Methods and Protocols最新文献

筛选
英文 中文
Parasitological Examination of the Digestive System of Wild Boar from a Practical Point of View-Endoparasitological Sampling under Field Conditions. 从实用角度对野猪消化系统进行寄生虫学检查--野外条件下的寄生虫学取样。
IF 2.3
Methods and Protocols Pub Date : 2024-08-21 DOI: 10.3390/mps7040065
Csaba Farkas, Alexandra Juhász, Balázs Fekete, Borisz Egri
{"title":"Parasitological Examination of the Digestive System of Wild Boar from a Practical Point of View-Endoparasitological Sampling under Field Conditions.","authors":"Csaba Farkas, Alexandra Juhász, Balázs Fekete, Borisz Egri","doi":"10.3390/mps7040065","DOIUrl":"10.3390/mps7040065","url":null,"abstract":"<p><p>From 2015 to 2023, we conducted a comprehensive study in the 11,893-hectare hunting area managed by the Marcal-Bitvaközi Hunting Company, characterised by its substantial wild boar population. The research was carried out across various settings, including a free-range wild boar garden during large-scale hunts and free-living areas during individual hunts. We examined 216 wild boars in total, with 173 individuals from free-living areas and 43 from free-range areas. Throughout the sample collection process, we encountered numerous technical challenges that are infrequently detailed in the professional literature, often mentioned only tangentially. This oversight in existing publications neglects the significance of addressing field sampling difficulties, which are crucial for ensuring the precision and accuracy of research. This paper details the equipment requirements, sampling methodologies, and practical solutions to streamline fieldwork. While our primary focus was on endoparasitic infections of the stomach and small intestine, the described methodologies and findings are broadly applicable to research involving all internal organs.</p>","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11356853/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142080916","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
Full Validation and Application to Clinical Research of a High-Performance Liquid Chromatography Method for the Assessment of Urinary 3-Indoxyl Sulfate in Pediatric Patients with Hematopoietic Stem Cell Transplant. 用于评估小儿造血干细胞移植患者尿液中 3-吲哚硫酸酯含量的高效液相色谱法的全面验证及在临床研究中的应用。
IF 2.3
Methods and Protocols Pub Date : 2024-08-19 DOI: 10.3390/mps7040064
Christian Ezequiel Olivetti, María Florencia Fernández, Jana Stojanova, Silvina Ruvinsky, Andrea Mangano, Paula Schaiquevich
{"title":"Full Validation and Application to Clinical Research of a High-Performance Liquid Chromatography Method for the Assessment of Urinary 3-Indoxyl Sulfate in Pediatric Patients with Hematopoietic Stem Cell Transplant.","authors":"Christian Ezequiel Olivetti, María Florencia Fernández, Jana Stojanova, Silvina Ruvinsky, Andrea Mangano, Paula Schaiquevich","doi":"10.3390/mps7040064","DOIUrl":"10.3390/mps7040064","url":null,"abstract":"<p><p>3-indoxyl sulfate (3-IS) results from a hepatic transformation of indole, a tryptophan degradation product produced by commensal gut bacteria. The metabolite has shown promise as a biomarker of dysbiosis and clinical outcomes following hematopoietic stem cell transplant (HSCT) in adults. Nonetheless, there is a paucity of data regarding microbiome health and outcomes in the pediatric HSCT setting. We developed and thoroughly validated an affordable high-performance liquid chromatography/fluorescence detector (HPLC-FLD) method to quantify 3-IS in urine for use in the pediatric setting. Chromatographic separation was achieved on a C18 column (250 × 4.6 mm × 5 μm) with a mobile phase consisting of pH 4.0 acetic acid-triethylamine buffer and acetonitrile (88:12, <i>v</i>/<i>v</i>), eluted isocratically at 1 mL/min. 3-IS fluorescence detection was set at excitation/emission of 280 and 375, respectively. The method was fully validated according to FDA-specified limits including selectivity, linearity (0.10 to 10.00 mg/L, r<sup>2</sup> > 0.997), intra- and inter-day accuracy, and precision. 3-IS stability was confirmed after three freeze-thaw cycles, for short- and medium-term on a benchtop and at 4 °C and for long-term up to 60 days at -20 °C. The validated method was used to quantify 3-IS in urine samples from HSCT pediatric patients.</p>","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11357030/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142080915","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
