BMC Research Notes最新文献

{"title":"BED-Craft for nanopore adaptive sampling: a tool for generating bed files with gene names as input data for enrichment sequencing.","authors":"Fuyuki Miya, Kenjiro Kosaki","doi":"10.1186/s13104-025-07152-z","DOIUrl":"10.1186/s13104-025-07152-z","url":null,"abstract":"<p><strong>Objective: </strong>Adaptive sampling, a nanopore sequencing method that enriches regions of interest (ROI), is cost-effective and useful. However, the process of defining targeted regions and creating the corresponding definition file (.bed file) are time-consuming and laborious. To simplify this process, we have developed a tool to easily create a .bed file for adaptive sampling directly from gene names.</p><p><strong>Results: </strong>The tool is freely available on GitHub at https://github.com/medicalbioinfo/BED-Craft . The input is a text file containing one or more gene names (symbols), and even with a large number of input genes (e.g., thousands), the resulting .bed file is generated in less than a second. The length of the buffer region added upstream and downstream of the ROI is designed to account for genome strand orientation, ensuring efficient adaptive sampling. The buffer length can also be modified by the user. The tool supports the genomes of human hg19, hg38, T2T-CHM13, and other species. For researchers unfamiliar with command-line input, a GUI version of the tool is also available at https://keio-cmg.jp/BED-Craft/ . This easy-to-use .bed file generation tool enables adaptive sampling by easily changing the target genes of interest in nanopore sequencing, and provide great benefits to researchers and diagnostic laboratories.</p>","PeriodicalId":9234,"journal":{"name":"BMC Research Notes","volume":"18 1","pages":"79"},"PeriodicalIF":1.6,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11844088/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143472351","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}

{"title":"Identification and attribution of weekly periodic biases in global epidemiological time series data.","authors":"Kit Gallagher, Richard Creswell, David Gavaghan, Ben Lambert","doi":"10.1186/s13104-025-07145-y","DOIUrl":"10.1186/s13104-025-07145-y","url":null,"abstract":"<p><strong>Objective: </strong>COVID-19 data exhibit various biases, not least a significant weekly periodic oscillation observed in case and death data from multiple countries. There has been debate over whether this may be attributed to weekly socialising and working patterns, or is due to underlying biases in the reporting process. We investigate these periodic reporting trends in epidemics of COVID-19 and cholera, and discuss the possible origin of these oscillations.</p><p><strong>Results: </strong>We present a systematic, global characterisation of these weekly biases and identify an equivalent bias in the current Haitian cholera outbreak. By comparing published COVID-19 time series to retrospective datasets from the United Kingdom (UK), we demonstrate that the weekly trends observed in the UK may be fully explained by biases in the testing and reporting processes. These conclusions play an important role in forecasting healthcare demand and determining suitable interventions for future infectious disease outbreaks.</p>","PeriodicalId":9234,"journal":{"name":"BMC Research Notes","volume":"18 1","pages":"78"},"PeriodicalIF":1.6,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11844129/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143467041","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}

{"title":"A deep learning approach: physics-informed neural networks for solving a nonlinear telegraph equation with different boundary conditions.","authors":"Alemayehu Tamirie Deresse, Alemu Senbeta Bekela","doi":"10.1186/s13104-025-07142-1","DOIUrl":"10.1186/s13104-025-07142-1","url":null,"abstract":"<p><p>The nonlinear Telegraph equation appears in a variety of engineering and science problems. This paper presents a deep learning algorithm termed physics-informed neural networks to resolve a hyperbolic nonlinear telegraph equation with Dirichlet, Neumann, and Periodic boundary conditions. To include physical information about the issue, a multi-objective loss function consisting of the residual of the governing partial differential equation and initial conditions and boundary conditions is defined. Using multiple densely connected neural networks, termed feedforward deep neural networks, the proposed scheme has been trained to minimize the total loss results from the multi-objective loss function. Three computational examples are provided to demonstrate the efficacy and applications of our suggested method. Using a Python software package, we conducted several tests for various model optimizations, activation functions, neural network architectures, and hidden layers to choose the best hyper-parameters representing the problem's physics-informed neural network model with the optimal solution. Furthermore, using graphs and tables, the results of the suggested approach are contrasted with the analytical solution in literature based on various relative error analyses and statistical performance measure analyses. According to the results, the suggested computational method is effective in resolving difficult non-linear physical issues with various boundary conditions.</p>","PeriodicalId":9234,"journal":{"name":"BMC Research Notes","volume":"18 1","pages":"77"},"PeriodicalIF":1.6,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837485/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143457066","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}

