bluuebunny/crossref_metadata_2025_split huggingface dataset:
SMGR: a joint statistical method for integrative analysis of single-cell multi-omics data
Authors: Song Qianqian , Zhu Xuewei , Jin Lingtao , Chen Minghan , Zhang Wei , Su Jing 
Published: July 2022

AbstractUnravelling the regulatory programs from single-cell multi-omics data has long been one of the major challenges in genomics, especially in the current emerging single-cell field. Currently there is a huge gap between fast-growing single-cell multi-omics data and effective methods for the integrative analysis of these inherent sparse and heterogeneous data. In this study, we have developed a novel method, Single-cell Multi-omics Gene co-Regulatory algorithm (SMGR), to detect coherent functional regulatory signals and target genes from the joint single-cell RNA-sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) data obtained from different samples. Given that scRNA-seq and scATAC-seq data can be captured by zero-inflated Negative Binomial distribution, we utilize a generalized linear regression model to identify the latent representation of consistently expressed genes and peaks, thus enables the identification of co-regulatory programs and the elucidation of regulating mechanisms. Results from both simulation and experimental data demonstrate that SMGR outperforms the existing methods with considerably improved accuracy. To illustrate the biological insights of SMGR, we apply SMGR to mixed-phenotype acute leukemia (MPAL) and identify the MPAL-specific regulatory program with significant peak-gene links, which greatly enhance our understanding of the regulatory mechanisms and potential targets of this complex tumor.
Model-Predicted Impact of ECG Monitoring Strategies During Bedaquiline Treatment
Authors: van Beek Stijn W , Tanneau Lénaïg , Meintjes Graeme , Wasserman Sean , Gandhi Neel R , Campbell Angie , Viljoen Charle A , Wiesner Lubbe , Aarnoutse Rob E , Maartens Gary , Brust James C M , Svensson Elin M 
Published: July 2022

Abstract

Background
The M2 metabolite of bedaquiline causes QT-interval prolongation, making electrocardiogram (ECG) monitoring of patients receiving bedaquiline for drug-resistant tuberculosis necessary. The objective of this study was to determine the relationship between M2 exposure and Fridericia-corrected QT (QTcF)-interval prolongation and to explore suitable ECG monitoring strategies for 6-month bedaquiline treatment.

Methods
Data from the PROBeX study, a prospective observational cohort study, were used to characterize the relationship between M2 exposure and QTcF. Established nonlinear mixed-effects models were fitted to pharmacokinetic and ECG data. In a virtual patient population, QTcF values were simulated for scenarios with and without concomitant clofazimine. ECG monitoring strategies to identify patients who need to interrupt treatment (QTcF &gt; 500 ms) were explored.

Results
One hundred seventy patients were included, providing 1131 bedaquiline/M2 plasma concentrations and 1702 QTcF measurements; 2.1% of virtual patients receiving concomitant clofazimine had QTcF &gt; 500 ms at any point during treatment (0.7% without concomitant clofazimine). With monthly monitoring, almost all patients with QTcF &gt; 500 ms were identified by week 12; after week 12, patients were predominantly falsely identified as QTcF &gt; 500 ms due to stochastic measurement error. Following a strategy with monitoring before treatment and at weeks 2, 4, 8, and 12 in simulations with concomitant clofazimine, 93.8% of all patients who should interrupt treatment were identified, and 26.4% of all interruptions were unnecessary (92.1% and 32.2%, respectively, without concomitant clofazimine).

Conclusions
Our simulations enable an informed decision for a suitable ECG monitoring strategy by weighing the risk of missing patients with QTcF &gt; 500 ms and that of interrupting bedaquiline treatment unnecessarily. We propose ECG monitoring before treatment and at weeks 2, 4, 8, and 12 after starting bedaquiline treatment.
Gauged sigma models and exceptional dressing cosets
Authors: Sakatani Yuho , Uehara Shozo 
Published: July 2022

