bluuebunny/crossref_metadata_2025 huggingface dataset:
Research in the Religious Realm: Intersectional Diversification and Dynamic Variances of Insider/Outsider Perspectives
Authors: Decoo Ellen
Published: January 2022

This article discusses insider/outsider perspectives in qualitative research among religious people. Focus is on the insider researcher. Even if researcher and participants share the same overall religious adherence or are members of the same denomination, various factors can differentiate them substantially, affecting insider/outsider perspectives. The methodological implications of this phenomenon are drawn from research on the perception of gender roles among Mormon women in Belgium. The mutual perception of researcher and participant can influence the data collection phase as value-laden issues are being discussed. To ensure the validity and objectivity of research in this context, positionalities of researcher and participants need to be clearly defined and methodological safeguards put into place. The analysis of the interactions between researcher and participants led to the identification of seven intersecting insider/outsider perspectives: denominational, congregational, social, religious, topical, lingual, and academic. Moreover, as compound insider/outsider positions move on several continua, various factors can change the perspectives during interviews. This article adds to the methodology of qualitative research by uncovering perspectives which researchers can consider or adapt when interviewing religious participants.
Investigations on the effect of silver nanoparticles on performance of coconut oil based cutting fluid in minimal fluid application
Authors: Robinson Gnanadurai Rengiah , Mesfin Solomon
Published: January 2022

In this work, an innovative nanocutting fluid, based on coconut oil was developed by dispersing silver nanoparticles (AgNPs) of size less than 50 nm. The tribological and physical properties of the prepared nanocutting fluid with different volumes of silver nanoparticles were studied. It was found that the addition of 4% by volume of nanoparticles enhanced the properties of the nanocutting fluid compared to the other concentrations studied, thus demonstrating its excellent tribological performance. The effect of the newly developed nanocutting fluid with 4% of silver nanoparticles on cutting performance was also investigated while machining AISI4340 steel with minimal fluid application. Results revealed that the cutting force, cutting temperature, and tool wear are reduced on an average by 22.6%, 12.6%, and 5.3% respectively. It was evident that efficient cooling and lubrication of nanocutting fluid dispersed with silver nanoparticles improved the cutting performance. The outcomes of this work can be considered as a development toward eco-friendly and sustainable machining.
Motion coordination control of planar 5R parallel quadruped robot based on SCPL-CPG
Authors: Chen Mingfang , Hu Kangkang , Zhang Yongxia , Qi Fengping
Published: January 2022

The parallel leg of the quadruped robot has good structural stiffness, accurate movement, and strong bearing capacity, but it is complicated to control. To solve this problem, a series connection of parallel legs (SCPL) was proposed, as well as a control strategy combined with the central pattern generator (CPG). With the planar 5R parallel leg as the research object, the SCPL analysis method was used to analyze the leg structure. The topology of CPG network was built with the Hopf oscillator as the unit model, and the CPG was the core to model the robot control system. By continuously adjusting the parameters in the CPG control system and changing the connection weight, and the smooth transition between gaits was realized. The simulation results show that the SCPL analysis method can be effectively used in the analysis of parallel legs, and the control system can realize the smooth transition between gaits, which verifies the feasibility and effectiveness of the proposed control strategy.
Research on cooperative optimization of multiphase pump impeller and diffuser based on adaptive refined response surface method
Authors: Cancan Peng , Xiaodong Zhang , Zhiguang Gao , Ju Wu , Yan Gong
Published: January 2022

Multiphase pumps play an important role in the exploitation of natural gas hydrate. Compared with ordinary pumps, they can handle fluids with higher gas volume fraction (GVF). Therefore, it is important to improve the performance of the pump under high GVF. A model pump is designed based on the design theory of axial flow pump and centrifugal pump inducer. The hydraulic performance of the model pump is verified by numerical simulation and experiment. The Sparse Grid method is applied to the design of experiment (DOE), and three different adaptive refined response surface methods (RSM) are applied to the build the approximate model. Refinement points and verification points are used to improve and verify the precision of the response surface, respectively. The model with high precision and high computational efficiency is obtained through comparison and analysis. The multi-objective optimization of the optimal response surface model is carried out by MOGA (Multi-Objective Genetic Algorithm) method. The pressure increment of the optimized model is increased by 38 kPa. The efficiency is significantly improved under large mass flow conditions. The hydraulic performance of the optimized model is compared with that of the basic model. And the reasons that affect the performance of the multiphase pump are analyzed.
Influential methods reports for group-randomized trials and related designs
Authors: Murray David M
Published: January 2022

