bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of bias adjustment in meta-analysis using data-based and opinion-based methods
Authors: Stone Jennifer C. , Furuya-Kanamori Luis , Aromataris Edoardo , Barker Timothy H. , Doi Suhail A.R. 
Published: February 2024

Introduction:
Several methods exist for bias adjustment of meta-analysis results, but there has been no comprehensive comparison with unadjusted methods. We compare 6 bias-adjustment methods with 2 unadjusted methods to examine how these different methods perform.

Methods:
We re-analyzed a meta-analysis that included 10 randomized controlled trials. Two data-based methods (Welton’s data-based approach and Doi’s quality effects model) and 4 opinion-informed methods (opinion-based approach, opinion-based distributions combined statistically with data-based distributions, numerical opinions informed by data-based distributions, and opinions obtained by selecting areas from data-based distributions) were used to incorporate methodological quality information into the meta-analytical estimates. The results of these 6 methods were compared with 2 unadjusted models: the DerSimonian-Laird random effects model and Doi’s inverse variance heterogeneity model.

Results:
The 4 opinion-based methods returned the random effects model estimates with wider uncertainty. The data-based and quality effects methods returned different results and aligned with the inverse variance heterogeneity method with some minor downward bias adjustment.

Conclusion:
Opinion-based methods seem to only add uncertainty rather than bias adjust.
A Hybrid Perspective of Vision-Based Methods for Estimating Structural Displacements Based on Mask Region-Based Convolutional Neural Networks
Authors: Xu Chuanchang , Lai Cass Wai Gwan , Wang Yangchun , Hou Jiale , Shao Zhufeng , Cai Enjian , Yang Xingjian 
Published: February 2024

Abstract
Vision-based methods have shown great potential in vibration-based structural health monitoring (SHM), which can be classified as target-based and target-free methods. However, target-based methods cannot achieve subpixel accuracy, and target-free methods are sensitive to environmental effects. To this end, this paper proposed a hybrid perspective of vision-based methods for estimating structural displacements, based on Mask region-based convolutional neural networks (Mask R-CNNs). In proposed methods, Mask R-CNN is used to first locate the target region and then target-free vision-based methods are used to estimate structural displacements from the located target. The performances of proposed methods were validated in a shaking table test of a cold formed steel (CFS) wall system. It can be seen that Mask R-CNN can significantly improve the accuracy of feature point matching results of the target-free method. The comparisons of estimated structural displacements using proposed methods are conducted and detailed into accuracy, stability, and computational burden, to guide the selection of the proper proposed method for the specific problem in vibration-based SHM. Proposed methods can also achieve even 1/15 pixel-level accuracy. Moreover, different image denoising methods in different lighting conditions are compared.
Gas Path Fault Diagnosis of Turboshaft Engine Based on Novel Transfer Learning Methods
Authors: Zhao Yong-Ping , Jin Hui-Jie , Liu Hao 
Published: February 2024

Abstract
Data-driven fault diagnosis method is widely used in the field of engine health management, which uses engine sensor data as input and engine faulty components as output for component-level fault diagnosis of the engine. The application premise of the general data-driven fault diagnosis method is that all data come from the same working conditions, that is, they belong to the same distribution. However, this assumption is not valid in the actual engine fault diagnosis, because the engine state will change with the increase of running time. In the meantime, collecting engine data is usually expensive, time-consuming, and laborious. To solve these problems, extreme learning machine (ELM)-based two transfer learning methods for fault diagnosis of turboshaft engines are proposed in this paper. One is joint solving ELM (JSELM), which regards the information of the target domain and source domain as similar and different parts, respectively, and knowledge is extracted from them at the same time. The other is model transfer-based ELM (MTELM), which uses the idea of pretraining. First, a general ELM classifier is trained with the source domain data and then fine-tuned with the target domain data. Both methods have a good real-time performance as the traditional ELM. When there are a few data in the target domain, they achieve much better classification accuracy than traditional ELM. Finally, experiments are carried out with turboshaft engine simulation data. The results show that both methods are effective, especially MTELM, which has better classification accuracy.
Adaptive Ensemble of Multi-Kernel Gaussian Process Regressions Based on Heuristic Model Screening for Nonparametric Modeling of Ship Maneuvering Motion
Authors: Jiang Lichao , Shang Xiaobing , Qi Xinyu , Ouyang Zilu , Zhang Zhi 
Published: February 2024

