bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of heterospecific pollen deposition on pollen tube growth depends on the phylogenetic relatedness between donor and recipient
Authors: Streher Nathália Susin , Bergamo Pedro Joaquim , Ashman Tia-Lynn , Wolowski Marina , Sazima Marlies 
Published: May 2020

AbstractCo-flowering plant species may interact via pollinators leading to heterospecific pollen transfer with consequences for plant reproduction. What determines the severity of heterospecific pollen effect on conspecific pollen performance is unclear, but it may depend on the phylogenetic relatedness of the interactors (pollen donors and recipient). The heterospecific pollen effect might also depend on the extent to which plants are exposed to heterospecific pollen over ecological or evolutionary timescales. For instance, generalist-pollinated plant species might tolerate heterospecific pollen more than specialists. Here, we tested whether heterospecific pollen effects are stronger between closely related species than phylogenetically distant ones in a tropical highland community. Then, based on these results, we determined whether responses to heterospecific pollen were stronger in generalized vs. specialized plant species. We applied heterospecific pollen from close (congeneric) or distant (different families) donors alone or with conspecific pollen on stigmas of three recipient species (one generalist, Sisyrinchium wettsteinii; and two specialists, Fuchsia campos-portoi and Fuchsia regia) and scored pollen tube performance in styles. In all species, pollen from closely related donors grew pollen tubes to the base of the style indicating a high potential to interfere with seed set. Conversely, distantly related heterospecific pollen had no effect on either specialist Fuchsia species, whereas enhanced performance of conspecific pollen was observed in generalist S. wettsteinii. The strong effect of phylogenetic relatedness of donor and recipient might have obscured the role of pollination specialization, at least for the three species examined here. Therefore, phylogenetic relatedness mediated the effect of heterospecific pollen on post-pollination success, with possible consequences for reproductive trait evolution and community assembly for further studies to explore.
PLIDflow: an open-source workflow for the online analysis of protein–ligand docking using galaxy
Authors: Ulzurrun Eugenia , Duarte Yorley , Perez-Wohlfeil Esteban , Gonzalez-Nilo Fernando , Trelles Oswaldo 
Published: May 2020

AbstractMotivationMolecular docking is aimed at predicting the conformation of small-molecule (ligands) within an identified binding site (BS) in a target protein (receptor). Protein–ligand docking plays an important role in modern drug discovery and biochemistry for protein engineering. However, efficient docking analysis of proteins requires prior knowledge of the BS, which is not always known. The process which covers BS identification and protein–ligand docking usually requires the combination of different programs, which require several input parameters. This is furtherly aggravated when factoring in computational demands, such as CPU-time. Therefore, these types of simulation experiments can become a complex process for researchers without a background in computer sciences.ResultsTo overcome these problems, we have designed an automatic computational workflow (WF) to process protein–ligand complexes, which runs from the identification of the possible BSs positions to the prediction of the experimental binding modes and affinities of the ligand. This open-access WF runs under the Galaxy platform that integrates public domain software. The results of the proposed method are in close agreement with state-of-the-art docking software.Availability and implementationSoftware is available at: https://pistacho.ac.uma.es/galaxy-bitlab.Contacteuv@uma.esSupplementary informationSupplementary data are available at Bioinformatics online.
Dataset-aware multi-task learning approaches for biomedical named entity recognition
Authors: Zuo Mei , Zhang Yang 
Published: May 2020

Abstract

Motivation
Named entity recognition is a critical and fundamental task for biomedical text mining. Recently, researchers have focused on exploiting deep neural networks for biomedical named entity recognition (Bio-NER). The performance of deep neural networks on a single dataset mostly depends on data quality and quantity while high-quality data tends to be limited in size. To alleviate task-specific data limitation, some studies explored the multi-task learning (MTL) for Bio-NER and achieved state-of-the-art performance. However, these MTL methods did not make full use of information from various datasets of Bio-NER. The performance of state-of-the-art MTL method was significantly limited by the number of training datasets.

Results
We propose two dataset-aware MTL approaches for Bio-NER which jointly train all models for numerous Bio-NER datasets, thus each of these models could discriminatively exploit information from all of related training datasets. Both of our two approaches achieve substantially better performance compared with the state-of-the-art MTL method on 14 out of 15 Bio-NER datasets. Furthermore, we implemented our approaches by incorporating Bio-NER and biomedical part-of-speech (POS) tagging datasets. The results verify Bio-NER and POS can significantly enhance one another.

