bluuebunny/crossref_metadata_2025_split huggingface dataset:
EasyMetagenome: A user‐friendly and flexible pipeline for shotgun metagenomic analysis in microbiome research
Authors: Bai Defeng , Chen Tong , Xun Jiani , Ma Chuang , Luo Hao , Yang Haifei , Cao Chen , Cao Xiaofeng , Cui Jianzhou , Deng Yuan‐Ping , Deng Zhaochao , Dong Wenxin , Dong Wenxue , Du Juan , Fang Qunkai , Fang Wei , Fang Yue , Fu Fangtian , Fu Min , Fu Yi‐Tian , Gao He , Ge Jingping , Gong Qinglong , Gu Lunda , Guo Peng , Guo Yuhao , Hai Tang , Liu Hao , He Jieqiang , He Zi‐Yang , Hou Huiyu , Huang Can , Ji Shuai , Jiang ChangHai , Jiang Gui‐Lai , Jiang Lingjuan , Jin Ling N. , Kan Yuhe , Kang Da , Kou Jin , Lam Ka‐Lung , Li Changchao , Li Chong , Li Fuyi , Li Liwei , Li Miao , Li Xin , Li Ye , Li Zheng‐Tao , Liang Jing , Lin Yongxin , Liu Changzhen , Liu Danni , Liu Fengqin , Liu Jia , Liu Tianrui , Liu Tingting , Liu Xinyuan , Liu Yaqun , Liu Bangyan , Liu Minghao , Lou Wenbo , Luan Yaning , Luo Yuanyuan , Lv Hujie , Ma Tengfei , Mai Zongjiong , Mo Jiayuan , Niu Dongze , Pan Zhuo , Qi Heyuan , Shi Zhanyao , Song Chunjiao , Sun Fuxiang , Sun Yan , Tian Sihui , Wan Xiulin , Wang Guoliang , Wang Hongyang , Wang Hongyu , Wang Huanhuan , Wang Jing , Wang Jun , Wang Kang , Wang Leli , Wang Shao‐kun , Wang Xinlong , Wang Yao , Xiao Zufei , Xing Huichun , Xu Yifan , Yan Shu‐yan , Yang Li , Yang Song , Yang Yuanming , Yao Xiaofang , Yousuf Salsabeel , Yu Hao , Lei Yu , Yuan Zhengrong , Zeng Meiyin , Zhang Chunfang , Zhang Chunge , Zhang Huimin , Zhang Jing , Zhang Na , Zhang Tianyuan , Zhang Yi‐Bo , Zhang Yupeng , Zhang Zheng , Zhou Mingda , Zhou Yuanping , Zhu Chengshuai , Zhu Lin , Zhu Yue , Zhu Zhihao , Zou Hongqin , Zuo Anna , Dong Wenxuan , Wen Tao , Chen Shifu , Li Guoliang , Gao Yunyun , Liu Yong‐Xin 
Published: February 2025

AbstractShotgun metagenomics has become a pivotal technology in microbiome research, enabling in‐depth analysis of microbial communities at both the high‐resolution taxonomic and functional levels. This approach provides valuable insights of microbial diversity, interactions, and their roles in health and disease. However, the complexity of data processing and the need for reproducibility pose significant challenges to researchers. To address these challenges, we developed EasyMetagenome, a user‐friendly pipeline that supports multiple analysis methods, including quality control and host removal, read‐based, assembly‐based, and binning, along with advanced genome analysis. The pipeline also features customizable settings, comprehensive data visualizations, and detailed parameter explanations, ensuring its adaptability across a wide range of data scenarios. Looking forward, we aim to refine the pipeline by addressing host contamination issues, optimizing workflows for third‐generation sequencing data, and integrating emerging technologies like deep learning and network analysis, to further enhance microbiome insights and data accuracy. EasyMetageonome is freely available at https://github.com/YongxinLiu/EasyMetagenome.
Ultra‐stretchable, super‐tough, and highly stable ion‐doped hydrogel for advanced robotic applications and human motion sensing
Authors: Hasany Masoud , Kohestanian Mohammad , Najafi Tireh Shabankareh Azar , Nezhad‐Mokhtari Parinaz , Mehrali Mehdi 
Published: February 2025

