bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ultrasonography Analysis of Vessels Around the Forehead Midline
Authors: Park Hyun Jin , Lee Ji-Hyun , Lee Kyu-Lim , Choi You-Jin , Hu Kyung-Seok , Kim Hee-Jin 
Published: December 2020

Abstract

Background
Filler injection into the glabella is well known to be a highly dangerous procedure due to the high risk of embolism and intravascular injection. Although it is conventional practice to insert the cannula into the middle of the forehead to perform injections into the glabella or radix, vascular structures can be observed in this region during anatomic dissection procedures.

Objectives
The aim of this study was to characterize the blood vessels around the forehead midline in order to provide crucial anatomic information for ensuring the safety of noninvasive procedures involving the forehead and glabella.

Methods
Ultrasonography image scanning was performed at the following 4 points on the forehead midline: trichion (P1), metopion (P2), halfway point between metopion and glabella (P3), and glabella (P4). The courses and locations of vessels were identified and classified according to their proximity to the forehead midline.

Results
Vessels coursing within 0.75 cm either side of the forehead midline were found in 34% to 50% of individuals. Arteries running near the forehead midline tended to be dominant on the right side of the forehead except in the P4 area. About half of the individuals had vessels in the P4 area, of which 96.7% were veins.

Conclusions
The present results indicate that there are superficial vessels running close to the midline of the forehead. This anatomic information can explain the higher incidence of vascular complications during conventional aesthetic procedures. To ensure safety, the cannula entry point or needle puncture point for glabella augmentation should be reconsidered.
PharmKG: a dedicated knowledge graph benchmark for bomedical data mining
Authors: Zheng Shuangjia , Rao Jiahua , Song Ying , Zhang Jixian , Xiao Xianglu , Fang Evandro Fei , Yang Yuedong , Niu Zhangming 
Published: December 2020

AbstractBiomedical knowledge graphs (KGs), which can help with the understanding of complex biological systems and pathologies, have begun to play a critical role in medical practice and research. However, challenges remain in their embedding and use due to their complex nature and the specific demands of their construction. Existing studies often suffer from problems such as sparse and noisy datasets, insufficient modeling methods and non-uniform evaluation metrics. In this work, we established a comprehensive KG system for the biomedical field in an attempt to bridge the gap. Here, we introduced PharmKG, a multi-relational, attributed biomedical KG, composed of more than 500 000 individual interconnections between genes, drugs and diseases, with 29 relation types over a vocabulary of ~8000 disambiguated entities. Each entity in PharmKG is attached with heterogeneous, domain-specific information obtained from multi-omics data, i.e. gene expression, chemical structure and disease word embedding, while preserving the semantic and biomedical features. For baselines, we offered nine state-of-the-art KG embedding (KGE) approaches and a new biological, intuitive, graph neural network-based KGE method that uses a combination of both global network structure and heterogeneous domain features. Based on the proposed benchmark, we conducted extensive experiments to assess these KGE models using multiple evaluation metrics. Finally, we discussed our observations across various downstream biological tasks and provide insights and guidelines for how to use a KG in biomedicine. We hope that the unprecedented quality and diversity of PharmKG will lead to advances in biomedical KG construction, embedding and application.
XGSEA: CROSS-species gene set enrichment analysis via domain adaptation
Authors: Cai Menglan , Hao Nguyen Canh , Mamitsuka Hiroshi , Li Limin 
Published: December 2020

Abstract

Motivation
Gene set enrichment analysis (GSEA) has been widely used to identify gene sets with statistically significant difference between cases and controls against a large gene set. GSEA needs both phenotype labels and expression of genes. However, gene expression are assessed more often for model organisms than minor species. Also, importantly gene expression are not measured well under specific conditions for human, due to high risk of direct experiments, such as non-approved treatment or gene knockout, and then often substituted by mouse. Thus, predicting enrichment significance (on a phenotype) of a given gene set of a species (target, say human), by using gene expression measured under the same phenotype of the other species (source, say mouse) is a vital and challenging problem, which we call CROSS-species gene set enrichment problem (XGSEP).

