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https://www.readbyqxmd.com/read/29216772/proteomic-cinderella-customized-analysis-of-bulky-ms-ms-data-in-one-night
#1
Olga Kiseleva, Ekaterina Poverennaya, Alexander Shargunov, Andrey Lisitsa
Proteomic challenges, stirred up by the advent of high-throughput technologies, produce large amount of MS data. Nowadays, the routine manual search does not satisfy the "speed" of modern science any longer. In our work, the necessity of single-thread analysis of bulky data emerged during interpretation of HepG2 proteome profiling results for proteoforms searching. We compared the contribution of each of the eight search engines (X!Tandem, MS-GF[Formula: see text], MS Amanda, MyriMatch, Comet, Tide, Andromeda, and OMSSA) integrated in an open-source graphical user interface SearchGUI ( http://searchgui...
November 13, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/29214361/forcegen-atomic-covalent-bond-value-derivation-for-gromacs
#2
Anthony Nash, Thomas Collier, Helen L Birch, Nora H de Leeuw
A large number of crystallographic protein structures include ligands, small molecules and post-translational modifications. Atomic bond force values for computational atomistic models of post-translational or non-standard amino acids, metal binding active sites, small molecules and drug molecules are not readily available in most simulation software packages. We present ForceGen, a Java tool that extracts the bond stretch and bond angle force values and equilibrium values from the Hessian of a Gaussian vibrational frequency analysis...
December 6, 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/29211758/rubus-a-compiler-for-seamless-and-extensible-parallelism
#3
Muhammad Adnan, Faisal Aslam, Zubair Nawaz, Syed Mansoor Sarwar
Nowadays, a typical processor may have multiple processing cores on a single chip. Furthermore, a special purpose processing unit called Graphic Processing Unit (GPU), originally designed for 2D/3D games, is now available for general purpose use in computers and mobile devices. However, the traditional programming languages which were designed to work with machines having single core CPUs, cannot utilize the parallelism available on multi-core processors efficiently. Therefore, to exploit the extraordinary processing power of multi-core processors, researchers are working on new tools and techniques to facilitate parallel programming...
2017: PloS One
https://www.readbyqxmd.com/read/29204168/pre-plan-technique-feasibility-in-multi-interstitial-endocavitary-perineal-gynecological-brachytherapy
#4
Silvia Rodriguez, Antonio Otal, Jose Richart, Jose Perez-Calatayud, Manuel Santos
Purpose: To present the implementation of a magnetic resonance imaging (MRI) pre-planning technique in multi-interstitial perineal and endocavitary gynecological brachytherapy. Material and methods: We used a new fully MRI-compatible applicator that is capable to engage titanium needles, and an intrauterine tandem, developed in our department for the treatment of gynecological cervical cancer patients. This applicator is an attempt to combine the technical advantages of the Martinez universal perineal interstitial template (MUPIT) with the improvement in dose distribution by adding an intrauterine probe with the imaging advantages of MRI-based brachytherapy, thus preserving the stability, geometry, and robustness of the implant, avoiding possible errors of free-hand needle placement...
October 2017: Journal of Contemporary Brachytherapy
https://www.readbyqxmd.com/read/29192088/complete-genome-sequence-of-bacillus-altitudinis-p-10-a-potential-bioprotectant-against-xanthomonas-oryzae-pv-oryzae-isolated-from-rice-rhizosphere-in-java-indonesia
#5
Anto Budiharjo, Haeyoung Jeong, Dyah Wulandari, Soohyun Lee, Choong-Min Ryu
Bacillus altitudinis P-10 was isolated from the rhizosphere of rice grown in an organic rice field and provides strong antagonism against the bacterial blight caused by Xanthomonas oryzae pv. oryzae in rice. Herein, we provide the complete genome sequence and a possible explanation of the antibiotic function of the P-10 strain.
November 30, 2017: Genome Announcements
https://www.readbyqxmd.com/read/29188446/ichrcloud-web-mobile-based-child-health-imprints-for-smart-healthcare
#6
Harpreet Singh, Raghuram Mallaiah, Gautam Yadav, Nitin Verma, Ashu Sawhney, Samir K Brahmachari
Reducing child mortality with quality care is the prime-most concern of all nations. Thus in current IT era, our healthcare industry needs to focus on adapting information technology in healthcare services. Barring few preliminary attempts to digitalize basic hospital administrative and clinical functions, even today in India, child health and vaccination records are still maintained as paper-based records. Also, error in manually plotting the parameters in growth charts results in missed opportunities for early detection of growth disorders in children...
November 29, 2017: Journal of Medical Systems
https://www.readbyqxmd.com/read/29186450/spectre-a-suite-of-phylogenetic-tools-for-reticulate-evolution
#7
Sarah Bastkowski, Daniel Mapleson, Andreas Spillner, Taoyang Wu, Monika Balvociute, Vincent Moulton
Summary: Split-networks are a generalization of phylogenetic trees that have proven to be a powerful tool in phylogenetics. Various ways have been developed for computing such networks, including split-decomposition, NeighborNet, QNet and FlatNJ. Some of these approaches are implemented in the user-friendly SplitsTree software package. However, to give the user the option to adjust and extend these approaches and to facilitate their integration into analysis pipelines, there is a need for robust, open-source implementations of associated data structures and algorithms...
