bluuebunny/crossref_metadata_2025_split huggingface dataset:
ClonoMatch: a tool for identifying homologous immunoglobulin and T-cell receptor sequences in large databases
Authors: Jones Taylor , Day Samuel B , Myers Luke , Crowe James E , Soto Cinque 
Published: November 2020

Abstract

Summary
B-cell receptor (BCR) and T-cell receptor (TCR) repertoires are generated through somatic DNA rearrangements and are responsible for the molecular basis of antigen recognition in the immune system. Next-generation sequencing (NGS) of DNA and the falling cost of sequencing due to continued development of these technologies have made sequencing assays an affordable way to characterize the repertoire of adaptive immune receptors (sometimes termed the ‘immunome’). Many new workflows have been developed to take advantage of NGS and have placed the resulting immunome datasets in the public domain. The scale of these NGS datasets has made it challenging to search through the Complementarity-determining region 3 (CDR3), which is responsible for imparting specific antibody-antigen interactions. Thus, there is an increasing demand for sequence analysis tools capable of searching through CDR3s from immunome data collections containing millions of sequences. To address this need, we created a software package called ClonoMatch that facilitates rapid searches in bulk immunome data for BCR or TCR sequences based on their CDR3 sequence or V3J clonotype.

Availability and implementation
Documentation, software support and the codebase are all available at https://github.com/crowelab/clonomatch. This software is distributed under the GPL v3 license.
DeMaSk: a deep mutational scanning substitution matrix and its use for variant impact prediction
Authors: Munro Daniel , Singh Mona 
Published: November 2020

Abstract

Motivation
Accurately predicting the quantitative impact of a substitution on a protein’s molecular function would be a great aid in understanding the effects of observed genetic variants across populations. While this remains a challenging task, new approaches can leverage data from the increasing numbers of comprehensive deep mutational scanning (DMS) studies that systematically mutate proteins and measure fitness.

Results
We introduce DeMaSk, an intuitive and interpretable method based only upon DMS datasets and sequence homologs that predicts the impact of missense mutations within any protein. DeMaSk first infers a directional amino acid substitution matrix from DMS datasets and then fits a linear model that combines these substitution scores with measures of per-position evolutionary conservation and variant frequency across homologs. Despite its simplicity, DeMaSk has state-of-the-art performance in predicting the impact of amino acid substitutions, and can easily and rapidly be applied to any protein sequence.

Availability and implementation
https://demask.princeton.edu generates fitness impact predictions and visualizations for any user-submitted protein sequence.

Supplementary information
Supplementary data are available at Bioinformatics online.
The sperm-specific form of lactate dehydrogenase is required for fertility and is an attractive target for male contraception (a review)
Authors: Goldberg Erwin 
Published: November 2020

AbstractThere has been a recent upsurge in the interest about contraceptive development, evidenced by the Contraceptive Special Issue of Biology of Reproduction [1], with research funding from the Male Contraceptive Initiative and the Bill and Melinda Gates Foundation. Support from the Contraceptive Research Branch of the Eunice Kennedy Shriver National Institutes of Child Health and Human Development continues with a marked change in focus in the funding announcements. This has motivated me to reflect on research, mostly from my laboratory starting in the 1960s to the present, on the development of a male contraceptive based on the sperm-specific glycolytic enzyme, lactate dehydrogenase C (LDHC4). This review considers the rationale behind this research, the development paths pursued, obstacles encountered, and the renewed interest in going forward toward development of a male contraceptive mediated by the inhibition of the sperm-specific form of LDHC. I will address how some papers published many years ago are relevant to the present goals of non-hormonal contraception and will mention about innovative technology now available that can advance this project. This review presumably will serve as an instructive guide for a research program with a focused program related to contraception. As an aside, many of the citations in this review are to most of the 26 publications in Biology of Reproduction co-authored by this investigator and collaborators from 1974 through 2020 not long after the first issue of BOR which was published in April 1969.
‘Our biographies are the same’: Juvenile Work in Mexican Drug Trafficking Organizations from the Perspective of a Collective Trajectory
Authors: Chomczyński Piotr A , Guy Roger 
Published: November 2020

