bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using Machine Learning and Natural Language Processing to Review and Classify the Medical Literature on Cancer Susceptibility Genes
Authors: Bao Yujia , Deng Zhengyi , Wang Yan , Kim Heeyoon , Armengol Victor Diego , Acevedo Francisco , Ouardaoui Nofal , Wang Cathy , Parmigiani Giovanni , Barzilay Regina , Braun Danielle , Hughes Kevin S. 
Published: September 2019

PURPOSE The medical literature relevant to germline genetics is growing exponentially. Clinicians need tools that help to monitor and prioritize the literature to understand the clinical implications of pathogenic genetic variants. We developed and evaluated two machine learning models to classify abstracts as relevant to the penetrance—risk of cancer for germline mutation carriers—or prevalence of germline genetic mutations. MATERIALS AND METHODS We conducted literature searches in PubMed and retrieved paper titles and abstracts to create an annotated data set for training and evaluating the two machine learning classification models. Our first model is a support vector machine (SVM) which learns a linear decision rule on the basis of the bag-of-ngrams representation of each title and abstract. Our second model is a convolutional neural network (CNN) which learns a complex nonlinear decision rule on the basis of the raw title and abstract. We evaluated the performance of the two models on the classification of papers as relevant to penetrance or prevalence. RESULTS For penetrance classification, we annotated 3,740 paper titles and abstracts and evaluated the two models using 10-fold cross-validation. The SVM model achieved 88.93% accuracy—percentage of papers that were correctly classified—whereas the CNN model achieved 88.53% accuracy. For prevalence classification, we annotated 3,753 paper titles and abstracts. The SVM model achieved 88.92% accuracy and the CNN model achieved 88.52% accuracy. CONCLUSION Our models achieve high accuracy in classifying abstracts as relevant to penetrance or prevalence. By facilitating literature review, this tool could help clinicians and researchers keep abreast of the burgeoning knowledge of gene–cancer associations and keep the knowledge bases for clinical decision support tools up to date.
Experimental Reproduction of Dynamic Fluctuation of TSH Receptor–Binding Antibodies Between Stimulation and Inhibition
Authors: Tagami Tetsuya , Hiroshima-Hamanaka Kaho , Umakoshi Hironobu , Tsuiki-Naruse Mika , Kusakabe Toru , Satoh-Asahara Noriko , Shimatsu Akira , Moriyama Kenji 
Published: September 2019

Abstract

Context
Hyperthyroidism in Graves disease (GD) is caused by autoantibody stimulation of the TSH receptor (TSHR). TSHR autoantibody (TSHR-Ab) activity is measured routinely by inhibition of labeled ligand (TSH or M22) binding to the TSHR [TSH-binding inhibitory immunoglobulins (TBIIs)] or by stimulation of cAMP production in isolated cells [TSH receptor–stimulating antibodies (TSAbs)]. Usually, measurements of TSHR-Abs by TBIIs agree reasonably well with TSAb values at least in the setting of hyperthyroidism, and both measurements tend to change in parallel during treatment with some exceptions. In this study, we describe three unusual cases, which illustrate nearly pure stimulating, blocking, or neutral properties of TSHR-Abs.

Objective
Whether patient serum TSHR-Abs can be reproduced by mixtures of human monoclonal autoantibodies to the TSHR was studied because the sera in most patients show moderate properties having both of TBII and TSAb activities.

Design
We compared the TBII and TSAb activities of serum from four unusual patients in detail with mixtures of human monoclonal TSHR-Abs (mAbs) M22 (stimulating), K1-18 (stimulating), and K1-70 (blocking).

Results
Characteristic of a patient’s serum was similar to M22 or K1-18, another was similar to K1-70, whereas another was similar to a mixture of K1-70 and M22 (or K1-18). Additionally, some patients seemed to have neutral TSHR-Abs in their sera.

