bluuebunny/crossref_metadata_2025_split huggingface dataset:
New cup out of old coffee: contribution of parental gene expression legacy to phenotypic novelty in coffee beans of the allopolyploid Coffea arabica L.
Authors: Combes Marie-Christine , Joët Thierry , Stavrinides Anna K , Lashermes Philippe 
Published: March 2022

Abstract

Background and Aims
Allopolyploidization is a widespread phenomenon known to generate novel phenotypes by merging evolutionarily distinct parental genomes and regulatory networks in a single nucleus. The objective of this study was to investigate the transcriptional regulation associated with phenotypic novelty in coffee beans of the allotetraploid Coffea arabica.

Methods
A genome-wide comparative transcriptomic analysis was performed in C. arabica and its two diploid progenitors, C. canephora and C. eugenioides. Gene expression patterns and homeologue expression were studied on seeds at five different maturation stages. The involvement of homeologue expression bias (HEB) in specific traits was addressed both by functional enrichment analyses and by the study of gene expression in the caffeine and chlorogenic acid biosynthesis pathways.

Key Results
Expression-level dominance in C. arabica seed was observed for most of the genes differentially expressed between the species. Approximately a third of the genes analysed showed HEB. This proportion increased during seed maturation but the biases remained equally distributed between the sub-genomes. The relative expression levels of homeologues remained relatively constant during maturation and were correlated with those estimated in leaves of C. arabica and interspecific hybrids between C. canephora and C. eugenioides. Functional enrichment analyses performed on genes exhibiting HEB enabled the identification of processes potentially associated with physiological traits. The expression profiles of the genes involved in caffeine biosynthesis mirror the differences observed in the caffeine content of mature seeds of C. arabica and its parental species.

Conclusions
Neither of the two sub-genomes is globally preferentially expressed in C. arabica seeds, and homeologues appear to be co-regulated by shared trans-regulatory mechanisms. The observed HEBs are thought to be a legacy of gene expression differences inherited from diploid progenitor species. Pre-existing functional divergences between parental species appear to play an important role in controlling the phenotype of C. arabica seeds.
Signaling repurposable drug combinations against COVID-19 by developing the heterogeneous deep herb-graph method
Authors: Yang Fan , Zhang Shuaijie , Pan Wei , Yao Ruiyuan , Zhang Weiguo , Zhang Yanchun , Wang Guoyin , Zhang Qianghua , Cheng Yunlong , Dong Jihua , Ruan Chunyang , Cui Lizhen , Wu Hao , Xue Fuzhong 
Published: March 2022

Abstract

Background
Coronavirus disease 2019 (COVID-19) has spurred a boom in uncovering repurposable existing drugs. Drug repurposing is a strategy for identifying new uses for approved or investigational drugs that are outside the scope of the original medical indication.

Motivation
Current works of drug repurposing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are mostly limited to only focusing on chemical medicines, analysis of single drug targeting single SARS-CoV-2 protein, one-size-fits-all strategy using the same treatment (same drug) for different infected stages of SARS-CoV-2. To dilute these issues, we initially set the research focusing on herbal medicines. We then proposed a heterogeneous graph embedding method to signaled candidate repurposing herbs for each SARS-CoV-2 protein, and employed the variational graph convolutional network approach to recommend the precision herb combinations as the potential candidate treatments against the specific infected stage.

Method
We initially employed the virtual screening method to construct the ‘Herb-Compound’ and ‘Compound-Protein’ docking graph based on 480 herbal medicines, 12,735 associated chemical compounds and 24 SARS-CoV-2 proteins. Sequentially, the ‘Herb-Compound-Protein’ heterogeneous network was constructed by means of the metapath-based embedding approach. We then proposed the heterogeneous-information-network-based graph embedding method to generate the candidate ranking lists of herbs that target structural, nonstructural and accessory SARS-CoV-2 proteins, individually. To obtain precision synthetic effective treatments forvarious COVID-19 infected stages, we employed the variational graph convolutional network method to generate candidate herb combinations as the recommended therapeutic therapies.

