bluuebunny/crossref_metadata_2025_split huggingface dataset:
Large-scale prediction of activity cliffs using machine and deep learning methods of increasing complexity
Authors: Tamura Shunsuke , Miyao Tomoyuki , Bajorath Jürgen 
Published: January 2023

AbstractActivity cliffs (AC) are formed by pairs of structural analogues that are active against the same target but have a large difference in potency. While much of our knowledge about ACs has originated from the analysis and comparison of compounds and activity data, several studies have reported AC predictions over the past decade. Different from typical compound classification tasks, AC predictions must be carried out at the level of compound pairs representing ACs or nonACs. Most AC predictions reported so far have focused on individual methods or comparisons of two or three approaches and only investigated a few compound activity classes (from 2 to 10). Although promising prediction accuracy has been reported in most cases, different system set-ups, AC definitions, methods, and calculation conditions were used, precluding direct comparisons of these studies. Therefore, we have carried out a large-scale AC prediction campaign across 100 activity classes comparing machine learning methods of greatly varying complexity, ranging from pair-based nearest neighbor classifiers and decision tree or kernel methods to deep neural networks. The results of our systematic predictions revealed the level of accuracy that can be expected for AC predictions across many different compound classes. In addition, prediction accuracy did not scale with methodological complexity but was significantly influenced by memorization of compounds shared by different ACs or nonACs. In many instances, limited training data were sufficient for building accurate models using different methods and there was no detectable advantage of deep learning over simpler approaches for AC prediction. On a global scale, support vector machine models performed best, by only small margins compared to others including simple nearest neighbor classifiers.
Graphical Abstract
Bacterial diversity associated with volatile compound accumulation in pit mud of Chinese strong-flavor baijiu pit
Authors: Shoubao Yan , Yonglei Jia , Qi Zhang , Shunchang Pu , Cuie Shi 
Published: January 2023

AbstractPit mud quality is a key parameter that impacts the quality of Chinese strong-flavor Baijiu production.This study was developed to explore spatial bacterial community distributions and the relationships between these distributions and the volatile compound accumulation within the pit mud used in the production of Chinese strong-flavor Baijiu. The results revealed Lactobacillus pasteurii and Limnochorda pilosa were found to be the dominant bacteria present in the upper wall, middle wall, and bottom pit mud layers, whereas the Clostridium genus was detectable at high levels in the lower layer of the pit wall and played a role in contributing to the overall aroma and flavor compounds in produced Chinese strong-flavor Baijiu, with Clostridium abundance being strongly correlated with caproic acid, ethyl caproate, ethyl butyrate, and hexanol levels as well as moderately correlated with butyric acid levels. The abundance of the Lactobacillus genus was positively correlated with levels of ethyl lactate, 1-butanol, and 2,3-butanediol. Limnochorda pilosa was closely associated with ethyl acetate levels. Additionally, the correlations between bacterial communities and chemical properties also investigated, and the results demonstrated PO43−, total carbon, K+, humus, NH4+-N, and Mg2+ levels significantly affected the bacterial community structure of pit mud, and they were positively correlated with the relative abundance of Clostridium. Together, these findings can serve as a foundation for future studies exploring the mechanisms whereby volatile compounds accumulate in different pit mud layers, which facilitates the fermentation regulation and pit mud quality improvement of Chinese strong-flavor Baijiu.
LncRNA–mRNA expression profile and functional network of vascular dysfunction in septic rats
Authors: Han Ye-Chen , Shen Zhu-Jun , Wang Yi-Ning , Xiang Ruo-Lan , Xie Hong-Zhi 
Published: January 2023

Abstract
Background
We used microarrays to analyse the changes in long non-coding RNAs (lncRNAs) and mRNAs in aorta tissue in model rats with lipopolysaccharide-induced sepsis and determined the lncRNA–mRNA and lncRNA–miRNA–mRNA functional networks.

