bluuebunny/crossref_metadata_2025_split huggingface dataset:
A coalescent-based method for population tree inference with haplotypes
Authors: Wu Yufeng 
Published: October 2014

Motivation: Population trees represent past population divergence histories. The inference of population trees can be useful for the study of population evolution. With the size of data increases in large-scale population genetic projects, such as the 1000 Genomes Project, there are new computational challenges for ancestral population inference, including population tree inference. Existing methods for population tree inference are mainly designed for unlinked genetic variants (e.g. single nucleotide polymorphisms or SNPs). There is a potential loss of information by not considering the haplotypes.
Results: In this article, we propose a new population tree inference method (called STELLSH) based on coalescent likelihood. The likelihood is for haplotypes over multiple SNPs within a non-recombining region, not unlinked variants. Unlike many existing ancestral inference methods, STELLSH does not use Monte Carlo approaches when computing the likelihood. For efficient computation, the likelihood model is approximated but still retains much information about population divergence history. STELLSH can find the maximum likelihood population tree based on the approximate likelihood. We show through simulation data and the 1000 Genomes Project data that STELLSH gives reasonably accurate inference results. STELLSH is reasonably efficient for data of current interest and can scale to handle whole-genome data.
Availability and implementation: The population tree inference method STELLSH has been implemented as part of the STELLS program: http://www.engr.uconn.edu/∼ywu/STELLS.html.
Contact: ywu@engr.uconn.edu
Supplementary information: Supplementary Data are available at Bioinformatics online.
Hepatitis E Vaccine to Prevent Morbidity and Mortality During Epidemics
Authors: Nelson Kenrad E. , Shih James W. K. , Zhang Jun , Zhao Qinjian , Xia Ningshao , Ticehurst John R. , Labrique Alain B. 
Published: October 2014

Abstract
Recurrent, large, waterborne epidemics of hepatitis E virus (HEV) occur regularly after monsoon rains contaminate water supplies in Asia or during humanitarian crises in Africa. These epidemics commonly affect thousands of persons, and it has a high mortality in pregnant women who become infected. Although a subunit HEV vaccine has been developed by Chinese investigators and was found to be highly effective and safe in a large clinical trial, this vaccine is only available in China. Until it is prequalified by the World Health Organization, the vaccine may not be available for use outside of China in low-income countries that lack national vaccine regulatory agencies. In this manuscript, we explore possible strategies for providing access to this potentially important vaccine for international use in responding to epidemics of HEV in low-resource countries.
Urinary Tract Infections in Male Veterans With Human Immunodeficiency Virus
Authors: Eccles-Radtke Caitlin , Rector Thomas S. , Cutting Andrea , Drekonja Dimitri M. 
Published: October 2014

Abstract
Treatment duration for men with urinary tract infection (UTI) and human immunodeficiency virus (HIV) infection is unknown. Fiscal year 2009 Veterans Affairs administrative data were used to compare men with HIV and UTI with non-HIV men with UTI. Antimicrobial selection and duration were similar. Shorter treatment (≤7 days) did not affect recurrence, suggesting that treatment beyond 7 days may be unnecessary.
Point-of-Use Mixing of Influenza H5N1 Vaccine and MF59 Adjuvant for Pandemic Vaccination Preparedness: Antibody Responses and Safety. A Phase 1 Clinical Trial
Authors: Mulligan Mark J. , Bernstein David I. , Frey Sharon , Winokur Patricia , Rouphael Nadine , Dickey Michelle , Edupuganti Srilatha , Spearman Paul , Anderson Edwin , Graham Irene , Noah Diana L. , Mangal Brian , Kim Sonnie , Hill Heather , Whitaker Jenifer , Emery William , Beck Allison , Stephens Kathy , Hartwell Brooke , Ogilvie Melinda , Rimann Nayoka , Osinski Eileen , Destefano Ellen , Gajadhar Theda , Strudwick Amanda , Pierce Karen , Lai Lilin , Yue Ling , Wang Dongli , Ying Carl , Cline Amy , Foltz Tara , Wagner Nancy , Dull Geraldine , Pacatte Thomas , Taggart Barbara , Johnson Valerie , Haller Logan , Looney Candi , Li Shixiong , May Megan , Myers Bridgette , May Rachel , Parker Lawanda , Cochran Nertaissa , Bowen Donna , Bell Michelle , Scoggins Jeffery , Burns Angela , Stablein Claire , Wolff Mark , Jolles Bernadette , Leung Brenda , Lambert Linda , Shorer Shy , Buchanan Wendy , Murray Suzanne , Chang Soju , Gorman Richard 
Published: October 2014

