bluuebunny/crossref_metadata_2025_split huggingface dataset:
Refined Causal Association Between Physical Activity Intensity and Depression: A Comprehensive Two-sample Mendelian Randomization Study
Authors: Pang Jinyong , Wei Xilin 
Published: October 2024

Abstract

Depression remains a significant public health issue with high morbidity and mortality worldwide, making it crucial to investigate the role and causality of different types of physical activities in relieving depression. This study utilized a two-sample Mendelian randomization (MR) approach to evaluate the causal relationship between various physical activities, strenuous sports and walking for pleasure, and both general and major depression. We used summary statistics from large-scale genome-wide association studies involving European ancestry participants. Causal associations were estimated using the inverse-variance weighted model, with additional validation through extensive sensitivity analyses. Meta-analysis was conducted to comprehensively estimate the effects of multiple MR analyses. Results from single MR analyses and meta-analyses showed no significant causal effect of strenuous sports on depression (general depression: logOR=-0.1405, p = 0.2984; major depression: logOR = 0.0453, p = 0.9293). In contrast, walking for pleasure demonstrated a significant causal effect in reducing general depression (logOR=-0.5398, p = 0.0069) and major depression (logOR=-1.9786, p = 0.0103). Reverse MR analyses found no causal association between genetic liability to depression and the physical activities tested. Our findings underscore the significant role of walking for pleasure in alleviating and preventing both general and major depression. However, strenuous sports do not show a statistically significant causal effect. Further research is warranted to explore physical activities with intensities similar to walking for pleasure as potential preventive or rehabilitative measures in depression therapy, either alone or alongside psychotherapy or pharmacotherapy.
CAESAR: a cross-technology and cross-resolution framework for spatial omics annotation
Authors: Liu Jin , Liu Wei , Chai Xiaoran , Zhang Xiao , Lin Zhixiang 
Published: October 2024

Abstract

The biotechnology of spatial omics has advanced rapidly over the past few years, with enhancements in both throughput and resolution. However, existing annotation pipelines in spatial omics predominantly rely on clustering methods and lack the flexibility to integrate extensive annotated information from single-cell RNA sequencing (scRNA-seq) due to discrepancies in spatial resolutions, species, or modalities. Here we introduce the CAESAR suite, an open-source software package that provides image-based spatial co-embedding of locations and genomic features. It uniquely transfers labels from scRNA-seq reference data, enabling the annotation of spatial omics datasets across different technologies, resolutions, species, and modalities, based on the conserved relationship between signature genes and cells/locations at an appropriate level of granularity. Notably, CAESAR enriches for location-level pathways, allowing for the detection of gradual biological pathway activation within spatially defined domain types. We demonstrate the advantages of CAESAR through a comprehensive analysis of five spatial omics datasets encompassing diverse technologies, resolutions, and modalities. Across these applications, CAESAR achieved substantial improvements in annotation accuracy (45.45%-4333.33%) by transferring cell-type labels from either multiple reference data, or across different species and modalities. As a result, CAESAR effectively recovers intricate structures in mouse olfactory bulb and embryo, and unveils tumor microenvironment heterogeneity, with exceptional efficiency and flexibility.
Diets influence dependency on synthetic nitrogen fertilizers
Authors: Simon Wolfram , Zanten Hannah Van , Hijbeek Renske 
Published: October 2024

Abstract

Europe’s nitrogen (N) crisis demands innovative food systems solutions to improve N cycling. This study modelled the potential of different diets and circular fertilization strategies to enhance food system N use efficiency (NUE), reduce N surplus, and minimize reliance on synthetic N fertilizers. Results show that circularity helps to improve NUE and total N losses but does not consistently improve N surplus per ha. Synthetic N fertilizer could be reduced by 95% if healthy diets were consumed in circular food systems, increasing NUE from the current 0.17 to 0.53. The reduction of synthetic N fertilizer led to increased use of manure and showed considerable trade-offs with land use and greenhouse gas emissions (GHGe). In contrast, circular systems in which vegan diets were consumed showed the lowest land use and GHGe and a relatively high NUE (~ 0.3). This emphasizes the importance of considering trade-offs and synergies between different environmental impacts when redesigning food systems.
Risk factors, prognostic factors, and nomograms for liver metastasis in patients with stage T is -T 2 colorectal cancer: a population-based study
Authors: Lin Zejin , Yi Taijun , Zhong Chengrui , Liang Yongling , Mai Ziyan , Li Xingyu , Wan Yunle , Li Guolin 
Published: October 2024