Conclusions
Our studies suggest that the characteristics of TSHR-Abs in the patient serum can be mimicked by mixtures of human mAbs to the TSHR, stimulating, blocking, and neutral if any.
Tepahtihquetl pan ce pilaltepetzin / A Village Healer
Authors: de la Cruz Sabina Cruz , Dufendach Rebecca 
Published: September 2019

Abstract
Sabina Cruz de la Cruz presents an auto-ethnohistory, an account written in her native language of Nahuatl based on her community experiences with illness and curing in the Huasteca region of Veracruz, Mexico. She documents her work with two curanderos to improve her poor health. The article is an invaluable record of contemporary, indigenous healing dialogue and traditions, some of which have similarities with colonial-era practices. It is an example of a collaboration between an ethnohistorian and an indigenous scholar writing her own history, and such collaborations will strengthen the field of ethnohistory.
BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services
Authors: Katayama Toshiaki , Kawashima Shuichi , Micklem Gos , Kawano Shin , Kim Jin-Dong , Kocbek Simon , Okamoto Shinobu , Wang Yue , Wu Hongyan , Yamaguchi Atsuko , Yamamoto Yasunori , Antezana Erick , Aoki-Kinoshita Kiyoko F. , Arakawa Kazuharu , Banno Masaki , Baran Joachim , Bolleman Jerven T. , Bonnal Raoul J. P. , Bono Hidemasa , Fernández-Breis Jesualdo T. , Buels Robert , Campbell Matthew P. , Chiba Hirokazu , Cock Peter J. A. , Cohen Kevin B. , Dumontier Michel , Fujisawa Takatomo , Fujiwara Toyofumi , Garcia Leyla , Gaudet Pascale , Hattori Emi , Hoehndorf Robert , Itaya Kotone , Ito Maori , Jamieson Daniel , Jupp Simon , Juty Nick , Kalderimis Alex , Kato Fumihiro , Kawaji Hideya , Kawashima Takeshi , Kinjo Akira R. , Komiyama Yusuke , Kotera Masaaki , Kushida Tatsuya , Malone James , Matsubara Masaaki , Mizuno Satoshi , Mizutani Sayaka , Mori Hiroshi , Moriya Yuki , Murakami Katsuhiko , Nakazato Takeru , Nishide Hiroyo , Nishimura Yosuke , Ogishima Soichi , Ohta Tazro , Okuda Shujiro , Ono Hiromasa , Perez-Riverol Yasset , Shinmachi Daisuke , Splendiani Andrea , Strozzi Francesco , Suzuki Shinya , Takehara Junichi , Thompson Mark , Tokimatsu Toshiaki , Uchiyama Ikuo , Verspoor Karin , Wilkinson Mark D. , Wimalaratne Sarala , Yamada Issaku , Yamamoto Nozomi , Yarimizu Masayuki , Kawamoto Shoko , Takagi Toshihisa 
Published: September 2019

Publishing databases in the Resource Description Framework (RDF) model is becoming widely accepted to maximize the syntactic and semantic interoperability of open data in life sciences. Here we report advancements made in the 6th and 7th annual BioHackathons which were held in Tokyo and Miyagi respectively. This review consists of two major sections covering: 1) improvement and utilization of RDF data in various domains of the life sciences and 2) meta-data about these RDF data, the resources that store them, and the service quality of SPARQL Protocol and RDF Query Language (SPARQL) endpoints. The first section describes how we developed RDF data, ontologies and tools in genomics, proteomics, metabolomics, glycomics and by literature text mining. The second section describes how we defined descriptions of datasets, the provenance of data, and quality assessment of services and service discovery. By enhancing the harmonization of these two layers of machine-readable data and knowledge, we improve the way community wide resources are developed and published. Moreover, we outline best practices for the future, and prepare ourselves for an exciting and unanticipatable variety of real world applications in coming years.
The grant is dead, long live the data - migration as a pragmatic exit strategy for research data preservation
Authors: Zielinski Tomasz , Hay Johnny , Millar Andrew J. 
Published: September 2019

Open research, data sharing and data re-use have become a priority for publicly- and charity-funded research. Efficient data management naturally requires computational resources that assist in data description, preservation and discovery. While it is possible to fund development of data management systems, currently it is more difficult to sustain data resources beyond the original grants. That puts the safety of the data at risk and undermines the very purpose of data gathering. PlaSMo stands for ‘Plant Systems-biology Modelling’ and the PlaSMo model repository was envisioned by the plant systems biology community in 2005 with the initial funding lasting until 2010. We addressed the sustainability of the PlaSMo repository and assured preservation of these data by implementing an exit strategy. For our exit strategy we migrated data to an alternative, public repository with secured funding. We describe details of our decision process and aspects of the implementation. Our experience may serve as an example for other projects in a similar situation. We share our reflections on the sustainability of biological data management and the future outcomes of its funding. We expect it to be a useful input for funding bodies.
Growth Response and Productivity of Sorghum for Bioenergy Production in South Texas
Authors: Chavez Jose C. , Enciso Juan , Ganjegunte Girisha , Rajan Nithya , Jifon John , Singh Vijay P. 
Published: September 2019

