text:
How Depression Hijacked My Soul, And How I Finally Wrenched It Back
An optimistic start
"Life is 10% what happens to you, 90% how you react to it." — Charles R. Swindoll
This is one of my favourite quotes and life philosophies. But what if you lose control over how you react to it?
Check phone. Again. Nope, he still hasn't texted. Heart lurches, stomach flips and brain tries desperately to recall That Nice Thing He Said which means that He Definitely Will Text. It's tough being an optimist, clinging onto those elusive gaps between the rain, and trying to ignore that you're getting drenched.
But I wouldn't have it any other way. I believe in life, and people, and the power of positivity. I appreciate how beautiful and precious life is and I walk around saying thank you for things – whether it be an amazing busker at a tube station or a fun weekend spent with friends. I appreciate how lucky I am to live in a safe country, to have a home and a loving family, and to live an abundant life that millions of people in this world can only dream of. I know I'm blessed and in moments of intense gratitude, I will look up to the sky and say thank you (in my head…mostly) to whoever may be listening. And really mean it. If I said it out loud you'd think I was trying to impersonate a Kansas City preacher. Without the Kansas City accent. You know what I mean.
This quote (I do love an inspirational quote) pretty much sums up my approach to life, and you can probably tell by now which side of the fence I'm on:
'There are only two ways to live your life. One is as though nothing is a miracle. The other is as though everything is a miracle.' (Albert Einstein)
As an optimist, I sympathised with depression and I respected its seriousness. But as an optimist, I was immune – right?
Surprising Fact #1: Optimists get depression.
In 2014, I went on a journey. To hell. This isn't an overstatement, it's a truthful summary of my experience. Here is my personal definition of depression:
Depression is a force that takes your soul and puts it in hell, then taunts your mind and body as you hopelessly struggle to get through the endless hours, days and months.
I am thankful every day that I found my way back. At my lowest, the first thing I would do upon waking up in the morning would be to google 'painless suicide methods'. Shout out to the Samaritans here whose sweet, 'Need help?' message would always pop up. I clearly needed something and it was comforting that, although it was an automated search engine asking, it was a real human who'd thought to ask. To that person and the Samaritans: thank you.
Highway to Hell: The journey begins
My journey started with some bad news from the diabetic clinic. Tests picked up that I have early stage kidney damage, a common diabetes complication. I was given some pills and not much advice, then sent on my merry way. I'll add here something I learnt recently at an event hosted by JDRF (excellent type 1 diabetes charity) from Paul Buchanan, founder of Team Blood Glucose and #GBdoc (excellent diabetes online community):
86 percent of diabetics will suffer from depression at some point in their lives.
86 per cent. The remaining 14 per cent probably get it when they're in their 80s and couldn't give two monkeys (not verified). I wouldn't, I'd say, "Sod it – pass the bloody cake". Anyway, 86 per cent of diabetics will suffer from depression, and in 24 years of being a type 1 diabetic, how many times do you think a medical professional has enquired after my mental wellbeing? I'll fill you in: zero.
Our society has got it all wrong. The health system focuses on the physical, but too often forgets that we are also cognitive and emotional beings. And when these parts of us fail, the consequences can be just as devastating. We have a long way to go to raise the status of mental health in this country, and therein lies the beating heart of this post.
So I got my diagnosis. In a nutshell, it consisted of, "We can detect it much earlier these days, we'll just keep an eye on it for now." I don't know about you, but I can spot quite an obvious follow-up question here: "Okay, then what?" Obviously, I sought further advice from Dr. Google, who told me that whilst I could stay at 'early stage' for up to 20 years or so, what I potentially had to look forward to at 'late stage' was deterioration in kidney function to the point where I'd eventually require dialysis/a transplant. When I first got this news, I was worried, but I had the same optimistic response as family and friends: it's a long way off, good it's been picked up early, it could be much worse, no point worrying yet, there are medical advancements all the time, stay positive. But while others could walk away from it, I was left with a suspended sentence hanging over my every thought. It was as if someone had given me an undetonated bomb to carry around in my handbag and said, "Don't worry, it'll be fine for now!"
Even if you think that you haven't given a second thought to how you'll live out your old age – I didn't think I had – you may be surprised. Because once I felt that a healthy and active later life was threatened, I realised what I'd subconsciously been taking for granted: that I would be running after my grandchildren, volunteering for a local charity, and revered as a wise pillar of the community (evidently, I was aiming high). One evening in Brixton I saw an old lady, I guessed late 70s, carrying a double-bass as she got off the tube. I smiled, and started thinking that was the kind of old lady that I wanted to be. But then this happy thought was cut short, as I was slapped in the face with the painful realization that this could suddenly be out of reach.
So once I'd dealt with the present, I followed my imagination down an increasingly dark path of destructive questions and observations, that I envied my friends for not having to contemplate:
- Will I be able to have kids?
- If I can have kids, is it fair, if I know that I could get really ill?
- I don't want my kids to be my carer.
- I don't want my partner to have to be my carer.
- Who on earth will want to be with me now anyway, knowing what could be in store?
- I don't want to be a burden to anyone.
- It's unfair and selfish to start a relationship with someone, or have kids, so I need to accept that I'll be on my own forever.
I will also admit that like many mid-late twenty-somethings, I was also borderline quarter-life crisis: wondering where I was going, criticizing decisions I'd made, and incredulous to be hurtling along a life path that I didn't remember choosing. I felt embarrassed by how little I'd achieved, and constantly compared myself to others. I don't know what it is about being 27, but you probably don't need me to tell you that it's a popular age for falling apart.
But I had time on my side. Oh, wait. And there, at that hopeless deadlock in my mind, lied the conditions for the perfect storm.
The Devil I Knew
I had experienced depression-like symptoms, let's say 'low mood', seven years previously which I eventually identified as being a side-effect of the pill. When I started recognising familiar feelings of a sadness that I seemed to feel on a biological level, I became concerned. I was upset, but I'd initially managed to be characteristically positive, grateful for friends' heartfelt offers of kidneys and even making jokes about it. I allowed myself to grieve because I'm a believer in 'riding things out', and I thought that letting out how I felt would enable me to move on. If I could deal with the worst case scenario, I could deal with anything. Apart from, I couldn't.
I clearly remember what I said to my mum around the time that I started recognising the tell-tale dark feelings: "I don't want to slide into depression." I'm recalling this because I want to make it clear that I wasn't unaware of what was happening. The theory behind Cognitive Behavioural Therapy (CBT) is applying rationale to irrational feelings, so this awareness should have provided me with some defence. But it didn't.
Surprising Fact #2: Depression is a master of disguise.
Even though I knew I had it, the majority of its effects, which changed me into someone unrecognisable, I didn't attribute to depression. Here are some of the reasons I thought I was feeling how I was:
- Personality change. I read somewhere that the biggest shift in personality comes in your late 20s. I concluded that I'd transformed into a miserable person and that was that. Forever. I knew that I'd been happy once but I could barely remember what it felt like, and I knew I'd never feel it again.
- Life is grim. Depression has a cunning way of showing you all the bad in the world, hiding all the good, and then portraying this bias view as the 'true' version. It certainly wasn't the case that I saw depression as an inevitable outcome of my situation, it was that I came to believe that life itself was nothing more than a desperately hard struggle. Once I fully believed this 'truth', I arrived at a point where I thought everyone ought to be miserable, considering the 'facts'. I couldn't understand how people around me were so full of joy; I concluded that they must all be kidding themselves.
- I'm a shit person. This was a big one. I was rubbish at everything. I couldn't have fun because I was boring, I couldn't hold a conversation because I had nothing interesting to say, and I couldn't be a decent friend because I was selfish. And actually, while I was depressed, I was. The little energy I had was taken up just getting myself through the day. I didn't have any strength left to support anyone else.
Life in Hell: Depression's tactical taunts
Depression has many fundamental elements. Interestingly, I only learnt about many of them months after I'd recovered. This is most likely because I attributed them to reasons 1 – 3 (mostly 3) above, and it was only with hindsight that I was able to sever this link and re-attribute the symptoms to depression – their true, deceitful creator.
1. Anxiety
Depression's BFF. A mental illness in its own right, and typically the first buddy depression calls over once it's hijacked your brain. Imagine you're about to jump out of an airplane.
You're 13,000ft above ground level, stood in the open door, heart racing, brain mashed, plane engine hammering in your ears. Now you're just about to jump and your heart feels like it's gripped in a vice. You feel a tap on the shoulder from behind – it's your boss: "Sorry George, I really need to know what your projected response rates are by segment for the Christmas mailing?" Feeling a mixture of incredulity and panic, your response would probably be along the lines of, "What? You think I can concentrate on anything right now?! I can't even process what you just said let alone answer the damn question!" You could probably get away with this if you were indeed stood in the doorway of a micro-aircraft, about to launch yourself out of it. Apart from, I wasn't – I was just in the office. But I had the exact feeling of being about to jump from 13,000ft, almost 24/7. And I mean the physical symptoms too; I demanded an ECG because I was convinced something must be wrong with my heart for it to be beating so fast all the time. In this constant state of on-edgeness, here are some activities that were near on impossible for my brain to carry out:
- Concentrating
- Holding a conversation
- Organising anything
- Making a decision
- Having even the smallest share of responsibility for something
- Remembering things I should remember
- Problem-solving (the worst)
- Talking in meetings
- Coherently responding to an email
Unsurprisingly, all of the above either feature or are implied in my job description. At work, I felt utterly incompetent. Any ambition I once had deserted me. I decided that I was only good enough for a stress-free, low-paid job where barely anything was expected of me. Luckily, my boss was understanding and supportive, but I still had to do my job. And naturally, anxiety didn't just affect me at work; functioning in social situations was a constant and exhausting challenge. Of all depression's demi-devils, anxiety was by far the most debilitating. And like my assumptions about 'personality change', I thought this state of anxiety would be permanent, too.
