bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tranexamic Acid Use in Foot and Ankle Surgery
Authors: Johns William L. , Walley Kempland C. , Seedat Raees , Jackson Benjamin , Boukhemis Karim , Gonzalez Tyler 
Published: December 2020

Background: There is a potential role for tranexamic acid (TXA) use in foot and ankle procedures; however, the benefits of this intervention have not been fully elucidated. The purpose of this study was to explore the safety, outcomes, and medical complication profile of the use of intravenous TXA in patients undergoing foot and ankle surgery. Methods: A prospective study with retrospective review of 241 patients undergoing elective and traumatic foot and ankle procedures was performed. One gram of intravenous (IV) TXA was administered prior to incision. Patients were followed and evaluated for medical comorbidities, intraoperative blood loss, wound complication, superficial and deep infections, hematoma formation, medical complications, 30-day hospital readmission rate, and return visits to the emergency department or urgent care setting prior to first postoperative visit. Descriptive statistics were used for subgroup analysis. Mean postoperative follow-up was 4.5 months. Results: Estimated blood loss in all cases was less than 20 mL. There was 1 case of superficial cellulitis (1/241, 0.4%), 1 deep infection after Achilles tendon repair (1/241, 0.4%), 4 cases of delayed wound healing (4/241, 1.6%), 1 instance of deep vein thrombosis (1/241, 0.4%), and 2 cases of postoperative pulmonary embolism (2/241, 0.8%). There were no instances of postoperative hematoma formation. There were no additional recorded thromboembolic events. There were no adverse drug reactions. There were no 30-day hospital readmissions or return visits to the emergency department or urgent care setting before the first postoperative visit. In a subgroup analysis, there was no significant difference in wound complications or infections between nondiabetics and diabetics ( P > .05) and traumatic and nontraumatic cases ( P > .05). Conclusions: The use of IV TXA in foot and ankle surgeries was associated with low risk of wound complications, infections, hematoma formation, thromboembolic events, and overall complication rates with minimal side effect profile. Perioperative tranexamic acid use may prove to be beneficial in foot and ankle surgery patients but especially in higher-risk patients such as those with diabetes, trauma, and those that are immunocompromised. Level of Evidence: Level IV, case series.
A novel methodological framework for testing automated vehicle functions
Authors: Török Árpád 
Published: December 2020

AbstractSince there are more and more highly automated vehicles in road transportation with various extremely safety-critical functions, it is crucial to intensify the development of testing methods. Following this consideration, this paper introduces a new methodological framework for evaluating automated vehicle functions. In the first step, the article proposes a method to select and calibrate the possibly applied and implemented control model. Following this, the developed approach suggests the comparison of the performed test results and the identified theoretical model outputs by evaluating the similarity of the investigated distributions based on statistical hypothesis tests. If the distributions of the real system’s output and the theoretical model’s output are close enough to each other, we can assume that the operation performance of the real system in the case of the investigated operation scenario is acceptable.
Graph embeddings on gene ontology annotations for protein–protein interaction prediction
Authors: Zhong Xiaoshi , Rajapakse Jagath C. 
Published: December 2020

AbstractBackgroundProtein–protein interaction (PPI) prediction is an important task towards the understanding of many bioinformatics functions and applications, such as predicting protein functions, gene-disease associations and disease-drug associations. However, many previous PPI prediction researches do not consider missing and spurious interactions inherent in PPI networks. To address these two issues, we define two corresponding tasks, namely missing PPI prediction and spurious PPI prediction, and propose a method that employs graph embeddings that learn vector representations from constructed Gene Ontology Annotation (GOA) graphs and then use embedded vectors to achieve the two tasks. Our method leverages on information from both term–term relations among GO terms and term-protein annotations between GO terms and proteins, and preserves properties of both local and global structural information of the GO annotation graph.ResultsWe compare our method with those methods that are based on information content (IC) and one method that is based on word embeddings, with experiments on three PPI datasets from STRING database. Experimental results demonstrate that our method is more effective than those compared methods.ConclusionOur experimental results demonstrate the effectiveness of using graph embeddings to learn vector representations from undirected GOA graphs for our defined missing and spurious PPI tasks.
Identifying diseases that cause psychological trauma and social avoidance by GCN-Xgboost
Authors: Xu Huijuan , Wang Hairong , Yuan Chenshan , Zhai Qinghua , Tian Xufeng , Wu Lei , Mi Yuanyuan 
Published: December 2020