Abstract
The Poisson–Lie (PL) T-duality is a generalized T-duality based on the Lie algebra of the Drinfel’d double. In particular, when we consider the PL T-duality of a coset space, the dual space is found to be a generalized coset space, which is called the dressing coset. We investigate an extension of the dressing cosets to the U-duality setup. We propose the gauged actions for various branes in M-theory and type IIB theory, where the generalized metric is constructed by using the exceptional Drinfel’d algebra (EDA) and the gauge algebra is a certain isotropic subalgebra of the EDA. By eliminating the gauge fields, the gauged action reduces to the standard brane action on a certain reduced background, which we call the exceptional dressing coset. We also propose an alternative definition of the exceptional dressing cosets based on Sfetsos’s approach and reproduce a known example of non-Abelian T-duality in the U-duality-covariant formulation.
Tracking the turnover of SARS-CoV-2 VOCs Gamma to Delta in a Brazilian state (Minas Gerais) with a high-vaccination status
Authors: Fonseca Paula L C , Moreira Filipe R R , de Souza Rafael M , Guimarães Natália R , Carvalho Nara O , Adelino Talita E R , Alves Hugo J , Alvim Luige B , Candido Darlan S , Coelho Helena P , Costa Alana V B , Costa Walyson C , de Carvalho Alex F , de Faria Bruna W F , de Lima Aline B , de Oliveira Eneida S , de Souza Carolina S A , de Souza Fernanda G , Dias Rillery C , Geddes Victor E V , Godinho Igor P , Gonçalves Alessandro L , Lourenço Karine L , Magalhães Rubens D M , Malta Frederico S V , Medeiros Eva L A , Mendes Fernanda S , Mendes Pedro H B de P , Mendonça Cristiane P T B , Menezes Andre L , Menezes Diego , Menezes Mariane T , Miguita Lucyene , Moreira Rennan G , Peixoto Renata B , Queiroz Daniel C , Ribeiro Adriana A , Ribeiro Ana Paula de B , Saliba Juliana W , Sato Hugo I , Silva Joice do P , Silva Natiely P , Faria Nuno R , Teixeira Santuza M R , da Fonseca Flávio G , Fernandes Ana Paula S M , Zauli Danielle A G , Januario José Nélio , de Oliveira Jaqueline S , Iani Felipe C de M , de Aguiar Renato S , de Souza Renan P 
Published: July 2022

Abstract
The emergence and global dissemination of Severe Acute Respiratory Syndrome virus 2 (SARS-CoV-2) variants of concern (VOCs) have been described as the main factor driving the Coronavirus Disease 2019 pandemic. In Brazil, the Gamma variant dominated the epidemiological scenario during the first period of 2021. Many Brazilian regions detected the Delta variant after its first description and documented its spread. To monitor the introduction and spread of VOC Delta, we performed Polymerase Chain Reaction (PCR) genotyping and genome sequencing in ten regional sentinel units from June to October 2021 in the State of Minas Gerais (MG). We documented the introduction and spread of Delta, comprising 70 per cent of the cases 8 weeks later. Comparing the viral loads of the Gamma and Delta dominance periods, we provide additional evidence that the latter is more transmissible. The spread and dominance of Delta did not culminate in the increase in cases and deaths, suggesting that the vaccination may have restrained the epidemic growth. Analysis of 224 novel Delta genomes revealed that Rio de Janeiro state was the primary source for disseminating this variant in the state of MG. We present the establishment of Delta, providing evidence of its enhanced transmissibility and showing that this variant shift did not aggravate the epidemiological scenario in a high immunity setting.
Provocative Discography
Authors: Pinto Manuel , Mehbod Amir A. , Swanberg Berit A. , Dawson John M. , Schellhas Kurt 
Published: July 2022

Study Design:
This was a retrospective cohort analysis.

Objective:
The objective of this study was to report the efficacy and safety profile of provocative discography.

Summary of Background Data:
It is reported that the provocative discogram as a diagnostic test for symptomatic degenerative disk disease induces disk degeneration.

Materials and Methods:
Discogram cases from 1998 to 2011 were identified. A matched control group with no discogram was identified. Both had pre–magnetic resonance imaging (MRI) and post-MRI with 5 years minimum between MRI studies. Statistics were generated by group for each level and for all levels combined.

Results:
The discogram cohort comprised 53 patients (193 disks). The control group had 51 subjects (255 disks). There were no significant demographic differences between the groups. Time intervals between the index and follow-up MRI were 11 and 8 years for the discogram and control groups, respectively. The most common injected level was L4–L5; the most painful level was L5–S1 (Visual Analog Scale=7.9); the most concordant level was L5–S1 (75%). The most deranged level as seen on discography was L5–S1 (98%). Degeneration from normal to abnormal MRI among discogram patients was 60%. For controls, the rate was 33%. The discogram and control cohorts were statistically different (P<0.01). Among discogram patients, 58% had a fusion surgery between MRI studies. Comparing the discogram group without interval fusion to controls, the degeneration rate was not different at a 5 years’ minimum follow-up.

