bluuebunny/crossref_metadata_2025_split huggingface dataset:
BEM: Mining Coregulation Patterns in Transcriptomics via Boolean Matrix Factorization
Authors: Liang Lifan , Zhu Kunju , Lu Songjian 
Published: January 2020

Abstract

Motivation
The matrix factorization is an important way to analyze coregulation patterns in transcriptomic data, which can reveal the tumor signal perturbation status and subtype classification. However, current matrix factorization methods do not provide clear bicluster structure. Furthermore, these algorithms are based on the assumption of linear combination, which may not be sufficient to capture the coregulation patterns.

Results
We presented a new algorithm for Boolean matrix factorization (BMF) via expectation maximization (BEM). BEM is more aligned with the molecular mechanism of transcriptomic coregulation and can scale to matrix with over 100 million data points. Synthetic experiments showed that BEM outperformed other BMF methods in terms of reconstruction error. Real-world application demonstrated that BEM is applicable to all kinds of transcriptomic data, including bulk RNA-seq, single-cell RNA-seq and spatial transcriptomic datasets. Given appropriate binarization, BEM was able to extract coregulation patterns consistent with disease subtypes, cell types or spatial anatomy.

Availability and implementation
Python source code of BEM is available on https://github.com/LifanLiang/EM_BMF.

Supplementary information
Supplementary data are available at Bioinformatics online.
A Possible Mechanism behind Faster Clearance and Higher Peak Concentrations of Cardiac Troponin I Compared with Troponin T in Acute Myocardial Infarction
Authors: Starnberg Karin , Fridén Vincent , Muslimovic Aida , Ricksten Sven-Erik , Nyström Susanne , Forsgard Niklas , Lindahl Bertil , Vukusic Kristina , Sandstedt Joakim , Dellgren Göran , Hammarsten Ola 
Published: January 2020

AbstractBackgroundAlthough cardiac troponin I (cTnI) and troponin T (cTnT) form a complex in the human myocardium and bind to thin filaments in the sarcomere, cTnI often reaches higher concentrations and returns to normal concentrations faster than cTnT in patients with acute myocardial infarction (MI).MethodsWe compared the overall clearance of cTnT and cTnI in rats and in patients with heart failure and examined the release of cTnT and cTnI from damaged human cardiac tissue in vitro.ResultsGround rat heart tissue was injected into the quadriceps muscle in rats to simulate myocardial damage with a defined onset. cTnT and cTnI peaked at the same time after injection. cTnI returned to baseline concentrations after 54 h, compared with 168 h for cTnT. There was no difference in the rate of clearance of solubilized cTnT or cTnI after intravenous or intramuscular injection. Renal clearance of cTnT and cTnI was similar in 7 heart failure patients. cTnI was degraded and released faster and reached higher concentrations than cTnT when human cardiac tissue was incubated in 37°C plasma.ConclusionOnce cTnI and cTnT are released to the circulation, there seems to be no difference in clearance. However, cTnI is degraded and released faster than cTnT from necrotic cardiac tissue. Faster degradation and release may be the main reason why cTnI reaches higher peak concentrations and returns to normal concentrations faster in patients with MI.
Ensemble Technique for Toxicity Prediction of Small Drug Molecules of the Antioxidant Response Element Signalling Pathway
Authors: Kumar Gupta Vishan , Singh Rana Prashant 
Published: January 2020

Abstract
The in-silico toxicity prediction techniques are useful to reduce rodents testing (in-vivo). Authors have proposed a computational method (in silico) for the toxicity prediction of small drug molecules using their various physicochemical properties (molecular descriptors), which can bind to the antioxidant response elements (AREs). The software PaDEL-Descriptor is used for extracting the different features of drug molecules. The ARE data set has total 7439 drug molecules, of which 1147 are active and 6292 are inactive, and each drug molecule contains 1444 features. We have proposed a novel ensemble-based model that can efficiently classify active (binding) and inactive (non-binding) compounds of the data set. Initially, we performed feature selection using random forest importance algorithm in R, and subsequently, we have resolved the class imbalance issue by ensemble learning method itself, where we divided the data set into five data frames, which have an almost equal number of active and inactive drug molecules. An ensemble model based upon the votes of four base classifiers is proposed, which gives an accuracy of 97.14%. The K-fold cross-validation is conducted to measure the consistency of the proposed ensemble model. Finally, the proposed ensemble model is validated on some new drug molecules and compared with some existing models.
Hydra: a method for strain-minimizing hyperbolic embedding of network- and distance-based data
Authors: Keller-Ressel Martin , Nargang Stephanie 
Published: January 2020

