bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bayesian abundance estimation from genetic mark-recapture data when not all sites are sampled: an example with the bowhead whale
Authors: Frasier Timothy R. , Petersen Stephen D. , Postma Lianne , Johnson Lucy , Heide-Jørgensen Mads Peter , Ferguson Steven H. 
Published: February 2019

AbstractEstimating abundance is one of the most fundamental and important aspects of population biology, with major implications on how the status of a population is perceived and thus on conservation and management efforts. Although typically based on one of two methods (distance sampling or mark-recapture), there are many individual identification methods that can be used for mark-recapture purposes. In recent years, the use of genetic data for individual identification and abundance estimation through mark-recapture analyses have increased, and in some situations such genetic identifications are more efficient than their field-based counterparts for population monitoring. One issue with mark-recapture analyses, regardless of which method of individual identification is used, is that the study area must provide adequate opportunities for “capturing” all individuals within a population. However, many populations are unevenly and widely distributed, making it unfeasible to adequately sample all necessary areas. Here we develop an analytical technique that accounts for unsampled locations, and provides a means to infer “missing” individuals from unsampled locations, and therefore obtain more accurate abundance estimates when it is not possible to sample all sites. This method is validated using simulations, and is used to estimate abundance of the Eastern Canada-West Greenland (EC-WG) bowhead whale population. Based on these analyses, the estimated size of this population is 9,089 individuals, with a 95% highest density interval of 5,107–17,079.
EpiMethylTag simultaneously detects ATAC-seq or ChIP-seq signals with DNA methylation
Authors: Lhoumaud Priscillia , Sethia Gunjan , Izzo Franco , Badri Sana , Cornwell MacIntosh , Kim Kyu-Tae , Landau Dan Avi , Skok Jane 
Published: February 2019

AbstractActivation of regulatory elements is thought to be inversely correlated with DNA methylation levels. However, it is difficult to determine whether DNA methylation is compatible with chromatin accessibility or transcription factor (TF) binding if assays are performed separately. We developed a low input, low sequencing depth method, EpiMethylTag that combines ATAC-seq or ChIP-seq (M-ATAC or M-ChIP) with bisulfite conversion, to simultaneously examine accessibility/TF binding and methylation on the same DNA.
Terahertz Circular Dichroism Spectroscopy of Biomaterials Enabled by Kirigami Polarization Modulators
Authors: Choi Won Jin , Cheng Gong , Huang Zhengyu , Zhang Shuai , Norris Theodore B. , Kotov Nicholas A. 
Published: February 2019

ABSTRACTSTerahertz circular dichroism (TCD) offers spectroscopic capabilities for understanding mesoscale chiral architecture and low-energy vibrations of macromolecules in (bio)materials1–5. However, the lack of dynamic polarization modulators comparable to polarization optics for other parts of electromagnetic spectrum impedes proliferation of TCD spectroscopy6–10. Here we show that tunable optical elements fabricated from patterned plasmonic sheets with periodic kirigami cuts make possible polarization modulation of THz radiation under application of mechanical strain. A herringbone pattern of microscale metal stripes enables dynamic range of polarization rotation modulation exceeding 80° over thousands of cycles. Upon out-of-plane buckling, the plasmonic stripes function as reconfigurable semi-helices of variable pitch aligned along the THz propagation direction. Several biomaterials, exemplified by elytrons of Chrysina gloriosa beetles, revealed distinct TCD fingerprints associated with the helical substructure in the biocomposite. Analogous kirigami modulators will also enable other applications in THz optics, such as polarization-based terahertz imaging and phase-encrypted telecommunication.
Red Sea SAR11 andProchlorococcusSingle-cell Genomes Reflect Globally Distributed Pangenomes
Authors: Thompson Luke R. , Haroon Mohamed F. , Shibl Ahmed A. , Cahill Matt J. , Ngugi David K. , Williams Gareth J. , Morton James T. , Knight Rob , Goodwin Kelly D. , Stingl Ulrich 
Published: February 2019

