bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fractional-order burgers model for coral concrete creep
Authors: Cao Jian , Wang Danshen , Zou Ziyi , Tu Ning 
Published: September 2024

Abstract
With the rapid development of marine engineering construction, coral aggregate has been widely applied in practical engineering. Its creep characteristics must be emphasized, but only a few experimental studies have been conducted, and theoretical research has not yet been reported. In this study, based on the traditional Burgers rheological model and using the fractional order software components Able dashpot, constructs a fractional order creep model for coral concrete and provides a calculation method. Comparison shows that the traditional Burgers rheological model cannot adjust the creep rate and development degree in calculations, resulting in a large deviation between its predicted results and experimental values. However, the fractional order model established in this paper aligns with the creep development law of coral concrete, and its calculated values match well with experimental values, making it suitable for predicting the creep characteristics of coral concrete under different water-cement ratios. Sensitivity analysis of the fractional order can achieve effective control over the prediction of creep development in coral concrete in practical engineering. The fractional order creep model established in this paper can provide a basis for predicting and evaluating the long-term performance of coral concrete in practical engineering.
Comparing Two-Step Approaches to Measuring Gender Identity: The Reliability and Applications of Asking About Sex Assigned at Birth versus Transgender Self-Identification
Authors: Tordoff Diana M , Minalga Brian , Catháin Nicole Ó , Fernandez Atlas , Gross Bennie , Glick Sara N ,   the Seattle Trans and Nonbinary Sexual Health (STARS) Advisory Board
Published: September 2024

Abstract
Inclusive measures of gender are critical for health equity research. This study compared the reliability and applications of two different approaches for measuring gender in response to emerging community concerns regarding the potential harms of asking about sex assigned at birth (SAAB) within transgender and gender diverse (TGD) populations. Using data from a 2021 survey of LGBTQ+ people in Washington state, we compared approaches for measuring gender via a two-step question that collected data on: (1) current gender and SAAB versus (2) current gender and transgender self-identification. Among 2,275 LGBTQ+ participants aged 9-81, 63% were cisgender, 35% TGD, and 2% were not categorized. There was near perfect agreement between the two methods in their ability to identify TGD participants (percent agreement=99.7%, unweighted Cohen’s Kappa=0.99). Among gender diverse participants, stratification by SAAB revealed differences in sexual health outcomes, while stratification by transgender self-identification revealed differences in access to gender-affirming care and lifetime experiences of discrimination. Ascertaining SAAB may be most useful for identifying sexual health disparities while transgender self-identification may better illuminate healthcare needs and social determinants of health among TGD people. Researchers and public health practitioners should critically consider the acceptability and relevance of SAAB questions to their research goals.
Higher-order correction of persistent batch effects in correlation networks
Authors: Micheletti Soel , Schlauch Daniel , Quackenbush John , Ben Guebila Marouen 
Published: September 2024

Abstract

Motivation
Systems biology analyses often use correlations in gene expression profiles to infer co-expression networks that are then used as input for gene regulatory network inference or to identify functional modules of co-expressed or putatively co-regulated genes. While systematic biases, including batch effects, are known to induce spurious associations and confound differential gene expression analyses (DE), the impact of batch effects on gene co-expression has not been fully explored. Methods have been developed to adjust expression values, ensuring conditional independence of mean and variance from batch or other covariates for each gene, resulting in improved fidelity of DE analysis. However, such adjustments do not address the potential for spurious differential co-expression (DC) between groups. Consequently, uncorrected, artifactual DC can skew the correlation structure, leading to the identification of false, non-biological associations, even when the input data are corrected using standard batch correction.

Results
In this work, we demonstrate the persistence of confounders in covariance after standard batch correction using synthetic and real-world gene expression data examples. We then introduce Co-expression Batch Reduction Adjustment (COBRA), a method for computing a batch-corrected gene co-expression matrix based on estimating a conditional covariance matrix. COBRA estimates a reduced set of parameters expressing the co-expression matrix as a function of the sample covariates, allowing control for continuous and categorical covariates. COBRA is computationally efficient, leveraging the inherently modular structure of genomic data to estimate accurate gene regulatory associations and facilitate functional analysis for high-dimensional genomic data.

