cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4910612
title: Supplementary Material for: Differential Allelic Expression of HTR1B in Suicide Victims: Genetic and Epigenetic Effect of the Cis-Acting Variants

description: <b><i>Objectives:</i></b> In the present study, we tested the allelic imbalance of the C861G single nucleotide polymorphism (SNP) of HTR1B in the frontal cortex of suicide victims. <b><i>Methods:</i></b> The study was conducted using 3 sets of samples. First, C861G allele-specific mRNA levels in the frontal cortex were compared between suicide (<i>n</i> = 13) and nonsuicide controls (<i>n</i> = 13) from the Stanley Medical Research postmortem brain collection. Second, we tested common variants in the HTR1B promoter for linkage disequilibrium (LD) with the C861G variant in an unrelated sample of suicide attempters (SA; <i>n</i> = 38) and non-SA (NSA; <i>n</i> = 42). Finally, we performed a family-based association study of the C861G and promoter variants in 162 nuclear families using suicidal behavior severity scores as phenotype. <b><i>Results:</i></b> We observed no alterations in the C/G expression ratio in suicide victims compared to nonsuicide controls (<i>p</i> = 0.370). When comparing the LD between the C861G and <i>cis</i>-acting SNPs, we did not find any differences in SA and NSA. There was no association between preferential transmission of <i>cis</i>-acting SNPs and suicidal behavior severity scores in both maternal and paternal meiosis. <b><i>Conclusions:</i></b> We found several promoter variants in LD that may potentially influence the allelic imbalance in the C861G variant. However, no evidence of allelic imbalance nor parent-of-origin effects of the C861G variant was observed in suicidal behavior. Further research is required to assess this marker in larger cohorts.
DOI: 10.6084/m9.figshare.4910639
title: Supplementary Material for: Patterns of Microglial Cell Activation in Alzheimer Disease and Frontotemporal Lobar Degeneration

description: <b><i>Aims:</i></b> Microglia-driven neuroinflammation can play an important role in the pathophysiology of neurodegenerative disorders. In this study, we sought to characterize the distribution of microglial cell activation in 2 neurodegenerative dementias with distinct protein signatures, Alzheimer disease (AD) and frontotemporal lobar degeneration (FTLD) of the TDP subtype, and to determine if there was an anatomical correlation with the phenotypes most commonly associated with these conditions. <b><i>Methods:</i></b> The distribution and extent of microglial cell activation was assessed semiquantitatively in the hippocampal formation, cortical gray matter, and subcortical white matter of CD68-immunostained sections of the frontal, temporal, parietal, and occipital cortices from 15 pathologically confirmed cases of AD, 13 cases of FTLD, and 18 controls. <b><i>Results:</i></b> Significantly higher levels of microglial cell activation occurred in the subiculum in AD and FTLD than in controls. Additionally, AD had higher microglial activation in the CA1 and FTLD in the hippocampal white matter than the controls. Microglial activation was greater in the dentate gyrus molecular layer in AD than in FTLD. In the cortical regions, the 2 pathological groups differed only in frontal white matter, with the FTLD group showing higher microglial scores. FTLD showed higher microglial activation in the white matter compared to the respective gray matter in the entorhinal, temporal, and frontal regions. <b><i>Conclusions:</i></b> Our work expands the knowledge of the distribution and magnitude of microglial activation in these disorders. Additionally, we found some microglial circuit-specific patterns that could help to explain some of the clinical overlap between AD and FTLD-TDP, namely in memory deficits.
DOI: 10.6084/m9.figshare.4910639.v1
title: Supplementary Material for: Patterns of Microglial Cell Activation in Alzheimer Disease and Frontotemporal Lobar Degeneration