Background. This article identifies the most influential methods reports for group-randomized trials and related designs published through 2020. Many interventions are delivered to participants in real or virtual groups or in groups defined by a shared interventionist so that there is an expectation for positive correlation among observations taken on participants in the same group. These interventions are typically evaluated using a group- or cluster-randomized trial, an individually randomized group treatment trial, or a stepped wedge group- or cluster-randomized trial. These trials face methodological issues beyond those encountered in the more familiar individually randomized controlled trial. Methods. PubMed was searched to identify candidate methods reports; that search was supplemented by reports known to the author. Candidate reports were reviewed by the author to include only those focused on the designs of interest. Citation counts and the relative citation ratio, a new bibliometric tool developed at the National Institutes of Health, were used to identify influential reports. The relative citation ratio measures influence at the article level by comparing the citation rate of the reference article to the citation rates of the articles cited by other articles that also cite the reference article. Results. In total, 1043 reports were identified that were published through 2020. However, 55 were deemed to be the most influential based on their relative citation ratio or their citation count using criteria specific to each of the three designs, with 32 group-randomized trial reports, 7 individually randomized group treatment trial reports, and 16 stepped wedge group-randomized trial reports. Many of the influential reports were early publications that drew attention to the issues that distinguish these designs from the more familiar individually randomized controlled trial. Others were textbooks that covered a wide range of issues for these designs. Others were “first reports” on analytic methods appropriate for a specific type of data (e.g. binary data, ordinal data), for features commonly encountered in these studies (e.g. unequal cluster size, attrition), or for important variations in study design (e.g. repeated measures, cohort versus cross-section). Many presented methods for sample size calculations. Others described how these designs could be applied to a new area (e.g. dissemination and implementation research). Among the reports with the highest relative citation ratios were the CONSORT statements for each design. Conclusions. Collectively, the influential reports address topics of great interest to investigators who might consider using one of these designs and need guidance on selecting the most appropriate design for their research question and on the best methods for design, analysis, and sample size.
Time trends with response-adaptive randomization: The inevitability of inefficiency
Authors: Korn Edward L , Freidlin Boris
Published: January 2022

Response-adaptive randomization, which changes the randomization ratio as a randomized clinical trial progresses, is inefficient as compared to a fixed 1:1 randomization ratio in terms of increased required sample size. It is also known that response-adaptive randomization leads to biased treatment effects if there are time trends in the accruing outcome data, for example, due to changes in the patient population being accrued, evaluation methods, or concomitant treatments. Response-adaptive-randomization analysis methods that account for potential time trends, such as time-block stratification or re-randomization, can eliminate this bias. However, as shown in this Commentary, these analysis methods cause a large additional inefficiency of response-adaptive randomization, regardless of whether a time trend actually exists.
The representation of Indigenous peoples in chronic disease clinical trials in Australia, Canada, New Zealand, and the United States
Authors: Umaefulam Valerie , Kleissen Tessa , Barnabe Cheryl
Published: January 2022

Background

Indigenous peoples are overrepresented with chronic health conditions and experience suboptimal outcomes compared with non-Indigenous peoples. Genetic variations influence therapeutic responses, thus there are potential risks and harm when extrapolating evidence from the general population to Indigenous peoples. Indigenous population–specific clinical studies, and inclusion of Indigenous peoples in general population clinical trials, are perceived to be rare. Our study (1) identified and characterized Indigenous population–specific chronic disease trials and (2) identified the representation of Indigenous peoples in general population chronic disease trials conducted in Australia, Canada, New Zealand, and the United States.

Methods

For Objective 1, publicly available clinical trial registries were searched from May 2010 to May 2020 using Indigenous population–specific terms and included for data extraction if in pre-specified chronic disease. For identified trials, we extracted Indigenous population group identity and characteristics, type of intervention, and funding type. For Objective 2, a random selection of 10% of registered clinical trials was performed and the proportion of Indigenous population participants enrolled extracted.

Results

In total, 170 Indigenous population–specific chronic disease trials were identified. The clinical trials were predominantly behavioral interventions (n = 95). Among general population studies, 830 studies were randomly selected. When race was reported in studies (n = 526), Indigenous individuals were enrolled in 172 studies and constituted 5.6% of the total population enrolled in those studies.

Conclusion

Clinical trials addressing chronic disease conditions in Indigenous populations are limited. It is crucial to ensure adequate representation of Indigenous peoples in clinical trials to ensure trial data are applicable to their clinical care.
Diversity training for health professionals: Preparedness to competently address intellectual disability in the Western Cape Province, South Africa
Authors: Smith Mario R , Papadakis Maryam , Munnik Erica
Published: January 2022

Diversity training for health professionals in South Africa has traditionally been conceptualized as differences in gender, race or ethnicity, culture and sexual orientation. More recently physical disability and mental illness was included as a dimension. Intellectual disabilities received lip service as a diversity concern. This paper reports on health professionals' perceptions of the extent to which diversity training prepared them to competently deal with intellectual disabilities. This explorative study included a purposive sample of 18 health care professionals experienced in intellectual disability services. Two focus groups were facilitated over three sessions. Transcripts were analysed thematically. Health professionals felt inadequately prepared to consider intellectual disabilities as a diversity issue. They could not effectively advocate for reasonable accommodation. There was a differential familiarity with issues related to diversity and intellectual disability with profession constituting an additional intersecting dimension of diversity. Health professions did not perceive their diversity training to prepare them to deal competently with intellectual disabilities.
Attention to bone health in follow-up of gynaecological cancers in tertiary care
Authors: O’Gorman Catherine A , Minnock Sorcha , Mulhall Joseph , Gleeson Noreen
Published: January 2022