AbstractHydrogel‐based sensors are recognized as key players in revolutionizing robotic applications, healthcare monitoring, and the development of artificial skins. However, the primary challenge hindering the commercial adoption of hydrogel‐based sensors is their lack of high stability, which arises from the high water content within the hydrogel structure, leading to freezing at subzero temperatures and drying issues if the protective layer is compromised. These factors result in a significant decline in the benefits offered by aqueous gel electrolytes, particularly in terms of mechanical properties and conductivity, which are crucial for flexible wearable electronics. Previous reports have highlighted several disadvantages associated with using cryoprotectant co‐solvents and lower mechanical properties for ion‐doped anti‐freezing hydrogel sensors. In this study, the design and optimization of a photocrosslinkable ionic hydrogel utilizing silk methacrylate as a novel natural crosslinker are presented. This innovative hydrogel demonstrates significantly enhanced mechanical properties, including stretchability (>1825%), tensile strength (2.49 MPa), toughness (9.85 MJ m–3), and resilience (4% hysteresis), compared to its non‐ion‐doped counterpart. Additionally, this hydrogel exhibits exceptional nonfreezing behavior down to −85°C, anti‐drying properties with functional stability up to 2.5 years, and a signal drift of only 5.35% over 2450 cycles, whereas the control variant, resembling commonly reported hydrogels, exhibits a signal drift of 149.8%. The successful application of the developed hydrogel in advanced robotics, combined with the pioneering demonstration of combinatorial commanding using a single sensor, could potentially revolutionize sensor design, elevating it to the next level and benefiting various fields.image
Impact of artificial intelligence on future clinical pharmacy research and scholarship
Authors: Chan Alexandre , Baker William L. , Abazia Daniel , Bauman Jerry , DeVane C. Lindsay , Goodlet Kellie J. , Hall Natalie , Hicks James Kevin , Jones Ellen , Lu Chi‐Hua , Moore Donald C. , Nelson Nicholas R. , Putney Kaylee , Sosa Aracely , Trujillo Toby , Zhou Crystal 
Published: February 2025

AbstractAlmost every facet of modern biomedical research involves artificial intelligence (AI). This ACCP commentary forecasts the role of AI in clinical pharmacy research and scholarship. The potential benefits/opportunities together with the limitations/challenges of AI are reviewed for stages of the scientific method including (1) developing the research question(s), study design, and execution; (2) data analysis; and (3) reporting and dissemination of clinical pharmacy research. Benefits and opportunities of AI in clinical pharmacy research include streamlining hypothesis generation and facilitating study design, overcoming limitations of traditional statistical analysis techniques, facilitating manuscript development and dissemination, and expediting peer review. Limitations and challenges of AI include the introduction of biases in subject recruitment; generation of false information, also known as “AI hallucinations”; concern of “black box” analyses that are difficult to validate; potential legal liabilities; lack of accountability; and the need for investigators to ensure the accuracy and integrity of AI‐generated content. In summary, rapid progress of AI capabilities has great potential to revolutionize and accelerate clinical pharmacy research and scholarship; however, it is also imperative to recognize and mitigate the challenges and limitations introduced by AI.
Lactic acid production by direct fermentation of agave fructans
Authors: Martha‐Lucero Nayeli , Cruz‐Guerrero Alma , Favela‐Torres Ernesto , Viniegra‐González Gustavo , Cira‐Chávez Luis Alberto , Estrada‐Alvarado María Isabel 
Published: February 2025

AbstractBACKGROUNDLactic acid (LA) is used in various industries and is produced mainly through lactic acid fermentation (LAF). The high cost of glucose, a common substrate, is a major challenge for LA production. Alternatives like fructans from agave are being explored for this purpose, including the production of probiotic beverages using the sap of agave leaves wasted in the field. This study aims to compare the kinetics of LA fermentation using agave fructans and glucose to identify the kinetic factors to be optimize for future use of this process.RESULTSThe study found that direct fructan fermentation by Lactobacillus bulgaricus delbrueckii (LDF) and Lactobacillus casei (LCF) achieved approximately half the productivity (P = 0.50, 0.59 gL−1/h) as compared to glucose fermentation with the same strains (P = 0.92, 1.33 gL−1/h) apparently because of the delay of fructan hydrolysis. The number of Colony Forming Units (CFU) increased following a logistic function, with a rapid decay observed for pH < 4, following first‐order kinetics. Despite the decay, CFU levels remained above 1E7 CFU/mL. This finding could be useful to produce probiotic beverages using agave leaves as a fermentation broth.CONCLUSIONThe LAB strains, Lacticaseibacillus casei NRRL B‐441 (LC) and Lactobacillus delbrueckii bulgaricus NRRL B‐763 (LD), efficiently utilize commercial agave fructans as the primary carbon source, converting them into LA without prior hydrolysis. Fermentation productivity using fructans was approximately half of that obtained with glucose. This supports using agave fructans and sap for innovative lactic acid fermentations, including probiotic beverages. © 2025 Society of Chemical Industry (SCI).
The Epidemiology of Ascites in a Multi‐Ethnic Asian Population
Authors: Sinnanaidu Ram Prasad , Poobalan Kumaraganapathy , Singh Aswinderjeet Singh Balwan , Nair Kishvan , Vijayananthan Anushya , Mahadeva Sanjiv 
Published: February 2025

