bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantification of aneuploidy in targeted sequencing data using ASCETS
Authors: Spurr Liam F , Touat Mehdi , Taylor Alison M , Dubuc Adrian M , Shih Juliann , Meredith David M , Pisano William V , Meyerson Matthew L , Ligon Keith L , Cherniack Andrew D , Li Yvonne Y , Beroukhim Rameen 
Published: November 2020

Abstract

Summary
The expansion of targeted panel sequencing efforts has created opportunities for large-scale genomic analysis, but tools for copy-number quantification on panel data are lacking. We introduce ASCETS, a method for the efficient quantitation of arm and chromosome-level copy-number changes from targeted sequencing data.

Availability and implementation
ASCETS is implemented in R and is freely available to non-commercial users on GitHub: https://github.com/beroukhim-lab/ascets, along with detailed documentation.

Supplementary information
Supplementary data are available at Bioinformatics online.
Robustifying genomic classifiers to batch effects via ensemble learning
Authors: Zhang Yuqing , Patil Prasad , Johnson W. Evan , Parmigiani Giovanni 
Published: November 2020

AbstractMotivationGenomic data are often produced in batches due to practical restrictions, which may lead to unwanted variation in data caused by discrepancies across batches. Such ‘batch effects’ often have negative impact on downstream biological analysis and need careful consideration. In practice, batch effects are usually addressed by specifically designed software, which merge the data from different batches, then estimate batch effects and remove them from the data. Here, we focus on classification and prediction problems, and propose a different strategy based on ensemble learning. We first develop prediction models within each batch, then integrate them through ensemble weighting methods.ResultsWe provide a systematic comparison between these two strategies using studies targeting diverse populations infected with tuberculosis. In one study, we simulated increasing levels of heterogeneity across random subsets of the study, which we treat as simulated batches. We then use the two methods to develop a genomic classifier for the binary indicator of disease status. We evaluate the accuracy of prediction in another independent study targeting a different population cohort. We observed that in independent validation, while merging followed by batch adjustment provides better discrimination at low level of heterogeneity, our ensemble learning strategy achieves more robust performance, especially at high severity of batch effects. These observations provide practical guidelines for handling batch effects in the development and evaluation of genomic classifiers.Availability and implementationThe data underlying this article are available in the article and in its online supplementary material. Processed data is available in the Github repository with implementation code, at https://github.com/zhangyuqing/bea_ensemble.Supplementary informationSupplementary data are available at Bioinformatics online.
Climatic control of mat vegetation communities on inselberg archipelagos in south-eastern Brazil
Authors: De Paula Luiza F A , Forzza Rafaela Campostrini , Azevedo Luísa O , Bueno Marcelo L , Solar Ricardo R C , Vanschoenwinkel Bram , Porembski Stefan 
Published: November 2020

AbstractGranite and/or gneiss inselbergs are excellent examples of geomorphologically stable island habitats, considered as old, climatically buffered, infertile landscapes (OCBILs). However, unlike oceanic islands, their underlying drivers of diversity patterns remain to be investigated. Here, we studied 24 inselbergs in south-eastern Brazil, aiming to understand the role of landscape variables and environmental conditions in the assembly of the characteristic extremophilic mat vegetation communities. We found that beta diversity was largely explained by climatic variables, whereas species richness did not vary among inselbergs. Classic determinants of the diversity of island communities do not generally seem to apply to these plant assemblages. Overall, these communities change along a coast-to-inland gradient that captures increased seasonality with a replacement of more hydrophilic taxa by more drought-tolerant taxa. Changes in species composition in space involved strong species replacement, with several widespread genera locally represented on distinct inselbergs by different narrowly distributed species. Despite the deterministic sorting of taxa based on climatic conditions, a substantial fraction of the beta diversity remained unexplained. This underlines the importance of historical processes, which are easier to notice in stable OCBIL regions, such as range expansion, local extinction, dispersal constraints and allopatric speciation.
Male hybrid sterility in the cattle-yak and other bovines: a review
Authors: Niayale Robert , Cui Yan , Adzitey Fredrick 
Published: November 2020