Objective:

Women with gynaecological cancers are at an increased risk of cancer treatment–induced bone loss, which impacts on their quality of life and overall survival. Clinical cancer follow-up reviews focus on cancer status and fail to attend to important health and quality-of-life issues. We questioned whether there was a care-gap between tertiary clinicians and primary care physicians in the management of bone health in this cohort. Significant care-gaps in relation to bone health have been demonstrated in other oncologic settings. The objective of this study was to determine the level of attention to bone health in the care of women living with and beyond gynaecological cancer at a tertiary referral centre for gynaecological oncology.

Methods:

Retrospective, observational cohort study of attention to bone health in the management and follow-up of gynaecological cancers.

Results:

This study shows that there has been suboptimal attention from the carers at a cancer centre to bone health during the oncological follow up of women undergoing treatment for gynaecological cancer. In those at particular risk of cancer treatment–induced bone loss (iatrogenic menopause and/or external beam pelvic radiotherapy), 52% of women had no reference to bone health in their notes, and 57% had no assessment of bone mineral density.

Conclusion:

Tertiary cancer carers may underestimate the importance of bone health or believe that it falls outside the remit of their gynaecologic oncology service. Further research is needed to explore whether these findings are indicative of a true care gap and to gain insight into possible corrective measures.
Diabetes Distal Peripheral Neuropathy: Subtypes and Diagnostic and Screening Technologies
Authors: Newlin Lew Kelley , Arnold Tracey , Cantelmo Catherine , Jacque Francky , Posada-Quintero Hugo , Luthra Pooja , Chon Ki H.
Published: January 2022

Diabetes distal symmetrical peripheral neuropathy (DSPN) is the most prevalent form of neuropathy in industrialized countries, substantially increasing risk for morbidity and pre-mature mortality. DSPN may manifest with small-fiber disease, large-fiber disease, or a combination of both. This review summarizes: (1) DSPN subtypes (small- and large-fiber disease) with attention to clinical signs and patient symptoms; and (2) technological diagnosis and screening for large- and small-fiber disease with inclusion of a comprehensive literature review of published studies from 2015-present ( N = 66). Review findings, informed by the most up-to-date research, advance critical understanding of DSPN large- and small-fiber screening technologies, including those designed for point-of-care use in primary care and endocrinology practices.
Book Review: From the inside out: The fight for environmental justice within government agencies by Jill Harrison
Authors: Dillon Lindsey
Published: January 2022

In From the Inside Out: The Fight for Environmental Justice within Government Agencies (MIT Press, 2019), Jill Harrison offers a nuanced study of why U.S. state agencies fail at implementing robust environmental justice (EJ) policies. Through a rigorous interview and ethnographic based methodology Harrison details the discourses, ideologies, and everyday practices and through which government agency staff, daily, undermine and even outright reject EJ policies and programs. The book is a richly empirical study that makes valuable contributions to academic and activist understandings of the government's failure to respond meaningfully to environmental injustices, and offers specific recommendations for how to reform government agencies. It is a timely monograph as EJ advocates seek to reimagine government agencies in the wake of the Trump administration, and in the context of an expanded public consciousness of racism following the killing of George Floyd and subsequent uprisings during the summer of 2020.
Differences in Shoulder Internal Rotation Strength Between Baseball Players With Ulnar Collateral Ligament Reconstruction and Healthy Controls
Authors: Kennedy Sean M. , Sheedy Philip , Klein Brooks , Gist Mason F. , Hannon Joseph P. , Conway John E. , Creed Kalyssa , Garrison J. Craig
Published: January 2022

Background:

Studies have indicated decreased shoulder internal rotation (IR) and external rotation (ER) strength in the throwing limb of baseball players after ulnar collateral ligament injury. There is limited evidence on the recovery of shoulder rotation strength after primary ulnar collateral ligament reconstruction (UCLR).

Hypothesis:

At the time of return to throwing, baseball players who underwent UCLR would demonstrate decreased IR and ER shoulder strength in the throwing arm as compared with healthy baseball players.

Study Design:

Cross-sectional study; Level of evidence, 3.

Methods:

Male competitive high school and collegiate baseball athletes participated in this study. Athletes who underwent UCLR were compared with healthy controls who were matched by age, height, weight, and position. Bilateral isometric shoulder ER and IR strength was measured using a handheld dynamometer for all participants at the time of initial evaluation (UCLR group) and throughout the course of a season (healthy group). Independent t tests were run to calculate mean differences in ER and IR shoulder strength between the groups, with significance set at P < .05.

