bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mortality risk in survivors of acute COVID-19 and the urinary proteome: Follow-up results from a multinational study that prospectively evaluated a proteomic urine test for early and accurate prognosis of critical course complications in patients with SARS-CoV-2 infection (CRIT-COV-U)
Authors: Siwy Justyna , Wendt Ralph , Keller Felix , Banasik Miroslaw , Peters Björn , Dudoignon Emmanuel , Mebazaa Alexandre , Gülmez Dilara , Spasovski Goce , Lazo Mercedes Salgueira , Mischak Harald , Hecking Manfred , Beige Joachim ,   UriCoV working group
Published: June 2024

AbstractSurvival prospects following SARS-CoV-2 infection extend beyond the acute phase, influenced by various factors including age, health conditions, and infection severity. We investigated mortality risk among 651 post-acute COVID-19 patients, assessing the association between urinary peptides and future death. Data spanning until December 2023 were collected from six countries, comparing mortality trends with age- and sex-matched non-infected controls. A death prediction classifier was developed and validated using pre-existing urinary peptidomics datasets. Notably, 13.98% of post-COVID-19 patients succumbed during the follow-up, with mortality rates significantly higher than non-infected controls, particularly evident in younger individuals (<65 years). Urinary peptide analysis identified 201 peptides linked to mortality, integrated into a predictive classifier (DP201). Higher DP201 scores, alongside age and BMI, significantly predicted death. These findings underscore the utility of urinary peptides in prognosticating post-acute COVID-19 mortality, offering insights for targeted interventions.
Visual Cortical Thickness Increases with Prolonged Artificial Vision Restoration
Authors: Stiles Noelle R. B. , Choupan Jeiran , Ameri Hossein , Patel Vivek R. , Shi Yonggang 
Published: June 2024

AbstractThe Argus II retinal prosthesis restores visual perception to late blind patients. It has been shown that structural changes occur in the brain due to late-onset blindness, including cortical thinning in visual regions of the brain. Following vision restoration, it is not yet known whether these visual regions are reinvigorated and regain a normal cortical thickness or retain the diminished thickness from blindness.We evaluated the cortical thicknesses of ten Argus II Retinal Prostheses patients, ten blind patients, and thirteen sighted participants. The Argus II patients on average had a thicker left Cuneus Cortex and Lateral Occipital Cortex relative to the blind patients. The duration of the Argus II use (time since implant in active users) significantly partially correlated with thicker visual cortical regions in the left hemisphere. Furthermore, in the two case studies (scanned before and after implantation), the patient with longer device use (44.5 months) had an increase in the cortical thickness of visual regions, whereas the shorter-using patient did not (6.5 months). Finally, a third case, scanned at three time points post-implantation, showed an increase in cortical thickness in the Lateral Occipital Cortex between 43.5 and 57 months, which was maintained even after 3 years of disuse (106 months).Overall, the Argus II patients’ cortical thickness was on average significantly rejuvenated in two higher visual regions and, patients using the implant for a longer duration had thicker visual regions. This research raises the possibility of structural plasticity reversing visual cortical atrophy in late-blind patients with prolonged vision restoration.
Data release and baseline analysis of the largest collection of 6-minute walk tests: the My Heart Counts Cardiovascular Health Study, a fully digital smartphone platform
Authors: Kim Daniel Seung , Schuetz Narayan , Johnson Anders , Tolas Alexander , Mantena Sriya , O’Sullivan Jack W , Hershman Steven G , King Abby C , Christle Jeffrey W , Oppezzo Marily , Rodriguez Fatima , Mattsson C. Mikael , Wheeler Matthew T , Taylor Herman A , Murphy Susan , Ashley Euan A 
Published: June 2024