Availability and implementation
Our source code is available at https://github.com/zmmzGitHub/MTL-BC-LBC-BioNER and all datasets are publicly available at https://github.com/cambridgeltl/MTL-Bioinformatics-2016.

Supplementary information
Supplementary data are available at Bioinformatics online.
Feature selection and classification of noisy proteomics mass spectrometry data based on one-bit perturbed compressed sensing
Authors: Xu Wenbo , Tian Yan , Wang Siye , Cui Yupeng 
Published: May 2020

Abstract

Motivation
The classification of high-throughput protein data based on mass spectrometry (MS) is of great practical significance in medical diagnosis. Generally, MS data are characterized by high dimension, which inevitably leads to prohibitive cost of computation. To solve this problem, one-bit compressed sensing (CS), which is an extreme case of quantized CS, has been employed on MS data to select important features with low dimension. Though enjoying remarkably reduction of computation complexity, the current one-bit CS method does not consider the unavoidable noise contained in MS dataset, and does not exploit the inherent structure of the underlying MS data.

Results
We propose two feature selection (FS) methods based on one-bit CS to deal with the noise and the underlying block-sparsity features, respectively. In the first method, the FS problem is modeled as a perturbed one-bit CS problem, where the perturbation represents the noise in MS data. By iterating between perturbation refinement and FS, this method selects the significant features from noisy data. The second method formulates the problem as a perturbed one-bit block CS problem and selects the features block by block. Such block extraction is due to the fact that the significant features in the first method usually cluster in groups. Experiments show that, the two proposed methods have better classification performance for real MS data when compared with the existing method, and the second one outperforms the first one.

Availability and implementation
The source code of our methods is available at: https://github.com/tianyan8023/OBCS.

Supplementary information
Supplementary data are available at Bioinformatics online.
Testing repeatability, measurement error and species differentiation when using geometric morphometrics on complex shapes: a case study of Patagonian lizards of the genus Liolaemus (Squamata: Liolaemini)
Authors: Vrdoljak Juan , Sanchez Kevin Imanol , Arreola-Ramos Roberto , Diaz Huesa Emilce Guadalupe , Villagra Alejandro , Avila Luciano Javier , Morando Mariana 
Published: May 2020

AbstractThe repeatability of findings is the key factor behind scientific reliability, and the failure to reproduce scientific findings has been termed the ‘replication crisis’. Geometric morphometrics is an established tool in evolutionary biology. However, different operators (and/or different methods) could act as large sources of variation in the data obtained. Here, we investigated inter-operator error in geometric morphometric protocols on complex shapes of Liolaemus lizards, as well as measurement error in three taxa varying in their difficulty of digitalization. We also examined the potential for these protocols to discriminate among complex shapes in closely related species. We found a wide range of inter-operator error, contributing between 19.5% and 60% to the total variation. Moreover, measurement error increased with the complexity of the quantified shape. All protocols were able to discriminate between species, but the use of more landmarks did not imply better performance. We present evidence that complex shapes reduce repeatability, highlighting the need to explore different sources of variation that could lead to such low repeatability. Lastly, we suggest some recommendations to improve the repeatability and reliability of geometric morphometrics results.
Ontogenetic and static allometry in the skull and cranial units of nine-banded armadillos (Cingulata: Dasypodidae:Dasypus novemcinctus)
Authors: Le Verger Kévin , Hautier Lionel , Bardin Jérémie , Gerber Sylvain , Delsuc Frédéric , Billet Guillaume 
Published: May 2020