It was also a terrible state to wake up in. I was so on edge that my morning alarm was enough to give me a near-on heart attack; I'd wake with a violent jolt and my heart feeling as though it were about to leap out of my chest.
In hindsight, this is funny: due to a complete lack of judgement, I agreed to go white water rafting with a friend. Here's an activity not to do if you're ever suffering from crippling anxiety: white water rafting. I was a wreck and I hated every goddamn second.
2. Depression slows you doooown.
While your heart may be racing, to your mind and body it's as if every thought and movement has to wade through tar. Just trying to function every day is ten times harder; living becomes exhausting. I remember how on some days just putting one foot in front of the other was so hard. All I can compare it to is how I imagine Anne Boleyn felt as she was walking to her execution. I'm speculating, but I'm going to guess she wasn't skipping.
All physical, mental and emotional endeavours required monstrous effort – just replying to a text was hard work, let alone trying to organise anything. Living the 'London Life' isn't sympathetic with a need to go slowly; London, and the friends within it, don't wait. I felt that life was moving ten times faster than I was and I couldn't keep up. Managing my diabetes, something I'd always coped with, became overwhelming. The strands of my life were unravelling and spiralling away from me at a terrifying speed, and the further away they spun, the more I panicked that I'd never get them back. I felt constantly overwhelmed by the simple act of living. It was as if I was treading water, I was expending all my energy on just staying alive. I had none left for anything else and I knew that I couldn't survive like this indefinitely. I was exhausted, and I was drowning.
3. Negativity
Depression re-wrote the script of my personality. For days on end, I'd get myself stuck going round and round in negative and highly destructive thought patterns. I worried about everything, and my anxiety caused me to make mountains out of matters that could be easily fixed. I thought I was a crap person but, due to the 'slowing down' effect, I didn't have the energy or motivation to make things better – and thus round and round I went.
I'd be woken by these negative thoughts in the middle of the night, and would lie awake worrying for hours. And then I'd worry that I'd be tired the next day. And then I'd worry that because I would be tired, I'd feel so much worse. And I did, and so it went on. This repetitive thinking is a classic symptom of depression and is known as 'ruminating' – a term introduced to me by my therapist (gosh, I feel so American – more on Caroline later).
I tried my best to masquerade as someone happy and 'normal', but often I didn't have the strength or desire to play the part, and negativity spilled into my words and behaviour. I became needy, constantly seeking reassurance. I'd typically appear at my most negative when I was simply exhausted of sustaining the cover-up. It was relentless and draining, and sometimes I just needed a break to express what I was really thinking, even if it was a toned-down version of it – I always kept my darkest thoughts hidden. I found myself drawn to many people and joining in, because this was far more consistent with how I was truly feeling and less tiring than feigning happiness. It brought me closer to blending in and enabled me to feel less 'weird'.
Friends and the world around me made being happy look effortless. When I hinted at how fed up I was feeling, many people's reaction was to tell me to "stay positive". I know they meant well, but it wasn't like I hadn't thought of that. It was just that rather than being the easily achievable task that their seemingly obvious suggestion implied, it was actually unbelievably hard. I was trying – I had life-affirming messages blu-tacked all over my wall – but still I couldn't reach the dizzy heights of 'feeling positive', and my failure to do so just made me feel useless and that I wasn't trying hard enough. But it was too difficult (and embarrassing) to explain this, so I just smiled. I felt like I was being judged, and criticized for being miserable when I didn't have enough reason to be. And I didn't think I had enough reason to be either, I told myself that 'things weren't bad enough' and this was a constant source of guilt. But here's something about depression: it is proudly non-discriminatory. There are no conditions for entry, it doesn't comply with logic, and it will welcome you with open arms – irrelevant of whether you, or anyone else, thinks it has enough 'reason' to.
I could tell that my gloominess was repelling my friends, and I feared that my constant despairing was pushing them further away from me still. It was plainly obvious to me that people were putting up with me, rather than enjoying my company. But this wasn't a revelation; it was how I was living with myself. I became a vacuous presence that drained others' energy, and I hated myself for it. But I didn't have any strength of my own and, like a parasite feeding on a host, it wasn't out of choice – it was my only means of survival.
It wasn't just through my personality that depression made itself known. Depression seizes control of your brain. What does your brain control? Every single cell in your body. I've already mentioned my racing heart; via your brain, your whole body is aware that something isn't right. As a woman, if you're suffering from chronic anxiety, stress and depression, your reproductive system can make the judgement that you're not in a fit state to be a mother, and temporarily shut down your ovaries. I went six months without having a period.
Occasionally, I'd be reminded of the person I'd once been when I saw an email or text I'd sent when I'd been the 'old' me. Rather than this being a source of hope, it left me incredulous. I could hardly recognise myself as someone who made jokes and texted someone for no reason other than something was funny. As far as I was concerned, cracking a joke was far, far superior to the elementary 'communication for beginners' that I was scarcely capable of. I'd send a text to try and arrange something, to see someone so I could try and give my heart some love, to ask after someone and desperately try to maintain a relationship. Everything was functional. I didn't have the strength to carry out anything that wasn't. I didn't recognise the glimpses of 'Old George' but at the same time, she was irrelevant. Because she didn't exist anymore.
4. Forgetfulness
This is one of the symptoms that falls into the group of those I learnt about only after I'd come out the other side. In my permanent state of on-edgeness, it felt like the only part of my brain I could access was a very thin layer around the outside – nothing would go in and I couldn't access any of the essential brain regions that I needed to be able to process and retain information. In my personal life, I forgot to ask after important events in friends' lives, I forgot what they'd said, I forgot the name of the bloke they were dating – and this recurrent uselessness just perpetuated my belief in spiteful number 3 – I was a shit person.
At work, it meant that I couldn't answer the most basic questions about campaigns I was in charge of, which further wounded my confidence. I even signed up to a brain training website in an attempt to exercise my mind back to remembering things. I forgot to use it.
5. Depression = An emotional black hole
It won't astonish you to learn that I felt miserable; it only took someone with a kind face to ask "How are you?" and I'd feel a lump rising in my throat. I got used to choking back tears. And I got used to not choking them back: in the shower, in the loo at work, and in the company of the friends I was closest to. There were times when nothing could bring me any joy. I'd berate myself for spending money on activities that left me just as miserable as before I'd started (let's not mention the white water rafting). More often than not, these occasions would actually leave me feeling worse, because they inevitably featured a social situation in which I would have failed to be normal. Due to the effect of depression on my personality, my confidence and self-esteem were at rock bottom, and this was only exacerbated through every occasion that exposed my useless social skills.
Depression's ability to self-perpetuate through its symptoms is one of the characteristics that makes it so destructive and dangerous. When you find yourself failing at basic conversation or crying in the shower whilst thinking about how best to kill yourself, you are acutely aware of just how far you've fallen, and the dire pit your life is in.
But what was worse than the sadness, was the void. The emotional black hole that left me dead inside. Making any kind of decision was impossible. I had an identity crisis because I didn't have any opinions. I didn't and couldn't care about anything. A close friend tried to help by encouraging me to compile a list of the things I wanted to achieve in my life. I just stared at the empty piece of paper and cried. I didn't know.
I remember the jealousy I felt towards one of my friends when she was upset about some guy who hadn't texted back – I envied that she could FEEL so much. Now that I had my kidneys to worry about it, it made everything else seem insignificant and I thought that the only stimulus that would be capable of provoking a response from me would have to be on a par with kidney failure. I couldn't empathise at all, I was just jealous because I thought I'd never be able to feel so intensely, about something so trivial, ever again. *Rolls eyes with irony* (No, he still hasn't bloody texted back.)
6. Self-destruction
It's shared experience that when we're feeling a bit crappy, we reach for a chocolate bar or some other vice, in a bid to fill the sense of emptiness caused by a break-up, an awful day at work, some sad news. But what if you feel crappy all the time? I don't know why when we're in this place, it's the things that are bad for us that call our name the loudest. But I do know that I can measure my level of happiness as the inverse proportion of how much I want to eat three pizzas followed by eight Wispas. This would be funnier if I wasn't diabetic. But is the fact that I am, and that bingeing on this kind of food is so bad for me, the reason it appeals so much? Probably. For others it may be alcohol, drugs, or even people (I'm not alluding to cannibalism here, 'spending time with' rather than 'consuming'.)
I'll admit to some artistic over-dramatisation: I never ate three pizzas or eight Wispas (in a row). But I did eat unnatural quantities of Bran Flakes. I would forbid myself from having another bowl and not possessing the necessary will power, i.e. some, I'd end up giving myself up to four insulin injections in a row to cover each additional carb hit.
And as if depression wasn't already doing a good enough job of it, I'd taunt myself. I would constantly find flaws in everything I did, compare myself to others, and remind myself of bullying number 3 – I was a shit person. I set unrealistically high expectations and criticized myself when I inevitably failed to meet them. And this was all in the context of feeling guilty for being depressed in the first place.
7. A devil's eye view
I've always been a believer that reality is subjective, and this is never truer than when you're depressed. I perceived the world around me through the bias lens of depression. I saw only the bad; the good was always obscured from view. A bleak outlook and the belief that you'll never get better is a classic feature of depression, but when you're going through it, it's actually more than that – it's as if the bleak view is the real one, and now you know the sorry truth. Every time I saw a homeless person on the street, the threat of this one day being me stuck to me like a magnet. In my mind's eye, I'd see my future self sitting there, once I'd lost everything because I hadn't been able to hold down a job. I saw war, poverty, meanness and life as being a hopeless journey towards old age, disease, and bits falling off. And because I was never going to marry or have kids, the future image I held of myself was of a lonely, decrepit old woman, living in a dilapidated, dark house with no one to look after me or care.
The sun was constantly behind a depressive black cloud in my mind – everything I pictured was always shrouded in darkness. Goodness, joy and fun existed in a different world on the other side of an impenetrable veil, as illusory as a dream. There was no way in, and no way of letting it into my world. So with a heavy heart, I turned my face away and tried to forget it existed. And depression, with its bias lens, was more than happy to assist.
