cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5466349.v1
title: Paper 2018 - PSIoT- ADVANCE - Latex Project

description: Draft paper - ADVANCE 2018
DOI: 10.6084/m9.figshare.5464396
title: SupplementalData-1.xlsx

description: Dataset is a list of publicly available genomes from NCBI's SRA with standardized metadata and verified serovar information using the SISTR platform. MLST information from the reference MLST database (http://mlst.warwick.ac.uk/) is contained in Supplemental Data 2<br>
DOI: 10.6084/m9.figshare.5464420
title: SupplementaryMaterial.docx

description: This a document containing the supplementary materials for the paper submitted to Systems.
DOI: 10.6084/m9.figshare.5464423
title: INTERPROSCAN results: PCA and discriminant analysis

description: results of Interproscan functional classification of the the ERP016024 dataset (as part of the EBI Metagenomics pipeline [Mitchell et al., Nucl. Acid Res. 2016] v3.0) were analysed using PCA and linear discriminant analysis.<br>"ERP016024_IPR_abundances_v3.0_PCA_subsistencestrategy_ populations.pdf":biplots of PCA based on InterPro functional terms relative abundance, showing the distribution of samples by groups of subsistence strategy (HG: hunter-gatheres, TF: traditional farmers, WC: Western controls) or populations (Aeta, Agta, Batak, Zambal, Casigurani, Tagbanua, Western controls) along the 6 first PC axis.<br><br>"ERP016024_IPR_abundances_v3.0.tsv_LDA_*vs*":tables summarize the results of a LDA with one discriminant function, i.e. separating pair of groups (HG vs TF, TF vs WC, WC vs HG). The top-ranking discriminating functional terms are reported.<br><br>Scripts used to analyse these results can be found on GitHub: https://github.com/flass/microbiomes/tree/master/scripts/interproThis work was published in the journal Molecular Ecology doi: 10.1111/mec.1443
DOI: 10.6084/m9.figshare.5464420.v1
title: SupplementaryMaterial.docx

description: This a document containing the supplementary materials for the paper submitted to Systems.
DOI: 10.6084/m9.figshare.5464381
title: Silicon photonic processor of two-qubit entangling quantum logic

description: Tomography datasets and plots for the data published in the paper: "Silicon photonic processor of two-qubit entangling quantum logic". <br>The data sets are reported as csv files, where each line contains:configuration, coincidence counts, accidentals.<br>The data were processed using Maximum Likelihood Tomography reconstructions, obtaining the probabilities for each configuration by subtracting from the coincidence counts the accidentals and renormalisation on the relative basis set. <br>Each filename contains the description of the relative measurement performed.<br>
DOI: 10.6084/m9.figshare.5464381.v1
title: Silicon photonic processor of two-qubit entangling quantum logic

description: Tomography datasets and plots for the data published in the paper: "Silicon photonic processor of two-qubit entangling quantum logic". <br>The data sets are reported as csv files, where each line contains:configuration, coincidence counts, accidentals.<br>The data were processed using Maximum Likelihood Tomography reconstructions, obtaining the probabilities for each configuration by subtracting from the coincidence counts the accidentals and renormalisation on the relative basis set. <br>Each filename contains the description of the relative measurement performed.<br>
DOI: 10.6084/m9.figshare.5464396.v1
title: SupplementalData-1.xlsx

description: Dataset is a list of publicly available genomes from NCBI's SRA with standardized metadata and verified serovar information using the SISTR platform. MLST information from the reference MLST database (http://mlst.warwick.ac.uk/) is contained in Supplemental Data 2<br>
DOI: 10.6084/m9.figshare.5464396.v2
title: SupplementalData-1.xlsx

description: Dataset is a list of publicly available genomes from NCBI's SRA with standardized metadata and verified serovar information using the SISTR platform. MLST information from the reference MLST database (http://mlst.warwick.ac.uk/) is contained in Supplemental Data 2<br>
DOI: 10.6084/m9.figshare.5464207
title: Oncologic Effectiveness and Safety of Bursectomy in Patients with Advanced Gastric Cancer: A Systematic Review and Updated Meta-Analysis

