cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3482579.v2
title: First record of a non-pollinating fig wasp (Hymenoptera: Sycophaginae) from Dominican amber, with estimation of the size of its host figs

description: Fig trees and their pollinating fig wasps arose about 75 million years ago in the Cretaceous period. Several other groups of chalcid wasps also utilize figs for larval development, including sycophagines, the putative sister group to pollinating fig wasps. Whereas stone and amber fossil pollinators are known, no fossils representing non-pollinating fig wasp groups have been confirmed previously. Here, we describe the first Sycophaginae from the <i>c</i>.15<i>–</i>20 Ma Dominican amber, <i>Idarnes thanatos</i> sp. nov. Farache, Rasplus, Pereira and Compton, and discuss its relationships within the <i>Idarnes carme</i> species group. Additionally, we use linear regression to compare body size, ovipositor sheaths length, and host fig size data from extant <i>Idarnes</i> species to estimate the size of its host figs. <i>Idarnes thanatos</i> was most likely associated with small to medium sized figs (diameter ≤1.0 cm), that were likely to have been dispersed by birds and primates. The discovery of this close relative of extant non-pollinating fig wasps suggests that early Miocene and modern fig wasp communities may share similar ecological and functional features.
DOI: 10.6084/m9.figshare.3482579.v1
title: First record of a non-pollinating fig wasp (Hymenoptera: Sycophaginae) from Dominican amber, with estimation of the size of its host figs

description: Fig trees and their pollinating fig wasps arose about 75 million years ago in the Cretaceous period. Several other groups of chalcid wasps also utilize figs for larval development, including sycophagines, the putative sister group to pollinating fig wasps. Whereas stone and amber fossil pollinators are known, no fossils representing non-pollinating fig wasp groups have been confirmed previously. Here, we describe the first Sycophaginae from the <i>c</i>.15<i>–</i>20 Ma Dominican amber, <i>Idarnes thanatos</i> sp. nov. Farache, Rasplus, Pereira and Compton, and discuss its relationships within the <i>Idarnes carme</i> species group. Additionally, we use linear regression to compare body size, ovipositor sheaths length, and host fig size data from extant <i>Idarnes</i> species to estimate the size of its host figs. <i>Idarnes thanatos</i> was most likely associated with small to medium sized figs (diameter ≤1.0 cm), that were likely to have been dispersed by birds and primates. The discovery of this close relative of extant non-pollinating fig wasps suggests that early Miocene and modern fig wasp communities may share similar ecological and functional features.
DOI: 10.6084/m9.figshare.3482576
title: Hayes_Saturday_1045_SalonD.pptm

description: A personal reflection of how good mentorship developed my career as a scientist and how members of the American Society of Ichthyologists and Herpetologists have duties to one another and to the public so the ASIH can exist for another 100 years.
DOI: 10.6084/m9.figshare.3482576.v1
title: Hayes_Saturday_1045_SalonD.pptm

description: A personal reflection of how good mentorship developed my career as a scientist and how members of the American Society of Ichthyologists and Herpetologists have duties to one another and to the public so the ASIH can exist for another 100 years.
DOI: 10.6084/m9.figshare.3482570
title: Supplementary Material for: Molecular Cytogenetic Mapping of Satellite DNA Sequences in Aegilops geniculata and Wheat

description: Fluorescence in situ hybridization (FISH) provides an efficient system for cytogenetic analysis of wild relatives of wheat for individual chromosome identification, elucidation of homoeologous relationships, and for monitoring alien gene transfers into wheat. This study is aimed at developing cytogenetic markers for chromosome identification of wheat and <i>Aegilops geniculata</i> (2n<i> = </i>4x<i> = </i>28, UgUgMgMg) using satellite DNAs obtained from flow-sorted chromosome 5Mg. FISH was performed to localize the satellite DNAs on chromosomes of wheat and selected <i>Aegilops</i> species. The FISH signals for satellite DNAs on chromosome 5Mg were generally associated with constitutive heterochromatin regions corresponding to C-band-positive chromatin including telomeric, pericentromeric, centromeric, and interstitial regions of all the 14 chromosome pairs of <i>Ae. geniculata</i>. Most satellite DNAs also generated FISH signals on wheat chromosomes and provided diagnostic chromosome arm-specific cytogenetic markers that significantly improved chromosome identification in wheat. The newly identified satellite DNA CL36 produced localized Mg genome chromosome-specific FISH signals in <i>Ae. geniculata</i> and in the M genome of the putative diploid donor species <i>Ae. comosa </i>subsp. <i>subventricosa</i> but not in <i>Ae. comosa</i>subsp. <i>comosa</i>, suggesting that the Mg genome of <i>Ae. geniculata</i> was probably derived from subsp. <i>subventricosa.</i>
DOI: 10.6084/m9.figshare.3482555
title: Supplementary Material for: Determinants of Physical Activity in Patients with Chronic Obstructive Pulmonary Disease: A 5-Year Prospective Follow-Up Study

