bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Petro‐Physical Model for Serpentinized Mantle and Origin of Natural Hydrogen in the Pyrenees
Authors: Pajang Sepideh , Mouthereau Frédéric , Robert Alexandra , Kumar Ajay , Callot Jean‐Paul 
Published: January 2025

AbstractThe relationships between the serpentinized continental mantle in orogens, its geophysical signature at depth and hydrogen seepages are poorly understood. A petro‐physical modeling approach accounting for serpentinization shows that a large domain of serpentinized mantle (1,800 km2) is present in the northern Pyrenees. The serpentinization reached a maximum of 40% during the mid‐Cretaceous rifting, according to the predicted temperature and pressure. Although high‐temperature serpentinization could have generated large quantify of hydrogen during the Mesozoic, the shallow and inactive faulting in Northern Pyrenees make this process unlikely to explain the entire serpentinization inferred by petro‐physical modeling. A combination of low‐temperature alteration of mafic and ultramafic rocks in the North Pyrenean Zone, active normal faulting in the North Pyrenean Fault, accumulation in local traps and transport of H2‐rich fluids along inactive but permeable fault may explain the hydrogen seepages observed today.
Sulfur‐to‐Iron Ratio as a Proxy for Degree of Organic Sulfurization
Authors: French K. L. , Birdwell J. E. 
Published: January 2025

AbstractThe degree of organic sulfurization is broadly relevant yet underreported. We present a statistically significant correlation between whole rock S/Fe and the measured degree of organic sulfurization in the thermally immature Cenomanian–Turonian Eagle Ford Group. This relationship shows a sink switch for sulfur from pyrite to organic matter. Excess iron and excess sulfur relative to pyrite, which are mathematically related to S/Fe, provide better insights into organic sulfurization than previous approaches that calculate excess iron relative to detrital iron based on aluminum concentrations. Organic sulfurization and S/Fe are tightly coupled in the Eagle Ford partially due to limited sulfur‐ and iron‐bearing components. Similar relationships could exist in other thermally immature, organic‐rich, anoxia‐prone, calcareous mudstones. The degree of organic sulfurization was estimated from S/Fe, which was used to map stratigraphic and regional variations of organic sulfurization across the Eagle Ford and to investigate how organic sulfurization relates to organic enrichment, organic preservation, and depositional redox chemistry. The extent of organic sulfurization is more tightly linked to organic preservation than enrichment. Together, organic sulfurization and Mo provide concordant evidence for depositional euxinia. The relationship between Mo and degree of organic sulfurization could indicate that sulfurized organic matter provides a pathway for Mo enrichment, but future work needs to disentangle direct mechanisms from indirect covariations between Mo, organic content, and degree of organic sulfurization. Whole rock elemental chemistry and programmed pyrolysis provide insights into organic sulfurization variations that can be upscaled and can guide subsequent detailed organic sulfur analyses.
Seismic Signatures of Fluctuating Fragmentation in Volcanic Eruptions
Authors: Coppess Katherine R. , Lam Fredric Y. K. , Dunham Eric M. 
Published: January 2025

AbstractFragmentation plays a critical role in eruption explosivity by influencing the eruptive jet and plume dynamics that may initiate hazards such as pyroclastic flows. The mechanics and progression of fragmentation during an eruption are challenging to constrain observationally, limiting our understanding of this important process. In this work, we explore seismic radiation associated with unsteady fragmentation. Seismic force and moment tensor fluctuations from unsteady fragmentation arise from fluctuations in fragmentation depth and wall shear stress (e.g., from viscosity variations). We use unsteady conduit flow models to simulate perturbations to a steady‐state eruption from injections of heterogeneous magma (specifically, variable magma viscosity due to crystal volume fraction variations). Changes in wall shear stress and pressure determine the seismic force and moment histories, which are used to calculate synthetic seismograms. We consider three heterogeneity profiles: Gaussian pulse, sinusoidal, and stochastic. Fragmentation of a high‐crystallinity Gaussian pulse produces a distinct very‐long‐period seismic signature and associated reduction in mass eruption rate, suggesting joint use of seismic, infrasound, and plume monitoring data to identify this process. Simulations of sinusoidal injections quantify the relation between the frequency or length scale of heterogeneities passing through fragmentation and spectral peaks in seismograms, with velocity seismogram amplitudes increasing with frequency. Stochastic composition variations produce stochastic seismic signals similar to observed eruption tremor, though computational limitations restrict our study to frequencies less than 0.25 Hz. We suggest that stochastic fragmentation fluctuations could be a plausible eruption tremor source.
ERG mediates the differentiation of hepatic progenitor cells towards immunosuppressive PDGFRα+ cancer-associated fibroblasts during hepatocarcinogenesis
Authors: Bai Haoran , Zhu Xinyu , Gao Lu , Feng Shiyao , Li Hegen , Gu Xiaoqiang , Xu Jiahua , Zong Chen , Hou Xiaojuan , Yang Xue , Jiang Jinghua , Zhao Qiudong , Wei Lixin , Zhang Li , Han Zhipeng , Liu Wenting , Qian Jianxin 
Published: January 2025

