bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-omics analysis of immune-related microbiome and prognostic model in head and neck squamous cell carcinoma
Authors: Liu Yingqiao , Lin Haitao , Zhong Weijun , Zeng Yudi , Zhou Guihai , Chen Zhifeng , Huang Shi , Zhang Leitao , Liu Xiqiang 
Published: April 2024

Abstract
Objectives
The aim of our study is to explore the transcriptional and microbial characteristics of head and neck cancer’s immune phenotypes using a multi-omics approach.

Materials and methods
Employing TCGA data, we analyzed head and neck squamous cell carcinoma (HNSCC) immune cells with CIBERSORT and identified differentially expressed genes using DESeq2. Microbial profiles, obtained from the TCMA database, were analyzed using LEfSe algorithm to identify differential microbes in immune cell infiltration (ICI) subgroups. Random Forest algorithm and deep neural network (DNN) were employed to select microbial features and developed a prognosis model.

Results
We categorized HNSCC into three immune subtypes, finding ICI-2 with the worst prognosis and distinct microbial diversity. Our immune-related microbiome (IRM) model outperformed the TNM staging model in predicting survival, linking higher IRM model scores with poorer prognosis, and demonstrating clinical utility over TNM staging. Patients categorized as low-risk by the IRM model showed higher sensitivity to cisplatin and sorafenib treatments.

Conclusions
This study offers a comprehensive exploration of the ICI landscape in HNSCC. We provide a detailed scenario of immune regulation in HNSCC and report a correlation between differing ICI patterns, intratumor microbiome, and prognosis. This research aids in identifying prime candidates for optimizing treatment strategies in HNSCC.

Clinical relevance
This study revealed the microbial signatures associated with immunophenotyping of HNSCC and further found the microbial signatures associated with prognosis. The prognostic model based on IRM microbes is helpful for early prediction of patient prognosis and assisting clinical decision-making.
Rare association between spinocerebellar ataxia and amyotrophic lateral sclerosis: a case series
Authors: Ferrari Valerio , Conti Matteo , Bovenzi Roberta , Cerroni Rocco , Pierantozzi Mariangela , Mercuri Nicola B. , Stefani Alessandro 
Published: April 2024

Abstract
Introduction
In this work, we describe a new case of association between SCA2 and MND.

Case Report
A 58-year-old man who was diagnosed with spinocerebellar ataxia type 2 presented dysphagia and a significant decline in his ability to walk, with a reduction in autonomy and the need to use a wheelchair. We performed electromyography and electroneurography of the four limbs and of the cranial district and motor-evoked potentials to study upper and lower motor neurons. Referring to the revised El Escorial criteria of 2015, ALS diagnosis was made.

Discussion
Considering different cases described in literature over the years, SCA2 could represent an important risk factor for developing ALS. In particular, the presence of alleles of ATXN2 with 27 and 28 CAG repeats seems to slightly decrease the risk of developing the disease, which would instead be progressively increased by the presence of alleles with 29, 30, 31, 32, and 33 repeats. The exact physiopathological mechanism by which the mutation increases the risk of developing the disease is currently unknown. Transcriptomic studies on mouse models have demonstrated the involvement of several pathways, including the innate immunity regulation by STING and the biosynthesis of fatty acid and cholesterol by SREBP.

Conclusion
CAG repeat expansions in the ATXN2 gene have been associated with variable neurological presentations, which include SCA2, ALS, Parkinsonism, or a combination of them. Further research is needed to understand the relationship between SCA2 and ALS better and explore molecular underlying mechanisms.
Genomic characterization and detection of potential therapeutic targets for peritoneal mesothelioma in current practice
Authors: van Kooten Job P. , Dietz Michelle V. , Dubbink Hendrikus Jan , Verhoef Cornelis , Aerts Joachim G. J. V. , Madsen Eva V. E. , von der Thüsen Jan H. 
Published: April 2024