ABSTRACTIntroductionAscites is a common condition seen by clinicians in secondary care. Data on the epidemiology of ascites in Asians is lacking.MethodologyA retrospective case record review was performed in this large, referral institution between January 2016 and December 2019. Clinical and epidemiological data of adult (age > 18 years) patients with ascites, identified from the Radiology database, were obtained from this institutions' electronic medical records.ResultsA total of 838 patients (median age 59.77 ± 14.46 years, 56% males, ethnicity: Chinese 41.9%, Malay 34.8%, Indian 22.7%) were included in the study. Malignancy (28.9%) and liver cirrhosis (27.9%) were the most common etiology of ascites. Most of the malignant etiology of ascites were due to female‐related (breast and ovarian) and gastrointestinal (colon, liver, pancreatic, bile duct) cancer. Liver cirrhosis‐related ascites was mostly due to metabolic‐associated fatty liver disease (MASLD, 35.5%) and hepatitis B infection (20.5%). An increased age (> 40 years) was associated with all causes of ascites. The etiology of ascites varied with ethnicity as follows: the most common cause of ascites was malignancy (37.6%) among ethnic Chinese, heart failure (20.5%) in ethnic Malays and chronic liver disease (43.7%) in ethnic Indians.ConclusionMalignancy and liver cirrhosis are the leading cause of ascites in a multi‐ethnic Asian population. Demographic factors, particularly ethnicity, have a strong influence on the etiology of ascites.
Surface Enhanced Raman Spectral Monitoring of 50 KDa Filtrate Portions of Blood Serum Samples of Patients with Iron Deficiency Anemia
Authors: Tariq Rabia , Khalil Muhammad Zeshan , Nawaz Haq , Majeed Muhammad Irfan , Rashid Nosheen , Albekairi Norah A. , Alshammari Abdulrahman , Kamran Ali , Hussain Munawar , Nawabzadi Seher , Afzal Saima , Rauf Shanza , Fatima Eman , Wasim Muhammad 
Published: February 2025

ABSTRACTSurface‐enhanced Raman spectroscopy (SERS) is considered powerful analytical technique that significantly enhances the Raman scattering which enables the detection of low concentration of biomolecular analytes of blood serum, which can lead to early diagnosis of diseases. The aim of this study is Surface enhanced Raman spectral monitoring of 50 KDa filtrate portions of blood serum samples of patients with iron deficiency anemia. The blood serum components include higher molecular weight fractions (HMWF) and lower molecular weight fractions (LMWF) of biomolecules. The biomarkers of iron deficiency anemia, which are low molecular weight fractions are suppressed by high molecular weight fraction hence hindering them from contributing in the diagnosis of the disease. The ultra‐filtration of the blood serum samples is performed using filtration devices of 50 KDa. The specific SERS spectral features related to biochemical markers of iron deficiency anemic subgroups (with different values of hemoglobin) from different blood serum samples are identified including 479, 535, 888, and 1300 cm−1. These SERS features can be associated with different biomarkers of iron deficiency anemia consisting of ferritin, hepcidin, iron bound transferrin, and erythropoietin. Moreover, chemometric statistical techniques including principal component analysis (PCA) and partial least square regression (PLSR) are used for qualitative analysis of variations between spectral data and quantitative prediction of hemoglobin concentration of iron deficiency anemia samples, respectively.
Atomic Dynamics and Structural Transformations in Chalcedony as a Model Cryptocrystalline Multiphase System at Non‐Ambient Conditions
Authors: Campomenosi Nicola , Murri Mara , Prencipe Mauro , Mihailova Boriana 
Published: February 2025

