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Mahsa Moein, Kamil Grzyb, Teresa Gonçalves Martins, Shinya Komoto, Francesca Peri, Alexander Crawford, Aymeric Fouquier d'Herouel, Alexander Skupin
Summary: Ca2+ is a central second messenger in eukaryotic cells that regulates many cellular processes. Recently, we have indicated that typical Ca2+ signals are not purely oscillatory as widely assumed but exhibit stochastic spiking with cell type and pathway specific characteristics. Here, we present CaSiAn (Calcium Signaling Analyzer), an open source software tool that allows for quantifying these signal characteristics including individual spike properties and time course statistics in a semi-automated manner...
April 12, 2018: Bioinformatics
Teguh Hari Sucipto, Tomohiro Kotaki, Kris Cahyo Mulyatno, Siti Churrotin, Amaliah Labiqah, Soegeng Soegijanto, Masanori Kameoka
Dengue virus (DENV) infection is a major health issue in tropical and subtropical areas. Indonesia is one of the biggest dengue endemic countries in the world. In the present study, the phylogenetic analysis of DENV in Bangkalan, Madura Island, Indonesia, was performed in order to obtain a clearer understanding of its dynamics in this country. A total of 359 blood samples from dengue-suspected patients were collected between 2012 and 2014. Serotyping was conducted using a multiplex Reverse Transcriptase-Polymerase Chain Reaction and a phylogenetic analysis of E gene sequences was performed using the Bayesian Markov chain Monte Carlo (MCMC) method...
2018: Journal of Tropical Medicine
Maximilian J Dombrowsky, Sven Jager, Benjamin Schiller, Benjamin E Mayer, Sebastian Stammler, Kay Hamacher
Gromacs is one of the most popular molecular simulation suites currently available. In this contribution we present streaMD, the first interface between Gromacs trajectory files and the statistical language R. The amount of data created due to ever increasing computational power renders fast and efficient analysis of trajectories into a challenge. Especially as standard approaches such as root-mean square fluctuations and the like provide only limited physical insight. In our streaMD package integration of the Gromacs I/O libraries with advanced, graph-based analysis methods as the java library Stream leads to both: improved speed and analysis depth...
April 17, 2018: Journal of Computational Chemistry
Andrea Hornakova, Markus List, Jilles Vreeken, Marcel H Schulz
Motivation: Genome-wide measurements of paired miRNA and gene expression data have enabled the prediction of competing endogenous RNAs (ceRNAs). It has been shown hat the sponge effect mediated by protein-coding as well as non-coding ceRNAs can play an important regulatory role in the cell in health and disease. Therefore many computational methods for the computational identification of ceRNAs have been suggested. In particular methods based on Conditional Mutual Information (CMI) have shown promising results...
April 6, 2018: Bioinformatics
Terje Toomistu
Indonesian transgender women, locally and internationally recognised as waria, share some lifestyle patterns that have emerged under conditions of limited social acceptance. These patterns include involvement in sex work. The high number of waria who are sex workers is usually explained in economic terms. However, their presence in certain locations around the city known for waria sex work is not only for work, and quite often not even for sex. Waria street nightlife fosters waria agency, which emerges from self-affirmation through pleasurable bodily practices involving intimate (sexual partners) and both proximate (other waria and men nearby) and distant others (structuring ideals)...
April 16, 2018: Culture, Health & Sexuality
Novy Helena Catharina Daulima
Pasung is a way of handling the mentally ill in the several Indonesian communities. In many cases, when the patients leave the hospital they are once again turned out by their families and returned to the pasung. This study aims to identify and explore the means of preventing mentally ill patients in the community from being subjected to pasung through a test of Daulima's Pasung Decision Questionnaire that measures a family's intention to use pasung. This study tested the content validity and reliability of Daulima's Pasung Decision Questionnaire by using the Spearman-Brown single test-single trial...
February 2018: Enfermería Clínica
Yasuaki Kusumoto, Yoshihiro Kita, Satomi Kusaka, Yoshinori Hiyama, Junko Tsuchiya, Toshiki Kutsuna, Hiroyuki Kameda, Saori Aida, Masaru Umeda, Tetsuya Takahashi
[Purpose] This study aimed to develop a tablet app that emulates paper questionnaires used in clinical care, and to verify the difference between the utility of tablet survey methods and paper questionnaire methods with elderly people. [Subjects and Methods] A tablet app was developed in the Java language. A questionnaire was provided to 30 community-dwelling elderly people. The subjects were randomly allocated to the group responding on the tablet (tablet group) or that responding to a paper-based questionnaire (questionnaire group)...