Abstract
Background.  Avian influenza A/H5N1 has threatened human health for nearly 2 decades. Avian influenza A vaccine without adjuvant is poorly immunogenic. A flexible rapid tactic for mass vaccination will be needed if a pandemic occurs.
Methods.  A multicenter, randomized, blinded phase 1 clinical trial evaluated safety and antibody responses after point-of-use mixing of influenza A/Indonesia/05/2005 (H5N1) vaccine with MF59 adjuvant. Field-site pharmacies mixed 3.75, 7.5, or 15 mcg of antigen with or without MF59 adjuvant just prior to intramuscular administration on days 0 and 21 of healthy adults aged 18–49 years.
Results.  Two hundred and seventy subjects were enrolled. After vaccination, titers of hemagglutination inhibition antibody ≥1:40 were achieved in 80% of subjects receiving 3.75 mcg + MF59 vs only 14% receiving 15 mcg without adjuvant (P &lt; .0001). Peak hemagglutination inhibition antibody geometric mean titers for vaccine + MF59 were ∼65 regardless of antigen dose, and neutralizing titers were 2- to 3-fold higher. Vaccine + MF59 produced cross-reactive antibody responses against 4 heterologous H5N1 viruses. Excellent safety and tolerability were demonstrated.
Conclusions.  Point-of-use mixing of H5N1 antigen and MF59 adjuvant achieved target antibody titers in a high percentage of subjects and was safe. The feasibility of the point-of-use mixing should be studied further.
Interplay of TGFb superfamily members governs optic fissure closure
Authors: Heermann Stephan , Eckert Priska , Mateo Juan L. , Roussa Eleni , Rahhal Belal , Zuniga Aimee , Krieglstein Kerstin , Wittbrodt Jochim 
Published: October 2014

AbstractThe optic fissure is a gap in the developing vertebrate eye and must be closed as development proceeds. A persisting optic fissure is referred to as coloboma, a major cause for blindness in children. Multiple factors have been linked to coloboma formation, however, the actual process of fissure closure is only poorly understood.Based on our findings we propose an important role of TGFb signaling for optic fissure closure. We show active TGFb signaling in the fissure margins, analyzed by a new TGFb signaling reporter zebrafish. We found BMP antagonists regulated by TGFb. These antagonists we also found expressed in the fissure margins. Finally we show a coloboma phenotype in a TGFb KO mouse. Microarray data analysis indicates intense TGFb dependent remodeling of the extracellular matrix (ECM) during optic fissure closure.We propose that TGFb is driving optic fissure closure by ECM remodeling. As previously shown, inhibition of BMP signaling is important for such TGFb dependent ECM remodeling. We show that this is achieved by the regulation of BMP antagonists, expressed in the optic fissure margins.
An Optical Clearing Technique for Plant Tissues Allowing Deep Imaging and Compatible with Fluorescence Microscopy
Authors: Warner Cherish A. , Biedrzycki Meredith L. , Jacobs Samuel S. , Wisser Randall J. , Caplan Jeffrey L. , Sherrier D. Janine 
Published: October 2014

Abstract
We report on a nondestructive clearing technique that enhances transmission of light through specimens from diverse plant species, opening unique opportunities for microscope-enabled plant research. After clearing, plant organs and thick tissue sections are amenable to deep imaging. The clearing method is compatible with immunocytochemistry techniques and can be used in concert with common fluorescent probes, including widely adopted protein tags such as GFP, which has fluorescence that is preserved during the clearing process.
The human herpesvirus 6 U21–U24 gene cluster is dispensable for virus growth
Authors: Jasirwan Chyntia , Tang Huamin , Kawabata Akiko , Mori Yasuko 
Published: October 2014

