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Varsha Manucha, Mary T Sessums, Jack Lewin, Israh Akhtar
The MiT family translocation renal cell carcinomas (RCCs) are relatively rare in comparison to the conventional RCC. The cytologic features overlap with conventional clear cell RCC and papillary RCCs, thereby making the diagnosis extremely challenging. Here, we describe a case of TFE3 translocation associated RCC in a 58-year-old patient, with emphasis on cytomorphologic features and clues toward this diagnostic entity. Correlating the cytohistologic findings and review of touch imprints revealed that presence of hyaline nodules resembling leisegang rings and psammoma bodies in cytologic smears from kidney tumors serve as an important clue in raising a suspicion for the diagnosis of MiT family translocation RCCs...
October 12, 2017: Diagnostic Cytopathology
Matteo Cesari, Jesper Mehlsen, Anne-Birgitte Mehlsen, Helge Bjarup Dissing Sorensen
T-wave amplitude (TWA) has been proposed as a marker of the innervation of the myocardium. Until now, TWA has been calculated manually or with poor algorithms, thus making its use not efficient in a clinical environment. We introduce a new wavelet-based algorithm for the delineation QRS complexes and T-waves, and the automatic calculation of TWA. When validated in the MIT/BIH Arrhythmia database, the QRS detector achieved sensitivity and positive predictive value of 99.84% and 99.87%, respectively. The algorithm was validated also on the QT database and it achieved sensitivity of 99...
2017: IEEE Journal of Translational Engineering in Health and Medicine
Sebastian Proost, Agnieszka Krawczyk, Marek Mutwil
BACKGROUND: Since experimental elucidation of gene function is often laborious, various in silico methods have been developed to predict gene function of uncharacterized genes. Since functionally related genes are often expressed in the same tissues, conditions and developmental stages (co-expressed), functional annotation of characterized genes can be transferred to co-expressed genes lacking annotation. With genome-wide expression data available, the construction of co-expression networks, where genes are nodes and edges connect significantly co-expressed genes, provides unprecedented opportunities to predict gene function...
October 10, 2017: BMC Bioinformatics
Elodie Blanc, Justin Caron, Charles Fant, Erwan Monier
While climate change impacts on crop yields has been extensively studied, estimating the impact of water shortages on irrigated crop yields is challenging because the water resources management system is complex. To investigate this issue, we integrate a crop yield reduction module and a water resources model into the MIT Integrated Global System Modeling framework, an integrated assessment model linking a global economic model to an Earth system model. We assess the effects of climate and socioeconomic changes on water availability for irrigation in the U...
August 2017: Earth's Future
Ali Mohammad Alqudah
Cardiac related biosignals modelling is very important for detecting, classification, compression and transmission of such health-related signals. This paper introduces a new, fast and accurate method for modelling the cardiac related biosignals (ECG and PPG) based on a mixture of Gaussian waves. For any signal, at first, the start and end of the ECG beat or PPG pulse is detected, then the baseline is detected then subtracted from the original signal, after that the signal is divided into two signals positive and negative, each modelled separately then incorporated together to form the modelled signal...
October 6, 2017: Journal of Medical Engineering & Technology
Luc Patiny, Michaël Zasso, Daniel Kostro, Andrés Bernal, Andrés M Castillo, Alejandro Bolaños, Miguel A Asencio, Norman Pellet, Matthew Todd, Nils Schloerer, Stefan Kuhn, Elaine Holmes, Sacha Javor, Julien Wist
NMR is a mature technique that is well established and adopted in a wide range of research facilities from laboratories to hospitals. This accounts for large amounts of valuable experimental data that may be readily exported into a standard and open format. Yet the publication of these data faces an important issue: raw data are not made available; instead, the information is slimed down into a string of characters (the list of peaks). Although historical limitations of technology explain this practice, it is not acceptable in the era of internet...
October 5, 2017: Magnetic Resonance in Chemistry: MRC
Tino Wetzig, Diana Kohn
No abstract text is available yet for this article.
October 2017: Journal der Deutschen Dermatologischen Gesellschaft, Journal of the German Society of Dermatology: JDDG
Rola M Saleeb, John R Srigley, Joan Sweet, Cedric Doucet, Virginie Royal, Ying-Bei Chen, Fadi Brimo, Andrew Evans
MiT family translocation tumors are a group of neoplasms characterized by translocations involving MiT family transcription factors. The translocation renal cell carcinomas, TFE3 (Xp11.2) and TFEB (t6;11) are known members of this family. Melanotic Xp11 translocation renal cancer is a more recently described entity. To date only 14 cases have been described. It is characterized by a distinct set of features including a nested epithelioid morphology, melanin pigmentation, labeling for markers of melanocytic differentiation, lack of labeling for markers of renal tubular differentiation, predominance in a younger age population and association with aggressive clinical behavior...
August 25, 2017: Pathology, Research and Practice
Joe Wandy, Yunfeng Zhu, Justin J J van der Hooft, Rónán Daly, Michael P Barrett, Simon Rogers
Motivation: We recently published MS2LDA, a method for the decomposition of sets of molecular fragment data derived from large metabolomics experiments. To make the method more widely available to the community, here we present, a web application that allows users to upload their data, run MS2LDA analyses and explore the results through interactive visualisations. Results: takes tandem mass spectrometry data in many standard formats and allows the user to infer the sets of fragment and neutral loss features that co-occur together (Mass2Motifs)...
