bluuebunny/crossref_metadata_2025_split huggingface dataset:
How to infer reliable diploid genotypes from NGS or traditional sequence data: from basic probability to experimental optimization
Authors: CHENUIL A. 
Published: March 2012

AbstractThe use of diploid sequence markers is still challenging despite the good quality of the information they provide. There is a common problem to all sequencing approaches [traditional cloning and sequencing of PCR amplicons as well as next‐generation sequencing (NGS)]: when no variation is found within the sequences from a given individual, homozygozity can never be asserted with certainty. As a consequence, sequence data from diploid markers are mostly analysed at the population (not the individual level) particularly in animal studies. This study aims at contributing to solve this. Using the Bayes theorem and the binomial law, useful results are derived, among which: (i) the number of sequence reads per individual (or sequencing depth) which is required to ensure, at a given probability threshold, that some heterozygotes are not considered erroneously as homozygotes, as a function of the observed heterozygozity (Ho) of the locus in the population; (ii) a way of estimating Ho from low coverage NGS data; (iii) a way of testing the null hypothesis that a genetic marker corresponds to a single and diploid locus, in the absence of data from controlled crosses; (iv) strategies for characterizing sequence genotypes in populations minimizing the average number of sequence reads per individual; (v) a rationale to decide which are the variations that one needs to consider along the sequence, as a function of the sequencing depth affordable, the level of polymorphism desired and the risk of sequencing error. For traditional sequencing technology, optimal strategies appear surprisingly different from the usual empirical ones. The average number of sequence reads required to obtain 99% of fully determined genotypes never exceeds six, this value corresponding to the worst situation when Ho equals 0.6. This threshold value of Ho is strikingly stable when the tolerated proportion of nonfully resolved genotypes varies in a reasonable range. These results do not rely on the Hardy–Weinberg equilibrium assumption or on diallelism of nucleotidic sites.
Pathogens of the bark beetle Ips cembrae: microsporidia and gregarines also known from other Ips species
Authors: Holuša J. , Lukášová K. , Wegensteiner R. , Grodzki W. , Pernek M. , Weiser J. 
Published: March 2012

AbstractThe objective of the current study was to identify pathogens of the large larch bark beetle, Ips cembrae, which is a secondary pest that has produced several local outbreaks across Europe in recent years. Beetles were collected from pheromone traps, trap trees and emergence traps (Larix decidua) during 2007 to 2011 at 10 study sites in central Europe. A total of 3379 mature and callow beetles were examined with a light microscope, and only two microsporidian pathogens [Chytridiopsis typographi and a diplokaryotic microsporidium (probably Nosema sp.)] and two gregarines (Gregarina typographi and Mattesia schwenkei) were found. Within the I. cembrae populations, the infection rate for C. typographi ranged from 2 to 58%. Nosema sp. occurred in only two beetles in 2007 (at two study sites). G. typographi was recorded only in Austria and Croatia and only in 1–2% of the beetles in those countries. Mattesia schwenkei was observed solely in Croatia in 0.6% of the beetles in that country. Only one fungal pathogen in the genus Fusarium was found and only in two mature beetles (0.7%) in 2010. The pathogen species found during our study of I. cembrae were very similar to the pathogens previously identified for Ips typographus. No species‐specific pathogen was detected.
Lactation Weight Loss in Primiparous Sows: Consequences for Embryo Survival and Progesterone and Relations with Metabolic Profiles
Authors: Hoving LL , Soede NM , Feitsma H , Kemp B 
Published: March 2012