A Mathematical Model of Pressure Ulcer Formation to Facilitate Prevention and Management. 压疮形成的数学模型有助于预防和管理。
IF 2.3
Methods and Protocols Pub Date : 2024-08-13 DOI: 10.3390/mps7040062
Ioannis G Violaris, Konstantinos Kalafatakis, Nikolaos Giannakeas, Alexandros T Tzallas, Markos Tsipouras
{"title":"A Mathematical Model of Pressure Ulcer Formation to Facilitate Prevention and Management.","authors":"Ioannis G Violaris, Konstantinos Kalafatakis, Nikolaos Giannakeas, Alexandros T Tzallas, Markos Tsipouras","doi":"10.3390/mps7040062","DOIUrl":"10.3390/mps7040062","url":null,"abstract":"<p><p>Pressure ulcers are a frequent issue involving localized damage to the skin and underlying tissues, commonly arising from prolonged hospitalization and immobilization. This paper introduces a mathematical model designed to elucidate the mechanics behind pressure ulcer formation, aiming to predict its occurrence and assist in its prevention. Utilizing differential geometry and elasticity theory, the model represents human skin and simulates its deformation under pressure. Additionally, a system of ordinary differential equations is employed to predict the outcomes of these deformations, estimating the cellular death rate in skin tissues and underlying layers. The model also incorporates changes in blood flow resulting from alterations in skin geometry. This comprehensive approach provides new insights into the optimal bed surfaces required to prevent pressure ulcers and offers a general predictive method to aid healthcare personnel in making informed decisions for at-risk patients. Compared to existing models in the literature, our model delivers a more thorough prediction method that aligns well with current data. It can forecast the time required for an immobilized individual to develop an ulcer in various body parts, considering different initial health conditions and treatment strategies.</p>","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11356783/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142080889","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
Evaluation of an Italian Population-Based Programme for Risk Assessment and Genetic Counselling and Testing for BRCA1/2-Related Hereditary Breast and Ovarian Cancer after 10 Years of Operation: An Observational Study Protocol. 意大利基于人口的 BRCA1/2 相关遗传性乳腺癌和卵巢癌风险评估、遗传咨询和检测计划运行 10 年后的评估:一项观察性研究计划。
IF 2.3
Methods and Protocols Pub Date : 2024-08-13 DOI: 10.3390/mps7040063
Stefano Ferretti, Priscilla Sassoli de Bianchi, Debora Canuti, Cinzia Campari, Laura Cortesi, Valentina Arcangeli, Elena Barbieri, Cecilia D'Aloia, Rita Danesi, Pierandrea De Iaco, Margherita De Lillo, Laura Lombardo, Gabriella Moretti, Antonino Musolino, Dante Palli, Caterina Palmonari, Mila Ravegnani, Alfredo Tafà, Alessandra Tononi, Daniela Turchetti, Claudio Zamagni, Valentina Zampiga, Lauro Bucchi, The Hboc Study Group
{"title":"Evaluation of an Italian Population-Based Programme for Risk Assessment and Genetic Counselling and Testing for BRCA1/2-Related Hereditary Breast and Ovarian Cancer after 10 Years of Operation: An Observational Study Protocol.","authors":"Stefano Ferretti, Priscilla Sassoli de Bianchi, Debora Canuti, Cinzia Campari, Laura Cortesi, Valentina Arcangeli, Elena Barbieri, Cecilia D'Aloia, Rita Danesi, Pierandrea De Iaco, Margherita De Lillo, Laura Lombardo, Gabriella Moretti, Antonino Musolino, Dante Palli, Caterina Palmonari, Mila Ravegnani, Alfredo Tafà, Alessandra Tononi, Daniela Turchetti, Claudio Zamagni, Valentina Zampiga, Lauro Bucchi, The Hboc Study Group","doi":"10.3390/mps7040063","DOIUrl":"10.3390/mps7040063","url":null,"abstract":"<p><p>Hereditary breast/ovarian cancer (HBOC) syndrome is caused by the inheritance of monoallelic germline BRCA1/2 gene mutations. If BRCA1/2 mutation carriers are identified before the disease develops, effective actions against HBOC can be taken, including intensive screening, risk-reducing mastectomy and salpingo-oophorectomy, and risk-reducing medications. The Italian National Prevention