cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3814239.v1
title: Similarity & Dissimilarity between Communities - Human feces, Pig feces, Hospital sewage - Different DNA Extraction Methods

description: The similarity and dissimilarity within and between microbial communities - from human feces, pig feces, and hospital sewage, processed with seven different DNA extraction protocols - was assessed using Jaccard and Bray Curtis distances, respectively. These figures relate to the article: <br>Berith E. Knudsen, Lasse Bergmark, Patrick Munk, Oksana Lukjancenko, Anders Priemé, Frank M. Aarestrup, Sünje J. Pamp (2016) Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition. <b><i>mSystems</i></b> Oct 2016, 1 (5) e00095-16; DOI: 10.1128/mSystems.00095-16 http://msystems.asm.org/content/1/5/e00095-16
DOI: 10.6084/m9.figshare.3814236
title: Songbird tap dancing produces non-vocal sounds<sup>*</sup>

description: Vocalizations have been elucidated in previous songbird studies, whereas less attention has been paid to non-vocal sounds. In the blue-capped cordon-bleu (<i>Uraeginthus cyanocephalus</i>), both sexes perform courtship displays that are accompanied by singing and distinct body movements (i.e. dance). Our previous study revealed that their courtship bobbing includes multiple rapid steps. This behaviour is quite similar to human tap dancing, because it can function as both visual and acoustic signals. To examine the acoustic signal value of such steps, we tested if their high-speed step movements produce non-vocal sounds that have amplitudes similar to vocal sounds. We found that step behaviour affected step sound amplitude. Additionally, the dancing step sounds were substantially louder than feet movement sounds in a non-courtship context, and the amplitude range overlapped with that of song notes. These results support the idea that in addition to song cordon-bleus produce acoustic signals with their feet.
DOI: 10.6084/m9.figshare.3814236.v1
title: Songbird tap dancing produces non-vocal sounds<sup>*</sup>

description: Vocalizations have been elucidated in previous songbird studies, whereas less attention has been paid to non-vocal sounds. In the blue-capped cordon-bleu (<i>Uraeginthus cyanocephalus</i>), both sexes perform courtship displays that are accompanied by singing and distinct body movements (i.e. dance). Our previous study revealed that their courtship bobbing includes multiple rapid steps. This behaviour is quite similar to human tap dancing, because it can function as both visual and acoustic signals. To examine the acoustic signal value of such steps, we tested if their high-speed step movements produce non-vocal sounds that have amplitudes similar to vocal sounds. We found that step behaviour affected step sound amplitude. Additionally, the dancing step sounds were substantially louder than feet movement sounds in a non-courtship context, and the amplitude range overlapped with that of song notes. These results support the idea that in addition to song cordon-bleus produce acoustic signals with their feet.
DOI: 10.6084/m9.figshare.3814224
title: La Rehabilitación Neuropsicológica en España: Historia y estado actual. Revista Neuropsicología, Neuropsiquiatría y Neurociencias, 16(1), 25-49

description: Este artículo dentro del monográfico titulado Rehabilitación Integral del Paciente con Daño Cerebral de la Revista Neuropsicología, Neuropsiquiatría y Neurociencias, Vol. 16 (1) realiza un recorrido por los pioneros de la neuropsicología de finales del siglo XIX, las contribuciones de profesionales españoles del siglo XX y las influencias de autores internacionales que ayudaron a conformar el panorama actual de la rehabilitación neuropsicológica en España. Para ofrecer una visión de la rehabilitación neuropsicológica actual se analizó la producción de artículos científicos y se mencionaron libros y programas de rehabilitación de autores con filiación en España. Además, con el apoyo de resultados de una encuesta realizada recientemente, se analizó el estado de la formación y los campos de intervención de los neuropsicólogos españoles. El estado de regularización de la práctica clínica se analizó utilizando como referente el documento de acreditación del profesional Experto en Neuropsicología Clínica elaborado por la Federación de Asociaciones de Neuropsicología Españolas (FANPSE) y aprobado en 2015 por el Consejo General de la Psicología de España que agrupa a todos los colegios oficiales de psicología del país. Finalmente se exponen varios retos que afronta la disciplina y se esbozan posibles vías de solución. Los desafíos se refieren a la escasa implantación en el sistema público de salud y la falta de reconocimiento de la neuropsicología clínica como especialidad, a la regulación y mejora de la formación especializada y a la paradójica situación legal actual que permite dos escenarios contrarios, uno donde la rehabilitación neuropsicológica se puede practicar sin obligatoriedad de una formación especializada y otro donde la formación y acreditación como Experto en Neuropsicología Clínica no permite ejercer.
DOI: 10.6084/m9.figshare.3814206.v1
title: Gabapentin for neuropathic pain - WHO EML application 2016

