cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12374978.v2
title: Effects of predation from functionally diverse predators on adult production and traits

description: Four days prior to the beginning of the experiment, 500ml plastic containers were filled with 400ml recerse osmosis water, 1 g dried oak (<i>Quercus virginiana</i>) leaves, and 0.05g dried decorated crickets (Gryllodes sigillatus), and 100 µl microbial inoculum from rain-filled buckets. Containers were covered with plastic lids with holes punched for ventilation. Cohorts of 150 newly hatched Aedes aegypti were placed in each container and exposed to one of five predator treatments: no predator, Mesocyclops longisetus, Corethrella appendiculata, Anopheles barberi, and diverse. Single predator species treatments received 3 individual predators of the same species, and the diverse treatments received one of each species. All predators used were late instars. Predators were removed on day 6. 0.5g dried oak leaves and 0.025g dried decorated crickets were added on days 16 and 30 to replenish food resources for <i>A. aegypti. </i>Containers were checked daily for <i>A. aegypti </i>pupae which were placed in glass vials and the number of days from hatching to pupation recorded (Daystop in data). Pupae were checked daily for adults, which were removed and the sex and the number of days to adulthood (Daystoa in data file) recorded. Female adults were placed in a drying oven at 70C for &gt;48 hours, after which their wing lengths were measured.
DOI: 10.6084/m9.figshare.12374702
title: Questionnaires

description: 2 Versions of questinnaire
DOI: 10.6084/m9.figshare.12374702.v1
title: Questionnaires

description: 2 Versions of questinnaire
DOI: 10.6084/m9.figshare.12374633
title: Study Questionnaire.docx-Factors associated with health facility delivery..docx

description: Questionnaire used for data collection
DOI: 10.6084/m9.figshare.12374633.v1
title: Study Questionnaire.docx-Factors associated with health facility delivery..docx

description: Questionnaire used for data collection
DOI: 10.6084/m9.figshare.12374258
title: Daily SST at 8 wave-exposed intertidal locations along the Atlantic Canadian coast

description: Daily SST (sea surface temperature) measured at 8 wave-exposed intertidal locations spanning 415 km of the Atlantic coast of Nova Scotia, Canada.<br>
DOI: 10.6084/m9.figshare.12374261
title: Ipad Use in Library Instruction --Culinary Medicine Program

description: The data represents results of a survey that was used to determine if a hands-on session using Ipads for library instruction was beneficial to participants in a culinary medicine curriculum. The session was conducted as part of the University of South Alabama Mitchell Cancer Institute’s Culinary Medicine Curriculum. The survey used a 5 point Likert scale. Survey data indicated that participants liked using the Ipads as a means of learning how to use MedlinePlus and wanted more time to learn about health resources.
DOI: 10.6084/m9.figshare.12374264
title: Library Instruction Survey for Culinary Medicine Program Evaluation

description: The purpose of this survey was to determine the effectiveness of a library component as part of the University of South Alabama Mitchell Cancer Institute’s Culinary Medicine Curriculum. The survey consisted of 10 questions using a 5-point Likert scale. Survey data was collected from the first two cohorts of participants in 2017 (n=16). The main purpose of the evaluation was to determine if the library component in the program was beneficial and justify the need for additional time to integrate hands-on activities during the session. The results indicate that the library session was beneficial to the program, participants wanted more time to explore the health resources, and a hands-on session would be helpful. With this data, librarians were able to justify additional time in the curriculum to program administrators.
DOI: 10.6084/m9.figshare.12374258.v1
title: Daily SST at 8 wave-exposed intertidal locations along the Atlantic Canadian coast

description: Daily SST (sea surface temperature) measured at 8 wave-exposed intertidal locations spanning 415 km of the Atlantic coast of Nova Scotia, Canada.<br>
DOI: 10.6084/m9.figshare.12374264.v1
title: Library Instruction Survey for Culinary Medicine Program Evaluation

description: The purpose of this survey was to determine the effectiveness of a library component as part of the University of South Alabama Mitchell Cancer Institute’s Culinary Medicine Curriculum. The survey consisted of 10 questions using a 5-point Likert scale. Survey data was collected from the first two cohorts of participants in 2017 (n=16). The main purpose of the evaluation was to determine if the library component in the program was beneficial and justify the need for additional time to integrate hands-on activities during the session. The results indicate that the library session was beneficial to the program, participants wanted more time to explore the health resources, and a hands-on session would be helpful. With this data, librarians were able to justify additional time in the curriculum to program administrators.
DOI: 10.6084/m9.figshare.12372014
title: Abundance of sessile species in wave-exposed intertidal habitats along the Atlantic Canadian coast