Results
There were 24 ranking lists, each containing top-10 herbs, targeting 24 SARS-CoV-2 proteins correspondingly, and 20 herb combinations were generated as the candidate-specific treatment to target the four infected stages. The code and supplementary materials are freely available at https://github.com/fanyang-AI/TCM-COVID19.
Knowledge-based BERT: a method to extract molecular features like computational chemists
Authors: Wu Zhenxing , Jiang Dejun , Wang Jike , Zhang Xujun , Du Hongyan , Pan Lurong , Hsieh Chang-Yu , Cao Dongsheng , Hou Tingjun 
Published: March 2022

Abstract
Molecular property prediction models based on machine learning algorithms have become important tools to triage unpromising lead molecules in the early stages of drug discovery. Compared with the mainstream descriptor- and graph-based methods for molecular property predictions, SMILES-based methods can directly extract molecular features from SMILES without human expert knowledge, but they require more powerful algorithms for feature extraction and a larger amount of data for training, which makes SMILES-based methods less popular. Here, we show the great potential of pre-training in promoting the predictions of important pharmaceutical properties. By utilizing three pre-training tasks based on atom feature prediction, molecular feature prediction and contrastive learning, a new pre-training method K-BERT, which can extract chemical information from SMILES like chemists, was developed. The calculation results on 15 pharmaceutical datasets show that K-BERT outperforms well-established descriptor-based (XGBoost) and graph-based (Attentive FP and HRGCN+) models. In addition, we found that the contrastive learning pre-training task enables K-BERT to ‘understand’ SMILES not limited to canonical SMILES. Moreover, the general fingerprints K-BERT-FP generated by K-BERT exhibit comparative predictive power to MACCS on 15 pharmaceutical datasets and can also capture molecular size and chirality information that traditional binary fingerprints cannot capture. Our results illustrate the great potential of K-BERT in the practical applications of molecular property predictions in drug discovery.
3DGT-DDI: 3D graph and text based neural network for drug–drug interaction prediction
Authors: He Haohuai , Chen Guanxing , Yu-Chian Chen Calvin 
Published: March 2022

AbstractMotivationDrug–drug interactions (DDIs) occur during the combination of drugs. Identifying potential DDI helps us to study the mechanism behind the combination medication or adverse reactions so as to avoid the side effects. Although many artificial intelligence methods predict and mine potential DDI, they ignore the 3D structure information of drug molecules and do not fully consider the contribution of molecular substructure in DDI.ResultsWe proposed a new deep learning architecture, 3DGT-DDI, a model composed of a 3D graph neural network and pre-trained text attention mechanism. We used 3D molecular graph structure and position information to enhance the prediction ability of the model for DDI, which enabled us to deeply explore the effect of drug substructure on DDI relationship. The results showed that 3DGT-DDI outperforms other state-of-the-art baselines. It achieved an 84.48% macro F1 score in the DDIExtraction 2013 shared task dataset. Also, our 3D graph model proves its performance and explainability through weight visualization on the DrugBank dataset. 3DGT-DDI can help us better understand and identify potential DDI, thereby helping to avoid the side effects of drug mixing.AvailabilityThe source code and data are available at https://github.com/hehh77/3DGT-DDI.
Structured Sparse Regularized TSK Fuzzy System for predicting therapeutic peptides
Authors: Guo Xiaoyi , Jiang Yizhang , Zou Quan 
Published: March 2022

AbstractTherapeutic peptides act on the skeletal system, digestive system and blood system, have antibacterial properties and help relieve inflammation. In order to reduce the resource consumption of wet experiments for the identification of therapeutic peptides, many computational-based methods have been developed to solve the identification of therapeutic peptides. Due to the insufficiency of traditional machine learning methods in dealing with feature noise. We propose a novel therapeutic peptide identification method called Structured Sparse Regularized Takagi–Sugeno–Kang Fuzzy System on Within-Class Scatter (SSR-TSK-FS-WCS). Our method achieves good performance on multiple therapeutic peptides and UCI datasets.
Biscuits, the World Cup and Nobel Prizes: The Puzzling Documentation of Shin Bet Interrogations
Authors: Ballas Irit , Dagan Netanel 
Published: March 2022

