cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5678878
title: Supplementary Material for: Regional Differences in Efficacy, Safety, and Biomarkers for Second-Line Axitinib in Patients with Advanced Hepatocellular Carcinoma: From a Randomized Phase II Study

description: <b><i>Background:</i></b> An unmet need exists for treatment of patients with advanced hepatocellular carcinoma (HCC) who progress on or are intolerant to sorafenib. A global randomized phase II trial (ClinicalTrial.gov No. NCT01210495) of axitinib, a vascular endothelial growth factor receptor 1-3 inhibitor, in combination with best supportive care (BSC) did not prolong overall survival (OS) over placebo/BSC, but showed improved progression-free survival in some patients. Subgroup analyses were conducted to identify potential predictive/prognostic factors. <b><i>Methods:</i></b> The data from this phase II study were analyzed for the efficacy and safety of axitinib/BSC in patients from Asia versus non-Asia versus Asian subgroups (Japan, Korea, or mainland China/Hong Kong/Taiwan) and predictive/prognostic values of baseline microRNAs and serum soluble proteins, using the Cox proportional hazards model. <b><i>Results:</i></b> Of 202 patients, 78 were from non-Asia and 124 from Asia (37 Japanese, 36 Korean, and 51 Chinese). No significant differences in OS were found between axitinib/BSC and placebo/BSC in non-Asians, Asians, or Asian subgroups. However, in an exploratory analysis, axitinib/BSC showed favorable OS in Asians, especially Japanese, when patients intolerant to prior antiangiogenic therapy were excluded from the data set. Axitinib/BSC was well tolerated by non-Asians and Asians alike. The presence of 4 circulating microRNAs, including miR-5684 and miR-1224-5p, or a level lower than or equal to the median protein level of stromal cell-derived factor 1 at baseline was significantly associated with longer OS in axitinib/BSC-treated Asians or non-Asians. <b><i>Conclusions:</i></b> Axitinib/BSC did not prolong survival over placebo/BSC in non-Asians, Asians, or Asian subgroups, but favorable OS with axitinib/BSC was observed in a subset of Japanese patients. A patient population that excludes sorafenib-intolerant patients might potentially be more suitable for clinical trials of new agents in advanced HCC. Since these results are very preliminary, further investigation is warranted. The potential predictive/prognostic value of several baseline microRNAs and soluble proteins identified in this study would require validation in prospective studies on a large cohort of patients.
DOI: 10.6084/m9.figshare.5678875
title: Identifying risk for language impairment in children from linguistically diverse low-income schools

description: <i>Purpose</i>: To improve screening procedures for children in a linguistically diverse context, we combined tasks known to reveal grammatical deficits in children with language impairment (LI) with training to facilitate performance on a verb elicitation task. <i>Method</i>: Sixty-four first grade children participated. The objective grammatical measures included elicitation of 12 past tense regular verbs preceded by a teaching phase (teach-test), the sentence recall (SR) subtest of the Clinical evaluation of language fundamentals (CELF-4), and a tally of all conjugated verbs from a narrative retell task. Given the widespread reliance on teacher observation for the referral of children suspected of having LI, we compared our results to the spoken language portion of the CELF-4 teacher observational rating scale (ORS). <i>Result</i>: Using teacher observation as a reference for comparison, the past tense elicitation task and the SR task yielded strong discriminating power, but the verb tally was relatively weak. However, combining the three tasks yielded the highest levels of sensitivity (75%) and specificity (92%) than any single measure on its own. <i>Conclusion</i>: This study contributes to alternative assessment practices by highlighting the potential utility of adding a teaching component prior to administering informal grammatical probes.
DOI: 10.6084/m9.figshare.5678875.v1
title: Identifying risk for language impairment in children from linguistically diverse low-income schools

