bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global Alliance for Genomics and Health Meets Bioconductor: Toward Reproducible and Agile Cancer Genomics at Cloud Scale
Authors: Carey Vincent J. , Ramos Marcel , Stubbs Benjamin J. , Gopaulakrishnan Shweta , Oh Sehyun , Turaga Nitesh , Waldron Levi , Morgan Martin 
Published: May 2020

PURPOSE Institutional efforts toward the democratization of cloud-scale data and analysis methods for cancer genomics are proceeding rapidly. As part of this effort, we bridge two major bioinformatic initiatives: the Global Alliance for Genomics and Health (GA4GH) and Bioconductor. METHODS We describe in detail a use case in pancancer transcriptomics conducted by blending implementations of the GA4GH Workflow Execution Services and Tool Registry Service concepts with the Bioconductor curatedTCGAData and BiocOncoTK packages. RESULTS We carried out the analysis with a formally archived workflow and container at dockstore.org and a workspace and notebook at app.terra.bio. The analysis identified relationships between microsatellite instability and biomarkers of immune dysregulation at a finer level of granularity than previously reported. Our use of standard approaches to containerization and workflow programming allows this analysis to be replicated and extended. CONCLUSION Experimental use of dockstore.org and app.terra.bio in concert with Bioconductor enabled novel statistical analysis of large genomic projects without the need for local supercomputing resources but involved challenges related to container design, script archiving, and unit testing. Best practices and cost/benefit metrics for the management and analysis of globally federated genomic data and annotation are evolving. The creation and execution of use cases like the one reported here will be helpful in the development and comparison of approaches to federated data/analysis systems in cancer genomics.
The use of the PD-1/PD-L1 pathway as an immunotherapy in oncological diseases, autoimmune diseases and infectious diseases
Authors: Madras Dominika Katarzyna , Rocka Agata Agnieszka , Szumna Klaudia Daria , Jasielski Patryk Piotr , Piędel Faustyna 
Published: May 2020

Introduction: PD-1 is programmed death receptor 1 belonging to the CD28 family of receptors. Immune cells have this receptor on their surface. PD-L1 allows cancer cells to avoid the host's response. Connection to the PD-1 receptor leads to the death of the immune cell.Objective: The use of PD-1 receptors in the treatment of oncological, autoimmune and infectious diseases.Abbreviated description of the state of knowledge: The development and progression of immunotherapy in recent years has resulted in the approval of five immunotherapy pathways targeting PD-1 (pembrolizumab and durvalumab) or PD-L1 (atezolizumab, nivolumab and avelumab) in patients with progression during or after cisplatin based chemotherapy. The latest updates show that in some types of cancer, positive PD-L1 expression has an effect on treatment effect and qualification. These therapies are used, among others in melanoma, lymphomas, kidney cancer or breast cancer. PD-1 is also used to treat autoimmune and infectious diseases.Conclusions: Understanding the mechanism of the PD-1/PD-L1 pathway allows to design targeted therapy for individuals. It has been already used in NSCLC treatment program, whether bladder cancer or melanoma. Immunotherapy increases the survival time of patients with advanced stages of cancer. The therapies targeting the PD-1/PD-L1 pathway in autoimmune and infectious diseases are in clinical trials.
Age-related relationship between the development of hyperplastic processes and VEGF expression in endometrial cells
Authors: Chumak Z. V. , Shapoval M. V. , Artyomenko V. V. 
Published: May 2020

The existence of a clear tendency to increase the prevalence of hormone-dependent diseases and endometrial cancer against the background of increasing the frequency of their occurrence and rejuvenation of the age of manifestation leads to the search for new possible markers of diagnosis and prognosis of the development of pathological process. Angiogenesis is one of the forms that lead to the formation of new blood vessels, with an increased metabolic need for perfusion of existing vessels. The vascular endothelial growth factor family (VEGF) is a protein that is the major inducer of angiogenesis. The objective: To study the expression of VEGF in endometrial cells in proliferative, hyperplastic, atrophic states at women’s different ages. Materials and methods. A retrospective analysis of medical records of the pathohistological bureau for the period 2014-2016 was conducted. 2196 pathomorphological findings of endometrial tissue specimens have been examined. Estimation of VEGF expression was performed in 417 endometrial specimens, in the cohorts of the study: in the reproductive, perimenopausal, postmenopausal periods, respectively, in groups with physiological endometrial proliferation phase, hyperplastic, atypical, atrophic endometrium. The results were statistically processed. Results and discussion. Analyzing the data presented, higher VEGF expression was detected in atypical hyperplasia in all age categories, but it was likely that higher rates were established in the postmenopausal period, with atypical endometrial hyperplasia, suggesting physicians' alertness to the process in this category. Probably low were indexes found at atrophic endometrium in this age category, which confirms the endometrial preservation of its growth factors, and in the presence of processes that stimulate the proliferation of the organ, they can trigger at the molecular-genetic level, neoplastic mechanisms. The data of the retrospective analysis confirm the growth of atypical form of hyperplastic processes and their maximum detection in the age categories 41 - 45 and 46 - 50 years old, and the beginning of detection of endometrial malignancy from the age of 46 - 50 years old, with a gradual increase with age. Conclusions. Expression of VEGF level in endometrial tissue cells as an inducer of angiogenesis can be a promising marker for the diagnosis of the risk of proliferative conditions and their prognosis, especially in relation to other markers characterizing immunohistochemical and molecular genetic cellular parameters.
Plant based diet and cardio-metabolic disease
Authors: Dąbrowska Justyna , Wójcik Magdalena , Borowik Joanna , Kuśmierczuk Kinga , Pieciewicz-Szczęsna Halina 
Published: May 2020