ContentsOur objective was to study reproductive consequences of lactation bodyweight loss occurring in primiparous sows with mild feed restriction and to relate these lactation weight losses and its consequences to metabolic profiles during lactation and subsequent early gestation. After weaning, 47 first‐litter sows were retrospectively assigned to a high– (HWL, >13.8%, n = 24) or low (LWL, ≤13.8%, n = 23)–weight loss group. Thirty‐six animals received an indwelling jugular vein catheter to determine lactational and gestational profiles of insulin‐like growth factor‐1 (IGF‐1), non‐esterified fatty acids (NEFA) and urea and gestational profiles of progesterone. At day 35 after insemination, sows were euthanized and their reproductive tract collected. Pregnancy rate was 75% (18/24) for HWL and 96% (22/23) for LWL sows. High–weight loss sows had a lower number of implantation sites (17.2 ± 0.8 vs 19.5 ± 0.7, respectively, p = 0.03) and a lower embryonic survival (65.6 ± 3.4 vs 77.4 ± 2.9%, p = 0.02), resulting in fewer vital embryos (14.9 ± 0.9 vs 16.8 ± 0.7, p = 0.07) than LWL sows. Progesterone peak values were reached later in HWL than in LWL sows (day 13.4 ± 0.5 vs 12.0 ± 0.5, respectively, p = 0.05). Gestational concentrations of IGF‐1, NEFA and urea were almost identical for HWL and LWL sows, whilst numerical differences were seen during lactation. The current study shows negative consequences of lactational weight loss in mildly feed‐restricted primiparous sows for embryonic survival and shows that these consequences seem only mildly related with metabolic alterations during lactation and not with metabolic alterations during subsequent gestation.
Provisional unicentric experience with an electronic incident reporting form in pediatric anesthesia
Authors: Montobbio Giovanni , Pini‐Prato Alessio , Guida Edoardo , Disma Nicola , Mameli Leila , Avanzini Stefano , Scali Roberto , Tuo Pietro , Jasonni Vincenzo , Mattioli Girolamo 
Published: March 2012

SummaryObjective:  To present and compare with literature our experience with an electronic anesthesia‐related incident reporting form as a quality control measure at Gaslini Children’s Hospital over a 19‐month period.Methods:  All events that occurred between March 2009 and September 2010 were recorded. We adopted an electronic reporting form included in the online recording process of every anesthetic procedure. Events were divided into near misses and adverse events. Adverse events were further divided into incidents, minor events, and major events. Patients were divided into three age‐groups: <1, between 1 and 3, and >3 years.Results:  A total of 12 850 anesthetics were performed. Eight (0.06%) near misses and 108 (0.8%) adverse events were reported. Adverse events occurred more frequently in infants. Of 108 events, 35 (32.4%), 61 (56.5%), and 12 (11.1%) were classified as incidents, minor, and major events, respectively. Of all the adverse events, 66 (61%) were respiratory, 27 (25%) organizational, six (5%) drug‐related, four (4%) cardiocirculatory, and five (5%) miscellaneous.Conclusions:  Infants were at the highest risk to experience adverse events. Although experimental electronic incident reporting proved to be feasible, there is reason to suspect that there was underreporting of near misses. Overreporting of near miss events may be enhanced by easier and more straightforward reporting forms as well as by better education for anesthetic providers about the importance of recognizing and reporting near misses.
HEALTH, VITAL GOALS, AND CENTRAL HUMAN CAPABILITIES
Authors: VENKATAPURAM SRIDHAR 
Published: March 2012

ABSTRACTI argue for a conception of health as a person's ability to achieve or exercise a cluster of basic human activities. These basic activities are in turn specified through free‐standing ethical reasoning about what constitutes a minimal conception of a human life with equal human dignity in the modern world. I arrive at this conception of health by closely following and modifying Lennart Nordenfelt's theory of health which presents health as the ability to achieve vital goals. Despite its strengths I transform Nordenfelt's argument in order to overcome three significant drawbacks. Nordenfelt makes vital goals relative to each community or context and significantly reflective of personal preferences. By doing so, Nordenfelt's conception of health faces problems with both socially relative concepts of health and subjectively defined wellbeing. Moreover, Nordenfelt does not ever explicitly specify a set of vital goals. The theory of health advanced here replaces Nordenfelt's (seemingly) empty set of preferences and society‐relative vital goals with a human species‐wide conception of basic vital goals, or ‘central human capabilities and functionings’. These central human capabilities come out of the capabilities approach (CA) now familiar in political philosophy and economics, and particularly reflect the work of Martha Nussbaum. As a result, the health of an individual should be understood as the ability to achieve a basic cluster of beings and doings—or having the overarching capability, a meta‐capability, to achieve a set of central or vital inter‐related capabilities and functionings.
Screening and Signaling in Communication*
Authors: Andina‐Díaz Ascensión 
Published: March 2012

