cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6803582
title: Supplementary Material for: No Protective Effect of Constitutive Activation of AMPK in Endothelial Cells on Vascular Function in Aged Obese Mice but Augmented α1-Adrenergic Contractions in Renal Arteries Reversible by Weight Loss

description: <b><i>Background:</i></b> Aging, obesity, and diabetes favor vascular dysfunction. Endothelial activation of adenosine monophosphate-activated protein kinase (AMPK) has protective effects in diabetes. <b><i>Methods:</i></b> Mice with constitutive endothelial activation of AMPK (CA-AMPK) were given a high fat diet to induce obesity or kept on standard chow as lean controls for up to 2 years. A subset of obese animals was changed to standard chow after 30 weeks of high fat feeding. En­dothelium-dependent and endothelium-independent responses were examined by isometric tension recording. <b><i>Results and Conclusion:</i></b> Endothelium-dependent nitric oxide (NO)- and apamin <i>plus</i> charybdotoxin-sensitive relaxations were preserved and similar between aortic or renal arterial preparations of lean and obese CA-AMPK mice and their wild-type littermates. Despite comparable release of vasoconstrictor prostanoids, cyclooxygenase-dependent contractions were enhanced during NO synthase inhibition in carotid arterial rings of obese CA-AMPK mice. Contractions to the α<sub>1</sub>-adrenoceptor agonist phenylephrine were augmented in renal arteries of obese animals, a genotype-independent phenomenon reversible by weight loss. These data indicate a higher α<sub>1</sub>-adrenergic reactivity in renal arteries of aged mice with obesity. The current results highlight the potential of weight loss to alleviate vascular dysfunction. However, endothelial activation of the AMPK pathway in obesity may not be sufficient to prevent vascular dysfunction without lifestyle changes.
DOI: 10.6084/m9.figshare.6803582.v1
title: Supplementary Material for: No Protective Effect of Constitutive Activation of AMPK in Endothelial Cells on Vascular Function in Aged Obese Mice but Augmented α1-Adrenergic Contractions in Renal Arteries Reversible by Weight Loss

description: <b><i>Background:</i></b> Aging, obesity, and diabetes favor vascular dysfunction. Endothelial activation of adenosine monophosphate-activated protein kinase (AMPK) has protective effects in diabetes. <b><i>Methods:</i></b> Mice with constitutive endothelial activation of AMPK (CA-AMPK) were given a high fat diet to induce obesity or kept on standard chow as lean controls for up to 2 years. A subset of obese animals was changed to standard chow after 30 weeks of high fat feeding. En­dothelium-dependent and endothelium-independent responses were examined by isometric tension recording. <b><i>Results and Conclusion:</i></b> Endothelium-dependent nitric oxide (NO)- and apamin <i>plus</i> charybdotoxin-sensitive relaxations were preserved and similar between aortic or renal arterial preparations of lean and obese CA-AMPK mice and their wild-type littermates. Despite comparable release of vasoconstrictor prostanoids, cyclooxygenase-dependent contractions were enhanced during NO synthase inhibition in carotid arterial rings of obese CA-AMPK mice. Contractions to the α<sub>1</sub>-adrenoceptor agonist phenylephrine were augmented in renal arteries of obese animals, a genotype-independent phenomenon reversible by weight loss. These data indicate a higher α<sub>1</sub>-adrenergic reactivity in renal arteries of aged mice with obesity. The current results highlight the potential of weight loss to alleviate vascular dysfunction. However, endothelial activation of the AMPK pathway in obesity may not be sufficient to prevent vascular dysfunction without lifestyle changes.
DOI: 10.6084/m9.figshare.6803513
title: Supplementary Material for: Clinical Impact of Preoperative Albumin-Globulin Ratio in Patients with Rectal Cancer Treated with Preoperative Chemoradiotherapy