AbstractRecent violence among drug trafficking organizations (DTOs) in Mexico has resulted in an ongoing demand for new recruits. Juveniles engage in a wide range of activities from lookouts in drug trafficking operations to high-risk activities, such as kidnapping and homicide. Based on ongoing ethnographic work in Mexico and referrals from correctional officials, we conducted in-depth biographical interviews with convicted and active cartel members (N = 79). Our data revealed that similar biographical experiences in communities characterized by a high degree of collectivism laid the groundwork for their entry and continued participation in criminal activity. Through inductive methods, we introduce a theoretical concept that we term a collective trajectory to help explain our subjects’ pathway and criminal careers in DTOs.
Applying graph database technology for analyzing perturbed co-expression networks in cancer
Authors: Simpson Claire M , Gnad Florian 
Published: November 2020

AbstractGraph representations provide an elegant solution to capture and analyze complex molecular mechanisms in the cell. Co-expression networks are undirected graph representations of transcriptional co-behavior indicating (co-)regulations, functional modules or even physical interactions between the corresponding gene products. The growing avalanche of available RNA sequencing (RNAseq) data fuels the construction of such networks, which are usually stored in relational databases like most other biological data. Inferring linkage by recursive multiple-join statements, however, is computationally expensive and complex to design in relational databases. In contrast, graph databases store and represent complex interconnected data as nodes, edges and properties, making it fast and intuitive to query and analyze relationships. While graph-based database technologies are on their way from a fringe domain to going mainstream, there are only a few studies reporting their application to biological data. We used the graph database management system Neo4j to store and analyze co-expression networks derived from RNAseq data from The Cancer Genome Atlas. Comparing co-expression in tumors versus healthy tissues in six cancer types revealed significant perturbation tracing back to erroneous or rewired gene regulation. Applying centrality, community detection and pathfinding graph algorithms uncovered the destruction or creation of central nodes, modules and relationships in co-expression networks of tumors. Given the speed, accuracy and straightforwardness of managing these densely connected networks, we conclude that graph databases are ready for entering the arena of biological data.
Relationships Between Sensorimotor Inhibition and Mobility in Older Adults With and Without Parkinson’s Disease
Authors: Martini Douglas N , Morris Rosie , Madhyastha Tara M , Grabowski Thomas J , Oakley John , Hu Shu-Ching , Zabetian Cyrus P , Edwards Karen L , Hiller Amie , Chung Kathryn , Ramsey Katrina , Lapidus Jodi A , Cholerton Brenna , Montine Thomas J , Quinn Joseph F , Horak Fay B 
Published: November 2020

Abstract

Background
Reduced cortical sensorimotor inhibition is associated with mobility and cognitive impairments in people with Parkinson’s disease (PD) and older adults (OAs). However, there is a lack of clarity regarding the relationships among sensorimotor, cognitive, and mobility impairments. The purpose of this study was to determine how cortical sensorimotor inhibition relates to impairments in mobility and cognition in people with PD and OAs.

Method
Cortical sensorimotor inhibition was characterized with short-latency afferent inhibition (SAI) in 81 people with PD and 69 OAs. Six inertial sensors recorded single- and dual-task gait and postural sway characteristics during a 2-minute walk and a 1-minute quiet stance. Cognition was assessed across the memory, visuospatial, executive function, attention, and language domains.

Results
SAI was significantly impaired in the PD compared to the OA group. The PD group preformed significantly worse across all gait and postural sway tasks. In PD, SAI significantly correlated with single-task foot strike angle and stride length variability, sway area, and jerkiness of sway in the coronal and sagittal planes. In OAs, SAI significantly related to single-task gait speed and stride length, dual-task stride length, and immediate recall (memory domain). No relationship among mobility, cognition, and SAI was observed.