Results:

A total of 86 baseball athletes participated in this study (43 UCLR group, 43 healthy group). At the time of return to throwing (mean ± SD, 194 ± 30 days postoperatively), the 2 groups demonstrated no significant differences in nonthrowing arm ER or IR strength ( P = .143 and .994, respectively). No significant difference was found between groups for throwing arm ER strength ( P = .921); however, the UCLR group demonstrated significantly less throwing arm IR strength than the healthy group (144.2 ± 27.8 vs 157.6 ± 27.1 N; P = .023).

Conclusion:

The results of this study demonstrate that throwing arm rotator cuff strength may not fully recover before the initiation of a return-to-throwing program after UCLR. These data provide a potential framework for clinicians to assist in the management and exercise prescription of the baseball athlete after UCLR and before medical release and the initiation of a return-to-throwing program.
Managing Type 2 Diabetes: Beliefs and Daily Practices in First Generation Asian Indians in the United States
Authors: Deol Rupinder M , Thompson Lisa M , Chun Kevin M , Chesla Catherine
Published: January 2022

Introduction

Diabetes management and control remain poor in Asian Indians (AI) and is influenced by personal beliefs and cultural practices. Since AIs have a high prevalence of diabetes and are more likely develop complications earlier than any other ethnic group, understanding their beliefs and practices of diabetes management is essential. The purpose of this study was to examine and understand beliefs and practices about diabetes self-management in first-generation AI Hindus and Sikhs.

Method

Interpretative phenomenology was used to interview 12 first generation AI participants with type 2 diabetes to elicit beliefs and daily self-management practices of diabetes. Interpretative and thematic analysis were completed.

Results

Diabetes self-management was a balancing act influenced by Ayurvedic principles, allopathy and dietary practices; gender roles, insufficient knowledge and culturally inappropriate diabetes education.

Discussion

Culturally appropriate strategies that incorporate Ayurvedic principles, dietary practices, gender roles should be developed to improve diabetes management.
Practical Risk Scoring System for Predicting Severity of COVID-19 Disease
Authors: Petersen Jeffrey , Jhala Darshana
Published: January 2022

Objectives:

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19 disease, has become an international pandemic with numerous casualties. It had been noted that the severity of the COVID-19 disease course depends on several clinical, laboratory, and radiological factors. This has led to risk scoring systems in various populations such as in China, but similar risk scoring systems based on the American veteran population are sparse, particularly with the vulnerable Veteran population. As a simple risk scoring system would be very useful, we propose a simple Jhala Risk Scoring System (JRSS) to assess the severity of disease risk.

Methods:

A retrospective review of all SARS-CoV-2 reverse transcriptase-polymerase chain reaction (RT-PCR) tests collected and performed at the regional Veterans Administration Medical Center (VAMC) serving the Philadelphia and surrounding areas from March 17th, 2020 to May 20th, 2020. Data was collected and analyzed in the same year. These tests were reviewed within the computerized medical record system for demographic, medical history, laboratory test history, and clinical course. Information from the medical records were then scored based on the criteria of the Jhala Risk Scoring System (JRSS).

Results:

The JRSS, based on age, ethnicity, presence of any lung disease, presence of cardiovascular disease, smoking history, and diabetes history with laboratory parameters correlated and predicted (with statistical significance) which patients would be hospitalized.

Conclusion:

The JRSS may play a role in informing which COVID-19 positive patients in the emergency room/urgent care for risk stratification.
Effects of Obesity Surgery on GERD and Esophageal Motility
Authors: Nguyen Anh D.
Published: January 2022

With the rising prevalence of obesity, bariatric surgery has become an increasingly popular treatment option. However, bariatric surgery can contribute to esophageal dysmotility and lead to worsening or development of GERD, two conditions that are already frequently seen in the obese population. We review the effects of the various types of bariatric surgeries on the esophagus, specifically focusing on sleeve gastrectomy, Roux-en-Y gastric bypass and laparoscopic adjustable gastric banding.
Surgical Management of Juvenile Idiopathic Arthritis Related Dentofacial Deformities
Authors: Wilson Walter H. , Waite Peter D. , Alrajhi Zeyad , Powell Kathlyn , Cron Randy Q. , Kinard Brian
Published: January 2022

Juvenile idiopathic arthritis (JIA) is the most common chronic rheumatologic disease of childhood and frequently affects the temporomandibular joints (TMJ). JIA TMJ management requires a team approach. Initially, TMJ JIA involvement is managed with systemic therapy or intra-articular medications to treat symptoms and limit the growth deformity, however may later require surgical intervention. This case series describes 4 patients with different presentations and treatments of juvenile idiopathic arthritis affecting the temporomandibular joints to illustrate a proposed treatment algorithm. This algorithm is not designed to be an absolute treatment regimen but a framework to help clarify the presenting problems and interventions that may be considered to treat JIA associated temporomandibular dysfunction and dentofacial deformity. This case series represents the variety of JIA temporomandibular joint disease and offers a graduated appropriate treatment algorithm.
The Expectations of Project Managers from Artificial Intelligence: A Delphi Study
Authors: Holzmann Vered , Zitter Daniel , Peshkess Sahar
Published: January 2022

