bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phenotypic Variation and Genetic Divergence in Natural Populations of Curmuca barb, Hypselobarbus curmuca (Hamilton, 1807) in the Rivers of the Western Ghats Biodiversity Hotspot, India
Authors: Mallegowda Jeevan Thiruguna , Lanthaimeilu Kamei , Devadas Dayal , Kumar Hirekudel Sanath , Jaiswar Ashok Kumar 
Published: February 2025

ABSTRACTHypselobarbus curmuca is an endemic fish species of Family Cyprinidae found in rivers and reservoirs of the Western Ghats, India. An interdisciplinary study was conducted to assess the population genetic structuring of the species with the help of conventional morphometric, image‐based truss network and genomic data of a nonprotein encoding mitochondrial DNA region (partial D‐loop −494 bp) (n = 106). Fishes were collected from five rivers of the Western Ghats, namely, Kali, Sharavathi and Chalakudy (west‐flowing) and Ghod and Tungabhadra (east‐flowing) (n = 294). Multivariate analysis of body measurements and truss distances revealed very weak separation among populations. The D‐loop sequence analysis showed that genetically distinct populations of fishes inhabit the studied rivers. Principal component analysis (PCA) and linear discriminant analysis (LDA) could not completely distinguish morphologically distinct populations. D‐loop sequence analysis indicated 13 haplotypes with low nucleotide diversity and 15 polymorphic sites, with location‐specific haplotypes. An overall haplotype diversity of 0.80 and nucleotide diversity of 0.00849 were found. The haplotype network and maximum likelihood phylogenetic tree showed three clusters with two most probable ancestors. Analysis of molecular variance (AMOVA) showed a high value (0.898) of the fixation index (FST) among the populations (p > 0.05). Neutrality test and mismatch distribution results indicated that the populations are currently subjected to selection. Application of an integrated approach to characterise the populations of H. curmuca in the wild supports the hypothesis of geographical barriers as major drivers of population genetic differentiation. Different riverine environments have not selected for morphological differences during the evolutionary process in the recent past and showed weak separation of populations. These findings can be utilised while designing conservation strategies for the species in the rivers of the Western Ghats, as the species faces threats due to exploitation in capture fisheries and trade in aquaculture.
Dynamic Mechanism of Short Peptide Additive Regulating Solvation Microenvironment of Zinc Ions
Authors: Li Yuting , Xiong Danyang , Zhu Jiabao , Mou Yulan , Yang Jinrong , He Xiao 
Published: February 2025

AbstractThe optimization electrolyte strategy through molecular additives to improve the stability of aqueous zinc‐ion batteries (AZIBs), which changes the solvation structure of hydrated zinc ions (Zn2+), generally relies on experimental trial and error, because the precise mechanism by which these additives alter the coordination environment of Zn2+ remains elusive. Here, we select the oligopeptide of mono‐, di‐, tri‐, and tetra‐glycine, as electrolyte additives to optimize the Zn2+ solvation microenvironment in AZIBs. Contrary to traditional views, we find that these additives modify the solvated structure of the Zn2+ by substituting sulfate ion (SO42−) in the preexistence of Zn2+‐SO42− ion pair, rather than water molecules in the first solvation shell, due to a high energy barrier to replace one of the coordinated water molecules of Zn2+. This observation is consistent with recent experimental result of the attenuating influence of glycine on the interaction between Zn2+ and SO42− confirmed by Fourier‐transform infrared spectroscopy. For the multifunctional triglycine, its favorable conformation is disrupted to accommodate the direct coordination of oxygen atoms with Zn2+, and Zn2+ is observed to migrate between distinct sites along the triglycine backbone. This work provides theoretical principles to rationally design advanced electrolytes for solvation modulation with high performance AZIBs.
Corporate Environmental Performance Leading Financial Performance: Impacts of Social Media Sentiment and Corporate Reputation
Authors: Islam Tiasha , Arunachalum Murugesh , Wellalage Nirosha , Benjamin Samuel 
Published: February 2025

