bluuebunny/crossref_metadata_2025_split huggingface dataset:
LBERT: Lexically aware Transformer-based Bidirectional Encoder Representation model for learning universal bio-entity relations
Authors: Warikoo Neha , Chang Yung-Chun , Hsu Wen-Lian 
Published: August 2020

Abstract

Motivation
Natural Language Processing techniques are constantly being advanced to accommodate the influx of data as well as to provide exhaustive and structured knowledge dissemination. Within the biomedical domain, relation detection between bio-entities known as the Bio-Entity Relation Extraction (BRE) task has a critical function in knowledge structuring. Although recent advances in deep learning-based biomedical domain embedding have improved BRE predictive analytics, these works are often task selective or use external knowledge-based pre-/post-processing. In addition, deep learning-based models do not account for local syntactic contexts, which have improved data representation in many kernel classifier-based models. In this study, we propose a universal BRE model, i.e. LBERT, which is a Lexically aware Transformer-based Bidirectional Encoder Representation model, and which explores both local and global contexts representations for sentence-level classification tasks.

Results
This article presents one of the most exhaustive BRE studies ever conducted over five different bio-entity relation types. Our model outperforms state-of-the-art deep learning models in protein–protein interaction (PPI), drug–drug interaction and protein–bio-entity relation classification tasks by 0.02%, 11.2% and 41.4%, respectively. LBERT representations show a statistically significant improvement over BioBERT in detecting true bio-entity relation for large corpora like PPI. Our ablation studies clearly indicate the contribution of the lexical features and distance-adjusted attention in improving prediction performance by learning additional local semantic context along with bi-directionally learned global context.

Availability and implementation
Github. https://github.com/warikoone/LBERT.

Supplementary information
Supplementary data are available at Bioinformatics online.
FuSe: a tool to move RNA-Seq analyses from chromosomal/gene loci to functional grouping of mRNA transcripts
Authors: Gupta Rajinder , Schrooders Yannick , Verheijen Marcha , Roth Adrian , Kleinjans Jos , Caiment Florian 
Published: August 2020

Abstract

Summary
Typical RNA sequencing (RNA-Seq) analyses are performed either at the gene level by summing all reads from the same locus, assuming that all transcripts from a gene make a protein or at the transcript level, assuming that each transcript displays unique function. However, these assumptions are flawed, as a gene can code for different types of transcripts and different transcripts are capable of synthesizing similar, different or no protein. As a consequence, functional changes are not well illustrated by either gene or transcript analyses. We propose to improve RNA-Seq analyses by grouping the transcripts based on their similar functions. We developed FuSe to predict functional similarities using the primary and secondary structure of proteins. To estimate the likelihood of proteins with similar functions, FuSe computes two confidence scores: knowledge (KS) and discovery (DS) for protein pairs. Overlapping protein pairs exhibiting high confidence are grouped to form ‘similar function protein groups’ and expression is calculated for each functional group. The impact of using FuSe is demonstrated on in vitro cells exposed to paracetamol, which highlight genes responsible for cell adhesion and glycogen regulation which were earlier shown to be not differentially expressed with traditional analysis methods.

Availability and implementation
The source code is available at https://github.com/rajinder4489/FuSe. Data for APAP exposure are available in the BioStudies database (http://www.ebi.ac.uk/biostudies) under accession numbers S-HECA143, S-HECA(158) and S-HECA139.

Supplementary information
Supplementary data are available at Bioinformatics online.
Bipartite tight spectral clustering (BiTSC) algorithm for identifying conserved gene co-clusters in two species
Authors: Sun Yidan Eden , Zhou Heather J , Li Jingyi Jessica 
Published: August 2020

Abstract

Motivation
Gene clustering is a widely used technique that has enabled computational prediction of unknown gene functions within a species. However, it remains a challenge to refine gene function prediction by leveraging evolutionarily conserved genes in another species. This challenge calls for a new computational algorithm to identify gene co-clusters in two species, so that genes in each co-cluster exhibit similar expression levels in each species and strong conservation between the species.