Availability and implementation
COBRA is available under the GLP3 open source license in R and Python in netZoo (https://netzoo.github.io).
KnotResolver: tracking self-intersecting filaments in microscopy using directed graphs
Authors: Khatri Dhruv , Yadav Shivani A , Athale Chaitanya A 
Published: September 2024

Abstract

Motivation
Quantification of microscopy time series of in vitro reconstituted motor-driven microtubule transport in “gliding assays” is typically performed using computational object tracking tools. However, these are limited to non-intersecting and rod-like filaments.

Results
Here, we describe a novel computational image-analysis pipeline, KnotResolver, to track image time series of highly curved self-intersecting looped filaments (knots) by resolving cross-overs. The code integrates filament segmentation and cross-over or “knot” identification based on directed graph representation, where nodes represent cross-overs and edges represent the path connecting them. The graphs are mapped back to contours and the distance to a reference minimized. The accuracy of contour detection is sub-pixel with a robustness to noise. We demonstrate the utility of KnotResolver by automatically quantifying “flagella-like” curvature dynamics and wave-like oscillations of clamped microtubules in a “gliding assay.”

Availability and implementation
The MATLAB-based source code is released as OpenSource and is available at https://github.com/CyCelsLab/MTKnotResolver.
Age and visual cortex inhibition: a TMS-MRS study
Authors: Simmonite Molly , Khammash Dalia , Michon Katherine J , Hamlin Abbey , Taylor Stephan F , Vesia Michael , Polk Thad A 
Published: September 2024

Abstract
Paired-pulse transcranial magnetic stimulation is a valuable tool for investigating inhibitory mechanisms in motor cortex. We recently demonstrated its use in measuring cortical inhibition in visual cortex, using an approach in which participants trace the size of phosphenes elicited by stimulation to occipital cortex. Here, we investigate age-related differences in primary visual cortical inhibition and the relationship between primary visual cortical inhibition and local GABA+ in the same region, estimated using magnetic resonance spectroscopy. GABA+ was estimated in 28 young (18 to 28 years) and 47 older adults (65 to 84 years); a subset (19 young, 18 older) also completed a paired-pulse transcranial magnetic stimulation session, which assessed visual cortical inhibition. The paired-pulse transcranial magnetic stimulation measure of inhibition was significantly lower in older adults. Uncorrected GABA+ in primary visual cortex was also significantly lower in older adults, while measures of GABA+ that were corrected for the tissue composition of the magnetic resonance spectroscopy voxel were unchanged with age. Furthermore, paired-pulse transcranial magnetic stimulation–measured inhibition and magnetic resonance spectroscopy–measured tissue-corrected GABA+ were significantly positively correlated. These findings are consistent with an age-related decline in cortical inhibition in visual cortex and suggest paired-pulse transcranial magnetic stimulation effects in visual cortex are driven by GABAergic mechanisms, as has been demonstrated in motor cortex.
The weighing process in patients on hemodialysis: an opportunity to improve volume management
Authors: Niknam Janosch , Mussnig Sebastian , Matthias Christoph , Waller Maximilian , Keil Nikolaus , Krenn Simon , Beige Joachim , Schneditz Daniel , Hecking Manfred 
Published: September 2024

ABSTRACT

Background
Hemodialysis relies on accurate body mass (BM) assessment to determine ultrafiltration volumes, but we have not identified published practice patterns disclosing how to handle clothing mass. Here we investigated the potential impact of clothing mass on predialysis BM determination, hypothesizing that a standardized template for clothing mass estimation enhances accuracy, compared with conventional practice.

Methods
Measurements included dressed and undressed BM predialysis. A pre-established template for average clothing mass was used to approximate undressed BM from clothed measurements. Differences from undressed BM were compared using Bland–Altman plots and tested for statistical significance using Wilcoxon signed rank tests.

Results
After excluding erroneous results, data from 48 patients were analyzed. Thirty-six patients (75%) did not habitually estimate clothing mass, but used their dressed BM as the predialysis BM, while the other 12 patients (25%) reported deducting a self-estimated clothing mass from their clothed predialysis BM. The differences from undressed BM were 0.819 ± 0.462 kg and 0.342 ± 0.321 kg in these two groups, respectively, indicating that patients underestimated clothing mass. Using the template to deduct clothing mass from clothed predialysis BM, these differences could be reduced to 0.197 ± 0.220 kg and 0.133 ± 0.135 kg, respectively. The average differences using the patient-reported BM and the template-based BM made up 39.4% and 8.6% of the average subsequent ultrafiltration volume, respectively, suggesting that potential overestimation of the actual ultrafiltration volume could be reduced.