Methods
Wistar rats were intraperitoneally injected with lipopolysaccharide, and the lncRNA and mRNA expression profiles in the aorta were evaluated using microarrays. The functions of the differentially expressed mRNAs were analysed using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses. We then constructed coding/non-coding co-expression and competing endogenous RNA networks to study the mechanisms related to sepsis in rats.

Results
We identified 503 differentially expressed lncRNAs and 2479 differentially expressed mRNAs in the model rats with lipopolysaccharide-induced sepsis. Mitochondrial fission process 1 (MTFP1) was the most significantly down-regulated mRNA. Bioinformatics analysis showed that the significantly down-regulated mRNAs in the sepsis models were in pathways related to mitochondrial structure, function, and energy metabolism. Coding/non-coding co-expression and competing endogenous RNA analyses were conducted using 12 validated lncRNAs in combination with all mRNAs. The coding/non-coding co-expression analysis showed that the 12 validated lncRNAs were mainly regulatory factors for abnormal energy metabolism, including mitochondrial structure damage and aberrant mitochondrial dynamics. The competing endogenous RNA analysis revealed that the potential functions of these 12 lncRNAs might be related to the inflammatory response.

Conclusion
We determined the differentially expressed lncRNAs and mRNAs in the aorta of septic rats using microarrays. Further studies on these lncRNAs will help elucidate the mechanism of sepsis at the genetic level and may identify potential therapeutic targets.
A remarkably diverse and well-organized virus community in a filter-feeding oyster
Authors: Jiang Jing-Zhe , Fang Yi-Fei , Wei Hong-Ying , Zhu Peng , Liu Min , Yuan Wen-Guang , Yang Li-Ling , Guo Ying-Xiang , Jin Tao , Shi Mang , Yao Tuo , Lu Jie , Ye Ling-Tong , Shi Shao-Kun , Wang Meng , Duan Ming , Zhang Dian-Chang 
Published: January 2023

AbstractBackgroundViruses play critical roles in the marine environment because of their interactions with an extremely broad range of potential hosts. Many studies of viruses in seawater have been published, but viruses that inhabit marine animals have been largely neglected. Oysters are keystone species in coastal ecosystems, yet as filter-feeding bivalves with very large roosting numbers and species co-habitation, it is not clear what role they play in marine virus transmission and coastal microbiome regulation.ResultsHere, we report a Dataset of Oyster Virome (DOV) that contains 728,784 nonredundant viral operational taxonomic unit contigs (≥ 800 bp) and 3473 high-quality viral genomes, enabling the first comprehensive overview of both DNA and RNA viral communities in the oysterCrassostrea hongkongensis. We discovered tremendous diversity among novel viruses that inhabit this oyster using multiple approaches, including reads recruitment, viral operational taxonomic units, and high-quality virus genomes. Our results show that these viruses are very different from viruses in the oceans or other habitats. In particular, the high diversity of novel circoviruses that we found in the oysters indicates that oysters may be potential hotspots for circoviruses. Notably, the viruses that were enriched in oysters are not random but are well-organized communities that can respond to changes in the health state of the host and the external environment at both compositional and functional levels.ConclusionsIn this study, we generated a first “knowledge landscape” of the oyster virome, which has increased the number of known oyster-related viruses by tens of thousands. Our results suggest that oysters provide a unique habitat that is different from that of seawater, and highlight the importance of filter-feeding bivalves for marine virus exploration as well as their essential but still invisible roles in regulating marine ecosystems.
Circular RNA circEMB promotes osteosarcoma progression and metastasis by sponging miR-3184-5p and regulating EGFR expression
Authors: Tan Jianye , Yang Bingsheng , Zhong Haobo , Luo Mengliang , Su Zexin , Xie Chao , Shi Meiling , Sun Chunhan , Lin Lijun 
Published: January 2023