description: The GitHub repository associated with this entry contains all the files required to generate the application (and supporting documents) the International Association for the Study of Pain (IASP) and the International Association of Hospice and Palliative Care (IAHPC) made to the 21st meeting of the WHO Expert Committee on Selection and Use of Essential Medicines (2017) for the inclusion of gabapentin on the WHO Model List of Essential Medicines for the treatment of neuropathic pain. <br>Follow the steps below to generate the application, appendices, and the executive summary. <br><b>If you use Git/GitHub </b>- Fork the repository to your GitHub account - Clone the repository to your computer - Open a terminal (Windows users should open a Git Bash terminal) and change the path to the root directory of the repository - Type 'make' (Windows users will need to download and install GNU Make beforehand) <br><b>If you do not use Git/GitHub</b> - Windows users must download and install: Git for Windows or any other Bash-like shell for Windows GNU Make - Download the respository as a zip file - Unzip the repository on your computer - Open a terminal and change the path to the root directory of the repository - Type 'make' <br><b>The following set-up was used to generate all files</b> - R version 3.2.4 (2016-03-10) running on RStudio v0.99.1243 for OSX <br>- Packages used (inclusive of: application.Rmd, appendices.Rmd, summary.Rmd, and all other analysis scripts): ggplot2 2.1.0, scales 0.4.0, gridExtra 2.2.1, xtable 1.8-2, pander 0.6.0, readr 1.0.0, strings 1.1.0, tidyr 0.6.0, nibble 1.2, dplyr 0.5.0.
DOI: 10.5287/bodleian:2ab66pq5b
title: A stand-alone magnetic guide for producing tuneable radical beams dataset
DOI: 10.6084/m9.figshare.3813975
title: Z'-factor Data

description: This is all the data needed to support "A high-content larval zebrafish brain imaging method for small molecule drug discovery"<br>by:<br>Harrison Liu, Steven Chen, Kevin Huang, Jeffrey Kim, Mo Han, Raffael Iovine, Julie Gendry, Pauline Pascal, Qiang Li, Yaping Sun, Zhiqiang Dong, Michelle Arkin, Su Guo*, Bo Huang*<br>that is currently under review (2016) by plos one.
DOI: 10.6084/m9.figshare.3813699
title: Formulating strategic problems with Systems Modeling Language

description: Prompted by difficulties inherent to causal analysis in problem formulation, and by a need for more formal and robust strategy and transformation design tools and frameworks, this article introduces a procedure for modeling strategic problems in the Systems Modeling Language (SysML). As a test bed for the procedure, we used the widely available Robin Hood strategic management case study. The modeling process fostered an enhanced understanding of the nature of the problem, and the resulting model proved rich and complex. The difficulties stemming from causal analysis were absent altogether, thus showing that SysML provides a good basis upon which to build a non-causal, systemic strategy and transformation design framework.
DOI: 10.6084/m9.figshare.3813699.v1
title: Formulating strategic problems with Systems Modeling Language

description: Prompted by difficulties inherent to causal analysis in problem formulation, and by a need for more formal and robust strategy and transformation design tools and frameworks, this article introduces a procedure for modeling strategic problems in the Systems Modeling Language (SysML). As a test bed for the procedure, we used the widely available Robin Hood strategic management case study. The modeling process fostered an enhanced understanding of the nature of the problem, and the resulting model proved rich and complex. The difficulties stemming from causal analysis were absent altogether, thus showing that SysML provides a good basis upon which to build a non-causal, systemic strategy and transformation design framework.
DOI: 10.6084/m9.figshare.3812274
title: HMGA1 silencing reduces stemness and temozolomide resistance in glioblastoma stem cells