description: Abundance (expressed as percent cover) of macroalgae and sessile invertebrates at the high and mid-intertidal zones of 8 wave-exposed locations spanning 415 km of the Atlantic coast of Nova Scotia, Canada (summer 2017).<br>
DOI: 10.6084/m9.figshare.12370637
title: VNIR spectra results.xlsx

description: Data archive for Figure 1 in Cutler et al. 2020 in The Planetary Science Journal. Reflectance spectra of samples before and after oxidation at 600°C: (A) alkali basalt, (B) diopside, (C) augite, (D) orthopyroxenite, and (E) olivine, modified<br>from Filiberto et al. (2020).<br>
DOI: 10.6084/m9.figshare.12370346
title: Metadata record for the manuscript: Olaparib for Metastatic Breast Cancer in a Patient with a Germline PALB2 Variant

description: <b>Summary</b>This metadata record provides details of the data supporting the claims of the related manuscript. The related study reports a patient with germline/somatic BRCA1/2 wild-type metastatic breast cancer (MBC), who had a dramatic response to the poly(adenosine diphosphate-ribose) polymerase (PARP) inhibitor olaparib of at least eight months’ duration. The patient was a 37-year-old woman with recurrent, hormone receptor-positive, HER2-negative MBC that had progressed despite hormonal therapy and palbociclib.<br><br><b>Data description and access</b>The tumour DNA sequencing data has been deposited in <i>NCBI Sequence Read Archive</i> and is available via accession: https://identifiers.org/ncbi/bioproject:PRJNA635377. The tumour DNA next generation sequencing (NGS) analysis is contained in the spreadsheet <b>Tumor DNA analysis.xlsx</b>, which is included with this data record; this file summarises the mutant allele frequency and copy number variations that were detected by NGS. The germline DNA sequencing can not be shared due to German data protection law considerations designed to safeguard patient anonymity. However, the authors confirm there were no other rare germline variants detected besides the reported PALB2 variant, which has previously been described and is available in <i>dbSNP </i>under this accession: https://identifiers.org/dbsnp:rs587782462.The data underlying Figure 1 in the related manuscript is contained in the spreadsheet <b>CA 15-3.xlsx</b>, included with this data record. <br><br><b>Ethics statement</b>Off-label treatment with olaparib in this patient with MBC lacking germline BRCA1/2 sequence variants affecting function was provided as compassionate use in the palliative setting in line with national regulations and did not require ethics committee approval. The patient provided written informed consent prior to initiation of treatment.
DOI: 10.6084/m9.figshare.12370346.v1
title: Metadata record for the manuscript: Olaparib for Metastatic Breast Cancer in a Patient with a Germline PALB2 Variant

description: <b>Summary</b>This metadata record provides details of the data supporting the claims of the related manuscript. The related study reports a patient with germline/somatic BRCA1/2 wild-type metastatic breast cancer (MBC), who had a dramatic response to the poly(adenosine diphosphate-ribose) polymerase (PARP) inhibitor olaparib of at least eight months’ duration. The patient was a 37-year-old woman with recurrent, hormone receptor-positive, HER2-negative MBC that had progressed despite hormonal therapy and palbociclib.<br><br><b>Data description and access</b>The tumour DNA sequencing data has been deposited in <i>NCBI Sequence Read Archive</i> and is available via accession: https://identifiers.org/ncbi/bioproject:PRJNA635377. The tumour DNA next generation sequencing (NGS) analysis is contained in the spreadsheet <b>Tumor DNA analysis.xlsx</b>, which is included with this data record; this file summarises the mutant allele frequency and copy number variations that were detected by NGS. The germline DNA sequencing can not be shared due to German data protection law considerations designed to safeguard patient anonymity. However, the authors confirm there were no other rare germline variants detected besides the reported PALB2 variant, which has previously been described and is available in <i>dbSNP </i>under this accession: https://identifiers.org/dbsnp:rs587782462.The data underlying Figure 1 in the related manuscript is contained in the spreadsheet <b>CA 15-3.xlsx</b>, included with this data record. <br><br><b>Ethics statement</b>Off-label treatment with olaparib in this patient with MBC lacking germline BRCA1/2 sequence variants affecting function was provided as compassionate use in the palliative setting in line with national regulations and did not require ethics committee approval. The patient provided written informed consent prior to initiation of treatment.
DOI: 10.6084/m9.figshare.12370307
title: New Zealand pollen

