cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14737233
title: EEG data and code: Reduced cerebellar rhythm by climbing fiber denervation causes motor rhythm deficits in mice and is associated with ataxia in patients

description: This package includes cerebellar EEG data for patients with cerebellar ataxia and codes for analysis
DOI: 10.5281/zenodo.14737234
title: EEG data and code: Reduced cerebellar rhythm by climbing fiber denervation causes motor rhythm deficits in mice and is associated with ataxia in patients

description: This package includes cerebellar EEG data for patients with cerebellar ataxia and codes for analysis
DOI: 10.15468/dl.g2tv7h
title: Occurrence Download

description: A dataset containing 993 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is ROC RSPB Farmland Species Survey Dataset"
 ]
}

 The dataset includes 993 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002027-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.28280489
title: Combinatorial Evolution of Artificial Tyroserleutide Transporters for Enhanced Cancer Therapy In Vivo

description: <b>Peptide transporters are integral membrane proteins responsible for the cellular uptake of di- and tripeptides from the extracellular environment, which play pivotal roles in nutrient absorption, antigen presentation, and cellular signaling. Despite their essential biological functions, the development of artificial peptide transporters capable of efficiently transporting charge-neutral peptides remains elusive. Herein, we introduce a novel class of peptide transporters involving the combinatorial integration of anion and cation transport functionalities. Notably, 5F-C12, which functions as a molecular tweezer, forms a stable 1:1 complex with charge-neutral peptide tyroserleutide—an anticancer agent currently in Phase III clinical trials—and actively facilitates its transmembrane transport by shielding it from the membrane's hydrophobic core, with an EC</b><sub><strong>50</strong></sub><b> value of 7.5 μM. Unprecedentedly, 5F-C12 could remarkably enhance the peptide’s bioavailability and exhibit a pronounced enhanced anticancer effect against MCF-7 breast cancer cells both </b><b><i>in vitro</i></b><b> and </b><b><i>in vivo</i></b><b>.</b>
DOI: 10.6084/m9.figshare.28280489.v1
title: Combinatorial Evolution of Artificial Tyroserleutide Transporters for Enhanced Cancer Therapy In Vivo

description: <b>Peptide transporters are integral membrane proteins responsible for the cellular uptake of di- and tripeptides from the extracellular environment, which play pivotal roles in nutrient absorption, antigen presentation, and cellular signaling. Despite their essential biological functions, the development of artificial peptide transporters capable of efficiently transporting charge-neutral peptides remains elusive. Herein, we introduce a novel class of peptide transporters involving the combinatorial integration of anion and cation transport functionalities. Notably, 5F-C12, which functions as a molecular tweezer, forms a stable 1:1 complex with charge-neutral peptide tyroserleutide—an anticancer agent currently in Phase III clinical trials—and actively facilitates its transmembrane transport by shielding it from the membrane's hydrophobic core, with an EC</b><sub><strong>50</strong></sub><b> value of 7.5 μM. Unprecedentedly, 5F-C12 could remarkably enhance the peptide’s bioavailability and exhibit a pronounced enhanced anticancer effect against MCF-7 breast cancer cells both </b><b><i>in vitro</i></b><b> and </b><b><i>in vivo</i></b><b>.</b>
DOI: 10.15468/dl.sdsujx
title: Occurrence Download

description: A dataset containing 94 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is USA.5_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Rhamphomyia Meigen, 1822"
 ]
}

 The dataset includes 94 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002029-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xz57tb
title: Occurrence Download

description: A dataset containing 197 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "OccurrenceStatus is Present",
 "TaxonKey is Lepus Linnaeus, 1758"
 ]
}

 The dataset includes 197 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002030-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dmqc6r
title: Occurrence Download

description: A dataset containing 1335 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is USA.5_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Empididae"
 ]
}

 The dataset includes 1335 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002032-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s94y7n
title: Occurrence Download

description: A dataset containing 46 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "OccurrenceStatus is Present",
 "TaxonKey is Bos taurus Linnaeus, 1758"
 ]
}