Conclusion
A standardized template for clothing mass may be useful to derive representative predialysis BM, leading to more precise ultrafiltration calculation. Exact BM determination might improve volume management in hemodialysis.
Beyond directed hypergraphs: heterogeneous hypergraphs and spectral centralities
Authors: Contreras-Aso Gonzalo , Criado Regino , Romance Miguel 
Published: September 2024

Abstract
The study of hypergraphs has received a lot of attention over the past few years, however up until recently there has been no interest in systems where higher order interactions are not undirected. In this article, we introduce the notion of heterogeneous hypergraphs from an algebraic point of view, which have traditional directed hypergraphs as a particular case. We furthermore analytically study the spectral centralities associated to some types of heterogeneous hypergraphs, extending previously defined eigenvector-like centrality measures to this new realm. We supplement the analytical arguments with some numerical comparisons of pairwise and higher order rankings, and we construct directed higher order networks from real data, which we then use for discussion and analysis.
How to conduct clinical research in cardiovascular imaging: a primer for clinical cardiologists and researchers—a statement of the European Association of Cardiovascular Imaging (EACVI) of the ESC
Authors: Muraru Denisa , Pontone Gianluca , Jurcut Ruxandra , Magne Julien , Donal Erwan , Stankovic Ivan , Anagnostopoulos Constantinos , Bartko Philipp E , Bijnens Bart , Fontana Marianna , Galli Elena , Michalski Blazej , Perazzolo Marra Martina , Pezel Théo , Rossi Alexia , Smiseth Otto A , Van de Veire Nico , Edvardsen Thor , Petersen Steffen E , Cosyns Bernard , Andreini Daniele , Bertrand Philippe , Delgado Victoria , Dweck Marc , Haugaa Kristina , Keenan Niall , Marwick Thomas H , Neglia Danilo 
Published: September 2024

Abstract
This statement from the European Association of Cardiovascular Imaging (EACVI) of the ESC aims to address the fundamental principles that guide clinical research in the field of cardiovascular imaging. It provides clinical researchers, cardiology fellows, and PhD students with a condensed, updated, and practical reference document to support them in designing, implementing, and conducting imaging protocols for clinical trials. Although the present article cannot replace formal research training and mentoring, it is recommended reading for any professional interested in becoming acquainted with or participating in clinical trials involving cardiovascular imaging.
Long-term outcomes of cardiogenic shock and cardiac arrest complicating ST-elevation myocardial infarction according to timing of occurrence
Authors: Kanhouche Gabriel , Nicolau Jose Carlos , de Mendonça Furtado Remo Holanda , Carvalho Luiz Sérgio , Dalçoquio Talia Falcão , Pileggi Brunna , de Sa Marchi Mauricio Felippi , Abi-Kair Pedro , Lopes Neuza , Giraldez Roberto Rocha , Baracioli Luciano Moreira , Lima Felipe Gallego , Hajjar Ludhmila Abrahão , Filho Roberto Kalil , de Brito Junior Fábio Sandoli , Abizaid Alexandre , Ribeiro Henrique Barbosa 
Published: September 2024

Abstract

Aims
Cardiogenic shock (CS) and cardiac arrest (CA) are serious complications in ST-elevation myocardial infarction (STEMI) patients, with lack of long-term data according to their timing of occurrence. This study sought to determine the incidence and relationship between the timing of occurrence and prognostic impact of CS and CA complicating STEMI in the long-term follow-up.

Methods and results
We conducted a retrospective analysis of consecutive STEMI patients treated between 2004 and 2017. Patients were divided into four groups based on the occurrence of neither CA nor CS, CA only, CS only, and both CA and CS (CA−CS−, CA+, CS+, and CA+CS+, respectively). Adjusted Cox regression analysis was used to assess the independent association between the CS and CA categories and mortality. A total of 1603 STEMI patients were followed for a median of 3.6 years. CA and CS occurred in the 12.2% and 15.9% of patients, and both impacted long-term mortality [adjusted hazard ratio (HR) = 2.59, 95% confidence interval (CI): 1.53–4.41, P &lt; 0.001; HR = 3.16, 95% CI: 2.21–4.53, P &lt; 0.001, respectively). CA+CS+ occurred in 7.3%, with the strongest association with higher mortality (adjusted HR = 5.36; 95% CI: 3.80–7.55, P &lt; 0.001). Using flexible parametric models with B-splines, the increased mortality was restricted to the first ∼10 months. In addition, overall mortality rates were higher at all timings (all with P &lt; 0.001), except for CA during initial cardiac catheterization (P &lt; 0.183).

