BMC Research Notes最新文献

{"title":"The expression of the lncRNAs USP30-AS1, ELFN1-AS1, GAS8-AS1, and SNHG11 in breast cancer samples from Iranian patients from 2014 to 2019: a cross-sectional study.","authors":"Ghazal Orak, Zahra Orak Chahartangi, Zahra Nazeri, Fereshteh Ameli, Maryam Adelipour","doi":"10.1186/s13104-024-07069-z","DOIUrl":"https://doi.org/10.1186/s13104-024-07069-z","url":null,"abstract":"<p><strong>Objective: </strong>Breast cancer is a widely prevalent and life-threatening malignancy that affects women worldwide. The identification of novel molecular markers associated with tumor progression is highly important for enhancing early detection, tailoring treatment approaches, and monitoring therapeutic outcomes. In this study, we investigated the expression patterns of four long noncoding RNAs (lncRNAs): USP30 antisense RNA1 (USP30-AS1), ELFN1 antisense RNA1 (ELFN1-AS1), GAS8 antisense RNA1 (GAS8-AS1), and small nucleolar RNA host gene 11 (SNHG11).</p><p><strong>Results: </strong>In breast cancer specimens, USP30-AS1 and GAS8-AS1 expression was decreased, whereas ELFN1-AS1 and SNHG11 expression was increased in breast cancer tissues compared with adjacent noncancer tissues. Decreased USP30-AS1 levels were associated with a smaller tumor size, lower tumor grade and stage, and the absence of lymphatic and vascular invasion. Lower GAS8-AS1 expression was associated with a lower tumor grade and positive estrogen and progestin receptor status. Elevated ELFN1-AS1 expression was associated with breast cancer that lacked P53 mutation. These changes suggest their promise as biomarkers for distinguishing between cancerous and noncancerous tissues.</p>","PeriodicalId":9234,"journal":{"name":"BMC Research Notes","volume":"18 1","pages":"4"},"PeriodicalIF":1.6,"publicationDate":"2025-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142930640","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Isolation and characterization of ɸEcM-vB1 bacteriophage targeting multidrug-resistant Escherichia coli.","authors":"Rania Abozahra, Dina Shlkamy, Sarah M Abdelhamid","doi":"10.1186/s13104-024-07033-x","DOIUrl":"10.1186/s13104-024-07033-x","url":null,"abstract":"<p><strong>Objectives: </strong>The aim of this study is to screen for, isolate and characterize a bacteriophage designated ɸEcM-vB1 with confirmed lytic activity against multidrug-resistant (MDR) E. coli. Methods done in this research are bacteriophage isolation, purification, titer determination, bacteriophage morphology, host range determination, bacteriophage latent period and burst size determination, genomic analysis by restriction enzymes, and bacteriophage total protein content determination.</p><p><strong>Results: </strong>ɸEcM-vB1 bacteriophage exhibited high lytic activity against different MDR E. coli isolates and showed stability over wide pH and temperature range. It belongs to the Myoviridae family of the caudovirales order according to TEM. It had a latent period of 5 min and an average burst size of 271.72 pfu/cell. Genomic analysis revealed that it is susceptible to digestion by EcoRI. Ten structural proteins were detected by SDS-PAGE. ɸEcM-vB1 is considered a promising candidate for phage therapy applications.</p>","PeriodicalId":9234,"journal":{"name":"BMC Research Notes","volume":"18 1","pages":"3"},"PeriodicalIF":1.6,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11699686/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142926716","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 generic and dynamic measure of health-related quality of life across a variety of health and disease conditions: insights from healthy individuals and patients with a variety of diagnoses.","authors":"Mohamad Adam Bujang, Wei Hong Lai, Xun Ting Tiong, Alex Ren Jye Kim, Masliyana Husin, Yvonne Yih Huan Jee, Nurul Fatma Diyana Ahmad, Clare Hui Hong Tan, Khoo Sing Yee, Yoon Khee Hon, Cheng Hoon Chew, Eileen Pin Pin Yap, Fazalena Johari, Alan Yean Yip Fong","doi":"10.1186/s13104-024-07037-7","DOIUrl":"10.1186/s13104-024-07037-7","url":null,"abstract":"<p><strong>Objectives: </strong>Health-Significant Quality of Life Measure (Health-SigQOLM) provides a generic and dynamic assessment of Health-related quality of life (HRQOL). This study aims to assess the HRQOL among healthy and non-healthy participants with varying chronic diseases.</p><p><strong>Results: </strong>Comparisons between healthy and non-healthy participants revealed statistically significant differences (p < 0.001) in the mean overall HRQOL score as well as across all its nine domains. Therefore, the Health-SigQOLM, along with its nine domains, is demonstrated to have adequate sensitivity in distinguishing between healthy and non-healthy study participants. This had supported the evidence that the Health-SigQOLM is a reliable and valid scale for measuring both generic and dynamic HRQOL.