Conclusions
Impaired SAI related to slower gait in OA and to increased gait variability and postural sway in people with PD, all of which have been shown to be related to increased fall risk.
Translating and validating the Health Literacy Questionnaire into Urdu: a robust nine-dimension confirmatory factor model
Authors: Saleem Ahsan , Steadman Kathryn J , Osborne Richard H , La Caze Adam 
Published: November 2020

Abstract
Pakistani migrants are one of the fastest-growing communities in Australia, and the majority speak Urdu at home. There is a lack of information regarding the health literacy of this population. This study aimed to translate the Health Literacy Questionnaire (HLQ) into Urdu and to explore its psychometric properties. A structured standardized procedure was followed to translate and validate HLQ into Urdu. Data were collected from 202 Pakistani migrants residing in Australia. The HLQ-Urdu was well understood by the respondents. The structural properties of HLQ-Urdu were close to the original HLQ. Data for all HLQ scales met pre-specified criteria for fit in the one-factor CFA model. The composite reliability was high, ranging from 0.84 to 0.91. A strict nine-factor CFA model was also fitted to the data with no cross-loadings or correlated residuals allowed, which showed excellent model fit statistics [χ2WLSMV = 1266.022 (df = 866, p = 0.000), comparative fit index  = 0.995, Tucker–Lewis index = 0.994, root mean square error of approximation = 0.050 and standardized root mean square residual = 0.069]. The Urdu version of HLQ showed robust psychometric properties. This HLQ-Urdu tool is now ready to be used to assess health literacy in Pakistani migrants in Australia. Availability of health literacy tools in migrant languages may help healthcare providers better understand the health literacy needs of migrant communities.
Evaluation of genetic effects on wild salmon populations from stock enhancement
Authors: Hagen Ingerid J , Ugedal Ola , Jensen Arne J , Lo Håvard , Holthe Espen , Bjøru Bjørn , Florø-Larsen Bjørn , Sægrov Harald , Skoglund Helge , Karlsson Sten 
Published: November 2020

Abstract
Many salmonid populations are of conservation concern, and the release of hatchery-produced juveniles is a frequently used measure to alleviate declines and increase harvest opportunities. While such releases may be of conservation value for some populations, stocking may also decrease the effective population size and subsequently impose additional strain on already threatened populations. In this study, we assessed how the cohort-wise effective number of breeders in five populations of Atlantic salmon (Salmo salar) were affected by supplementation. Altogether, 19 cohorts were studied (2–7 cohorts per population) by estimating the proportion hatchery-released individuals and the effective number of wild and captive breeders in each cohort of the respective populations. We show that the effect of releasing captive-bred individuals varies both between populations and between years within the same population. A Ryman–Laikre effect—where the effective number of breeders has decreased as a consequence of supplementation—was observed for 11 cohorts. We discuss how supplementation can be adapted to optimize the effective population size, demonstrate that evaluation of supplementation can be reliably achieved, and show that supplementation programmes that lead to high proportions of hatchery-origin fish on spawning grounds are more likely to induce a Ryman–Laikre effect.
Impact of long-term quorum sensing inhibition on uropathogenic Escherichia coli
Authors: Henly E L , Norris K , Rawson K , Zoulias N , Jaques L , Chirila P G , Parkin K L , Kadirvel M , Whiteoak C , Lacey M M , Smith T J , Forbes S 
Published: November 2020

Abstract

Background
Quorum sensing is an extracellular bacterial communication system used in the density-dependent regulation of gene expression and development of biofilms. Biofilm formation has been implicated in the establishment of catheter-associated urinary tract infections and therefore quorum sensing inhibitors (QSIs) have been suggested as anti-biofilm catheter coating agents. The long-term effects of QSIs in uropathogens is, however, not clearly understood.

Objectives
We evaluated the effects of repeated exposure to the QSIs cinnamaldehyde, (Z)-4-bromo-5(bromomethylene)-2(5H)-furanone-C30 (furanone-C30) and 4-fluoro-5-hydroxypentane-2,3-dione (F-DPD) on antimicrobial susceptibility, biofilm formation and relative pathogenicity in eight uropathogenic Escherichia coli (UPEC) isolates.

