bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synthesis of causal and surrogate models by non-equilibrium thermodynamics in biological systems
Authors: Sakurada Kazuhiro , Ishikawa Tetsuo 
Published: October 2023

Abstract
There is no general way to describe the time evolution of life phenomena in terms of governing equations or physical laws. In biology, models of causal mechanisms and information processing have been used to explain life phenomena for which initial conditions, causes, and consequences are known. Recently, surrogate models of biological phenomena have been developed based on machine learning of large amounts of data, enabling highly accurate prediction of changes in the state of living systems. However, these surrogate models are black boxes. Therefore, the reliability and reproducibility of the models are abrogated by data bias. Biological systems form a multi-hierarchical structure from chromosomes to ecosystems, creating coherent order through the exchange of matter, energy, and messages. Messages have the force to change the state of the biological system. We have focused on this point and developed a signaling force field theory. Here, we show that this theory allows us to describe time-evolving phenomena in biological systems by synthesizing causal and surrogate models.
Insight into mRNA and its regulating pathways in the susceptibility and resistance to malaria infection by RNA sequencing
Authors: Kataria Poonam , Chaudhary Amrendra , Chauhan Rubika , Kalkal Meenu , Surela Neha , Das Jyoti , Das Emily 
Published: October 2023

Abstract
Background: Malaria is a severe febrile sickness transmitted by Plasmodium parasites. During murine malaria infection, the host immune response exhibits distinct variations in response to two strains of Plasmodium yoelii (P. yoelii 17XL and P. yoelii XNL), which are known to be associated with varying levels of parasite virulence and malaria severity. The study focuses on change in molecular mechanisms that regulate transcriptional activity as well as the gene networks involved in pathogenesis and defence during lethal and non-lethal malaria infections at different time points.
Methods: The gene expression profiles of mRNAs in control mice, Py.17XNL, and Py.17XL infected animals were evaluated using RNA sequencing and bioinformatics methods, and the differentially expressed mRNAs were validated using RT-qPCR. These DE mRNAs were identified as, cellular components, molecular functions, and biological processes utilizing Kyoto Encyclopaedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses.
Results: The results reveal several differentially expressed mRNAs that were associated with T-cell differentiation, cytokine receptor activity, and other related processes. Some of these genes, including Erfe, Hk1, and Podxl, are found to be significantly expressed in lethal infections, potentially contributing to increased parasitaemia and susceptibility.
Conclusion: This study provides significant insights into the gene expression patterns that may be used to investigate the molecular mechanisms of the host's response to both lethal and non-lethal malaria infections. These mechanisms are involved in both the pathogenesis of the disease and the immune defence against malaria infection.
Persistence of marine bacterial plasmid in the house fly (Musca domestica): marine-derived antimicrobial resistance genes have a chance of invading the human environment
Authors: Nawata Kanoko , Kadoya Aya , Suzuki Satoru 
Published: October 2023

Abstract
The house fly is known to be a vector of antibiotic-resistant bacteria (ARB) in animal farms. It is also possible that the house fly contributes to the spread of ARB and antibiotic resistance genes (ARGs) among various environments. We hypothesized that ARB and ARGs present in marine fish and fishery food may gain access to humans via the house fly. We show herein that pAQU1, a marine bacterial ARG-bearing plasmid, persists in the house fly intestine for 5 days after fly ingestion of marine bacteria. In the case of Escherichia coli bearing the same plasmid, the persistence period exceeded 7 days. This interval is sufficient for transmission to human environments, meaning that the house fly is capable of serving as a vector of marine-derived ARGs. Time course monitoring of the house fly intestinal microflora showed that the initial microflora was occupied abundantly with Enterobacteriaceae. Experimentally ingested bacteria dominated the intestinal environment immediately following ingestion; however, after 72 h, the intestinal microflora recovered to resemble that observed at baseline, when diverse genera of Enterobacteriaceae were seen. Given that pAQU1 in marine bacteria and E. coli were detected in fly excrement (defined here as any combination of feces and regurgitated material) at 7 days post bacterial ingestion, we hypothesize that the house fly may serve as a vector for transmission of ARGs from marine items and fish to humans via contamination with fly excrement.
Early Modulation of the Gut Microbiome by Female Sex Hormones Alters Amyloid Pathology and Microglial Function
Authors: Saha Piyali , Weigle Ian , Slimmon Nicholas , Blauth Pedro , Patel Priyam , Zhang Xiaogiong , Cao Yajun , Michalkiewicz Julia , Gomm Ashley , Zhang Can , Tanzi Rudolph , Dylla Nicholas , Al-Hendy Ayman , Sisodia Sangram 
Published: October 2023