Abstract

Background: Liver metastasis(LM) is the primary cause of mortality in patients with colorectal cancer. The incidence of liver metastasis in patients with stage Tis-T2 colorectal cancer is uncommon, and there is limited research available. While nomograms have been increasingly utilized in oncology, there is a lack of studies focusing on the diagnosis and prognostic assessment of liver metastasis in patients with stage Tis-T2 colorectal cancer.
Methods: The data of patients with stage Tis-T2 colorectal cancer diagnosed between 2010 and 2015 were extracted from the Surveillance, Epidemiology, and End Results (SEER) database. Univariate and multivariate logistic regression analyses were conducted to identify the independent risk factors for liver metastasis in patients with stage Tis-T2 colorectal cancer. Additionally, both univariate and multivariate Cox proportional hazards regression analyses were performed to determine the independent prognostic factors in patients with stage Tis-T2 colorectal cancer who had liver metastasis. Subsequently, two nomograms were developed and the results were assessed using receiver operating characteristic (ROC) curves, calibration curves, and decision curve analysis (DCA).
Results: A total of 1,1116 patients diagnosed with stage Tis-T2 colorectal cancer were studied, among whom 190 (1.71%) developed liver metastasis. The identified independent risk factors for liver metastasis in these patients included age, sex, primary tumor size, serum CEA levels, N stage, and histological type. Furthermore, sex, race, primary tumor size, serum CEA levels, and chemotherapy were found to be independent factors influencing the prognosis of patients with stage Tis-T2 colorectal cancer who developed liver metastasis. The accuracy of predicting the risk and prognosis of liver metastasis in these patients was confirmed through various analyses such as ROC curves, calibration curves, DCA curves, and Kaplan-Meier survival curves on both training and validation sets using two nomograms.
Conclusions: The two nomograms are considered effective tools for predicting the risk of liver metastasis in patients with stage Tis-T2 colorectal cancer, as well as predicting the prognosis of patients with liver metastasis.These tools can aid in clinical decision-making.
Prediction of précised biomarkers by expression-network-survival-based approach for breast cancer bone metastasis
Authors: Bhardwaj Mahima , Peele K. Abraham , Singh Sachidanand 
Published: October 2024

Abstract

Background: About 70% of Breast Cancer (BCa) patients have Bone Metastasis (BM), the prediction of précised biomarkers for BM from BCa would guide focused treatment by early interventions to prevent or delay BM.
Method: In this study, the datasets (GSE103357, GSE55715, GSE2034, GSE14776 and GSE137842) were retrieved from the Gene Expression Omnibus (GEO). These datasets comprise of gene expression patterns of 232 samples of tumor cells from BCa and 84 samples of metastatic tumor cells from BM to understand molecular mechanism underlying in development of BCa-BM. Common differentially expressed genes (DEGs) were identified by performing meta-analysis implying ImaGEO. A protein-protein interaction (PPI) network was constructed from high throughput experiments using STRING (Search Tool for the Retrieval of Interacting Genes). Analysis of the PPI-Interactome and their sorted hub genes was performed using centrality parameters viz., degree, clustering coefficient, closeness, and betweenness centrality which are statistically and biologically significant plug-ins added in Cytoscape 3.9.1. To understand the likely course of the progression of BCa to BM survival analysis was performed using GEPIA2 and validation was done by TCGA (The Cancer Genome Atlas). To characterize the précised potential biomarkers the functional enrichment analysis, Pathway analysis and Gene Ontology (GO) studies was performed by Funrich 3.1.3.
Result: 90 common DEGs were acquired from our study among all 5 datasets, out of which 28 and 62 constitute down- and up-regulated genes respectively. Where among these 90 DEGs, 18 genes were showing unambiguous connections with each other. 12 genes were identified significant through the topological analysis performed by the above said centrality parameters of interactome and were also showing worse survival outcome in disease free survival analysis. Five genes (RACGAP1, PPP1CC, RAD23A, PSMD1 and RPL26L1) among the 12 genes were identified as hub genes and were validated by TCGA, 3 genes (RPL26L1, PSMD1, and RAD23A) were identified to show poorer disease-free survival, also RPL26L1 was identified to show worst overall survival across all samples. 3 genes (RACGAP1, PPP1CC, and RAD23A) were literature reviewed potential diagnostic biomarkers in cancer progression, including breast cancer bone metastasis. RPL26L1 is significant potential biomarker identified with upregulation in BCa-BM samples with worse overall survival. These reported and significantly identified genes intersect notably cell growth, skeletal muscle development, and cell communication
Conclusion: Our expression-based network-based approach successfully prioritized précised biomarkers for breast cancer bone metastasis.
Functional validation of somatic variability in TP53 and KRAS for prediction of platinum sensitivity and prognosis in epithelial ovarian carcinoma patients
Authors: Allah Mohammad Al Obeed , Ali Esraa , Krus Ivona , Holý Petr , Haničinec Vojtěch , Ambrozkiewicz Filip , Rob Lukáš , Hruda Martin , Mrhalová Marcela , Kopečková Kateřina , Bartáková Alena , Bouda Jiří , Souček Pavel , Václavíková Radka 
Published: October 2024

