bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole Genome Analysis Identifies Homologous Recombination Deficiency in Cancers with BRCA1/2 Wild-Type and BRCA1/2 Structural Variants
Authors: Mosquera Juan Miguel , Assaad Majd , Hadi Kevin , Levine Max , Guevara Daniela , Patel Minal , Tranquille Marvel , King Abigail , Otilano John , Semaan Alissa , Gundem Gunes , Medina-Martínez Juan , Sigouros Michael , Manohar Jyothi , Kuo Hui-Hsuan , Wilkes David , Andreopoulou Eleni , Chapman-Davis Eloise , Tagawa Scott , Sboner Andrea , Ocean Allyson J. , Shah Manish , Papaemmanuil Elli , Sternberg Cora , Holcomb Kevin , Nanus David , Elemento Olivier 
Published: November 2024

Abstract

Purpose
Homologous recombination deficiency (HRD) impacts cancer treatment strategies, particularly effective utilization of PARP inhibitors. However, the variability of different HRD assays has hampered the selection of oncology patients who may benefit from these therapies. Our study aims to use the whole genome landscape to better define HRD in a pan-cancer cohort.
Methods
We employed a novel whole genome sequencing (WGS) HRD classifier that includes genome-wide signatures associated with HRD to analyze 580 tumor/normal paired samples. The HRD phenotype was correlated with genomic variants in BRCA1/2 and other homologous recombination repair genes. The results were compared to other assays and, in a subset, with commercial HRD tests, correlating them with treatment responses.
Results
HRD phenotype was identified in various cancers including breast (21%), pancreaticobiliary (20%), gynecological (17%), prostate (9%), upper gastrointestinal (GI) (2%), and other cancers (1%). HRD cases were not confined to BRCA1/2 mutations; 24% of HRD cases were BRCA1/2 wild-type. A diverse range of gene alterations involved in HRD were elucidated, including biallelic mutations in FANCF, XRCC2, and FANCC, and deleterious structural variants. In a subset of 15 cases, the WGS-based classifier offered more insights and a better correlation to treatment response when compared to other assays.
Conclusion
HRD is a biomarker used to determine which cancer patients would benefit from PARP inhibitors. However, a lack of harmonization of tests to determine HRD status makes it challenging to interpret their results. Our study highlights the use of comprehensive WGS analysis to better predict HRD and elucidates new genomic mechanisms associated with this phenotype.
Clinical significance and pathogenesis of GBP5 in infectious mononucleosis associated liver injury
Authors: Li Yan , Tang Jiamei , Ma Yulan , Yan Yujuan , Cheng Fangfang , Wang Kun 
Published: November 2024

Abstract

Background
Infectious mononucleosis (IM) is a common disease in children; however, liver injury is its most common complication. However, the pathogenesis of IM complicated with liver injury is ambiguous. Thus, this study aimed to explore the potential mechanism of IM-associated liver injury.
Methods
This study was conducted at the Children’s Hospital of Soochow University by collecting peripheral blood of 70 hospitalized children with IM. These patients were categorized into the liver injury (LIG, n = 35) and the non-liver injury groups (NLIG, n = 35), respectively. Subsequently, PBMCs and plasma were separated and obtained. PBMCs transcriptome sequencing was performed in two groups (5 cases in each group), and significantly differentially expressed genes (DEGs) were screened. Additionally, GO function enrichment, KEGG enrichment and GSEA analyses were performed. RT-PCR helped to detect the relative GBP5, NLRP3 and caspase-1 expressions in two groups (30 cases in each group) while the two groups’ caspase-1, IL-1β and IL-18 in plasma levels were measured by ELISA. Thus, clinical and laboratory datas of 60 hospitalized children with IM were evaluated.
Results
Transcriptome sequencing results showed that 171 DEGs were screened in the NLIG group, compared with the LIG. Among them, 154 DEGs were up-regulated, and 17 were down-regulated, respectively. KEGG and GSEA analyses showed that IM-associated liver injury is correlated with a NOD-like receptor signaling pathway. Statistically significant differences were observed in the white blood cell and lymphocyte counts, CD3+CD4+ T cells, CD3+CD8+T cells, alanine aminotransferase (ALT), aspartate transaminase (AST), and lactate dehydrogenase (LDH) of the two groups (p < 0.05). Compared with NLIG, GBP5, NLRP3 and caspase-1 expressions in PBMCs, as well as the caspase-1, IL-1β and IL-18 in plasma levels, were significantly higher in LIG (p < 0.001). A correlation analysis revealed a positive correlation of GBP5 with LDH, ALT, AST, CD3+CD8+T cells and NLRP3 (p < 0.05).
Conclusions
Our findings demonstrate that GBP5 contributes to liver injury in IM children through the NLRP3-dependent pathway.
Challenges and Prospects for the Substitution of Plastic Products with Jute in the context of Bangladesh – A Social Study
Authors: Masum Md. Mehedi Hassan , Zuthi Mst. Farzana Rahman , Khan Farjana , Hoque Asiful , Pal Sudip Kumar , Emon Ahasan Ul Islam , Das Sujit Ranjan , Kraft Eckhard , Kühlewindt Susanne 
Published: November 2024

