cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1621438.v1
title: Raman spectroscopy detects melanoma and the tissue surrounding melanoma using tissue engineered melanoma models

description: ABSTRACTInvasion of melanoma cells from the primary tumour involves interaction with adjacent tissues and extracellular matrix. The extent of this interaction is not fully understood. In this study Raman spectroscopy was applied to cryo-sections of established 3D models of melanoma in human skin. Principal component analysis was used to investigate differences between the tumour and normal tissue and between the peri-tumour area and the normal skin. Two human melanoma cells lines A375SM and C8161 were investigated and compared in 3D melanoma models. Changes were found in protein conformations and tryptophan configurations across the entire melanoma samples, in tyrosine orientation and in more fluid lipid packing only in tumour dense areas, and in increased glycogen content in the peri-tumour areas of melanoma. Raman spectroscopy revealed changes around the perimeter of a melanoma tumour as well as detecting differences between the tumour and the normal tissue.
DOI: 10.6084/m9.figshare.1621429
title: Association of Inhaled Corticosteroids with Incident Pneumonia and Mortality in COPD Patients; Systematic Review and Meta-Analysis

description: <i>Background:</i> Inhaled corticosteroids are commonly prescribed for patients with severe COPD. They have been associated with increased risk of pneumonia but not with increased pneumonia-associated or overall mortality. <i>Methods:</i> To further examine the effects of inhaled corticosteroids on pneumonia incidence, and mortality in COPD patients, we searched for potentially relevant articles in PubMed, Medline, CENTRAL, EMBASE, Scopus, Web of Science and manufacturers' web clinical trial registries from 1994 to February 4, 2014. Additionally, we checked the included and excluded studies' bibliographies. We subsequently performed systematic review and meta-analysis of included randomized controlled trials and observational studies on the topic. <i>Results:</i> We identified 38 studies: 29 randomized controlled trials and nine observational studies. The estimated unadjusted risk of pneumonia was increased in randomized trials: RR 1.61; 95% CI 1.35–1.93, <i>p</i> &lt; 0.001; as well as in observational studies: OR 1.89; 95% CI 1.39–2.58, <i>p</i> &lt; 0·001. Six randomized trials and seven observational studies were useful in estimating unadjusted risk of pneumonia ­case-fatality: RR 0.91; 95% CI 0.52–1.59, <i>p</i> = 0.74; and OR 0.72; 95% CI 0.59–0.88, <i>p</i> = 0.001, respectively. Twenty-nine randomized trials and six observational studies allowed estimation of unadjusted risk of overall mortality: RR 0.95; 95% CI 0.85–1.05, <i>p</i> = 0.31; and OR 0.79; 95% CI 0.65–0.97, <i>p</i> = 0.02, respectively. <i>Conclusions:</i> Despite a substantial and significant increase in unadjusted risk of pneumonia associated with inhaled corticosteroid use, pneumonia fatality and overall mortality were found not to be increased in randomized controlled trials and were decreased in observational studies.
DOI: 10.6084/m9.figshare.1621429.v1
title: Association of Inhaled Corticosteroids with Incident Pneumonia and Mortality in COPD Patients; Systematic Review and Meta-Analysis

description: <i>Background:</i> Inhaled corticosteroids are commonly prescribed for patients with severe COPD. They have been associated with increased risk of pneumonia but not with increased pneumonia-associated or overall mortality. <i>Methods:</i> To further examine the effects of inhaled corticosteroids on pneumonia incidence, and mortality in COPD patients, we searched for potentially relevant articles in PubMed, Medline, CENTRAL, EMBASE, Scopus, Web of Science and manufacturers' web clinical trial registries from 1994 to February 4, 2014. Additionally, we checked the included and excluded studies' bibliographies. We subsequently performed systematic review and meta-analysis of included randomized controlled trials and observational studies on the topic. <i>Results:</i> We identified 38 studies: 29 randomized controlled trials and nine observational studies. The estimated unadjusted risk of pneumonia was increased in randomized trials: RR 1.61; 95% CI 1.35–1.93, <i>p</i> &lt; 0.001; as well as in observational studies: OR 1.89; 95% CI 1.39–2.58, <i>p</i> &lt; 0·001. Six randomized trials and seven observational studies were useful in estimating unadjusted risk of pneumonia ­case-fatality: RR 0.91; 95% CI 0.52–1.59, <i>p</i> = 0.74; and OR 0.72; 95% CI 0.59–0.88, <i>p</i> = 0.001, respectively. Twenty-nine randomized trials and six observational studies allowed estimation of unadjusted risk of overall mortality: RR 0.95; 95% CI 0.85–1.05, <i>p</i> = 0.31; and OR 0.79; 95% CI 0.65–0.97, <i>p</i> = 0.02, respectively. <i>Conclusions:</i> Despite a substantial and significant increase in unadjusted risk of pneumonia associated with inhaled corticosteroid use, pneumonia fatality and overall mortality were found not to be increased in randomized controlled trials and were decreased in observational studies.
DOI: 10.6084/m9.figshare.1621425
title: Microarray analysis of transcripts with elevated expressions in the rat medial or lateral habenula suggest fast GABAergic excitation in the medial habenula and habenular involvement in the regulation of feeding and energy balance

