bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide association study of glucocerebrosidase activity modifiers.
Authors: Somerville Emma N. , Krohn Lynne , Senkevich Konstanin , Yu Eric , Ahmad Jamil , Asayesh Farnaz , Ruskey Jennifer A. , Speigelman Dan , Fahn Stanley , Waters Cheryl , Sardi S. Pablo , Alcalay Roy N. , Gan-Or Ziv 
Published: June 2024

Abstract

One of the most common genetic risk factors for Parkinson’s disease (PD) are variants in GBA1, which encodes the lysosomal enzyme glucocerebrosidase (GCase). GCase deficiency has been associated with an increased PD risk, but not all individuals with low GCase activity are carriers of GBA1 mutations, suggesting other factors may be acting as modifiers. We aimed to discover common variants associated with GCase activity, as well as replicate previously reported associations, by performing a genome-wide association study using two independent cohorts: a Columbia University cohort consisting of 697 PD cases and 347 controls and the Parkinson’s Progression Markers Initiative (PPMI) cohort consisting of 357 PD cases and 163 controls. As expected, GBA1 variants have the strongest association with decreased activity, led by p.N370S (beta = -4.36, se = 0.32, p = 5.05e-43). We also identify a novel association in the GAA locus (encoding for acid alpha-glucosidase, beta = -0.96, se = 0.17, p = 5.23e-09) that may be the result of an interaction between GCase and acid alpha-glucosidase based on various interaction analyses. Lastly, we show that several PD-risk loci are potentially associated with GCase activity. Further research will be needed to replicate and validate our findings and to uncover the functional connection between acid alpha-glucosidase and GCase.
Evaluating the multifarious anti-cancer activity of Laos Kaempferia parviflora (black ginger) on human melanoma cell lines
Authors: Park Gyun Seok , Shin Juhyun , Hong Seongwoo , Saini Ramesh Kumar , Gopal Judy , Oh Jae-Wook 
Published: June 2024

Abstract

Cancer has become a consistent concern globally and has become increasingly fatal. Malignant melanoma is a rising concern, with its increased mortality. Kaempferia parviflora (KP) commonly known as black ginger is well known for its medicinal contributions.
Methods: For the first time, in the following study we have investigated the anti-melanoma potential of Laos KP extracts in human cell lines. KP extracts in methanol, DCM, ethyl acetate and hexane were tested against two melanoma cell lines. The Mu-2-related death-inducing gene (MUDENG, MuD) protein association with the KPE extracts were also investigated. The results showed that KPE enhanced apoptotic cells in the absence and presence of pan-caspase inhibitor Z-VAD-FMK. Interestingly, these apoptotic cells were significantly suppressed by the caspase inhibitor. Moreover, elevated Mitochondrial Membrane Potential (MMP) and intracellular reactive oxygen species (ROS) levels, suggestive of KPEs mitochondrial-mediated apoptosis in melanoma cells, were also confirmed. KPE treatment increased MMP levels, upregulated the generation of ROS in A375 cells but not in A2058 cells. However, pretreatment with an ROS scavenger (NAC) suppressed KPE-induced cell death and ROS generation. These results clearly pointed out to KPE-induced mitochondrial-mediated apoptotic cell death as the mechanism behind the inhibition of the human melanoma cells.
Balancing environmental sustainability with the social goals of scientific organisations: a ‘COM-B’ behaviour change strategy to reduce greenhouse gas emissions from international scientific conferences, meetings and educational events
Authors: Richards David , Bellon Filip , Goñi-Fuste Blanca , Grech Joseph , Hollowood Lorna , Mezzalira Elisabetta , Möhler Ralph , Perez-de-Gracia David , Seckin Muzeyyen , Velonaki Venetia , Teixeira-Santos Luísa , Deschodt Mieke 
Published: June 2024