Abstract
Hybridization is important for both animal breeders attempting to fix new phenotypic traits and researchers trying to unravel the mechanism of reproductive barriers in hybrid species and the process of speciation. In interspecies animal hybrids, gains made in terms of adaptation to environmental conditions and hybrid vigor may be offset by reduced fertility or sterility. Bovine hybrids exhibit remarkable hybrid vigor compared to their parents. However, the F1 male hybrid exhibits sterility, whereas the female is fertile. This male-biased sterility is consistent with the Haldane rule where heterogametic sex is preferentially rare, absent, or sterile in the progeny of two different species. The obstacle of fixing favorable traits and passing them to subsequent generations due to the male sterility is a major setback in improving the reproductive potential of bovines through hybridization. Multiperspective approaches such as molecular genetics, proteomics, transcriptomics, physiology, and endocrinology have been used by several researchers over the past decade in an attempt to unravel the potential mechanisms underlying male hybrid sterility. However, the mechanism of sterility in the hybrid male is still not completely unravelled. This review seeks to provide an update of the mechanisms of the sterility in the cattle-yak and other bovines.
PET-MRI nanoparticles imaging of blood–brain barrier damage and modulation after stroke reperfusion
Authors: Debatisse Justine , Eker Omer Faruk , Wateau Océane , Cho Tae-Hee , Wiart Marlène , Ramonet David , Costes Nicolas , Mérida Inés , Léon Christelle , Dia Maya , Paillard Mélanie , Confais Joachim , Rossetti Fabien , Langlois Jean-Baptiste , Troalen Thomas , Iecker Thibaut , Le Bars Didier , Lancelot Sophie , Bouchier Baptiste , Lukasziewicz Anne-Claire , Oudotte Adrien , Nighoghossian Norbert , Ovize Michel , Contamin Hugues , Lux François , Tillement Olivier , Canet-Soulas Emmanuelle 
Published: November 2020

Abstract
In an acute ischaemic stroke, understanding the dynamics of blood–brain barrier injury is of particular importance for the prevention of symptomatic haemorrhagic transformation. However, the available techniques assessing blood–brain barrier permeability are not quantitative and are little used in the context of acute reperfusion therapy. Nanoparticles cross the healthy or impaired blood–brain barrier through combined passive and active processes. Imaging and quantifying their transfer rate could better characterize blood–brain barrier damage and refine the delivery of neuroprotective agents. We previously developed an original endovascular stroke model of acute ischaemic stroke treated by mechanical thrombectomy followed by positron emission tomography-magnetic resonance imaging. Cerebral capillary permeability was quantified for two molecule sizes: small clinical gadolinium Gd-DOTA (&lt;1 nm) and AGuIX® nanoparticles (∼5 nm) used for brain theranostics. On dynamic contrast-enhanced magnetic resonance imaging, the baseline transfer constant Ktrans was 0.94 [0.48, 1.72] and 0.16 [0.08, 0.33] ×10−3 min−1, respectively, in the normal brain parenchyma, consistent with their respective sizes, and 1.90 [1.23, 3.95] and 2.86 [1.39, 4.52] ×10−3 min−1 in choroid plexus, confirming higher permeability than brain parenchyma. At early reperfusion, Ktrans for both Gd-DOTA and AGuIX® nanoparticles was significantly higher within the ischaemic area compared to the contralateral hemisphere; 2.23 [1.17, 4.13] and 0.82 [0.46, 1.87] ×10−3 min−1 for Gd-DOTA and AGuIX® nanoparticles, respectively. With AGuIX® nanoparticles, Ktrans also increased within the ischaemic growth areas, suggesting added value for AGuIX®. Finally, Ktrans was significantly lower in both the lesion and the choroid plexus in a drug-treated group (ciclosporin A, n = 7) compared to placebo (n = 5). Ktrans quantification with AGuIX® nanoparticles can monitor early blood–brain barrier damage and treatment effect in ischaemic stroke after reperfusion.
Pterostilbene accelerates wound healing by modulating diabetes-induced estrogen receptor β suppression in hematopoietic stem cells
Authors: Xie Weiguo , Zhou Xueqing , Hu Weigang , Chu Zhigang , Ruan Qiongfang , Zhang Haimou , Li Min , Zhang Hongyu , Huang Xiaodong , Yao Paul 
Published: November 2020