description: <b>Objective:</b> Glioblastoma multiforme (GBM) develops from a small subpopulation of stem-like cells, which are endowed with the ability to self-renew, proliferate and give rise to progeny of multiple neuroepithelial lineages. These cells are resistant to conventional chemo- and radiotherapy and are hence also responsible for tumor recurrence. HMGA1 overexpression has been shown to correlate with proliferation, invasion, and angiogenesis of GBMs and to affect self-renewal of cancer stem cells from colon cancer. The role of HMGA1 in GBM tumor stem cells is not completely understood. <b>Research design and methods:</b> We have investigated the role of HMGA1 in brain tumor stem cell (BTSC) self-renewal, stemness and resistance to temozolomide by shRNA- mediated HMGA1 silencing. <b>Results:</b> We first report that HMGA1 is overexpressed in a subset of BTSC lines from human GBMs. Then, we show that HMGA1 knockdown reduces self-renewal, sphere forming efficiency and stemness, and sensitizes BTSCs to temozolomide. Interestingly, HMGA1 silencing also leads to reduced tumor initiation ability <i>in vivo</i>. <b>Conclusions:</b> These results demonstrate a pivotal role of HMGA1 in cancer stem cell gliomagenesis and endorse HMGA1 as a suitable target for CSC-specific GBM therapy.
DOI: 10.6084/m9.figshare.3812274.v1
title: HMGA1 silencing reduces stemness and temozolomide resistance in glioblastoma stem cells

description: <b>Objective:</b> Glioblastoma multiforme (GBM) develops from a small subpopulation of stem-like cells, which are endowed with the ability to self-renew, proliferate and give rise to progeny of multiple neuroepithelial lineages. These cells are resistant to conventional chemo- and radiotherapy and are hence also responsible for tumor recurrence. HMGA1 overexpression has been shown to correlate with proliferation, invasion, and angiogenesis of GBMs and to affect self-renewal of cancer stem cells from colon cancer. The role of HMGA1 in GBM tumor stem cells is not completely understood. <b>Research design and methods:</b> We have investigated the role of HMGA1 in brain tumor stem cell (BTSC) self-renewal, stemness and resistance to temozolomide by shRNA- mediated HMGA1 silencing. <b>Results:</b> We first report that HMGA1 is overexpressed in a subset of BTSC lines from human GBMs. Then, we show that HMGA1 knockdown reduces self-renewal, sphere forming efficiency and stemness, and sensitizes BTSCs to temozolomide. Interestingly, HMGA1 silencing also leads to reduced tumor initiation ability <i>in vivo</i>. <b>Conclusions:</b> These results demonstrate a pivotal role of HMGA1 in cancer stem cell gliomagenesis and endorse HMGA1 as a suitable target for CSC-specific GBM therapy.
DOI: 10.6084/m9.figshare.3811686
title: Simkins, Bonier, and Benowitz-Fredericks Master Data.xlsx

description: In birds, exposure to testosterone during embryonic development can suppress immune function; however, it is unclear whether this is caused by direct stimulation of androgen receptors. Estradiol is synthesized from testosterone by the enzyme aromatase, and this conversion is a necessary step in many signaling pathways that are ostensibly testosterone-dependent. Many lines of evidence in mammals indicate that estradiol can affect immune function. We tested the hypothesis that immunosuppressive effects of avian <i>in ovo</i> testosterone exposure are mediated by conversion to estradiol by aromatase, using Fadrozole to inhibit aromatization of endogenous testosterone during a crucial period of embryonic immune system development in domestic chickens (<i>Gallus gallus</i>). We then measured total IgY antibody count, response to PHA challenge, mass of thymus and bursa of Fabricius, and plasma testosterone post-hatch on days 3 and 18. We predicted that if immunomodulation by testosterone is dependent on aromatization, then Fadrozole treatment would lead to elevated immune activity by inhibiting estrogen production. Conversely, if testosterone inhibits immune function directly by binding to androgen receptors, then Fadrozole treatment would likely not alter immune function. Fadrozole treated birds had decreased day 3 plasma IgY antibody titers but there was a strong trend towards increased day 18 thymic mass. Furthermore, Fadrozole treatment generated a positive relationship between testosterone and thymic mass in males, and tended to increase day 18 IgY levels for a given bursal mass in females. There was no effect on PHA response, bursal mass, or plasma testosterone at either age. Overall, Fadrozole treated birds tended to have elevated indicators of immune function, implicating aromatization as a relevant pathway through which developmental exposure to testosterone can affect immunity.
DOI: 10.6084/m9.figshare.3811686.v1
title: Simkins, Bonier, and Benowitz-Fredericks Master Data.xlsx

