bluuebunny/crossref_metadata_2025_split huggingface dataset:
PoLoBag: Polynomial Lasso Bagging for signed gene regulatory network inference from expression data
Authors: Ghosh Roy Gourab , Geard Nicholas , Verspoor Karin , He Shan 
Published: July 2020

AbstractMotivationInferring gene regulatory networks (GRNs) from expression data is a significant systems biology problem. A useful inference algorithm should not only unveil the global structure of the regulatory mechanisms but also the details of regulatory interactions such as edge direction (from regulator to target) and sign (activation/inhibition). Many popular GRN inference algorithms cannot infer edge signs, and those that can infer signed GRNs cannot simultaneously infer edge directions or network cycles.ResultsTo address these limitations of existing algorithms, we propose Polynomial Lasso Bagging (PoLoBag) for signed GRN inference with both edge directions and network cycles. PoLoBag is an ensemble regression algorithm in a bagging framework where Lasso weights estimated on bootstrap samples are averaged. These bootstrap samples incorporate polynomial features to capture higher-order interactions. Results demonstrate that PoLoBag is consistently more accurate for signed inference than state-of-the-art algorithms on simulated and real-world expression datasets.Availability and implementationAlgorithm and data are freely available at https://github.com/gourabghoshroy/PoLoBag.Supplementary informationSupplementary data are available at Bioinformatics online.
Rapid and inexpensive whole-genome sequencing of SARS-CoV-2 using 1200 bp tiled amplicons and Oxford Nanopore Rapid Barcoding
Authors: Freed Nikki E , Vlková Markéta , Faisal Muhammad B , Silander Olin K 
Published: July 2020

Abstract
Rapid and cost-efficient whole-genome sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019, is critical for understanding viral transmission dynamics. Here we show that using a new multiplexed set of primers in conjunction with the Oxford Nanopore Rapid Barcode library kit allows for faster, simpler, and less expensive SARS-CoV-2 genome sequencing. This primer set results in amplicons that exhibit lower levels of variation in coverage compared to other commonly used primer sets. Using five SARS-CoV-2 patient samples with Cq values between 20 and 31, we show that high-quality genomes can be generated with as few as 10 000 reads (∼5 Mbp of sequence data). We also show that mis-classification of barcodes, which may be more likely when using the Oxford Nanopore Rapid Barcode library prep, is unlikely to cause problems in variant calling. This method reduces the time from RNA to genome sequence by more than half compared to the more standard ligation-based Oxford Nanopore library preparation method at considerably lower costs.
UPLC-ESI/Q-TOF MS/MS Method for Determination of Vildagliptin and its Organic Impurities
Authors: Ferrazza Alves Giordani Camila , Campanharo Sarah , Ribeiro Wingert Nathalie , Maronesi Bueno Lívia , Wittckind Manoel Joanna , Virginia Garcia Cássia , Maria Volpato Nadia , Dineck Iop Gabrielle , de Azevedo Mello Paola , Marlon de Moraes Flores Erico , Eva Scherman Schapoval Elfrides , Steppe Martin 
Published: July 2020

AbstractVildagliptin (VLG) corresponds to a drug used for the treatment of diabetes mellitus. This disease requires continuous treatment, and so the control of impurities present in it is important to assure the quality of this drug. Thus, it is necessary to use sensitive and selective detection techniques and the ultra-performance liquid chromatography is a better option compared with high-performance liquid chromatography because it enhances the separation efficiency with a shorter analysis time and an increased resolution. This research analysis was accomplished by using liquid chromatography/tandem mass spectrometry, and the quantification was performed by using an extracted ion from the VLG drug and its main organic impurities of synthesis. During the validation process, following international standards, the method proved to be linear for the tree substances (R2 = 0.997–0.998) and the analysis of variance showed a non-significant linearity deviation (P &gt; 0.05). Three critical factors were selected to evaluate method robustness with a full factorial experimental design, and the changes in the parameters were found to be not significant for the quantification of VLG and its impurities. The ultra-performance liquid chromatography-tandem mass spectrometry for the determination of impurities in VLG was precise, accurate and robust proving to be effective for analysis in the pharmaceutical industry and to improve the quality, safety and effectiveness of the new drug developed.
Clinical Application of Multiple Reaction Monitoring-Mass Spectrometry to Human Epidermal Growth Factor Receptor 2 Measurements as a Potential Diagnostic Tool for Breast Cancer Therapy
Authors: Do Misol , Kim Hyunsoo , Yeo Injoon , Lee Jihyeon , Park In Ae , Ryu Han Suk , Kim Youngsoo 
Published: July 2020