Results
Here, we develop the bipartite tight spectral clustering (BiTSC) algorithm, which identifies gene co-clusters in two species based on gene orthology information and gene expression data. BiTSC novelly implements a formulation that encodes gene orthology as a bipartite network and gene expression data as node covariates. This formulation allows BiTSC to adopt and combine the advantages of multiple unsupervised learning techniques: kernel enhancement, bipartite spectral clustering, consensus clustering, tight clustering and hierarchical clustering. As a result, BiTSC is a flexible and robust algorithm capable of identifying informative gene co-clusters without forcing all genes into co-clusters. Another advantage of BiTSC is that it does not rely on any distributional assumptions. Beyond cross-species gene co-clustering, BiTSC also has wide applications as a general algorithm for identifying tight node co-clusters in any bipartite network with node covariates. We demonstrate the accuracy and robustness of BiTSC through comprehensive simulation studies. In a real data example, we use BiTSC to identify conserved gene co-clusters of Drosophila melanogaster and Caenorhabditis elegans, and we perform a series of downstream analysis to both validate BiTSC and verify the biological significance of the identified co-clusters.

Availability and implementation
The Python package BiTSC is open-access and available at https://github.com/edensunyidan/BiTSC.

Supplementary information
Supplementary data are available at Bioinformatics online.
ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes
Authors: Moshiri Niema 
Published: August 2020

Abstract

Motivation
In molecular epidemiology, the identification of clusters of transmissions typically requires the alignment of viral genomic sequence data. However, existing methods of multiple sequence alignment (MSA) scale poorly with respect to the number of sequences.

Results
ViralMSA is a user-friendly reference-guided MSA tool that leverages the algorithmic techniques of read mappers to enable the MSA of ultra-large viral genome datasets. It scales linearly with the number of sequences, and it is able to align tens of thousands of full viral genomes in seconds. However, alignments produced by ViralMSA omit insertions with respect to the reference genome.

Availability and implementation
ViralMSA is freely available at https://github.com/niemasd/ViralMSA as an open-source software project.

Supplementary information
Supplementary data are available at Bioinformatics online.
Regional extracorporeal membrane oxygenation retrieval service during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic: an interdisciplinary team approach to maintain service provision despite increased demand
Authors: Rafiq Muhammad U , Valchanov Kamen , Vuylsteke Alain , Taghavi Fouad J , Iyer Swetha B , Sudarshan Catherine D , Fowles Jo-Anne , Anderson Simon , Govender Pooveshni , Holmes Miranda , White Alexander , Mishra Abhi , Mwaura Lucy , Jenkins David P 
Published: August 2020

Abstract

OBJECTIVES
Coronavirus disease 2019 is a new contagious disease that has spread rapidly across the world. It is associated with high mortality in those who develop respiratory complications and require admission to intensive care. Extracorporeal membrane oxygenation (ECMO) is a supportive therapy option for selected severely ill patients who deteriorate despite the best supportive care. During the coronavirus disease 2019 pandemic, extra demand led to staff reorganization; hence, cardiac surgery consultants joined the ECMO retrieval team. This article describes how we increased service provisions to adapt to the changes in activity and staffing.

METHODS
The data were collected from 16 March 2020 to 8 May 2020. The patients were referred through a dedicated Web-based referral portal to cope with increasing demand. The retrieval team attended the referring hospital, reviewed the patients and made the final decision to proceed with ECMO.

RESULTS
We reported 41 ECMO retrieval runs during this study period. Apart from staffing changes, other retrieval protocols were maintained. The preferred cannulation method for veno-venous ECMO was drainage via the femoral vein and return to the right internal jugular vein. There were no complications reported during cannulation or transport.

CONCLUSIONS
Staff reorganization in a crisis is of paramount importance. For those with precise transferrable skills, experience can be gained quickly with appropriate supervision. Therefore, the team members were selected based on skill mix rather than on roles that are more traditional. We have demonstrated that an ECMO retrieval service can be reorganized swiftly and successfully to cope with the sudden increase in demand by spending cardiac surgeons services to supplement the anaesthetic-intensivist roles.
The effect of minimally invasive pectus excavatum repair on thoracic scoliosis
Authors: İşcan Mehlika , Kılıç Burcu , Turna Akif , Kaynak Mehmet Kamil 
Published: August 2020