description: <i>Purpose</i>: To improve screening procedures for children in a linguistically diverse context, we combined tasks known to reveal grammatical deficits in children with language impairment (LI) with training to facilitate performance on a verb elicitation task. <i>Method</i>: Sixty-four first grade children participated. The objective grammatical measures included elicitation of 12 past tense regular verbs preceded by a teaching phase (teach-test), the sentence recall (SR) subtest of the Clinical evaluation of language fundamentals (CELF-4), and a tally of all conjugated verbs from a narrative retell task. Given the widespread reliance on teacher observation for the referral of children suspected of having LI, we compared our results to the spoken language portion of the CELF-4 teacher observational rating scale (ORS). <i>Result</i>: Using teacher observation as a reference for comparison, the past tense elicitation task and the SR task yielded strong discriminating power, but the verb tally was relatively weak. However, combining the three tasks yielded the highest levels of sensitivity (75%) and specificity (92%) than any single measure on its own. <i>Conclusion</i>: This study contributes to alternative assessment practices by highlighting the potential utility of adding a teaching component prior to administering informal grammatical probes.
DOI: 10.6084/m9.figshare.5678839
title: Enclosure design for flock-level, chronic exposure of birds to air contaminant mixtures

description: The objective of this study was to design an enclosure suitable for studying the ecotoxicological effects of vehicle emissions on groups of wild birds without compromising welfare. Two, adjacent enclosures sheltered from sunlight, wind and rain, were bird-proofed and wrapped with thick polyethylene sheeting. Emissions were directed into the treatment enclosure from the exhaust of a light-duty gasoline truck, using flexible, heat-proof pipe, with joins sealed to prevent leakage. During active exposure, the engine was idled for 5 h/day, 6 days/week for 4 weeks. Fans maintained positive pressure (controls) and negative pressure (treatment), preventing cross-contamination of enclosures and protecting investigators. Four sets of passive, badge-type samplers were distributed across each enclosure, measuring nitrogen dioxide, sulfur dioxide and volatile organic compounds (NO<sub>2</sub>, SO<sub>2</sub> and VOCs, respectively), and were complemented by active monitors measuring VOCs and particulate matter (2.5 µm diameter, PM<sub>2.5</sub>). We found that the concentrations of NO<sub>2</sub>, SO<sub>2</sub> and PM<sub>2.5</sub> were not different between treatment and control enclosures. Volatile organic compounds (e.g. benzene, toluene, ethylbenzene and xylenes) were approximately six times higher in the treatment enclosure than control (13.23 and 2.13 µg m<sup>−1</sup>, respectively). In conclusion, this represents a successful, practical design for studying the effects of sub-chronic to chronic exposure to realistic mixtures of vehicle exhaust contaminants, in groups of birds. Recommended modifications for future research include a chassis dynamometer (vehicle treadmill), to better replicate driving conditions including acceleration and deceleration.
DOI: 10.6084/m9.figshare.5678839.v1
title: Enclosure design for flock-level, chronic exposure of birds to air contaminant mixtures

description: The objective of this study was to design an enclosure suitable for studying the ecotoxicological effects of vehicle emissions on groups of wild birds without compromising welfare. Two, adjacent enclosures sheltered from sunlight, wind and rain, were bird-proofed and wrapped with thick polyethylene sheeting. Emissions were directed into the treatment enclosure from the exhaust of a light-duty gasoline truck, using flexible, heat-proof pipe, with joins sealed to prevent leakage. During active exposure, the engine was idled for 5 h/day, 6 days/week for 4 weeks. Fans maintained positive pressure (controls) and negative pressure (treatment), preventing cross-contamination of enclosures and protecting investigators. Four sets of passive, badge-type samplers were distributed across each enclosure, measuring nitrogen dioxide, sulfur dioxide and volatile organic compounds (NO<sub>2</sub>, SO<sub>2</sub> and VOCs, respectively), and were complemented by active monitors measuring VOCs and particulate matter (2.5 µm diameter, PM<sub>2.5</sub>). We found that the concentrations of NO<sub>2</sub>, SO<sub>2</sub> and PM<sub>2.5</sub> were not different between treatment and control enclosures. Volatile organic compounds (e.g. benzene, toluene, ethylbenzene and xylenes) were approximately six times higher in the treatment enclosure than control (13.23 and 2.13 µg m<sup>−1</sup>, respectively). In conclusion, this represents a successful, practical design for studying the effects of sub-chronic to chronic exposure to realistic mixtures of vehicle exhaust contaminants, in groups of birds. Recommended modifications for future research include a chassis dynamometer (vehicle treadmill), to better replicate driving conditions including acceleration and deceleration.
DOI: 10.6084/m9.figshare.5678806
title: rawGeneExpData.mat

description: This dataset is originated from the raw dataset published in http://archive.broadinstitute.org/mpr/CNS. It is only used to show the effectiveness of our analysis method.
DOI: 10.6084/m9.figshare.5678737
title: Dataset1 and putative SNPs under selection