Artificial intelligence (AI) technologies are rapidly developing these days and are expected to impact the field of project management on multiple levels; however, there remains a high level of uncertainty regarding the effect that AI might have on project management practices. This article aims to address this topic based on a Delphi study with a panel of 52 project management experts who reflected on future potential AI applications for the project management Knowledge Areas. The article provides a visionary perspective that can be further translated into practical solutions in the near and far future to improve project management practices.
Predicting the targets of IRF8 and NFATc1 during osteoclast differentiation using the machine learning method framework cTAP
Authors: Wang Honglin , Joshi Pujan , Hong Seung-Hyun , Maye Peter F. , Rowe David W. , Shin Dong-Guk
Published: January 2022

Background

Interferon regulatory factor-8 (IRF8) and nuclear factor-activated T cells c1 (NFATc1) are two transcription factors that have an important role in osteoclast differentiation. Thanks to ChIP-seq technology, scientists can now estimate potential genome-wide target genes of IRF8 and NFATc1. However, finding target genes that are consistently up-regulated or down-regulated across different studies is hard because it requires analysis of a large number of high-throughput expression studies from a comparable context.

Method

We have developed a machine learning based method, called, Cohort-based TF target prediction system (cTAP) to overcome this problem. This method assumes that the pathway involving the transcription factors of interest is featured with multiple “functional groups” of marker genes pertaining to the concerned biological process. It uses two notions, Gene-Present Sufficiently (GP) and Gene-Absent Insufficiently (GA), in addition to log2 fold changes of differentially expressed genes for the prediction. Target prediction is made by applying multiple machine-learning models, which learn the patterns of GP and GA from log2 fold changes and four types of Z scores from the normalized cohort’s gene expression data. The learned patterns are then associated with the putative transcription factor targets to identify genes that consistently exhibit Up/Down gene regulation patterns within the cohort. We applied this method to 11 publicly available GEO data sets related to osteoclastgenesis.

Result

Our experiment identified a small number of Up/Down IRF8 and NFATc1 target genes as relevant to osteoclast differentiation. The machine learning models using GP and GA produced NFATc1 and IRF8 target genes different than simply using a log2 fold change alone. Our literature survey revealed that all predicted target genes have known roles in bone remodeling, specifically related to the immune system and osteoclast formation and functions, suggesting confidence and validity in our method.

Conclusion

cTAP was motivated by recognizing that biologists tend to use Z score values present in data sets for the analysis. However, using cTAP effectively presupposes assembling a sizable cohort of gene expression data sets within a comparable context. As public gene expression data repositories grow, the need to use cohort-based analysis method like cTAP will become increasingly important.
Comparative genome analysis of plant ascomycete fungal pathogens with different lifestyles reveals distinctive virulence strategies
Authors: Wang Yansu , Wu Jie , Yan Jiacheng , Guo Ming , Xu Lei , Hou Liping , Zou Quan
Published: January 2022

Background

Pathogens have evolved diverse lifestyles and adopted pivotal new roles in both natural ecosystems and human environments. However, the molecular mechanisms underlying their adaptation to new lifestyles are obscure. Comparative genomics was adopted to determine distinct strategies of plant ascomycete fungal pathogens with different lifestyles and to elucidate their distinctive virulence strategies.

Results

We found that plant ascomycete biotrophs exhibited lower gene gain and loss events and loss of CAZyme-encoding genes involved in plant cell wall degradation and biosynthesis gene clusters for the production of secondary metabolites in the genome. Comparison with the candidate effectome detected distinctive variations between plant biotrophic pathogens and other groups (including human, necrotrophic and hemibiotrophic pathogens). The results revealed the biotroph-specific and lifestyle-conserved candidate effector families. These data have been configured in web-based genome browser applications for public display (http://lab.malab.cn/soft/PFPG). This resource allows researchers to profile the genome, proteome, secretome and effectome of plant fungal pathogens.

Conclusions

Our findings demonstrated different genome evolution strategies of plant fungal pathogens with different lifestyles and explored their lifestyle-conserved and specific candidate effectors. It will provide a new basis for discovering the novel effectors and their pathogenic mechanisms.
N7-methylguanosine modification of lncRNAs in a rat model of hypoxic pulmonary hypertension: a comprehensive analysis
Authors: Wang Huan , Chen Ren Biao , Zhang Si Ni , Zhang Rui Feng
Published: January 2022

Background

Long non-coding RNAs (lncRNAs) play a critical role in the pathogenesis of hypoxic pulmonary hypertension (HPH). The role of N7-methylguanosine (m7G) modification in lncRNAs has received increased attentions in recent years. However, the m7G-methylation of lncRNA in HPH has yet to be determined. We have therefore performed a transcriptome-wide analysis of m7G lncRNAs in HPH.