Introduction: Modern lifestyle, especially diet have a great impact on health. The number of people suffering from conditions related to lifestyle is growing rapidly. Illnesses related to lifestyle, specifically to diet are large health and economic burdens, which makes them the leading priorities of our time. Coronary heart disease (CHD), stroke, type 2 diabetes, and obesity are some of cardio-metabolic diseases related to diet. Plant-based diets are dietary patterns in which a high intake of plant food is emphasized and the intake of animal products is limited. Plant based diet was associated with decreased risk of cardio-metabolic disease.The aim of the study: The purpose of this systemic review was to collect and analyse current data of plant based diet and its effect on health.Material and method: Standard criteria were used to review the literature data. The search of articles in the PubMed and Google Scholar database was carried out using the following keywords: plant based diet, vegetarian diet, cardiovascular disease, type 2 diabetes, hypercholesterolemia.Description of the state of knowledge: Red meat and, especially processed meat, is source of cholesterol, saturated fatty acids, and sodium, which makes it a risk factors for metabolic disorders. Healthy plant based diet can positively affect cardiovascular health in many ways. High fiber content makes those diets low in energy density, flavonoids that are present in fruits and vegetables and also high content of antioxidants. Plant based diet was also shown to be helpful in reducing weight.Summary: Many risk factors of cardio-metabolic disease are related to our lifestyle and dietary choices . Changes towards plant based diet can be beneficial for our health in many ways. Healthy plant based diet should be considered as a nonpharmaceutical approach to prevent and treat cardio-metabolic diseases.
Does Competition Improve Analysts’ Forecast Informativeness?
Authors: Banerjee Sanjay 
Published: May 2020

This paper studies the effect of competition on analysts’ forecast informativeness. Analysts compete to achieve a higher rank in forecast accuracy. Competition can impair, improve, or have no effect on analysts’ forecast informativeness. Competition impairs informativeness if and only if the prior uncertainty of the economic state is high, and analysts’ private signals are positively correlated conditional on the state. The more intense the competition in terms of a higher prize-to-penalty ratio and a stronger signal correlation, the less informative the forecasts. The higher the number of competing analysts, the greater the likelihood that analyst forecasts are less informative.This paper was accepted by Suraj Srinivasan, accounting.
High-speed fiber-optic scanning nonlinear endomicroscopy for imaging neuron dynamics in vivo
Authors: Park Hyeon-Cheol , Guan Honghua , Li Ang , Yue Yuanlei , Li Ming-Jun , Lu Hui , Li Xingde 
Published: May 2020

Fiber-optic-based two-photon fluorescence endomicroscopy is emerging as an enabling technology for in vivo histological imaging of internal organs and functional neuronal imaging on freely-behaving animals. However, high-speed imaging remains challenging due to the expense of miniaturization and lack of suited fast beam scanners. For many applications, a higher imaging speed is highly desired, especially for monitoring functional dynamics such as transient dendritic responses in neuroscience. This Letter reports the development of a fast fiber-optic scanning endo-microscope with an imaging speed higher than 26 frames/s. In vivo neural dynamics imaging with the high-speed endomicroscope was performed on a freely-behaving mouse over the primary motor cortex that expressed GCaMP6m. The results demonstrate its capability of real-time monitoring of transient neuronal dynamics with very fine temporal resolution.
Gender Matters: Characteristics of Hepatocellular Carcinoma in Women From a Large, Multicenter Study in the United States
Authors: Phipps Meaghan , Livanos Alexandra , Guo Averill , Pomenti Sydney , Yeh Jonathan , Dakhoul Lara , Burney Heather , Kettler Carla , Liu Hao , Miller Ethan , Gawrieh Samer , deLemos Andrew , Scanga Andrew , Chalasani Naga , Wattacheril Julia 
Published: May 2020

INTRODUCTION:
Hepatocellular carcinoma (HCC) is the fourth leading cause of cancer-related death worldwide, affecting men to women at a ratio of about 4:1. Risk factors, characteristics, and outcomes for HCC in women in the United States remain poorly understood; therefore, we aim to explore gender differences further.

