cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7806641.v1
title: Association of FOSL1 copy number alteration and triple negative breast tumors

description: Abstract Copy number alterations (CNAs) are a frequent feature in human breast cancer, and one of the hallmarks of genomic instability. The FOSL1, GSTP1 and CCND1 genes are located at 11q13, a cytoband commonly affected by CNA in breast cancer, with relevant function in progression and invasion. Our main goal was to analyze CNAs of these genes and determine their association with breast cancer subtypes. Seventy-three cases of invasive breast tumors [52 Luminal, 7 HER2+ and 14 triple negative (TNBC) subtypes] were analyzed by TaqMan assays. CNAs were observed for all genes, with gains more frequently observed. Gains of the FOSL1 gene were observed in 71% of the cases. This gene was the only one with a statistically significant difference (p&lt;0.001) among tumor subtypes, with increased copy number in TNBC compared to luminal and HER2+. No significant association of CNA and clinical and histopathological parameters from the patients was observed. Additional studies in larger breast cancer patient cohorts based on more refined molecular subtypes are necessary to confirm the observed association of FOSL1 gain with aggressive breast tumors phenotypes.
DOI: 10.6084/m9.figshare.7806647.v1
title: Science and evolution

description: Abstract Evolution is both a fact and a theory. Evolution is widely observable in laboratory and natural populations as they change over time. The fact that we need annual flu vaccines is one example of observable evolution. At the same time, evolutionary theory explains more than observations, as the succession on the fossil record. Hence, evolution is also the scientific theory that embodies biology, including all organisms and their characteristics. In this paper, we emphasize why evolution is the most important theory in biology. Evolution explains every biological detail, similar to how history explains many aspects of a current political situation. Only evolution explains the patterns observed in the fossil record. Examples include the succession in the fossil record; we cannot find the easily fossilized mammals before 300 million years ago; after the extinction of the dinosaurs, the fossil record indicates that mammals and birds radiated throughout the planet. Additionally, the fact that we are able to construct fairly consistent phylogenetic trees using distinct genetic markers in the genome is only explained by evolutionary theory. Finally, we show that the processes that drive evolution, both on short and long time scales, are observable facts.
DOI: 10.26180/5c7f10ec15f9f
title: Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from south and southeast Asia: Table S1

description: Supporting information for Wyres et al "Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from south and southeast Asia."
DOI: 10.6084/m9.figshare.7806581
title: Thinking Styles dataset

description: A dataset containing TSI-R2 and MDRAI responses (includes rows with missing data).
DOI: 10.6084/m9.figshare.7806602
title: Data and Code Archive for "Automated, predictive, and interpretable inference of C. elegans escape dynamics"

description: This file archive contains data and code used to support the publication "Automated, predictive, and interpretable inference of <i>C. elegans</i> escape dynamics," to appear in the Proceedings of the National Academy of Sciences USA.<br>Using the data and code in this archive, along with other openly available code (including particularly <i>Sir Isaac</i>), should allow one to reproduce all analysis and figures from the paper.
DOI: 10.6084/m9.figshare.7806602.v1
title: Data and Code Archive for "Automated, predictive, and interpretable inference of C. elegans escape dynamics"

description: This file archive contains data and code used to support the publication "Automated, predictive, and interpretable inference of <i>C. elegans</i> escape dynamics," to appear in the Proceedings of the National Academy of Sciences USA.<br>Using the data and code in this archive, along with other openly available code (including particularly <i>Sir Isaac</i>), should allow one to reproduce all analysis and figures from the paper.
DOI: 10.25376/hra.7806569
title: NK Depletion Dataverse Files.zip

description: This is the raw data of the results published in the current study.<br>
DOI: 10.6084/m9.figshare.7806566
title: Sequence similarity searches for morphine biosynthesis enzymes in bacteria yields putative targets for understanding associations between infection and opiate administration