Abstract

Background
Delayed wound healing is one of the major complications of diabetes mellitus and is characterized by prolonged inflammation, delayed re-epithelialization and consistent oxidative stress, although the detailed mechanism remains unknown. In this study, we aimed to investigate the potential role and effect of pterostilbene (PTE) and hematopoietic stem cells (HSCs) on diabetic wound healing.

Methods
Diabetic rats were used to measure the epigenetic changes in both HSCs and peripheral blood mononuclear cells (PBMCs). A cutaneous burn injury was induced in the rats and PTE-treated diabetic HSCs were transplanted for evaluation of wound healing. In addition, several biomedical parameters, including gene expression, oxidative stress, mitochondrial function and inflammation in macrophages, were also measured.

Results
Our data showed that PTE had a much stronger effect than resveratrol on accelerating diabetic wound healing, likely because PTE can ameliorate diabetes-induced epigenetic changes to estrogen receptor β promoter in HSCs, while resveratrol cannot. Further investigation showed that bone marrow transplantation of PTE-treated diabetic HSCs restores diabetes-induced suppression of estrogen receptor β and its target genes, including nuclear respiratory factor-1 and superoxide dismutase 2, and protects against diabetes-induced oxidative stress, mitochondrial dysfunction and elevated pro-inflammatory cytokines in both PBMCs and macrophages, subsequently accelerating cutaneous wound healing.

Conclusions
HSC may play an important role in wound healing through transferring epigenetic modifications to subsequent PBMCs and macrophages by differentiation, while PTE accelerates diabetic wound healing by modulating diabetes-induced epigenetic changes in HSCs. Thus, PTE may be a novel therapeutic strategy for diabetic wound healing.
Evaluating mucus exudation dynamics through isotopic enrichment and turnover of skin mucus fractions in a marine fish model
Authors: Ordóñez-Grande Borja , Fernández-Alacid Laura , Sanahuja Ignasi , Sánchez-Nuño Sergio , Fernández-Borràs Jaume , Blasco Josefina , Ibarz Antoni 
Published: November 2020

Abstract
Fish skin mucus is composed of insoluble components, which form the physical barrier, and soluble components, which are key for interrelationship functions. Mucus is continuously secreted, but rates of production and exudation are still unknown, as are the underlying mechanisms. Using stable isotope analysis, here, we evaluate skin mucus turnover and renewal in gilthead sea bream, separating raw mucus and its soluble and insoluble fractions. Isotopic abundance analysis reveals no differences between mucus and white muscle, thus confirming mucus samples as reliable non-invasive biomarkers. Mucus production was evaluated using a single labelled meal packaged in a gelatine capsule, with both 13C and 15N, via a time-course trial. 13C was gradually allocated to skin mucus fractions over the first 12 h and was significantly (4-fold) higher in the soluble fraction, indicating a higher turnover of soluble mucus components that are continuously produced and supplied. 15N was also gradually allocated to mucus, indicating incorporation of new proteins containing the labelled dietary amino acids, but with no differences between fractions. When existent mucus was removed, dietary stable isotopes revealed stimulated mucus neoformation dependent on the components. All this is novel knowledge concerning skin mucus dynamics and turnover in fish and could offer interesting non-invasive approaches to the use of skin mucus production in ecological or applied biological studies such as climate change effects, human impact, alterations in trophic networks or habitat degradation, especially of wild-captured species or protected species.
“Daughterlands”: Personal and Political Mappings in Scottish Women’s Poetry
Authors: Norquay Glenda 
Published: November 2020