METHODS:
Patients diagnosed with HCC between January 2000 and June 2014 at 5 large centers were identified. Clinical information, tumor characteristics, and survival data were extracted manually. The presence of underlying cirrhosis was assessed based on published criteria.

RESULTS:
Of 5,327 patients with HCC in our cohort, 1,203 (22.6%) were women. There were important differences in the underlying etiology of liver disease between the 2 genders (P < 0.0001): women had a significantly higher frequency of nonalcoholic fatty liver disease (23% vs 12%) and lower frequency of alcoholic liver disease (5% vs 15%). The proportion of noncirrhotic HCC was significantly higher among women (17% vs 10%, P < 0.0001). Women had less-advanced HCC at presentation by tumor, node, metastasis staging (P < 0.0001) and a higher proportion within Milan criteria (39% vs 35%, P = 0.002). Women had a greater overall survival (2.5 ± 2.9 years vs 2.2 ± 2.7 years, P = 0.0031).

DISCUSSION:
The frequency of underlying nonalcoholic fatty liver disease and noncirrhotic HCC were significantly higher in women than men in this large cohort. Women presented with less-advanced HCC and had a greater overall survival. Further investigation is warranted to explore potential mechanisms and implications for these gender differences, especially with noncirrhotic HCC (see Visual Abstract, Supplementary Digital Content 1, http://links.lww.com/AJG/B535).
Colorectal Cancer Litigation: 1988–2018
Authors: Panuganti Pranati L. , Hartnett Davis A. , Eltorai Adam E. M. , Eltorai Mahmoud I. , Daniels Alan H. 
Published: May 2020

INTRODUCTION:
The purpose of this study was to examine colorectal cancer (CRC) malpractice suits over the past 20 years in the United States and evaluate the most common allegations, lawsuit outcomes, indemnity payment amounts, patient outcomes, and physician characteristics.

METHODS:
The malpractice section of VerdictSearch, a legal database, was queried for cases in which CRC was a principle component of the lawsuit. Legal notes were used to characterize plaintiff allegations, verdict, financial compensation, and case year. Clinical history for each case were analyzed for patient demographics, medical outcomes, and physician characteristics.

RESULTS:
A total of 240 CRC-related malpractice cases (1988–2018) were collected, resulting in defense (n = 101, 42.1%), plaintiff (n = 37, 15.4%), or settlement (n = 96, 40%) verdict. The primary defendants were often primary care physicians (n = 61, 25.4%) and gastroenterologists (n = 55, 22.9%). Most common plaintiff allegations are failure to perform diagnostic colonoscopy for patients with symptoms (n = 67, 27.9%), failure to perform screening colonoscopy according to screening guidelines (n = 46, 19.2%), or failure to detect CRC with colonoscopy (n = 45, 18.7%). A common alleged error in diagnosis before the median year of 2005 was failure to detect CRC by the noncolonoscopic methods (<2005: n = 22, 24.2%; >2005: n = 3, 3.09%).

DISCUSSION:
Plaintiff-alleged errors in diagnosis are consistently the most common reason for CRC malpractice litigation in the past 20 years, whereas specific diagnostic allegations (i.e., failure to screen vs failure to detect) and methods used for surveillance may vary over time. It is important to identify such pitfalls in CRC screening and explore areas for improvement to maximize patient care and satisfaction and reduce physician malpractice litigations.
Die Zukunft des Heidelberger Bibliothekssystems im Spiegel des CATS-Forschungsbaus
Authors: Probst Veit , Balzuweit Rike 
Published: May 2020