Abstract
It is well-established that women are disproportionately affected by Alzheimer’s disease (AD). The mechanisms underlying this sex-specific disparity are not fully understood, but several factors that are often associated-including interactions of sex hormones, genetic factors, and the gut microbiome-likely contribute to the disease's etiology. Here, we have examined the role of sex hormones and the gut microbiome in mediating Aβ amyloidosis and neuroinflammation in APPPS1-21 mice. We report that postnatal gut microbiome perturbation in female APPPS1-21 mice leads to an elevation in levels of circulating estradiol. Early stage ovariectomy (OVX) leads to a reduction of plasma estradiol that is correlated with a significant alteration of gut microbiome composition and reduction in Aβ pathology. On the other hand, supplementation of OVX-treated animals with estradiol restores Aβ burden and influences gut microbiome composition. The reduction of Aβ pathology with OVX is paralleled by diminished levels of plaque-associated MGnD-type microglia while estradiol supplementation of OVX-treated animals leads to a restoration of activated microglia around plaques. In summary, our investigation elucidates the complex interplay between sex-specific hormonal modulations, gut microbiome dynamics, metabolic perturbations, and microglial functionality in the pathogenesis of Alzheimer's disease.
The Risk of Malnutrition and its Impact on Quality of Life in Head and Neck Cancer
Authors: Theurer Julie , Lynch Mark , Jovanovic Nedeljko , Doyle Philip 
Published: October 2023

Abstract
Objectives
Individuals with head and neck cancer (HNCa) are at an increased risk of malnutrition. Therefore, the use of self-administered, outpatient nutrition screens that seek information specific to nutritional concerns may yield benefits of identifying a need for intervention which may facilitate improved treatment outcomes and quality of life (QOL).
Methods
In this descriptive, cohort case series conducted at a tertiary care center, fifty participants (36 men, 14 women) completed one demographic and two QOL surveys, a nutrition assessment, two nutrition self-screening tools, and an ease-of-use questionnaire. Results obtained from nutrition screens were compared to those of the nutrition assessment. Additionally, the relationships between QOL, nutrition status, and demographics were examined.
Results
Thirty-two percent of participants were identified as nutritionally compromised. In this patient population, the sensitivity and specificity for the PG-SGA SF and Pt-Global Application were found to be 81.25% and 100%, and 68.76% and 100%, respectively. Additionally, alterations in nutrition status were associated with QOL.
Conclusions
Data suggest that self-administered nutrition screens may be a viable option which enable proactive identification of nutritional concerns associated with HNCa.
Decoding the Genetic Links Between Substance Use Disorder and Cancer Vulnerability
Authors: Su Xin , Mo Xiaoyan , Kan Jun , Zhang Bei 
Published: October 2023