Methods
MICs, MBCs and minimum biofilm eradication concentrations and antibiotic susceptibility were determined. Biofilm formation was quantified using crystal violet. Relative pathogenicity was assessed in a Galleria mellonella model. To correlate changes in phenotype to gene expression, transcriptomic profiles were created through RNA sequencing and variant analysis of genomes was performed in strain EC958.

Results
Cinnamaldehyde and furanone-C30 led to increases in susceptibility in planktonic and biofilm-associated UPEC. Relative pathogenicity increased after cinnamaldehyde exposure (4/8 isolates), decreased after furanone-C30 exposure (6/8 isolates) and varied after F-DPD exposure (one increased and one decreased). A total of 9/96 cases of putative antibiotic cross-resistance were generated. Exposure to cinnamaldehyde or F-DPD reduced expression of genes associated with locomotion, whilst cinnamaldehyde caused an increase in genes encoding fimbrial and afimbrial-like adhesins. Furanone-C30 caused a reduction in genes involved in cellular biosynthetic processes, likely though impaired ribonucleoprotein assembly.

Conclusions
The multiple phenotypic adaptations induced during QSI exposure in UPEC should be considered when selecting an anti-infective catheter coating agent.
Quantification of Amyloid-β in Plasma by Simple and Highly Sensitive Immunoaffinity Enrichment and LC-MS/MS Assay
Authors: Iino Takuya , Watanabe Shunsuke , Yamashita Kazuto , Tamada Eiya , Hasegawa Takehiro , Irino Yasuhiro , Iwanaga Shigeki , Harada Amane , Noda Kenta , Suto Kouzou , Yoshida Tomokazu 
Published: November 2020

AbstractBackgroundNumerous immunoassays have been developed to quantify amyloid β1-40 (Aβ40) and amyloid β1-42 (Aβ42). Nevertheless, given the low concentration of Aβ and the high levels of interfering factors in plasma, quantification of plasma Aβ is still challenging. To overcome the problems related to the specificity of Aβ immunoassays, this study aimed to develop an immunoaffinity enrichment and LC-MS/MS (IA-MS) assay.MethodsWe developed an IA-MS assay using antibody-labeled magnetic beads for purification and LC-MS/MS for Aβ quantification. To avoid the loss of Aβ due to aggregation in acidic buffer, we used alkaline elution buffer for immunoaffinity enrichment. The concentrations of the Aβs in plasma samples were measured, and the correlation between the plasma and cerebrospinal fluid (CSF) Aβ42/Aβ40 ratio was also evaluated.ResultsThe intensities of the Aβ mass peaks were significantly higher with the alkaline elution buffer than with the acidic elution buffer (Aβ40: 3.6-fold, Aβ42: 5.4-fold). This assay exhibited high reproducibility (intra-assay and inter-assay precision, %CV &lt;15), and the working ranges of Aβ40 and Aβ42 were determined to be 21.7 to 692.8 pg/mL and 5.6 to 180.6 pg/mL, respectively. The concentrations of Aβ40 and Aβ42 in plasma were measured by IA-MS, and the plasma Aβ42/Aβ40 ratio was correlated with the CSF Aβ42/Aβ40 ratio (rs = 0.439, P &lt; 0.01).ConclusionsThe IA-MS assay has sufficient analytic performance for measuring endogenous Aβ40 and Aβ42 in plasma. This assay can lead to new lines of clinical discovery related to amyloid pathology.
83 Evaluation of transmammary-delivered firocoxib and an ethyl chloride spray to mitigate pain associated with processing procedures in piglets
Authors: Viscardi Abbie V , Shirtcliff Elizabeth , Eppler Emily , Miller Savannah , Coetzee Johann 
Published: November 2020