Conclusions:
The L5–S1 intervertebral disk level was the most painful, concordant, and deranged level as seen on discogram. Patients who underwent a provocative discogram and interval fusion had a higher rate of subsequent degeneration than similar low back pain sufferers with no discogram. Degeneration rates were comparable at 5 years’ minimum follow-up between discogram patients without interval spine fusion and patients without discogram exposure. The provocative discogram did not accelerate degeneration among these patients.
Adoption and Deadoption of Medications to Treat Hospitalized Patients With COVID-19
Authors: Barbash Ian J. , Davis Billie S. , Minturn John S. , Kahn Jeremy M. 
Published: July 2022

OBJECTIVES:
The COVID-19 pandemic was characterized by rapidly evolving evidence regarding the efficacy of different therapies, as well as rapidly evolving health policies in response to that evidence. Data on adoption and deadoption are essential as we learn from this pandemic and prepare for future public health emergencies.

DESIGN:
We conducted an observational cohort study in which we determined patterns in the use of multiple medications to treat COVID-19: remdesivir, hydroxychloroquine, IV corticosteroids, tocilizumab, heparin-based anticoagulants, and ivermectin. We analyzed changes both overall and within subgroups of critically ill versus Noncritically ill patients.

SETTING:
Data from Optum’s deidentified Claims-Clinical Dataset, which contains multicenter electronic health record data from U.S. hospitals.

PATIENTS:
Adults hospitalized with COVID-19 from January 2020 to June 2021.

INTERVENTIONS:
None.

MEASUREMENTS AND MAIN RESULTS:
Of 141,533 eligible patients, 34,515 (24.4%) required admission to an ICU, 14,754 (10.4%) required mechanical ventilation, and 18,998 (13.4%) died during their hospitalization. Averaged over the entire time period, corticosteroid use was most common (47.0%), followed by remdesivir (33.2%), anticoagulants (19.3%), hydroxychloroquine (7.3%), and tocilizumab (3.4%). Usage patterns varied substantially across treatments. For example, hydroxychloroquine use peaked in March 2020 and leveled off to near zero by June 2020, whereas the use of remdesivir, corticosteroids, and tocilizumab all increased following press releases announcing positive results of large international trials. Ivermectin use increased slightly over the study period but was extremely rare overall (0.4%).

CONCLUSIONS:
During the COVID-19 pandemic, medication treatment patterns evolved reliably in response to emerging evidence and changes in policy. These findings may inform efforts to promote optimal adoption and deadoption of treatments for acute care conditions.
Progesterone and Preterm Birth
Authors: Standard Venus , Jones-Beatty Kimberly , Joseph-Lemon Lodz , Marcelle Ebony , Morris Charlotte E. , Williams Trinisha , Brown Tracie , Oura Haley Shizuka , Stapleton Susan , Jolles Diana R. 
Published: July 2022

Background:
Progesterone has been the standard of practice for the prevention of preterm birth for decades. The drug received expedited Food and Drug Administration approval, prior to the robust demonstration of scientific efficacy.

Methods:
Prospective research from the American Association of Birth Centers Perinatal Data Registry, 2007-2020. Two-tailed t tests, logistic regression, and propensity score matching were used.

Results:
Midwifery-led care was underutilized by groups most at risk for preterm birth and was shown to be effective at maintaining low preterm birth rates. The model did not demonstrate reliable access to progesterone. People of color are most at risk of preterm birth, yet were least likely to receiving progesterone treatment. Progesterone was not demonstrated to be effective at decreasing preterm birth when comparing the childbearing people with a history of preterm birth who used the medication and those who did not within this sample.

