bluuebunny/crossref_metadata_2025_split huggingface dataset:
Troponin I Tyrosine Phosphorylation Beneficially Accelerates Diastolic Function
Authors: Salyer Lorien G. , Salhi Hussam E. , Brundage Elizabeth A. , Shettigar Vikram , Sturgill Sarah L. , Zanella Helena , Templeton Benjamin , Abay Eaman , Emmer Kathryn M. , Lowe Jeovanna , Rafael-Fortney Jill A. , Parinandi Narasimham , Foster D. Brian , McKinsey Timothy A. , Woulfe Kathleen C. , Ziolo Mark T. , Biesiadecki Brandon J. 
Published: December 2023

BACKGROUND:
A healthy heart is able to modify its function and increase relaxation through post-translational modifications of myofilament proteins. While there are known examples of serine/threonine kinases directly phosphorylating myofilament proteins to modify heart function, the roles of tyrosine (Y) phosphorylation to directly modify heart function have not been demonstrated. The myofilament protein TnI (troponin I) is the inhibitory subunit of the troponin complex and is a key regulator of cardiac contraction and relaxation. We previously demonstrated that TnI-Y26 phosphorylation decreases calcium-sensitive force development and accelerates calcium dissociation, suggesting a novel role for tyrosine kinase–mediated TnI-Y26 phosphorylation to regulate cardiac relaxation. Therefore, we hypothesize that increasing TnI-Y26 phosphorylation will increase cardiac relaxation in vivo and be beneficial during pathological diastolic dysfunction.

METHODS:
The signaling pathway involved in TnI-Y26 phosphorylation was predicted in silico and validated by tyrosine kinase activation and inhibition in primary adult murine cardiomyocytes. To investigate how TnI-Y26 phosphorylation affects cardiac muscle, structure, and function in vivo, we developed a novel TnI-Y26 phosphorylation-mimetic mouse that was subjected to echocardiography, pressure-volume loop hemodynamics, and myofibril mechanical studies. TnI-Y26 phosphorylation-mimetic mice were further subjected to the nephrectomy/DOCA (deoxycorticosterone acetate) model of diastolic dysfunction to investigate the effects of increased TnI-Y26 phosphorylation in disease.

RESULTS:
Src tyrosine kinase is sufficient to phosphorylate TnI-Y26 in cardiomyocytes. TnI-Y26 phosphorylation accelerates in vivo relaxation without detrimental structural or systolic impairment. In a mouse model of diastolic dysfunction, TnI-Y26 phosphorylation is beneficial and protects against the development of disease.

CONCLUSIONS:
We have demonstrated that tyrosine kinase phosphorylation of TnI is a novel mechanism to directly and beneficially accelerate myocardial relaxation in vivo.
Remarks on a Recent Study of the Śrīmālādevīsiṁhanādanirdeśasūtra
Authors: Silk Jonathan A. 
Published: December 2023

Abstract
The Śrīmālādevīsiṁhanādanirdeśasūtra is preserved in toto in one Tibetan and two Chinese translations, in addition to which we have access to a fragmentary Sanskrit manuscript and a considerable number of Sanskrit quotations, contributing to a sizable amount of the text now being available in Sanskrit. The present contribution takes as its impetus a recent contribution on the sūtra and its ideas about tathāgatagarbha, offering a survey of the state of the field of study of the text in its Indian context, and several suggestions for improved understandings.
A New Reading of the Bactrian Part of the Dašt-i Nāwur Trilingual (DN I)
Authors: Halfmann Jakob , Bonmann Svenja , Fries Simon , Korobzow Natalie 
Published: December 2023

Abstract
The trilingual Kushan royal inscription of Dašt-i Nāwur has been the subject of scholarly controversies since the time of its first scientific publication (Fussman 1974), with different authors defending opposing views and mutually incompatible readings, in particular of the Bactrian part of the inscription (e.g. Davary & Humbach 1976; Sims-Williams & Cribb 1996; Fussman 1998). Progress in the understanding of the inscription has been hampered by inadequate photographic documentation, but also by the comparatively small amount of information on the Bactrian language that was available at the time of its first publication. A color photograph of the Bactrian inscription probably taken in 1969, which was unavailable to earlier editors, has now been made publicly accessible by the Collège de France as part of the estate of the late Gérard Fussman. This article presents a new reading of the inscription based on this photograph, diverging in many respects from earlier interpretations. It includes a response to the recent re-edition of Palunčić et al. (2023), who have also taken the new photograph into account but reached different conclusions.
Momentum Transport in Organized Shallow Cumulus Convection
Authors: Savazzi Alessandro C. M. , Nuijens Louise , de Rooy Wim , Janssens Martin , Siebesma A. Pier 
Published: December 2023

