cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10066544
title: The first 500-meter, long-term winter wheat grain protein content dataset for China from multi-source data

description: In China, the demand for precise perception of wheat Grain Protein Content (GPC) has gained increased urgency, driven by the rising demands in the food consumption market and intensifying international market competition. However, due to the lack of extensive, prolonged high-resolution benchmark data, previous GPC studies have primarily focused on experimental fields, small geographic units, and limited temporal scopes. Additionally, the diversified geographical landscape in China introduces spatiotemporal heterogeneity and intricacy to the influence of wheat GPC, further amplifying the challenges of large-scale GPC estimation. To address this challenge and the data gap, the first 500-meter spatial resolution, long-term winter wheat dataset covering major planting regions in China (CNWheatGPC-500) was created by integrating multi-source data from ERA5 and MODIS.
DOI: 10.5281/zenodo.10572564
title: Bochum-Hordel Westfalen-Apotheke

description: Historical questionnaire/s 1924/1948 and index cards, partly selected enclosures regarding the history of aGerman pharmacy, catalogued via Kalliope portal (Historischer Fragebogen 1924/1948 und Karteikarten, ggf.gemeinfreie Anlagen zur Apothekengeschichte; als Katalog dient das Nachlassportal Kalliope):https://kalliope-verbund.info/DE-611-BF-70963[Funktion: Im Findbuch anzeigen]

Please note: The Kalliope catalogue entry might indicate related material in the archival folder which cannotbe published due to copyright or other legal restrictions (NB: Das Katalogisat bei Kalliope kann auch aufMaterialien - teils erheblichen Umfangs - verweisen, die aus archiv- oder urheberrechtlichen Gründen nichtveröffentlicht werden dürfen).
DOI: 10.6084/m9.figshare.24805728
title: Supplementary Material for: Efficacy of Levetiracetam as add-on therapy in the treatment of seizures in neonates

description: Introduction
There is no consensus regarding the efficacy of add-on therapy with levetiracetam (LEV) in the treatment of seizures in neonates. The aim of this study was to evaluate the efficacy of add–on therapy with LEV, for achieving &gt;80% seizure reduction after phenobarbital (PB) treatment.

Methods
Retrospective cohort study of near term neonates admitted to the neonatal intensive care unit with EEG confirmed seizures despite treatment with PB as first-line therapy and using LEV as 2nd, 3rd or 4th line treatment. Antiseizure medication (ASM) was administered according to national guidelines. All neonates were monitored with 2-channel amplitude-integrated electroencephalography (aEEG). The total seizure burden in minutes, 2 hours before and 4 hours after administration of LEV was calculated using raw EEG. Primary outcome was the efficacy of LEV in achieving &gt;80% seizure reduction. The efficacy of additional midazolam (MDZ) and lidocaine (LDC) was also calculated.

Results
A total of 47 full-term neonates were included. The mean total loading dose of LEV was 40 mg/kg (36-44 mg/kg). Seizure etiology consisted of hypoxic-ischemic encephalopathy (n=11), hemorrhagic or ischemic stroke (n=16), central nervous system infection (n= 8), genetic (n=8), metabolic disorders (n=3), and unknown (n=1). Following LEV administration, &gt;80% seizure reduction was observed in 17% (8/47) of neonates, whereas it was 23% (6/26) after MDZ and 92% (23/25) after LDC administration.

Discussion 
Although the cumulative loading dose of LEV was low and the group of infants studied was heterogeneous, the efficacy of LEV as add-on therapy for the treatment of seizures in neonates was limited. The highest seizure reduction rate was seen after LDC administration.
DOI: 10.6084/m9.figshare.24805728.v2
title: Supplementary Material for: Efficacy of Levetiracetam as add-on therapy in the treatment of seizures in neonates

description: Introduction
There is no consensus regarding the efficacy of add-on therapy with levetiracetam (LEV) in the treatment of seizures in neonates. The aim of this study was to evaluate the efficacy of add–on therapy with LEV, for achieving &gt;80% seizure reduction after phenobarbital (PB) treatment.

Methods
Retrospective cohort study of near term neonates admitted to the neonatal intensive care unit with EEG confirmed seizures despite treatment with PB as first-line therapy and using LEV as 2nd, 3rd or 4th line treatment. Antiseizure medication (ASM) was administered according to national guidelines. All neonates were monitored with 2-channel amplitude-integrated electroencephalography (aEEG). The total seizure burden in minutes, 2 hours before and 4 hours after administration of LEV was calculated using raw EEG. Primary outcome was the efficacy of LEV in achieving &gt;80% seizure reduction. The efficacy of additional midazolam (MDZ) and lidocaine (LDC) was also calculated.