Abstract
We introduce hydra (hyperbolic distance recovery and approximation), a new method for embedding network- or distance-based data into hyperbolic space. We show mathematically that hydra satisfies a certain optimality guarantee: it minimizes the ‘hyperbolic strain’ between original and embedded data points. Moreover, it is able to recover points exactly, when they are contained in a low-dimensional hyperbolic subspace of the feature space. Testing on real network data we show that the embedding quality of hydra is competitive with existing hyperbolic embedding methods, but achieved at substantially shorter computation time. An extended method, termed hydra+, typically outperforms existing methods in both computation time and embedding quality.
Parenting in a warming world: thermoregulatory responses to heat stress in an endangered seabird
Authors: Cook Timothée R , Martin Rowan , Roberts Jennifer , Häkkinen Henry , Botha Philna , Meyer Corlia , Sparks Emilee , Underhill Leslie G , Ryan Peter G , Sherley Richard B 
Published: January 2020

AbstractThe frequency of extreme weather events, including heat waves, is increasing with climate change. The thermoregulatory demands resulting from hotter weather can have catastrophic impacts on animals, leading to mass mortalities. Although less dramatic, animals also experience physiological costs below, but approaching, critical temperature thresholds. These costs may be particularly constraining during reproduction, when parents must balance thermoregulation against breeding activities. Such challenges should be acute among seabirds, which often nest in locations exposed to high solar radiation and predation risk. The globally endangered bank cormorant Phalacrocorax neglectus breeds in southern Africa in the winter, giving little scope for poleward or phenological shifts in the face of increasing temperatures. Physiological studies of endangered species sensitive to human disturbance, like the bank cormorant, are challenging, because individuals cannot be captured for experimental research. Using a novel, non-invasive, videographic approach, we investigated the thermoregulatory responses of this seabird across a range of environmental temperatures at three nesting colonies. The time birds spent gular fluttering, a behaviour enhancing evaporative heat loss, increased with temperature. Crouching or standing birds spent considerably less time gular fluttering than birds sitting on nests (ca 30% less at 22°C), showing that postural adjustments mediate exposure to heat stress and enhance water conservation. Crouching or standing, however, increases the vulnerability of eggs and chicks to suboptimal temperatures and/or expose nest contents to predation, suggesting that parents may trade-off thermoregulatory demands against offspring survival. We modelled thermoregulatory responses under future climate scenarios and found that nest-bound bank cormorants will gular flutter almost continuously for several hours a day by 2100. The associated increase in water loss may lead to dehydration, forcing birds to prioritize survival over breeding, a trade-off that would ultimately deteriorate the conservation status of this species.
Prot2HG: a database of protein domains mapped to the human genome
Authors: Stanek David , Bis-Brewer Dana M , Saghira Cima , Danzi Matt C , Seeman Pavel , Lassuthova Petra , Zuchner Stephan 
Published: January 2020

Abstract

Genetic variation occurring within conserved functional protein domains warrants special attention when examining DNA variation in the context of disease causation. Here we introduce a resource, freely available at www.prot2hg.com, that addresses the question of whether a particular variant falls onto an annotated protein domain and directly translates chromosomal coordinates onto protein residues. The tool can perform a multiple-site query in a simple way, and the whole dataset is available for download as well as incorporated into our own accessible pipeline. To create this resource, National Center for Biotechnology Information protein data were retrieved using the Entrez Programming Utilities. After processing all human protein domains, residue positions were reverse translated and mapped to the reference genome hg19 and stored in a MySQL database. In total, 760 487 protein domains from 42 371 protein models were mapped to hg19 coordinates and made publicly available for search or download (www.prot2hg.com). In addition, this annotation was implemented into the genomics research platform GENESIS in order to query nearly 8000 exomes and genomes of families with rare Mendelian disorders (tgp-foundation.org). When applied to patient genetic data, we found that rare (&lt;1%) variants in the Genome Aggregation Database were significantly more annotated onto a protein domain in comparison to common (&gt;1%) variants. Similarly, variants described as pathogenic or likely pathogenic in ClinVar were more likely to be annotated onto a domain. In addition, we tested a dataset consisting of 60 causal variants in a cohort of patients with epileptic encephalopathy and found that 71% of them (43 variants) were propagated onto protein domains. In summary, we developed a resource that annotates variants in the coding part of the genome onto conserved protein domains in order to increase variant prioritization efficiency.

