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"Exceptional times call for exceptional measures", or so the mantra goes these days. The Great Lockdown has lead us to close ourselves in our own homes – but has also locked away many of our civil and political rights, such as the freedom of assembly or the normal functioning of parliamentary systems.
Not that quarantine measures aren't justified, when the choice is between temporary containment or widespread viral contagion. Laws and norms – the constitutional-legal order of a society – are set for those circumstances the legislator can foresee. Contrary to a war, which still requires a formal declaration at a definite point in time, a global pandemic does not abide by the principles of international law – how could it? – and hits without warning.
The state of exception
A crisis of such magnitude, then, naturally calls for urgent and forceful actions in response. For such actions to be undertaken, the Executive branch of government requires to wield emergency powers, which are provided for in most, if not all, modern constitutions. Farsighted constitutional forefathers, who had just lived through the horrors of fascist authoritarian regimes and the Second World War, rightfully delineated the reach and duration of such "State of exception" provisions. They sought to establish, in the words of German philosopher Carl Schmitt [1], the conditions for and constraints on a "commissarial dictatorship": a momentary suspension of the constitutional order aimed at preserving the constitutional order itself. And yet, as later philosophers rightfully remarked,[2] who's to say that the "sovereign" – he who wields emergency powers during a state of exception – would return them once the crisis passes?
Emergency measures in the EU
Elements of a "state of exception" can be found in the European response to the COVID-19 outbreak. Forget the usual "bad kids on the block", Hungary and Poland: ruling-by-decree, the suspension of elections and parliaments' sessions, restrictions to personal freedoms, have become the norm across Member States. Measures that are justified – and rightly so – by the need to protect the inviolable right to life of citizens. Discomfort has, however, began to surface. In Spain, the contention over the state of emergency could be dictated by the opportunity to exploit the structural weakness of a minority Government for short-term electoral gains. But partisan political interest can't always be the excuse.
It is the right of Parliaments to oversee and the duty of the oppositions – as extremist and filthy their policy proposal may be – to question the actions of Governments. In Italy, the country I know best, the confinement measures have largely been decided by Prime Ministerial decrees, administrative acts with "the power law", which however crucially lack in parliamentary oversight. They have been preferred – for reasons unknown – to other instruments foreseen in the Italian Constitution, which are equally time-bound and that the Government can adopt autonomously, such as law-decrees and legislative decrees. These must be converted into law at a later stage, which allows then for ex-post parliamentary oversight.
The question, rather than whether such measures are momentarily justified, is to whether the precedents we are setting today will stick around after the health crisis. The state of exception is, in fact, the Hotel California of modern democracies: you may "check out anytime [you] like / but [you] can never leave".
- "McGruff/It was all worth it!" by Emily Horne and Joey Comeau (reproduced with permission)
A state of permanent emergency
Western politics has been living in a state of permanent emergency for the past two decades, and emergency-like powers have been used without restraint also in times of peace. Under the guise of ensuring swift legislative processes at EU level, most EU legislation has in the past decade effectively neglected the Treaty-mandated processes in favour of the so-called "trilogues": informal (and thus untransparent) negotiations between the Commission, Council and Parliament on legislative texts. It wouldn't be unconceivable to consider this a mild – yet persistent – version of the Schmittian state of exception.
Let us be very clear: the Commission (as the EU's executive) could hardly ever become an authoritarian institution, not least because it is not "sovereign": it lacks the competences and the tools to assume the emergency powers required to unilaterally impose its will, with all due respect to those who lose their Eurosceptic voices shouting the opposite. As federalists, this is part of our fundamental battle: that no level of Government – local, regional, national, European, global – be ever "sovereign" in the Schmittian sense, able to indefinitely suspend the constitutional order and the rights of its citizens.
Therein also lies the strength and weakness of parliamentary democracies. Parliamentary and judicial processes are slow-by-design, as they are set to distil the elements of a decision to allow for their careful consideration and a well-informed public debate.[3] Decisions taken in secluded, smoke-free rooms are undoubtedly swift, but they will hardly reinforce citizens' confidence in the EU. Can decisions taken in a permanent state of exception, with an eye to the next electoral round, rather than the next generation, really prepare us for the deep and structural changes of the world to come?
The struggle ahead
As some of us edge towards the end of our COVID-19 lockdown period, many questions have surfaced as to how we will slowly return to our previous live: work outside our homes, maintaining social distancing, how we will deal with and pay for the prolonged recession that will outlast an otherwise relatively short-lived (yet not less severe) health crisis. But the question very few seem to ask is that of how we will deal with the lasting effects of the pandemic crisis on our democracies.
A fraught citizenry is easily seduced by the illusions of governmental grandeur: the firm wooden desks from whence quarantines are announced, on a background of golden tapestries and governmental insignias, the subtle suggestion that the Executive is, and will always be, a well-meaning and kind protector - and that, dear reader, is far from certain. A feeble voice in the back of your head is trying to draw attention to the flipside of this situation: read out in the same monotonous voice of the same Prime Minister, it's a statement that democratic checks and balances have, for now, ceased to apply - and that, dear reader, is the truth.
Oh, emergencies are a beguilling call to absolutism, and the powerful are addicted to the sweet pitch of these sirens. That which starts sweet ends bitter, and that which starts bitter doesn't always end sweet. That is why we should cherish parliamentary democracy and its slow processes; and that is also why we cannot give up on our struggle as radical democrats and federalists.


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Turn On:
The White House has announced that President Bush will hold a press conference on Thursday night at 8:30 EDT to discuss his plans for Social Security. What that means for your chance to watch Alan Arkin guest-star as Grace's dad on "Will & Grace" (originally scheduled for 8:30 p.m. EDT on NBC) or the season -- and possible series -- finale of Fox's "Tru Calling" (9 p.m. EDT) one can only guess. But surely, surely, the WB won't postpone its home-makeover show spoof "Mobile Home Disaster" (9 p.m. EDT), right?
Morning Briefing:
Cute as two buttons: While the celeb-gossip world has had its gaze fixed unswervingly on possible couple (and People mag "beautiful people") Brad Pitt and Angelina Jolie (even to the point of creating cover images of them together out of old images), definite couple Tom Cruise, 42, and Katie Holmes, 26, have slipped quietly under the radar into apparently happy companionship. After the duo was photographed looking cozy in Rome, where Cruise is due to accept an award this week, spokespeople for both Cruise and Holmes confirmed that they are "dating." Holmes recently split with her boyfriend of five years -- and erstwhile fiancé -- Chris Klein, shortly after he was arrested for drunk driving. (Newsday, Reuters, N.Y. Daily News)
Jackson trial update: In what the Associated Press is calling a "startling setback to the prosecution," Debbie Rowe, Michael Jackson's ex-wife and the mother of his two eldest children, took the stand on Wednesday and testified that her statements in a video made to counteract the deleterious P.R. effects of Martin Bashir's "Living With Michael Jackson" documentary were not scripted. The prosecution had told the jury that Rowe would testify that Jackson's people had told her what to say, but Rowe said her words were all her own. "I didn't want anyone to be able to come back to me and say my interview was rehearsed," said the former dermatological nurse who was married to Jackson for three years. "As Mr. Jackson knows, no one can tell me what to say." In what may be good news for the prosecution, however, Rowe -- who testified that she and Jackson "never shared a home" and also that she was allowed just eight hours with her children every 45 days -- said that she was not entirely truthful on the video, which she made voluntarily in an attempt "to be reunited with the children and be reacquainted with their dad." Explaining her reasons for dissembling on film, Rowe said, "My personal life was my personal life and no one's business." (Associated Press, N.Y. Post)
Note to self, take apology lessons from this woman: Air America talk-show host Randi Rhodes has expressed remorse for an audio skit that joked about shooting President Bush, which ran on her show this week and sparked some alarm in D.C. "If the bit was understood to be a threat against the president, I need to apologize to the president of the United States, and I do. I also need to apologize to the Secret Service [which] has a very, very serious job. If they had to take two seconds out of their day to look into me, I apologize for that. ... But where is the apology when they threaten judges from the Senate floor or from the House floor? Or where's the investigation into Ann Coulter's mouth?" Rhodes said Wednesday on her show. "[My apology] is sincere. I feel bad that anybody would feel threatened by comedy. That's one thing, but I also feel bad that it wasn't funny. And I also feel bad that there could be a perception that I would be advocating violence against anybody, let alone the president of the United States of America. It's no secret that I think he's a terrible president, but I don't think that anybody should have violence advocated against them in any way, shape or form ever! ... That [skit] will never see the light of day again. It was bad." (WorldNetDaily.com, Drudge)
Also: Judi Dench says Pierce Brosnan will return as James Bond in the upcoming 007 flick "Casino Royale," telling the British tabloid the Mirror, "Despite the fact that everyone on the face of the Earth has been tested as his possible replacement, he'll be doing it again, and it'll be announced come summer." The film's producers are declining to comment. (The Mirror via Megastar.co.uk) ... Ricky Gervais, of the BBC's "The Office," and his production partner Stephen Merchant have signed a deal with HBO to bring a show called "Extras," about an aspiring actor, to U.S. cable TV. "It's an honor to be on the same channel that gave us 'The Sopranos,' and they made me an offer I couldn't refuse," quipped Gervais. (Reuters/Hollywood Reporter) ... Conservative radio host Laura Ingraham appears to be on the mend after undergoing breast-cancer surgery on Wednesday. The cancer does not appear to have spread and the operation "couldn't have gone better," her surgeon said. (N.Y. Post) ... The author of "Stories From a Moron: Real Stories Rejected by Real Magazines," one "Ed Broth," is likely none other than Jerry Seinfeld, who penned the book's foreword. (Page Six) ... A blue-and-white gingham dress worn by Judy Garland in "The Wizard of Oz" has been sold for #140,000 (approx. $267,000) at auction. (Time Out) ... Oh, and you won't want to miss this New York Times article (by occasional Salon contributor Dana Vachon) on high-powered guys swimming naked in NYC. (N.Y. Times)
Money Quote:
Paris Hilton on -- what else? -- herself: "I always wanted to build a brand. Barbie's a brand. I knew I could be like that -- an American princess." (N.Y. Daily News)
-- Amy Reiter
Bookmark The Fix here. To send a hot tip to The Fix, click here.