ABSTRACTThe six-minute walk test (6MWT) is a sub-maximal exercise test used clinically as a measure of functional capacity. With the emergence of advanced sensors, 6MWTs were commonly performed remotely via smartphones and other devices. The My Heart Counts Cardiovascular Health Study is a smartphone application that serves as a digital platform for studies of human cardiovascular health. It has been used to perform 30,475 6MWTs on 25,539 unique participants. Here, we report on the associations of demographic and clinical variables with 6MWT distance at baseline (N=4,576), validating prior associations with male gender, height, and baseline physical activity with 6MWT distance in multivariable regression analysis. We also report associations of 6MWT baseline distance with working status (+26.8m +5.2m, P<0.001) and feeling depressed (−3.78m, +0.79m, P<0.001). In a subset of participants who conducted repeat 6MWTs separated by at least 1-week but no greater than 3-months (N=2,269), we found that use of theMy Heart Countsapp resulted in a statistically significant increase in 6MWT distance (+21.5m +5.72m,P<0.001). Finally, we present the public data release of our 30,475 6MWTs and the launch of a webpage-based data viewer of summary-level statistics, to compare the relative health of an individual by their age, gender, and chronic disease status. Given the importance of 6MWTs in assessment of functional capacity, our publicly-available data will serve an important purpose as a healthy and disease-specific reference for investigators worldwide.
Panacea: A foundation model for clinical trial search, summarization, design, and recruitment
Authors: Lin Jiacheng , Xu Hanwen , Wang Zifeng , Wang Sheng , Sun Jimeng 
Published: June 2024

AbstractClinical trials are fundamental in developing new drugs, medical devices, and treatments. However, they are often time-consuming and have low success rates. Although there have been initial attempts to create large language models (LLMs) for clinical trial design and patient-trial matching, these models remain task-specific and not adaptable to diverse clinical trial tasks. To address this challenge, we propose a clinical trial foundation model namedPanacea, designed to handle multiple tasks, including trial search, trial summarization, trial design, and patient-trial matching. We also assemble a large-scale dataset, namedTrialAlign, of 793,279 trial documents and 1,113,207 trial-related scientific papers, to infuse clinical knowledge into the model by pre-training. We further curateTrialInstruct, which has 200,866 of instruction data for fine-tuning. These resources enablePanaceato be widely applicable for a range of clinical trial tasks based on user requirements.We evaluatedPanaceaon a new benchmark, namedTrialPanorama, which covers eight clinical trial tasks. Our method performed the best on seven of the eight tasks compared to six cutting-edge generic or medicine-specific LLMs. Specifically,Panaceashowed great potential to collaborate with human experts in crafting the design of eligibility criteria, study arms, and outcome measures, in multi-round conversations. In addition, Panacea achieved 14.42% improvement in patient-trial matching, 41.78% to 52.02% improvement in trial search, and consistently ranked at the top for five aspects of trial summarization. Our approach demonstrates the effectiveness ofPanaceain clinical trials and establishes a comprehensive resource, including training data, model, and benchmark, for developing clinical trial foundation models, paving the path for AI-based clinical trial development.
How to Detect the Early Cardiac Functional Change and Predict Heart Failure in Paroxysmal Atrial Fibrillation? A Prospective Cohort Study
Authors: Cheng Lei , Bao Lilian , Zhuang Xinyu , Yan Fangying , Gao Xiufang , Zhou Peng , Zhao Yikai , Yang Ke , Zhang Qi , Huang Guoqian , Bao Liwen 
Published: June 2024

AbstractBackgrounds20-30% atrial fibrillation (AF) may result in heart failure (HF). Noninvasive left ventricle myocardial work (LVMW) is a fairly new method for detecting LV function. We aimed to evaluate whether LVMW could detect the LV change function in paroxysmal atrial fibrillation (PAF) and predict HF incident.MethodsIn this prospective cohort study, 146 PAF subjects and 63 non-PAF subjects matched by age and gender set as the controls were enrolled. Noninvasive LVMW parameters, including global work index, global constructive work, global wasted work (GWW) and global work efficiency (GWE) were obtained from LV pressure-strain loop by 2D speckle tracking imaging. LA volume index (LAVI) was measured by 3D echocardiography. AF burden (AFB) was evaluated by questionnaire. The primary outcome was the incident HF.AFB deterioration was evaluated at the end of follow up. Stata15.0 and R4.1 were used for data analysis and description.ResultsThe average age was 66.2±11.4 years and comprised 55% males in PAF. Compared with the controls, PAF had significantly elevated GWW (143.7±88.3mmHg% vs 115.5±59.6mmHg%, p<0.001) and impaired GWE (92.3±7.5% vs 93.8±2.8%, p=0.035) and they were correlated with increased LAVImax and LAVImin. Those with higher AFB showed significantly decreased LAEF and increased LAVImin. During the average 40.5 months follow-up, 9.9% PAF developed HF and ablation reduced the HF occurrence. In the non-ablation subgroup, baseline decreased LAEF rather than LVMW was a strong predictor for HF. As expected, AFB deterioration was strongly associated with HF incident.ConclusionsElevated GWW was detected by LVMW and it was strongly correlated with LA dilation in PAF. Higher AFB had adverse effect on LAVImin. Restoring sinus rhythm was significant for HF prevention, especially for PAF with lower LAEF.Clinical PerspectiveWhat is new?Although GLS and LVEF remained normal, subtle LV dysfunction of elevated GWW and impaired GWE could be detected by LVMW in the early stage of PAF.Increased LAVImin, rather than LAEF, was strongly associated with elevated GWW and higher AF burden in PAF.Restoring sinus rhythm was important to early stage of PAF for HF prevention, especially in PAF with lower LAEF.What are the clinical implications?It is significant for PAF to protect LV function by maintaining sinus rhythm or keeping AFB at minimal-mild stage, even from the very early stage.Increased LAVImin is an important indicator for detecting LV dysfunction in PAF and the underlying mechanism needs to be discovered.
Emerging Applications of NLP and Large Language Models in Gastroenterology and Hepatology: A Systematic Review
Authors: Omar Mahmud , SharIf Kassem , Glicksberg Benjamin , Nadkarni Girish N , Klang Eyal 
Published: June 2024