AbstractRecords kept by security authorities documenting potentially violent encounters are generally characterized by technocratic language and parsimonious content, which is intended to project an image of objective and impartial state officials. A qualitative analysis of 688 records covering interrogations of suspects in terror activities by the Israeli Security Agency (Shin Bet) presents a very different picture. They consist of representations of (1) hospitality—caring for the well-being of the person under interrogation; (2) camaraderie—amicable conversations between interrogator and interrogee; and (3) moral conviction—impassioned political or moral debates regarding the Israeli–Palestinian conflict. The analysis shows how unconventional documentation techniques in security interrogations may be used to preserve legitimacy; bolster professional prestige and makes a sophisticated use of a sense of secrecy.
Single-cell transcriptomes in the heart: when every epigenome counts
Authors: Gromova Tatiana , Gehred Natalie D , Vondriska Thomas M 
Published: March 2022

AbstractThe response of an organ to stimuli emerges from the actions of individual cells. Recent cardiac single-cell RNA-sequencing studies of development, injury, and reprogramming have uncovered heterogeneous populations even among previously well-defined cell types, raising questions about what level of experimental resolution corresponds to disease-relevant, tissue-level phenotypes. In this review, we explore the biological meaning behind this cellular heterogeneity by undertaking an exhaustive analysis of single-cell transcriptomics in the heart (including a comprehensive, annotated compendium of studies published to date) and evaluating new models for the cardiac function that have emerged from these studies (including discussion and schematics that depict new hypotheses in the field). We evaluate the evidence to support the biological actions of newly identified cell populations and debate questions related to the role of cell-to-cell variability in development and disease. Finally, we present emerging epigenomic approaches that, when combined with single-cell RNA-sequencing, can resolve basic mechanisms of gene regulation and variability in cell phenotype.
Gender-related presentation, surgical treatment, outcome and failure to rescue after surgery for type A aortic dissection: results from a multicentre registry
Authors: Francica Alessandra , Vendramin Igor , Salizzoni Stefano , D’Onofrio Augusto , Gatti Giuseppe , Rinaldi Mauro , Gerosa Gino , Pappalardo Aniello , Livi Ugolino , Faggian Giuseppe , Onorati Francesco 
Published: March 2022

Abstract

OBJECTIVES
Reports on gender-related differences in perioperative characteristics and the outcome after surgery for type A acute aortic dissection are contradictory.

METHODS
Perioperative characteristics, outcome and overall or itemized failure-to-rescue rates were collected retrospectively and dichotomized by gender in patients operated on at 5 referral institutions. A propensity score matched analysis was performed to compared males and females with similar preoperative risk profiles. Multivariable analysis assessed gender-related predictors of 30-day mortality.

RESULTS
A total of 1271 patients were collected. Females (on average, 63 years old) developed type A acute aortic dissection, with differences in clinical presentation (number of intimal tears, thoracic pain at the onset of symptoms). Female-reported characteristics included lower frozen elephant trunk and elephant trunk procedures, higher femoral perfusion, retrograde cerebral perfusion and retrograde cardiopulmonary bypass restart after deep hypothermic circulatory arrest (P &lt; 0.05). The 30-day mortality was 19.8%, without a gender-related difference (P = 0.37). No substantial differences in hospital outcome and in items related to failure to rescue were reported. A total of 256 propensity score matched pairs of males and females were investigated. Previous differences in surgical techniques and strategies were still confirmed; however, a higher incidence of postoperative permanent coma (P = 0.02) was reported in the female population.

CONCLUSIONS
Different surgical techniques and operative strategies were used on the 2 genders, with a lower complexity in females. However, there were no differences in hospital outcome between genders, except for the higher incidence of coma in female patients.
Sex differences in mortality after first time, isolated coronary artery bypass graft surgery: a systematic review and meta-analysis of randomized controlled trials
Authors: Matthews Stacey , Buttery Amanda , O’Neil Adrienne , Sanders Julie , Marasco Silvana , Fredericks Suzanne , Martorella Geraldine , Keenan Niamh , Ghanes Anand , Wynne Rochelle 
Published: March 2022

Abstract

Aim
Reports of sex-specific differences in mortality after coronary artery bypass graft surgery (CABGS) are contradictory. The review aim was to determine whether CABGS is differentially efficacious than alternative procedures by sex, on short- and longer-term mortality.