Eventually, I wound up isolated on a sad, dark and lonely island, cut off from everyone and everything I loved, where happiness didn't exist. By this point, my self-esteem was so low that I didn't think I deserved anything better, and my sense of reality was so skewed that I didn't believe the world had anything better to offer. I was exhausted of faking happiness – I only tried for the sake of the people around me, and because I was scared of being judged and pushing people away even further. I'd tried and failed at attempts at fun – it didn't work and this had been proven time and time again. Succumbing became a much more sensible and appealing option. I just wanted to curl up in the sanctuary of my bed and hide from the world, with no responsibilities, nothing expected of me, and without having to be anything to anyone. I became obsessed with wanting security; suddenly money came above values that had previously been core to what I stood for. I'd lost my values and everything that made me 'me': I had no idea who I was anymore. I felt no joy, and knew I'd never feel it again. So I started questioning what I was living for. I didn't know.
Pits of Hell
This is the point I'd arrived at when I found myself searching 'painless suicide methods' on Google first thing in the morning. I didn't only think this was the best option for me, I thought it would be best for everyone. I was toxic, useless and pathetic. I trivialized my life and its meaning; if I could tell myself that my life wasn't a big deal in the first place, then ending it didn't seem a big deal either. Despite feeling guilt at the inevitable commuter chaos, jumping in front of a train seemed an appealing and sure-fire method. Until I was horrified to learn that often in this scenario, a flying body part hits and injures a stander-by. I certainly didn't want to harm anyone else, especially in such a horrifying manner, so trains were categorically ruled out. I had the vague idea that on an upcoming trip to Kefalonia, there would be a plethora of suitable cliffs that I could throw myself from into the Ionian sea or a reliably hard rock. But the survival rate was alarmingly high for this method, and I was keener for guaranteed death. When the Malaysia Airlines flight MH17 was shot down in Eastern Ukraine, killing everyone on board, I wished I could have been on it. I felt guilty that so many people who deserved to live had lost their lives, when I would have happily swapped places and given them mine, so that they could have done a worthier job of living.
Fighting the Devil: What helped
I knew, even more than before, that I should be making the most of my life. But as I was going round in circles about how I could make things better, I kept coming back to the same place: I couldn't act on anything while my head was so messed up. This was the root problem that I needed to fix in order to get anywhere. And it was a challenge in itself, organising as much as calling the doctor and navigating the Bupa referral path (challenging enough even when you're not depressed) took a lot of effort. But this achievement alone was something I was proud of – it was a step in the direction of getting better, and an act of positivity that I'd actually managed to accomplish. When I spoke (cried) to the doctor, he was fairly aloof and patronising – and unwittingly ironic when he concluded, "The biggest problem is that people don't tell us".
Once I was referred to Caroline, a psychotherapist, I felt a sense of power from the fact that I was doing something that might help.
And that's what depression doesn't want you to know; that while it may be self-perpetuating, so is strength, confidence and hope.
This emergence of hope into my consciousness marked a clear turning point. In my first session, I cried more than I talked. I learnt that everything I was feeling were actually classic symptoms of depression, which led me to view it in a more clinical light, and helped remove some blame. Discussing it openly with an intelligent and non-judgemental professional was empowering. Talking about it out loud and tackling it turned it into something that could be tackled. Rather than instinctively obeying depression's voice, I began questioning and criticizing it. I no longer viewed it as a credible authority but as a bloody evil bastard. Knowledge = power. Finally, I was dislodging depression's voice and rediscovering my own.
Singing in the Choir
The only activity that reliably (this factor was key) managed to lift my mood and bring a window of respite, was singing at choir. Like a memory stirred, it reminded me of the happier person I'd once been, and it was the closest I felt to being her. It brought my soul within reach, and nourished it with a restorative antidote to depression's venom.
Choir opened a crack in the doorway into that elusive world of happiness that I couldn't otherwise reach. It allowed the light from that forgotten place to stream in, and I basked in its heavenly glow.
Choir gave me a foot-hold on recovery; feeling just 'okay' was a miracle in itself, which offered a glimmer of hope that I was heading in the direction of 'good'. Sometimes the effect lasted into the next day. I'd feel lighter when I walked to the station in the morning as if someone had removed the tar from the atmosphere. It's no coincidence that I was at my lowest during the summer break.
Singing gave me something – the only thing – I could consistently enjoy and also the only thing I could be good at. It was also comforting that, even in my most wretched projection of the future, I would always have singing, and choir, and friends to sing with. Thank you Starling Arts, I know mine's not the only soul you've saved.
There has been much research carried out in recent years on the psychological benefits of group singing, and you can read a whole post about this in Starling Arts' own blog here. (If you're inspired to improve your own mental wellbeing through singing, check out Starling Arts' four London-based choirs here.)
There were actually very few people I was open with about how I was truly feeling. Much of what appears in this blog, I am sharing for the first time (including the saying thank you to the sky bit, I'm going to get ripped for that). But the people I could be honest with were my angels and saviors. The ones who listened to me decry the world and taint it with my depressive brush, and were still there, asking if I wanted to go for another coffee. The ones who made the effort to see me, rather than the other way round. I need to credit my ex-boyfriend here, who, despite us having broken up a few months before, held me after I got the kidney diagnosis and was there when others weren't. I know how miserable I was when I wasn't putting a huge amount of effort into pretending I was fine, but I could relax and be my honest, depressive self with him; putting up with me was above and beyond his duty as ex-boyfriend. Knowing that someone cared enough to still be there when I took off the mask and the pasted smile, really helped get me through.
Being honest with people helped me feel connected to the world I otherwise felt severed from. Hanging onto this link, however thin the thread, was so important. I valued the people who knew me well, because they were the ones who knew that this wasn't me, and that was a huge relief and comfort. To the friends and family who helped keep me tethered to the world – thank you. Never underestimate the difference you can make to someone.
Knowing I wasn't alone
350 million people of all ages around the world are currently suffering from depression. A fair few then. Hearing others' stories and knowing that they were going through the same torment helped to remove the unjust feeling of shame that too often accompanies depression. It's awful feeling like you're the 'weirdo'. Here are some names you will probably recognise: J.K. Rowling, Stephen Fry, Halle Berry (also a type 1 diabetic), Jon Bon Jovi, Abraham Lincoln, David Walliams, William Churchill, Helena Bonham Carter, Brian May, Brad Pitt, Charles Dickens, Woody Allen, Beyoncé, William Blake, Oprah Winfrey, Eric Clapton, Bob Dylan, Dolly Parton, Mark Twain, Michelangelo, and Isaac Newton. The aforementioned (eclectic) group of well-known personalities have all suffered from depression. And while it may have debilitated them for a time, they've gone on to use their minds to convey extraordinary and diverse talent. It doesn't matter what's bothering us in life, knowing we're not alone can make a powerful difference.
Self-defense: Arm yourself
There were a few other forms of weaponry that I picked up along the way; whether you're depressed, stressed or waiting for a text, they're helpful defense against an onslaught of mental anarchy:
- Mindfulness. You can practice this in many ways – classes, apps, courses. It is essentially the practice of observing your thoughts and letting them pass, rather than maniacally latching onto them with a panicked, knee-jerk response. It is an awareness of mind that eventually enables you to control how you react to thoughts and external stimuli; it's the difference between, "Ok, that could make me feel a bit stressed" and "AAAAAAAH crap crap crap!" (not the official definition).
- Sleep. (You know this.)
- Exercise. Even if it's just a stroll – endorphins are a mini-army in your bloodstream. But equally, don't punish yourself for not doing any. You're the only one judging.
- Having a routine. I found the stability element reassuring.
- Tiny goals. Reward yourself for sending that text or going to that social event. If you start acknowledging all these mini-triumphs, you'll gradually build confidence.
- Distraction. It's not a long-term cure, but often preferable to being inside your messed-up head. If you can find a film, an activity, anything to temporarily distract you, it's at least a break. Especially if it's funny – depression hates laughter.
- Getting out in nature. On holiday in Greece, I was at a pretty low point. But one blissful moment was when I went swimming out in the bay: it was beautiful, rugged and wild, and there was something about the simplicity of it and being out where nobody could judge me and life wasn't going crazy-fast, that helped calm my heart and mind.
- Knowing it will pass. Your brain is an organ, and like any other part of your body, it sometimes gets ill. Or breaks. But like a virus or a broken leg, you WILL recover from it. Don't let depression's voice convince you otherwise.
- Adding some bullet proof layers. In his book, How to do Everything and be Happy, author and self-help guru, Peter Jones, talks about five 'bullet proof layers' for beating the blues, which feature many of the above and include basics like 'put your pants on', i.e. get up, put on some decent clothes, do your makeup/shave. The book in its entirety is excellent if you're not as far as being depressed, but are perhaps stuck in a bit of a rut and need a kick-start to set some goals and actually achieve them. I can't recommend his 'mumbo jumbo and jargon free' approach to self-help enough.
And here's something not to do:
Don't compare yourself to others.
It's very easy (and very harmful) to scroll through Facebook and create a fictional superhuman from the snapshots of everyone you see. This person, naturally, is having The Best Time ALL the time, attends every event featured in Time Out, has set up a pioneering enterprise, has informed opinions on every political and global news story, one billion friends, owns a house, is cultured, athletic, always on holiday, a member of ten thousand social clubs, has countless impressive hobbies, a high-flying job, fifteen inspirational projects on the go, has won an award for that other thing, has – undoubtedly – 'made something of themselves', definitely never has a night in, is adored by everyone…get the picture? It's not real, but even if there are some impassioned and heroic (and knackered) folk whose lives resemble this, they are not doing it all at the same time. We are (with a few exceptions, e.g. Hitler) each our own worst enemy. It is highly likely that the only person judging you is you. Everyone else is too busy working their own lives out. Make your own goals; it's not a bad thing to be ambitious, but it is a bad thing to measure your own success against the cumulative achievements of every other human being in the whole world. It's bonkers. Give yourself a break and be kind to yourself.