description: Dataset 1 contains the called genotypes for 60 plains zebras, 3 Grevy's zebras, 3 mountain zebras and one Quagga zebra. A total of 98,512 SNPs were called. The data is based on the RADseq technology. We used a missingness filter of 0.2 and excluded monomorphic sites.<br>We also include a list of SNPs inferred from pcadapt, which are putatively under selection.<br><br>
DOI: 10.6084/m9.figshare.5678701
title: Long-term dynamics of the bacterial community in a Swedish full-scale wastewater treatment plant

description: The operational efficiency of activated sludge wastewater treatment plants depends to a large extent on the microbial community structure of the activated sludge. The aims of this paper are to describe the composition of the bacterial community in a Swedish full-scale activated sludge wastewater treatment plant, to describe the dynamics of the community and to elucidate possible causes for bacterial community composition changes. The bacterial community composition in the activated sludge was described using 16S rRNA gene libraries and monitored for 15 months by a terminal restriction fragment (T-RF) length polymorphism (T-RFLP) analysis of the 16S rRNA gene. Despite variable environmental conditions, a large fraction of the observed T-RFs were present at all times, making up at least 50% in all samples, possibly representing a relatively stable core fraction of the bacterial community. However, the proportions of the different T-RFs in this fraction as well as the T-RFs in the more variable fraction showed a significant variation over time and temperature. The difference in community composition between summer and winter coincided with observed differences in floc structure. These observations suggest a relationship between floc properties and bacterial community composition, although additional experiments are required to determine causality.
DOI: 10.6084/m9.figshare.5678701.v1
title: Long-term dynamics of the bacterial community in a Swedish full-scale wastewater treatment plant

description: The operational efficiency of activated sludge wastewater treatment plants depends to a large extent on the microbial community structure of the activated sludge. The aims of this paper are to describe the composition of the bacterial community in a Swedish full-scale activated sludge wastewater treatment plant, to describe the dynamics of the community and to elucidate possible causes for bacterial community composition changes. The bacterial community composition in the activated sludge was described using 16S rRNA gene libraries and monitored for 15 months by a terminal restriction fragment (T-RF) length polymorphism (T-RFLP) analysis of the 16S rRNA gene. Despite variable environmental conditions, a large fraction of the observed T-RFs were present at all times, making up at least 50% in all samples, possibly representing a relatively stable core fraction of the bacterial community. However, the proportions of the different T-RFs in this fraction as well as the T-RFs in the more variable fraction showed a significant variation over time and temperature. The difference in community composition between summer and winter coincided with observed differences in floc structure. These observations suggest a relationship between floc properties and bacterial community composition, although additional experiments are required to determine causality.
DOI: 10.6084/m9.figshare.5678551
title: Additional file 8 of On the impact of relatedness on SNP association analysis

description: Perl script for converting HapMap genotype data. This Perl script requires the sample list of Additional file 6, the SNP list of Additional file 7 and HapMap raw data. The HapMap project website is not available anymore, however, genotype data can still be retrieved from ftp://ftp.ncbi.nlm.nih.gov/hapmap/genotypes/2010-08_phaseII+III/ . The converted genotypes are saved in a CSV file. Folder and file locations must be adapted before running the script. Running the script on an Intel Xeon X5560 CPU (2.80 GHz) required 800 MB RAM and took about 5 minutes. (PL 2 kb)
DOI: 10.6084/m9.figshare.5678551.v1
title: Additional file 8 of On the impact of relatedness on SNP association analysis

description: Perl script for converting HapMap genotype data. This Perl script requires the sample list of Additional file 6, the SNP list of Additional file 7 and HapMap raw data. The HapMap project website is not available anymore, however, genotype data can still be retrieved from ftp://ftp.ncbi.nlm.nih.gov/hapmap/genotypes/2010-08_phaseII+III/ . The converted genotypes are saved in a CSV file. Folder and file locations must be adapted before running the script. Running the script on an Intel Xeon X5560 CPU (2.80 GHz) required 800 MB RAM and took about 5 minutes. (PL 2 kb)
DOI: 10.6084/m9.figshare.5678533
title: Additional file 7 of On the impact of relatedness on SNP association analysis