description: <i>Background:</i> Although many studies examined determinants of physical activity in patients with chronic obstructive pulmonary disease (COPD), most were cross-sectional and focused on single determinants only. <i>Objectives:</i> The aim of this study was to determine how COPD patients' physical activity changes over time and to identify the determinants of physical activity using multivariable and longitudinal methods. <i>Methods:</i> In a prospective cohort study, 409 primary care patients with COPD in the Netherlands and Switzerland were followed for up to 5 years. Physical activity was assessed at baseline and every 6 months using the Longitudinal Aging Study Amsterdam Physical Activity Questionnaire (LAPAQ) adapted to a 0- to 23-point scale. We studied the associations between determinants at baseline and patients' long-term physical activity levels using linear mixed models. <i>Results:</i> Unadjusted analysis showed an overall gradual decline in physical activity (0.22 points of the LAPAQ scale every 6 months, 95% CI: 0.17-0.28; p &lt; 0.001). In multivariable analyses, baseline determinants that were independently associated (p ≤ 0.05) with lower long-term physical activity levels included (starting from coefficients with the smallest p value) lower exercise capacity, older age, working, more smoking pack-years, more fatigued, male sex, lower educational levels, previously not in fitness programs, more depressed, lower lung function, lower overall health status, and more prescription drug use. <i>Conclusions:</i> We found that physical activity of COPD patients may decline more than reported in the healthy elderly. Longitudinal analysis identified independent determinants of physical activity, which allows the identification of patients having low physical activity levels and who may benefit from physical activity interventions.
DOI: 10.6084/m9.figshare.3482555.v1
title: Supplementary Material for: Determinants of Physical Activity in Patients with Chronic Obstructive Pulmonary Disease: A 5-Year Prospective Follow-Up Study

description: <i>Background:</i> Although many studies examined determinants of physical activity in patients with chronic obstructive pulmonary disease (COPD), most were cross-sectional and focused on single determinants only. <i>Objectives:</i> The aim of this study was to determine how COPD patients' physical activity changes over time and to identify the determinants of physical activity using multivariable and longitudinal methods. <i>Methods:</i> In a prospective cohort study, 409 primary care patients with COPD in the Netherlands and Switzerland were followed for up to 5 years. Physical activity was assessed at baseline and every 6 months using the Longitudinal Aging Study Amsterdam Physical Activity Questionnaire (LAPAQ) adapted to a 0- to 23-point scale. We studied the associations between determinants at baseline and patients' long-term physical activity levels using linear mixed models. <i>Results:</i> Unadjusted analysis showed an overall gradual decline in physical activity (0.22 points of the LAPAQ scale every 6 months, 95% CI: 0.17-0.28; p &lt; 0.001). In multivariable analyses, baseline determinants that were independently associated (p ≤ 0.05) with lower long-term physical activity levels included (starting from coefficients with the smallest p value) lower exercise capacity, older age, working, more smoking pack-years, more fatigued, male sex, lower educational levels, previously not in fitness programs, more depressed, lower lung function, lower overall health status, and more prescription drug use. <i>Conclusions:</i> We found that physical activity of COPD patients may decline more than reported in the healthy elderly. Longitudinal analysis identified independent determinants of physical activity, which allows the identification of patients having low physical activity levels and who may benefit from physical activity interventions.
DOI: 10.6084/m9.figshare.3482546
title: Tests on Thin Reinforced Concrete Walls Subjected to In-plane and Out-of-plane Cyclic Loading - TW4 (4/4) & TW5 (1/3)

