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Wu Liu, María Martinón-Torres, Yousuke Kaifu, Xiujie Wu, Reiko T Kono, Chun-Hsiang Chang, Pianpian Wei, Song Xing, Wanbo Huang, José María Bermúdez de Castro
OBJECTIVES: This study presents the first detailed morphological description and comparison of a Middle Pleistocene hominin mandibular fragment (PA 831) and associated teeth from the Hexian site in Eastern China. We aim to investigate where the Hexian mandible fits within the genus Homo variability in the light of an increased and better characterized Asian fossils record. METHODS: Comparative samples include Pleistocene Homo mandibles and teeth from Africa, Asia, and Europe, as well as earlier African hominins (Australopithecus and early Homo) and Holocene recent humans...
January 21, 2017: American Journal of Physical Anthropology
Evelyn W Williams, Elliot M Gardner, Robert Harris, Arunrat Chaveerach, Joan T Pereira, Nyree J C Zerega
BACKGROUND AND AIMS: The breadfruit genus (Artocarpus, Moraceae) includes valuable underutilized fruit tree crops with a centre of diversity in Southeast Asia. It belongs to the monophyletic tribe Artocarpeae, whose only other members include two small neotropical genera. This study aimed to reconstruct the phylogeny, estimate divergence dates and infer ancestral ranges of Artocarpeae, especially Artocarpus, to better understand spatial and temporal evolutionary relationships and dispersal patterns in a geologically complex region...
January 10, 2017: Annals of Botany
Andrés Mejías, Reyes S Herrera, Marco A Márquez, Antonio José Calderón, Isaías González, José Manuel Andújar
There are several specific solutions for accessing sensors and actuators present in any process or system through a TCP/IP network, either local or a wide area type like the Internet. The usage of sensors and actuators of different nature and diverse interfaces (SPI, I2C, analogue, etc.) makes access to them from a network in a homogeneous and secure way more complex. A framework, including both software and hardware resources, is necessary to simplify and unify networked access to these devices. In this paper, a set of open-source software tools, specifically designed to cover the different issues concerning the access to sensors and actuators, and two proposed low-cost hardware architectures to operate with the abovementioned software tools are presented...
January 5, 2017: Sensors
Sajad Mirzaei, Yufeng Wu
MOTIVATION: Haplotypes from one or multiple related populations share a common genealogical history. If this shared genealogy can be inferred from haplotypes, it can be very useful for many population genetics problems. However, with the presence of recombination, the genealogical history of haplotypes is complex and cannot be represented by a single genealogical tree. Therefore, inference of genealogical history with recombination is much more challenging than the case of no recombination...
January 8, 2017: Bioinformatics
Miroslav Radojević, Erik Meijering
MOTIVATION: The functionality of neurons and their role in neuronal networks is tightly connected to the cell morphology. A fundamental problem in many neurobiological studies aiming to unravel this connection is the digital reconstruction of neuronal cell morphology from microscopic image data. Many methods have been developed for this, but they are far from perfect, and better methods are needed. RESULTS: Here we present a new method for tracing neuron centerlines needed for full reconstruction...
January 8, 2017: Bioinformatics
Philipp Bruland, Martin Dugas
BACKGROUND: Data capture for clinical registries or pilot studies is often performed in spreadsheet-based applications like Microsoft Excel or IBM SPSS. Usually, data is transferred into statistic software, such as SAS, R or IBM SPSS Statistics, for analyses afterwards. Spreadsheet-based solutions suffer from several drawbacks: It is generally not possible to ensure a sufficient right and role management; it is not traced who has changed data when and why. Therefore, such systems are not able to comply with regulatory requirements for electronic data capture in clinical trials...
January 7, 2017: BMC Medical Informatics and Decision Making
Katrin Tebel, Vivien Boldt, Anne Steininger, Matthias Port, Grit Ebert, Reinhard Ullmann
BACKGROUND: The analysis of DNA copy number variants (CNV) has increasing impact in the field of genetic diagnostics and research. However, the interpretation of CNV data derived from high resolution array CGH or NGS platforms is complicated by the considerable variability of the human genome. Therefore, tools for multidimensional data analysis and comparison of patient cohorts are needed to assist in the discrimination of clinically relevant CNVs from others. RESULTS: We developed GenomeCAT, a standalone Java application for the analysis and integrative visualization of CNVs...