Abstract
Background
With the rapid development of medical treatment, many patients not only consider the survival time, but also care about the quality of life. Changes in physical, psychological and social functions after and during treatment have caused a lot of troubles to patients and their families. Based on the bio-psycho-social medical model theory, mental health plays an important role in treatment. Therefore, it is necessary for medical staff to know the diseases which have high potential to cause psychological trauma and social avoidance (PTSA).

Results
Firstly, we obtained diseases which can cause PTSA from literatures. Then, we calculated the similarities of related-diseases to build a disease network. The similarities between diseases were based on their known related genes. Then, we obtained these diseases-related proteins from UniProt. These proteins were extracted as the features of diseases. Therefore, in the disease network, each node denotes a disease and contains the information of its related proteins, and the edges of the network are the similarities of diseases. Then, graph convolutional network (GCN) was used to encode the disease network. In this way, each disease’s own feature and its relationship with other diseases were extracted. Finally, Xgboost was used to identify PTSA diseases.

Conclusion
We developed a novel method ‘GCN-Xgboost’ and compared it with some traditional methods. Using leave-one-out cross-validation, the AUC and AUPR were higher than some existing methods. In addition, case studies have been done to verify our results. We also discussed the trajectory of social avoidance and distress during acute survival of breast cancer patients.
NDRindex: a method for the quality assessment of single-cell RNA-Seq preprocessing data
Authors: Xiao Ruiyu , Lu Guoshan , Guo Wanqian , Jin Shuilin 
Published: December 2020

Abstract
Background
Single-cell RNA sequencing can be used to fairly determine cell types, which is beneficial to the medical field, especially the many recent studies on COVID-19. Generally, single-cell RNA data analysis pipelines include data normalization, size reduction, and unsupervised clustering. However, different normalization and size reduction methods will significantly affect the results of clustering and cell type enrichment analysis. Choices of preprocessing paths is crucial in scRNA-Seq data mining, because a proper preprocessing path can extract more important information from complex raw data and lead to more accurate clustering results.

Results
We proposed a method called NDRindex (Normalization and Dimensionality Reduction index) to evaluate data quality of outcomes of normalization and dimensionality reduction methods. The method includes a function to calculate the degree of data aggregation, which is the key to measuring data quality before clustering. For the five single-cell RNA sequence datasets we tested, the results proved the efficacy and accuracy of our index.

Conclusions
This method we introduce focuses on filling the blanks in the selection of preprocessing paths, and the result proves its effectiveness and accuracy. Our research provides useful indicators for the evaluation of RNA-Seq data.
Using earth mover’s distance for viral outbreak investigations
Authors: Melnyk Andrew , Knyazev Sergey , Vannberg Fredrik , Bunimovich Leonid , Skums Pavel , Zelikovsky Alex 
Published: December 2020

Abstract
Background
RNA viruses mutate at extremely high rates, forming an intra-host viral population of closely related variants, which allows them to evade the host’s immune system and makes them particularly dangerous. Viral outbreaks pose a significant threat for public health, and, in order to deal with it, it is critical to infer transmission clusters, i.e., decide whether two viral samples belong to the same outbreak. Next-generation sequencing (NGS) can significantly help in tackling outbreak-related problems. While NGS data is first obtained as short reads, existing methods rely on assembled sequences. This requires reconstruction of the entire viral population, which is complicated, error-prone and time-consuming.

Results
The experimental validation using sequencing data from HCV outbreaks shows that the proposed algorithm can successfully identify genetic relatedness between viral populations, infer transmission direction, transmission clusters and outbreak sources, as well as decide whether the source is present in the sequenced outbreak sample and identify it.

