School districts looking for interventions to prevent teen drug use and boost students' mental health may soon have one less place to turn.
Martha Yeide of the Development Services Group, Inc., the contractor for the center, confirmed that it received a letter Dec. 28 telling the group to stop work by Jan. 26, six months before the contract was scheduled to expire. The contract was ended "for the convenience of the government, not for cost," and there have been no moves to switch the site to a new contractor, suggesting NIMH may take it offline or leave it as a static site. The NIH has not yet responded to a request for more information.
The announcement comes during a somewhat tumultuous period for advocates of evidence-based policy. The fiscal 2018 budget proposals in both the House and the Senate include millions of dollars in cuts to research across agencies (Congress may vote on a final omnibus spending bill later this month), and last month the Centers for Disease Control and Prevention were advised not to use words like "evidence-based" and "science-based" in the agency's 2019 budget request. While an evidence-based policy bill backed by House Speaker Paul Ryan has passed that chamber, its sister bill has not moved out of committee in the Senate.
Correction: An earlier version of this post listed SAMHSA as part of the National Institutes of Health; it is part of the Health and Human Services Administration.


In general, PHARMAC will not apply a subsidy to a new medicine unless it is offered at a price lower than currently available subsidized medicines in the same therapeutic class or unless the producer is willing to lower its price on another medicine already subsidized in another class. Pharmaceuticals can also be delisted if a competing product is selected to serve the market as the result of a tender or if a cheaper alternative becomes available and the manufacturer of the original product refuses to discount its price to that of the lower-priced alternative. PHARMAC's use of reference pricing, the practice of doing trade-off deals between classes of drugs, and tendering practices can negatively affect a company's revenue return on its intellectual property.
I don't know what insurance policies the USTR provides its employees, but they might spend a little time looking at the HMO industry in the US to better understand what PHARMAC is up to.
December 3, 1999, PhRMA's 2000 NTE submission. This is an extensive attack on New Zealand's efforts to control costs through HMO style price negotiations.
Decembe 18, 2002. Lesley Springall for the Independent. Govt sneaks patent law change through Parliament. This news story is about a research provision in the IP law very much like the Bolar Provision in U.S. law.


The truth is also crass in numbers. The driver in a car with the half-light switched on will see a pedestrian on an average of fifty meters away. If the pedestrian carries a reflective tape, it is visible at 350 meters distance. With the main beam turned on, the reflex is even more efficient. The law states that pedestrians should use reflexes – yet half of Finns do not do so, according to information from the Swedish Transport Safety Agency.
"This applies to common sense: use reflexes for others in the traffic to see you," says Camilla Fri-Bergström.
Even in the enlightened urban environment, it can be difficult to get a view of cyclists and pedestrians. Immune windows, shadows from bushes and trees and various light sources can affect the field of view. Dirty windscreens and bad lanterns can further aggravate the situation.
Since 2003, it has been mandatory to use reflex in the enlightened urban environment. In a new proposal for road traffic law, the reflex section still shines with its absence – something that has caused the Swedish Transport Administration to shudder.
"The statutory is a guideline also for media and education, private individuals and municipalities. No one has been disturbed by the rule for 35 years," says CEO Anna-Liisa Tarvainen in a press release.
And although the law recommends the use of reflective vest, the one who does not meet meets some penalties.
Toothless, says Ola Lindholm from the insurance company Lokaltapiola Sydkusten.
If you get hit, it doesn't matter if you wear reflective clothing with reflective fabrics or not when looking at potential benefits. The circumstances determine: has the person gone on the right side of the road? Everyone has an obligation to follow the rules in this respect, says Ola Lindholm, whoever goes on the wrong side of the road may have been involved and caused the accident.
Fortunately, such accidents are relatively few and emphasize that generalizing rules are difficult to give since nothing is black and white.
Ola Lindholm herself thinks that a single reflex is not worth much – here is the reflective vest that applies.
It is quite lean with a reflex that dangles at knee height when moving on a dark road.


HEALTHY LIVING — About 400,000 Americans may be getting highly invasive back surgery unnecessarily.
A local doctor says he's found great success taking care of ruptured disks through a tiny incision.
Dr. Ditsworth says he has done thousands of patients with higher than a 90 percent success rate. His findings are published in the "Surgical Neurology."


text:
Call of Duty Modern Warfare 2 PS4 vs PS5: Should You Upgrade?
Muhammad Ali Bari September 19, 2022
The Call of Duty Modern Warfare 2 beta is currently underway, and we now have a reasonable idea of how the game will perform come launch on both the PS4 and PS5.
It's worth mentioning, however, that these performance stats for the PS4 and PS5 versions of Call of Duty Modern Warfare 2 are all based on the beta, and, therefore, its performance may change in its final build.
Call of Duty Modern Warfare 2 uses horizontal dynamic resolution with temporal reconstruction, which has also been the case with prior entries in the series. For the first time, however, it's possible to modify the Field of View (FOV) on all platforms, including PS4, all the way up to 120. In the comparison footage seen above, it is set to 90.
The PS5 version features better shadows, ambient occlusion, LOD, anisotropic filtering and some higher resolution textures compared to the PS4 and PS4 Pro version. The quality and performance seen on the PS4 and PS4 Pro is very similar to that of the Call of Duty Modern Warfare (2019). Based on the game's graphical makeup, it's a cross-gen game that has been developed with the limitation of the previous-gen consoles in mind.
In terms of performance, the Call of Duty Modern Warfare 2 beta currently does not have offer a 120fps mode for PS5. The game runs at 60fps on Sony's current-gen machine, regardless of whether you play at 60hz or 120hz. Meanwhile, the performance is slightly uneven in the PS4 version. In some areas, it fails to hit its target frame rate of 60fps.
Call of Duty Modern Warfare II is the sequel to Call of Duty Modern Warfare, which was released in 2019. On October 25, 2019, the latter was released for Microsoft Windows, PlayStation 4, and Xbox One. It is the sixteenth installment in the Call of Duty series and a reboot of the Modern Warfare sub-series.
Deathloop Resolution And Frame Rate For Xbox Series S and X
Wo Long: Fallen Dynasty PS5 vs Xbox Series X Resolution And Frame Rate: Which Runs It Better?
Call Of Duty Warzone 2.0 & Modern Warfare 2 Have An Almost 200 GB File Size
Muhammad Ali Bari November 12, 2022
Modern Warfare 2 Premium Expansion Launches In 2023, Equal To "Full Release"
Muhammad Ali Bari November 8, 2022
Call Of Duty: Modern Warfare 2 Review (PS5) – Half-baked, Yet Highly Entertaining
Call Of Duty Modern Warfare 2: How To Gain XP & Level Up Fast
The Callisto Protocol Massively Underperforms, Has Reported Budget Of $160M
Monster Hunter Rise Frame Rate, Resolution & Cross-Save Details For PS4/PS5/XSX/XB1
Hogwarts Legacy PC System Requirements, PS5/Xbox Series Resolution & Frame Rate Revealed
Atomic Heart 14 Mins Gameplay Footage Leaked, Comparison Shows Improved Visuals

redpajama_set_name: RedPajamaCommonCrawl


text:
Keep Fighting: The Billy Bremner Story (Paperback)
By Paul Harrison
Billy Bremner is a football legend. During his years playing for Leeds Utd and Scotland, his passion for the game and his commitment to the cause made him into one of the all-time greats. Now, 20 years after his tragically early death, Keep Fighting - The Billy Bremner Story is published in paperback for the very first time. When Bremner died in 1997 at the age of just 54, author Paul Harrison was working with him on a new book telling the story of his life. Now, that unique material from extensive interviews has been brought together in Keep Fighting: The Billy Bremner Story. It covers Bremner's life from his early years in Scotland, his move to Leeds Utd and the glory days of the Don Revie era, his distinguished international career and his later move into football management. In his own words, find out what Billy Bremner thought of life at Leeds Utd, about his exploits for Scotland, his footballing friends and those he clashed with. There are stories of winning the League Championship and the FA Cup with Leeds, playing for Scotland in the World Cup, his controversial ban from international football and the libel action he won against a Sunday newspaper. And there's Bremner's own forthright views about some of the biggest names in football, from Don Revie to Brian Clough and Gary Sprake to Kevin Keegan. Keep Fighting is a unique, no-holds-barred account of the life of Billy Bremner - straight-talker and footballing legend - and is a fitting tribute to one of the all-time greats of the game.
Paul Harrison is a sports writer with numerous books published on football. His most recent works include Northern and Proud and The Elland Road Encyclopedia. Harrison also writes for football magazines FourFourTwo, World Soccer, and Leeds Leeds Leeds. In addition, he provides marketing and media consultancy to football clubs and players.
Publisher: Black & White Publishing
Biography & Autobiography / Sports
Sports & Recreation / Soccer


text:
<?php

namespace Apps\Console;

use Ffcms\Console\Command;
use Ffcms\Core\Helper\FileSystem\File;
use Ffcms\Core\Helper\Type\Arr;
use Ffcms\Core\Helper\Type\Str;
use Symfony\Component\Console\Input\InputInterface;
use Symfony\Component\Console\Input\InputOption;
use Symfony\Component\Console\Output\OutputInterface;