description: <b><i>Objective:</i></b> The serum albumin-globulin ratio (AGR) is associated with malignancy outcomes. However, among patients with rectal cancer (RC) who undergo neoadjuvant chemoradiotherapy (nCRT), the clinical and prognostic significance of the pretreatment AGR is unclear. <b><i>Methods:</i></b> We investigated whether the pre-nCRT AGR can help predict oncological outcomes in patients with RC receiving nCRT. We analyzed 114 patients with RC who received nCRT followed by total mesorectal excision at our institution. <b><i>Results:</i></b> A lower AGR in pre-nCRT serum was significantly correlated with shorter overall survival and disease-free survival in patients with nCRT-treated RC. In multivariate analysis, a high carcinoembryonic antigen (CEA) level and a low AGR in pre-nCRT serum were independent predictors of a poor prognosis in these patients. Furthermore, combining the AGR with CEA provided a more accurate indicator of poor prognosis and early recurrence in these patients. In particular, a low pre-nCRT AGR was a stronger indicator of a poor prognosis and early recurrence in patients without than with pathological lymph node metastasis. Combining the pre-nCRT AGR with CEA could more precisely stratify patients’ oncological outcome risks. <b><i>Conclusion:</i></b> Assessment of the pretreatment AGR with or without CEA can guide postoperative treatment in patients with RC who undergo nCRT.
DOI: 10.6084/m9.figshare.6803513.v1
title: Supplementary Material for: Clinical Impact of Preoperative Albumin-Globulin Ratio in Patients with Rectal Cancer Treated with Preoperative Chemoradiotherapy

description: <b><i>Objective:</i></b> The serum albumin-globulin ratio (AGR) is associated with malignancy outcomes. However, among patients with rectal cancer (RC) who undergo neoadjuvant chemoradiotherapy (nCRT), the clinical and prognostic significance of the pretreatment AGR is unclear. <b><i>Methods:</i></b> We investigated whether the pre-nCRT AGR can help predict oncological outcomes in patients with RC receiving nCRT. We analyzed 114 patients with RC who received nCRT followed by total mesorectal excision at our institution. <b><i>Results:</i></b> A lower AGR in pre-nCRT serum was significantly correlated with shorter overall survival and disease-free survival in patients with nCRT-treated RC. In multivariate analysis, a high carcinoembryonic antigen (CEA) level and a low AGR in pre-nCRT serum were independent predictors of a poor prognosis in these patients. Furthermore, combining the AGR with CEA provided a more accurate indicator of poor prognosis and early recurrence in these patients. In particular, a low pre-nCRT AGR was a stronger indicator of a poor prognosis and early recurrence in patients without than with pathological lymph node metastasis. Combining the pre-nCRT AGR with CEA could more precisely stratify patients’ oncological outcome risks. <b><i>Conclusion:</i></b> Assessment of the pretreatment AGR with or without CEA can guide postoperative treatment in patients with RC who undergo nCRT.
DOI: 10.6084/m9.figshare.6803498
title: Stomach adenocarcinoma

description: microRNA expression of Stomach adenocarcinoma samples. Data from TGCA (https://cancergenome.nih.gov/)
DOI: 10.6084/m9.figshare.6803498.v1
title: Stomach adenocarcinoma

description: microRNA expression of Stomach adenocarcinoma samples. Data from TGCA (https://cancergenome.nih.gov/)
DOI: 10.6084/m9.figshare.6803465
title: Dataset for: <sup>1</sup>H and <sup>13</sup>C Assignments of 6-, 8- 9- Substituted Purines
DOI: 10.6084/m9.figshare.6803438
title: shallow water systems denitrification

description: <b>denitrification and Water-periphytic biofilm-sediment properties</b>
DOI: 10.6084/m9.figshare.6803417
title: Supplementary Material for: Increasing the Sensitivity of Functional Status Assessment in the Preclinical Range (Normal to Mild Cognitive Impairment): Exploring the IADL-Extended Approach

description: <b><i>Background/Aims:</i></b> Dementia exhibits an insidious onset consisting of cognitive, behavioral, and functional impairment. We explored a functional continuum that extends assessment beyond the clinical instrumental activities of daily living (IADL) range and into advanced activities of daily living. <b><i>Methods:</i></b> We examined the predictive power (Cox regression; <i>n</i> = 2,471) of a unidimensional IADL-extended (IADL-x) scale for incident mild cognitive impairment (MCI). We also examined “time to MCI” as an outcome measure. <b><i>Results:</i></b> Each additional task endorsed on the IADL-x hierarchy (e.g., endorsing participation in 6 vs. 5 activities) resulted in a 10% reduction in MCI risk (HR 0.90, 95% CI 0.85–0.94, <i>p</i> &lt; 0.001). For the fully adjusted model the risk reduction dropped to 6%. The odds of incident MCI within 2 years (for those below the median IADL-x total score) was 2.5 times higher (OR 2.60, 95% CI 1.52–4.4, <i>p</i> &lt; 0.001) and 2 times higher for incident MCI within the next 5 years (OR 1.93, 95% CI 1.76–3.2, <i>p</i> &lt; 0.01). <b><i>Conclusion:</i></b> The IADL-x metric appears to be a valid approach for determining the risk of MCI based on one’s position along a formal hierarchy of function.
DOI: 10.6084/m9.figshare.6803417.v1
title: Supplementary Material for: Increasing the Sensitivity of Functional Status Assessment in the Preclinical Range (Normal to Mild Cognitive Impairment): Exploring the IADL-Extended Approach