description: <i>Purpose/Aim</i>: In the past few decades some researchers have questioned whether bursectomy for gastric cancer is essential from an oncological point of view and no consistent recommendations have been proposed. The aim of this systematic review with meta-analysis is to investigate the oncologic effectiveness and safety of bursectomy for the treatment of advanced gastric cancer patients. <i>Materials and Methods</i>: We planned and performed this systematic review and meta-analysis in accordance with Preferred Reporting Items for Systematic Review and Meta-analysis (PRISMA) statement and Cochrane Handbook for Systematic Reviews of Intervention. <i>Results</i>: Overall, four studies with a total of 1,340 patients met inclusion criteria. The pooled hazard ratio for overall survival between the bursectomy versus nonbursectomy groups was [HR = 0.85, 95% CI 0.66–1.11, <i>p</i> =.252]. Interestingly, the pooled HR between the two groups in serosa-positive cases subgroup, showed a significant improvement of overall survival rate in favor of bursectomy [HR = 0.72, 95% CI 0.73–0.99, <i>p</i> Conclusions: Bursectomy represents a surgical procedure that might be able to improve overall survival in serosa positive gastric cancer patients. However, a definitive conclusion could not be made because of the studies’ methodological limitations. This meta-analysis points to the urgent need of high quality, large-scaled, clinical trials with short- as well as long-term evaluation comparing bursectomy with non bursectomy procedures, in a controlled randomized manner, helping future researches and establishing a modern and tailored approach to gastric cancer.
DOI: 10.6084/m9.figshare.5464195
title: Theory Of Universal Origins.pdf

description: About a century ago, Albert Einstein realized how the Theory of Newton's Universal Gravitation was inadequate to describe nature and needed to be revised in order to be neatly incorporated into the relativistic scheme with its undesirable instantaneous force shortcomings. Since then we have come to adopt the relativistic high energy tensor theory of General Relativity, which saw its inception into mainstream physics in the year 1916. General Relativity has stood firm against varied tests, such as: gravitational lensing, perihelion of mercury, gravitational time dilation, PSR1913+16 etc, but with the steady advancement of Quantum Mechanics, and its overwhelming experimental success, we are yet again faced with the same problem that was faced a century ago, but this time, the problem is much worse, and the elephant in the room is General Relativity. The fact that General relativity and Quantum mechanics, share different views in the description of space and time or space-time, with quantum mechanics in favor of the latter and general relativity of the former; does not allow one to have a smooth transition from one representation to the other. This automatically implies that for scenarios where both quantum mechanics and gravity / general relativity are required, then that scenario is unsolvable with our current model of physics (hence either General Relativity or Quantum Mechanics is flawed). It becomes clear from the microscopic realm of quantum mechanics and the cosmological problems associated with General Relativity, such as dark energy, dark matter, the inflation force... perhaps a bit closer to home for general relativity being the singularities inherent in its own equations, and the very nature of General Relativity, allowing mostly approximate solutions (reason why most physicist, even today still cling to Newtonian dynamics), because of this and more a new theory of gravity is required – the much anticipated “Quantum Gravity” – just as it was required those many years ago. In the theory that I propose, we will see how from the most basic concepts of quantum mechanics, a theory of gravity can emerge that has the power to not only be mathematically simpler than General Relativity, explain dark energy, dark matter and inflation without any ad-hoc mechanisms, but also have the power to unify all the forces of nature into a single unified theory of everything.<br>
DOI: 10.6084/m9.figshare.5464207.v1
title: Oncologic Effectiveness and Safety of Bursectomy in Patients with Advanced Gastric Cancer: A Systematic Review and Updated Meta-Analysis

description: <i>Purpose/Aim</i>: In the past few decades some researchers have questioned whether bursectomy for gastric cancer is essential from an oncological point of view and no consistent recommendations have been proposed. The aim of this systematic review with meta-analysis is to investigate the oncologic effectiveness and safety of bursectomy for the treatment of advanced gastric cancer patients. <i>Materials and Methods</i>: We planned and performed this systematic review and meta-analysis in accordance with Preferred Reporting Items for Systematic Review and Meta-analysis (PRISMA) statement and Cochrane Handbook for Systematic Reviews of Intervention. <i>Results</i>: Overall, four studies with a total of 1,340 patients met inclusion criteria. The pooled hazard ratio for overall survival between the bursectomy versus nonbursectomy groups was [HR = 0.85, 95% CI 0.66–1.11, <i>p</i> =.252]. Interestingly, the pooled HR between the two groups in serosa-positive cases subgroup, showed a significant improvement of overall survival rate in favor of bursectomy [HR = 0.72, 95% CI 0.73–0.99, <i>p</i> Conclusions: Bursectomy represents a surgical procedure that might be able to improve overall survival in serosa positive gastric cancer patients. However, a definitive conclusion could not be made because of the studies’ methodological limitations. This meta-analysis points to the urgent need of high quality, large-scaled, clinical trials with short- as well as long-term evaluation comparing bursectomy with non bursectomy procedures, in a controlled randomized manner, helping future researches and establishing a modern and tailored approach to gastric cancer.
DOI: 10.6084/m9.figshare.5464168
title: FEM-Microplane-Q4-Exponencial-RedMesh-2.xml