/**
 * Class GeneratorControllerCommand. Generate controller carcase
 * @package Apps\Console
 */
class GeneratorControllerCommand extends Command
{
    /**
     * Register command and options
     */
    public function configure()
    {
        $this->setName('generator:controller')
            ->setDescription('Generate default controller template')
            ->addOption('loader', 'loader', InputOption::VALUE_OPTIONAL, 'Set which loader will be used to create controller. Example: front, admin, install')
            ->addOption('name', 'name', InputOption::VALUE_OPTIONAL, 'Set new controller name');
    }

    /**
     * Execute generator create controller command
     * @param InputInterface $input
     * @param OutputInterface $output
     * @throws \Exception
     * @return int
     */
    public function execute(InputInterface $input, OutputInterface $output)
    {
        // get options from input
        $loader = $this->optionOrAsk('loader', 'Loader name(front|admin|api)', 'front');
        $name = $this->optionOrAsk('name', 'Controller name');

        $loader = ucfirst(Str::lowerCase($loader));
        $name = ucfirst(Str::lowerCase($name));

        // check loader definition
        if (!Arr::in($loader, ['Front', 'Admin', 'Api'])) {
            throw new \Exception('Wrong definition for loader. You shoud use front, admin, api');
        }

        // prepare code & write
        $template = File::read('/Private/Carcase/' . $loader . '/Controller.tphp');
        $code = Str::replace(['%name%'], [$name], $template);

        $savePath = '/Apps/Controller/' . $loader . '/' . $name . '.php';
        File::write($savePath, $code);

        $output->write('Controller are successful created: ' . $savePath);

        return 0;
    }
}

redpajama_set_name: RedPajamaGithub


Aaron Muldoon gives a personal reflection on the individuality of Taste Coffee Shop, and the different coffee drinking styles in St Andrews.
It's no secret that our British and American students have a tendency to join different sports teams, take different classes, and form societies – even friendship groups – around their compatriots. The story is no different when it comes to the many other nationalities. But don't despair, dear readers. For at 148 North Street, at the very least, we are all just citizens of the Universe.
The eclectic mix of Taste's patrons reflects a much wider diversity than even their nationalities would suggest. Unlike every other coffee shop in town, it has resisted conforming to a "customer cliché." We can all picture that fluffy female trotting around Pret in her Canada Goose and black ankle boots as she carefully selects which superfood salad to indulge in today. What about the overly-romantic couple who orders the pancake stack at North Point? They hold hands and giggle about what they will name their children and take horizontal snapchats of their feast despite knowing deep down that nobody will ever rotate their phone just to get a better look at what exactly they are having for breakfast.
And then there are misguided folk who go to Starbucks. The philistines who are so culturally and politically uninformed that they think nothing of supporting a huge, swindling corporation ahead of a local business. Blindly hooked on the allure of loyalty card stamps, these people are potentially the crude oil fuelling the engines of capitalism and globalisation. They are people whose aspirations are to own a detached house in suburbia, drive a Ford Mondeo and feed their kids Birdseye fish-fingers at dinner whilst they discuss their upcoming annual holiday to Benidorm.
There is no cliché of the person who goes to Taste and this is extremely important for maintaining its unique atmosphere. It seems to attract people who are self-aware and independently minded enough to care about where they spend their half-hour of downtime during the day. Someone once told me about an individual who visits the cafe and has never owned a smartphone. "His first name is Alex but nobody can be sure about his surname because he doesn't have Facebook," my informant explains. Casting my eyes around the space, I wouldn't be surprised to see someone who looks like they've walked straight off a NY Fashion Week runway sitting right beside another who looks like they've climbed straight out of a skip. There are whispers that one frosty morning, even Vice Chancellor Sally Mapstone hopped across North Street from her abode on the Scores for a quick Taste visit.
So what is Taste doing that makes it so special? Let us begin with the interior. There is no way to avoid the fact that Taste is about the size of a telephone box. But what better way to induce conversation between the patrons than have them crammed together like cattle in a trailer? The décor is a cross between a second hand furniture store and a garden shed, but the division of the seating area, leading into a bar along the window and a low sofa along the back wall, helps create the dynamic and both intimate and bustling atmosphere. The tables are sticky – but in a good way, and the single pane windows steam up every night, adding to the overall hygge.
There is something wonderful about the students who work here compared to the other coffee shops too. Take Northpoint, for instance. The staff are dour and you are never made to feel especially welcome. At least they have some character – which is more than can be said for the forlorn, glassy eyed Starbucks employees – slaving around behind the counter, crushed by the weight of the multinational corporations they serve as their individuality and freedom of expression is ground out of them with every extra of commercialism they send over the counter.
At Taste, the staff are an intrinsic part of the tapestry. Their nonchalant attitude to customers is rather fantastic; making coffee at their own pace and calling over to people to come collect their drinks if they aren't in the mood to serve them. I leave thinking, "Maybe if I keep coming back, I'll end up being as cool as them." Sometimes a customer is gifted with the added bonus of some decent latte art — but again, this is very mood dependent. The staff are an essential part of Taste's appeal. But they aren't just staff. They are totems of the the way of life that Taste represents.
It pains me to write this, but my beloved hole in the wall simply can't compete with Pret on the food front. To the right of the counter there is a half-heartedly stacked fridge with some pre-made sandwiches. To anyone who has had the pleasure of trying a freshly made ciabatta sandwich from Eataly, or even Rocca, Taste's equivalent seems like a sandwich genetics experiment gone horribly wrong. The fillings include soggy roast peppers, Aldi-grade chorizo and pesto that tastes weirdly like metal – but the merciless toasting process obliterates any last whimpering sign of life in these over-refrigerated sandwiches anyway.
The standard improves a little as you move toward the towering baskets of croissants and the oat biscuits kept in a cookie jar (a nice touch). And once you reach the windowsill display of all sorts of fresh tray bake delights, things start to look a lot more promising. As for the coffee? Well there's no point wasting time talking about that. I am sure you are all aware that there are different types of coffee. There is coffee for strutting along Market Street when you are bored and coffee for the Sunday night of revision week; strong coffee, weak coffee, frothy coffee, not so frothy coffee, coffee from this bean, and coffee from that bean. Whatever. It doesn't really matter. I doubt the person who actually chooses what bean to grind can even tell the difference let alone determine their superiority.
My favourite part of Taste is the small wooden bench that sits outside. Those three planks of wood are so much more than just that. The bench epitomises the simplistic beauty and raw practicality of the whole place — cool, but without really trying. Taste take-away cups are like Tinder. Carrying one of them around town with you, all you need to do is nod at another Taste cup holder and you know you have made a friend for life. After such an encounter it is not unusual for a feeling of warmth to spread all over your body. It's the feeling that we are not alone in this world. The feeling that we are one of the chosen people. Taste isn't a cult, per se. It is more a way of life — and I mean this with only a touch of sarcasm. It's nothing to do with the coffee, but you can definitely taste the difference.
Next articleCAPOD: what's on offer?


text:
Q: Python3 Function returning only first values I'm trying to make a function that opens a textfile, counts the words and then returns the top 7 words in percent. However when I run the code with "return" it only retrieves the first value but "print" gives me what I need + a "None".
def count_wfrequency(fname):
    with open(fname,"r") as f:
        dictionary = dict()
        for line in f:
            line = line.rstrip()
            delaorden = line.split()
            for word in delaorden:
                dictionary[word] = dictionary.get(word,0) + 1

        tmp = list()
        for key, value in dictionary.items():
            tmp.append((value, key))
            tmp.sort(reverse=True)

        for value, key in tmp[:7]:
            b = ("{0:.0f}%".format(value / len(tmp)* 100))

            print(key, b, end=", ")

the 9%, to 6%, of 5%, and 4%, in 3%, a 3%, would 2%, Frequency of words: None

What am I doing wrong?
edit: To clarify, I want to make it so that it prints out "Frequency of words: the 9%, to 6%...and so on.
Trying to use the function like this:
if args.word_frequency:
        print("Frequency of words: {}".format(funk.count_wfrequency(args.filename)))