Abstract
Cancer-associated fibroblasts (CAFs) play important roles in the occurrence and development of hepatocellular carcinoma (HCC) and are a key component of the immunosuppressive microenvironment. However, the origin of CAFs has not been fully elucidated. We employed single-cell sequencing technology to identify the dynamic changes in different subsets of fibroblasts at different time points in rat primary HCC model. Inflammation-associated CAFs (Pdgfrα
+ CAFs) were subsequently identified, which demonstrated a significant correlation with the survival duration of HCC patients and a dual role in the tumour microenvironment (TME). On the one hand, they secrete the chemokines CCL3 and CXCL12, which recruit macrophages to the tumour site. On the other hand, they produce TGFβ, inducing the polarization of these macrophages towards an immunosuppressive phenotype. According to the in vitro and in vivo results, hepatic progenitor cells (HPCs) can aberrantly differentiate into PDGFRα+ CAFs upon stimulation with inflammatory cytokine. This differentiation is mediated by the activation of the MAPK signaling pathway and the downstream transcription factor ERG via the TLR4 receptor. Downregulating the expression of ERG in HPCs significantly reduces the number of PDGFRα+ CAFs and the infiltration of tumour-associated macrophages in HCC, thereby suppressing hepatocarcinogenesis. Collectively, our findings elucidate the distinct biological functions of PDGFRα+ cancer-associated fibroblasts (PDGFRα+ CAFs) within the TME. These insights contribute to our understanding of the mechanisms underlying the establishment of an immunosuppressive microenvironment in HCC, paving the way for the exploration of novel immunotherapeutic strategies tailored for HCC treatment.
The clinical-stage drug BTZ-043 accumulates in murine tuberculosis lesions and efficiently acts against Mycobacterium tuberculosis
Authors: Römpp Andreas , Treu Axel , Kokesch-Himmelreich Julia , Marwitz Franziska , Dreisbach Julia , Aboutara Nadine , Hillemann Doris , Garrelts Moritz , Converse Paul J. , Tyagi Sandeep , Gerbach Sina , Gyr Luzia , Lemm Ann-Kathrin , Volz Johanna , Hölscher Alexandra , Gröschel Leon , Stemp Eva-Maria , Heinrich Norbert , Kloss Florian , Nuermberger Eric L. , Schwudke Dominik , Hoelscher Michael , Hölscher Christoph , Walter Kerstin 
Published: January 2025

Abstract
The development of granulomas with central necrosis harboring Mycobacterium tuberculosis (Mtb) is the hallmark of human tuberculosis (TB). New anti-TB therapies need to effectively penetrate the cellular and necrotic compartments of these lesions and reach sufficient concentrations to eliminate Mtb. BTZ-043 is a novel antibiotic showing good bactericidal activity in humans in a phase IIa trial. Here, we report on lesional BTZ-043 concentrations severalfold above the minimal-inhibitory-concentration and the substantial local efficacy of BTZ-043 in interleukin-13-overexpressing mice, which mimic human TB pathology of granuloma necrosis. High-resolution MALDI imaging further reveals that BTZ-043 diffuses and accumulates in the cellular compartment, and fully penetrates the necrotic center. This is the first study that visualizes an efficient penetration and accumulation of a clinical-stage TB drug in human-like centrally necrotizing granulomas and that also determines its lesional activity. Our results most likely predict a substantial bactericidal effect of BTZ-043 at these hard-to-reach sites in TB patients.
Curating global datasets of structural linguistic features for independence
Authors: Graff Anna , Chousou-Polydouri Natalia , Inman David , Skirgård Hedvig , Lischka Marc , Zakharko Taras , Barbieri Chiara , Bickel Balthasar 
Published: January 2025

