bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pharmacological network-based study on interventional mechanism of Baitouweng Decoction for treatment of colitis-associated cancer
Authors: Cao Qianqian , Zhang Kaiyu , Yao Dan , Chen Peiyao 
Published: December 2023

Abstract
Background Baitouweng Decoction, a traditional Chinese medicine formula prescribed for the treatment of colitis-associated cancer, has shown promising efficacy. However, the bioactive components and mechanisms remain unclear.
Methods Obtaining the components included in Baitouweng Decoction through the TCMSP, TCMID, TCMIP component database of traditional Chinese medicine (TCM) and combined with literatures. Predicting targets of the components included in Baitouweng Decoction through PharmMapper Server platform. Verifying relationship between the targets of Baitouweng Decoction and colitis-associated cancer by comparing the disease targets from GeneCards with chemotherapeutic molecular target of colitis-associated cancer from DrugBank; Building networks of "herb-component-target" and "component-target" by Cytoscape; Finally, analysing the pathway of Baitouweng Decoction in the treatment of colitis-associated cancer, which based on DAVID database.
Results Getting 98 components and 87 targets (including 12 key components and 11 main targets) from the "herb-component-target" network of Baitouweng Decoction in the treatment of Colitis-Associated Colorectal Cancer; KEGG pathway mainly involves Cancer pathways, prostate cancer, proteoglycans in cancer, PI3K-Akt signaling pathway, EGFR tyrosine kinase inhibitors, etc. GO are mainly related to oxygenate response, protein tyrosine kinase activity, cytoplasmic vesicles, etc. The results of molecular docking showed that limonin, candotoxin A and fraxin had good binding ability with HRAS, IGF1, MAP2K1and HSP90AA1.
Conclusions Analysing with literature reports and forecast result, Baitouweng Decoction can induce the progression of colitis-associated cancer and promote tumor cell apoptosis at multiple levels and in different ways by mediating EGFR and its downstream signal pathway.
The symptom cluster and core symptoms of early recovery in patients after esophageal cancer surgery: A network analysis
Authors: Ji YongZhi , Zhang Yunfang , Shi Ziyue , Wang Panpan , Chen Tingzi , Fan Zhibo , Jiang Enshe 
Published: December 2023

Abstract
Background
Patients with esophageal cancer, one month after surgery, undergo a transitional period before discharge, which may trigger a range of emotional and physical adjustments, including physical and psychological symptoms. Although current research examines individual symptoms in isolation, it is crucial to comprehend the relationships between symptoms and the core symptoms for effective symptom management.
Objective
Our study aims to describe symptoms in patients in the early stages of postoperative recovery from esophageal cancer, identify symptom clusters, and explore core symptoms and the relationship between symptoms.
Methods
This study was a cross-sectional investigation utilizing convenience sampling to select 281 postoperative esophageal cancer patients from two hospitals in Henan Province, China. A self-administered general information questionnaire and Anderson's Gastrointestinal Tumour Symptom Evaluation Scale were employed to survey the symptoms. Symptom clusters were extracted via exploratory factor analysis, and a symptom network was constructed using R. Network analysis was used to estimate correlations among symptoms.
Results
Our study identified difficulty swallowing(86.8%), pain (86.8%), and feeling of sad(83.3%) as the most prevalent symptoms. Four symptom clusters were extracted: the eating-related symptom cluster, the fatigue and sleep symptom cluster, the difficulty swallowing and psychological symptom cluster, and the digestive reconstruction symptom cluster. In the symptom network, feeling of sad (rs = 0.979) and fatigue (rs = 0.845) had the largest value of strength centrality.
Conclusion
Multiple symptoms and symptom clusters are apparent in patients in the early stages of postoperative recovery from esophageal cancer. Feeling of sad and fatigue are the core symptoms in patients in the early stages of postoperative recovery from esophageal cancer. Healthcare professionals can design accurate interventions based on these core symptoms, reducing the role of sadness and fatigue in the symptom network and improving patients' quality of life.
Cybersecurity Attack Detection using Gradient Boosting Classifier
Authors: Kumar N. Chaitanya , Sabeena Jasmine 
Published: December 2023