AbstractEvidence suggests many marine bacteria are cosmopolitan, with widespread but sparse strains poised to seed abundant populations upon conducive growth conditions. However, studies supporting this “microbial seed bank” hypothesis have analyzed taxonomic marker genes rather than whole genomes/metagenomes, leaving open the possibility that disparate ocean regions harbor endemic gene content. The Red Sea is isolated geographically from the rest of the ocean and has a combination of high irradiance, high temperature, and high salinity that is unique among the ocean; we therefore asked whether it harbors endemic gene content. We sequenced and assembled single-cell genomes of 21 SAR11 (subclades Ia, Ib, Id, II) and 5Prochlorococcus(ecotype HLII) cells from the Red Sea and combined them with globally-sourced reference genomes to cluster genes into ortholog groups (OGs). Ordination of OG composition could distinguish clades, including phylogenetically crypticProchlorococcusecotypes LLII and LLIII. Compared with reference genomes, 1% ofProchlorococcusand 17% of SAR11 OGs were unique to the Red Sea genomes (RS-OGs). Most (83%) RS-OGs had no annotated function, but 65% of RS-OGs were expressed in diel Red Sea metatranscriptomes, suggesting they could be functional. SearchingTaraOceans metagenomes, RS-OGs were as likely to be found as non-RS-OGs; nevertheless, Red Sea and other warm samples could be distinguished from cooler samples using the relative abundances of OGs. The results suggest that the prevalence of OGs in these surface ocean bacteria is largely cosmopolitan, with differences in population metagenomes manifested by differences in relative abundance rather than complete presence-absence of OGs.
External location of touch is constructed post-hoc based on limb choice
Authors: Maij Femke , Seegelke Christian , Medendorp W. Pieter , Heed Tobias 
Published: February 2019

AbstractWhen humans indicate on which hand a tactile stimulus occurred, they often err when their hands are crossed. This finding seemingly supports the view that the automatically determined touch location in external space affects limb assignment: the crossed right hand is localized in left space, and this conflict presumably provokes hand assignment errors. Here, participants judged on which hand the first of two stimuli, presented during a bimanual movement, had occurred, and then indicated its external location by a reach-to-point movement. When participants incorrectly chose the hand stimulated second, they pointed to where that hand had been at the correct, first time point, though no stimulus had occurred at that location. This behavior suggests that stimulus localization depended on hand assignment, not vice versa. It is, thus, incompatible with the notion of automatic computation of external stimulus location upon occurrence. Instead, humans construct external touch location post-hoc and on demand.
The genomic basis of mood instability: identification of 46 loci in 363,705 UK Biobank participants, genetic correlation with psychiatric disorders, and association with gene expression and function
Authors: Ward Joey , Tunbridge Elizabeth M. , Sandor Cynthia , Lyall Laura M. , Ferguson Amy , Strawbridge Rona J. , Lyall Donald M. , Cullen Breda , Graham Nicholas , Johnston Keira J.A. , Webber Caleb , Escott-Price Valentina , ODonovan Michael , Pell Jill P. , Bailey Mark E.S. , Harrison Paul J. , Smith Daniel J. 
Published: February 2019

AbstractGenome-wide association studies (GWAS) of psychiatric phenotypes have tended to focus on categorical diagnoses, but to understand the biology of mental illness it may be more useful to study traits which cut across traditional boundaries. Here we report the results of a GWAS of mood instability (MI) as a trait in a large population cohort (UK Biobank, n=363,705). We also assess the clinical and biological relevance of the findings, including whether genetic associations show enrichment for nervous system pathways. Forty six unique loci associated with MI were identified with a heritability estimate of 9%. Linkage Disequilibrium Score Regression (LDSR) analyses identified genetic correlations with Major Depressive Disorder (MDD), Bipolar Disorder (BD), Schizophrenia (SZ), anxiety and Post Traumatic Stress Disorder (PTSD). Gene-level and gene set analyses identified total 244 significant genes and 6 enriched gene sets. Tissue expression analysis from the SNP level data found enrichment in multiple brain regions, and eQTL analyses highlighted an inversion on chromosome 17 plus two brain-specific eQTLs. Additionally, we used a Phenotype Linkage Network (PLN) analysis and community analysis to assess for enrichment of nervous system gene sets using mouse orthologue databases. The PLN analysis found enrichment in nervous system PLNs for a community containing serotonin and melatonin receptors. In summary, this work has identified novel loci, tissues, and gene sets contributing to MI as a normal trait and will inform future work on the biology of mood and psychotic disorders, and to point the way towards potential for new stratified medicine approaches and the identification of novel trans-diagnostic drug targets.
Adaptation to binocular anticorrelation results in increased neural excitability
Authors: Rideaux Reuben , Michael Elizabeth , Welchman Andrew E 
Published: February 2019

