bluuebunny/crossref_metadata_2025_split huggingface dataset:
The demographic history of populations experiencing asymmetric gene flow: combining simulated and empirical data
Authors: Paz‐Vinas I. , Quéméré E. , Chikhi L. , Loot G. , Blanchet S. 
Published: May 2013

AbstractPopulation structure can significantly affect genetic‐based demographic inferences, generating spurious bottleneck‐like signals. Previous studies have typically assumed island or stepping‐stone models, which are characterized by symmetric gene flow. However, many organisms are characterized by asymmetric gene flow. Here, we combined simulated and empirical data to test whether asymmetric gene flow affects the inference of past demographic changes. Through the analysis of simulated genetic data with three methods (i.e. bottleneck, M‐ratio and msvar), we demonstrated that asymmetric gene flow biases past demographic changes. Most biases were towards spurious signals of expansion, albeit their strength depended on values of effective population size and migration rate. It is noteworthy that the spurious signals of demographic changes also depended on the statistical approach underlying each of the three methods. For one of the three methods, biases induced by asymmetric gene flow were confirmed in an empirical multispecific data set involving four freshwater fish species (Squalius cephalus, Leuciscus burdigalensis, Gobio gobio and Phoxinus phoxinus). However, for the two other methods, strong signals of bottlenecks were detected for all species and across two rivers. This suggests that, although potentially biased by asymmetric gene flow, some of these methods were able to bypass this bias when a bottleneck actually occurred. Our results show that population structure and dispersal patterns have to be considered for proper inference of demographic changes from genetic data.
An exploration of jealousy in nursing: A Kleinian analysis
Authors: Evans Alicia M , Traynor Michael , Glass Nel 
Published: May 2013

It is well established that nursing practice produces considerable anxiety, and it can also give rise to envy and jealousy. While envy in nursing was identified in the literature more than 50 years ago, there remains a paucity of articles addressing either envy or jealousy for nurses. In a recent research study on current experiences of clinical practice, we analysed a fragment of nurses’ speech via Klein's theory of jealousy. The results revealed that the nurses expressed jealousy at the privilege afforded to doctors. We argue that it is important to acknowledge jealousy in nursing practice because it has the potential for ‘spoiling’ effective care delivery and as such, can have detrimental ramifications in the health system. Also, jealousy may keep the nurse from fully focusing on their nursing practice in that it divides the nurse's attention and so limits the nurse's treatment of the patient. Nurses’ jealousy of doctors is a taboo topic in nursing, and yet it warrants serious consideration due to the potential deleterious consequences that can arise when this dynamic is present.
Association between reflux and symptoms during ambulatory reflux monitoring: pros and cons of existing methods
Authors: Bredenoord A. J. , Smout A. J. P. M. 
Published: May 2013

AbstractAmbulatory reflux monitoring provides information on the quantity of gastroesophageal reflux and, if symptoms are registered during the study, provides insights into the relation between symptoms and reflux. Several symptom‐reflux association analysis indices have been developed to express the relationship between onset of symptom and reflux in a numerical way. One of these indices is the binomial symptom index, introduced by Ghillebert et al. in 1990. The binomial symptom index can be used to study the relationship between symptoms and acid reflux. In this issue of Neurogastroenterology and Motility Barriga‐Rivera et al. describe the use of Monte Carlo simulations to investigate the effect of random changes in reflux rates and symptom occurrences on binomial symptom index outcome. Their analysis shows that this index can be used to measure the strength of reflux symptom association. Performing symptom‐reflux association analysis is important as the outcome has been shown to be reproducible and can be used as a predictor to response to acid‐suppressive treatment. Despite some limitations, use of symptom‐reflux association analysis is a valuable clinical tool that can provide unique insights into the cause of a patient's symptoms.
Fast Covariance Estimation for Innovations Computed from a Spatial Gibbs Point Process
Authors: Coeurjolly Jean‐François , Rubak Ege 
Published: May 2013