AbstractScottish women’s poetry in recent years has evinced an interest in mapping daughterhood, frequently through linguistic negatives that challenge binary thinking. This essay argues that such “daughterlands” offer an imaginative alternative to the more familiar “motherland”: encompassing past, present, and future and positioning women in multiple roles, they have played a transformative role in the poetic imagining of “Scotland” in the new millennium. The essay considers the deployment of daughterly spaces by influential writers such as Carol Ann Duffy, Liz Lochhead, Jackie Kay, and Kathleen Jamie and then traces more recent instantiations by a younger generation of poets such as Claire Askew, Theresa Muñoz, and Em Strang. In conclusion, it demonstrates the experiential and metaphoric potential of daughterhood for shaping broad political thinking in an explicitly public poem by Kay.
A hybrid approach toward biomedical relation extraction training corpora: combining distant supervision with crowdsourcing
Authors: Sousa Diana , Lamurias Andre , Couto Francisco M 
Published: November 2020

AbstractBiomedical relation extraction (RE) datasets are vital in the construction of knowledge bases and to potentiate the discovery of new interactions. There are several ways to create biomedical RE datasets, some more reliable than others, such as resorting to domain expert annotations. However, the emerging use of crowdsourcing platforms, such as Amazon Mechanical Turk (MTurk), can potentially reduce the cost of RE dataset construction, even if the same level of quality cannot be guaranteed. There is a lack of power of the researcher to control who, how and in what context workers engage in crowdsourcing platforms. Hence, allying distant supervision with crowdsourcing can be a more reliable alternative. The crowdsourcing workers would be asked only to rectify or discard already existing annotations, which would make the process less dependent on their ability to interpret complex biomedical sentences. In this work, we use a previously created distantly supervised human phenotype–gene relations (PGR) dataset to perform crowdsourcing validation. We divided the original dataset into two annotation tasks: Task 1, 70% of the dataset annotated by one worker, and Task 2, 30% of the dataset annotated by seven workers. Also, for Task 2, we added an extra rater on-site and a domain expert to further assess the crowdsourcing validation quality. Here, we describe a detailed pipeline for RE crowdsourcing validation, creating a new release of the PGR dataset with partial domain expert revision, and assess the quality of the MTurk platform. We applied the new dataset to two state-of-the-art deep learning systems (BiOnt and BioBERT) and compared its performance with the original PGR dataset, as well as combinations between the two, achieving a 0.3494 increase in average F-measure. The code supporting our work and the new release of the PGR dataset is available at https://github.com/lasigeBioTM/PGR-crowd.
ncVarDB: a manually curated database for pathogenic non-coding variants and benign controls
Authors: Biggs Harry , Parthasarathy Padmini , Gavryushkina Alexandra , Gardner Paul P 
Published: November 2020

AbstractVariants within the non-coding genome are frequently associated with phenotypes in genome-wide association studies. These non-coding regions may be involved in the regulation of gene expression, encode functional non-coding RNAs, or influence splicing and other cellular functions. We have curated a list of characterized non-coding human genome variants based on the published evidence that indicates phenotypic consequences of the variation. In order to minimize annotation errors, two curators have independently verified the supporting evidence for pathogenicity of each non-coding variant in the published literature. The database consists of 721 non-coding variants linked to the published literature describing the evidence of functional consequences. We have also sampled 7228 covariate-matched benign controls, that have a population frequency of over 5%, from the single nucleotide polymorphism database (dbSNP151) database. These were sampled controlling for potential confounding factors such as linkage with pathogenic variants, annotation type (untranslated region, intron, intergenic, etc.) and variant type (substitution or indel). The dataset presented here represents a curated repository, with a potential use for the training or evaluation of algorithms used in the prediction of non-coding variant functionality.Database URL: https://github.com/Gardner-BinfLab/ncVarDB.
Evolutionary History of Mitochondrial Genomes in Discoba, Including the Extreme Halophile Pleurostomum flabellatum (Heterolobosea)
Authors: Ettahi Khaoula , Lhee Duckhyun , Sung Ji Yeon , Simpson Alastair G B , Park Jong Soo , Yoon Hwan Su 
Published: November 2020