ABSTRACTThroughout the brain, information from individual sources converges onto higher order neurons. For example, information from the two eyes first converges in binocular neurons in area V1. Many neurons appear tuned to similarities between sources of information, which makes intuitive sense in a system striving to match multiple sensory signals to a single external cause, i.e., establish causal inference. However, there are also neurons that are tuned to dissimilar information. In particular, many binocular neurons respond maximally to a dark feature in one eye and a light feature in the other. Despite compelling neurophysiological and behavioural evidence supporting the existence of these neurons (Cumming & Parker, 1997; Janssen, Vogels, Liu, & Orban, 2003; Katyal, Vergeer, He, He, & Engel, 2018; Kingdom, Jennings, & Georgeson, 2018; Tsao, Conway, & Livingstone, 2003), their function has remained opaque. To determine how neural mechanisms tuned to dissimilarities support perception, here we use electroencephalography to measure human observers’ steady-state visually evoked potentials (SSVEPs) in response to change in depth after prolonged viewing of anticorrelated and correlated random-dot stereograms (RDS). We find that adaptation to anticorrelated RDS results in larger SSVEPs, while adaptation to correlated RDS has no effect. These results are consistent with recent theoretical work suggesting ‘what not’ neurons play a suppressive role in supporting stereopsis (Goncalves & Welchman, 2017); that is, selective adaptation of neurons tuned to binocular mismatches reduces suppression resulting in increased neural excitability.
Thrombin cleaves and activates the protease-activated receptor 2 dependent on thrombomodulin co-receptor availability
Authors: Heuberger Dorothea M. , Franchini Alessandro G. , Madon Jerzy , Schuepbach Reto A. 
Published: February 2019

AbstractIntroductionProtease-activated receptors (PARs) evolved to react to extracellular proteolytic activity. In mammals, three of the four PARs (PAR1, PAR3, and PAR4) that are expressed respond to the prototypical procoagulant enzyme thrombin, whereas PAR2 was assumed to resist activation by thrombin. To date, involvement of cell surface thrombin-recruiting co-receptors such as thrombomodulin (TM), which potentially facilitates PAR2 cleavage, has not been addressed. Thus, we examined whether TM-bound thrombin cleaved PAR2 and tested biological responses such as nuclear factor kappa B (NF-κB) DNA binding activity and cytokine release.Materials and MethodsWe examined 293T cells overexpressing PAR2 and TM for thrombin recruitment by TM promoting PAR2 cleavage. To test for the TM–thrombin interactions required for PAR2 cleavage and to map cleavage sites on PAR2, mutant constructs of TM or PAR2 were engineered. Biological effects because of PAR2 activation were investigated using an NF-κB reporter system and cytokine release.Results and ConclusionsWe identified that, at low to moderate concentrations, thrombin cleaved PAR2 in a TM co-receptor-dependent manner with cleavage efficiency comparable to that of trypsin. In TM’s presence, thrombin efficiently cleaved both, PAR1 and PAR2, albeit kinetics differed. Whereas the majority of surface expressed PAR1 was immediately cleaved off, prolonged exposure to thrombin resulted in few additional cleavage. In contrast, PAR2 cleavage was sustained upon prolonged exposure to thrombin. However, TM EGF-like domain 5 was required and TM chondroitin sulfate (CS) proteoglycan sites serine 490 and serine 492 assisted in PAR2 cleavage, while thrombin preferentially cleaved at arginine 36 on PAR2’s N-terminus. Note that thrombin-induced activation of NF-κB via PAR2 resulted in release of interleukin-8. Thus, we provide a novel concept of how thrombin efficiently cleaves PAR2 in a TM-dependent manner, resulting in pro-inflammatory interleukin-8 release. This unexpected pro-inflammatory role of TM, promoting cleavage and activation of PAR2 by thrombin, may lead to novel therapeutic options for treating inflammatory and malignant diseases.
Novel risk genes and mechanisms implicated by exome sequencing of 2,572 individuals with pulmonary arterial hypertension
Authors: Zhu Na , Pauciulo Michael W. , Welch Carrie L. , Lutz Katie A. , Coleman Anna W. , Gonzaga-Jauregui Claudia , Wang Jiayao , Grimes Joseph M. , Martin Lisa J. , He Hua ,   PAH Biobank, Shen Yufeng , Chung Wendy K. , Nichols William C. 
Published: February 2019