description: Dataset first used in the paper <i>Precise automatic classification of 46 different pollen types with convolutional neural networks</i> [0].<br><br>The images are dark field microscope images captured on the Classifynder system. The Classifynder (formerly knownas AutoStage) is documented in [1]. It was designed as a complete ’standalone’ system for automated pollen analysis. The system uses basic shape features to identify the locations of objects of interest (i.e. pollen grains) in conventional microscope slides under a low-power objective. It then switches to a higher power objective and visits the location of each pollen object to capture an image of it to be used for classification.<br>Objects are imaged at different focus levels, producing a ’Z-stack’. The system subsets the best-focused portions of each object Z-stack images, and then combines them to<br>produce a single composite image, followed by segmentation from the background. This image is then falsely colored to show depth.<br>[0] http://doi.org/10.1371/journal.pone.0229751[1] http://www.sciencedirect.com/science/article/pii/S0034666711001205
DOI: 10.6084/m9.figshare.12370187
title: Analysis of prostate cancer serum samples and healthy controls using recombinant antibody microarrays.

description: Serum samples collected from prostate cancer (PC) patients (nmPC=non-metastatic PC, mPC = metastatic PC) and healthy controls, HC (including the subgroups HC-1 and HC-2) were biotinylated and analyzed using antibody-based microarrays. Along the process, a quality control sample (QCpool) consisting of pooled human serum from five healthy individuals, biotinylated at one occasion, was also included in each assay.<br>In total, 363 serum samples (derived from prostate cancer patients and healthy controls) were analyzed using an antibody microarray consisting of 363 antibodies (scFv). The IMMray Evaluation Software (IES, Immunovia AB, Lund, Sweden) was used to align and quantify spot signal intensities. Using IES, local background was subtracted from each spot signal. Each data-point was represented by a mean spot intensity signal calculated based on three spot replicates per antibody. If the replicate coefficient of variation (CV) exceeded 15% from the mean value, the mean spot intensity was based on the two remaining replicates, which displayed most similar signals. In addition, all mean signals were trimmed, where 5% of the lower and upper extreme values were discarded, leading to the raw data file "Raw data_363 clinical samples and 136 QCpool samples_363 abs". Missing values (noted with NA) were replaced by bagged tree imputation, and acquired mean signal intensities were log2 transformed and normalized using Bayes algorithm ComBat to adjust for batch (print-to-print) variation. This data is available in the file "Normalized log2 data_363 clinical samples_363 abs".<br> In addition, 136 QCpool samples which were analyzed in the antibody microarray were also processed (separately) in a similar way as described above, and the data is available in the file "Normalized log2 _QCpool data".<br>
DOI: 10.25392/leicester.data.12370145
title: Zamudio et al Environmental Microbiology 2020 SUPPELMENTARY DATA 10.1111/1462-2920.15111

description: Zamudio R, RD Haigh, JD Ralph, M De Ste Croix, T Tasara, K Zurfluh, MJ Kwun, AD Millard, SD Bentley, NJ Croucher, R Stephan, MR Oggioni. 2020. Lineage specific evolution and gene flow in Listeria monocytogenes is independent of bacteriophages. Environmental Microbiology. 2020 doi 10.1111/1462-2920.15111<br> Listeria monocytogenes is a foodborne pathogen causing systemic infection with high mortality. To allow efficient tracing of outbreaks a clear definition of the genomic signature of a cluster of related isolates is required, but lineage specific characteristics call for a more detailed understanding of evolution. In our work we used core genome MLST (cgMLST) to identify new outbreaks combined to core genome SNP analysis to characterize the population structure and gene flow between lineages. Whilst analysing differences between the four lineages of L. monocytogenes we have detected differences in the recombination rate, and interestingly also divergence in the SNP differences between sub-lineages. In addition, the exchange of core genome variation between the lineages exhibited a distinct pattern, with lineage III being the best donor for horizontal gene transfer. Whilst attempting to link bacteriophage mediated transduction to observed gene transfer, we found an inverse correlation between phage presence in a lineage and the extent of recombination. Irrespective of the profound differences in recombination rates observed between sub-lineages and lineages we found that the previously proposed cut-off of 10 allelic differences in cgMLST can be still considered valid for the definition of a foodborne outbreak cluster of L. monocytogenes.<br>
DOI: 10.25392/leicester.data.12370145.v1
title: Zamudio et al Environmental Microbiology 2020 SUPPELMENTARY DATA 10.1111/1462-2920.15111