Abstract
Background
Cancer is a leading cause of mortality and morbidity globally and burdens public health heavily. Cannabis and opioids are promising applications for cancer pain management. However, due to their widespread abuse and addiction potential, they have become the focus of public health attention. They may have critical long-term health effects, raising concerns about their possible association with cancer risk. However, their relationship with cancer vulnerability is highly controversial. This Mendelian randomization (MR) study aimed to investigate the causal relationship of cannabis use disorder (CUD) and opioids use disorder (OUD) on cancer vulnerability.
Methods
Two-sample MR study using summary statistics from genome-wide association studies (GWAS), FinnGen, and UK Biobank. The primary method was inverse-variance weighted (IVW), and we included a range of sensitivity analyses to assess the robustness of the findings.
Findings:
We found the IVW results showed a causal association between OUD and bladder cancer (OR = 1.040, 95% CI 1.004–1.078, P = 0.029, adj. P = 0.125), acute myeloid leukemia (OR = 0.931, 95% CI 0.885–0.978, P = 0.005, adj. P = 0.061) and ovarian cancer (OR = 0.937, 95% CI 0.891–0.984, P = 0.010, adj. P = 0.064). Sensitivity analysis is directionally consistent with IVW. In the reverse MR analysis, none of the methods produced statistically significant proof of a connection between OUD and three cancers (all P > 0.05). However, OUD did not prove a genetic causal relationship with other cancers (P > 0.05). We found no relevant evidence of a statistically significant potential causal effect of CUD on cancers (P > 0.05).
Summary: This study suggests that OUD may be causally linked to bladder, AML, and ovarian cancer, which needs to be further evaluated in extensive population studies.
Chronic intracranial recordings in the basal ganglia reveal patient-specific circadian rhythms in Parkinson's disease
Authors: de Hemptinne Coralie , Cagle Jackson , de Araujo Tiberio , Johnson Kara , Yu Jun , Fanty Lauren , Sarmento Filipe , Little Simon , Okun Michael , Wong Joshua 
Published: October 2023

Abstract

Adaptive deep brain stimulation (aDBS) is a promising therapeutic approach for subjects with Parkinson’s disease (PD) using neural signals as feedback control to adjust the level of therapy. However, the circadian fluctuation of neural signals may alter these control signals and possibly result in suboptimal therapy. We report a large retrospective cohort including 119 subjects with PD (165 hemispheres) with globus pallidus internus (GPi) and subthalamic nucleus (STN) activity recorded chronically in the home environment. Both GPi and STN activity was significantly altered by circadian rhythms. The direction of the circadian rhythm (increase versus decrease at night) depended on the frequency band in both the GPi and STN. The use of long-acting extended released dopaminergic medications significantly impacted the circadian rhythms in the GPi target. These findings demonstrate the variability of chronic circadian rhythms and suggest that aDBS will likely need to account for these patient-specific fluctuations to ensure successful implementation in real-world environments.
Nmu receptor of Siberian sturgeon (Acipenser baerii) and its role in food intake
Authors: Tang Ni , Kang Qin , Wu Hongwei , Li Yingzi , Yao Qin , Zhang Xin , Li Zhiqiong 
Published: October 2023

Abstract
Neuromedin U (NMU) exerts an annorexigenic role in mammals. In fish, only one study in gold-fish has identified neuromedin U receptors (NMURs), but the information about NMURs in ap-petite regulation is limited. To clarify the response mode of NMURs and the signal transduction pathway in NMU regulation of Feeding of Siberian sturgeon, the cDNA of nmur1 and nmur2 of Siberian sturgeon has been cloned and both of them are widely expressed in the 22 tissues ex-amined, especially higher in brain and gastrointestinal tract. Nmur1 and nmur2 were significant-ly upregulated after feeding. Long term fasting resulted in a significant downregulation of nmur1 in the hypothalamus, which returned to normal level after re-feeding, while the expres-sion pattern of nmur1 in the liver was completely opposite. In addition, after i.p. injection NMU-25, the nmur2 mRNA level significantly increased in hypothalamus and ileum. After i.c.v. injection NMU-25, the levels of nmur1 mRNA and nmur2 mRNA were significantly increased in the hypothalamus. NMURs of Siberian sturgeon can be activated by different nutritional states and are closely related to specific tissues and duration and the inhibitory effect of NMU-25 on appetite may be mediated jointly by NMUR1 and NMUR2 in the central nervous system, while in peripheral tissues, it may mainly be achieved through NMUR2. Our study, as a whole, laid the foundation for further exploring the molecular mechanism of NMU in appetite control in a fish model.
An Integrated Framework for Reference Site Selection and Benchmarking Soil Health Studies
Authors: Das Saurav , Hird Aaron , Maharjan Bijesh , Stephenson Mitchell , Kariyawasam Lithma 
Published: October 2023