ABSTRACTIn this paper, we derive an exact formula for the covariance of two innovations computed from a spatial Gibbs point process and suggest a fast method for estimating this covariance. We show how this methodology can be used to estimate the asymptotic covariance matrix of the maximum pseudo‐likelihood estimator of the parameters of a spatial Gibbs point process model. This allows us to construct asymptotic confidence intervals for the parameters. We illustrate the efficiency of our procedure in a simulation study for several classical parametric models. The procedure is implemented in the statistical software R, and it is included in spatstat, which is an R package for analyzing spatial point patterns.
Reducing Implicit Prejudice
Authors: Lai Calvin K. , Hoffman Kelly M. , Nosek Brian A. 
Published: May 2013

AbstractImplicit prejudices are social preferences that exist outside of conscious awareness or control. In this review, we summarize evidence for three mechanisms that influence the expression of implicit prejudice: associative change, contextual change, and change in control over implicit prejudice. We then review the evidence (or lack thereof) for answers to five open issues in implicit prejudice reduction research: (1) what shows effectiveness in real‐world application; (2) what doesn't work for implicit prejudice reduction; (3) what interventions produce long‐term changes in implicit prejudice; (4) measurement diversity in implicit prejudice reduction research; and (5) the relationship between implicit prejudice and behavior. Addressing these issues provides an agenda for clarifying the conditions and implications of reducing implicit prejudice.
The Dynamic Relationship Between Accuracy and Bias in Social Perception Research
Authors: Stern Chadly , West Tessa V. , Schoenthaler Antoinette 
Published: May 2013

AbstractHow do perceivers make accurate social judgments? A substantial amount of evidence suggests that perceivers' judgments are often quite accurate even when they do not have direct access to the truth, in part because they make judgments through biased processes. In the present article, we examine the dynamic relationship between bias and accuracy in social perception research. We outline how bias and accuracy are theoretically and empirically distinct processes and describe the importance (and difficulty) of defining and measuring both truth variables and bias variables in order to make empirical conclusions in accuracy research. Additionally, we examine how both bias variables (e.g., stereotypes, perceivers' own beliefs) and truth variables exert an influence on how perceivers make social judgments, as well as the extent to which judgments are accurate. Lastly, we provide steps that researchers can take in order to examine the relationship between bias and accuracy in their own research.
Village registers for vital registration in rural Malawi
Authors: Singogo E. , Kanike E. , van Lettow M. , Cataldo F. , Zachariah R. , Bissell K. , Harries A. D. 
Published: May 2013

AbstractPaper‐based village registers were introduced 5 years ago in Malawi as a tool to measure vital statistics of births and deaths at the population level. However, usage, completeness and accuracy of their content have never been formally evaluated. In Traditional Authority Mwambo, Zomba district, Malawi, we assessed 280 of the 325 village registers with respect to (i) characteristics of village headmen who used village registers, (ii) use and content of village registers, and (iii) whether village registers provided accurate information on births and deaths. All village headpersons used registers. There were 185 (66%) registers that were regarded as 95% completed, and according to the registers, there were 115 840 people living in the villages in the catchment area. In 2011, there were 1753 births recorded in village registers, while 6397 births were recorded in health centre registers in the same catchment area. For the same year, 199 deaths were recorded in village registers, giving crude death rates per 100 000 population of 189 for males and 153 for females. These could not be compared with death rates in health centre registers due to poor and inconsistent recording in these registers, but they were compared with death rates obtained from the 2010 Malawi Demographic Health Survey that reported 880 and 840 per 100 000 for males and females, respectively. In conclusion, this study shows that village registers are a potential source for vital statistics. However, considerable inputs are needed to improve accuracy of births and deaths, and there are no functional systems for the collation and analysis of data at the traditional authority level. Innovative ways to address these challenges are discussed, including the use of solar‐powered electronic village registers and mobile phones, connected with each other and the health facilities and the District Commissioner's office through the cellular network and wireless coverage.
Decorin‐PEI nanoconstruct attenuates equine corneal fibroblast differentiation
Authors: Donnelly Kevin S. , Giuliano Elizabeth A. , Sharma Ajay , Tandon Ashish , Rodier Jason T. , Mohan Rajiv R. 
Published: May 2013