AbstractBackground and AimIn the last two years, natural language processing (NLP) has transformed significantly with the introduction of large language models (LLM). This review updates on NLP and LLM applications and challenges in gastroenterology and hepatology.MethodsRegistered with PROSPERO (CRD42024542275) and adhering to PRISMA guidelines, we searched six databases for relevant studies published from 2003 to 2024, ultimately including 57 studies.ResultsOur review notes an increase in relevant publications in 2023-2024 compared to previous years, reflecting growing interest in newer models such as GPT-3 and GPT-4. The results demonstrate that NLP models have enhanced data extraction from electronic health records and other unstructured medical data sources. Key findings include high precision in identifying disease characteristics from unstructured reports and ongoing improvement in clinical decision-making. Risk of bias assessments using ROBINS-I, QUADAS-2, and PROBAST tools confirmed the methodological robustness of the included studies.ConclusionNLP and LLMs can enhance diagnosis and treatment in gastroenterology and hepatology. They enable extraction of data from unstructured medical records, such as endoscopy reports and patient notes, and for enhancing clinical decision-making. Despite these advancements, integrating these tools into routine practice is still challenging. Future work should prospectively demonstrate real-world value.
Tuning the performance of a TphR-based terephthalate biosensor with a design of experiments approach
Authors: Gonzalez Guadalupe Alvarez , Chacón Micaela , Butterfield Thomas , Dixon Neil 
Published: June 2024

AbstractTranscription factor-based biosensors are genetic tools that aim to predictability link the presence of a specific input stimuli to a tailored gene expression output. The performance characteristics of a biosensor fundamentally determines its potential applications. However, current methods to engineer and optimise tailored biosensor responses are highly nonintuitive, and struggle to investigate multidimensional sequence/design space efficiently. In this study we employ a design of experiments (DoE) approach to build a framework for efficiently engineering activator-based biosensors with tailored performances, and we apply the framework for the development of biosensors for the polyethylene terephthalate (PET) plastic degradation monomer terephthalate (TPA). We simultaneously engineer the core promoter and operator regions of the responsive promoter, and by employing a dual refactoring approach, we were able to explore an enhanced biosensor design space and assign their causative performance effects. The approach employed here serves as a foundational framework for engineering transcriptional biosensors and enabled development of tailored biosensors with enhanced dynamic range and diverse signal output, sensitivity, and steepness. We further demonstrate its applicability on the development of tailored biosensors for primary screening of PET hydrolases and enzyme condition screening, demonstrating the potential of statistical modelling in optimizing biosensors for tailored industrial and environmental applications.Abstract FigureGraphical Abstract. Employment of a DoE framework for fine-tuning biosensor performance.HighlightsBioinformatic mining of allosteric transcription factors to produce TPA biosensorsEfficient sampling of complex sequence-function relationships of genetic circuitsModelling to learn and optimise biosensor genetic circuitsApplication of biosensors for primary and secondary enzyme screening applications
Ethylene Receptor Gain- and Loss-of-function Mutants Reveal an ETR1-dependent Transcriptional Network in Roots
Authors: Khoury Maleana G. , Harkey Alexandria F. , Mühlemann Joëlle K. , Olex Amy L. , Houben Maarten , Binder Brad M. , Muday Gloria K. 
Published: June 2024