Abstract

Single-use plastics are a major environmental concern in developing countries like Bangladesh due to their non-biodegradable nature. Finding sustainable alternatives is crucial to reduce reliance on these harmful plastics and mitigate pollution. This study aims to explore the public opinions on plastic pollution and investigate the challenges and potential for substituting plastics with jute. The study also provides essential recommendations for addressing these challenges and fostering the successful substitution of plastics with jute-based alternatives. A thorough social study was carried out in two major cities of Bangladesh, involving 212 participants through face-to-face questionnaire surveys. The selected participants represented diverse demographics in terms of age, gender, occupation, and education level. The findings reveal broad support for plastic recyclability, with many participants favoring jute and paper bags as alternatives to plastics. However, most individuals show little concern for reusing plastic products. Moreover, more than half of the total participants, spanning various demographics, have been exposed to plastic waste reduction campaigns. Furthermore, two-thirds of participants from diverse age groups, occupations, education levels, and genders support the introduction of higher pricing, such as additional tax, as measures to reduce plastic pollution. The correlation and Principal Component Analysis (PCA) plot reveal clustering patterns aligning plastic recycling, extra charges on plastic, and the availability of jute products with socio-demographic variables. Despite favorable views on jute, participants highlight high prices and limited availability as major barriers to adopting jute alternatives. Most of the participants call for additional support to the jute sector, with consensus favoring increased subsidies from the Government of Bangladesh and recognition of the significance of investing in research.
Selective Modulation of Aryl Hydrocarbon Receptor by Coptisine in MAFLD
Authors: Zhu Xiliang , Liu Qi , Cheng Zhaoyun , Luo Yi 
Published: November 2024

Abstract

Background:
Metabolic-associated fatty liver disease (MAFLD) is a multifaceted condition driven by disrupted lipid metabolism and chronic inflammation, influenced by genetic, environmental, and dietary factors. The Aryl Hydrocarbon Receptor (AHR) has emerged as a critical regulator in this context, mediating responses to various environmental and dietary signals. The dual role of AHR in MAFLD is complex, with some ligands exacerbating liver damage while others confer protective effects, suggesting that AHR’s impact may be highly context-dependent.
Methods:
This study analyzed single-cell RNA sequencing (scRNA-seq) data to explore the metabolic and transcriptional heterogeneity of hepatocyte subpopulations in a high-sucrose, high-fat diet (HSDFD)-induced MAFLD model. Virtual screening identified potential AHR-targeting compounds, leading to the selection of CPT for further study. The efficacy of CPT was evaluated through in vivo and in vitro assays, including Cellular Thermal Shift Assay (CETSA), Drug Affinity Responsive Target Stability (DARTS), Western blotting, immunohistochemistry (IHC), immunofluorescence, and Bodipy staining. These methods were employed to elucidate the molecular interactions between AHR and its ligands, and to assess CPT’s impact on lipid accumulation and AHR-mediated transcriptional activity.
Results:
Our findings reveal significant alterations in hepatocyte subpopulation dynamics under HSDFD conditions, with subpopulations such as Rasd1(hi), Galnt17(hi), and Lpin1(-) displaying enhanced metabolic activity. Transcriptional regulation analysis identified a reorganization of the M1 regulon module, with differential AHR activity across subpopulations. Notably, CPT emerged as a potent AHR-targeting compound, effectively reducing lipid accumulation and restoring CYP1A1 expression in MAFLD models. Structural and dynamic analyses demonstrated that CPT induces specific conformational changes in AHR, leading to a transcriptional environment that favors lipid metabolism and oxidative stress management.
Conclusion:
This study highlights the complex role of AHR in MAFLD and underscores the therapeutic potential of CPT in modulating AHR activity to mitigate lipid dysregulation. The findings provide valuable insights for developing targeted therapies that leverage the AHR/CYP1A1 pathway to treat MAFLD.
Defect Passivation of Hafnium Oxide Ferroelectric Tunnel Junction Using Forming Gas Annealing for Neuromorphic Applications
Authors: Nguyen Manh-Cuong , Min Kyung Kyu , Shin Wonjun Kyu , Yim Jiyong , Choi Rino , Kwon Daewoong 
Published: November 2024

