bluuebunny/crossref_metadata_2025 huggingface dataset:
Balloon-assisted maturation of autogenous arteriovenous fistulae: A randomized controlled prospective study
Authors: Elkassaby Mohammed , Elsaadany Nashaat , Mowaphy Khaled , Soliman Mosaad
Published: December 2020

Background

Current guidelines recommend referral of patient with renal failure for access creation 6 months before planned dialysis. There is a growing cohort of patients that require long-term hemodialysis without adequate preparation. Temporary dialysis catheters and rapid access arteriovenous grafts (AVG) are far from being an ideal solution in this scenario. In an effort to expedite maturation of autogenous arteriovenous fistulae (AVF), balloon-assisted maturation (BAM) was advised by some authors. This technique still lacks the support of high-level evidence studies. We investigated the ability of intra-operative BAM to induce early functional maturation of AVFs.

Methods

This is a prospective randomized controlled study conducted in a tertiary referral center, with a catchment area of more than 15 million population. Cases were divided into two groups; Group (A), where BAM technique was performed, while in the control group (B), the standard technique was used (NO BAM) for creation of AVFs.

Results

Between June 2017 and May 2019, 300 cases were recruited from a total of 648 primary AVF creation instances. Patients’ age ranged from 19 to 89 (mean 51.17 ±SD 15.5) years. Group A (BAM) included 52.3% ( n = 157) AVFs, while Group B included 47.7% ( n = 143) AVFs. The average maturation time was 3.7 weeks (SD ± 1.3, 95% CI 3.55–3.95) and 5.91 weeks (SD ± 2.2, 95% CI 5.55–6.26) for both groups, respectively ( p = 0.0001). 78.3% of the AVFs that underwent BAM showed early maturation within 2–4 weeks vs 32.2% only in the NO BAM group ( p = 0.002). Successful functional maturation was higher among cases of the BAM group (93%), compared to the NO BAM group (77%) ( p = 0.001). Complication rates were 9.6% and 4.9% in the two groups, respectively ( p = 0.042).

Conclusion

BAM can play a pivotal role in helping the dialysis society meet the goals of the Fistula First Initiative, keeping in mind that this comes with an increased risk of complications. BAM should be considered only when unplanned early access to long-term dialysis is required.
The leadership of ICT coordinators: A distributed perspective
Authors: Woo David
Published: December 2020

Educational leadership is essential to implement information and communications technologies in schools but the leadership practice of information and communications technologies coordinators, a position role that supports teachers to implement information and communications technologies, appears limited. The present study applies a distributed perspective to leadership and investigates aspects of information and communications technologies coordinator context that would facilitate leadership. Twenty-seven information and communications technologies coordinators were surveyed on their schools’ structures and mechanisms that mediate their leadership practice. Descriptive statistics show that a wide range of structures and mechanisms in different quantities and with different qualities can be available to coordinators. The majority of coordinators have neither additional position roles nor a teaching load, but the coordinators have organizational unit assignments and attend daily, routine interactions. A case study illustrates how specific structures and mechanisms would facilitate leadership for information and communications technologies implementation. It is recommended to design an information and communications technologies coordinator role as a formal position role, for a school to employ more than one information and communications technologies coordinator, and to develop an information and communications technologies coordinator’s teaching load, organizational unit assignments and routine interactions according to school needs. Several possible populations of information and communications technologies coordinators are identified for further research.
Critical care transfers and COVID-19: Managing capacity challenges through critical care networks
Authors: Pett Eleanor , Leung Hai Lin , Taylor Emily , Chong Martin Shao Foong , Hla Teddy Tun Win , Sartori Giulia , Sathianathan Vivian , Husain Tariq , Suntharalingam Ganesh , Rosenberg Alexander , Walsh Angela , Wigmore Timothy
Published: December 2020

The intensive care units in North West London are part of one of the oldest critical care networks in the UK, forming a mature and established strategic alliance to share resources, experience and knowledge for the benefit of its patients. North West London saw an early surge in COVID-19 admissions, which urgently threatened the capacity of some of its intensive care units even before the UK government announced lockdown. The pre-existing relationships and culture within the network allowed its members to unite and work rapidly to develop agile and innovative solutions, protecting any individual unit from becoming overwhelmed, and ultimately protecting its patients. Within a short 50-day period 223 patients were transferred within the network to distribute pressures. This unprecedented number of critical care transfers, combined with the creation of extra capacity and new pathways, allowed the region to continue to offer timely and unrationed access to critical care for all patients who would benefit from admission. This extraordinary response is a testament to the power and benefits of a regionally networked approach to critical care, and the lessons learned may benefit other healthcare providers, managers and policy makers, especially in regions currently facing new outbreaks of COVID-19.
Therapeutic interventions for COVID-19: a living overview of reviews
Authors: Khalili Malahat , Chegeni Maryam , Javadi Sara , Farokhnia Mehrdad , Sharifi Hamid , Karamouzian Mohammad
Published: December 2020