Plan mandates the creation of regional BRCA genetic testing programmes. So far, however, only informal data have been reported on their implementation. We have designed a study aimed at evaluating the results of a population-based programme for risk assessment and genetic counselling and testing for BRCA1/2-related HBOC that is underway in the Emilia-Romagna region (northern Italy). The programme-which is entirely free-includes basic screening with an estimate of the likelihood of carrying a BRCA1/2 mutation using a familial risk assessment tool, a closer examination of women with suspected risk increase, an assessment of the need for further genetic counselling and, if needed, genetic testing and risk-reducing interventions. In this paper, the design of the programme and the protocol of the study are presented. The study has an observational, historical cohort design. Eligible are the women found to be at an increased risk of HBOC (profile 3 women). The main objectives are (i) to determine the precision of the programme in measuring the level of risk of HBOC for profile 3 women; (ii) to determine the characteristics of profile 3 women and their association with the risk management strategy chosen; (iii) to compare the age at onset, histologic type, tumour stage, molecular subtype, and prognosis of breast/ovarian cancers observed in the cohort of profile 3 women with the features of sporadic cancers observed in the general female population; (iv) to determine the level and the determinants of adherence to recommendations; and (v) to determine the appropriateness and timing of risk-reducing surgery and medications. Investigating the quality and results of the programme is necessary because the best practices in risk assessment and genetic counselling and testing for BRCA1/2-related cancer and the challenges they encounter should be identified and shared. The study has the potential to provide sound empirical evidence for the factors affecting the effectiveness of this type of service.</p>","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11357531/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142080914","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
The Sri Lanka Mother and Newborn Growth (S-MaNGro) Cohort: Protocol of a Nationwide Prospective Study. 斯里兰卡母亲与新生儿成长(S-MaNGro)队列:全国性前瞻性研究协议。
IF 2.3
Methods and Protocols Pub Date : 2024-08-06 DOI: 10.3390/mps7040061
Malshani Lakshika Pathirathna, Megumi Haruna, Satoshi Sasaki, Kaori Yonezawa, Yuriko Usui, Yasuhiro Hagiwara
{"title":"The Sri Lanka Mother and Newborn Growth (S-MaNGro) Cohort: Protocol of a Nationwide Prospective Study.","authors":"Malshani Lakshika Pathirathna, Megumi Haruna, Satoshi Sasaki, Kaori Yonezawa, Yuriko Usui, Yasuhiro Hagiwara","doi":"10.3390/mps7040061","DOIUrl":"10.3390/mps7040061","url":null,"abstract":"<p><p>Perinatal cohort studies with a prospective longitudinal design are critical for determining the effects of early-life exposures on offspring's health outcomes. The Sri Lanka Mother and Newborn Growth cohort study aims to investigate the impact of maternal nutritional and psychosocial factors on newborns' birth weight in the Sri Lankan context. This paper presents the methodology of participant recruitment, follow-ups, an overview of measurements, and planned data analyses. This study included a nationally representative sample of Sri Lankan pregnant women recruited in their first trimester of pregnancy. Follow-up assessments were conducted once during the second and third trimesters of pregnancy and after the baby's birth, prospectively tracking the women's dietary intake, mental health, hemoglobin concentrations, and gestational weight gain data. Once the participants delivered their babies, the data on gestational age, sex of the newborn, birth weight, length and occipitofrontal circumference at birth, and mode of delivery were collected. Between August 2022 and August 2023, we recruited 2000 first-trimester pregnant women to the cohort and continued to follow up with them until the baby's birth. The response rates were 90.4%, 81.4%, and 75.2% in the first, second, and third follow-ups. We plan to analyze the data in July 2024. We expect this study to provide valuable insights into various early-life exposures affecting neonatal birth weight. The study's findings will serve as a valuable information resource for a broader scientific community, enabling the development of effective policies to prevent low-birth-weight deliveries in low-resource settings.</p>","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11356845/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142080919","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