Abstract

Forming gas annealing (FGA) is applied to HfOx ferroelectric tunnel junction (FTJ) synaptic devices to passivate defects and reduce trap-assisted-tunneling (TAT). Without FGA, TAT caused by defects in metal–ferroelectric–insulator–semiconductor (MFIS) FTJ stack dominates the conduction mechanism in FTJs and results in no memory window (MW). The reduction of defects or TAT after FGA reveals the effect of polarization switching on the FTJ performance. Consequently, linear/symmetric potentiation and depression (P/D) characteristics of FTJ after FGA with stable repeatability are obtained. Owing to the FGA-induced linearity and symmetricity of P/D, a learning accuracy of approximately 90% is achieved via pattern recognition simulations utilizing HfOx FTJ crossbar.
Parents' Information Needs and Perceptions of Chatbots for Self-Medicating Their Children: A Descriptive Qualitative Study
Authors: Wei Xueyi , Chen Xiuwen , Yue Liqing , Liao Peng 
Published: November 2024

Abstract

This qualitative study aimed to better understand parents’ information needs and perceptions of chatbots for self-medicating their children and developing chatbots for self-medication. A qualitative study using semi-structured interviews were conducted with parents with at least one child between October 2023 and December 2023. The interview data were analysed using a thematic analysis method. A total of 26 participants were interviewed by trained interviewers. Four key themes were identified: 1) Multiple information needs for self-medication; 2) Factors promoting the use of chatbots in self-medication; 3) Factors hindering the use of chatbots in self-medication; and 4) Expectations and suggestions for chatbots design. This study provides a detailed understanding of parents' information needs for self-medicating their children, as well as barriers and facilitators to using chatbots, informing the future design of conversational interfaces that could help improve parents' practice of self-medicating their children.
Results of round-robin testing for determining capillarity properties of vegetal concrete
Authors: Sandrine Marceau , Picandet Vincent , Gloria M’hamed Yassin Rajiv da 
Published: November 2024

Abstract

This study aims at presenting a new proposal to perform the water capillary absorption test of hemp concretes, and to establish the parameters useful for analyzing the obtained results. Based on the standards of traditional materials, such as concrete and mortar, a protocol was proposed and executed by 8 laboratories through a round robin test. Homogeneous hemp concrete cubic specimens of edge 150 mm were cast, distributed to the laboratories, where they were conditioned before being submitted to the test. By adopting the new test procedure, it was possible to obtain consistent results after analyzing in both square root of time and log-time regimes. For each regime, two parameters couples CA and k (square root of time regime), IRA and K1 (log-time regime) were used to compare the obtained data, and validate successfully the round robin test.
Changes in Lung mechanics with High-Flow Nasal Cannula compared to nasal CPAP in Preterm Infants
Authors: Katheria Anup , Ines Felix , Hough Judith , Rich Wade , Morales Ana , Sanjay Shashank , Poeltler Debra , Finer Neil 
Published: November 2024