AbstractGroup 1 pulmonary arterial hypertension (PAH) is a rare disease with high mortality despite recent therapeutic advances. Pathogenic remodeling of pulmonary arterioles leads to increased pulmonary pressures, right ventricular hypertrophy and heart failure. Mutations in bone morphogenetic protein receptor type 2 and other risk genes predispose to disease, but the vast majority of non-familial cases remain genetically undefined. To identify new risk genes, we performed exome sequencing in a large cohort from the National Biological Sample and Data Repository for PAH. By statistical association of rare deleterious variants, we found tissue kallikrein 1 and gamma glutamyl carboxylase as new candidate risk genes for idiopathic PAH associated with a later age-of-onset and relatively moderate disease phenotype compared to bone morphogenetic receptor type 2. Both genes play important roles in vascular hemodynamics and inflammation but have not been implicated in PAH previously. These data suggest new genes, pathogenic mechanisms and therapeutic targets for this lethal vasculopathy.
ENDOSOMAL MEMBRANE TENSION CONTROLS ESCRT-III-DEPENDENT INTRA-LUMENAL VESICLE FORMATION
Authors: Mercier Vincent , Larios Jorge , Molinard Guillaume , Goujon Antoine , Matile Stefan , Gruenberg Jean , Roux Aurélien 
Published: February 2019

AbstractPlasma membrane tension strongly affects cell surface processes, such as migration, endocytosis and signalling. However, it is not known whether membrane tension of organelles regulates their functions, notably intracellular traffic. The ESCRT-III complex is the major membrane remodelling complex that drives Intra-Lumenal Vesicle (ILV) formation on endosomal membranes. Here, we made use of a new fluorescent membrane tension probe to show that ESCRT-III subunits are recruited onto endosomal membranes when membrane tension is reduced. We find that tension-dependent recruitment is associated with ESCRT-III polymerization and membrane deformation in vitro, and correlates with increased ILVs formation in ESCRT-III decorated endosomes in vivo. Finally, we find that endosomal membrane tension decreases when ILV formation is triggered by EGF under physiological conditions. These results indicate that membrane tension is a major regulator of ILV formation and of endosome trafficking, leading us to conclude that membrane tension can control organelle functions.One Sentence SummaryMembrane tension decrease facilitates membrane remodeling by ESCRT-III polymerization during intra-lumenal vesicle formation.
Associations between absolute neutrophil count and lymphocyte-predominant breast cancer
Authors: Yoon Chang Ik , Park So Eun , Cha Yoon Jin , Bae Soong June , Cha Chi Hwan , Lee Da Young , Ahn Sung Gwe , Jeong Joon 
Published: February 2019

AbstractTumor-infiltrating lymphocytes (TILs) might be associated with host-cell mediated immunity, which could be partly reflected by peripheral blood cell counts. We aimed to investigate whether peripheral blood cell counts are associated with TILs in breast cancer. Between August 2016 and July 2018, we evaluated the percentage of stromal TILs in breast cancer patients who underwent primary surgery, using the standardized methodology proposed by the international TIL Working Group. Lymphocyte-predominant breast cancer (LPBC) was defined as tumors having high TIL levels (≥ 50%). Peripheral blood cell counts including absolute neutrophil counts (ANC), absolute lymphocyte counts (ALC) and neutrophil-to-lymphocyte ratio (NLR) was obtained from pretreatment laboratory data. Of the 684 patients, 99 (17.2%) had LPBC, and 478 (82.8%) had non-LBPC. In a comparison of 3 markers of peripheral blood counts, LPBC had a significantly lower mean ANC than non-LPBC (3,330 vs. 3,660;P=0.004), but the other means were not different. Decreasing ANC was an independent clinical factor in predicting LPBC (OR: 0.736, 95% CI: 0.591-0.917;P=0.004). Low peripheral ANC might be linked with LPBC, supporting the hypothesis that systemic immune cell counts might be associated with the tumor-immune microenvironment.
Crystal Structure of the Dog Allergen Can f 6
Authors: Clayton Gina M , White Janice , Kappler John W , Chan Sanny K 
Published: February 2019