Abstract
Gaussian process regression (GPR) is a commonly used approach for establishing the nonparametric models of ship maneuvering motion, and its performance depends on the selection of the kernel function. However, no single kernel function can be universally applied to all nonparametric models of ship maneuvering motion, which may compromise the robustness of GPR. To address this issue, an adaptive ensemble of multi-kernel GPRs based on heuristic model screening (AEGPR-HMS) is proposed in this paper. In the proposed method, four kernel functions are involved in constructing the ensemble model. The HMS method is introduced to determine the weights of individual-based GPR models, which can be adaptively assigned according to the baseline GPR model. To determine the hyper-parameters of these kernel functions, the genetic algorithm is also employed to compute the optimal values. The KVLCC2 tanker provided by the SIMMAN 2008 workshop is used to validate the performance of the proposed method. The results demonstrate that the AEGPR-HMS is an efficient and robust method for nonparametric modeling of ship maneuvering motion.
Amoebicidal effect of synthetic indoles against
Acanthamoeba
spp.: a study of cell death
Authors: Sifaoui Ines , Rodríguez-Expósito Rubén L. , Reyes-Batlle María , Dumpiérrez Ramos Alejandra , Diana-Rivero Raquel , García-Tellado Fernando , Tejedor David , Piñero José E. , Lorenzo-Morales Jacob 
Published: February 2024

ABSTRACT

Organic and synthetic chemistry plays a crucial role in drug discovery fields. Moreover, chemical modifications of available molecules to enhance their efficacy, selectivity and safety have been considered as an attractive approach for the development of new bioactive agents. Indoles, a versatile group of natural heterocyclic compounds, have been widely used in pharmaceutical industry due to their broad spectrum of activities including antimicrobial, antitumoral and anti-inflammatory among others. Herein, we report the amoebicidal activity of different indole analogs on
Acanthamoeba castellanii
Neff. Among the 40 tested derivatives, eight molecules were able to inhibit this protistan parasite. The structure-activity relationship (SAR) analysis of their anti-
Acanthamoeba
activity would suggest that a carboxylation of C-3 position and the incorporation of halogen as chlorine/fluorine would enhance their biological profile, presumably by increasing their lipophilicity and therefore their ability to cross the cell membrane. Fluorescence image base system was used to investigate the effect of indole 6o c-6 on the cytoskeleton network and various programmed cell death features. We were able to highlight that the methyl 6-chloro-1H-indole-3-carboxylate could induce program cell death by the mitochondrial dysfunction.
Identification of bacterial dissimilatory antimonate reductase AnrA: genes and proteins involved in antimonate respiration and resistance in
Geobacter
sp. strain SVR
Authors: Kambara Ryoya , Yamamura Shigeki , Amachi Seigo 
Published: February 2024

ABSTRACT

Geobacter
sp. strain SVR uses antimonate [Sb(V)] as a terminal electron acceptor for anaerobic respiration. Here, we visualized a possible key enzyme, periplasmic Sb(V) reductase (Anr), via active staining and non-denaturing gel electrophoresis. Liquid chromatography-tandem mass spectrometry analysis revealed that a novel dimethyl sulfoxide (DMSO) reductase family protein, WP_173201954.1, is involved in Anr. This protein was closely related with AnrA, a protein suggested to be the catalytic subunit of a respiratory Sb(V) reductase in
Desulfuribacillus stibiiarsenatis
. The
anr
genes of strain SVR (
anrXSRBAD
) formed an operon-like structure, and their transcription was upregulated under Sb(V)-respiring conditions. The expression of
anrA
gene was induced by more than 1 µM of antimonite [Sb(III)]; however, arsenite [As(III)] did not induce the expression of
anrA
gene. Tandem mass tag-based proteomic analysis revealed that, in addition to Anr proteins, proteins in the following categories were upregulated under Sb(V)-respiring conditions: (i) Sb(III) efflux systems such as Ant and Ars; (ii) antioxidizing proteins such as ferritin, rubredoxin, and thioredoxin; (iii) protein quality control systems such as HspA, HslO, and DnaK; and (iv) DNA repair proteins such as UspA and UvrB. These results suggest that strain SVR copes with antimony stress by modulating pleiotropic processes to resist and actively metabolize antimony. To the best of our knowledge, this is the first report to demonstrate the involvement of AnrA in Sb(V) respiration at the protein level. Furthermore, this is the first example to show high expression of the Ant system proteins in the Sb(V)-respiring bacterium.