Abstract
In the rapidly evolving digital landscape, cybersecurity attacks have become increasingly sophisticated, posing monumental threats to organi- zations and individuals alike. Among the myriad of cyber threats, our focus in this paper is on detecting anomalies indicative of potential cy- ber attacks, specifically targeting network traffic. Detecting these attacks promptly and accurately is not just a technical challenge but a necessity to ensure data integrity, user trust, and operational continuity. This paper presents a comprehensive approach to detect such cybersecurity anoma- lies using the Gradient Boosting Classifier, a machine learning algorithm renowned for its predictive prowess. Our proposed solution encompasses advanced data preprocessing techniques, meticulous feature engineering, and rigorous model evaluation metrics. The applications of such a detec- tion system are vast, spanning across sectors like finance, healthcare, and e-commerce, acting as a bulwark against data breaches and unauthorized intrusions. The paper outlines our methodology, from data acquisition and preprocessing to modeling and evaluation, providing a blueprint for effective cyber attack detection.
Weaning protocol to reduce mechanical ventilation time in children admitted to pediatric intensive care units: Protocol for a Systematic Review and Meta-Analysis
Authors: Almeida Suzana Cristina , Souza Rayany Cristina , Azevedo Ingrid Guerra , Silva Ivanízia Soares da , Azevedo Vivian Mara Gonçalves de Oliveira 
Published: December 2023

Abstract

Background
Invasive Mechanical ventilation (IMV) is necessary for most Pediatric Intensive Care Units (PICU) patients. Although it is a complex process, weaning should be performed as soon as possible due to the adverse effects of IMV. This review aims to identify whether the use of a weaning protocol in a PICU, compared to usual care, can reduce the duration of IMV, length of stay in the PICU, mortality, and adverse events in children.
Methods
The strategy review and selective reports were developed using the population, intervention, comparison, outcome, and study design (PICOS) format. PUBMED, EMBASE, CINHAL, Web of Science, Cochrane Central Register of Controlled Trials, International Clinical Trials Registration Platform, and gray literature will be systematically searched for randomized controlled trials (RCTs). The studies’ methods should have been compared to protocol and nonprotocol weaning in children older than 28 days and younger than 18 years old, assisted at the PICU, and mechanically ventilated through an endotracheal tube. The risk of bias will be evaluated using the Cochrane Risk of Bias Tool for Randomized Trials. A meta-analysis will be conducted to compare the differences in the outcomes if at least two studies are sufficiently homogeneous concerning participants, interventions, and outcome measures. Subgroup analyses will also be performed looking for protocol type, indication for IMV, clinical condition, and age group differences.
Discussion
The results will synthesize the weaning protocol in a PICU and compare it to usual care to provide information to guide the pediatric intensivist therapist in weaning children from mechanical ventilation.
Systematic review registration: PROSPERO CRD42023399650.
A molecular T-pentomino for separating BTEX hydrocarbons
Authors: MacGillivray Leonard , Hartwick Christopher , Reinheimer Eric 
Published: December 2023

Abstract
The development of methods to separate molecules (e.g., petrochemicals) are exceedingly important industrially, particularly to purify fuels and polymer precursors.1 A common approach for separations is to crystallize an organic molecule that acts as a host by either providing an enforced covalent cavity (intrinsic cavity) or that packs inefficiently (extrinsic cavity).2 Here we report a self-assembled molecule with a shape that is highly biased to completely enclosed space and, thereby, pack efficiently yet has the property of hosting and allowing for the separation of BTEX hydrocarbons (i.e., benzene, toluene, ethylbenzene, xylenes).1 The components of the host are held together by N→B bonds and form a diboron assembly with a molecular shape that conforms to a T-shaped pentomino.3 A T-pentomino is a polyomino, which is a plane figure that tiles a plane without cavities and holes, and we show the T-shaped molecule to crystallize into one of six limited polymorphic structures for T-pentomino tiling.4 The separations of the BTEX hydrocarbons occur at mild conditions while rejecting similarly shaped aromatics such as xylene isomers, thiophene, and styrene. Our observation on the structure and tiling of the host to conform to a T-pentomino allows us to develop a theory on how novel synthetic molecules that mimic the structures and packing of polyominoes3 can be synthesized and - quite counterintuitively - developed into a system of hosts with cavities used for selective and useful separations.
Mechanical and morphological properties of cellulose nanocrystals synthesized from industrial hemp agro-waste
Authors: Heacock Jesse A. , Sun Yu , Li Yan Vivian 
Published: December 2023