AbstractIn Arabidopsis, a family of five receptors mediates ethylene responses in roots, with Ethylene Response 1 (ETR1) controlling increases in root hair proliferation and decreases in lateral root formation. To define the ETR1-dependent gene regulatory network (GRN) controlling root development, we profiled the root transcriptome from Col-0 and theetr1-3gain-of-function andetr1-7loss-of-function mutants in the presence and absence of ethylene or the ethylene precursor aminocyclopropane-1-carboxylic acid (ACC). We identified 4,522 differentially expressed (DE) transcripts in Col-0 roots with altered abundance in response to ethylene and/or ACC treatment, most with larger magnitude changes induced by ethylene. These included 553 DE transcripts that were ETR1-dependent, defined by a lack of response to treatment with ethylene and/or ACC in ethylene-insensitiveetr1-3and constitutively altered inetr1-7in the presence and absence of treatment relative to untreated Col-0. Within these ETR1 dependent transcripts were ethylene biosynthesis genes and transcription factors.ACC OXIDASE 2(ACO2)andACO3convert ACC to ethylene and were ETR1-dependent, andACOpromoter fusions were ACC regulated in root tissues in appropriate locations to control root development, withACO5localized to root hairs. Abundance of ETR1-dependent transcripts that were predicted to encode transcription factors and ACOs were examined in Col-0 and anein3eil1mutant with and without ACC treatment, revealing that the ETR1 and EIN3/EIL1 canonical ethylene signaling pathway regulated some, but not all, of these transcriptional responses. Together, these findings reveal features of an ETR1-dependent GRN that controls both ethylene synthesis and root growth and development.
Elucidating the kinetic and thermodynamic insight into regulation of glycolysis by lactate dehydrogenase and its impact on tricarboxylic acid cycle and oxidative phosphorylation in cancer cells
Authors: Zeng Siying , Wang Yuqi , Ying Minfeng , Jin Chengmeng , Ying Chang , Wang Di , Wu Hao , Hu Xun 
Published: June 2024

AbstractLactate dehydrogenase (LDH) stands at the intersection of pyruvate metabolism. While it is believed that inhibition of LDH redirects pyruvate to mitochondrial metabolism, suppressing glycolysis and boosting oxidative phosphorylation, the mechanism remains largely unexplored. We found that individual LDH A or B knockouts had minimal impact on glycolysis, tricarboxylic acid cycle (TCAC), or oxidative phosphorylation (OXPHOS). However, combining LDH knockout with LDH inhibitor GNE-140 significantly suppressed these processes. Inhibition of LDH led to an increase in free NADH concentration and a decrease in free NAD+concentration, the reduced free NAD+concentration inhibited GAPDH, disrupting the balance of glycolytic intermediates, which were linked with thermodynamic shift of the Gibbs free energy of reactions between phosphofructokinase 1 (PFK1) and phosphoglycerate mutase (PGAM) in the glycolytic pathway, favoring their reverse direction. This disrupted glycolysis led to impaired TCAC and mitochondrial respiration due to reduced pyruvate and glutamine carbon influx into TCAC. Under hypoxia, LDH inhibition had a stronger effect, inducing energy crisis, redox imbalance, and cancer cell death. Our study reveals LDH’s intricate control over glycolysis, TCAC, and mitochondrial respiration, highlighting the interplay of enzyme kinetics and thermodynamics in metabolic pathways—a crucial aspect for understanding metabolic regulation.Impact statementThe biochemical mechanism underlying the flux regulation of glycolytic flux by lactate dehydrogenase in cancer cells, which have remained largely unexplored, is deciphered.Funding informationThis work has been supported in part by China Natural Science Foundation projects (82073038, 81772947), a key project (2018C03009) funded by Zhejiang Provincial Department of Sciences and Technologies, the Fundamental Research Funds for the Central Universities (226-2024-00062), to X.H.
Spiral to stripe transition in the two-dimensional Hubbard model
Authors: Scholle Robin , Metzner Walter , Vilardi Demetrio , Bonetti Pietro M. 
Published: June 2024