subset: commoncrawl


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If you need ideas for celebrating your wedding anniversary, take a few tips from Beyoncé. To celebrate her almost-decade-long marriage to Jay Z, the songstress just released a new studio version of her 2015 track "Die With You" for their ninth wedding anniversary, having already shared a stripped-down version of the track that year to celebrate her and Jay Z's then-seventh wedding anniversary. On the hook, Yoncé sings, "'Cause darling I wake up just to sleep with you / I open my eyes so I could see with you / And I live so I can die with you." The songstress also released a touching video montage exclusively on TIDAL (of course) to go along with the ballad. Scenes of the couple at home, at their wedding, on vacation, in the hospital and hanging with Blue Ivy pepper the heartwarming video, which fans have been fawning over.
One to always outdo herself, the singer didn't stop with the release of the single and video. She also released a playlist. For "IV EVER EVER," Beyoncé handpicked 63 tracks from the likes of Sade, D'Angelo, Bilal, Frank Ocean and more to celebrate her love for Jay.
Travel down memory lane with the hottest chick in the game wearing Jay Z's chain when you press play on "Die With You" below. Use your good TIDAL membership to see the full version and to listen to the playlist Beyoncé curated for her bae so you can jam to the sounds of their love and celebrate the couple's wedding anniversary.


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Keep updated
Introducing TAP2BREW; No longer waiting in the queue! Order your favourites and pay ahead. You will now be able to order your favourite Costa Coffee items with a simple TAP from your devices from our Mriehel and Tower Road Sliema outlets.How will this work?
TAP to Serve; Order In-storeSimply sit down at your table, either through your phone camera or through ourloyalty app scan the QR code found on the table, select the items you'd like, proceedto checkout and relax while our Baristas prepare your order and conveniently bring itto you at your table.TAP to Collect; Order from anywhereRunning late for work and do not have the time to wait to order your coffee? Log intowww.tap2brew.com or click on Pay & Collect on our loyalty app Costa Club Malta.Choose your items, location and time of pick up and our Baristas will make sureyou'll find your order ready waiting for pick up when you arrive in store.BONUS REWARDS!To continue celebrating International Coffee Day, download our app Costa Club Malta to receive your FREE primo sized coffee coupon to be redeemed throughout October!
Happy Brewing and Happy International Coffee Day!


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Alabama Information
HVAC Contractors and Techs - CEU RequirementsCEU Requirements: 4 hours per year. If 8 hours are taken in 1 year, 4 of those hours can carry over to the next year licensing period. CEUS must be completed by December 31 of each year.
Licensing Agency: Alabama Board of Heating & Air Conditioning Contractors
Certificate of Completion information is forwarded to the AHJ within 2 business days.


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Large Dog Special Iron Cage Outdoor Kennel 4x2x2m Pet Puppy House Enclosure Run
This versatile dog kennel has multiple uses: playing, exercising, training, or simply keeping your dogs safe. It will be the perfect play paradise for your furry friends! This large dog kennel provides ample exercise space while the chain link mesh all around helps prevent mischief and unexpected accidents, while enabling ventilation. The dog kennel is made of galvanised steel. The hinged door swings outwards and ensures extra security and safety for your dogs thanks to the lockable latch system.
Material: Galvanised steel frame & mesh. Overall dimensions: 385 x 192 x 195 cm (L x W x H).
Door size: 45 x 170 cm (W x H). Ground surface area: 8 m2. Inner dimensions: 186.2 x 376 x 195 cm (W x D x H). Nice to meet you, look forward to cooperate with you.
- Brand: Unbranded/Generic
- MPN: Does not Apply
- Material: Galvanised steel frame & mesh
- Dog Size: 45 x 170 cm (W x H)


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I'm defining "Barack and Chill" as:
What Hawaii residents have to patiently do while awaiting delays caused by President Barack Obama's annual holiday stay.
If you don't Barack and chill, you wouldn't handle delays like this as the freeways are shutdown for the Presidential motorcade making its way to Hickam for their departure.
#HITraffic on H1 from Aiea to Halawa is extra congested due to the First Family's departur… https://t.co/Pw7ENLVsti pic.twitter.com/oel0XNzapM
— GoAkamai (@goakamai) January 3, 2016


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Panic Attacks in Pregnancy
by admin
Hi. I'm Joanie. I've had some issues through out the years with depression and anxiety. But I'd never had a panic attack or anxiety attack until I found out about being pregnant with twins. All the questions, concerns, and added stresses overloaded my system. I didn't even know what they were until I went to the doctor. My heart would race, head would pound, and I'd feel short of breath and light headed or shaky.
I thought at first it may be related to my asthma, but my rescue inhaler did nothing or made it worse. (Not fun when you're already freaking out!) So after three "attacks", two in one weekend, I decided if I can't breathe … neither can the babies, so I went to my doc. She flat out told me what it was; I was in shock. I was not even thinking about stressful things when they happened! Heck, I woke up from a nap the one time and five minutes later, boom. So she put me on a heart monitor to be safe and did routine blood work. All tests were good. Relief … not so much.
How does a pregnant women treat "attacks" when you can't take the meds? "Breathe into a paper bag" was the advice given. I ended up in the ER later that week with another "attack." This time I had gotten upset and emotional about my pregnancy; darn it, the doctor was right. It's all in my head, consciously or not. So now that I'm more aware of the situation, I've been doing better. And I started seeing a therapist to have an objective view on a lot of issues—not just this pregnancy. And it does seem to help … besides, when talking to people who have no personal feelings or attachments to you, you are more honest! So if any of this happens to you, you'll now know you're not alone. Good luck to you all!


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About the Council on Aging Grey Bruce
Our Vision
A community that respects, values and empowers its older adult population.
Our Mission Statement
To be a collective voice supporting the experience of aging through education and leadership providing older adults with the opportunity to participate fully in society.
Board Executive Committee
- Chair
- Tanya Shute
- 1 st Vice Chair
- Wally Halliday
- 2 nd Vice Chair
- Sharron Colter
- Secretary
- Frank Emptage
- Treasurer
- David Bradley
- Members at Large
- Randy Hughes
- Lynn Silverton
- Past Co-Chairs
- Tanya Shute
- Wally Halliday
- Communications
- Wally Halliday
- OACA Representative & Alternate Representative
- David Bradley (Rep)
- Sharron Colter (Alt)
The Strategy
To develop Community Advisory Committees in each of the 17 Municipalities of Grey and Bruce Counties. These Community Advisory Committees (CACs) made up of municipal residents will interface with the older adult residents in there community and bring forward their concerns and issues along with any proposed solutions they may have, to their Municipal Council and the Council On Aging. The CACs will be the eyes, ears, and conscience of the municipality in there community. Each CAC will select one of their member to sit on the Council on Aging, giving each municipality equal representation. This whole concept is designed to give older adult residents in Grey Bruce a COLLECTIVE VOICE!!!
Our COA Goals
- To provide older adults in Grey Bruce with a platform to make their Collective Voice heard at the Municipal, County, and Provincial levels.
- To encourage Municipalities to embed the Age Friendly Community concept in their strategic plans to resolve issues and concerns of their older adult residents.