description: SNP selection of HapMap genotype data. This file contains a list of HapMap SNP identifiers used for our analyses. rsid (reference SNP identifier) refers to the first column of the genotype data files as provided by HapMap. (CSV 10000 kb)
DOI: 10.6084/m9.figshare.5678533.v1
title: Additional file 7 of On the impact of relatedness on SNP association analysis

description: SNP selection of HapMap genotype data. This file contains a list of HapMap SNP identifiers used for our analyses. rsid (reference SNP identifier) refers to the first column of the genotype data files as provided by HapMap. (CSV 10000 kb)
DOI: 10.6084/m9.figshare.5678515
title: Additional file 6 of On the impact of relatedness on SNP association analysis

description: Sample selection of HapMap genotype data. This file provides annotations for 174 HapMap CEU samples. The columns FID (family identifier), IID (individual identifier), dad, mom, sex (1=male, 2=female), pheno (always 0), population (always CEU) correspond to the columns of relationships_w_pops_121708.txt filtered for CEU samples as provided by HapMap. The column ctr contains a unique trio identifier and equals NA when the sample does not belong to a complete trio family. The reason for exclusion is provided where applicable, otherwise NA is stated and the sample is included in our study. (CSV 8 kb)
DOI: 10.6084/m9.figshare.5678515.v1
title: Additional file 6 of On the impact of relatedness on SNP association analysis

description: Sample selection of HapMap genotype data. This file provides annotations for 174 HapMap CEU samples. The columns FID (family identifier), IID (individual identifier), dad, mom, sex (1=male, 2=female), pheno (always 0), population (always CEU) correspond to the columns of relationships_w_pops_121708.txt filtered for CEU samples as provided by HapMap. The column ctr contains a unique trio identifier and equals NA when the sample does not belong to a complete trio family. The reason for exclusion is provided where applicable, otherwise NA is stated and the sample is included in our study. (CSV 8 kb)
DOI: 10.6084/m9.figshare.5678500
title: Additional file 5 of On the impact of relatedness on SNP association analysis

description: Pairwise relatedness estimates of HapMap samples. This file contains a matrix of pairwise relatedness estimates resulting from the preliminary analysis of 174 HapMap CEU samples. Sample identifiers for the pair of individuals under consideration are given in the first row and in the first column, respectively. A value of -1 occurs if pairwise relatedness could not be estimated because of disjoint SNP sets. (CSV 571 kb)
DOI: 10.6084/m9.figshare.5678500.v1
title: Additional file 5 of On the impact of relatedness on SNP association analysis

description: Pairwise relatedness estimates of HapMap samples. This file contains a matrix of pairwise relatedness estimates resulting from the preliminary analysis of 174 HapMap CEU samples. Sample identifiers for the pair of individuals under consideration are given in the first row and in the first column, respectively. A value of -1 occurs if pairwise relatedness could not be estimated because of disjoint SNP sets. (CSV 571 kb)
DOI: 10.6084/m9.figshare.5678497
title: MOESM3 of Synthesis, structure and toxicity evaluation of ethanolamine nitro/chloronitrobenzoates: a combined experimental and theoretical study

description: Additional file 3. Cif file for compound 2.
DOI: 10.6084/m9.figshare.5678497.v1
title: MOESM3 of Synthesis, structure and toxicity evaluation of ethanolamine nitro/chloronitrobenzoates: a combined experimental and theoretical study

description: Additional file 3. Cif file for compound 2.
DOI: 10.6084/m9.figshare.5678479
title: MOESM2 of Synthesis, structure and toxicity evaluation of ethanolamine nitro/chloronitrobenzoates: a combined experimental and theoretical study

description: Additional file 2. Cif file for compound 1.
DOI: 10.6084/m9.figshare.5678479.v1
title: MOESM2 of Synthesis, structure and toxicity evaluation of ethanolamine nitro/chloronitrobenzoates: a combined experimental and theoretical study

description: Additional file 2. Cif file for compound 1.
DOI: 10.6084/m9.figshare.5678464
title: Additional file 3 of On the impact of relatedness on SNP association analysis

description: Maxima script for deriving expected variance inflation. This script can be used with Maxima [30] for deriving formulae for the expected variance inflation Îť f;m;câ ˛ for synthetic family studies. (WXM 1 kb)
DOI: 10.6084/m9.figshare.5678464.v1
title: Additional file 3 of On the impact of relatedness on SNP association analysis

