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John K Chan, James J Java, Katherine Fuh, Bradley J Monk, Daniel S Kapp, Thomas Herzog, Jeffrey Bell, Robert Young
OBJECTIVES: To determine the association between timing of adjuvant therapy initiation and survival of early stage ovarian cancer patients. METHODS: Data were obtained from women who underwent primary surgical staging followed by adjuvant therapy from two Gynecologic Oncology Group trials (protocols # 95 and 157). Kaplan-Meier estimates and Cox proportional hazards model adjusted for covariates were used for analyses. RESULTS: Of 497 stage I-II epithelial ovarian cancer patients, the median time between surgery and initiation of adjuvant therapy was 23days (25th-75th%: 12-33days)...
October 19, 2016: Gynecologic Oncology
Esteban Alejandro Lopez, Orozimbo Alves Costa, Deborah Viviane Ferrari
Purpose: The purpose of this research note is to describe the development and technical validation of the Mobile Based Assistive Listening System (MoBALS), a free-of-charge smartphone-based remote microphone application. Method: MoBALS Version 1.0 was developed for Android (Version 2.1 or higher) and was coded with Java using Eclipse Indigo with the Android Software Development Kit. A Wi-Fi router with background traffic and 2 affordable smartphones were used for debugging and technical validation comprising, among other things, multicasting capability, data packet loss, and battery consumption...
October 1, 2016: American Journal of Audiology
Noriyoshi Tsujino, Yu Nishihara, Daisuke Yamazaki, Yusuke Seto, Yuji Higo, Eiichi Takahashi
Seismic shear wave anisotropy is observed in Earth's uppermost lower mantle around several subducted slabs. The anisotropy caused by the deformation-induced crystallographic preferred orientation (CPO) of bridgmanite (perovskite-structured (Mg,Fe)SiO3) is the most plausible explanation for these seismic observations. However, the rheological properties of bridgmanite are largely unknown. Uniaxial deformation experiments have been carried out to determine the deformation texture of bridgmanite, but the dominant slip system (the slip direction and plane) has not been determined...
October 17, 2016: Nature
Amanda N Fader, James Java, Meaghan Tenney, Stephanie Ricci, Camille C Gunderson, Sarah M Temkin, Nick Spirtos, Christina L Kushnir, Michael L Pearl, Oliver Zivanovic, Krishnansu S Tewari, David O'Malley, Ellen M Hartenbach, Chad A Hamilton, Natalie S Gould, Robert S Mannel, William Rodgers, Joan L Walker
OBJECTIVES: We sought to analyze the clinicopathologic features, recurrence patterns and survival outcomes of women with high-grade uterine cancer (UC) enrolled on The Gynecologic Oncology Group (GOG) LAP2 trial. METHODS: This is a post-hoc analysis of LAP-2 patients with grade 3 endometrioid adenocarcinoma (ENDO), uterine serous (USC), clear cell (CC) and carcinosarcoma (CS). Demographics, clinicopathologic features, and recurrence patterns, were compared by histology and surgical approach...
October 12, 2016: Gynecologic Oncology
Sehar Yousaf, Abid Hussain, Shafiqur Rehman, Muhammad Shahbaz Aslam, Zaigham Abbas
A lot of treatment strategies available for diabetes but its complications are still a medical problem around the globe. It demands to find out some alternative therapeutic measures. In order to investigate the anti-diabetic potential of probiotics and natural extracts, this study was designed. Accordingly, a local source of yogurt probiotic strain Lactobacillus fermentum was isolated and characterized that showed its probiotic properties. Besides this, natural extracts of plants fruits like java plum (Syzygium cumini) and bitter gourd (M...
September 2016: Pakistan Journal of Pharmaceutical Sciences
Arlene E Garcia-Soto, James J Java, Wilberto Nieves Neira, J Matthew Pearson, David E Cohn, Shashikant B Lele, Krishnansu S Tewari, Joan L Walker, Angeles Alvarez Secord, Deborah K Armstrong, Larry J Copeland
OBJECTIVES: To determine the relationship of the time from surgery to intraperitoneal (IP) chemotherapy (TSIC) initiation with survival of patients with stage III epithelial ovarian cancer (EOC) patients using ancillary data from cooperative group clinical trials. METHODS: Data from 420 patients with stage III EOC treated with IP chemotherapy under GOG-0114 and 172 were reviewed. The Cox proportional hazards model was used to evaluate independent prognostic factors and estimate their covariate-adjusted effects on PFS and OS...