Abstract
This study investigates momentum transport in shallow cumulus clouds as simulated with the Dutch Atmospheric Large Eddy Simulation (DALES) for a 150 × 150 km2 domain east of Barbados during 9 days of EUREC4A. DALES is initialized and forced with the mesoscale weather model HARMONIE–AROME and subjectively reproduces observed cloud patterns. This study examines the evolution of momentum transport, which scales contribute to it, and how they modulate the trade winds. Daily-mean momentum flux profiles show downgradient zonal momentum transport in the subcloud layer, which turns countergradient in the cloud layer. The meridional momentum transport is nontrivial, with mostly downgradient transport throughout the trade wind layer except near the top of the surface layer and near cloud tops. Substantial spatial and temporal heterogeneity in momentum flux is observed with much stronger tendencies imposed in areas of organized convection. The study finds that while scales < 2 km dominate momentum flux at 200 m in unorganized fields, submesoscales carry up to 50% of the zonal momentum flux in the cloud layer in organized fields. For the meridional momentum flux, this fraction is even larger near the surface and in the subcloud layer. The scale dependence of the momentum flux is not explained by changes in convective or boundary layer depth. Instead, the results suggest the importance of spatial heterogeneity, increasing horizontal length scales, and countergradient transport in the presence of organized convection.
The Tamil Version of the Three-Factor Eating Questionnaire-R18V2: Reliability and Factor Structure Among Persons with Schizophrenia
Authors: Swarnameenaa G. , Durairaj Jothilakshmi , Hariharan Nithyashri , Madhavan Vaishnavi K. , Arunachaleeswaran Pavithra , Venkatraman Lakshmi , Sankaranarayanan Anoop , Ramachandran Padmavati 
Published: December 2023

Background: Persons with schizophrenia (PwS) are vulnerable to developing disordered eating behaviors. However, standardized tools to assess disordered eating patterns are unavailable in the regional language, Tamil. Different versions of the Three-Factor Eating Questionnaire (TFEQ) have been used to measure disordered eating patterns among PwS worldwide. This study aimed to assess the factor structure and reliability of the Tamil version of TFEQ-R18V2 among Tamil-speaking PwS. Methods: Over three months, 135 PwS, aged 18–65 years, who attended the outpatient department of a tertiary mental health service provider in Chennai, completed the Tamil version of TFEQ-R18V2. Thirty PwS completed the tool after two weeks to assess its test–retest reliability. The factor structure of the tool was explored using principal component analysis. Results: The sample included 75 (55.6%) males and 60 (44.4%) females with a mean (±SD) age of 40.1 (±9.8) years and a mean duration of illness of 11.99 (± 8.72) years. Internal consistency and test–retest reliability of the Tamil version were 0.84 and 0.532, respectively. A five-factor structure emerged from the factor analysis, with 65.67% of the variance. Conclusion: The Tamil version of TFEQ-R18V2 emerged as a reliable tool to assess disordered eating patterns among Tamil-speaking PwS.
Methylthioadenosine Phosphorylase and Breast Cancer 1 Protein-Associated Protein 1 as Biomarkers for the Peritoneal Mesothelioma
Authors: Chen Yue , Du Xuemei , Gao Ying , Wu Heliang , Zhao Hongyu , Su Yandong 
Published: December 2023