description: <b><i>Aims:</i></b> Microglia-driven neuroinflammation can play an important role in the pathophysiology of neurodegenerative disorders. In this study, we sought to characterize the distribution of microglial cell activation in 2 neurodegenerative dementias with distinct protein signatures, Alzheimer disease (AD) and frontotemporal lobar degeneration (FTLD) of the TDP subtype, and to determine if there was an anatomical correlation with the phenotypes most commonly associated with these conditions. <b><i>Methods:</i></b> The distribution and extent of microglial cell activation was assessed semiquantitatively in the hippocampal formation, cortical gray matter, and subcortical white matter of CD68-immunostained sections of the frontal, temporal, parietal, and occipital cortices from 15 pathologically confirmed cases of AD, 13 cases of FTLD, and 18 controls. <b><i>Results:</i></b> Significantly higher levels of microglial cell activation occurred in the subiculum in AD and FTLD than in controls. Additionally, AD had higher microglial activation in the CA1 and FTLD in the hippocampal white matter than the controls. Microglial activation was greater in the dentate gyrus molecular layer in AD than in FTLD. In the cortical regions, the 2 pathological groups differed only in frontal white matter, with the FTLD group showing higher microglial scores. FTLD showed higher microglial activation in the white matter compared to the respective gray matter in the entorhinal, temporal, and frontal regions. <b><i>Conclusions:</i></b> Our work expands the knowledge of the distribution and magnitude of microglial activation in these disorders. Additionally, we found some microglial circuit-specific patterns that could help to explain some of the clinical overlap between AD and FTLD-TDP, namely in memory deficits.
DOI: 10.6084/m9.figshare.4910585
title: Supplementary Material for: Genetic Polymorphisms in Aromatase (cyp19a1) Are Not Associated with Gonadal Phenotypes in Red-Eared Slider Turtle Hatchlings Developed at a Pivotal Temperature

description: Embryonic gonad sex in many reptilian species is determined by the incubation temperature of the egg, a differentiation process known as temperature-dependent sex determination (TSD). Incubation at the pivotal temperature (PvT) results in approximately an equal number of offspring of both sexes. We investigated the potential contribution of genetic variations that drives the gonadal differentiation into testes or ovaries under this temperature in the red-eared slider turtle (<i>Trachemys scripta</i>). Four male and 4 female hatchlings of eggs that had been incubated at the PvT were examined for polymorphisms at an approximately 23-kb region of the aromatase (<i>cyp19a1</i>) gene. By aligning the red-eared slider aromatase gene to a reference genome of the western painted turtle (<i>Chrysemys picta bellii</i>), we discovered 22 exonic and 1,268 intronic polymorphisms. Of these, 12 (55%) exonic polymorphisms were unique to the individuals of the red-eared slider; 10 were synonymous and 2 were nonsynonymous changes. We found no pattern in these genetic variants as well as intronic variants that are consistently different between male and female hatchlings at the PvT. Overall, our study suggests that polymorphisms within the aromatase gene - at least by themselves - do not constrain the gonad sex differentiation in embryos developed at the PvT.
DOI: 10.6084/m9.figshare.4910579
title: Supplementary Material for: Three-Year Clinical Outcome of Patients with Coronary Disease and Increased Event Risk Treated with Newer-Generation Drug-Eluting Stents: From the Randomized DUTCH PEERS Trial

description: <b><i>Objective:</i></b> Limited data is available on the long-term outcome of patients with increased cardiovascular event risk, treated with newer-generation durable polymer drug-eluting stents (DES). <b><i>Methods:</i></b> We therefore assessed 3-year follow-up data of high-risk versus low- to intermediate-risk patients of the randomized DUTCH PEERS trial (NCT01331707). In both risk groups we also compared patients treated with Resolute Integrity versus Promus Element DES. Patients were categorized as “high-risk” if they met ≥1 of the following criteria: (1) diabetes (17.9%); (2) previous myocardial infarction (21.9%); (3) previous coronary revascularization (25.8%); (4) chronic renal failure (3.5%); (5) left ventricular ejection fraction ≤30% (1.5%); and (6) age ≥75 years (17.3%). <b><i>Results:</i></b> At the 3-year follow-up, the incidence of the composite endpoint target vessel failure (TVF) (13.2 vs. 7.5%; logrank <i>p</i> &lt; 0.001) and 2 of its components - cardiac death (4.7 vs. 1.5%; logrank <i>p</i> &lt; 0.001) and target vessel revascularization (7.3 vs. 4.7%; logrank <i>p</i> = 0.03) - was higher in high-risk (<i>n</i> = 957) versus low- to intermediate-risk patients (<i>n</i> = 854). Among high-risk patients, treatment with Resolute Integrity (<i>n</i> = 481) and Promus Element stents (<i>n</i> = 476) was similarly safe and efficacious (TVF: 13.3 vs. 13.1%; logrank <i>p</i> = 0.95; definite-or-probable stent thrombosis: 1.7 vs. 1.7%; logrank <i>p</i> = 1.00). <b><i>Conclusions:</i></b> The newer-generation Resolute Integrity and Promus Element stents showed similar results in terms of safety and efficacy for treating high-risk patients, who had significantly higher event rates than patients with low-to-intermediate risk.
DOI: 10.6084/m9.figshare.4910576
title: II.5 - Agrogenom genomic blocks of evolutionary events (first pass)

