bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhanced Prognostic Signature for Lung Adenocarcinoma through Integration of Adjacent Normal and Tumor Gene Expressions
Authors: Hao Mingyue , Li Dandan , Chen Weihao , Xiong Ming , Wang Xinkun , Qiao Yuanyuan , Ma Wei 
Published: January 2024

Abstract
Background: Cancer prognosis-related signatures have traditionally been constructed based on gene expression profiles derived from tumor tissues. However, the potential benefits of incorporating gene expression profiles from normal tissues in improving signature performance have not been explored.
Methods: In this study, we developed three prognosis models for lung adenocarcinoma (LUAD) using gene expression profiles from tumor tissues, normal tissues, and a combination (COM) of both, sourced from The Cancer Genome Atlas (TCGA). To ensure comparability, we followed the same workflow for all three models.
Results: When applied to the TCGA LUAD dataset, the tumor-derived model exhibited the best overall performance, with the exception of calibration analysis, where the normal-derived model performed better. The COM-derived model demonstrated intermediate performance. To validate the models, we applied them to three independent test datasets. Surprisingly, the COM-derived model showed the best performance, while the normal-derived model showed the worst. Notably, in the overall survival (OS) analysis, the low-risk group defined by the COM-derived model consistently exhibited longer mean survival times. In contrast, the tumor-derived model did not consistently show the same trend. The normal-derived model consistently produced opposite results. In discrimination analysis, no significant differences were observed. The COM-derived model demonstrated good discrimination ability for short time periods, while the tumor-derived model showed better performance for longer periods. In calibration analysis, both the COM and tumor-derived models exhibited similar absolute prediction errors, which were better than those of the normal-derived model. However, the tumor-derived model tended to underestimate survival rates.
Conclusions: Overall, the COM-derived model demonstrated the best generalization ability. The superior performance of the tumor-derived model in the TCGA LUAD dataset might be attributed to overfitting. Additionally, our results suggest that appropriate combinations of gene expression data from tumor and normal tissues can enhance the predictive power of prognosis signatures.
Differentiating Biomarker Features and Familial Characteristics
of B-SNIP Psychosis Biotypes
Authors: Parker David , Trotti Rebekah , McDowell Jennifer , Keedy Sarah , Keshavan Matcheri , Pearlson Godfrey , Gershon Elliot , Ivleva Elena , Huang Ling-Yu , Sauer Kodiak , Hill Scot , Sweeny John , Tamminga Carol , Clementz Brett 
Published: January 2024

Abstract
Idiopathic psychosis shows considerable biological heterogeneity across cases. B-SNIP used psychosis-relevant biomarkers to identity psychosis Biotypes, which will aid etiological and targeted treatment investigations. Psychosis probands from the B-SNIP consortium (n = 1907), their first-degree biological relatives (n = 705), and healthy participants (n = 895) completed a biomarker battery composed of cognition, saccades, and auditory EEG measurements. ERP quantifications were substantially modified from previous iterations of this approach. Multivariate integration reduced multiple biomarker outcomes to 11 “bio-factors”. Twenty-four different approaches indicated bio-factor data among probands were best distributed as three subgroups. Numerical taxonomy with k-means constructed psychosis Biotypes, and rand indices evaluated consistency of Biotype assignments. Psychosis subgroups, their non-psychotic first-degree relatives, and healthy individuals were compared across bio-factors. The three psychosis Biotypes differed significantly on all 11 bio-factors, especially prominent for general cognition, antisaccades, ERP magnitude, and intrinsic neural activity. Rand indices showed excellent consistency of clustering membership when samples included at least 1100 subjects. Canonical discriminant analysis described composite bio-factors that simplified group comparisons and captured neural dysregulation, neural vigor, and stimulus salience variates. Neural dysregulation captured Biotype-2, low neural vigor captured Biotype-1, and deviations of stimulus salience captured Biotype-3. First-degree relatives showed similar patterns as their Biotyped proband relatives on general cognition, antisaccades, ERP magnitudes, and intrinsic brain activity. Results extend previous efforts by the B-SNIP consortium to characterize biologically distinct psychosis Biotypes. They also show that at least 1100 observations are necessary to achieve consistent outcomes. First-degree relative data implicate specific bio-factor deviations to the subtype of their proband and may inform studies of genetic risk.
Light-driven C-H activation mediated by 2D transition metal dichalcogenides
Authors: Zheng Yuebing , Li Jingang , Zhang Di , Guo Zhongyuan , Jiang Xi , Larson Jonathan , Zhu Haoyue , Zhang Tianyi , Gu Yuqian , Blankenship Brian , Chen Min , Wu Zilong , Huang Suichu , Kostecki Robert , Minor Andrew , Grigoropoulos Costas , Akinwande Deji , Terrones Mauricio , Redwing Joan , Li Hao 
Published: January 2024