Now: Back on earth
Though I know that depression might have another pop, it doesn't scare me. I know I'll be okay because now that I've come through the other side, it can't fool me into believing that I never will. I've got hard evidence and more experience than I'd wish on my worst enemy. It's a bit like chickenpox in the sense that now that I've experienced depression, my mind knows how to recognize it and fight it off. And I am armed, ready and damn determined to fight. I will defend myself against that hellish force with all the strength of my being – my life and soul depend on it.
I know immunity isn't guaranteed, but I actually feel better equipped than someone who has never been through depression. Interestingly, I'm not just back to feeling how I did before I was depressed, I actually feel happier than I have done in years. You may have recognized some of the symptoms of depression, or lesser versions of them, in yourself at times. That's because one or two at a time, in small doses, are just the same factors that contribute to us feeling a bit rubbish – brought on by stress, low self-esteem, or being stuck in a rut. You might not even notice they're there or identify them as the culprit of your bad mood. But all at once and at ten times the velocity, and you're heading down a slippery slope. So I'd probably been feeling some of this for years, but now that I've been forced to apply science to how I'm feeling and distil all the elements, I can identify the triggers individually and nip them in the bud. This elevated awareness acts like a safety net, catching me if I start to fall and allowing me to yank my mind back to tranquility and optimism.
I can still scarcely believe how easy it is now to be me and live. For months I was imprisoned in a living hell and now that I'm free, I feel like a caged springbok released back to the wild: I'm bursting with energy and a voracious eagerness to throw my arms to the sky and run and dance and sing and laugh, and make up for lost time by doing all the things I'd forgotten I was capable of.
Now, as much as I don't advocate stressing yourself out by comparing yourself to an amalgamation of your Facebook news feed, I'll admit to setting fairly high standards for myself: there is a lot on both my 'Live Life Now' and 'Wish' lists (again, see How to do Everything and be Happy). But these goals and aspirations are my own, carefully chosen, and unique to my passions and values.
While I'm happy now to live by quotes (last one, promise) such as:
'There is no passion to be found playing small, in settling for a life less than the one you are capable of living', (Nelson Mandela), when I was depressed, the pressure of aspiring to goals like this was crippling. However, going through it did teach me how miserable we can make ourselves by setting unattainable expectations.
I'm not any less ambitious now, but alongside that ambition and all those shoot-for-the-stars quotes, I remember this one (oops, one more):
'You can do anything, but not everything.'
I have this as a sign in my room, and it's the reassuring voice that says 'Be nice to yourself, you're doing fine', and drowns out the racket of 'She's doing it, why aren't you?'
I'm so relieved that I'm back to being someone who, rather than sapping the love and energy of others, can actually give some back. When depression stole my ability to support and cherish the people I loved, I lost a fundamental part of who I was. It was the part of me that gave most meaning to my existence, and the one that I'm most delighted, and grateful, to have back. These days, I've got positive energy overflowing and I relish every opportunity to share it.
I remember when just feeling okay was a miracle; now I feel fantastic, often I feel positively WONDERFUL, and that is something I am thankful for every single day.
And this is self-perpetuating too; I feel wonderful because I feel wonderful, so then I feel even more…wonderful.
And I can FEEL. This post has taken me almost four weeks to write, and about three paragraphs ago, the boy called to dump me. (I knew it was coming – in our last text exchange, I put a kiss and he didn't. Doomed.) Because I'm a hopeless romantic and ridiculously emotional (in regular mode), I was pretty cut up about this. I felt like I'd been brutally shoved off cloud nine back to…Tinder. Oh Jesus. The anguish, the heartache – I could dance down the street with the sheer JOY I'm filled with just for being able to FEEL either of these emotions. Because now I truly know that I'm back: body, mind, heart…and soul.
To anyone going through depression now, you will smile, and laugh, and love life again – I guarantee it. Oh, and you're awesome.
No Soul Left Behind: How you can help
Help. Fight. Stigma.
While I was depressed, I felt like I needed an excuse for myself, but I couldn't say depression so I didn't have one. Most of the time when I was feeling utterly awful and didn't mention it, it was out of guilt for bringing up a gloomy topic. When I was told to "stay positive", I inferred that this was the polite thing to do.
If you break a leg, no one expects you to be able to walk properly. You get a plaster cast, crutches, sympathy, time off work, and enthusiastic well-wishers queuing up to write on your cast. If I'd had a broken leg, I wouldn't have felt guilty or ashamed for not being able to use it. If I'd had a brain tumor, I wouldn't have felt guilty for forgetting things or struggling with brain functions. So why, when I had a mental illness, i.e. an illness of the most complex and sophisticated organ in the body – the brain – did I feel such shame? You shouldn't be ashamed of having an illness. And surely, due to its limitless complexity, the brain is one of the most likely parts of your body to go wrong in the first place. It wasn't my fault, but due to its nature, depression told me it was and stigma helped perpetuate that belief. I was suicidal, coping on hardly any sleep, and felt worse than I ever had done in my life. But I didn't have one day off work because I was scared of being judged for having 'depression' or 'mental illness' on my record. This culture needs to change. I'm not saying it would have been the best idea to completely succumb and lie in bed all day, but a bit of a break would have helped.
Society needs to recognize that depression is a real, psychological condition and a formidable killer: 90 percent of people who commit suicide are suffering from a mental illness at the time. You may need to read this next harrowing statistic twice: in the past year alone, more men in the UK have died by suicide than all British soldiers fighting in all wars since 1945. We need to eradicate the shame and stigma that harbors depression, and dispel the ridiculous and outdated idea that it somehow 'isn't real' or that people choose to be depressed. This last notion is so ridiculous it's laughable.
One of the few positives from my experience is what I have learned, especially with regard to the people close to me. I can proudly say that some of the best and most successful people I know have suffered from mental illness. I would, of course, say the same about physical illness, but that wouldn't be a big deal. Just like it shouldn't be for the cerebral equivalent. I'm not even sure why we need to differentiate. If someone says they've got a migraine, you don't feel awkward but at the same time, you adapt your behavior to be considerate of it. It would be lovely if this were one day true for depression. This article is hopefully contributing to the fight to change attitudes, and so can you.
Here's how:
- Talk openly about mental health. Just by saying, "my friend had depression, she's great now and she's written a blog about it", could help someone because you don't know who's listening, or what hidden demons they might be facing.
- Be there. If you know or suspect a friend is depressed, you don't have to talk about the deep stuff in order to help. If you're not into that or have a more 'laddish' relationship, then ask them out for a beer and crack a few jokes if you're better at that. But keep asking to meet up, even if they appear to be having a rubbish time. Chances are they appreciate it more than they're capable of showing.
- Publicly support mental health. Share this post, posts from mental health charities, and general support of mental health on social media – anything that shows your friends that you're open to mental illness and won't judge them. It could make the difference between them talking to you, or bottling it up and getting no one else's opinion on the shit view they hold of themselves other than depression's, which will always agree.
- Help to reduce stress. Facilitate removing as many potential worries and burdens as you can, e.g. by offering to take the lead on organizing something. If you're a line manager, talk to your report about redistributing some of their work and alleviating some responsibilities.
- Don't make someone feel any weirder. Think twice before pulling a strange look, or uttering a low and drawn-out "okaaaaay" under your breath.
- Be kind. This should go without saying, but in a fast-paced and high-pressured world, kindness isn't always prioritized. You don't know what battles the people around you are facing. Don't roll your eyes if a colleague is a bit slow with the figures. Instead of getting impatient and snapping, check in with them: "You don't seem your normal self today, are you okay?" When someone is in an incredibly vulnerable position, potentially with a pre-formed suicide plan, your words have the potential to push them over the edge, or pull them back.
- Don't instinctively flee from negativity. We're told from all manner of sources to steer clear of 'toxic people' – the ones whose negative energy brings us down – but what if someone isn't 'toxic' per se, but is just having a really tough time right now? You know your friends – if someone is unusually negative and dispassionate, check if they're really ok.
- Help with distraction. Suggest an activity and for God's sake be the one to organize it.
- Don't try and be a therapist. Listen and be open, boost their confidence if you can, but saying things like "you should do that" is generally not helpful, because inevitably 'that' will be harder than you could possibly imagine.
- Sign petitions. Lend your support to campaigns that are fighting for mental health services.
Further resources
- The Samaritans: If you're in the UK, call them 24 hours a day on 08457 90 90 90. If you're elsewhere, visit Befrienders Worldwide to find a helpline in your country.
- Mind: Provide advice and support to anyone experiencing a mental health problem, as well as campaigning to improve mental health services, raise awareness and promote understanding.
- Headspace: Mindfulness app and website with guided meditations to promote peace of mind and wellbeing.
- CALM: Campaign Against Living Miserably. You may have seen the #MANDICTIONARY billboard ads. CALM is a charity dedicated to preventing male suicide, in part by 'challenging a culture that prevents men seeking help when they need it'. (I think my acronym is better: Campaign Against Lad Mentality.) Their helpline is open 5pm-midnight in the UK: 0800 58 58 58, or you can use their webchat service.
- Matt Haig's book, Reasons to Stay Alive, has had glowing reviews, including from Stephen Fry. This guy has been through depression, and has eloquently held two fingers up at it by turning depression's doctrine on its head. Matt says: 'I wrote this book because the oldest clichés remain the truest. Time heals. The bottom of the valley never provides the clearest view. The tunnel does have light at the end of it, even if we haven't been able to see it . . . Words, just sometimes, really can set you free.'
- #GBdoc: Supportive online community hosting free weekly tweet chats for diabetics.
- Team Blood Glucose: Social enterprise set up to help all those with, or at risk of diabetes learn how to use activity, sports and exercise as a core tool in the management of diabetes.
- JDRF: Type 1 diabetes charity that hosts local diabetic 'Discovery' events for meeting other type 1s and learning about research.