description: Full article is available in "Brain Structure and Function":http://link.springer.com/article/10.1007/s00429-016-1195-zby Franziska Wagner, René Bernard, Christian Derst, Leon French and Rüdiger W. Veh.In vertebrates the “anti-reward-system” mainly is represented by the habenula and its medial (MHb) and especially lateral (LHb) complexes. So far, considerable knowledge has accumulated especially concerning subnuclear structures and the connectivities of MHb and LHb subnuclei. The present investigation aimed to obtain novel information, whether MHb or LHb or their subnuclei display characteristic gene products, which may shed more light on biological functions of these areas. Using microarray analysis of mRNAs expressed in microdissected habenular and thalamic control areas yielded expression values of 17,745 RNAs representing protein-coding genes, to which annotated gene names could be assigned. High relative values of genes with known expression in MHb, LHb or thalamus in the corresponding areas indicated a high precision of the microdissection procedure. <strong>File descriptions</strong> Supplemental Table 1: Expression matrix with gene symbols and normalized values for each ref-seq probe. Supplemental Table 2: The first 100 transcripts with the highest absolute expression in MHb and LHb.Supplemental Table 3: Transcripts with enhanced expression in the lateral habenula as compared to the thalamus (FDR &lt; 0.05 and fold change &gt; 1.5). A “+” in column J or K indicates that this gene also is included in the indicated table and correspondingly depicted in the intersections of Figure 1. Gene ontology biological process terms are listed in the last column.Supplemental Table 4: Transcripts with enhanced expression in the lateral habenula as compared to the thalamus (FDR &lt; 0.2 and fold change &gt; 1.5). A “+” in column J or K indicates that this gene also is included in the indicated table and correspondingly depicted in the intersections of Figure 1. Gene ontology biological process terms are listed in the last column.<br>Supplemental Table 5: Genes deferentially expressed between medial and the lateral habenula (FDR &lt; 0.05 and absolute fold change &gt; 1.5). A “+” in column J or K indicates that this gene also is included in the indicated table and correspondingly depicted in the intersections of Figure 1. Gene ontology biological process terms are listed in the last column.<br>Supplemental Table 6: Gene ontology term enrichment results (six sheets in one table). These results were computed by ErmineJ. Gene Ontology files were downloaded on June 2015. Enrichment was tested on genes that had a corrected p &lt; 0.05 for each direction of change. Except for the LHb-Thal comparisons due to a limited number of genes that pass FDR &lt; 0.05. For these LHb-Thal comparisons the area under the receiver operating curve enrichment (AROC) method was applied.
DOI: 10.6084/m9.figshare.1621404
title: new fileset

description: Final project for Decision Pathways class. Includes Matlab models with code, excel based game on water resources and economics, interactive twine feature, presentation of our research in a word document as well as powerpoint.
DOI: 10.6084/m9.figshare.1621405
title: North_Carolina_Clapper_Rail_Data

description: Stable Nitrogen and Carbon and Mercury values from feathers pulled from the breasts of Clapper Rails in museums.
DOI: 10.6084/m9.figshare.1621425.v2
title: Microarray analysis of transcripts with elevated expressions in the rat medial or lateral habenula suggest fast GABAergic excitation in the medial habenula and habenular involvement in the regulation of feeding and energy balance