description: Blocks of evolutionary events ( gene duplication, D, or transfer, T) involving several neighbour genes ; this is a first pass of running the script getblockevents.py to find congruent neighbouring events across gene family trees.This will allow (at the next step) to pick the optimal events amongst the set of mutually exclusive events retained as possible for a gene tree node at the previous step (see item #II.4).<br><br>getblockevents_out.<b>l.</b>*/ folders are results of parallel jobs searching for neighbouring genes in extant ("leaf") genomes involved in similar events, i.e. <b>leaf blocks</b>; each job searched separately within a set of replicon (or contigs). This search is performed with a greedy algorithm covering chromosome; "gap" genes without signal for a congruent event are first allowed, and then tested for compatibility and eventually rejected if negative.<br>getblockevents_out.<b>a</b>.*/ folder is the result of the single job that searched for leaf blocks linking to the same events in gene trees, to reconstruct the one <b>ancestral block</b> of genes from which descend the extant blocks of co-evolved gene.<br><br>The file structure in <i>getblockevents_out.</i><i>l.</i><i>*/</i> folders is similar:- <i>blocks/</i> folder: one file per replicon listing genes involved in a block- <i>before_split_blocks.stats</i> file: stats on blocks generated by the greedy algorithm recognizing similar events based on their event characteristics, i.e. the sets of possible recipient and donor species;- <i>transferred_blocks.stats</i> file: stats on blocks after the compatibility of common events with gap gene trees was checked and incopatibility resolved by splitting the initial blocks into several blocks.<br>[omitted here for space sake, several Gb altogether]:- <i>block_trees/</i> folder: the gene trees associated to the block events - <i>replicon.shelve</i> file: the serialized Python objects containing all the genes borne by a replicon/contig and the event block that link them.<br> file structure in <i>getblockevents_out.a</i><i>.</i><i>*/:</i>- <i>ancestral_blocks</i> file: list of all ancestral blocks and the leaf blocks they link to;<br>[similar files as described above for leaf blocks]- <i>blocks_events.mat</i> file: summary of block events recorded between donor and recipient (ancestral) species pairs[omitted here for space sake, several Gb for 1 file]:- <i>ancblocks.shelve</i> file:the serialized Python objects containing all the ancestral blocks and the leaf blocks linked to them
DOI: 10.6084/m9.figshare.4910579.v1
title: Supplementary Material for: Three-Year Clinical Outcome of Patients with Coronary Disease and Increased Event Risk Treated with Newer-Generation Drug-Eluting Stents: From the Randomized DUTCH PEERS Trial

description: <b><i>Objective:</i></b> Limited data is available on the long-term outcome of patients with increased cardiovascular event risk, treated with newer-generation durable polymer drug-eluting stents (DES). <b><i>Methods:</i></b> We therefore assessed 3-year follow-up data of high-risk versus low- to intermediate-risk patients of the randomized DUTCH PEERS trial (NCT01331707). In both risk groups we also compared patients treated with Resolute Integrity versus Promus Element DES. Patients were categorized as “high-risk” if they met ≥1 of the following criteria: (1) diabetes (17.9%); (2) previous myocardial infarction (21.9%); (3) previous coronary revascularization (25.8%); (4) chronic renal failure (3.5%); (5) left ventricular ejection fraction ≤30% (1.5%); and (6) age ≥75 years (17.3%). <b><i>Results:</i></b> At the 3-year follow-up, the incidence of the composite endpoint target vessel failure (TVF) (13.2 vs. 7.5%; logrank <i>p</i> &lt; 0.001) and 2 of its components - cardiac death (4.7 vs. 1.5%; logrank <i>p</i> &lt; 0.001) and target vessel revascularization (7.3 vs. 4.7%; logrank <i>p</i> = 0.03) - was higher in high-risk (<i>n</i> = 957) versus low- to intermediate-risk patients (<i>n</i> = 854). Among high-risk patients, treatment with Resolute Integrity (<i>n</i> = 481) and Promus Element stents (<i>n</i> = 476) was similarly safe and efficacious (TVF: 13.3 vs. 13.1%; logrank <i>p</i> = 0.95; definite-or-probable stent thrombosis: 1.7 vs. 1.7%; logrank <i>p</i> = 1.00). <b><i>Conclusions:</i></b> The newer-generation Resolute Integrity and Promus Element stents showed similar results in terms of safety and efficacy for treating high-risk patients, who had significantly higher event rates than patients with low-to-intermediate risk.
DOI: 10.6084/m9.figshare.4910585.v1
title: Supplementary Material for: Genetic Polymorphisms in Aromatase (cyp19a1) Are Not Associated with Gonadal Phenotypes in Red-Eared Slider Turtle Hatchlings Developed at a Pivotal Temperature