- How to do Everything and be Happy: Peter Jones's original self-book has now become a series, blog and philosophy.
- The World Health Organisation's Black Dog video by Matthew Johnstone is an excellent and sincere representation of the signs and effects of depression.
- Tiny Buddha: Aiming to help us re-balance our lives in a complex world, this website is full of wisdom, quotes, tips and stories to 'help us help ourselves and each other'.


text:
SANTA CLARA, Calif. – Trent Baalke was promoted to general manager of the San Francisco 49ers on Tuesday night.
Now, let the coaching search begin.
Baalke was formally hired as the team's new GM, though he had largely been considered the front-runner for about a week. He will take on more responsibility from his most recent post as vice president of player personnel, including taking the lead on finding a new coach.
With Baalke in place, the Niners are in position to make a serious run at Stanford coach Jim Harbaugh — perhaps starting as soon as Wednesday morning, though it is believed the sides have already had contact.
Harbaugh, with plenty of suitors coming his way, returned to the Bay Area earlier Tuesday evening from a 40-12 Orange Bowl victory over Virginia Tech in Miami. The Cardinal finished at 12-1.
Baalke had interviewed extensively on Saturday with team president Jed York, who has said he would let the general manager pick the team's next coach.
"Trent has done an exceptional job in his role as vice president of player personnel and throughout his tenure with the 49ers," York said in a statement. "I have had the benefit of watching Trent closely in the recent months and have been very impressed with his knowledge and leadership. I am confident that Trent will find the 49ers an excellent head coach who will lead us to great success in the coming years."
Mike Singletary was fired after a 25-17 loss at St. Louis on Dec. 26 that eliminated the 49ers from playoff contention for an eighth straight year. That was after San Francisco was picked to win the NFC West following an unbeaten preseason.
York insisted last week he would conduct a national search for the GM position but ultimately decided to promote from within. The 49ers had been without a general manager since Scot McCloughan's abrupt departure last March in what York called a "mutual parting."
Baalke, who spent time before last Sunday's 38-7 season-ending win against Arizona shaking hands with several fans in the stands at Candlestick Park, has been with the organization for six years.
"I would like to thank Jed York and the York family for this tremendous opportunity," Baalke said in a statement. "It is an honor to be named the general manager of the San Francisco 49ers, a franchise with a history filled by some of the game's greatest players, coaches and executives. I look at this role as one of great responsibility — to not only the history of the franchise, but also to the 49ers faithful. My entire focus is now dedicated to finding the next head coach of the 49ers."
He was director of player personnel from 2008-09, overseeing the college and pro personnel departments. He first joined the franchise in 2005 as the 49ers' Western Region scout, a position he held through 2007.
Baalke orchestrated the contract extensions of two key 49ers this season: four-time Pro Bowl linebacker Patrick Willis and star tight end Vernon Davis. Those are two significant moves since Baalke took over football operations after McCloughan left, along with leading the team's 2010 draft.
In May, Willis received a $50 million, five-year contract extension that takes him through the 2016 season and includes $29 million in guaranteed money. He earns $10 million per season. Davis was rewarded with a five-year deal paying him $37 million overall, with $34 million guaranteed.
Baalke also drafted rookie starting offensive linemen Anthony Davis and Mike Iupati with the 11th and 17th overall picks, respectively.
His other draft picks last season also played significant roles as rookies.
Baalke also worked four years in the scouting department for the Washington Redskins prior to coming to San Francisco and has coached in the college game.

subset: commoncrawl


text:
Man Facing 142 Charges Posted Incriminating Photos on Instagram
A Florida man suspected of organizing several so-called "dinner time" burglaries in the Boynton Beach area was arrested after posting a series of incriminating photos on Instagram.
The photos, posted at duce22ceritfied (sic), show Depree Johnson and others posing with guns, cash, and drugs.
The months-long investigation into the break-ins at local senior communities led authorities to Johnson's Lake Worth home, where they found "numerous pieces of jewelry ... (including) watches, charms, necklaces and loose diamonds, as well as two stolen firearms."
All told, the Palm Beach County Sheriff's Office recovered some $250,000 worth of loot.
Johnson was subsequently booked on 142 charges, including possession of weapons/ammunition by a convicted felon.


text:
By Hammer Nutrition
Athletes searching for training protocols to improve strength using EMS (electrical muscle stimulation) find a variety of plans. Some find a mixed training plan that incorporates the variety of strength training programs week by week. In a mixed training plan, the programs selected account for the demands of a particular sport and whether or not the athlete is in a precompetitive or competitive phase of their training. Other plans focus on building one kind of strength for a minimum of three weeks and continue it for up to eight weeks. Can you expect similar results from these different approaches to building strength? The answer is no, so pick the kind of plan that helps you meet your goals.
An important consideration when selecting workouts that best meet your needs is "muscle specificity," a concept that helps accurately predict the outcome of the whole spectrum of training practices. While it's a simple concept, it can help any athlete make decisions about how best to meet their athletic goals.
Muscle specificity can apply to any and all characteristics of skeletal muscle function. Whether it's the energy delivery system, (aerobic, anaerobic, or alactate,), the speed at which a muscle contracts (slowly, quickly, and everything in between), the amount of force applied at various points throughout a muscle's range of motion, or the kind of muscle contraction (concentric, eccentric, or isometric), the muscle can be trained specifically. The flip side is that specific training produces specific results. Just because one is well trained to sprint has little to do with how well that individual can perform if not sprinting. We all have experienced this firsthand.
It's not only the workouts you do, but also how many times per week and how many weeks you consistently do it that affect the outcome. When it comes to building strength, one time per week will show some improvement initially, but the rate of gain will quickly slow down and plateau. Two times per week is far better for gaining the desired adaptations, and continued improvement will last for many more weeks. Given that you need to recover from NMES strength training, three times per week is often enough to acquire the maximum amount of gain and the proper amount of recovery.
How many weeks the training is extended affects the amount of gain as well. Measured significant improvement takes about three weeks to realize when using the Strength and Resistance programs. Up to six weeks is required to see a significant improvement with the Endurance building program. The inevitable plateau from weeks of training in a specific way occurs in about 8 weeks when using the Strength and Resistance programs, and 10-12 weeks when employing the Endurance program. Once a plateau is reached, change the way in which you train to avoid stale performances.
Below are two possible approaches to training with a Compex. There are a lot of similarities between Scenarios One and Two; the major difference is in the number of weeks that a particular program is applied. The results will be different as well. In Scenario One, the gains will come, but they won't be fully developed in one area. This is a way to touch more bases and spread the gains out over a broader set of adaptations. In Scenario Two, the programs are applied over many weeks and the gains are significantly greater, but the set of adaptations are narrow and focused.
Which way is better? "Better" depends on what kind of outcome you desire. I like to employ both methods. During off-season, Scenario Two makes more sense to me. Once the three specific adaptations that result from applying the Strength, Resistance, and Endurance programs are fully developed and you're close to the season's competitions, switching to Scenario One to maintain the gains and focus more on the intensity and volume that comes from practicing your particular sport makes a good deal of sense. Not a new approach and certainly not the only approach, it is a common one used in a majority of sports. Like any approach that works, it doesn't ignore the principles of muscle specificity, training frequency, and plateau effect.
No matter what approach you take, build strength with a Compex. It works! HN


text:
Difference between revisions of "Minimac: 1000 Genomes Imputation Cookbook"
|Line 327:
|Line 327:
[http://www.eurac.edu/en/research/institutes/centerofbiomedicine/Software/GWAtoolbox.html GWAtoolbox]
[http://www.eurac.edu/en/research/institutes/centerofbiomedicine/Software/GWAtoolbox.html GWAtoolbox]
== Questions and Comments ==
== Questions and Comments ==
Please contact [mailto:firstname.lastname@example.com Goncalo Abecasis], [mailto:firstname.lastname@example.com Christian Fuchsberger (minimac)] or [mailto:firstname.lastname@example.com Yun Li (MaCH)].
Please contact [mailto:firstname.lastname@example.com Goncalo Abecasis], [mailto:firstname.lastname@example.com Christian Fuchsberger (minimac)] or [mailto:firstname.lastname@example.com Yun Li (MaCH)].
Revision as of 18:55, 27 August 2012
This page documents how to impute 1000 Genome SNPs using Minimac, which is typically the preferred approach for imputation using large reference panels such as the 1000 Genomes data. For pointers on how to carry out 1000 Genomes Imputation using IMPUTE2, see IMPUTE2:_1000_Genomes_Imputation_Cookbook.
Before reading this tutorial, you might find it useful to spend a few minutes reading through the main Minimac documentation.
Getting Started
Your Own Data
To get started, you will need to store your data in Merlin format pedigree and data files, one per chromosome. For details, of the Merlin file format, see the Merlin tutorial.
Within each file, markers should be stored by chromosome position. Alleles should be stored in the forward strand and can be encoded as 'A', 'C', 'G' or 'T' (there is no need to use numeric identifiers for each allele).
The latest reference panel generated by the 1000 Genomes project uses NCBI Build 37 (HG 19). Make sure that your data is on Build 37 (or Minimac may ignore genotyped markers whose names have changed in build 37). If you are trying to convert your data from an earlier genome build to build 37, you'll probably find the dbSNP merge table (table description on the NCBI website), which logs rs# changes between dbSNP builds, and the UCSC online liftOver tool, which converts genome positions between different genome builds, to be quite useful. We have aslo documented ( Link) a general procedure to convert genome positions and rs number between builds.
If you are planning to use imputation with the MetaboChip, you might find a list of SNPs whose order varies between NCBI genome build 36 and 37 convenient. Here it is: List of Metabochip SNPs Whose Order Changes With Build
Note: For the most recent reference panel in VCF format by default GWAS SNPs are expected to be in the chr:pos format e.g. 1:1000; otherwise, for GWAS SNPs in the rs..... format you have to set the --rs flag
Quality Control
You should apply standard quality control filters to the set of SNPs that you use as input to the imputation procedure. These filters are typically study specific but usually a series of per marker and per individual quality checks.