Background:

Coronavirus disease 2019 (COVID-19) has rapidly spread worldwide, but safe and effective treatment options remain unavailable. Numerous systematic reviews of varying qualities have tried to summarize the evidence on the available therapeutic interventions for COVID-19. This overview of reviews aims to provide a succinct summary of the findings of systematic reviews on different pharmacological and non-pharmacological therapeutic interventions for COVID-19.

Methods:

We searched PubMed, Embase, Google Scholar, Cochrane Database of Systematic Reviews, and WHO database of publications on COVID-19 from 1 December 2019 through to 11 June 2020 for peer-reviewed systematic review studies that reported on potential pharmacological or non-pharmacological therapies for COVID-19. Quality assessment was completed using A MeaSurement Tool to Assess systematic Reviews-2 (AMSTAR-2) measure.

Results:

Out of 816 non-duplicate studies, 45 were included in the overview. Antiviral and antibiotic agents, corticosteroids, and anti-malarial agents were the most common drug classes used to treat COVID-19; however, there was no direct or strong evidence to support their efficacy. Oxygen therapy and ventilatory support was the most common non-pharmacological supportive care. The quality of most of the included reviews was rated as low or critically low.

Conclusion:

This overview of reviews demonstrates that although some therapeutic interventions may be beneficial to specific subgroups of COVID-19 patients, the available data are insufficient to strongly recommend any particular treatment option to be used at a population level. Future systematic reviews on COVID-19 treatments should adhere to the recommended systematic review methodologies and ensure that promptness and comprehensiveness are balanced. The reviews of this paper are available via the supplemental material section.
Accuracy of the Helicobacter pylori diagnostic tests in patients with peptic ulcer bleeding: a systematic review and network meta-analysis
Authors: Vörhendi Nóra , Soós Alexandra , Anne Engh Marie , Tinusz Benedek , Szakács Zsolt , Pécsi Dániel , Mikó Alexandra , Sarlós Patrícia , Hegyi Péter , Eröss Bálint
Published: December 2020

Introduction:

Some studies suggest that the accuracy of Helicobacter pylori diagnostic tests is decreased in peptic ulcer bleeding (PUB). We aimed to assess the accuracy of diagnostic tests for H. pylori in patients with PUB in a diagnostic test accuracy (DTA) network meta-analysis.

Methods:

A systematic search was carried out in seven databases until November 2019. We collected or calculated true and false positive and negative values, and constructed 2×2 diagnostic contingency tables with reference standards including histology, rapid urease test, urea breath test, serology, stool antigen test, culture, and polymerase chain reaction. We ranked the index tests by the superiority indices (SI) and calculated pooled sensitivity and specificity of each test.

Discussion:

Our search yielded 40 eligible studies with 27 different diagnostic strategies for H. pylori. In 32 articles, the reference standard was a combination of multiple tests. In 12 studies, the index tests were compared with a single testing method. We analyzed seven networks with the reference standards against a single or a combination of diagnostic index tests. None of the index tests had better diagnostic accuracy (SI between 9.94 and 2.17) compared with the individual index tests as all the confidence intervals included 1. Combined testing strategies had higher sensitivities (0.92–0.62) and lower specificities (0.85–0.46) while single tests proved to have higher specificities (0.83–0.77) and lower sensitivities (0.73–0.42).

Conclusion:

Use of combined tests may have a rationale in clinical practice due to their higher sensitivities. The differences between the included DTA studies limited the comparison of the testing strategies.
Immunosuppressive agents for rheumatoid arthritis: a systematic review of clinical trials and their current development stage
Authors: Blaess Julien , Walther Julia , Petitdemange Arthur , Gottenberg Jacques-Eric , Sibilia Jean , Arnaud Laurent , Felten Renaud
Published: December 2020

Aims:

With the arrival of conventional synthetic (csDMARDs), biological (bDMARDS) and then targeted synthetic (tsDMARDs) disease-modifying anti-rheumatic drugs, the therapeutic arsenal against rheumatoid arthritis (RA) has recently expanded. However, there are still some unmet needs for patients who do not achieve remission and continue to worsen despite treatments. Of note, most randomized controlled trials show that, for methotrexate-inadequate responders, only 20% of patients are ACR70 responders. With our better understanding of RA pathogenesis, finding new treatments is a necessary challenge. The objective of our study was to analyse the whole pipeline of immunosuppressive and immunomodulating drugs evaluated in RA and describe their mechanisms of action and stage of clinical development.

