bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insights into Electroreceptor Development and Evolution from Molecular Comparisons with Hair Cells
Authors: Baker Clare V H , Modrell Melinda S 
Published: May 2018

AbstractThe vertebrate lateral line system comprises a mechanosensory division, with neuromasts containing hair cells that detect local water movement (“distant touch”); and an electrosensory division, with electrosensory organs that detect the weak, low-frequency electric fields surrounding other animals in water (primarily used for hunting). The entire lateral line system was lost in the amniote lineage with the transition to fully terrestrial life; the electrosensory division was lost independently in several lineages, including the ancestors of frogs and of teleost fishes. (Electroreception with different characteristics subsequently evolved independently within two teleost lineages.) Recent gene expression studies in a non-teleost actinopterygian fish suggest that electroreceptor ribbon synapses employ the same transmission mechanisms as hair cell ribbon synapses, and show that developing electrosensory organs express transcription factors essential for hair cell development, including Atoh1 and Pou4f3. Previous hypotheses for electroreceptor evolution suggest either that electroreceptors and hair cells evolved independently in the vertebrate ancestor from a common ciliated secondary cell, or that electroreceptors evolved from hair cells. The close developmental and putative physiological similarities implied by the gene expression data support the latter hypothesis, i.e., that electroreceptors evolved in the vertebrate ancestor as a “sister cell-type” to lateral line hair cells.
Finite-region boundedness and stabilization for 2D continuous-discrete systems in Roesser model
Authors: Hua Dingli , Wang Weiqun , Yu Weiren , Wang Yixiang 
Published: May 2018

Abstract
This paper investigates the finite-region boundedness (FRB) and stabilization problems for two-dimensional continuous-discrete linear Roesser models subject to two kinds of disturbances. For two-dimensional continuous-discrete system, we first put forward the concepts of finite-region stability and FRB. Then, by establishing special recursive formulas, sufficient conditions of FRB for two-dimensional continuous-discrete systems with two kinds of disturbances are formulated. Furthermore, we analyze the finite-region stabilization issues for the corresponding two-dimensional continuous-discrete systems and give generic sufficient conditions and sufficient conditions that can be verified by linear matrix inequalities for designing the state feedback controllers which ensure the closed-loop systems FRB. Finally, viable experimental results are demonstrated by illustrative examples.
Semi-infinite Plücker Relations and Weyl Modules
Authors: Feigin Evgeny , Makedonskyi Ievgen 
Published: May 2018

Abstract
The goal of this paper is two-fold. First, we write down the semi-infinite Plücker relations, describing the Drinfeld–Plücker embedding of the (formal version of) semi-infinite flag varieties in type A. Second, we study the homogeneous coordinate ring, that is, the quotient by the ideal generated by the semi-infinite Plücker relations. We establish the isomorphism with the algebra of dual global Weyl modules and derive a new character formula.
Connectedness and Lyubeznik Numbers
Authors: Núñez-Betancourt Luis , Spiroff Sandra , Witt Emily E 
Published: May 2018

AbstractWe investigate the relationship between connectedness properties of spectra and the Lyubeznik numbers, numerical invariants defined via local cohomology. We prove that for complete equidimensional local rings, the Lyubeznik numbers characterize when connectedness dimension equals 1. More generally, these invariants determine a bound on connectedness dimension. Additionally, our methods imply that the Lyubeznik number $\lambda _{1,2}(A)$ of the local ring $A$ at the vertex of the affine cone over a projective variety is independent of the choice of its embedding into projective space.
Regional variation in chronic kidney disease and associated factors in hypertensive individuals in rural South Asia: findings from control of blood pressure and risk attenuation—Bangladesh, Pakistan and Sri Lanka
Authors: Feng Liang , de Silva Hithanadura Asita , Jehan Imtiaz , Naheed Aliya , Kasturiratne Anuradhani , Himani Gulshan , Hasnat Mohammad Abul , Jafar Tazeen H 
Published: May 2018

Abstract

Background
We aimed to determine the prevalence of chronic kidney disease (CKD) and its cross-country variation among hypertensive individuals in rural Bangladesh, Pakistan and Sri Lanka. We also explored the factors associated with CKD in these populations.

