cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12834263
title: Supplementary Material for: Retinal Ganglion Cell Topography and Spatial Resolving Power in Echolocating and Non-Echolocating Bats

description: Bats are nocturnal mammals known for their ability to echolocate, yet all bats can see, and most bats of the family Pteropodidae (fruit bats) do not echolocate – instead they rely mainly on vision and olfaction to forage. We investigated whether echolocating bats, given their limited reliance on vision, have poorer spatial resolving power (SRP) than pteropodids and whether tongue click echolocating fruit bats differ from non-echolocating fruit bats in terms of visual performance. We compared the number and distribution of retinal ganglion cells (RGCs) as well as the maximum anatomical SRP derived from these distributions in 4 species of bats: <i>Myotis daubentonii</i>, a laryngeal echolocating bat from the family Vespertilionidae, <i>Rousettus aegyptiacus</i>, a tongue clicking echolocating bat from the family Pteropodidae, and <i>Pteropus alecto</i> and <i>P. poliocephalus</i>, 2 non-echolocating bats (also from the Pteropodidae). We find that all 3 pteropodids have a similar number (≈200,000 cells) and distribution of RGCs and a similar maximum SRP (≈4 cycles/degree). <i>M. daubentonii</i> has fewer (∼6,000 cells) and sparser RGCs than the pteropodids and thus a significantly lower SRP (0.6 cycles/degree). <i>M. daubentonii</i> also differs in terms of the distribution of RGCs by having a unique dorsal area of specialization in the retina. Our findings are consistent with the existing literature and suggest that <i>M. daubentonii</i> likely only uses vision for orientation, while for pteropodids vision is also important for foraging.
DOI: 10.6084/m9.figshare.12834011
title: Supplementary Material for: A Novel Gain-of-Function <b><i>KCND3</i></b> Variant Associated with Brugada Syndrome

description: Brugada syndrome (BrS) is a known cause of sudden cardiac death (SCD) characterized by abnormal electrocardiograms and fatal arrhythmias. The variants in <i>KCND3</i> encoding the K<sub>V</sub>4.3 potassium-channel (the α-subunit of the I<sub>to</sub>) have seldom been reported in BrS. This study aimed to identify novel <i>KCND3</i> variants associated with BrS and elucidate BrS pathogenesis. High-depth targeted sequencing was performed and the electrophysiological properties of the variants were detected by whole-cell patch-clamp methods in a cultured-cell expressing system. The transcriptional levels of K<sub>V</sub>4.3 in different genotypes were studied by real-time PCR. Western blot was used to assess channel protein expression. A novel <i>KCND3</i>heterozygous variant, c.1292G&gt;A (Arg431His, R431H), was found in the proband. Whole-cell patch-clamp results revealed a gain-of-function phenotype in the variant, with peak I<sub>to</sub> current density increased and faster recovery from inactivation. The expression of mutant Kv4.3 membrane protein increased and the cytoplasmic protein decreased, demonstrating that the membrane/cytoplasm ratio was significantly different. In conclusion, a novel <i>KCND3</i> heterozygous variant was associated with BrS. The increased I<sub>to</sub> current explained the critical role of <i>KCND3</i> in the pathogenesis of BrS. Genetic screening for <i>KCND3</i> could be useful for understanding the pathogenesis of BrS and providing effective risk stratification in the clinic.
DOI: 10.6084/m9.figshare.12834014
title: original DATA. 2020

description: Dataset.
DOI: 10.6084/m9.figshare.12833996
title: Supplementary Material for: Greater Attendance at a Community Weight Loss Programme over the First 12 Weeks Predicts Weight Loss at 2 Years