description: The present dataset describes an experimental campaign on five thin T-shaped reinforced concrete walls. The tests aimed at assessing the influence of wall thickness on member stability, the role of lap splices on damage distribution and displacement ductility, and the effects of the simultaneous application of out-of-plane loading on the member response.Further data can be downloaded from the links below.<br> If you use the data, please cite: Almeida, J. P., O. Prodan, A. Rosso, and K. Beyer. 2016. Tests on Thin Reinforced Concrete Walls Subjected to in-Plane and out-of-Plane Cyclic Loading. <i>Earthquake Spectra</i>.
DOI: 10.6084/m9.figshare.3482504
title: Supplementary Material for: Risk of Ophthalmic Adverse Effects in Patients Treated with MEK Inhibitors: A Systematic Review and Meta-Analysis

description: <i>Objectives:</i> This meta-analysis aims to evaluate the risk of ophthalmic adverse effects associated with MEK inhibitors. <i>Methods:</i> A literature search was conducted in PubMed and the Cochrane Library to identify randomized clinical trials (RCTs) which have been designed to evaluate the efficacy and safety of MEK inhibitors. Overall risk of ophthalmic adverse effects, chorioretinopathy, retinal detachment, blurred vision, uveitis, and eye haemorrhage were the assessed outcomes. Peto odds ratios (ORs) with their 95% confidence intervals (CIs) were pooled. Between-study heterogeneity was assessed using I2 statistics. <i>Results:</i> Thirteen RCTs were included in this meta-analysis. Overall, MEK inhibitors were associated with an increased risk of ophthalmic adverse effects (OR 2.24; 95% CI 1.75-2.87; p &lt; 0.0001; I2 = 86.5%). An increased risk was also estimated for chorioretinopathy (OR 5.44; 95% CI 2.89-10.23; p &lt; 0.0001; I2 = 0%), retinal detachment (OR 6.54; 95% CI 3.28-13.03; p &lt; 0.0001; I2 = 0%), and blurred vision (OR 2.30; 95% CI 1.50-3.54; p &lt; 0.0001; I2 = 60.1%), but not for uveitis (OR 0.99; 95% CI 0.14-7.03; p = 0.991; I2 = 2.9%) or eye haemorrhage (OR 0.72; 95% CI 0.04-12.39; p = 0.824; I2 = 29.8%). <i>Conclusions:</i> Treatment with MEK inhibitors seems to increase the risk of ophthalmic adverse effects. A need for monitoring the safety of this class of drugs exists. Regulators, clinicians, and other health care professionals must, together, be involved in this process.
DOI: 10.6084/m9.figshare.3482477
title: Supplementary Material for: CFH Y402H and VEGF Polymorphisms and Anti-VEGF Treatment Response in Exudative Age-Related Macular Degeneration

description: <i>Purpose:</i> The aim of this study was to evaluate the prevalence of single nucleotide polymorphisms (SNPs) in complement factor H (CFH) Y402H and VEGF rs2146323 and rs699947 in exudative age-related macular degeneration (AMD) and their relationship with intravitreal anti-VEGF treatment response. <i>Methods:</i> A total of 109 exudative AMD patients and 70 controls were included. Patients were classified as ‘good responders' and ‘nonresponders' based on the changes in best corrected visual acuity, central foveal thickness, lesion size, and the persistence of retinal hemorrhage after three dosages of anti-VEGF. We examined CFH, VEGF rs2146323 and rs699947 SNPs, and plasma interleukin-6 (IL-6) levels in both groups. <i>Results:</i> In total, 42 patients (38.5%) and 11 controls (15.7%) had homozygote wild genotype TT (p = 0.002). The variant C allele frequency was 45% in controls and 31.7% in patients (p = 0.011). A and C allele frequencies for VEGF rs699947 and rs2416323 were similar between the control and patient groups (p = 0.947, p = 0.378). Both SNPs were similar in responders and nonresponders. No significant difference was detected between plasma IL-6 levels of the control and AMD groups (p = 0.594), but the levels were higher in good responders than nonresponders (p &lt; 0.001). <i>Conclusion:</i> CFH Y402H SNP might be protective for AMD in the Turkish population. VEGF rs2146323 and rs699947 SNPs have no relationship to exudative AMD formation, and none of these seem to have any effect on anti-VEGF response.
DOI: 10.6084/m9.figshare.3482453
title: Supplementary Material for: Colorectal Cancer with BRAF D594G Mutation Is Not Associated with Microsatellite Instability or Poor Prognosis