description: Embryonic gonad sex in many reptilian species is determined by the incubation temperature of the egg, a differentiation process known as temperature-dependent sex determination (TSD). Incubation at the pivotal temperature (PvT) results in approximately an equal number of offspring of both sexes. We investigated the potential contribution of genetic variations that drives the gonadal differentiation into testes or ovaries under this temperature in the red-eared slider turtle (<i>Trachemys scripta</i>). Four male and 4 female hatchlings of eggs that had been incubated at the PvT were examined for polymorphisms at an approximately 23-kb region of the aromatase (<i>cyp19a1</i>) gene. By aligning the red-eared slider aromatase gene to a reference genome of the western painted turtle (<i>Chrysemys picta bellii</i>), we discovered 22 exonic and 1,268 intronic polymorphisms. Of these, 12 (55%) exonic polymorphisms were unique to the individuals of the red-eared slider; 10 were synonymous and 2 were nonsynonymous changes. We found no pattern in these genetic variants as well as intronic variants that are consistently different between male and female hatchlings at the PvT. Overall, our study suggests that polymorphisms within the aromatase gene - at least by themselves - do not constrain the gonad sex differentiation in embryos developed at the PvT.
DOI: 10.6084/m9.figshare.4910381
title: Pairwise comparisons between cell fractions from adipose tissue

description: Annotated pairwise comparisons between all FACS-sorted fractions from adipose tissue. Usage note:Columns are separed with ; (not tab or comma)
DOI: 10.6084/m9.figshare.19959990
title: Additional file 6 of Antioxidant potential of Pediococcus pentosaceus strains from the sow milk bacterial collection in weaned piglets

description: Additional file 6: Figure S9. (a) Alpha diversity comparisons of the gut microbiomes including Ace, Chao, Sobs index, Shannon index, Shannoneven index, Simpson index, Simpsoneven index and Faith's phylogenetic diversity index which were analyzed using a Kruskal-Wallis H test and Tukey-Kramer post hoc test with 95% confidence level. Data are the mean ± s.d (n = 7). ns, no significant differences. (b) Rarefaction curves for Shannon indices at the genus level in the colon contents. Figure S10. (a) Bar charts of relative abundance at the family level in the control and treated groups. (b) Comparison of microbial genera between the high dose group and control. (c) Comparison of microbial families between high dose group and control. Significantly differentially abundant taxa were identified by the Wilcoxon rank-sum test. *p &lt; 0.05; **p &lt; 0.01. Figure S11. (a) Linear discriminant analysis score (log10) with a threshold value of 4 from phylum to genus level. (b) Differences in relative abundance of the variable genera in the colonic microbiota among three group. Each data represented the mean and SEM of relative abundance of each genus (n = 7). One-way analysis of variance and Duncan’s multiple comparison test to determine the statistical. Different letters in the same graph indicate significant statistical differences (p &lt; 0.05).
DOI: 10.6084/m9.figshare.23631368.v1
title: Mechanistic assessment of aerosol transport in a SFR cover gas space under operating condition