Method
We studied baseline data from the Control of Blood Pressure and Risk Attenuation-Bangladesh, Pakistan and Sri Lanka (COBRA-BPS) trial, an ongoing cluster randomized controlled trial on 2643 hypertensive adults ≥40 years of age from 30 randomly selected rural clusters, 10 in each of the three countries. CKD was defined as an estimated glomerular filtration rate (eGFR) &lt;60 mL/min/1.73 m2 or a urine albumin:creatinine ratio (UACR)  ≥30 mg/g. Determinants for CKD were assessed using logistic regression analysis.

Results
The overall prevalence of CKD was 38.1% (95% confidence interval 36.2–40.1%): 21.5% with eGFR &lt;60 mL/min/1.73 m2 and 24.4% with UACR ≥30 mg/g. CKD prevalence varied across the three countries (58.3% in Sri Lanka, 36.4% Bangladesh and 16.9% Pakistan; P &lt;0.001). The factors independently associated with higher odds of CKD were older age, being unmarried, higher 24-h urinary sodium excretion, presence of diabetes, elevated systolic blood pressure, diuretic use and living in Bangladesh or Sri Lanka (versus Pakistan).

Conclusions
The prevalence of CKD is alarmingly high in community-dwelling hypertensive adults, with significant cross-country variation in South Asia. Our findings underscore the urgency for further research into the etiology of CKD and address associated factors in targeted public health strategies with hypertension care outreach services in rural South Asia.

ClinicalTrials.gov
NCT02657746
Inflammation Associates With Impaired Small Arterial Elasticity Early in HIV Disease
Authors: Peterson Tess E , Huppler Hullsiek Katherine , Wyman Engen Nicole , Kumarasamy Nagalingeswaran , Lebech Anne-Mette , Liappis Angelike , Papadopoulos Antonios , Polizzotto Mark N , Schreiner Pamela J , Duprez Daniel , Baker Jason V ,   INSIGHT START (Strategic Timing of AntiRetroviral Treatment) Study Group
Published: May 2018

Abstract
We estimated small arterial elasticity and used linear regression to evaluate its association with inflammatory biomarkers among antiretroviral therapy–naïve, HIV-positive patients with high CD4+ counts. After adjustment, high-sensitivity C-reactive protein and interleukin-6 were inversely associated with small arterial elasticity. These data suggest that systemic inflammation may contribute to vascular dysfunction even in very early HIV disease.
Utility of Immunohistochemistry in Distinguishing Primary Adnexal Carcinoma From Metastatic Breast Carcinoma to Skin and Squamous Cell Carcinoma
Authors: Valencia-Guerrero Aida , Dresser Karen , Cornejo Kristine M. 
Published: May 2018

Abstract:
The distinction between primary adnexal carcinoma (PAC) from metastatic breast carcinoma (BrCa) to skin and squamous cell carcinoma (SCC), particularly those with ductal differentiation (SCCDD), can be quite challenging, despite adequate history. The aim of the study was to determine the utility of an immunohistochemistry (IHC) panel to differentiate these entities and apply them to ambiguous tumors. Twenty-seven PAC, 7 metastatic BrCa, 28 SCC, and 16 ambiguous cases (SCCDD vs. PAC, n = 13 and metastatic BrCa vs. PAC, n = 3) were analyzed using CD23, PAX5, D2-40, P63, and CD117 immunohistochemistry. A total of 9 (33%) PAC were CD117 positive, whereas all metastatic BrCa and SCC were negative (P = 0.0002). D2-40 was expressed in 16 (59%) PAC and 16 (57%) SCC cases, but none of the metastatic BrCa cases (P = 0.0041). Of the 13 ambiguous tumors with a differential diagnosis of SCCDD versus PAC, all were positive for P63, 10 were positive for D2-40, and 1 was positive for CD117. Of the 3 ambiguous tumors with a differential diagnosis of PAC versus metastatic BrCA, 2 were positive for CD117, whereas none showed reactivity for D2-40 or P63. All cases were negative for CD23 and PAX5. Our study indicates that CD117 reactivity favors a PAC with a sensitivity and specificity of 33% and 100%, respectively. D2-40 and P63 expression highlighted both PAC and SCC and seems to be useful in excluding metastatic BrCa with a sensitivity and specificity of 58% and 100%, and 98% and 100%, respectively. Despite previous reports, CD23 and PAX5 do not seem to be useful.
Healthy ageing delays the neural processing of face features relevant for behaviour by 40 ms
Authors: Jaworska Katarzyna , Yi Fei , Ince Robin A.A. , van Rijsbergen Nicola J. , Schyns Philippe G. , Rousselet Guillaume A. 
Published: May 2018