description: <br>
DOI: 10.6084/m9.figshare.5464150
title: Rizzuto et al. Activity Data set

description: This is the data set associated with Rizzuto et al. Foraging constraints reverse the scaling of activity time in carnivores.
DOI: 10.6084/m9.figshare.5464150.v1
title: Rizzuto et al. Activity Data set

description: This is the data set associated with Rizzuto et al. Foraging constraints reverse the scaling of activity time in carnivores.
DOI: 10.6084/m9.figshare.5463934
title: Influence of habitat modification by livestock on páramo bird abundance in southern Andes of Ecuador

description: Livestock grazing on natural grasslands is widespread with negative consequences to biodiversity. In the High Andes, páramo grassland is a distinctive ecosystem where the influence of livestock grazing on páramo birds is poorly documented. We assessed the influence of habitat modification of páramo grassland related to livestock grazing on bird habitat guilds in the southern Andes of Ecuador. We recorded birds occurring along transects located in areas which showed a gradient (low to high) of grazing pressure. We found a decrease in abundance of páramo specialists in transects with more grazing pressure. We interpret this habitat modification as loss of key habitat necessary for habitat-specialized birds.
DOI: 10.6084/m9.figshare.5463940
title: BARM Counts Redoxcline 2014

description: Tables with counts per sample and gene/annotation.The counts are either sum of raw counts of reads mapping or sum of tpm values. The counts for taxonomy are given in individual files per level and in a combined file for all levels. These counts are from two stations; the Boknis Eck station and the Gotland Basin.
DOI: 10.6084/m9.figshare.5463934.v2
title: Influence of habitat modification by livestock on páramo bird abundance in southern Andes of Ecuador

description: Livestock grazing on natural grasslands is widespread with negative consequences to biodiversity. In the High Andes, páramo grassland is a distinctive ecosystem where the influence of livestock grazing on páramo birds is poorly documented. We assessed the influence of habitat modification of páramo grassland related to livestock grazing on bird habitat guilds in the southern Andes of Ecuador. We recorded birds occurring along transects located in areas which showed a gradient (low to high) of grazing pressure. We found a decrease in abundance of páramo specialists in transects with more grazing pressure. We interpret this habitat modification as loss of key habitat necessary for habitat-specialized birds.
DOI: 10.6084/m9.figshare.5463781
title: Table S1 from Starvation effects on nitrogen and carbon stable isotopes of animals: an insight from meta-analysis of fasting experiments

description: The all data of the meta-analysis on starvation effects on nitrogen and carbon stable isotopes of animals
DOI: 10.6084/m9.figshare.5463781.v1
title: Table S1 from Starvation effects on nitrogen and carbon stable isotopes of animals: an insight from meta-analysis of fasting experiments

description: The all data of the meta-analysis on starvation effects on nitrogen and carbon stable isotopes of animals
DOI: 10.6084/m9.figshare.5463787
title: Cue-based decision rules of cleaner fish in a biological market task

description: Data for: Wismer et al (in prep) Cue-based decision rules of cleaner fish in a biological market task<br>Data collected by SW and AP. Please refer to the manuscript for data collection methods and statistical analyses. For questions or to notify the authors if any errors are identified in the data, please contact Sharon Wismer [McAfoose] (Sharon_Wismer@hotmail.com) and/or Dominique Roche (dominique.roche@mail.mcgill.ca).<br>
DOI: 10.6084/m9.figshare.5463733
title: BARM Counts Transect Cruise 2014