Phytochemical Composition and Antimicrobial and Antibiofilm Effect of Myrciaria cauliflora Hydroethanolic Extract against Staphylococcus aureus and Acinetobacter baumannii. Myrciaria cauliflora 水乙醇提取物的植物化学成分及对金黄色葡萄球菌和鲍曼不动杆菌的抗菌和抗生物膜作用
IF 2.3
Methods and Protocols Pub Date : 2024-08-04 DOI: 10.3390/mps7040060
Luciane Dias de Oliveira, Ana Luisa Monteiro Ribeiro, Sthéfani de Oliveira Dias, Geovani Moreira da Cruz, Raquel Teles de Menezes, Lara Steffany de Carvalho, Mariana Gadelho Gimenez Diamantino, Thaís Cristine Pereira, Maria Cristina Marcucci, Amjad Abu Hasna
{"title":"Phytochemical Composition and Antimicrobial and Antibiofilm Effect of <i>Myrciaria cauliflora</i> Hydroethanolic Extract against <i>Staphylococcus aureus</i> and <i>Acinetobacter baumannii</i>.","authors":"Luciane Dias de Oliveira, Ana Luisa Monteiro Ribeiro, Sthéfani de Oliveira Dias, Geovani Moreira da Cruz, Raquel Teles de Menezes, Lara Steffany de Carvalho, Mariana Gadelho Gimenez Diamantino, Thaís Cristine Pereira, Maria Cristina Marcucci, Amjad Abu Hasna","doi":"10.3390/mps7040060","DOIUrl":"10.3390/mps7040060","url":null,"abstract":"<p><p><i>Staphylococcus aureus</i> and <i>Acinetobacter baumannii</i> are opportunistic pathogens, and both are involved in different oral infections. This work aimed to analyze the phytochemical composition of <i>Myrciaria cauliflora</i> hydroethanolic extract and to evaluate its antimicrobial and antibiofilm action against <i>Staphylococcus aureus</i> (ATCC 6538) and <i>Acinetobacter baumannii</i> (ATCC 19606; multi-resistant clinical strains 58004, 50098, 566006, and H557). <i>Myrciaria cauliflora</i> hydroethanolic extract was prepared, and the content of soluble solids, flavonoids, and phenols was quantified. High-performance liquid chromatography (HPLC) was performed later. The minimum inhibitory concentration was determined using the broth microdilution method according to the Clinical and Laboratory Standards Institute, standard M7-A6, and subsequently, its minimum bactericidal concentration was determined. Then, the most effective concentrations were analyzed against biofilms. Statistical analysis was performed using the ANOVA method with Tukey's test. The soluble solids content in the prepared hydroethanolic extract of <i>M. cauliflora</i> was 2.22%. Additionally, the total flavonoid content, measured using the quercetin standard curve, was 0.040 mg/mL. Furthermore, the total phenol content, determined using the gallic acid standard curve, was 0.729 mg/mL. HPLC analysis presented peaks of gallic acid (11.80 m), p-coumaric acid (12.09 m), cinnamic acid derivative (19.02 m), and ellagic acid (29.83 m). The extract demonstrated antimicrobial and antibiofilm action against all tested strains. However, the most effective antibacterial concentration against all the tested bacteria was 5.55 mg/mL. Therefore, these chemical components justify that <i>M. cauliflora</i> hydroethanolic extract is effective in reducing biofilm formation in <i>S. aureus</i> (standard strain) and <i>A. baumannii</i> (standard and clinical strains).</p>","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11357044/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142080917","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
Research on the Design and Performance of Plant Volatile Organic Compounds Water Removal Device Based on Optimized Filler Ratio. 基于优化填充率的工厂挥发性有机化合物脱水装置的设计与性能研究
IF 2.3
Methods and Protocols Pub Date : 2024-07-31 DOI: 10.3390/mps7040059
Yali Yuan, Huasen Wang, Zhihong Sun, Chao Yu