AbstractFast and accurate face processing is critical for everyday social interactions, but it declines and becomes delayed with age, as measured by both neural and behavioural responses. Here, we addressed the critical challenge of understanding how ageing changes neural information processing mechanisms to delay behaviour. Young (20-36 years) and older (60-86 years) adults performed the basic social interaction task detecting a face vs. noise while we recorded their electroencephalogram (EEG). In each participant, using a new information theoretic framework we reconstructed the features supporting face detection behaviour, and also where, when and how EEG activity represents them. We found that occipital-temporal pathway activity dynamically represents the eyes of the face images for behaviour ∼170 ms post-stimulus, with a 40 ms delay in older adults that underlies their 200 ms behavioural deficit of slower reaction times. Our results therefore demonstrate how ageing can change neural information processing mechanisms that underlie behavioural slow down.Author summaryOlder adults are consistently slower than young adults in a variety of behavioural perceptual tasks. So far, it has been unclear if the underlying cause of the behavioural delay relates to attentional or perceptual differences in encoding visual information, or slower neural processing speed, or other neural factors. Our study addresses these questions by showing that in a basic social interaction task (discriminating faces from noise), young and older adults encoded the same visual information (eyes of the face) to perform the task. Moreover, early brain activity (within 200 ms following stimulus onset) encoded the same visual information (again, eyes of the face) in both groups, but was delayed and weaker in older adults. These early delays in information encoding were directly related to the observed behavioural slowing in older adults, showing that differences in early perceptual brain processes can contribute to the motor response.
Fundamental Differences: A Basis Set for Characterizing Inter-Individual Variation in Resting State Connectomes
Authors: Sripada Chandra , Angstadt Mike , Rutherford Saige , Kessler Daniel , Kim Yura , Yee Mike , Levina Liza 
Published: May 2018

SummaryResting state functional connectomes are massive and complex. It is an open question, however, whether connectomes differ across individuals in a correspondingly massive number of ways, or whether most differences take a small number of characteristic forms. We systematically investigated this question and found clear evidence of low-rank structure in which a modest number of connectomic components, around 50-150, account for a sizable portion of inter-individual connectomic variation. This number was convergently arrived at with multiple methods including estimation of intrinsic dimensionality and assessment of reconstruction of out-of-sample data. We demonstrate that these connectomic components enable prediction of a broad array of neurocognitive and clinical variables. In addition, using stochastic block modeling-based methods, we show these components exhibit extensive community structure reflecting interrelationships between intrinsic connectivity networks. We propose that these connectivity components form an effective basis set for quantifying and interpreting inter-individual connectomic differences, and for predicting behavioral/clinical phenotypes.
Fast open modification spectral library searching through approximate nearest neighbor indexing
Authors: Bittremieux Wout , Meysman Pieter , Noble William Stafford , Laukens Kris 
Published: May 2018

AbstractOpen modification searching (OMS) is a powerful search strategy that identifies peptides carrying any type of modification by allowing a modified spectrum to match against its unmodified variant by using a very wide precursor mass window. A drawback of this strategy, however, is that it leads to a large increase in search time. Although performing an open search can be done using existing spectral library search engines by simply setting a wide precursor mass window, none of these tools have been optimized for OMS, leading to excessive runtimes and suboptimal identification results. Here we present the ANN-SoLo tool for fast and accurate open spectral library searching. ANN-SoLo uses approximate nearest neighbor indexing to speed up OMS by selecting only a limited number of the most relevant library spectra to compare to an unknown query spectrum. This approach is combined with a cascade search strategy to maximize the number of identified unmodified and modified spectra while strictly controlling the false discovery rate, as well as a shifted dot product score to sensitively match modified spectra to their unmodified counterparts. ANN-SoLo achieves state-of-the-art performance in terms of speed and the number of identifications. On a previously published human cell line data set, ANN-SoLo confidently identifies more spectra than SpectraST or MSFragger and achieves a speedup of an order of magnitude compared to SpectraST.ANN-SoLo is implemented in Python and C++. It is freely available under the Apache 2.0 license athttps://github.com/bittremieux/ANN-SoLo.
GREIN: An Interactive Web Platform for Reanalyzing GEO RNA-seq Data
Authors: Mahi Naim Al , Najafabadi Mehdi Fazel , Pilarczyk Marcin , Kouril Michal , Medvedovic Mario 
Published: May 2018