description: TableS1.xls - Seventy proteins that were found the top 100 hits from the T6ODM and CODM searches.
DOI: 10.6084/m9.figshare.7806581.v1
title: Thinking Styles dataset

description: A dataset containing TSI-R2 and MDRAI responses.
DOI: 10.6084/m9.figshare.7806581.v2
title: Thinking Styles dataset

description: A dataset containing TSI-R2 and MDRAI responses (includes rows with missing data).
DOI: 10.25376/hra.7806569.v1
title: NK Depletion Dataverse Files.zip

description: This is the raw data of the results published in the current study.<br>
DOI: 10.6084/m9.figshare.7806566.v2
title: Sequence similarity searches for morphine biosynthesis enzymes in bacteria yields putative targets for understanding associations between infection and opiate administration

description: TableS1.xls - Seventy proteins that were found the top 100 hits from the T6ODM and CODM searches.
DOI: 10.6084/m9.figshare.7806548.v1
title: Agent-based Planning Portfolio

description: This dataset contains a portfolio of different datasets with generated plans for agents that represent multiple options to choose from. The following datasets are included so far:<br>1. Synthetic2. Residential energy consumption3. Bike sharing 4. Charging control of electric vehicles<br>These portfolio of agent plans has been used to study the collective learning algorithm of EPOS, the Economic Planning and Optimized Selections: http://epos-net.org
DOI: 10.6084/m9.figshare.7806548.v2
title: Agent-based Planning Portfolio

description: This dataset contains a portfolio of different datasets with generated plans for agents that represent multiple options to choose from. The following datasets are included so far:<br>1. Synthetic2. Residential energy consumption3. Bike sharing 4. Charging control of electric vehicles<br>These portfolio of agent plans has been used to study the collective learning algorithm of EPOS, the Economic Planning and Optimized Selections: http://epos-net.org
DOI: 10.6084/m9.figshare.7806458
title: Migraine burden and costs in France: a nationwide claims database analysis of triptan users

description: <b>Objectives:</b> To estimate the burden of migraine in the population of French patients identified as specific migraine acute treatment users compared to a control group. <b>Methods:</b> A cross-sectional retrospective analysis was performed on the Echantillon Généraliste des Bénéficiaires claims database, a 1/97 random sample of the French public insurance database. A representative sample of all adults with at least one delivery of triptans, ergot derivatives or acetylsalicylic acid/metoclopramide (all drugs with a specific label in migraine acute treatment – SMAT) in 2014 was selected with a control group matched on age, gender and geographic region. Among triptan users, a sub-group of over-users was defined according to their level of triptan uptake expressed in defined daily doses (DDD – a standard daily dose of treatment of acute migraine) per month over 3 months and more, was also compared with controls. The cost analysis was performed in a societal perspective for direct costs. Sick leave indirect costs were estimated using the human capital approach. <b>Results:</b> In total 8639 SMAT users (mean age: 44.6 years; 78.7% women) were selected representing a crude prevalence rate of 1.7%. The annual per capita total healthcare expenditures were higher by €280 in this group compared to controls (€2463 vs. €2183). Triptans contributed 47.8% to this extra cost. They used significantly (<i>p</i> <b>Conclusions:</b> Due to its high prevalence, migraine costs generate a significant societal burden. The group of over-users concentrates high per capita direct and indirect costs.
DOI: 10.6084/m9.figshare.7806548.v3
title: Agent-based Planning Portfolio

description: This dataset contains a portfolio of different datasets with generated plans for agents that represent multiple options to choose from. The following datasets are included so far:<br>1. Synthetic2. Residential energy consumption3. Bike sharing 4. Charging control of electric vehicles5. Fog computing load-balancing<br>These portfolio of agent plans has been used to study the collective learning algorithm of EPOS, the Economic Planning and Optimized Selections: http://epos-net.org
DOI: 10.6084/m9.figshare.7806431
title: Targeting avoidance via compound extinction