description: Full article is available in "Brain Structure and Function":http://link.springer.com/article/10.1007/s00429-016-1195-zby Franziska Wagner, René Bernard, Christian Derst, Leon French and Rüdiger W. Veh.In vertebrates the “anti-reward-system” mainly is represented by the habenula and its medial (MHb) and especially lateral (LHb) complexes. So far, considerable knowledge has accumulated especially concerning subnuclear structures and the connectivities of MHb and LHb subnuclei. The present investigation aimed to obtain novel information, whether MHb or LHb or their subnuclei display characteristic gene products, which may shed more light on biological functions of these areas. Using microarray analysis of mRNAs expressed in microdissected habenular and thalamic control areas yielded expression values of 17,745 RNAs representing protein-coding genes, to which annotated gene names could be assigned. High relative values of genes with known expression in MHb, LHb or thalamus in the corresponding areas indicated a high precision of the microdissection procedure. <strong>File descriptions</strong> Supplemental Table 1: Expression matrix with gene symbols and normalized values for each ref-seq probe. Supplemental Table 2: The first 100 transcripts with the highest absolute expression in MHb and LHb.Supplemental Table 3: Transcripts with enhanced expression in the lateral habenula as compared to the thalamus (FDR &lt; 0.05 and fold change &gt; 1.5). A “+” in column J or K indicates that this gene also is included in the indicated table and correspondingly depicted in the intersections of Figure 1. Gene ontology biological process terms are listed in the last column.Supplemental Table 4: Transcripts with enhanced expression in the lateral habenula as compared to the thalamus (FDR &lt; 0.2 and fold change &gt; 1.5). A “+” in column J or K indicates that this gene also is included in the indicated table and correspondingly depicted in the intersections of Figure 1. Gene ontology biological process terms are listed in the last column.<br>Supplemental Table 5: Genes deferentially expressed between medial and the lateral habenula (FDR &lt; 0.05 and absolute fold change &gt; 1.5). A “+” in column J or K indicates that this gene also is included in the indicated table and correspondingly depicted in the intersections of Figure 1. Gene ontology biological process terms are listed in the last column.<br>Supplemental Table 6: Gene ontology term enrichment results (six sheets in one table). These results were computed by ErmineJ. Gene Ontology files were downloaded on June 2015. Enrichment was tested on genes that had a corrected p &lt; 0.05 for each direction of change. Except for the LHb-Thal comparisons due to a limited number of genes that pass FDR &lt; 0.05. For these LHb-Thal comparisons the area under the receiver operating curve enrichment (AROC) method was applied.
DOI: 10.6084/m9.figshare.1621425.v1
title: Microarray analysis of transcripts with elevated expression in the rat medial or lateral habenula

description: Full article is available in "Brain Structure and Function":http://link.springer.com/article/10.1007/s00429-016-1195-zby Franziska Wagner, René Bernard, Christian Derst, Leon French and Rüdiger W. Veh.In vertebrates the “anti-reward-system” mainly is represented by the habenula and its medial (MHb) and especially lateral (LHb) complexes. So far, considerable knowledge has accumulated especially concerning subnuclear structures and the connectivities of MHb and LHb subnuclei. The present investigation aimed to obtain novel information, whether MHb or LHb or their subnuclei display characteristic gene products, which may shed more light on biological functions of these areas. Using microarray analysis of mRNAs expressed in microdissected habenular and thalamic control areas yielded expression values of 17,745 RNAs representing protein-coding genes, to which annotated gene names could be assigned. High relative values of genes with known expression in MHb, LHb or thalamus in the corresponding areas indicated a high precision of the microdissection procedure. <strong>File descriptions</strong> Supplemental Table 1: Expression matrix with gene symbols and normalized values for each ref-seq probe. Supplemental Table 2: The first 100 transcripts with the highest absolute expression in MHb and LHb.Supplemental Table 3: Transcripts with enhanced expression in the lateral habenula as compared to the thalamus (FDR &lt; 0.05 and fold change &gt; 1.5). A “+” in column J or K indicates that this gene also is included in the indicated table and correspondingly depicted in the intersections of Figure 1. Gene ontology biological process terms are listed in the last column.Supplemental Table 4: Transcripts with enhanced expression in the lateral habenula as compared to the thalamus (FDR &lt; 0.2 and fold change &gt; 1.5). A “+” in column J or K indicates that this gene also is included in the indicated table and correspondingly depicted in the intersections of Figure 1. Gene ontology biological process terms are listed in the last column.<br>Supplemental Table 5: Genes deferentially expressed between medial and the lateral habenula (FDR &lt; 0.05 and absolute fold change &gt; 1.5). A “+” in column J or K indicates that this gene also is included in the indicated table and correspondingly depicted in the intersections of Figure 1. Gene ontology biological process terms are listed in the last column.<br>Supplemental Table 6: Gene ontology term enrichment results (six sheets in one table). These results were computed by ErmineJ. Gene Ontology files were downloaded on June 2015. Enrichment was tested on genes that had a corrected p &lt; 0.05 for each direction of change. Except for the LHb-Thal comparisons due to a limited number of genes that pass FDR &lt; 0.05. For these LHb-Thal comparisons the area under the receiver operating curve enrichment (AROC) method was applied.
DOI: 10.6084/m9.figshare.1621400
title: Azadirachtin(A) Distinctively Modulates Subdomain 2 of Actin – Novel Mechanism to Induce Depolymerization revealed by Molecular Dynamics Study