Database URL: www.prot2hg.com
European citizens’ perspectives on direct-to-consumer genetic testing: an updated systematic review
Authors: Hoxhaj Ilda , Stojanovic Jovana , Boccia Stefania 
Published: January 2020

Abstract

Background
Direct-to-consumer genetic tests (DTC-GTs) are genetic tests for a medical or non-medical trait that are sold directly to the public, usually ordered without the engagement of a healthcare professional. Our aim was to explore the knowledge, attitudes and behaviors toward DTC-GTs among European citizens.

Methods
We updated the most recent systematic review on citizens’ perspectives toward DTC-GTs. Relevant English language studies were searched on PubMed, ISI Web of Science, Scopus, Embase and Google Scholar from October 2014 to April 2019. We extended our search on Scopus without publication date restriction, since it was not included in the former review. Eligible studies were conducted in European countries and reported original data. The quality of the studies was evaluated using a checklist developed by Kmet et al.

Results
We included six studies conducted in European countries between 2015 and 2018. The studies were performed among general population in the Netherlands, students in Italy and Greece, laypeople in Germany and older adults in Switzerland. The level of awareness, in overall low, differed by country and population group. Most of the participants were interested in undergoing a DTC-GT, mainly for knowing the risk predisposition to a common disease. Concerns were raised about tests’ validity and utility and data privacy.

Conclusions
Our review shows that European citizens, overall, have a low level of knowledge on DTC-GTs and a high interest in their purchase. This understanding might contribute to the development of educational programs in order to the increase of general public capabilities to make appropriate health decisions.
Emphasizing iterative practices for a sequential course-based undergraduate research experience in microbial biofilms
Authors: Light Caitlin J , Fegley Megan , Stamp Nancy 
Published: January 2020

ABSTRACT
Iteration is a fundamental area of course design in course-based undergraduate research experiences (CUREs). Iteration includes development of many skills necessary for laboratory work, experimental design, data analysis, communication and teamwork. With a focus on the microbial biofilm research track of the First-year Research Immersion (FRI) program, the perceptions of four student cohorts were examined at the end of the three-term CURE sequence, relative to exposure to iterative tasks, learning gains and benefits from the research experience. Based on results from the first two cohorts, substantial changes were made in the CURE sequence to increase iterative tasks and discussion with students about the iterative nature of research. In turn, the results for the latter cohorts reached FRI program targets. In sum, novice researchers benefit from a deliberate step-wise approach for developing skills to meet the requirements and understand the complex role of iteration in real research.
Effect of betaine and selenium on the growth and photosynthetic pigment production in Dunaliella salina as biostimulants
Authors: Constantinescu-Aruxandei Diana , Vlaicu Alexandru , Marinaș Ioana Cristina , Vintilă Alin Cristian Nicolae , Dimitriu Luminița , Oancea Florin 
Published: January 2020

ABSTRACT
The aim of our study was to establish the effect of selenium and betaine on the growth of D. salina, accumulation of photosynthetic pigments and antioxidant activity of the hydrophobic fraction. This approach was an attempt to demonstrate ‘microalgae biostimulant’ effects, similar to ‘plant biostimulant’ effects, i.e. increased tolerance to abiotic stress and enhanced accumulation of bioactive compounds. A high-throughput assay was done in 24-well microplates, at 15% NaCl and different concentrations of sodium selenite (0, 0.5, 2 and 8 µM) or betaine (0, 5, 50 and 500 µM). Both selenium and betaine induced a slight delay in algae growth during the actively growing stage but the final density reached similar values to the control. Betaine significantly enhanced (50%–100%) carotenoids and chlorophyll a accumulation, in a concentration depending manner. Antioxidant activity increased almost 3-fold in extracts of algae treated with 50 µM betaine. Selenium had a much more discrete effect than betaine on pigments biosynthesis. The antioxidant activity of the extracts increased 2-fold in the presence of Se compared to the control. Our work proves that it is possible to enhance production and activity of bioactive compounds from microalgae by using ingredients, which already proved to act as plant biostimulants.
Fertilization of Norway spruce forest with wood ash and nitrogen affected both tree growth and composition of chemical defence
Authors: Hanssen Kjersti Holt , Asplund Johan , Clarke Nicholas , Selmer Ruben , Nybakken Line 
Published: January 2020