Abstract

Objective
To estimate the environmental impact of two exemplar in-person academic events and, using the COM-B behaviour change framework of capability, opportunity, motivation, identify strategies that could be applied by organisers and participants to reduce this impact.
Methods
We calculated the greenhouse gas (GHG) emissions from two European PhD summer schools, one geographically peripheral and one central, organised by a European academic society, the European Academy of Nursing Science. We used participant distances from home university cities to the event sites to calculate individual GHG travel emissions. We incorporated on-site emissions into per-participant totals, and examined the relative contributions of travel and on-site factors to individual and total event emissions. We calculated the financial costs of individual participant attendance.
Results
Our exemplar events contributed between 41 tonnes and 99 tonnes CO2e emissions per event, a per-participant mean between 0.324, (SD 0.173) and 0.724, (SD 0.263) tonnes, representing 2 to 5.5 times the daily per-person European average. Distance from home was the largest contributor to emissions, with the peripheral event associated with 2.5 times the emissions of the central event, driven by aviation as flying was the only viable means to travel long distances. On-site emissions were no more than 26% of the total event emissions profiles. Costs were similar for both events.
Implications
Whilst organisers can provide participants with the opportunity to travel shorter distances and to sites where ground-based travel options are available, participants may not act on opportunities unless their capabilities and motivation are enhanced. We describe a behaviour change programme, structured using the COM-B model, that identifies strategies for organisers and participants to use to reduce the GHG emissions of academic events. A multi-component behavioural change programme including environmental change, enablement, education, incentivisation and persuasion is likely to be more successful than single strand approaches.
Molecular Dynamics Simulations Study: The Master Role of Solvation Free Energy for Topoisomerase Activity
Authors: dhar Murali , Vandana Km , pandey Vinayak , Tiwari Rakesh Kumar 
Published: June 2024

Abstract

Topoisomerase enzymes are vital players in DNA manipulation, crucial for maintaining its topological structure, and a cornerstone of molecular biology. Among these enzymes, Topoisomerase-IB (Topo-IB) has a unique role in relieving DNA torsional stress using phosphorylated tyrosine bonds (PTR), which are crucial for changing DNA topology. Our study, employing molecular dynamics simulations and diverse analytical tools, delves into the structural intricacies governing Topo-IB activity. Key to our findings is the discovery of Lysine 318 (Lys 318) within the core domain as a major contributor to Topo-IB's function. Lys 318's role in generating polar solvation energy crucially stabilizes enzymatic activity. Furthermore, we highlight the pivotal role of hydrogen bond dynamics in orchestrating Topo-IB's activity, showcasing the intricate interplay of molecular interactions during DNA manipulation. Overall, our study unveils the molecular mechanisms driving Topo-IB's function, spotlighting Lys 318 and hydrogen bond dynamics as central elements. These insights deepen our grasp of DNA topology modulation and offer promising avenues for developing pharmacological interventions targeting Topo-IB, with implications across various pathophysiological contexts.
A qualitative evaluation of the effectiveness of behaviour change techniques used in the Healthy Eating and Active Lifestyles for Diabetes (HEAL-D) intervention
Authors: Moore Amanda P , Rivas Carol , Harding Seeromanie , Goff Louise M 
Published: June 2024

Abstract

Background
Type 2 diabetes (T2D) is up to three times more common in people of Black African and Black Caribbean heritage living in the UK, compared to their White British counterparts. Structured education is the cornerstone of care but is less successful for people from minority ethnic groups. Healthy Eating and Active Lifestyles for Diabetes (HEAL-D) was developed to support diabetes self-management in people of Black African and Caribbean heritage living with T2D in the UK. The intervention was designed using COM-B/behaviour change wheel methodology to specify the theory of change. In a process evaluation study, we explored how the selected behaviour change techniques (BCTs) and components supported behaviour change in the intervention.
Methods
Focus groups and interviews were conducted with participants who were randomised to receive the HEAL-D intervention in a feasibility trial. A topic guide directed discussions to explore experiences of HEAL-D, key learnings and impact, and behaviour change; the interviews gave the opportunity to probe further the focus group themes and areas requiring clarification. Sessions were audio-recorded and transcribed. Framework analysis was used to explore how the selected BCTs supported behaviour change in those attending HEAL-D.
Results
Thirty-six participants took part in one or both activities (44% Black African, 50% Black Caribbean, 6% Mixed race; 61% female, 83% first-generation; mean age 59.5, SD 10.02). Participants reported increased physical activity, reduced carbohydrate portion size and engagement in weight monitoring behaviour. BCTs to increase social opportunity (social comparison, social support) and shift motivational barriers (credible sources and modelling) were effective in addressing cultural barriers around diet, stigma and health beliefs. BCTs to develop capability (demonstration, instruction, information on health consequences) were effective because of the cultural salience of the developed components. Less impactful BCTs were problem solving, graded tasks, goal setting, and feedback on outcomes.
Conclusions
BCTs identified in the development of the HEAL-D intervention were acceptable and effective, particularly useful were those promoting social opportunity as normative cultural habits and beliefs can conflict with diabetes self-management guidance. In addition, lifestyle interventions should include opportunity for experiential learning alongside culturally salient information provision.
Trial registration
number: NCT03531177; May 18th 2018
Risk factors for systemic inflammatory response syndrome after radical prostatectomy for prostate cancer: A prospective study
Authors: Chen Yu , Liao Chaoyu , Li Siyue , Zhou Luqiang , Zhu Jingzhen , Fu Weihua , Zheng Ji , Song Caiping 
Published: June 2024