Conclusions:
This study adds to the body of research that demonstrates midwifery-led care and low preterm birth rates. The ineffectiveness of progesterone in the prevention of preterm birth among people at risk was demonstrated.
Prediction of Renal Function in Living Kidney Donors and Recipients of Living Donor Kidneys Using Quantitative Histology
Authors: Buus Niels Henrik , Nielsen Cecilie Mølgaard , Skov Karin , Ibsen Lotte , Krag Søren , Nyengaard Jens Randel 
Published: July 2022

Background.
Living kidney donors (LKDs) are at increased risk of chronic kidney disease, whereas transplant recipients experience progressive reduction of graft function. We examined the predictive value of quantitative stereology on renal function in LKDs and recipients of living donor kidneys, based on perioperative biopsies from the donated kidney.

Methods.
Cortex volume of both donor kidneys was determined by contrast-enhanced computed tomography and single-kidney glomerular filtration rate (GFR) by 51chrome-EDTA clearance together with renography. Glomerular density was used to estimate total glomeruli number in addition to glomerular volume, glomerular sclerosis, kidney fibrosis, and arteriole dimensions. GFR measurements were repeated 1 y after transplantation in both LKDs and recipients. Associations between GFR at follow-up and cortex volume and histomorphometric parameters after adjustment of age, gender, body mass index, smoking status, 24-h blood pressure, and single-kidney GFR were examined.

Results.
We included 49 LKDs (age, 51 ± 12 y) and 51 recipients (age, 44 ± 13 y). At follow-up, GFR was 71 ± 16 mL/min in LKDs and 61 ± 18 mL/min in recipients with hyperfiltration being more prominent in LKDs (30.4%) as compared to recipients (16.4%; P < 0.05). One-year GFR in donors correlated to cortex volume (P < 0.001) but not to any histological parameters, whereas GFR in recipients correlated to the amount of interstitial fibrosis (P < 0.01) but not to other histological parameters or cortex volume.

Conclusions.
Kidney cortex volume, but not renal histology parameters, predicts 1-y renal outcome in LKDs. In contrast, the amount of interstitial fibrosis, but not cortex volume, predicts 1-y graft function in recipients.
Students' adoption of e-learning: evidence from a Moroccan business school in the COVID-19 era
Authors: Alami Youssef , El Idrissi Issam 
Published: July 2022

PurposeThis article aims to study the determinants of e-learning acceptability by university students based on their experiences with distance learning during the coronavirus disease 2019 (COVID-19) pandemic.Design/methodology/approachA questionnaire was used to collect data from 448 students enrolled in a Moroccan business school's fourth and fifth years. The technology acceptance model (TAM) was the primary framework used for this analysis, into which variables from the expectation confirmation model were injected, namely facilitating conditions, social influence, expectation confirmation and satisfaction. The proposed conceptual model was tested and evaluated using the partial least squares structural equation modeling (PLS-SEM) technique. Then the authors have offered an in-depth analysis by employing the importance-performance map analysis (IPMA) approach.FindingsThe investigation suggested that the proposed measurement scale effectively assesses the factors impacting students' decision to continue using e-learning in the future. This study’s results show that e-learning acceptance depends significantly on the students' satisfaction, perceived ease of use (PEU) and perceived usefulness (PU). In contrast, the facilitating conditions are not a valid measurement scale to determine students' attitudes toward e-learning.Originality/valueThis is one of the first studies in the Moroccan context to evaluate e-learning acceptability by management students after COVID-19 using a unique research model.
A method for the ontology-based risk management of PPP construction projects
Authors: Jiang Xiaoyan , Wang Sai , Liu Yong , Xia Bo , Skitmore Martin , Nepal Madhav , Ghanbaripour Amir Naser 
Published: July 2022

Purpose
With the increasing complexity of public–private partnership (PPP) projects, the amount of data generated during the construction process is massive. This paper aims to develop a new information management method to cope with the risk problems involved in dealing with such data, based on domain ontologies of the construction industry, to help manage PPP risks, share and reuse risk knowledge.

Design/methodology/approach
Risk knowledge concepts are acquired and summarized through PPP failure cases and an extensive literature review to establish a domain framework for risk knowledge using ontology technology to help manage PPP risks.

Findings
The results indicate that the risk ontology is capable of capturing key concepts and relationships involved in managing PPP risks and can be used to facilitate knowledge reuse and storage beneficial to risk management.

Research limitations/implications
The classes in the risk knowledge ontology model constructed in this research do not yet cover all the information in PPP project risks and need to be further extended. Moreover, only the framework and basic methods needed are developed, while the construction of a working ontology model and the relationship between implicit and explicit knowledge is a complicated process that requires repeated modifications and evaluations before it can be implemented.