Results
For XGSEP, we propose the CROSS-species gene set enrichment analysis (XGSEA), with three steps of: (1) running GSEA for a source species to obtain enrichment scores and $p$-values of source gene sets; (2) representing the relation between source and target gene sets by domain adaptation; and (3) using regression to predict $p$-values of target gene sets, based on the representation in (2). We extensively validated the XGSEA by using five regression and one classification measurements on four real data sets under various settings, proving that the XGSEA significantly outperformed three baseline methods in most cases. A case study of identifying important human pathways for T -cell dysfunction and reprogramming from mouse ATAC-Seq data further confirmed the reliability of the XGSEA.

Availability
Source code of the XGSEA is available through https://github.com/LiminLi-xjtu/XGSEA.
ProkSeq for complete analysis of RNA-Seq data from prokaryotes
Authors: Mahmud A K M Firoj , Delhomme Nicolas , Nandi Soumyadeep , Fällman Maria 
Published: December 2020

AbstractSummarySince its introduction, RNA-Seq technology has been used extensively in studies of pathogenic bacteria to identify and quantify differences in gene expression across multiple samples from bacteria exposed to different conditions. With some exceptions, tools for studying gene expression, determination of differential gene expression, downstream pathway analysis and normalization of data collected in extreme biological conditions is still lacking. Here, we describe ProkSeq, a user-friendly, fully automated RNA-Seq data analysis pipeline designed for prokaryotes. ProkSeq provides a wide variety of options for analysing differential expression, normalizing expression data and visualizing data and results.Availability and implementationProkSeq is implemented in Python and is published under the MIT source license. The pipeline is available as a Docker container https://hub.docker.com/repository/docker/snandids/prokseq-v2.0, or can be used through Anaconda: https://anaconda.org/snandiDS/prokseq. The code is available on Github: https://github.com/snandiDS/prokseq and a detailed user documentation, including a manual and tutorial can be found at https://prokseqV20.readthedocs.io.Supplementary informationSupplementary data are available at Bioinformatics online.
UniBioDicts: Unified access to Biological Dictionaries
Authors: Zobolas John , Touré Vasundra , Kuiper Martin , Vercruysse Steven 
Published: December 2020

Abstract

Summary
We present a set of software packages that provide uniform access to diverse biological vocabulary resources that are instrumental for current biocuration efforts and tools. The Unified Biological Dictionaries (UniBioDicts or UBDs) provide a single query-interface for accessing the online API services of leading biological data providers. Given a search string, UBDs return a list of matching term, identifier and metadata units from databases (e.g. UniProt), controlled vocabularies (e.g. PSI-MI) and ontologies (e.g. GO, via BioPortal). This functionality can be connected to input fields (user-interface components) that offer autocomplete lookup for these dictionaries. UBDs create a unified gateway for accessing life science concepts, helping curators find annotation terms across resources (based on descriptive metadata and unambiguous identifiers), and helping data users search and retrieve the right query terms.

Availability and implementation
The UBDs are available through npm and the code is available in the GitHub organisation UniBioDicts (https://github.com/UniBioDicts) under the Affero GPL license.

Supplementary information
Supplementary data are available at Bioinformatics online.
Virxicon: a lexicon of viral sequences
Authors: Kudla Mateusz , Gutowska Kaja , Synak Jaroslaw , Weber Mirko , Bohnsack Katrin Sophie , Lukasiak Piotr , Villmann Thomas , Blazewicz Jacek , Szachniuk Marta 
Published: December 2020

Abstract

Motivation
Viruses are the most abundant biological entities and constitute a large reservoir of genetic diversity. In recent years, knowledge about them has increased significantly as a result of dynamic development in life sciences and rapid technological progress. This knowledge is scattered across various data repositories, making a comprehensive analysis of viral data difficult.

Results
In response to the need for gathering a comprehensive knowledge of viruses and viral sequences, we developed Virxicon, a lexicon of all experimentally acquired sequences for RNA and DNA viruses. The ability to quickly obtain data for entire viral groups, searching sequences by levels of taxonomic hierarchy—according to the Baltimore classification and ICTV taxonomy—and tracking the distribution of viral data and its growth over time are unique features of our database compared to the other tools.