Results
A total of 47 full-term neonates were included. The mean total loading dose of LEV was 40 mg/kg (36-44 mg/kg). Seizure etiology consisted of hypoxic-ischemic encephalopathy (n=11), hemorrhagic or ischemic stroke (n=16), central nervous system infection (n= 8), genetic (n=8), metabolic disorders (n=3), and unknown (n=1). Following LEV administration, &gt;80% seizure reduction was observed in 17% (8/47) of neonates, whereas it was 23% (6/26) after MDZ and 92% (23/25) after LDC administration.

Discussion 
Although the cumulative loading dose of LEV was low and the group of infants studied was heterogeneous, the efficacy of LEV as add-on therapy for the treatment of seizures in neonates was limited. The highest seizure reduction rate was seen after LDC administration.
DOI: 10.6084/m9.figshare.24805728.v1
title: Supplementary Material for: Efficacy of Levetiracetam as add-on therapy in the treatment of seizures in neonates

description: Introduction
There is no consensus regarding the efficacy of add-on therapy with levetiracetam (LEV) in the treatment of seizures in neonates. The aim of this study was to evaluate the efficacy of add–on therapy with LEV, for achieving &gt;80% seizure reduction after phenobarbital (PB) treatment.

Methods
Retrospective cohort study of near term neonates admitted to the neonatal intensive care unit with EEG confirmed seizures despite treatment with PB as first-line therapy and using LEV as 2nd, 3rd or 4th line treatment. Antiseizure medication (ASM) was administered according to national guidelines. All neonates were monitored with 2-channel amplitude-integrated electroencephalography (aEEG). The total seizure burden in minutes, 2 hours before and 4 hours after administration of LEV was calculated using raw EEG. Primary outcome was the efficacy of LEV in achieving &gt;80% seizure reduction. The efficacy of additional midazolam (MDZ) and lidocaine (LDC) was also calculated.

Results
A total of 47 full-term neonates were included. The mean total loading dose of LEV was 40 mg/kg (36-44 mg/kg). Seizure etiology consisted of hypoxic-ischemic encephalopathy (n=11), hemorrhagic or ischemic stroke (n=16), central nervous system infection (n= 8), genetic (n=8), metabolic disorders (n=3), and unknown (n=1). Following LEV administration, &gt;80% seizure reduction was observed in 17% (8/47) of neonates, whereas it was 23% (6/26) after MDZ and 92% (23/25) after LDC administration.

Discussion 
Although the cumulative loading dose of LEV was low and the group of infants studied was heterogeneous, the efficacy of LEV as add-on therapy for the treatment of seizures in neonates was limited. The highest seizure reduction rate was seen after LDC administration.
DOI: 10.6084/m9.figshare.25040093.v2
title: Complete dataset of seed ingestion by Anatidae in North America (Almeida et al. 2024)

description: This dataset comprises five tables used in Almeida et al. 2024.. 'complete_dataset.csv' has studies with information on seeds ingested by Anatidae species in North America. 'qualitative_matrix.csv' has a general qualitative waterfowl by plant species matrix indicating the presence or absence of each seed species in the diet of each waterfowl species. 'quantitative_matrix.csv' has a quantitative matrix containing the occurrence of each seed species in the diet of each bird species, in which we included the number of individual birds (or faecal samples) sampled in each study. 'waterfowl_traits.csv' contains trait values for each waterfowl species. 'plant_traits.csv' contains trait values for each plant species that was found to be ingested by North American waterfowl.
DOI: 10.6084/m9.figshare.25075282
title: Bayesian Hyperbolic Multidimensional Scaling

description: <b>Multidimensional scaling (MDS) is a widely used approach to representing high-dimensional, dependent data. MDS works by assigning each observation a location on a low-dimensional geometric manifold, with distance on the manifold representing similarity. We propose a Bayesian approach to multidimensional scaling when the low-dimensional manifold is hyperbolic. Using hyperbolic space facilitates representing tree-like structures common in many settings (e.g. text or genetic data with hierarchical structure). A Bayesian approach provides regularization that minimizes the impact of measurement error in the observed data and assesses uncertainty. We also propose a case-control likelihood approximation that allows for efficient sampling from the posterior distribution in larger data settings, reducing computational complexity from approximately</b>O(n2)<b>to <i>O</i>(<i>n</i>). We evaluate the proposed method against state-of-the-art alternatives using simulations, canonical reference datasets, Indian village network data, and human gene expression data. Code to reproduce the result in the paper is available at</b>https://github.com/peterliu599/BHMDS.
DOI: 10.6084/m9.figshare.25075282.v1
title: Bayesian Hyperbolic Multidimensional Scaling