description: <i>Objective:</i><i>BRAF</i> D594G mutations in colorectal cancer patients are not clearly understood. We retrospectively investigated the clinicopathological features of colorectal cancers with <i>BRAF</i> D594G mutations. <i>Methods:</i> We selected 908 colorectal cancer patients who underwent surgical resection from January 2008 to January 2013, and assessed <i>BRAF</i>, <i>KRAS</i>, microsatellite instability, and CpG island methylator phenotype (CIMP). <i>Results:</i> We detected <i>BRAF</i> D594G in 7 patients and <i>BRAF</i> V600E in 45 patients. The clinicopathological features of cancers with <i>BRAF</i> D594G mutation were similar to those with <i>BRAF</i> wild-type, but differed from those with <i>BRAF</i> V600E mutations. Regarding microsatellite instability status, 44.4% of cases with <i>BRAF</i>V600E mutations exhibited high microsatellite instability, compared to 14.3% of those with <i>BRAF</i> D594G mutations and 4.4% of those with <i>BRAF</i> wild-type. There were no CIMP-positive tumors in cancers with <i>BRAF</i> D594G mutations, whereas 67.8% of tumors with <i>BRAF</i> V600E mutations were CIMP-positive. In stage IV cancers, the survival rates of patients at 2 years were 8.5, 50.0, and 68.2% in the <i>BRAF</i> V600E mutation, <i>BRAF</i> D594G mutation, and <i>BRAF</i> wild-type groups, respectively.<i>Conclusion:</i> Colorectal cancers with <i>BRAF</i> D594G mutations exhibit similar clinicopathological features, microsatellite instability status, and prognosis as those with <i>BRAF</i> wild-type.
DOI: 10.6084/m9.figshare.3482453.v1
title: Supplementary Material for: Colorectal Cancer with BRAF D594G Mutation Is Not Associated with Microsatellite Instability or Poor Prognosis

description: <i>Objective:</i><i>BRAF</i> D594G mutations in colorectal cancer patients are not clearly understood. We retrospectively investigated the clinicopathological features of colorectal cancers with <i>BRAF</i> D594G mutations. <i>Methods:</i> We selected 908 colorectal cancer patients who underwent surgical resection from January 2008 to January 2013, and assessed <i>BRAF</i>, <i>KRAS</i>, microsatellite instability, and CpG island methylator phenotype (CIMP). <i>Results:</i> We detected <i>BRAF</i> D594G in 7 patients and <i>BRAF</i> V600E in 45 patients. The clinicopathological features of cancers with <i>BRAF</i> D594G mutation were similar to those with <i>BRAF</i> wild-type, but differed from those with <i>BRAF</i> V600E mutations. Regarding microsatellite instability status, 44.4% of cases with <i>BRAF</i>V600E mutations exhibited high microsatellite instability, compared to 14.3% of those with <i>BRAF</i> D594G mutations and 4.4% of those with <i>BRAF</i> wild-type. There were no CIMP-positive tumors in cancers with <i>BRAF</i> D594G mutations, whereas 67.8% of tumors with <i>BRAF</i> V600E mutations were CIMP-positive. In stage IV cancers, the survival rates of patients at 2 years were 8.5, 50.0, and 68.2% in the <i>BRAF</i> V600E mutation, <i>BRAF</i> D594G mutation, and <i>BRAF</i> wild-type groups, respectively.<i>Conclusion:</i> Colorectal cancers with <i>BRAF</i> D594G mutations exhibit similar clinicopathological features, microsatellite instability status, and prognosis as those with <i>BRAF</i> wild-type.
DOI: 10.6084/m9.figshare.3482450
title: Supplementary Material: Tables

description: <b>Tables Legend</b><br><b>Table S1.</b> Unionida mitochondrial genomes used in the phylogenetics analysis.<b><br></b><b>Table S2.</b> DNA alignment length before and after using Guidance for each mitochondrial gene used in this study.<b><br></b><b>Table S3.</b> Amino acid alignment length before and after using Guidance for each mitochondrial gene used and the best fit model used in the phylogenetic inference. Residue masking was also applied to the alignments: on average less than 1% of the aligned residues were masked.<br><b>Table S4.</b> Supporting values for each branch of the four trees generated in this study (ML-DNA, ML-AA, BI-DNA, BI-AA).<br><b>Table S5. </b>Normalized Robinson and Foulds distances between concatenated mtDNA trees (BI-AA, BI-DNA, ML-AA and ML-DNA) and two-gene trees or single gene trees. The suffixes have the following interpretation: "<b>_AA</b>", gene tree inferred from amino acid sequences; "<b>_P123</b>", gene tree inferred from DNA sequences using all three codon positions; "<b>_P12</b>", gene tree inferred from DNA sequences using all first and second codon positions. Distances highlighted in bold indicate the minimum value recorded for a given category (single gene tree, two-gene tree) relative to a specific concatenated mtDNA tree (columns 2 to 5).<br><b>Table S6. </b>Mitogenomic features of the F- and M- haplotypes of <i>Unio delphinus</i>.
DOI: 10.6084/m9.figshare.3482450.v1
title: Supplementary Material: Tables