November 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29186339/bioalcidae-samjs-and-vcffilterjs-object-oriented-formatters-and-filters-for-bioinformatics-files
#8
Pierre Lindenbaum, Richard Redon
Motivation: Reformatting and filtering bioinformatics files are common tasks for bioinformaticians. Standard linux tools and specific programs are usually used to perform such tasks but there is still a gap between using these tools and the programming interface of some existing libraries. Results: In this context, we wrote a set of tools named bioalcidae, samjs and vcffilterjs that reformat or filter files using a javascript engine or a pure java expression and taking advantage of the java API for high-throughput sequencing data (htsjdk)...
November 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29186322/sapp-functional-genome-annotation-and-analysis-through-a-semantic-framework-using-fair-principles
#9
Jasper J Koehorst, Jesse C J van Dam, Edoardo Saccenti, Vitor A P Martins Dos Santos, Maria Suarez-Diez, Peter J Schaap
Summary: To unlock the full potential of genome data and to enhance data interoperability and reusability of genome annotations we have developed SAPP, a Semantic Annotation Platform with Provenance. SAPP is designed as an infrastructure supporting FAIR de novo computational genomics but can also be used to process and analyse existing genome annotations. SAPP automatically predicts, tracks and stores structural and functional annotations and associated dataset- and element-wise provenance in a Linked Data format, thereby enabling information mining and retrieval with Semantic Web technologies...
November 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29186321/mapping-free-variant-calling-using-haplotype-reconstruction-from-k-mer-frequencies
#10
Peter Audano, Shashidhar Ravishankar, Fredrik Vannberg
Motivation: The standard protocol for detecting variation in DNA is to map millions of short sequence reads to a known reference and find loci that differ. While this approach works well, it cannot be applied where the sample contains dense variants or is too distant from known references. De novo assembly or hybrid methods can recover genomic variation, but the cost of computation is often much higher. We developed a novel k-mer algorithm and software implementation, Kestrel, capable of characterizing densely-packed SNPs and large indels without mapping, assembly, or de Bruijn graphs...
November 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29186288/reproducible-and-flexible-simulation-experiments-with-ml-rules-and-sessl
#11
T Warnke, T Helms, A M Uhrmacher
Summary: The modeling language ML-Rules allows specifying and simulating complex systems biology models at multiple levels of organization. The development of such simulation models involves a wide variety of simulation experiments and the replicability of generated simulation results requires suitable means for documenting simulation experiments. Embedded domain-specific languages, such as SESSL, cater both requirements. With SESSL, the user can integrate diverse simulation experimentation methods and third-party software components into an executable, readable simulation experiment specification...
November 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29186140/phylogeography-of-the-termite-macrotermes-gilvus-and-insight-into-ancient-dispersal-corridors-in-pleistocene-southeast-asia
#12
G Veera Singham, Ahmad Sofiman Othman, Chow-Yang Lee
Dispersal of soil-dwelling organisms via the repeatedly exposed Sunda shelf through much of the Pleistocene in Southeast Asia has not been studied extensively, especially for invertebrates. Here we investigated the phylogeography of an endemic termite species, Macrotermes gilvus (Hagen), to elucidate the spatiotemporal dynamics of dispersal routes of terrestrial fauna in Pleistocene Southeast Asia. We sampled 213 termite colonies from 66 localities throughout the region. Independently inherited microsatellites and mtDNA markers were used to infer the phylogeographic framework of M...
2017: PloS One
https://www.readbyqxmd.com/read/29182608/impact-of-tumour-histology-on-survival-in-advanced-cervical-carcinoma-an-nrg-oncology-gynaecologic-oncology-group-study
#13
Leigh G Seamon, James J Java, Bradley J Monk, Richard T Penson, Jubilee Brown, Robert S Mannel, Anna Oaknin, Mario M Leitao, Eric L Eisenhauer, Harry J Long, Shu Y Liao, Krishnansu S Tewari
BACKGROUND: Based primarily on studies concerning early-stage tumours (treated surgically), and locally advanced disease (treated with chemoradiation), the prognosis for women with adenocarcinoma (AC) or adenosquamous (AS) carcinoma has been reported to be poorer than those with squamous cell carcinoma (SCCA) of the cervix. It is unclear whether differences in prognosis also persist in the setting of recurrent or metastatic disease treated using chemotherapy doublets with or without bevacizumab...
November 28, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/29179744/levels-trends-and-correlates-of-unmet-need-for-family-planning-among-postpartum-women-in-indonesia-2007-2015
#14
Siswanto Agus Wilopo, Althaf Setyawan, Anggriyani Wahyu Pinandari, Titut Prihyugiarto, Flourisa Juliaan, Robert J Magnani
BACKGROUND: Although Indonesia has relatively high contraceptive prevalence, postpartum family planning (PP-FP) has not been a particular point of emphasis. This article reports the results of analyses undertaken in order to (1) better understand levels and trends in unmet need for family planning among postpartum women, (2) assess the extent to which unmet need is concentrated among particular population sub-groups, and (3) assess the policy priority that PP-FP should have in relation to other interventions...