{"title":"Hemoglobin phenotypes of children attending pediatric clinics in Lomé, Togo, 2022.","authors":"Yao Rodion Konu, Fiali Ayawa Lack, Oumarou I Wone Adama, Harold Régis Kouanfack, Kokou Herbert Gounon, Kokou François Sogbo, Kodzovi Mawulé Corcellar Womey, Ounoo Elom Takassi, Maléwé Kolou, Didier Koumavi Ekouevi","doi":"10.1186/s13104-025-07150-1","DOIUrl":"10.1186/s13104-025-07150-1","url":null,"abstract":"<p><strong>Objective: </strong>To provide an up-to-date data, we aim to estimate the frequency of sickle cell disease among children in the pediatric clinics of the Sylvanus Olympio University Hospital, Lome, Togo, in 2022.</p><p><strong>Results: </strong>A total of 317 children with a median age of 8 years (Interquartile range: 4-12) were included. Both parents knew their Hb phenotype in 7.3% of cases. Nineteen children had sickle cell disease (6.0%) and about 15.6% of the children had sickle cell trait AS. This study found a high frequency of children with sickle cell disease seen in pediatric clinics. We therefore emphasize the need for continued education to improve knowledge of the hemoglobin phenotype at community level and the importance of premarital screening to reduce this burden in the country.</p>","PeriodicalId":9234,"journal":{"name":"BMC Research Notes","volume":"18 1","pages":"76"},"PeriodicalIF":1.6,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837640/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143448369","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}

{"title":"Antiviral activity of silver nanoparticles against H1N1 influenza virus.","authors":"Manya Seyfi, Arash Letafati, Fahime Edalat, Somayeh Shatizadeh Malekshahi, Neda Pirbonyeh, Afagh Moattari","doi":"10.1186/s13104-025-07143-0","DOIUrl":"10.1186/s13104-025-07143-0","url":null,"abstract":"<p><strong>Background: </strong>Influenza virus is a significant cause of annual global respiratory disease and death. According to the limited availability of effective drugs and vaccines, innovative antivirals are currently being investigated as possible strategies to contain the spread of infectious agents. Among the various types of nanoparticles, silver nanoparticles (Ag-NPs) have attracted great interest due to their exceptional physicochemical properties. This study aims to investigate the antiviral activity of Ag-NPs against the influenza A virus (IAV)/H1N1.</p><p><strong>Methods: </strong>The MTT assay was used to determine the possible cytotoxicity of the Ag-NPs. Madin-Darby canine kidney (MDCK) cells were exposed to Ag-NPs extract in conjunction with 100 cell culture infectious dose 50% (CCID50) of virus administered at time intervals during the infection process. The antiviral activity of the extract was evaluated under pre-treatment, post-treatment, and simultaneous assay. Viral titer reduction was assayed using hemagglutination (HA) and CCID50 assays. Viral RNA relative quantification by real-time Polymerase Chain Reaction approach was performed in each experimental condition.</p><p><strong>Results: </strong>The study yielded significant findings regarding the inhibitory effects of Ag-NPs on the IAV/H1N1. Silver nanoparticles showed dose-dependent inhibition of the virus, with the strongest effect observed when administered simultaneously with the virus which the virus titer exhibited a substantial decrease from 5 Log10 in the control group to 1 Log10 in the initial samples, further reducing to 2 Log10 per milliliter at lower concentrations. Notably, Ag-NPs demonstrated a greater reduction in virus titer during the simultaneous stage, showing a statistically significant difference (P < 0.05) between the control and experimental groups). The reduction in viral titer was also evident in both pre- and post-inoculation stages, although the effects were different.</p><p><strong>Conclusion: </strong>Silver nanoparticles possess inhibitory effects on the growth of the IAV/H1N1, with a significant reduction in virus titer. These findings suggest the potential of Ag-NPs as effective antiviral agents and highlight opportunities for further research and potential clinical applications in combating IAV (H1N1) infections.</p>","PeriodicalId":9234,"journal":{"name":"BMC Research Notes","volume":"18 1","pages":"75"},"PeriodicalIF":1.6,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11834247/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143448425","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}

