bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biopsia transrectal ecodirigida de la próstata: estado del arte y guía práctica de consejos y trucos
Authors: Chavarriaga Soto Julián , Ocampo María Antonia , Gutiérrez Andrés Felipe 
Published: July 2018

Introducción y Objetivos La biopsia transrectal de la próstata (BTRP), fue propuesta por primera vez en 1937 y hasta 1981 se realizó la primera biopsia ecodirigida, actualmente es la vía de acceso a la próstata más utilizada por su fácil curva de aprendizaje como por el alto rendimiento diagnóstico, sin embargo, en el Reino Unido, el 68% de los urólogos no realizan BTRP porque consideran que no han recibido suficiente entrenamiento. El objetivo de este estudio es describir las diferentes técnicas utilizadas en la actualidad, las complicaciones del procedimiento y aportar una guía de consejos y trucos implementada en varios centros de referencia a la hora de realizar una BTRP para prevenir complicaciones, mejorar el desempeño de la prueba y del urólogo y estandarizar el método de toma de la BTRP.
Materiales y Métodos Realizamos una búsqueda en las bases de datos de PubMed, MEDLINE, SciELO utilizando las palabras claves “Transrectal ultrasound biopsy of the prostate” “tips and tricks” “Transperineal biopsy of the prostate” “Magnetic resonance imaging targeted biopsy” “MRI/US fusion biopsy”, basados en la literatura y en la experiencia de los autores de más de 1100 biopsias anuales entre los diferentes centros de referencia. Brindamos una guía práctica de consejos y trucos para facilitar el desempeño del urólogo en la BTRP.
Resultados La biopsia transrectal de próstata ecodirigida continúa siendo la primera opción para el abordaje diagnóstico del paciente con sospecha clínica de cáncer de próstata, es de gran importancia estandarizar el esquema de toma de la biopsia, y en nuestro caso recomendamos utilizar un esquema de 12 cores, definir la profilaxis antibióticas y la duración del tratamiento, y el uso de analgesia o anestesia local. Presentamos los consejos y trucos que hemos utilizado en nuestra práctica clínica en varios centros de referencia.
Renal Function in Cirrhosis: A Critical Review of Available Tools
Authors: Piano Salvatore , Brocca Alessandra , Angeli Paolo 
Published: July 2018

AbstractPatients with cirrhosis have a high prevalence of renal dysfunction. The susceptibility to renal dysfunction is due to both the severe splanchnic arterial vasodilation and the systemic inflammation observed in these patients. An accurate assessment of renal function is recommended in all patients with cirrhosis. Indeed, the renal function assessment guides the management of patients, helps to refine prognosis and to define transplant strategies. Despite its limitations, serum creatinine is still the most used biomarker for the estimation of glomerular filtration rate (GFR) and the assessment of acute kidney injury (AKI) in patients with cirrhosis. New biomarkers of GFR such as cystatin C may improve the assessment of GFR and the prognostic stratification in these patients. AKI is a life-threatening complication and needs a timely management. The differential diagnosis between hepatorenal syndrome (HRS) and acute tubular necrosis (ATN) is tricky in clinical practice. New biomarkers of kidney injury, such as neutrophil gelatinase-associated lipocalin and interleukin-18, represent useful tools in refining the discrimination between HRS and ATN. Patients with HRS need a prompt treatment with vasoconstrictors and albumin and a rapid evaluation for liver transplant eligibility. In this article, the authors reviewed the available tools in the diagnosis and management of renal dysfunction in cirrhosis.
Management Strategies for Diastasis Recti
Authors: Nahabedian Maurice 
Published: July 2018

AbstractDiastasis recti is a relatively common condition in which there is a midline abdominal bulge that can affect a variety of individuals. The etiology and diagnosis is well understood and optimal management depends on the degree of severity. Patients at high risk for diastasis recti include multiparous women, obese patients, and those with multiple previous operations. Diagnosis includes clinical examination and assessment of symptoms. Physical characteristics include a midline abdominal bulge without a fascial defect. Classification systems are based on the degree of separation between the paired midline rectus and myofascial deformity. Optimal management varies and includes simple plication of the midline defect, extensive plication of the anterior abdominal wall, and sometimes the use of resorbable or nonresorbable mesh.
A Comprehensive Review of Hepatic Sarcoid
Authors: Deutsch-Link Sasha , Fortuna Danielle , Weinberg Ethan 
Published: July 2018