December 2017: Journal of Physical Therapy Science
M Sivade Dumousseau, M Koch, A Shrivastava, D Alonso-López, J De Las Rivas, N Del-Toro, C W Combe, B H M Meldal, J Heimbach, J Rappsilber, J Sullivan, Y Yehudi, S Orchard
BACKGROUND: A number of different molecular interactions data download formats now exist, designed to allow access to these valuable data by diverse user groups. These formats include the PSI-XML and MITAB standard interchange formats developed by Molecular Interaction workgroup of the HUPO-PSI in addition to other, use-specific downloads produced by other resources. The onus is currently on the user to ensure that a piece of software is capable of read/writing all necessary versions of each format...
April 11, 2018: BMC Bioinformatics
Emy Koestanti S, Wiwik Misaco, Sri Chusniati, Lilik Maslachah
Background: Brucellosis in pigs at East Java Indonesia has not only cause great economic losses due to a decrease in productivity of livestock but also are zoonotic. Infection on free brucelosis pigs were initially begun with the infected pigs both male and female, or the use of superior male pigs together. The elimination of the disease either on a group or population is considered as the most effective way to prevent the spread of the disease in pigs. Prevention efforts mainly addressed to vaccination, sanitary maintenace and government policy...
2018: African Journal of Infectious Diseases
Dharin Serebrina Arfiputri, Afif Nurul Hidayati, Samsriyaningsih Handayani, Evy Ervianti
Background: Vulvovaginal Candidiasis (VVC) is one-third of vaginitis case. About 75% of women will have at least one episode of VVC. Complication of VVC can be unfavorable to impact the patient's quality of life. Knowing its risk factors can prevent someone suffering from pathological VVC and its sequelae. The purpose of this study was to identify risk factors of VVC. Materials and Methods: A descriptive retrospective study was conducted by total sampling to 213 medical records of VVC patients from 869 fluor albus patients in Sexually Transmitted Infection (STI) Division, Dermatology and Venereology Outpatient Clinic in Dr...
2018: African Journal of Infectious Diseases
Hosizah Markam, Harry Hochheiser, Kuntoro Kuntoro, Hari Basuki Notobroto
Documentation requirements for the Indonesian integrated antenatal care (ANC) program suggest the need for electronic systems to address gaps in existing paper documentation practices. Our goals were to quantify midwives' documentation completeness in a primary healthcare center, understand documentation challenges, develop a tool, and assess intention to use the tool. We analyzed existing ANC records in a primary healthcare center in Bangkalan, East Java, and conducted interviews with stakeholders to understand needs for an electronic system in support of ANC...
2018: Perspectives in Health Information Management
Ryan Rebernick, Lauren Fahmy, Christopher Glover, Mandar Bawadekar, Daeun Shim, Caitlyn L Holmes, Nicole Rademacher, Hemanth Potluri, Christie M Bartels, Miriam A Shelef
Background: Neutrophil extracellular traps (NETs), extracellular structures composed of decondensed chromatin and antimicrobial molecules, are released in a process called NETosis. NETs, which are part of normal host defense, have also been implicated in multiple human diseases. Unfortunately, methods for quantifying NETs have limitations which constrain the study of NETs in disease. Establishing optimal methods for NET quantification holds the potential to further elucidate the role of NETs in normal and pathologic processes...
2018: Biological Procedures Online
V A Chistyakov, Y V Denisenko, A B Bren
One of the important components of the concept of aging-phenoptosis (programmed aging) is the notion of aging as an accelerator of evolution having the rank of subconcept. For many reasons, the main being the problematic experimental testing of evolutionary hypotheses, verification of the above-mentioned subconcept can be based primarily on analysis of the internal inconsistency of heuristic models and their correspondence to undisputedly observed facts. To illustrate the acceleration mechanism, and most importantly to structure the evolutionary process in communities that include naturally weakened individuals, V...