Objectives Combination of Breast Cancer 1 protein-associated protein 1 (BAP1) and methylthioadenosine phosphorylase (MTAP) in the peritoneal mesothelioma (PeM) has yet to be explored. We aim to assess the diagnostic value of combined BAP1 and MTAP to distinguish biphasic mesothelioma (BM) from epithelioid mesothelioma (EM) with reactive stroma in peritoneum, as well as its prognostic value in PeM. Methods This is a retrospective study from June 2014 to December 2021. This study included 18 cases of BM and 27 cases of EM with reactive stroma, excluded sarcomatoid, and EM without reactive stroma cases, and clinicopathological information was collected. The associations between MTAP and BAP1 levels and clinicopathological features or prognosis were analyzed. Clinical follow-up data were reviewed to correlate with pathological prognostic factors using Kaplan–Meier estimator and univariate/multivariate Cox proportional hazards regression models. Results Loss/decrease of BAP1/MTAP was observed in 6 (33.3%) BM cases and 12 (44.4%) EM cases. In 5 (27.8%) cases, loss of or decreased BAP1/MTAP expression was observed in both EC and SC of BM. BAP1/MTAP loss/decrease was observed in 12 (44.4%) cases of only EC of EM but not in reactive stroma. Compared with histology alone, a combination of BAP1 and MTAP immunohistochemistry (IHC) in spindled PeM provides a more objective mean to distinguish BM from EM with reactive stroma. Loss/decrease of BAP1/MTAP was associated with peritoneal cancer index (PCI) score ( P = 0.047) and completeness of cytoreduction (CC) score ( P = 0.038). BM patients have worse overall survival (OS) than EM with reactive stroma ( P = 0 .007). Conclusions Combination of BAP1/MTAP by IHC is helpful for differential diagnosis of peritoneal BM from EM with reactive stroma. Nevertheless, BAP1/MTAP may help to evaluate the biological behavior of PeM.
Genome-wide association study of preserved ratio impaired spirometry (PRISm)
Authors: Higbee Daniel H. , Lirio Alvin , Hamilton Fergus , Granell Raquel , Wyss Annah B. , London Stephanie J. , Bartz Traci M. , Gharib Sina A. , Cho Michael H. , Wan Emily , Silverman Edwin , Crapo James D. , Lominchar Jesus V.T. , Hansen Torben , Grarup Niels , Dantoft Thomas , Kårhus Line , Linneberg Allan , O'Connor George T. , Dupuis Josée , Xu Hanfie , De Vries Maaike M. , Hu Xiaowei , Rich Stephen S. , Barr R. Graham , Manichaikul Ani , Wijnant Sara R.A. , Brusselle Guy G. , Lahousse Lies , Li Xuan , Hernández Cordero Ana I. , Obeidat Ma'en , Sin Don D. , Harris Sarah E. , Redmond Paul , Taylor Adele M. , Cox Simon R. , Williams Alexander T. , Shrine Nick , John Catherine , Guyatt Anna L. , Hall Ian P. , Davey Smith George , Tobin Martin D. , Dodd James W. 
Published: December 2023

BackgroundPreserved ratio impaired spirometry (PRISm) is defined as a forced expiratory volume in 1 s (FEV1) <80% predicted and FEV1/forced vital capacity ≥0.70. PRISm is associated with respiratory symptoms and comorbidities. Our objective was to discover novel genetic signals for PRISm and see if they provide insight into the pathogenesis of PRISm and associated comorbidities.MethodsWe undertook a genome-wide association study (GWAS) of PRISm in UK Biobank participants (Stage 1), and selected single nucleotide polymorphisms (SNPs) reaching genome-wide significance for replication in 13 cohorts (Stage 2). A combined meta-analysis of Stage 1 and Stage 2 was done to determine top SNPs. We used cross-trait linkage disequilibrium score regression to estimate genome-wide genetic correlation between PRISm and pulmonary and extrapulmonary traits. Phenome-wide association studies of top SNPs were performed.Results22 signals reached significance in the joint meta-analysis, including four signals novel for lung function. A strong genome-wide genetic correlation (rg) between PRISm and spirometric COPD (rg=0.62, p<0.001) was observed, and genetic correlation with type 2 diabetes (rg=0.12, p=0.007). Phenome-wide association studies showed that 18 of 22 signals were associated with diabetic traits and seven with blood pressure traits.ConclusionThis is the first GWAS to successfully identify SNPs associated with PRISm. Four of the signals, rs7652391 (nearest geneMECOM), rs9431040 (HLX), rs62018863 (TMEM114) and rs185937162 (HLA-B), have not been described in association with lung function before, demonstrating the utility of using different lung function phenotypes in GWAS. Genetic factors associated with PRISm are strongly correlated with risk of both other lung diseases and extrapulmonary comorbidity.
Extensive acute and sustained changes to neutrophil proteomes post-SARS-CoV-2 infection
Authors: Long Merete B. , Howden Andrew J.M. , Keir Holly R. , Rollings Christina M. , Giam Yan Hui , Pembridge Thomas , Delgado Lilia , Abo-Leyah Hani , Lloyd Amy F. , Sollberger Gabriel , Hull Rebecca , Gilmour Amy , Hughes Chloe , New Benjamin J.M. , Cassidy Diane , Shoemark Amelia , Richardson Hollian , Lamond Angus I. , Cantrell Doreen A. , Chalmers James D. , Brenes Alejandro J. 
Published: December 2023