Methods:

We conducted a systematic review of all drugs in clinical development in RA, in 17 online registries of clinical trials.

Results:

The search yielded 4652 trials, from which we identified 243 molecules. Those molecules belong to csDMARDs ( n = 22), bDMARDs ( n = 118), tsDMARDs ( n = 103). Twenty-four molecules are already marketed in RA in at least one country: eight csDMARDs, 10 bDMARDs and six tsDMARDs. Molecules under current development are mainly bDMARDs ( n = 34) and tsDMARDs ( n = 33). Seven of those have reached phase III. A large number of molecules (150/243, 61.7%) have been withdrawn.

Conclusion:

Despite the availability of 24 marketed molecules, the development of new targeted molecules is ongoing with a total of 243 molecules in RA. With seven molecules currently reaching phase III, we can expect an increase in the armamentarium in the years to come.
Still Where, Not If, You’re Poor: International Baccalaureate Opportunities to Learn International-Mindedness and Proximity to U.S. Cities
Authors: Thier Michael , Beach Paul T.
Published: December 2020

By matching International Baccalaureate (IB) and non-IB U.S. public schools based on state, grade span, and enrollment, we used recent public data to confirm relations among a hierarchy of school characteristics and whether schools made available any of IB’s four programs. We fortified prior claims regarding how poverty, minority concentration, and geographic locale as a function of proximity to cities relate to IB availability, a proxy for opportunity to learn international-mindedness. Our proximity approach to data from public schools and a descriptive look at data from private schools highlighted the unique importance of proximity to cities in identifying where IB opportunities do and do not exist. We conclude by specifying recommendations for decision-makers who might need resources to make IB implementation viable or to win local hearts and minds before doing so.
“I Thought I Knew You, Two”: A Performative Response to Norman Denzin and Tami Spry’s Wild West Show at ICQI 2018
Authors: Alexander Bryant Keith
Published: December 2020

For the 2018 Autoethnography Special Interest Group at the International Congress of Qualitative Inquiry (ICQI), Norman Denzin and Tami Spry did an integrative co-performance of each other’s autoethnography linked with a western motif. Each of the originating pieces of their performance texts were pre-published in Special Issues edited by this author. The author of this piece was invited to engage a performative response to the performance, and ostensibly entered the textual and embodied performance as a third companion on a western journey discovering new insights of both presenters in the performance of each as the other. 1
Yield of Head Imaging in Ambulatory and Hospitalized Patients With SARS-CoV-2: A Multi-Center Study of 8675 Patients
Authors: Greenway Melanie R. F. , Erben Young , Huang Josephine F. , Siegel Jason L. , Lamb Christopher J. , Badi Mohammed K. , Sakusic Amra , Gopal Neethu , Meschia James F. , Lin Michelle P.
Published: December 2020

Background and Purpose:

To describe the neurological and cerebrovascular findings in patients who tested positive for SARS-CoV-2 and underwent head imaging in ambulatory and inpatient settings.

Methods:

Consecutive patients aged ≥18 years with SARS-CoV-2 infection diagnosed or treated at Mayo Clinic sites from 3/11/2020 to 7/23/2020 with head CT or brain MRI within 30 days of SARS-CoV-2 diagnosis were included. Demographics, medical history, indication for SARS-CoV-2 testing, neurologic symptoms, indication for brain imaging, neuroimaging findings, etiology of cerebrovascular events, and hospital course were abstracted from medical records.

Results:

Of 8,675 patients with SARS-CoV-2, 180 (2.07%) had head imaging. Mean age of the entire cohort was 42 ± 18 years, whereas mean age of those with head imaging was 62 ± 19 years. Common indications for imaging were headache (34.4%), encephalopathy (33.4%), focal neurologic symptom (16.7%), and trauma (13.9%). While 86.1% of patients who underwent head imaging had normal exams, cerebrovascular events occurred in 18 patients (0.21% of the total cohort). Of patients with cerebrovascular events, 8 (44.5%) had acute infarct; 6 (33.3%), acute intracranial hemorrhage; 5 (2.8%), subacute infarct; and 1 (0.6%) posterior reversible encephalopathy syndrome. In the thirteen patients with ischemic stroke, 6 (46.2%) had cryptogenic stroke; 3 (23.1%), other defined causes; 2 (15.4%), small vessel stroke; 1 (7.7%), large vessel stroke; and 1 (7.7%) cardioembolic stroke.

