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Privacy-Preservation for Publishing Sample Availability Data with Personal Identifiers 个人标识符发布样本可用性数据的隐私保护
Journal of medical and bioengineering Pub Date : 1900-01-01 DOI: 10.12720/JOMB.4.2.117-125
A. Gholami, E. Laure, P. Somogyi, O. Spjuth, Salman Niazi, J. Dowling
{"title":"Privacy-Preservation for Publishing Sample Availability Data with Personal Identifiers","authors":"A. Gholami, E. Laure, P. Somogyi, O. Spjuth, Salman Niazi, J. Dowling","doi":"10.12720/JOMB.4.2.117-125","DOIUrl":"https://doi.org/10.12720/JOMB.4.2.117-125","url":null,"abstract":"Medical organizations collect, store and process vast amounts of sensitive information about patients. Easy access to this information by researchers is crucial to improving medical research, but in many institutions, cumbersome security measures and walled-gardens have created a situation where even information about what medical data is out there is not available. One of the main security challenges in this area, is enabling researchers to cross-link different medical studies, while preserving the privacy of the patients involved. In this paper, we introduce a privacy-preserving system for publishing sample availability data that allows researchers to make queries that crosscut different studies. That is, researchers can ask questions such as how many patients have had both diabetes and prostate cancer, where the diabetes and prostate cancer information originates from different clinical registries. We realize our solution by having a two-level anonymiziation mechanism, where our toolkit for publishing availability data first pseudonymizes personal identifiers and then anonymizes sensitive attributes. Our toolkit also includes a web-based server that stores the encrypted pseudonymized sample data and allows researchers to execute cross-linked queries across different study data. We believe that our toolkit contributes a first step to support the privacy preserving publication of data containing personal identifiers.","PeriodicalId":437476,"journal":{"name":"Journal of medical and bioengineering","volume":"73 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129837370","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: 9
Single Nucleotide Variant Calling Tools for RNA-Seq RNA-Seq单核苷酸变异调用工具
Journal of medical and bioengineering Pub Date : 1900-01-01 DOI: 10.12720/JOMB.2.2.84-87
Yunqin Chen, Jia Wei
{"title":"Single Nucleotide Variant Calling Tools for RNA-Seq","authors":"Yunqin Chen, Jia Wei","doi":"10.12720/JOMB.2.2.84-87","DOIUrl":"https://doi.org/10.12720/JOMB.2.2.84-87","url":null,"abstract":"Dissecting the transcriptome is essential for understanding the functional element of genome and molecular constituents of cells and tissues, and also important for revealing the cancer mechanism. Highthroughput RNA sequencing (RNA-Seq) has enabled whole genome and transcriptome single nucleotide variant (SNV) discovery in cancer. In recent years, a number of SNV identification methods have been published from both public and commercial sources. Here we presented an overview and evaluation of these attempts on SNV calling. We defined a set of criteria and compared the performance of four tools (GATK, Samtools, VarScan and Array Studio) based on these criteria, and we further provided advices on lowering false positive mutation rate. ","PeriodicalId":437476,"journal":{"name":"Journal of medical and bioengineering","volume":"118 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132911989","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
Production and Characterization of Xylanases from Fungal Isolate Aspergillus Terreus and Development of Low Cost Fermentation Media 土曲霉木聚糖酶的生产、鉴定及低成本发酵培养基的开发
Journal of medical and bioengineering Pub Date : 1900-01-01 DOI: 10.12720/jomb.5.1.15-18
Prachi Kaushik, A. Malik
{"title":"Production and Characterization of Xylanases from Fungal Isolate Aspergillus Terreus and Development of Low Cost Fermentation Media","authors":"Prachi Kaushik, A. Malik","doi":"10.12720/jomb.5.1.15-18","DOIUrl":"https://doi.org/10.12720/jomb.5.1.15-18","url":null,"abstract":"Fungal isolate, Aspergillus terreus, was utilized for the production of hydrolytic enzymes through solid state fermentation of wheat bran. After 5 days of incubation, 116 U/g xylanase, 1.53 fpu/g cellulase and 16.99 cmc/g carboxymethyl cellulase was produced. The optimum pH and temperature for the activity of xylanase enzyme was found to be pH 5 and 60oC. The zymogram analysis of the native enzyme shows the presence of single xylanase band with the molecular weight of 91.67 KDa. Low cost nutrient supplements such as the corn cob as the carbon substrate and biogas slurry as the nitrogen supplement can offer a low cost medium for the production of xylanase enzyme by A. terreus.","PeriodicalId":437476,"journal":{"name":"Journal of medical and bioengineering","volume":"268 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134059829","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: 2
Missing Value Estimation in DNA Microarrays Using B-Splines 基于b样条的DNA微阵列缺失值估计