Abstract

C-H bond activation enables the facile synthesis of new chemicals. While C-H activation in short-chain alkanes has been widely investigated, it remains largely unexplored for long-chain organic molecules. Here, we report light-driven C-H activation in complex organic materials mediated by 2D transition metal dichalcogenides (TMDCs) and the resultant solid-state synthesis of luminescent carbon dots in a spatially-resolved fashion. We unravel the efficient H adsorption and a lowered energy barrier of C-C coupling mediated by 2D TMDCs to promote C-H activation. Our results shed light on 2D materials for C-H activation in organic compounds for applications in organic chemistry, environmental remediation, and photonic materials.
Engagement of Aotearoa New Zealand Dairy farmers with the Restricted Veterinary Medicine process: implications for One Health and antimicrobial resistance – A pilot study.
Authors: Arden Kurt , Rosanowski Sarah , Laven Richard , Mueller Kristina 
Published: January 2024

Abstract

Background:
Reducing antimicrobial resistance (AMR) requires a multidisciplinary One Health approach, which necessitates buy-in from all stakeholders. In Aotearoa New Zealand, where the dairy industry is one of the largest users of antibiotics, there are ongoing efforts to optimise antibiotic usage (AMU) to minimise the development of AMR. These include regulations around the veterinary authorisation of the use of antibiotics by farmers without the need for a specific prescription (“the RVM process”) and programmes such as the New Zealand Veterinary Association’s antibiotic ‘Traffic Light System’. The goal of this pilot study was to develop and trial a questionnaire to determine how much Aotearoa dairy farmers understand about One Health, AMR, the RVM process and how their actions regarding AMU affect the wider environment.
Methods:
A 55-question semi-structured questionnaire was piloted on 15 dairy farms in the Manawatu district of the North Island of Aotearoa via an in-person semi-structured interview between September and November 2021.
Results:
None of the interviewed farmers knew of the term One Health. However, the majority found the RVM process to be of use on their farm, although admitted they generally felt frustration regarding AMR, seeing it as a blockage to productivity, and lacked awareness regarding how their actions were related to its development. Of the farmers interviewed over half had not heard of the traffic light system, and of those who had, one admitted they refused to adhere to it.
Conclusions:
This study’s novel findings have highlighted that there are notable gaps within dairy farmer understanding of AMU, AMR and One Health as well as highlighting that veterinarians are not keeping their clients informed of their important role and engagement within One Health. There is still a lot more work to do with regards to vets, farmers and industry representatives working together to embrace One Health. Simple solutions would be to encourage farmers returning unused drugs to their veterinarians for correct disposal and to actively engage farmers further regarding AMU and AMR, so that these end-product users do not feel disconnected from the process.
Unraveling the Intertwined Threads of Insomnia and Sarcopenia in Cognitive and Functional Decline in Octogenarians
Authors: Filho Elias Rocha de Azevedo , Koeche Cristiane , Bueno Flavia Fagundes , de Nóbrega Otávio Toledo , Alves Vicente Paulo , Silva Henrique Salmazo da , Moraes Clayton Franco , Freitas Wladimir M. , Campos-Staffico Alessandra M. , de Carvalho Luiz Sérgio Fernandes 
Published: January 2024

