cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7265645
title: The value of ‘having a go’: Trialing a project-based learning activity to inform curriculum design

description: Active, student-centered pedagogies such as project-based learning (PjBL) can offer significant potential for engaging undergraduates with complex sustainability issues. Driven by institution-wide curriculum changes and informed by educational theories and evidence from previous studies, a trial PjBL activity was designed and delivered on three separate occasions, to three different student groups, at a university in the United Kingdom. In these trials, students from geography, Earth, and environmental science (GEES) programs worked in small (5 to 6 people), multiple-discipline teams to explore a single research question focused on a global sustainability issue. The perceptions and experiences of the trial participants (students and faculty) were investigated using data from surveys and interviews, and the findings applied to designing a new, multiple-disciplinary module focused on energy and climate change. In general, all participants engaged positively with the PjBL approach, although issues around the nature and extent of support available to the students and appropriate methods of assessing PjBL outputs emerged as requiring further consideration. The findings demonstrate that a single research question need not constrain the approach students take when completing a PjBL activity and identify clear potential benefits in terms of developing students’ wider professional skills. This study also highlights the value to curriculum developers in trialing new pedagogic approaches, as the opportunity to “have a go” enabled potential issues for learners and instructors to be identified and mitigated prior to the final module design and implementation.
DOI: 10.6084/m9.figshare.7265645.v1
title: The value of ‘having a go’: Trialing a project-based learning activity to inform curriculum design

description: Active, student-centered pedagogies such as project-based learning (PjBL) can offer significant potential for engaging undergraduates with complex sustainability issues. Driven by institution-wide curriculum changes and informed by educational theories and evidence from previous studies, a trial PjBL activity was designed and delivered on three separate occasions, to three different student groups, at a university in the United Kingdom. In these trials, students from geography, Earth, and environmental science (GEES) programs worked in small (5 to 6 people), multiple-discipline teams to explore a single research question focused on a global sustainability issue. The perceptions and experiences of the trial participants (students and faculty) were investigated using data from surveys and interviews, and the findings applied to designing a new, multiple-disciplinary module focused on energy and climate change. In general, all participants engaged positively with the PjBL approach, although issues around the nature and extent of support available to the students and appropriate methods of assessing PjBL outputs emerged as requiring further consideration. The findings demonstrate that a single research question need not constrain the approach students take when completing a PjBL activity and identify clear potential benefits in terms of developing students’ wider professional skills. This study also highlights the value to curriculum developers in trialing new pedagogic approaches, as the opportunity to “have a go” enabled potential issues for learners and instructors to be identified and mitigated prior to the final module design and implementation.
DOI: 10.6084/m9.figshare.7265636
title: Health Science Librarianship and Health Informatics Offerings at Institutions 2015-2017

description: These datasets consist of health informatics education and health science librarianship offerings, based on public facing academic institution websites and online course catalogs. Data is organized by institution and includes: the course or degree offered, whether the library program at the instution is involved, and the URLs for the programs. Data is associated with the following paper: <i>Raszewski, R., Dwyer, J. and Griffin, T. Health Informatics Educational Offerings through ALA-accredited LIS Programs. JELIS; Vol 60; Issue 1; DOI: 10.3138/jelis.60.1.2018-0032</i><br>Data dictionary and code book are included.
DOI: 10.25377/sussex.7265624
title: Khalil Attallah, Abdullah Hamdan and Hanya Teyah discussing the Ottoman period and World War I

description: Khalil Attallah, Abdullah Hamdan and Hanya Teyah interviewed by Fared Yousef. <br>They discuss the following: Ottoman rule in Bethlehem during World War I; Palestinian economic situation couldn’t handle the war; Ottoman authorities stole from the people; trade and industry declined; when the Ottomans entered the war the situation worsened; spread of disease and the locust plague destroyed all the food; forced military conscription – Arabs who were recruited were treated badly and some ran away but those who were caught were killed; Ottomans used to cut down the trees to use as fuel for the trains – this worsened the starvation; when the locusts came people used to bury their food in a hole in the ground; when there was a lack of water diseases spread more quickly; drought of 1916 caused great unrest as people were demanding bread; people used to share their food with those who didn’t have enough to eat. <br>Original audio: 2 cassette tapes. Transcript: summary. In the original collection at Bethlehem University these cassette tapes were categorised as File 7a and 7b of Box 1. <br>This fileset exists as part of the Ottoman Empire and World War I collection within the Bethlehem University Oral History project of the Planet Bethlehem Archive.
DOI: 10.25377/sussex.7265627
title: Ahmad Quais discussing the Ottoman period and World War I

