bluuebunny/crossref_metadata_2025_split huggingface dataset:
Denisovan Ancestry in East Eurasian and Native American Populations
Authors: Qin Pengfei , Stoneking Mark 
Published: April 2015

AbstractAlthough initial studies suggested that Denisovan ancestry was found only in modern human populations from island Southeast Asia and Oceania, more recent studies have suggested that Denisovan ancestry may be more widespread. However, the geographic extent of Denisovan ancestry has not been determined, and moreover the relationship between the Denisovan ancestry in Oceania and that elsewhere has not been studied. Here we analyze genome-wide SNP data from 2493 individuals from 221 worldwide populations, and show that there is a widespread signal of a very low level of Denisovan ancestry across Eastern Eurasian and Native American (EE/NA) populations. We also verify a higher level of Denisovan ancestry in Oceania than that in EE/NA; the Denisovan ancestry in Oceania is correlated with the amount of New Guinea ancestry, but not the amount of Australian ancestry, indicating that recent gene flow from New Guinea likely accounts for signals of Denisovan ancestry across Oceania. However, Denisovan ancestry in EE/NA populations is equally correlated with their New Guinea or their Australian ancestry, suggesting a common source for the Denisovan ancestry in EE/NA and Oceanian populations. Our results suggest that Denisovan ancestry in EE/NA is derived either from common ancestry with, or gene flow from, the common ancestor of New Guineans and Australians, indicating a more complex history involving East Eurasians and Oceanians than previously suspected.
Mycobacterial infection induces a specific human innate immune response
Authors: Blischak John D. , Tailleux Ludovic , Mitrano Amy , Barreiro Luis B. , Gilad Yoav 
Published: April 2015

AbstractThe innate immune system provides the first response to pathogen infection and orchestrates the activation of the adaptive immune system. Though a large component of the innate immune response is common to all infections, pathogen-specific responses have been documented as well. The innate immune response is thought to be especially critical for fighting infection withMycobacterium tuberculosis(MTB), the causative agent of tuberculosis (TB). While TB can be deadly, only 5-10% of individuals infected with MTB develop active disease. The risk for disease susceptibility is, at least partly, heritable. Studies of inter-individual variation in the innate immune response to MTB infection may therefore shed light on the genetic basis for variation in susceptibility to TB. Yet, to date, we still do not know which properties of the innate immune response are specific to MTB infection and which represent a general response to pathogen infection. To begin addressing this gap, we infected macrophages with eight different bacteria, including different MTB strains and related mycobacteria, and studied the transcriptional response to infection. Although the ensued gene regulatory responses were largely consistent across the bacterial infection treatments, we were able to identify a novel subset of genes whose regulation was affected specifically by infection with mycobacteria. Genetic variants that are associated with regulatory differences in these genes should be considered candidate loci for explaining inter-individual susceptibility TB.Author SummaryTuberculosis (TB) is a deadly disease responsible for millions of deaths annually. It is caused by infection withMycobacterium tuberculosis(MTB), an ancient human pathogen. Approximately a third of the world’s population is infected with MTB, yet only an estimated 5-10% of individuals will develop an active form of the disease. While this variation in TB susceptibility has been demonstrated to be heritable, we still know little about its underlying genetic basis. The genetic variation that affects TB susceptibility likely involves the innate immune system, which is our first line of defense against invading pathogens, because infection with MTB does not prevent future infections. However, we do not fully understand how the innate immune system differs in its response to MTB versus other bacteria. To investigate this further, we infected macrophages with MTB, related mycobacteria, and other bacteria, and measured how their gene expression levels changed in response. We identified a subset of genes that respond preferentially to infection with mycobacterial species. These genes provide insight into the interactions between MTB and the innate immune system and are candidate loci for explaining inter-individual susceptibility to TB.
Evolutionarily induced alternative states and coexistence in systems with apparent competition
Authors: Schreiber Sebastian J. , Patel Swati 
Published: April 2015