AbstractIn this paper, we analyze a model of repeated strategic communication between a sender and a receiver. The sender has private information on a policy‐relevant variable but does not know the receiver's motives. Together with the desire of the sender to please the receiver and the desire of the receiver to be pleased, the two‐sided incomplete information creates an interesting communication problem in which players can choose to use information strategically. We analyze various modes of communication, which allow for information transmission, and we compare them in terms of both the quality of the policy implemented and the welfare of the players.
Learning Out of Leaders
Authors: Mougeot Mathilde , Picard Dominique , Tribouley Karine 
Published: March 2012

SummaryThe paper investigates the estimation problem in a regression-type model. To be able to deal with potential high dimensions, we provide a procedure called LOL—for learning out of leaders—with no optimization step. LOL is an autodriven algorithm with two thresholding steps. A first adaptive thresholding helps to select leaders among the initial regressors to obtain a first reduction of dimensionality. Then a second thresholding is performed on the linear regression on the leaders. The consistency of the procedure is investigated. Exponential bounds are obtained, leading to minimax and adaptive results for a wide class of sparse parameters, with (quasi) no restriction on the number p of possible regressors. An extensive computational experiment is conducted to emphasize the practical good performances of LOL.
TLR2 and TLR4 gene polymorphisms in Turkish vitiligo patients
Authors: Karaca N. , Ozturk G. , Gerceker B.T. , Turkmen M. , Berdeli A. 
Published: March 2012

AbstractBackground  It has been shown that toll like receptors (TLR) may be involved in some inflammatory skin diseases such as psoriasis, atopic dermatitis. Vitiligo is an acquired pigmentation disorder of unknown aetiology. A number of genes playing a role in inflammatory response may be associated with development of vitiligo.Objectives  To investigate whether there is an association between TLR 2 and TLR4 gene polymorphisms in Turkish patients with vitiligo.Methods  A total of 100 patients (59 women and 41 men) with vitiligo and 100 controls (58 women and 42 men) were included in the study. The TLR2 gene Arg753Gln and TLR4 gene Asp299Gly and Thr399Ile polymorphisms were genotyped by using polymerase chain reaction and restriction fragment length polymorphism method. The data were analysed by Mann–Whitney U‐test, chi‐squared test and logistic regression analysis.Results  Significant difference was found in the distribution of TLR2 Arg753Gln genotype and in the allele frequencies TLR2 753Gln between vitiligo patients and healthy subjects (P < 0.05). The distribution of TLR4 Asp299Gly genotype was significantly higher in the patient group (10%) than in the control group (%2) (P < 0.05). The TLR4 Thr399Ile distribution did not show any difference in both vitiligo and healthy groups.Conclusions  Our findings suggest that Toll‐like receptor 2 gene Arg753Gln and Toll‐like receptor 4 Asp299Gly gene polymorphisms are associated with vitiligo susceptibility in Turkish patients.
Long‐term outcomes of interruption and retreatment vs. continuous therapy with adalimumab for psoriasis: subanalysis of REVEAL and the open‐label extension study
Authors: Papp K. , Menter A. , Poulin Y. , Gu Y. , Sasso E.H. 
Published: March 2012

AbstractBackground  REVEAL was a 52‐week study of adalimumab for moderate to severe psoriasis. At Week 33, adalimumab‐treated patients with sustained responses (PASI ≥75 at Weeks 16 and 33) were re‐randomized to receive adalimumab or placebo. Subsequently, they could receive adalimumab in an open‐label extension (OLE) study.Objective  To compare long‐term efficacy and safety of adalimumab 40 mg every other week (eow), given as continuous treatment or with one period of interruption followed by retreatment.Methods  Patients who were re‐randomized to adalimumab or placebo at REVEAL Week 33 and received ≥1 dose of OLE adalimumab were analysed as the continuous and retreatment groups, respectively, for >2 years of OLE treatment with adalimumab 40 mg eow. LOCF was used for missing efficacy data.Results  At OLE Weeks 0, 12 and 24, PASI 75 response rates were 84%, 84%, 86% with continuous treatment (N = 233) vs. 45%, 71%, 79% with retreatment (N = 227). Thereafter, efficacies were slightly greater for continuous treatment but similar between groups, with PASI 75 response rates at OLE Week 108 of 75% vs. 73% respectively. Retreatment was most effective for patients with ≥PASI 50 responses when retreatment was initiated. Adverse event rates for retreatment were equal to or lower than those for continuous treatment.Conclusions  In psoriasis patients with sustained PASI 75 responses to adalimumab, long‐term efficacy of retreatment after a ≤19‐week interruption was similar to efficacy achieved with >3 years continuous treatment. Adalimumab retreatment provided the best results when initiated before responses had declined below PASI 50.
Morphology and development of the placentae in Eulamprus quoyii group skinks (Squamata: Scincidae)
Authors: Murphy Bridget F. , Brandley Matthew C. , Murphy Christopher R. , Thompson Michael B. 
Published: March 2012