description: Maxima script for deriving expected variance inflation. This script can be used with Maxima [30] for deriving formulae for the expected variance inflation Îť f;m;câ ˛ for synthetic family studies. (WXM 1 kb)
DOI: 10.6084/m9.figshare.24947649
title: Weather data

description: Weather data test 1
DOI: 10.6084/m9.figshare.24947649.v2
title: Weather data

description: Weather data test 1
DOI: 10.6084/m9.figshare.24947649.v1
title: Weather data for China

description: Weather data for China
DOI: 10.25949/21728318
title: Nelson et al Groundwater microbial assemblages in the Murray-Darling Basin (16S rDNA)

description: Samples of groundwater were collected from sites across the southern Murray Darling Basin on 2 occasions and analysed to characterise the microbial communities in the water. Water quality data were also collected.Microbial assemblage data derived from Illumina sequencing of 16S rDNA amplicons. Sequence data were processed using Greenfield Hybrid Analysis Pipeline (GHAP) v2.2, created by CSIRO Australia (available at https://cloudstor.aarnet.edu.au/plus/s/ pUvwME6fMeCcX - zL). Taxonomic assignment is based on the Ribosomal Database Project (RDP) Classifier (Wang, Garrity et al. 2007). OTUs were assigned using a 97% similarity threshold). Low abundant OTUs (&lt;10), organelles and unassigned taxa at kingdom level were removed.
DOI: 10.25949/21728318.v1
title: Nelson et al Groundwater microbial assemblages in the Murray-Darling Basin (16S rDNA)

description: Samples of groundwater were collected from sites across the southern Murray Darling Basin on 2 occasions and analysed to characterise the microbial communities in the water. Water quality data were also collected.Microbial assemblage data derived from Illumina sequencing of 16S rDNA amplicons. Sequence data were processed using Greenfield Hybrid Analysis Pipeline (GHAP) v2.2, created by CSIRO Australia (available at https://cloudstor.aarnet.edu.au/plus/s/ pUvwME6fMeCcX - zL). Taxonomic assignment is based on the Ribosomal Database Project (RDP) Classifier (Wang, Garrity et al. 2007). OTUs were assigned using a 97% similarity threshold). Low abundant OTUs (&lt;10), organelles and unassigned taxa at kingdom level were removed.
DOI: 10.21227/fr6t-6t64
title: Aerial Image (Roads & Sidewalks/ Crosswalks)

description: In this study called "GeoSAM", we leverage high-resolution orthorectified imagery and GIS data to train and evaluate the GeoSAM model, aimed at improving the segmentation of mobility infrastructure in urban environments. Orthorectified images, provided by the U.S. Geological Survey, serve as a precise and corrected form of aerial imagery, which, along with GIS data, are used to create accurate annotation labels. Our methodology involves using these datasets across two distinct regions within Washington DC for model training and evaluation. Additionally, to assess the model's generalization capabilities, we introduce image tiles from Cambridge—a city not seen during training—thereby testing GeoSAM's ability to adapt and perform in new, unseen environments. The images prepared for GeoSAM are of (1024x1024) resolution, with a zoom level of 20, assembled from adjacent tiles to meet the required dimensions. This approach underscores the robustness and wide applicability of GeoSAM across various geographical locations, demonstrating its potential in enhancing the accuracy of urban infrastructure mapping through advanced image processing techniques.
DOI: 10.25345/c5pk07c5t
title: MassIVE MSV000094021 - Leishmania LRV and VPs36 metabolomics studies
title: Parasites metabolomics profile using HILIC column on negative mode
DOI: 10.5281/zenodo.10579184
title: MSI(Mass spectrum imaging) dataset for MS-DIAL5 tutorial

description: This dataset is used for the tutorial of msi data analysis in MS-DIAL5. It contains:



zip file of ".d files" used for mass spectrometry imaging data analysis


 

This dataset has been selected from the Dataset 2 of 

DROP Met:  DM0048. ACSL6 facilitates the local distribution of di-DHA- and ULC-PUFA-containing phospholipids in the retina to support normal visual function in mice

The dataset is associated with the following paper.





Kuroha, S. et al. Long chain acyl‐CoA synthetase 6 facilitates the local distribution of di‐docosahexaenoic acid‐ and ultra‐long‐chain‐PUFA‐containing phospholipids in the retina to support normal visual function in mice. The FASEB Journal 37, e23151 (2023).