Abstract
Data from Discoba (Heterolobosea, Euglenozoa, Tsukubamonadida, and Jakobida) are essential to understand the evolution of mitochondrial genomes (mitogenomes), because this clade includes the most primitive-looking mitogenomes known, as well some extremely divergent genome information systems. Heterolobosea encompasses more than 150 described species, many of them from extreme habitats, but only six heterolobosean mitogenomes have been fully sequenced to date. Here we complete the mitogenome of the heterolobosean Pleurostomum flabellatum, which is extremely halophilic and reportedly also lacks classical mitochondrial cristae, hinting at reduction or loss of respiratory function. The mitogenome of P. flabellatum maps as a 57,829-bp-long circular molecule, including 40 coding sequences (19 tRNA, two rRNA, and 19 orfs). The gene content and gene arrangement are similar to Naegleria gruberi and Naegleria fowleri, the closest relatives with sequenced mitogenomes. The P. flabellatum mitogenome contains genes that encode components of the electron transport chain similar to those of Naegleria mitogenomes. Homology searches against a draft nuclear genome showed that P. flabellatum has two homologs of the highly conserved Mic60 subunit of the MICOS complex, and likely lost Mic19 and Mic10. However, electron microscopy showed no cristae structures. We infer that P. flabellatum, which originates from high salinity (313‰) water where the dissolved oxygen concentration is low, possesses a mitochondrion capable of aerobic respiration, but with reduced development of cristae structure reflecting limited use of this aerobic capacity (e.g., microaerophily).
Ambient noise correlation analysis of S-net records: extracting surface wave signals below instrument noise levels
Authors: Takagi Ryota , Toyokuni Genti , Chikasada Naotaka 
Published: November 2020

SUMMARY
We applied ambient noise cross-correlation analysis to the cabled ocean bottom seismic network offshore northeast Japan (Seafloor observation network for earthquakes and tsunamis along the Japan Trench: S-net) to extract surface waves propagating in the ocean area of the forearc region. We found two types of peculiar pulses in the cross-correlation functions (CCFs) of ambient seismic noise records: periodic pulses mainly every minute and sharp pulses around the lag time zero. These pulses strongly contaminate the surface wave signals in the CCFs at frequencies below ∼0.1 Hz. The periodic pulses originate from periodic instrument noises, while the zero-lag pulses originate from random instrument noises which are coherent within station pairs. By developing solutions to remove the periodic and zero-lag pulses based on the characteristics of the pulses, we succeeded in extracting Rayleigh and Love wave signals from the S-net records at 0.03–0.3 Hz, while the surface wave signals at 0.03–0.1 Hz were not visible without the application of these solutions. These solutions widen the frequency range of analysis, and may be applicable to other seismic networks, particularly to recent dense but non-broad-band networks. We identified the fundamental and first higher modes of Rayleigh waves and the fundamental mode of the Love wave. The extracted surface wave signals can constrain the shear wave velocity structure from the sediment to seismogenic zone around the megathrust plate boundary in the forearc region.
Intruders in a Balancing Act: Black Economic Empowerment, Transitional Justice and Investment Arbitration Tribunals
Authors: Le Moli Ginevra 
Published: November 2020

Abstract
This article examines the role of ad hoc investment arbitration tribunals in arbitrating highly sensitive matters in transitional justice contexts, focusing on disputes arising from black economic empowerment (BEE) policies in countries formerly under racially discriminatory regimes. After an overview of the investment protection system, the article introduces the historical context of BEE policies. It subsequently analyses three main disputes, one against South Africa and two against Zimbabwe, where white concession holders and landowners relied on Bilateral Investment Treaties to claim compensation for the consequences of BEE mining and land redistribution policies. These disputes provide a testing ground to shed light on the role of investment arbitration in the context of transitional justice. The article concludes that such a role essentially amounts to an intrusion in the perilous ‘balancing act’ of managing a transitional justice process.