</p>","PeriodicalId":9234,"journal":{"name":"BMC Research Notes","volume":"18 1","pages":"2"},"PeriodicalIF":1.6,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11697485/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142926715","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 effect of dexmedetomidine vs. atracurium on intubation condition in children - a randomized clinical trial.","authors":"Mohammad Alipour, Samira Ghanei, Shahrzad Sheikh, Masoud Ghanei, Ahmad Nemati, Shabnam Niroumand","doi":"10.1186/s13104-024-07072-4","DOIUrl":"10.1186/s13104-024-07072-4","url":null,"abstract":"<p><strong>Background: </strong>Using neuromuscular blocking agents (NMBA) in pediatric induction protocol is a challenging matter. Therefore, in this study, we aimed to find a safer way for anesthesia in children. We compared the effects of dexmedetomidine with atracurium on intubation conditions in children aged 6-12 years under general anesthesia. If dexmedetomidine has the similar effect as atracurium, we can use it for intubation and anesthesia of children in situations where the use of atracurium is challenging for any reason.</p><p><strong>Methods: </strong>This clinical trial was carried out on children between 6 and 12 years in Mashhad University of Medical Sciences, Mashhad, Iran between January 2018 and February 2020. Participants candidates for tracheal intubation and general anesthesia were enrolled. Patients were distributed into two groups: Patients received Dexmedetomidine (Group D) and patients received Atracurium (Group A).</p><p><strong>Results: </strong>We enrolled 25 patients in each group. Most of them were male. The intubation quality score consists of 5 items including laryngoscopy, vocal cord, coughing, jaw relaxation and limb movement was assessed between two groups. This score had no statistically significant difference between study groups. Immediately after induction and one minute after it, heart rate was statistically significant higher in group A than group D (P < 0.001 & P = 0.04 respectively). All of the intubations in our study were successful. More coughing was seen in group A compared with group D (P = 0.01).</p><p><strong>Conclusion: </strong>In children aged 6-12 years, the administration of intravenous dexmedetomidine 1mcg/kg over a period of 10 min before the induction of anesthesia with sufentanil 0.3 µg/kg and propofol 3 mg/kg showed no statistically significant difference in quality of intubation score when compared to the use of 0.5 mg/kg atracurium to facilitate intubation. Decreased heart rate and less coughing were observed when using dexmedetomidine. This trial was registered retrospectively in the Iranian Clinical Trials Registry at 2021-24-05 ( https://www.irct.ir/ ), and its registration number is IRCT20201028049177N1.</p>","PeriodicalId":9234,"journal":{"name":"BMC Research Notes","volume":"18 1","pages":"1"},"PeriodicalIF":1.6,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11694357/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142913585","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":"Comparison of baseline global gene expression profiles of prostate cancer cell lines LNCaP and DU145.","authors":"Khalid Ahmed, Zhannur Omarova, Alisalman Sheikh, Gulzhan Abuova, Kulsoom Ghias, Syed Hani Abidi","doi":"10.1186/s13104-024-07050-w","DOIUrl":"10.1186/s13104-024-07050-w","url":null,"abstract":"<p><strong>Introduction: </strong>DU145 and LNCaP are classic prostate cancer cell lines. Characterizing their baseline transcriptomics profiles (without any intervention) can offer insights into baseline genetic features and oncogenic pathways that should be considered while interpreting findings after various experimental interventions such as exogenous gene transfection or drug treatment.</p><p><strong>Methods: </strong>LNCaP and DU145 cell lines were cultured under normal conditions, followed by RNA extraction, cDNA conversion, library preparation, and RNA sequencing using the Illumina NovaSeq platform. The sequences were analyzed to identify differentially expressed genes (DEGs) and for gene ontology (GO) and pathway enrichment.</p><p><strong>Results: </strong>A total of 3916 and 2301 genes were found to be differentially upregulated and downregulated between LNCaP and DU145 cell lines, respectively. The GO and pathway analysis of up-regulated DEGs indicated significant enrichment of genes involved in extracellular matrix organization and cell-substrate adhesion, while down-regulated genes are involved in epithelial cell migration, cell death regulation, and cell proliferation.</p><p><strong>Conclusion: </strong>The results showed significant differences in baseline gene expression and cellular pathways that may account for the varying metastatic potentials between LNCaP and DU145 cell lines, which should be considered when interpreting findings after experimental interventions.