Abstract
The increasing availability of cross-linguistic databases dedicated to documenting morphosyntactic, lexical and phonological features has proliferated the use of such data for studies on language evolution and human history. However, most of these databases were not designed to ensure independence of features, such that it is not valid to jointly use all their features in large-scale statistical analyses assuming independence of inputs. Here, we curate published data from five large linguistic databases to generate two global-scale cross-linguistic datasets: GBI (from the Grambank dataset), and TLI (using inputs from the World Atlas of Language Structures, AUTOTYP, PHOIBLE and Lexibank). The datasets minimize logical dependencies of features and forms of strong statistical dependencies that go beyond phylogenetic and geographical signal. They are also made available in densified form, reducing the proportion of missing data. We document our curation principles and workflows to ensure reusability of this framework with other inputs or thresholds of independence. Our curation steps on both datasets reveal robust and comparable global patterns of structural linguistic diversity.
Association of chronic stress during studies with depressive symptoms 10 years later
Authors: Weinmann Tobias , Wibowo Razan , Forster Felix , Gerlich Jessica , Wengenroth Laura , Weinmayr Gudrun , Genuneit Jon , Nowak Dennis , Vogelberg Christian , Radon Katja , Herbig Britta 
Published: January 2025

Abstract
The long-tern implications of stress during university for individuals’ mental health are not well understood so far. Hence, we aimed to examine the potential effect of stress while studying at university on depression in later life. We analysed data from two waves of the longitudinal Study on Occupational Allergy Risks. Using the ‘work overload’ and ‘proving oneself’ scales of the Trier Inventory for Chronic Stress and the Patient Health Questionnaire-2 (PHQ-2), participants reported chronic stress during university (2007–2009, mean age 22.2 years, T1) and depressive symptoms ten years later (2017–2018, mean age 31.6 years, T2). We performed linear regression analyses to explore the association between stress during university (T1) and later depressive symptoms (T2). Participants (N = 548, 59% female) indicated rather low levels of stress and depression (PHQ-2 mean score: 1.14 (range: 0–6)). We observed evidence for a linear association between overload at T1 and depression at T2 (regression coefficient (B) = 0.270; 95% confidence interval (CI) = 0.131 to 0.409; standardised regression coefficient (β) = 0.170). Our analyses yielded evidence for an association between chronic stress while studying and risk of depressive symptoms later in life. This finding underlines the importance of implementing sustainable preventive measures against stress among students.
First record of microplastic contamination in adult endemic amazonian anuran species
Authors: e Souza-Ferreira Maria Luiza Cunha , dos Reis Adrian José Oliveira , Ferreira Erikson Bruno Loseiro , Dipold Jessica , Freitas Anderson Z. , Wetter Niklaus U. , de Oliveira-Bahia Verônica Regina Lobato , Vieira Thiago Bernardi 
Published: January 2025

Abstract
The microplastics (MPs), due to their high dispersion and bioaccumulation rates, have been identified in various animal groups, such as anuran amphibians during both larval and adult stages. However, current studies on adult anuran amphibians focus on assessing only one exposure route, the digestive system, while other routes remain underestimated. Therefore, this present study aimed to evaluate the degree of contamination in the digestive, respiratory, and integumentary systems, in situ, of two endemic Amazonian adult anuran species (Physalaemus ephippifer and Boana multifasciata). From this, we identified and characterized microplastic particles for each exposure route, assessed the effects of morphometric measures on the total MP contamination level and in the gastrointestinal tract (GIT). Additionally, we determined different contamination indices and how they vary according to species and systems. Based on our data, the digestive and integumentary exposure routes showed the highest contamination levels for both species. Additionally, variations in MP contamination levels indicated that P. ephippifer had a higher level of MP contamination. Thus, this study provides the first evidence of microplastic exposure through respiratory and integumentary routes in adult anurans in situ, and it is the first to identify MP contamination in terrestrial biomonitors in the Amazon.
Benchmarking protein language models for protein crystallization
Authors: Mall Raghvendra , Kaushik Rahul , Martinez Zachary A. , Thomson Matt W. , Castiglione Filippo 
Published: January 2025