BackgroundNeutrophils are important in the pathophysiology of coronavirus disease 2019 (COVID-19), but the molecular changes contributing to altered neutrophil phenotypes following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are not fully understood. We used quantitative mass spectrometry-based proteomics to explore neutrophil phenotypes immediately following acute SARS-CoV-2 infection and during recovery.MethodsProspective observational study of hospitalised patients with PCR-confirmed SARS-CoV-2 infection (May to December 2020). Patients were enrolled within 96 h of admission, with longitudinal sampling up to 29 days. Control groups comprised non-COVID-19 acute lower respiratory tract infection (LRTI) and age-matched noninfected controls. Neutrophils were isolated from peripheral blood and analysed using mass spectrometry. COVID-19 severity and recovery were defined using the World Health Organization ordinal scale.ResultsNeutrophil proteomes from 84 COVID-19 patients were compared to those from 91 LRTI and 42 control participants. 5800 neutrophil proteins were identified, with >1700 proteins significantly changed in neutrophils from COVID-19 patients compared to noninfected controls. Neutrophils from COVID-19 patients initially all demonstrated a strong interferon signature, but this signature rapidly declined in patients with severe disease. Severe disease was associated with increased abundance of proteins involved in metabolism, immunosuppression and pattern recognition, while delayed recovery from COVID-19 was associated with decreased granule components and reduced abundance of metabolic proteins, chemokine and leukotriene receptors, integrins and inhibitory receptors.ConclusionsSARS-CoV-2 infection results in the sustained presence of circulating neutrophils with distinct proteomes suggesting altered metabolic and immunosuppressive profiles and altered capacities to respond to migratory signals and cues from other immune cells, pathogens or cytokines.
PET-CT-guidedversusCT-guided biopsy in suspected malignant pleural thickening: a randomised trial
Authors: de Fonseka Duneesha , Arnold David T. , Smartt Helena J.M. , Culliford Lucy , Stadon Louise , Tucker Emma , Morley Anna , Zahan-Evans Natalie , Bibby Anna C. , Lynch Geraldine , Mishra Eleanor , Khan Shahul , Haris Mohammed , Steer Henry , Lewis Leon , Ionescu Alina , Harvey John , Blyth Kevin , Rahman Najib M. , Edey Anthony E. , Rogers Chris A. , Maskell Nick A. 
Published: December 2023

BackgroundPleural biopsy is the gold standard for diagnosis of pleural malignancy but a significant proportion will have an inconclusive biopsy despite ongoing clinical suspicion of malignancy. We investigated whether positron emission tomography-computed tomography (PET-CT) targeted pleural biopsy is superior to standard CT-guided pleural biopsy following an initial non-diagnostic biopsy.MethodsThe TARGET trial was a multicentre, parallel group randomised trial. Patients with a previous inconclusive pleural biopsy but an ongoing suspicion of pleural malignancy were randomised (1:1) to receive either CT-guided biopsy (standard care) or PET-CT followed by a targeted CT biopsy (intervention). The primary outcome was pleural malignancy correctly identified from the trial biopsy.ResultsBetween September 2015 and September 2018, 59 participants were randomised from eight UK hospital sites: 29 to CT-only followed by targeted biopsy and 30 to PET-CT followed by targeted biopsy. The proportion of pleural malignancy correctly identified was similar between the groups (risk ratio 1.03 (95% CI 0.83–1.29); p=0.77). The sensitivity of the trial biopsy to identify pleural malignancy was 79% (95% CI 54–94%) in the CT-only groupversus81% (95% CI 54–96%) in the PET-CT group.ConclusionsThe results do not support the practice of PET-CT to guide pleural biopsies in patients with a previous non-diagnostic biopsy. The diagnostic sensitivity in the CT-only group was higher than anticipated and supports the practice of repeating a CT-guided biopsy following an inconclusive result if clinical suspicion of malignancy persists.
Rail Internal Defect Detection Method Based on Enhanced Network Structure and Module Design Using Ultrasonic Images
Authors: Wu Fupei , Xie Xiaoyang , Ye Weilin 
Published: December 2023

AbstractImproving the detection accuracy of rail internal defects and the generalization ability of detection models are not only the main problems in the field of defect detection but also the key to ensuring the safe operation of high-speed trains. For this reason, a rail internal defect detection method based on an enhanced network structure and module design using ultrasonic images is proposed in this paper. First, a data augmentation method was used to extend the existing image dataset to obtain appropriate image samples. Second, an enhanced network structure was designed to make full use of the high-level and low-level feature information in the image, which improved the accuracy of defect detection. Subsequently, to optimize the detection performance of the proposed model, the Mish activation function was used to design the block module of the feature extraction network. Finally, the proposed rail defect detection model was trained. The experimental results showed that the precision rate and $${F}_{1}$$