January 6, 2017: BMC Bioinformatics
J Richart, A Otal, S Rodriguez, M Santos, J Perez-Calatayud
PURPOSE: ABS and GEC-ESTRO have recommended MRI T2 for image guided brachytherapy. Recently, a new applicator (Benidorm Template, TB) has been developed in our Department (Rodriguez et al 2015). TB is fully MRI compatible because the Titanium needles and it allows the use of intrauterine tandem. Currently, TPS applicators library are not currently available for non-rigid applicators in case of interstitial component as the TB.The purpose of this work is to present the development of a library for the TB, together with its use on a pre-planning technique...
June 2016: Medical Physics
C Wu
PURPOSE: To implement an automatic electronic PDF plan reporting tool for Philips Pinnacle treatment planning system (TPS) METHODS: An electronic treatment plan reporting software is developed by us to enable fully automatic PDF report from Pinnacle TPS to external EMR programs such as MOSAIQ. The tool is named "plan2pdf". plan2pdf is implemented using Pinnacle scripts, Java and UNIX shell scripts, without any external program needed. plan2pdf supports full auto-mode and manual mode reporting...
June 2016: Medical Physics
K-H Song, C-H Yoo, S-I Lim, B-Y Choe
PURPOSE: The objective of this study is to evaluate the relaxation time of methylene resonance in comparison with other lipid resonances. METHODS: The examinations were performed on a 3.0T MRI scanner using a four-channel animal coil. Eight more Sprague-Dawley rats in the same baseline weight range were housed with ad libitum access to water and a high-fat (HF) diet (60% fat, 20% protein, and 20% carbohydrate). In order to avoid large blood vessels, a voxel (0.8×0...
June 2016: Medical Physics
Y Tschudi
PURPOSE: To create an automatic workflow for evaluation of thresholds of restricted diffusion, based on Apparent Diffusion Coefficient (ADC) values in multiparametric (mp)MRI of the prostate. To investigate the association of these volumes with biopsy Gleason Score (GS). METHODS: Patients with prostate cancer, imaged on 3T Discovery MR750 (GE, Waukesha, WI) magnet were selected from departmental database based on the presence of mpMRI exam. All subsequent analyses were performed using Java plugins in MIM (MIM, Cleveland, Ohio)...
June 2016: Medical Physics
K-H Song, S-I Lim, C-H Yoo, B-Y Choe
PURPOSE: The objective of this study is to compare lipid contents using localized point-resolved spectroscopy (PRESS) and stimulated echo acquisition mode (STEAM) sequences to assess lipid resonances in the liver, using in vivo high-resolution spectra at 9.4 T. METHODS: The examinations were performed on a Bruker 9.4T scanner using 4-channel animal coil for higher resolution. We used PRESS (repetition time [TR]/ TE = 3500/20 ms; number of signal averages [NSA] = 128; acquisition data points = 2048) and STEAM (TR/TM/TE = 3500/10/20 ms; NSA = 128; acquisition data points = 2048)...
June 2016: Medical Physics
Alex V Kochetov, Jens Allmer, Alexandra I Klimenko, Bulat S Zuraev, Yury G Matushkin, Sergey A Lashin
MOTIVATION: Protein synthesis is not a straight forward process and one gene locus can produce many isoforms, for example, by starting mRNA translation from alternative start sites. altORF evaluator (altORFev) predicts alternative open reading frames within eukaryotic mRNA translated by a linear scanning mechanism and its modifications (leaky scanning and reinitiation). The program reveals the efficiently translated altORFs recognized by the majority of 40S ribosomal subunits landing on the 5'-end of an mRNA...