description: <b>Tables Legend</b><br><b>Table S1.</b> Unionida mitochondrial genomes used in the phylogenetics analysis.<b><br></b><b>Table S2.</b> DNA alignment length before and after using Guidance for each mitochondrial gene used in this study.<b><br></b><b>Table S3.</b> Amino acid alignment length before and after using Guidance for each mitochondrial gene used and the best fit model used in the phylogenetic inference. Residue masking was also applied to the alignments: on average less than 1% of the aligned residues were masked.<br><b>Table S4.</b> Supporting values for each branch of the four trees generated in this study (ML-DNA, ML-AA, BI-DNA, BI-AA).<br><b>Table S5. </b>Normalized Robinson and Foulds distances between concatenated mtDNA trees (BI-AA, BI-DNA, ML-AA and ML-DNA) and two-gene trees or single gene trees. The suffixes have the following interpretation: "<b>_AA</b>", gene tree inferred from amino acid sequences; "<b>_P123</b>", gene tree inferred from DNA sequences using all three codon positions; "<b>_P12</b>", gene tree inferred from DNA sequences using all first and second codon positions. Distances highlighted in bold indicate the minimum value recorded for a given category (single gene tree, two-gene tree) relative to a specific concatenated mtDNA tree (columns 2 to 5).<br><b>Table S6. </b>Mitogenomic features of the F- and M- haplotypes of <i>Unio delphinus</i>.
DOI: 10.6084/m9.figshare.3482447
title: Molecular modeling study for the design of novel acetyl-CoA carboxylase inhibitors using 3D QSAR, molecular docking and dynamic simulations

description: Acetyl-CoA carboxylase (ACC) enzyme plays an important role in the regulation of biosynthesis and oxidation of fatty acids. ACC is a recognized drug target for the treatment of obesity and diabetes. Combination of ligand and structure-based <i>in silico</i> methods along with activity and toxicity prediction provides best lead compounds in the drug discovery process. In this study, a data-set of 100 ACC inhibitors were used for the development of comparative molecular field analysis (CoMFA) and comparative molecular similarity index matrix analysis (CoMSIA) models. The generated contour maps were used for the design of novel ACC inhibitors. CoMFA and CoMSIA models were used for the predication of activity of designed compounds. <i>In silico</i> toxicity risk prediction study was carried out for the designed compounds. Molecular docking and dynamic simulations studies were performed to know the binding mode of designed compounds with the ACC enzyme. The designed compounds showed interactions with key amino acid residues important for catalysis, and good correlation was observed between binding free energy and inhibition of ACC.
DOI: 10.6084/m9.figshare.3482447.v1
title: Molecular modeling study for the design of novel acetyl-CoA carboxylase inhibitors using 3D QSAR, molecular docking and dynamic simulations

description: Acetyl-CoA carboxylase (ACC) enzyme plays an important role in the regulation of biosynthesis and oxidation of fatty acids. ACC is a recognized drug target for the treatment of obesity and diabetes. Combination of ligand and structure-based <i>in silico</i> methods along with activity and toxicity prediction provides best lead compounds in the drug discovery process. In this study, a data-set of 100 ACC inhibitors were used for the development of comparative molecular field analysis (CoMFA) and comparative molecular similarity index matrix analysis (CoMSIA) models. The generated contour maps were used for the design of novel ACC inhibitors. CoMFA and CoMSIA models were used for the predication of activity of designed compounds. <i>In silico</i> toxicity risk prediction study was carried out for the designed compounds. Molecular docking and dynamic simulations studies were performed to know the binding mode of designed compounds with the ACC enzyme. The designed compounds showed interactions with key amino acid residues important for catalysis, and good correlation was observed between binding free energy and inhibition of ACC.