AbstractSarcoidosis is a multisystem inflammatory disease, which is characterized by the development of noncaseating granulomas amid healthy tissue. While most commonly affecting the mediastinum and/or lungs, sarcoid can also affect the liver, resulting in “hepatic sarcoid.” The spectrum of disease in hepatic sarcoid is variable, ranging from asymptomatic or mild liver enzyme abnormalities to end-stage liver disease requiring liver transplantation. Because clinically-significant hepatic sarcoid is rare, research on epidemiology, clinical manifestations, and treatment is limited. The mainstays of hepatic sarcoid treatment have involved steroids and more recently, ursodeoxycholic acid; however, novel immunomodulatory agents provide new possibilities for management. Questions remain regarding screening, diagnostic modalities, and what to treat with and when. The purpose of this review is to summarize the available research on the epidemiology, clinical course, and management of hepatic sarcoid, and identify gaps in our knowledge to motivate future research.
Immunohistochemical Markers for Schwannomas, Neurofibromas and Malignant Peripheral Nerve Sheath Tumors—What Can the Recent Literature Tell Us?
Authors: Guedes-Corrêa José , Cardoso Rodrigo 
Published: July 2018

Introduction Schwannomas and neurofibromas are the two most common benign neoplasms of the peripheral nerve sheath, and although they are generally easy to distinguish, in some cases, they can closely resemble one another. Furthermore, malignant peripheral nerve sheath tumors (MPNSTs), another example of peripheral nerve sheath neoplasm, may likewise constitute, due to their morphology and lack of specific immunohistochemical markers, a challenging diagnostic.
Objective To bring attention to new and promising biomarkers for schwannomas, neurofibromas and MPNSTs and to outline, based on the recent literature, a immunohistochemical profile for each neoplasm at hand, as well as to emphasize the need for further studies that could help us understand their diagnostic potential and disrupt our dependence of limited and nonspecific biomarkers.
Methods An overview of the recent literature published in English on both the classical promising immunohistochemical markers of schwannomas, neurofibromas and MPNSTs was performed. We discarded case reports.
Conclusions There is still a lack of specific biomarkers for peripheral nerve tumors. However, plenty of new immunohistochemical markers have been coming to light with presumed higher specificity and more diverse helpful uses than the classical ones. For example, Sox10 is a good biomarker for differentiating schwannomas and neurofibromas from sarcomas, calretinin schwannomas from neurofibromas, TLE1 and HMGA2 MPNSTs from sarcomas, and nestin, EGFR, p16 and Ki-67 MPNSTs from different types of schwannomas and neurofibromas. There is still need for further studies; however, the potential of some of these promising markers, among others, should not be disregarded.
Selection of an ASIC1a-blocking combinatorial antibody that protects cells from ischemic death
Authors: Qiang Min , Dong Xue , Zha Zhao , Zuo Xiao-Kun , Song Xing-Lei , Zhao Lixia , Yuan Chao , Huang Chen , Tao Pingdong , Hu Qin , Li Wei-Guang , Hu Wanhui , Li Jie , Nie Yan , Buratto Damiano , Zonta Francesco , Ma Peixiang , Yu Zheng , Liu Lili , Zhang Yi , Yang Bei , Xie Jia , Xu Tian-Le , Qu Zhihu , Yang Guang , Lerner Richard A. 
Published: July 2018

Significance
Unfortunately, the need for ideal medical treatment of acute ischemic stroke is still largely unmet. One of the contributing factors to the deleterious neuronal death is the opening of acid-sensing ion channels (ASICs) at reduced pH, which in turn, activates other calcium-permeable channels that initiate the catastrophic cascade. Here, we report the discovery of an antibody that blocks the ASIC1a with high specificity and potency. Infusion of this antibody reduces the damaged area from brain ischemia in the murine stroke model. We hypothesize that using antibodies to target ASIC1a is a valid approach for future stroke therapy. The antibody that we report here has the potential to be further developed as drug candidate.
DoRes within CellMissy: dose-response analysis on cell migration and related data
Authors: Sergeant Gwendolien , Martens Lennart , Van Troys Marleen , Masuzzo Paola 
Published: July 2018