Abstract

Aim
Exploring the risk factors for systemic inflammatory response syndrome in prostate cancer patients after radical surgery, establishing a risk warning model, and validating it.
Methods
A prospective selection was conducted on 309 patients who underwent radical prostatectomy in our hospital from March 2022 to March 2024. They were divided into two groups based on whether SIRS occurred after surgery: the SIRS group (n =46) and the non-SIRS group (n =263). Logistic regression analysis was performed on possible related factors to construct a column chart risk model. Internal validation of the column chart model for predicting postoperative SIRS was performed using the Bootstrap method with 1000 repeated samples.
Results
The results of multivariate logistic regression analysis showed that operative time, diabetes mellitusm, preoperative indwelling catheterization, urinary catheter retention time, pathologic diagnosis (OR ＞ 1, P ＜0.05). A column chart prediction model was established based on the risk factors affecting postoperative SIRS, and internal validation was performed using bootstrap method with 1000 repeated samples. The predicted values of the calibration curve were basically consistent with the actual values, and the Hosmer Lemeshow goodness of fit test was performed χ2 = 11.851, P = 0.158, the area under the ROC curve is 0.844 (95%CI: 0.792-0.897).
Conclusions
The occurrence of SIRS in prostate cancer patients after radical surgery is influenced by multiple factors, and the risk warning model established based on these factors has good predictive performance.
Pretransplantation risk factors for MRD after allogeneic stem cell transplantation in AML patients: A prospective study
Authors: Chang Ying-Jun , Li Si-Qi , Yu Chunzi , Xu Lan-Ping , Wang Yu , Zhang Xiao-hui , Chen Huan , Chen Yuhong , Wang Fengr-Rong , Sun Yuqian , Yan Chen-Hua , Lv Meng , Mo Xiao-Dong , Liu Yanrong , Liu Kaiyan , Zhao Xiaosu , Zhao Xiang-Yu , Huang Xiaojun 
Published: June 2024

Abstract

We aimed to explore the risk factors for measurable residual disease (MRD) positivity after allogeneic stem cell transplantation (allo-SCT) in AML patients. A total of 478 AML patients receiving allo-SCT were prospectively enrolled. The cumulative incidences of post-SCT MRD positivity at 100 days, 360 days and 3 years were 4.6%, 12.1% and 18.3%, respectively. Positive pre-SCT MRD was a risk factor for post-SCT MRD positivity at both 360 days and 3 years (P < 0.001). European LeukemiaNet (ELN) 2022 and 2017 risk stratification was a risk factor for positive post-SCT MRD at 100 days and 360 days (P = 0.020 and 0.047, respectively). A scoring system for predicting post-SCT MRD positivity at 360 days was established by using pre-SCT MRD and ELN 2017 risk stratification. The cumulative incidence of positive post-SCT MRD at 3 years was 13.2%, 23.6%, and 43.9% for patients with scores of 0, 1, and 2, respectively (P < 0.001). Multivariate analysis demonstrated that the scoring system was associated with a higher cumulative incidence of post-SCT MRD positivity, leukemia relapse and inferior survival. Our data indicate that positive pre-SCT MRD status, ELN 2022 risk stratification and 2017 risk stratification are independent risk factors for positive post-SCT MRD status in AML patients.
Pan-cancer analysis of Ischemic stroke-related innate immune genes screened by machine learning
Authors: Li Liang , Zhan Zhenrun , He Xiaoyuan , Zhao Tingting 
Published: June 2024