ABSTRACTThe vast amount of RNA-seq data deposited in Gene Expression Omnibus (GEO) and Sequence Read Archive (SRA) is still a grossly underutilized resource for biomedical research. To remove technical roadblocks for reusing these data, we have developed a web-application GREIN (GEO RNA-seq Experiments Interactive Navigator) which provides user-friendly interfaces to manipulate and analyze GEO RNA-seq data. GREIN is powered by the back-end computational pipeline for uniform processing of RNA-seq data and the large number (>6,500) of already processed datasets. The front-end user interfaces provide a wealth of user-analytics options including sub-setting and downloading processed data, interactive visualization, statistical power analyses, construction of differential gene expression signatures and their comprehensive functional characterization, and connectivity analysis with LINCS L1000 data. The combination of the massive amount of back-end data and front-end analytics options driven by user-friendly interfaces makes GREIN a unique open-source resource for re-using GEO RNA-seq data. GREIN is accessible at:https://shiny.ilincs.org/grein, the source code at:https://github.com/uc-bd2k/grein, and the Docker container at:https://hub.docker.com/r/ucbd2k/grein.
Recurrent loss-of-function mutations reveal costs to OAS1 antiviral activity in primates
Authors: Carey Clayton M. , Govande Apurva , Cooper Juliane M. , Hartley Melissa K. , Kranzusch Philip J. , Elde Nels C. 
Published: May 2018

ABSTRACTImmune responses counteract infections and can also cause collateral damage to hosts. We investigated functional outcomes of variation in the rapidly evolving antiviral double-stranded RNA (dsRNA) sensing factor Oligoadenylate Synthetase 1 (OAS1) in primates as a model for understanding how individual immune pathways evolve to minimize deleterious effects on host fitness. Upon binding of dsRNAs, OAS1 polymerizes ATP into 2′–5′ linked oligoadenylate (2-5A), which in turn activates Latent Ribonuclease (RNase L) to kill virus infected cells. OAS1 can undergo auto-activation by host encoded RNAs, raising the question of how it might evolve to mitigate RNase L-mediated cytotoxicity. Using a new yeast-based growth assay, we observed a pattern of frequent loss of 2-5A synthesis by OAS1 from several species. In gorillas, we identified a polymorphism in a conserved substrate binding residue that severely decreases catalytic function. In contrast, lowered 2-5A generation previously associated with variation in humans results from production of unstable OAS1 isoforms. Examination of OAS1 function in monkeys revealed a spectrum of activities, including the complete loss of 2-5A synthesis in tamarins. Frequent loss of catalytic activity in primates suggests that costs associated with OAS1 activation can be so detrimental to host fitness that its pathogen-protective effects are repeatedly forfeited.
CRISPRO Identifies Functional Protein Coding Sequences Based on Genome Editing Dense Mutagenesis
Authors: Schoonenberg Vivien A. C. , Cole Mitchel A. , Yao Qiuming , Macias-Treviño Claudio , Sher Falak , Schupp Patrick G. , Canver Matthew C. , Maeda Takahiro , Pinello Luca , Bauer Daniel E. 
Published: May 2018

AbstractCRISPR/Cas9 pooled screening permits parallel evaluation of comprehensive guide RNA libraries to systematically perturb protein coding sequences in situ and correlate with functional readouts. For the analysis and visualization of the resulting datasets we have developed CRISPRO, a computational pipeline that maps functional scores associated with guide RNAs to genome, transcript, and protein coordinates and structure. No available tool has similar functionality. The ensuing genotype-phenotype linear and 3D maps raise hypotheses about structure-function relationships at discrete protein regions. Machine learning based on CRISPRO features improves prediction of guide RNA efficacy. The CRISPRO tool is freely available at gitlab.com/bauerlab/crispro.
Temperature-dependent nanomechanics and topography of bacteriophage T7
Authors: Vörös Zsuzsanna , Csík Gabriella , Herényi Levente , Kellermayer Miklós 
Published: May 2018