description: Tables with counts per sample and gene/annotation.The counts are either sum of raw counts of reads mapping or sum of tpm values. The counts for taxonomy are given in individual files per level and in a combined file for all levels. These counts are for the transect cruise of the Baltic Sea conducted by IOW (Leibniz Institute for Baltic Sea Research Warnemünde) on the summer of 2014.
DOI: 10.6084/m9.figshare.5463733.v1
title: BARM Counts Transect Cruise 2014

description: Tables with counts per sample and gene/annotation.The counts are either sum of raw counts of reads mapping or sum of tpm values. The counts for taxonomy are given in individual files per level and in a combined file for all levels. These counts are for the transect cruise of the Baltic Sea conducted by IOW (Leibniz Institute for Baltic Sea Research Warnemünde) on the summer of 2014.
DOI: 10.6084/m9.figshare.5463739.v2
title: BRAIN Journal - An Energy-Saving Concept of the Smart Building Power Grid with Separated Lines for Standby Devices

description: <i>Abstract</i><br>Standby power takes 5-10 % of the residential electricity around the world. Some countries lose more than 14 % of the total electricity used in the residential sector. Hence, a new energysaving concept that could help to decrease the power losses is discussed in this paper. Firstly, the two power lines of infrastructure for continuously connected equipment and for standby devices is proposed for new smart buildings. Secondly, the segmented infrastructure with unified hardware units is proposed for existing smart buildings (the new one can apply this principle as well). The contactors (i.e. unified hardware units) consist of the NodeMcu Lua ESP8266 WiFi IoT development board, ACS712T ELC-30A current sensor, and the Songle relay. The automatic mode is based on three steps: measurement of the current using ACS712T ELC-30A sensor in all segments except the root; switching off the relays with the current less than or equal to any number in the historical data; switching off the root contactor if all the descendent relays (i.e. contactors) are switched off. Second step represents the linear classification with sliding window in machine learning. The software consists of two parts, low-level Arduino sketches and high-level C# Windows form app. They are connected by MQTT broker Mosquitto. The proposed concept was successfully tested using a prototype with three segments, one of which includes smart lighting. The payback period is of approximately one month and a half for the whole-building switch concept.<br><b>Find more at:</b><b>https://www.edusoft.ro/brain/index.php/brain/article/view/633</b><br>
DOI: 10.6084/m9.figshare.5463655
title: Supplementary Material for: An Intact Kidney Slice Model to Investigate Vasa Recta Properties and Function in situ

description: <b><i>Background:</i></b> Medullary blood flow is via vasa recta capillaries, which possess contractile pericytes. In vitro studies using isolated descending vasa recta show that pericytes can constrict/dilate descending vasa recta when vasoactive substances are present. We describe a live kidney slice model in which pericyte-mediated vasa recta constriction/dilation can be visualized in situ. <b><i>Methods:</i></b> Confocal microscopy was used to image calcein, propidium iodide and Hoechst labelling in ‘live’ kidney slices, to determine tubular and vascular cell viability and morphology. DIC video-imaging of live kidney slices was employed to investigate pericyte-mediated real-time changes in vasa recta diameter. <b><i>Results:</i></b> Pericytes were identified on vasa recta and their morphology and density were characterized in the medulla. Pericyte-mediated changes in vasa recta diameter (10–30%) were evoked in response to bath application of vasoactive agents (norepinephrine, endothelin-1, angiotensin-II and prostaglandin E<sub>2</sub>) or by manipulating endogenous vasoactive signalling pathways (using tyramine, <i>L</i>-NAME, a cyclo-oxygenase (COX-1) inhibitor indomethacin, and ATP release). <b><i>Conclusions:</i></b> The live kidney slice model is a valid complementary technique for investigating vasa recta function in situ and the role of pericytes as regulators of vasa recta diameter. This technique may also be useful in exploring the role of tubulovascular crosstalk in regulation of medullary blood flow.
DOI: 10.6084/m9.figshare.5463655.v1
title: Supplementary Material for: An Intact Kidney Slice Model to Investigate Vasa Recta Properties and Function in situ