 The dataset includes 46 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002033-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13997011
title: LYCEUM: Learning to call copy number variants on low coverage ancient genomes

description: Copy number variants (CNVs) are pivotal in driving phenotypic variation that facilitates species adaptation. They are significant contributors to various disorders, making ancient genomes cru- cial for uncovering the genetic origins of disease susceptibility across populations. However, detecting CNVs in ancient samples poses substantial challenges due to several factors. Ancient DNA (aDNA) is often highly degraded, and this degradation is further complicated by contamination from micro- bial DNA and DNA from closely related species, introducing additional noise into sequencing data. Finally, the typically low coverage of aDNA renders accurate CNV detection particularly difficult. Conventional CNV calling algorithms, optimized for high coverage and long reads, often underper- form in such conditions. To address these limitations, we introduce LYCEUM, a deep learning-based CNV caller specifically designed for low-coverage aDNA. LYCEUM performs transfer learning from a model designed to detect CNVs in another noisy data domain, whole exome sequencing then it per- forms fine-tuning with a few aDNA samples for which semi-ground truth CNV calls are available. Our findings demonstrate that LYCEUM accurately identifies CNVs even in highly downsampled genomes, maintaining robust performance across a range of coverage levels. Thus, LYCEUM offers researchers a reliable solution for CNV detection in challenging ancient genomic datasets.
description: This repository contains processed samples, groundtruth data, and CNV predictions for real and simulated datasets to reproduce the analyses in the paper: LYCEUM: Learning to Call Copy Number Variants on Low-Coverage Ancient Genomes.
DOI: 10.5281/zenodo.13997010
title: LYCEUM: Learning to call copy number variants on low coverage ancient genomes

description: Copy number variants (CNVs) are pivotal in driving phenotypic variation that facilitates species adaptation. They are significant contributors to various disorders, making ancient genomes crucial for uncovering the genetic origins of disease susceptibility across populations. However, detecting CNVs in ancient DNA (aDNA) samples poses substantial challenges due to several factors: (i) aDNA is often highly degraded; (ii) contamination from microbial DNA and DNA from closely related species introduce additional noise into sequencing data; and finally, (iii) the typically low coverage of aDNA renders accurate CNV detection particularly difficult. Conventional CNV calling algorithms, which are optimized for high coverage read-depth signals, underperform under such conditions. To address these limitations, we introduce LYCEUM, the first machine learning-based CNV caller for aDNA. To overcome challenges related to data quality and scarcity, we employ a two-step training strategy. First, the model is pre-trained on whole genome sequencing data from the 1000 Genomes Project, teaching it CNV-calling capabilities similar to conventional methods. Next, the model is fine-tuned using high- confidence CNV calls derived from only a few existing high-coverage aDNA samples. During this stage, the model adapts to making CNV calls based on the downsampled read depth signals of the same aDNA samples. LYCEUM achieves accurate detection of CNVs even in typically low-coverage ancient genomes. We also observe that the segmental deletion calls made by LYCEUM show correlation with the demographic history of the samples and exhibit patterns of negative selection inline with natural selection.
description: This repository contains processed samples, groundtruth data, and CNV predictions for real and simulated datasets to reproduce the analyses in the paper: LYCEUM: Learning to Call Copy Number Variants on Low-Coverage Ancient Genomes.
DOI: 10.5281/zenodo.14739221
title: LYCEUM: Learning to call copy number variants on low coverage ancient genomes