December 30, 2016: Bioinformatics
Yongjun Piao, Seong Keon Lee, Eun-Joon Lee, Keith D Robertson, Huidong Shi, Keun Ho Ryu, Jeong-Hyeon Choi
MOTIVATION: Chromatin accessibility plays a key role in epigenetic regulation of gene activation and silencing. Open chromatin regions allow regulatory elements such as transcription factors and polymerases to bind for gene expression while closed chromatin regions prevent the activity of transcriptional machinery. Recently, Methyltransferase Accessibility Protocol for individual templates-Bisulfite Genome Sequencing (MAPit-BGS) and nucleosome occupancy and methylome sequencing (NOMe-seq) have been developed for simultaneously profiling chromatin accessibility and DNA methylation on single molecules...
December 29, 2016: Bioinformatics
Ralf Eggeling, Ivo Grosse, Jan Grau
: Recent studies have shown that the traditional position weight matrix model is often insufficient for modeling transcription factor binding sites, as intra-motif dependencies play a significant role for an accurate description of binding motifs. Here, we present the Java application InMoDe, a collection of tools for learning, leveraging and visualizing such dependencies of putative higher order. The distinguishing feature of InMoDe is a robust model selection from a class of parsimonious models, taking into account dependencies only if justified by the data while choosing for simplicity otherwise...
December 28, 2016: Bioinformatics
Erry Yudhya Mulyani, Mury Kuswari, Sudikno, Sandjaja, Fitrah Ernawati
BACKGROUND AND OBJECTIVES: Vitamin A deficiency is particularly common among children younger than 5 years. In 2011, a study conducted in West Java revealed that the prevalence of vitamin A deficiency in children aged 6-11 months, 12-23 months, and 24-59 months was 18.2%, 15.2%, and 9.9%, respectively. The present study analysed the differences in vitamin A intake and serum retinol in all the preschool children from Grobogan and Kudus, Central Java. METHODS AND STUDY DESIGN: The baseline data of vitamin A efficacy were analysed...
December 2016: Asia Pacific Journal of Clinical Nutrition
Martha Zakrzewski, Carla Proietti, Jonathan J Ellis, Shihab Hasan, Marie-Jo Brion, Bernard Berger, Lutz Krause
: Calypso is an easy-to-use online software suite that allows non-expert users to mine, interpret and compare taxonomic information from metagenomic or 16S rDNA datasets. Calypso has a focus on multivariate statistical approaches that can identify complex environment-microbiome associations. The software enables quantitative visualizations, statistical testing, multivariate analysis, supervised learning, factor analysis, multivariable regression, network analysis and diversity estimates...
December 24, 2016: Bioinformatics
Sijin He, May Yong, Paul M Matthews, Yike Guo
MOTIVATION: TranSMART has a wide range of functionalities for translational research and a large user community, but it does not support imaging data. In this context, imaging data typically includes 2D or 3D sets of magnitude data and metadata information. Imaging data may summarise complex feature descriptions in a less biased fashion than user defined plain texts and numeric numbers. Imaging data also is contextualised by other data sets and may be analysed jointly with other data that can explain features or their variation...
December 24, 2016: Bioinformatics
Csaba Turzó, Péter Juhász, Zoltán Papp, Zoltán Szöllősi
INTRODUCTION AND AIM: The practices of autopsies and waivers in three Hungarian counties subject to the same statutory framework in a 5-year interval have been examined, with special attention to cases of non-natural death. METHOD: The summary data included in the post mortem examination certificates, for the years between 2006 and 2010, in a breakdown according to counties, covering all cases of death were analysed. The work was assisted by a Java-based software programme...
December 2016: Orvosi Hetilap
Toshihiro Tokiwa, Atsushi Kojima, Shun Sasaki, Rie Kubota, Kazunori Ike
Five individuals of the domestic Java sparrows, Lonchura oryzivora (Aves: Estrildidae), were examined for coccidian parasites. Sporulated oocysts had two sporocysts containing four sporozoites each. Sporulated oocysts (n=30) were spherical, with a two splinter-like polar granules. Oocyst size was 22.1×20.7 (20.0-25.0×20.0-22.5)μm. They had a thick wall that consisted of a pale yellow outer layer and a dark yellow inner layer, and lacked micropyle and residuum. Sporocysts (n=60) were elongated ovoid 14.1×9...
December 18, 2016: Parasitology International
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