IMPORTANCE

Antimony (Sb) exists mainly as antimonite [Sb(III)] or antimonate [Sb(V)] in the environment, and Sb(III) is more toxic than Sb(V). Recently, microbial involvement in Sb redox reactions has received attention. Although more than 90 Sb(III)-oxidizing bacteria have been reported, information on Sb(V)-reducing bacteria is limited. Especially, the enzyme involved in dissimilatory Sb(V) reduction, or Sb(V) respiration, is unclear, despite this pathway being very important for the circulation of Sb in nature. In this study, we demonstrated that the Sb(V) reductase (Anr) of an Sb(V)-respiring bacterium (
Geobacter
sp. SVR) is a novel member of the dimethyl sulfoxide (DMSO) reductase family. In addition, we found that strain SVR copes with Sb stress by modulating pleiotropic processes, including the Ant and Ars systems, and upregulating the antioxidant and quality control protein levels. Considering the abundance and diversity of putative
anr
genes in the environment, Anr may play a significant role in global Sb cycling in both marine and terrestrial environments.
Recapitulation of the Powassan virus life cycle in cell culture
Authors: Song Jingwei , Hong Jiayao , Yang Chen , Zhang Yu , Li Zhuoyang , He Peifeng , Ding Qiang 
Published: February 2024

ABSTRACT

Powassan virus (POWV) is a tick-borne flavivirus known for causing fatal neuroinvasive diseases in humans. Recently, there has been a noticeable increase in POWV infections, emphasizing the urgency of understanding viral replication, pathogenesis, and developing interventions. Notably, there are no approved vaccines or therapeutics for POWV, and its classification as a biosafety level-3 (BSL-3) agent hampers research. To overcome these obstacles, we developed a replicon system, a self-replicating RNA lacking structural proteins, making it safe to operate in a BSL-2 environment. We constructed a POWV replicon carrying the Gaussia luciferase (Gluc) reporter gene and blasticidin (BSD) selectable marker. Continuous BSD selection led to obtain a stable POWV replicon-carrying Huh7 cell lines. We identified cell culture adaptive mutations G4079A, G4944T and G6256A, resulting in NS2A
R195K
, NS3
G122G
, and NS3
V560M
, enhancing RNA replication. We demonstrated the utility of the POWV replicon system for high-throughput screening (HTS) assay to identify promising antivirals against POWV replication. We further explored the applications of the POWV replicon system, generating single-round infectious particles (SRIPs) by transfecting Huh7-POWV replicon cells with plasmids encoding viral capsid (C), premembrane (prM), and envelope (E) proteins, and revealed the distinct antigenic profiles of POWV with ZIKV. In summary, the POWV replicon and SRIP systems represent crucial platforms for genetic and functional analysis of the POWV life cycle and facilitating the discovery of antiviral drugs.

IMPORTANCE
In light of the recent surge in human infections caused by POWV, a biosafety level-3 (BSL-3) classified virus, there is a pressing need to understand the viral life cycle and the development of effective countermeasures. To address this, we have pioneered the establishment of a POWV RNA replicon system and a replicon-based POWV SRIP system. Importantly, these systems are operable in BSL-2 laboratories, enabling comprehensive investigations into the viral life cycle and facilitating antiviral screening. In summary, these useful tools are poised to advance our understanding of the POWV life cycle and expedite the development of antiviral interventions.
RpoS and the bacterial general stress response
Authors: Bouillet Sophie , Bauer Taran S. , Gottesman Susan 
Published: February 2024