Abstract

Background
Human epidermal growth factor receptor 2 (HER2) is often overexpressed in breast cancer and correlates with a worse prognosis. Thus, the accurate detection of HER2 is crucial for providing the appropriate measures for patients. However, the current techniques used to detect HER2 status, immunohistochemistry and fluorescence in situ hybridization (FISH), have limitations. Specifically, FISH, which is mandatory for arbitrating 2+ cases, is time-consuming and costly. To address this shortcoming, we established a multiple reaction monitoring-mass spectrometry (MRM-MS) assay that improves on existing methods for differentiating HER2 status.

Methods
We quantified HER2 expression levels in 210 breast cancer formalin-fixed paraffin-embedded (FFPE) tissue samples by MRM-MS. We aimed to improve the accuracy and precision of HER2 quantification by simplifying the sample preparation through predicting the number of FFPE slides required to ensure an adequate amount of protein and using the expression levels of an epithelial cell-specific protein as a normalization factor when measuring HER2 expression levels.

Results
To assess the correlation between MRM-MS and IHC/FISH data, HER2 quantitative data from MRM-MS were divided by the expression levels of junctional adhesion molecule A, an epithelial cell-specific protein, prior to statistical analysis. The normalized HER2 amounts distinguished between HER2 2+/FISH-negative and 2+/FISH-positive groups (AUROC = 0.908), which could not be differentiated by IHC. In addition, all HER2 status were discriminated by MRM-MS.

Conclusions
This MRM-MS assay yields more accurate HER2 expression levels relative to immunohistochemistry and should help to guide clinicians toward the proper treatment for breast cancer patients, based on their HER2 expression.
Breeding success of Eleonora’s Falcon in Cyprus revisited using survey techniques for cliff-nesting species
Authors: Hadjikyriakou Thomas G , Kassinis Nikolaos , Skarlatos Dimitrios , Charilaou Pantelis , Kirschel Alexander N G 
Published: July 2020

AbstractThe global breeding population of Eleonora’s Falcon (Falco eleonorae) is distributed from the Canary Islands in the west, across the Mediterranean Sea, to Cyprus in the east. The remoteness of nesting colonies, which are predominantly located on sea cliffs and islets, renders breeding success estimation a challenging task, requiring a composite approach to assess each of the breeding stages. Early estimates of the breeding success of Eleonora’s Falcon suggested that the Akrotiri colony in Cyprus had the lowest breeding success among all the colonies throughout the species’ breeding range, at a level seemingly unsustainable, suggesting the colony might have been in danger of gradual extinction. Here we use a diversity of survey methods including boat, ground, and aerial surveys, with the incorporation of photography and photogrammetry, to reassess the breeding success and the effect of nest characteristics on the Eleonora’s Falcon breeding population in Cyprus. During a 6-yr study, we found that Cyprus hosts ~138 ± 8 breeding pairs and that breeding success equals 1.54 ± 0.85 fledglings per breeding pair, and thus is considerably higher than previous estimates. In addition, by analyzing temporal variation in breeding and nest characteristics, we found that early breeding and reuse of nests positively influence breeding success, but physical nest characteristics have a limited effect on colony productivity. The range of survey methods employed, as well as the array of photography techniques utilized, enhanced the efficiency and accuracy of this study, allowing us to overcome the challenge of inaccessibility of nesting cliffs.
Intervention Outcomes, Anxiety, Self-Esteem, and Self-Efficacy With DHH Students in Universities
Authors: Pandya Samta P 
Published: July 2020