Zusammenfassung
Seit 2006 hat die Universitätsbibliothek Heidelberg fünf Bibliotheksneubauten sowie fünf große Sanierungsmaßnahmen im Gesamtvolumen von rund 133 Millionen Euro angestoßen. Höhepunkt der Bauaktivitäten 2019 war die Neueröffnung der Bibliothek des Center for Asian and Transcultural Studies (CATS). Mit dem Forschungsbau nach Art. 91b GG ist die größte deutsche Asienbibliothek nach der Ostasienabteilung der Staatsbibliothek zu Berlin entstanden. Der Bau ist Schlussstein langjähriger Reorganisationsprozesse, mit denen die Universitätsbibliothek Heidelberg die Voraussetzungen dafür geschaffen hat, sechs asienwissenschaftliche Institutsbibliotheken unter einem Dach zusammenzuführen.
Valoración de un cambio de protocolo del cribado prenatal mediante la inclusión del diagnóstico prenatal no invasivo
Authors: Cabra-Rodríguez Rocío , Bueno Rodríguez Guadalupe , Santos Rosa Cristina , Castaño López Miguel Ángel , Delgado Muñoz Sonia , León-Justel Antonio 
Published: May 2020

Resumen

Objetivos
El diagnóstico prenatal no invasivo (DPNI) es un test que permite detectar en la sangre materna las principales alteraciones cromosómicas del feto durante el embarazo. El objetivo es evaluar el DPNI, valorando su rendimiento dentro del Programa Andaluz de Cribado de Anomalías Congénitas del Sistema Sanitario Público Andaluz.

Métodos
Estudio observacional retrospectivo en el que se analizan los DPNI realizados desde su incorporación, además del número de procedimientos diagnósticos invasivos tras la implementación del DPNI en gestantes incluidas en el programa entre marzo del año 2016 y agosto del 2017.

Resultados
Se realizaron 6.258 cribados combinados en gestantes de primer y segundo trimestre, con una cobertura de la población del 95%; se obtuvo un cálculo de riesgo elevado (≥1/280) en 250 gestantes, de los cuales el DPNI se aplicó en 200 gestantes después de asumir las pérdidas. La sensibilidad obtenida fue de 100% (IC 95%:76,84 a 100%) y la especificidad de 99,46% (IC 95%:97,04 a 99,99%).

Conclusiones
Este test es muy sensible, con alta especificidad. En nuestro estudio, la incorporación del DPNI en la práctica clínica minimiza las pérdidas fetales y reduce en un 70% la realización de procedimientos invasivos.
Repellent rings at titanium cylinders against overgrowth by fibroblasts
Authors: Fosodeder Peter , Baumgartner Werner , Steinwender Clemens , Hassel Achim Walter , Florian Camilo , Bonse Jörn , Heitz Johannes 
Published: May 2020

Abstract
The invention of new miniaturized and smart medical implants continues in all medical fields, including miniaturized heart pacemakers. These implants often come with a titanium (Ti) casing, which may have to be removed after several months or years and shall therefore not be completely overgrown by cells or scar tissue after implantation. Scar tissue is mainly formed by fibroblast cells and extracellular matrix proteins like collagen produced by them. Suppression of fibroblast growth at Ti surfaces could be achieved by 800 nm femtosecond laser-ablation creating self-organized sharp spikes with dimensions in the 10 μm-range which are superposed by fine sub-μm parallel ripples. On flat Ti control samples, the best results regarding suppression of cell growth were obtained on spike-structures which were additionally electrochemically anodized under acidic conditions. When Ti cylinders with a diameter of 8 mm (similar as the pacemakers) were placed upright in a culture of murine fibroblasts, a multi-layer cell growth up to a height of at least 1.5 mm occurred within 19–22 days. We have demonstrated that a laser-structured and anodized ring around the Ti cylinder surface is an effective way to create a barrier that murine fibroblasts were not able to overgrow within this time.
Auf den Leib eingeschrieben, auf das Foto gebannt? – Fotografische Konturen des muslimischen Leibes in Russisch-Mittelasien vor 1917. Ein Versuch zur historischen Körpersoziologie
Authors: Sidikov Bakhodir 
Published: May 2020

Abstrakt

Inscribed on the body, locked within the photo? – Photographic contours of Muslim body in Russian Central Asia before 1917. An essay of historical sociology of the body

Der folgende Beitrag besteht aus zwei Teilen. Im ersten Teil werden sowohl theoretische Überlegungen und Konzepte wie auch methodologische Annäherungen an das oben angekündigte Thema vorgestellt. Im zweiten Teil werden ausgewählte historische Ansichtskartenfotografien aus Russisch-Mittelasien vor 1917 praxeologisch (praxistheoretisch) analysiert mit dem Ziel, relevante historische Inhalte zu generieren. Der Zeitraum der Analyse orientiert sich an dem Aufkommen der Ansichtskarte an der Wende vom 19. zum 20. Jahrhundert. In dieser Zeit etabliert sie sich in Europa bzw. Russland als das erste globale Massenkommunikationsmedium.
Holzheid 2011.
Der Umbruch der Bibliothekslandschaft in SBZ und früher DDR im Spiegel einer kleinen Spezialbibliothek
Authors: Altekamp Stefan 
Published: May 2020