Abstract

Background
Ischemic stroke (IS), also known as acute cerebral infarction (ACI), is the most common clinical cerebrovascular disease. It is currently believed that the occurrence of IS has some genetic background factors, and the differential expression of several genes may affect the occurrence and prognosis of IS. In this study, we used bioinformatic big data analysis to screen IS-related differential genes and perform pathway and functional analysis. Pan-cancer analysis of hub genes was also performed.
Methods
The data of differentially expressed gene profiles in peripheral blood of IS patients and normal subjects were selected from GEO database, and the DEGs were screened. The screened differential genes were subjected to weighted gene co-expression analysis and machine learning calculations, and the obtained core genes were subjected to functional analysis. Finally, immune-related hub genes were analyzed for pan-cancer analysis.
Results
The GSE16561 dataset of 501 differentially expressed genes in IS patients and normal control population was then continued with WGCNA analysis to screen the core set of genes. They were analyzed for GO, KEGG, DO, and GSEA enrichment and were mainly enriched for bacterial infectious diseases, primary immunodeficiency diseases, lymphocyte differentiation and proliferation, monocyte differentiation, positive regulation of cell adhesion, T cell receptor signaling pathway, and hematopoietic cell lines. Next, SVM, LASSO and RF operations were performed to screen out hub genes and to analyze them for immune infiltration. Finally, pan-cancer analysis revealed that ID3 was associated with multiple cancer d prognosis and immune infiltration.
Conclusion
ID3 may be associated with IS occurrence and is expected to be a new target for IS prevention and treatment. Meanwhile, ID3 has also been found to be associated with the prognosis of various cancers, which may provide new ideas for future intervention and prognosis improvement of cancer progression.
Machine learning prediction of pathological complete response to neoadjuvant chemotherapy with peritumoral breast tumor ultrasound radiomics: compare with intratumoral radiomics and clinicopathologic predictors
Authors: Yao Jiejie , Zhou Wei , Jia Xiaohong , Zhu Ying , Chen Xiaosong , Zhan Weiwei , Zhou Jianqiao 
Published: June 2024

Abstract

Purpose
Noninvasive, accurate and novel approaches to predict patients who will achieve pathological complete response (pCR) after neoadjuvant chemotherapy (NAC) could assist precise treatment strategies. The aim of this study was to explore machine learning (ML)-based peritumoral ultrasound radiomics signature (PURS), compared with intratumoral radiomics (IURS) and clinicopathologic factors, for early prediction of pCR.
Methods
We analyzed 358 locally advanced breast cancer patients (250 in the training set and 108 in the test set), who accepted NAC and post NAC surgery at our institution. The PURS and IURS of baseline breast tumors were extracted by using 3D-slicer and PyRadiomics software. Five ML classifiers including linear discriminant analysis (LDA), support vector machine (SVM), random forest (RF), logistic regression (LR), and adaptive boosting (AdaBoost) were applied to construct radiomics models for the prediction of pCR. The performance of PURS, IURS models and clinicopathologic predictors were assessed with respect to sensitivity, specificity, accuracy and the areas under the curve (AUCs).
Results
For the PURS models, the RF classifier achieved better efficacy (AUC of 0.889) than LR (0.849), AdaBoost (0.823), SVM (0.746) and LDA (0.732) in the test set. For the IURS models, the RF classifier also obtained a maximum AUC of 0.931 than 0.920 (AdaBoost), 0.875 (LR), 0.825 (SVM), and 0.798 (LDA) in the test set. The RF-based PURS yielded higher predictive ability (AUC, 0.889; 95% CI: 0.814, 0.947) than clinicopathologic factors (AUC, 0.759; 95% CI: 0.657, 0.861; p < 0.05), but lower efficacy compared with IURS (AUC, 0.931; 95%CI: 0.865, 0.980; p < 0.05).
Conclusion
The peritumoral US radiomics, as a novel potential biomarker, may be a promising clinical approach to guide precise therapy decisions.
Diagnostic predictive model for distinguishing intravascular large B-cell lymphoma among patients with fever of unknown origin
Authors: Chen Chao , Di Yiao , Zhuang Zhe , Li Zepeng , Jia Congwei , Shi Ximin , Zhao Danqing , Wang Wei , Zhang Wei , Zhou Daobin , Zhang Yan 
Published: June 2024