redpajama_set_name: RedPajamaStackExchange


text:
October 2009 , 126:521 | Cite as
Linguistic and maternal genetic diversity are not correlated in Native Mexicans
Karla Sandoval
Leonor Buentello-Malo
Rosenda Peñaloza-Espinosa
Heriberto Avelino
Antonio Salas
Francesc Calafell
David Comas
Mesoamerica, defined as the broad linguistic and cultural area from middle southern Mexico to Costa Rica, might have played a pivotal role during the colonization of the American continent. The Mesoamerican isthmus has constituted an important geographic barrier that has severely restricted gene flow between North and South America in pre-historical times. Although the Native American component has been already described in admixed Mexican populations, few studies have been carried out in native Mexican populations. In this study, we present mitochondrial DNA (mtDNA) sequence data for the first hypervariable region (HVR-I) in 477 unrelated individuals belonging to 11 different native populations from Mexico. Almost all of the Native Mexican mtDNAs could be classified into the four pan-Amerindian haplogroups (A2, B2, C1, and D1); only two of them could be allocated to the rare Native American lineage D4h3. Their haplogroup phylogenies are clearly star-like, as expected from relatively young populations that have experienced diverse episodes of genetic drift (e.g., extensive isolation, genetic drift, and founder effects) and posterior population expansions. In agreement with this observation, Native Mexican populations show a high degree of heterogeneity in their patterns of haplogroup frequencies. Haplogroup X2a was absent in our samples, supporting previous observations where this clade was only detected in the American northernmost areas. The search for identical sequences in the American continent shows that, although Native Mexican populations seem to show a closer relationship to North American populations, they cannot be related to a single geographical region within the continent. Finally, we did not find significant population structure in the maternal lineages when considering the four main and distinct linguistic groups represented in our Mexican samples (Oto-Manguean, Uto-Aztecan, Tarascan, and Mayan), suggesting that genetic divergence predates linguistic diversification in Mexico.
American Continent Mexican Population Linguistic Group Native American Population Linguistic Family
The online version of this article (doi: 10.1007/s00439-009-0693-y) contains supplementary material, which is available to authorized users.
Although largely explored by many disciplines, the peopling of the Americas remains as an issue of intense debate. The tempo and mode in which modern humans colonized the New World through Beringia to the rest of the American continent remains unclear; with numerous hypotheses have been proposed in the last few decades (Campbell and Mithum 1979; Chakraborty and Weiss 1991; Greenberg et al. 1986; Laughlin 1988; Spencer et al. 1977; Szathmary et al. 1983; Wallace et al. 1985). However, a date of entry into the Americas roughly consistent with the archaeological record, has been placed around 15,000–17,000 years before present (ybp), followed by subsequent episodes of reduced population size, compatible with the current low genetic diversity observed in present day Native American populations (Mulligan et al. 2004).
Interest in the settlement of the New World has boosted genetic studies in Native American populations. These studies are based mainly on the analysis of the mitochondrial (mtDNA), a genome inherited exclusively throughout the maternal line. Most extant Native American mtDNAs, if not of recent admixture, descend from four main founding haplogroups, initially baptized as A, B, C, D (Torroni et al. 1993a) and further characterized as A2, B2, C1, and D1 (Achilli et al. 2008; Fagundes et al. 2008; Perego et al. 2009; Tamm et al. 2007); and five minor lineages, namely C4c, D2a, D3, D4h3, and X2a (Achilli et al. 2008; Bandelt et al. 2003; Brown et al. 1998; Fagundes et al. 2008; Schurr et al. 1990; Tamm et al. 2007; Torroni et al. 1992, 1993a). Based on mtDNA sequence data, Bonatto and Salzano (1997) proposed the hypothesis of a single and early migration that entered into the New World through Beringia where the population settled, expanded and diversified before the further colonization of the rest of the American continent. This "Out of Beringia" model, in contrast to the previous multiple migration scenarios for the Pleistocene peopling of the Americas, was compatible with recent studies supporting a single migration scenario. For instance, according to Tamm et al. (2007) and Fagundes et al. (2008), the ancestral population left from northeast Asia during the Last Glacial Maximum, defined as an interval centered on 21,000 ybp (Clark and Mix 2002), crossed through the Bering Strait bearing the five founder lineages and remained isolated long enough to generate the pan-American haplogroups A2, B2, C1, D1, and X2a (Achilli et al. 2008), which were distributed southward probably following a Pacific coastal route. This pattern of dispersion is indeed found in the actual distribution of Uto-Aztecan languages extending from the Western Plateau and Coast of California to Nicaragua in Central America (Miller 1983) and Oto-Manguean languages found from Middle America (Northeast Mexico) to Nicaragua and Honduras in Central America (Suaréz 1983). Recently, Perego et al. (2009) have reported the variation at two rare American mtDNA haplogroups D4h3 and X2a, based on complete genome sequencing of the mtDNA molecule, signaling for the first time the existence of two distinctive and almost concomitant Paleo-Indian migrations routes which would have occurred 15–17 kya from Beringia.
Specific geographic regions of the continent might have played a key role during the colonization of the Americas. One such region is the linguistic and cultural area called Mesoamerica (Campbell et al. 1986; Kirchhoff 1943; Pailes and Whitecotton 1995), which extends from middle southern Mexico to Guatemala, Belize, Honduras, El Salvador, Nicaragua, and Costa Rica, in which ancient native populations shared languages, traditions, customs, and history (López-Austin and Luján 2001). This evidence suggests that Mesoamerica represented a geographic bottleneck and possibly limited the gene flow between North and South America, and concentrated an invaluable source of diversity in that region. In fact, present day Mexican territories, which cover most of Mesoamerica, harbor one of the richest ethnic and linguistic diversities of the continent. Thus, Mexico has eleven linguistic families divided into 68 major linguistic groups which include 291 living languages and seven extinct ones (Inali 2007).
Despite the abundant genetic data on different Native American groups across the continent, the patterns of variability of Native Mexicans still remain unclear. Some prospective studies based on uniparental markers (Barrot et al. 2005; Buentello-Malo et al. 2003; Collins-Schramm et al. 2004; Rangel-Villalobos et al. 1999, 2000, 2001a, b) showed a relative genetic homogeneity of Mexican autochthonous populations. Other studies based on mixed urban samples (Mestizos) (Bonilla et al. 2005; Cerda-Flores et al. 2002a, b; Green et al. 2000) indicated that these groups are basically the result of admixture between Native Americans and Europeans but provided a poor idea about the genetic structure and diversity of autochthonous populations. Moreover, studies focused on ancient mtDNA (González-Oliver et al. 2001) have shown the presence of haplogroup A2, B2, and C1 (following the most recent nomenclature) mtDNA lineages in pre-Columbians; and analyses of extant mtDNA based on restriction enzymes have also shown the presence of the four major Amerindian haplogroups in Mexican samples (Penaloza-Espinosa et al. 2007). A deep genetic characterization of a larger number of Native Mexican populations might give insights, not only on the complex relationships between autochthonous groups inside Mexico, but also on the reconstruction of the human history of the Americas.
Here, we present mtDNA sequence data for 477 unrelated individuals belonging to eleven different native populations from Mexico, namely, Triqui, Tarahumara, Purépecha, Otomí, Mixtec, Nahua Xochimilco, Nahua Zitlala, Nahua Ixhuatlancillo, Nahua Necoxtla, Maya, and Pima. For the first time, an exhaustive analysis of maternal lineages in Native Mesoamerican populations is reported and the results are discussed within the context of continental genetic variation by constructing a mtDNA database with published reported sequences from populations from North, Central, and South America.
Population sampling
A total of 477 unrelated Mexican individuals from 11 populations were sampled with their appropriate informed consent. All individuals were native speakers with two generation-local unrelated ancestors. The geographic location of collected samples is shown in Fig. 1 and comprised 107 Triquis, 15 Tarahumaras, 34 Purépechas, 68 Otomíes, 35 Nahuas from Xochimilco, 14 Nahuas from Zitlala, 10 Nahuas from Ixhuatlancillo, 25 Nahuas from Necoxtla, 19 Mixtecs, 98 Pimas, and 52 Mayas. An additional sample of 23 Quechua individuals from Peru was included and used for population comparisons as part of the Native American database. All sequences are available at Supplementary Table S1.
Map of Mexican populations sampled. Pima (PM), Tarahumara (R), Otomí (O), Purépecha (P), Nahua from Xochimilco (Nx), Nahua from Ixhuatlancillo (Ni), Nahua from Necoxtla (Na), Nahua from Zitlala (Nz), Mixtec (M), Triqui (T), and Maya (MY)
Mitochondrial DNA genotyping
DNA was extracted from blood samples using standard phenol chloroform method (Sambrook et al. 1982) and FTA® extraction according to the supplier's protocol. DNA from Pimas, Mayas, and Quechuas was directly provided from the laboratory of Judith R. Kidd and Kenneth K. Kidd (Yale University, New Haven, CT, USA) where lymphoblastoid cell lines are maintained. The mtDNA control region was amplified using primers L15996 and H408 (Vigilant et al. 1989). PCR products were subsequently purified with GFX PCR DNA Kit (Amersham Biosciences, GE Healthcare Bio-Sciences AB, Uppsala, Sweden). Both strands of the hypervariable region I (HVRI) were sequenced with the Big Dye Terminator v3.1 Cycle Sequencing kit (Applied Biosystems, Carlsbad, CA, USA) using primers L15996 and H16401 (Vigilant et al. 1989). The sequence from positions 16024 to 16391 was determined (Anderson et al. 1981) for each individual. Length polymorphisms observed in the C-stretch from position 16184 to 16193 were not considered in those analyses involving population samples collected from the literature, due to lack of consistency when reporting variation at this region. In order to properly classify some sequences into haplogroups, additional markers in the mtDNA coding region were analyzed. The 9-bp tandem repeat (CCCCCTCTA) in the COII/tRNALys intergenic region, defining haplogroup B in Native Americans, was amplified using primers L8196 (5′-ACA GTT TCA TGC CCA TGG TC-3′) and H8297 (5′-ATG CTA AGT TAG CCT TAC AG-3′) and run into a 4% agarose gel (Comas et al. 2004). A diagnostic restriction enzyme (AluI for position 5176) was used to categorize haplogroup D, using the primers L5054 (5′-TAG GAT GAA TAA TAG CAG CTC TAC CG-3′), and H5189 (5′-GGG TGG ATG GAA TTA AGG GTG T-′3).