description: Avoidance towards innocuous cues is a key diagnostic criterion across anxiety-related disorders. Importantly, the most effective intervention for anxiety-related disorders, exposure therapy with response prevention, sometimes does not prevent the relapse of anxiety's symptomatology. We tested whether extinction effects, the experimental proxy of exposure, are enhanced by increasing the discrepancy between the prediction of an unpleasant event happening (shock presentation), and the actual event (shock omission). Forty-eight individuals first saw pictures of three stimuli. Two pictures (CSA, CSB) were followed by a shock (US) and one (CS-) was not. Next, participants learned to avoid the US by pressing a computer key. An extinction and response prevention procedure followed. In the first part of it, participants saw unreinforced presentations of all CSs. In the second part, the <i>single</i> group saw unreinforced presentations of the CSA and CS-. The <i>compound</i> group encountered compound unreinforced presentations of the CSA and CSB, and separate presentations of the CS-. Return of avoidance and fear was tested after unsignalled presentations of the US. Compound extinction resulted in comparable reduction of fear and avoidance compared to standard extinction. We discuss how future research could enhance extinction effects by adding costs to the avoidance behaviour.
DOI: 10.6084/m9.figshare.7806458.v1
title: Migraine burden and costs in france: a nationwide claims database analysis of triptan users

description: <b><i>Objectives:</i></b> To estimate the burden of migraine in the population of French patients identified as specific migraine acute treatment users as compared to a control group. <b><i>Methods:</i></b> A cross-sectional retrospective analysis was performed on the “Echantillon Généraliste des Bénéficiaires” claims database, a 1/97 random sample of the French public insurance database. A representative sample of all adults with at least one delivery of triptans, ergot derivatives or acetylsalicylic acid/metoclopramide (all drugs with a Specific label in Migraine Acute Treatment - SMAT) in 2014 was selected with a control group matched on age, gender and geographic region. Among triptan users, a sub-group of over-users was defined according to their level of triptan uptake expressed in Defined Daily Doses (DDD - a standard daily dose of treatment of acute migraine) per month over 3 months and more, was also compared with controls. The cost analysis was performed in a societal perspective for direct costs. Sick leaves indirect costs were estimated using the human capital approach. <b><i>Results:</i></b> 8,639 SMAT users (mean age: 44.6 years; 78.7% of women) were selected representing a crude prevalence rate of 1.7%. The annual per capita total healthcare expenditures were higher by €280 in this group as compared to controls (€2,463 vs €2,183). Triptans contributed for 47.8% to this extra cost. They used significantly (p <b><i>Conclusions:</i></b> Due to its high prevalence, migraine costs generate a significant societal burden. The group of over-users concentrates high per capita direct and indirect costs.
DOI: 10.6084/m9.figshare.7806458.v2
title: Migraine burden and costs in France: a nationwide claims database analysis of triptan users

description: <b>Objectives:</b> To estimate the burden of migraine in the population of French patients identified as specific migraine acute treatment users compared to a control group. <b>Methods:</b> A cross-sectional retrospective analysis was performed on the Echantillon Généraliste des Bénéficiaires claims database, a 1/97 random sample of the French public insurance database. A representative sample of all adults with at least one delivery of triptans, ergot derivatives or acetylsalicylic acid/metoclopramide (all drugs with a specific label in migraine acute treatment – SMAT) in 2014 was selected with a control group matched on age, gender and geographic region. Among triptan users, a sub-group of over-users was defined according to their level of triptan uptake expressed in defined daily doses (DDD – a standard daily dose of treatment of acute migraine) per month over 3 months and more, was also compared with controls. The cost analysis was performed in a societal perspective for direct costs. Sick leave indirect costs were estimated using the human capital approach. <b>Results:</b> In total 8639 SMAT users (mean age: 44.6 years; 78.7% women) were selected representing a crude prevalence rate of 1.7%. The annual per capita total healthcare expenditures were higher by €280 in this group compared to controls (€2463 vs. €2183). Triptans contributed 47.8% to this extra cost. They used significantly (<i>p</i> <b>Conclusions:</b> Due to its high prevalence, migraine costs generate a significant societal burden. The group of over-users concentrates high per capita direct and indirect costs.
DOI: 10.6084/m9.figshare.7806431.v1
title: Targeting avoidance via compound extinction