description: The cover gas space is an inert isolation layer provided for sodium systems in sodium-cooled fast reactors. During normal reactor operation, sodium aerosols are generated continuously in the cover gas space. Understanding the complex dynamics of the evolution and transport of the aerosol is essential from the perspective of the reactor operation. Such assessments provides vital insights into deposition patterns of aerosols to the components mounted on the roof slab. In the present manuscript, the evolution and transport of aerosol in the cover gas space as well as in roof-slab annular gaps are studied in detail with the help of computational fluid dynamics tool. The present model is validated against the experimental data from the literature. There is good agreement between temperature variation, aerosol number and mass concentration across the cover gas height. Post validation, the study of thermal and aerosol transport in the full-scale reactor cover gas for a medium-sized reference reactor is carried out. It is observed that aerosol sizes greater than ∼31 <i>μm</i> are mostly concentrated near either the sodium pool surface, component wall or near the vessel boundary. It is found that the average mass concentration in the cover gas space is uniform (∼ 29 g/m<sup>3</sup>). However, the annular regions are found to have a non-uniform distribution of aerosols with heavier particles confined to the lower annular regions in wavy like patterns having the same Count Mean Diameter (CMD) as in the bulk cover gas space. The CMD in the top annular regions is ∼ 2 <i>μm</i>. A coupled analysis of aerosol transport in cover gas space and roof-slab annular gaps using modified aerosolEulerFoam is carried out.Validation of the numerical model is performed with data from two experiments (Furukawa et al., 1984; Kumar et al., 2015). Where, average aerosol mass concentration and size distributions were compared.Detailed aerosol transport studies for the full scale primary cover gas of the reference reactor is carried out.Aerosol size greater than ∼31 <i>μm</i> are mostly concentrated near either sodium pool surface, component wall or near the vessel boundary. A coupled analysis of aerosol transport in cover gas space and roof-slab annular gaps using modified aerosolEulerFoam is carried out. Validation of the numerical model is performed with data from two experiments (Furukawa et al., 1984; Kumar et al., 2015). Where, average aerosol mass concentration and size distributions were compared. Detailed aerosol transport studies for the full scale primary cover gas of the reference reactor is carried out. Aerosol size greater than ∼31 <i>μm</i> are mostly concentrated near either sodium pool surface, component wall or near the vessel boundary.
DOI: 10.6084/m9.figshare.12097095.v1
title: Additional file 1 of Diagnosis of severe scrub typhus infection by next-generation sequencing:a case report

description: Additional file 1.
DOI: 10.6084/m9.figshare.14720961
title: Fast and Separable Estimation in High-Dimensional Tensor Gaussian Graphical Models

description: In the tensor data analysis, the Kronecker covariance structure plays a vital role in unsupervised learning and regression. Under the Kronecker covariance model assumption, the covariance of an <i>M</i>-way tensor is parameterized as the Kronecker product of <i>M</i> individual covariance matrices. With normally distributed tensors, the key to high-dimensional tensor graphical models becomes the sparse estimation of the <i>M</i> inverse covariance matrices. Unable to maximize the tensor normal likelihood analytically, existing approaches often require cyclic updates of the <i>M</i> sparse matrices. For the high-dimensional tensor graphical models, each update step solves a regularized inverse covariance estimation problem that is computationally nontrivial. This computational challenge motivates our study of whether a noncyclic approach can be as good as the cyclic algorithms in theory and practice. To handle the potentially very high-dimensional and high-order tensors, we propose a separable and parallel estimation scheme. We show that the new estimator achieves the same minimax optimal convergence rate as the cyclic estimation approaches. Numerically, the new estimator is much faster and often more accurate than the cyclic approach. Moreover, another advantage of the separable estimation scheme is its flexibility in modeling, where we can easily incorporate user-specified or specially structured covariances on any modes of the tensor. We demonstrate the efficiency of the proposed method through both simulations and a neuroimaging application. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.12097098
title: Additional file 1 of Impact of spring freshet flooding and summer rainfall flooding on the water quality of an alpine barrier lake

description: Additional file 1. River flow.
DOI: 10.6084/m9.figshare.12097101
title: Additional file 2 of Impact of spring freshet flooding and summer rainfall flooding on the water quality of an alpine barrier lake

description: Additional file 2. River water quality.
DOI: 10.6084/m9.figshare.12097101.v1
title: Additional file 2 of Impact of spring freshet flooding and summer rainfall flooding on the water quality of an alpine barrier lake

description: Additional file 2. River water quality.
DOI: 10.25387/g3.9478253
title: Supplemental Material for Lei et al., 2019

description: Supplemental figures and tables.
DOI: 10.25387/g3.9478253.v2
title: Supplemental Material for Lei et al., 2019

description: Supplemental figures and tables.
DOI: 10.25387/g3.9478253.v1
title: Supplemental Material for Lei et al., 2019

description: Supplemental figures and tables.
DOI: 10.5281/zenodo.10624834
title: craterocephalus_marjoriae_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.5281/zenodo.10624835
title: craterocephalus_marjoriae_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.6084/m9.figshare.12097116
title: Additional file 4 of Impact of spring freshet flooding and summer rainfall flooding on the water quality of an alpine barrier lake

description: Additional file 4. Hydraulic power plant.
DOI: 10.6084/m9.figshare.12097098.v1
title: Additional file 1 of Impact of spring freshet flooding and summer rainfall flooding on the water quality of an alpine barrier lake

description: Additional file 1. River flow.