BMC Research Notes最新文献_第6页

A dataset for machine learning-based QSAR models establishment to screen beta-lactamase inhibitors using the FARM -BIOMOL chemical library. 使用 FARM -BIOMOL 化学物质库筛选 beta-内酰胺酶抑制剂的基于机器学习的 QSAR 模型数据集。

IF 1.6

BMC Research Notes Pub Date : 2025-03-03 DOI: 10.1186/s13104-025-07159-6

Thanet Pitakbut, Jennifer Munkert, Wenhui Xi, Yanjie Wei, Gregor Fuhrmann

{"title":"A dataset for machine learning-based QSAR models establishment to screen beta-lactamase inhibitors using the FARM -BIOMOL chemical library.","authors":"Thanet Pitakbut, Jennifer Munkert, Wenhui Xi, Yanjie Wei, Gregor Fuhrmann","doi":"10.1186/s13104-025-07159-6","DOIUrl":"10.1186/s13104-025-07159-6","url":null,"abstract":"Objectives: Beta-lactamase is a bacterial enzyme that deactivates beta-lactam antibiotics, and it is one of the leading causes of antibiotic resistance problems globally. In current drug discovery research, molecular simulation, like molecular docking, has been routinely integrated to virtually screen an enzyme inhibitory effect. However, a commonly known limitation of molecular docking is a low percent success rate. Previously, we reported a proof-of-concept of combining machine learning with a quantitative structure-activity relationship (QSAR) model that overcame this limitation ( https://doi.org/10.1186/s13065-024-01324-x ). Here, we presented and navigated the dataset used in our previous report, including sixty trained models (thirty for random forest and another thirty for logistic regression).Data description: This data note has three essential parts. The first part is an in vitro beta-lactamase inhibitory screening of eighty-nine bioactive molecules. The second part consisted of three molecular docking approaches (AutoDock Vina, DOCK6, and consensus docking). The last part is machine learning integrated with QSAR models. Therefore, this data note is vital for further model development to increase performance.","PeriodicalId":9234,"journal":{"name":"BMC Research Notes","volume":"18 1","pages":"91"},"PeriodicalIF":1.6,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11877915/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143540193","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Regional soil salinity analysis using stepwise M5 decision tree.

IF 1.6

BMC Research Notes Pub Date : 2025-03-03 DOI: 10.1186/s13104-025-07097-3

Khalil Ghorbani, Soraya Bandak, Laleh Rezaei Ghaleh, Saeed Mehri, Aynaz Lotfata

{"title":"Regional soil salinity analysis using stepwise M5 decision tree.","authors":"Khalil Ghorbani, Soraya Bandak, Laleh Rezaei Ghaleh, Saeed Mehri, Aynaz Lotfata","doi":"10.1186/s13104-025-07097-3","DOIUrl":"10.1186/s13104-025-07097-3","url":null,"abstract":"Objective: The study aimed to evaluate the potential of multispectral satellite images in soil salinity assessment using linear multiple regression and the M5 decision tree regression method. Therefore, 96 soil samples were collected and correlated with 15 independent spectral information and Landsat 8 satellite image indices.Results: Due to the nonlinear relationship between EC and spectral bands, linear regression results were unsatisfactory, with the highest correlation coefficient of 58% and an RMSE of 0.78. The M5 decision tree regression model provided better results, with a correlation coefficient of 73% and an RMSE of 0.29 after establishing 9 regression relationships, successfully estimating the natural logarithm of EC. The B64, NDII, and S2 indices are the most influential in remotely sensed soil salinity estimation. Furthermore, the M5 model, utilizing six regression equations, demonstrates a 37.18% improvement in accuracy compared to a multivariate linear regression approach. Factors such as vegetation cover, soil moisture, and uneven moisture content of samples during collection contributed to errors in assessing soil salinity using satellite images.","PeriodicalId":9234,"journal":{"name":"BMC Research Notes","volume":"18 1","pages":"90"},"PeriodicalIF":1.6,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11877688/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143540195","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Morphological characteristics of microenvironment in the human thymus during fetal development.