AbstractFrequent evolutionary changes in reproductive mode have produced a wide range of placental structures in viviparous squamate reptiles. Closely related species with different placental structures and resolved phylogenetic relationships are particularly useful for reconstructing how placentae might have transformed during the evolutionary process. We used light microscopy to study placental morphology in mid‐ to late stage embryos of four closely related species of Eulamprus, a genus of viviparous scincid lizards that we had reason to suspect may display significant interspecific variation in placental morphology. Embryos from all four species possess a chorioallantoic placenta, an omphaloplacenta and an interomphalopleuric membrane, characteristics present in other viviparous skinks. However, unlike other viviparous skinks but characteristic of oviparous skinks, the allantois expands to surround the yolk sac in each species, supplanting the omphalopleure with a larger area of chorioallantois until a chorioallantoic placenta surrounds the entire egg in one specimen that is only a few days from birth. All four Eulamprus species share the same extraembryonic membrane morphology, but the cellular morphology of the uterine epithelium in the chorioallantoic placenta and omphaloplacenta varies between species. We determined that the interomphalopleuric membrane is a shared derived character of the Eulamprus quoyii species group. New phylogenetic information indicates that variation in the chorioallantoic placenta is a result of two independent transitions, but that variation in the omphaloplacenta can be explained using a single change within the species studied. Our results indicate that E. quoyii group skinks are a valuable model for investigating the evolution of viviparity, as extraembryonic membrane development in these species shows features characteristic of both oviparous and viviparous skinks.
A national survey of UK health libraries investigating the cost of interlibrary loan services and assessing the accessibility to key orthopaedic journals
Authors: Tahim Arpan , Stokes Oliver , Vedi Vikas 
Published: March 2012

AbstractBackground:  NHS Library Services are utilised by NHS staff and junior trainees to locate scientific papers that provide them with the evidence base required for modern medical practice. The cost of accessing articles can be considerable particularly for junior trainees.Objectives:  This survey looks at variations in cost of journal article loans and investigates access to particular orthopaedic journals across the country.Methods:  A national survey of UK Health Libraries was performed. Access to and costs of journals and interlibrary loan services were assessed. Availability of five wide‐reaching orthopaedic journals was investigated.Results:  Seven hundred and ten libraries were identified. One hundred and ten libraries completed the questionnaire (16.7%). Of these, 96.2% reported free access to scientific journals for users. 99.1% of libraries used interlibrary loan services with 38.2% passing costs on to the user at an average of £2.99 per article. 72.7% of libraries supported orthopaedic services. Journal of Bone and Joint Surgery (British) had greatest onsite availability.Conclusions:  The study demonstrates fluctuations in cost of access to interlibrary loan services and variation in access to important orthopaedic journals. It provides a reflection of current policy of charging for the acquisition of medical evidence by libraries in the UK.
THE PROBLEMATIZATION OF MEDICAL TOURISM: A CRITIQUE OF NEOLIBERALISM
Authors: SMITH KRISTEN 
Published: March 2012