AbstractBackgroundOsteosarcoma (OSA) is the most prevalent type of bone cancer with a high rate of metastasis. Circular RNAs (CircRNAs) play an essential role in multiple aspects of tumour biology. This study aimed to elucidate the role of circEMB in OSA.MethodscircRNAs related to OSA invasion were identified via RNA sequencing and qRT-PCR. The relationship between circEMB levels and clinicopathological features of OSA was examined using the clinical specimens and data of 53 patients with OSA. Several in vivo and in vitro experiments, including intravital imaging, whole-transcriptome sequencing, transwell assay, flow cytometry, dual-luciferase reporter assay, RIP assay, RNA pull-down assay and RNA-FISH, were performed to examine the effects of circEMB on the malignant behaviour of OSA.ResultsA novel circRNA, named circEMB (hsa_circ_001310), was identified in this study. circEMB can promote the malignant behaviour of OSA. In vitro experiments revealed that circEMB knockdown decreased cell proliferation, inhibited tumour invasion and metastasis; increased apoptosis and resulted in G1/S phase arrest. In vivo experiments revealed that circEMB knockdown inhibited tumour growth and metastasis in xenograft-bearing mice. Mechanistically, circEMB affects the malignant behaviour of OSA by mediating EGFR as an miR-3184-5p sponge. In addition, the circEMB/miR-3184-5p/EGFR axis modulates methotrexate (MTX) resistance in OSA.ConclusionsCircEMB plays a critical role in promoting cancer via the miR-3184-5p/EGFR pathway, indicating that circEMB may serve as a therapeutic target for OSA.
Mortality analysis among sepsis patients in and out of intensive care units using the Japanese nationwide medical claims database: a study by the Japan Sepsis Alliance study group
Authors: Oami Takehiko , Imaeda Taro , Nakada Taka‑aki , Abe Toshikazu , Takahashi Nozomi , Yamao Yasuo , Nakagawa Satoshi , Ogura Hiroshi , Shime Nobuaki , Umemura Yutaka , Matsushima Asako , Fushimi Kiyohide 
Published: January 2023

AbstractBackgroundA substantial number of sepsis patients require specialized care, including multidisciplinary care, close monitoring, and artificial organ support in the intensive care unit (ICU). However, the efficacy of ICU management on clinical outcomes remains insufficiently researched. Therefore, we tested the hypothesis that ICU admission would increase the survival rate among sepsis patients.MethodsWe conducted a retrospective study using the nationwide medical claims database of sepsis patients in Japan from 2010 to 2017 with propensity score matching to adjust for baseline imbalances. Patients aged over 20 years, with a combined diagnosis of presumed serious infection and organ failure, were included in this study. The primary outcome studied was the in-hospital mortality among non-ICU and ICU patients. In addition to propensity score matching, we performed a multivariable logistic regression analysis for the primary outcome. As the treatment policy was not extracted from the database, we performed sensitivity analyses to determine mortality differences in adults (20 ≤ age ≤ 64), independent patients, patients without malignant tumors, based on the assumption that treatment intensity is likely to increase in those population.ResultsAmong 1,167,901 sepsis patients (974,289 in non-ICU and 193,612 in ICU settings), the unadjusted in-hospital mortality was 22.5% among non-ICU patients and 26.2% among ICU patients (3.7% [95% CI 3.5–3.9]). After propensity score matching, the in-hospital mortality was 29.2% among non-ICU patients and 25.8% among ICU patients ($$-$$-3.4% [95% CI$$-$$-3.7 to$$-$$-3.1]). In-hospital mortality with a multivariable regression analysis ($$-$$-5.0% [95% CI$$-$$-5.2 to$$-$$-4.8]) was comparable with the results of the propensity score matching analysis. In the sensitivity analyses, the mortality differences between non-ICU and ICU in adults, independent patients, and patients without malignant tumors were$$-$$-2.7% [95% CI$$-$$-3.3 to$$-$$-2.2],$$-$$-5.8% [95% CI$$-$$-6.4 to$$-$$-5.2], and$$-$$-1.3% [95% CI$$-$$-1.7 to$$-$$-1.0], respectively.ConclusionsHerein, using the nationwide medical claims database, we demonstrated that ICU admission was potentially associated with decreasing in-hospital mortality among sepsis patients. Further investigations are warranted to validate these results and elucidate the mechanisms favoring ICU management on clinical outcomes.
The Frail-LESS (LEss Sitting and Sarcopenia in Frail older adults) intervention to improve sarcopenia and maintain independent living via reductions in prolonged sitting: a randomised controlled feasibility trial protocol
Authors: Bailey Daniel P. , Kilbride Cherry , Harper Jamie H. , Victor Christina , Brierley Marsha L. , Hewson David J. , Chater Angel M. 
Published: January 2023