IF 1.6

BMC Research Notes Pub Date : 2025-03-03 DOI: 10.1186/s13104-025-07109-2

Nemanja Maletin, Nikola Denda, Stefan Borocki, Zoran Golušin, Aleksandar Rašković, Aleksandra Fejsa-Levakov, Bojana Andrejić Višnjić, Jelena Amidžić

{"title":"Morphological characteristics of microenvironment in the human thymus during fetal development.","authors":"Nemanja Maletin, Nikola Denda, Stefan Borocki, Zoran Golušin, Aleksandar Rašković, Aleksandra Fejsa-Levakov, Bojana Andrejić Višnjić, Jelena Amidžić","doi":"10.1186/s13104-025-07109-2","DOIUrl":"10.1186/s13104-025-07109-2","url":null,"abstract":"Background: The thymus is a key organ for the development of T cells. T cell precursors first migrate from the bone marrow to the thymus. During maturation, these precursors require interactions with various types of cells that form the thymic microenvironment, such as epithelial, mesenchymal, and other immune cells not belonging to the T lineage. The aim of this study was to examine the changes in the number and diameter of Hassall's corpuscles, as well as the density and distribution of epithelial cells (p63+) and macrophages (CD68+).Methods: Twenty-five fetal thymus samples were examined, divided into five groups according to gestational age. The samples were processed using standard histological methods and immunohistochemical staining.Results: The study showed that the number and diameter of Hassall's corpuscles gradually increased during fetal development, with a significant increase from the 14th to the 38th gestational week. The average diameter of Hassall's corpuscles was largest in the age group of 34-38 weeks. The density of p63 + epithelial cells decreased in correlation with gestational week, while the density of CD68 + macrophages significantly increased, particularly in the thymic medulla, towards the end of the fetal period.Conclusions: An increase in the number and size of Hassall's corpuscles during fetal development was recorded, while the density of epithelial cells decreased and the density of macrophages increased.","PeriodicalId":9234,"journal":{"name":"BMC Research Notes","volume":"18 1","pages":"92"},"PeriodicalIF":1.6,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11877800/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143540194","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Language and racial disparities in treatment initiation for patients with pulmonary non-tuberculous mycobacteria.

IF 1.6

BMC Research Notes Pub Date : 2025-03-01 DOI: 10.1186/s13104-025-07126-1

Olabimpe Asupoto, Shamsuddin Anwar, Leo K Westgard, Majd Alsoubani, Tine Vindenes, Alysse G Wurcel

引用次数: 0

Nanopore sequencing-based genotyping suggested an association between CYP2D6 function and susceptibility to anxiety and depression. 基于纳米孔测序的基因分型表明，CYP2D6 功能与焦虑症和抑郁症的易感性之间存在关联。

IF 1.6

BMC Research Notes Pub Date : 2025-02-27 DOI: 10.1186/s13104-025-07156-9

Eng Wee Chua, Harsheni Karunanathie, Kevina Yanasegaran, Simran Maggo, Ping Siu Kee, Martin Kennedy, Mohd Rizal Abdul Manaf, Pei Yuen Ng

{"title":"Nanopore sequencing-based genotyping suggested an association between CYP2D6 function and susceptibility to anxiety and depression.","authors":"Eng Wee Chua, Harsheni Karunanathie, Kevina Yanasegaran, Simran Maggo, Ping Siu Kee, Martin Kennedy, Mohd Rizal Abdul Manaf, Pei Yuen Ng","doi":"10.1186/s13104-025-07156-9","DOIUrl":"10.1186/s13104-025-07156-9","url":null,"abstract":"Objective: CYP2D6 activity has been inconsistently associated with anxious and depressive personality traits. The inconsistency may stem from limitations of targeted genotyping, employed in most previous studies, leading to undetected errors in metabolic classification. Using a nanopore sequencing-based method, we comprehensively genotyped CYP2D6 alleles in a small cohort of 96 Malaysians and re-examined the relationship between CYP2D6 activity and susceptibility to anxiety and depression.Results: In keeping with prior studies, CYP2D6*10 was found to be the most common defective allele. Nearly half of the (48.5%) participants were classified as intermediate and poor metabolizers. Linear regression analysis suggested that impaired CYP2D6 activity could be a predictor of anxiety and depression, consistent with the putative role of CYP2D6 in the synthesis of serotonin and dopamine, the mood-boosting neurotransmitters. We hope this brief report will prompt larger-scale studies to further elucidate the contribution of CYP2D6 to the genetic underpinnings of mental well-being.","PeriodicalId":9234,"journal":{"name":"BMC Research Notes","volume":"18 1","pages":"88"},"PeriodicalIF":1.6,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11869584/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143522590","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Candida albicans cell-free extract against human gastric cancer; an in-vitro study.