Abstract. Biomass sorghum ( (L.) Moench) is widely recognized for its high biomass yield potential, high efficiency in converting solar energy into biomass, and high efficiency in water use for biofuel production. Therefore, it could be a sustainable alternative to traditional food/feed crops in south Texas. The objectives of this investigation were to: (1) quantify the growth response and dry biomass productivity of a forage sorghum hybrid (Pioneer 877F) and two high-biomass sorghum hybrids (Blade ES 5140 and Blade ES 5200) in south Texas, (2) determine the radiation use efficiency (RUE) and water use efficiency (WUE) of the sorghum hybrids over two years, and (3) identify variations in WUE and water used among the hybrids. The experiments were conducted at the Texas A&amp;M AgriLife Research Center at Weslaco, Texas, during the 2015 and 2016 growing seasons. There were significant differences among hybrids during the two years in dry biomass, RUE, and WUE. The highest productivities and efficiencies were observed in the biomass hybrids. Blade ES 5200 produced an average dry biomass of 32.8 Mg ha-1 with a leaf area index (LAI) of 6.0 m2 m-2, RUE of 4.92 g MJ-1, and WUE of 6.98 kg m-3. In contrast to the biomass hybrids, the forage hybrid produced the lowest yields. The average dry biomass observed was 20.9 Mg ha-1 with an LAI of 2.6 m2 m-2, RUE of 3.52 g MJ-1, and WUE of 4.28 kg m-3. Our results show that biomass sorghum hybrids can produce up to 66% more biomass than forage hybrids, and they have potential for producing as much as 33 Mg ha-1 with 530 mm of water using drip irrigation in south Texas. Keywords: Biomass sorghum, Crop growth rate, Radiation use efficiency, Water use efficiency.
Design and Testing of an Impact Sensor Using Two Crossed Polyvinylidene Fluoride (PVDF) Films
Authors: Sun Ying , Cao Rui , Lu Zhan , Nie Xin , Li Zhaokai , Yu Yonghua , Tian Hongping , Qian Xiangqun , Wang Jianping 
Published: September 2019

Abstract. Impact sensors are widely used to detect grain losses in harvesters. Using polyvinylidene fluoride (PVDF) films as sensing elements is a promising way to improve sensor performance due to their high sensitivity, stability, and flexibility. However, the overlap of collision signals significantly reduces the accuracy of a sensor. To solve this problem, a novel impact sensor with two crossed PVDF films was designed and investigated. This sensor has two orthogonal layers of sensing elements that both respond to impacts, which creates positioning information for the impacts. Because of the sensor’s structure, a signal processing method was designed based on multisensor fusion theory. Tests were performed to verify the performance of the proposed impact sensor. The average signal-to-noise ratios (SNRs) for impacted PVDF films were 34.79 and 20.23 dB, respectively, for the upper and lower layers, while the average signal-to-clutter ratios (SCRs) for nonimpacted films were 21.90 and 10.05 dB, respectively. The sensor also has an extremely high detection efficiency of at least 1528 collisions per second and can identify particles that impact at the same time. Keywords: Grain loss detection, Impact sensors, Multisensor fusion, Particle impact tests, PVDF films.
Tahu yang Difermentasi Rhizopus sp. Menurunkan Kadar Glukosa Darah Tikus Putih(Rattus norvegicus)
Authors: Melati Eldaa Putik Bunga , Wiboworini Budiyanti , Subariyanti Briandani 
Published: September 2019