Journal of medical and bioengineering Pub Date : 1900-01-01 DOI: 10.12720/JOMB.2.2.88-92
Sujay Saha, K. Dey, Riddhiman Dasgupta, Anirban Ghose, K. Mullick
{"title":"Missing Value Estimation in DNA Microarrays Using B-Splines","authors":"Sujay Saha, K. Dey, Riddhiman Dasgupta, Anirban Ghose, K. Mullick","doi":"10.12720/JOMB.2.2.88-92","DOIUrl":"https://doi.org/10.12720/JOMB.2.2.88-92","url":null,"abstract":"Gene expression profiles generated by the high- throughput microarray experiments are usually in the form of large matrices with high dimensionality. Unfortunately, microarray experiments can generate data sets with multiple missing values, which significantly affect the performance of subsequent statistical analysis and machine learning algorithms. Numerous imputation algorithms have been proposed to estimate the missing values. However, most of these algorithms fail to take into account the fact that gene expressions are continuous time series, and deal with gene expression profiles in terms of discrete data. In this paper, we present a new approach, FDVSplineImpute, for time series gene expression analysis that permits the estimation of missing observations using B-splines of similar genes from fuzzy difference vectors. We have used smoothing splines to relax the fit of the splines so that they are less prone to over fitting the data. Our algorithm shows significant improvement over the current state-of-the-art methods in use. ","PeriodicalId":437476,"journal":{"name":"Journal of medical and bioengineering","volume":"19 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133315066","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: 10
How and Why Cancer should be Better Handled in the 1Billion + India 在拥有10多亿人口的印度，如何更好地治疗癌症
Journal of medical and bioengineering Pub Date : 1900-01-01 DOI: 10.12720/JOMB.1.1.17-19
Shaheen Shah, Safa Shaheen
{"title":"How and Why Cancer should be Better Handled in the 1Billion + India","authors":"Shaheen Shah, Safa Shaheen","doi":"10.12720/JOMB.1.1.17-19","DOIUrl":"https://doi.org/10.12720/JOMB.1.1.17-19","url":null,"abstract":"","PeriodicalId":437476,"journal":{"name":"Journal of medical and bioengineering","volume":"344 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132808950","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
Manufacture of Lyophilized Cortical Bone Particles for Bone Filling Applications by Machining Methods 用机械加工方法制造用于骨填充物的冻干皮质骨颗粒
Journal of medical and bioengineering Pub Date : 1900-01-01 DOI: 10.12720/JOMB.2.1.32-36
Lina María González Bernal, Fabio A. Rojas
{"title":"Manufacture of Lyophilized Cortical Bone Particles for Bone Filling Applications by Machining Methods","authors":"Lina María González Bernal, Fabio A. Rojas","doi":"10.12720/JOMB.2.1.32-36","DOIUrl":"https://doi.org/10.12720/JOMB.2.1.32-36","url":null,"abstract":"Abstract— Initially was conducted a study of the properties that bone particles for bone filling applications must fulfill and the influence of these properties on the shape and size of the particles. Then we studied the shape and size of commercial particles and determined a geometry that can satisfy these properties with a better assessment than previously studied particles. Then a factorial experiment is design where we studied the parameters that are influential in the process of cutting and the particles that best meet the preselected geometry were selected.","PeriodicalId":437476,"journal":{"name":"Journal of medical and bioengineering","volume":"87 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114548524","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
Balance assessment in older people using inertial sensors 用惯性传感器评估老年人的平衡能力
Journal of medical and bioengineering Pub Date : 1900-01-01 DOI: 10.12720/JOMB.4.2.139-144
M. Ghahramani, F. Naghdy, D. Stirling, G. Naghdy, J. Potter
{"title":"Balance assessment in older people using inertial sensors","authors":"M. Ghahramani, F. Naghdy, D. Stirling, G. Naghdy, J. Potter","doi":"10.12720/JOMB.4.2.139-144","DOIUrl":"https://doi.org/10.12720/JOMB.4.2.139-144","url":null,"abstract":"People at the age of 65 and above are drastically at the risk of falling. Falls among elderly may occur because of many physical factors such as natural deterioration of motor function or other disease related problems such as stroke, Parkinson's or Alzheimer's disease. The methods reported in the literature to assess the risk of falling in older people are often subjective, qualitative, retrospective and inaccurate. An objective, quantifiable approach to assess the risk of falling in elderly by analysing body movement using inertial sensors is conducted. Initial results of the experimental work and analysis carried out on three subjects, one older person with impaired balance and two younger people with normal balance are reported. The sensors are mounted on the subjects' chests and they are asked to conduct balance tests. The results of the data analysis indicate that the elderly subject has disturbed and involuntary chest movements. This demonstrates the potential of the method to assess balance and the risk of fall in older people. Index Terms--balance assessment for older people, fall risk assessment between the elderly, gait and posture analysis Language: en","PeriodicalId":437476,"journal":{"name":"Journal of medical and bioengineering","volume":"16 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128076333","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: 3