AbstractThis article reports the impact of an online spiritual counseling (OSC) program in mitigating anxiety and building self-esteem and academic self-efficacy among deaf and hard-of-hearing (DHH) students in universities. Compared to online relaxation sessions, the OSC was more effective. Male DHH students and those whose parents were highly qualified exhibited less anxiety and higher self-esteem and self-efficacy at pretest (T1). Post-test (T2) male students having better educated parents responded better to the OSC. T2 anxiety was lower and self-esteem and academic self-efficacy was higher for liberal arts students and having stay-at-home parents compared with science and commerce students and whose parents worked outside home. Self-esteem was also positively moderated by better economic class and presence of siblings. Intervention compliance in terms of regular attendance and self-practice mediated the relationship between sociodemographic predictors and outcomes. Results support the biopsychosocial model and encourage the implementation of the OSC with DHH university students.
Effects of Vocal Training on Thyroarytenoid Muscle Neuromuscular Junctions and Myofibers in Young and Older Rats
Authors: Shembel Adrianna C , Lenell Charles , Chen Sophia , Johnson Aaron M 
Published: July 2020

Abstract
The purpose of this investigation was to determine the effects of vocal training on neuromuscular junction (NMJ) morphology and muscle fiber size and composition in the thyroarytenoid muscle, the primary muscle in the vocal fold, in younger (9-month) and older (24-month) Fischer 344 × Brown Norway male rats. Over 4 or 8 weeks of vocal training, rats of both ages progressively increased their daily number of ultrasonic vocalizations (USVs) through operant conditioning and were then compared to an untrained control group. Neuromuscular junction morphology and myofiber size and composition were measured from the thyroarytenoid muscle. Acoustic analysis of USVs before and after training quantified the functional effect of training. Both 4- and 8-week training resulted in less NMJ motor endplate dispersion in the lateral portion of the thyroarytenoid muscle in rats of both ages. Vocal training and age had no significant effects on laryngeal myofiber size or type. Vocal training resulted in a greater number of USVs with longer duration and increased intensity. This study demonstrated that vocal training induces laryngeal NMJ morphology and acoustic changes. The lack of significant effects of vocal training on muscle fiber type and size suggests vocal training significantly improves neuromuscular efficiency but does not significantly influence muscle strength changes.
Vaginal neutrophils eliminate sperm by trogocytosis
Authors: Olivera-Valle I , Latorre M C , Calvo M , Gaspar B , Gómez-Oro C , Collazos A , Breton A , Caballero-Campo P , Ardoy M , Asensio F , Sánchez-Mateos P , Pérez-Millan F , Relloso M 
Published: July 2020

Abstract

STUDY QUESTION
What is the vaginal polymorphonuclear (PMN) spermicidal mechanism to reduce the excess of sperm?

SUMMARY ANSWER
We show that PMNs are very efficient at killing sperm by a trogocytosis-dependent spermicidal activity independent of neutrophil extracellular traps (NETs).

WHAT IS KNOWN ALREADY
Trogocytosis has been described as an active membrane exchange between immune cells with a regulatory purpose. Recently, trogocytosis has been reported as a mechanism which PMNs use to kill tumour cells or Trichomonas vaginalis.

STUDY DESIGN, SIZE, DURATION
We used in vivo murine models and human ex vivo sperm and PMNs to investigate the early PMN–sperm response.

PARTICIPANTS/MATERIALS, SETTING, METHODS
We set up a live/dead sperm detection system in the presence of PMNs to investigate in vivo and ex vivo PMN-spermicidal activity by confocal microscopy, flow cytometry and computer-assisted sperm analysis (SCA).

MAIN RESULTS AND THE ROLE OF CHANCE
We revealed that PMNs are highly efficient at killing sperm by way of a NETs-independent, contact-dependent and serine proteases-dependent engulfment mechanism. PMNs ‘bite’ sperm and quickly reduce sperm motility (within 5 min) and viability (within 20 min) after contact.

LARGE SCALE DATA
N/A

LIMITATIONS, REASONS FOR CAUTION
This study was conducted using murine models and healthy human blood PMNs; whether it is relevant to human vaginal PMNs or to cases of infertility is unknown.

WIDER IMPLICATIONS OF THE FINDINGS
Vaginal PMNs attack and immobilize excess sperm in the vagina by trogocytosis because sperm are exogenous and may carry pathogens. Furthermore, this mechanism of sperm regulation has low mucosal impact and avoids an exacerbated inflammatory response that could lead to mucosal damage or infertility.