Methods and results
EMBASE, CINAHL, Medline, and the Cochrane Library were searched. Inclusion criteria: English language, randomized controlled trials from 2010, comparing isolated CABGS to alternative revascularization. Analyses were included Mantel–Haenszel fixed-effects modelling, risk of bias (Cochrane RoB2), and quality assessment (CONSORT). PROSPERO Registration ID: CRD42020181673. The search yielded 4459 citations, and full-text review of 29 articles revealed nine studies for inclusion with variable time to follow-up. Risk of mortality for women was similar in pooled analyses [risk ratio (RR) 0.94, 95% confidence interval (CI) 0.84–1.05, P = 0.26] but higher in sensitivity analyses excluding ‘high risk’ patients (RR 1.22, 95% CI 1.01–1.48, P = 0.04). At 30 days and 10 years, in contrast to men, women had an 18% (RR 0.82, 95% CI 0.66–1.02, P = 0.08) and 19% (RR 0.81, 95% CI 0.69–0.95, P = 0.01) mortality risk reduction. At 1–2 years women had a 7% (RR 1.07, 95% CI 0.69–1.64, P = 0.77), and at 2–5 years a 25% increase in risk of mortality compared with men (RR 1.25, 95% CI 1.03–1.53, P = 0.03). Women were increasingly under-represented over time comprising 41% (30 days) to 16.7% (10 years) of the pooled population.

Conclusion
Meta-analysis revealed inconsistent sex-specific differences in mortality after CABGS. Trials with sex-specific stratification are required to ensure appropriate sex-differentiated treatments for revascularization.
Biotechnological use of dairy by-products for the production and microencapsulation of the food preservative enterocin CRL35
Authors: Farizano Juan V , Díaz Vergara Ladislao I , Masias Emilse , Baillo Ayelén A , Torino María I , Fadda Silvina , Vanden Braber Noelia L , Montenegro Mariana A , Saavedra Lucila , Minahk Carlos 
Published: March 2022

Abstract
Bacteriocins from Gram-positive bacteria have been proposed as natural food preservative and there is a need for large-scale production for commercial purposes. The aim of the present work is to evaluate whey, a cheese industrial by-product, for the production and microencapsulation of enterocin CRL35. Whey proved to be a promising basal medium for bacterial growth although the bacteriocin production was quite low. However, it could be much favored with the addition of yeast extract at concentrations as low as 0.5%. Besides improving bacteriocin production, this peptide was successfully microencapsulated by spray drying using whey protein concentrate and a chitosan derivative as wall materials. Microcapsules averaging 10 ± 5 μm diameter were obtained, with good structural integrity and high antimicrobial activity with a stability of at least 12 weeks at 4°C. In summary, sustainable bacteriocin production and microencapsulation was achieved recycling whey or its derivatives. In addition, the formulation owns high antimicrobial activity with a long shelf life. The development of a food preservative may represent a green solution for handling whey.
Effects of temperature and water saturation on the elastic moduli of sandstone and mudstone from the Lufeng geothermal field: experimental results and theoretical model
Authors: Zou Guangui , Zeng Hu , Gong Fei , Yin Caiyun , Li Shengqi , Peng Suping , Xu Zhengwei 
Published: March 2022