Abstract
Piglets raised in commercial production systems in the U.S. undergo painful management procedures, including surgical castration, tail docking and ear notching, without analgesia or anesthesia provision for pain relief. This is a significant animal welfare concern. There is an immediate need to identify the most practical and effective analgesia or anesthesia option for use on-farm. The objective of this study was to assess the efficacy of 2.0mg/kg firocoxib, administered to the sow and delivered transmammary to her piglets, and a vapocoolant spray (ethyl chloride) to reduce processing pain. Five-day old male and female Yorkshire-cross piglets were used. 2.0mg/kg firocoxib was administered to the sow intramuscularly 7h prior to processing piglets. An ethyl chloride spray was applied to the ears, tail and scrotum of the piglets immediately before ear notching, tail docking and surgical castration, respectively. Piglets were assigned to one of four treatment groups: firocoxib and vapocoolant spray (FV; n=32), firocoxib only (F; n=32), vapocoolant spray only (V; n=32), no treatment (CON; n=32). The observation period was from 24h pre- to 48h post-processing (specific time points = baseline, 0h, 1h, 2h, 4h, 7h, 24h, 30h, 36h, 48h). Preliminary results found piglets displayed significantly more pain-related behaviors at 24h and 30h post-processing than at most other time points (p&lt; 0.05). Piglets had significantly higher cranial temperatures at 7h post-processing than all other time points (p&lt; 0.05). There was a trend in FV and F piglets having a higher cranial temperature at 36h post-processing compared to V and CON piglets (p=0.08). All piglets had significantly higher hair cortisol levels at 4 vs 20-days old (p&lt; .0001); however, there were no significant treatment effects on cranial temperature, hair cortisol or pain behavior, suggesting firocoxib and the ethyl chloride spray were unable to significantly reduce piglet pain post-processing. Further study analysis is needed to confirm these initial findings.
196 Feeding and nutritional strategies to improve welfare of group-housed gestating sows
Authors: Li Yuzhi 
Published: November 2020

Abstract
Gestating sows in group-housing systems usually face two major welfare challenges: aggression when mixing with unfamiliar pen-mates and a lack of satiety due to restricted feeding. The two issues might be related because that hungry animals may be frustrated so that they may be more aggressive than animals that are in satiety. To restricted-fed gestating sows, one of the strategies to reduce aggression at mixing is to increase feed intake for a short period of time around mixing. Research showed that this strategy could reduce aggression among sows during feeding in competitive feeding systems, but had very limited effects on aggression during the initial period of mixing. Likewise, neither providing feed when moving sows in group-pens nor dividing the daily ration into multiple meals affected aggression caused by mixing. There is evidence that supplementation of an excessive amount of Tryptophan in the diet could reduce aggression in growing and finishing pigs. However, effects of dietary Tryptophan on reducing aggression among sows during mixing is less evident. Possibly, sows are more persistent in fighting for dominance hierarchy than young pigs. Although high fiber diets had limited effects on reducing aggression among sows at mixing, providing fermentable fibers in the diet could increase satiety in sows. Increasing satiety could reduce stereotypies, reduce aggression for maintaining dominance hierarchy, and increase resting time, which consequently will improve welfare of group-housed gestating sows.
110 Managing Feed Efficiency to Improve Dairy Farm Margin
Authors: Brouk Micheal J 
Published: November 2020

Abstract
Dairy farm margin has continued to be a challenge for the dairy industry. Several years of challenging milk prices with limited relief from high feed costs and increasing production cost have continued to erode the net margin of US dairy farms. As dairy producers continue to operate in a challenging economic environment, discoveries are being made in various farm efficiencies to improve farm margin. Increased management intensity on all aspects of the dairy farm is resulting in the discover of and improvement of many individual efficiency factors. Key areas of economic efficiency include feed, animal reproduction, replacement animals, labor and resource allocation. Often the answer to improved efficiency involves more than just reduced production cost, but also in the improvement of production to reduce the cost per unit of milk produced. Identifying and focusing on the important factors that can improve overall farm efficiency will enable producers to weather the economic challenges. For dairy producers, one of the complications is the biology of the dairy cow and understanding how to utilize the biology correctly for improved efficiency of milk production. Improved efficiency of milk production requires attention to details in many areas of the dairy. Identifying the correct areas of deficiencies, establishing corrective plans of action and then careful evaluation of the impact of changes are all key to the overall success of improving dairy farm margins and efficiencies.