Availabilityand implementation
Virxicon is a publicly available resource, updated weekly. It has an intuitive web interface and can be freely accessed at http://virxicon.cs.put.poznan.pl/.
Consistency guarantees for greedy permutation-based causal inference algorithms
Authors: Solus L , Wang Y , Uhler C 
Published: December 2020

SummaryDirected acyclic graphical models are widely used to represent complex causal systems. Since the basic task of learning such a model from data is NP-hard, a standard approach is greedy search over the space of directed acyclic graphs or Markov equivalence classes of directed acyclic graphs. As the space of directed acyclic graphs on $p$ nodes and the associated space of Markov equivalence classes are both much larger than the space of permutations, it is desirable to consider permutation-based greedy searches. Here, we provide the first consistency guarantees, both uniform and high dimensional, of a greedy permutation-based search. This search corresponds to a simplex-like algorithm operating over the edge-graph of a subpolytope of the permutohedron, called a directed acyclic graph associahedron. Every vertex in this polytope is associated with a directed acyclic graph, and hence with a collection of permutations that are consistent with the directed acyclic graph ordering. A walk is performed on the edges of the polytope maximizing the sparsity of the associated directed acyclic graphs. We show via simulated and real data that this permutation search is competitive with current approaches.
Real-Time Lived Experience of Social Work Students in Their Field Training during the Coronavirus Crisis: Insights from Photovoice-Based Research
Authors: Malka Menny 
Published: December 2020

Abstract
The present paper is based on a photovoice study conducted with sixteen undergraduate social work students in their third year of study, examining their real-time lived experience of their fieldwork training in the immediate aftermath of the outbreak of the coronavirus pandemic. The findings of the study, based on an analysis of sixty-six photovoices, indicate four main narratives encapsulating the students’ real-time lived experiences: (i) the challenges of encountering the crisis; (ii) conceptualizing the experience; (iii) coping practices; (iv) perspectives for the future. The findings are discussed in the light of shared traumatic reality theory and transformative learning theory. Following the use of the photovoice methodology, the research conclusions encourage the assimilation of creative and entrepreneurial models of teaching and practice, in order to enable the inclusion of different types of knowledge and life experiences in different learning and research spaces.
Nucleus Accumbens Stimulation Modulates Inhibitory Control by Right Prefrontal Cortex Activation in Obsessive-Compulsive Disorder
Authors: Lopez-Sosa Fernando , Reneses Blanca , Sanmartino Florencia , Galarza-Vallejo Ana , Garcia-Albea Julia , Cruz-Gomez Alvaro J , Yebra Mar , Oliviero Antonio , Barcia Juan A , Strange Bryan A , Gonzalez-Rosa Javier J 
Published: December 2020

Abstract
Inhibitory control is considered a compromised cognitive function in obsessive-compulsive (OCD) patients and likely linked to corticostriatal circuitry disturbances. Here, 9 refractory OCD patients treated with deep brain stimulation (DBS) were evaluated to address the dynamic modulations of large-scale cortical network activity involved in inhibitory control after nucleus accumbens (NAc) stimulation and their relationship with cortical thickness. A comparison of DBS “On/Off” states showed that patients committed fewer errors and exhibited increased intraindividual reaction time variability, resulting in improved goal maintenance abilities and proactive inhibitory control. Visual P3 event-related potentials showed increased amplitudes during Go/NoGo performance. Go and NoGo responses increased cortical activation mainly over the right inferior frontal gyrus and medial frontal gyrus, respectively. Moreover, increased cortical activation in these areas was equally associated with a higher cortical thickness within the prefrontal cortex. These results highlight the critical role of NAc DBS for preferentially modulating the neuronal activity underlying sustained speed responses and inhibitory control in OCD patients and show that it is triggered by reorganizing brain functions to the right prefrontal regions, which may depend on the underlying cortical thinning. Our findings provide updated structural and functional evidence that supports critical dopaminergic-mediated frontal-striatal network interactions in OCD.
Human Immunodeficiency Virus Is Associated With Higher Levels of Systemic Inflammation Among Kenyan Adults Despite Viral Suppression
Authors: Masyuko Sarah J , Page Stephanie T , Polyak Stephen J , Kinuthia John , Osoti Alfred O , Otieno Fredrick C , Kibachio Joseph M , Mogaka Jerusha N , Macharia Paul M , Chohan Bhavna H , Wogner Jessica , O’Connor Aidan , Temu Tecla M , Zifodya Jerry S , Otedo Amos , Nakanjako Damalie , Hughes James P , Farquhar Carey 
Published: December 2020