AbstractBackgroundSarcopenia is a progressive and generalised loss of muscle mass and function with advancing age and is a major contributor to frailty. These conditions lead to functional disability, loss of independence, and lower quality of life. Sedentary behaviour is adversely associated with sarcopenia and frailty. Reducing and breaking up sitting should thus be explored as an intervention target for their management. The primary aim of this study, therefore, is to examine the feasibility, safety, and acceptability of conducting a randomised controlled trial (RCT) that evaluates a remotely delivered intervention to improve sarcopenia and independent living via reducing and breaking up sitting in frail older adults.MethodsThis mixed-methods randomised controlled feasibility trial will recruit 60 community-dwelling older adults aged ≥ 65 years with very mild or mild frailty. After baseline measures, participants will be randomised to receive the Frail-LESS (LEss Sitting and Sarcopenia in Frail older adults) intervention or serve as controls (usual care) for 6 months. Frail-LESS is a remotely delivered intervention comprising of tailored feedback on sitting, information on the health risks of excess sitting, supported goal setting and action planning, a wearable device that tracks inactive time and provides alerts to move, health coaching, and peer support. Feasibility will be assessed in terms of recruitment, retention and data completion rates. A process evaluation will assess intervention acceptability, safety, and fidelity of the trial. The following measures will be taken at baseline, 3 months, and 6 months: sitting, standing, and stepping using a thigh-worn activPAL4 device, sarcopenia (via hand grip strength, muscle mass, and physical function), mood, wellbeing, and quality of life.DiscussionThis study will determine the feasibility, safety, and acceptability of evaluating a remote intervention to reduce and break up sitting to support improvements in sarcopenia and independent living in frail older adults. A future definitive RCT to determine intervention effectiveness will be informed by the study findings.Trial registrationISRCTN, ISRCTN17158017; Registered 6 August 2021,https://www.isrctn.com/ISRCTN17158017
A hybrid decision support system with golden cut and bipolar q-ROFSs for evaluating the risk-based strategic priorities of fintech lending for clean energy projects
Authors: Wan Qilong , Miao Xiaodong , Wang Chenguang , Dinçer Hasan , Yüksel Serhat 
Published: January 2023

AbstractIn the last decade, the risk evaluation and the investment decision are among the most prominent issues of efficient project management. Especially, the innovative financial sources could have some specific risk appetite due to the increasing return of investment. Hence, it is important to uncover the risk factors of fintech investments and investigate the possible impacts with an integrated approach to the strategic priorities of fintech lending. Accordingly, this study aims to analyze a unique risk set and the strategic priorities of fintech lending for clean energy projects. The most important contributions to the literature can be listed as to construct an impact-direction map of risk-based strategic priorities for fintech lending in clean energy projects and to measure the possible influences by using a hybrid decision making system with golden cut and bipolar q-rung orthopair fuzzy sets. The extension of multi stepwise weight assessment ratio analysis (M-SWARA) is applied for weighting the risk factors of fintech lending. The extension of elimination and choice translating reality (ELECTRE) is employed for constructing and ranking the risk-based strategic priorities for clean energy projects. In this process, data is obtained with the evaluation of three different decision makers. The main superiority of the proposed model by comparing with the previous models in the literature is that significant improvements are made to the classical SWARA method so that a new technique is created with the name of M-SWARA. Hence, the causality analysis between the criteria can also be performed in this proposed model. The findings demonstrate that security is the most critical risk factor for fintech lending system. Moreover, volume is found as the most critical risk-based strategy for fintech lending. In this context, fintech companies need to take some precautions to effectively manage the security risk. For this purpose, the main risks to information technologies need to be clearly identified. Next, control steps should be put for these risks to be managed properly. Furthermore, it has been determined that the most appropriate strategy to increase the success of the fintech lending system is to increase the number of financiers integrated into the system. Within this framework, the platform should be secure and profitable to persuade financiers.
Prescribing pattern of anti-psychotic medications in patients with dementia in Oman: a retrospective observational study
Authors: Al-Rashdi Zainab , Al-Mahrouqi Tamadhir , Al-Shamli Siham , Panchatcharam Sathiya , Al-Busaidi Fatema , Al-Afani Reem , Al-Balushi Naser , Al-Sinawi Hamed 
Published: January 2023