Abstract
Introduction: Although insomnia and sarcopenia may seem unrelated in the context of older adult health, recent evidence has revealed shared underlying pathophysiological pathways. However, the extent to which these two factors jointly impact crucial clinical outcomes still needs to be determined. This study aimed to elucidate the associations of insomnia and sarcopenia with cognitive impairment and functional decline, shedding light on potential mechanistic connections.
Methods: In this observational study, we scrutinized data collected from 493 individuals aged ≥80 years between 2016 and 2018. Sarcopenia was assessed using the EWGSOP2 criteria, insomnia was assessed using the Insomnia Severity Index, functional status was assessed using the Instrumental Activity of Daily Living Scale, and cognition was assessed using the Mini Mental Condition Examination. The baseline assessments included blood lipid, IFN-γ, IL-2, IL-4, IL-6, IL-10, and CRP levels and DNA methylation.
Results: Insomnia alone was not associated with cognitive impairment or functional dependence. However, sarcopenia alone increased the odds of cognitive impairment by a factor of 2.6 (95% confidence interval [CI] 1.2 - 5.6, p = 0.011), although it did not impact functional decline. When examined together, insomnia and sarcopenia were associated with 4.8-fold increased odds of cognitive impairment (95% CI 2.1 - 10.9, p <0.001) and 7.1-fold increased odds of functional decline (95% CI 1.7 - 29.0, p = 0.007) compared to those with neither condition. Lipid profiles and inflammatory marker levelsdid not differ, but sarcopenic individuals had significantly greater DNA methylation (p <0.001).
Conclusions: Insomnia and sarcopenia synergistically increase the risk of cognitive impairment and functional decline among long-lived older adults. Sarcopenia alone impacted cognition in individuals, whichcould be related to the increase in inflammation-independent DNA methylation observed among individuals with sarcopenia.
Point mutations in the ygiV promoter region lead to cystobactamid resistance and reduced virulence in E. coli
Authors: Müller Rolf , Risch Timo , Kolling Dominik , Mostert Dietrich , Seedorf Tim , Heimann Dominik , Kohnhäuser Daniel , Deschner Felix , Fries Franziska , Solga Danny , Hilgers Jil-Sophie , Dastbaz Jan , Hirsch Anna , Brönstrup Mark , Kirschning Andreas , Herrmann Jennifer , Sieber Stephan 
Published: January 2024

Abstract
Antimicrobial resistance is one of the major health threats of the modern world. Thus, new structural classes of antimicrobial compounds are needed in order to overcome existing resistance. Cystobactamids as such a new compound class inhibit the well-established target bacterial type II topoisomerases while exhibiting superior antibacterial and resistance-breaking properties. Understanding potential mechanisms of emerging resistances is crucial in the development of novel antibiotics as they directly impact the future therapeutic application and market success. Therefore, the frequency and molecular basis of cystobactamid resistance in Escherichia coli was analyzed. High-level resistant E. coli mutants were selected and found to harbor single nucleotide polymorphisms in the promotor region of the ygiV gene, causing an upregulation of the respective protein. These stable mutations are contrary to what was observed as resistance genotype in the structurally related albicidins, where ygiV gene amplifications were identified causing resistance. Overexpression of YgiV in the mutants was additionally amplified upon cystobactamid exposition, showing further adaptation to this compound class under treatment. YgiV binds cystobactamids with high binding affinity, thereby preventing their interaction with the antimicrobial targets topoisomerase IV and DNA gyrase. Additionally, we observed stabilization of the gyrase cleavage complex by YgiV itself, suggesting a further protective effect against topoisomerase poisoning. Moreover, tested cystobactamid-resistant mutants show reduced motility and fimbrial protein expression, indicating an overall decreased virulence and potentially pathogenicity, associated with ygiV promotor mutations.
Validity of a visual analogue scale to measure and value perceived level of sanitation – evidence from Ghana and Mozambique
Authors: Cheung Ho Hei , Adriano Zaida , Dwumfour-Asare Bismark , Nyarko Kwabena B. , Scott Pippa , Nala Rassul , Brown Joe , Cumming Oliver , Ross Ian 
Published: January 2024