Abstract

Background
Systemic inflammation independently predicts future cardiovascular events and is associated with a 2-fold increase in cardiovascular disease (CVD) risk among persons living with human immunodeficiency virus (PLHIV). We examined the association between inflammatory markers, HIV status, and traditional CVD risk factors.

Methods
We conducted a cross-sectional study of Kenyan adults with and without HIV seeking care at Kisumu County Hospital. Using a multiplex immunoassay, we measured interleukin (IL) 1β, IL-6, tumor necrosis factor α (TNF-α), and high-sensitivity C-reactive protein (hsCRP) concentrations. We compared inflammatory marker concentrations by HIV status using the Wilcoxon rank-sum test. Multivariable linear regression was used to evaluate associations between inflammatory biomarkers and HIV status, adjusting for CVD risk factors.

Results
We enrolled 286 PLHIV and 277 HIV-negative participants. Median duration of antiretroviral therapy for PLHIV was 8 years (interquartile range, 4–10) and 96% were virally suppressed. PLHIV had a 51% higher mean IL-6 concentration (P &lt; .001), 39% higher mean IL-1β (P = .005), 40% higher mean TNF-α (P &lt; .001), and 27% higher mean hsCRP (P = .008) compared with HIV-negative participants, independent of CVD risk factors. Male sex, older age, and obesity were associated with higher concentrations of inflammatory markers. Restricting to PLHIV, viral load of ≥1000 copies/mL was associated with higher TNF-α levels (P = .013).

Conclusions
We found higher levels of systemic inflammatory biomarkers among PLHIV who were virally suppressed, and this was independent of traditional CVD risk factors. Further longitudinal analyses to determine whether these inflammatory markers predict future CVD events, and are possible therapeutic targets among PLHIV, are warranted.
Biomarkers to Distinguish Bacterial From Viral Pediatric Clinical Pneumonia in a Malaria-Endemic Setting
Authors: Gillette Michael A , Mani D R , Uschnig Christopher , Pellé Karell G , Madrid Lola , Acácio Sozinho , Lanaspa Miguel , Alonso Pedro , Valim Clarissa , Carr Steven A , Schaffner Stephen F , MacInnis Bronwyn , Milner Danny A , Bassat Quique , Wirth Dyann F 
Published: December 2020

Abstract

Background
Differential etiologies of pediatric acute febrile respiratory illness pose challenges for all populations globally, but especially in malaria-endemic settings because the pathogens responsible overlap in clinical presentation and frequently occur together. Rapid identification of bacterial pneumonia with high-quality diagnostic tools would enable appropriate, point-of-care antibiotic treatment. Current diagnostics are insufficient, and the discovery and development of new tools is needed. We report a unique biomarker signature identified in blood samples to accomplish this.

Methods
Blood samples from 195 pediatric Mozambican patients with clinical pneumonia were analyzed with an aptamer-based, high-dynamic-range, quantitative assay (~1200 proteins). We identified new biomarkers using a training set of samples from patients with established bacterial, viral, or malarial pneumonia. Proteins with significantly variable abundance across etiologies (false discovery rate &lt;0.01) formed the basis for predictive diagnostic models derived from machine learning techniques (Random Forest, Elastic Net). Validation on a dedicated test set of samples was performed.