AbstractA large part of extant and past mammalian morphological diversity is related to variation in size through allometric effects. Previous studies suggested that craniofacial allometry is the dominant pattern underlying mammalian skull shape variation, but cranial allometries were rarely characterized within cranial units such as individual bones. Here, we used 3D geometric morphometric methods to study allometric patterns of the whole skull (global) and of cranial units (local) in a postnatal developmental series of nine-banded armadillos (Dasypus novemcinctus ssp.). Analyses were conducted at the ontogenetic and static levels, and for successive developmental stages. Our results support craniofacial allometry as the global pattern along with more local allometric trends, such as the relative posterior elongation of the infraorbital canal, the tooth row reduction on the maxillary, and the marked development of nuchal crests on the supraoccipital with increasing skull size. Our study also reports allometric proportions of shape variation varying substantially among cranial units and across ontogenetic stages. The multi-scale approach advocated here allowed unveiling previously unnoticed allometric variations, indicating an untapped complexity of cranial allometric patterns to further explain mammalian morphological evolution.
SLC12A2 variants cause a neurodevelopmental disorder or cochleovestibular defect
Authors: McNeill Alisdair , Iovino Emanuela , Mansard Luke , Vache Christel , Baux David , Bedoukian Emma , Cox Helen , Dean John , Goudie David , Kumar Ajith , Newbury-Ecob Ruth , Fallerini Chiara , Renieri Alessandra , Lopergolo Diego , Mari Francesca , Blanchet Catherine , Willems Marjolaine , Roux Anne-Francoise , Pippucci Tommaso , Delpire Eric 
Published: May 2020

Abstract
The SLC12 gene family consists of SLC12A1–SLC12A9, encoding electroneutral cation-coupled chloride co-transporters. SCL12A2 has been shown to play a role in corticogenesis and therefore represents a strong candidate neurodevelopmental disorder gene. Through trio exome sequencing we identified de novo mutations in SLC12A2 in six children with neurodevelopmental disorders. All had developmental delay or intellectual disability ranging from mild to severe. Two had sensorineural deafness. We also identified SLC12A2 variants in three individuals with non-syndromic bilateral sensorineural hearing loss and vestibular areflexia. The SLC12A2 de novo mutation rate was demonstrated to be significantly elevated in the deciphering developmental disorders cohort. All tested variants were shown to reduce co-transporter function in Xenopus laevis oocytes. Analysis of SLC12A2 expression in foetal brain at 16–18 weeks post-conception revealed high expression in radial glial cells, compatible with a role in neurogenesis. Gene co-expression analysis in cells robustly expressing SLC12A2 at 16–18 weeks post-conception identified a transcriptomic programme associated with active neurogenesis. We identify SLC12A2 de novo mutations as the cause of a novel neurodevelopmental disorder and bilateral non-syndromic sensorineural hearing loss and provide further data supporting a role for this gene in human neurodevelopment.
Quantifying the Polygenic Architecture of the Human Cerebral Cortex: Extensive Genetic Overlap between Cortical Thickness and Surface Area
Authors: van der Meer Dennis , Frei Oleksandr , Kaufmann Tobias , Chen Chi-Hua , Thompson Wesley K , O’Connell Kevin S , Monereo Sánchez Jennifer , Linden David E J , Westlye Lars T , Dale Anders M , Andreassen Ole A 
Published: May 2020

Abstract
The thickness of the cerebral cortical sheet and its surface area are highly heritable traits thought to have largely distinct polygenic architectures. Despite large-scale efforts, the majority of their genetic determinants remain unknown. Our ability to identify causal genetic variants can be improved by employing brain measures that better map onto the biology we seek to understand. Such measures may have fewer variants but with larger effects, that is, lower polygenicity and higher discoverability. Using Gaussian mixture modeling, we estimated the number of causal variants shared between mean cortical thickness and total surface area, as well as the polygenicity and discoverability of regional measures. We made use of UK Biobank data from 30 880 healthy White European individuals (mean age 64.3, standard deviation 7.5, 52.1% female). We found large genetic overlap between total surface area and mean thickness, sharing 4016 out of 7941 causal variants. Regional surface area was more discoverable (P = 2.6 × 10−6) and less polygenic (P = 0.004) than regional thickness measures. These findings may serve as a roadmap for improved future GWAS studies; knowledge of which measures are most discoverable may be used to boost identification of genetic predictors and thereby gain a better understanding of brain morphology.
Progress Towards Elimination of Hepatitis C Infection Among People Who Inject Drugs in Australia: The ETHOS Engage Study
Authors: Valerio Heather , Alavi Maryam , Silk David , Treloar Carla , Martinello Marianne , Milat Andrew , Dunlop Adrian , Holden Jo , Henderson Charles , Amin Janaki , Read Phillip , Marks Philippa , Degenhardt Louisa , Hayllar Jeremy , Reid David , Gorton Carla , Lam Thao , Dore Gregory J , Grebely Jason 
Published: May 2020