All the mtDNAs could be allocated to the Native American haplogroups A2, B2, C1, D1, and D4h3, with the exception of one Pima and one Quechua bearing West Eurasian haplogroups R1 and T, respectively. These two sequences were not considered for computational analysis. We follow Tamm et al. (2007), Fagundes et al. (2008), Achilli et al. (2008), and Perego et al. (2009) for the nomenclature of Native American clades. We are aware that HVRI alone is unable to distinguish Native American clades from their closest neighbors in northeast Asia; it is, however, commonly accepted that most of the variation belonging to haplogroups A, B, C, and D observed in Native Americans can be attributed to the American sub-lineages A2, B2, C1, and D1. This is particularly true for Mexico, where there is not known historical documentation supporting recent gene flow from Asian populations. We, therefore, use in what follows the latter nomenclature in the present study. Distinction of the minor Native American sub-clades, C4c, D2a, D3, D4h3, and X2a, as well as sub-lineages within A2, B2, C1, and D1, is also challenged by the limited resolution provided by the HVRI segment; some of these lineage, however, are characterized by diagnostic sites in this region (Achilli et al. 2008; Perego et al. 2009).
Intrapopulation genetic diversity parameters were computed using DnaSP software v4.0 (Rozas et al. 2003). The mean number of pairwise differences and the weighted intra-linage mean pairwise (WIMP) differences (Hurles et al. 2002) were calculated using the Arlequin program v3.1 (Excoffier et al. 2005).
A median joining network (Bandelt et al. 1995) was constructed using the Network 4.5.0.0 package (http://www.fluxus-engineering.com/) for each of the four main haplogroups (A2, B2, C1, and D1) found in Mexican populations. Positions 16024 to 16391 were considered and nucleotide position was given a weight as in Brandstätter et al. (2008) (Bandelt et al. 2006). The dating method employed (Saillard et al. 2000) is based on the average number of mutations accumulated from an ancestral sequence as a linear function of time and mutation rate. Values of ρ and σ were converted to age estimates using the most recent mutation rate available for the HVS-I segment of one transition per 18,845 years (in the sequence range 16090–16365) (Soares et al. 2009). This method was also performed with Network 4.5.0.0 program.
In order to compare the present Mexican results with other Native American populations, HVRI sequences from 52 Native American sample populations were collected from the literature (Supplementary Table S2). We removed from this database a total of 12 sequences belonging to non-Native American haplogroups (Achilli et al. 2008), considered to be the result of recent admixture with European and African individuals. For some analyses, population samples were grouped into major subcontinental areas: North (879 individuals from Alaska to southern Mexico), Central (234 individuals from Guatemala to Panama), and South America (1,633 individuals from Colombia southwards) (Table S2). For some analyses, Mexican samples were also considered as a separate category from North, Central, and South America. A spatial analysis of the molecular variance (SAMOVA) was also performed using the SAMOVA 1.0 program (Dupanloup et al. 2002) by presetting different numbers of population groups. This approach defines groups of populations that are geographically homogeneous and maximizes the proportion of total genetic variance due to differences between groups. Population genetic structure was tested through analysis of molecular variance (AMOVA) (Excoffier et al. 1992) using the Arlequin program v3.1 (Excoffier et al. 2005). Genetic relationships among Mexican and continental populations were analyzed by means of pairwise genetic differences and haplogroup absolute frequencies. The former were calculated using Arlequin program v3.1 (Excoffier et al. 2005) and represented in a Multidimensional Scaling plot (MDS) and the latter were used to construct a Correspondence Analysis (CA) plot using STATISTICA 7 package (http://www.statsoft.com).
In order to compare Mexican mtDNA sequences within the American framework, sequence variation within the range 16090 to 16362 (Anderson et al. 1981) was used for inter-population comparisons. Each mitochondrial sequence found in Mexico was compared with the dataset (Supplementary Table S3). To estimate the most likely source ancestral population (North, Central, or South America) of each of the Mexican mtDNA observed in our study, we followed a Bayesian approach: the probability of each of the subcontinental regions was computed as \( P_{{0{\text{s}}}} = {\frac{1}{n}}\sum\nolimits_{i = 1}^{n} {k_{i}{\frac{{p_{{i{\text{s}}}} }}{{p_{{i{\text{c}}}} }}}} \) where n is the number of Mexican sequences matching at least one mtDNA in the whole continental database; k i the number of times the sequence i is found in the Mexican sample; p is the frequency of the sequence i in the subcontinental region database; and p ic the frequency of the sequence i in the whole continental database. To provide confidence intervals for each of the estimations for the subcontinental regions, we also computed the standard deviations as \( SD(P_{{0{\text{s}}}} ) = \sqrt {{\frac{{p_{{0{\text{s}}}} (1 - p_{{0{\text{s}}}} )}}{n}}} \) (Mendizabal et al. 2008).
Mitochondrial DNA diversity in Native Mexican populations
A total of 118 different sequences were found in the 477 Mexican individuals analyzed in the present study. The genetic diversity found in Mexican samples is summarized in Table 1. Three different estimates for the expected number of unique sequences in the different populations sampled are also provided (Egeland and Salas 2008) in Table 1, indicating that the samples sizes for the 12 ethnic groups analyzed in the present study cover reasonably well the expected variation at the HVRI segment. In addition, the sample coverage parameter (C; for definition see also Egeland and Salas 2008) also indicates that sample sizes represent in most of the cases more than 60% of the expected haplotypes in the populations; only the Quechua sample from Peru seems to represent only a very small proportion of the expected number of haplotypes in the population (~9%; data not shown). The results showed that Pimas (0.54 ± 0.05) and Triquis (0.55 ± 0.05) presented the lowest sequence diversity values despite their larger sample sizes. The average pairwise differences by population range from 1.69 to 7.42. Although most Mexican populations presented high sequence diversity and moderate mean pairwise differences, the WIMP differences value was low in all samples, suggesting that Mexican samples present a composition of distantly phylogenetic related haplogroups with low to moderate internal diversity.
Diversity parameters for the first mtDNA hypervariable region (HVRI) in eleven Mexican native populations
HD (SE)
H (SE)
Theta S
C (%)
Triqui
0.550 (0.057)
Tarahumara
Purépecha
Otomí
Mixtec
N.Xochimilco
N.Zitlala
N.Ixhuatlancillo
N.Necoxtla
Pimaa
n number of individuals, K number of different sequences, S number of variable positions, HD haplotype diversity, SE standard errors, H nucleotide diversity, Theta S Watterson's theta values, M mean number of pairwise differences, WIMP weighted intra-lineage mean pairwise differences, N 1 , N 2 , N 3 different estimates for the expected total number of unique sequences, C refers to sample coverage; see Egeland and Salas (2008) for definitions
aOne Pima sequence belonging to haplogroup R1 was excluded from the analyses
All Mexican sequences were classified into the five Amerindian haplogroups A2, B2, C1, D1, and D4h3, according to Achilli et al. (2008) and Perego et al. (2009), with the exception of one Pima individual who presented a sequence probably belonging to the Eurasian haplogroup R1 as suggested by the presence of exact matches (16278T 16311C) to other sample populations where coding region information was also available (Macaulay et al. 1999). This sequence was excluded from subsequent analyses (Table 1). The most frequent haplogroup in Native Mexican populations was haplogroup A2 (50.5%), followed by C1 (28.5%), B2 (17.6%), D1 (2.7%), and D4h3 (0.4%) (Table 2). With respect to the pan-American haplogroups, we noted that the composition of Native Mexicans contrasts with the pattern reported by Salzano (2002) based on restriction endonuclease analysis, in which Mexican and Central American samples have higher frequencies of haplogroups A2 and B2 when compared with C1 and D1. This is especially relevant in the Pima and Tarahumara samples were C1 is very frequent compared to other Mexican samples. We did not find the minor haplogroup X2a, which has been reported at low frequencies in North American samples and absent in South America (see Perego et al. 2009 for a recent analysis of this haplogroup based on complete genome sequences). The highest expected frequency (F) of the unobserved X2a haplogroup in the population can be estimated assuming that the pattern of variability follows a Poisson distribution and using a confidence interval of 95%; then 1 − e−Fn = 0.95, where n represents sample size. Therefore, the maximum frequency of the X2a haplogroup in native Mexican populations given our sample size would be 0.6% (see Egeland and Salas 2008 for some caveats concerning this approach).
Absolute haplogroup frequencies of Native Mexican Populations (in parenthesis relative frequencies)
D4h3
3 (3.06)
Total Mexican sample
13 (2.7)
n number of individuals
It is worth mentioning that the occurrences of two out of the three D4h3 mtDNAs observed in our samples were in one Mexican Tarahumara and one Peruvian Quechua, both living in the West side of the continent, as predicted by the results of (Perego et al. 2009), who postulated that this haplogroup spread into the Americas along the Pacific Coast. The third occurrence of D4h3 was in the Nahua from Ixhualtlancillo, a population living in the narrow region of southern Mexico, where it is also expected to find some members of this lineage (as it will probably occur in other studies on native populations living in other Mesoamerican countries).
The most common haplotypes are shared by almost all the populations. However, it is interesting to note that the pattern of haplotype frequencies varies significantly between populations (independently of their sample sizes). To give an example, haplotype 16111T 16223T 16290T 16319A 16362C makes up ~66% of the Triqui population, ~64% of the Nahuas from Zitlala, but it is ~10% of the Otomí sample and it is absent in Pima. The fact that these haplotypes are common in America and are phylogenetically related to each other (see below) indicates that genetic drift has played an important role in modulating their spatial distribution in Mexico.
In order to investigate the genetic relationship between the mtDNAs observed in our sample set, a median joining network was constructed for each of the most common mitochondrial haplogroups, namely A2, B2, C1, and D1. The four networks clearly have a star-like pattern and do not present any well-defined cluster (for an example of haplogroup A, see Supplementary Figure S1). The estimated ages for the four haplogroups were dated in a wide range of 18–31 kya. Given that recent studies by Tamm et al. (2007); Achilli et al. (2008) and Perego et al. (2009) based on complete genome analysis provided more recent ages for the four main Native American haplogroups; the ages obtained here probably represent an overestimate of the real haplogroup coalescent times likely due to the low resolution provided by the HVRI segment analyzed in the present study.