AbstractOBJECTIVESThe Nuss technique comprises the placement of an intrathoracic bar behind the sternum. However, besides improving the body posture through the correction of the pectus excavatum (PE), this procedure may cause or worsen thoracic scoliosis as a result of the considerable stress loaded on the chest wall and the thorax. Our goal was to investigate the impact of the Nuss procedure on the thoracic spinal curvature in patients with PE.METHODSA total of 100 patients with PE who underwent the Nuss procedure were included in the study and evaluated retrospectively. The Haller index (HI), asymmetry index and sternal torsion angle were calculated from thoracic computed tomography images before the operation. To evaluate the scoliosis in the T2–T8 thoracic vertebrae, Cobb angles were calculated on a plain chest X-ray before the Nuss operation and after the removal of the bar. Cobb angles were classified as normal (5°), scoliotic posture (5°–10°) and scoliosis (&gt;10°). All angles before and after the Nuss operation were compared. The patients were followed up for a mean of 41 months. Substernal bars were removed after a mean of 33 months.RESULTSThe mean age of the patients was 19.6 ± 6.7 years. The Cobb angle was statistically significantly increased in all patients (P = 0.01), male patients (P = 0.01) and children (P = 0.046) but not in adults (P = 0.11) and female patients (P = 0.54). The Cobb angle was increased in patients with severe (HI ≥ 3.5) but not in patients with moderate (3.2 &lt; HI &lt; 3.5) or mild (2.0 &lt; HI &lt; 3.2) PE deformity.CONCLUSIONSThe present study shows that the Cobb angle indicates that the severity of thoracic scoliosis increases following the Nuss procedure, particularly in male patients, in patients with mild and moderate sternal torsion angle and in those with a high preoperative HI. This alteration might be due to correctional forces and torque applied by the bar. Patients undergoing the Nuss procedure for the correction of PE should be followed up strictly for timely diagnosis and management of the scoliosis.
Clinical outcomes of complete versus incomplete revascularization in patients treated with coronary artery bypass grafting: insights from the TiCAB trial
Authors: Schaefer Andreas , Conradi Lenard , Schneeberger Yvonne , Reichenspurner Hermann , Sandner Sigrid , Tebbe Ulrich , Nowak Bernd , Stritzke Jan , Kastrati Adnan , Schunkert Heribert , Scheidt Moritz von ,   for the TiCAB investigators
Published: August 2020

Abstract

OBJECTIVES
In this post hoc analysis of the Ticagrelor in coronary artery bypass grafting (CABG) trial, we aimed to analyse patients treated with CABG receiving either complete revascularization (CR) or incomplete revascularization (ICR) independent from random allocation to either ticagrelor or aspirin.

METHODS
Of 1859 patients enrolled in the Ticagrelor in CABG trial, 1550 patients (83.4%) received CR and 309 patients (16.6%) ICR. Outcomes were evaluated regarding all-cause mortality, cardiovascular death, myocardial infarction (MI), repeat revascularization, stroke and bleeding within 12 months after CABG.

RESULTS
Baseline parameters revealed significant differences regarding clinical presentation (stable angina pectoris: CR 68.9% vs ICR 71.2%, instable angina pectoris: 14.1% vs 7.8%, non-ST elevation MI: 17.0% vs 21.0%, P ˂ 0.01), lesion characteristics (chronic total occlusion: CR 91.3% vs ICR 96.8%, P ˂ 0.01), operative technique [off-pump coronary artery bypass surgery (OPCAB): CR 3.0% vs ICR 6.1%, P ˂ 0.01] and number of utilized grafts (total number of grafts: 2.69/patient vs 2.49/patient, P ˂ 0.001). ICR patients displayed a significantly increased risk of repeat revascularization [hazard ratio (HR) 1.91, 95% confidence interval (CI) 1.16–3.16; P &lt; 0.01] and percutaneous coronary intervention (HR 1.95, 95% CI 1.13–3.35; P &lt; 0.05) within 12 months after CABG. Higher risk for repeat revascularization in ICR patients was independent from random allocation to either ticagrelor or aspirin and persisted after adjustment for baseline imbalances.

CONCLUSIONS
Patients with ICR presented more stable at the time of admission, but received less grafts, highly likely due to a higher rate of chronic total occlusion lesions and performed OPCAB. Although mortality presented no difference between groups, our results suggest that patients benefit from CR with regard to prevention of repeat revascularization.
Comparative Genomics Underlines Multiple Roles of Profftella, an Obligate Symbiont of Psyllids: Providing Toxins, Vitamins, and Carotenoids
Authors: Nakabachi Atsushi , Piel Jörn , Malenovský Igor , Hirose Yuu 
Published: August 2020