AbstractPeritoneal mesothelioma (PeM) is an aggressive tumor with limited treatment options. The current study aimed to evaluate the value of next generation sequencing (NGS) of PeM samples in current practice. Foundation Medicine F1CDx NGS was performed on 20 tumor samples. This platform assesses 360 commonly somatically mutated genes in solid tumors and provides a genomic signature. Based on the detected mutations, potentially effective targeted therapies were identified. NGS was successful in 19 cases. Tumor mutational burden (TMB) was low in 10 cases, and 11 cases were microsatellite stable. In the other cases, TMB and microsatellite status could not be determined. BRCA1 associated protein 1 (BAP1) mutations were found in 32% of cases, cyclin dependent kinase inhibitor 2A/B (CDKN2A/B) and neurofibromin 2 (NF2) mutations in 16%, and ataxia-telangiectasia mutated serine/threonine kinase (ATM) in 11%. Based on mutations in the latter two genes, potential targeted therapies are available for approximately a quarter of cases (i.e., protein kinase inhibitors for three NF2 mutated tumors, and polyADP-ribose polymerase inhibitors for two ATM mutated tumors). Extensive NGS analysis of PeM samples resulted in the identification of potentially effective targeted therapies for about one in four patients. Although these therapies are currently not available for patients with PeM, ongoing developments might result in new treatment options in the future.
Effects of moisture and aging upon decomposition of methyl iodide by reduced silver mordenite
Authors: Goettsche Heinrik , Raja Krishnan , Sabbarwall Piyush , Utgikar Vivek 
Published: April 2024

AbstractReduced silver mordenite has been considered as a sorbent for the capture of organic iodides, especially methyl iodide, from off-gases produced by aqueous used nuclear fuel reprocessing operations. The adsorption capacity of this material has been unpredictable especially when NOx and water are present. Previous work has found that a catalytic decomposition reaction is occurring on the surface but few determinations have been made of the kinetics of this reaction. The work presented tested the adsorption behavior and apparent catalytic reaction rate in humid conditions and compared those to dry conditions testing. Both experiments observed a first order reaction with rate constants of 0.0847 L/g sorbent/s and 0.1202 L/g sorbent/s respectively. Such a reduction in apparent rate constant is possibly due to either water obstructing methyl iodide adsorption or product desorption limitation. Changes in the adsorption profile were also apparent between these two, with the humid conditions experiment reaching saturation sooner than the dry conditions experiment. Additionally, an experiment into the effects of sorbent storage in a controlled laboratory environment was performed. The performance of the sorbent materials that were stored with silver in the zerovalent state was slightly inferior to those materials that were stored in ionic form (Ag+) and reduced to zerovalent silver immediately prior to subjecting them to sorption test. The materials stored with silver in the ionic form (and reduced just prior to application) behaved essentially similarly to the freshly synthesized (and reduced) sorbents in the sorption tests. This suggests that zerovalent silver experiences some oxidation resulting in deactivation of some sites.
Evaluation of markers of immunity in different metastatic immune microenvironments suggests more suppression within breast to liver metastases in breast cancer
Authors: Hsu Robert , Al-zubeidy Batul , Flores Daniel , Nazarian Ari , Baugh Aaron , Gonzalez Edgar , Castanon Sofi , Xiu Joanne , Kang Irene , Spicer Darcy , Lenz Heinz Josef , Dara Lily , Ademuyiwa Foluso O. , Korn W. Michael , Irshad Sheeba , Chan Isaac S. , Roussos Torres Evanthia T. 
Published: April 2024

Abstract
Purpose
Programmed death receptor ligand-1 (PD-L1) expression and tumor mutational burden (TMB) are approved screening biomarkers for immune checkpoint inhibition (ICI) in advanced triple negative breast cancer. We examined these biomarkers along with characterization of the tumor microenvironment (TME) between breast tumors (BrTs), axillary metastases (AxMs), liver metastases (LvMs), non-axillary lymph node metastases, and non-liver metastases to determine differences related to site of metastatic disease.

Methods
3076 unpaired biopsies from breast cancer patients were analyzed using whole transcriptome sequencing and NextGen DNA depicting TMB within tumor sites. The PD-L1 positivity was determined with VENTANA PD-L1 (SP142) assay. The immune cell fraction within the TME was calculated by QuantiSeq and MCP-counter.

Results
Compared to BrT, more LvM samples had a high TMB (≥ 10 mutations/Mb) and fewer LvM samples had PD-L1+ expression. Evaluation of the TME revealed that LvM sites harbored lower infiltration of adaptive immune cells, such as CD4+, CD8+, and regulatory T-cells compared with the BrT foci. We saw differences in innate immune cell infiltration in LvM compared to BrT, including neutrophils and NK cells.