Abstract

Summary
In cancer research, cell-based assays are used to assess cell migration and invasion. The major bottleneck is the lack of automated tools to visualize and analyse the large amounts of biological dose-response data produced. To address this challenge, we have developed an automated and free software package for dose-response analyses, DoRes, which is released as an add-on of the freely available and open-source tool CellMissy, dedicated to the management and analysis of cell migration data. DoRes implements non-linear curve fitting functionality into a robust, user-friendly and flexible software package with the possibility of importing a tabular file or starting from a cell migration experiment. We demonstrate the ability of the software by analysing public dose-response data and a typical cell migration experiment, and show that the extracted dose-response parameters and the calculated statistical values are consistently comparable to those of the widely used, commercial software GraphPad Prism.

Availability and implementation
The software here presented is a new module in CellMissy, an open-source and cross-platform package dedicated to the management, storage and analysis of cell migration data. The new module is written in Java, and inherits the cross-platform support from CellMissy. Source code and binaries are freely available under the Apache2 open-source licence at https://github.com/compomics/cellmissy/.

Supplementary information
Supplementary data are available at Bioinformatics online.
4mCPred: machine learning methods for DNA N4-methylcytosine sites prediction
Authors: He Wenying , Jia Cangzhi , Zou Quan 
Published: July 2018

Abstract

Motivation
N4-methylcytosine (4mC), an important epigenetic modification formed by the action of specific methyltransferases, plays an essential role in DNA repair, expression and replication. The accurate identification of 4mC sites aids in-depth research to biological functions and mechanisms. Because, experimental identification of 4mC sites is time-consuming and costly, especially given the rapid accumulation of gene sequences. Supplementation with efficient computational methods is urgently needed.

Results
In this study, we developed a new tool, 4mCPred, for predicting 4mC sites in Caenorhabditis elegans, Drosophila melanogaster, Arabidopsis thaliana, Escherichia coli, Geoalkalibacter subterraneus and Geobacter pickeringii. 4mCPred consists of two independent models, 4mCPred_I and 4mCPred_II, for each species. The predictive results of independent and cross-species tests demonstrated that the performance of 4mCPred_I is a useful tool. To identify position-specific trinucleotide propensity (PSTNP) and electron-ion interaction potential features, we used the F-score method to construct predictive models and to compare their PSTNP features. Compared with other existing predictors, 4mCPred achieved much higher accuracies in rigorous jackknife and independent tests. We also analyzed the importance of different features in detail.

Availability and implementation
The web-server 4mCPred is accessible at http://server.malab.cn/4mCPred/index.jsp.

Supplementary information
Supplementary data are available at Bioinformatics online.
Herd Immunity Likely Protected the Men Who Have Sex With Men in the Recent Hepatitis A Outbreak in San Diego, California
Authors: Smith Davey , Huynh Christina , Moore Adam J , Frick Andrew , Anderson Christy , Porrachia Magali , Scott Brianna , Stous Sarah , Schooley Robert , Little Susan , Santos AsherLev T 
Published: July 2018

Abstract
A high seroprevalence of hepatitis A virus (81%) among human immunodeficiency virus–negative high-risk men who have sex with men is likely why this community was largely spared from a recent hepatitis A virus outbreak in San Diego, California.
Automated mapping of laboratory tests to LOINC codes using noisy labels in a national electronic health record system database
Authors: Parr Sharidan K , Shotwell Matthew S , Jeffery Alvin D , Lasko Thomas A , Matheny Michael E 
Published: July 2018