description: <b>Multidimensional scaling (MDS) is a widely used approach to representing high-dimensional, dependent data. MDS works by assigning each observation a location on a low-dimensional geometric manifold, with distance on the manifold representing similarity. We propose a Bayesian approach to multidimensional scaling when the low-dimensional manifold is hyperbolic. Using hyperbolic space facilitates representing tree-like structures common in many settings (e.g. text or genetic data with hierarchical structure). A Bayesian approach provides regularization that minimizes the impact of measurement error in the observed data and assesses uncertainty. We also propose a case-control likelihood approximation that allows for efficient sampling from the posterior distribution in larger data settings, reducing computational complexity from approximately</b>O(n2)<b>to <i>O</i>(<i>n</i>). We evaluate the proposed method against state-of-the-art alternatives using simulations, canonical reference datasets, Indian village network data, and human gene expression data. Code to reproduce the result in the paper is available at</b>https://github.com/peterliu599/BHMDS.
DOI: 10.6084/m9.figshare.22920755
title: Supplementary Material for: Thrombolysis for acute wake-up and unclear onset strokes with alteplase at 0.6 mg/kg in clinical practice: THAWS2 Study

description: Introduction: The aim of this study was to determine the safety and efficacy of intravenous (IV) alteplase at 0.6 mg/kg for patients with acute wake-up or unclear onset strokes in clinical practice.
Methods: This multicenter observational study enrolled acute ischemic stroke patients with last-known-well time &gt;4.5 h who had mismatch between DWI and FLAIR and were treated with IV alteplase. The safety outcomes were symptomatic intracranial hemorrhage (sICH) after thrombolysis, all-cause deaths and all adverse events. The efficacy outcomes were favorable outcome defined as an mRS score of 0–1 or recovery to the same mRS score as the premorbid score, complete independence defined as an mRS score of 0–1 at 90 days, and change in NIHSS at 24 h from baseline.
Results: Sixty-six patients (35 females; mean age, 74±11 years; premorbid complete independence, 54 [82%]; median NIHSS on admission, 11) were enrolled at 15 hospitals. Two patients (3%) had sICH. Median NIHSS changed from 11 (IQR, 6.75–16.25) at baseline to 5 (3–12.25) at 24 h after alteplase initiation (change, –4.8±8.1). At discharge, 31 patients (47%) had favorable outcome and 29 (44%) had complete independence. None died within 90 days. Twenty-three (35%) also underwent mechanical thrombectomy (no sICH, NIHSS change of –8.5±7.3), of whom 11 (48%) were completely independent at discharge.
Conclusions: In real-world clinical practice, IV alteplase for unclear onset stroke patients with DWI-FLAIR mismatch provided safe and efficacious outcomes comparable to those in previous trials. Additional mechanical thrombectomy was performed safely in them.
DOI: 10.6084/m9.figshare.24886560
title: Codes and data used for the Manuscript titled "<b>Diet-induced miRNAs regulate adult neurogenesis and functional activity of nascent neurons in the hypothalamus</b>"

description: Neurogenesis in the hypothalamus upon high fat diet (HFD) feeding regulates the feeding circuit. HFD induces the neurogenesis of β2 tanycytes in young- adult mice. However, molecular mechanisms of tanycytic neurogenesis and their functional integration into the feeding circuitry is poorly understood. We investigated the role of miRNAs in the regulation of HFD-induced tanycytic neurogenesis. miRNA arrays identified a cohort of HFD-induced, differentially-regulated miRNAs in BrdU<sup>+</sup> β2-tanycytes. These miRNAs arise from different chromosomes, rather than a single cluster. <i>In silico</i> network analysis on the predicted targets of all five HFD-induced miRNAs and reporter assays identified a subset of targets that influence neurogenesis and neuronal differentiation. HFD-induced miRNAs drive a molecular program leading to the functional integration of nascent neurons; introduction of a miRNA sponge sequestering all five miRNAs abolishes it. Diet-regulated newborn neurons preferentially differentiate into AgRP+ neurons that functionally integrate into the feeding circuit.
DOI: 10.6084/m9.figshare.24886560.v1
title: Codes and data used for the Manuscript titled "<b>Diet-induced miRNAs regulate adult neurogenesis and functional activity of nascent neurons in the hypothalamus</b>"