Abstract

Background: Concerning the dismal prognosis of chemoresistant patients with epithelial ovarian carcinoma (EOC), we aimed to validate the findings of a previous whole exome sequencing study on 50 patients using an orthogonal Sanger sequencing method on the same patients and a separate set of 127 EOC patients (N=177).
Methods: We focused on TP53 as a frequently mutated gene relevant for chemosensitivity, included KRAS as an additional therapeutically relevant target, complemented study with transcript levels of both genes, and compared results with clinical parameters.
Results: All variants in TP53 and KRAS detected by exome sequencing were confirmed. KRAS mutated patients had significantly more frequently FIGO stages I or II (p=0.007) and other than high-grade serous tumor subtypes (nonHGSCs) (p<0.001), which was connected with lower KRAS transcript levels (p=0.004). Patients with nonHGSCs harboring TP53 missense variants disrupting the DNA binding loop had significantly poorer platinum-free interval than the rest (p=0.008). Tumors bearing nonsense, frameshift, or splice site TP53 variants had a significantly lower TP53 transcript level, while those with missense variants had significantly higher levels than wild-types (p<0.001). The normalized intratumoral TP53 and KRAS transcript levels were correlated, and three patients with both genes co-mutated had extremely poor survival.
Conclusions: Our study points to KRAS as a target for future therapy of nonHGSCs and reveals the prognostic value of TP53variants in the DNA binding loop.
Construction and verification of nomogram prediction model for non-suicidal self-injury in adolescents with depression
Authors: Gao Yuehong , Wang Yanchi , Chen Yun , Shi Jiajia , Mao Xiaoli , Wang Jinhong , He Jialu , Huang Hongmei , xu Xujuan Xu 
Published: October 2024