November 28, 2017: BMC Women's Health
https://www.readbyqxmd.com/read/29174555/predictive-modeling-for-determination-of-microscopic-residual-disease-at-primary-cytoreduction-an-nrg-oncology-gynecologic-oncology-group-182-study
#15
Neil S Horowitz, G Larry Maxwell, Austin Miller, Chad A Hamilton, Bunja Rungruang, Noah Rodriguez, Scott D Richard, Thomas C Krivak, Jeffrey M Fowler, David G Mutch, Linda Van Le, Roger B Lee, Peter Argenta, David Bender, Krishnansu S Tewari, David Gershenson, James J Java, Michael A Bookman
OBJECTIVE: Microscopic residual disease following complete cytoreduction (R0) is associated with a significant survival benefit for patients with advanced epithelial ovarian cancer (EOC). Our objective was to develop a prediction model for R0 to support surgeons in their clinical care decisions. METHODS: Demographic, pathologic, surgical, and CA125 data were collected from GOG 182 records. Patients enrolled prior to September 1, 2003 were used for the training model while those enrolled after constituted the validation data set...
November 22, 2017: Gynecologic Oncology
https://www.readbyqxmd.com/read/29171165/readtools-a-universal-toolkit-for-handling-sequence-data-from-different-sequencing-platforms
#16
D Gómez-Sánchez, C Schlötterer
Sequencing whole genomes has become a standard research tool in many disciplines including Molecular Ecology, but the rapid technological advances in combination with several competing platforms has resulted in a confusing diversity of formats. This lack of standard formats causes several problems, such as undocumented pre-processing steps or the loss of information in downstream software tools, which do not account for the specifics of the different available formats. ReadTools is an open source Java toolkit designed to standardize and pre-process read data from different platforms...
November 24, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29166193/traditional-method-of-initial-diarrhea-treatment-in-children
#17
Kristian Ade Chandra, Dessie Wanda
Diarrhea is the most common cause of death in children. For diarrhea, home treatment should be administered by parents to prevent diarrheal complications. The purpose of this research was to investigate the traditional method of diarrhea treatment in Tegal regency, Central Java, Indonesia. A descriptive study was conducted with the aim of describing the traditional method of home treatment for diarrhea in children. The study sample included families with children who were experiencing or had experienced diarrhea and had received traditional medicine...
2017: Comprehensive Child and Adolescent Nursing
https://www.readbyqxmd.com/read/29166192/maternal-self-efficacy-of-pregnant-indonesian-teens-development-and-validation-of-an-indonesian-version-of-the-young-adult-maternal-confidence-scale-and-measurement-of-its-validity-and-reliability
#18
Desy Ayu Wardani, Imami Nur Rachmawati, Dewi Gayatri
Pregnant teens often feel uncertain in the last trimester about their ability to take care of their baby. At this time, maternal confidence in the ability to care for the baby is an important step in the preparation for becoming a mother. The purpose of this study was to examine the validity and reliability of an Indonesian version of the Young Adult Maternal Confidence Scale (YAMCS) as an instrument to measure maternal self-efficacy of pregnant teens in the last trimester. The study consisted of 90 pregnant teens, age of respondents less than 19 years and living in 1 of 3 sub-districts: Cilember, Sukamanah and Megamendung, Bogor Regency...
2017: Comprehensive Child and Adolescent Nursing
https://www.readbyqxmd.com/read/29166183/the-development-of-an-interactive-health-education-model-based-on-the-djuwita-application-for-adolescent-girls
#19
Sri Djuwitaningsih, Setyowati
Alarming incidents of maternal deaths in Indonesia are due to three major causes: bleeding, sepsis, and hypertension, in addition to other non-obstetric causes and unsafe abortions. Adolescent girls contributed to maternal mortality based on early marriage, unwanted pregnancy, and childbirth. Prevention efforts have been taken through government programs and non-governmental organizations, but in practice those were considered ineffective. Thus, a preventative effort in the form of health education should be made, preferably embedded in a popular mobile application that most teenagers would be apt to use...
2017: Comprehensive Child and Adolescent Nursing
https://www.readbyqxmd.com/read/29151821/streamqre-modular-specification-and-efficient-evaluation-of-quantitative-queries-over-streaming-data
#20
Konstantinos Mamouras, Mukund Raghothaman, Rajeev Alur, Zachary G Ives, Sanjeev Khanna
Real-time decision making in emerging IoT applications typically relies on computing quantitative summaries of large data streams in an efficient and incremental manner. To simplify the task of programming the desired logic, we propose StreamQRE, which provides natural and high-level constructs for processing streaming data. Our language has a novel integration of linguistic constructs from two distinct programming paradigms: streaming extensions of relational query languages and quantitative extensions of regular expressions...
June 2017: Proceedings of the ACM SIGPLAN ... Conference on Programming Language Design and Implementation
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