description: Copy number variants (CNVs) are pivotal in driving phenotypic variation that facilitates species adaptation. They are significant contributors to various disorders, making ancient genomes crucial for uncovering the genetic origins of disease susceptibility across populations. However, detecting CNVs in ancient DNA (aDNA) samples poses substantial challenges due to several factors: (i) aDNA is often highly degraded; (ii) contamination from microbial DNA and DNA from closely related species introduce additional noise into sequencing data; and finally, (iii) the typically low coverage of aDNA renders accurate CNV detection particularly difficult. Conventional CNV calling algorithms, which are optimized for high coverage read-depth signals, underperform under such conditions. To address these limitations, we introduce LYCEUM, the first machine learning-based CNV caller for aDNA. To overcome challenges related to data quality and scarcity, we employ a two-step training strategy. First, the model is pre-trained on whole genome sequencing data from the 1000 Genomes Project, teaching it CNV-calling capabilities similar to conventional methods. Next, the model is fine-tuned using high- confidence CNV calls derived from only a few existing high-coverage aDNA samples. During this stage, the model adapts to making CNV calls based on the downsampled read depth signals of the same aDNA samples. LYCEUM achieves accurate detection of CNVs even in typically low-coverage ancient genomes. We also observe that the segmental deletion calls made by LYCEUM show correlation with the demographic history of the samples and exhibit patterns of negative selection inline with natural selection.
description: This repository contains processed samples, groundtruth data, and CNV predictions for real and simulated datasets to reproduce the analyses in the paper: LYCEUM: Learning to Call Copy Number Variants on Low-Coverage Ancient Genomes.
DOI: 10.5519/qd.pgtobu4y
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (2073 records)
DOI: 10.3886/e188081v1
title: Data set data set sharing

description: This data set has responses of 361 respondents
DOI: 10.3886/e188081
title: Data set data set sharing

description: This data set has responses of 361 respondents
DOI: 10.3886/e188081v2
title: Data set data set sharing

description: This data set has responses of 361 respondents
DOI: 10.15468/dl.qv95w4
title: Occurrence Download

description: A dataset containing 54872 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "OccurrenceStatus is Present",
 "TaxonKey is Falco Linnaeus, 1758"
 ]
}

 The dataset includes 54872 records from 70 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002034-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qyjbq6
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "OccurrenceStatus is Present",
 "TaxonKey is Leptotyphlops Fitzinger, 1843"
 ]
}

 The dataset includes 23 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002035-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25345/c5kw57w63
title: MassIVE MSV000096957 - GNPS Costus speciosus fbmn analysis of spirostanols
title: GNPS analysis of Costus speciosus extract for spirostanol glycosides
DOI: 10.15468/dl.bj6q3k
title: Occurrence Download

description: A dataset containing 52255 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "OccurrenceStatus is Present",
 "TaxonKey is Chiroptera"
 ]
}

 The dataset includes 52255 records from 97 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002036-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.18112/openneuro.ds005880.v1.0.1
title: BIDS Dataset for the Diminished Seventh Chord
DOI: 10.6084/m9.figshare.28280495
title: Data.xlsx

description: 2021 年 9 月初，选择了 Cainan 、 Guanlichu 和 Beishawo，EP、CM 和 HP 在这里分布均匀。NS 和 MS 之间的距离为 38 公里，MS 和 SS 之间的距离为 31 公里，NS 和 SS 之间的距离为 65 公里。根据多年的观察，三个采样点的气候条件基本相同（每年可探测的降雨量 [&gt; 0.2 毫米] 为 66.7 毫米;如果降雪，则深度约为 13-15 毫米），但在土壤物理和化学性质上存在很大差异，土壤粒径和生物结皮发育水平最直观。在同一地点为每个物种随机设置大小为 20 m × 20 m 的 6 个样地。在每个样地中为同一物种选择 5 株大小相近的健康单株，并将每个个体视为 1 个重复。由于植物分布不均，每个地点每个物种的实际植物数量（复制）各不相同，范围在 30 到 38 之间。三个站点的 EP 、 CM 和 HP 个体总数分别为 92 、 95 和 104 人。随后，在中冠层中充分收集完全成熟和暴露在阳光下的 ABs。然后将植物样本放入装有冰袋的泡沫盒中，并立即运送到实验室。在实地调查期间还测量了植物大小。EP、CM 和 HP 的平均冠径分别为 18.61 ± 1.12、94.68 ± 10.12 和 185.41 ± 15.45 厘米;平均株高分别为 16.82 ± 0.95、57.20 ± 4.43 和 223.47 ± 19.38 厘米。将植物样品在75 °C的烘箱中干燥至恒重。将干燥的叶子样品在振动盘式研磨机 （MM400， Retsch GmbH Inc.， Haan， Germany） 中研磨成粉末，并储存在拉链袋中。<sup>-1</sup>） 和 N （mg<sup>g-1</sup>） 浓度。<sup>-1</sup>） 浓度。<sup>−1</sup>FP640， Jingke Co.， Shanghai， China） 测量叶 K （mg g -1） 浓度。然后计算化学计量比。为了比较三个地点之间土壤特性的差异，收集了土壤样本并评估了生物结皮的发展。在每 20 m × 20 m 样地收集 1 个 0−10 cm 深度的混合土壤样品。土壤在实验室中风干，然后过筛。首先，采用筛分法测定土壤粒径，筛孔尺寸为 0.05、0.1、0.25、0.45 和 1 mm;为了更清楚地探究土壤粒径与植物养分之间的关系，φ &lt; 0.25 mm 的粒径被定义为细沙，φ &gt; 0.45 mm 的粒径被视为粗砂（Fu et al.， 2022;He et al.， 2018）。接下来，土壤有机碳（OC，g kg-1）、总氮（TN，g kg-1）、总磷（TP，g kg-1）、总钾（TK，g kg-1）、有效氮（AN，mg kg-1）和速效磷（AP，mg kg-1）、速效钾（AK，mg kg-1）、土壤pH值和电导率（EC，μS cm-1）的浓度根据Bao（2000）的标准方法确定。<br><br><br><br>
DOI: 10.6084/m9.figshare.28280519
title: Raw data for cytokine ELISA and antigen recall assays