F
1

score of the proposed method were as high as 98%, while the model’s recall rate reached 99%. Specifically, good detection results were achieved for different types of defects, which provides a reference for the engineering application of internal defect detection. Experimental results verified the effectiveness of the proposed method.
Rainfall modeling using two different neural networks improved by metaheuristic algorithms
Authors: Sammen Saad Sh. , Kisi Ozgur , Ehteram Mohammad , El-Shafie Ahmed , Al-Ansari Nadhir , Ghorbani Mohammad Ali , Bhat Shakeel Ahmad , Ahmed Ali Najah , Shahid Shamsuddin 
Published: December 2023

AbstractRainfall is crucial for the development and management of water resources. Six hybrid soft computing models, including multilayer perceptron (MLP)–Henry gas solubility optimization (HGSO), MLP–bat algorithm (MLP–BA), MLP–particle swarm optimization (MLP–PSO), radial basis neural network function (RBFNN)–HGSO, RBFNN–PSO, and RBFGNN–BA, were used in this study to forecast monthly rainfall at two stations in Malaysia (Sara and Banding). Different statistical measures (mean absolute error (MAE) and Nash–Sutcliffe efficiency (NSE) and percentage of BIAS (PBIAS)) and a Taylor diagram were used to assess the models’ performance. The results indicated that the MLP–HGSO performed better than the other models in forecasting rainfall at both stations. In addition, transition matrices were computed for each station and year based on the conditional probability of rainfall or absence of rainfall on a given month. The values of MAE for testing processes for the MLP–HGSO, MLP–PSO, MLP–BA, RBFNN–HGSO, RBFNN–BA, and RBFNN–PSO at the first station were 0.712, 0.755, 0.765, 0.717, 0.865, and 0.891, while the corresponding NSE and PBIAS values were 0.90–0.23, 0.83–0.29, 0.85–0.25, 0.87–0.27, 0.81–0.31, and 0.80–0.35, respectively. For the second station, the values of MAE were found 0.711, 0.743, 0.742, 0.719, 0.863 and 0.890 for the MLP–HGSO, MLP–PSO, MLP–BA, RBFNN–HGSO, RBFNN–BA, and RBFNN–PSO during testing processes and the corresponding NSE–PBIAS values were 0.92–0.22, 0.85–0.28, 0.89–0.26, 0.91–0.25, 0.83–0.31, 0.82–0.32, respectively. Based on the outputs of the MLP–HGSO, the highest rainfall was recorded in 2012 with a probability of 0.72, while the lowest rainfall was recorded in 2006 with a probability of 0.52 at the Sara Station. In addition, the results indicated that the MLP–HGSO performed better than the other models within the Banding Station. According to the findings, the hybrid MLP–HGSO was selected as an effective rainfall prediction model.
Expectations of duplicate gene retention under the gene duplicability hypothesis
Authors: Wilson Amanda E. , Liberles David A. 
Published: December 2023

Abstract
Background
Gene duplication is an important process in evolution. What causes some genes to be retained after duplication and others to be lost is a process not well understood. The most prevalent theory is the gene duplicability hypothesis, that something about the function and number of interacting partners (number of subunits of protein complex, etc.), determines whether copies have more opportunity to be retained for long evolutionary periods. Some genes are also more susceptible to dosage balance effects following WGD events, making them more likely to be retained for longer periods of time. One would expect these processes that affect the retention of duplicate copies to affect the conditional probability ratio after consecutive whole genome duplication events. The probability that a gene will be retained after a second whole genome duplication event (WGD2), given that it was retained after the first whole genome duplication event (WGD1) versus the probability a gene will be retained after WGD2, given it was lost after WGD1 defines the probability ratio that is calculated.

Results
Since duplicate gene retention is a time heterogeneous process, the time between the events (t1) and the time since the most recent event (t2) are relevant factors in calculating the expectation for observation in any genome. Here, we use a survival analysis framework to predict the probability ratio for genomes with different values of t1 and t2 under the gene duplicability hypothesis, that some genes are more susceptible to selectable functional shifts, some more susceptible to dosage compensation, and others only drifting. We also predict the probability ratio with different values of t1 and t2 under the mutational opportunity hypothesis, that probability of retention for certain genes changes in subsequent events depending upon how they were previously retained. These models are nested such that the mutational opportunity model encompasses the gene duplicability model with shifting duplicability over time. Here we present a formalization of the gene duplicability and mutational opportunity hypotheses to characterize evolutionary dynamics and explanatory power in a recently developed statistical framework.

Conclusions
This work presents expectations of the gene duplicability and mutational opportunity hypotheses over time under different sets of assumptions. This expectation will enable formal testing of processes leading to duplicate gene retention.