Conclusions
Introduced algorithm allows to cluster genetically related samples, infer transmission directions and predict sources of outbreaks. Validation on experimental data demonstrated that algorithm is able to reconstruct various transmission characteristics. Advantage of the method is the ability to bypass cumbersome read assembly, thus eliminating the chance to introduce new errors, and saving processing time by allowing to use raw NGS reads.
Mixed reality for teaching catheter placement to medical students: a randomized single-blinded, prospective trial
Authors: Schoeb D. S. , Schwarz J. , Hein S. , Schlager D. , Pohlmann P. F. , Frankenschmidt A. , Gratzke C. , Miernik A. 
Published: December 2020

Abstract
Background
Cost-effective methods to facilitate practical medical education are in high demand and the “mixed-reality” (MR) technology seems suitable to provide students with instructions when learning a new practical task. To evaluate a step-by-step mixed reality (MR) guidance system for instructing a practical medical procedure, we conducted a randomized, single-blinded prospective trial on medical students learning bladder catheter placement.

Methods
We enrolled 164 medical students. Students were randomized into 2 groups and received instructions on how to perform bladder catheter placement on a male catheterization training model. One group (107 students) were given their instructions by an instructor, while the other group (57 students) were instructed via an MR guidance system using a Microsoft HoloLens. Both groups did hands on training. A standardized questionnaire covering previous knowledge, interest in modern technologies and a self-evaluation was filled out. In addition, students were asked to evaluate the system’s usability. We assessed both groups’s learning outcome via a standardized OSCE (objective structured clinical examination).

Results
Our evaluation of the learning outcome revealed an average point value of 19.96 ± 2,42 for the control group and 21.49 ± 2.27 for the MR group - the MR group’s result was significantly better (p = 0.00). The self-evaluations revealed no difference between groups, however, the control group gave higher ratings when evaluating the quality of instructions. The MR system’s assessment showed less usability, with a cumulative SUS (system usability scale) score of 56.6 (lower half) as well as a cumulative score of 24.2 ± 7.3 (n = 52) out of 100 in the NASA task load index.

Conclusions
MR is a promising tool for instructing practical skills, and has the potential to enable superior learning outcomes. Advances in MR technology are necessary to improve the usability of current systems.

Trial registration
German Clinical Trial Register ID: DRKS00013186
Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity
Authors: Utter Daniel R. , Borisy Gary G. , Eren A. Murat , Cavanaugh Colleen M. , Mark Welch Jessica L. 
Published: December 2020

Abstract
Background
The increasing availability of microbial genomes and environmental shotgun metagenomes provides unprecedented access to the genomic differences within related bacteria. The human oral microbiome with its diverse habitats and abundant, relatively well-characterized microbial inhabitants presents an opportunity to investigate bacterial population structures at an ecosystem scale.

Results
Here, we employ a metapangenomic approach that combines public genomes with Human Microbiome Project (HMP) metagenomes to study the diversity of microbial residents of three oral habitats: tongue dorsum, buccal mucosa, and supragingival plaque. For two exemplar taxa, Haemophilus parainfluenzae and the genus Rothia, metapangenomes reveal distinct genomic groups based on shared genome content. H. parainfluenzae genomes separate into three distinct subgroups with differential abundance between oral habitats. Functional enrichment analyses identify an operon encoding oxaloacetate decarboxylase as diagnostic for the tongue-abundant subgroup. For the genus Rothia, grouping by shared genome content recapitulates species-level taxonomy and habitat preferences. However, while most R. mucilaginosa are restricted to the tongue as expected, two genomes represent a cryptic population of R. mucilaginosa in many buccal mucosa samples. For both H. parainfluenzae and the genus Rothia, we identify not only limitations in the ability of cultivated organisms to represent populations in their native environment, but also specifically which cultivar gene sequences are absent or ubiquitous.