Abstract
The problem of protein structure determination is usually solved by X-ray crystallography. Several in silico deep learning methods have been developed to overcome the high attrition rate, cost of experiments and extensive trial-and-error settings, for predicting the crystallization propensities of proteins based on their sequences. In this work, we benchmark the power of open protein language models (PLMs) through the TRILL platform, a be-spoke framework democratizing the usage of PLMs for the task of predicting crystallization propensities of proteins. By comparing LightGBM / XGBoost classifiers built on the average embedding representations of proteins learned by different PLMs, such as ESM2, Ankh, ProtT5-XL, ProstT5, xTrimoPGLM, SaProt with the performance of state-of-the-art sequence-based methods like DeepCrystal, ATTCrys and CLPred, we identify the most effective methods for predicting crystallization outcomes. The LightGBM classifiers utilizing embeddings from ESM2 model with 30 and 36 transformer layers and 150 and 3000 million parameters respectively have performance gains by 3-
$$5\%$$
than all compared models for various evaluation metrics, including AUPR (Area Under Precision-Recall Curve), AUC (Area Under the Receiver Operating Characteristic Curve), and F1 on independent test sets. Furthermore, we fine-tune the ProtGPT2 model available via TRILL to generate crystallizable proteins. Starting with 3000 generated proteins and through a step of filtration processes including consensus of all open PLM-based classifiers, sequence identity through CD-HIT, secondary structure compatibility, aggregation screening, homology search and foldability evaluation, we identified a set of 5 novel proteins as potentially crystallizable.
Thermal conductivity and balanced performance in infrared nonlinear optical multicomponent chalcogenides LixAg1−xGayIn1−ySe2
Authors: Isaenko L. I. , Xu Bohui , Korzhneva K. E. , Gong Pifu , Samoshkin D. A. , Kurus A. F. , Lin Zheshuai 
Published: January 2025

Combined machine-learning with experimental evaluations, the thermal conductivities in IR nonlinear optical chalcogenides LixAg1−xGayIn1−ySe2 series are investigated, and three compositions exhibit balanced properties.
Nonunion Rate following Ulnar Shortening Osteotomy using Brand-Specific Systems: A Systematic Review
Authors: Pasdar Pouria , Shariyate Mohammad Javad , Ghayyad Kassem , Bachoura Abdo , Kachooei Amir R. 
Published: January 2025

Abstract
Objectives This study aims to compare nonunion rates between conventional plates versus specific systems for ulnar shortening osteotomy (USO).
Materials and Methods To identify relevant studies, we searched various databases, including MEDLINE via Ovid, Embase.com, Web of Science Core Collection, Cochrane CENTRAL via Wiley, and Google Scholar. The level of evidence was assessed independently by three evaluators. Preferred reporting items for systematic reviews (PRISMA) recommendations were followed during the study selection process, which involved applying inclusion and exclusion criteria. All studies that reported the postoperative nonunion rates and mentioned the manufacturer of the fixation device were included. A total of 42 studies were analyzed, with information retrieved on osteotomy type, fixation type, manufacturer, bone union period, and nonunion rate for each study.
Results A total of 42 relevant articles were included in this study, with a total sample size of 1617 cases. The nonunion rate with the conventional plates was 5% (41 nonunion out of 815 cases).The reported nonunion rate was 0% (0 out of 67 cases) for the Stryker Trauma plates, 1.9% (three nonunion out of 157 cases) for the Rayhack plates, 4% (11 nonunion out of 271 cases) for the Acumed plates, 10.3% (3 nonunion out of 29 cases) for the specialized AO plates and 5% (14 nonunion and out of 278 cases) for the TriMed plates.
Conclusion Despite advances in plate designs for USO, the overall nonunion rate with USO-specific systems is almost comparable to that of conventional plates. So, it seems likely that the surgical technique and patient characteristics may play a more significant role than the type of device when planning for a USO. Cost and time savings should be weighed and considered when choosing between the less expensive conventional plates versus USO-specific systems.
Level of Evidence Prognostic level IV
Dorsal Triangular Fibrocartilage Complex Arthroscopic Repair
Authors: Woo Arthur On-Fai , Chau Wai-Wang , Tse Wing-Lim , Mak Michael Chu-Kay , Ho Pak-Cheong , Koo Jeffrey Justin Siu-Cheong 
Published: January 2025