STUDY FUNDING/COMPETING INTEREST(S)
This work was partially supported by Ministry of Economy and Competitiveness ISCIII-FIS grants, PI16/00050, and PI19/00078, co-financed by ERDF (FEDER) Funds from the European Commission, ‘A way of making Europe’ and IiSGM intramural grant II-PI-MRC-2017. M.R. holds a Miguel Servet II contract (CPII14/00009). M.C.L. holds IiSGM intramural contract. There are no competing interests.
The Effects of Roughness and Wetness on Salamander Cling Performance
Authors: O’Donnell Mary Kate , Deban Stephen M 
Published: July 2020

SynopsisAnimals clinging to natural surfaces have to generate attachment across a range of surface roughnesses in both dry and wet conditions. Plethodontid salamanders can be aquatic, semi-aquatic, terrestrial, arboreal, troglodytic, saxicolous, and fossorial and therefore may need to climb on and over rocks, tree trunks, plant leaves, and stems, as well as move through soil and water. Sixteen species of salamanders were tested to determine the effects of substrate roughness and wetness on maximum cling angle. Substrate roughness had a significant effect on maximum cling angle, an effect that varied among species. Substrates of intermediate roughness (asperity size 100–350 µm) resulted in the poorest attachment performance for all species. Small species performed best on smooth substrates, while large species showed significant improvement on the roughest substrates (asperity size 1000–4000 µm), possibly switching from mucus adhesion on a smooth substrate to an interlocking attachment on rough substrates. Water, in the form of a misted substrate coating and a flowing stream, decreased cling performance in salamanders on smooth substrates. However, small salamanders significantly increased maximum cling angle on wetted substrates of intermediate roughness, compared with the dry condition. Study of cling performance and its relationship to surface properties may cast light onto how this group of salamanders has radiated into the most speciose family of salamanders that occupies diverse habitats across an enormous geographical range.
Resolution of the identity ofPinnotheres latipesHombron & Jacquinot, 1846 and description of a new species ofViridotheresManning, 1996 (Decapoda: Brachyura: Pinnotheridae): two symbionts of bivalve molluscs
Authors: Ahyong Shane T 
Published: July 2020

AbstractPinnotherid crabs are well known as obligate associates of other marine invertebrates, frequently bivalve molluscs. Knowledge of the Australian pinnotherid crab fauna is expanded by description of a new species of Viridotheres Manning, 1996, representing the first record of the genus from Western Australia. The new species of Viridotheres is most similar to V. gracilis (Bürger, 1895) from the Philippines and V. takedai Ahyong, Komai & Watanabe, 2012 from Japan, but is unique in the genus in the elongated maxilliped 3 palp that distinctly overreaches the propodal apex. The identity of the poorly known northern Australian species, Pinnotheres latipes Hombron & Jacquinot, 1846, originally described from the Northern Territory, is resolved by designation of a neotype that places the species in the genus Nepinnotheres Manning, 1993. Nepinnotheres latipescomb. nov. is widespread in northern Australia and commonly hosted by the bivalve mollusc Pinna Linnaeus, 1758. Previous Australian records of Nepinnotheres cardii (Bürger, 1895) and N. edwardsi (De Man, 1888) from Australia are referable to N. latipes. Nepinnotheres latipes is one of only five known pinnotherids having androgynous males. Few pinnotherids are known from males, so estimating the extent of androgyny in Pinnotheridae must await discovery of males of additional species.
Linking population performance to nutritional condition in an alpine ungulate
Authors: Stephenson Thomas R , German David W , Cassirer E Frances , Walsh Daniel P , Blum Marcus E , Cox Mike , Stewart Kelley M , Monteith Kevin L 
Published: July 2020