description: Zamudio R, RD Haigh, JD Ralph, M De Ste Croix, T Tasara, K Zurfluh, MJ Kwun, AD Millard, SD Bentley, NJ Croucher, R Stephan, MR Oggioni. 2020. Lineage specific evolution and gene flow in Listeria monocytogenes is independent of bacteriophages. Environmental Microbiology. 2020 doi 10.1111/1462-2920.15111<br> Listeria monocytogenes is a foodborne pathogen causing systemic infection with high mortality. To allow efficient tracing of outbreaks a clear definition of the genomic signature of a cluster of related isolates is required, but lineage specific characteristics call for a more detailed understanding of evolution. In our work we used core genome MLST (cgMLST) to identify new outbreaks combined to core genome SNP analysis to characterize the population structure and gene flow between lineages. Whilst analysing differences between the four lineages of L. monocytogenes we have detected differences in the recombination rate, and interestingly also divergence in the SNP differences between sub-lineages. In addition, the exchange of core genome variation between the lineages exhibited a distinct pattern, with lineage III being the best donor for horizontal gene transfer. Whilst attempting to link bacteriophage mediated transduction to observed gene transfer, we found an inverse correlation between phage presence in a lineage and the extent of recombination. Irrespective of the profound differences in recombination rates observed between sub-lineages and lineages we found that the previously proposed cut-off of 10 allelic differences in cgMLST can be still considered valid for the definition of a foodborne outbreak cluster of L. monocytogenes.<br>
DOI: 10.6084/m9.figshare.12370187.v1
title: Analysis of prostate cancer serum samples and healthy controls using recombinant antibody microarrays.

description: Serum samples collected from prostate cancer (PC) patients (nmPC=non-metastatic PC, mPC = metastatic PC) and healthy controls, HC (including the subgroups HC-1 and HC-2) were biotinylated and analyzed using antibody-based microarrays. Along the process, a quality control sample (QCpool) consisting of pooled human serum from five healthy individuals, biotinylated at one occasion, was also included in each assay.<br>In total, 363 serum samples (derived from prostate cancer patients and healthy controls) were analyzed using an antibody microarray consisting of 363 antibodies (scFv). The IMMray Evaluation Software (IES, Immunovia AB, Lund, Sweden) was used to align and quantify spot signal intensities. Using IES, local background was subtracted from each spot signal. Each data-point was represented by a mean spot intensity signal calculated based on three spot replicates per antibody. If the replicate coefficient of variation (CV) exceeded 15% from the mean value, the mean spot intensity was based on the two remaining replicates, which displayed most similar signals. In addition, all mean signals were trimmed, meaning that 5% of the lower and upper extreme values were discarded. Missing values were replaced by bagged tree imputation, and acquired mean signal intensities were log2 transformed and normalized using Bayes algorithm ComBat to adjust for batch (print-to-print) variation. This data is available in the file "Normalized log2 data_363 clinical samples_363 abs".<br> In addition, 136 QCpool samples which were analyzed in the antibody microarray were also processed (separately) in a similar way as described above, and the data is available in the file "Normalized log2 _QCpool data".<br>
DOI: 10.6084/m9.figshare.12370106
title: ProMIS NGS datasets - Test 1-4

description: NGS data output from Illumina NextSeq 500 generated in the proof-of-concept study for the ProMIS assay.<br>NGS raw data (BCL files) generated from the NextSeq 500 was demultiplexed by the sample index reads using bcl2fastq2 Conversion Software v2.20 (Illumina) and ran through an in-house pipeline written in Java programming language to count the total number of scFv-specific tags for each sample available here:https://github.com/sunnyveerla/ProMIS/blob/master/ProMIS.java<br>For our analysis we used only reads that passed the sequencer chastity filter and had base call quality for each base over Q30 (Phred Quality score).<br>Data for Test 4 is divided into 2 parts due to file size limitation in Figshare.
DOI: 10.6084/m9.figshare.12370187.v3
title: Analysis of prostate cancer serum samples and healthy controls using recombinant antibody microarrays.