Abstract
The rapid increase of industrial hemp growth in the US has resulted in a significant increase of hemp agro-waste, suggesting a need of counteracting the increasing agro-waste and promoting sustainable farming practice. One attractive solution is to treat hemp agro-waste with ammonium persulfate (APS), resulting in cellulose nanocrystals (CNCs) which are biofriendly and environmental-friendly alternatives to petroleum-based materials. However, most existing work on CNC extraction focuses on other cellulose sources such as cotton, wheat, and rice. There has been a lack of work on hemp, particularly hemp agro-waste using APS treatment. In this study, the one-step treatment was followed by purification to remove impurities and hence to colloidally stabilize CNCs in aqueous solutions. The resulting CNCs had an average length of 190 nm and average height of 4 nm. The mechanical analysis of individual CNCs using Force-Distance Spectroscopy suggested a Young’s modulus of 2.19 ± 0.15 GPa, maximum loading force of 6.29 ± 0.09 nN, and adhesion energy of 1.57 ± 1.12e-16 J. No statistical differences between purified and unpurified CNCs were found in Young’s modulus and maximum loading forces measurements, suggesting the impurities had minimum impact on mechanical strength. The results highlight hemp agro-waste as a valuable resource and the one-step APS treatment as an eco-friendly and efficient method to produce CNCs.
Causal relationship between gut microbiota and constipation: a two-sample Mendelian randomization study
Authors: He Nan , Li Guangzhao , Zhang Shenghuan , sheng kai 
Published: December 2023

Abstract
Background
As one of the most common gastrointestinal disorders, recent study has shown that dysfunction in the gut microbiota might lead to constipation. However, the causality between the gut microbiota and constipation is unclear.
Methods
Genome-Wide Association Studies (GWAS) used to obtain the summary-level data of constipation through IEU OpenGWAS database, and constipation was used as outcome. In addition, MiBioGen was used to gain the summary data of gut microbiota, including Ruminiclostridium 9, Intestinibacter, Anaerotruncus, Butyricimonas and Hungatella, which were used as exposure factors. Univariable Mendelian randomization (MR) analysis was used to evaluate the causality of gut microbiota on constipation. In briefly, Inverse-variance weighted (IVW) method was regarded as a main method to estimate the causality of gut microbiota and constipation, and supplemented by other four methods, including MR-egger, Weighted median, Simple mode and Weighted mode. Finally, funnel plot, heterogeneity test, horizontal pleiotropy test and leave-one-out test were used to evaluate the reliability of MR results.
Results
Ruminiclostridium 9 and Intestinibacter were causally associated with constipation and were the protective factors for constipation based on the MR analysis of IVW. The causal odds ratio (OR) values of Ruminiclostridium 9 and Intestinibacter were 0.75 (95% confidence interval (CI) 0.73–0.78; P < 0.001) and 0.89 (95% CI 0.86–0.93; P < 0.001) for constipation. Moreover, Anaerotruncus, Butyricimonas and Hungatella were also causally associated with constipation but were the risk factors for constipation. The OR values of Anaerotruncus, Butyricimonas and Hungatella were 1.08 (95% CI 1.02–1.13; P = 0.007), 1.07 (95% CI 1.01–1.13; P = 0.015), 1.03 (95% CI 1.00-1.06; P = 0.037) respectively. Furthermore, validation by funnel plot, heterogeneity test and horizontal pleiotropy test showed that MR results were reliable.
Conclusion
Ruminiclostridium 9, Intestinibacter, Anaerotruncus, Butyricimonas and Hungatella were identified as causalities of constipation, which provided a basis for understanding pathology of constipation and new insights into prevention and treatment.
Comprehensive pan-cancer analysis reveals clinical and immunological significance of ATP7A as a potential biomarker in hepatic carcinoma
Authors: Teng Luojun , Zhao Ruinan , Wang Weishan , Yao Guoxiang 
Published: December 2023