Genetic structure of Native Mexican populations
An AMOVA was performed in order to define the population structure of Mexican indigenous populations according to geographic and linguistic criteria (Table 3). When all Mexican populations were considered as a single group, 19.23% (p < 0.01) of the genetic variance was found between populations, showing a relevant genetic heterogeneity among Native Mexican populations. A significant proportion of the variance (19.17%; p < 0.01) was found between groups when populations were classified into northern (Tarahumara and Pima) and central-southern groups (Triqui, Purépecha, Otomí, Nahua, Mixtec, and Maya), meaning that significant mtDNA differences between the northern and central-southern Mexican populations exist, however no statistical differences were found between central (Purépecha, Otomí, and Nahua) and southern (Triqui, Mixtec, and Maya) groups (4.35%, p = 0.15). When the geographical location of the samples was taken into account in a SAMOVA analysis, the first grouping of populations was again Tarahumara and Pima versus the rest of populations, and subsequent partitions of the variance rendered only individual populations without a geographical structure (data not shown).
Results of the analysis of molecular variance (AMOVA) of Native Americans
Among groups
Among populations within groups
Within populations
Mexican populationsa
Linguistic classificationb
−0.45 ns
Mexican northern populationsc
9.05**
American populationsd
Geographic classificatione
0.65 ns
American populations and Mexicansf
ns non-significant
* p < 0.05; ** p < 0.01
aThe eleven Mexican population samples analyzed
bMexican population samples were grouped according to their linguistic families
cNorthern samples (Tarahumara and Pima) were compared to Central-Southern samples
dAll Native American populations from the present database
eNative American population samples grouped according to their sub-continental regions (North, Central and South)
fFour groups: populations from North, Central, South America, and the Mexicans
Four major linguistic families found in Mexico were represented in our studied populations: Oto-Manguean (Mixtec, Triqui and Otomí), Uto-Aztecan (Nahua populations, Tarahumara and Pima), Tarascan (Purépecha) and Mayan (Maya). A non-significant −0.45% of the variance was explained by these linguistic groups, suggesting a lack of correlation between mtDNA genetic diversity and linguistic classification.
Mexican populations within the American genetic landscape
In order to compare the mtDNA diversity found in Mexico to the rest of the American continent, a Correspondence Analysis (CA) based on haplogroup frequencies was performed considering the whole set of populations included in our dataset (Fig. 2). The two-dimension plot accounts for 53.49% of the total variation whereas 28.31% is explained by the first dimension. Although the distribution along the second dimension (25.18%) slightly suggests a North-South pattern, no particular clustering of populations can be clearly detected. It is noteworthy that most Mexican populations are closely related to other North and Central American populations, with the clear exception of Pima and Tarahumara which appear considerably separated from the rest. A similar pattern is shown when a MDS analysis is performed at a continental scale; that is, no clear clusters, and a few outliers caused by low sequence diversity, such as Pima and Triqui (Mexico), Ayoreo (Bolivia and northern Paraguay) and Emerillon (French Guiana) were observed (data not shown).
Two-dimension Correspondence Analysis (CA) plot of Native American populations based on absolute haplogroup frequencies. Triangles stand for Northern, diamonds for Central, and circles for Southern populations. Mexican populations are shown in gray and haplogroups are underlined
An AMOVA considering all Native American populations showed a high degree of heterogeneity between populations (16.86% of the genetic variance; p < 0.01). It is noteworthy that this mtDNA heterogeneity is of a similar magnitude to that observed considering only Mexican populations. In order to ascertain whether this heterogeneity was caused by geographical factors, three continental groups (North, Central and South) were considered (Table S2). The AMOVA showed that a non-significant 0.65% (p = 0.15) of the genetic variance was due to differences between these three sub-continental groups, whereas the genetic variance within the three groups remained highly significant (16.44%, p < 0.01), pointing to an important genetic heterogeneity within the sub-continental areas and a lack of continental structure. When Mexican samples were considered as a separate category from northern, central and southern groups, a mere 1.09% (p = 0.046) of the genetic variance was attributed to differences among groups, whereas the genetic heterogeneity within groups remained highly significant (16.08%, p < 0.01).
To obtain rough estimates for the relationship of Mexican mtDNA lineages at a finer scale, we searched exact matching sequences in our dataset. This analysis assumes that the frequencies found nowadays are representatives of extinct populations. Although this assumption is somehow unrealistic due to the dramatic genetic drift events experienced by most of the Native American populations, this proxy is still useful to better describe the geographical distribution of haplotype Mexican sequences within the American continent. All the Mexican lineages were compared to our dataset of 2,746 published Native American sequences (Table S2) divided into the three main aforementioned geographical regions (North, Central, and South). Only 21 Native Mexican lineages, representing 59% of the individuals, were also found in the America dataset (Table S3). The average of the proportions of Mexican sequences found in each geographical region can be used as a proxy to infer the relationship of these populations within the continent. Thus, the distribution of the Native Mexican sequences could be described as follows: 46.29% (SD 2.98%) to North, 15.86% (SD 2.19%) to Central and 37.83% (SD 2.89%) to South America. As expected, the mtDNA variability observed in Mexicans cannot be allocated to a single geographical region within the continent (due to the lack of a clear geographical structure in the Americas as shown, e.g., in the AMOVA analysis). However, the Mexican mtDNA pool shows a closer relationship to northern American populations.
Native American populations show a unique pattern of genetic diversity as a result of different demographic processes—population bottlenecks, founder effects, genetic drift—involved in the colonization of the New World and the posterior European contact and African slave trade (Mulligan et al. 2004; Salas et al. 2004). Presently Mexico is mainly inhabited by two distinct population groups: (1) the so-called 'Mestizos', a term used in the country and widely accepted by Mexicans to designate individuals of recent admixed ancestry (although the term is meaningless from a genetic point of view; see comments in Salas et al. (2004)), and (2) the native indigenous Mexican groups defined by their language, cultural traits, ethnicity, oral history and customs as part of their cultural complexity. Despite 'Mestizos' representing nearly 95% of the Mexican population (INEGI 2007), the Native American component is highly prevalent in their gene pool. Thus, for instance, the study by Cerda-Flores et al. (2002a) based on short tandem repeats showed the admixed percentage contribution of 'Mestizo' Mexicans from northeastern locations as deriving from Spanish (54.99 ± 3.44), Amerindian (39.99 ± 2.57) and African (5.02 ± 2.82). The analysis of the mtDNA in 'Mestizos' has shown that their maternal component is an admixture of Native American (89.1%), European (5.4%), and African (4.5%) lineages (Green et al. 2000).
Besides the intrinsic interest of exploring the variability of Native American groups, their analysis is also pivotal to understand the genetic composition of admixed populations in the Americas. Our results show that the majority of the mtDNAs of autochthonous Mexican individuals can be allocated to one of the four most common Native American haplogroups (A2, B2, C1, D1) (Achilli et al. 2008). We did not observe the mtDNA contribution of African and European ancestry, with the exception of one Pima individual who presented a Eurasian lineage that could be attributed to recent gene flow. The haplogroup distribution observed is similar to that found in an ancient Maya population in which haplogroup A2 accounted for most of the samples (84%) followed by C1 (8%) and B2 (4%), although haplogroup D1 was not found (González-Oliver et al. 2001).
It is noteworthy that no traces of haplogroup X2a were observed in our native Mexican populations. In contrast with haplogroups A2 to D1, which have an East Asian origin (Torroni et al. 1993b), haplogroup X has its origins in West Eurasia, and its entrance into the Americas is more controversial. Haplogroup X2a is not present in Central and South Native American populations (Perego et al. 2009) and represents a clade that lacks close relatives in the Old Word, including Siberia (Reidla et al. 2003). Our results point to a geographical limit in Mesoamerica beyond which haplogroup X2a is not found. Fagundes et al. (2008) suggested that this haplogroup was part of the gene pool of a single Native American founding population and its low frequency is probably due to a failed expansion as a result of its geographic location in the expansion wave and/or its low initial frequency. The most recent study of Perego et al. (2009) suggested however that X2a could have moved from Beringia directly into the North American regions located East of the Rocky Mountains; the X2a expansion could have occurred in the Great Plains region, where the terminal part of the glacial corridor ended, and is in complete agreement with both the extent of diversity and distribution of X2a observed in modern Native American populations. The absence of X2a in our samples supports the idea that Mesoamerica played an important role during the colonization of the continent, restricting this haplogroup to the northernmost lands and shaping the diversity of the other founder haplogroups on their way down to Central and South America.
We have shown a relevant genetic heterogeneity of indigenous groups within Mexico, probably due to processes such as extensive isolation, genetic drift, and founder effects. These demographic events have modulated the distinctive patterns of frequencies of the four main Native American haplogroups in the different Mexican populations. Some populations, in particular the northernmost Tarahumara and Pima, showed larger genetic distances from the rest of the Mexican populations and different haplogroup spectra. When our mtDNA sequences were analyzed together within the continental landscape, no particular structure was detected for the Mexican populations, and sub-continental division does not account for the genetic differences among Native American populations. These results point to a common origin of Native American populations, including the Mexican groups, with extensive isolation and genetic drift, which might have produced an extremely high heterogeneity in their haplogroup patterns.