description: Serum samples collected from prostate cancer (PC) patients (nmPC=non-metastatic PC, mPC = metastatic PC) and healthy controls, HC (including the subgroups HC-1 and HC-2) were biotinylated and analyzed using antibody-based microarrays. Along the process, a quality control sample (QCpool) consisting of pooled human serum from five healthy individuals, biotinylated at one occasion, was also included in each assay.<br>In total, 363 serum samples (derived from prostate cancer patients and healthy controls) were analyzed using an antibody microarray consisting of 363 antibodies (scFv). The IMMray Evaluation Software (IES, Immunovia AB, Lund, Sweden) was used to align and quantify spot signal intensities. Using IES, local background was subtracted from each spot signal. Each data-point was represented by a mean spot intensity signal calculated based on three spot replicates per antibody. If the replicate coefficient of variation (CV) exceeded 15% from the mean value, the mean spot intensity was based on the two remaining replicates, which displayed most similar signals. In addition, all mean signals were trimmed, where 5% of the lower and upper extreme values were discarded, leading to the raw data file "Raw data_363 clinical samples and 136 QCpool samples_363 abs". Missing values (noted with NA) were replaced by bagged tree imputation, and acquired mean signal intensities were log2 transformed and normalized using Bayes algorithm ComBat to adjust for batch (print-to-print) variation. This data is available in the file "Normalized log2 data_363 clinical samples_363 abs".<br> In addition, 136 QCpool samples which were analyzed in the antibody microarray were also processed (separately) in a similar way as described above, and the data is available in the file "Normalized log2 _QCpool data".<br>
DOI: 10.6084/m9.figshare.12370091
title: nitrate budget

description: caefEfewf
DOI: 10.6084/m9.figshare.12370187.v2
title: Analysis of prostate cancer serum samples and healthy controls using recombinant antibody microarrays.

description: Serum samples collected from prostate cancer (PC) patients (nmPC=non-metastatic PC, mPC = metastatic PC) and healthy controls, HC (including the subgroups HC-1 and HC-2) were biotinylated and analyzed using antibody-based microarrays. Along the process, a quality control sample (QCpool) consisting of pooled human serum from five healthy individuals, biotinylated at one occasion, was also included in each assay.<br>In total, 363 serum samples (derived from prostate cancer patients and healthy controls) were analyzed using an antibody microarray consisting of 363 antibodies (scFv). The IMMray Evaluation Software (IES, Immunovia AB, Lund, Sweden) was used to align and quantify spot signal intensities. Using IES, local background was subtracted from each spot signal. Each data-point was represented by a mean spot intensity signal calculated based on three spot replicates per antibody. If the replicate coefficient of variation (CV) exceeded 15% from the mean value, the mean spot intensity was based on the two remaining replicates, which displayed most similar signals. In addition, all mean signals were trimmed, meaning that 5% of the lower and upper extreme values were discarded. Missing values were replaced by bagged tree imputation, and acquired mean signal intensities were log2 transformed and normalized using Bayes algorithm ComBat to adjust for batch (print-to-print) variation. This data is available in the file "Normalized log2 data_363 clinical samples_363 abs".<br> In addition, 136 QCpool samples which were analyzed in the antibody microarray were also processed (separately) in a similar way as described above, and the data is available in the file "Normalized log2 _QCpool data".<br>
DOI: 10.6084/m9.figshare.12370091.v1
title: nitrate budget

description: caefEfewf
DOI: 10.6084/m9.figshare.12370037
title: Exhibit Tables

description: Exhibit table to run code<br>
DOI: 10.6084/m9.figshare.12370001
title: Reproducible Code.R

description: Code to reproducible local government revenue shock<br>
DOI: 10.6084/m9.figshare.12370037.v1
title: Exhibit Tables

description: Exhibit table to run code<br>
DOI: 10.6084/m9.figshare.12369995
title: localgovt_revenue.xlsx

description: Data file to accompany local government revenue shock paper<br>
DOI: 10.6084/m9.figshare.12369995.v1
title: localgovt_revenue.xlsx

description: Data file to accompany local government revenue shock paper<br>
DOI: 10.6084/m9.figshare.12370001.v1
title: Reproducible Code.R

description: Code to reproducible local government revenue shock<br>