description: <b><i>Background:</i></b> There is considerable heterogeneity in long-term weight loss among people referred to obesity treatment programmes. It is unclear whether attendance at face-to-face sessions in the early weeks of the programme is an independent predictor of long-term success. <b><i>Objective:</i></b> To investigate whether frequency of attendance at a community weight loss programme over the first 12 weeks is associated with long-term weight change. <b><i>Methods:</i></b> Participants were randomised to receive brief support only (control, <i>n</i> = 211), or a weight loss programme for 12 weeks (<i>n</i> = 530) or 52 weeks (<i>n</i> = 528). This study included participants with data on session attendance over the first 12 weeks (<i>n</i> = 889) compared to the control group. The association between attendance (continuously) and weight loss was explored using a linear model. A multi-level mixed-effects linear model was used to investigate whether attendance (categorised as 0, 1, 2–5, 6—9, and 10–12 sessions) was associated with weight loss at 3, 12, and 24 months compared to the control. <b><i>Results:</i></b> For every session attended in the first 12 weeks, the average weight loss was –0.259 kg/session at 24 months (<i>p</i> = 0.005). Analysis by attendance group found only those attending 10–12 sessions had significantly greater weight loss (–7.5 kg [95% CI –8.1 to –6.9] at 12 months; –4.7 kg [95% CI –5.3 to –4.1] at 24 months) compared to the control group (–3.4 [95% CI –4.5 to –2.4] at 12 months, –2.5 [95% CI –3.5 to –1.5] at 24 months). Early attendance was higher for people ≥70 years, but there was no evidence of a difference by gender, ethnicity, education, or income. <b><i>Conclusions:</i></b> Greater attendance at a community weight loss programme in the first 12 weeks is associated with enhanced weight loss up to 24 months. Regular attendance at a programme could be used as a criterion for continued provision of weight loss services to maximise the cost-effectiveness of interventions.
DOI: 10.6084/m9.figshare.12834014.v1
title: original DATA. 2020

description: Dataset.
DOI: 10.6084/m9.figshare.12834011.v1
title: Supplementary Material for: A Novel Gain-of-Function <b><i>KCND3</i></b> Variant Associated with Brugada Syndrome

description: Brugada syndrome (BrS) is a known cause of sudden cardiac death (SCD) characterized by abnormal electrocardiograms and fatal arrhythmias. The variants in <i>KCND3</i> encoding the K<sub>V</sub>4.3 potassium-channel (the α-subunit of the I<sub>to</sub>) have seldom been reported in BrS. This study aimed to identify novel <i>KCND3</i> variants associated with BrS and elucidate BrS pathogenesis. High-depth targeted sequencing was performed and the electrophysiological properties of the variants were detected by whole-cell patch-clamp methods in a cultured-cell expressing system. The transcriptional levels of K<sub>V</sub>4.3 in different genotypes were studied by real-time PCR. Western blot was used to assess channel protein expression. A novel <i>KCND3</i>heterozygous variant, c.1292G&gt;A (Arg431His, R431H), was found in the proband. Whole-cell patch-clamp results revealed a gain-of-function phenotype in the variant, with peak I<sub>to</sub> current density increased and faster recovery from inactivation. The expression of mutant Kv4.3 membrane protein increased and the cytoplasmic protein decreased, demonstrating that the membrane/cytoplasm ratio was significantly different. In conclusion, a novel <i>KCND3</i> heterozygous variant was associated with BrS. The increased I<sub>to</sub> current explained the critical role of <i>KCND3</i> in the pathogenesis of BrS. Genetic screening for <i>KCND3</i> could be useful for understanding the pathogenesis of BrS and providing effective risk stratification in the clinic.
DOI: 10.6084/m9.figshare.12833996.v1
title: Supplementary Material for: Greater Attendance at a Community Weight Loss Programme over the First 12 Weeks Predicts Weight Loss at 2 Years

description: <b><i>Background:</i></b> There is considerable heterogeneity in long-term weight loss among people referred to obesity treatment programmes. It is unclear whether attendance at face-to-face sessions in the early weeks of the programme is an independent predictor of long-term success. <b><i>Objective:</i></b> To investigate whether frequency of attendance at a community weight loss programme over the first 12 weeks is associated with long-term weight change. <b><i>Methods:</i></b> Participants were randomised to receive brief support only (control, <i>n</i> = 211), or a weight loss programme for 12 weeks (<i>n</i> = 530) or 52 weeks (<i>n</i> = 528). This study included participants with data on session attendance over the first 12 weeks (<i>n</i> = 889) compared to the control group. The association between attendance (continuously) and weight loss was explored using a linear model. A multi-level mixed-effects linear model was used to investigate whether attendance (categorised as 0, 1, 2–5, 6—9, and 10–12 sessions) was associated with weight loss at 3, 12, and 24 months compared to the control. <b><i>Results:</i></b> For every session attended in the first 12 weeks, the average weight loss was –0.259 kg/session at 24 months (<i>p</i> = 0.005). Analysis by attendance group found only those attending 10–12 sessions had significantly greater weight loss (–7.5 kg [95% CI –8.1 to –6.9] at 12 months; –4.7 kg [95% CI –5.3 to –4.1] at 24 months) compared to the control group (–3.4 [95% CI –4.5 to –2.4] at 12 months, –2.5 [95% CI –3.5 to –1.5] at 24 months). Early attendance was higher for people ≥70 years, but there was no evidence of a difference by gender, ethnicity, education, or income. <b><i>Conclusions:</i></b> Greater attendance at a community weight loss programme in the first 12 weeks is associated with enhanced weight loss up to 24 months. Regular attendance at a programme could be used as a criterion for continued provision of weight loss services to maximise the cost-effectiveness of interventions.
DOI: 10.6084/m9.figshare.12833885
title: Supplementary Material for: Area Deprivation and Risk of Death and CKD Progression: Long-Term Cohort Study in Patients under Unrestricted Nephrology Care