AbstractViruses are nanoscale infectious agents which may be inactivated by heat treatment. Although heat inactivation is thought to be caused by the release of genetic material from the capsid, the thermally-induced structural changes in viruses are little known. Here we measured the heat-induced changes in the properties of T7 bacteriophage particles exposed to two-stage (65 °C and 80 °C) thermal effect by using AFM-based nanomechanical and topographical measurements. We found that exposure to 65 °C caused the release of genomic DNA due to the loss of the capsid tail which leads to a destabilization of the T7 particles. Further heating to 80 °C surprisingly led to an increase in mechanical stability due to partial denaturation of the capsomeric proteins kept within the global capsid arrangement.
Methicillin-Resistant Staphylococcus Aureus CC22-MRSA-IV as an Agent of Dairy Cow Intramammary Infections
Authors: Magro Giada , Rebolini Marta , Berettac Daniele , Piccinini Renata 
Published: May 2018

ABSTRACTMethicillin-resistantS. aureus(MRSA) lineages have become major responsible of healthcare-and community-associated infections in human population. Bovine MRSA are sporadically detected in the dairy herd, but its presence might enhance the risk of zoonosis. Some lineages are able to lose the specific host tropism, being easily transmitted from animals to humans and vice-versa. The present study aims at clarifying the epidemiology of MRSA intramammary infections in a closed dairy herd, which was running a mastitis control program since years. Quarter milk samples were collected from all lactating cows once a week for 9 weeks and bacteriologically tested. At the end of the follow-up period, also a self taken nasal swab of the milker was analysed. Three cows (12.5%) were MRSA positive, a four showed a transient infection and an MRSA was isolated also from the milker. Somatic cell counts of the infected quarters fluctuated from 1,000 to 1,800,000 cells/mL. All isolates were genotyped using DNA microarrays and identified as the epidemic UK-EMRSA-15 grouping in CC22. All strains carried the genes for β-lactam and macrolide resistance. The milker isolate differed from cow isolates mainly for the absence of the untruncated β-haemolysin and the presence of the immune evasion cluster. The milker had been volunteering in a nursing home since months, thus playing the role of MRSA vector into the herd. Our results showed the adaptive capacity of such MRSA to the bovine host. Therefore, we suggest that CC22-MRSA should be regarded as a potential cause of humanosis in dairy cattle herds.
Piwi mutant germ cells transmit a form of heritable stress that promotes longevity
Authors: Heestand Bree , McCarthy Ben , Simon Matt , Lister-Shimauchi Evan H. , Frenk Stephen , Ahmed Shawn 
Published: May 2018

SummaryTheC. elegansArgonaute protein PRG-1/Piwi and associated piRNAs protect metazoan genomes by silencing transposons and other types of foreign DNA. Asprg-1mutants are propagated, their fertility deteriorates prior to the onset of a reproductive arrest phenotype that resembles a starvation-induced stress response. We found that late-generationprg-1mutants with substantially reduced fertility were long-lived, whereas early- or mid-generationprg-1mutants had normal lifespans. Loss of the stress response transcription factor DAF-16 caused mid- or late-generationprg-1mutants to live very short lives, whereas overexpression of DAF-16 enabled both mid- and late-generationprg-1mutants to live long. Cytoplasmic P-bodies that respond to stress increased in long-lived late-generationprg-1mutants and were transmitted to F1 but not F2 cross-progeny. Moreover, moderate levels of heritable stress shorten late-generationprg-1mutant longevity when DAF-16 or P bodies are deficient. Together, these results suggest that the longevity of late-generationprg-1mutants is a hormetic stress response. However, dauer larvae that occur in response to stress were not observed in late-generationprg-1mutants. Small germ cell nucleoli that depended on germline DAF-16 were present in late-generationprg-1mutants but were not necessary for their longevity. We propose thatprg-1mutant germ cells transmit a form of heritable stress, high levels of which promote longevity and strongly reduce fertility. The heritable stress transmitted by PRG-1/Piwi mutant germ cells may be generally relevant to epigenetic inheritance of longevity.Core message of paperprg-1/Piwi mutants with strongly reduced fertility live long and longevity is transmitted for one generation to F1 cross progeny. Stress granules are increased and germ cell nucleoli are small for long-lived Piwi mutants and their F1 progeny. Loss ofdaf-16stress response transcription factor ordcap-1P body protein causes very short life for worms whenprg-1mutant fertility is moderately reduced, whereas moderate fertility is sufficient to extend lifespan when somatic DAF-16 is overexpressed. We propose thatprg-1mutant germ cells transmit a heritable epigenetic factor that is stressful and elicits two hormetic stress responses: reproductive arrest and longevity.