bluuebunny/crossref_metadata_2025_split huggingface dataset:
BERT4Bitter: a bidirectional encoder representations from transformers (BERT)-based model for improving the prediction of bitter peptides
Authors: Charoenkwan Phasit , Nantasenamat Chanin , Hasan Md Mehedi , Manavalan Balachandran , Shoombuatong Watshara 
Published: February 2021

Abstract

Motivation
The identification of bitter peptides through experimental approaches is an expensive and time-consuming endeavor. Due to the huge number of newly available peptide sequences in the post-genomic era, the development of automated computational models for the identification of novel bitter peptides is highly desirable.

Results
In this work, we present BERT4Bitter, a bidirectional encoder representation from transformers (BERT)-based model for predicting bitter peptides directly from their amino acid sequence without using any structural information. To the best of our knowledge, this is the first time a BERT-based model has been employed to identify bitter peptides. Compared to widely used machine learning models, BERT4Bitter achieved the best performance with an accuracy of 0.861 and 0.922 for cross-validation and independent tests, respectively. Furthermore, extensive empirical benchmarking experiments on the independent dataset demonstrated that BERT4Bitter clearly outperformed the existing method with improvements of 8.0% accuracy and 16.0% Matthews coefficient correlation, highlighting the effectiveness and robustness of BERT4Bitter. We believe that the BERT4Bitter method proposed herein will be a useful tool for rapidly screening and identifying novel bitter peptides for drug development and nutritional research.

Availabilityand implementation
The user-friendly web server of the proposed BERT4Bitter is freely accessible at http://pmlab.pythonanywhere.com/BERT4Bitter.

Supplementary information
Supplementary data are available at Bioinformatics online.
Novel mineral regulatory pathways in ovine pregnancy: I. phosphate, klotho signaling, and sodium-dependent phosphate transporters
Authors: Stenhouse Claire , Halloran Katherine M , Newton Makenzie G , Gaddy Dana , Suva Larry J , Bazer Fuller W 
Published: February 2021

AbstractAppropriate mineralization of the fetal skeleton requires an excess of phosphate in the fetus compared to the mother. However, mechanisms for placental phosphate transport are poorly understood. This study aimed to identify phosphate regulatory pathways in ovine endometria and placentae throughout gestation. Suffolk ewes were bred with fertile rams upon visual detection of estrus (Day 0). On Days 9, 12, 17, 30, 70, 90, 110, and 125 of pregnancy (n = 3–14/Day), ewes were euthanized and hysterectomized. Phosphate abundance varied across gestational days in uterine flushings, allantoic fluid, and homogenized endometria and placentae (P &lt; 0.05). The expression of mRNAs for sodium-dependent phosphate transporters (SLC20A1 and SLC20A2) and klotho signaling mediators (FGF7, FGF21, FGF23, FGFR1–4, KL, KLB, ADAM10, and ADAM17) were quantified by qPCR. Day 17 conceptus tissue expressed SLC20A1, SLC20A2, KLB, FGF7, FGF21, FGF23, FGFR1, and FGFR2 mRNAs. Both sodium-dependent phosphate transporters and klotho signaling mediators were expressed in endometria and placentae throughout gestation. Gestational day influenced the expression of SLC20A1, ADAM10, ADAM17, FGF21, FGFR1, and FGFR3 mRNAs in both endometria and placentae (P &lt; 0.05). Gestational day influenced endometrial expression of FGF7 (P &lt; 0.001), and placental expression of FGF23 (P &lt; 0.05). Immunohistochemistry confirmed that both FGF23 and KL proteins were expressed in endometria and placentae throughout gestation. The observed spatiotemporal profile of KL-FGF signaling suggests a potential role in the establishment of pregnancy and regulation of fetal growth. This study provides a platform for further mechanistic investigation into the role for KL-FGF signaling in the regulation of phosphate transport at the ovine maternal–conceptus interface.
Being the Gatekeeper: How Thinking about Sharing Affects Neural Encoding of Information
Authors: Chan Hang-Yee , Scholz Christin , Baek Elisa C , O’Donnell Matthew B , Falk Emily B 
Published: February 2021