Abstract

Objective: To compare the degree of atelectasis in preterm infants on nasal continuous airway pressure (nCPAP) versus high-flow nasal cannula (HFNC) at 8 L/min.
Study Design: A cross-over study of preterm infants <29 weeks gestational age (GA) receiving nCPAP and underwent 6-hours of HFNC at 8 L/min before returning to nCPAP. Electrical Impedance Tomography (EIT) was used to measure lung mechanics in dependent silent spaces (DSS), end-expiratory lung volume (EELV), ventral/dorsal center of ventilation (CoV-VD), and relative tidal stretch.
Results: 80 infants were recruited. There were no differences in estimated marginal mean measurements of DSS (p=0.76), EELV (p=0.68), CoV-VD (p=0.05), and relative tidal stretch (p=0.42) between respiratory support modes.
Conclusion: This study of premature infants <29 weeks GA at birth demonstrated no significant difference in DSS. EIT was able to detect real-time changes in the distribution of ventilation which may allow clinicians to identify infants at substantial risk to failure.
ClinicalTrials.gov ID: NCT03700606
Investigating the improvement of the quality of heavy crude oil and reducing the concentration of asphaltene hydrocarbons using microwaves radiation during acidizing based on hydrochloric acid
Authors: Tanhaei Hadi , Dehaghani Amir Hossein Saeedi 
Published: November 2024

Abstract

Acidizing boosts well production, while microwave radiation techniques and hybrid methods are emerging to enhance hydrocarbon extraction and oil production efficiency. In this research, the interaction between microwave radiation and working acid on crude oil was systematically investigated. Crude oil samples were positioned adjacent to an acid solution and subsequently subjected to microwave radiation at power levels of 1300 watt(100% Microwave) and 780 watt (60% Microwave) for durations of 1, 2, and 3 minutes. A comprehensive suite of analyses was performed, including viscometric assessments, interfacial tension measurements, density measurements, asphaltene quantification via extraction tests, sludge analysis, nuclear magnetic resonance (NMR) spectroscopy, pH measurements, and Fourier transform infrared spectroscopy (FTIR). The results indicate that the polarity of both the crude oil and the acid solution enhances the absorption of microwave radiation. FTIR analysis revealed an increase in polar functional groups relative to non-polar groups, suggesting significant molecular interactions, which NMR test also proves this trend. Furthermore, viscometric and surface tension tests demonstrated that increased polarity correlates with enhanced microwave absorption. The combined method, which is characterized by the simultaneous presence of polar acid solution and an electromagnetic field, led to alternating fluctuations (increase and decrease) of surface tension, viscosity, density, pH, and sludge during the tested process. It also caused a decrease in the concentration of asphaltene hydrocarbons, The reason for these intermittent changes is the simultaneous effects of changes in the strength of acid solutions and increasing or decreasing the power of microwave radiation at a certain time.
The Relationship of α-Klotho Level with Vitamin D, Calcium, Phosphorus and Parathyroid Hormone in the Ankylosing Spondylitis
Authors: Dogan Burcu , Toçoğlu Aysel , Tuzun Sabah , Akçay Ülkü , Altaş Ayfer , Gönüllü Emel , Tamer Ali 
Published: November 2024

Abstract

This study aimed to evaluate the relationship between -klotho levels and 25(OH)-vitamin D, calcium, phosphorus, and parathyroid hormone (PTH) in ankylosing spondylitis (AS) patients.
Eighty-five patients aged 18-65, admitted to outpatient clinics between August 1 and September 1, 2019, were included. Patients with AS for at least 5 years (32, 37.6%) were assigned to the AS group, while those without known diseases (53, 62.4%) were placed in the healthy group. The -klotho level was 0.60 [0.33] ng/mL in the AS group and 0.68 [1.59] ng/mL in the healthy group (p=0.209). In the AS group, those with vitamin D deficiency had a klotho level of 0.599 [1.751] ng/mL, compared to 0.605 [0.499] ng/mL in those without (p=0.952). In the healthy group, levels were 1.309 [10.110] ng/mL and 0.641 [0.879] ng/mL, respectively (p=0.195). No significant relationships were found between -klotho levels and vitamin D, PTH, calcium, phosphorus, or ALP in either group. Although some studies suggest a link between vitamin D and -klotho, further research is needed.
A Sustainable Risk Assessment Method for Workers With Disabilities – An ICT-Based Tool to Help SMEs Managers
Authors: TRIFU Alina , DARABONT Doru Costin , CIOCÎRLEA Vicentiu , IVAN Iulian Madalin , BADEA Daniel Onuț 
Published: November 2024