description: Raw data for cytokine ELISA and antigen recall assays
DOI: 10.5281/zenodo.10473109
title: Worldwide Delineation of Multi-Tier City-Regions

description: Urban centres are pivotal in shaping societies, yet a systematic global analysis of how countries are organized around multiple urban centres is lacking. We enhance understanding by delineating city-regions worldwide, classifying over 30,000 urban centres into four tiers-town, small, intermediate, and large city-based on population size and mapping their catchment areas based on travel time, differentiating between primary and secondary city-regions. Employing a 3-hour travel time cutoff, we identify 1,403 primary city-regions, increasing to 4,210 with a 1-hour cutoff, more indicative of commuting times. Our findings reveal significant interconnectedness among urban centres and with their surrounding areas, with 3.2 billion people having physical access to multiple tiers within an hour, and 4.7 billion within three hours. Notably, among people living in or closest to towns or small cities, twice as many have easier access to intermediate than to large cities, underscoring intermediate cities' crucial role in connecting surrounding populations. This systematic identification of city-regions globally, uncovers diverse organisational patterns across urban tiers, influenced by geography, level of development and infrastructure, offering a valuable spatial dataset for regional planning, economic development, and resource management.
description: City-region CSV files are added.
DOI: 10.5281/zenodo.10473110
title: Worldwide Delineation of Multi-Tier City-Regions

description: Urban centres shape societies, but there is no systematic global approach analysing how countries are organized around multiple urban centres. We advance understanding by delineating 6,100 city–regions worldwide using a novel framework classifying 30,000 urban centres into four tiers and mapping their nested catchment areas based on travel time accessibility. Our results show extensive interconnectedness among urban centres and with their surrounding areas, with 3.2 billion people having physical access to multiple tiers with 1-hour travel time, rising to 4.7 billion for 3-hours travel time. Importantly, among people living in or near towns and small cities, access to intermediate cities is far greater than to large cities. This highlights the essential role intermediate cities play in engaging surrounding populations. For the first time, city–regions around the world are identified systematically, showing great diversity in how societies are organized across urban tiers, depending on geography and national income. The associated spatial dataset is a powerful tool for regional planning, economic development, and natural resource management.
DOI: 10.5281/zenodo.10512398
title: Worldwide Delineation of Multi-Tier City-Regions