{"title":"The influence of genetic variants of IL-6 (-174 G/C) and INFγ (+ 874 A/T) and their impact on anemic Sudanese children with kidney failure.","authors":"Abier Abdelaziz Makkawi Abdelrahman Makkawi, Salah Eldin GumaaElzaki GumaaElzaki, Nahla Allam Allam, Nadia Madani Mohammed Ahmed Mohammed, Nazik Elmalaika Obaid Seid Ahmed Husain Husain","doi":"10.1186/s13104-025-07095-5","DOIUrl":"10.1186/s13104-025-07095-5","url":null,"abstract":"<p><strong>Objectives: </strong>To investigate the influence of genetic variants IL-6 (-174 G/C) and interferon-gamma (IFNγ) (+ 874 A/T) on beta-globin gene expression, inflammation markers such as C-reactive protein (CRP), and their diagnostic impact on anemic Sudanese children with kidney failure.</p><p><strong>Results: </strong>Severe and moderate anemia were observed in 88.9% of children aged 5-15 years. Semi-quantified molecular analysis of allele-specific genomic content (Lane%) revealed a correlation with disease severity. For interferon-gamma (+ 874 A/T), the AA genotype expressed the highest beta-globin gene Lane% value (5.22 ± 2.15), with beta-globin gene expression showing diagnostic utility at an area under the curve (AUC) of 0.646 (95% confidence interval (CI): 0.472-0.820). For IL-6 (-174 G/C), the CC genotype exhibited the highest Lane% value (5.82 ± 2.34), and Lane% content was more diagnostic compared to beta-globin gene expression, with an AUC of 0.715 (95% CI: 0.471-0.959). C-reactive protein showed significant diagnostic value as a marker of inflammation, with AUC values for interferon-gamma at 0.618 (95% CI: 0.443-0.793) and IL-6 at 0.663 (95% CI: 0.502-0.823). These findings highlight the role of IL-6 and interferon-gamma genetic variants in the severity of anemia and their diagnostic potential in children with kidney failure.</p>","PeriodicalId":9234,"journal":{"name":"BMC Research Notes","volume":"18 1","pages":"70"},"PeriodicalIF":1.6,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11831838/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143439991","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}

{"title":"Nationwide spatial epidemiological dataset of over 100,000 influenza-like illness notifications in Iran by county (2015-2019).","authors":"Atieh Sedghian, Shahab MohammadEbrahimi, Benn Sartorius, Behzad Kiani","doi":"10.1186/s13104-025-07139-w","DOIUrl":"10.1186/s13104-025-07139-w","url":null,"abstract":"<p><strong>Objectives: </strong>This data note documents influenza-like illness (ILI) notifications in Iran by county from 2015 to 2019 as a pre-COVID-19 dataset, providing individual and spatial data for further comprehensive spatiotemporal analysis. Due to the high contagion rate of ILI and global health impact, precise geographic mapping serves as a critical tool for public health officials and researchers to monitor, mitigate, and predict epidemics. By utilizing advanced spatial-temporal epidemiological analysis to study disease occurrence patterns, this geodatabase can enable a better understanding and more effective management of ILIs in the future.</p><p><strong>Data description: </strong>This is the most comprehensive dataset of all individual ILI notifications in Iran between 2015 and 2019 by date of notification and county (398 counties). The database includes two data files, a help file, and a data usage agreement: Data File 1 is an Excel (.xlsx) file detailing demographic and clinical information from 109,919 ILI notifications nationwide, covering county and date of notification, patient demographics, admission details, sample types, differential diagnosis, medical history, mortality details, test results, and symptoms. Data File 2 contains spatiotemporal information in polygon shapefiles (.shp), mapping ILI notification locations by county with data on case counts for each year, total population, gender distribution, and geographic coordinates.</p>","PeriodicalId":9234,"journal":{"name":"BMC Research Notes","volume":"18 1","pages":"72"},"PeriodicalIF":1.6,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11834186/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143440053","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}