AbstractBighorn sheep (Ovis canadensis) can live in extremely harsh environments and subsist on submaintenance diets for much of the year. Under these conditions, energy stored as body fat serves as an essential reserve for supplementing dietary intake to meet metabolic demands of survival and reproduction. We developed equations to predict ingesta-free body fat in bighorn sheep using ultrasonography and condition scores in vivo and carcass measurements postmortem. We then used in vivo equations to investigate the relationships between body fat, pregnancy, overwinter survival, and population growth in free-ranging bighorn sheep in California and Nevada. Among 11 subpopulations that included alpine winter residents and migrants, mean ingesta-free body fat of lactating adult females during autumn ranged between 8.8% and 15.0%; mean body fat for nonlactating females ranged from 16.4% to 20.9%. In adult females, ingesta-free body fat &gt; 7.7% during January (early in the second trimester) corresponded with a &gt; 90% probability of pregnancy and ingesta-free body fat &gt; 13.5% during autumn yielded a probability of overwinter survival &gt; 90%. Mean ingesta-free body fat of lactating females in autumn was positively associated with finite rate of population increase (λ) over the subsequent year in bighorn sheep subpopulations that wintered in alpine landscapes. Bighorn sheep with ingesta-free body fat of 26% in autumn and living in alpine environments possess energy reserves sufficient to meet resting metabolism for 83 days on fat reserves alone. We demonstrated that nutritional condition can be a pervasive mechanism underlying demography in bighorn sheep and characterizes the nutritional value of their occupied ranges. Mountain sheep are capital survivors in addition to being capital breeders, and because they inhabit landscapes with extreme seasonal forage scarcity, they also can be fat reserve obligates. Quantifying nutritional condition is essential for understanding the quality of habitats, how it underpins demography, and the proximity of a population to a nutritional threshold.
Explaining mammalian abundance and elevational range size with body mass and niche characteristics
Authors: Wen Zhixin , Feijó Anderson , Cheng Jilong , Du Yuanbao , Ge Deyan , Xia Lin , Yang Qisen 
Published: July 2020

Abstract
Recent work on tropical montane small mammals and birds has shown that abundance–elevational range size relationships (i.e., the relationship between abundance of a species and its elevational range size) can be manifested in a number of distinct generalized patterns. To understand why different patterns occur, one first must understand the causal mechanisms behind patterns of interspecific variation in species abundance and elevational range size. Using small mammal data along five elevational gradients in Southwest China, we assessed the relative importance of body mass, niche position (i.e., how typical the environmental conditions in which a species occurs are of the full set of conditions under consideration) and niche breadth in explaining the interspecific variation in mean abundance of species of small mammals, and elevational range size. Niche position and niche breadth were calculated using outlying mean index analysis based on 24 environmental variables. The relative importance of body mass, niche position, and niche breadth, in explaining the mean abundance and elevational range size of species were examined using phylogenetic regression and phylogenetic path analyses. Along each of five elevational gradients, body mass maintained a nonsignificant (P &gt; 0.05) relationship both with mean abundance and elevational range size when the effects of phylogeny were taken into account. Niche position had a negative effect on mean abundance and elevational range size (species with a niche position close to edge environmental conditions were rarer and had smaller elevational range sizes) across five gradients (significant negative effect: three gradients for mean abundance; five gradients for elevational range size). Conversely, a positive effect of niche breadth on mean abundance and elevational range size was observed consistently, yet the effect was significant only for some gradients (mean abundance: two gradients; elevational range size: four gradients). Our study suggests that niche position and niche breadth both are good predictors of abundance and elevational range size of montane small mammals; niche position and niche breadth therefore play a strong role in the formation of abundance–elevational range size relationship.
Evaluation of accuracy in the determination of crystal structure factors using large-angle convergent-beam electron diffraction patterns
Authors: Morikawa Daisuke , Tsuda Kenji 
Published: July 2020

Abstract
The accuracy of electron density distribution analysis using large-angle convergent-beam electron diffraction (LACBED) patterns is evaluated for different convergence angles. An orbital ordered state of FeCr2O4 is used as an example of the analysis. Ideal orbital-ordered and non-ordered states are simulated by using orbital scattering factors. LACBED patterns calculated for the orbital-ordered state were used as hypothetical experimental data sets. Electron density distribution of the Fe 3d orbitals has been successfully reconstructed with a higher accuracy from LACBED patterns with convergence angles larger than 15.2 mrad, which is 4 times as large as that for conventional convergent-beam electron diffraction patterns. Excitation of particular Bloch waves with the aid of LACBED patterns has a key role in the accurate analysis of electron density distributions.