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[pictured: a party too cool for me]
Yeah, so this exchange pretty much sums it up:
So if I'm not doing a lot of talking at a party or other visit, this is one of the reasons why!
[pictured: a party too cool for me]
Yeah, so this exchange pretty much sums it up:
So if I'm not doing a lot of talking at a party or other visit, this is one of the reasons why!
Ok, if you're not familiar with the phrase and concept of 'uncanny valley,' go read up.
Back? Cool.
Being autistic is like being living in an uncanny valley.
We humans are most comfortable with humans who act like humans and robots who act like robots. Mixing the two together creates an eerie revulsion that jars our expectations and freaks us out.
And of course, how do people describe us higher-functioning autistics? Monotone. Focused. Cold. Rational. Unemotional.
Instead of thinking it was always personal, or that it was my weight, acne, whatever, I should have just rationalized it as "Oh, duh, these people have a reflexive avulsion to humans with robotic tendencies!"
If only.
We're not robots. We're just different.
Where many would become derailed by emotion, we won't. Where others make poor decisions based on anger, spite, and hate, we don't. Where some bask in the warmth of others and feel the benefit of feelings, well, sometimes we can't.
We're no less human. I'm no less human.
I might not look you in the eye. I might flap and jitter while walking and waiting. I probably won't get worked up about hot-button, emotional topics. And my elevated prosody isn't your computer's dictionary talking.
I can't help that you're revolted. And I also cannot pretend to be a normal human the way normal humans don't have to pretend.
If you can, try to see beyond the uncanny valley.
My wife is fond of joking, "Hunter was a Navy brat. Now he's just a brat." I don't object, as it's quite true.
As is the case with many military kids, we often consider joining the service ourselves.
But apparently, that would have been a bad fit for me.
Could I make it through basic? Eh, probably not. Could I survive wearing those big goofy glasses? Not likely.
Beyond that, there was something more fundamental and situational.
I remember frustrating my dad to no end growing up. He was quick to point out my skills, but I tended to get in the way of my own potential.
"Hunter," he said, "you could be just about anything you want! A lawyer, a doctor, an anesthesiologist! But — not an Air Force pilot."
"Why not?" I asked.
"Because you always have to ask why."
He clarified:
"When you're flying your jet, and you get that order to EJECT, EJECT — you're not going to have time to say 'Gee officer, why do I have to eject?' There's nothing wr—' and then BOOM!" he exclaimed, "you're hit by a missile."
It'd be some sweet irony to write this and say, "Well, hah — I'm a Lieutenant Colonel in the Air Force with over 200 sorties flown—"
It's always mine to question why.
That mindset doesn't always fit everywhere.
I'm far from a rebel – I mean, I survived four years of Pensacola Christian College of all places. But I'm not always a rule-follower either.
I'd like to say I'm just unnaturally curious, but I'm too lazy for that.
There's a different sort of autistic slant.
We're quick to question logic — we need things to make sense.
I know that's not the way the world, society, people always work. But the autistic mind rests in understanding, putting pieces together — if they fit, then that helps dispel so much objection, reaction, and question.
There's a world of difference between "I'm not sold, but I see the logic," vs. "I don't even understand the intent here."
I'm always one to make reply,
And never cease to reason why,
Theirs but to do and (try not to) die (if I don't have to)
And for what it's worth, I could always fly commercial airliners. Not like I'd need to rationalize ejecting out of one of those . . .


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Solasta - meaning luminous or shining in Scottish Gaelic is a textured cowl to make any yarn shine. This elegant shawl has simple knitting stitches, lace mesh pattern and only takes one skein of lovely yarn. This pattern is charted and includes written instructions.
Kit includes & 1 skein of Anzula Squishy (80% merino wool, 10% cashmere, 10% nylon) and pattern (pdf file sent to your email).