Conclusion
CS and CA complicating patients presenting with STEMI were associated with higher long-term mortality rate, especially in the first 10 months. Both CS+ and CA+ at any timeframe impacted outcomes, except for CA+ during the initial cardiac catheterization, although this will have to be confirmed in larger future studies, given the relatively small number of patients.
Shortened radiofrequency delivery time to optimize efficiency and safety of pulmonary vein isolation with the radiofrequency balloon: insights from the COLLABORATE registry
Authors: Almorad Alexandre , Rocca Domenico Giovanni Della , Del Monte Alvise , Vijgen Johan , Koopman Pieter , Worck René , Johannessen Arne , Lepièce Caroline , de Ravenstein Antoine de Meester , Strisciuglio Teresa , Poggi Sara , Stabile Giuseppe , La Greca Carmelo , Kheir Joseph Antoine , Jesel-Morel Laurence , El Haddad Milad , Hossein Amin , Audiat Charles , Scacciavillani Roberto , Pannone Luigi , de Asmundis Carlo , Chierchia Gian-Battista 
Published: September 2024

Abstract

Aims
Previous clinical studies on pulmonary vein isolation (PVI) with a radiofrequency balloon (RFB) reported safe and effective procedures using conventional ablation settings with 20/60 s RF delivery via posterior/anterior (PST/ANT) electrodes. The latest evidence suggests that reducing the application time to 15 s (s) on the posterior wall when facing the oesophageal region is as effective as applying 20 s. To prospectively assess whether reducing RF time on PST/ANT segments to 15/45 s can ensure sufficient quality of lesion metrics and compare the new shortened ablation settings with the conventional one in terms of safety, and effectiveness at 1-year.

Methods and results
A total of 641 patients from seven European centres were enrolled in a collaborative registry, with 374 in the conventional RF delivery group and 267 in the shortened RF delivery group. Procedural outcomes, lesion metrics, and safety profiles were assessed and compared between the groups. Freedom of any atrial tachycarrythmias at one year was 85.4% and 88.2% in the SHRT and CONV groups, respectively. The shortened RF delivery strategy was associated with significantly shorter procedure times (median 63.5 vs. 96.5 min, P &lt; 0.001) and shortened fluoroscopy exposure (median 10.0 vs. 14.0 min, P &lt; 0.001) compared to conventional delivery. Efficacy metrics, including first-pass isolation rates and time to isolation, were comparable between groups. Shortened RF delivery was associated with a lower incidence of procedural complications (1.4% vs. 5.3%, P = 0.04) and optimized thermal characteristics.

Conclusion
Analyses from the COLLABORATE registry demonstrate that shortening RF energy delivery times to 15/45 s (PST/ANT) during PVI with the RFB resulted in comparable freedom from recurrent atrial tachyarrhythmia compared to conventional delivery times with comparable efficiency and safety.
In-depth Analysis of the HIV Reservoir Confirms Effectiveness and Safety of Dolutegravir/Lamivudine in a Phase 4 Randomized Controlled Switch Trial (RUMBA)
Authors: De Scheerder Marie-Angélique , Degroote Sophie , Delporte Mareva , Kiselinova Maja , Trypsteen Wim , Vincke Lara , De Smet Evelien , Van Den Eeckhout Bram , Schrooyen Loïc , Verschoore Maxime , Muccini Camilla , Vanherrewege Sophie , Caluwe Els , De Buyser Stefanie , Gerlo Sarah , Blomme Evy , Vandekerckhove Linos 
Published: September 2024

Abstract

Background
Reducing the number of active compounds for lifelong human immunodeficiency virus (HIV) treatment is of interest, especially to reduce potential long-term side effects. So far, available data assessing viral control support the robustness and safety of 2DR (2-drug regimen) antiretroviral therapy compared to 3DR. However, further in-depth investigations of the viral reservoirs are mandatory to guarantee long-term safety of these regimens regarding stable intact HIV-1 DNA copies, HIV-1 RNA transcripts, and sustained immunological control.