</p>","PeriodicalId":9234,"journal":{"name":"BMC Research Notes","volume":"17 1","pages":"398"},"PeriodicalIF":1.6,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11689513/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142909306","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":"Reducing DNA extraction costs through factorial design for the DNAdvance Kit.","authors":"Carson J Neal, Zachery D Zbinden, Michael E Douglas, Marlis R Douglas","doi":"10.1186/s13104-024-07063-5","DOIUrl":"10.1186/s13104-024-07063-5","url":null,"abstract":"<p><strong>Objective: </strong>Extracting DNA is essential in wildlife genetic studies, and numerous methods are available. However, the process is costly and time-consuming for non-model organisms, including most wildlife species. Therefore, we optimized a cost-efficient protocol to extract DNA from the muscle tissue of White-tailed Deer using the DNAdvance kit (Beckman Coulter), a magnetic-bead-based approach. We devised a 3 × 3 factorial design using combinations of tissue mass (10 mg, 50 mg, or 100 mg) and reaction volume (25%, 33%, and 50% of the manufacturer's recommended volumes). DNA was extracted for N = 81 tissue sub-samples (9 replicates/treatment).</p><p><strong>Results: </strong>Our target yield was 500 ng of genomic DNA per sample, sufficient for population genetic assessments. A combination of 50 mg tissue and 25% reaction volume yielded enough DNA at the lowest cost. The factorial design revealed that varying tissue mass and reagent volume significantly affected extracted DNA yield. Our study demonstrates that sufficient DNA can be extracted at 75% lower costs than the manufacturer's standard protocol. Other researchers can directly use our modified DNAdvance protocol to perform cost-effective DNA extractions.</p>","PeriodicalId":9234,"journal":{"name":"BMC Research Notes","volume":"17 1","pages":"397"},"PeriodicalIF":1.6,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11684086/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142906546","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":"Seroprevalence of bovine Herpesvirus-1, bovine viral diarrhoea virus, Neospora caninum and Coxiella burnetii in dairy cows in Ethiopia.","authors":"Gebrerufael Girmay, Bezina Arega Emeru, Desiye Tesfaye Tegegne, Shelema Kelbesa Bora, Workitu Firomsa Gudeta, Betelhem Seyoum Dersso, Beksisa Urge Hurrisa, Gebremeskel Mamu Werid, Shimels Tikuye Yalew, Yohannes Equar Messele","doi":"10.1186/s13104-024-07059-1","DOIUrl":"10.1186/s13104-024-07059-1","url":null,"abstract":"<p><strong>Background: </strong>The reproductive problem is an animal health-related bottleneck that constrains livestock genetic improvement efforts in tropical countries such as Ethiopia. The infectious causes of reproductive disorders are one cause of decreased reproductive efficiency. This study aimed to determine the seroprevalence to Bovine Herpesvirus-1 (BHV1), Bovine Viral Diarrhea Virus (BVDV), Neospora caninum (N. caninum) and C. burnetii (C. burnetii) exposures in dairy cows with reproductive disorders in selected areas of Ethiopia. Overall, 164 serum samples were collected from October 2018 to May 2019 from animals with a history of reproductive disorders. The collected sera were tested for antibody titers to Brucella species, N. caninum, BVDV, BHV1, C. burnetii and Chlamydophila abortus (C. abortus) using Rose Bengal and ELISA.</p><p><strong>Results: </strong>The apparent seroprevalence of BHV1, BVDV, N. caninum and C. burnetii were 61%, 33.5%, 4.9% and 0.6%, respectively. Among the selected study areas, the mean apparent seroprevalence was significantly greater in Bishoftu (35.9%), Holeta (34.2%) and Adaberga (28.6%) than in Mekelle (9.9%) and Ambo (16.2%). Among the specific seroprevalence in specific areas, BHV1 was the most common in Adaberga, with an apparent seroprevalence of 92.9%. Similarly, the seroprevalence of BVDV was the highest in Holeta, with an apparent seroprevalence of 73.3%. On the other hand, no seropositive animal to Brucella spp. or C. abortus was found in these study areas.</p><p><strong>Conclusion: </strong>BVDV and BHV1 seroprevalence was higher in dairy cattle with a history of reproductive disorder in Ethiopia as compared to the seroprevalence of N. caninum and C. burnetii.</p>","PeriodicalId":9234,"journal":{"name":"BMC Research Notes","volume":"17 1","pages":"394"},"PeriodicalIF":1.6,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11684144/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142906622","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":"Factors associated with decision-making on fertility among rural women in the central district of Tamil Nadu.","authors":"Geetha Jeganathan, Sampath Kumar Srinivasan, Senthilkumar Ramasamy, Pitchaimani Govindharaj","doi":"10.1186/s13104-024-07054-6","DOIUrl":"10.1186/s13104-024-07054-6","url":null,"abstract":"<p><strong>Introduction: </strong>Fertility decision-making is an important factor affecting the Total Fertility Rate. Good communication between partners encourages shared decision-making and equal participation. Women's decision-making plays an important role in determining their reproductive health and fertility behaviour. Therefore, this study aimed to assess the decision-making of rural women on fertility.