Abstract

Intravascular large B-cell lymphoma (IVLBCL) is relatively rare. Due to the lack of distinctive symptoms, the diagnosis is difficult. Fever of unknown origin (FUO) is the most common symptom. This study retrospectively analyzed IVLBCL patients and FUO patients between February 2015 and October 2023. Diagnostic predictive models were constructed using multivariable logistic regression in the training cohort including 42 IVLBCL patients and 45 FUO patients. Model 1 consisted of peripheral edema, hypoxemia, neurological symptoms, hemophagocytic lymphohistiocytosis, and interstitial lung abnormalities on CT, exhibited good diagnostic efficiency (AUC = 0.928). Model 2 consisted of peripheral edema, hypoxemia, neurological symptoms and Interleukin-10/Interleukin-6 concentration ratio, showed a higher diagnostic ability than Model 1 (AUC = 0.982, p = 0.023). The diagnostic abilities of models were validated internally in leave-one-out validation and externally in the validation cohort. As some medical institutions may lack the capability to test for interleukin concentration, Model 1 can be used to help the diagnosis of IVLBCL in these institutions. Based on Model 1 and Model 2, we established and validated two integer-based scoring systems for clinical practice. Most patients (58%) were histologically diagnosed by random skin biopsy, and the positive rate of random skin biopsy was 79.5%.
Evaluation of Shell Powders of Bush Mango and Hamburger Bean as Eco-friendly Fluid Loss Control Additives in Drilling Mud
Authors: Nwiyoronu Kayii Joe , Onuoha Oriji , Chukunedum Onojake Mudiagha , Obuzor Gloria 
Published: June 2024

Abstract

Fluid loss within a permeable formation is one of the expensive problems encounter during drilling of a wellbore. Commercially available materials such as Hydroxyl Ethyl Cellulose (HEC), Polyanionic Cellulose (PAC), and Carboxyl Methyl Cellulose (CMC) are employed to minimize fluid loss but they are costly and cause increased viscosity when faced with high salinity and hardness. This study evaluate the application of shell powders of hamburger bean and bush mango as eco-friendly and cheap filtration control additives in water-based mud. Sixteen samples were formulated with different concentrations (5g, 10g, 15g and 20g) of the shell powders. The effect of the additives on the rheological property was determined. Filtration test was determined using API 13B-I LPLP filter press. Results obtained showed that 15g and 20g of Bush mango reduced fluid loss, while the mud samples with hamburger beans exhibited a progressive decrease in filtration rate as the hamburger bean content increased. Both Bush Mango and Hamburger Bean-based mud produced cake thickness between 1.2-1.8 mm. The overall result indicates that Hamburger bean provide effective filtration control than Bush mango.
The prevalence and susceptibility patterns of Multi-Drug Resistant Organisms in neurosurgical Patients: a retrospective analysis
Authors: Al-Mufargi Younis , Busaidi Fatma Al , Balushi Yasmine Al , Malki Teeba Al , Hamdani Marwa Al , Al-Saadi Tariq , Alkhatri Rajwa , Yazidi Thuraya AL , Saidi Sultan AL 
Published: June 2024

Abstract

Background
This study investigates the prevalence and susceptibility patterns of multidrug-resistant organisms (MDROs) causing post-neurosurgical meningitis in a region lacking prior data, emphasizing the importance of appropriate antimicrobial therapy in neurosurgical cases.
Methods and Study Design
: A retrospective study at Khoula Hospital (KH) in Oman analyzed medical records of 238 neurology and neurosurgery patients from January to December 2019. Data included patient demographics, diagnoses, antimicrobial resistance profiles, and hospital stay lengths, analyzed through statistical methods on SPSS software.
Results
The study found a MDRO prevalence rate of 26.1%, with the most common diagnosis being cerebrovascular diseases. High resistance rates were seen in various antibiotic classes. No significant associations were found between MDRO presence, hospital stay lengths, gender, or age. MDR alone was the most prevalent infection type.
Discussion
Antimicrobial resistance poses challenges in neurosurgical patients, highlighting the need for tailored treatment strategies. More research is needed to confirm these findings and guide clinical practices, but this study provides valuable insights into MDRO prevalence and resistance patterns in central nervous system conditions.