Abstract
Two billion people globally lack access to a basic toilet, and sanitation is a critical determinant of health and wellbeing. Evaluations of sanitation programmes typically measure disease or behaviour, and visual analogue scales (VAS) have not been used to measure users’ feelings about their level of sanitation. In this study, we assess the validity of a sanitation VAS numbered 0–10, with end-anchors best and worst imaginable sanitation. In Kumasi, Ghana, we surveyed 291 participants before and after uptake of a container-based sanitation service. In Maputo, Mozambique, we surveyed 424 participants from treatment groups of a prior trial. We assessed construct validity by testing hypothesised associations between VAS scores and toilet characteristics, and by respondents valuing three hypothetical sanitation states. We assessed responsiveness by comparing VAS with/without interventions. There was evidence (p < 0.05) for 60% of hypothesised associations in Ghana, and 100% in Mozambique. For responsiveness, there was a 3.4 point increase (2.1 SD) in VAS 10 weeks post- intervention in Ghana, and a 2.9 point difference (1.3 SD) in Mozambique. In valuation exercises, the mean was higher (p < 0.001) for the objectively better state. The sanitation VAS could be useful in economic evaluation, in valuing sanitation states or levels of service, to identify which improvements achieve quality of life gains most efficiently.
Associated factors of frailty in patients with chronic heart failure: A systematic review and meta-analysis
Authors: Liu Si , Xiong Xiao-yun , Liu Meng-die , Xiang Qin , Zhang Mei-jun , Chen Hua 
Published: January 2024

Abstract
Background: Although some researchers have explored the influencing factors of frailty in chronic heart failure (CHF) patients, frailty is affected by many factors, and their conclusions are inconsistent. This review aims to systematically evaluate the factors affecting frailty in CHF patients to provide an evidence-based basis for risk prediction, treatment plans, and the prevention of health outcomes in clinical settings.
Methods: EMBASE, the Cochrane Library, PubMed, Web of Science, CINAHL, Chinese Biological Medicine (CBM), CNKI, and Wan Fang databases were searched up to August 10, 2023, to identify observational studies to assemble the factors affecting frailty in CHF patients. Two independent reviewers assessed the quality of included studies using corresponding assessment tools. RevMan 5.4 was used for meta-analysis and sensitivity analysis. Stata 18 MP was used for publication bias assessment.
Results: 14 articles including 4310 patients were included. 16 influencing factors were identified, and the factors with statistical significance were age (OR=1.11, 95% CI=1.07-1.16, p<0.001), NYHA functional class (OR=3.15, 95% CI=2.46-4.04, p<0.001), albumin (OR=0.86, 95% CI=0.77-0.95, p=0.005), haemoglobin (OR=0.86, 95% CI=0.76-0.97, p=0.01), cerebrovascular accidents (OR=2.31, 95% CI=1.49-3.06, P<0.001), number of comorbidities (OR=1.24, 95%CI=1.05-1.47, P=0.01), left ventricular ejection fraction (LVEF) (OR=0.88, 95% CI=0.78-0.99, p=0.03), duration of hospitalization (OR=1.14, 95% CI=1.05-1.23, p=0.001) and left atrial diameter (OR=1.12, 95% CI=1.05-1.20, P=0.0006).
Conclusions: While this review and meta-analysis found that age, NYHA functional class, albumin, haemoglobin, cerebrovascular accidents, comorbidity, LVEF, duration of hospitalization, left atrial diameter were associated with frailty in patients with chronic heart failure, the study heterogeneity shows the need for better-designed studies to further clarify the influencing factors of frailty in CHF patients and develop disease prediction models based on an algorithm for predicting the risk of frailty more accurately.
The prognosis model of glioblastoma was constructed based on lactic acid metabolism-related genes
Authors: Lu Feng , Jiang Xiaohang , Zheng Guangwei , Zeng Guangming 
Published: January 2024