Conclusion:

In ambulatory and hospitalized patients with SARS-CoV-2 infection, the rate of head imaging is low, with common indications of encephalopathy and headache. Cerebrovascular events occurred rarely, and cryptogenic stroke was the most common stroke mechanism.
Processing employees’ personal data during the Covid-19 pandemic
Authors: Suder Seili
Published: December 2020

While needing to ensure the health and safety of their employees during the Covid-19 pandemic, employers face many burning data protection questions, including under what conditions they can process employees’ personal data (in particular health data) and whether gathering personal data concerning employees’ medical history, trips and contacts with infected persons, is allowed. This article focuses on issues that are problematic, based on the analysis of guidance issued by the European Data Protection Board, as well as national data protection authorities and practitioners from 20 countries in response to these concerns. The first section of the article analyses concepts of personal data and health data in the context of Covid-19. Then the article proceeds with exploring what possible legal bases employers can use to process employees’ personal data in general, and health data in particular, under the General Data Protection Regulation when applying different measures to combat Covid-19. In the latter part of the article two practical questions raised by employers – concerning the checking of employees’ body temperatures and informing them of possible infection – are discussed. The analysis indicates that national data protection authorities seem to look for a reasonable and pragmatic approach regarding compliance with the GDPR in light of the Covid-19 emergency. However, their guidance differs in several areas and the views in between nation states are not always aligned. A more specific, clear and uniform pan-European vision concerning the processing of employees’ data in times of emergency is needed to better protect employees and limit the spread of the virus.
Ethical and Moral Competences of Upper Secondary Students: A Comparative Study
Authors: Peng (彭正梅) Zhengmei , Benner Dietrich , Nikolova Roumiana , Ivanov Stanislav , Peng (彭韬) Tao
Published: December 2020

Purpose:

This article presents the theoretical framework, research design, methodology, and main findings of the comparative measurement of ethical–moral competences of 15-year-old upper secondary students in Shanghai, under the ETiK-International-Shanghai project.

Design/Approach/Methods:

By dividing the ethical–moral competences into the categories of basic ethical–moral knowledge, ethical–moral judgment competence, and competence in developing ethical–moral action plans, a survey of 2,036 students was conducted, using a reliable and valid testing instrument.

Findings:

In general, 15-year-olds from homes with more educational resources perform higher in all three scales across all countries taken under consideration in our study. Furthermore, school practices, teaching, as well as quantity and quality of instruction play a very important role in the moral education process and especially in developing students’ proficiency levels of ethical–moral knowledge, reasoning competence, as well as students’ high abilities in developing moral action plans. When relevant educational background factors are held constant, Chinese students show lower average scores on basic ethical–moral knowledge and moral judgment competence. With exception of the tested Vienna students, all other European samples scored better than the Chinese students—also on the test for developing ethical–moral action plans. However, Chinese students are especially able to display outstanding empathy when dealing with suffering, misfortune, and sorrow, as well as in their willingness to help others.

Originality/Value:

The findings of this article can foster thinking about which topics should be further discussed to improve the ethical–moral knowledge and competences of Chinese students and highlight requirements for the further development of moral education in China at the levels of teaching, curriculum, teacher education, and research.
Resident Involvement in Arthroscopic Knee Surgery Is Not Associated With Increased Short-term Risk to Patients
Authors: Basques Bryce A. , Saltzman Bryan M. , Korber Shane S. , Bolia Ioanna K. , Mayer Erik N. , Bach Bernard R. , Verma Nikhil N. , Cole Brian J. , Weber Alexander E.
Published: December 2020

Background:

Whether resident involvement in surgical procedures affects intra- and/or postoperative outcomes is controversial.

Purpose/Hypothesis:

The purpose of this study was to compare operative time, adverse events, and readmission rate for arthroscopic knee surgery cases with and without resident involvement. We hypothesized that resident involvement would not negatively affect these variables.

Study Design:

Cohort study; Level of evidence, 3.

Methods:

A retrospective review of the prospectively maintained National Surgical Quality Improvement Program was performed. Patients who underwent arthroscopic knee surgery between 2005 and 2012 were identified. Multivariate Poisson regression with robust error variance was used to compare the rates of postoperative adverse events and readmission within 30 days between cases with and without resident involvement. Multivariate linear regression was used to compare operative time between cohorts. Because of multiple statistical comparisons, a Bonferroni correction was used, and statistical significance was set at P < .004.