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In today's medical marketplace, physicians such as urologists and ObGyns are finding it more and more difficult to keep doors open in the face of deceased reimbursements and patients who lack medical insurance. Additionally, attracting new patients is harder than ever, thanks to the prevalence of websites which allow patients to rate their doctors, sometimes leaving bad reviews which do not adequately depict the situation from both sides.
Unfortunately, one bad word-of-mouth review can lead to decreased business. Listed here are the primary sources of patient complaints in ObGyn and urology practices, as well as tips for overcoming these issues.
Long Wait Times
Long wait times are a top patient complaint for both urologists and gynecologists. In some instances, long wait times can be attributed to emergency cases that doctors must attend to immediately, which is outside of the doctor's control. If a urologist or gynecologist frequently deals with emergency cases that throw off the day's schedule, it can be beneficial to work a couple 15 – 20 minute "open" appointment slots into the day in order to deal with these cases without throwing off the equilibrium of the entire practice.
In other instances, patients must deal with long wait times because of other patients. When patients are routinely late for appointments, this inconsideration puts a strain on the entire work flow and can make it difficult for a doctor to remain on time with his or her other appointments. If this problem is a continual concern, doctors can include time buffers between patients – or start charging repeat offenders a fee for tardiness.
Finally, many doctors must keep a strict schedule of patients to meet quotas for the day in order to be profitable, due to the current state of medical reimbursements. If being overbooked is the main reason for long wait times, doctors can audit their practice to look for ways of streamlining daily routines and improving efficiency as much as possible.
Two ways to effectively combat long wait times are: automated text messaging appointment reminder systems and calls to patients confirming appointment times. Text messages have a 98% open rate in the U.S., so you are virtually assured that a message sent to a patient will be seen. Text message reminders about appointments can drastically reduce no-show rates and help get patients to their appointments on time, which in turn lower waiting times because it streamlines the flow of patients throughout the day. Furthermore, practices calling patients just prior to their appointments has a similar impact and allows for easily rescheduling if a conflict has arisen for the patient.
Not Taking Pain Seriously
Recent studies have indicated that women's pain is not taken as seriously as men's pain, particularly when it is gynecological. Indeed, women are shown to be treated less aggressively until it is proven beyond doubt that their symptoms are just as severe as that of male patients. In general, women report more severe pain1 than men, and have more frequent incidences of pain for longer duration, but are time and again treated less aggressively – despite no biological difference between their pain mechanisms. In fact, the medical community has a term for this phenomenon: the Yentl Syndrome2, which is defined as the necessity of women to prove they are as sick as men to be taken as seriously.
While this complaint is common among women, men complain that their urologists might not take their pain as seriously as well. This phenomenon is likely due to the fact that urologists see patients with the same symptoms every day, and that pain is one of the most common complaints.
In both instances, it is important to remember to have empathy for patients, and to treat each one as an individual. Women and men should be treated equally, and each patient's discomfort should be considered a cause for concern.
Poor Bedside Manner
Another common complaint among patients is poor bedside manner, especially when it comes to the sensitive topics that urologists and ObGyns face daily. In a recent study of top complaints among dissatisfied patients, 43.1% listed poor bedside manner as their most relevant issue with their physician. What comprises poor bedside manner? In this instance, the perception of arrogance, lack of listening skills, and indifference were the top offenders. While doctors often feel as though their interpersonal skills should not be judged as a basis of their medical technique, the truth is that patients have little else to go by when choosing a physician.
Patients particularly found poor bedside manner with their ObGyn to be troublesome during labor. While it can be hard to calm first time parents, doctors should aim to lend an empathetic ear instead of rattling off a list of what makes them qualified for the job. Similarly, urologists should remember that when a patient's reproductive organs are not working properly, good bedside manner is necessary to keep a tense situation from escalating.
Poor Customer Service
Good customer service is important in any service industry, especially when it comes to medical practices. In fact, 35.3% of patients complain about poor customer service, which is wide ranging. For instance, inability to schedule timely follow up appointments was one concern that patients had, which is disconcerting for clients with a serious health problem.
Rude treatment by front staff was also a major concern. For many patients, seeing a specialist such as a urologist or ObGyn can be stressful, and rude or unaccommodating receptionists or nurses can be especially frustrating. While working in healthcare is not for the faint of heart, it is important that each patient is treated politely.
For other patients, the difficulty of talking to a person on the phone is especially aggravating. To clear up phone lines, physicians can set up online appointment scheduling, which streamlines the entire process. It is also useful to track patient phone calls and monitor when clients are most likely to call with emergencies or for appointment scheduling. During "down times," staff can use this opportunity to confirm appointments and perform follow up phone calls without tying up the phone lines or placing too many patients on hold.
Not hearing back about test results in a timely manner
Along with poor customer service, patients complaint about physicians who do not alert clients to abnormal test results in a timely manner. This grievance is a serious one, and is complained about surprisingly often. When doctors operate on a "no news is good news" policy, it is important that physicians reach out to patients quickly when a problem is discovered. Not only is this method courteous, but it also allows patients to be treated as quickly as possible. To reach patients in a timely manner, many doctors have turned to mailing test results which came back normal directly to the patient, and only calling when results require follow up tests or treatment. Ultimately, a patient should never wait more than a week to find out something is seriously wrong, or get stuck playing phone tag with the receptionist.
Not calling in prescriptions
Similarly – and perhaps even more seriously – an all too common complaint is physicians that do not call in prescriptions in a timely manner. Oftentimes, patients with this concern have gone to the pharmacy to pick up their medication, only to be told by the pharmacist that the doctor has not yet called. This problem is often due to negligence of the doctor, and results in patients that are unable to take their medication consistently. This type of behavior can cause mistrust in doctors, and a lot of frustration for the patient.
However, patients often do not realize that doctors must comply with restrictive privacy rules and out-of-date technology that hinders efficiency in this regard. Doctors should audit their in-house processes, and work towards improving efficiency if these factors are affecting a patient's care. While many complaints that a patient has about a doctor can be brushed aside, not filling prescriptions on time is a grievous offense that can cost a doctor many future patients.
Not consulting with referring physician
When patients are referred to specialists such as urologists, gynecologists, and urogynecologists, the reason is often because the patient is a special or advanced case. Therefore, it is not surprising that patients become frustrated when the specialist does not consult with the referring physician. Even worse, sometimes specialists fail to fully assess the patient and simply diagnose the symptoms based on the referring doctor's notes. When this situation occurs, the patient can feel that his or her time or money was wasted.
While consulting is difficult between two doctors based on their busy schedules, it is important that the specialist respect that the referring doctor felt the case was more complicated than what he or she could handle. Urologists and gynecologists should use their best judgment when examining a patient, but be as thorough as possible when determining that the new client has the exact disease the original physician assumed.
False Diagnoses
Urology and gynecology are two fields where misdiagnoses can be especially troublesome to individuals. Indeed, 21.5% of patients complained of misdiagnoses from their doctors. In urology, the top offenders are urinary incontinence disorders, interstitial cystitis, chronic pelvic pain, and bladder cancer. Many of these disorders have similar symptoms, and specialists tend to diagnose common diseases before knowing the full scope of the problem – especially when the same disorders are observed every day with little variability among symptoms.
In the gynecology field, pelvic organ prolapse and miscarriage can be incorrectly diagnosed. Pelvic organ prolapse causes symptoms of urinary incontinence in women, which affects 1 in 3 adult females. However, a pelvic organ prolapse can affect one of five pelvic organs, and is a common complication of childbirth. Doctors should fully investigate whether a pelvic organ prolapse is to blame when a woman complains of stress or urge incontinence.
An alarming revelation that was made in the past decade is that ultrasound guidelines for the first trimester of pregnancy may result in a false diagnosis of nonviability of the fetus. In one study, researchers found that 1 in 23 pregnancies in the United States are misdiagnosed as nonviable, prior to women undergoing procedures to clean out the uterus. New guidelines for first trimester ultrasound have been released, which are aimed at reducing the number of these misdiagnoses.
Surgical Mistakes
While misdiagnoses are frustrating, 21.5% of patients also cited surgical mistakes as a source of frustration. Unfortunately, surgeons are not immune to human error. While thousands – if not millions – of surgeries around the globe are performed daily without error, the small percentage of incidences which do occur often speak loudest. In general, the three most common errors during surgery are wrong site surgery, wrong surgical procedure performed, and surgery performed on the wrong patient. While errors are likely to occur given the nature of surgery, these three errors are wholly preventable.
Indeed, in one study, preventable adverse events was the leading cause of death in the United States, and in New York alone 3.7% of hospital admissions were due to preventable adverse errors caused by medical professionals. Therefore, nearly 100,000 deaths per year in the United States can be prevented by surgical staff. While these complaints by patients are frustrating and indeed can harm a physician's business, the fact of the matter is that surgical mistakes are a serious and life-threatening problem.
Not Listening to Patient Complaints
Another common complaint that patients have about their doctors – primarily in specialty fields – is physicians who do not adequately listen to the patient. While doctors seek the most accurate and relevant information possible, when only given a 15 – 20 minute time slot with each patient a doctor can feel rushed to make a quick judgment about the patient's condition. Therefore, doctors might hear 4 out of 6 symptoms that a patient is experiencing, then cut him or her off to prescribe treatment. While this method is efficient for the doctor, it is frustrating for the patient. In many instances, such as when BPH or genuine stress incontinence is suspected, the doctor has seen countless similar cases in his or her lifetime and can make that judgment with high confidence, yet the patient is generally left feeling as though his or her feelings did not matter. Even worse, when the quick diagnosis is wrong, patients can feel especially cheated of both time and money. Even when a patient presents his or her symptoms and appears "textbook," take the additional few minutes to hear out the patient completely.
Being Close-Minded to Non-Traditional Medicine
Non-traditional treatments are gaining traction, such as meditation, yoga, acupuncture, and herbal supplements. While there is evidence that some holistic techniques may be complementary to conventional medicine, such as acupuncture for women's reproductive health3, other "remedies" might counteract traditional medicine. A good example is St. John's Wort4, which diminishes the efficiency of the birth control pill, as well as certain antibiotics. However, the initial response many physicians have when their patients are discussing non-traditional medicine can cause patients not to disclose this information altogether. Not only is a teaching opportunity into the patient's health lost, but doctors may be missing important contraindications, simply because the patient did not want to be sneered at for taking an herbal supplement. Open lines of communication are key when it comes to overcoming this complaint source.
"Private" Discussions
Urologists and gynecologists treat patients with sensitive problems every day. Infertility, erectile dysfunction, cancer, and incontinence are only a handful of the personal problems that bring people to see a urologist or ObGyn. Therefore, many patients wish for their conversations to be completely private and out of earshot of other clients. However, one common complaint among visitors of urology and gynecology practices is perceived lack of privacy, particularly when discussing the patient's condition. Care should be taken to ensure the privacy of each patient, and for doctors not to discuss patient specifics with other physicians or nurses within earshot of other people.
Too-Early Hospital Release
As physicians and hospital staff are aware, patient turnover after in-patient procedures directly affects revenue. However, a significant problem arises when patients are released from the hospital too early. This trend is especially evident in women and newborns. In the past 40 years, the length of a hospital stay following delivery has drastically decreased. Indeed, there has been question recently whether early discharge of mothers and their newborns is safe. Additionally, there is evidence5 which suggests early discharge correlates with higher incidences of infant readmission to the hospital, increased attendance rates at hospital emergency departments related to infant health issues, more contacts with health professionals regarding infant health following discharge, maternal readmission to the hospital, more maternal health issues, increased incidences of maternal depression, anxiety, and fatigue following birth, and increased risk of breastfeeding problems.
In addition, urology patients that have serious urinary complaints – such as difficulty voiding – are sometimes released from the hospital too soon following surgery. While many patients dealt with these symptoms prior to surgery, post-operatively it is important to question whether the patient is fit to go home given the current problems. Ultimately, a release from the hospital too soon can result in serious complications that require additional medical appointments or hospitalization, which is why this complaint is common.
Ultimately, the primary sources of patient complaints in ObGyn and urology practices can be lumped into three categories: patient inconvenience (i.e. long wait times), patient – doctor interactions (i.e. poor bedside manner), and questions regarding physician competency (i.e. misdiagnoses).
While some of these complaints are unavoidable, such as long wait times due to emergencies, other issues can be overcome with enhanced attention to daily processes within the clinic. The most egregious complaints, such as surgical mistakes, can largely be overcome with implementation of better practices and closer attention to detail. Overall, doctors must recognize that just like any other service industry, customer service is important, and word of mouth complaints can be damaging to a business.
About BHN
BHN provides mobile diagnostics to over 300 urology and ObGyn practices across the country. One of our primary services is urodynamics testing, where we provide the equipment, staff, and supplies to deliver turn-key urodynamics testing on site our our customers' locations. If you would like more information on our urodynamics testing services, please kick on the button below.
- Hoffmann DE, Tarzian AJ. The girl who cried pain: a bias against women in the treatment of pain. J Law Med Ethics. 2001;29(1):13-27.
- Merz CN. The Yentl syndrome is alive and well. Eur Heart J. 2011;32(11):1313-5.
- Cochrane S, Smith CA, Possamai-Inesedy A, Bensoussan A. Acupuncture and women's health: an overview of the role of acupuncture and its clinical management in women's reproductive health. International Journal of Women's Health. 2014;6:313-325. doi:10.2147/IJWH.S38969.
- Murphy PA, Kern SE, Stanczyk FZ, Westhoff CL. Interaction of St. John's Wort with oral contraceptives: effects on the pharmacokinetics of norethindrone and ethinyl estradiol, ovarian activity and breakthrough bleeding. Contraception. 2005;71(6):402-8.
- Jones E, Taylor B, MacArthur C, Pritchett R, Cummins C. The effect of early postnatal discharge from hospital for women and infants: a systematic review protocol. Systematic Reviews. 2016;5:24. doi:10.1186/s13643-016-0193-9.