Conclusions
Our findings provide insights into population structure and biogeography in the mouth and form specific hypotheses about habitat adaptation. These results illustrate the power of combining metagenomes and pangenomes to investigate the ecology and evolution of bacteria across analytical scales.
Analysis of poverty, income inequality and their effects on food insecurity in southern Ethiopia
Authors: Debebe Sisay , Zekarias Efta Hizkiel 
Published: December 2020

Abstract
Background
Reduction of poverty and income inequality, and ensuring food security is the main goal of the Ethiopian government. In response, declines of national poverty were observed over time, but it is still a worrying concern as a significant proportion of the population remains poor. However, the trends of income inequality are rising substantially over time and thereby might exacerbate the food insecurity status in the country. This study aims to measure, identify determinants, and analyze the effects of poverty and income inequality on food insecurity status of households in Sawla town of southern Ethiopia.

Methodology
A two-stage sampling technique was used to select 227 sampled households’ heads. This study applied descriptive statistics, Foster Greer Thorbecke approach, binary logistic, and quantile regression models to analyze the data.

Results
The finds of this study reveals that 34% of households are living below the poverty line with a poverty gap index of 11% and severity index of 5.6%. The average income inequality with Gini coefficient index is found to be 0.447. Both poverty and income inequality result is quite larger than the national average of the country. The sample households are food insecure with 20.7% depth and 13% severity indexes of food insecurity. The levels of poverty and income inequality are more worrisome among the food-insecure households. Moreover, the logistic regression model shows that levels of education, family size, being divorced, the main occupation, savings, and house ownership negatively and significantly affected the household level of poverty. Quantile regression model result shows that age, level of education, income, family size, health, savings, remittances, electric, credit, and house ownership affected households’ level of income of the study area.

Conclusion
The study suggests strengthening the existing welfare-oriented strategies by undertaking intra-household resource allocations for women, encouraging participation of diversified business activities, promoting the use of family planning methods, strengthening formal education, microfinance institution and housing program by targeting impoverished households in the town.
Erythrocytosis and iron status in Eisenmenger syndrome: an illustrative case study
Authors: Condliffe Robin 
Published: December 2020

Abstract
Background
Patients with Eisenmenger syndrome are chronically hypoxaemic and should therefore mount a secondary erythrocytosis. This response can be attenuated by iron deficiency. Historically, patients with Eisenmenger-associated erythrocytosis often underwent venesection but recent data have challenged this practice.

Case presentation
An illustrative case of a 30-year-old female with Eisenmenger syndrome secondary to a ventricular septal defect is discussed. Her resting saturations on room air were 84%. She was receiving pulmonary arterial hypertension targeted therapy with sildenafil 25 mg three times a day and bosentan 125 mg twice daily. Her local haematologist was planning on therapeutic venesection as her haematocrit was elevated at 0.57. Her haemoglobin was 16.7 g/dl, ferritin levels were 15 μg/L and transferrin saturations were 10.5%. What are the indications for venesection? Should she receive iron supplementation instead? Data to help guide decision-making are reviewed and a clinical approach is suggested.

Conclusions
Iron status should be regularly checked in Eisenmenger syndrome patients and replaced appropriately. There is no role for routine venesection in patients with Eisenmenger syndrome; this should be reserved for the small proportion of patients with symptoms of hyperviscosity in the absence of dehydration.
Risk factors for suicide in Bangladesh: case–control psychological autopsy study
Authors: Arafat S. M. Yasir , Mohit M. A. , Mullick Mohammad S. I. , Kabir Russell , Khan Murad M. 
Published: December 2020

Background
Suicide is an important, understudied public health problem in Bangladesh, where risk factors for suicide have not been investigated by case–control psychological autopsy study.

Aims
To identify the major risk factors for suicide in Dhaka, Bangladesh.

Methods
We designed a matched case–control psychological autopsy study. We conducted a semi-structured interview with the next-of-kin of 100 individuals who died by suicide and 100 living controls, matched for age, gender and area of residence. The study was conducted from July 2019 to July 2020.