October 7, 2016: Gynecologic Oncology
Rashmi G S Phulari, Rajendrasinh S Rathore, Trupti Pramod Talegaon
BACKGROUND: Various clinical and histological factors have helped in predicting the survival of patients with oral squamous cell carcinoma (OSCC). However, there has been a need for more specialized diagnostic and prognostic factors to avoid subjective variation among opinion. Thus, fractal dimension (FD) can be used as an index of the morphological changes that the epithelial cells undergo during their transformation into neoplastic cell. In oral cancer study, nuclear FD (NFD) can be used as a quantitative index to discriminate between normal, dysplastic and neoplastic oral mucosa...
September 2016: Journal of Oral and Maxillofacial Pathology: JOMFP
Charles Girardot, Jelle Scholtalbers, Sajoscha Sauer, Shu-Yi Su, Eileen E M Furlong
BACKGROUND: The yield obtained from next generation sequencers has increased almost exponentially in recent years, making sample multiplexing common practice. While barcodes (known sequences of fixed length) primarily encode the sample identity of sequenced DNA fragments, barcodes made of random sequences (Unique Molecular Identifier or UMIs) are often used to distinguish between PCR duplicates and transcript abundance in, for example, single-cell RNA sequencing (scRNA-seq). In paired-end sequencing, different barcodes can be inserted at each fragment end to either increase the number of multiplexed samples in the library or to use one of the barcodes as UMI...
October 8, 2016: BMC Bioinformatics
Qi Zheng, Elizabeth A Grice
Accurate mapping of next-generation sequencing (NGS) reads to reference genomes is crucial for almost all NGS applications and downstream analyses. Various repetitive elements in human and other higher eukaryotic genomes contribute in large part to ambiguously (non-uniquely) mapped reads. Most available NGS aligners attempt to address this by either removing all non-uniquely mapping reads, or reporting one random or "best" hit based on simple heuristics. Accurate estimation of the mapping quality of NGS reads is therefore critical albeit completely lacking at present...
October 2016: PLoS Computational Biology
Lee-Sim Lim, Gábor Csorba, Cheng-Min Wong, Akbar Zubaid, Sultana Parvin Habeebur Rahman, Jayaraj Vijaya Kumaran, Faisal Ali Anwarali Khan, Joe Chun-Chia Huang, Nazalan Najimudin, Tamás Görföl
The Southeast Asian species of Hypsugo are rare bats, except for H. cadornae and H. pulveratus, which are distributed throughout the Indomalayan region. Hypsugo macrotis is restricted to Peninsular Malaysia, Sumatra, Java and adjacent islands, and is known only from a handful of specimens. Here we report a new locality record of the species from Seremban, Peninsular Malaysia, which also represents the first known building-dweller colony of any Hypsugo from the region. We discuss the taxonomic status of two morphologically similar species, H...
September 22, 2016: Zootaxa
Toshio Kawai
A new armored searobin, Peristedion richardsi sp. nov., is described on the basis of three specimens collected from the deep sea (485-600 m) off Java, Indonesia. This new species differs from the Indo-West Pacific congeners in having anterior edge of the 4th sensory pore of the rostral projection located anterior to the anterior edge of the premaxilla, perifacial rim prominent starting near anterior margin of lower jaw, spatulate rostral projection with very narrow interspace between both rostral projections, rostral projection width 1...
September 28, 2016: Zootaxa
Alden King-Yung Leung, Tsz-Piu Kwok, Raymond Wan, Ming Xiao, Pui-Yan Kwok, Kevin Y Yip, Ting-Fung Chan
MOTIVATION: Optical mapping is a technique for capturing fluorescent signal patterns of long DNAmolecules (in the range of 0.1 Mbp to 1 Mbp). Recently, it has been complementing the widely-used short-read sequencing technology by assisting with scaffolding and detecting large and complex structural variations. Here, we introduce a fast, robust and accurate tool called OMBlast for aligning optical maps, the set of signal locations on the molecules generated from optical mapping. Our method is based on the seed-and-extend approach from sequence alignment, with modifications specific to optical mapping...
September 30, 2016: Bioinformatics
Seungmok Choi, Minsoo Kim, Changhee Kim, Jae-Kwan Hwang, Wonku Kang
Although xanthorrhizol, a sesquiterpenoid oil isolated from the rhizoma of Curcuma xanthorrhiza Roxb. known as Java turmeric, represents a variety of pharmacological activities, to date, there have been no validated determination methods of xanthorrhizol in biological samples. Thus, we developed a liquid chromatographic method using a tandem mass spectrometry for the determination of xanthorrhizol in rat plasma. After simple protein precipitation with acetonitrile including diclofenac (internal standard, IS), the analytes were chromatographed on a reversed-phased column with a mobile phase of 20mM ammonium acetate aqueous solution and acetonitrile (20:80, v/v)...