Abstract
Background
Aggression, agitation, psychosis, and sleep disturbances are common behavioral symptoms of people with dementia and they can be distressing for both individuals and their carers. Due to their potential side effects, antipsychotic medications are recommended only for severe behavioral and psychological symptoms of dementia (BPSD). This study explores the prevalence, patterns, and associated factors with antipsychotic drug use among patients with dementia attending geriatric psychiatry services at Sultan Qaboos University Hospital (SQUH). Using a retrospective cross-sectional design, this study examines antipsychotic use among elderly patients aged 60 years or older with dementia who attended geriatric psychiatry services from January 2020 to December 2021. The following information was solicited: socio-demographic factors, type and severity of dementia, presence of co-morbid medical or mental illness, the psychotropic medications prescribed, the anti-psychotic medication use, duration of use, and the indication of use were solicited as well. A multivariate logistic regression analysis was conducted.

Results
The total prevalence of anti-psychotic use among elderly patients with dementia was 56.6%, and among them, 59% were prescribed anti-psychotics for more than 2 years. Being female, having non-Alzheimer’s dementia, experiencing severe stages of dementia, and having other medical or mental co-morbid conditions were independent predictors of antipsychotic drug use (odds ratio [OR] =1.85, confidence interval [CI] =1.04–3.30; OR=2.77, C.I. 1.52–5.04; OR=4.47, C.I. 2.18–9.18; and OR=2.54, C.I. 1.11–5.78, respectively).

Conclusions
Antipsychotic medication use is prevalent among elderly patients with dementia in Oman. The results from this study will help the policymakers and psychiatrists in Oman to plan for the use of non-pharmacological strategies as the first line of management for BPSD.
Employing in silico investigations to determine the cross-kingdom approach for Curcuma longa miRNAs and their human targets
Authors: Saiyed Atiyabanu N. , Vasavada Abhay R. , Johar S. R. Kaid 
Published: January 2023

Abstract
Background
Plant elements and extracts have been used for centuries to treat a wide range of diseases, from cancer to modern lifestyle ailments like viral infections. These plant-based miRNAs have the capacity to control physiological and pathological conditions in both humans and animals, and they might be helpful in the detection and treatment of a variety of diseases. The present study investigates the miRNA of the well-known spice Curcuma Longa and its prospective targets using a variety of bioinformatics techniques.

Results
Using the integrative database of animal, plant, and viral microRNAs known as miRNEST 2.0, nine C. longa miRNAs were predicted. psRNA target service foretells the presence of 23 human target genes linked to a variety of disorders. By interacting with a variety of cellular and metabolic processes, miRNAs 167, 1525, and 756 have been found to be critical regulators of tumour microenvironment. SARS-cov2 and influenza A virus regulation have been connected to ZFP36L1 from miRNA 1525 and ETV5 from miRNA 756, respectively.

Conclusions
The current cross-kingdom study offers fresh knowledge about how to increase the effectiveness of plant-based therapies for disease prevention and serves as a platform for in vitro and in vivo research development.

Graphical abstract