description: In birds, exposure to testosterone during embryonic development can suppress immune function; however, it is unclear whether this is caused by direct stimulation of androgen receptors. Estradiol is synthesized from testosterone by the enzyme aromatase, and this conversion is a necessary step in many signaling pathways that are ostensibly testosterone-dependent. Many lines of evidence in mammals indicate that estradiol can affect immune function. We tested the hypothesis that immunosuppressive effects of avian <i>in ovo</i> testosterone exposure are mediated by conversion to estradiol by aromatase, using Fadrozole to inhibit aromatization of endogenous testosterone during a crucial period of embryonic immune system development in domestic chickens (<i>Gallus gallus</i>). We then measured total IgY antibody count, response to PHA challenge, mass of thymus and bursa of Fabricius, and plasma testosterone post-hatch on days 3 and 18. We predicted that if immunomodulation by testosterone is dependent on aromatization, then Fadrozole treatment would lead to elevated immune activity by inhibiting estrogen production. Conversely, if testosterone inhibits immune function directly by binding to androgen receptors, then Fadrozole treatment would likely not alter immune function. Fadrozole treated birds had decreased day 3 plasma IgY antibody titers but there was a strong trend towards increased day 18 thymic mass. Furthermore, Fadrozole treatment generated a positive relationship between testosterone and thymic mass in males, and tended to increase day 18 IgY levels for a given bursal mass in females. There was no effect on PHA response, bursal mass, or plasma testosterone at either age. Overall, Fadrozole treated birds tended to have elevated indicators of immune function, implicating aromatization as a relevant pathway through which developmental exposure to testosterone can affect immunity.
DOI: 10.6084/m9.figshare.3811680
title: intropolis: exon-exon junctions across publicly available RNA-seq samples on the Sequence Read Archive

description: All exon-exon junctions detected by Rail-RNA across 21,504 human RNA-seq samples from the Sequence Read Archive, as studied in the paper "Human splicing diversity across the Sequence Read Archive" by Abhinav Nellore, Andrew E. Jaffe, Jean-Philippe Fortin, José Alquicira-Hernández, Leonardo Collado-Torres, Siruo Wang, Robert A. Phillips III, Nishika Karbhari, Kasper D. Hansen, Ben Langmead, and Jeffrey T. Leek. File formats are described at http://intropolis.rail.bio .
DOI: 10.6084/m9.figshare.3811587
title: Leonarduzzi_TGG_data.zip

description: Data used in analyses presented by Leonarduzzi et al. in the manuscript "Effective gene flow in a historically fragmented area at the southern edge of silver fir (<i>Abies alba</i> Mill.) distribution." <i>Tree Genetics & Genomes</i>, 12:95<br>
DOI: 10.6084/m9.figshare.3811371
title: Nonlinear structured illumination using a fluorescent proteins activating at the readout wavelength_S1 Raw data.zip

description: Raw data of a scientific article with a topic on nonlinear structured illumination microscopy:Nonlinear structured illumination using a fluorescent proteins activating at the readout wavelength
DOI: 10.6084/m9.figshare.3811371.v1
title: S1 Raw data.zip

description: Raw data of a scientific article with a topic on nonlinear structured illumination microscopy:Nonlinear structured illumination using a fluorescent proteins activating at the readout wavelength
DOI: 10.6084/m9.figshare.3811371.v3
title: Nonlinear structured illumination using a fluorescent proteins activating at the readout wavelength_S1 Raw data.zip

description: Raw data of a scientific article with a topic on nonlinear structured illumination microscopy:Nonlinear structured illumination using a fluorescent proteins activating at the readout wavelength
DOI: 10.6084/m9.figshare.3811371.v2
title: S1 Raw data.zip

description: Raw data of a scientific article with a topic on nonlinear structured illumination microscopy:Nonlinear structured illumination using a fluorescent proteins activating at the readout wavelength
DOI: 10.6084/m9.figshare.3811338
title: HMG-CoA Reductase inhibitors: an updated review of patents of novel compounds and formulations (2011-2015)