<p><strong><em>Introductions : </em></strong><em>Control</em><em>l</em><em>ing of blood glucose would be important </em><em>to prevent </em><em>many complications</em><em> of </em><em>DM.</em><em> Consuming fiber is one</em><em> way to maintain blood glucose </em><em>level</em><em>. These amount of fiber could be obtained in tofu fermented by <span style="text-decoration: underline;">Rhizopus sp</span>. This research aimed to know the effect of tofu fermented by <span style="text-decoration: underline;">Rhizopus sp.</span></em><em> in controlling </em><em> blood glucose level of diabetic induced white rats (<span style="text-decoration: underline;">Rattus norvegicus</span>).</em></p><p><strong><em>Methods : </em></strong><em>This research was a laboratoric-experimental study. The subjects were <span style="text-decoration: underline;">Rattus norvegicus</span>grouped randomly. The total 30 <span style="text-decoration: underline;">Rattus norvegicus</span> were injected by Alloxan 15mg/100gramBW, then</em><em> randomly allocated</em><em> into 5 group, positive control group (glibenclamide 0</em><em>.</em><em>05mg/100gramBW/day), negative control group (aquadest), and treatment groups with different doses of fermented tofu (</em><em>0.025gram/100 gramB</em><em>W</em><em>/</em><em>day; </em><em>0.050gram/100 gramBW/</em><em>day; </em><em>0.100gram/100gramBW/</em><em>day). The</em><em> research</em><em> design was </em><em>Pretest and Posttest Control Group Design</em><em>. The</em><em> fasting blood glucose were measured</em><em>before Alloxan injection (day-2), after Alloxan injection (day-5), and after the treatments (day-19).</em></p><p><strong><em>Result</em></strong><strong><em>s</em></strong><strong><em> : </em></strong><em>there was</em><em> a </em><em>significant decreas</em><em>e</em><em> of blood glucose level in all treatment groups and positive control (p = 0</em><em>.</em><em>001). Post Hoc Test showed </em><em>a</em><em> significant difference between all treatment groups and positive control group compared to negative control group (p = 0</em><em>.</em><em>001).</em></p><p><strong><em>Conclusion :</em></strong><em>Tofu fermented by <span style="text-decoration: underline;">Rhizopus sp</span>. was able to decrease blood glucose level in diabetic rats (<span style="text-decoration: underline;">Rattus norvegicus</span>).</em></p><p><em> </em></p><p><strong><em>Keyword </em></strong><em>: Tofu fermented</em><em>, </em><em><span style="text-decoration: underline;">Rhizopus sp</span></em><em><span style="text-decoration: underline;">.</span></em><em>, blood glucose level, alloxan, glibenclamide</em><strong></strong></p>
Epidemiology of insulin-dependent diabetes mellitus
Authors: Dedov I. I. , Suntsov Yu. I. , Kudryakova S. V. , Ryzhkova S. G. 
Published: September 2019

The epidemiology of diabetes mellitus (DM) is a section of diabetology that includes the study of the basic laws of the formation of the epidemiological situation and the epidemiological conditions in relation to this disease, as well as environmental, social and biological factors that determine the dynamics of its main epidemiological characteristics.
The end points of the epidemic process are the prevalence of cases of the disease, their frequency and mortality of patients with diabetes. Each of these characteristics is determined by many factors that can change their importance, priority and even lose it over time.
The epidemiological approach to solving a number of diabetological problems is based on the same principles as the epidemiology of other noncommunicable diseases: cardiovascular, oncological and some others. The main ones: the object of study is the population (population); the study of the disease is carried out in vivo of its development and course; in the researcher’s field of vision, the whole set of factors that can be associated with the fact of the development of the disease.
RESÚMENES DE TESIS: DOCTORADO EN CIENCIAS BIOLÓGICAS
Authors: Vignatti Maria Del Carmen 
Published: September 2019