AbstractObjectiveStandards such as the Logical Observation Identifiers Names and Codes (LOINC®) are critical for interoperability and integrating data into common data models, but are inconsistently used. Without consistent mapping to standards, clinical data cannot be harmonized, shared, or interpreted in a meaningful context. We sought to develop an automated machine learning pipeline that leverages noisy labels to map laboratory data to LOINC codes.Materials and MethodsAcross 130 sites in the Department of Veterans Affairs Corporate Data Warehouse, we selected the 150 most commonly used laboratory tests with numeric results per site from 2000 through 2016. Using source data text and numeric fields, we developed a machine learning model and manually validated random samples from both labeled and unlabeled datasets.ResultsThe raw laboratory data consisted of &gt;6.5 billion test results, with 2215 distinct LOINC codes. The model predicted the correct LOINC code in 85% of the unlabeled data and 96% of the labeled data by test frequency. In the subset of labeled data where the original and model-predicted LOINC codes disagreed, the model-predicted LOINC code was correct in 83% of the data by test frequency.ConclusionUsing a completely automated process, we are able to assign LOINC codes to unlabeled data with high accuracy. When the model-predicted LOINC code differed from the original LOINC code, the model prediction was correct in the vast majority of cases. This scalable, automated algorithm may improve data quality and interoperability, while substantially reducing the manual effort currently needed to accurately map laboratory data.
Patient and healthcare provider views on a patient-reported outcomes portal
Authors: Cronin Robert M , Conway Douglas , Condon David , Jerome Rebecca N , Byrne Daniel W , Harris Paul A 
Published: July 2018

Abstract

Background
Over the past decade, public interest in managing health-related information for personal understanding and self-improvement has rapidly expanded. This study explored aspects of how patient-provided health information could be obtained through an electronic portal and presented to inform and engage patients while also providing information for healthcare providers.

Methods
We invited participants using ResearchMatch from 2 cohorts: (1) self-reported healthy volunteers (no medical conditions) and (2) individuals with a self-reported diagnosis of anxiety and/or depression. Participants used a secure web application (dashboard) to complete the PROMIS® domain survey(s) and then complete a feedback survey. A community engagement studio with 5 healthcare providers assessed perspectives on the feasibility and features of a portal to collect and display patient provided health information. We used bivariate analyses and regression analyses to determine differences between cohorts.

Results
A total of 480 participants completed the study (239 healthy, 241 anxiety and/or depression). While participants from the tw2o cohorts had significantly different PROMIS scores (p &lt; .05), both cohorts welcomed the concept of a patient-centric dashboard, saw value in sharing results with their healthcare provider, and wanted to view results over time. However, factors needing consideration before widespread use included personalization for the patient and their health issues, integration with existing information (eg electronic health records), and integration into clinician workflow.

Conclusions
Our findings demonstrated a strong desire among healthy people, patients with chronic diseases, and healthcare providers for a self-assessment portal that can collect patient-reported outcome metrics and deliver personalized feedback.
Strategy for Assessing New Drug Value in Orphan Diseases: An International Case Match Control Analysis of the PROPEL Study
Authors: O’Connor Owen A , Marchi Enrica , Volinn Weining , Shi Jin , Mehrling Thomas , Kim Won Seog 
Published: July 2018

AbstractBackgroundAlthough randomized studies are designed to assess overall survival (OS) benefit, the conduct of regulatory studies in patients with orphan diseases can be timely and costly without offering the same commercial return on the investment. The peripheral T-cell lymphomas (PTCL) represent a rare group of heterogeneous lymphoid malignancies with very poor prognosis. PROPEL was a pivotal phase II study that led to the accelerated approval of pralatrexate for patients with relapsed or refractory PTCL.MethodsAn international database of 859 patients was assembled from four institutions with an interest in PTCL, of which 386 were considered eligible for matching against the PROPEL criteria. Using a rigorous propensity score matching algorithm, a unique 1:1 case match of 80 patients was performed.ResultsThe analysis demonstrated an OS benefit for the PROPEL population with a median OS of 4.07 and 15.24 months (hazard ratio = 0.432, 95% confidence interval = 0.298 to 0.626), respectively, for the control and PROPEL populations. Highly statistically significant improvements in OS were noted for the PROPEL population about the subtype of PTCL (save anaplastic large cell lymphoma) and all age groups, including the elderly (>65 years of age). For patients on PROPEL, there was a statistically significant prolongation in progression free survival compared with the line of prior therapy, including those with refractory disease.ConclusionIn the context of this case-match-control study, patients treated on PROPEL experienced an OS advantage compared with an international database of historical controls. This information can help inform critical decision-making regarding clinical studies in PTCL.
Japanese Philosophy
Authors: Asakura Tomomi 
Published: July 2018