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John Hughes posted an update 4 years, 10 months ago
Hi. This is how far I have got my project. I have the head upright on the basic shoulder parts. I have my servos on order so I will be doing some work on wiring it up soon. The Shoulder area is not totally stable and I was wondering what extra parts add on the bottom to give it some stablity until I am ready to move on. Can any one direct me to the parts that add on next? Kind Regards Ian
Damian got a pic of his inmoov a few Post down ( Muiti-Coloured one),,, he has got the Front and Back Chest Plates plus the 2 Center Beams Fully built — ,, Personally i would do that ,, but do not Permanently join them together — you can permanently join each of the smaller plate pieces together in to Make the 4 Major section ( Front/Back Plates and x2 Center Beam) but don't permanently join those 4 Major section together ,,,,,


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Wellness in the center of Florence
An oasis where you can rediscover the lost quiet and purify yourself from everyday stress. Treat yourself to a massage and take care of yourself. A magical space for the body and the mind. Allow your senses to free themselves while sipping a herbal tea, a regenerating experience.


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A long and proud tradition
Movies about social class inequality have been around for a very long time because, after all, social class inequality is nothing new, and the issue has only become more pressing here in the 21st century.
Even if you're the most hardcore Capitalist around, I hope you'll agree that massive corporations preventing competition in favor of holding their markets hostage is just plain bad, and it's led to a new class of hyper-wealth that is inherently immoral.
Now that we've gotten that out of the way, let's get back to movies. Classic films like Mr. Smith Goes to Washington, Roma, They Live, and many, many more have attempted to tackle the subject of class inequality and the problems it creates in just about every culture and every country around the world.
Thankfully, these movies focus on being entertaining first, and the messaging tends to be at least a little bit subtle, well, maybe not so much in They Live, but for the most part this holds true.
Part of the strangeness behind Parasite's success, both the success of the filmmaking as well as the many awards its gathered over the past several months, is that Bong Joon-Ho is not a stranger to making movies that grapple with class disparity, and even more interesting, his past work has not been subtle in the least when it comes to this topic.
Snowpiercer is maybe the most blunt of his entire filmography.
If you don't already know the premise, it's set in a sci-fi post-apocalypse where surviving humans travel on a train that never stops, making use of a mysterious fuel source. The rich people live in the front portions of the train, and the poor and crammed in the absolute rear, forced to fight amongst themselves and even kill/eat each other just to survive.
Don't get me wrong, it's still a great movie, and the messaging still works, but subtlety is just not part of the equation in that one.
But Parasite is different in so many ways.
And no, it's not terribly subtle, either. Changes in premise, approach, tone, and character vault Parasite to a different level.
Yes, we root for the main characters the whole way through, but also can't, in good conscience, label them as "the good guys."
Everything in the movie is more complex than it first seems, ya know, kind of like real life.
Shades of gray
The week before the Academy Awards, Parasite had a small re-release in black and white, or, more accurately, a very specific grayscale version of the movie.
(The only other contemporary example of this strange choice is Mad Max: Fury Road, which itself had a limited run of the Black & Chrome edition. Apparently George Miller always wanted the movie to be shot and shown in black and white, but the studio wasn't too hot on the idea, and honestly, after seeing the Black & Chrome edition, I'm not either.)
Why did Bong and Co. make this choice? Well, according to him it was to highlight the shades of gray in the movie. Get it?
It may sound a bit cringey, but the thing is, he's allowed to be indulgent with this one.
The movie, for one, is just that good, but it also just nails the moral ambiguity of its shocking plot. It's allowed to have a black and white release; this isn't a student film shot in 16mm, it's a killer examination of how an inhuman system impacts the people who have to live within it.
As we already talked about, this premise is not exactly novel, but rarely is it handled with such skill.
Plenty has already been written about our family of protagonists. They're all incredibly likable and, more importantly, each of them is actually skilled and talented, a point which has been noted in a number of interviews with the cast.
In a way, that genuine skill gives the characters a kind of morality halo in the mind of the viewer, glazing over some of the objectively terrible things they do.
When the focus shifts to the rich family, skill isn't really addressed. Their child creates terrible paintings reminiscent of Basquiat, and we never learn what their daughter, or the mother, are supposed to be good at, if anything. Maybe the father has a very demanding job, maybe not.
But here's the most interesting aspect of the rich family, and I praise Bong for including this in what might otherwise have been yet another painfully on-the-nose class commentary: they're kind, or at the very least ambivalent.
The rich folks don't realize that their wealth, status, and power is problematic.
Warning: heady philosophical and ethical content ahead.
In 1963, political theorist Hannah Arendt reported on the trial of Adolf Eichmann, a man responsible, in large part, for the Holocaust.
I know, but we'll get back to movies very soon. Hang in there, champ.
Arendt's pieces were originally published in the New Yorker, and a year later, a book was published with some extra content, titled Eichmann in Jerusalem: A Report on the Banality of Evil.
It's incredibly well-written and you should read it, but for now, I'll try to communicate the central concept that subsequent philosophers pulled from it.
The core takeaway is that many (if not all) people who do bad things do so without fully understanding the full extent of their actions or even that those actions are indeed evil.
This is like the Cliff's Notes of the Cliff's Notes of the book, so please forgive the oversimplification.
But it checks out: lots of people who do bad stuff don't think they're doing bad stuff. In one way it's thanks to varying moral sensibilities, sure, but it's also just how humans work. If you need an example, I dunno, look at contemporary American politics and guess who I'm referring to.
For those of you who are relatively new to anti-Capitalist discourse, well, for one I have a few books you might be interested in, but I should also tell you that a recurring theme is that the biggest villain of all is capital itself, a product of the system.
But if you're making a movie about the evils of an entire economic system, then you most likely need a visual stand-in. Spielberg's solution to this problem has always been to insert a very obvious corporate villain character. Yes, each character is a villain in their own right, but they also represent a larger, more abstract idea. Ya know, symbolism.
But here's where Parasite catapults itself into Very Good Movie Land: there is no such character. Even the rich family's house doesn't really serve this purpose. The evil is still there. In fact, it has a huge presence in the movie.
In Parasite, an unjust system is represented by the movie's overall tone. In other words, the way the movie feels mimics the way it feels to be poor and desperate in real life.
Yes, there are brief moments of hope, there are fantasies and playful times with family, but the one consistent sensation is an acute sense of impending doom. There's no real safety, even when things seem pretty alright. You're never that far away from being homeless, or horribly ill, or just becoming a permanent underfoot character.
Even if you, as a viewer, are very well set up and have two small boats and a mid-tier luxury car or even a tesla (good for you, man, the environment says thanks), the middle section of the movie (no big spoilers here) will fill you with dread. The movie is going to put you into the shoes of people who live on the margins of society, at least with regards to finances.
Very good movies do this. Whether you like it or not, you will be fully immersed and experience the events of the film alongside the characters.
This isn't the only way to make a great movie, but it sure helps, especially if you're hoping to win some very prestigious awards.
The legacy of Parasite
I'm no expert, but it's time to predict the future!
We're still in the honeymoon period with Parasite. Somewhat recently it swept the Oscars and people who didn't see the movie praised the sweep as a sign of increased diversity at the Oscars, which is confusing to me.
But even those of us who watched the movie last fall still feel pretty good about it and feel validated by its wins at the Oscars and at Cannes, even though we definitely don't reeeaaallly care about those institutions anyway, right?
So how will Parasite age over time? Will it suffer the fate of The Artist, a pretty bad French film that won Best Picture and was then forgotten by every person on the planet, except for me, because I was destined to remind you about it right now?
Parasite has staying power, and a lot of that is thanks to the subject matter, the aforementioned class war content, but it also has to do with the incredible dedication to craft going on here.
Whether or not you're a film geek, the individual elements of a film are extremely important, and when they're all in place and executed well, the gestalt is tangibly satisfying.
The cinematography, casting, performances, set design, pacing, editing, score, direction, writing, blocking, and lighting of Parasite are fantastic.
It often gets classified as a drama, but really it's so many things. It's funny and sad and brutal and thoughtful, and frequently it's several of these things at the same time.
The movie's versatility makes it easier to watch. It never feels like homework, and for anyone looking to get into arthouse film in general, that's a huge bonus.
Believe the hype: Parasite is a darn good film that's worth watching. The only hope here is that it isn't Bong's peak.