Abstract
Copper death has emerged as a potent tool in clearing cancer cells. The ATPase Copper Transporting Alpha (ATP7A) plays a pivotal role in in maintaining intracellular copper ion homeostasis, yet a comprehensive pan-cancer analysis of its molecular function and clinical relevance remains elusive. In this study, we systematically examined the expression levels of ATP7A across various malignancies using data from the TCGA database, delving into its expression patterns, prognostic significance, potential regulatory impact on the immune microenvironment, as well as its association with tumor mutation burden and microsatellite instability in a pan-cancer context. Our investigation revealed downregulation of ATP7A in colon cancer, ovarian cancer, and pancreatic carcinoma, while observing upregulation in liver hepatocellular carcinoma, lung adenocarcinoma, and glioblastoma. Furthermore, heightened expression of ATP7A was found to be linked to poorer prognosis in Kidney renal clear cell carcinoma and Brain Lower Grade Glioma. Notably, ATP7A demonstrated a positive correlation with immune scores in LGG, and conversely, exhibited a negative correlation with immune scores in bladder urothelial carcinoma, breast invasive carcinoma, lung squamous cell carcinoma, and thyroid carcinoma. Leveraging Cibersortx software for the calculation of immune cell infiltration scores using global gene expression profiles of patients, we observed a strong association between ATP7A expression levels and the abundance of tumor-infiltrating immune cells. Additionally, our analysis unveiled significant correlations between ATP7A expression and PDL1 expression, tumor mutation burden (TMB), and microsatellite instability (MSI), suggesting its potential as a biomarker for immune checkpoint blockade (ICB) therapy. In summary, our study presents an encompassing pan-cancer analysis of ATP7A, providing a foundational framework for ATP7A-based precision medicine strategies.
Pharmacovigilance study of Rucaparib based on the FDA Adverse Event Reporting System(FAERS)
Authors: Fangying Si , Ying Xue , Xiaojing Lu , Zhao Yin , zhang Du Shu 
Published: December 2023

Abstract
Rucaparib was approved for the treatment of ovarian and prostate cancers. The aim of the study was to assess rucaparib-related adverse events (AEs) through data mining using the US Food and Drug Administration Adverse Event Reporting System (FAERS).We analyzed adverse event (AE) reports in the FAERS between 2016 Q4 and 2022 Q2. Disproportionality analyses were performed during data mining to quantify the signals of rucaparib-related AEs. Of 13,638,847 reports collected from the FAERS database, 7436 reports of rucaparib related AEs were identified . A total of 95 preferred terms (PTs) with significant disproportionality in 11 system organ classes (SOCs) were retained. Unexpected significant AEs, such as small intestinal obstruction, intestinal mass, intestinal obstruction, decreased glomerular filtration rate, have been also reported. The median time-to-onset of rucaparib-associated AEs was 32 days (interquartile range [IQR], 15–88 days). Time-to-onset of acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS) were 525 and 522.5 days, for photosensitivity reaction and sunburn, time-to-onset were 44 and 62 days, and for neuropathy peripheral and taste disorder, time-to-onset were 49.5 and 60.5 days. Our study identified potential new AE signals that might provide important support for clinical monitoring of rucaparib, supporting its rational use in clinical practice.
Balancing Privacy and Explainability in Federated Learning
Authors: Teixeira Rafael , Almeida Leonardo , Rodrigues Pedro , Corona Julio , Antunes Mário , Aguiar Rui L. 
Published: December 2023

Abstract

As we advance towards future generations of communication networks, such as 6G, Artificial Intelligence (AI) and Machine Learning (ML) will assume an increasingly pivotal role in network optimization, management, and operation. In this context, the pursuit of reliability in ML models has emerged as a highly active area of research. Explainable AI (XAI) is an essential tool to unravel the underlying mechanisms of network behaviour, enabling a deeper understanding of the decisions made by black-box models in future-generation networks. This paper investigates the impact of Federated Learning (FL) on explainability by evaluating the correlation between the feature importance derived from models trained using four different FL approaches and the model trained using a conventional single-host approach. The analysis utilizes two publicly available datasets, two XAI metrics, and two correlation metrics. The findings reveal a high correlation between FL and single-host trained models in three of the four FL approaches, suggesting that some FL approaches failed to capture similar patterns.
Impact of directly acting-antivirals and behavior change due to the COVID 19 pandemic on HCV micro-elimination in MSM in Germany
Authors: Ingiliz Patrick , Lutz Thomas , Schewe Knud , Baumgarten Axel , Krznaric Ivanka , Mauss Stefan , Christensen Stefan , Bickel Markus , Schmidt Axel Jeremias , Sabranski Michael , He Feng , Jain Sonia , Martin Nastasha Kaleta , Rockstroh Jürgen K. , Boesecke Christoph 
Published: December 2023