Efectos de la exposición perinatal a estrógenos ambientales sobre la diferenciación de la glándula mamaria durante la gestación y la lactanciaGabriela Anahí Altamirano
Desarrollo de un inóculo probiótico para pollos parrilleros y monitoreo durante su tránsito intestinal y en órganos del medio internoJesica Evelyn Blajman
Subunidades Fksp del complejo β-1,3- D-Glucan sintasa de Candida glabrata: Rol en la síntesis de la pared celular, en la resistencia a las equinocandinas y como marcadores de resistencia clínicaCatiana Beatriz Dudiuk
Caracterización funcional y molecular de los rizobios noduladores de Desmanthus virgatus aislados en suelos argentinosLaura Viviana Fornasero
Rol de la adhesión mediada por Cadherina ECarolina Daniela Galetto
Conservación de la diversidad del sotobosque en bosques de Nothofagus pumilio bajo distintos tipos de aprovechamiento forestalEmilce Andrea Gallo
Diseño y optimización de un proceso de producción de muteínas de interferón-α2b humano con mayor actividad biológica mediante glicosilación en células de mamíferoAgustina Gugliotta
Staphylococcus aureus con sensibilidad disminuida a tigeciclina. Análisis de los mecanismos de resistencia involucradosMelina Elizabeth Herrera
Evaluación de novedosas metodologías analíticas ambientalmente compatibles para monitoreo terapéutico y estudios farmacocinéticos de antirretrovirales en fluidos biológicosGabriel Alejandro Hunzicker
Efectos de largo plazo del uso del suelo sobre la comunidad de lombrices de tierra (Annelida, Oligochaeta) en la provincia de Santa FeCarolina Elisabet Masin
Modificación de implantes cardiovasculares con propiedades anti-restenóticas y anti-trombóticas: tratamiento de superficie y liberación controlada de drogasLucila Navarro
Biología reproductiva de especies de aves del río Paraná Medio, ArgentinaPamela Olguin
Fagos autóctonos de Leuconostoc: caracterización, interacción con sus cepas sensibles e implicancias industrialesSilvina Pujato
Contaminación acuática por glifosato: efecto sobre especies nativas y eficiencia de procesos de remediaciónUlises Reno
Influencia de los patrones de expresión, la conservación y la divergencia de secuencias de los factores de transcripción HD-Zip I de Arabidopsis thaliana sobre su función biológicaPamela Anahí Ribone
Caracterización del metabolismo antioxidante y de reparación del daño oxidativo en Leptospira spp. Estudio de la relevancia de la homeostasis redox en la viabilidad de las bacteriasNatalia Sasoni
Ensambles de macrófitas en ambientes de la llanura aluvial del Río Paraná Medio: factores que inciden a distintas escalasBerenice Schneider
Desarrollo de estrategias analíticas basadas en técnicas cromatográficas y modelado quimiométrico para la determinación de ácido retinoico y principios activos de uso veterinario en muestras de interés biológicoCarla Mariela Teglia
Biogeografía evolutiva de pseudocangrejos de agua dulce de la familia Aeglidae (Crustacea: Anomura)Georgina Tumini
Electronic books A scientometric assessment of global literature during 1993 2018
Authors: Gupta B .M. , Dhawan SM 
Published: September 2019

Purpose - This paper provides a quantitative and qualitative description of global research output in the “electronic books” published during 1993-18” based on select bibliometric indicators.
Design/Methodology/Approach - The study sourced sample data (2116 publications) from Scopus database covering period 1993-2018. The study analyzed data on a series of bibliometric measures (like average annual growth, citations per paper, international collaborative papers, relative citation index, activity index, top productive countries, organizations, authors, journals, and highly cited papers).
Findings - ‘E-books’ is fast emerging as a research topic in the domain of library and information science. Top 10 most productive countries in the subject account for 73.25% of global literature. The USA leads with 38.42% global publications share whereas other 9 of top 10 top productive countries are distant cousins contributing 1.61% to 8.74% share. United Kingdom registered the highest citation impact per paper and relative citation index (12.08 and 1.61). Bar-Ilan University, Israel was the most productive organization and H. Falk was the most productive author. Publishing Research Quarterly is the most popular journal in e-books.
Originality/value – This is the one of the comprehensive studies of its kind that provides a quantitative and qualitative description of research studies on the ‘e-books’.
DROUGHT HAZARD CHARACTERISTIC USING SOIL MOISTURE DEFICIT INDEX MODELLING
Authors: Fitria Lulu Mari , Fathurrohmah Septiana 
Published: September 2019

Drought happen when the rainfall decreases in the extreme condition for long period of time (above normal). Drought hazard mapping can be analyzed by various approaches, like environmental approach, ecological approach, hydrological approach, meteorological approach, geological approach, agricultural approach, and many other. Meteorological, Climatological, and Geophysical Agency (in Indonesia a.k.a BMKG) measures the drought hazard by utilizing Standardized Precipitation Index (SPI)The comparison of rainfall rate through SPI has positive correlation with drought type, for example SPI 3 indicates agricultural drought; while SPI 6, SPI 9 and SPI 12 indicate hydrological drought. The analysis of drought hazard level also can be done using soil moisture level measurement. Soil moisture is the result of water shortages in the hydroclimatological concept. Soil moisture analysis utilizes several influenced variables, such as soil water, precipitation, evapotranspiration, and percolation. Each of variables was analyzed using GIS as a method of soil moisture modeling. Drought index level analysis is using soil moisture deficit index, which indicates that drought occurs if the index score less than (-0.5). Some assumptions used in this modeling are both SMDI modeling using WHC (Water Holding Capacity) and without using WHC. This modeling used medium term analysis during 2007-2012 to prove the occurrence of extreme drought on 2009 and 2012 for measurement of drought level in agriculture area. Based on SMDI, it is known that the dangers of SMDI drought have positive correlation to SPI 3, SPI 6, SPI 9, and SPI 12, where SPI is in accordance with the interpretation of meteorolgy, agriculture, and hydrological drought indices.