Results

Differentially-expressed m7Gs were detected in HPH, and m7G lncRNAs were significantly upregulated compared with non-m7G lncRNAs in HPH. Importantly, this was the first time that the upregulated m7G lncXR_591973 and m7G lncXR_592398 were identified in HPH.

Conclusion

This study provides the first m7G transcriptome-wide analysis of HPH. Importantly, two HPH-associated m7G lncRNAs were identified, although their clinical significance requires further validation.
A novel graph-based k-partitioning approach improves the detection of gene-gene correlations by single-cell RNA sequencing
Authors: Xu Heng , Hu Ying , Zhang Xinyu , Aouizerat Bradley E. , Yan Chunhua , Xu Ke
Published: January 2022

Background

Gene expression is regulated by transcription factors, cofactors, and epigenetic mechanisms. Coexpressed genes indicate similar functional categories and gene networks. Detecting gene-gene coexpression is important for understanding the underlying mechanisms of cellular function and human diseases. A common practice of identifying coexpressed genes is to test the correlation of expression in a set of genes. In single-cell RNA-seq data, an important challenge is the abundance of zero values, so-called “dropout”, which results in biased estimation of gene-gene correlations for downstream analyses. In recent years, efforts have been made to recover coexpressed genes in scRNA-seq data. Here, our goal is to detect coexpressed gene pairs to reduce the “dropout” effect in scRNA-seq data using a novel graph-based k-partitioning method by merging transcriptomically similar cells.

Results

We observed that the number of zero values was reduced among the merged transcriptomically similar cell clusters. Motivated by this observation, we leveraged a graph-based algorithm and develop an R package, scCorr, to recover the missing gene-gene correlation in scRNA-seq data that enables the reliable acquisition of cluster-based gene-gene correlations in three independent scRNA-seq datasets. The graphically partitioned cell clusters did not change the local cell community. For example, in scRNA-seq data from peripheral blood mononuclear cells (PBMCs), the gene-gene correlation estimated by scCorr outperformed the correlation estimated by the nonclustering method. Among 85 correlated gene pairs in a set of 100 clusters, scCorr detected 71 gene pairs, while the nonclustering method detected only 4 pairs of a dataset from PBMCs. The performance of scCorr was comparable to those of three previously published methods. As an example of downstream analysis using scCorr, we show that scCorr accurately identified a known cell type (i.e., CD4+ T cells) in PBMCs with a receiver operating characteristic area under the curve of 0.96.

Conclusions

Our results demonstrate that scCorr is a robust and reliable graph-based method for identifying correlated gene pairs, which is fundamental to network construction, gene-gene interaction, and cellular omic analyses. scCorr can be quickly and easily implemented to minimize zero values in scRNA-seq analysis and is freely available at https://github.com/CBIIT-CGBB/scCorr.
Characterization of non-specific lipid transfer protein (nsLtp) gene families in the Brassica napus pangenome reveals abundance variation
Authors: Liang Yu , Huang Yang , Chen Kang , Kong Xiangdong , Li Maoteng
Published: January 2022

Background

Brassica napus is an important agricultural species, improving stress resistance was one of the main breeding goals at present. Non-specific lipid transfer proteins (nsLTPs) are small, basic proteins which are involved in some biotic or abiotic stress responses. B. napus is susceptible to a variety of fungal diseases, so identify the BnLTPs and their expression in disease responses is very important. The common reference genome of B. napus does not contain all B. napus genes because of gene presence/absence variations between individuals. Therefore, it was necessary to search for candidate BnLTP genes in the B. napus pangenome.

Results

In the present study, the BnLTP genes were identified throughout the pangenome, and different BnLTP genes were presented among varieties. Totally, 246 BnLTP genes were identified and could be divided into five types (1, 2, C, D, and G). The classification, phylogenetic reconstruction, chromosome distribution, functional annotation, and gene expression were analyzed. We also identified potential cis-elements that respond to biotic and abiotic stresses in the 2 kb upstream regions of all BnLTP genes. RNA sequencing analysis showed that the BnLTP genes were involved in the response to Sclerotinia sclerotiorum infection. We identified 32 BnLTPs linked to blackleg resistance quantitative trait locus (QTL).

Conclusion

The identification and analysis of LTP genes in the B. napus pangenome could help to elucidate the function of BnLTP family members and provide new information for future molecular breeding in B. napus.
Impact of nutritional status on prognosis in acute myocardial infarction patients undergoing percutaneous coronary intervention
Authors: Kanda Daisuke , Ikeda Yoshiyuki , Takumi Takuro , Tokushige Akihiro , Sonoda Takeshi , Arikawa Ryo , Anzaki Kazuhiro , Kosedo Ippei , Ohishi Mitsuru
Published: January 2022

Background

Malnutrition affects the prognosis of cardiovascular disease. Acute myocardial infarction (AMI) has been a major cause of death around the world. Thus, we investigated the impact of malnutrition as defined by Geriatric Nutritional Risk Index (GNRI) on mortality in AMI patients.