Conclusions
LvMs are less likely to express PD-L1+ tumor cells but more likely to harbor high TMB as compared to BrTs. Unlike AxMs, LvMs represent a more immunosuppressed TME and demonstrate lower gene expression associated with adaptive immunity compared to BrTs. These findings suggest biopsy site be considered when interpreting results that influence ICI use for treatment and further investigation of immune composition and biomarkers expression by metastatic site.
Aneuploidy detection in pooled polar bodies using rapid nanopore sequencing
Authors: Madritsch Silvia , Arnold Vivienne , Haider Martha , Bosenge Julia , Pfeifer Mateja , Weil Beatrix , Zechmeister Manuela , Hengstschläger Markus , Neesen Jürgen , Laccone Franco 
Published: April 2024

Abstract
Purpose
Various screening techniques have been developed for preimplantation genetic testing for aneuploidy (PGT-A) to reduce implantation failure and miscarriages in women undergoing in vitro fertilisation (IVF) treatment. Among these methods, the Oxford nanopore technology (ONT) has already been tested in several tissues. However, no studies have applied ONT to polar bodies, a cellular material that is less restrictively regulated for PGT-A in some countries.

Methods
We performed rapid short nanopore sequencing on pooled first and second polar bodies of 102 oocytes from women undergoing IVF treatment to screen for aneuploidy. An automated analysis pipeline was developed with the expectation of three chromatids per chromosome. The results were compared to those obtained by array-based comparative genomic hybridisation (aCGH).

Results
ONT and aCGH were consistent for 96% (98/102) of sample ploidy classification. Of those samples, 36 were classified as euploid, while 62 were classified as aneuploid. The four discordant samples were assessed as euploid using aCGH but classified as aneuploid using ONT. The concordance of the ploidy classification (euploid, gain, or loss) per chromosome was 92.5% (2169 of 2346 of analysed chromosomes) using aCGH and ONT and increased to 97.7% (2113/2162) without the eight samples assessed as highly complex aneuploid using ONT.

Conclusion
The automated detection of the ploidy classification per chromosome and shorter duplications or deletions depending on the sequencing depth demonstrates an advantage of the ONT method over standard, commercial aCGH methods, which do not consider the presence of three chromatids in pooled polar bodies.
Exploring the Benefits and Acceptance of Blended Positive Psychotherapy as an Adjunctive Treatment for Clients with Residual Depressive Symptoms: A Mixed-Method Study
Authors: Vergeer-Hagoort Femke , Kraiss Jannis T. , Drossaert Constance H. C. , Bohlmeijer Ernst T. 
Published: April 2024

AbstractA proof-of-concept study was conducted to explore the acceptability and potential benefits of a blended positive psychotherapy intervention for clients with residual depressive symptoms. A single-arm pilot study was conducted in 2022 and 2023 with 24 Dutch adults experiencing residual depressive symptoms after treatment. Clients who had recently received an evidence-based treatment for depressive disorder were approached to participate in this study through opportunity sampling. The intervention consisted of nine sessions with a therapist and a six-week self-guided digital positive psychology intervention. Acceptability was examined using semi-structured interviews (n = 15). Participants filled out questionnaires pre- (n = 21), mid- (n = 14) and post-intervention (n = 8). Potential benefits were assessed in terms of changes in mental well-being (MHC-SF), depression (PHQ-9) and personal recovery (QPR). Quantitative data and qualitative data were analysed using linear mixed-effects models and framework analysis, respectively. The analyses were primarily based on Sekhon’s theoretical framework of acceptability. Linear mixed-effects analyses showed changes over time in most mental health indicators, including mental well-being (Hedge’s g = 1.58), depression (g = 1.43) and personal recovery (g = 1.96). Most of the interviewed participants considered blended positive psychotherapy a valuable adjunctive treatment; it connected well with their wish to become more positive in their daily life without ignoring difficult experiences. For some participants, shifting towards a positive treatment approach was difficult, resulting in early dropout. This study’s findings suggest that blended positive psychotherapy is acceptable to most people with residual depressive symptoms after treatment. Its impact is yet to be established in larger samples of studies involving more robust designs.
Patrilocality at the Beginning of Farming? An Isotopic Approach from SE Moravia
Authors: Morell-Rovira Berta , Tvrdý Zdeněk , Díaz-Zorita Bonilla Marta , Bickle Penny , Tóth Peter , Přichystal Michal , Bedáňová Alžběta , Masclans Alba 
Published: April 2024