Abstract
Introduction
Directly-acting antivirals (DAA) are the cornerstone to reach HCV elimination. In men who have sex with men (MSM) with HIV coinfection, recently acquired HCV infection (RAHCV) is common. Sexual practices and reinfection rates may hamper micro-elimination despite high treatment rates.
Methods
The cohort included MSM with RAHCV from 2014 to 2021. The patients’ demographic, clinical, behavioral, and laboratory data were documented, as well as treatment and reinfection outcomes.
Results
237 men with RAHCV were included, 216 (91%) were PLWH. Median age was 46 years (IQR: 39–52), median CD4 count was 660/mm3 (IQR: 527–835).
The annual incidence of RAHCV remained between 0.28% and 0.43%, but dropped to 0.02% in 2021 during the onset of the COVID-pandemic almost reaching micro-elimination. The reinfection incidence was 15.5 per 100 patient-years (95%-CI: 12.6-18.8), reinfection was associated with use of crystal methamphetamine (p=0.032) and ketamine (p=0.042). 31.3% had multiple reinfections, four reinfections occurred in PrEP users.
Conclusions
High treatment and cure rates did not lead to HCV elimination. A change in sexual behavior, potentially imposed by COVID-19 restrictions, led to micro-elimination in the NoCo cohort. As RAHCV is prevalent in HIV-positive and -negative MSM, surveillance is necessary to consolidate elimination goals.
How to customize Common Data Models for rare diseases: an OMOP-based implementation and lessons learned
Authors: Ahmadi Najia , Zoch Michele , Guengoeze Oya , Facchinello Carlo , Mondorf Antonia , Stratmann Katharina , Musleh Khader , Erasmus Hans-Peter , Tchertov Jana , Gebler Richard , Schaaf Jannik , Frischen Lena , Nasirian Azadeh , Dai Jiabin , Henke Elisa , Tremblay Douglas , Srisuwananuk Andrew , Bornhäuser Martin , Röllig Christoph , Eckardt Jan-Niklas , Middeke Jan Moritz , Wolfien Markus , Sedlmayr Martin 
Published: December 2023

Abstract

Background
Given the geographical sparsity of Rare Diseases (RDs), assembling a cohort is often a challenging task. Common Data Models (CDM) can harmonize disparate sources of data that can be the basis of decision support systems and artificial intelligence-based studies, leading to new insights in the field. This work is sought to support the design of large-scale multi-center studies for rare diseases.
Methods
In an interdisciplinary group, we derived a list of elements of RDs in three medical domains (endocrinology, gastroenterology, and pneumonology) according to specialist knowledge and clinical guidelines in an iterative process. We then defined a RDs data structure that matched all our data elements and built Extract, Transform, Load (ETL) processes to transfer the structure to a joint CDM. To ensure interoperability of our developed CDM and its subsequent usage for further RDs domains, we ultimately mapped it to Observational Medical Outcomes Partnership (OMOP) CDM. We then included a fourth domain, hematology, as a proof-of-concept and mapped an acute myeloid leukemia (AML) dataset to the developed CDM.
Results
We have developed an OMOP-based rare diseases common data model (RD-CDM) using data elements from the three domains (endocrinology, gastroenterology, and pneumonology) and tested the CDM using data from the hematology domain. The total study cohort included 61,697 patients. After aligning our modules with those of Medical Informatics Initiative (MII) Core Dataset (CDS) modules, we leveraged its ETL process. This facilitated the seamless transfer of demographic information, diagnoses, procedures, laboratory results, and medication modules from our RD-CDM to the OMOP. For the phenotypes and genotypes, we developed a second ETL process. We finally derived lessons learned for customizing our RD-CDM for different RDs.
Discussion
This work can serve as a blueprint for other domains as its modularized structure could be extended towards novel data types. An interdisciplinary group of stakeholders that are actively supporting the project's progress is necessary to reach a comprehensive CDM.
Conclusion
The customized data structure related our RD-CDM can be used to perform multi-center studies to test data-driven hypotheses on a larger scale and take advantage of the analytical tools offered by the OHDSI community.