ABSTRACTHuman herpesvirus 6 (HHV‐6) is a T‐lymphotrophic virus belongs to the genus Roseolovirus within the beta herpesvirus subfamily. The U20–U24 gene cluster is unique to Roseoloviruses; however, both their function and whether they are essential for virus growth is unknown. Recently, bacterial artificial chromosome (BAC) techniques have been used to investigate HHV‐6A. This study describes generation of a virus genome lacking U21–U24 (HHV‐6ABACΔU21–24) and shows that infectious virus particles can be reconstituted from this BAC DNA. Our data indicate that the HHV‐6 U21–U24 gene cluster is dispensable for virus propagation.
Molecular characterization of dengue and chikungunya virus strains circulating in New Delhi, India
Authors: Afreen Nazia , Deeba Farah , Khan Wajihul H. , Haider Shakir H. , Kazim Syed Naqui , Ishrat Romana , Naqvi Irshad Hussain , Shareef Mohammad Y. , Broor Shobha , Ahmed Anwar , Parveen Shama 
Published: October 2014

AbstractDengue and chikungunya are acute viral infections with overlapping clinical symptoms. Both diseases are transmitted by common mosquito vectors resulting in their co‐circulation in a region. Molecular and serological tests specific for both dengue and chikungunya infections were performed on 87 acute phase blood samples collected from patients with suspected dengue/chikungunya infections in Delhi from September to December, 2011. RT‐PCR and IgM ELISA were performed to detect dengue virus (DENV) and chikungunya virus (CHIKV). NS1 and IgG ELISA were also performed to detect DENV specific antigen and secondary DENV infection. DENV infection was detected in 49%, CHIKV infection in 29% and co‐infection with DENV and CHIKV in 10% of the samples by RT‐PCR. DENV serotypes 1, 2 and 3 were detected in this study. Nine DENV‐1 strains, six DENV‐2 strains and 20 CHIKV strains were characterized by DNA sequencing and phylogenetic analysis of their respective envelope protein genes. DENV‐1 strains grouped in the American African genotype, DENV‐2 strains in the Cosmopolitan genotype and CHIKV strains in the East Central South African genotype by phylogenetic analysis. This is one of the few studies reporting the phylogeny of two dengue virus serotypes (DENV‐1 and DENV‐2) and CHIKV. Surveillance and monitoring of DENV and CHIKV strains are important for design of strategies to control impending epidemics.
Herbivore effect traits and their impact on plant community biomass: an experimental test using grasshoppers
Authors: Deraison Hélène , Badenhausser Isabelle , Börger Luca , Gross Nicolas 
Published: October 2014

Summary

Using trait‐based approaches to study trophic interactions may represent one of the most promising approaches to evaluate the impact of trophic interactions on ecosystem functioning. To achieve this goal, it is necessary to clearly identify which traits determine the impact of one trophic level on another.

Using functionally contrasting grasshopper species, we tested the ability of multiple traits (morphological, chemical and biomechanical) to predict herbivore impact on the biomass of a diverse plant community. We set‐up a cage experiment in an old species rich grassland field and evaluated how multiple candidate grasshopper effect traits mediated herbivore impact on plant biomass.

Grasshoppers had different impact on plant community biomass (consuming up to 60% of plant community biomass). Grasshopper impact was positively correlated with their incisive strength while body size or grasshopper C:N ratio exhibited low predictive ability. Importantly, the strong relationship between the incisive strength and the impact was mediated by the grasshopper feeding niche, which was well predicted in our study by two simple plant traits (leaf dry matter content, leaf C:N ratio). Feeding niche differences between grasshoppers were explained by differences in incisive strength, highlighting the fundamental linkage between grasshopper effect traits and their niche.

Our study contributes to the development of the trait‐based approach in the study of trophic interactions by providing a first experimental test of the relationship between herbivore effect traits, their impact on plant community biomass, and in a larger extent on ecosystem functioning. By comparing the relative importance of multiple interacting grasshopper traits, our study showed that incisive strength was a key effect trait which determined grasshopper feeding niche and its relative impact on plant community biomass.
Bringing animal personality research into the food web arena
Authors: Kalinkat Gregor 
Published: October 2014

The consumption rate of the crab Panopeus herbstii feeding on the mussel Brachidontes exustus depends on predator and prey body size as well as the predator individual activity level. Photo credit: Kathryn Levasseur.imageThe consumption rate of the crab Panopeus herbstii feeding on the mussel Brachidontes exustus depends on predator and prey body size as well as the predator individual activity level. Photo credit: Kathryn Levasseur.