Results
The odds ratios for the risk factors were 15.33 (95% CI, 4.76–49.30) for the presence of a psychiatric disorder, 17.75 (95% CI, 6.48–48.59) for life events, 65.28 (95% CI, 0.75–5644.48) for previous attempts and 12 (95% CI, 1.56–92.29) for sexual abuse.

Conclusions
The presence of a psychiatric disorder, immediate life events, previous suicidal attempts and sexual abuse were found as significant risk factors for suicide in Dhaka, Bangladesh.
Applications of statistical physics to study climate phenomena and contribute to overall adaptation efforts(a)
Authors: Blesić S. 
Published: December 2020

AbstractThis paper provides a brief review of the interesting physics that arises from the use of detrending methods for time series analysis for the study of phenomena related to problems of adaptation to climate change. It presents illustrative examples of some of the newly developed or already existent methodological solutions that can be used to study climate phenomena, and of three sectors —public health, infrastructure and cultural heritage— where statistical physics tools can be utilized. In the context of adaptation to climate change statistical physics can offer data-led understandings that are of wider value to the scientific community and applicable local-scale insights.
Disruption of a Hedgehog-Foxf1-Rspo2 signaling axis leads to tracheomalacia and a loss of Sox9+ tracheal chondrocytes
Authors: Nasr Talia , Holderbaum Andrea M. , Chaturvedi Praneet , Agarwal Kunal , Kinney Jessica L. , Daniels Keziah , Trisno Stephen L. , Ustiyan Vladimir , Shannon John M. , Wells James M. , Sinner Debora , Kalinichenko Vladimir V. , Zorn Aaron M. 
Published: December 2020

ABSTRACT
Congenital tracheomalacia, resulting from incomplete tracheal cartilage development, is a relatively common birth defect that severely impairs breathing in neonates. Mutations in the Hedgehog (HH) pathway and downstream Gli transcription factors are associated with tracheomalacia in patients and mouse models; however, the underlying molecular mechanisms are unclear. Using multiple HH/Gli mouse mutants, including one that mimics Pallister–Hall Syndrome, we show that excessive Gli repressor activity prevents specification of tracheal chondrocytes. Lineage-tracing experiments show that Sox9+ chondrocytes arise from HH-responsive splanchnic mesoderm in the fetal foregut that expresses the transcription factor Foxf1. Disrupted HH/Gli signaling results in (1) loss of Foxf1, which in turn is required to support Sox9+ chondrocyte progenitors, and (2) a dramatic reduction in Rspo2, a secreted ligand that potentiates Wnt signaling known to be required for chondrogenesis. These results reveal an HH-Foxf1-Rspo2 signaling axis that governs tracheal cartilage development and informs the etiology of tracheomalacia.
This article has an associated First Person interview with the first author of the paper.
Theoretical and methodological approaches to understanding the concepts of "vitality" and "subjective vitality" in the framework of the conceptual model for the development of subjective vitality of the heads of internal affairs bodies
Authors: Maltseva Tatyana 
Published: December 2020

Today, the definition of “subjective vitality” is interpreted in many research works as the experience of a person being full of energy, the vital forces available to her. Therefore, there is a need to consider the relationship and difference in the scientific understanding and development of such ends as “life force” and “subjective vitality”. The concept of “life force”, used in modern literature, is devoid of both a supernatural character and the functions of a natural science fact.
The energy aspect of human functioning is more developed in our opinion in psychological research than in philosophical and natural sciences. For the first time, a description of the energetic component of a personality in line with psychology is found in works performed in line with a psychoanalytic direction. In the dynamic psychology of K. Levin, an approach to the energy component of the personality is described. E. Byrne believed that human energy can be directed inward, towards himself, and outward. From the perspective of describing the nature of vital energy, V. Reich's approach has been developed. According to A. Lowen, a single energy, enclosed in the body, manifests itself both in psychic phenomena and in movements; this energy is bioenergy. In the work of practical psychologists, one can find a difference in understanding of vital energy and energy.