SUMMARY
The key issue in the 3-D seismic exploration of geothermal reservoirs is to determine how the petrophysical properties of geothermal reservoirs change with temperature. In this paper, physical experiments on six rock samples from the Yunnan Lufeng geothermal field were used to analyse the effect of temperature on the elastic moduli of dry rock. The laboratory measurements show that under formation pressure conditions, the bulk modulus and shear modulus of the studied rock decrease linearly with increasing temperature, and the rock moduli exhibit approximately linear relationships with temperature. Gassmann's equation can be used to predict the influence of pore fluid on the P- and S-wave velocities of the rocks. To include the temperature effect in Gassmann's equation, we separately considered the rock matrix and pore fluid; we combined thermoelastic theory to introduce the influence of temperature on the rock into Gassmann's equation and directly considered the influence of temperature on the pore fluid. The effects of fluid on the physical properties of rocks were evaluated based on Gassmann's equation while considering the effect of temperature. The results show that the rock shear modulus is affected by temperature more than the bulk modulus is, which implies that the S-wave information is more sensitive to temperature. When the uniform water saturation is less than 95 per cent, temperature is the main factor influencing the rock bulk modulus. When the uniform water saturation is greater than 95 per cent, the fluid is the main factor influencing the rock bulk modulus, and the rock shear modulus is affected by only temperature. Fluid replacement with Gassmann's equation achieves results that are more consistent with laboratory measurements when the influence of temperature is considered. Gassmann's equation considering the effect of temperature reveals crucial dependences of the seismic wave velocities and elastic moduli on temperature and fluid content.
An algorithm to assess the heating strategy of buildings in cold climates: a case study of Germany
Authors: Mazhar Abdur Rehman , Zou Yuliang , Zeng Cheng , Shen Yongliang , Liu Shuli 
Published: March 2022

Abstract
Two-thirds of the final energy consumption of the EU residential sector goes towards space heating of buildings, yet a huge portion of the population still suffers from energy poverty. Identifying optimum heating strategies of current buildings would be a solution to this crisis, which is the main aim of the developed algorithm in this research. The algorithm incorporates a modified version of the simple hourly method from the ISO 13790 standard to determine the hourly heating load and indoor temperatures of buildings based on any heating strategy. Flexibility in the input of building and weather data make this tool versatile with practicality towards building users and policymakers. With this algorithm, a case study to evaluate three commonly used domestic heating strategies has been established for nine different residential buildings in typical cold winter conditions in Germany. Most EU households heat their buildings either continuously throughout the day at fixed temperatures, sporadically at fixed times or at peak loads during the evening. The continuous heating strategy is rated the best consuming minimal energy with consistent temperatures and optimal thermal comfort ranges. The sporadic and peak load heating strategies provide fluctuating indoor temperatures with high standard deviations of up to 8.70°C while consuming a similar cumulative energy to the continuous heating strategy. Additionally, both these aforementioned strategies augment energy poverty and promote indoor mould formation on the building envelope caused by water vapor condensation. Consequently, this algorithm can be applicable to any building type of any region.
A randomized controlled trial of a pharmacist-led intervention to enhance knowledge of Vietnamese patients with type 2 diabetes mellitus
Authors: Nguyen Thao H , Tran Tam T T , Nguyen Nguyet K , Diep Han G , Vo Son D , Taxis Katja , Pham Suol T , Nguyen Thang 
Published: March 2022

Abstract

Objectives
We aimed to assess whether a pharmacist-led intervention enhances knowledge, medication adherence and glycemic control in patients with type 2 diabetes mellitus (T2DM).

Methods
We conducted a single-blinded randomized controlled trial in Vietnam. Individuals with T2DM were recruited from a general hospital and randomly allocated to intervention and routine care. The intervention group received routine care plus counselling intervention by a pharmacist, including providing drug information and answering individual patients’ queries relating to T2DM and medications, which had not been done in routine care. We assessed the outcomes: knowledge score as measured by the Diabetes Knowledge Questionnaire, self-reported adherence and fasting blood glucose (FBG) at the 1-month follow-up.

Key findings
A total of 165 patients (83 intervention, 82 control) completed the study; their mean age was 63.33 years, and 49.1% were males. The baseline characteristics of the patients were similar between the groups. At 1-month follow-up, the pharmacist’s intervention resulted in an improvement in all three outcomes: knowledge score [B = 5.527; 95% confidence intervals (CI): 3.982 to 7.072; P &lt; 0.001], adherence [odds ratio (OR) = 9.813; 95% CI: 2.456 to 39.205; P = 0.001] and attainment of target FBG (OR = 1.979; 95% CI: 1.029 to 3.806; P = 0.041).

Conclusions
The pharmacist-led intervention enhanced disease knowledge, medication adherence and glycemic control in patients with T2DM. This study provides evidence of the benefits of pharmacist counselling in addition to routine care for T2DM outpatients in a Vietnam population.