The Americas are one of the most linguistically diverse regions in the world comprising about 150 linguistic stocks (Nichols 1992). In addition, languages in the Americas show a striking and unparalleled diversity in their grammatical structures. Divergence across populations is caused by genetic drift; however, the differences diminish by extensive contact between populations, i.e., by genetic exchange. The principles governing genetic and linguistic patterns are of different nature and, therefore, it is not uncommon to observe differences between them (Comas et al. 2008). In the Mexican samples analyzed, four major linguistic families are represented (Oto-Manguean, Uto-Aztecan, Tarascan, and Mayan). However, we did not find a correlation between linguistic affiliation and their mtDNA gene pool when populations were grouped according to their linguistic families. The genetic differences between linguistic groups were not significant, which concomitantly translates into a high genetic heterogeneity within linguistic groups. This heterogeneity and the lack of correlation between mtDNA diversity and linguistic affiliation could be explained by the extensive isolation between Mexican indigenous populations. Nonetheless, Tarahumara and Pima show a certain degree of genetic differentiation from the other nine groups, which could be explained by cultural isolation beyond language; note that these are the only two populations analyzed that lay out of the Mesoamerican area. This fact contrasts with the Nahua populations, which despite being affiliated with Uto-Aztecan, the same linguistic family as Tarahumara and Pima, do belong to the cultural-geographical Mesoamerican group. Overall, the data suggest that the Mesoamerican geographic barrier could explain population differences between Native American groups due to genetic drift.
In summary, our findings suggest that the mtDNA diversity patterns in Native Mexicans have been mainly driven by genetic drift. Native Mexicans have preserved their native mtDNA background with almost no contribution from European and/or African populations. Although linguistic structure in Mexicans is highly stratified, we did not observe a correlation between linguistic and mtDNA patterns. Despite the fact that mtDNA represents just a small fraction of the human genome, it has been demonstrated once more to be useful to unravel demographic events in human populations. However, it would be worth exploring other genomic regions in Mexican DNA where natural selection could have played an important role in modulating their variation, providing the necessary adaptive skills in their way to the colonization of South America.
We would like to thank Andrés Moreno-Estrada, Isabel Mendizabal, Chiara Batini (Unitat de Biologia Evolutiva, UPF), Michelle Gardner (Department of Molecular Neuroscience, Institute of Neurology, University College London) for their comments and help; Mònica Vallés (Unitat de Biologia Evolutiva, UPF), Stéphanie Plaza and Roger Anglada (Servei Genòmica, UPF) for their technical support; and Kenneth Kidd and Judith Kidd (Yale University) for kindly providing Pima, Mayan and Quechua samples. This research was supported by the Agencia Española de Cooperación Internacional (AECI, Programa de Cooperación Interuniversitaria e Investigación Científica entre España e Iberoamérica) (A/7694/07) and Direcció General de Recerca, Generalitat de Catalunya (2005SGR/00608). Karla Sandoval received a fellowship from the Consejo Nacional de Ciencia y Tecnología (CONACyT), México.
This article is distributed under the terms of the Creative Commons Attribution Noncommercial License which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are credited.
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Supplementary material 1 (TIFF 4418 kb)
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Supplementary material 2 (XLS 51 kb)
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Haplogroup frequencies classified by population in the dataset used for comparison to the Mexican sequences analyzed in the present study (DOC 328 kb)
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Mitochondrial DNA sequences found in Mexico with their haplogroup classification and number of (identical) matches in the database used for comparison. Only positions from 16090 to 16362 were taken into account in the comparison database (DOC 60 kb)
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1.Institute of Evolutionary Biology (UPF-CSIC)CEXS-UPF-PRBBBarcelonaSpain
2.Instituto de Investigaciones AntropológicasUniversidad Nacional Autónoma de MéxicoMexico CityMexico
3.Unidad de Investigación Médica en Genética HumanaCentro Medico Nacional, Siglo XXI, IMSSMexico CityMexico
4.Department of LinguisticsMax Planck Institute for Evolutionary AnthropologyLeipzigGermany
5.Unidade de Xenética, Instituto de Medicina Legal, Departamento de Anatomía Patolóxica e Ciencias Forenses, Facultade de MedicinaUniversidade de Santiago de CompostelaGaliciaSpain
6.CIBER de Epidemiología y Salud PúblicaBarcelonaSpain
Sandoval, K., Buentello-Malo, L., Peñaloza-Espinosa, R. et al. Hum Genet (2009) 126: 521. https://doi.org/10.1007/s00439-009-0693-y
Received 17 February 2009
Accepted 25 May 2009
DOI https://doi.org/10.1007/s00439-009-0693-y
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A hydraulic manifold manufacturer contacted Dura-Bar Metal Services because they were unable to procure cold drawn 12L14 steel in the size that was required to manufacture a custom manifold for a major construction equipment OEM. The customer contacted Dura-Bar Metal Services because a line at the end user was about to be shut down if manifolds could not be produced and shipped as scheduled.
Dura-Bar Metal Services had worked with the end user previously and qualified Dura-Bar grade 65-45-12 ductile iron for manifolds. To keep the end user's line from shutting down, we were able to saw cut 65-45-12 plate to the customer's specification and deliver the blanks for machining in three business days.
Step two was to design a special size bar that would be cast, four-side milled and cut-to-length to provide the best size and cost option for the manifold manufacturer. Dura-Bar Metal Services was able to provide just in time delivery of cut-to-length slugs that shipped directly to the client's machining center.
Dura-Bar Metal Services was able to provide four-sided milled blanks to a +/-0.005" tolerance and was able to cut those blanks to a +/-0.005" tolerance as well. These value-added processes allowed the customer to use the saw cut faces, eliminating a machining operation and significantly reducing the machine cycle time for the manifold. This increased the number of manifolds produced per hour and the profitability for the client.
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Monmouthshire County Council has granted its first licence to a resident to grow fruit, vegetables and herbs on council-owned land just twelve months after approving its Community Food Growing policy. The licence grants Alison Newsam of Abergavenny the right to cultivate the St Helen's Road Incredible Edible plot, where with the help of neighbours Alison has transformed an area of overgrown shrubs into an area supporting pollinating plants to sustain insects plus tomatoes, runner beans, rhubarb and strawberries. All produce is offered free to anyone who wants to harvest them. More licences are expected elsewhere in the county. Further information on the Community Food Growing policy may be obtained by contacting Sustainability and Community Officer Alison Howard: alisonhoward@monmouthshire.gov.uk or 01633 644844.
If you are interested in getting involved in any of the following volunteering projects please contact Morag Sinton on 01633 644663 or email moragsinton@monmouthshire.gov.uk – looking after counters of people using the Wye Valley Walk, surveying the condition of bridges, and installing small bridges – all with training provided.
An on-line toolkit for anyone interested in volunteering to support walking and riding will be launched at 3pm at the Centenary Hall, Usk on Wednesday, 26 November – contact zara@adventa.org.uk.
The new Vale of Usk Local Action Group, which will oversee the 2014-20 Rural Development Programme for Monmouthshire and Newport (and possibly Torfaen) is seeking members. Go to http://www.monmouthshire.gov.uk/home/2014/10/22/become-a-member-of-the-new-vale-of-usk-local-action-group/ to learn more and apply – by 31 October.
Monmouthshire CC has rejected Welsh Government proposals that it should merge voluntarily with Newport CC or any other neighbouring council, believing that a robust business case has not been made by Wales Government. Instead they will explore with others options based on joint working but maintaining local democracy and accountability in Monmouthshire.
Already with a reputation for refusing windfarms, the UK Government has moved to curtail the growth of solar farms. Earlier this month it was announced that subsidies for large scale solar farms would end in April, and now Environment Secretary Liz Truss has labelled these a blight on the countryside, taking up land that could be used for crops. She will withdraw agricultural subsidies from these fields despite their availability for grazing sheep and other small animals. These subsidies are devolved to the Welsh Government which now has to decide whether to follow suit, and it will be interesting to see whether planning authorities will feel the need to toughen their controls.
The Federation of City Farms and Community Gardens wants to recruit a SE Wales Development Worker, 4 days a week. More at https://www.farmgarden.org.uk/about-us/jobs. Apply by 30 October.
How Could Energy Efficiency Be Improved?
Welsh Government is consulting on how they could improve energy efficiency performance in Wales, the most cost-effective way to support the move to a low carbon energy system. At this stage they want to hear your views on how to achieve this – http://wales.gov.uk/consultations/environmentandcountryside/energy-efficiency-strategy-for-wales/?lang=en. Deadline 8 January.
Usk has won the gold award for the best large village at the 50th Britain in Bloom UK Final awards ceremony. This is after winning the Wales in Bloom award for the small rural town category for the 33rd year in a row.
Welsh Government is consulting on their detailed proposals for the new pre-application procedures provided for in the Planning (Wales) Bill – http://wales.gov.uk/consultations/planning/frontloading-the-development-management-system/?status=open&lang=en – Deadline 16 January.
Welsh Government is consulting on how they can support their existing policies on design and inclusive access without the need for Design and Access Statements, which are not to be mandatory under a provision of the Planning (Wales) Bill. Go to http://wales.gov.uk/consultations/planning/design-in-the-planning-process/?lang=en. Deadline 16 January.