AbstractPredators often consume multiple prey and by mutually subsidizing a shared predator, the prey may reciprocally harm each other. When predation levels are high, this apparent competition can culminate in a prey species being displaced. Coupling quantitative genetics and Lotka-Volterra models, we study how predator evolution alters this and other ecological outcomes. These models account for a trade-off between the predator’s attack rates on two prey species. We provide a mathematical characterization of a strong form of persistence–permanence–for which there is a global attractor bounded away from extinction. When the evolutionary dynamics occur at a sufficiently slower time scale than the ecological dynamics, we also characterize attractors and their basins’ of attraction using singular perturbation theory and a graphical approach to the eco-evolutionary dynamics. Our results show that eco-evolutionary feedbacks can mediate permanence at intermediate trade-offs in the attack rates. However, at strong trade-offs, permanence is lost. Despite this loss of permanence, there can be attractors supporting coexistence. These attractors, however, may coincide with attractors at which the predator is excluded. Our results highlight that evo-evolutionary feedbacks can alter community structure by mediating coexistence or leading to trait-dependent alternative stable states.
Suppression of Arbuscule Degeneration in Medicago truncatula phosphate transporter4 Mutants Is Dependent on the Ammonium Transporter 2 Family Protein AMT2;3
Authors: Breuillin-Sessoms Florence , Floss Daniela S. , Gomez S. Karen , Pumplin Nathan , Ding Yi , Levesque-Tremblay Veronique , Noar Roslyn D. , Daniels Dierdra A. , Bravo Armando , Eaglesham James B. , Benedito Vagner A. , Udvardi Michael K. , Harrison Maria J. 
Published: April 2015

Abstract
During arbuscular mycorrhizal (AM) symbiosis, the plant gains access to phosphate (Pi) and nitrogen delivered by its fungal symbiont. Transfer of mineral nutrients occurs at the interface between branched hyphae called arbuscules and root cortical cells. In Medicago truncatula, a Pi transporter, PT4, is required for symbiotic Pi transport, and in pt4, symbiotic Pi transport fails, arbuscules degenerate prematurely, and the symbiosis is not maintained. Premature arbuscule degeneration (PAD) is suppressed when pt4 mutants are nitrogen-deprived, possibly the result of compensation by PT8, a second AM-induced Pi transporter. However, PAD is also suppressed in nitrogen-starved pt4 pt8 double mutants, negating this hypothesis and furthermore indicating that in this condition, neither of these symbiotic Pi transporters is required for symbiosis. In M. truncatula, three AMT2 family ammonium transporters are induced during AM symbiosis. To test the hypothesis that suppression of PAD involves AMT2 transporters, we analyzed double and triple Pi and ammonium transporter mutants. ATM2;3 but not AMT2;4 was required for suppression of PAD in pt4, while AMT2;4, but not AMT2;3, complemented growth of a yeast ammonium transporter mutant. In summary, arbuscule life span is influenced by PT4 and ATM2;3, and their relative importance varies with the nitrogen status of the plant.
Ethylene Responses in Rice Roots and Coleoptiles Are Differentially Regulated by a Carotenoid Isomerase-Mediated Abscisic Acid Pathway
Authors: Yin Cui-Cui , Ma Biao , Collinge Derek Phillip , Pogson Barry James , He Si-Jie , Xiong Qing , Duan Kai-Xuan , Chen Hui , Yang Chao , Lu Xiang , Wang Yi-Qin , Zhang Wan-Ke , Chu Cheng-Cai , Sun Xiao-Hong , Fang Shuang , Chu Jin-Fang , Lu Tie-Gang , Chen Shou-Yi , Zhang Jin-Song 
Published: April 2015