AbstractObjectiveTo explore (i) the potential of polyethylenimine (PEI) nanoparticles as a vector for delivering genes into equine corneal fibroblasts (ECFs) using green fluorescent protein (GFP) marker gene, (ii) whether PEI nanoparticle‐mediated decorin (DCN) gene therapy could be used to inhibit fibrosis in the equine cornea using an in vitro model.ProcedurePolyethylenimine–DNA nanoparticles were prepared at nitrogen‐to‐phosphate (N‐P) ratio of 15 by mixing 22 kDa linear PEI and a plasmid encoding either GFP or DCN. ECFs were generated from donor corneas as previously described. Initially, GFP was introduced into ECFs using PEI nanoparticles to confirm gene delivery, then DCN was introduced to evaluate for antifibrotic effects. GFP gene delivery was confirmed with real‐time qPCR and ELISA. Changes in fibrosis after DCN therapy were quantified by measuring α‐smooth muscle actin (αSMA) mRNA and protein levels with qPCR, immunostaining, and immunoblotting. Cytotoxicity was determined by evaluating cell morphology, cellular viability, and TUNEL assay.ResultsPolyethylenimine‐green fluorescent protein‐treated cultures showed 2.2 × 104 GFP plasmid copies/μg of cellular DNA and 2.1 pg of GFP/100 μL of lysate. PEI–DCN delivery significantly attenuated TGFβ‐induced transdifferentiation of fibroblasts to myofibroblasts (2‐fold decrease of αSMA mRNA; P = 0.05) and significant inhibition of αSMA (49 ± 14.2%; P < 0.001) in immunocytochemical staining and immunoblotting were found. Furthermore, PEI–DNA nanoparticle delivery did not alter cellular phenotype at 24 h and cellular viability was maintained.ConclusionsTwenty‐two kilo dalton Polyethylenimine nanoparticles are safe and effective for equine corneal gene therapy in vitro. PEI‐mediated DCN gene delivery is effective at inhibiting TGFβ‐mediated fibrosis in this model.
Minimum Core Genome Sequence Typing of Bacterial Pathogens: a Unified Approach for Clinical and Public Health Microbiology
Authors: Chen Chen , Zhang Wen , Zheng Han , Lan Ruiting , Wang Haiyin , Du Pengcheng , Bai Xuemei , Ji Shaobo , Meng Qiong , Jin Dong , Liu Kai , Jing Huaiqi , Ye Changyun , Gao George F. , Wang Lei , Gottschalk Marcelo , Xu Jianguo 
Published: May 2013

ABSTRACT

Bacterial pathogens impose a heavy health burden worldwide. In the new era of high-throughput sequencing and online bioinformatics, real-time genome typing of infecting agents, and in particular those with potential severe clinical outcomes, holds promise for guiding clinical care to limit the detrimental effects of infections and to prevent potential local or global outbreaks. Here, we sequenced and compared 85 isolates of
Streptococcus suis
, a zoonotic human and swine pathogen, wherein we analyzed 32 recognized serotypes and 75 sequence types representing the diversity of the species and the human clinical isolates with high public health significance. We found that 1,077 of the 2,469 genes are shared by all isolates. Excluding 201 common but mobile genes, 876 genes were defined as the minimum core genome (MCG) of the species. Of 190,894 single-nucleotide polymorphisms (SNPs) identified, 58,501 were located in the MCG genes and were referred to as MCG SNPs. A population structure analysis of these MCG SNPs classified the 85 isolates into seven MCG groups, of which MCG group 1 includes all isolates from human infections and outbreaks. Our MCG typing system for
S. suis
provided a clear separation of groups containing human-associated isolates from those containing animal-associated isolates. It also separated the group containing outbreak isolates, including those causing life-threatening streptococcal toxic shock-like syndrome, from sporadic or less severe meningitis or bacteremia-only isolates. The typing system facilitates the application of genome data to the fields of clinical medicine and epidemiology and to the surveillance of
S. suis
. The MCG groups may also be used as the taxonomical units of
S. suis
to define bacterial subpopulations with the potential to cause severe clinical infections and large-scale outbreaks.
Optimization of a Ligase Detection Reaction-Fluorescent Microsphere Assay for Characterization of Resistance-Mediating Polymorphisms in African Samples of Plasmodium falciparum
Authors: LeClair Norbert P. , Conrad Melissa D. , Baliraine Frederick N. , Nsanzabana Christian , Nsobya Samuel L. , Rosenthal Philip J. 
Published: May 2013