AbstractLipocalins represent the most important protein family of the mammalian respiratory allergens. Four of the seven named dog allergens are lipocalins: Can f 1, Can f 2, Can f 4, and Can f 6. We present the structure of Can f 6 along with data on the biophysical and biological activity of this protein in comparison with other animal lipocalins. The Can f 6 structure displays the classic lipocalin calyx-shaped ligand binding cavity within a central β-barrel similar to other lipocalins. Despite low sequence identity between the different dog lipocalin proteins, there is a high degree of structural similarity. On the other hand, Can f 6 has a similar primary sequence to cat, horse, mouse lipocalins as well as a structure that may underlie their cross reactivity. Interestingly, the entrance to the ligand binding pocket is capped by a His instead of the usually seen Tyr that may help select its natural ligand binding partner. Our highly pure recombinant Can f 6 is able to bind to human IgE (hIgE) demonstrating biological antigenicity.
Ranking the barriers of sustainable textile and apparel supply chains
Authors: Raut Rakesh , Gardas Bhaskar B. , Narkhede Balkrishna 
Published: February 2019

PurposeTextile and Apparel (T&A) sector significantly influences socio-economic and environmental dimensions of the sustainability. The purpose of this paper is proposed to establish the interrelationship among the critical barriers to the sustainable development of T&A supply chains by using a multi-criteria decision-making approach and to obtain a ranking of the barriers.Design/methodology/approachIn the present investigation through literature review and from expert opinions, 14 significant challenges to the sustainable growth of T&A sector have identified. For establishing the interrelationship and for developing a structural model of the identified challenges, interpretive structural modelling (ISM) methodology is employed.FindingsThe results of the investigation revealed that lack of effective governmental policies (B8), poor infrastructure (B4), lack of effective level of integration (B6), low foreign investment (B13) and demonetization (B12) are the top most significant challenges.Research limitations/implicationsThe model development based on the expert inputs from the industry and academia, these inputs could be biased influencing the accuracy of the model. Also, inclusion more factors for the analysis will improve the reliability of the model.Originality/valueThis research is intended to guide the policy and decision makers for improving overall the growth of the T&A supply chain.
Ensuring environmental performance in green leases: the role of facilities managers
Authors: Rameezdeen Raufdeen , Zuo Jian , Ochoa Paniagua Jorge , Wood Anthony , Do Phuong 
Published: February 2019

PurposeA green lease incorporates sustainability practices to reduce a building’s negative impact on the environment. Facilities managers play an important role in ensuring these best practices are implemented during the operational stage of a building; however, green leasing is an under-researched area in the emerging field of sustainable facilities management (SFM). This paper aims to investigate the common barriers encountered in ensuring environmental performance when a green lease agreement is in operation between a landlord and tenant.Design/methodology/approachThis research was conducted in three stages using the principal-agent problem as the theoretical foundation for data collection. Stages 1 and 2 used semi-structured interviews to collect data with policy/corporate-level professionals, landlord and facilities management representatives who have considerable experience in green leases. Stage 3 used document reviews based on summative content analysis to further evaluate the extent of the contextual use of green leasing concepts as used within the facilities management community.FindingsThe study confirmed a strong incentive gap and information asymmetry between the landlord and facilities manager, forming a typical double principal-agent problem when the split incentives between the landlord and tenants are also taken into consideration, which results in agents acting on their own self-interest rather than the interests of the principal. Goal alignment is found to be key for the successful operation and management of a building throughout its life; when present, these goal conflicts can lead to disharmony between the parties to the contract.Research limitations/implicationsThe study proposes a few practical measures to close the gaps in incentive and information asymmetry that create the principal-agent problem, while providing recommendations to the facilities management professional community. These recommendations could be included in future revisions of the SFM guidelines or code of practices used by the industry. Although this study exposed a rather neglected area of the facilities manager’s role in green leases, the findings are limited by the relatively small sample size used for the interviews.Originality/valueThis study contributes to the SFM body of knowledge from a green lease perspective, and the theoretical framework in the double principal-agent problem introduced in the study could be used in future research endeavours.