We obtain an almost complete understanding of the mean-field phase diagram of the two-dimensional Hubbard model on a square lattice with a sizable next-nearest-neighbor hopping and a moderate interaction strength. In particular, we clarify the nature of the transition region between the spiral and the stripe phase. Complementing previous [] real-space Hartree-Fock calculations on large finite lattices, we solve the mean-field equations for coplanar unidirectional magnetic order directly in the thermodynamic limit, and we determine the nature of the magnetic states right below the mean-field critical temperature T* by a Landau free-energy analysis. While the magnetic order for filling factors n≥1 is always of Néel type, for n≤1 the following sequence of magnetic states is found as a function of increasing hole-doping: Néel, planar circular spiral, multispiral, and collinear spin-charge stripe states. Multispiral states are superpositions of several spirals with distinct wave vectors, and lead to concomitant charge order. We finally point out that nematic and charge orders inherited from the magnetic order can survive even in the presence of fluctuations, and we present a corresponding qualitative phase diagram.

Published by the American Physical Society
2024
Barriers to the implementation of enterprise risk management in Indian construction firms
Authors: Prakash Anand , Ambekar Sudhir 
Published: June 2024

Purpose
Implementing enterprise risk management (ERM) systems in construction firms of developing countries like India is critical for targeting strong risk management strategies that support their growth. It requires such firms to holistically understand the major barriers in terms of their definitions, relationships with one another and interdependencies. Thus, this study aims to identify, model and analyze the barriers to implementing ERM in construction firms using interpretive structural modeling (ISM).

Design/methodology/approach
This study used a Delphi process to identify barriers to the implementation of ERM in Indian construction firms, ISM to model them and Matrice d’Impacts Croisés Multiplication Appliquée à un Classement (MICMAC) to analyze their interrelationships.

Findings
The study’s results revealed that individual-level factors are the most important among the barriers present at the lowest level in the hierarchical model, whereas organizational commitment with the highest dependence power is present at the highest level in the hierarchical model.

Research limitations/implications
Since the usage of ERM in the construction industry is highly culture-dependent and may have regional nuances, the data on ERM usage might accurately reflect the Indian construction industry but may not apply to other regions.

Practical implications
This study can be used to develop effective strategies to improve the implementation of ERM in construction firms in developing countries like India.

Social implications
ERM is crucial for managing risks in Indian construction firms due to the high degree of complexity and uncertainty associated with construction projects coming from changes due to technological advancement, regulatory changes, changes in consumer preferences, global competition and other socioeconomic and political factors.

Originality/value
The study’s results will help researchers and practitioners working in the construction industry of developing countries like India to identify the challenges in adopting ERM systems. It will guide construction firms to appropriately develop risk management strategies for managing the inevitable risks in their complex project environments. This will help improve their contribution to the country’s economic development.
Topology and parameter optimization of IPM motor considering mechanical strength by stress and connection constraints
Authors: Takenouchi Kou , Hiruma Shingo , Mifune Takeshi , Matsuo Tetsuji 
Published: June 2024

Purpose
The purpose of this study is to apply the topology and parameter optimization (TPO) to interior permanent magnet (IPM) motors to obtain the optimized shape with higher torque, lower ripple and sufficient mechanical strength.

Design/methodology/approach
The constraints regarding the maximum stress, connectivity and mesh quality were considered to achieve not only high electrical performance but also high mechanical strength. To enhance the accuracy of the finite element analysis of the elastic analysis, this paper used body-fitted mesh adaptation technique to avoid the stress concentration.

Findings
The proposed method in this study resulted in feasible shapes with sufficiently high strength compared to previous studies. It is also shown that TPO yielded IPM motors with higher torque compared to topology optimization (TO) with fixed parameters.

Practical implications
Different from the existing studies on topology optimization of IPM motors, the mechanical strength is even considered by evaluating the stress values. Therefore, in the practical phase, geometries can be designed that are less likely to be damaged due to deformation, even in the high-speed rotation range.

Originality/value
This paper performed TO and parameter optimization (PO) simultaneously, considering not only the electrical performance but also the mechanical strength. Furthermore, the mechanical strength was evaluated more precisely by devising the elastic analysis conditions and mesh generation.