Abstract
Information transmission in a society depends on individuals’ intention to share or not. Yet, little is known about whether being the gatekeeper shapes the brain’s processing of incoming information. Here, we examine how thinking about sharing affects neural encoding of information, and whether this effect is moderated by the person’s real-life social network position. In an functional magnetic resonance imaging study, participants rated abstracts of news articles on how much they wanted to read for themselves (read) or—as information gatekeepers—to share with a specific other (narrowcast) or to post on their social media feed (broadcast). In all conditions, consistent spatial blood oxygen level-dependent patterns associated with news articles were observed across participants in brain regions involved in perceptual and language processing as well as higher-order processes. However, when thinking about sharing, encoding consistency decreased in higher-order processing areas (e.g., default mode network), suggesting that the gatekeeper role involves more individualized processing in the brain, that is, person- and context-specific. Moreover, participants whose social networks had high ego-betweenness centrality (i.e., more likely to be information gatekeeper in real life) showed more individualized encoding when thinking about broadcasting. This study reveals how gatekeeping shapes our brain’s processing of incoming information.
A System-Wide Understanding of the Human Olfactory Percept Chemical Space
Authors: Kowalewski Joel , Huynh Brandon , Ray Anandasankar 
Published: February 2021

Abstract
The fundamental units of olfactory perception are discrete 3D structures of volatile chemicals that each interact with specific subsets of a very large family of hundreds of odorant receptor proteins, in turn activating complex neural circuitry and posing a challenge to understand. We have applied computational approaches to analyze olfactory perceptual space from the perspective of odorant chemical features. We identify physicochemical features associated with ~150 different perceptual descriptors and develop machine-learning models. Validation of predictions shows a high success rate for test set chemicals within a study, as well as across studies more than 30 years apart in time. Due to the high success rates, we are able to map ~150 percepts onto a chemical space of nearly 0.5 million compounds, predicting numerous percept–structure combinations. The chemical structure-to-percept prediction provides a system-level view of human olfaction and opens the door for comprehensive computational discovery of fragrances and flavors.
Isotopic niche provides an insight into the ecology of a symbiont during its geographic expansion
Authors: González-Ortegón Enrique , Perez-Miguel Marta , Navas Jose I , Drake Pilar , Cuesta Jose A 
Published: February 2021

Abstract
The study of the recent colonization of a symbiont and its interaction with host communities in new locations is an opportunity to understand how they interact. The use of isotopic ratios in trophic ecology can provide measurements of a species’ isotopic niche, as well as knowledge about how the isotopic niches between symbiont and host species overlap. Stable isotope measurements were used to assess the sources of carbon assimilated by the host species (the bivalves Mytilus galloprovincialis and Scrobicularia plana) and their associated symbiont pea crab Afropinnotheres monodi, which occurs within these bivalves’ mantle cavities. The mixing model estimates suggest that all of them assimilate carbon from similar sources, particularly from pseudofaeces and particulate organic matter in this symbiotic system based on filter feeding. The symbiotic species occupy comparable trophic levels and its association seems to be commensal or parasitic depending on the duration of such association. The pea crab A. monodi reflects a sex-specific diet, where males are more generalist than the soft females because the latter’s habitat is restricted to the host bivalve. The high isotopic overlap between soft females and M. galloprovincialis may reflect a good commensal relationship with the host.
The role of pharmacogenomics in contemporary cardiovascular therapy: a position statement from the European Society of Cardiology Working Group on Cardiovascular Pharmacotherapy
Authors: Magavern Emma Forton , Kaski Juan Carlos , Turner Richard M , Drexel Heinz , Janmohamed Azara , Scourfield Andrew , Burrage Daniel , Floyd Christopher N , Adeyeye Elizabeth , Tamargo Juan , Lewis Basil S , Kjeldsen Keld Per , Niessner Alexander , Wassmann Sven , Sulzgruber Patrick , Borry Pascal , Agewall Stefan , Semb Anne Grete , Savarese Gianluigi , Pirmohamed Munir , Caulfield Mark J 
Published: February 2021