Abstract

Background
Accurate identification of adolescents with depression at high risk of non-suicidal self-harm and implementation of appropriate interventions are critical to reducing the risk of self-harm. This study used the nomogram technique to develop a predictive model for predicting non-suicidal self-injury (NSSI) behavior in adolescents with depression.
Methods
Convenience sampling was used to examine 596 adolescents with depression. Data from one hospital were used as training and internal validation sets (n = 455) and data from two other hospitals as external validation sets (n = 144). In the former, nine optimal predictors were identified by combining the results of one-way analysis, LASSO regression, and binary logistic regression. These predictors were used to construct a graphical column-line model of the NSSI. The receiver operator characteristic (ROC) curve, the area under the curve (AUC), the Hosmer-Lemeshow test, and calibration curves were used to test the discrimination and calibration of the training and internal and external validation sets of the predictive model, and decision curve analysis (DCA) was used to measure clinical applicability.
Results
Predictors included in the delivery model, history of peer NSSI, parental psychiatric history, sleep duration, social life events, self-esteem, psychological resilience, social support, and degree of depression (P < 0.05). The area under the ROC curve of the model was 0.880 (P < 0.001), and the Hosmer-Lemeshow test (χ2 = 7.19, P = 0.516), showed a maximum Jordan index of 0.668, a specificity of 0.765 and a sensitivity of 0.933. For clinical applicability analyses, the nomogram prediction model had a significant net gain for almost all risk threshold probabilities. In particular, there was a significant net gain for threshold probabilities of 0.1-1.0. Both internal and external validation of the model showed good discrimination, calibration, and clinical applicability.
Conclusion
The constructed nomogram risk prediction model performs well and can effectively predict the occurrence of NSSI in adolescents with depression, which is scientifically instructive and worthy of further promotion.
Effectiveness of tranexamic acid in reducing hidden blood loss during laparoscopic sleeve gastrectomy: a randomized clinical trial
Authors: Bieniaszewski Ksawery , Szymański Michał , Nowicki Piotr , Wilczyński Maciej , Bigda Justyna , Proczko-Stepaniak Monika 
Published: October 2024

Abstract

Introduction:
Obesity and its related metabolic complications are an increasing challenge for healthcare systems. Bariatric surgery is an effective treatment, but it is associated with potential adverse events, including postoperative bleeding. Enhanced Recovery After Bariatric Surgery (ERABS) protocols aim to reduce length of hospital stay, but they also reduce time for patients monitoring. Tranexamic acid (TXA), an antifibrinolytic agent, has shown promise in reducing bleeding in various surgeries, but its use in bariatric procedures remains under-researched. This study aims to evaluate the effectiveness of TXA in reducing postoperative bleeding following laparoscopic sleeve gastrectomy (SG).
Material and methods:
A single-center, single-blinded, randomized controlled trial was conducted at the University Clinical Center, Medical University of Gdańsk, Poland, between July 2022 and June 2023. A total of 238 patients undergoing SG were randomized to receive either TXA or no pharmacological intervention. The primary outcome was the haemoglobin concentration in abdominal drainage post-surgery. Secondary outcomes included total blood loss, drainage volume, need for blood transfusion, and postoperative complications. Statistical analysis was performed using intention-to-treat and per-protocol strategies.
Results:
A significant reduction in haemoglobin concentration in the drainage samples was observed in the TXA group (p=0.003). However, no significant differences were found in overall blood loss, drainage volume, necessity for blood transfusions or extended hospital stay between groups.
Conclusion:
TXA administration during SG reduces postoperative, abdominal bleeding as measured by haemoglobin concentration in abdominal drainage without affecting overall blood loss. These findings support further research into the routine use of TXA as part of the ERABS protocol in bariatric surgery. Further multicenter trials are needed to confirm the broader applicability and safety of TXA in this setting.
Trial registration: ClinicalTrials.gov (blinded).
Quantifying Uncertainty in Economics Policy Predictions: A Bayesian &amp; Monte Carlo based Data-Driven Approach
Authors: Rahaman Shafeeq Ur , Abdul Mahe Jabeen 
Published: October 2024

Abstract

Economic policy uncertainty relates to the unpredictability in government policies that can impact economic decision-making. High policy uncertainty can lead to less investment, slower economic growth, and increased volatility in financial markets. This study aims to quantify the uncertainty by employing a data-driven approach based on Bayesian Hierarchical Modeling (BHM) and Markov Chain Monte Carlo simulations. This research focuses essentially on key policy domains such as monetary policy, fiscal policy, and trade policy where uncertainty underlies crucial influences upon economic decisions. The methodology integrates data collection, feature scaling, normalization, Bayesian inference using MCMC simulations, uncertainty quantification and policy prediction to produce predictive insights under various economic scenarios. The Bayesian Hierarchical Model was employed to estimate the relationships between macroeconomic variables and policy outcomes. The posterior distribution results revealed significant predictors, with certain factors like monetary policy uncertainty exerting a substantial negative impact, while others such as equity market-related uncertainty showed positive influence. A rigorous uncertainty quantification step provided credible intervals for predicted outcomes with a 95% credible interval ranging between 0.276 - 0.359. This enabled an assessment of the potential variability in predictions based on differing levels of economic uncertainty. The study concluded with policy predictions generated under two distinct economic scenarios. Under conditions of high uncertainty, the predicted policy outcome was -0.2346, while a moderate uncertainty scenario resulted in a less negative outcome of -0.2060. These results demonstrate the sensitivity of economic policy predictions to varying levels of uncertainty. The findings provide a robust framework for understanding and quantifying uncertainty in economic policy-making. By applying BHM and Monte Carlo methods, this study contributes to the development of more resilient and adaptive economic strategies in the face of uncertainty.
Influence of the physiochemical parameters on the occurrence of E. coli bacteria in a small and shallow reservoir
Authors: Volf Goran , Sušanj Čule Ivana , Zorko Sonja 
Published: October 2024