description: Avoidance towards innocuous cues is a key diagnostic criterion across anxiety-related disorders. Importantly, the most effective intervention for anxiety-related disorders, exposure therapy with response prevention, sometimes does not prevent the relapse of anxiety's symptomatology. We tested whether extinction effects, the experimental proxy of exposure, are enhanced by increasing the discrepancy between the prediction of an unpleasant event happening (shock presentation), and the actual event (shock omission). Forty-eight individuals first saw pictures of three stimuli. Two pictures (CSA, CSB) were followed by a shock (US) and one (CS-) was not. Next, participants learned to avoid the US by pressing a computer key. An extinction and response prevention procedure followed. In the first part of it, participants saw unreinforced presentations of all CSs. In the second part, the <i>single</i> group saw unreinforced presentations of the CSA and CS-. The <i>compound</i> group encountered compound unreinforced presentations of the CSA and CSB, and separate presentations of the CS-. Return of avoidance and fear was tested after unsignalled presentations of the US. Compound extinction resulted in comparable reduction of fear and avoidance compared to standard extinction. We discuss how future research could enhance extinction effects by adding costs to the avoidance behaviour.
DOI: 10.6084/m9.figshare.7806278
title: A musculoskeletal shoulder simulation of moment arms and joint reaction forces after medialization of the supraspinatus footprint in rotator cuff repair

description: A non-anatomical reinsertion of the supraspinatus medially to the original footprint to avoid over-tensioning of the tendon in large and retracted tears is one surgical option in rotator cuff (RC) repair. The purpose of the study was to determine the biomechanical effects on the glenohumeral joint with regard to this surgical technique. A modified musculoskeletal computational shoulder model was used to evaluate the change in moment arms and muscle forces of the RC and the co-contracting muscles and the alteration of the joint reaction forces (compressive and shear forces) after reinsertion of the supraspinatus 5 mm, 10 mm, 15 mm and 20 mm medially to the original footprint. A medialization of the supraspinatus reduces its moment arm in glenohumeral abduction. In case of a medialization of the attachment of 15 mm and 20 mm, the supraspinatus restricts glenohumeral abduction at 54° and 68°. In glenohumeral forward flexion and in lower degrees of internal rotation the moment arm of the supraspinatus increases for a medialized tendon attachment and decreases in external rotation in relation to the anatomical condition. A medialization of the supraspinatus insertion point yields in an increase in muscle force for abduction, internal and external rotation. In the present model a medially non-anatomic reinsertion reduces significantly the compressive glenohumeral joint reaction and the glenohumeral stability. Moreover, the results show that a medialization of the supraspinatus leads to a reduction of the supraspinatus moment arm especially in abduction. This leads to an increase of a compensatory supraspinatus load for stabilization the humerus in space, which may potentially cause a postoperative overload of the tendon-bone-complex.
DOI: 10.6084/m9.figshare.7806278.v1
title: A musculoskeletal shoulder simulation of moment arms and joint reaction forces after medialization of the supraspinatus footprint in rotator cuff repair