ABSTRACT

Genetic polymorphisms in the malaria parasite
Plasmodium falciparum
mediate alterations in sensitivity to important antimalarial drugs. Surveillance for these polymorphisms is helpful in assessing the prevalence of drug resistance and designing strategies for malaria control. Multiple methods are available for the assessment of
P. falciparum
genetic polymorphisms, but they suffer from low throughput, technical limitations, and high cost. We have optimized and tested a multiplex ligase detection reaction-fluorescent microsphere (LDR-FM) assay for the identification of important
P. falciparum
genetic polymorphisms. For 84 clinical samples from Kampala, Uganda, a region where both transmission intensity and infection complexity are high, DNA was extracted from dried blood spots, genes of interest were amplified, amplicons were subjected to multiplex ligase detection reactions to add bead-specific oligonucleotides and biotin, fragments were hybridized to magnetic beads, and polymorphism prevalences were assessed fluorometrically in a multiplex format. A total of 19 alleles from the
pfcrt
,
pfmdr1
,
pfmrp1
,
pfdhfr
, and
pfdhps
genes were analyzed by LDR-FM and restriction fragment length polymorphism (RFLP) analyses. Considering samples with results from the two assays, concordance between the assays was good, with 78 to 100% of results identical at individual alleles, most nonconcordant results differing only between a mixed and pure genotype call, and full disagreement at individual alleles in only 0 to 3% of results. We estimate that the LDR-FM assay offers much higher throughput and lower cost than RFLP. Our results suggest that the LDR-FM system offers an accurate high-throughput means of classifying genetic polymorphisms in field samples of
P. falciparum
.
Constitutive Interferon-Inducible Protein 16-Inflammasome Activation during Epstein-Barr Virus Latency I, II, and III in B and Epithelial Cells
Authors: Ansari Mairaj Ahmed , Singh Vivek Vikram , Dutta Sujoy , Veettil Mohanan Valiya , Dutta Dipanjan , Chikoti Leela , Lu Jie , Everly David , Chandran Bala 
Published: May 2013

ABSTRACT

Epstein-Barr virus (EBV), etiologically linked with human B-cell malignancies and nasopharyngeal carcinoma (NPC), establishes three types of latency that facilitate its episomal genome persistence and evasion of host immune responses. The innate inflammasome responses recognize the pathogen-associated molecular patterns which lead into the association of a cytoplasmic sensor such as NLRP3 and AIM2 proteins or nuclear interferon-inducible protein 16 (IFI16) with adaptor ASC protein (apoptosis-associated speck-like protein with a caspase recruitment domain) and effector procaspase-1, resulting in active caspase-1 formation which cleaves the proforms of inflammatory interleukin-1β (IL-1β), IL-18, and IL-33 cytokines. Whether inflammasome responses recognize and respond to EBV genome in the nuclei was not known. We observed evidence of inflammasome activation, such as the activation of caspase-1 and cleavage of pro-IL-1β, -IL-18, and -IL-33, in EBV latency I Raji cells, latency II NPC C666-1 cells, and latency III lymphoblastoid cell lines (LCL). Interaction between ASC with IFI16 but not with AIM2 or NLRP3 was detected in all three latencies and during EBV infection of primary human B cells. IFI16 and cleaved caspase-1, IL-1β, IL-18, and IL-33 were detected in the exosomes from Raji cells and LCL. Though EBV nuclear antigen 1 (EBNA1) and EBV-encoded small RNAs (EBERs) are common to all forms of EBV latency, caspase-1 cleavage was not detected in cells expressing EBNA1 alone, and blocking EBER transcription did not inhibit caspase-1 cleavage. In fluorescence
in situ
hybridization (FISH) analysis, IFI16 colocalized with the EBV genome in LCL and Raji cell nuclei. These studies demonstrated that constant sensing of latent EBV genome by IFI16 in all types of latency results in the constitutive induction of the inflammasome and IL-1β, IL-18, and IL-33 maturation.
Genome-Wide Characterization of Endogenous Retroviruses in the Bat Myotis lucifugus Reveals Recent and Diverse Infections
Authors: Zhuo Xiaoyu , Rho Mina , Feschotte Cédric 
Published: May 2013