description: Neurogenesis in the hypothalamus upon high fat diet (HFD) feeding regulates the feeding circuit. HFD induces the neurogenesis of β2 tanycytes in young- adult mice. However, molecular mechanisms of tanycytic neurogenesis and their functional integration into the feeding circuitry is poorly understood. We investigated the role of miRNAs in the regulation of HFD-induced tanycytic neurogenesis. miRNA arrays identified a cohort of HFD-induced, differentially-regulated miRNAs in BrdU<sup>+</sup> β2-tanycytes. These miRNAs arise from different chromosomes, rather than a single cluster. <i>In silico</i> network analysis on the predicted targets of all five HFD-induced miRNAs and reporter assays identified a subset of targets that influence neurogenesis and neuronal differentiation. HFD-induced miRNAs drive a molecular program leading to the functional integration of nascent neurons; introduction of a miRNA sponge sequestering all five miRNAs abolishes it. Diet-regulated newborn neurons preferentially differentiate into AgRP+ neurons that functionally integrate into the feeding circuit.
DOI: 10.5281/zenodo.5513495
title: Calpain DEK1 acts as a developmental switch gatekeeping cell fate transitions

description: This is the supplementary data archive for our study showing that:


Calpain DEK1 acts as a developmental switch gatekeeping cell fate transitions


Abstract: Calpains are cysteine proteases that control cell fate transitions. Although calpains are viewed as modulatory proteases displaying severe, pleiotropic phenotypes in eukaryotes, human calpain targets are also directed to the N-end rule degradatory pathway. Several of these destabilized targets are transcription factors, hinting at a gene regulatory role. Here, we analyze the gene regulatory networks of Physcomitrium patens and characterize the regulons that are deregulated in DEK1 calpain mutants. Predicted cleavage patterns of regulatory hierarchies in the five DEK1-controlled subnetworks are consistent with the gene’s pleiotropy and the regulatory role in cell fate transitions targeting a broad spectrum of functions. Network structure suggests DEK1-gated sequential transition between cell fates in 2D to 3D development. We anticipate that both our method combining phenotyping, transcriptomics and data science to dissect phenotypic traits and our model explaining the calpain’s role as a switch gatekeeping cell fate transitions will inform biology beyond plant development.
DOI: 10.5281/zenodo.5513496
title: Calpain DEK1 acts as a developmental switch gatekeeping cell fate transitions

description: This is the supplementary data archive for our study showing that:


Calpain DEK1 acts as a developmental switch gatekeeping cell fate transitions


Abstract: Calpains are cysteine proteases that control cell fate transitions. Although calpains are viewed as modulatory proteases displaying severe, pleiotropic phenotypes in eukaryotes, human calpain targets are also directed to the N-end rule degradatory pathway. Several of these destabilized targets are transcription factors, hinting at a gene regulatory role. Here, we analyze the gene regulatory networks of Physcomitrium patens and characterize the regulons that are deregulated in DEK1 calpain mutants. Predicted cleavage patterns of regulatory hierarchies in the five DEK1-controlled subnetworks are consistent with the gene’s pleiotropy and the regulatory role in cell fate transitions targeting a broad spectrum of functions. Network structure suggests DEK1-gated sequential transition between cell fates in 2D to 3D development. We anticipate that both our method combining phenotyping, transcriptomics and data science to dissect phenotypic traits and our model explaining the calpain’s role as a switch gatekeeping cell fate transitions will inform biology beyond plant development.
DOI: 10.6084/m9.figshare.25075319.v1
title: Codes and data used for the Manuscript titled "<b>Diet-induced miRNAs regulate adult neurogenesis and functional activity of nascent neurons in the hypothalamus</b>"

description: Neurogenesis in the hypothalamus upon high fat diet (HFD) feeding regulates the feeding circuit. HFD induces the neurogenesis of β2 tanycytes in young- adult mice. However, molecular mechanisms of tanycytic neurogenesis and their functional integration into the feeding circuitry is poorly understood. We investigated the role of miRNAs in the regulation of HFD-induced tanycytic neurogenesis. miRNA arrays identified a cohort of HFD-induced, differentially-regulated miRNAs in BrdU<sup>+</sup> β2-tanycytes. These miRNAs arise from different chromosomes, rather than a single cluster. <i>In silico</i> network analysis on the predicted targets of all five HFD-induced miRNAs and reporter assays identified a subset of targets that influence neurogenesis and neuronal differentiation. HFD-induced miRNAs drive a molecular program leading to the functional integration of nascent neurons; introduction of a miRNA sponge sequestering all five miRNAs abolishes it. Diet-regulated newborn neurons preferentially differentiate into AgRP+ neurons that functionally integrate into the feeding circuit.
DOI: 10.6084/m9.figshare.25075319
title: Codes and data used for the Manuscript titled "<b>Diet-induced miRNAs regulate adult neurogenesis and functional activity of nascent neurons in the hypothalamus</b>"