description: Azadirachtin(A) (AZA) a potential insecticide from neem binds to actin and induces depolymerization in <i>Drosophila.</i> AZA binds to the pocket same as that of Latrunculin A (LAT) but LAT inhibits actin polymerization by stiffening the actin structure and affects the ADP-ATP exchange. The mechanism by which AZA induces actin depolymerization is not clearly understood. Therefore, different computational experiments were conducted to delineate the precise mechanism of AZA induced actin depolymerization. Molecular dynamics studies showed that AZA strongly interacted with subdomain 2 and destabilised the interactions between subdomain 2 of one actin and subdomain 1 & 4 of the adjacent actin, causing the separation of actin subunits. The separation was observed between subdomain 3 of subunit n and subdomain 4 of subunit n+2. However, the specific triggering point for the separation of the subunits was the destabilisation of direct interactions between subdomain 2 of subunit n (Arg39, Val45, Gly46 and Arg62) and subdomain 4 of subunit n+2 (Asp286, Ile287, Asp288, Ile289, Asp244 and Lys291). These results reveal a unique mechanism of an actin filament modulator that induces depolymerization. This mechanism of AZA can be used to design similar molecules against mammalian actins for cancer therapy.
DOI: 10.6084/m9.figshare.12848777.v1
title: The characteristics of dockless electric rental scooter-related injuries in a large U.S. city

description: To describe the characteristics of dockless electric rental scooter ("e-scooter")-related injuries presenting to two emergency departments in one large U.S. city. This observational cohort study utilized the city’s public health syndromic surveillance system to prospectively identify patients with e-scooter-related injuries presenting between September and November 2018. The medical records for all adult patients treated at the two participating emergency departments were manually reviewed to extract demographic and clinical data. Cases involving mobility scooters or non-electric scooters were excluded. For the 124 included adult patients with e-scooter-related injuries, the median age was 30 years (IQR: 22-43), they were predominantly male (59.7%), and approximately half (51.6%) arrived by ambulance. Falling from the scooter (84.7%) was the most common mechanism; twelve patients (9.7%) had collided with a motor vehicle. Head and face injuries (45.5%) were common; only 2 patients (1.6%) were documented as wearing a helmet at the time of injury. Most patients (n = 112, 90.3%) required imaging, more than half (n = 78, 62.9%) required an emergency department procedure, and 26 (21.0%) required surgical intervention. Most patients were discharged home, but 35 (28.2%) were admitted to hospital. Two patients (1.6%) were admitted to the intensive care unit. E-scooters are an emerging transportation technology associated with a wide range of potentially serious injuries that consume substantial emergency department and hospital resources. Head injuries are a particular concern, as few e-scooter riders are wearing helmets at the time of injury.
DOI: 10.6084/m9.figshare.1621405.v1
title: North_Carolina_Clapper_Rail_Data

description: Stable Nitrogen and Carbon and Mercury values from feathers pulled from the breasts of Clapper Rails in museums.
DOI: 10.6084/m9.figshare.12848777
title: The characteristics of dockless electric rental scooter-related injuries in a large U.S. city

description: To describe the characteristics of dockless electric rental scooter ("e-scooter")-related injuries presenting to two emergency departments in one large U.S. city. This observational cohort study utilized the city’s public health syndromic surveillance system to prospectively identify patients with e-scooter-related injuries presenting between September and November 2018. The medical records for all adult patients treated at the two participating emergency departments were manually reviewed to extract demographic and clinical data. Cases involving mobility scooters or non-electric scooters were excluded. For the 124 included adult patients with e-scooter-related injuries, the median age was 30 years (IQR: 22-43), they were predominantly male (59.7%), and approximately half (51.6%) arrived by ambulance. Falling from the scooter (84.7%) was the most common mechanism; twelve patients (9.7%) had collided with a motor vehicle. Head and face injuries (45.5%) were common; only 2 patients (1.6%) were documented as wearing a helmet at the time of injury. Most patients (n = 112, 90.3%) required imaging, more than half (n = 78, 62.9%) required an emergency department procedure, and 26 (21.0%) required surgical intervention. Most patients were discharged home, but 35 (28.2%) were admitted to hospital. Two patients (1.6%) were admitted to the intensive care unit. E-scooters are an emerging transportation technology associated with a wide range of potentially serious injuries that consume substantial emergency department and hospital resources. Head injuries are a particular concern, as few e-scooter riders are wearing helmets at the time of injury.
DOI: 10.6084/m9.figshare.1621404.v1
title: new fileset