description: <b><i>Background/Aims:</i></b> Dementia exhibits an insidious onset consisting of cognitive, behavioral, and functional impairment. We explored a functional continuum that extends assessment beyond the clinical instrumental activities of daily living (IADL) range and into advanced activities of daily living. <b><i>Methods:</i></b> We examined the predictive power (Cox regression; <i>n</i> = 2,471) of a unidimensional IADL-extended (IADL-x) scale for incident mild cognitive impairment (MCI). We also examined “time to MCI” as an outcome measure. <b><i>Results:</i></b> Each additional task endorsed on the IADL-x hierarchy (e.g., endorsing participation in 6 vs. 5 activities) resulted in a 10% reduction in MCI risk (HR 0.90, 95% CI 0.85–0.94, <i>p</i> &lt; 0.001). For the fully adjusted model the risk reduction dropped to 6%. The odds of incident MCI within 2 years (for those below the median IADL-x total score) was 2.5 times higher (OR 2.60, 95% CI 1.52–4.4, <i>p</i> &lt; 0.001) and 2 times higher for incident MCI within the next 5 years (OR 1.93, 95% CI 1.76–3.2, <i>p</i> &lt; 0.01). <b><i>Conclusion:</i></b> The IADL-x metric appears to be a valid approach for determining the risk of MCI based on one’s position along a formal hierarchy of function.
DOI: 10.6084/m9.figshare.6803438.v1
title: shallow water systems denitrification

description: <b>denitrification and Water-periphytic biofilm-sediment properties</b>
DOI: 10.6084/m9.figshare.6803405
title: Dataset for: 5α-Cyprinol sulfate: Complete NMR assignment and revision of earlier published data, including the submission of a computer-readable assignment in NMReDATA format

description: No description available
DOI: 10.6084/m9.figshare.6803405.v1
title: Dataset for: 5α-Cyprinol sulfate: Complete NMR assignment and revision of earlier published data, including the submission of a computer-readable assignment in NMReDATA format

description: No description available
DOI: 10.6084/m9.figshare.6803276
title: Brain mass and body mass datasets and phylogenies linked to brain-body allometry and the encephalization of birds and mammals

description: This dataset consists of 6 <b>.xlsx</b> Excel format spreadsheet files and 6 <b>.nex</b> Nexus format phylogenetic data files recording body mass, brain volume and brain mass data for 4,587 of amphibians, birds, cartilaginous fishes, mammals, reptiles, and teleost fishes.<br>The related study investigates the influence of reduced phenotypic integration between brain and body size on encephalization in birds and mammals. This research addresses the requirement for a comparison of intraspecific allometries across a wide range of taxa to address theoretical arguments for a decoupling of phenotypic integration between brain and body size.<br>The Excel files contain observations as rows (note that each observation may include multiple samples) with following variables: brain mass (g), body mass (g), brain volume (mm3 or ml), sex, age class, collected date, collected location, sample size, specimen ID (for museum specimens), references and remarks. Clades from Order to Species (or Subspecies where relevant) are provided for each observation. In specific Excel files the following variables are included: SVL (snout to vent length), standard length (i.e. excluding caudal fin) and total length for fishes, and geographical coordinates. 20,213 observations are included.<br>'Remarks' is a free text value that may include for example details of data conversion and methodology or specimen collection locations. <br>Data acquisition methods specific to the sample are described in referenced articles. Citations should be made for original references.<br>The following data files are included:<b>Tsuboi_etal_NEE_amphibian.xlsx </b>- amphibians<br><b>Tsuboi_etal_NEE_bird.xlsx </b>- birds<br><b>Tsuboi_etal_NEE_mammal.xlsx </b>- mammals<br><b>Tsuboi_etal_NEE_reptile.xlsx </b>- reptiles<br><b>Tsuboi_etal_NEE_shark_ray.xlsx </b>- sharks and rays<br><b>Tsuboi_etal_NEE_teleost.xlsx </b>- teleost fishes<br>In Nexus files, time-calibrated phylogenies are given. Phylogenies of Chondrichthyes and Amphibia were time-calibrated by the authors. Other phylogenies are used unchanged from those associated with original articles (references are found in the main text), except for taxon identities which we modified to the most updated taxa according to the International Taxonomic Information System (ITIS).<br>Each Nexus file contains a 'Trees' block containing phylogenetic trees described using the Newick format.<br>The following phylogenetic tree files are included:<b>amp_phylo_calib.nex </b>- amphibians<br><b>bird_phylo.nex </b>- birds<br><b>mammal_phylo.nex </b>- mammals<br><b>rep_phylo.nex </b>- reptiles<br><b>shark_phylo_calib.nex </b>- sharks and rays<br><b>tel_phylo.nex </b>- teleost fishes<br>
DOI: 10.6084/m9.figshare.6803276.v1
title: Brain mass and body mass datasets and phylogenies linked to brain-body allometry and the encephalization of birds and mammals