Abstract

Comparative soil health studies are critical in soil conservation and gauging the success of different management practices in soil improvement. A primary challenge in these studies is the selection of a consistent natural reference site. Current choices vary widely, from minimally disturbed areas to pristine prairies. This methodological paper underscores the need for deliberate and thoughtful reference site selection for benchmark soil properties. Utilizing the State-and-transition models (STM), the study introduces a framework for this selection, drawing upon the ecological site (ES), and reference plant communities detailed in an ecological site description (ESD) within a respective Major Land Resource Area (MLRA). This study advocates for a localized classification within the framework of the Cropland Reference Ecological Unit (CREU), emphasizing the significance of local precipitation and soil data to ensure unbiased comparisons. Soil samples from eastern (MLRA106) and western (MLRA67A) Nebraska were collected, representing distinct pedogenetic and climatic differences. Analysis of SOM within an MLRA region displayed substantial variations, suggesting potential biases and complexities in soil health gap calculations when using reference sites and croplands not in the same MLRA, soil types (texture class), or precipitation zone. However, refining the comparisons by delineating MLRA, soil, and precipitation zones within the framework of CREU yielded more consistent and realistic comparative data. The integration of the MLRA and ES, complemented by granular soil and precipitation data provides a robust method for establishing soil health benchmark data.
Excessive cleavage of von Willebrand factor multimers by ADAMTS13 may predict progression of transplant-associated thrombotic microangiopathy
Authors: Matsumoto Masanori , Yamada Shinya , Sakai Kazuya , Kubo Masayuki , Hirokazu Okumura , Asakura Hidesaku , Miyamoto Toshihiro 
Published: October 2023

Abstract
Transplant-associated thrombotic microangiopathy (TA-TMA) is a fatal complication of hematopoietic stem cell transplantation (HSCT). Since little is known about multimer changes of von Willebrand factor (VWF) in TA-TMA, VWF-degradation product (DP) was analyzed to unravel the mechanism of change in the VWF multimer and disease course. This study enrolled 14 patients who underwent allogeneic HSCT at a single institute. VWF-associated markers were measured in blood samples collected every 7 days. There were two patients of definite TMA, and six patients that presented with probable TMA that did not progress to definite TMA. Each plasma sample was classified into three groups: definite TMA, probable TMA, and non-TMA. VWF multimer analysis showed the absence of high-molecular-weight (HMW)-VWF multimers in probable TMA, whereas the appearance of unusually-large VWF multimers was observed in definite TMA. The median value of the VWF-DP/VWF:antigen ratio in probable TMA was elevated to 4.17, suggesting that excessive cleavage of VWF multimers by VWF cleaving enzyme, ADAMTS13, resulted in the loss of HMW-VWF multimers. During the transition from probable to definite TMA, drastic VWF multimer changes imply a switch from bleeding to thrombotic tendencies. Extensive VWF-DP and VWF multimer analyses provided novel insights.
Assessing Urban Park Equity in Chaoyang District, Beijing using Online Review Data
Authors: Zou Ning , Mi Xiayuan , Xiao Yang , Li Yunyuan , Hu Nan 
Published: October 2023

Abstract
Urban parks are essential components of urban ecosystems, providing vital ecological resources for city residents. However, the rapid expansion of high-density urban areas has led to an unequal distribution of park resources, raising growing concerns about spatial equity. To address these challenges, we employed an improved Gaussian two-step floating catchment area (2SFCA) method, considering park quality variations and integrating sentiment scores from park reviews to calculate a comprehensive park accessibility index, accounting for both supply and demand dynamics among park users. The results demonstrate the significance of park management, as users prioritise convenience and cleanliness of public facilities. Recreational quality significantly influences park distribution equity, with areas near Beijing’s initial greenbelt zone showing improved accessibility (IA). Nonetheless, our analysis exposes disparities in urban park resource allocation within the Chaoyang District, indicating relative inequity. Spatial supply and demand mismatches, especially in the northwest and southeast, are evident. To enhance park layout equity, we recommend strategies like identifying and repurposing underused spaces, establishing pocket parks and micro-green areas, and improving recreational facilities. It is crucial to address the needs of vulnerable groups such as older residents and children. These insights stress the importance of ensuring fair urban park access to enhance the well-being of all city residents.
Non-linear relationship between pulse pressure and the risk of prediabetes： A 5-year cohort study in Chinese Adults
Authors: Huang Zhenhua , Wang Fangxi , Xiao Xiaoyong , Liu Dehong , Deng Zhe 
Published: October 2023