Practical implications
The ontology provides a basis for turning PPP risk information into risk knowledge to allow the effective sharing and communication of project risks between different project stakeholders. It can also have the potential to help reduce the dependence on subjectivity by mining, using and storing tacit knowledge in the risk management process.

Originality/value
The apparent suitability of the nine classes of PPP risk knowledge (project model, risk type, risk occurrence stage, risk source, risk consequence, risk likelihood, risk carrier, risk management measures and risk case) is identified, and the proposed construction method and steps for a complete domain ontology for PPP risk management are unique. A combination of criteria- and task-based evaluations is also developed for assessing the PPP risk ontology for the first time.
Attitudes of nursing students towards mental health and the influence of social desirability: a cross-sectional study
Authors: Giralt Palou Rosa , Prat Vigué Gemma , Romeu-Labayen Maria , Tort-Nasarre Glòria 
Published: July 2022

Purpose
Identifying negative attitudes toward mental illness among students on nursing undergraduate degrees can help to design teaching strategies able to reduce the stigma attached to this condition. This study aims to assess attitudes toward mental health and intentions regarding future behavior in university nursing students initiating their training in the treatment of mental health problems (MHPs).

Design/methodology/approach
A descriptive, observational and cross-sectional study was designed. A sample of 162 nursing students completed scales to assess their attitudes toward mental health, stigma, predicted behavior and social desirability. Simple and a multiple linear regression was performed adjusted for the social desirability scale result.

Findings
Nursing students with previous experience of MHPs presented positive attitudes and behavioral intentions toward mental illness. Those who had no such experience before their training in mental health nursing presented certain stigmatizing attitudes. Attitudes toward MHPs may be affected by stigma and also by social desirability bias. The training in mental health care given to nursing students should aim to reduce its influence to help them carry out their future duties efficiently and compassionately.

Originality/value
This study demonstrates the relevance of university teaching plans, which should place special emphasis on promoting knowledge and developing skills and attitudes in nursing students undergoing training in mental health care to ensure optimal levels of performance in their future careers.
Industry globalization: construct, measurement and variation across industries
Authors: Sambharya Rakesh B. , Contractor Farok J. , Rasheed Abdul A. 
Published: July 2022

Purpose
The purpose of this paper is to identify some of the major issues relating to the conceptualization and operationalization of industry globalization.

Findings
Globalized industries have four important characteristics: cross-border product flows, cross-border capital flows, dispersal of global value chains and global competition. However, lack of availability of data limits our ability to develop an operationalization that encompasses all these four aspects of globalization.

Practical implications
The authors identify some of the most important factors driving industry globalization as well as the major impediments to globalization.

Originality/value
Although the term “globalization” has attained a nearly “taken for granted” status, its meaning is rather vaguely specified and is often context dependent. This paper delineates the domain of the construct and identifies many of the practical issues in operationalizing the construct.
How does green intellectual capital affect environmental performance? Evidence from manufacturing firms in Ghana
Authors: Boso Richard Kwasi , Adusei Enoch , Demah Emmanuel 
Published: July 2022

Purpose
Industrialization has contributed to global environmental problems, especially in developed countries, but increasingly so in developing ones as well. Leveraging on the natural resource-based view theory, this study aims to examine the mediating role of environmental consciousness (EC) on the relationship between green intellectual capital (IC) and environmental performance among manufacturing firms in Ghana against a backdrop of increasing national drive towards greater industrialization.

Design/methodology/approach
This study used a cross-sectional survey design to obtain data from 245 manufacturing firms using purposive sampling technique. Structural equation modelling was used to test for the hypothesized relationships among variables.

Findings
Evidence suggests that green IC has a significantly positive effect on environmental performance. Furthermore, it was found that green IC has a positive and significant effect on EC, but EC only mediated the relationship between green IC and environmental performance.

Practical implications
Manufacturing firms within emerging economies like Ghana can improve on their green practices by incorporating these findings in their business models, while research could be guided to focus their inquiries on this and related genre of scholarly work.

Originality/value
This study is an early-stage study to identify EC as a variable which mediates the relationship between green IC and environmental performance among manufacturing firms in an emerging economy like Ghana.