Per marker quality checks typically evaluate:
- Genotype completeness (markers with relatively high missingness rates are typically excluded)
- Hardy Weinberg equilibrium (markers with clear deviations from Hardy Weinberg proportions are typically excluded)
- Duplicate concordance (markers with high discordance rates are excluded)
- Mendelian inconsistencies (when parent-offspring pairs are available, markers with an excess of Mendelian inconsistencies are typically excluded).
- Polymorphism check (monomorphic markers can represent assay failures and are typically excluded).
Per individual quality checks typically include:
- Check for per sample completeness (samples with high missingness rates are typically excluded)
- Check for per sample heterozygosity (samples with unusual heterozygosity are typically excluded)
- Inspection of principal component or multi-dimensional scaling plots (genetic ancestry outliers are usually excluded)
- Check for related individuals (if related samples are identified, the analysis plan must be adjusted or they must be removed)
With older genotyping platforms, low frequency SNPs are also often excluded because they are hard to genotype accurately. With more modern genotyping arrays, the accuracy of genotype calls for low frequency SNPs is less of a concern.
Two good ways to verify that you have used appropriate quality control steps are to generate a Q-Q plot for your dataset and to calculate a genomic control parameter. If these are not satisfactory, it may be useful to investigate before proceeding to imputation.
Reference Haplotypes
Reference haplotypes generated by the 1000 Genomes project and formatted so that they are ready for analysis are available from the MaCH download page. In our hands, it is ideal to always use the most recent release since generation of additional sequence data, improvements in variant discovery, genotyping and haplotyping strategies typically result in noticeable improvements in data quality. When this page was written, the most recent release of 1000 Genomes project haplotypes was the Integrated Phase I release, including 1092 individuals. We recommend to use the reduced GIANT all population panel (no monomorphic and singleton sites) GIANT.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL.vcf.gz.tgz
Furthermore, we provide also a Metabochip specific reference panel (GIANT.metabo.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL.vcf.gz.tgz). This reduced reference panel is a time saver, since it focuses on the well-imputable fine-mapping regions.
Minimac Imputation
Minimac relies on a two step approach. First, the samples that are to be analyzed must be phased into a series of estimated haplotypes. Second, imputation is carried out directly into these phased haplotypes. As newer reference panels become available, only the second step must be repeated.
Pre-phasing - MaCH
A convenient way to haplotype your sample is to use MaCH. A typical MaCH command line to estimate phased haplotypes might look like this:
mach1 -d chr1.dat -p chr1.ped --rounds 20 --states 200 --phase --interim 5 --sample 5 --prefix chr$chr.haps
This will request that MaCH estimate haplotypes for your sample, using 20 iterations of its Markov sampler and conditioning each update on up to 200 haplotypes. A summary description of these parameters follows (but for a more complete description, you should go to the MaCH website):
-d sample.dat
|Data file in Merlin format. Markers should be listed according to their order along the chromosome.
-p sample.ped
|Pedigree file in Merlin format. Alleles should be labeled on the forward strand.
--states 200
|Number of haplotypes to consider during each update. Increasing this value will typically lead to better haplotypes, but can dramatically increase computing time and memory use. A value of 200 - 400 is typical. If computing time is a constraints, you may consider decreasing this parameter to 100. If you have substantial computing resources, consider increasing this value to 600 or even 800.
--rounds 20
|Iterations of the Markov sampler to use for haplotyping. Typically, using 20-30 rounds should give good results. To obtain better results, it is usually better to increase the
--states parameter.
--interim 5
|Request that intermediate results should be saved to disk periodically. These will facilitate analyses in case a run doesn't complete.
--sample 5
|Request that random (but plausible) sets of haplotypes for each individual should be drawn every 5 iterations. This parameter is optional, but for some rare variant analyses, these alternative haplotypes can be very useful. If you are not short of disk space, you should consider enabling this parameter.
|Tell MaCH to estimate phased haplotypes for each individual.
|Reduce memory use at the cost of approximately doubling runtime.
You should be able to run this step in parallel and in our cluster we'd use:
foreach chr (`seq 1 22`)
runon -m 4096 mach -d chr$chr.dat -p chr$chr.ped --rounds 20 --states 200 --phase --interim 5 --sample 5 --prefix chr$chr.haps
Imputation into Phased Haplotypes - minimac
Imputing genotypes using minimac is a straightforward process: after selecting a set of reference haplotypes, plugging-in the target haplotypes from the previous step and setting the number of rounds to use for estimating model parameters (which describe the length and conservation of haplotype stretches shared between the reference panel and your study samples), imputation should proceed rapidly. Because marker names can change between dbSNP versions, it is usually a good idea to include aliases file that provides mappings between earlier marker names and the current preferred name for each polymorphism.
A typical minimac command line, where the string $chr should be replaced with an appropriate chromosome number, might look like this:
== using a VCF reference panel == minimac --vcfReference --refHaps ref.vcf.gz --haps target.hap.gz --snps target.snps.gz --rounds 5 --states 200 --prefix results Note: GWAS SNPs (file --snps target.snps.gz) are by default expected to be in the chr:pos format e.g. 1:1000 and on build37/hg19; otherwise, please set the --rs flag
A detailed description of all minimac options is available elsewhere. Here is a brief description of the above parameters:
--refHaps ref.hap.gz
|Reference haplotypes (e.g. from MaCH download page)
|This option specifies that the provided --refHaps file is provided in VCF format , no --refSNPs file needed.
--snps chr.snps
|SNPs in phased haplotypes. These should largely be a subset of the SNPs in the reference panel.
--haps chr.haps.gz
|Phased haplotypes where missing genotypes will be imputed.
--prefix imputed
|Optionally, a string that is used to help generate output file names.
Again, you can speed-up things by running this step in parallel and in our cluster we'd use:
foreach chr (`seq 1 22`)
runon -m 1024 minimac --refHaps ref.hap.$chr.gz --vcfReference \
--haps chr$chr.haps.gz --snps chr.$chr.snps --prefix chr$chr.imputed
Further Time Savings
The recipe above imputes whole chromosomes, one a time. A further time savings is possible by imputing chromosomes in chunks, a process that can be facilitated using the ChunkChromosome tool. This tool automates some of the manual editing steps that would be required to divide each chromosome into more manageable chunks. It also interfaces with minimac to ensure SNPs that overlap between chunks are only imputed once.
Recall that the original analysis script might have looked like this:
# Build SNP lists for each chromosome
foreach chr (`seq 1 22`)
awk '{ if ($1 == "M") print $2; }' < chr${chr}.dat > chr${chr}.snps
# Estimate haplotypes for all individuals, one chromosome at a time
foreach chr (`seq 1 22`)
mach -d chr$chr.dat -p chr$chr.ped --rounds 20 --states 200 --phase --sample 5 --prefix chr$chr.haps >& chr$chr-mach.log &
# Impute into phased haplotypes
foreach chr (`seq 1 22`)
minimac --refHaps ref.hap.$chr.gz --vcfReference \
--haps chr$chr.haps.gz --snps chr$chr.snps --prefix chr$chr.imputed >& chr$chr-minimac.log &
A modified script, using ChunkChromosome would look like this (chr:pos GWAS SNP IDs):
@ length = 2500
@ overlap = 500
# Estimate haplotypes for all individuals, in 2500 marker chunks, with 500 marker overhang
foreach chr (`seq 1 22`)
ChunkChromosome -d chr$chr.dat -n $length -o $overlap
foreach chunk (chunk*-chr$chr.dat)
mach -d $chunk -p chr$chr.ped --prefix ${chunk:r} \
--rounds 20 --states 200 --phase --sample 5 >& ${chunk:r}-mach.log &
# Impute into phased haplotypes
foreach chr (`seq 1 22`)
foreach chunk (chunk*-chr$chr.dat)
set haps = /data/1000g/hap/all/20101123.chr$chr.hap.gz
set snps = /data/1000g/snps/chr$chr.snps
minimac --refHaps $haps --refSnps $snps --vcfReference \
--haps ${chunk:r}.gz --snps ${chunk}.snps --autoClip autoChunk-chr$chr.dat \
--prefix ${chunk:r}.imputed >& ${chunk:r}-minimac.log &
Using ChunkChromosome would look like this (rs GWAS SNP IDs):
@ length = 2500
@ overlap = 500
# Estimate haplotypes for all individuals, in 2500 marker chunks, with 500 marker overhang
foreach chr (`seq 1 22`)
ChunkChromosome -d chr$chr.dat -n $length -o $overlap
foreach chunk (chunk*-chr$chr.dat)
mach -d $chunk -p chr$chr.ped --prefix ${chunk:r} \
--rounds 20 --states 200 --phase --sample 5 >& ${chunk:r}-mach.log &
# Impute into phased haplotypes
foreach chr (`seq 1 22`)
foreach chunk (chunk*-chr$chr.dat)
set haps = /data/1000g/hap/all/20101123.chr$chr.hap.gz
set snps = /data/1000g/snps/chr$chr.snps
minimac --refHaps $haps --refSnps $snps --vcfReference --rs --snpAliases dbsnp134-merges.txt.gz \
--haps ${chunk:r}.gz --snps ${chunk}.snps --autoClip autoChunk-chr$chr.dat \
--prefix ${chunk:r}.imputed >& ${chunk:r}-minimac.log &
Although the loss in accuracy will typically be small, analyses of small chromosome chunks will necessarily result in slightly less accurate results. The differences will be large in populations where haplotype sharing is expected to extend further (for example, in Finland and Sardinia we find that haplotypes can be estimated accurately over several megabases and focusing on small chunks of chromosome will make these matches harder to identify).