Abstract
Previous research has established a strong link between pulse pressure (PP) and diabetes, but there is limited investigation into the connection between PP and prediabetes. This study aims to explore the potential association between PP and prediabetes. A retrospective cohort study encompassed 202,320 Chinese adults who underwent health check-ups between 2010 and 2016. Prediabetes was defined in accordance with the World Health Organization (WHO) criteria, indicating impaired fasting glucose, with fasting blood glucose levels ranging from 6.1 to 6.9 mmol/l. To assess the PP-prediabetes relationship, we employed Cox regression analysis, sensitivity analysis, and subgroup analysis. Cox proportional hazards regression, coupled with cubic spline functions and smooth curve fitting, helped elucidate the non-linear PP-prediabetes relationship. Upon adjusting for confounding factors, we observed a positive association between PP and prediabetes (HR: 1.15, 95% CI: 1.11-1.18, P < 0.0001). Participants in the fourth quartile (PP ≥ 51 mmHg) had a 73% higher likelihood of developing prediabetes compared to those in the first quartile (PP < 36 mmHg) (HR: 1.73, 95% CI: 1.52-1.97, P < 0.0001). Moreover, the relationship between PP and prediabetes was non-linear. A two-piece Cox proportional hazards regression model identified an inflection point at 40 mmHg for PP (P for log-likelihood ratio test = 0.047). Sensitivity and subgroup analyses corroborated the robustness of our findings.Our study reveals a non-linear correlation between PP and prediabetes, signifying an increased risk of prediabetes when PP levels exceed 40 mmHg. This discovery has significant clinical implications for early prediabetes prevention and intervention, ultimately contributing to improved patient outcomes and quality of life.
Patients as teachers: a within-subjects randomized pilot experiment of patient-led online learning modules for health professionals
Authors: Ndjaboue Ruth , Beaudoin Caroline , Comeau Sandrine , Dagnault Anne , Dogba Maman Joyce , Numainville Sarah , Racine Charles , Straus Sharon , Tremblay Marie-Claude , Witteman Holly O. 
Published: October 2023

Abstract

Purpose: Many health professions education programs involve people with lived experience as expert speakers. Such presentations may help learners better understand the realities of living with chronic illness or experiencing an acute health problem. However, lectures from only one or a small number of people may not adequately illustrate the perspectives and experiences of a diverse patient cohort. Additionally, logistical constraints such as public health restrictions or travel barriers may impede in-person presentations, particularly among people who have more restrictions on their time. Health professions education programs may benefit from understanding the potential effects of online patient-led presentations with a diverse set of speakers. We aimed to explore whether patient-led online learning modules about diabetes care would influence learners’ responses to clinical scenarios and to collect learners’ feedback about the modules.
Method: This within-subjects randomized experiment involved 26 third-year medical students at Université Laval in Quebec, Canada. Participation in the experiment was an optional component within a required course. Prior to the intervention, participating learners responded to three clinical scenarios randomly selected from a set of six such scenarios. Each participant responded to the other three scenarios after the intervention. The intervention consisted of patient-led online learning modules incorporating segments of narratives from 21 patient partners (11 racialized or Indigenous) describing why and how clinicians could provide patient-centered care. Working with clinical teachers and psychometric experts, we developed a scoring grid based on the biopsychosocial model and set 0.6 as a passing score. Independent evaluators, blinded to whether each response was collected before or after the intervention, then scored learners’ responses to scenarios using the grid. We used Fisher’s Exact test to compare proportions of passing scores before and after the intervention.
Results: Learners’ overall percentage of passing scores prior to the intervention was 66%. Following the intervention, the percentage of passing scores was 76% (p = 0.002). Overall, learners expressed appreciation and other positive feedback regarding the patient-led online learning modules.
Discussion: Findings from this experiment suggest that learners can learn to provide better patient-centered care by watching patient-led online learning modules created with diverse patients.