{"title":"Assessment of antibiofilm and quorum quenching potencies of environmental bacteria in controlling biofilm of food spoilage bacteria.","authors":"Christine Charen, Diana Elizabeth Waturangi","doi":"10.1186/s13104-025-07141-2","DOIUrl":"10.1186/s13104-025-07141-2","url":null,"abstract":"<p><strong>Objectives: </strong>This research aims to investigate anti-quorum sensing and antibiofilm activity of supernatants from environmental bacteria against the biofilm formed by food spoilage bacteria such as Bacillus cereus, Bacillus subtilis, and Shewanella putrefaciens.</p><p><strong>Results: </strong>Supernatants were generated from ten environmental bacteria isolates (A19, A30, A32, A40, B10, B212, C1, J70, J73, and T152), with four isolates (A19, A32, A40, B212) showed anti-quorum sensing activity against Chromobacterium violaceum wild type as indicator bacteria. In inhibition and destruction assays, the highest percentage inhibition of 81.42% and 81.33% by B10 and B212, respectively, against B. cereus and J73 against B. subtilis was recorded at 87.45%. While A32, T152, and C1 performed the highest destruction against B. cereus, B. subtilis, and S. putrefaciens with percentages of 45.4%, 83.81%, 74.81%, respectively. Observation using light microscopy and Scanning Electron Microscopy (SEM) revealed C, O, Na, Mg, Al, Si, K, and Ca elements were detected which might play role in biofilm formation. Based on 16s rRNA sequencing, the environmental bacteria isolates were identified as Enterobacter, Acinetobacter, Acinetobacter, Pantoea genera, C1, and T152. These results imply that these bacteria have destructing and inhibiting potential against Bacillus cereus, Bacillus subtillis, Shewanella putrefaciens.</p>","PeriodicalId":9234,"journal":{"name":"BMC Research Notes","volume":"18 1","pages":"71"},"PeriodicalIF":1.6,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11834272/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143440045","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}

{"title":"Correction: Deriving GWAS summary estimates for paternal smoking in UK biobank: a GWAS by subtraction.","authors":"Benjamin Woolf, Hannah M Sallis, Marcus R Munafò, Dipender Gill","doi":"10.1186/s13104-024-06972-9","DOIUrl":"10.1186/s13104-024-06972-9","url":null,"abstract":"","PeriodicalId":9234,"journal":{"name":"BMC Research Notes","volume":"18 1","pages":"74"},"PeriodicalIF":1.6,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11834237/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143440048","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}

{"title":"Accuracy of anti-mycobacterial protein 51 antibodies as a biomarker for latent TB infection in asymptomatic HIV positive individuals: a cross-sectional diagnostic study.","authors":"Josephine Victo Namugga, Carol Musubika, Stuart Niwagaba, Jonathan Mayito, Obondo James Sande","doi":"10.1186/s13104-025-07134-1","DOIUrl":"10.1186/s13104-025-07134-1","url":null,"abstract":"<p><strong>Objective: </strong>To evaluate the diagnostic accuracy of anti-Mycobacterial Protein 51 (MPT51) antibodies in latent Tuberculosis (TB) detection among asymptomatic Human Immune Virus (HIV) positive individuals using Interferon Gamma Release Assay (IGRA) (QuantiFERON-TB Gold Plus) as the gold standard and determine the factors associated with anti-MPT51 antibody positivity among asymptomatic HIV positive individuals.</p><p><strong>Results: </strong>Considering QuantiFERON-TB Gold Plus as the gold standard, antibody reactivity to MPT51 revealed sensitivity of 32.6% (95% CI 24.5-40.6), specificity of 56.1% (95% CI 47.6-64.6), positive predictive value of 61.7% (95% CI 53.4-70.1) and negative predictive value of 27.7% (95% CI 20-35.4). Among the factors tested, none was independently associated with an increased risk of antibody reactivity against MPT51.</p>","PeriodicalId":9234,"journal":{"name":"BMC Research Notes","volume":"18 1","pages":"73"},"PeriodicalIF":1.6,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11834177/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143440031","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}