ABSTRACTThis study examines the interplay between social media sentiment (SMS) and corporate reputation (CR) in shaping the relationship between corporate environmental performance (CEP) and corporate financial performance (CFP). Using a dataset of S&P 500 companies from 2017 to 2022, the results indicate that both CR and SMS positively influence the CEP–CFP relationship. However, when firms have weak reputations, a strong social media presence does not translate positive CEP into improved CFP. This research is among the first to explore the combined impact of SMS and CR on the CEP–CFP relationship, addressing the notable gap in the literature. In addition, the empirical findings offer insights into resource‐based views, legitimacy and ethical investment theories by demonstrating environmental performance as a competitive advantage. This aligns with the ethical investment theory's premise that stakeholders value environmentally responsible business practices. Finally, the study provides practical implications for managers, emphasising the importance of prioritising efforts to build and maintain a positive reputation for effective communication through social media.
Multi‐Institutional Analysis of Survival and Recurrence Patterns of Different Pathological Regression Types After Neoadjuvant Chemoradiotherapy or Radiotherapy for Esophageal Squamous Cell Carcinoma
Authors: Zhao Fangdong , Wang Qifeng , Han Weiming , Maitudi Wubulaishan , Cao Fuliang , Zhang Tian , Chen Xi , Dong Jie , Gong Lei , Shang Xiaobin , Jiang Hongjing , Zhang Wencheng , Pang Qingsong , Xiao Zefen , Wang Ping , Tang Peng 
Published: February 2025

ABSTRACTBackgroundThe recurrence patterns of different types of pathologic regression of the primary tumor and lymph nodes in patients with esophageal squamous cell carcinoma (ESCC) after neoadjuvant chemoradiotherapy (NCRT) are little known, especially in ypT0N+ patients.MethodsWe included 582 patients with ESCC who had esophagectomy after NCRT or neoadjuvant radiotherapy (NRT) from 3 institutions. The patients were divided into 4 groups: ypT0N0, ypT0N+, ypT+N0, and ypT+N+ according to the type of pathological regression of the primary tumor and lymph nodes. Survival, recurrence pattern and timing, and potential prognostic factors were compared.ResultsA total of 179 patients were classified as ypT0N0, 227 patients as ypT + N0, 45 patients as ypT0N+, and 131 patients as ypT + N+. The median follow‐up was 31.7 months in all patients. The restricted mean survival time (RMST) of ypT0N0, ypT + N0, ypT0N+, and ypT + N+ patients decreased sequentially (70.64, 63.84, 55.93 and 39.96 months) and the recurrence rates increased sequentially (22.3%, 29.5%, 44.4% and 54.2%). Both the overall survival (OS) and recurrence‐free survival (RFS) in the ypT0N+ group were significantly lower than those in the ypT0N0 group (HR: 2.226, p = 0.007; HR: 2.271, p = 0.003). The distant metastasis (DM) pattern in ypT0N+ was similar to that of ypT + N+, and higher than that of ypN0 (25.6% vs 14.3%, HR: 1.970, p = 0.040).ConclusionsESCC patients with various pathological regression types after receiving NCRT or NRT had significantly different survival rates. ypT0N+ patients had a lower survival rate and higher DM rate than ypT0N0 patients. For these lymph node‐positive patients, adjuvant chemotherapy does not appear to improve their prognosis.
Molecular Subtyping and Therapeutic Targeting of IFNG‐Driven Immunogenic Cell Death in Lung Adenocarcinoma
Authors: Li Lifeng , Yang Yaqi , Peng Mengle , Wang Biyue , Zhu Lili , Chen Chengxin , Fan Zhirui , Duan Xiaoran , Xue Ruyue , Lv Xuefeng , Cheng Ming , Zhao Jie 
Published: February 2025

ABSTRACTBackgroundImmunogenic cell death (ICD) can be triggered by various therapies to induce anti‐tumor immune responses, significantly enhancing treatment effectiveness, and is widely utilized in tumor immunotherapy.MethodsLUAD data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) validated ICD‐related molecular subtypes via consensus clustering. Clinical features, ICD genes, driver genes, mutations, tumor microenvironment, immune checkpoints, and drug sensitivity were compared. RT‐qPCR, Western blot, immunofluorescence, ELISA, flow cytometry, and tube formation assays validated findings.ResultsDifferential expression of 33 ICD genes was observed between tumor and normal tissues. These genes were clustered into two groups via consensus clustering and validated with GEO data. Prognostic analysis indicated superior outcomes in cluster 2 across TCGA and GEO cohorts. Significant disparities in clinicopathological characteristics like stage, gender, and age were noted between subtypes. Cluster 2 exhibited heightened expression of ICD‐related genes, driver genes, immune checkpoints, and immune cells. Cluster 2 also showed increased sensitivity to chemotherapy drugs. IFNG overexpression in A549 and H1299 cells induced CRT exposure, HMGB1 release, and ATP secretion, thereby promoting dendritic cell maturation and enhancing CD8+ T cell function. Additionally, IFNG boosted tumor angiogenesis via HMGB1 pathways, which could be mitigated by HMGB1 inhibition.ConclusionIdentification of novel ICD‐related molecular subtypes holds promise for guiding personalized therapies, assessing prognosis, and predicting immunotherapy efficacy in LUAD. IFNG emerges as a potential prognostic biomarker and therapeutic target, influencing both the tumor microenvironment and angiogenesis. These findings offer new insights into therapeutic strategies targeting IFNG‐mediated pathways in LUAD.
A Novel Method to Calibrate Spring‐Network Cell Model in Hydrodynamic Flow
Authors: Anandan Aravind , Maleki Mehdi , Thomann Céline , Perraud Axelle , Chatelin Robin , Ohayon Avigaël , Marquette Christophe , Courtial Edwin‐Joffrey 
Published: February 2025