Abstract
Der Beitrag analysiert die konkreten Auswirkungen von Entnazifizierung, Umverteilung von Bibliotheksgut, Bezugsmöglichkeiten im Antiquariatsbuchhandel und Angeboten der Buchreproduktion in Fotografie und Mikroformen auf die Bestandsgeschichte einer Spezialbibliothek vor dem Hintergrund des Umbruchs der Bibliothekslandschaft in der Sowjetischen Besatzungszone und der frühen DDR.
Acht Lehren aus acht Jahren Open Access
Authors: Fund Sven 
Published: May 2020

Abstract
Knowledge Unlatched war die erste Initiative, die die Finanzierung von Monographien in den Geistes- und Sozialwissenschaften im Open Access verfügbar gemacht hat. Seitdem werden jährliche Pledging-Runden durchgeführt. Das Modell ist zwischenzeitlich deutlich gewachsen und umfasst auch Zeitschriften und andere Produktkategorien. Der Beitrag betrachtet aus der Insider-Perspektive die zentralen Learnings. Sie sind für Verlage, Bibliotheken und Forschungsfinanzierer, aber auch für vergleichbare Initiativen von Bedeutung für die Weiterentwicklung des Ansatzes.
Die Buchpublikationen der „Academic Communities“ in Dänemark und den Niederlanden: Rückschlüsse für globale Publikationsstrategien
Authors: Tausch Arno 
Published: May 2020

Abstract
Unser Aufsatz hat zahlreiche Kriterien entwickelt, mit denen die Bibliometrie und Szientometrie des auf akademische Bücher spezialisierten Verlagswesens betrieben werden kann. Wir testen den Einfluss von Messgrößen, wie sie auf Grund von Altmetrics, Entlehnungsstatistiken, Libcitation nach OCLC Worldcat und anderen Unionskatalogen in Industrie- und Entwicklungsländern, subjektivem Ranking durch academic communities und Zitierungen im Book Citation Index gewonnen werden können. 57 global operierende Buchverlage, über die sämtliche Daten vorhanden sind, stehen dabei im Mittelpunkt. All diese Daten haben eine Relevanz für die Publikationsstrategie-Beratung der Wissenschaft durch die Bibliotheksdienste im 21. Jahrhundert. Die Innovation dieses Aufsatzes besteht vor allem in der Verwendung von neuen Daten über die Publikationspräferenz zweier renommierter akademischer communities in Europa, nämlich Dänemark (landesweit) und von der Reichsuniversität Groningen in den Niederlanden in der multivariaten Analyse. Unsere Auswertungen zeigen, dass sowohl Ansätze, die auf die Zitierungen im Book Citation Index oder auf Größen der Libcitation (globale Verbreitung im OCLC Worldcat) ausschließlichen Wert legen, die komplexe Realität des heutigen internationalen Publikationswesens nicht erfassen. Nirgends haben Daten des Book Citation Index oder Libcitation (globale Verbreitung im OCLC Worldcat) jene überragende Bedeutung für die Publikationsentscheidungen der dänischen und niederländischen Wissenschaftler, wie bisherige Prototheorien des globalen Publikationswesens bisher annahmen. Bei den dänischen Wissenschaftlern scheint der Faktor „size and high quality“ der ausschlaggebende zu sein. Für Groningen kommt als determinierender Faktor noch die international anerkannte Verlagsqualität hinzu. Vergleiche unserer Ergebnisse mit den landesweiten subjektiven Verlagseinschätzungen der einzigen Wissenschaftscommunity, wo solche Daten erhoben wurden (Spanien) bestätigen unsere multivariaten Ergebnisse.
Analyzing the Effect of Mandatory Water Restrictions on Water Usage
Authors: Dronyk-Trosper Trey , Stitzel Brandli 
Published: May 2020

Abstract
As water rights and water usage become an ever more important part of municipalities’ and states’ way of life, it becomes important to understand what policies can be effective for encouraging conservation of water. One method that has been employed at various times and throughout numerous communities is to limit outdoor watering days. We use a dataset with over 3 million property-month observations during the 2007–2015 period in Norman, Oklahoma, to identify whether the periodic implementation of mandatory water restrictions reduces water usage. Our data allow us to exploit variance in the timing of these water restriction programs. Our findings indicate that this policy reduces water consumption by 0.7 % of total water consumption. Additionally, we use home assessment prices to identify heterogeneity in this response, finding that high priced homes are more responsive to water use restrictions.