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pplacer performs phylogenetic placement.
pplacer [options] [alignment]
|Specify the path to the reference package.
|Specify the reference tree filename.
|Specify the reference alignment filename.
|Supply a phyml stats.txt or a RAxML info file giving the model parameters.
|Specify the directory containing the reference information.
|Calculate posterior probabilities.
|Substitution model. Protein: LG, WAG, or JTT. Nucleotides: GTR.
|Use model frequencies instead of reference alignment frequencies.
|Number of categories for discrete gamma model.
|Specify the shape parameter for a discrete gamma model.
|1st stage branch len optimization tolerance (2nd stage to 1e-5). Default: 0.01.
|Relative error for the posterior probability calculation. Default is 0.01.
|Use a uniform prior rather than exponential.
|Use an informative exponential prior based on rooted distance to leaves.
|Lower bound for the informative prior mean. Default is 0.
|Starting pendant branch length. Default is 0.1.
|Set the maximum ML pendant branch length. Default is 2.
|The cutoff for determining figs. Default is 0; specify 0 to disable.
|Evaluate all likelihoods to ensure that the best location was selected.
|Write out a tree showing the discrepancies between the best complete and observed locations.
|Write out a tree showing the figs on the tree.
|Maximum number of strikes for baseball. 0 -> no ball playing. Default is 6.
|Set the size of the strike box in log likelihood units. Default is 3.
|Set the maximum number of pitches for baseball. Default is 40.
|Desired likelihood cutoff for fantasy baseball mode. 0 -> no fantasy.
|Fraction of fragments to use when running fantasy baseball. Default is 0.1.
|Write alignment masked to the region without gaps in the query.
|Set verbosity level. 0 is silent, and 2 is quite a lot. Default is 1.
|Specify the directory to write place files to.
|Specify the output file name
|Only check out the files then report. Do not run the analysis.
|Write out the likelihood of the reference tree, calculated two ways.
|The number of child processes to spawn when doing placements. Default is 2.
|Display timing information after the pplacer run finishes.
|Don't pre-mask sequences before placement.
|Write out the pre-masked sequences to the specified fasta file before placement.
|Specify a file to write out MAP sequences for MRCAs and corresponding placements.
|Specify cutoff for inclusion in MAP sequence file. Default is 0.8.
|Add the percent identity of the query sequence to the nearest MAP sequence to each placement.
|The maximum number of placements we keep. Default is 7.
|Throw away anything that has ml_ratio below keep_factor times (best ml_ratio). Default is 0.01.
|Classify with MRCAs instead of a painted tree.
|Split query alignment into the specified number of groups.
|Always refine the model before placing.
|Instead of doing large allocations, mmap the given file. It will be created if it doesn't exist.
|When pre-masking, silently discard sequences which don't overlap the mask.
|Write out the version number and exit.
|Display this list of options
|Display this list of options
Pplacer places query sequences on a fixed reference phylogenetic tree according to a reference alignment. In maximum likelihood (ML) mode, pplacer tries to find the attachment location and the pendant branch length which maximize the likelihood of the tree with pendant branch length attached. In Bayesian posterior probability (PP) mode, pplacer tries to find the edge attachment which maximizes the posterior probability of a fragment placement on an edge conditioned on the reference tree (with branch lengths).
A basic pplacer run looks like:
pplacer -c my.refpkg aln.fasta
with a reference package. Running pplacer with a reference package is simple and produces taxonomic annotations which can be used for classification and visualization (see, for example classify and fat). If you wish to override specific parts of the reference package, you can do so with command line options.
A "reference package" is simply a collection of files including a reference tree, a reference alignment, and associated taxonomic information. We have the beginnings of a reference package database which we hope in the future to be a comprehensive resource for phylogenetic placement. It's just started, and we would love to have your submissions. For now most users will have to make a reference package using our taxtastic package.
aln.fasta is the alignment file.
It should have the reference sequences which were used to make the reference tree, aligned with the query sequences to be placed on the reference tree.
The reference sequences must have identical names to those used in the reference tree.
It's possible to split the alignment into two files (the reference sequences and the query sequences); in that case you need to make sure that those alignments are in the same frame and have the same length.
This splitting was obligatory in v1.0.
The alignment can be in FASTA format (with a
.fasta or
.fa suffix) or Stockholm format (with a
.sto or
.sth suffix).
Migrating from pplacer v1.0¶
There are a couple of differences between the present version and the previous version of pplacer which are worth knowing about.
- Rather than having a plain text ".place" output file, we now have a JSON-format file which contains the placements
- Reference packages encapsulate reference information, making it easy to do placement and taxonomic annotation
- Alignments can now be supplied as a single file, rather than being split into reference and query alignments
- Much better: faster, taxonomic integration, etc
mokaphyhave been replaced by a single binary called
rpprbinary for preparing reference packages
Pre-masking and masking¶
One of the primary design goals of pplacer is to have it work efficiently and consistently when placing short reads in what might be a longer alignment. As part of achieving these design goals, we have put effort into two masking procedures, which are fairly strict in their interpretation of what is informative in a sequence alignment. Specifically, we consider columns that are gap in a query sequence or all gap in the reference alignment to not be informative for the placement of that query sequence. This is a different statement than saying that a column does not impact the phylogenetic likelihood, and indeed columns that are all gap except for one sequence do change the likelihood in all implementations that interpret gaps as missing data (this is true for essentially all phylogenetic inference software).
We call the first procedure "pre-masking," and it ignores columns that are all gap in either the reference alignment or the query alignment.
This has been the default behavior since v1.1alpha08, but it can be disabled with the
--no-pre-mask flag.
You can see the effect of pre-masking by supplying a file name to the
--write-pre-masked flag.
However, in certain situations this can lead to sequences other than the given sequence influencing the likelihood. Specifically, imagine that we have two sequences A and B that are non-gap in column sets X and Y, respectively, and that there are no all-gap columns in the reference alignment. Say that X and Y are disjoint sets. If we ran pplacer with pre-masking on A alone, or B alone, the alignment columns would be subset to X and Y, respectively. However, if we run them together, the columns would be subset to the union of X and Y. Then, when we are placing A in the presence of B, A's gap entries in Y will influence the likelihood (similarly for B in the presence of A). These effects are subtle but nonzero.
Therefore, we have a second procedure, which we call "masking," that only computes likelihoods for the columns in each placement that are informative in that placement.
This ensures identical behavior when sequences are run separately or together, and also makes things faster.
This is now the default behavior, and you can see the results of masking by supplying the
--write-masked flag.
(Careful when using this, as it will make one fasta file for each query sequence.)
When placing metagenomic sequences onto trees built from very wide alignments (such as concatenations), we suggest using the "groups" feature.
Using, say,
--groups 5 will divide the alignment into 5 evenly spaced sectors across the width of the alignment.
The reads are then grouped into which sector they fit into best, and each group is run sequentially.
In combination with the pre-masking, this can result in a very substantial reduction of memory usage, because the likelihood vectors are calculated for one sector (plus a bit extra) at a time.
Note that these gains will be eliminated if you have reads that span the whole reference alignment.
Using this feature will not change the result except possibly for likelihood computations where the query sequence has a gap; these likelihoods are not meaningful, so if there is a substantial difference when you use groups your alignment is lacking signal!
JSON format specification¶
The JSON format is described in detail in our paper on the phylogenetic
placement format. Each document is a JSON object with a minimum of four keys:
placements, and
version. Another key,
metadata, is optional. Other keys in the root object are ignored.
|The version of the JSON format as an integer.
|The reference tree as a string, in "edge-numbered Newick" format.
|An array of placements.
|An array of strings corresponding to the data given in the placements array.