The first symptom of CJD is rapidly progressive dementia, leading to memory loss, personality changes, and hallucinations. Other frequently occurring features include anxiety, depression, paranoia, obsessive-compulsive symptoms, and psychosis. This is accompanied by physical problems such as speech impairment, jerky movements (myoclonus), balance and coordination dysfunction (ataxia), changes in gait, rigid posture, and seizures. The duration of the disease varies greatly, but sporadic (non-inherited) CJD can be fatal within months or even weeks. In some people, the symptoms can continue for years. In most patients, these symptoms are followed by involuntary movements and the appearance of an atypical diagnostic electroencephalogram tracing. Most victims die six months after initial symptoms appear, often of pneumonia due to impaired coughing reflexes. About 15% of patients survive for two or more years. Some patients have been known to live 4–5 years with mostly psychological symptoms until the disease progresses causing more physical symptoms leading to a diagnosis and inevitable death usually within the first year of diagnosis.
The symptoms of CJD are caused by the progressive death of the brain's nerve cells, which is associated with the build-up of abnormal prion proteins forming amyloids. When brain tissue from a CJD patient is examined under a microscope, many tiny holes can be seen where whole areas of nerve cells have died. The word "spongiform" in "transmissible spongiform encephalopathies" refers to the sponge-like appearance of the brain tissue.
Transmissible spongiform encephalopathy diseases are caused by prions. Prions are proteins that occur normally in neurons of the central nervous system (CNS). As of 2007 , these proteins are thought to affect signaling processes, damaging neurons and resulting in degeneration that causes the spongiform appearance in the affected brain.
The CJD prion is dangerous because it promotes refolding of native proteins into the diseased state. The number of misfolded protein molecules will increase exponentially and the process leads to a large quantity of insoluble protein in affected cells. This mass of misfolded proteins disrupts neuronal cell function and causes cell death. Mutations in the gene for the prion protein can cause a misfolding of the dominantly alpha helical regions into beta pleated sheets. This change in conformation disables the ability of the protein to undergo digestion. Once the prion is transmitted, the defective proteins invade the brain and are produced in a self-sustaining feedback loop.
These neurodegenerative diseases are commonly called prion diseases.
People can also acquire CJD genetically through a mutation of the gene that codes for the prion protein (PRNP). This occurs in only 5-10% of all CJD cases. An EU study determined that "87% of cases were sporadic, 8% genetic, and 5% iatrogenic."
The disease has also been shown to result from use of human growth hormone obtained from the pituitary glands of persons who died from Creutzfeldt–Jakob Disease, though the known incidence of this cause is (as of April 2004) quite small. The risk of infection via cadaveric HGH in the US ceased when the medication was withdrawn in 1985.
It is thought that humans can contract the disease by consuming material from animals infected with the bovine form of the disease. The only suspected cases to arise thus far have been vCJD with cases in the UK and Canada. But there are also fears—based on animal studies —that consuming beef or beef products containing prion particles can also cause the development of classic CJD. When BSE material infects humans, the resulting disease is known as (new) variant CJD (nvCJD).
Prions, the infectious agent of CJD, may not be inactivated by means of routine surgical instrument sterilization procedures. The World Health Organization and the US Centers for Disease Control and Prevention recommend that instrumentation used in such cases be immediately destroyed after use; short of destruction, it is recommended that heat and chemical decontamination be used in combination to process instruments that come in contact with high-infectivity tissues. No cases of iatrogenic transmission of CJD have been reported subsequent to the adoption of current sterilization procedures, or since 1976. Copper-hydrogen peroxide has been suggested as an alternative to the current recommendation of sodium hydroxide or sodium hypochlorite. Thermal depolymerization also destroys prions in infected organic and inorganic matter, since the process chemically attacks protein at the molecular level, although more effective and practical methods involve destruction by combinations of detergents and enzymes similar to biological washing powders.
In 2004, a report published in the Lancet medical journal showed that vCJD can be transmitted by blood transfusions. The finding alarmed healthcare officials because a large epidemic of the disease could result in the near-future. A blood test for vCJD infection is possible but is not yet available for screening blood donations. Significant restrictions exist to protect the blood supply. The UK government banned anyone who had received a blood transfusion since January 1980 from donating blood. From 1999 there has been a ban in the UK for using UK blood to manufacture fractional products such as albumin. Whilst these restrictions may go some way to preventing a self-sustaining epidemic of secondary infections the number of infected blood donations is unknown and could be considerable as a study by the Health Protection Agency show around 1 in 2000 people in the UK shows signs of vCJD infection. In June 2013 the government was warned that deaths-then at 176-could rise five-fold through blood transfusions.
On May 28, 2002, the United States Food and Drug Administration instituted a policy that excludes from donation anyone having spent at least six months in certain European countries (or three months in the United Kingdom) from 1980 to 1996. Given the large number of U.S. military personnel and their dependents residing in Europe, it was expected that over 7% of donors would be deferred due to the policy. Later changes to this policy have relaxed the restriction to a cumulative total of five years or more of civilian travel in European countries (six months or more if military). The three-month restriction on travel to the UK, however, has not been changed.
The American Red Cross' policy is as follows: During the period January 1, 1980, to December 31, 1996, spending a total time of three months or more in the Channel Islands, England, the Falkland Islands, the Isle of Man, Gibraltar, Northern Ireland, Scotland, and Wales precludes individuals from donating. Moreover, spending a total time of five years or more after January 1, 1980 (to present), in the above-mentioned countries and/or any country in Europe (except the former USSR), also precludes donation. People with a biologic relative having been diagnosed with CJD or vCJD are unable to donate. Biologic relative in this setting means mother, father, sibling, grandparent, aunt, uncle, or child.
The Singapore Red Cross precludes potential donors having spent a cumulative time of three months or more in the United Kingdom between 1980 and 1996.
In New Zealand, the New Zealand Blood Service (NZBS) in 2000 introduced measures to preclude permanently donors having resided in the United Kingdom (including the Isle of Man and the Channel Islands) for a total of six months or more between January 1980 and December 1996. The measure resulted in ten percent of New Zealand's active blood donors at the time becoming ineligible to donate blood. In 2003, the NZBS further extended restrictions to preclude permanently donors having had received a blood transfusion in the United Kingdom since January 1980, and in April 2006, restrictions were further extended to include the Republic of Ireland and France.
Similar regulations are in place in Germany, where anyone having spent six months or more living in the UK between January 1980 and December 1996 is permanently banned from donating blood.
In Canada, individuals are not eligible to donate blood or plasma if they have spent a cumulative total of three months in the United Kingdom or France from January 1, 1980, to December 31, 1996. They are also ineligible if they have spent a cumulative total of five years or more in Western Europe outside the U.K. or France since 1980, or if they have had a blood transfusion in the U.K., France or Western Europe since 1980.
The Association of Blood Donors of Denmark precludes potential donors having spent a cumulative time of at least 12 months in the United Kingdom between 1 January 1980 and 31 December 1996.
The Swiss Blutspendedienst SRK precludes potential donors having spent a cumulative time of at least six months in the United Kingdom between 1 January 1980 and 31 December 1996.
In Poland, anyone having spent cumulatively six months or longer between 1 January 1980 and 31 December 1996 in the UK, Ireland, or France is permanently barred from donating.