description: Final project for Decision Pathways class. Includes Matlab models with code, excel based game on water resources and economics, interactive twine feature, presentation of our research in a word document as well as powerpoint.
DOI: 10.6084/m9.figshare.1621397
title: Benzoxazolinone Detoxification by <i>N</i>-Glucosylation: The Multi-Compartment- Network of <i>Zea mays</i> L

description: The major detoxification product in maize roots after 24h benzoxazolin-2(3<i>H</i>)-one (BOA) exposure was identified as glucoside carbamate resulting from rearrangement of BOA-<i>N</i>-glucoside, but the pathway of <i>N</i>-glucosylation, enzymes involved and the site of synthesis were previously unknown. Assaying whole cell proteins revealed the necessity of H<sub>2</sub>O<sub>2</sub> and Fe<sup>2</sup><sup>+</sup> ions for glucoside carbamate production. Peroxidase produced BOA radicals are apparently formed within the extraplastic space of the young maize root. Radicals seem to be the preferred substrate for <i>N</i>-glucosylation, either by direct reaction with glucose or, more likely, the <i>N</i>-glucoside is released by glucanase/glucosidase catalyzed hydrolysis from cell wall components harboring fixed BOA. The processes are accompanied by alterations of cell wall polymers. Glucoside carbamate accumulation could be suppressed by the oxireductase inhibitor 2-bromo-4´-nitroacetophenone and by peroxidase inhibitor 2,3-butanedione. Alternatively, activated BOA molecules with an open heterocycle may be produced by microorganisms (e.g., endophyte <i>Fusarium verticillioides</i>) and channeled for enzymatic <i>N</i>-glucosylation. Experiments with transgenic <i>Arabidopsis</i> lines indicate a role of maize glucosyltransferase BX9 in BOA-<i>N</i>-glycosylation. Western blots with BX9 antibody demonstrate the presence of BX9 in the extraplastic space. Proteomic analyses verified a high BOA responsiveness of multiple peroxidases in the apoplast/cell wall. BOA incubations led to shifting, altered abundances and identities of the apoplast and cell wall located peroxidases, glucanases, glucosidases and glutathione transferases (GSTs). GSTs could function as glucoside carbamate transporters. The highly complex, compartment spanning and redox-regulated glucoside carbamate pathway seems to be mainly realized in Poaceae. In maize, carbamate production is independent from benzoxazinone synthesis.
DOI: 10.6084/m9.figshare.1621400.v1
title: Azadirachtin(A) Distinctively Modulates Subdomain 2 of Actin – Novel Mechanism to Induce Depolymerization revealed by Molecular Dynamics Study

description: Azadirachtin(A) (AZA) a potential insecticide from neem binds to actin and induces depolymerization in <i>Drosophila.</i> AZA binds to the pocket same as that of Latrunculin A (LAT) but LAT inhibits actin polymerization by stiffening the actin structure and affects the ADP-ATP exchange. The mechanism by which AZA induces actin depolymerization is not clearly understood. Therefore, different computational experiments were conducted to delineate the precise mechanism of AZA induced actin depolymerization. Molecular dynamics studies showed that AZA strongly interacted with subdomain 2 and destabilised the interactions between subdomain 2 of one actin and subdomain 1 & 4 of the adjacent actin, causing the separation of actin subunits. The separation was observed between subdomain 3 of subunit n and subdomain 4 of subunit n+2. However, the specific triggering point for the separation of the subunits was the destabilisation of direct interactions between subdomain 2 of subunit n (Arg39, Val45, Gly46 and Arg62) and subdomain 4 of subunit n+2 (Asp286, Ile287, Asp288, Ile289, Asp244 and Lys291). These results reveal a unique mechanism of an actin filament modulator that induces depolymerization. This mechanism of AZA can be used to design similar molecules against mammalian actins for cancer therapy.