AbstractBackgroundEvaluating progress towards hepatitis C virus (HCV) elimination is critical. This study estimated prevalence of current HCV infection and HCV treatment uptake among people who inject drugs (PWID) in Australia.MethodsThe Enhancing Treatment of Hepatitis C in Opioid Substitution Settings Engage is an observational study of PWID attending drug treatment clinics and needle and syringe programs (NSPs). Participants completed a questionnaire including self-reported treatment history and underwent point-of-care HCV RNA testing (Xpert HCV Viral Load Fingerstick; Cepheid).ResultsBetween May 2018 and September 2019, 1443 participants were enrolled (64% injected drugs in the last month, 74% receiving opioid agonist therapy [OAT]). HCV infection status was uninfected (28%), spontaneous clearance (16%), treatment-induced clearance (32%), and current infection (24%). Current HCV was more likely among people who were homeless (adjusted odds ratio, 1.47; 95% confidence interval, 1.00–2.16), incarcerated in the previous year (2.04; 1.38–3.02), and those injecting drugs daily or more (2.26; 1.43–2.42). Among those with previous chronic or current HCV, 66% (n = 520/788) reported HCV treatment. In adjusted analysis, HCV treatment was lower among females (.68; .48–.95), participants who were homeless (.59; .38–.96), and those injecting daily or more (.51; .31–.89). People aged ≥45 years (1.46; 1.06–2.01) and people receiving OAT (2.62; 1.52–4.51) were more likely to report HCV treatment.ConclusionsUnrestricted direct-acting antiviral therapy access in Australia has yielded high treatment uptake among PWID attending drug treatment and NSPs, with a marked decline in HCV prevalence. To achieve elimination, PWID with greater marginalization may require additional support and tailored strategies to enhance treatment.
Partial Protective Effect of Bivalent Human Papillomavirus 16/18 Vaccination Against Anogenital Warts in a Large Cohort of Dutch Primary Care Patients
Authors: Woestenberg Petra J , Guevara Morel Alejandra E , Bogaards Johannes A , Hooiveld Mariëtte , Schurink-van ‘t Klooster Tessa M , Hoebe Christian J P A , van der Sande Marianne A B , van Benthem Birgit H B 
Published: May 2020

Abstract

Background
There is ongoing debate about the possible protective effect of the bivalent human papillomavirus (2vHPV) vaccine, targeting oncogenic types HPV-16/18, against anogenital warts (AGWs), commonly attributed to HPV-6/11. We performed a retrospective registry-based open cohort study to assess the effect of 2vHPV vaccination on AGWs.

Methods
We linked general practice (ie, primary care) data from women born between 1993 and 2002, who had been eligible for HPV vaccination in the Netherlands, to the Dutch national immunization registry on an individual level. Women were followed until their first AGW diagnosis or end of follow-up. Adjusted incidence rate ratios (aIRRs) were estimated using Poisson regression with vaccination status as a time-dependent exposure.

Results
We linked data of 96 468 women with a total of 328 019 years observation time and 613 AGW diagnoses (incidence: 1.87/1000 person-years). At the end of follow-up, 61% were 2vHPV vaccinated (≥ 1 dose) of whom 91% were fully vaccinated. The AGW incidence was lower among those with ≥ 1 dose vs 0 doses (aIRR, 0.75 [95% confidence interval {CI}, .64–.88]). The effect of vaccination was stronger after full vaccination (aIRR, 0.72 [95% CI, .61–.86]) and for women who were offered vaccination at 12–13 years of age (aIRR, 0.69 [95% CI, .51–.93]) vs those at 13–16 years of age (aIRR, 0.77 [95% CI, .64–.93]).