description: A non-anatomical reinsertion of the supraspinatus medially to the original footprint to avoid over-tensioning of the tendon in large and retracted tears is one surgical option in rotator cuff (RC) repair. The purpose of the study was to determine the biomechanical effects on the glenohumeral joint with regard to this surgical technique. A modified musculoskeletal computational shoulder model was used to evaluate the change in moment arms and muscle forces of the RC and the co-contracting muscles and the alteration of the joint reaction forces (compressive and shear forces) after reinsertion of the supraspinatus 5 mm, 10 mm, 15 mm and 20 mm medially to the original footprint. A medialization of the supraspinatus reduces its moment arm in glenohumeral abduction. In case of a medialization of the attachment of 15 mm and 20 mm, the supraspinatus restricts glenohumeral abduction at 54° and 68°. In glenohumeral forward flexion and in lower degrees of internal rotation the moment arm of the supraspinatus increases for a medialized tendon attachment and decreases in external rotation in relation to the anatomical condition. A medialization of the supraspinatus insertion point yields in an increase in muscle force for abduction, internal and external rotation. In the present model a medially non-anatomic reinsertion reduces significantly the compressive glenohumeral joint reaction and the glenohumeral stability. Moreover, the results show that a medialization of the supraspinatus leads to a reduction of the supraspinatus moment arm especially in abduction. This leads to an increase of a compensatory supraspinatus load for stabilization the humerus in space, which may potentially cause a postoperative overload of the tendon-bone-complex.
DOI: 10.6084/m9.figshare.7806266
title: Individual and stable autoantibody repertoires in healthy individuals

description: In the era towards precision medicine, we here present the individual specific autoantibody signatures of 193 healthy individuals. The self-reactive IgG signatures are stable over time in a way that each individual profile is recognized in longitudinal sampling. The IgG autoantibody reactivity towards an antigen array comprising 335 protein fragments, representing 204 human proteins with potential relevance to autoimmune disorders, was measured in longitudinal plasma samples from 193 healthy individuals. This analysis resulted in unique autoantibody barcodes for each individual that were maintained over one year’s time. The reactivity profiles, or signatures, are person specific in regards to the number of reactivities and antigen specificity. Two independent data sets were consistent in that each healthy individual displayed reactivity towards 0–16 antigens, with a median of six. Subsequently, four selected individuals were profiled on in-house produced high-density protein arrays containing 23,000 protein fragments representing 14,000 unique protein coding genes. Based on a unique, broad and deep longitudinal profiling of autoantibody reactivities, our results demonstrate a unique autoreactive profile in each analyzed healthy individual. The need and interest for broad-ranged and high-resolution molecular profiling of healthy individuals is rising. We have here generated and assessed an initial perspective on the global distribution of the self-reactive IgG repertoire in healthy individuals, by investigating 193 well-characterized healthy individuals.HighlightsA unique longitudinal profiling of autoantibody repertoires in healthy individualsAutoantibody profiles are highly individual and stable over timeAll individuals display IgG binding to human protein fragmentsThe specificity of disease associated autoantigens needs to be thoroughly characterizedThe identification of a small set of highly reactive autoantigensImportance of stringent antigen and sample specific cut-offs for defining reactivity A unique longitudinal profiling of autoantibody repertoires in healthy individuals Autoantibody profiles are highly individual and stable over time All individuals display IgG binding to human protein fragments The specificity of disease associated autoantigens needs to be thoroughly characterized The identification of a small set of highly reactive autoantigens Importance of stringent antigen and sample specific cut-offs for defining reactivity
DOI: 10.6084/m9.figshare.7806263
title: The most relevant chromosomal abnormalities in the north of Rio Grande do Sul, Brazil: 26 years of cytogenetic analysis

description: From 1992 to 2018, cytogenetic analyses were successfully performed to explore the chromosomal abnormalities of 729 patients, who utilised a pioneering counselling service in the city of Passo Fundo in the northern part of the Brazilian state of Rio Grande do Sul. This city is characterised by a large conglomerate of private and public hospitals. A classical cytogenetic analysis and G-banding were performed using the patient samples. Although normal karyotypes were observed for 562 of the cases, 167 individuals evidenced chromosomal alterations. Among those, 110 exhibited numerical alterations (65.86%), 41 demonstrated structural modifications (24.55%) and 16 showed both numerical and structural chromosomal changes (9.58%). This study describes the diversity of the chromosomal alterations in this region, which have not been previously examined. After 26 years of study, the findings are discussed herein in a self-critical form.