{"title":"Research on the Design and Performance of Plant Volatile Organic Compounds Water Removal Device Based on Optimized Filler Ratio.","authors":"Yali Yuan, Huasen Wang, Zhihong Sun, Chao Yu","doi":"10.3390/mps7040059","DOIUrl":"10.3390/mps7040059","url":null,"abstract":"<p><p>This study focuses on the development and optimization of a water removal device for biogenic volatile organic compounds (BVOCs) from plant emissions. BVOCs play a crucial role in various ecological processes and have potential therapeutic effects on human health. However, it is challenging to accurately detect and analyze BVOCs due to their very low concentrations and interference by water vapor. This study systematically evaluates different filler materials and ratios to alleviate water vapor interference while maintaining BVOCs' integrity. The experimental results demonstrate that the combination of MgSO<sub>4</sub> + Na<sub>2</sub>SO<sub>4</sub> mixed filling and CuSO<sub>4</sub> layered filling in a 3:3:1 ratio can effectively improve the collection efficiency and detection accuracy of BVOCs. Meanwhile, the effectiveness of the device in improving the detection of volatile compounds in plant samples is also confirmed by the VOC verification experiments on <i>Michelia maudiae</i> and <i>Cinnamomum camphora</i> tree species after mechanical damage. The experimental results show that the device is effective in improving the detection of volatile compounds in plant samples. The findings provide a powerful technical means for exploring the role of BVOCs in environmental monitoring and scientific research.</p>","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11357541/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142080918","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
A Multicenter, Single-Arm, Prospective Trial to Evaluate Efficacy and Safety of Dose-Dense Methotrexate, Vinblastine, Doxorubicin, and Carboplatin (DD-MVACarbo) Chemotherapy for Cisplatin-Ineligible Patients with Advanced Urothelial Cancer: Study Protocol of the CARBUNCLE Trial. 一项多中心、单臂、前瞻性试验,评估对符合顺铂条件的晚期尿路上皮癌患者进行剂量密集型甲氨蝶呤、长春新碱、多柔比星和卡铂(DD-MVACarbo)化疗的有效性和安全性:CARBUNCLE 试验研究方案》。
IF 2.3
Methods and Protocols Pub Date : 2024-07-29 DOI: 10.3390/mps7040058
Makito Miyake, Satoshi Anai, Yusuke Iemura, Kazuki Ichikawa, Tatsuki Miyamoto, Atsushi Tomioka, Masaomi Kuwada, Yoshitaka Itami, Yukinari Hosokawa, Yoshiaki Matsumura, Eijiro Okajima, Kazumasa Torimoto, Nobutaka Nishimura, Mitsuru Tomizawa, Takuto Shimizu, Shunta Hori, Yosuke Morizawa, Daisuke Gotoh, Yasushi Nakai, Kiyohide Fujimoto
{"title":"A Multicenter, Single-Arm, Prospective Trial to Evaluate Efficacy and Safety of Dose-Dense Methotrexate, Vinblastine, Doxorubicin, and Carboplatin (DD-MVACarbo) Chemotherapy for Cisplatin-Ineligible Patients with Advanced Urothelial Cancer: Study Protocol of the CARBUNCLE Trial.","authors":"Makito Miyake, Satoshi Anai, Yusuke Iemura, Kazuki Ichikawa, Tatsuki Miyamoto, Atsushi Tomioka, Masaomi Kuwada, Yoshitaka Itami, Yukinari Hosokawa, Yoshiaki Matsumura, Eijiro Okajima, Kazumasa Torimoto, Nobutaka Nishimura, Mitsuru Tomizawa, Takuto Shimizu, Shunta Hori, Yosuke Morizawa, Daisuke Gotoh, Yasushi Nakai, Kiyohide Fujimoto","doi":"10.3390/mps7040058","DOIUrl":"10.3390/mps7040058","url":null,"abstract":"<p><p>Unresectable, metastatic, advanced urothelial carcinoma (aUC) is an aggressive disease and is treated with platinum-containing first-line chemotherapy, followed by immune checkpoint inhibitors and antibody-drug conjugates. Response to first-line chemotherapy is a vital priority in sequential treatment strategies because a better response to first-line chemotherapy is associated with a better response to subsequent therapies. Gemcitabine plus carboplatin chemotherapy is conventionally recommended for cisplatin-ineligible patients. This multicenter, single-arm prospective trial will investigate whether dose-dense methotrexate, vinblastine, doxorubicin, and carboplatin (DD-MVACarbo) chemotherapy is superior to gemcitabine plus carboplatin chemotherapy in terms of efficacy in platinum-naïve, cisplatin-ineligible patients with aUC. After screening and registration, a total of 46 patients will be treated with this novel chemotherapy regimen. The primary endpoint is the objective response rate. The secondary endpoints include disease control rate, patient-reported outcomes, and adverse events. No evidence of this novel intervention is available as of July 2024. The results are expected to change the standard of care and improve the management of patients with aUC.</p>","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11356861/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142080890","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