description: <b><i>Background:</i></b> Area deprivation index (ADI) associates with prognosis in non-dialysis CKD. However, no study has evaluated this association in CKD patients under unrestricted nephrology care. <b><i>Methods:</i></b> We performed a long-term prospective study to assess the role of deprivation in CKD progression and mortality in stage 1–4 CKD patients under regular nephrology care, living in Naples (Italy). We used ADI calculated at census block levels, standardized to mean values of whole population in Naples, and linked to patients by georeference method. After 12 months of “goal-oriented” nephrology treatment, we compared the risk of death or composite renal outcomes (end-stage kidney disease or doubling of serum creatinine) in the tertiles of standardized ADI. Estimated glomerular filtration rate (eGFR) decline was evaluated by mixed effects model for repeated eGFR measurements. <b><i>Results:</i></b> We enrolled 715 consecutive patients (age: 64 ± 15 years; 59.1% males; eGFR: 49 ± 22 mL/min/1.73 m<sup>2</sup>). Most (75.2%) were at the lowest national ADI quintile. At referral, demographic, clinical, and therapeutic features were similar across ADI tertiles; after 12 months, treatment intensification allowed better control of hypertension, proteinuria, hypercholesterolaemia, and anaemia with no difference across ADI tertiles. During the subsequent long-term follow-up (10.5 years [interquartile range 8.2–12.6]), 166 renal events and 249 deaths were registered. ADI independently associated with all-cause death (<i>p</i> for trend = 0.020) and non-cardiovascular (CV) mortality (<i>p</i> for trend = 0.045), while CV mortality did not differ (<i>p</i> for trend = 0.252). Risk of composite renal outcomes was similar across ADI tertiles (<i>p</i> for trend = 0.467). The same held true for eGFR decline (<i>p</i> for trend = 0.675). <b><i>Conclusions:</i></b> In CKD patients under regular nephrology care, ADI is not associated with CKD progression, while it is associated with all-cause death due to an excess of non-CV mortality.
DOI: 10.6084/m9.figshare.12833915
title: Supplementary Material for: Effectiveness and Safety of the European Society of Cardiology 0-/1-h Troponin Rule-Out Protocol: The Design of the ESC-TROP Multicenter Implementation Study

description: Chest pain is one of the most common complaints at the emergency department (ED), and it is commonly the perceived likelihood of acute coronary syndrome (ACS) that drives management. Guidelines from the European Society of Cardiology (ESC) recommend the use of a 0-/1-h high-sensitivity cardiac troponin T (hs-cTnT) protocol to rule out or in ACS, but this is mostly based on observational studies. The aim of the ESC-TROP trial is to determine the safety and effectiveness of the ESC 0-/1-h hs-cTnT protocol when implemented in routine care. Adult chest pain patients at 5 EDs in the Skåne Region, Sweden, are included in the trial. The 0-/1-h hs-cTnT ESC protocol supplemented with clinical assessment and electrocardiography (ECG) is implemented at 3 EDs, and the other 2 EDs act as concurrent controls. Outcomes will be evaluated during the 10 months after the implementation and the corresponding 10 months of the previous year. The 2 co-primary outcomes are (a) acute myocardial infarction (AMI) and all-cause death within 30 days in patients discharged from the ED, and (b) ED length of stay of the same patients. Secondary outcomes include the proportion of chest pain patients discharged from the ED and the number of ruled-out patients undergoing objective testing within 30 days. The ESC-TROP trial will determine the performance and applicability of the 0-/1-h hs-cTnT ESC protocol supplemented with clinical assessment and ECG when implemented in routine ED care. It will provide evidence whether 0-/1-h hs-cTnT testing is safe, effective, and feasible, and whether widespread implementation as recommended by ESC guidelines should be supported.
DOI: 10.6084/m9.figshare.12833840
title: Table S2: Putative MRO proteins of Barthelona sp. strain PAP020 and their predicted subcellular localizations. from Barthelonids represent a deep-branching metamonad clade with mitochondrion-related organelles predicted to generate no ATP