Abstract
The Asian citrus psyllid Diaphorina citri (Insecta: Hemiptera: Psylloidea), a serious pest of citrus species worldwide, harbors vertically transmitted intracellular mutualists, Candidatus Profftella armatura (Profftella_DC, Gammaproteobacteria: Burkholderiales) and Candidatus Carsonella ruddii (Carsonella_DC, Gammaproteobacteria: Oceanospirillales). Whereas Carsonella_DC is a typical nutritional symbiont, Profftella_DC is a unique defensive symbiont with organelle-like features, including intracellular localization within the host, perfect infection in host populations, vertical transmission over evolutionary time, and drastic genome reduction down to much less than 1 Mb. Large parts of the 460-kb genome of Profftella_DC are devoted to genes for synthesizing a polyketide toxin; diaphorin. To better understand the evolution of this unusual symbiont, the present study analyzed the genome of Profftella_Dco, a sister lineage to Profftella_DC, using Diaphorina cf. continua, a host psyllid congeneric with D. citri. The genome of coresiding Carsonella (Carsonella_Dco) was also analyzed. The analysis revealed nearly perfect synteny conservation in these genomes with their counterparts from D. citri. The substitution rate analysis further demonstrated genomic stability of Profftella which is comparable to that of Carsonella. Profftella_Dco and Profftella_DC shared all genes for the biosynthesis of diaphorin, hemolysin, riboflavin, biotin, and carotenoids, underlining multiple roles of Profftella, which may contribute to stabilizing symbiotic relationships with the host. However, acyl carrier proteins were extensively amplified in polyketide synthases DipP and DipT for diaphorin synthesis in Profftella_Dco. This level of acyl carrier protein augmentation, unprecedented in modular polyketide synthases of any known organism, is not thought to influence the polyketide structure but may improve the synthesis efficiency.
Food Fingerprinting: Using a Two-Tiered approach to Monitor and Mitigate Food Fraud in Rice
Authors: McGrath Terence F , Shannon Maeve , Chevallier Olivier P , Ch Ratnasekhar , Xu Fei , Kong Fanzhou , Peng Hong , Teye Ernest , Akaba Selorm , Wu Di , Wu Libiao , Cai Qiang , Le Nguyen Doan Duy , Le Van Viet Man , Pandor Sufyan , Kapil Arun P , Zhang Guangtao , McBride Mary , Elliott Christopher T 
Published: August 2020

Abstract

Background
Rice is an important staple food that is consumed around the world. Like many foods, the price of rice varies considerably, from very inexpensive for a low-quality product to premium pricing for highly prized varieties from specific locations. Therefore, like other foods it is vulnerable to economically motivated adulteration through substitution or misrepresentation of inferior-quality rice for more expensive varieties.

Objective
In this article we describe results of a research project focused on addressing potential food fraud issues related to rice supplies in China, India, Vietnam, and Ghana. Rice fraud manifests differently in each country; therefore, tailored solutions were required.

Method
Here we describe a two-tiered testing regime of rapid screening using portable Near Infrared technology supported by second tier testing using mass spectrometry-based analysis of suspicious samples.

Results
Portable Near Infrared spectroscopy models and laboratory-based Gas Chromatography-Mass Spectrometry methods were developed to differentiate between: high-value Basmati rice varieties and their potential adulterants; six Geographic Indicated protected rice varieties from specific regions within China; various qualities of rice in Ghana and Vietnam; and locally produced and imported rice in Ghana. Furthermore, an Inductively Coupled Plasma-Mass Spectrometry method was developed to support the Chinese rice varieties methods as well as a Liquid Chromatography Quadrupole Time-of-Flight Mass Spectrometry method for quality differentiation in Vietnam.

Conclusions/Highlights
This two-tier approach can provide a substantially increased level of testing through rapid screening outside of the laboratory with the reassurance of corroborating mass spectrometry-based laboratory analysis to support decision making.
Setting Up an Abbreviated Breast MRI Program: Our Two-year Implementation Experience
Authors: Marshall Holly N , Plecha Donna M 
Published: August 2020