AbstractThis research combines Strontium (87Sr/86Sr) and Oxygen (δ18O) isotope analysis to challenge the prevailing interpretation of patrilocal exogamic practices among eastern European Early Neolithic Linearbandkeramik (LBK) communities. Patrilocality has been considered the key factor influencing the mobility patterns of central Europe’s first farmers (c. 5500–4900 cal. BC), especially in the south-eastern Moravian region (Czech Republic). Focusing our attention on both male and female tooth enamel samples from cemeteries, settlement graves and small clusters of graves, this paper reassesses the correlation between mobility, biological sex, and funerary practices. This task is accomplished by establishing a new isotopic footprint using new 87Sr/86Sr data, as well as significantly increasing the number of sampled individuals for 87Sr/86Sr and δ18O. The outcome of this research contributes to a better understanding of the mobility patterns among early farmers in central Europe, challenging existing theories and providing new insights into their social and cultural dynamics.
Combining machine learning with computational fluid dynamics using OpenFOAM and SmartSim
Authors: Maric Tomislav , Fadeli Mohammed Elwardi , Rigazzi Alessandro , Shao Andrew , Weiner Andre 
Published: April 2024

AbstractCombining machine learning (ML) with computational fluid dynamics (CFD) opens many possibilities for improving simulations of technical and natural systems. However, CFD+ML algorithms require exchange of data, synchronization, and calculation on heterogeneous hardware, making their implementation for large-scale problems exceptionally challenging. We provide an effective and scalable solution to developing CFD+ML algorithms using open source software OpenFOAM and SmartSim. SmartSim provides an Orchestrator that significantly simplifies the programming of CFD+ML algorithms enables scalable data exchange between ML and CFD clients. We show how to leverage SmartSim to effectively couple different segments of OpenFOAM with ML, including pre/post-processing applications, function objects, and mesh motion solvers. We additionally provide an OpenFOAM sub-module with examples that can be used as starting points for real-world applications in CFD+ML.
Dissipativity Analysis of Memristive Inertial Competitive Neural Networks with Mixed Delays
Authors: Yang Jin , Jian Jigui 
Published: April 2024

AbstractWithout altering the inertial system into the two first-order differential systems, this paper primarily works over the global exponential dissipativity (GED) of memristive inertial competitive neural networks (MICNNs) with mixed delays. For this purpose, a novel differential inequality is primarily established around the discussed system. Then, by applying the founded inequality and constructing some novel Lyapunov functionals, the GED criteria in the algebraic form and the linear matrix inequality (LMI) form are given, respectively. Furthermore, the estimation of the global exponential attractive set (GEAS) is furnished. Finally, a specific illustrative example is analyzed to check the correctness and feasibility of the obtained findings.
Statistical analysis of flood risk perception: a case study for Eastern Black Sea Basin, Turkey
Authors: Anılan Tuğçe , Bayram Selahattin , Sayıl Mahmut Cenk , Yüksek Osman 
Published: April 2024

AbstractIt is very essential in terms of flood risk management to consider social expectations such as risk perception, flood awareness, preparedness, and socio-economic dynamics together with engineering designs. Understanding the way people perceive flood risk can enhance our capability of improving existing flood risk management methods, thus helps us creating disaster resilient societies. In this study, results of a questionnaire which was used for a previous study and had been administered to participants from Eastern Black Sea Region of Turkey were further investigated using statistical methods. The main aim was to understand how demographic factors such as age, gender and education level affect people’s flood risk perception. It was also desired to see that whether they were aware of the parties responsible for taking mitigation measures, or whether they know about possible flood mitigation measures or not. Using the same data with the previous study, but in addition using SPSS software to do statistical analysis, questionnaire results were investigated using convenient statistical tests for each parameter, analysis results were interpreted, and conclusions were drawn. Same tests were conducted using weight coefficients adopted using a certain methodology which is explained in the paper, in order to make a better investigation. Also, results were compared with the results of the previous study. It was seen that there were some consistencies and contradictions between the results of the previous study and this study’s results.
Quantifying future changes of flood hazards within the Broadland catchment in the UK
Authors: Gudde Ross , He Yi , Pasquier Ulysse , Forstenhäusler Nicole , Noble Ciar , Zha Qianyu 
Published: April 2024