AbstractWe fertilized a Norway spruce (Picea abies (L.) Karst.) stand on rich mineral soil with 3 t ha−1 of wood ash (ASH), 150 kg ha−1 of nitrogen (N) or a combination of wood ash and nitrogen (ASH + N), in addition to unfertilized control plots. After five growing seasons, we remeasured the trees and took core samples. Current- and previous-year needles were sampled and analyzed for total nitrogen and carbon, low-molecular weight phenolics and condensed tannins. Annual volume increment and standing volume were significantly higher in the ASH + N treatment than in control plots after 5 years. N gave a significant positive effect on basal area growth in the third year, after which the effect diminished. The ASH + N treated trees, on the other hand, showed an increasing basal area growth trend throughout the period. ASH reduced the total concentration of low-molecular weight phenolic compounds significantly in current-year needles. Phenolic acids increased under both ASH and ASH + N, while flavonoids decreased significantly under the same treatments compared to N. By including annual growth rate before fertilization in the analyses, the effect of N-treatment on flavonoids was positive only in trees with higher growth rates, and in those trees the concentration was higher than in both ASH-treated plots and controls. An acetophenone, constituting more than half of the total low-molecular weight phenolics concentration, was strongly reduced under all fertilization treatments. These results demonstrate that in addition to effects on tree growth, fertilization of the forest floor also has a strong influence on other metabolic processes of trees, with potential implications for ecosystem functioning.
Differential Expression in Testis and Liver Transcriptomes from Four Species of Peromyscus (Rodentia: Cricetidae)
Authors: Lindsey Laramie L , Platt Roy N , Phillips Caleb D , Ray David A , Bradley Robert D 
Published: January 2020

AbstractThe genus Peromyscus represents a rapidly diverged clade of Cricetid rodents that contains multiple cryptic species and has a propensity for morphologic conservation across its members. The unresolved relationships in previously proposed phylogenies reflect a suspected rapid adaptive radiation. To identify functional groups of genes that may be important in reproductive isolation in a reoccurring fashion across the Peromyscus phylogeny, liver and testis transcriptomes from four species (P. attwateri, P. boylii, P. leucopus, and P. maniculatus) were generated and differential expression (DE) tests were conducted. Taxa were selected to represent members diverged from a common ancestor: P. attwateri + P. boylii (clade A), and P. leucopus + P. maniculatus (clade B). Comparison of clades (A vs. B) suggested that 252 transcripts had significant DE in the liver data set, whereas significant DE was identified for 657 transcripts in the testis data set. Further, 45 genes had DE isoforms in the 657 testis transcripts and most of these functioned in major reproductive roles such as acrosome assembly, spermatogenesis, and cell cycle processes (meiosis). DE transcripts in the liver mapped to more broad gene ontology terms (metabolic processes, catabolic processes, response to chemical, and regulatory processes), and DE transcripts in the testis mapped to gene ontology terms associated with reproductive processes, such as meiosis, sperm motility, acrosome assembly, and sperm–egg fusion. These results suggest that a suite of genes that conduct similar functions in the testes may be responsible for the adaptive radiation events and potential reoccurring speciation of Peromyscus in terms of reproduction through varying expression levels.
Bring Back the Rat!
Authors: Carter Christy S , Richardson Arlan , Huffman Derek M , Austad Steven 
Published: January 2020