Toscano, B.J. & Griffen,B.D. (2014) . Journal of Animal Ecology, 83, 1469–1477.
While the concept of consistent behavioural differences among individuals of the same population has gained a lot of scientific attention over the last decade, its implementation into a community context with a focus on species‐level interactions is still in its infancy. In their study on the effects of animal personalities on predator–prey functional responses of mussel‐eating crabs, Toscano & Griffen (2014) introduce a promising avenue for future research synthesizing concepts and ideas from animal behaviour and food web ecology. More precisely, by showing that the interplay of animal personalities and predator and prey body sizes significantly alters the outcome of predator–prey interactions, this study provides important evidence that the concept of animal personalities needs greater consideration if we want to refine and improve current models of predator–prey interactions and the impact of individual‐level variation on quantitative food‐web dynamics.
Influence of temperature on the reproductive success, brood development and brood fitness of the eastern larch beetle Dendroctonus simplexLeConte
Authors: McKee Fraser R. , Aukema Brian H. 
Published: October 2014

Abstract

The eastern larch beetle Dendroctonus simplex LeConte colonizes the phloem of tamarack Larix laricina (Du Roi) K. Koch, preferring recently dead or moribund trees weakened by insect defoliation or other factors that predispose trees to beetle attack.
Outbreaks of eastern larch beetles are typically localized, of short duration, and collapse when the supply of stressed hosts is exhausted. Although rare, landscape‐level outbreaks of eastern larch beetles can occur if large areas of tamarack become stressed.
From 2000 onward, an ongoing outbreak of eastern larch beetles in the Great Lakes Region of North America has resulted in extensive mortality to more than 75 000 ha of tamarack forest in Minnesota, U.S.A. This outbreak has no known biotic predisposing factor, such as extensive defoliation. Trends of recent climate warming, however, are suspected to be a contributing factor.
Current efforts to model the effects of climate on eastern larch beetle population dynamics are hampered by an absence of data relating beetle developmental biology to temperature. In a laboratory study, we studied eastern larch beetle reproductive success, larval development and offspring fitness at temperatures in the range 9.9–29.4 °C.
Offspring production was similar across temperatures. Successful brood development occurred at 9.9 °C, whereas the minimum and optimal developmental temperatures were calculated to be 7.5 and 27.9 °C, respectively. Offspring size and lipid content were maximized between 20 and 22 °C.
Our results indicate a potential trade‐off between temperatures that maximizes eastern larch beetle offspring fitness versus developmental rate. The implications of such a trade‐off are discussed with respect to beetle population dynamics.
Subpopulations of Macrophages within Eutopic Endometrium of Endometriosis Patients
Authors: Takebayashi Akie , Kimura Fuminori , Kishi Yohei , Ishida Mitsuaki , Takahashi Akimasa , Yamanaka Akiyoshi , Wu Di , Zheng Luyi , Takahashi Kentaro , Suginami Hiroshi , Murakami Takashi 
Published: October 2014

ProblemEndometriosis is recognized as a chronic inflammatory disease and is related to immune response. There have been reports that revealed the different distribution of macrophage within the eutopic endometrium of women with endometriosis. Macrophages are functionally polarized into M1 and M2 cell lineages. We studied a difference in the subpopulations of M1 and M2 macrophages within the eutopic endometrium in patients with or without endometriosis to investigate how the eutopic endometrium is stimulated immunologically.Method of studyThirty‐six patients with endometriosis (endometriosis group) and 37 without endometriosis (non‐endometriosis group) were analyzed. Paraffin‐embedded endometrial specimens were used for the study. Consecutive sections were used for immunostaining of CD68 (pan‐macrophage marker) and CD163 (M2 macrophage marker). Cells positive for each marker were quantified, and the ratio of M2 macrophages in pan‐macrophages was calculated.ResultThe endometriosis group had a significantly higher number of pan‐macrophages than the control group in all phases (P < 0.05). The ratios of M2 macrophages in pan‐macrophages were significantly lower in all phases in the endometriosis group (P < 0.05).ConclusionThe macrophage population slants toward M1 in the endometrium of endometriosis patients. The endometrium appeared to be stimulated by some organelles and/or substances that induce M1 in endometriosis patients.
Carboxyhaemoglobin formation and ECG changes during hysteroscopic surgery, transurethral prostatectomy and tonsillectomy using bipolar diathermy
Authors: Overdijk L. E. , van Kesteren P. J. M. , de Haan P. , Schellekens N. C. J. , Dijksman L. M. , Hovius M. C. , van den Berg R. G. , Bakkum E. A. , Rademaker B. M. P. 
Published: October 2014