|An object containing metadata about the generation of this collection of placements.
An "edge-numbered Newick" tree is simply a Newick format tree with integers in curly braces which provide a well-defined numbering of edges. These edge numbers are used to specify the edges on which the placements lie.
Currently there are three versions of the placefile format accepted by
2, and
3, though only version 3 will be generated.
Differences between versions
1 and
There are only two differences between versions 1 and 2: the format of the
Newick tree in the
tree field has changed, and
marginal_prob was
renamed to
marginal_like in version 2.
Version 1 used a slightly different version of edge-numbered Newick trees for
tree field, where edge numbers were specified in square brackets
instead of curly braces. Both this kind of Newick tree and version 1 of the
JSON format are now deprecated.
Differences between versions
2 and
Version 3 replaces the separate
n and
m keys in placement objects with
a more general
nm key that can associate mass with each name.
Format summary¶
The pplacer suite currently uses the following field names:
|The edge number from the provided
tree as an integer.
|ML log likelihood as a float.
|ML likelihood weight ratio as a float.
|ML distance from the distal side of the edge as a float.
|ML pendant branch length as a float.
|The posterior probability of a placement on the edge.
|The marginal likelihood of a placement on the edge. [1]
|The marginal likelihood of a placement on the edge. [2]
tax_id from a reference package as a string.
|The percent identity between this sequence and the corresponding MAP sequence.
|The number of overlapping sites between this sequence and the corresponding MAP sequence.
guppy to be able to load a JSON file, it must have
distal_length, and
pendant_length fields. All other fields are optional, but if one of
post_prob and
marginal_like are specified, both must be specified.
Each entry in the
placements array is an object with the following keys:
|A string or array of strings corresponding to the name or names of the sequences placed here. [5]
|An array of arrays containing placement data in the same order as
|(optional) A float that represents the mass of this placement. If this key is specified,
n must only be or contain a single string. [1] [4]
|An array of
[name, mass] pair arrays representing the mass for each sequence placed here. [3]
An example JSON document follows, with the first placement showing uncertainty in location, and the second showing two reads that had identical placements but different masses:
"tree": "((A:0.2{0},B:0.09{1}):0.7{2},C:0.5{3}){4};",
[[1, -2578.16, 0.777385, 0.004132, 0.0006],
[0, -2580.15, 0.107065, 0.000009, 0.0153]
"n": ["fragment1", "fragment2"]
{"p": [[2, -2576.46, 1.0, 0.003555, 0.000006]],
"nm": [["fragment3", 1.5], ["fragment4", 2]]}
"pplacer -c tiny.refpkg frags.fasta"
"version": 3,
["edge_num", "likelihood", "like_weight_ratio",
"distal_length", "pendant_length"]
|(1, 2) New in format version
|Removed in format version
|New in format version
|Removed in format version
|This key will not ever be generated by any program in the pplacer suite as of format version
3, but will continue to be accepted by
guppy and
Making alignments for use with pplacer¶
There are several options and formats for providing alignments of reference and query sequences. Examples below illustrate various steps in the sequence alignment process.
Examples using Infernal¶
Infernal is an excellent package for searching and aligning sequences using RNA secondary structure information.
Creating a reference alignment¶
The first step in any pipeline involving Infernal (assuming you already have an alignment profile but are not working from a reference package) is to create an alignment of reference sequences. See the Infernal docs for a description of options not mentioned here. For example:
cmalign --hbanded --sub --dna -1 -o refalign.sto profile.cm refseqs.fasta
Inputs to this command include an alignment profile (
profile.cm) and unaligned reference sequences (
The output file, identified using the
-o option, contains the aligned reference sequences in Stockholm format.
-1 (that's a one, not an L) specifies non-interleaved output, one sequence per line.
Merging reference and query sequences¶
Query sequences must be aligned with respect to the reference sequences. This is easily accomplished using two calls to cmalign. First, align the query sequences just like the reference sequences above:
cmalign --hbanded --sub --dna -1 -o qalign.sto profile.cm qseqs.fasta
Next, merge the reference and query alignments using the
--merge option:
cmalign --merge --hbanded --sub --dna -1 -o merged.sto profile.cm refalign.sto qalign.sto
merged.sto contains a single alignment of both reference and query sequences, and can be used with pplacer as follows after making a reference tree and accompanying statistics file:
pplacer -t reference_tree -s statistics_file merged.sto
Using a reference package¶
A closely related example involves alignment with the profile and reference sequences included in a reference package (
my.refpkg - note that names may vary in a reference package).
So now we skip creation of the reference alignment.
First, create the query alignment:
cmalign --hbanded --sub --dna -1 -o qalign.sto my.refpkg/profile.cm qseqs.fasta
...then merge:
cmalign --merge --hbanded --sub --dna -1 \
-o mergedWithRefpkg.sto \
my.refpkg/profile.cm my.refpkg/refalign.sto qalign.sto
Now it is even easier to write the pplacer command:
pplacer -c my.refpkg mergedWithRefpkg.sto
Examples using HMMER¶
HMMER is another excellent package for searching and aligning sequences by the Eddy group, which can align amino acid and nucleotide sequences.
Assume that we have a reference alignment
refseqs.sto in Stockholm format. We first build an HMM:
hmmbuild refseqs.hmm refseqs.sto
Then we can use it to make a combined alignment with the reference sequences and the reads:
hmmalign -o combo.sto --mapali refseqs.sto refseqs.hmm qseqs.fasta
Now we can run pplacer:
pplacer -t rpoB.tre -s RAxML_info.rpoB combo.sto
... or with a reference package:
pplacer -c rpoB.refpkg combo.sto
Making reference trees¶
We save the log file so it can get parsed and become part of the reference package.
Nucleotide alignments¶
FastTree should be used in the following way when making nucleotide reference trees for use with pplacer:
FastTree -nt -gtr -log vaginal.log vaginal.fasta > vaginal.tre
In particular, do not use the
-gamma option, but do use the
-gtr option.
Amino Acid alignments¶
FastTree should be used in the following way when making amino acid reference trees for use with pplacer:
FastTree -log TIGR00001.log TIGR00001.fasta > TIGR00001.tre
-gamma should not be used.
phyml and RAxML¶
PHYML and RAxML are two nice packages for making ML trees that are supported for use with pplacer. Pplacer only knows about the GTR, WAG, LG, and JTT models, so use those to build your trees. If you are fond of another model and can convince me that I should implement it, I will.
Both of these packages implement gamma rate variation among sites, which accomodates that some regions evolve more quickly than others. That's generally a good thing, but if you have millions of query sequences, you might have to run pplacer with fewer rate parameters to make it faster.
I run RAxML like so, on similar alignments (the "F" suffix on PROTGAMMAWAGF means to use the empirical amino acid frequencies):
raxmlHPC -m GTRGAMMA -n test -s nucleotides.phy
raxmlHPC -m PROTGAMMAWAGF -n test -s amino_acids.phy
pplacer does not support using the CAT model from RAxML, although a similar model is available via FastTree.
PHYML can be run like so, on non-interleaved (hence the -q) phylip-format alignments:
phyml -q -d nt -m GTR -i nucleotides.phy
phyml -q -d aa -m WAG -i amino_acids.phy
Note that pplacer only works with phyml version 3.0 (the current version).
Both of these programs emit "statistics files": files that describe the phylogenetic model used.
Pplacer then uses those same statistics to place your reads.
For RAxML, they are called something like
RAxML_info.test, whereas for PHYML they are called something like
If your taxon names have too many funny symbols, pplacer will get confused. We have had a difficult time with the wacky names exported by the otherwise lovely software geneious. If you have a tree which isn't getting parsed properly by pplacer, and you think it should be, send it to us and we will have a look.
Avoid giving pplacer a reference tree with lots of very similar sequences. It's a waste of time– pplacer must evaluate the resultant branches like any others. Identical sequences are especially bad, and the resultant zero length branches will make pplacer complain.
If you give pplacer a reference tree which has been rooted in the middle of an edge, you will get a warning like:
Warning: pplacer results make the most sense when the given tree is multifurcating
at the root. See manual for details.
In pplacer the two edges coming off of the root have the same status as the rest of the edges; therefore they will counted as two separate edges. That will lead to artifactually low likelihood weight ratio and posterior probabilities for query sequences placed on those edges. This doesn't matter if your query sequences do not get placed next to the root, but you can avoid the problem altogether by rooting the tree at an internal node, or by leaving the outgroup in and rerooting the output trees.