Methods

In 268 consecutive AMI patients who underwent percutaneous coronary intervention (PCI), associations between all-cause death and baseline characteristics including malnutrition (GNRI < 92.0) and Global Registry of Acute Coronary Events (GRACE) risk score were assessed.

Results

Thirty-three patients died after PCI. Mortality was higher in the 51 malnourished patients than in the 217 non-malnourished patients, both within 1 month after PCI (p < 0.001) and beyond 1 month after PCI (p = 0.017). Multivariate Cox proportional hazards regression modelling using age, left ventricular ejection fraction and GRACE risk score showed malnutrition correlated significantly with all-cause death within 1 month after PCI (hazard ratio [HR] 7.04; 95% confidence interval [CI] 2.30–21.51; p < 0.001) and beyond 1 month after PCI (HR 3.10; 95% CI 1.70–8.96; p = 0.037). There were no significant differences in area under the receiver-operating characteristic (ROC) curve between GRACE risk score and GNRI for predicting all-cause death within 1 month after PCI (0.90 vs. 0.81; p = 0.074) or beyond 1 month after PCI (0.69 vs. 0.71; p = 0.87). Calibration plots comparing actual and predicted mortality confirmed that GNRI (p = 0.006) was more predictive of outcome than GRACE risk score (p = 0.85) beyond 1 month after PCI. Furthermore, comparison of p-value for interaction of malnutrition and GRACE risk score for all-cause death within 1 month after PCI, beyond 1 month after PCI, and the full follow-up period after PCI were p = 0.62, p = 0.64 and p = 0.38, respectively.

Conclusions

GNRI may have a potential for predicting the mortality in AMI patients especially in beyond 1 month after PCI, separate from GRACE risk score. Assessment of nutritional status may help stratify the risk of AMI mortality.
A validation study of data in the National Tonsil Surgery Register in Sweden: high agreement with medical records ensures that data can be used to monitor clinical practices and outcomes
Authors: Lundström Filip , Odhagen Erik , Alm Fredrik , Hemlin Claes , Nerfeldt Pia , Sunnergren Ola
Published: January 2022

Background

The ambition of the National Tonsil Surgery Register in Sweden (NTSRS) is to improve otorhinolaryngological care by monitoring trends in the clinical practices, complications, and outcomes of tonsil surgery. The NTSRS collects data from both surgeons and patients and provides the participating clinics with daily updated data on a publicly available website. On the website, national and local results can be compared and monitored. The use of NTSRS data necessitates that the data is valid, but the NTSRS has not yet been validated. With approximately half of the registered patients responding to the postoperative questionnaires, an analysis of responders and non-responders is also necessary. The aim of this study was to assess the criterion validity of NTSRS data. Another aim was to compare the characteristics and rates of complications between postoperative questionnaire responders and non-responders.

Methods

Data in the NTSRS were compared with data in electronic medical records. The 200 most recent surgeries, up to 31 Dec 2019, in each of 11 surgical units were included. Criterion validity was analysed in terms of observed agreement, Cohens kappa, Gwet’s AC1, and positive and negative agreement. The sign test was used to analyse systematic differences between the NTSRS and the medical records. Comparisons of rates between groups were made with Fisher’s exact test, the chi-square test, and Fisher’s non-parametric permutation test.

Results

A total of 1991 registrations were included in the study. All variables showed very high observed agreement ranging from 0.91 to 1.00, and all variables had AC1 values corresponding to almost perfect agreement. The analysis of questionnaire responders and non-responders showed no statistically significant differences regarding age, indication, or type of surgery. The proportion of women was higher in the responder group. The rate of reoperation due to bleeding was higher in the responder group, but there were no differences regarding other complications.

Conclusions

The results of this study show that data in the NTSRS have criterion validity. The NTSRS is thus well suited for monitoring the clinical practices and outcomes of tonsil surgery. The quality of the data also implies that the registry can be used in both clinical improvement projects and research.
Oncologic patients’ misconceptions may impede enrollment into clinical trials: a cross-sectional study
Authors: Asher Nethanel , Raphael Ari , Wolf Ido , Pelles Sharon , Geva Ravit
Published: January 2022

Background

Clinical trials are an essential source for advances in oncologic care, yet the enrollment rate is only 2-4%. Patients' reluctance to participate is an important barrier. This study evaluates patients' level of understanding and attitudes towards clinical trials.