ABSTRACTOne of the primary challenges encountered during the extrusion bioprinting process involves managing mechanical stresses within the printer nozzle. These stresses ultimately have an impact on the health and functionality of the cells within the printed structure. Statistical models in bioprinting predict cell damage but are empirical, disregard key interactions, and lack single‐cell prediction. Our ultimate objective is to develop an efficient validated computational model simulating human dermal fibroblast deformability in extrusion bioprinting, considering all important interactions. The spring‐network model shows promise in simulating cellular deformation. However, its widespread adoption and efficiency rely on a significant challenge of accurately calibrating model coefficients. This calibration process is complex due to the lack of a manual method tailored for eukaryotic cells suspended in hydrodynamic flow. In this study, we described a new method to calibrate the model coefficients manually for human dermal fibroblasts. To achieve this calibration, experimental data of human dermal fibroblasts passing through narrow microfluidics constriction was used. The calibration process was initiated by using coefficients associated with red blood cells and subsequently adjusted by comparing the model's behavior with experimental data. The elastic coefficients were calibrated to closely replicate the entry time observed in the experiments with a 5% error margin. However, notable differences persisted in the cell deformation behavior between simulation and experiment. Moreover, adding membrane viscosity minimally reduced transient cell deformation by less than 10% without affecting steady‐state deformation.
Mitogenomic Analysis of Glirids (Gliridae) and Squirrels (Sciuridae) From Türkiye: Evolutionary and Taxonomic Implications Within the Suborder Sciuromorpha
Authors: İbiş Osman , Selçuk Ahmet Yesari , Teber Saffet , Baran Mehmet , Koepfli Klaus‐Peter , Kefelioğlu Haluk , Tez Coşkun 
Published: February 2025

ABSTRACTGliridae and Sciuridae, the most impressive mammalian radiations within the suborder Sciuromorpha, encompass a total of 327 extant species. This study aimed to: (i) characterize the mitogenomes of three sciurid (Spermophilus citellus, Spermophilus taurensis, and Spermophilus xanthoprymnus) and three glirid (Glis glis, Dryomys nitedula, and Dryomys laniger) species from Türkiye; (ii) elucidate the phylogeographic relationships within D. laniger and D. nitedula using both mitogenomes and mitochondrial cytochrome b (CYTB) sequences; and (iii) reconstruct the phylogenetic relationships among extant members of the suborder Sciuromorpha. Sixteen new mitogenomes were sequenced from Turkish samples, containing 37 genes (2 ribosomal RNAs, 13 protein‐coding genes, 22 transfer RNAs), exhibiting similarity to those of other Gliridae and Sciuridae species. Based on mitogenomic data, Bayesian Inference and Maximum Likelihood phylogenetic analyses revealed two major phylogroups corresponding to the two families, Gliridae and Sciuridae, which were both monophyletic. Analyses of mitogenomic and CYTB sequences revealed at least two major lineages (i: Anatolia and ii: Lesser Caucasus and Alborz) of D. nitedula in the Anatolian region of Türkiye. The mitochondrial CYTB data indicated that D. laniger exhibited at least two major lineages (Eastern and Western), whereas D. nitedula comprised multiple lineages and sublineages. The mean genetic distance between the two mitogenomic lineages of D. nitedula was 7.69%. Based on the CYTB data, the mean genetic distance between the Eastern and Western lineages of D. laniger was 7%, whereas the mean genetic distances among the lineages of D. nitedula ranged from 6% to 13%. Major lineages of both D. laniger and D. nitedula might be considered distinct species throughout the species' range. This study demonstrates that complete mitogenomes for reconstructing the Gliridae phylogeny provides important information for revealing phylogenetic and phylogeographic relationships.
HLA evolutionary divergence score after donor lymphocyte infusion following allogeneic hematopoietic stem cell transplantation
Authors: Le Grand Sophie , Villemonteix Juliette , Daguindau Etienne , Fort Marylise , Caillat‐Zucman Sophie , Allain Vincent , Dormoy Anne , De Mas Veronique , Delabesse Eric , Recher Christian , Peffault de Latour Regis , Vallet Nicolas , Michonneau David , Guenounou Sarah , Huynh Anne 
Published: February 2025