X Chromosome Imputation
minimac (version 8.15.12 or newer) supports the imputation of genotypes on the X chromosome (reference haplotypes can be found here)
1. Split X chromosome pedigree file by sex
- For females: follow the same protocol as for autosomes
- For males
- Convert the pedigree file into a MaCH haplotype file (missing genotypes should be encoded as: "0" or "." or "N" )
- <Example of a male only pedigree file; hemizygous males appear as homozygotes >
- ...
- <End of pedigree file>
- <Example of the corresponding haplotype file>
- ...
- <End of the corresponding haplotype file>
2. Impute non-pseudo-autosomal part by sex
Impute females and males separately
minimac --refHaps chrX.no.auto.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL.vcf.gz --vcfReference --haps females.hap --snps females.snps minimac --refHaps chrX.no.auto.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL.vcf.gz --vcfReference --haps males.hap --snps males.snps
3. Impute pseudo-autosomal part by sex
Impute females and males separately
minimac --refHaps chrX.auto.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL.vcf.gz --vcfReference --haps females.hap --snps females.snps minimac --refHaps chrX.auto.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL.vcf.gz --vcfReference --haps males.hap --snps males.snps
Imputation quality evaluation
Minimac hides each of the genotyped SNPs in turn and then calculates 3 statistics:
- looRSQ - this is the estimated rsq for that SNP (as if SNP weren't typed).
- empR - this is the empirical correlation between true and imputed genotypes for the SNP. If this is negative, the SNP alleles are probably flipped.
- empRSQ - this is the actual R2 value, comparing imputed and true genotypes.
These statistics can be found in the *.info file
Be aware that, unfortunately, imputation quality statistics are not directly comparable between different imputation programs (MaCH/minimac vs. Impute vs. Beagle etc.).
GWAS result QC and SNP harmonization
More details to follow; in the meantime please check our GWAtoolbox R-package out:
Questions and Comments
Please contact Goncalo Abecasis, Christian Fuchsberger (minimac) or Yun Li (MaCH).


text:
Here's the latest article from the Addictions & Children site at BellaOnline.com.
Aram's Letter
Part 3 of Arams' Story:
Please visit addictionsandchildren.bellaonline.com for even more great content about Addictions & Children.
I hope to hear from you sometime soon, either in the forum or in response to this email message. I thrive on your feedback!
Have fun passing this message along to family and friends, because we all love free knowledge!
Susan Hubenthal, Addictions & Children Editor
One of hundreds of sites at BellaOnline.com


text:
The Corinthian Creed
by Shawn McEvoy
Be on your guard, stand firm in faith, be men of courage, be strong; do everything in love. - 1 Corinthians 16:13-14
Today's verse hangs on a board on the wall of my son. But years ago, long before my son was even an inkling, I came across that verse as I was sending my own father one of many letters I composed over the years to share with him the importance of salvation, and the value of life in Christ. My sister, mother, and I came to know the Lord in 1980, but it took another 17 years, seven months, and 26 days worth of praying, heart softening, and brokenness for Dan McEvoy to surrender.
And it wasn't this letter or the above verse that pushed him into it. No, this letter I was writing simply to tell him how blessed I was to have begun dating a woman (who eventually became my wife) for whom faith came first, and I was giving God all the glory and credit and all that good stuff, and probably telling him how God delights in blessing those who trust in Him.
With the letter I enclosed a quick-and-dirty page of graphic art involving the aforementioned verse from Corinthians in some fancy font, with a clip-art picture of a sailboat, kind of as a visual aid to my letter, indicating, I suppose, what it was like for the man of God to live in this world under the Captaincy of Christ.
Well, so. After he died in 2001, I found that letter and piece of "art" in my father's desk, looking as if it had been read and glanced at often. Something in me knew then that if I were ever to have a son, I'd commit to raising him to manhood under these same five principles:
- Be on your guard. Be ready, be alert. Expect God to be involved, expect Satan to attack. Let the wonder of creation still catch your eye.
- Stand firm in faith. Be unmoved because you know intimately that of which you believe in. Become biblically literate.
- Be a man of courage. Fear is not from God (2 Timothy 1:7), so go your way boldly. The worst that can happen – even death – still ends in victory and glory for the Christian.
- Be strong. Physically, yes, let's take care of ourselves, and present our bodies as holy. But remember that the Lord is the strength of the strong (Ephesians 6:10), and that "when I am weak, then I am strong" (2 Corinthians 12:10).
- Do everything in love. Here's your motivation, because he that doesn't love doesn't know God (1 John 4:8), and the world shall know you by your love (John 13:35).
So when Jordan was born, and we had the dedication service at our church, that's the verse we selected to have read. When he was about two-and-a-half, he started reciting it by memory and making up arm/hand motions to go with it. We call it our "Man-Creed."
But here's the secret: these couple verses from the closing of Paul's first letter to Corinth aren't first-and-foremost for Jordan… they're for me.
When I first realized that, it caught me, ironically enough, "off my guard." I had been more than happy to tell my own father how to "be a man," and was perfectly willing to raise my son to be one according to the Word. How, I wonder, did I intend to do so without living out the credo, making it my own?
The Commentary Critical and Explanatory on the Whole Bible comments upon the 1 Corinthians passage thusly: "[Paul] shows that they ought to make their hopes of salvation to depend not on Apollos or any other teacher; that it rests with themselves." Yes, and on how I am willing to live, or better, whether I am willing to let my life be of greater worth than my words.
I don't know about the other guys out there, but it definitely helps me to have something to live by, to recite, to write on my heart, ponder the meaning of, and connect to other scriptures as I strive to be a man after God's own heart. And it doesn't hurt that this creed I now try to follow is affecting its third generation in my family.
Intersecting Faith & Life: Allow me to recommend teaching your child – no matter how young – to recite Bible verses that reflect who they are and can be in Christ, and make it real in their lives. But while you're doing it, "be on your guard." One of them may just become your own credo.
Further Reading
Ephesians 6:10
Creed: More than Words
Why Memorize Scripture?
Check out fantastic resources on Faith, Family, and Fun at Crosswalk.com!
Want to grow your prayer life? The So Much More Podcast shows you how to create space to be with God. This podcast, hosted by Jodie Niznik, introduces you to two types of scripture experiences: Lectio Divina and Imaginative Prayer. Join our growing prayer community today!


text:
Shady contractors and home repair scams can cost you. Discover tips to protect yourself from repair scams by learning how to spot home repair fraud.
Clouds aren't the only things that roll in with tornadoes, hurricanes, wild fires or other types of severe weather. Also on that horizon are unscrupulous contractors trying to scam you. Home repair scams arrive in the aftermath of storms as shady contractors cash in by delivering substandard or incomplete work. Help protect yourself, your money, and your home from repair rip-offs by learning to spot the red flags.
What are warning signs of a shady contractor?
Be watchful of the following tactics. And remember, trust your gut. If you don't get a good feeling about the contractor, don't use them.
- Offers unsolicited services: If a contactor stops by and gives you an unexpected estimate for projects like driveway sealing, chimney rebuilds and roof repair — projects that are commonly pitched to homeowners.
- Has "material left over": Be cautious if the quote includes a reduced price on the work because of "materials left over from a job down the street".
- Home demonstration discount: If the quote includes a discount for using your home as a demonstration.
- Extra pushy: Employs pushy door-to-door sales tactics.
- Limited time offers: If the contractor says you need to place a deposit immediately to secure a spot in his schedule or to get a good price on material.
- Not local: Appear to be from out of town or working out of a pickup truck.
- Demands immediate payment in full: You should not pre-pay for any work.
- Accepts cash only: Always a red flag.
- Provides no written contract: All the details of the work should be written out in advance.
- No references: And are not willing to produce them.
- No insurance or licensing: Fails to provide proof of insurance and proper licensing.
- Finance through a friend: Suggest financing or recommend financing through someone they know.
- Ask you to secure any required permits: Most communities require the contractor to acquire the proper permits.
- Not insured: Don't take promises of insurance compensation for any repairs.
What should you look out for after a contractor begins a project?
- Calls from subcontractors: Subcontractors are reaching out to you personally for payment for work completed.
- Pricey unexpected expenses: It is common to have unexpected expenses arise, but when they are frequent or very expensive. Make sure to reach out to a home inspector or call another reputable contractor in your area for a second opinion.
- Lack of activity: There is no activity on the job site during peak working hours.
- Poor communication regarding progress: If your contractor stops returning your calls and is not showing up to the job site, contact your local Better Business Bureau.
- Shoddy tools and low grade materials: Ensure the material the contractor is using matches what he listed on the estimate.
Ways to protect yourself from shady contractors
When looking for a contractor to remodel, renovate your home or to help you recover from a weather disaster, consider these tips.
- Get multiple quotes from local established businesses.
- Take time to make your decision.
- Do your research. Look into professional affiliations and Better Business Bureau reports, and follow up on references from previous clients.
- Check for up-to-date licenses, and verify insurance protection.
- Insist on written estimates and a contract that includes contact information, important dates, and a breakdown of costs. According to Federal Trade Commission rulings, you may be able to cancel a contract of more than $25 within three business days of signing it at your home or in a seller's temporary business location.
The National Association of Home Builders offers additional tips for hiring a dependable professional contractor. For storm repair tips, visit the Better Business Bureau website. And before you hire any contractor for storm-related repairs, always contact your insurance agent to be sure repairs will be covered.


text:
A recent feature on the politics page of The Christian Post discusses the issue of income inequality in America, and various Christian proposals for the best way to address it. Professor Ron Sider of Palmer Theological Seminary argues that the appropriate response to the "enormously centralized" economic and political power we see in America today is for the government to redistribute wealth via tax hikes on the rich and increased public investment in our poorest citizens. From the article:
"[S]ider supported higher taxes on the rich and a combination of tax breaks and education reforms to help the poor. He supported an upper income tax rate of 50 percent for those making over $5 million per year. He also called for the federal government to tax dividends and capital gains at the same rate as other income,' which would target the rich and raise more money to reduce the deficit.