Abstract
Background Dorsal triangular fibrocartilage complex (TFCC) is a newer entity of its family, which was not included in the Palmer classification. We believe that tear of the dorsal TFCC can cause pain and disability. Literature on this type of tear is limited, in addition, outcomes post-repair, especially arthroscopically, are scarce.
Purposes This article defines dorsal TFCC anatomy and investigates the clinical and functional outcomes post-TFCC dorsal tear arthroscopic repair.
Methods An 18-year retrospective review of 32 patients with arthroscopic repair of TFCC dorsal tears was performed. We categorised our patients into group (1) with only isolated TFCC dorsal tear and group (2) also with other concomitant TFCC tear. We evaluated their clinical and functional outcomes and also compared the two groups with other cofactors.
Results The mean follow-up period was 44 months. In the isolated dorsal tear group (N = 17), the wrist performance score was improved from 29 to 37 (p = 0.01), the Visual Analog Scale (VAS) score was improved from 6 to 3 (p < 0.01), Modified Mayo Wrist Score (MMWS) was improved from 60 to 74 (p = 0.01), and the hand grip strength was improved from 18 to 28 kg (p = 0.05). In the complex tear group (N = 9), VAS score was improved from 6 to 3 (p = 0.01) and the MMWS was improved from 44 to 79 (p = 0.01). Distal radioulnar joint stability was improved in the isolated group, achieving 100% stability after surgery (p < 0.01). No prognostic factors were identified. We noticed that patients who had surgery 9 months post-injury, would have the highest improvement on wrist flexion (p = 0.03), comparing with those who had surgery at other time points.
Conclusion We define dorsal TFCC as the area located between the horizontal dorsal superficial radioulnar ligament and the vertical dorsal capsular wall, that is, the extensor carpi ulnaris subsheath and extensor digiti minimi sheath. To our knowledge, internationally, we have operated and collected the largest series of TFCC dorsal tear arthroscopic repair. Our patients were benefited with significant pain relief with improved daily activities performance.
Clinical Relevance Dorsal TFCC tear can cause symptoms and is often missed, even during arthroscopic examination. We should consider offering wrist arthroscopy to patient who suffers from ulnar-sided wrist pain, even with negative radiological findings and 9 months post-injury, for diagnostic and therapeutic purposes.
Rare Presentation of Moyamoya Disease with an Acute Subdural Hemorrhage from a Rare Location of Aneurysm-Related Moyamoya Disease
Authors: Komonchan Surasak , Wattanasen Yodkhwan 
Published: January 2025

AbstractSpontaneous acute subdural hematoma is uncommon and usually caused by coagulopathy or other bleeding disorders, malignancy, intracranial hypotension, and abnormal intracranial vessels. We present unique cases of acute spontaneous subdural hematoma from moyamoya disease. There are a few cases reported, and we review previous literature and describe bleeding sources from aneurysms related to moyamoya disease in highly unusual locations.
Combination Therapy of 5-Fluorouracil and Triamcinolone Acetonide with Compression Therapy after Surgical Excision in the Management of Keloids in Ears
Authors: Lamba Randeep Singh , Pargal Pinki , Salwan Anurag , P.M Junaise , Nigam Pallavi , Bansal Noopur 
Published: January 2025

Abstract
Background Any deviation from the normal process of wound healing leads to excessive scar formation in the form of keloid or hypertrophic scar.
Materials and Methods The study included 120 candidates with keloids divided equally into two groups, A and B, of 60 patients each. After surgical excision, group A received combination therapy of intramarginal 5-fluorouracil (5-FU) and triamcinolone acetonide (TCA), while group B received only TCA, followed by compression therapy in both.
Results Eighty-seven patients had keloids on ear lobules, 25 (20.8%) on helix, and 8 (6.7%) over multiple locations on ear. Ninety-two (76.7%) had keloids over bilateral, 18 (15%) on left, and 10 (8.3%) on right ear. Sixty-three (52.5%) belonged to third, 65 (54.2%) to fourth, and 8 (6.7%) to fifth decade of life. Overall recurrence rate was 21.7 and 38.3% in group A and B, respectively. Recurrence was seen in 2 from group A (male:female 2:0) and 4 from group B (male:female 3:1) at 3 months, in 7 from group A (male:female 5:2) and 13 in group B (male:female 8:5) at 6 months, and in 4 from group A (male:female 3:1) and 6 from group B (male:female 5:1) at 1 year. Overall, pain was reported by 9 and 7 from group A and B, respectively, and burning sensation by 3 and 1 from group A and B, respectively. Ulceration was noted in 2, wound dehiscence in 1 and transient hyperpigmentation in 2 from group A. Based on the Vancouver Scar Scale, outcome on follow-up had an average of 3.5 at 3 months, 4.2 at 6 months, and 4.8 at 1 year in group A, and 3.8 at 3 months, 4.7 at 6 months, and 5.4 at 1 year in group B.
Conclusion Multimodal approach of combination therapy of intramarginal 5-FU and TCA with compression therapy after surgical excision of keloids in ears yields lower recurrence rate when compared with TCA alone. Chances of recurrence are more common in males than females. Though intramarginal 5-FU in combination with TCA has more localized side effects than TCA alone yet lower recurrence rate and better results in the long term can overcome the mild severity of these side effects.