Results:

A total of 29,539 patients who underwent arthroscopic knee surgery were included in the study, and 11.3% of these patients had a resident involved with the case. The overall rate of adverse events was 1.62%. On multivariate analysis, resident involvement was not associated with increased rates of adverse events or readmission. Resident cases had a mean 6-minute increase in operative time ( P < .001).

Conclusion:

Overall, resident involvement in arthroscopic knee surgery was not associated with an increased risk of adverse events or readmission. Resident involvement was associated with only a mean increased operative time of 6 minutes, a difference that is not likely to be clinically significant. These results support the safety of resident involvement with arthroscopic knee surgery.
Effect of Ulnar Collateral Ligament Reconstruction on Pitch Accuracy, Velocity, and Movement in Major League Baseball Pitchers
Authors: McKnight Braden , Heckmann Nathanael D. , Chen Xiao T. , Hindoyan Kevork , Hill J. Ryan , Goldbeck Graham , Omid Reza , Hatch George F. “Rick” , Charlton Timothy P.
Published: December 2020

Background:

Ulnar collateral ligament (UCL) reconstruction is frequently performed on Major League Baseball (MLB) pitchers. Previous studies have investigated the effects of UCL reconstruction on fastball and curveball velocity, but no study to date has evaluated its effect on fastball accuracy or curveball movement among MLB pitchers.

Purpose/Hypothesis:

The primary purpose of this study was to determine the effects of UCL reconstruction on fastball accuracy, fastball velocity, and curveball movement in MLB pitchers. Our hypothesis was that MLB pitchers who underwent UCL reconstruction would return to their presurgery fastball velocity, fastball accuracy, and curveball movement. The secondary purpose of this study was to determine which factors, if any, were predictive of poor performance after UCL reconstruction.

Study Design:

Case-control study; Level of evidence, 3.

Methods:

MLB pitchers who underwent UCL reconstruction surgery between 2011 and 2012 were identified. Performance data including fastball velocity, fastball accuracy, and curveball movement were evaluated 1 year preoperatively and up to 3 years of play postoperatively. A repeated-measures analysis of variance with a Tukey-Kramer post hoc test was used to determine statistically significant changes in performance over time. Characteristic factors and presurgery performance statistics were compared between poor performers (>20% decrease in fastball accuracy) and non—poor performers.

Results:

We identified 56 pitchers with a total of 230,995 individual pitches for this study. After exclusion for lack of return to play (n = 14) and revision surgery (n = 3), 39 pitchers were included in the final analysis. The mean presurgery fastball pitch-to-target distance was 32.9 cm. There was a statistically significant decrease in fastball accuracy after reconstruction, which was present up to 3 years postoperatively ( P = .007). The mean presurgery fastball velocity of 91.82 mph did not significantly change after surgery ( P = .194). The mean presurgery curveball movement of 34.49 cm vertically and 5.89 cm horizontally also did not change significantly ( P = .937 and .161, respectively).

Conclusion:

Fastball accuracy among MLB pitchers significantly decreased after UCL reconstruction for up to 3 years postoperatively. There were no statistically significant differences in characteristic factors or presurgery performance statistics between poor and non--poor performers.
IJV’s political ties and R&D strategy: Asymmetric contingencies of market versus governmental policy turbulence
Authors: Yang Jie , Ma Jieqiong , Doty D Harold , Lee Jeoung Yul
Published: December 2020

The purpose of this article is to empirically explore (1) the impact of political ties on international joint ventures’ (IJVs) R&D strategy and (2) the moderating effects of market turbulence and governmental policy turbulence on the relationship between IJV political ties and R&D investment in China. Our sample consists of 1,344 observations taken from 224 IJVs over a period of 6 years (2012–2017), and we applied hierarchical moderated regression analysis (HMRA) with panel data to analyze our three hypotheses. Our findings show that IJVs with political ties tend to invest more in R&D than their counterparts without political ties. Interestingly, this positive relationship grows stronger with high market turbulence, but wanes under high governmental policy turbulence. While the issues regarding the importance of political ties to IJVs competing in China have been discussed, the issues related to why political ties influence IJV’s decisions on R&D investment have been largely overlooked. Hence, this study applies the environmental contingency view to fill this gap and shows how asymmetric contingencies for market turbulence and governmental policy turbulence occur in this context.

JEL CLASSIFICATION: M1
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

Since 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

Background

Protein–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.

Results

We 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.

Conclusion

Our 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

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

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

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

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

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

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

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

This 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

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.