Abstract

Sustainability and workplace safety are deeply interconnected, both playing a crucial role in fostering a healthy and responsible work environment. In the realm of workplace safety, sustainability encompasses practices and policies designed to protect employee well-being, safeguard the environment, and ensure the organization's long-term success. Also, the metalwork welding industry is dominated by small and medium-sized enterprises (SMEs) that do not have full-time staff for occupational health and safety and, as is well known, industry-wide, that occupational accident and disease rates are often twice as high among SMEs compared to large enterprises. Furthermore, considering that the issue of workers with disabilities in very rare approached in the OSH world, the authors of the paper responds to the needs of such small and medium-sized enterprises by proposing a risk assessment method that is addressed to managers and staff with attributions regarding occupational safety and health of disabled workers in SMEs where welding activities are carried out, to help them identify the risks and to know what measures must be taken.
Preparation and adsorption properties of microsphere geopolymers based on calcium carbide slag-fly ash
Authors: Liao Yinnian , Ma Xiaoqing , Zou Jinchi , Zhao Mengqi , Chen Dejun , Xu Dayu 
Published: November 2024

Abstract

In this work, using fly ash and calcium carbide slag as mixed precursors, hydrogen peroxide and sodium dodecyl sulfate as mixed foaming agents, porous microsphere geopolymer was prepared by suspension curing technology to remove Cu (II) from aqueous solution. Because the Ca (OH) 2 in calcium carbide slag effectively improves the pozzolana activity of fly ash, more C-S-H gel is produced in the geopolymerization process, and the foaming process makes the material have larger specific surface area and better adsorption properties. The results show that the specific surface area of the material is 63.46 m2·g-1, the product regeneration rate is 83.20%, the optimal adsorption conditions are pH = 5, and the adsorption capacity was 118.48 mg·g-1. At the same time, it is found that the pseudo-first-order kinetic model and the Langmuir isotherm model can be applied to adsorption kinetics and isothermal adsorption respectively. Adsorption mechanisms may include physisorption and chemisorption. The adsorption capacity of this product for Cu(II) is better than that of other similar products, which has great potential in the field of heavy metal adsorption and provides a new idea for the resourceful use of industrial by-products.
Feasibility of Self-Expanding Transcatheter Pulmonary Valves in Patients with Pyramidal RVOT: Favorable Mid-term Outcomes
Authors: Zhu Wenhao , Xia Zhiyuan , Kai Jeffrey Chan Shi , Wan Junyi , Xu Liang , Li Yihang , Zhang Jingnan , Tse Gary , Fang Fang , Zhang Gejun 
Published: November 2024

Abstract

Background
Transcatheter pulmonary valve replacement (TPVR) has been acknowledged as a common and beneficial treatment for significant pulmonary regurgitation (PR), but data are still lacking about the mid-term effects of self-expanding valve implantation in patients with pyramidal right ventricular outflow tract (RVOT).
Methods
This study was a multicenter retrospective analysis involving consecutive patients who underwent intentional TPVR between May 27, 2014, and September 14, 2023. Baseline characteristics and immediate/mid-term echocardiographic variables were gathered and compared among patients with pyramidal RVOT and those with other RVOT configurations. The primary endpoint of immediate device success rate and secondary endpoint within one year post-procedure were also evaluated in both groups.
Results
A total of 68 patients were enrolled in the study. The primary endpoint showed a marginal difference between the two groups, with a significance level of P = 0.067 (86.7% in the pyramid-type group versus 100% in other types). At 1-year follow-up, the secondary endpoint demonstrated no intergroup differences in outcome (91.7% versus 86.0%; P = 0.605). Echocardiographic improvement and mid-term clinical outcomes were comparable in both groups (all P > 0.05). However, prosthesis valves implanted in pyramidal RVOT were observed to be more prone to developing trivial regurgitation within the first month (6 out of 11, 54.5% versus 7 out of 45, 15.6%; P = 0.016).
Conclusions
Despite slightly lower immediate device success rates, the outcomes of Venus P-Valve implantation in pyramidal RVOT were not only acceptable but favorable during mid-term echocardiographic and clinical follow-up. The utilization of self-expanding valves has significantly broadened the indications for TPVR, necessitating specific morphology assessments to better guide future procedures.