In Vitro Anti-Inflammatory Activities of Red Gemor (Nothaphoebe cf Umbelliflora) 红宝石(Nothaphoebe cf bellliflora)体外抗炎活性的研究
Journal of medical and bioengineering Pub Date : 1900-01-01 DOI: 10.12720/jomb.4.4.312-317
Y. Arifin, S. Hamidah, Sudin Panjaitan, E. Suhartono
{"title":"In Vitro Anti-Inflammatory Activities of Red Gemor (Nothaphoebe cf Umbelliflora)","authors":"Y. Arifin, S. Hamidah, Sudin Panjaitan, E. Suhartono","doi":"10.12720/jomb.4.4.312-317","DOIUrl":"https://doi.org/10.12720/jomb.4.4.312-317","url":null,"abstract":"Gemor (Nothaphoebe cf umbelliflora) is a tree species that found naturally in swampy forest of Sumatra and Kalimantan, Indonesia. The anti-inflammation activity of red gemor plant parts have not been investigated, therefore many study should be performed. Thus our study aimed to investigate the anti-inflammation effect of different parts of red gemor. Phytochemical analysis of diffrent parts of red gemor extracts revealed the presence of various biochemical compounds such as alkaloids, flavonoids, phenolic compounds, triterpenoids and steroid. The antiinflammatory activities was determined by inhibition protein denaturation method. Result of this study revealed there is inhibitory action on protein denaturation. The percentage inhibition varied from 20,154 to 71,667 for highest concentration to the lowest concentration. The IC50 was found to be 60 for twig, 47,8 for bark, and 116,2 for leaves of red gemor. To determined which one of the phytochemical constituent in diffrent parts of red gemor are most influence in anti-inflammation activity, we used linear correlation between IC 50 with alkaloid and flavonid content in different parts of red gemor. The result suggest that flavonoid are the most influence to protein denaturation (R = 0,9927). The results of the present study suggest that the diffrent parts of red gemor have antiinflammation activity. The anti-inflammation activity of different parts of red gemor due to the phytochemical constituents content in different parts of red gemor, such as flavonoid and alkaloid.","PeriodicalId":437476,"journal":{"name":"Journal of medical and bioengineering","volume":"5 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133757033","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: 7
Lactoferrin, Isolation,Purification and Antimicrobial Effects 乳铁蛋白的分离纯化及抑菌作用
Journal of medical and bioengineering Pub Date : 1900-01-01 DOI: 10.12720/jomb.3.3.203-206
F. Moradian, Ramisa Sharbafi, A. Rafiei
{"title":"Lactoferrin, Isolation,Purification and Antimicrobial Effects","authors":"F. Moradian, Ramisa Sharbafi, A. Rafiei","doi":"10.12720/jomb.3.3.203-206","DOIUrl":"https://doi.org/10.12720/jomb.3.3.203-206","url":null,"abstract":"Lactoferrin (Lf) is an 80 kDa iron-binding glycoprotein with multifunctional properties and useful for clinical and commercial applications. Currently, Lf has some advantages including, immune system modulation, antibacterial activity and as antioxidant in infant and adult of human as well as animal health. In the present study, antibacterial activity of Lf has been scrutinized after isolation and purification from cow’s milk colostrums against Pseudomonas aeroginosa. Lf purified using CMsephadex C50, a cation exchange chromatography. Bacterial samples were isolated from scald patients and microbial activity was confirmed by biochemical tests. Different concentration of Lf (0, 200, 400, 500, 600 and 700 μg/ml) treated on Pseudomonas colonies as well as E.coli( DH5α) as positive control for two days. Our result indicated LF was effective on Pseudomonas growth and the least and the inset inhibitory concentration were 400,and 700 μg/ml, respectively. The result showed that The Lf has more strong effect than other previous studies. ","PeriodicalId":437476,"journal":{"name":"Journal of medical and bioengineering","volume":"69 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134044037","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: 16
Extraction of Ultrasonography Images Using Ratio of Geometric Operations 利用几何运算比率提取超声图像
Journal of medical and bioengineering Pub Date : 1900-01-01 DOI: 10.12720/jomb.4.3.206-212
R. Supriyanti, Ades Wahyu Dwi Susilo, Y. Ramadhani, Arwita Mulyawati, H. Widodo
{"title":"Extraction of Ultrasonography Images Using Ratio of Geometric Operations","authors":"R. Supriyanti, Ades Wahyu Dwi Susilo, Y. Ramadhani, Arwita Mulyawati, H. Widodo","doi":"10.12720/jomb.4.3.206-212","DOIUrl":"https://doi.org/10.12720/jomb.4.3.206-212","url":null,"abstract":"","PeriodicalId":437476,"journal":{"name":"Journal of medical and bioengineering","volume":"20 8","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133650864","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: 2
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