SUMMARY

The general stress response (GSR) is a widespread strategy developed by bacteria to adapt and respond to their changing environments. The GSR is induced by one or multiple simultaneous stresses, as well as during entry into stationary phase and leads to a global response that protects cells against multiple stresses. The alternative sigma factor RpoS is the central GSR regulator in
E. coli
and conserved in most γ-proteobacteria. In
E. coli
, RpoS is induced under conditions of nutrient deprivation and other stresses, primarily via the activation of RpoS translation and inhibition of RpoS proteolysis. This review includes recent advances in our understanding of how stresses lead to RpoS induction and a summary of the recent studies attempting to define RpoS-dependent genes and pathways.
Draft genome sequence of antibiotic-resistant
Shigella
flexneri
MTR_GR_V146 strain isolated from a tomato (
Solanum lycopersicum
) sample collected from a peri-urban area of Bangladesh
Authors: Islam Md. Saiful , Pramanik Pritom Kumar , Rana Md. Liton , Ullah Md. Ashek , Neloy Fahim Haque , Ramasamy Srinivasan , Schreinemachers Pepijn , Oliva Ricardo , Rahman Md. Tanvir 
Published: February 2024

ABSTRACT

This study announces the genome sequence of the
Shigella flexneri
MTR_GR_V146 strain isolated from a tomato (
Solanum lycopersicum
) sample in Bangladesh. This strain has a 4,624,521 bp genome length (coverage: 73.07×), 2 CRISPR arrays, 1 plasmid, 52 predicted antibiotic resistance genes, and 53 virulence factor genes.
Earliest observation of the tetracycline destructase
tet(X3
)
Authors: Grenier Frédéric , Lévesque Simon , Rodrigue Sébastien , Haraoui Louis-Patrick 
Published: February 2024

ABSTRACT

Tigecycline is an antibiotic of last resort for infections with carbapenem-resistant
Acinetobacter baumannii
. Plasmids harboring variants of the tetracycline destructase gene
tetX
promote rising tigecycline resistance rates. We report the earliest observation of
tet(X3
) in a clinical strain predating tigecycline’s commercialization, suggesting selective pressures other than tigecycline contributed to its emergence.

IMPORTANCE

We present the earliest observation of a
tet
(
X3
)-positive bacterial strain, predating by many years the earliest reports of this gene so far. This finding is significant as tigecycline is an antibiotic of last resort for carbapenem-resistant
Acinetobacter baumannii
(CRAB), which the World Health Organization ranks as one of its top three critical priority pathogens, and
tet
(
X3
) variants have become the most prevalent genes responsible for enabling CRAB to become tigecycline resistant. Moreover, the
tet
(
X3
)-positive strain we report is the first and only to be found that predates the commercialization of tigecycline, an antibiotic that was thought to have contributed to the emergence of this resistance gene. Understanding the factors contributing to the origin and spread of novel antibiotic resistance genes is crucial to addressing the major global public health issue, which is antimicrobial resistance.
Diagnostic utility of point-of-care ultrasound and optical coherence tomography for papilloedema in children: a prospective pilot study
Authors: Chiu Hannah H , Al-Farsi Nouf , Wong Agnes M F , Davis Adrienne , Tessaro Mark O , Wan Michael J 
Published: February 2024

Background/AimsPapilloedema is an important sign of serious neurological disease, but it can be difficult to detect on funduscopy. The purpose of this study was to determine the diagnostic accuracy of point-of-care ultrasound (POCUS) and optical coherence tomography (OCT) for detecting papilloedema in children.MethodsThis was a prospective observational study at a tertiary care paediatric hospital. Patients were eligible for the study if they underwent a lumbar puncture with opening pressure and had high-quality POCUS and OCT imaging.ResultsA total of 63 eyes from 32 patients were included in the study, 41 (65%) with papilloedema and 22 (35%) without. There were statistically significant differences between the groups in the optic disc elevation (ODE) (p<0.001) and optic nerve sheath diameter (ONSD) (p<0.001) on POCUS, and in the average retinal nerve fibre layer (rNFL) thickness on OCT (p<0.001). Average rNFL thickness had the highest diagnostic accuracy with an area under the curve (AUC) of 0.999 and a 100% sensitivity and 95% specificity for papilloedema (threshold value of ≥108 µm). ODE had an AUC of 0.866 and a 93% sensitivity and 55% specificity (threshold value of ≥0.5 mm). ONSD had an AUC of 0.786 and a 93% sensitivity and 45% specificity (threshold value of ≥5.5 mm).ConclusionBoth OCT and POCUS are potentially useful tools to help diagnose papilloedema in children. Larger studies are needed to further define the role and accuracy of POCUS and OCT in assessing papilloedema in children.
Aerobic exercise interventions for promoting cardiovascular health and mobility after stroke: a systematic review with Bayesian network meta-analysis
Authors: Moncion Kevin , Rodrigues Lynden , Wiley Elise , Noguchi Kenneth S , Negm Ahmed , Richardson Julie , MacDonald Maureen Jane , Roig Marc , Tang Ada 
Published: February 2024