February 2018: Biochemistry. Biokhimii︠a︡
Shuai Jiang, Yubin Xie, Zhihao He, Ya Zhang, Yuli Zhao, Li Chen, Yueyuan Zheng, Yanyan Miao, Zhixiang Zuo, Jian Ren
Background: Large-scale genome sequencing projects have identified many genetic variants for diverse diseases. A major goal of these projects is to characterize these genetic variants to provide insight into their function and roles in diseases. N6-methyladenosine (m6A) is one of the most abundant RNA modifications in eukaryotes. Recent studies have revealed that aberrant m6A modifications are involved in many diseases. Findings: In this study, we present a user-friendly web server called "m6ASNP" that is dedicated to the identification of genetic variants targeting m6A modification sites...
April 2, 2018: GigaScience
Mehmet Demir, Yigit Akin, Kubra Asena Kapakin Terim, Mehmet Gulum, Evren Buyukfirat, Halil Ciftci, Ercan Yeni
OBJECTIVES: Apoptosis effect of oral alpha-blockers is known in the prostate. Apoptosis index of silodosin has not been proved, yet. Aims are to present apoptosis index of silodosin in prostate and to compare this with other currently used alpha-blocker's apoptosis indexes together with their clinical effects. MATERIALS AND METHODS: Benign prostatic hyperplasia (BPH) patients were enrolled among those admitted to urology outpatient clinic between June 2014 and June 2015...
March 18, 2018: International Braz J Urol: Official Journal of the Brazilian Society of Urology
Jorge González-Domínguez, Roberto R Expósito
Biclustering techniques are gaining attention in the analysis of large-scale datasets as they identify two-dimensional submatrices where both rows and columns are correlated. In this work we present ParBiBit, a parallel tool to accelerate the search of interesting biclusters on binary datasets, which are very popular on different fields such as genetics, marketing or text mining. It is based on the state-of-the-art sequential Java tool BiBit, which has been proved accurate by several studies, especially on scenarios that result on many large biclusters...
2018: PloS One
Manuel Rodríguez-Martínez
Social media has become an important platform to gauge public opinion on topics related to our daily lives. In practice, processing these posts requires big data analytics tools since the volume of data and the speed of production overwhelm single-server solutions. Building an application to capture and analyze posts from social media can be a challenge simply because it requires combining a set of complex software tools that often times are tricky to configure, tune, and maintain. In many instances, the application ends up being an assorted collection of Java/Scala programs or Python scripts that developers cobble together to generate the data products they need...
June 2017: Proceedings. IEEE International Congress on Big Data
Flynn R Hill, Antoine M van Oijen, Karl E Duderstadt
Single-molecule approaches present a powerful way to obtain detailed kinetic information at the molecular level. However, the identification of small rate changes is often hindered by the considerable noise present in such single-molecule kinetic data. We present a general method to detect such kinetic change points in trajectories of motion of processive single molecules having Gaussian noise, with a minimum number of parameters and without the need of an assumed kinetic model beyond piece-wise linearity of motion...
March 28, 2018: Journal of Chemical Physics
Penny Humaidah Hamid, Yuli Purwandari Kristianingrum, April Hari Wardhana, Sigit Prastowo, Liliana Machado Ribeiro da Silva
Avian coccidiosis is a huge problem worldwide. Heavily infected animals that show severe clinical signs and coccidiostat resistance are causing important economic losses. The present study aimed to update the recent cases of coccidiosis in Central Java, Indonesia, and to show the importance of the disease in the region. A total of 699 samples were obtained from different chicken breed. Different Eimeria species were detected in 175 individuals (25.04%). Three different groups of chicken breed were considered: local chicken (autochthonous chickens of Sentul and Jawa), commercial broiler, and layer...
2018: Veterinary Medicine International
I Nyoman Giri Putra, Yuliana Fitri Syamsuni, Beginer Subhan, Made Pharmawati, Hawis Madduppa
The Indo-Malay Archipelago is regarded as a barrier that separates organisms of the Indian and Pacific Oceans. Previous studies of marine biota from this region have found a variety of biogeographic barriers, seemingly dependent on taxon and methodology. Several hypotheses, such as emergence of the Sunda Shelf and recent physical oceanography, have been proposed to account for the genetic structuring of marine organisms in this region. Here, we used six microsatellite loci to infer genetic diversity, population differentiation and phylogeographic patterns of Enhalus acoroides across the Indo-Malay Archipelago...
2018: PeerJ
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