Methods
The RUMBA study is the first prospective randomized controlled trial evaluating the impact of switch from 3DR to 2DR on the viral reservoir. Participants on any stable second-generation integrase strand transfer inhibitor-based 3DR regimen with HIV-1 RNA &lt; 50 copies/mL plasma for at least 3 months were randomized to switch to dolutegravir/lamivudine (DTG/3TC, n = 89) or to switch or stay on bictegravir/emtricitabine/tenofovir alafenamide (B/F/TAF, n = 45). After 48 weeks, virological, immunological, and metabolic parameters were evaluated.

Results
We did not observe a significant difference in change over time in the mean number of intact HIV-1 DNA copies/million CD4+ T cells with DTG/3TC compared to B/F/TAF. There was no evidence in this study that switching to DTG/3TC increased the active reservoir by HIV-1 transcription. No significant changes in proinflammatory cytokines or major immune cell subsets were observed. Changes in exhaustion and activation of specific cellular subsets were small and bidirectional. Metabolic outcomes are similar between the treatment regimens.

Conclusions
This study confirms the safety of DTG/3TC compared to B/F/TAF through viral control after in-depth investigations of the intact HIV-1 reservoir, HIV-1 transcription, and inflammatory markers.

Clinical Trials Registration
NCT04553081.
Exploring native arsenic (As)-resistant bacteria: unveiling multifaceted mechanisms for plant growth promotion under As stress
Authors: Yan Yaoyao , Chang Wenying , Tian Peili , Chen Jiying , Jiang Jiayin , Dai Xianzhu , Jiang Tao , Luo Feng , Yang Caiyun 
Published: September 2024

Abstract

Aims
This study explores the plant growth-promoting effect (PGPE) and potential mechanisms of the arsenic (As)-resistant bacterium Flavobacterium sp. A9 (A9 hereafter).

Methods and results
The influences of A9 on the growth of Arabidopsis thaliana, lettuce, and Brassica napus under As(V) stress were investigated. Additionally, a metabolome analysis was conducted to unravel the underlying mechanisms that facilitate PGPE. Results revealed that A9 significantly enhanced the fresh weight of Arabidopsis seedlings by 62.6%–135.4% under As(V) stress. A9 significantly increased root length (19.4%), phosphorus (25.28%), chlorophyll content (59%), pod number (24.42%), and weight (18.88%), while decreasing As content (48.33%, P ≤ .05) and oxidative stress of Arabidopsis. It also significantly promoted the growth of lettuce and B. napus under As(V) stress. A9 demonstrated the capability to produce ≥31 beneficial substances contributing to plant growth promotion (e.g. gibberellic acid), stress tolerance (e.g. thiamine), and reduced As accumulation (e.g. siderophores).

Conclusions
A9 significantly promoted the plant growth under As stress and decreased As accumulation by decreasing oxidative stress and releasing beneficial compounds.
Molecular and biochemical characterization of a plant-like iota-class glutathione S-transferase from the halotolerant cyanobacterium Halothece sp. PCC7418
Authors: Samsri Sasiprapa , Kortheerakul Chananwat , Kageyama Hakuto , Waditee-Sirisattha Rungaroon 
Published: September 2024

Abstract

Aims
This study identifies a unique glutathione S-transferase (GST) in extremophiles using genome, phylogeny, bioinformatics, functional characterization, and RNA sequencing analysis.

Methods and Results
Five putative GSTs (H0647, H0729, H1478, H3557, and H3594) were identified in Halothece sp. PCC7418. Phylogenetic analysis suggested that H0647, H1478, H0729, H3557, and H3594 are distinct GST classes. Of these, H0729 was classified as an iota-class GST, encoding a high molecular mass GST protein with remarkable features. The protein secondary structure of H0729 revealed the presence of a glutaredoxin (Grx) Cys-Pro-Tyr-Cys (C-P-Y-C) motif that overlaps with the N-terminal domain and harbors a topology similar to the thioredoxin (Trx) fold. Interestingly, recombinant H0729 exhibited a high catalytic efficiency for both glutathione (GSH) and 1-chloro-2, 4-dinitrobenzene (CDNB), with catalytic efficiencies that were 155- and 32-fold higher, respectively, compared to recombinant H3557. Lastly, the Halothece gene expression profiles suggested that antioxidant and phase II detoxification encoding genes are crucial in response to salt stress.

Conclusion
Iota-class GST was identified in cyanobacteria. This GST exhibited a high catalytic efficiency toward xenobiotic substrates. Our findings shed light on a diversified evolution of GST in cyanobacteria and provide functional dynamics of the genes encoding the enzymatic antioxidant and detoxification systems under abiotic stresses.