Abstract
There is a strong and ever-growing body of evidence regarding the use of pharmacogenomics to inform cardiovascular pharmacology. However, there is no common position taken by international cardiovascular societies to unite diverse availability, interpretation, and application of such data, nor is there recognition of the challenges of variation in clinical practice between countries within Europe. Aside from the considerable barriers to implementing pharmacogenomic testing and the complexities of clinically actioning results, there are differences in the availability of resources and expertise internationally within Europe. Diverse legal and ethical approaches to genomic testing and clinical therapeutic application also require serious thought. As direct-to-consumer genomic testing becomes more common, it can be anticipated that data may be brought in by patients themselves, which will require critical assessment by the clinical cardiovascular prescriber. In a modern, pluralistic and multi-ethnic Europe, self-identified race/ethnicity may not be concordant with genetically detected ancestry and thus may not accurately convey polymorphism prevalence. Given the broad relevance of pharmacogenomics to areas, such as thrombosis and coagulation, interventional cardiology, heart failure, arrhythmias, clinical trials, and policy/regulatory activity within cardiovascular medicine, as well as to genomic and pharmacology subspecialists, this position statement attempts to address these issues at a wide-ranging level.
WhatsApp as part of an EFL programme: participation and interaction
Authors: Mackay Jessica , Andria Maria , Tragant Elsa , Pinyana Àngels 
Published: February 2021

Abstract
This study examines the results of an intervention conducted with adult EFL learners in Barcelona, Spain, to foster engagement with the target language outside class time. As part of the programme, the messaging service WhatsApp was used to carry out a range of voluntary communicative tasks, in learners’ own time. Familiarity with this tool made it easy to use, and learner feedback was positive. Analysis of the resulting chat transcript indicated that (1) off-task participation increased as learners appropriated the space as a vehicle for their own communication, (2) off-task interactions fell predominantly into two categories: administrative and social, and (3) despite being voluntary and unevaluated, with minimum teacher intervention, English was overwhelmingly the language of choice within these interactions. We hope this study can serve as an example of the possibilities offered by the WhatsApp medium in an EFL context.
Factors associated with A1C reduction with GLP-1 agonist or SGLT-2 inhibitor use
Authors: Davis Hanifah , Heilmann Rachel , Milchak Jessica , Delate Thomas 
Published: February 2021

Abstract

Background
While use of glucagon-like peptide-1 (GLP-1) agonists and sodium-glucose cotransporter-2 (SGLT-2) inhibitors reduces the risk of atherosclerotic cardiovascular disease outcomes and lowers glycosylated haemoglobin (A1C), evidence on patient characteristics associated with clinically relevant A1C reduction is lacking.

Objective
The objective of this retrospective cohort study was to identify patient characteristics associated with A1C reduction with initial GLP-1 or SGLT-2 use.

Methods
Patients with type 2 diabetes and a baseline A1C ≥7% who were dispensed a GLP-1 or SGLT-2 between 01/01/10 and 12/31/17 were included. Patients were categorized as having a ≥1% or &lt;1% A1C reduction during the 90–365 days after GLP-1/SGLT-2 initiation. Patient characteristics were collected during the 180 days prior to initiation. Multivariable logistic and linear regression modelling was performed to identify characteristics associated with a ≥1% A1C reduction and absolute change in A1C, respectively.

Results
Five hundred and seventy-two patients were included with 261 (46%) and 311 (54%) having and not having an ≥1% A1C reduction. Patients were primarily middle-aged, female, white, non-Hispanic and had a high burden of chronic disease. Characteristics associated with a ≥1% A1C reduction included: GLP-1/SGLT-2 persistence, congestive heart failure comorbidity, phentermine dispensing, care management team (CMT) enrollee and higher baseline A1C. Characteristics associated with absolute A1C reduction included: age, baseline A1C, CMT enrollee, GLP-1/SGLT-2 persistence and a phentermine dispensing.