In the Czech Republic, anyone having spent more than six months in the UK or France between the years 1980 and 1996 or received transfusion in the UK after the year 1980 is not allowed to donate blood.
In the U.S., the FDA has banned import of any donor sperm, motivated by a risk of Creutzfeldt–Jakob disease, inhibiting the once popular import of Scandinavian sperm. The risk, however, is not known, since artificial insemination has not been studied as a route of transmission.
There is no known way to prevent sporadic CJD. If you have a family history of neurological disease, you may benefit from talking with a genetics counselor, who can help you sort through the risks associated with your situation.
Single-use kits for spinal taps (lumbar punctures).
The risk of contracting vCJD in the United States remains extremely low. Only three cases have been reported in the U.S. According to the Centers for Disease Control and Prevention, strong evidence suggests that these cases were acquired abroad — two in the United Kingdom and one in Saudi Arabia.
In the United Kingdom, where the majority of vCJD cases have occurred, fewer than 200 cases have been reported. CJD incidence peaked between 1999 and 2000 and has been declining since.
MRI of the brain—often shows high signal intensity in the caudate nucleus and putamen bilaterally on T2-weighted images.
Research in 2010 and 2011 identified a possible blood test for CJD. The test attempts to identify the prion responsible for the disease. However, it has not yet been demonstrated if it is able to detect the prions in early stages of the disease.
Diffusion Weighted Imaging (DWI) images are the most sensitive. In about 24% of cases DWI shows only cortical hyperintensity; in 68%, cortical and subcortical abnormalities; and in 5%, only subcortical anomalies. The involvement of the thalamus can be found in sCJD, is even stronger and constant in vCJD.
Clinical testing for CJD has always been an issue. Diagnosis has been based mostly on clinical and physical examination of symptoms. In recent years, studies have shown that the tumour marker Neuron-specific enolase (NSE) is often elevated in CJD cases, however its diagnostic utility is seen primarily when combined with a test for the 14-3-3 protein. As of 2010, screening tests to identify infected asymptomatic individuals, such as blood donors, are not yet available, though methods have been proposed and evaluated.
In 2010, a team from New York described detection of PrPSc even when initially present at only one part in one hundred billion (10−11) in brain tissue. The method combines amplification with a novel technology called surround optical fiber immunoassay (SOFIA) and some specific antibodies against PrPSc. After amplifying and then concentrating any PrPSc, the samples are labelled with a fluorescent dye using an antibody for specificity and then finally loaded into a micro-capillary tube. This tube is placed in a specially constructed apparatus so that it is totally surrounded by optical fibres to capture all light emitted once the dye is excited using a laser. The technique allowed detection of PrPSc after many fewer cycles of conversion than others have achieved, substantially reducing the possibility of artefacts, as well as speeding up the assay. The researchers also tested their method on blood samples from apparently healthy sheep that went on to develop scrapie. The animals' brains were analysed once any symptoms became apparent. The researchers could therefore compare results from brain tissue and blood taken once the animals exhibited symptoms of the diseases, with blood obtained earlier in the animals' lives, and from uninfected animals. The results showed very clearly that PrPSc could be detected in the blood of animals long before the symptoms appeared. After further development and testing, this method could be of great value in surveillance as a blood or urine-based screening test for CJD. In 2014 a human study showed a nasal brushing method that can accurately detect PrP in the olfactory epithelial of CJD patients. . This finding creates new opportunities for minimally invasive detection of CJD.
The classic histologic appearance is spongiform change in the gray matter: the presence of many round vacuoles from one to 50 micrometres in the neuropil, in all six cortical layers in the cerebral cortex or with diffuse involvement of the cerebellar molecular layer. These vacuoles appear glassy or eosinophilic and may coalesce. Neuronal loss and gliosis are also seen. Plaques of amyloid-like material can be seen in the neocortex in new-variant CJD.
However, vacuolization can be seen in other disease states. Diffuse cortical vacuolization occurs in Alzheimer's, and superficial cortical vacuolization occurs in ischemia and frontotemporal dementia. These vacuoles appear clear and punched-out. Larger vacuoles encircling neurons, vessels, and glia are a possible processing artifact.
Prognosis of Creutzfeldt-Jakob Disease: Poor. Typically death within 12 months. Prognosis for Creutzfeldt-Jakob Disease: About 90 percent of patients die within 1 year. In the early stages of disease, patients may have failing memory, behavioral changes, lack of coordination and visual disturbances. As the illness progresses, mental deterioration becomes pronounced and involuntary movements, blindness, weakness of extremities, and coma may occur. (Source: excerpt from NINDS Creutzfeldt-Jakob Disease Information Page: NINDS) Duration of Creutzfeldt-Jakob Disease: In more than 85 percent of cases, the duration of CJD is less than 1 year (median: 4 months) after onset of symptoms. (Source: excerpt from Facts About Creutzfeldt-Jakob Disease: CDC-OC).
As of 2015 , no generally accepted treatment for CJD exists; the disease is invariably fatal and research continues. An experimental treatment was given to a Northern Irish teenager, Jonathan Simms, beginning in January 2003. The medication, called pentosan polysulphate (PPS) and used to treat interstitial cystitis, is infused into the patient's lateral ventricle within the brain. PPS does not seem to stop the disease from progressing, and both brain function and tissue continue to be lost. However, the treatment is alleged to slow the progression of the otherwise untreatable disease, and may have contributed to the longer than expected survival of the seven patients studied. Simms died in 2011. The CJD Therapy Advisory Group to the UK Health Departments advises that data are not sufficient to support claims that pentosan polysulphate is an effective treatment and suggests that further research in animal models is appropriate. A 2007 review of the treatment of 26 patients with PPS finds no proof of efficacy because of the lack of accepted objective criteria.
Scientists have investigated using RNA interference to slow the progression of scrapie in mice. The RNA blocks production of the protein that the CJD process transforms into prions. This research is unlikely to lead to a human therapy for many years.
Both amphotericin B and doxorubicin have been investigated as potentially effective against CJD, but as yet there is no strong evidence that either drug is effective in stopping the disease. Further study has been taken with other medical drugs, but none are effective. However, drugs to reduce suffering do exist, and include valproate, an anticonvulsant agent, clonazepam and benzodiazepine, to reduce muscle jerks.
Scientists from the University of California, San Francisco are currently running a treatment trial for sporadic CJD using quinacrine, a medicine originally created for malaria. Pilot studies showed quinacrine permanently cleared abnormal prion proteins from cell cultures, but results have not yet been published on their clinical study. The efficacy of quinacrine was also assessed in a rigorous clinical trial in the UK and the results were published in Lancet Neurology, and concluded that quinacrine had no measurable effect on the clinical course of CJD.
In a 2013 paper published in the Proceedings of the National Academy of Sciences, scientists from The Scripps Research Institute reported that Astemizole, a medication approved for human use, has been found to have anti-prion activity and may lead to a treatment for Creutzfeldt–Jakob disease.
Fatal Brain Disease in Deer, Elk, Moose Spreading; Danger for Humans?
No added diagnostic value of non-phosphorylated tau fraction (p-taurel) in CSF as a biomarker for differential dementia diagnosis.
Disinfection of Tonometers: A Report by the American Academy of Ophthalmology.
An autopsy case of Creutzfeldt-Jakob disease with a prion protein gene codon 180 mutation presenting with pathological laughing and an exaggerated startle reaction.
A Case Report of Probable Sporadic Creutzfeldt-Jakob Disease: How to Approach Early Diagnosis?
A patient with a 'typical presentation' of Wernicke encephalopathy was found to have sporadic Creutzfeldt-Jakob disease.