Abstract
Mammography is the long-standing screening tool for detecting breast cancer. Breast MRI is the most sensitive screening modality; however, it has been reserved for patients who are at an increased risk of developing breast cancer. Abbreviated breast MRI (AB-MRI) overcomes the limitations of cost and scanner time when considering screening patients at average or slightly elevated risk. This paper discusses the practical considerations for implementing an AB-MRI program on many levels, after our two-year experience. One of the first steps in introducing an AB-MRI program, since there is no standardized protocol, is determining and implementing a protocol. Since there is no Current Procedural Terminology code for an AB-MRI, a self-pay charge should be established. Adjusting MRI scheduling templates to accommodate the 10-minute AB-MRI exam is helpful. Communication with the breast team and the education of referring physicians is a key step to ensure awareness of a new screening option. As the AB-MRI program is incorporated into a practice, auditing of routine screening outcomes several months after commencement is invaluable to the continued success of the program.
Effects of medium-chain fatty acids as alternatives to ZnO or antibiotics in nursery pig diets
Authors: Dahmer Payton L , Leubcke Grace E , Lerner Annie B , Jones Cassandra K 
Published: August 2020

Abstract
The objective of this experiment was to evaluate the effects of medium-chain fatty acids (MCFA) on nursery pig performance in place of ZnO and carbadox. In this trial, 360 weanling pigs (DNA 200 × 400; 5.4 ± 0.07 kg BW) were fed for 35 d, with 6 pigs/pen and 10 replicate pens/treatment. Upon weaning, pigs were weighed and allotted to pens based on BW in a completely randomized design to one of six treatment diets: 1) Negative control (no added ZnO or carbadox); 2) Control + 3,000 ppm ZnO in phase 1 and 2,000 ppm ZnO in phase 2; 3) Control + 50 g/ton carbadox; 4) Control + C6:C8:C10 MCFA blend; 5) Control + Proprietary Oil Blend (Feed Energy Corp.); and 6) Control + monolaurate blend (FORMI GML from ADDCON). Treatment diets were fed through two dietary phases and a common diet fed through phase three. Pigs and feeders were individually weighed on a weekly basis to determine average daily gain (ADG) and average daily feed intake (ADFI). From days 0 to 19, pigs being fed the ZnO or Carbadox diets had the greatest ADG. These pigs had significantly higher (P &lt; 0.05) ADG than pigs fed the control or Feed Energy Proprietary Oil Blend, whereas pigs fed the C6:C8:C10 blend or FORMI GML diets had similar (P &gt; 0.05) ADG compared with those fed carbadox. These effects were primarily driven by feed intake, which was greatest (P &lt; 0.05) in pigs fed ZnO and carbadox. Treatment diet had a marginally significant effect (P = 0.078) on G:F. Increased day 19 BW (P &lt; 0.05) was observed for pigs fed ZnO and carbadox compared with the negative control, whereas other treatments were intermediate. Additionally, blood data and fecal scores were collected throughout the trial. On day 21, pigs fed ZnO or carbadox had higher (P &lt; 0.0001) glucose values than those fed the Feed Energy Proprietary Oil Blend, with other diets being intermediate, showing potential health benefits of carbadox. Although ZnO resulted in higher glucose values, it may also contribute to hepatic issues. Although replacing ZnO and carbadox with MCFA did not result in significant changes in gut microflora, it did affect fecal consistency by softening the feces during the treatment period. Overall, these results show that ZnO and carbadox are valuable additives to help maximize growth performance in early stages of the nursery. Some MCFA products, like FORMI GML, may result in similar performance, whereas others restrict it. Thus, additional research is needed to study the effectiveness of MCFA to replace ZnO or feed-based antibiotics.
Cognitive declines after perioperative covert stroke: Recent advances and perspectives
Authors: Yu Shiqiu , Li Peiying 
Published: August 2020

Purpose of review
With the aging of the population, there are increasing number of aged patients who require surgical interventions. Perioperative covert stroke is emerging as an important health threat and social burden that could affect patients’ long-term neurological outcomes.

Recent findings
Recent findings of the association between perioperative covert stroke with long-term cognitive declines of surgical patients highlighted the significance of the silent cognitive function killer—perioperative covert stroke. Considering the devastating long-term consequence of the asymptomatic covert stroke, early diagnosis and prevention are turning out as crucial problems to tackle. The evolving brain imaging techniques, such as multimodel MRI sequences are not only able to detect early, small and subtle injuries of the acute ischemic lesions, but also quite advantageous in capturing the preexisting brain vascular diseases that are considered as important risk factors of covert stroke. However, effective predictive markers are still lacking to identify high risk patients for perioperative covert stroke, rendering an unmet need of investigations in this regard.

Summary
The present review will summarize recent findings in perioperative covert stroke and highlight future perspectives of its early diagnosis and the impact of postoperative cognitive impairments.