For the poor, 'biblical justice demands access to the productive resources so they can earn their own way,' Sider argued. In the information age, the productive resource is knowledge, so he supported education reforms to help the poorest Americans. He suggested a major trial period for both school vouchers and public school reform. Whichever most helps the minority poor should be universally implemented.
Sider argued that, rather than segregating themselves into 'white suburban enclaves,' Christians should advocate for spending more money on public schools, especially in minority areas. They should also support food stamps, Pell Grants, and increasing tax refunds for the poor. He would reform government along this principle — 'If you work full time responsibly, you ought to get to 125% of the poverty level and have health insurance.'"
Mr. Sider's proposals appeal to sentiment, but are ultimately ill-conceived. Few would argue with his observation that wealth and special interests play too great a role in America's political and economic landscape. The solution is not, however, to tip the scale in the other direction by soaking the rich and increasing government control over public education. A better approach is to take the thumb off the scale and let markets and charities do their work. Economic justice should not be the result of competing special interests advocating for bigger and bigger slices of government largesse. Economic justice should be the result of free, virtuous, and lawfully acting individuals and groups interacting with others in their community for their own betterment and that of others, with each contributing their time and talent and each reaping rewards commensurate with their efforts and talents. Would such a model result in income equality? Most certainly not, but it would result in a fair and level playing field. It would realize the American dream of equal opportunity that has drawn immigrants to these shores for the last 300 years.
Of course, no one is saying that government doesn't have an obligation to help those who can't help themselves. Civilized societies have always recognized a collective obligation to help the weak and the vulnerable, and government has a role to play in this equation. It is naïve and ignores the lessons of history, however, to think that the best solution is for government to enforce income equality through punitive tax policy and an expanded welfare state. This approach belies the same old social engineering mentality that has wrought so much human misery and suffering over the last century. When governments try to legislate the perfect society, they inevitably resort to oppression and tyranny in order to eliminate variety and establish total control. In the end, everyone suffers as productivity and liberty are suppressed
As a theologian, Sider should understand that human beings are sinful. As an observer of human nature, he should certainly recognize the truth of Lord Acton's observation that "power corrupts, and absolute power corrupts absolutely." In light of these immutable truths it's hard to understand why Sider would place so much trust in government to right society's wrongs. You can be sure that increased power will be abused and that the politicians will use it as a vehicle for buying and controlling another constituency in order to perpetuate their personal power. While we should all strive for a just society, let us not fall victim to the deluded notion that government is the best instrument for achieving that goal. Instead, we should strive as individuals and families and churches to stand as examples of hard work, thrift, self-denial, and charity, and let those virtues do their work in transforming society.
As for education, the facts do not support Sider's position. Federal spending on education has gone up steadily over the decades, with little to show for it. Money means little when it is controlled by unaccountable bureaucrats who care more about appeasing the teachers' unions than they do about educating children. Here again, markets can be a much more effective agent of transformation, because markets are based on performance, demand accountability to customers, and are stimulated to perform by competitors. Reforms like school choice, vouchers, and charter schools have been shown to work, yet they are opposed by the federal educational apparatus at every turn. The special interests at the NEA and their political patsies prefer the status quo, because the status quo keeps them in power.
Bottom line, in this life we will not achieve utopia, and most certainly not through government. The Founders understood this, which is why they went to such great lengths to establish limited government and to put in place checks and balances. The American people would be better off to take their focus off of Washington, D.C., and concentrate instead on building virtuous communities. Professor Sider's so-called "biblical solution" is likely only to create a governmental Frankenstein.
Publication date: December 31, 2013


text:
Plastic Challenge: Beth Terry, Week 21
Location:Oakland, California, United States
Name: Beth Terry
Week: 21
Personal Info:
I am the founder of MyPlasticfreeLife.com and have been collecting my plastic and attempting to live as plastic-free as possible since June of 2007.
See my previous years' tallies at:
Beth Terry's personal blog:
List of plastic items REFUSED this week. (Yay!)
Plastic cups, bottles, bags, produce bags, and more…
Total items collected: 6
Total weight: 1.2 oz
Items: Recyclable
Items: Nonrecyclable
1-2) Packing tape from 2 cases of Plastic-Free books.
3-4) Packing slip pouches from 2 cases of Plastic-Free books.
I explain the packing tape and packing slip pouches in my post about receiving my books here: /2012/05/compost-this-book-but-first-check-out-how-cool-it-is/. Read below for further explantion.
5) One plastic envelope window. Read about what envelope windows are made from: /2009/04/year-2-week-42-results-05-oz-of-plastic/
6) Piece of tape — don't remember the source.
What items can I easily replace with plastic free or less plastic alternatives?
I have asked my publishing company to skip the plastic pouch. I don't need a packing slip, since they email me the invoice. They have agreed not to include the plastic pouch for future shipments.
I have also asked the person who sent the window envelope to send envelopes without windows in the future, and he has agreed.
What items would I be willing to give up if a plastic free alternative doesn't exist?
What items are essential and seem to have no plastic-free alternative?
The plastic packing tape does not have an alternative, unfortunately, because the books have all been packed up by the printer, so that horse has already left the barn. If we do a second printing, I will request plastic-free tape, but for the rest of this year, as long as I sell books, I am going to have plastic packaging tape in my tallies. *Sigh*


text:
Growing up in Brooklyn as the child of Nigerian immigrants, 33-year-old Adepero Oduye knew how to wear two hats. Inside her home, she was an obedient Nigerian child, eating beef stews for breakfast and wearing the traditional garb. But in school, she was a Brooklyn kid who hung out with friends and listened to rap. This duality would prepare Oduye for her breakout performance as the lead in the independent film Pariah, a coming of age story of a young African American teen searching for her sexual identity and acceptance.
"I was straddling two worlds," said Oduye. "It was little Nigeria in the house and then going to school I remember feeling like I was different."
But it was tragedy that made her turn to acting. Oduye's father, who was studying to become a doctor, died unexpectedly when she was 19, leaving her mother to care for all seven children. Oduye and her older siblings helped out with whatever money they were able to make from their jobs, but it was difficult. She was a premed student at Cornell University at the time, and she realized she did not want to be a doctor.
"That was the wake up call," said Oduye, who is at once soft spoken and yet animated and vivacious. "Life is short. If you know what you want to do, you have to at least try."
Her mother did not understand her choice.
"She didn't see it as a profession," she said. "Acting was not for people like us. For her, movies were not for African or black people. I remember thinking, 'Yes, mom, I know I am black but I still want to act.' She knew instinctively it was going to be a hard road."
And so Oduye began her long journey into acting. She played bit parts in theater and on television shows such as Law & Order. But it was not until 2006 that she received an email that would change her life. It was a casting call for Pariah, a short film being made by Dee Rees, a graduate student at New York University's film school. Oduye donned on her little brother's baggy jeans, shirt and cap and walked in for the audition thinking maybe she could land a spot as an extra.
But Rees knew immediately she had found Alike, the 17-year-old protagonist of the film who is desperately trying to be herself and yet not disappoint her traditional and devout parents.
"I needed someone who could be as beautiful as a masculine identified woman as in a feminine identified way," said Rees. "Also one of the things that I was looking for was someone who had an outsider experience. Adepero had been in situations where she felt she was on the outside because of her heritage."
Pariah touches on the often-taboo subject of homosexuality among African American and Latino women in New York. It is an underground scene, with the women hitting clandestine clubs playing roles of either butch or femme and then hiding the reality from their families or risk rejection. The film was semi-autobiographical for Rees, who was raised Methodist and whose parents initially refused to accept her homosexuality.
Like most independent films, it was a long process from script to screen. The short was accepted into the Sundance Screenwriters' Lab in 2007 where they developed it further. Raising the money to make the film was extremely difficult for a film many financiers considered edgy but "small" and "specific."
Producer Nekisa Cooper hit up every independent film financing avenue she could think of and approached Spike Lee, who agreed to executive produce the film. Oduye and the cast dove into the parts with research by reading Audre Lorde's Zami and going into Dave & Buster's gaming restaurant in Times Square dressed as masculine lesbians, to watch people's reactions.
Although Oduye is not grappling with the same issues as her character, she found an affinity for Alike's struggle to unmask her true self. She was brought back to the time many years ago when she was hired to work as an improv actor for a teen job program at the Center for Family Life in Brooklyn. For that brief moment in time, she felt she could truly express herself through acting.
"I identified with that feeling of not feeling free," she said. "You know there is a person deep down inside of you that is beautiful but is covered with all this stuff. You know it is there but you want to uncover all that stuff and be the person you are meant to be."
Pariah premiered at this year's Sundance Film Festival and was bought by Focus Features.
The journey created a tight bond between the cast and crew. Cooper and Rees now consider Oduye a close friend. Oduye knitted caps and baked cakes for the crew during production. Both director and producer sound like proud parents when they recall how much Oduye's expectations of herself have changed.
"She has come into herself," said Cooper. "She didn't think she could be the lead in a film five years ago. She had bit parts in movies but I think that this has changed her dramatically. We have seen her grow in confidence."
Added Rees, "She is full of grace, friendly, and genuine. She is a really well rounded person."
Oduye, who looks a decade younger than her real age, knows that with her features and skin color, Hollywood will be a hard place to crack. On the day of the interview, she is startlingly beautiful wearing a red silk dress and soft, small diamond earrings contrasting against her smooth dark skin. But she is undaunted and knows exactly where she wants to take her career.
"It has been challenging, but at the end of the day it has made me who I am and I like the actor that I am today," she said. "The journey has made it clear what kind of work I want to do and what kind of people I want to be with. I want to tell authentic, real stories with real characters."
She knows that Pariah's story is not "small" and "specific" but a universal story. For one, it has touched her Nigerian mother to the core.
"After Sundance, my mother was in Nigeria and she called me and said 'Pariah needs to come to Africa because they are killing people here because they are gay,'" said Oduye, smiling broadly. "She never talks about LGBT issues anywhere. But my participation in this film opened her mind up a little more. If that can happen to my mother, anything is possible."