A Protocol to Extract a Specific Genomic Region from a Public Whole-Genome Database and Modify Analytical Bin Length for Population Genetic Studies. 从公共全基因组数据库中提取特定基因组区域并为群体遗传研究修改分析区间长度的规程。
IF 2.3
Methods and Protocols Pub Date : 2024-07-27 DOI: 10.3390/mps7040057
Muhammad Shoaib Akhtar, Shoji Kawamura
{"title":"A Protocol to Extract a Specific Genomic Region from a Public Whole-Genome Database and Modify Analytical Bin Length for Population Genetic Studies.","authors":"Muhammad Shoaib Akhtar, Shoji Kawamura","doi":"10.3390/mps7040057","DOIUrl":"10.3390/mps7040057","url":null,"abstract":"<p><p>With the advent of \"next-generation\" sequencing and the continuous reduction in sequencing costs, an increasing amount of genomic data has emerged, such as whole-genome, whole-exome, and targeted sequencing data. These applications are popular not only in mega sequencing projects, such as the 1000 Genomes Project and UK BioBank, but also among individual researchers. Evolutionary genetic analyses, such as the dN/dS ratio and Tajima's <i>D</i>, are demanded more and more for whole-genome-level population data. These analyses are often carried out under a uniform custom bin size across the genome. However, these analyses require subdivision of a genomic region into functional units, such as protein-coding regions, introns, and untranslated regions, and computing these genetic measures for large-scale data remains challenging. In a recent investigation, we successfully devised a method to address this issue. This method requires a multi-sample VCF file containing population data, a reference genome, target regions in the BED file, and a list of samples to be included in the analysis. Given that the targeted regions are extracted in a new VCF file, targeted population genetic analysis can be performed. We conducted Tajima's D analysis using this approach on intact and pseudogenes, as well as non-coding regions.</p>","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11357298/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142080913","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
Image Processing Analysis of Plant Morphometry with Examples from the Genus Sedum (Crassulaceae) 以景天科植物为例,对植物形态测量进行图像处理分析
IF 2.3
Methods and Protocols Pub Date : 2024-07-24 DOI: 10.3390/mps7040056
Mădălina Borcă, Alexandru Borcă, A. Ciobîcă, Gabriela Halitchi, A. Stoie
{"title":"Image Processing Analysis of Plant Morphometry with Examples from the Genus Sedum (Crassulaceae)","authors":"Mădălina Borcă, Alexandru Borcă, A. Ciobîcă, Gabriela Halitchi, A. Stoie","doi":"10.3390/mps7040056","DOIUrl":"https://doi.org/10.3390/mps7040056","url":null,"abstract":"The complex systematics of the genus Sedum, the difficulties of its classification and the ambiguity of the concrete identification of the taxa brought about the need to implement a measurement system adaptable to field conditions, so as to facilitate the accuracy of data collection, avoiding the etiolation of samples and, therefore, the deterioration of the morphological structures subject to analysis. Thus, our study describes a digitization of the classic method of making measurements using millimeter paper, thus facilitating the subsequent statistical processing of quantifiable values. Depending on the number of pixels in the photos taken and the pixel/millimeter ratio, a variable measurement scale can be created depending on the size of the analyzed taxomes. The method used adds to the classic taxonomy, which is based on the analysis of morphological characteristics to determine the species of these succulent plants. The applicability of our method is shown by means of the example of an analysis performed on the flowers of the native species of the genus Sedum in the territory of Romania.","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141810240","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}
引用次数: 0
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信