description: This dataset consists of 6 <b>.xlsx</b> Excel format spreadsheet files and 6 <b>.nex</b> Nexus format phylogenetic data files recording body mass, brain volume and brain mass data for 4,587 of amphibians, birds, cartilaginous fishes, mammals, reptiles, and teleost fishes.<br>The related study investigates the influence of reduced phenotypic integration between brain and body size on encephalization in birds and mammals. This research addresses the requirement for a comparison of intraspecific allometries across a wide range of taxa to address theoretical arguments for a decoupling of phenotypic integration between brain and body size.<br>The Excel files contain observations as rows (note that each observation may include multiple samples) with following variables: brain mass (g), body mass (g), brain volume (mm3 or ml), sex, age class, collected date, collected location, sample size, specimen ID (for museum specimens), references and remarks. Clades from Order to Species (or Subspecies where relevant) are provided for each observation. In specific Excel files the following variables are included: SVL (snout to vent length), standard length (i.e. excluding caudal fin) and total length for fishes, and geographical coordinates. 20,213 observations are included.<br>'Remarks' is a free text value that may include for example details of data conversion and methodology or specimen collection locations. <br>Data acquisition methods specific to the sample are described in referenced articles. Citations should be made for original references.<br>The following data files are included:<b>Tsuboi_etal_NEE_amphibian.xlsx </b>- amphibians<br><b>Tsuboi_etal_NEE_bird.xlsx </b>- birds<br><b>Tsuboi_etal_NEE_mammal.xlsx </b>- mammals<br><b>Tsuboi_etal_NEE_reptile.xlsx </b>- reptiles<br><b>Tsuboi_etal_NEE_shark_ray.xlsx </b>- sharks and rays<br><b>Tsuboi_etal_NEE_teleost.xlsx </b>- teleost fishes<br>In Nexus files, time-calibrated phylogenies are given. Phylogenies of Chondrichthyes and Amphibia were time-calibrated by the authors. Other phylogenies are used unchanged from those associated with original articles (references are found in the main text), except for taxon identities which we modified to the most updated taxa according to the International Taxonomic Information System (ITIS).<br>Each Nexus file contains a 'Trees' block containing phylogenetic trees described using the Newick format.<br>The following phylogenetic tree files are included:<b>amp_phylo_calib.nex </b>- amphibians<br><b>bird_phylo.nex </b>- birds<br><b>mammal_phylo.nex </b>- mammals<br><b>rep_phylo.nex </b>- reptiles<br><b>shark_phylo_calib.nex </b>- sharks and rays<br><b>tel_phylo.nex </b>- teleost fishes<br>
DOI: 10.6084/m9.figshare.6803264
title: Herbarium genomics retraces the origins of C<sub>4</sub>-specific carbonic anhydrase in Andropogoneae (Poaceae)

description: Natural history collections are traditionally used for taxonomic research, but their relevance can extend into studies of molecular evolution as illustrated here using the example of C<sub>4</sub> photosynthesis. This complex trait boosts growth in open and warm conditions and evolved numerous times, providing multiple comparisons among C<sub>3</sub> and C<sub>4</sub> relatives. Previous genomic studies relied on comparisons of model species which are often separated by long-time divergence. The large C<sub>4</sub> group Andropogoneae (Poaceae) was usually compared to relatively distant C<sub>3</sub> taxa. Early-diverging C<sub>4</sub> Andropogoneae and closely related C<sub>3</sub> taxa are known but are difficult to collect and hence have not been sequenced yet. We show here that genome scans generated from herbarium samples can be used to retrace the evolution of <i>βca</i> genes, which encode beta carbonic anhydrase, an enzyme of the C<sub>4</sub> pathway. Genomic fragments encompassing <i>βca</i> genes were assembled for specimens of phylogenetic importance, and their comparison to model grasses made it possible to distinguish changes that happened during the transition to C<sub>4</sub> from those that preceded or followed it. Tandem gene duplications occurred during the early grass diversification, and the duplicate that retained the ancestral alternative exon conferring chloroplast localization was later co-opted for C<sub>4</sub> photosynthesis. Early transition to C<sub>4</sub> photosynthesis apparently relied on an increase of the cytosolic alternative transcript without drastic changes in the <i>βca</i> gene, which occurred later during the diversification of C<sub>4</sub> groups. These insights into the genomic rearrangements linked to the evolution of an adaptive trait highlight the potential of natural history collections for genomic analyses.
DOI: 10.6084/m9.figshare.6803264.v2
title: Herbarium genomics retraces the origins of C<sub>4</sub>-specific carbonic anhydrase in Andropogoneae (Poaceae)