Abstract
Ethylene and abscisic acid (ABA) act synergistically or antagonistically to regulate plant growth and development. ABA is derived from the carotenoid biosynthesis pathway. Here, we analyzed the interplay among ethylene, carotenoid biogenesis, and ABA in rice (Oryza sativa) using the rice ethylene response mutant mhz5, which displays a reduced ethylene response in roots but an enhanced ethylene response in coleoptiles. We found that MHZ5 encodes a carotenoid isomerase and that the mutation in mhz5 blocks carotenoid biosynthesis, reduces ABA accumulation, and promotes ethylene production in etiolated seedlings. ABA can largely rescue the ethylene response of the mhz5 mutant. Ethylene induces MHZ5 expression, the production of neoxanthin, an ABA biosynthesis precursor, and ABA accumulation in roots. MHZ5 overexpression results in enhanced ethylene sensitivity in roots and reduced ethylene sensitivity in coleoptiles. Mutation or overexpression of MHZ5 also alters the expression of ethylene-responsive genes. Genetic studies revealed that the MHZ5-mediated ABA pathway acts downstream of ethylene signaling to inhibit root growth. The MHZ5-mediated ABA pathway likely acts upstream but negatively regulates ethylene signaling to control coleoptile growth. Our study reveals novel interactions among ethylene, carotenogenesis, and ABA and provides insight into improvements in agronomic traits and adaptive growth through the manipulation of these pathways in rice.
Collaborating across health and social care: joint funding an adult protection Coordinator post in Caerphilly, UK
Authors: Giordano Andrea , Neville Alison 
Published: April 2015

Purpose
– The purpose of the paper is to improve the consistency and quality of the response to vulnerable adults who experience abuse and neglect within NHS, independent healthcare and social care settings is noted by practitioners, agencies and patients. Health and social care policy frameworks promote principles of service improvement and consistency, along with a focus on outcomes and resource effectiveness and interagency collaboration. The Protection of Vulnerable Adults (POVA) coordinator role carries the responsibility of coordinating a response to individual referrals of abuse and neglect as described as part of the Designated Lead Manager role in the Wales Interim POVA Policy and Procedures for the POVA from abuse (Wales Adult Protection Coordinators Group, 2013).

Design/methodology/approach
– This paper will explore the benefits realised through a registered nurse being seconded from the Aneurin Bevan University Health Board into a newly created joint adult protection Health Coordinator post within the Caerphilly County Borough Council social services department POVA team.

Findings
– This is the first example of such partnership working in adult protection in Wales and has provided a number of benefits in relation to: providing adult protection advice; coordinating the response to referrals of vulnerable adult abuse and neglect within health and social care settings; carrying out or buddying others to complete adult protection investigations; facilitating the two day non-criminal POVA investigation training course and, awareness raising within the local Health Board. The development of a student nurse placement in the social services POVA team cements the multiagency collaborative approach that this development sought to achieve.

Originality/value
– The need to improve the consistency and quality of the response to vulnerable adults who experience abuse and neglect within NHS, independent healthcare and social care settings is noted by practitioners, agencies and patients.
Reproducibility of Facial Soft Tissue Thickness Measurements Using Cone‐Beam CT Images According to the Measurement Methods
Authors: Hwang Hyeon‐Shik , Choe Seon‐Yeong , Hwang Ji‐Sup , Moon Da‐Nal , Hou Yanan , Lee Won‐Joon , Wilkinson Caroline 
Published: April 2015

AbstractThe purpose of this study was to establish the reproducibility of facial soft tissue (ST) thickness measurements by comparing three different measurement methods applied at 32 landmarks on three‐dimensional cone‐beam computed tomography (CBCT) images. Two observers carried out the measurements of facialSTthickness of 20 adult subjects usingCBCTscan data, and inter‐ and intra‐observer reproducibilities were evaluated. The measurement method of “perpendicular to bone” resulted in high inter‐ and intra‐observer reproducibility at all 32 landmarks. In contrast, the “perpendicular to skin” method and “direct” method, which measures a distance between one point on bone and the other point on skin, presented low reproducibility. The results indicate that reproducibility could be increased by identifying the landmarks on hard tissue images, rather than onSTimages, and the landmark description used in this study can be used in the establishment of reliable tissue depth data usingCBCTimages.
Forensic Applicability of Femur Subtrochanteric Shape to Ancestry Assessment in Thai and White American Males
Authors: Tallman Sean D. , Winburn Allysha P. 
Published: April 2015