Conclusions
This is the largest population-based study so far to examine the effect of 2vHPV vaccination on AGWs, with reliable individual information on AGW diagnoses and vaccination status. The results indicate that 2vHPV vaccination partially protects against AGWs, especially when administered in early adolescence.
Analysis of the Infection Status of Healthcare Workers in Wuhan During the COVID-19 Outbreak: A Cross-sectional Study
Authors: Zheng Lichun , Wang Xiang , Zhou Chongchong , Liu Qin , Li Shuang , Sun Qin , Wang Mengjia , Zhou Qian , Wang Wenmei 
Published: May 2020

Abstract

Background
Healthcare workers (HCWs) at the frontline are facing a substantial risk of infection during the coronavirus disease 2019 (COVID-19) outbreak.

Methods
We acquired information and data on general information on and infection and death status of HCWs in Wuhan during the COVID-19 outbreak and completed statistical analyses.

Results
We obtained the data on 2457 infected cases among HCWs in Wuhan, China. More than half of the infected individuals were nurses (52.06%), whereas 33.62% of infected cases were doctors and 14.33% of cases were medical staff. In particular, the case infection rate of nurses (2.22%) was remarkably higher than that of doctors (1.92%). Most infected cases among HCWs were female (72.28%). A majority of the infected HCWs (89.26%) came from general hospitals, followed by specialized hospitals (5.70%) and community hospitals (5.05%). The case infection rate of HCWs (2.10%) was dramatically higher than that of non-HCWs (0.43%). The case fatality rate of HCWs (0.69%) was significantly lower than that of non-HCWs (5.30%).

Conclusions
The infection risk of HCWs is clearly higher than that of non-HCWs. HCWs play an essential role in fighting the pandemic. The analysis of the infection status of HCWs is essential to attract enough attention from the public, provide effective suggestions for government agencies, and improve protective measures for HCWs.
Local Pollination-Based Moth Search Algorithm for Task-Scheduling Heterogeneous Cloud Environment
Authors: Gokuldhev M , Singaravel G 
Published: May 2020

Abstract
Nowadays, Cloud computing is a new computing model in the field of information technology and research. Generally, the cloud environment aims in providing the resource that depends upon the user’s necessity. The major problem caused by cloud computing is task scheduling. Nevertheless, the previous scheduling methods concentrate only on the resource needs, memory, implementation time and cost. In this paper, we introduced an optimal task-scheduling algorithm of the local pollination-based moth search algorithm (LPMSA), which is the hybridization of moth search algorithm (MSA) and flower pollination algorithm (FPA). The proposed LPMSA chooses an optimal solution for proper task scheduling in the cloud. Moreover, the exploitation capacity of MSA is improved by using the local search of the FPA algorithm. In this work, we use 2-fold simulation processes that are implemented under the platform of JAVA. The proposed LPMSA for task-scheduling performance is evaluated using low and high heterogeneous machines with uniform and non-uniform parameters. The experimental analysis demonstrates that the proposed LPMSA approach is well suitable for cloud task scheduling thereby reducing the makespan and energy consumption during proper task scheduling.
Mismatched light and temperature cues disrupt locomotion and energetics via thyroid-dependent mechanisms
Authors: Le Roy Amélie , Seebacher Frank 
Published: May 2020

AbstractAnimals integrate information from different environmental cues to maintain performance across environmental gradients. Increasing average temperature and variability induced by climate change can lead to mismatches between seasonal cues. We used mosquitofish (Gambusia holbrooki) to test the hypotheses that mismatches between seasonal temperature and light regimes (short days and warm temperature and vice versa) decrease swimming performance, metabolic rates and mitochondrial efficiency and that the responses to light and temperature are mediated by thyroid hormone. We show that day length influenced thermal acclimation of swimming performance through thyroid-dependent mechanisms. Oxygen consumption rates were influenced by acclimation temperature and thyroid hormone. Mitochondrial substrate oxidation rates (state three rates) were modified by the interaction between temperature and day length, and mitochondrial efficiency (P/O ratios) increased with warm acclimation. Using P/O ratios to calibrate metabolic (oxygen consumption) scope showed that oxygen consumption did not predict adenosine triphosphate (ATP) production. Unlike oxygen consumption, ATP production was influenced by day length in a thyroid-dependent manner. Our data indicate that oxygen consumption alone should not be used as a predictor of ATP production. Overall, the effects of thyroid hormone on locomotion and energetics were reversed by mismatches such as warm temperatures on short days. We predict that mid to high latitudes in North America and Asia will be particularly affected by mismatches as a result of high seasonality and predicted warming over the next 50 years.