ABSTRACT

The microbiological quality of water plays a crucial role in the relationship among human, animal, and environmental health. This research gives insight into the relationship between concentrations of Escherichia coli bacteria and physiochemical parameters in water, which is captured from the Butoniga reservoir and then used for treatment in the drinking water treatment plant Butoniga. Analysis was carried out using statistical analysis through the Pearson correlation coefficient and supported with PCA. The conducted analysis revealed that turbidity and Fe have the highest correlation coefficients with E. coli bacteria. Turbidity was also identified as a potential indicator for E. coli bacteria. Additionally, parameters such as Mn and UV 254 were also found to be closely related to E. coli bacteria, alongside turbidity and Fe. Furthermore, a relationship between E. coli bacteria and different water intakes was conducted. This shows that higher concentrations of E. coli bacteria were present when water was captured from lower water intakes, characterized by increased water turbidity. Thus, the research results provide important information on influential water quality parameters related to E. coli bacteria, especially in the Butoniga reservoir and related drinking water treatment plant, creating a foundation for future water quality management.
Modifiable Risk Factors Related to Oral Diseases in Youth Cuban Baseball Sportsmen
Authors: Méndez-Romero Jailín , Ríos-Garit Jesús 
Published: October 2024

Background
Oral health care closes the cycle of medical assistance integrated with sports, becoming a specialized service of great value in Cuba; however, oral diseases in young athletes are very frequent. For effective prevention, it is necessary to know the modifiable risk factors related to these diseases.

Objective
This study aimed to determine the relationship between risk factors and oral diseases in baseball sportsmen from the sports initiation school of Villa Clara, Cuba.

Material and Methods
A descriptive, correlational, and cross-sectional study was carried out in the young baseball athletes (N=60) of the 15U (n=30) and 18U (n=30) divisions (M=15.33; SD=1.49). Data were analyzed using empirical frequency distribution and descriptive statistics. Data normality was tested using asymmetry, kurtosis, and the Kolmogorov-Smirnov test. Mann-Whitney U test was used to determine differences in the risk factors and oral diseases between divisions, and the Tau_b Kendall correlation coefficient was used to determine relationships between both groups of variables.

Results
Improper tooth brushing, cariogenic diet, and inefficient oral hygiene were the main risk factors, while dental caries, gingivitis, and malocclusions were the oral diseases most notable. Athletes of higher division have greater toxic habits and a cariogenic diet; however, they brush more frequently and have more efficient oral hygiene. Except for the presence of malocclusions, the rest of the conditions are related to the determined risk factors.

Conclusion

The knowledge about the relationship between risk factors and oral conditions allows to base the design of educational intervention actions focused on the promotion of adequate oral health behaviors in the athletes, which shows the relevance of odontology in sports.
“It Doesn’t Make Sense”: Professional Skepticism As Sensemaking
Authors: Xu Gina , Yang Cherrie 
Published: October 2024

SUMMARY
Professional skepticism is a fundamental yet complex aspect of auditing. To understand how auditors exercise skepticism in practice, Xu, Yang, and Fukofuka (2023) conducted qualitative research based on stories provided by auditors. The study identified that professional skepticism is like a sensemaking process. It is triggered and unfolded through auditors’ actions and interactions with their audit teams and clients. These findings highlight the importance of understanding how auditors act, converse, and interact with clients to effectively exercise professional skepticism, which has important implications for auditing firms and practitioners.