AbstractAncestry assessment from the postcranial skeleton presents a significant challenge to forensic anthropologists. However, metric dimensions of the femur subtrochanteric region are believed to distinguish between individuals of Asian and non‐Asian descent. This study tests the discriminatory power of subtrochanteric shape using modern samples of 128 Thai and 77 White American males. Results indicate that the samples' platymeric index distributions are significantly different (p ≤ 0.001), with the Thai platymeric index range generally lower and the White American range generally higher. While the application of ancestry assessment methods developed from Native American subtrochanteric data results in low correct classification rates for the Thai sample (50.8–57.8%), adapting these methods to the current samples leads to better classification. The Thai data may be more useful in forensic analysis than previously published subtrochanteric data derived from Native American samples. Adapting methods to include appropriate geographic and contemporaneous populations increases the accuracy of femur subtrochanteric ancestry methods.
Determined to Die! Ability to Act Following Multiple Self‐inflicted Gunshot Wounds to the Head. The Cook County Office of Medical Examiner Experience (2005–2012) and Review of Literature
Authors: Arunkumar Ponni , Maiese Aniello , Bolino Giorgio , Gitto Lorenzo 
Published: April 2015

AbstractCases of multiple (considered 2+) self‐inflicted gunshot wounds are a rarity and require careful examination of the scene of occurrence; thorough consideration of the decedent's psychiatric, medical, and social histories; and accurate postmortem documentation of the gunshot wounds. We present a series of four cases of multiple self‐inflicted gunshot wounds to the head from the Cook County Medical Examiner's Office between 2005 and 2012 including the first case report of suicide involving eight gunshot wounds to the head. In addition, a review of the literature concerning multiple self‐inflicted gunshot wounds to the head is performed. The majority of reported cases document two gunshot entrance wound defects. Temporal regions are the most common affected regions (especially the right and left temples). Determining the capability to act following a gunshot wound to the head is necessary in crime scene reconstruction and in differentiation between homicide and suicide.
A SNP test to identify Africanized honeybees via proportion of ‘African’ ancestry
Authors: Chapman Nadine C. , Harpur Brock A. , Lim Julianne , Rinderer Thomas E. , Allsopp Michael H. , Zayed Amro , Oldroyd Benjamin P. 
Published: April 2015

AbstractThe honeybee, Apis mellifera, is the world's most important pollinator and is ubiquitous in most agricultural ecosystems. Four major evolutionary lineages and at least 24 subspecies are recognized. Commercial populations are mainly derived from subspecies originating in Europe (75–95%). The Africanized honeybee is a New World hybrid of A. m. scutellata from Africa and European subspecies, with the African component making up 50–90% of the genome. Africanized honeybees are considered undesirable for bee‐keeping in most countries, due to their extreme defensiveness and poor honey production. The international trade in honeybees is restricted, due in part to bans on the importation of queens (and semen) from countries where Africanized honeybees are extant. Some desirable strains from the United States of America that have been bred for traits such as resistance to the mite Varroa destructor are unfortunately excluded from export to countries such as Australia due to the presence of Africanized honeybees in the USA. This study shows that a panel of 95 single nucleotide polymorphisms, chosen to differentiate between the African, Eastern European and Western European lineages, can detect Africanized honeybees with a high degree of confidence via ancestry assignment. Our panel therefore offers a valuable tool to mitigate the risks of spreading Africanized honeybees across the globe and may enable the resumption of queen and bee semen imports from the Americas.
A new method for studying population genetics of cyst nematodes based on Pool‐Seq and genomewide allele frequency analysis
Authors: Mimee Benjamin , Duceppe Marc‐Olivier , Véronneau Pierre‐Yves , Lafond‐Lapalme Joël , Jean Martine , Belzile François , Bélair Guy 
Published: April 2015