description: We here report the phylogenetic position of barthelonids, small anaerobic flagellates previously examined using light microscopy alone. <i>Barthelona</i> spp. were isolated from geographically distinct regions and we established five laboratory strains. Transcriptomic data generated from one <i>Barthelona</i> strain (PAP020) were used for large-scale, multi-gene phylogenetic (phylogenomic) analyses. Our analyses robustly placed strain PAP020 at the base of the Fornicata clade, indicating that barthelonids represent a deep-branching Metamonad clade. Considering the anaerobic/microaerophilic nature of barthelonids and preliminary electron microscopy observations on strain PAP020, we suspected that barthelonids possess functionally and structurally reduced mitochondria (i.e. mitochondrion-related organelles or MROs). The metabolic pathways localized in the MRO of strain PAP020 were predicted based on its transcriptomic data and compared with those in the MROs of fornicates. We here propose that strain PAP020 is incapable of generating ATP in the MRO, as no mitochondrial/MRO enzymes involved in substrate-level phosphorylation were detected. Instead, we detected the putative cytosolic ATP-generating enzyme (acetyl-CoA synthetase), suggesting that strain PAP020 depends on ATP generated in the cytosol. We propose two separate losses of substrate-level phosphorylation from the MRO in the clade containing barthelonids and (other) fornicates.
DOI: 10.6084/m9.figshare.12833885.v1
title: Supplementary Material for: Area Deprivation and Risk of Death and CKD Progression: Long-Term Cohort Study in Patients under Unrestricted Nephrology Care

description: <b><i>Background:</i></b> Area deprivation index (ADI) associates with prognosis in non-dialysis CKD. However, no study has evaluated this association in CKD patients under unrestricted nephrology care. <b><i>Methods:</i></b> We performed a long-term prospective study to assess the role of deprivation in CKD progression and mortality in stage 1–4 CKD patients under regular nephrology care, living in Naples (Italy). We used ADI calculated at census block levels, standardized to mean values of whole population in Naples, and linked to patients by georeference method. After 12 months of “goal-oriented” nephrology treatment, we compared the risk of death or composite renal outcomes (end-stage kidney disease or doubling of serum creatinine) in the tertiles of standardized ADI. Estimated glomerular filtration rate (eGFR) decline was evaluated by mixed effects model for repeated eGFR measurements. <b><i>Results:</i></b> We enrolled 715 consecutive patients (age: 64 ± 15 years; 59.1% males; eGFR: 49 ± 22 mL/min/1.73 m<sup>2</sup>). Most (75.2%) were at the lowest national ADI quintile. At referral, demographic, clinical, and therapeutic features were similar across ADI tertiles; after 12 months, treatment intensification allowed better control of hypertension, proteinuria, hypercholesterolaemia, and anaemia with no difference across ADI tertiles. During the subsequent long-term follow-up (10.5 years [interquartile range 8.2–12.6]), 166 renal events and 249 deaths were registered. ADI independently associated with all-cause death (<i>p</i> for trend = 0.020) and non-cardiovascular (CV) mortality (<i>p</i> for trend = 0.045), while CV mortality did not differ (<i>p</i> for trend = 0.252). Risk of composite renal outcomes was similar across ADI tertiles (<i>p</i> for trend = 0.467). The same held true for eGFR decline (<i>p</i> for trend = 0.675). <b><i>Conclusions:</i></b> In CKD patients under regular nephrology care, ADI is not associated with CKD progression, while it is associated with all-cause death due to an excess of non-CV mortality.
DOI: 10.6084/m9.figshare.12833840.v1
title: Table S2: Putative MRO proteins of Barthelona sp. strain PAP020 and their predicted subcellular localizations. from Barthelonids represent a deep-branching metamonad clade with mitochondrion-related organelles predicted to generate no ATP

description: We here report the phylogenetic position of barthelonids, small anaerobic flagellates previously examined using light microscopy alone. <i>Barthelona</i> spp. were isolated from geographically distinct regions and we established five laboratory strains. Transcriptomic data generated from one <i>Barthelona</i> strain (PAP020) were used for large-scale, multi-gene phylogenetic (phylogenomic) analyses. Our analyses robustly placed strain PAP020 at the base of the Fornicata clade, indicating that barthelonids represent a deep-branching Metamonad clade. Considering the anaerobic/microaerophilic nature of barthelonids and preliminary electron microscopy observations on strain PAP020, we suspected that barthelonids possess functionally and structurally reduced mitochondria (i.e. mitochondrion-related organelles or MROs). The metabolic pathways localized in the MRO of strain PAP020 were predicted based on its transcriptomic data and compared with those in the MROs of fornicates. We here propose that strain PAP020 is incapable of generating ATP in the MRO, as no mitochondrial/MRO enzymes involved in substrate-level phosphorylation were detected. Instead, we detected the putative cytosolic ATP-generating enzyme (acetyl-CoA synthetase), suggesting that strain PAP020 depends on ATP generated in the cytosol. We propose two separate losses of substrate-level phosphorylation from the MRO in the clade containing barthelonids and (other) fornicates.
DOI: 10.6084/m9.figshare.12833834
title: Table S1: Amino acid positions and coverages of the 148 single-gene alignments used in this study from Barthelonids represent a deep-branching metamonad clade with mitochondrion-related organelles predicted to generate no ATP