ABSTRACTThe behaviour of chalcedony, a natural polycrystalline system consisting of cryptocrystalline (i.e., submicron‐sized) quartz and moganite, has been investigated via in situ Raman spectroscopy under non‐ambient conditions, complemented by hybrid Hartree–Fock/density‐functional‐theory (HF‐DFT) simulations of moganite phonon modes at high pressure. The combined experimental and computational results clearly indicate that the peak neat 503 cm−1 arises exclusively from the moganite SiO4‐ring mode rather than from OH librations of silanol groups. At high pressure and room temperature, the quartz fraction in chalcedony becomes metastable against coesite at 2.4 GPa and develops structural defects because of the anisotropic elastic strain arising from the interaction between cryptocrystalline moganite and quartz under the applied hydrostatic compressible stress. This process can trigger amorphization of quartz at pressures lower than those commonly observed in a quartz single crystal. At high temperature and ambient pressure, both quartz and moganite Raman peaks measured in chalcedony are excellent markers of both moganite and quartz α‐β transformations. Further, we show that upon heating–cooling cycles of chalcedony, a part of the moganite fraction transforms into quartz, if the temperature of α‐β quartz phase transition is crossed, confirming the overall metastability of the moganite structure with respect to that of α quartz. Moreover, the α‐β moganite transition affects the rate of phonon softening on quartz on the approach to the phase‐transition temperature. Our results demonstrate that the mutual impact of quartz and moganites is achieved via an admixture of phonons belonging to different phases but having the same symmetry and type of atomic vibrations, emphasizing the key role of Raman spectroscopy in studying structural transformations in multiphase systems.
Differences in bed elevation shape subtidal mussel bed stability under high‐energy hydrodynamic events
Authors: Zhao Zhiyuan , de Smit Jaco C. , Capelle Jacob J. , Grandjean Tim , Wu Mingxuan , Gerkema Theo , van de Koppel Johan , Bouma Tjeerd J. 
Published: February 2025

AbstractEscalating high‐energy hydrodynamic events, like storms, represent a significant manifestation of global climate change, causing detrimental impacts on various ecosystems and potentially triggering thresholds that result in abrupt shifts in ecosystem states. Despite the potential of such thresholds, few studies have explicitly addressed them. This gap is particularly notable for subtidal ecosystems due to technological challenges in detecting responses of organisms enduring constant submersion. This study focused on subtidal soft‐bottom mussel beds through the development of Biophys loggers for in situ monitoring of the fine‐scale behavior of mussel clusters under hydrodynamic disturbances and a statistical model based on an 11‐yr dataset to perform regional‐scale assessments of mussel bed stability. Multisite monitoring in the Dutch Wadden Sea revealed spatial heterogeneity in mussel bed mobility threshold (i.e., near‐bed orbital velocity inducing mussel movement), with predictable patterns along elevation gradients. Stability assessment in this region demonstrated that mussel beds in shallower areas (i.e., at higher bed elevations) exhibited higher stability than those in deeper areas, a difference that was attributed to the longer return interval of the mobility thresholds in shallow regions. These findings suggest that conditions such as bed elevation can modulate the stress tolerance of mussels and thereby influence the stability of subtidal soft‐bottom mussel beds. This study provides an approach for assessing mussel bed stability, which can also be extended to other comparable ecosystems, such as oyster reefs, to address their stability under climate change, thereby informing strategic management.
Market Reaction to Corporate Governance Reform: Evidence From China
Authors: Wei Haitian , Mohd‐Rashid Rasidah , Fawzi Agung Masyad , Ooi Chai‐Aun , Wei Haixuan 
Published: February 2025

ABSTRACTConsidering the market's different opinions on ESG, this study examines the market reaction to corporate governance reform within the context of ESG disclosure. By employing the event study methodology, it is demonstrated that the Chinese market exhibited an adverse reaction to the announcement of corporate governance reform. Furthermore, this study uses the ordinary least squares (OLS) model to demonstrate that ESG performance has a negative impact on cumulative abnormal return. It finds that the Chinese market had negative views about ESG disclosure. The findings have significant implications for the understanding of investor behavior and ESG‐related policies in emerging markets.
TBP Repeat Expansion Analysis in Patients Carrying Heterozygous STUB1 Variants
Authors: De Winter Jonathan , Van de Vondel Liedewei , Van Schil Kristof , Deconinck Tine , Storm Katrien , Geens Karine , Sommeling Charlotte , Crosiers David , Marechal Emke , De Ridder Willem , De Jonghe Peter , Baets Jonathan 
Published: February 2025