AbstractCyst nematodes are important agricultural pests responsible for billions of dollars of losses each year. Plant resistance is the most effective management tool, but it requires a close monitoring of population genetics. Current technologies for pathotyping and genotyping cyst nematodes are time‐consuming, expensive and imprecise. In this study, we capitalized on the reproduction mode of cyst nematodes to develop a simple population genetic analysis pipeline based on genotyping‐by‐sequencing and Pool‐Seq. This method yielded thousands of SNPs and allowed us to study the relationships between populations of different origins or pathotypes. Validation of the method on well‐characterized populations also demonstrated that it was a powerful and accurate tool for population genetics. The genomewide allele frequencies of 23 populations of golden nematode, from nine countries and representing the five known pathotypes, were compared. A clear separation of the pathotypes and fine genetic relationships between and among global populations were obtained using this method. In addition to being powerful, this tool has proven to be very time‐ and cost‐efficient and could be applied to other cyst nematode species.
For testing the significance of regression coefficients, go ahead and log‐transform count data
Authors: Ives Anthony R. 
Published: April 2015

Summary

The rise in the use of statistical models for non‐Gaussian data, such as generalized linear models (GLMs) and generalized linear mixed models (GLMMs), is pushing aside the traditional approach of transforming data and applying least‐squares linear models (LMs). Nonetheless, many least‐squares statistical tests depend on the variance of the sum of residuals, which by the Central Limit Theorem converge to a Gaussian distribution for large sample sizes. Therefore, least‐squares LMs will likely have good performance in assessing the statistical significance of regression coefficients.

Using simulations of count data, I compared GLM approaches for testing whether regression coefficients differ from zero with the traditional approach of applying LMs to transformed data. Simulations assumed that variation among sample populations was either (i) negative binomial or (ii) log‐normal Poisson (i.e. log‐normal variation among populations that were then sampled by a Poisson distribution). I used the simulated data to conduct tests of the hypotheses that regression coefficients differed from zero; I did not investigate statistical properties of the coefficient estimators, such as bias and precision.

For negative binomial simulations whose assumptions closely matched the GLMs, the GLMs were nonetheless prone to type I errors (false positives) especially when there was more than one predictor (independent) variable. After correcting for type I errors, however, the GLMs provided slightly better statistical power than LMs. For log‐normal‐Poisson simulations, both a GLMM and the LMs performed well, but under some simulated conditions the GLMs had high type I error rates, a deadly sin for statistical tests.

These results show that, while GLMs have slight advantages in power when they are properly specified, they can lead to badly wrong conclusions about the significance of regression coefficients if they are mis‐specified. In contrast, transforming data and applying least‐squares linear analyses provide robust statistical tests for significance over a wide range of conditions. Thus, the traditional approach of transforming data and applying LMs is still useful.
Variation and response to experimental warming in a New Zealand cushion plant species
Authors: Cranston Brittany H. , Monks Adrian , Whigham Peter A. , Dickinson Katharine J. M. 
Published: April 2015

AbstractCold adapted plants, such as cushion plants, may be particularly sensitive to climate warming because of their compact growth form and high branch density. In the oceanic southern hemisphere, cushion communities tend to have large range distributions at low latitudes (sea level to low alpine), thus providing an opportunity to test the effects of temperature on plant morphology and reproduction across gradients. Using Donatia novae‐zelandiae as a model species, we compared the leaf morphology, reproduction and responses to warming. Two low‐alpine sites (Maungatua (880 m a.s.l.), Blue Mountains (1000 m a.s.l.)) and two sea‐level sites (Waituna 1 (0 m a.s.l.), Waituna 2 (0 m a.s.l.)) in South Island, New Zealand were used. Donatia novae‐zelandiae cushions differed significantly between the high‐elevation and sea‐level sites both morphologically and in terms of reproduction. High‐elevation cushions produced more flowers (threefold more flowers per plant) and seeds (sevenfold more seeds per capsule) than at sea level, but leaves were larger at sea level (in length and specific leaf area). The cushions were also twice as compact at the high‐elevation sites. After two growing seasons of artificial warming, seed production (35%), leaf length (7%) and width (13%), and specific leaf area (63%) significantly decreased in D. novae‐zelandiae plants; flower production was not significantly affected. Cushion plant morphology and reproduction were significantly affected by environmental drivers at their establishment sites, but all populations responded negatively to artificial warming of 1–3°C. Many cushion plants are considered keystone species because of their propensity to facilitate the growth and establishment of other plant species, the inferred negative effects of global warming on cushion plant species may have a cascading effect on other alpine plant groups.