AbstractFlooding represents the greatest natural threat to the UK, presenting severe risk to populations along coastlines and floodplains through extreme tidal surge and hydrometeorological events. Climate change is projected to significantly elevate flood risk through increased severity and frequency of occurrences, which will be exacerbated by external drivers of risk such as property development and population growth throughout floodplains. This investigation explores the entire flood hazard modelling chain, utilising the nonparametric bias correction of UKCP18 regional climate projections, the distributed HBV-TYN hydrological model and HEC-RAS hydraulic model to assess future manifestation of flood hazard within the Broadland Catchment, UK. When assessing the independent impact of extreme river discharge and storm surge events as well as the impact of a compound event of the two along a high emission scenario, exponential increases in hazard extent over time were observed. The flood extent increases from 197 km2 in 1990 to 200 km2 in 2030, and 208 km2 in 2070. In parallel, exponential population exposure increases were found from 13,917 (1990) to 14,088 (2030) to 18,785 (2070). This methodology could see integration into policy-based flood risk management by use of the developed hazard modelling tool for future planning and suitability of existing infrastructure at a catchment scale.
The contributions of transcription skills to paper-based and computer-based text composing in the early years
Authors: Malpique Anabela Anabela , Asil Mustafa , Pino-Pasternak Deborah , Ledger Susan , Teo Timothy 
Published: April 2024

AbstractDigital tools are an integral part of most writing communities across the globe, enhancing the criticality of gaining a comprehensive understanding of both paper and computer-based writing acquisition and development. The relationships between transcription skills and children’s paper-based writing performance are well documented. Less is known about the relationships between transcription skills and children’s computer-based writing performance. In this study, we examined the unique contributions of transcription skills (i.e., handwriting automaticity, keyboarding automaticity and spelling) in predicting Grade 2 students (N = 544) paper-based and computer-based writing performance (i.e., compositional quality and productivity) after controlling for other student-level factors (i.e., gender, word reading, reading comprehension, and attitudes towards writing) and classroom-level factors (i.e., amount of time teaching handwriting, keyboarding, and spelling). Multilevel modelling showed that, compared to handwriting automaticity, spelling skills accounted for a larger percentage of unique variance in predicting paper-based compositional quality; handwriting automaticity accounted for a larger percentage of unique variance in explaining paper-based compositional productivity. Findings further showed that keyboarding automaticity accounted for a larger percentage of unique variance in students’ computer-based compositional quality and productivity when compared to spelling. Gender and word reading skills were also found to be uniquely related to students’ writing performance across modalities. These findings underscore the need for educators to address and nurture the automaticity of inscription and spelling skills to enhance students' compositional quality and productivity, whether in traditional paperbased or computer-based text composing.
An empirical analysis of individual and collective determinants of international research collaboration
Authors: de Frutos-Belizón Jesús , García-Carbonell Natalia , Guerrero-Alba Félix , Sánchez-Gardey Gonzalo 
Published: April 2024

AbstractInternational research collaboration is a crucial determinant of scientific productivity, but it remains an underdeveloped task for governments, universities and research systems. Despite important economic and institutional efforts to promote collaborations, not all researchers establish successful international connections during their academic careers. This lack of international contacts hinders knowledge transfer from a broader perspective, limiting, in a way, the advancement of science. This paper analyses these factors—individual and collective—affecting research collaboration in the international context through a hierarchical multiple regression analysis of a sample of 954 Spanish academic researchers. We found that collective factors such as research team social capital—including structural and cognitive dimensions—and team orientation toward research and team productivity clearly affect international collaboration levels. Furthermore, contrary to our expectations, researchers’ human capital and motivation, and the principal investigator’s knowledge-oriented leadership, exerted only a very weak effect, which also is discussed in the paper’s final section.