</p><p><strong>Methods: </strong>A household survey was conducted by using a multi-stage sample with 407 married women aged 18-45 years, having at least one child and living in Tiruchirappalli District, Tamil Nadu were recruited for this study. A semi-structured questionnaire was used to collect data about the demographic status and decision-making related to fertility.</p><p><strong>Results: </strong>Of the 407 participants, 70% were aged between 26 and 40 years, 73% were working as farmers and labourers and 77% were living in nuclear families. In decision-making on the usage of contraception, 25%, 27% and 27% of their decision were taken by themselves, their spouse, and both the participants and their spouse respectively. In spacing of childbirth, 53% took decisions concurrently with their husband. Among the participants, 40%, of their intake of food in the pre-and post-natal period was decided by them and 44% of women preferred the institutional delivery for childbirth by themselves.</p><p><strong>Conclusion: </strong>The study reveals that women tend to prefer sharing and involving their spouses in making decisions on fertility-related issues. Additionally, they exhibit greater support during the pre- and post-natal periods for women.</p>","PeriodicalId":9234,"journal":{"name":"BMC Research Notes","volume":"17 1","pages":"395"},"PeriodicalIF":1.6,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11684057/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142906490","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 characterization of 17 novel polynucleotide microsatellite markers in Ocypode stimpsoni (Decapoda: Ocypodidae).","authors":"Ha Yeun Song, Young Ji Choi, Dea-Sung Lee, Hyun Ki Choi, Kyung Min Choi, Kang-Yeol Yu, Namki Cho, Seungki Lee","doi":"10.1186/s13104-024-07049-3","DOIUrl":"10.1186/s13104-024-07049-3","url":null,"abstract":"<p><strong>Objective: </strong>The ghost crab Ocypode stimpsoni (Decapoda) is designated as a protected marine species in Korea due to its declining population. In this study, we successfully identified 17 microsatellite markers for O. stimpsoni through next-generation sequencing.</p><p><strong>Results: </strong>Out of the 63 loci examined, 26 were effectively amplified in a sample of 100 individuals. These 17 loci, comprising four tri-nucleotide and 13 tetra-nucleotide repeats, exhibited a range of 4 to 26 alleles per locus (with an average of 14.1 alleles) across 100 samples from three O. stimpsoni populations. The mean observed and expected heterozygosities were calculated to be 0.885 and 0.836, respectively. These 17 newly identified polymorphic microsatellite loci hold valuable utility for investigating the genetic structure and diversity of this protected marine species.</p>","PeriodicalId":9234,"journal":{"name":"BMC Research Notes","volume":"17 1","pages":"396"},"PeriodicalIF":1.6,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11684255/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142906494","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":"ERCPMP: an endoscopic image and video dataset for colorectal polyps morphology and pathology.","authors":"Mojgan Forootan, Mohsen Rajabnia, Ahmad R Mafi, Hamed Azhdari Tehrani, Erfan Ghadirzadeh, Mahziar Setayeshfar, Zahra Ghaffari, Mohammad Tashakoripour, Mohammad Reza Zali, Hamidreza Bolhasani","doi":"10.1186/s13104-024-07062-6","DOIUrl":"10.1186/s13104-024-07062-6","url":null,"abstract":"<p><p>This dataset contains demographic, morphological and pathological data, endoscopic images and videos of 191 patients with colorectal polyps. Morphological data is included based on the latest international gastroenterology classification references such as Paris, Pit and JNET classification. Pathological data includes the diagnosis of the polyps including Tubular, Villous, Tubulovillous, Hyperplastic, Serrated, Inflammatory and Adenocarcinoma with Dysplasia Grade & Differentiation.Objectives: Today the most important challenge of developing accurate algorithms for medical prediction, detection, diagnosis, treatment and prognosis is data. ERCPMP is an Endoscopic Image and Video Dataset for Recognition of Colorectal Polyps Morphology and Pathology. This dataset can be used for developing deep learning algorithms for polyps detection, classification, and segmentation.Data description: Images were captured with Olympus colonoscope and are presented in RGB format, JPG type with the resolution of 368 * 256 pixels and 96 dpi. The name of each file (image or video) includes pathological diagnosis, grade and JNet classification of the related polyp.</p>","PeriodicalId":9234,"journal":{"name":"BMC Research Notes","volume":"17 1","pages":"393"},"PeriodicalIF":1.6,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11682631/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142892413","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}