description: We here report the phylogenetic position of barthelonids, small anaerobic flagellates previously examined using light microscopy alone. <i>Barthelona</i> spp. were isolated from geographically distinct regions and we established five laboratory strains. Transcriptomic data generated from one <i>Barthelona</i> strain (PAP020) were used for large-scale, multi-gene phylogenetic (phylogenomic) analyses. Our analyses robustly placed strain PAP020 at the base of the Fornicata clade, indicating that barthelonids represent a deep-branching Metamonad clade. Considering the anaerobic/microaerophilic nature of barthelonids and preliminary electron microscopy observations on strain PAP020, we suspected that barthelonids possess functionally and structurally reduced mitochondria (i.e. mitochondrion-related organelles or MROs). The metabolic pathways localized in the MRO of strain PAP020 were predicted based on its transcriptomic data and compared with those in the MROs of fornicates. We here propose that strain PAP020 is incapable of generating ATP in the MRO, as no mitochondrial/MRO enzymes involved in substrate-level phosphorylation were detected. Instead, we detected the putative cytosolic ATP-generating enzyme (acetyl-CoA synthetase), suggesting that strain PAP020 depends on ATP generated in the cytosol. We propose two separate losses of substrate-level phosphorylation from the MRO in the clade containing barthelonids and (other) fornicates.
DOI: 10.6084/m9.figshare.12833834.v1
title: Table S1: Amino acid positions and coverages of the 148 single-gene alignments used in this study from Barthelonids represent a deep-branching metamonad clade with mitochondrion-related organelles predicted to generate no ATP

description: We here report the phylogenetic position of barthelonids, small anaerobic flagellates previously examined using light microscopy alone. <i>Barthelona</i> spp. were isolated from geographically distinct regions and we established five laboratory strains. Transcriptomic data generated from one <i>Barthelona</i> strain (PAP020) were used for large-scale, multi-gene phylogenetic (phylogenomic) analyses. Our analyses robustly placed strain PAP020 at the base of the Fornicata clade, indicating that barthelonids represent a deep-branching Metamonad clade. Considering the anaerobic/microaerophilic nature of barthelonids and preliminary electron microscopy observations on strain PAP020, we suspected that barthelonids possess functionally and structurally reduced mitochondria (i.e. mitochondrion-related organelles or MROs). The metabolic pathways localized in the MRO of strain PAP020 were predicted based on its transcriptomic data and compared with those in the MROs of fornicates. We here propose that strain PAP020 is incapable of generating ATP in the MRO, as no mitochondrial/MRO enzymes involved in substrate-level phosphorylation were detected. Instead, we detected the putative cytosolic ATP-generating enzyme (acetyl-CoA synthetase), suggesting that strain PAP020 depends on ATP generated in the cytosol. We propose two separate losses of substrate-level phosphorylation from the MRO in the clade containing barthelonids and (other) fornicates.
DOI: 10.6084/m9.figshare.12833774
title: R0186_20170816a_videos

description: Rat 0186, skilled reaching data collected on 8/16/2017 in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.12833768
title: R0187_20170921a_videos

description: Rat 0187, skilled reaching data collected on 9/21/2017 in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.12833768.v1
title: R0187_20170921a_videos

description: Rat 0187, skilled reaching data collected on 9/21/2017 in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.12833774.v1
title: R0186_20170816a_videos

description: Rat 0186, skilled reaching data collected on 8/16/2017 in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.12833720
title: Solid-state petrological assimilations in high-grade metamorphic terrains: A reaction-diffusion modelling approach

description: This folder contains the data used to determine the fractal dimension of the four interface types and the mafic relics within felsic rocks. These are documented from the high-grade gneissic terrain of Chotanagpur Granite Gneissic Complex, Eastern India, and also simulated in numerical modelling in the present study.<br>