description: Urban centres shape societies, but there is no systematic global approach analysing how countries are organized around multiple urban centres. We advance understanding by delineating 6,100 city–regions worldwide using a novel framework classifying 30,000 urban centres into four tiers and mapping their nested catchment areas based on travel time accessibility. Our results show extensive interconnectedness among urban centres and with their surrounding areas, with 3.2 billion people having physical access to multiple tiers with 1-hour travel time, rising to 4.7 billion for 3-hours travel time. Importantly, among people living in or near towns and small cities, access to intermediate cities is far greater than to large cities. This highlights the essential role intermediate cities play in engaging surrounding populations. For the first time, city–regions around the world are identified systematically, showing great diversity in how societies are organized across urban tiers, depending on geography and national income. The associated spatial dataset is a powerful tool for regional planning, economic development, and natural resource management.
description: The Excel files are updated to display the numbers reported in the manuscript by default.
DOI: 10.5281/zenodo.11187634
title: Worldwide Delineation of Multi-Tier City-Regions

description: Urban centres are pivotal in shaping societies, yet a systematic global analysis of how countries are organized around multiple urban centres is lacking. We enhance understanding by delineating city-regions worldwide, classifying over 30,000 urban centres into four tiers-town, small, intermediate, and large city-based on population size and mapping their catchment areas based on travel time, differentiating between primary and secondary city-regions. Employing a 3-hour travel time cutoff, we identify 1,403 primary city-regions, increasing to 4,210 with a 1-hour cutoff, more indicative of commuting times. Our findings reveal significant interconnectedness among urban centres and with their surrounding areas, with 3.2 billion people having physical access to multiple tiers within an hour, and 4.7 billion within three hours. Notably, among people living in or closest to towns or small cities, twice as many have easier access to intermediate than to large cities, underscoring intermediate cities' crucial role in connecting surrounding populations. This systematic identification of city-regions globally, uncovers diverse organisational patterns across urban tiers, influenced by geography, level of development and infrastructure, offering a valuable spatial dataset for regional planning, economic development, and resource management.
description: City-region CSV files are added.
DOI: 10.6084/m9.figshare.28280516
title: Raw data for in vivo and ex vivo data

description: Raw data for in vivo and ex vivo data
DOI: 10.6084/m9.figshare.28280474
title: Original data.

description: The rock cavy, a social rodent, emits alarm calls to signal danger. These calls are believed to be adjusted depending on the type of predator and the urgency of the threat. To confirm this, we aimed to compare the acoustic responses of free-range Kerodon rupestris in different threat contexts. The study was conducted in two conservation units located in the Brazilian semiarid region known as the Caatinga. All alarm calls were collected using the ad libitum method. Calls were classified through aural and visual inspection using Raven Pro software. Discriminant function analysis was applied to test the classification of vocal types. To assess differences in vocalization quantities and acoustic parameters, generalized mixed linear models were used, followed by Tukey post hoc tests when appropriate. Our results showed that rock cavies emitted two vocal types (alarm whistle and fast alarm whistle) in threat contexts. It was observed that both the type of threat and the proximity of the threat affected the intervals between pulses of the alarm whistles. Rocky cavies emitted alarm whistles with longer intervals between pulses when faced with threats from humans and dogs than birds of prey, tayra and ocelot. When the threat was closer, the rocky cavies emitted alarm whistles with shorter intervals between pulses. Fast alarm whistles were emitted only by rock cavy close to potential hunting predators. This study highlights that the distance from the threat and different threats influence adjustments in K. rupestris alarm calls. The rock cavy signals higher-degree dangers by emitting faster calls with shorter intervals between pulses.
DOI: 10.15468/dl.arg8xk
title: Occurrence Download

description: A dataset containing 68 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Catalpa speciosa (Warder ex Barney) Warder ex Engelm."
 ]
}

 The dataset includes 68 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002037-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ztkknb
title: Occurrence Download

description: A dataset containing 136556 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((19.92671 42.97933,42.27158 42.97933,42.27158 53.75628,19.92671 53.75628,19.92671 42.97933))",
 "Month is one of (May, June, July)",
 "OccurrenceStatus is Present",
 "TaxonKey is Aves",
 "Year 1000-1999"
 ]
}

 The dataset includes 136556 records from 90 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002025-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.