ObjectiveTo determine the superiority of aerobic exercise (AE) interventions on key outcomes of stroke recovery, including cardiorespiratory fitness (V̇O2peak, primary outcome), systolic blood pressure (SBP) and mobility (6 min Walk Test (6MWT) distance and 10 m Usual Gait Speed) after stroke.Data sourcesMEDLINE, EMBASE, Web of Science, CINAHL, CENTRAL, SPORTDiscus, PsycINFO and AMED Allied and Complementary Medicine were searched from inception to February 2023.Eligibility criteriaRandomised controlled trials were included that compared the effects of any AE interventions (low-intensity, moderate-intensity, high-intensity continuous training (HICT), high-intensity interval training (HIIT)) to no exercise, usual care or other AE interventions in individuals poststroke.AnalysesSystematic review with Bayesian network meta-analysis (NMA) methodology was employed. Surface under the cumulative ranking curve (SUCRA) values were used to rank interventions. The Grading of Recommendations, Assessment, Development and Evaluation minimally contextualised framework for NMA was followed.ResultsThere were 28 studies (n=1298) included in the NMA for V̇O2peak, 11 (n=648) for SBP, 28 (n=1494) for 6MWT and 18 (n=775) for the 10 m Usual Gait Speed. The greatest effect on V̇O2peak, 6MWT and 10 m Usual Gait Speed was observed after HIIT and HICT. No differences between interventions were found for SBP. SUCRA values identified HIIT as the superior AE intervention for all outcomes of interest. HIIT was the most effective intervention for improving V̇O2peak (2.9 mL/kg/min (95% credible interval 0.8 to 5.0) moderate certainty) compared with usual care.ConclusionThis NMA suggests that higher-intensity AE is superior to traditional low-intensity to moderate-intensity AE for improving outcomes after stroke.
Access to telehealth and changes in diabetes care patterns during the pandemic: evidence from a large integrated health system in the Southeast USA
Authors: Oviedo Sofia A , McDonald Bennett , Gander Jennifer C , Ali Mohammed K , Harding Jessica L 
Published: February 2024

IntroductionTo examine the role of telehealth in diabetes care and management during versus pre-COVID-19 pandemic.Research design and methodsWe included adults (≥18 years) with prevalent diabetes as of January 1, 2018, and continuously enrolled at Kaiser Permanente Georgia through December 31, 2021 (n=22,854). We defined pre (2018–2019) and during COVID-19 (2020–2021) periods. Logistic generalized estimating equations (GEEs) assessed the within-subject change in adherence to seven annual routine care processes (blood pressure (BP), hemoglobin A1C (HbA1c), cholesterol, creatinine, urine-albumin-creatinine ratio (UACR), eye and foot examinations) pre versus during COVID-19 among telehealth users (ie, more than one telehealth visit per year per period) and non-telehealth users. Linear GEE compared mean laboratory measurements pre versus during COVID-19 by telehealth use.ResultsThe proportion of telehealth users increased from 38.7% (2018–2019) to 91.5% (2020–2021). During (vs pre) the pandemic, adherence to all care processes declined in telehealth (range: 1.6% for foot examinations to 12.4% for BP) and non-telehealth users (range: 1.9% for foot examinations to 40.7% for BP). In telehealth users, average HbA1c (mean difference: 0.4% (95% CI 0.2% to 0.6%), systolic BP (1.62 mm Hg (1.44 to 1.81)), and creatinine (0.03 mg/dL (0.02 to 0.04)), worsened during (vs pre) COVID-19, while low density lipoprotein (LDL) cholesterol improved (−9.08 mg/dL (−9.77 to −8.39)). For UACR, odds of elevated risk of kidney disease increased by 48% (OR 1.48 (1.36–1.62)). Patterns were similar in non-telehealth users.ConclusionsTelehealth use increased during the pandemic and alleviated some of the observed declines in routine diabetes care and management.