Conclusions
The results of this study provide practitioners with guidance on the patients who are most likely to have a clinically relevant A1C reduction with GLP-1 or SGLT-2 use.
Modelling growing stock volume of forest stands with various ALS area-based approaches
Authors: Parkitna Karolina , Krok Grzegorz , Miścicki Stanisław , Ukalski Krzysztof , Lisańczuk Marek , Mitelsztedt Krzysztof , Magnussen Steen , Markiewicz Anna , Stereńczak Krzysztof 
Published: February 2021

Abstract
Airborne laser scanning (ALS) is one of the most innovative remote sensing tools with a recognized important utility for characterizing forest stands. Currently, the most common ALS-based method applied in the estimation of forest stand characteristics is the area-based approach (ABA).
The aim of this study was to analyse how three ABA methods affect growing stock volume (GSV) estimates at the sample plot and forest stand levels. We examined (1) an ABA with point cloud metrics, (2) an ABA with canopy height model (CHM) metrics and (3) an ABA with aggregated individual tree CHM-based metrics. What is more, three different modelling techniques: multiple linear regression, boosted regression trees and random forest, were applied to all ABA methods, which yielded a total of nine combinations to report. An important element of this work is also the empirical verification of the methods for estimating the GSV error for individual forest stand. All nine combinations of the ABA methods and different modelling techniques yielded very similar predictions of GSV for both sample plots and forest stands. The root mean squared error (RMSE) of estimated GSV ranged from 75 to 85 m3 ha−1 (RMSE% = 20.5–23.4 per cent) and from 57 to 64 m3 ha−1 (RMSE% = 16.4–18.3 per cent) for plots and stands, respectively. As a result of the research, it can be concluded that GSV modelling with the use of different ALS processing approaches and statistical methods leads to very similar results. Therefore, the choice of a GSV prediction method may be more determined by the availability of data and competences than by the requirement to use a particular method.
Genome announcement ofSteinernema khuongiand its associated symbiont from Florida
Authors: Baniya Anil , DiGennaro Peter 
Published: February 2021

AbstractCitrus root weevil (Diaprepes abbreviates) causes significant yield loss in citrus, especially in Florida. A promising source of control for this pest is biological control agents, namely, native entomopathogenic nematodes (EPNs) within the genus Steinernema. Two species of endemic EPN in Florida are S. diaparepesi, abundant within the central ridge, and S. khuongi, dominating the flatwood regions of the state. These citrus-growing regions differ significantly in their soil habitats, which impacts the potential success of biological control measures. Although the genome sequence of S. diaprepesi is currently available, the genome sequence of S. khuongi and identity of the symbiotic bacteria is still unknown. Understanding the genomic differences between these two nematodes and their favored habitats can inform successful biological control practices. Here, MiSeq libraries were used to simultaneously sequence and assemble the draft genome of S. khuongi and its associated symbionts. The final draft genome for S. khuongi has 8,794 contigs with a total length of ∼82 Mb, a largest contig of 428,226 bp, and N50 of 46 kb; its BUSCO scores indicate that it is &gt; 86% complete. An associated bacterial genome was assembled with a total length of ∼3.5 Mb, a largest contig at 116,532 bp, and N50 of 17,487 bp. The bacterial genome encoded 3,721 genes, similar to other Xenorhabdus genomes. Comparative genomics identified the symbiotic bacteria of S. khuongi as Xenorhabdus poinarii. These new draft genomes of a host and symbiont can be used as a valuable tool for comparative genomics with other EPNs and its symbionts to understand host range and habitat suitability.
Religious Involvement and Cognitive Functioning at the Intersection of Race–Ethnicity and Gender Among Midlife and Older Adults
Authors: Henderson Andrea K , Walsemann Katrina M , Ailshire Jennifer A 
Published: February 2021

AbstractObjectivesTo investigate the association between religious involvement and cognitive functioning at the intersections of race–ethnicity and gender among midlife and older adults, and to determine if psychosocial factors help explain this relationship.MethodThe sample included 14,037 adults aged 50+ from the Health and Retirement Study (HRS). We utilized measures from the HRS 2010 and 2012 Core interviews and Leave-Behind questionnaires and estimated our models using linear regression.ResultsCompared to individuals who frequently attended religious services, infrequent religious service attendance was related to poorer cognitive functioning. Religiosity was inversely associated with cognitive functioning at baseline, but the relationship varied by race/gender subgroup. Greater religiosity was associated with better cognitive functioning among Black women, but lower cognitive functioning among White men and women. Psychosocial factors did little to explain the inverse association between religiosity and cognitive functioning.DiscussionResults suggest the association between religious involvement and cognitive functioning is varied and complex, and largely dependent on important social identities. The findings have important implications for investigating health-protective factors, like religious involvement, using an intersectional perspective.
Local-scale phase velocity estimation using ambient seismic noise: comparison between passive seismic interferometry and conventional frequency–wavenumber methods
Authors: Karaaslan Aylin , Kocaoğlu Argun , Özalaybey Serdar 
Published: February 2021