ABSTRACT

Bats are increasingly recognized as reservoir species for a variety of zoonotic viruses that pose severe threats to human health. While many RNA viruses have been identified in bats, little is known about bat retroviruses. Endogenous retroviruses (ERVs) represent genomic fossils of past retroviral infections and, thus, can inform us on the diversity and history of retroviruses that have infected a species lineage. Here, we took advantage of the availability of a high-quality genome assembly for the little brown bat,
Myotis lucifugus
, to systematically identify and analyze ERVs in this species. We mined an initial set of 362 potentially complete proviruses from the three main classes of ERVs, which were further resolved into 13 major families and 86 subfamilies by phylogenetic analysis. Consensus or representative sequences for each of the 86 subfamilies were then merged to the Repbase collection of known ERV/long terminal repeat (LTR) elements to annotate the retroviral complement of the bat genome. The results show that nearly 5% of the genome assembly is occupied by ERV-derived sequences, a quantity comparable to findings for other eutherian mammals. About one-fourth of these sequences belong to subfamilies newly identified in this study. Using two independent methods, intraelement LTR divergence and analysis of orthologous loci in two other bat species, we found that the vast majority of the potentially complete proviruses identified in
M. lucifugus
were integrated in the last ∼25 million years. All three major ERV classes include recently integrated proviruses, suggesting that a wide diversity of retroviruses is still circulating in
Myotis
bats.
Geology, hydrology, and mechanics of a slow-moving, clay-rich landslide, Honolulu, Hawaii
Authors: Baum Rex L. , Reid Mark. E. 
Published: May 2013

Abstract
The Alani-Paty landslide has damaged streets, utilities, and homes built on a debris apron in Honolulu, Oahu, Hawaii. Failure of weathered, crudely stratified, highly plastic, debris-apron deposits has created several similar landslides in southeastern Oahu. The Alani-Paty landslide affects about 60 residential lots. It is about 300 m long, 160 m wide, 7-10 m thick, and consists of two main kinematic elements that are separated by a right-lateral shear zone. One element has moved about 4 m, mainly by translation, down a slope of about 12°, and the adjacent element has moved about 3 m down a slope of 9°. Longitudinal stretching in the upslope third and shortening in the downslope two-thirds characterize deformation in each element; landslides in Ohio, Utah, and Colorado have deformed similarly. Smectite-rich clay layers within the deposits are medium to stiff, and measured angles of residual friction range from 6° to 11° with cohesion intercepts less than 12.5 kPa. Saturated hydraulic conductivity within the landslide decreases with depth; below the slip surface, the hydraulic conductivity increases. Rainfall infiltrates at the ground surface, percolates downward and perches on the zone of low hydraulic conductivity near the slip surface, keeping the slide mostly saturated year round. The main body of the landslide moves during rainy periods, when the ten-day average rainfall exceeds 25 mm/day and the pore-water pressures in the upslope quarter of the landslide increase 10-30 kPa. Pore pressure increases within the landslide occur 1-2 days following the onset of rainfall and result from infiltration of rainfall and runoff; after materials above the perennial water table become saturated, downward propagating pressure waves triggered by bursts of intense rainfall produce further, short-lived increases in pore pressure. This elevated pore pressure at the slip surface triggers movement. The ground-water response in the upslope quarter of the landslide is relatively rapid compared to responses in other landslides described in the literature.