description: Natural history collections are traditionally used for taxonomic research, but their relevance can extend into studies of molecular evolution as illustrated here using the example of C<sub>4</sub> photosynthesis. This complex trait boosts growth in open and warm conditions and evolved numerous times, providing multiple comparisons among C<sub>3</sub> and C<sub>4</sub> relatives. Previous genomic studies relied on comparisons of model species which are often separated by long-time divergence. The large C<sub>4</sub> group Andropogoneae (Poaceae) was usually compared to relatively distant C<sub>3</sub> taxa. Early-diverging C<sub>4</sub> Andropogoneae and closely related C<sub>3</sub> taxa are known but are difficult to collect and hence have not been sequenced yet. We show here that genome scans generated from herbarium samples can be used to retrace the evolution of <i>βca</i> genes, which encode beta carbonic anhydrase, an enzyme of the C<sub>4</sub> pathway. Genomic fragments encompassing <i>βca</i> genes were assembled for specimens of phylogenetic importance, and their comparison to model grasses made it possible to distinguish changes that happened during the transition to C<sub>4</sub> from those that preceded or followed it. Tandem gene duplications occurred during the early grass diversification, and the duplicate that retained the ancestral alternative exon conferring chloroplast localization was later co-opted for C<sub>4</sub> photosynthesis. Early transition to C<sub>4</sub> photosynthesis apparently relied on an increase of the cytosolic alternative transcript without drastic changes in the <i>βca</i> gene, which occurred later during the diversification of C<sub>4</sub> groups. These insights into the genomic rearrangements linked to the evolution of an adaptive trait highlight the potential of natural history collections for genomic analyses.
DOI: 10.6084/m9.figshare.6803237
title: all_Data

description: Human pose estimation
DOI: 10.6084/m9.figshare.6803237.v1
title: all_Data

description: Human pose estimation
DOI: 10.6084/m9.figshare.6803183
title: Supplementary Material for: The Extended C-Terminal α-Helix of the HypC Chaperone Restricts Recognition of Large Subunit Precursors by the Hyp-Scaffold Machinery during [NiFe]-Hydrogenase Maturation in <b><i>Escherichia coli</i></b>

description: Members of the HypC protein family are chaperone-like proteins that play a central role in the maturation of [NiFe]-hydrogenases (Hyd). <i>Escherichia coli</i> has a second copy of HypC, called HybG, and, as a component of the HypDEF maturation scaffold, these proteins help synthesize the NiFe-cofactor and guide the scaffold to its designated hydrogenase large subunit precursor. HypC is required to synthesize active Hyd-1 and Hyd-3, while HybG facilitates Hyd-2 and Hyd-1 synthesis. To identify determinants on HypC that allow it to discriminate against Hyd-2, we made amino acid exchanges in 3 variable regions, termed VR1, VR2, and VR3, of HypC, that make it more similar to HybG. Region VR3 includes a HypC-specific C-terminal α-helical extension, and this proved particularly important in preventing the maturation of Hyd-2 by HypC. Truncation of this extension on HypC increased Hyd-2 activity in the absence of HybG, while retaining maturation of Hyd-3 and Hyd-1. Combining this truncation with amino acid exchanges in VR1 and VR2 of HypC negatively affected the synthesis of active Hyd-1. The C-terminus of <i>E. coli</i> HypC is thus a key determinant in hindering Hyd-2 maturation, while VR1 and VR2 appear more important for Hyd-1 matu­ration.
DOI: 10.6084/m9.figshare.6803147
title: <i>In silico</i> design of chiral dimers to direct the synthesis of a chiral zeolite

description: We have applied <i>in silico</i> materials design in an effort to design chiral organic structure directing agents (OSDAs) for the synthesis of enantiomerically enriched STW zeolite. To do so, we have used both exhaustive virtual screening of a limited set of symmetrical imidazolium dimers and a multi-objective genetic algorithm to effectively search a larger virtual combinatorial chemistry space that is too vast for an exhaustive approach.