SUMMARYWe present a new processing scheme that uses passive seismic interferometry (PSI) followed by multichannel analysis of surface waves (MASW), which we call the 2-D PSI-MASW method, to obtain Rayleigh wave phase velocity dispersion (PVD) information. In this scheme, we first use the principles of PSI to form multidirectional cross-correlations (CCs) then project the CCs onto a 1-D virtual array and apply the phase-shift transform as in MASW processing. We compare PVD information obtained by this method with those of the conventional beam-power based frequency–wavenumber decomposition (CVFK) method using ambient seismic noise (ASN) data collected by local-scale 2-D arrays deployed at three selected sites in Bursa, Turkey. By analysing the ASN data from these sites, we show that similar multimodal PVD curves can be obtained with the two methods over a broad frequency range (∼2–23 Hz) within the wavenumber resolution and aliasing limits. However, in one of our sites where the 2-D array configuration has a considerable antisymmetry, we show that the 1-D virtual array used in the 2-D PSI-MASW method has a better array response function in terms of wavenumber resolution and suppression of side-lobes leading to superior mode resolution and separation than that of the CVFK method, which shows strong directional variations. Furthermore, unlike the CVFK method, the 2-D PSI-MASW method takes advantage of temporal stacking of CCs ensuring weak but coherent Rayleigh wave signals present in the ASN wavefield to be strengthened and has the potential for better extraction of PVD information. We conclude that by using a 2-D array with spatial coverage providing a wide range of directions and distances, reliable PVD information can be obtained even if the ASN sources are not concentrated in the stationary phase zones. Thus, we suggest that the 2-D PSI-MASW method is highly advantageous for the extraction of reliable PVD information owing to the multidirectional CCs provided by the 2-D array configurations. We also report that using only a single receiver line in the interferometric approach results in biased and/or incomplete PVD information due to the non-isotropic ASN source distribution at all three sites we analysed. In conclusion, our results clearly indicate that the 2-D PSI-MASW method can be used as complementary or alternative to the CVFK method to extract multimodal Rayleigh wave PVD information in local-scale seismological studies.
Nanopore direct RNA sequencing detects DUX4-activated repeats and isoforms in human muscle cells
Authors: Mitsuhashi Satomi , Nakagawa So , Sasaki-Honda Mitsuru , Sakurai Hidetoshi , Frith Martin C , Mitsuhashi Hiroaki 
Published: February 2021

AbstractFacioscapulohumeral muscular dystrophy (FSHD) is an inherited muscle disease caused by misexpression of the DUX4 gene in skeletal muscle. DUX4 is a transcription factor, which is normally expressed in the cleavage-stage embryo and regulates gene expression involved in early embryonic development. Recent studies revealed that DUX4 also activates the transcription of repetitive elements such as endogenous retroviruses (ERVs), mammalian apparent long terminal repeat (LTR)-retrotransposons and pericentromeric satellite repeats (Human Satellite II). DUX4-bound ERV sequences also create alternative promoters for genes or long non-coding RNAs, producing fusion transcripts. To further understand transcriptional regulation by DUX4, we performed nanopore long-read direct RNA sequencing (dRNA-seq) of human muscle cells induced by DUX4, because long reads show whole isoforms with greater confidence. We successfully detected differential expression of known DUX4-induced genes and discovered 61 differentially expressed repeat loci, which are near DUX4–ChIP peaks. We also identified 247 gene–ERV fusion transcripts, of which 216 were not reported previously. In addition, long-read dRNA-seq clearly shows that RNA splicing is a common event in DUX4-activated ERV transcripts. Long-read analysis showed non-LTR transposons including Alu elements are also transcribed from LTRs. Our findings revealed further complexity of DUX4-induced ERV transcripts. This catalogue of DUX4-activated repetitive elements may provide useful information to elucidate the pathology of FSHD. Also, our results indicate that nanopore dRNA-seq has complementary strengths to conventional short-read complementary DNA sequencing.