"Baseball" is one way that pplacer substantially increases the speed of placement, especially on very large trees. Baseball is a game where the player with the bat has a certain number of unsuccessful attempts, called "strikes", to hit the ball.
Pplacer applies this logic as follows. Before placing placements, the algorithm gathers some extra information at each edge which makes it very fast to do a quick initial evaluation of those edges. This initial evaluation of the edges gives the order with which those edges are evaluated in a more complete sense. We will call full evaluations "pitches." We start with the edge that looks best from the initial evaluation; say that the ML attachment to that edge for a given query has log likelihood L. Fix some positive number D, which we call the "strike box." We proceed down the list in order until we encounter the first placement which has log likelihood less than L - D, which we call a "strike." Continue, allowing some number of strikes, until we stop doing detailed evaluation of what are most likely rather poor parts of the tree.
You can control the behavior of baseball playing using the
--strike-box, and
--max-pitches options.
If, for any reason, you wish to disable baseball playing, simply add
--max-strikes to zero (this also disables the
--max-pitches option).
Having control over these options raises the question of how to set them.
The answer to this question can be given by pplacer's "fantasy baseball" feature.
To gain an understanding of the tradeoff between runtime and accuracy, it analyzes all
--max-pitches best locations.
It then runs the baseball algorithm with each combination of strike box (from 0 to the specified
--strike-box) and max strikes (from 1 to the specified
Using these different settings the program reports
- the "batting average," i.e. the number of times the baseball algorithm with those settings achieved the optimal location obtained by evaluating all
--max-pitchesbest locations; found in the file prefix.batting_avg.out
- the "log likelihood difference," i.e. the difference between the ML log likelihood achieved by the baseball algorithm with those settings compared to the best obtained by evaluating all
--max-pitchesbest locations; found in the file prefix.like_diff.out
- the "number of trials," i.e. the number of locations fully evaluated by the baseball algorithm with those settings; found in the file prefix.n_trials.out
The fantasy mode is invoked by telling pplacer what average likelihood difference you would like via the
--fantasy option.
You can also tell it to run an evenly-spaced fraction of the query sequences in fantasy mode using the
--fantasy-frac option, which gives you an idea of the optimal run parameters for the rest of the sequences. For example:
pplacer --max-strikes 10 --strike-box 10 --fantasy 0.05 --fantasy-frac 0.02 -r example.fasta...
says to run pplacer trying all of the combinations of max strikes and strike box up to 10, looking for the optimal combination which will give an average log likelihood difference of 0.05, and running on 2% of the query sequences.
If, for any reason, you wish to disable baseball playing, simply add
--max-strikes to zero (this also disables the
--max-pitches option).
You can use R to plot these matrices in a heat-map like fashion like so:
ba > read.table("reads_nodups.batting_avg.out")
image(x=c(0:nrow(ba)-1),xlab= "strike box", ylab= "number of strikes", \
y=c(1:ncol(ba)-1),z=as.matrix(ba), main="batting average")
Note that we have set things up so that turning on posterior probability with
-p now changes the default search parameters to make a deeper search as follows:
--keep-at-most 20
--keep-factor 0.001
--max-strikes 20
You can set these to anything you like by using these flags after the
Fig ranking¶
"Fig ranking" is a way to reduce the number of initial comparisons done by using the structure of the reference tree. This initial phase is not the bottleneck for trees on a thousand or so taxa, but it is for trees on tens of thousands of taxa or more.
If a value is specified as
--fig-cutoff x, pplacer will find subtrees of
the reference tree (that we call figs) on the reference tree such that no two
leaves in the cluster have a distance of greater than
x. Each leaf is
contained in exactly one fig. A representative edge of the fig is chosen as
follows: say n is the most proximal node contained in the fig; the
representative is the edge descending from n to the subtree with the greatest
number of leaves.
With a collection of figs, pplacer will rank each of the representative edges by the initial evaluation likelihood given a query sequence. For each fig, in this order, pplacer selects all of the edges within the fig as well as all of the edges proximal to the fig up to the root of the tree. These edges are ranked by the same initial evaluation likelihood before pplacer attempts to place the query sequence on each in turn. No edge will be attempted twice; if the same edge is proximal to two separate figs, it will only be attempted when the first fig is evaluated.
As each fig is evaluated for a query sequence, pplacer will also select any
figs ordered immediately after the current fig where the difference between
that fig's representative likelihood and the current fig's representative
likelihood is less than the value of the
--strike-box parameter. Each of
these figs' sets of edges are then merged into the current fig's edge set.
To test the accuracy of fig evaluation vs. full evaluation, the
--fig-eval-all flag can be specified to do both fig and full evaluation,
then show the percentage of sequences where the best location chosen by full
evaluation and fig evaluation is the same.
--fig-eval-all must be specified
to specify the
--fig-eval-discrepancy-tree flag. If this flag is specified,
a tree will be written out showing the locations chosen by both methods for
each sequence where the two differ.
The colored trees written out by the
--fig-tree and
--fig-eval-discrepancy-tree flags shows figs as colored subtrees within the
reference tree.
Model refinement¶
By default when using the FastTree CAT model, the site rate categories used directly from the FastTree run. This is not possible, however, when a different reference alignment is supplied than was used to build the tree. This can happen when supplying an integrated reference and query alignment.
When the site rates cannot be used directly, the model gets "refined".
Currently, this only actually means something for the CAT model, in which case
it infers site categories. You can force this behavior by using the
--always-refine flag.
Memory usage¶
The amount of memory pplacer needs will vary depending on the reference package and input alignment and is directly proportional to the number of sites after pre-masking and the number of nodes on the reference tree. As mentioned in the FAQ, placing on a GTRGAMMA RAxML tree will use about four times as much memory as placing on a FastTree tree.
To see how much memory would be used for by the part of pplacer which uses the
most memory (i.e. internal nodes), pass the
--pretend flag and it will be
displayed. pplacer will use more memory than this value, but for most analyses,
this will be by far the biggest allocation.
In cases when there isn't enough memory for pplacer to use for internal nodes,
or it's otherwise disadvantageous to use physical memory, it's possible to
instead tell pplacer to
mmap(2) a file instead using the
--mmap-file flag.
This will, very roughly, perform disk IO instead of using physical memory.
You will see that pplacer will use the same amount of address space, but less
physical memory. In terms of
top(1) on linux,
VIRT will stay the same
RES will decrease. The speed of pplacer will also become at least
partially dependent on the speed of the drive where the mmap file is located;
with an SSD you might not see any difference from using physical memory, while
with a spinning metal drive there might be some slowdown. Placing the file on
an NFS mount is likely not ideal for this reason.
The implementation and underlying behavior of mmap may vary between platforms
(the link above is only for linux out of convenience), but pplacer will always
mmap(2) with
PROT_READ | PROT_WRITE and
It's also possible to pass a directory for the value of the
flag; this will create a temporary file in that directory, and then unlink it
after opening it. The data will be written to the drive, but when the process
exits, the last reference to that filesystem entry will be removed and it will
get cleaned up.


text:
24 Hawkeyes to Watch | Fight For Iowa | Hawk Talk Monthly – November | Hawkeye Fan Shop — A Black & Gold Store – https://hawkeyefanshop.com/?utm_source=HawkeyeSports&utm_medium=HawkeyeSports&utm_campaign=HawkeyeSports
AUSTIN, Texas — Freshman Oliver Okonkwo and sophomore Joe Tyler had continued success on Sunday at the Longhorn Invitational on Sunday.
Okonkwo was crowned Flight B White champion, while Tyler advanced all the way to the championship match in the Flight C Gold after three straight victories.
In Okonkwo's Flight B championship matchup he faced off against Miami's Kaya Gore. Okonkwo beat Gore in a tight three-set match, 2-6, 6-4, 6-1. Tyler fell in his match (6-4, 6-3) to Houston's Mohamed Abdel-Aziz.
The Hawkeyes have concluded their fall season and will return to action for their home opener Jan. 19, 2019, when they host Western Michigan and Marquette in a doubleheader.
Flight B White
Oliver Okonkwo (UI) def. Kaya Gore (UM): 2-6, 6-4, 6-1
Flight C Gold
Mohamed abdel-Aziz (UH) def. Joe Tyler (UI): 6-4, 6-3