AbstractDonor lymphocyte infusion (DLI) prevents acute myeloid leukemia (AML) or myelodysplastic syndrome (MDS) relapses following hematopoietic stem cell transplantation. Given the life‐threatening toxicities such as graft versus host disease (GVHD), the identification of variables associated with response without toxicities is warranted. We hypothesized that HLA evolutionary divergence (HED), defined by the diversity between two given alleles of the same HLA gene, may be such a factor. A retrospective multicenter case‐control study was conducted to evaluate the outcomes of pre‐emptive (preDLI) and prophylactic DLI (proDLI) regarding their HED score, in AML or MDS patients. DLI‐treated patients were matched with controls (1:2 matched) from French transplantation centers according to hospital, hemopathy, donor type, and risk classification. In total, 201 patients were included (N = 147 in the preDLI group, N = 54 in the proDLI group). Relapse‐free survival was significantly better in the preDLI group (hazard ratio [HR] = 0.23, 95% confidence interval [CI]: 0.14–0.55, p < 0.001) than in controls. However, this benefit was offset by a higher incidence of severe GVHD (HR = 4.88, 95% CI: 2.30–10.32, p < 0.001). HED A, B, C, DQA1, DQB1, DPB1, and DRB1 were calculated for 65 DLI‐treated patients. High‐class II HED was significantly associated with higher GVHD and relapse‐free survival (GRFS, HR = 0.33, 95% CI: 0.20–0.77, p = 0.005). Specific DQAB associations directly improved GRFS (HR = 0.23, 95% CI: 0.09–0.58, p = 0.004). In conclusion, screening the class II HED score identifies patients eligible for DLI treatment who will benefit the most from this strategy.
miR‐207 Suppresses the Progression of SiO2‐Induced Pulmonary Fibrosis by Targeting Smad3 to Regulate the TGF‐β1/Smad3 Signaling Pathway in C57BL/6 Mice
Authors: Zhao Jia‐hui , Li Shuang , Du Shu‐ling , Han Gui‐zhi , Li Huan , Shao Bo , Liu Xia , Zhou Yuting , Zhang Zhao‐qiang 
Published: February 2025

ABSTRACTSilicosis is a worldwide occupational disease characterized by irreversible pulmonary fibrosis. Recent studies have showed that microRNAs (miRNAs) may play a crucial role in silicosis progression by modulating fibrosis‐related gene express. In this study, we selected miR‐207 as our research subject because we found that miR‐207 can be match with Smad3 using bioinformatic techniques, which might silence the key fibrosis‐related TGF‐β1/Smad3 signal pathway. In this study, the mice were given silica suspension (20 µg/µL, 80 µL) via nostril once a day for 16 days to establish silicosis models, and then were transfected with miR‐207 mimic or inhibitor. The mice which were given phosphate‐buffered saline (PBS) (80 µL) via nostril were used as control. All mice were killed on Day 45 after the first exposure to dust, after which their lungs were removed for pathological observation and to measure the hydroxyproline content. Then, real‐time polymerase chain reaction and Western blot analysis were applied to detect the relative expression levels of TGF‐β1/Smad3 signaling pathway indicators (TGF‐β1, TGF‐βR, and Smad3), and myofibroblast transformation indicators (α‐SMA and Fn). Results showed that the lung pathological images of silicosis model group mice showed significant fibrosis, and TGF‐β1, TGF‐βR, Smad3, α‐SMA, and Fn were all highly upregulated compared with the control group mice. Intervention with miR‐207 mimics significantly inhibited pulmonary fibrosis in silicosis mice by downregulation of TGF‐β1/Smad3 and inhibiting of myofibroblast formation. Whereas these phenomena were not observed in silicosis mice treated with miR‐207 inhibitor. The results demonstrated that miR‐207 can block the progression of SiO2‐induced pulmonary fibrosis by targeting the TGF‐β/Smad3 signaling pathway.
Scaling of the GROMACS Molecular Dynamics Code to 65k CPU Cores on an HPC Cluster
Authors: Kutzner Carsten , Miletić Vedran , Palacio Rodríguez Karen , Rampp Markus , Hummer Gerhard , de Groot Bert L. , Grubmüller Helmut 
Published: February 2025