description: <b><i>Background:</i></b> Medullary blood flow is via vasa recta capillaries, which possess contractile pericytes. In vitro studies using isolated descending vasa recta show that pericytes can constrict/dilate descending vasa recta when vasoactive substances are present. We describe a live kidney slice model in which pericyte-mediated vasa recta constriction/dilation can be visualized in situ. <b><i>Methods:</i></b> Confocal microscopy was used to image calcein, propidium iodide and Hoechst labelling in ‘live’ kidney slices, to determine tubular and vascular cell viability and morphology. DIC video-imaging of live kidney slices was employed to investigate pericyte-mediated real-time changes in vasa recta diameter. <b><i>Results:</i></b> Pericytes were identified on vasa recta and their morphology and density were characterized in the medulla. Pericyte-mediated changes in vasa recta diameter (10–30%) were evoked in response to bath application of vasoactive agents (norepinephrine, endothelin-1, angiotensin-II and prostaglandin E<sub>2</sub>) or by manipulating endogenous vasoactive signalling pathways (using tyramine, <i>L</i>-NAME, a cyclo-oxygenase (COX-1) inhibitor indomethacin, and ATP release). <b><i>Conclusions:</i></b> The live kidney slice model is a valid complementary technique for investigating vasa recta function in situ and the role of pericytes as regulators of vasa recta diameter. This technique may also be useful in exploring the role of tubulovascular crosstalk in regulation of medullary blood flow.
DOI: 10.6084/m9.figshare.5463631
title: Supplementary Material for: Mutation Analysis of NPHS1 in a Worldwide Cohort of Congenital Nephrotic Syndrome Patients

description: <b><i>Background:</i></b> Congenital nephrotic syndrome (CNS) is defined as nephrotic syndrome that manifests within the first 3 months of life. Mutations in the <i>NPHS1</i> gene encoding nephrin, are a major cause for CNS. Currently, more than 173 different mutations of <i>NPHS1</i> have been published as causing CNS, affecting most exons. <b><i>Methods:</i></b> We performed mutation analysis of NPHS1 in a worldwide cohort of 20 families (23 children) with CNS. All 29 exons of the NPHS1 gene were examined using direct sequencing. New mutations were confirmed by demonstrating their absence in 96 healthy control individuals. <b><i>Results:</i></b> We detected disease-causing mutations in 9 of 20 families (45%). Seven of the families showed a homozygous mutation, while two were compound heterozygous. In another 2 families, single heterozygous <i>NPHS1</i> mutations were detected. Out of 10 different mutations discovered, 3 were novel, consisting of 1 splice site mutation and 2 missense mutations. <b><i>Conclusion:</i></b> Our data demonstrate that the spectrum of <i>NPHS1</i> mutations is still expanding, involving new exons, in patients from a diverse ethnic background.
DOI: 10.6084/m9.figshare.5463631.v1
title: Supplementary Material for: Mutation Analysis of NPHS1 in a Worldwide Cohort of Congenital Nephrotic Syndrome Patients

description: <b><i>Background:</i></b> Congenital nephrotic syndrome (CNS) is defined as nephrotic syndrome that manifests within the first 3 months of life. Mutations in the <i>NPHS1</i> gene encoding nephrin, are a major cause for CNS. Currently, more than 173 different mutations of <i>NPHS1</i> have been published as causing CNS, affecting most exons. <b><i>Methods:</i></b> We performed mutation analysis of NPHS1 in a worldwide cohort of 20 families (23 children) with CNS. All 29 exons of the NPHS1 gene were examined using direct sequencing. New mutations were confirmed by demonstrating their absence in 96 healthy control individuals. <b><i>Results:</i></b> We detected disease-causing mutations in 9 of 20 families (45%). Seven of the families showed a homozygous mutation, while two were compound heterozygous. In another 2 families, single heterozygous <i>NPHS1</i> mutations were detected. Out of 10 different mutations discovered, 3 were novel, consisting of 1 splice site mutation and 2 missense mutations. <b><i>Conclusion:</i></b> Our data demonstrate that the spectrum of <i>NPHS1</i> mutations is still expanding, involving new exons, in patients from a diverse ethnic background.
DOI: 10.6084/m9.figshare.5463604
title: BARM Counts LMO 2012

description: Tables with counts per sample and gene/annotation.The counts are either sum of raw counts of reads mapping or sum of tpm values. The counts for taxonomy are given in individual files per level and in a combined file for all levels. These counts are for the time series data of Hugerth et al (2015) from the Linnaeus Microbial Observatory (LMO) in the Baltic Sea.
DOI: 10.6084/m9.figshare.5463508
title: Reproducibility of Shear Wave Elastography.xlsx

description: Dataset of subjects in which were performed a hepatic shear wave elastography and a measure of fibrosis. The fibrosis stage was classified with Metavir score.