Japanese philosophy can be viewed, in a very simple way, as consisting of three historical phases: the classical thought, modern philosophy, and contemporary philosophy. In the first and classical phase, theoretical speculation in Japan is usually seen as a variation of East Asian intellectual tradition. Japanese thinkers from the seventh century to the eighteenth century used to work in this cultural sphere, which basically consists of Confucianism and Sinicized Buddhism, using classical Chinese for formal writing; they are by no means blind followers of Chinese thinkers, contributing to the development of philosophical speculation in the East Asian framework. During the Edo period (1603–1868), however, some thinkers started to depart from this framework by drawing either on the indigenous culture or on the knowledge of occidental civilization, which eventually led to the modernization, or Westernization, of Japanese society. The second, or modern, phase of Japanese philosophy began with the full-fledged introduction of Western philosophy during the Meiji period (1868–1912). As a result, there arose a theoretical task to synthesize Eastern and Western frameworks, and many pioneering works were produced in the first half of the twentieth century. The best-known modern Japanese philosopher is Nishida Kitarō (b. 1870–d. 1945). The Kyoto school of philosophy was formed through his influence, which shares the ambition to make “contributions to philosophy” with the Eastern tradition—especially Mahayana Buddhism—in the background. However, the Kyoto school had fallen into disrepute in the mid-twentieth century when Japan underwent a tremendous social and cultural change. The third and contemporary phase of Japanese philosophy spans from the postwar reconstruction of Japan to the present, when eminent researchers gather in the University of Tokyo and lead philosophical studies under the framework either of analytic or continental context, mostly refraining from mentioning the Eastern tradition. Recent philosophical research in Japan is increasingly getting free from such academic frameworks, producing some remarkable results; however, most of these contemporary works remain little known overseas.
Mourning Dove (Syilx Okanagan)
Authors: Lamont Victoria 
Published: July 2018

Mourning Dove (Syilx Okanagan, b. c. 1882–1888–d. 1936) was the second Indigenous woman in the United States to publish a novel, and she is a foundational figure in Indigenous American literature. Her novel Cogewea introduced what are now prominent themes in Indigenous writing: the mixed-blood figure poised between Indigenous and white cultures, critique of the trope of the “disappearing Indian,” and affirmation of Indigenous culture in the face of government policies designed to eradicate it. Mourning Dove lived during a period of profound dislocation for her people. At the turn of the twentieth century, the 1890 massacre at Wounded Knee was in recent memory, Indigenous tribes were forced from what remained of their traditional territories and confined to reservations, and children were sent to schools designed to assimilate them. Ironically, the very education Mourning Dove received at these schools enabled her to become an important activist and advocate for Indigenous people and their culture. Not surprisingly given colonial conditions, basic biographical details about Mourning Dove are uncertain. Records and family accounts give competing birthdates between 1882 and 1888. Her English name was Christine Quintasket, her Indigenous name was Humishuma, and her pen name was Mourning Dove. She grew up on the Colville reservation in Washington State and identified with the Syilx Okanagan tribe, whose traditional territory spans the US-Canada border. While historical documents suggest she was of wholly Indigenous ancestry, she identified herself as mixed blood. Mourning Dove attended both mission and BIA (Bureau of Indian Affairs) schools, as well as a clerical college in Calgary, Alberta, Canada, where she studied typing and English language. To support herself, she worked primarily as an agricultural laborer. Determined to be a writer, Mourning Dove managed to produce a novel, a collection of traditional Okanagan narratives, and an autobiography despite poverty, chronic health problems, and two difficult marriages. Her first work, the novel Cogewea, was written between 1912 and 1914, and it likely would not have been published without the assistance of Lucullus McWhorter, amateur ethnographer and activist for Indigenous people. The two met in 1914 and became close friends and collaborators. With McWhorter’s help, Cogewea was finally published in 1928, followed by Coyote Stories, a selection of traditional Okanagan narratives, in 1933. Mourning Dove’s autobiography was published posthumously in 1990. In addition to her writing, Mourning Dove was active in tribal politics and advocacy for Indigenous people. She died in 1936.