AbstractBackgroundThe cooccurrence of intermediate (40–49 CAG/CAA) TBP repeat expansions with STUB1 variants questions the pathogenicity of monoallelic STUB1 variants in cerebellar ataxia.ObjectiveThe objective of this study was to describe the phenotypic spectrum of heterozygous STUB1 variants with or without intermediate TBP repeat expansions.MethodsWe determined the presence of TBP repeat expansions and STUB1 variants in six families with cerebellar ataxia.ResultsCooccurrence of both genotypes in one family resulted in cerebellar ataxia, involving cognitive and extrapyramidal complications. Variable degrees of cerebellar ataxia and cognitive impairment were found in four families carrying a heterozygous STUB1 variant and normal TBP alleles. Finally, we report one patient with a mild late‐onset cerebellar ataxia carrying an intermediate expanded TBP allele without the presence of a STUB1 variant.ConclusionsHeterozygous STUB1 variants are associated with a milder phenotype and reduced penetrance compared with the cosegregation with intermediate TBP alleles, which causes a fully penetrant complicated form of cerebellar ataxia. © 2025 International Parkinson and Movement Disorder Society.
The Age‐Dependent Anticancer Efficacy of Agaricus blazei Murill Polysaccharide in Colon Cancer
Authors: Xu Yongzhao , Xu Tianxiong , Huang Chujun , Amakye William Kwame , Li Kaiqiang , Zhu Ying , Ren Jiaoyan 
Published: February 2025

ABSTRACTAgaricus blazei Murill polysaccharide (ABMP) has been found to exhibit significant immune regulatory effects, making them a promising candidate for complementary to the pharmacological treatment of colorectal cancer immune‐related diseases. As the prevalence of colorectal cancer among younger individuals increases, the possible age‐dependent anticancer modulatory effect of ABMP has not been clarified. This study evaluated the age‐dependent immunoregulatory efficacy of polysaccharides extraction from A. blazei in colon tumor. Hematoxylin‐eosin staining, immunohistochemistry, and vibrational spectroscopic image analysis of subcutaneous tumor tissues after ABMP preventive intervention for 14 weeks were analyzed in depth. In vivo data demonstrated that ABMP could more effectively inhibit the growth of tumor in mice at 8 compared with 12 months old without toxic side effect. Concurrently, Raman imaging spectroscopy analysis showed that ABMP preventive intervention could significantly reduce the lipid content in the tumor microenvironment (TME) of 8‐month‐old subcutaneous tumor‐bearing mice, suggesting that the changes in lipid content in TME are closely related to anticancer activity. These results stress the importance of considering age as a factor in polysaccharide adjuvant anticancer therapy. This work highlights for the first time that age is a key determinant in the ABMP preventive effectiveness by affecting lipid levels in the TME of tumor‐bearing mice, thereby exerting anticancer activity.
Predictive Value of Perioperative Blood Lactic Acid Levels for Postoperative Crisis in Myasthenia Gravis Patients Undergoing Thymectomy
Authors: Zou Jianyong , Yao Xiaojing , Liu Zhihao , Liu Zhenguo , Zhu Haoshuai , Zhang Xin , Chen Zhenguang , Su Chunhua 
Published: February 2025

ABSTRACTIntroduction/AimsPostoperative myasthenic crisis (POMC), which occurs specifically after thymectomy in myasthenia gravis (MG) patients, is a serious complication with known risk factors such as prior myasthenic crisis. However, the predictive value of perioperative blood lactic acid levels (BLAL) for POMC remains unclear. This study aims to determine whether changes in perioperative BLAL can predict POMC in MG patients undergoing thymectomy.MethodsA total of 340 patients diagnosed with MG and undergoing thymectomy at the First Affiliated Hospital of Sun Yat‐sen University were enrolled (January 2008–September 2018). Multivariate logistic regression analyses were employed to discern independent factors linked with POMC.ResultsAmong the patients with POMC, notable differences including higher Myasthenia Gravis Foundation of America (MGFA) stage, and history of preoperative myasthenic crisis were observed. Higher postoperative lactic acid levels and the extent of changes were more prevalent in the POMC group. The multivariate analysis unveiled history of myasthenic crisis (odds ratio, OR: 67.18), postoperative BLAL change ratio greater than 50% (OR: 2.86), the video‐assisted thoracoscopic surgery (VATS) approach (OR: 4.33), and higher preoperative BLAL (OR per unit: 2.68) were associated with POMC. Both continuous and grouped lactic acid models demonstrated a good predictive capability, yielding area under the curve (AUC) values of 0.84 and 0.83, respectively. The optimal threshold for 24‐h postoperative BLAL was 1.98 mmol/L.DiscussionThese findings offer valuable insights for clinical decision‐making and monitoring of prognosis in managing patients with MG. Future research should explore further the underlying mechanisms linking elevated lactate levels to POMC.