IF 1.6

BMC Research Notes Pub Date : 2025-02-27 DOI: 10.1186/s13104-025-07081-x

Babak Pakbin, Shaghayegh Pishkhan Dibazar, Samaneh Allahyari, Faezeh Mohammadi, Reza Ovissipour, Amir Peymani, Arian Amirvaresi

{"title":"Candida albicans cell-free extract against human gastric cancer; an in-vitro study.","authors":"Babak Pakbin, Shaghayegh Pishkhan Dibazar, Samaneh Allahyari, Faezeh Mohammadi, Reza Ovissipour, Amir Peymani, Arian Amirvaresi","doi":"10.1186/s13104-025-07081-x","DOIUrl":"10.1186/s13104-025-07081-x","url":null,"abstract":"Objective: Yeast cell-free extracts and supernatants contain several compounds such as β-glucan, mannan, chitin, and mannoprotein with potent antitumor and other health-promoting activities. Candida albicans have been frequently and widely isolated from different habitats compared to other yeasts. The supernatant extracted from this yeast also contains β-glucan, chitin, and mannan compounds. This study investigates the anticancer, apoptosis-inducing, and downregulation of proinflammatory gene expression activities in normal and drug-resistant human stomach cancer cells (EPG and RDB cell lines) after 24 and 48 h treatment.Results: We found that Candida albicans supernatant-induced apoptosis suppressed the survivin gene expression in both cell lines and suppressed the expression of IL-8 and NF-ƙB genes in normal stomach cancer cells. IC50 for EPG cells were 1599 µg/mL and 1040 µg/mL after 24 and 48 h treatment, respectively; and for RDB cells were 877 µg/mL and 675 µg/mL after 24 and 48 h treatment, respectively. Consequently, this work suggests that Candida albicans supernatant can potentially protect against and treat human stomach cancer.","PeriodicalId":9234,"journal":{"name":"BMC Research Notes","volume":"18 1","pages":"87"},"PeriodicalIF":1.6,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11869586/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143522588","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Cubic non-polynomial spline on piecewise mesh for singularly perturbed reaction differential equations with robin type boundary conditions.

IF 1.6

BMC Research Notes Pub Date : 2025-02-26 DOI: 10.1186/s13104-025-07117-2

Bethelhem Esayas Ayele, Tesfaye Aga Bullo, Gemechis File Duressa

引用次数: 0

Buddhist temples as driving force of dementia-friendly society: a qualitative analysis of community-based integrated care in Buddhist temple caregiver cafés.

IF 1.6

BMC Research Notes Pub Date : 2025-02-26 DOI: 10.1186/s13104-025-07151-0

Chiaki Ura, Tsuyoshi Okamura, Akinori Takase, Yukan Ogawa, Ryosho Shoji

{"title":"Buddhist temples as driving force of dementia-friendly society: a qualitative analysis of community-based integrated care in Buddhist temple caregiver cafés.","authors":"Chiaki Ura, Tsuyoshi Okamura, Akinori Takase, Yukan Ogawa, Ryosho Shoji","doi":"10.1186/s13104-025-07151-0","DOIUrl":"10.1186/s13104-025-07151-0","url":null,"abstract":"Objective: Outside the Japanese government's community-based integrated care system, Buddhist temples are emerging as a resource to support caregivers of individuals with dementia living at home. However, we must critically analyze the views of secular professionals who are familiar with these activities. Thus, this study aimed to explore the characteristics and potential of caregiver cafés hosted in Buddhist temples from the perspective of healthcare and welfare professionals providing community-based integrated care by conducting two-step research: (1) a preliminary survey with Buddhist priests to understand the phenomenon; and (2) semi-structured interviews with staff providing community-based integrated care to explore its implementation.Results: According to 13 Buddhist priests who organized the caregiver cafés, most temples held cafés once every month or two, while all collaborated with the community-based integrated care system. A thematic analysis of semi-structured interviews of 15 healthcare and welfare professionals identified two major categories (\"temples as social resources\" and \"temples and priests leveraging their strengths\") and six subcategories from 143 discourses. The results indicated that temples and priests could be important social resources in community-based care systems by utilizing caregiver cafés in a society facing a shortage of care workers and an increasing number of individuals requiring care.","PeriodicalId":9234,"journal":{"name":"BMC Research Notes","volume":"18 1","pages":"85"},"PeriodicalIF":1.6,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11863499/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143514585","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identification of a novel transcript of mouse Sdha. 鉴定小鼠 Sdha 的新转录本。

IF 1.6

BMC Research Notes Pub Date : 2025-02-25 DOI: 10.1186/s13104-025-07149-8

María J Esteban-Amo, Amaia Telleria, Dino Gobelli, Pablo Serrano-Lorenzo, Juan J Tellería, María T Pérez-García, Piotr Kozlowski, Miguel Á de la Fuente, María Simarro

引用次数: 0

Chronic obstructive Pulmonary Disease (COPD) in non-smoking Sri Lankan adults; a cross-sectional study.

IF 1.6

BMC Research Notes Pub Date : 2025-02-25 DOI: 10.1186/s13104-025-07146-x

K D Gunasekera, Wadl Amarasiri, A R Wickremasinghe, Bpr Perera, Ucm Undugodage, A Fernando, Hkms Silva, A Sadikeen, W Gunasinghe

引用次数: 0