description: <b>Introduction</b>: Statins are remarkably safe and efficient medications that are the mainstay of hypercholesterolemia treatment and have proven to be an invaluable tool to lower the risk of acute cardiovascular events. These compounds are inhibitors of 3-hydroxy-methylglutaryl CoA reductase (HMG-R), the rate-limiting enzyme in cholesterol biosynthesis. In spite of their success, they present undesirable side effects and are now loosing patent protection, which provides a great opportunity for the development of new and improved statins. <b>Areas covered</b>: This review summarizes the new patents for HMG-R inhibitors for the 2011–2015 period. Combinations of existing statins with other drugs are also addressed, as well as novel applications of existing statins. <b>Expert opinion</b>: Recent efforts for the discovery of HMG-CoA-R inhibitors has resulted in several new molecules. Most of these are based on commercially available statins, including sterol and terpenoid derivatives. A few peptides have also been patented. However, the origin of the side effects caused by previous statins continues to be, to a large extent, unknown. Although the patents published in the past 5 years are promising, and might result in new drugs, there is still no way to know if they will present reduced toxicity. Only future clinical trials will answer this question.
DOI: 10.6084/m9.figshare.3811338.v1
title: HMG-CoA Reductase inhibitors: an updated review of patents of novel compounds and formulations (2011-2015)

description: <b>Introduction</b>: Statins are remarkably safe and efficient medications that are the mainstay of hypercholesterolemia treatment and have proven to be an invaluable tool to lower the risk of acute cardiovascular events. These compounds are inhibitors of 3-hydroxy-methylglutaryl CoA reductase (HMG-R), the rate-limiting enzyme in cholesterol biosynthesis. In spite of their success, they present undesirable side effects and are now loosing patent protection, which provides a great opportunity for the development of new and improved statins. <b>Areas covered</b>: This review summarizes the new patents for HMG-R inhibitors for the 2011–2015 period. Combinations of existing statins with other drugs are also addressed, as well as novel applications of existing statins. <b>Expert opinion</b>: Recent efforts for the discovery of HMG-CoA-R inhibitors has resulted in several new molecules. Most of these are based on commercially available statins, including sterol and terpenoid derivatives. A few peptides have also been patented. However, the origin of the side effects caused by previous statins continues to be, to a large extent, unknown. Although the patents published in the past 5 years are promising, and might result in new drugs, there is still no way to know if they will present reduced toxicity. Only future clinical trials will answer this question.
DOI: 10.6084/m9.figshare.3811314
title: Stress-associated radiation effects in pygmy wood mouse <i>Apodemus uralensis</i> (Muridae, Rodentia) populations from the East-Urals Radioactive Trace

description: This work is based on the comparative analysis of data obtained in the course of monitoring pygmy wood mouse populations (<i>Apodemus uralensis</i> Pallas, 1811) in the East-Urals Radioactive Trace (EURT) area and background territories. The effect of population size and its interaction with the radioactivity on biochemical parameters in the spleen and adrenal glands was studied. The concentrations of total lipids, proteins, DNA and RNA, activity of glucose-6-phosphate isomerase and catalase as well as the level of lipid peroxidation (LPO) were evaluated. The functional-metabolic shifts seen with large population sizes were characterized by delipidisation of adrenocortical cells, increased LPO as the main mechanism for steroidogenesis, growth of the protein components of the adrenal glands to maintain their hyperfunction, as well as immunosuppression associated with the restriction of carbohydrates providing splenocytes, reduction of DNA synthesis, and the development of a pro-/antioxidant imbalance. Reactivity of the neuroendocrine and hematopoietic systems of animals experiencing a high population density was higher in the EURT zone compared with the reference group. This difference can be explained by the additional stress from the chronic radiation exposure. The level of LPO, catalase activity, and DNA/protein ratio in the spleen and the total protein content in the adrenal glands were the most sensitive to the interaction of population size and radiation exposure. The harmful effect (distress) of the interaction of non-radiation and radiation factors can manifest when there is a population abundance above 30 ind./100 trap–day and a radiation burden which exceeds the lower boundary of the Derived Consideration Reference Levels, which is above 0.1 mGy/day.