SummaryDiathermy is known to produce a mixture of waste products including carbon monoxide. During transcervical hysteroscopic surgery, carbon monoxide might enter the circulation leading to the formation of carboxyhaemoglobin. In 20 patients scheduled for transcervical hysteroscopic resection of myoma or endometrium, carboxyhaemoglobin was measured before and at the end of the surgical procedure, and compared with levels measured in 20 patients during transurethral prostatectomy, and in 20 patients during tonsillectomy. Haemodynamic data, including ST‐segment changes, were recorded. Levels of carboxyhaemoglobin increased significantly during hysteroscopic surgery from median (IQR [range]) 1.0% (0.7–1.4 [0.5–4.9])% to 3.5% (2.0–6.1 [1.3–10.3]%, p < 0.001), compared with levels during prostatectomy or tonsillectomy. Significant ST‐segment changes were observed in 50% of the patients during hysteroscopic surgery. Significant correlations were observed between the increase in carboxyhaemoglobin and the maximum ST‐segment change (ρ = −0.707, p < 0.01), between the increase in carboxyhaemoglobin and intravasation (ρ = 0.625; p < 0.01), and between intravasation and the maximum ST‐segment change (ρ = −0.761; p < 0.01). The increased carboxyhaemoglobin levels during hysteroscopic surgery appear to be related to the amount of intravasation and this could potentially be a contributing factor to the observed ST‐segment changes.
The association of thyroid peroxidase antibody risk loci with susceptibility to and phenotype of Graves' disease
Authors: Kuś Aleksander , Szymański Konrad , Peeters Robin P. , Miśkiewicz Piotr , Porcu Eleonora , Pistis Giorgio , Sanna Serena , Naitza Silvia , Płoski Rafał , Medici Marco , Bednarczuk Tomasz 
Published: October 2014

SummaryBackgroundDespite great progress, the genetic basis of Graves' disease (GD) remains poorly understood. Recently, a population‐based genomewide association study (GWAS) identified five novel loci (ATXN2/SH2B3, MAGI3, BACH2, TPO and KALRN) as significantly associated with the presence of thyroid peroxidase autoantibodies (TPOAbs), whereas several other loci showed suggestive association.MethodsIn this study, we investigated 16 single nucleotide polymorphisms (SNPs) associated with TPOAbs for the association with susceptibility to and phenotype of GD in a cohort of 647 patients with GD and 769 controls from a Polish Caucasian population.ResultsSNPs within/near HCP5 (rs3094228, P = 1·6 × 10−12, OR = 1·88), MAGI3 (rs1230666, P = 1·9 × 10−5, OR = 1·51) and ATXN2/SH2B3 (rs653178, P = 0·0015, OR = 1·28) loci were significantly associated with susceptibility to GD. Allele frequencies differed significantly in subgroups of patients with GD stratified by age of GD onset for HCP5 (P = 0·0014, OR = 1·50) and showed a suggestive difference for MAGI3 (P = 0·0035, OR = 1·50) SNPs. Although rs11675434 located near TPO showed no association with GD susceptibility, it was significantly associated with the presence of clinically evident Graves' ophthalmopathy (GO, P = 5·2 × 10−5, OR = 1·64), and this effect was independent from smoking status, age of GD onset and gender.ConclusionsThis is the first study showing an association of the ATXN2/SH2B3 locus with susceptibility to GD. Furthermore, we observed a novel significant association within the HLA region at a SNP located near HCP5 and confirmed the association of the MAGI3 locus with GD susceptibility. HCP5 and MAGI3 SNPs were further correlated with age of GD onset. Finally, we identified TPO as a new susceptibility locus for GO.
Advances in Interaction with 3D Environments
Authors: Jankowski J. , Hachet M. 
Published: October 2014

AbstractVarious interaction techniques have been developed for interactive 3D environments. This paper presents an up‐to‐date and comprehensive review of the state of the art of non‐immersive interaction techniques for Navigation, Selection & Manipulation, and System Control, including a basic introduction to the topic, the challenges and an examination of a number of popular approaches. We also introduce 3D Interaction Testbed (3DIT) to firstly allow a ‘hands‐on' understanding of 3D interaction principles, and secondly to create an open platform for defining evaluation methods, stimuli as well as representative tasks akin to those found in other disciplines of science. We hope that this survey can aid both researchers and developers of interactive 3D applications in having a clearer overview of the topic and in particular can be useful for practitioners and researchers that are new to the field of interactive 3D graphics.