Abstract

Related studies have shown that lactate played a key role in immune escape and metastasis. Exploring the roles of lactic acid metabolism-related genes (LRGs) in glioblastoma (GBM) has great significance for clinic treatment of GBM.The target genes were obtained by intersecting the differentially expressed genes (DEGs) and the module genes. Biomarkers of GBM were screened out to construct the survival risk model, and the nomogram of GBM was constructed to clinically predict the survival of GBM patients. Moreover, the gene set enrichment analysis (GSEA) and the tumor micro-environment analysis were conducted to study the functions of different risk groups and the potential mechanism of GBM. Furthermore, the drug sensitivity analysis were carried out to provide theoretical support for clinical treatment of GBM.The risk score was constructed with six biomarkers, including CALN1, CDHR1, CRTAC1, GNAL, SLC7A14, and SPHKAP, and SLC7A14 was negative factors of GBM. Based on it, the prognostic model was constructed with age, IDH status, grade, and risk score. Noticeable, the clinical risk of GBM were associated with proliferation, migration, apoptosis, and immune related signaling pathways. In addition, the level of immune escape was higher in high risk group, and samples in high risk group were more sensitive to Vinorelbine_2048, Paclitaxel_1080, Docetaxel_1007, Gefitinib_1010, Erlotinib_1168, and etc. drugs. In this study, we identified six LRGs, including CALN1, CDHR1, CRTAC1, GNAL, SLC7A14, and SPHKAP. These findings might help to deepen the understanding of the regulatory mechanism of LRGs in GBM.
A Mixed Media Approach Using Locally Available Neutralizing Materials for the Passive Treatment of Acid Mine Drainage
Authors: Pocaan Joshua Pascual , Turingan Casey Oliver A. , Tabelin Carlito Baltazar , Zoleta Joshua B. , Arima Takahiko , Park Ilhwan , Ito Mayumi , Orbecido Aileen H. 
Published: January 2024

Abstract
Acid mine drainage (AMD)—the strongly acidic and highly polluted effluents from mine sites—are generally managed via active or passive treatment. Active treatment strategies are effective but requires continuous input of energy, chemicals and manpower making them unsustainable in the long term. Because of this, passive treatment is explored as a more sustainable alternative especially for abandoned and legacy mines. Recent studies of the authors have explored the use limestone and waste materials like low-grade ores (LGO), fly ash (FA), and concrete wastes for AMD treatment and found that although these materials generated alkalinity individually, they could only partially remove sulfate (SO42−) and some heavy metals. To address this limitation, a mixed media approach using these four materials is proposed to neutralize the pH of AMD and maximize heavy metals (Cu, Fe, Mn, Ni, and Al) and SO42− removal. A total of twenty (20) mixtures of the four materials were identified based on the response surface methodology (RSM) experimental design. Laboratory-scale experiments using simulated AMD were performed to assess the performance of each mixture by monitoring the pH, oxidation-reduction potential (Eh), electrical conductivity (EC), metal concentrations, and SO42− concentration. Based on the results, three optimized mixed media compositions were identified in wt%: (i) 43% LGO, 40% limestone, 17% CW; (ii) 44% LGO, 51% limestone, 6% CW; and (iii) 89% limestone, 11% LGO. Overall, simulated AMD passively treated by the optimized mixed media compositions met the Philippine effluent standards except for SO42−. Simulated AMD treated by the optimized mixed media achieved pH values of < 9 and removal efficiencies for Cu, Fe, Mn, Ni, and Al of about 99%, 99%, 98%, 70%, and 96%, respectively.
On the suitability of a Convolutional Neural Network based RCM-Emulator for fine spatio-temporal precipitation.
Authors: Doury Antoine , Somot Samuel , Gadat Sébastien 
Published: January 2024

Abstract

High resolution climate models are necessary to capture local precipitation but are too expensive to explore the uncertainties associated with future projections. To solve this resolution-uncertainty dilemma, Doury et al (2022) proposed a neural network based RCM-emulator for the near-surface temperature, at a daily and 12km-resolution. It uses existing RCM simulations to learn the relationship between low-resolution predictors and high resolution surface variables. When trained the emulator can be applied to any GCM simulation to produce ensembles of high resolution emulated simulations. This study assess the suitability of applying the RCM-emulator for precipitation thanks to a novel asymmetric loss function targeting to reproduce the entire precipitation distribution over any grid point.
In perfect model evaluation, the resulting emulator shows striking ability to reproduce the RCM original series with an excellent spatio-temporal correlation. In particular, a very good behaviour is obtained for the two tails of the distribution, measured by the number of dry days and the 99th quantile. Moreover, it creates consistent precipitation objects with a slight lack of precision. The emulator quality holds for all simulations of the same RCM, with any driving GCM, ensuring transferability of the tool to GCMs never downscaled by the RCM.
A first showcase of downscaling GCM simulations showed that the RCMemulator brings significant added-value with respect to the GCM as it produces adequate high resolution spatial structure and extremes’ intensity. Nevertheless, further work is needed to understand the differences that occur with the RCM and establish a relevant evaluation framework for GCM applications.