September 28, 2016: Journal of Pharmaceutical and Biomedical Analysis
Peter G Rose, James J Java, Mark A Morgan, Angeles Alvarez-Secord, Joshua P Kesterson, Frederick B Stehman, David P Warshal, William T Creasman, Parviz Hanjani, Robert T Morris, Larry J Copeland
PURPOSE: GOG 152 was a randomized trial of secondary cytoreductive surgery (SCS) in patients with suboptimal residual disease (residual tumor nodule >1cm in greatest diameter) following primary cytoreductive surgery for advanced stage ovarian cancer. The current analysis was undertaken to evaluate the impact of disease findings at SCS on progression-free survival (PFS) and overall survival (OS). METHODS: Among the 550 patients enrolled on GOG-152, two-hundred-sixteen patients were randomly assigned following 3cycles of cisplatin and paclitaxel to receive SCS...
September 27, 2016: Gynecologic Oncology
Mayra Sousa Gomes, Paulo Rogério Ferreti Bonan, Vitor Yuri Nicolau Ferreira, Laudenice de Lucena Pereira, Ricardo João Cruz Correia, Hélder Bruno da Silva Teixeira, Daniel Cláudio Pereira
PURPOSE: To develop a mobile application (app) for oral cancer screening. METHODS: The app was developed using Android system version 4.4.2, with JAVA language. Information concerning sociodemographic data and risk factors for oral cancer development, e.g., tobacco and alcohol use, sun exposure and other contributing factors, such as unprotected oral sex, oral pain and denture use, were included. We surveyed a population at high risk for oral cancer development and then evaluated the sensitivity/specificity/accuracy and predictive values of clinical oral diagnosis between two blinded trained examiners, who used movies and data from the app, and in loco oral examination as gold-standard...
September 20, 2016: Technology and Health Care: Official Journal of the European Society for Engineering and Medicine
Daniel LaFave, Duncan Thomas
The farm household model has played a central role in improving the understanding of small-scale agricultural households and non-farm enterprises. Under the assumptions that all current and future markets exist and that farmers treat all prices as given, the model simplifies households' simultaneous production and consumption decisions into a recursive form in which production can be treated as independent of preferences of household members. These assumptions, which are the foundation of a large literature in labor and development, have been tested and not rejected in several important studies including Benjamin (1992)...
September 2016: Econometrica: Journal of the Econometric Society
Alexander Seitinger, Andrea Rappelsberger, Harald Leitich, Michael Binder, Klaus-Peter Adlassnig
INTRODUCTION: Clinical decision support systems (CDSSs) are being developed to assist physicians in processing extensive data and new knowledge based on recent scientific advances. Structured medical knowledge in the form of clinical alerts or reminder rules, decision trees or tables, clinical protocols or practice guidelines, score algorithms, and others, constitute the core of CDSSs. Several medical knowledge representation and guideline languages have been developed for the formal computerized definition of such knowledge...
August 12, 2016: Artificial Intelligence in Medicine
Matthew C DeLorenzo, Dee H Wu, Kai Yang, Isaac B Rutel
The purpose of this study was to introduce and describe the development of RadShield, a Java-based graphical user interface (GUI), which provides a base design that uniquely performs thorough, spatially distributed calculations at many points and reports the maximum air-kerma rate and barrier thickness for each barrier pursuant to NCRP Report 147 methodology. Semiautomated shielding design calculations are validated by two approaches: a geometry-based approach and a manual approach. A series of geometry-based equations were derived giv-ing the maximum air-kerma rate magnitude and location through a first derivative root finding approach...
2016: Journal of Applied Clinical Medical Physics
Guy Divita, Marjorie E Carter, Le-Thuy Tran, Doug Redd, Qing T Zeng, Scott Duvall, Matthew H Samore, Adi V Gundlapalli
INTRODUCTION: Substantial amounts of clinically significant information are contained only within the narrative of the clinical notes in electronic medical records. The v3NLP Framework is a set of "best-of-breed" functionalities developed to transform this information into structured data for use in quality improvement, research, population health surveillance, and decision support. BACKGROUND: MetaMap, cTAKES and similar well-known natural language processing (NLP) tools do not have sufficient scalability out of the box...
2016: EGEMS
Ricardo Andrade, Martin Wannagat, Cecilia C Klein, Vicente Acuña, Alberto Marchetti-Spaccamela, Paulo V Milreu, Leen Stougie, Marie-France Sagot
BACKGROUND: What an organism needs at least from its environment to produce a set of metabolites, e.g. target(s) of interest and/or biomass, has been called a minimal precursor set. Early approaches to enumerate all minimal precursor sets took into account only the topology of the metabolic network (topological precursor sets). Due to cycles and the stoichiometric values of the reactions, it is often not possible to produce the target(s) from a topological precursor set in the sense that there is no feasible flux...
2016: Algorithms for Molecular Biology: AMB
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