description: Neurogenesis in the hypothalamus upon high fat diet (HFD) feeding regulates the feeding circuit. HFD induces the neurogenesis of β2 tanycytes in young- adult mice. However, molecular mechanisms of tanycytic neurogenesis and their functional integration into the feeding circuitry is poorly understood. We investigated the role of miRNAs in the regulation of HFD-induced tanycytic neurogenesis. miRNA arrays identified a cohort of HFD-induced, differentially-regulated miRNAs in BrdU<sup>+</sup> β2-tanycytes. These miRNAs arise from different chromosomes, rather than a single cluster. <i>In silico</i> network analysis on the predicted targets of all five HFD-induced miRNAs and reporter assays identified a subset of targets that influence neurogenesis and neuronal differentiation. HFD-induced miRNAs drive a molecular program leading to the functional integration of nascent neurons; introduction of a miRNA sponge sequestering all five miRNAs abolishes it. Diet-regulated newborn neurons preferentially differentiate into AgRP+ neurons that functionally integrate into the feeding circuit.
DOI: 10.5281/zenodo.10360967
title: Hyytiälä SMEAR II Scots pine shoot and forest floor CO2 and water vapour exchange rates 2009-2019

description: This dataset consists of Scots pine shoot and forest floor CO2 and H2O exchange rates, measured at Hyytiälä SMEAR II site in southern Finland, in years 2009-2019.

Methodology is shortly explained in Methods of shoot gas exchange rate measurements.docx

Data columns are explained in Flux_readme.txt

Data for each year and individual chamber is in separate files, with 2- or 3-digit extension.

2-digit extensions are for soil chamber (forest floor gas exchange).

3-digit extensions are for Scots pine shoot chambers.
DOI: 10.5281/zenodo.10360968
title: Hyytiälä SMEAR II Scots pine shoot and forest floor CO2 and water vapour exchange rates 2009-2019

description: This dataset consists of Scots pine shoot and forest floor CO2 and H2O exchange rates, measured at Hyytiälä SMEAR II site in southern Finland, in years 2009-2019.

Methodology is shortly explained in Methods of shoot gas exchange rate measurements.docx

Data columns are explained in Flux_readme.txt

Data for each year and individual chamber is in separate files, with 2- or 3-digit extension.

2-digit extensions are for soil chamber (forest floor gas exchange).

3-digit extensions are for Scots pine shoot chambers.
DOI: 10.12751/g-node.v7wkqe
title: Dataset - Effects of chronic ingestion of soy peptide supplementation on juvenile social isolation

description: This dataset is supplementing a research paper. We provide all numeric data and 16S rRNA sequencing data (fastq files) generated and analyzed during the study.
description: IsSupplementTo: Tamura et al., Chronic ingestion of soy peptide supplementation reduces aggressive behavior and abnormal fear memory caused by juvenile social isolation that is not published yet. Scientific Reports, submitted.
DOI: 10.25824/redu/w33hjm
title: Figure S3

description: Variation partitioning analysis (VPA). The VPA was used to determine the effects of Locality, Grape Variety, Time/Collection and Soil Chemistry, on the variation in the structure of the microbial community.
DOI: 10.25824/redu/s19aa0
title: Table S4

description: Network analysis to assess complexity and integrity of bacterial groups at the class level by grape variety.
DOI: 10.25824/redu/inkqro
title: Table S3

description: Classification of soil nutrient status present in rhizospheric grapevine soil. The macronutrient contents (K+, Ca2+, Mg2+ in cmolc/dm3 and P in mg.dm3), pH in CaCl2, soil organic matter (SOM), potential acidity (H+Al), cation exchange capacity (CEC) and base saturation (V%) were evaluated
DOI: 10.25824/redu/snytw9
title: Figure S2

description: Statistical analysis using PERMANOVA for nutrients of the soil.
DOI: 10.25824/redu/0raoty
title: Figure S1

description: Rarefaction curves based on the V3-V4 region of the 16S rRNA gene obtained from the rhizospheric grape soil samples. Cabernet sauvignon (CSPL), Malbec (MPL), Syrah (SPL) and Syrah (ST) from two different vineyard in State of São Paulo.
DOI: 10.25824/redu/yu26pq
title: Table S1

description: ASV count table
DOI: 10.25824/redu/k38jc5
title: Table S2

description: Phylogenetic classification of ASVs