Results
Significantly different abundances between bacterial and viral infections (219 proteins) and bacterial infections and mixed (viral and malaria) infections (151 proteins) were found. Predictive models achieved &gt;90% sensitivity and &gt;80% specificity, regardless of number of pathogen classes. Bacterial pneumonia was strongly associated with neutrophil markers—in particular, degranulation including HP, LCN2, LTF, MPO, MMP8, PGLYRP1, RETN, SERPINA1, S100A9, and SLPI.

Conclusions
Blood protein signatures highly associated with neutrophil biology reliably differentiated bacterial pneumonia from other causes. With appropriate technology, these markers could provide the basis for a rapid diagnostic for field-based triage for antibiotic treatment of pediatric pneumonia.
Low dialysis potassium bath is associated with lower mortality in end-stage renal disease patients admitted to hospital with severe hyperkalemia
Authors: Singh Tripti , Alagasundaramoorthy Sayee , Gregory Andrew , Astor Brad C , Maursetter Laura 
Published: December 2020

Abstract

Background
Hyperkalemia is a modifiable risk factor for sudden cardiac death, a leading cause of mortality in hemodialysis (HD) patients. The optimal treatment of hyperkalemia in hospitalized end-stage renal disease (ESRD) patients is nonexistent in literature, which has prompted studies from outpatient dialysis to be extrapolated to inpatient care. The goal of this study was to determine if low-potassium dialysate 1 mEq/L is associated with higher mortality in hospitalized ESRD patients with severe hyperkalemia (serum potassium &gt;6.5 mmol/L).

Methods
We conducted a retrospective study of all adult ESRD patients admitted with severe hyperkalemia between January 2011 and August 2016.

Results
There were 209 ESRD patients on HD admitted with severe hyperkalemia during the study period. Mean serum potassium was 7.1 mmol/L. In-hospital mortality or cardiac arrest in ESRD patients with severe hyperkalemia was 12.4%. Median time to dialysis after serum potassium result was 2.0 h (25, 75 interquartile range 0.9, 4.2 h). Totally, 47.4% of patients received dialysis with 1 mEq/L concentration potassium bath. The use of 1 mEq/L potassium bath was associated with significantly lower mortality or cardiac arrest in ESRD patients admitted with severe hyperkalemia (odds ratio 0.27, 95% confidence interval 0.09–0.80, P = 0.01).

Conclusion
We conclude that use of 1 mEq/L potassium bath for treatment of severe hyperkalemia (&gt;6.5 mmol/L) in hospitalized ESRD patients is associated with decreased in-hospital mortality or cardiac arrest.
CorkOakDB—The Cork Oak Genome Database Portal
Authors: Arias-Baldrich Cirenia , Silva Marta Contreiras , Bergeretti Filippo , Chaves Inês , Miguel Célia , Saibo Nelson J M , Sobral Daniel , Faria Daniel , Barros Pedro M 
Published: December 2020

Abstract
Quercus suber (cork oak) is an evergreen tree native to the Mediterranean basin, which plays a key role in the ecology and economy of this area. Over the last decades, this species has gone through an observable decline, mostly due to environmental factors. Deciphering the mechanisms of cork oak’s response to the environment and getting a deep insight into its biology are crucial to counteract biotic and abiotic stresses compromising the stability of a unique ecosystem. In the light of these setbacks, the publication of the genome in 2018 was a major step towards understanding the genetic make-up of this species. In an effort to integrate this information in a comprehensive, accessible and intuitive format, we have developed The Cork Oak Genome Database Portal (CorkOakDB). The CorkOakDB is supported by the BioData.pt e-infrastructure, the Portuguese ELIXIR node for biological data. The portal gives public access to search and explore the curated genomic and transcriptomic data on this species. Moreover, CorkOakDB provides a user-friendly interface and functional tools to help the research community take advantage of the increased accessibility to genomic information. A study case is provided to highlight the functionalities of the portal. CorkOakDB guarantees the update, curation and data collection, aiming to collect data besides the genetic/genomic information, in order to become the main repository in cork oak research.
Database URL: http://corkoakdb.org/