ABSTRACTWe benchmarked the performance of the GROMACS 2024 molecular dynamics (MD) code on a modern high‐performance computing (HPC) cluster with AMD CPUs on up to 65,536 CPU cores. We used five different MD systems, ranging in size from about 82,000 to 204 million atoms, and evaluated their performance using two different Message Passing Interface (MPI) libraries, Intel‐MPI and Open‐MPI. The largest system showed near‐perfect strong scaling up to 512 nodes or 65,536 cores, maintaining a parallel efficiency above 0.9 even at the highest level of parallelization. Energy efficiency for a given number of nodes was generally equal to or slightly better than parallel efficiency. We achieved peak performances of 687 ns/d for the 82k atom system, 116 ns/d for the 53M atom system, and about 35 ns/d for the largest 204M atom system. These results demonstrate that highly optimized software running on a state‐of‐the‐art HPC cluster provides sufficient computing power to simulate biomolecular systems at the mesoscale of viruses and organelles, and potentially small cells in the near future.
So Many Choices: A Guide to Selecting Among Methods to Adjust for Observed Confounders
Authors: Keele Luke , Grieve Richard 
Published: February 2025

ABSTRACTNon‐randomised studies (NRS) typically assume that there are no differences in unobserved baseline characteristics between the treatment groups under comparison. Traditionally regression models have been deployed to estimate treatment effects adjusting for observed confounders but can lead to biased estimates if the model is missspecified, by making incorrect functional form assumptions. A multitude of alternative methods have been developed which can reduce the risk of bias due to model misspecification. Investigators can now choose between many forms of matching, weighting, doubly robust, and machine learning methods. We review key concepts related to functional form assumptions and how those can contribute to bias from model misspecification. We then categorize the three frameworks for modeling treatment effects and the wide variety of estimation methods that can be applied to each framework. We consider why machine learning methods have been widely proposed for estimation and review the strengths and weaknesses of these approaches. We apply a range of these methods in re‐analyzing a landmark case study. In the application, we examine how several widely used methods may be subject to bias from model misspecification. We conclude with a set of recommendations for practice.
Predictive Power of Pharyngolaryngeal Secretion Accumulations for Penetration and Aspiration in Head and Neck Cancer Patients
Authors: Hötzel J. , Zaretsky E. , Goeze A. , Hey C. 
Published: February 2025

Abstract
Pharyngolaryngeal secretions, penetration, and aspiration belong to the cardinal symptoms of swallowing disorders in head and neck cancer patients. In order to provide safe swallowing diagnostics, it is of interest whether pharyngolaryngeal secretion accumulations can be used as a predictor for penetration and aspiration of food and liquids. This study analyzed the predictive power of pharyngolaryngeal secretion accumulations for the penetration and aspiration in head and neck cancer patients. Between 2016 – 2024, 403 head and neck cancer patients underwent swallowing diagnostics via Fiberoptic Endoscopic Evaluation of Swallowing (FEES). Pharyngolaryngeal secretions were graded with the secretion severity rating scale (SSRS) by Murray et al., penetration and aspiration with the penetration-aspiration scale (PAS) by Rosenbek et al. Both scales were cross-tabulated and correlated with each other. Possible influencing factors on PAS were analyzed by Spearman’s correlations and Kruskal–Wallis-H-tests: patients’ age, tumor stage and site, type of the oncological therapy, and time of examination. A linear regression and a Categorical Principal Components Analysis were utilized for the same purpose. Higher SSRS and PAS values tended to co-occur. In univariate calculations, the tumor stage and time of examination showed significant correlations with PAS. In multivariate analyses, the tumor stage, patients’ age, but above all the SSRS were shown to be significant influencing factors on PAS. Pharyngolaryngeal secretion accumulations can be used for the prediction of aspiration of food and liquids and thus for the improvement of safety of the swallowing diagnostics via FEES.