Methods

This cross-sectional study was conducted in the oncology department and day care unit at the oncology division Tel Aviv Sourasky Medical Center, Israel. From January 2015 to September 2016. Two-hundred patients’ currently receiving active anti-cancer therapy at a large tertiary hospital completed an anonymous questionnaire comprised of demographic information, past experience in clinical research and basic knowledge on clinical trials.

Results

The majority of respondents did not meet the minimum knowledge level criteria. In those who replied they would decline to participate in a clinical trial, concern were related to potential assignment to the placebo arm, provision of informed consent and trust issues with their oncologist. Those with sufficient knowledge were significantly more interested in participating. Patients with past experience in clinical trials had a higher level of academic education, were less religious, had a better understanding of medical research and were inclined to participate in future research.

Conclusions

Misperceptions of clinical trials may contribute substantially to the unwillingness to participate in them.
Simple Excel and ICD-10 based dataset calculator for the Charlson and Elixhauser comorbidity indices
Authors: Prommik Pärt , Tootsi Kaspar , Saluse Toomas , Strauss Eiki , Kolk Helgi , Märtson Aare
Published: January 2022

Background

The Charlson and Elixhauser Comorbidity Indices are the most widely used comorbidity assessment methods in medical research. Both methods are adapted for use with the International Classification of Diseases, which 10th revision (ICD-10) is used by over a hundred countries in the world. Available Charlson and Elixhauser Comorbidity Index calculating methods are limited to a few applications with command-line user interfaces, all requiring specific programming language skills. This study aims to use Microsoft Excel to develop a non-programming and ICD-10 based dataset calculator for Charlson and Elixhauser Comorbidity Index and to validate its results with R- and SAS-based methods.

Methods

The Excel-based dataset calculator was developed using the program’s formulae, ICD-10 coding algorithms, and different weights of the Charlson and Elixhauser Comorbidity Index. Real, population-wide, nine-year spanning, index hip fracture data from the Estonian Health Insurance Fund was used for validating the calculator. The Excel-based calculator’s output values and processing speed were compared to R- and SAS-based methods.

Results

A total of 11,491 hip fracture patients’ comorbidities were used for validating the Excel-based calculator. The Excel-based calculator’s results were consistent, revealing no discrepancies, with R- and SAS-based methods while comparing 192,690 and 353,265 output values of Charlson and Elixhauser Comorbidity Index, respectively. The Excel-based calculator’s processing speed was slower but differing only from a few seconds up to four minutes with datasets including 6250–200,000 patients.

Conclusions

This study proposes a novel, validated, and non-programming-based method for calculating Charlson and Elixhauser Comorbidity Index scores. As the comorbidity calculations can be conducted in Microsoft Excel’s simple graphical point-and-click interface, the new method lowers the threshold for calculating these two widely used indices.

Trial registration

retrospectively registered.
The uptake and use of a minimum data set (MDS) for older people living and dying in care homes: a realist review
Authors: Musa Massirfufulay Kpehe , Akdur Gizdem , Brand Sarah , Killett Anne , Spilsbury Karen , Peryer Guy , Burton Jennifer Kirsty , Gordon Adam Lee , Hanratty Barbara , Towers Ann-Marie , Irvine Lisa , Kelly Sarah , Jones Liz , Meyer Julienne , Goodman Claire
Published: January 2022

Background

Care homes provide long term care for older people. Countries with standardised approaches to residents’ assessment, care planning and review (known as minimum data sets (MDS)) use the aggregate data to guide resource allocation, monitor quality, and for research. Less is known about how an MDS affects how staff assess, provide and review residents’ everyday care. The review aimed to develop a theory-driven understanding of how care home staff can effectively implement and use MDS to plan and deliver care for residents.

Methods

The realist review was organised according to RAMESES (Realist And Meta-narrative Evidence Synthesis: and Evolving Standards) guidelines. There were three overlapping stages: 1) defining the scope of the review and theory development on the use of minimum data set 2) testing and refining candidate programme theories through iterative literature searches and stakeholders’ consultations as well as discussion among the research team; and 3) data synthesis from stages 1 and 2. The following databases were used MEDLINE via OVID, Embase, CINAHL (Cumulative Index to Nursing and Allied Health Literature), ASSIA [Applied Social Sciences Citation Index and Abstracts]) and sources of grey literature.

Results

Fifty-one papers informed the development of three key interlinked theoretical propositions: motivation (mandates and incentives for Minimum Data Set completion); frontline staff monitoring (when Minimum Data Set completion is built into the working practices of the care home); and embedded recording systems (Minimum Data Set recording system is integral to collecting residents’ data). By valuing the contributions of staff and building on existing ways of working, the uptake and use of an MDS could enable all staff to learn with and from each other about what is important for residents’ care

Conclusions

Minimum Data Sets provides commissioners service providers and researchers with standardised information useful for commissioning planning and analysis. For it to be equally useful for care home staff it requires key activities that address the staff experiences of care, their work with others and the use of digital technology.

Registration

PROSPERO registration number CRD42020171323.