ABSTRACTThe past two decades have seen the extensive privatisation and marketisation of health care in an ever reaching number of developing countries. Within this milieu, medical tourism is being promoted as a rational economic development strategy for some developing nations, and a makeshift solution to the escalating waiting lists and exorbitant costs of health care in developed nations. This paper explores the need to problematize medical tourism in order to move beyond one dimensional neoliberal discourses that have, to date, dominated the arena. In this problematization, the paper discusses a range of understandings and uses of the term ‘medical tourism’ and situates it within the context of the neoliberal economic development of health care internationally. Drawing on theory from critical medical anthropology and health and human rights perspectives, the paper critically analyzes the assumed independence between the medical tourism industry and local populations facing critical health issues, where social, cultural and economic inequities are widening in terms of access, cost and quality of health care. Finally, medical tourism is examined in the local context of India, critiquing the increasingly indistinct roles played by government and private sectors, whilst linking these shifts to global market forces.
NEWS MEDIA REPORTS OF PATIENT DEATHS FOLLOWING ‘MEDICAL TOURISM’ FOR COSMETIC SURGERY AND BARIATRIC SURGERY
Authors: TURNER LEIGH 
Published: March 2012

ABSTRACTContemporary scholarship examining clinical outcomes in medical travel for cosmetic surgery identifies cases in which patients traveled abroad for medical procedures and subsequently returned home with infections and other surgical complications. Though there are peer‐reviewed articles identifying patient deaths in cases where patients traveled abroad for commercial kidney transplantation or stem cell injections, no scholarly publications document deaths of patients who traveled abroad for cosmetic surgery or bariatric surgery. Drawing upon news media reports extending from 1993 to 2011, this article identifies and describes twenty‐six reported cases of deaths of individuals who traveled abroad for cosmetic surgery or bariatric surgery. Over half of the reported deaths occurred in two countries. Analysis of these news reports cannot be used to make causal claims about why the patients died. In addition, cases identified in news media accounts do not provide a basis for establishing the relative risk of traveling abroad for care instead of seeking elective cosmetic surgery at domestic health care facilities. Acknowledging these limitations, the case reports suggest the possibility that contemporary peer‐reviewed scholarship is underreporting patient mortality in medical travel. The paper makes a strong case for promoting normative analyses and empirical studies of medical travel. In particular, the paper argues that empirically informed ethical analysis of ‘medical tourism’ will benefit from rigorous studies tracking global flows of medical travelers and the clinical outcomes they experience. The paper contains practical recommendations intended to promote debate concerning how to promote patient safety and quality of care in medical travel.
The paraoxonase‐1 pathway is not a major bioactivation pathway of clopidogrel in vitro
Authors: Ancrenaz V , Desmeules J , James R , Fontana P , Reny J‐L , Dayer P , Daali Y 
Published: March 2012

BACKGROUND AND PURPOSE Clopidogrel is a prodrug bioactivated by cytochrome P450s (CYPs). More recently, paraoxonase‐1 (PON1) has been proposed as a major contributor to clopidogrel metabolism. The purpose of this study was to assess the relative contribution of CYPs and PON1 to clopidogrel metabolism in vitro.EXPERIMENTAL APPROACH Clopidogrel metabolism was studied in human serum, recombinant PON1 enzyme (rePON1), pooled human liver microsomes (HLMs), HLMs with the CYP2C19*1/*1 genotype and HLMs with the CYP2C19*2/*2 genotype. Inhibition studies were also performed using specific CYP inhibitors and antibodies. Clopidogrel and its metabolites were measured using LC/MS/MS method.KEY RESULTS PON1 activity was highest in the human serum and there was no difference in PON1 activity between any of the HLM groups. The production of clopidogrel's active metabolite (clopidogrel‐AM) from 2‐oxo‐clopidogrel in pooled HLMs was approximately 500 times that in serum. When 2‐oxo‐clopidogrel was incubated with rePON1, clopidogrel‐AM was not detected. Clopidogrel‐AM production from 2‐oxo‐clopidogrel was lower in CYP2C19*2/*2 HLMs compared with CYP2C19*1/*1 HLMs, while PON1 activity in HLMs with both genotypes was similar. Moreover, incubation with inhibitors of CYP3A, CYP2B6 and CYP2C19 significantly reduced clopidogrel bioactivation while a PON1 inhibitor, EDTA, had only a weak inhibitory effect.CONCLUSION AND IMPLICATIONS This in vitro study shows that the contribution of PON1 to clopidogrel metabolism is limited at clinically relevant concentrations. Moreover, CYP2C19, CYP2B6 and CYP3A play important roles in the bioactivation of clopidogrel.