September 14, 2017: Bioinformatics
Tarmo Äijö, Christian L Müller, Richard Bonneau
Motivation: The number of microbial and metagenomic studies has increased drastically due to advancements in next-generation sequencing-based measurement techniques. Statistical analysis and the validity of conclusions drawn from (time series) 16S rRNA and other metagenomic sequencing data is hampered by the presence of significant amount of noise and missing data (sampling zeros). Accounting uncertainty in microbiome data is often challenging due to the difficulty of obtaining biological replicates...
September 13, 2017: Bioinformatics
Sara Brin Rosenthal, Julia Len, Mikayla Webster, Aaron Gary, Amanda Birmingham, Kathleen M Fisch
Motivation: Network biology is widely used to elucidate mechanisms of disease and biological processes. The ability to interact with biological networks is important for hypothesis generation and to give researchers an intuitive understanding of the data. We present visJS2jupyter, a tool designed to embed interactive networks in Jupyter notebooks to streamline network analysis and to promote reproducible research. Results: The tool provides functions for performing and visualizing useful network operations in biology, including network overlap, network propagation around a focal set of genes, and co-localization of two sets of seed genes...
September 14, 2017: Bioinformatics
Fabiano B Menegidio, Daniela L Jabes, Regina Costa de Oliveira, Luiz R Nunes
Summary: This manuscript introduces and describes Dugong, a Docker image based on Ubuntu 16.04, which automates installation of more than 3500 bioinformatics tools (along with their respective libraries and dependencies), in alternative computational environments. The software operates through a user-friendly XFCE4 graphic interface that allows software management and installation by users not fully familiarized with the Linux command line and provides the Jupyter Notebook to assist in the delivery and exchange of consistent and reproducible protocols and results across laboratories, assisting in the development of open science projects...
September 4, 2017: Bioinformatics
Jiayin Ling, John P Voccio, Seungyong Hahn, Timing Qu, Juan Bascuñán, Yukikazu Iwasa
This paper presents construction details and test results of a persistent-mode 0.5-T MgB2 magnet developed at the Francis Bitter Magnet Lab, MIT. The magnet, of 276-mm inner diameter and 290-mm outer diameter, consisted of a stack of 8 solenoidal coils with a total height of 460 mm. Each coil was wound with monofilament MgB2 wire, equipped with a persistent-current switch and terminated with a superconducting joint, forming an individual superconducting loop. Resistive solder joints connected the 8 coils in series...
February 2017: Superconductor Science & Technology
Steven Foltz, Wen-Wei Liang, Mingchao Xie, Li Ding
Summary: MIRMMR predicts microsatellite instability status in cancer samples using methylation and mutation information, in contrast to existing methods that rely on observed microsatellites. Additionally, MIRMMR highlights those genetic alterations contributing to microsatellite instability. Availability: Source code is freely available at under the MIT license, implemented in R, and supported on Unix/OS X operating systems. Supplementary information: Supplementary data are available at Bioinformatics online...
August 17, 2017: Bioinformatics
Alba Gutiérrez-Sacristán, Carles Hernández-Ferrer, Juan R González, Laura I Furlong
Motivation: Psychiatric disorders have a great impact on morbidity and mortality. Genotype-phenotype resources for psychiatric diseases are key to enable the translation of research findings to a better care of patients. PsyGeNET is a knowledge resource on psychiatric diseases and their genes, developed by text mining and curated by domain experts. Results: We present psygenet2r, an R package that contains a variety of functions for leveraging PsyGeNET database and facilitating its analysis and interpretation...
August 17, 2017: Bioinformatics
Jennifer Berglund
At the age of 14, Linda Griffith experienced such abnormally painful periods that her doctor had already put her on birth control pills. They helped but only a little. In graduate school, a boyfriend convinced her to go off the pills, and her periods became so painful, she couldn't walk.
September 2017: IEEE Pulse
Liuqing Wei, Xuemin Zhang, Zhen Li, Jingyao Liu
In the Multiple Identity Tracking (MIT) task, categorical distinctions between targets and distractors have been found to facilitate tracking (Wei, Zhang, Lyu, & Li in Frontiers in Psychology, 7, 589, 2016). The purpose of this study was to further investigate the reasons for the facilitation effect, through six experiments. The results of Experiments 1-3 excluded the potential explanations of visual distinctiveness, attentional distribution strategy, and a working memory mechanism, respectively. When objects' visual information was preserved and categorical information was removed, the facilitation effect disappeared, suggesting that the visual distinctiveness between targets and distractors was not the main reason for the facilitation effect...
September 27, 2017: Attention, Perception & Psychophysics
Elif Yaman Dosdogru, Feyza Nur Gorken, Arzu Pinar Erdem, Evren Oztas, Gulnaz Marsan, Elif Sepet, Zeynep Aytepe
PURPOSE: The aim of this study was to assess the association between the presence of maxillary incisor trauma (MIT) with age, gender, dentition type, the degree of overjet (OJ), lip form, respiratory type and dental arch form in patients with Class II division 1 dental malocclusion. SUBJECTS AND METHODS: 256 patients (mean age: 15.80 ± 2.2) were included in this study. The patients' gender, dentition type, superior lip form, dental arch form and respiratory type were recorded...
2017: J Istanb Univ Fac Dent
Mohamed Elgendi, Marianna Meo, Derek Abbott
A robust and numerically-efficient method based on two moving average filters, followed by a dynamic event-related threshold, has been developed to detect P and T waves in electrocardiogram (ECG) signals as a proof-of-concept. Detection of P and T waves is affected by the quality and abnormalities in ECG recordings; the proposed method can detect P and T waves simultaneously through a unique algorithm despite these challenges. The algorithm was tested on arrhythmic ECG signals extracted from the MIT-BIH arrhythmia database with 21,702 beats...
October 17, 2016: Bioengineering
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