AbstractAs 2020 is “The Year of the Rat” in the Chinese astrological calendar, it seems an appropriate time to consider whether we should bring back the laboratory rat to front-and-center in research on the basic biology of mammalian aging. Beginning in the 1970s, aging research with rats became common, peaking in 1992 but then declined dramatically by 2018 as the mouse became preeminent. The purpose of this review is to highlight some of the historical contributions as well as current advantages of the rat as a mammalian model of human aging, because we suspect at least a generation of researchers is no longer aware of this history or these advantages. Herein, we compare and contrast the mouse and rat in the context of several biological domains relevant to their use as appropriate models of aging: phylogeny/domestication, longevity interventions, pathology/physiology, and behavior/cognition. It is not the goal of this review to give a complete characterization of the differences between mice and rats, but to provide important examples of why using rats as well as mice is important to advance our understanding of the biology of aging.
Genome and population sequencing of a chromosome-level genome assembly of the Chinese tapertail anchovy (Coilia nasus) provides novel insights into migratory adaptation
Authors: Xu Gangchun , Bian Chao , Nie Zhijuan , Li Jia , Wang Yuyu , Xu Dongpo , You Xinxin , Liu Hongbo , Gao Jiancao , Li Hongxia , Liu Kai , Yang Jian , Li Quanjie , Shao Nailin , Zhuang Yanbing , Fang Dian , Jiang Tao , Lv Yunyun , Huang Yu , Gu Ruobo , Xu Junmin , Ge Wei , Shi Qiong , Xu Pao 
Published: January 2020

Abstract

Background
Seasonal migration is one of the most spectacular events in nature; however, the molecular mechanisms related to this phenomenon have not been investigated in detail. The Chinese tapertail, or Japanese grenadier anchovy, Coilia nasus, is a valuable migratory fish of high economic importance and special migratory dimorphism (with certain individuals as non-migratory residents).

Results
In this study, an 870.0-Mb high-quality genome was assembled by the combination of Illumina and Pacific Biosciences sequencing. Approximately 812.1 Mb of scaffolds were linked to 24 chromosomes using a high-density genetic map from a family of 104 full siblings and their parents. In addition, population sequencing of 96 representative individuals from diverse areas along the putative migration path identified 150 candidate genes, which are mainly enriched in 3 Ca2+-related pathways. Based on integrative genomic and transcriptomic analyses, we determined that the 3 Ca2+-related pathways are critical for promotion of migratory adaption. A large number of molecular markers were also identified, which distinguished migratory individuals and non-migratory freshwater residents.

Conclusions
We assembled a chromosome-level genome for the Chinese tapertail anchovy. The genome provided a valuable genetic resource for understanding of migratory adaption and population genetics and will benefit the aquaculture and management of this economically important fish.
Incidence and Predictors of Flares in the Postpartum Year Among Women With Inflammatory Bowel Disease
Authors: Yu Amy , Friedman Sonia , Ananthakrishnan Ashwin N 
Published: January 2020

Abstract

Background
The postpartum period is marked by physiological and psychological stresses that may impact activity in inflammatory bowel disease. The predictors and outcomes of disease activity during this period have not been well characterized.

Methods
We performed a retrospective review of inflammatory bowel disease patients who underwent successful pregnancy and live birth at 2 referral institutions. Data on patient and disease factors including disease activity before and during pregnancy were abstracted from the medical records. We noted whether therapy was dose-reduced or stopped during pregnancy at each trimester and after delivery. Multivariable logistic regression of independent predictors of postpartum flare was performed, adjusting for relevant covariates.

Results
We identified a total of 206 eligible women (mean age, 33.2 years). Of these, 97 (47%) had a diagnosis of Crohn’s disease, whereas the remainder had ulcerative colitis. Nearly half the women delivered vaginally (53%), and the rest delivered by Caesarean section (47%). In the entire cohort, 65 (31.6%) experienced a postpartum flare within the year after delivery. In multivariable analysis, development of a postpartum flare was predicted by disease activity during the third trimester (odds ratio [OR], 6.27; 95% confidence interval [CI], 2.81–17.27), therapy de-escalation during pregnancy (OR, 3.00; 95% CI, 1.03–8.68), and therapy de-escalation after pregnancy (OR, 4.43; 95% CI, 1.55–12.65). Postpartum disease flare was not related to disease type, duration of disease, or mode of childbirth.

Conclusions
One-third of women with inflammatory bowel disease may experience disease flare during the postpartum year. Continued optimization of therapy before, during, and after pregnancy is essential to prevent this morbidity.