description: Ahmad Qnais interviewed by Fatimah Asad. <br>He discusses the following: World War I; Ottomans took men for military conscription and some people paid them not to take their sons; Ahmad’s father was able to pay for his two children to avoid conscription but not the third; the reason for the Ottoman Empire's involvement in the war was to betray the Arabs; relations between the Arabs and the Ottoman Empire (Turks) were bad – Ottomans only cared about taxes; starvation set in for the Arabs while the Turkish soldiers were fine; locusts destroyed the crops during the locust plague of 1915 and people burned them; people used to be kind and respectful to each other; when the British came they brought money and took the gold; relations between Arabs and Jews at that time were good, until Britain supported Zionism and confiscated the Arabs’ firearms, giving them to Jews instead. <br>Original audio: 2 cassette tapes. Transcript: summary. In the original collection at Bethlehem University these cassette tapes were categorised as File 8 of Box 1. <br>This fileset exists as part of the Ottoman Empire and World War I collection within the Bethlehem University Oral History project of the Planet Bethlehem Archive.
DOI: 10.7284/118738
title: Flowmeter data collected during research cruise SKQ201510S using a Krohne Optiflux 5000 instrument system onboard the platform RV Sikuliaq

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7265585
title: Forecast SB2: XXI AFORE BANORTE

description: The objective of this data is to show the AFORES classification SB2 and the yield of the investment in the SIEFORES to the prediction of contributions and yields in the period analyzed with a confidence level between 80 and 95%. The database obtained from https://figshare.com/articles/SIEFORES_BASIC_2_SB2_/7210022
DOI: 10.7284/118741
title: Fluorometer data collected during research cruise SKQ201510S using a Turner Cyclops-7 instrument system onboard the platform RV Sikuliaq

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/118742
title: GNSS (Global Navigation Satellite System) data collected during research cruise SKQ201510S using a C&C C-Nav 3050 instrument system onboard the platform RV Sikuliaq

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7265579
title: R. bonasus and L. erinacea embryo fin transcriptomes

description: Using bycatch of commercial fisheries, samples from embryos undergoing paired fin development were collected from a wild population of cownose rays (<i>Rhinoptera bonasus; Rbo</i>) in Chesapeake Bay. RNA extractions were made from various fin domains and sequenced on an Illumina HiSeq4000 and Illumina MiSeq. Adapters and low quality sequences from cownose ray data were trimmed from fastq files using the TrimGalore wrapper for Cutadapt and FastQC. Overlapping reads were combined with Flash prior to assembly and orphaned reads were retained. To reduce the impact of genetic variability, data from fin domains of only three individuals were used in the assembly, including: two regions of a stage one embryo (broad anterior pectoral fin region and mid-anterior pectoral fin), one region of a stage seven embryo (clasper) and eight regions of stage three embryos (cephalic lobe, anterior pectoral fin, mid-anterior pectoral fin, mid-pectoral fin, mid-posterior pectoral fin, posterior pectoral fin, zipper region, and pelvic fin). Sequencing with both HiSeq (stage 3 samples, 100bp PE reads) and MiSeq (stage 1 and stage 7 samples, 300 bp PE reads) was conducted to help generate full length transcripts. Abyss was used to assemble contiguous sequences (contigs) from the paired end (PE) and orphaned sequence data with 10 kmer sizes ranging from 25-70 nucleotides. Contigs of 500 nucleotides or greater were summarized according to similarity (e-value &lt; 1e-160) with BLAST+ tools. <br>Using iterative BLAST searches and pairwise alignments, contig sequences with strong e-values (&lt;1e-10) were annotated and used in the final transcriptome. Specifically, initial screening and annotation of contigs was conducted iteratively by best-reciprocal-blast using peptide, coding sequence, and non-coding libraries from Danio rerio (GRCz10) with BLAST+ tools and a minimum e-value threshold of 0.1. Each R. bonasus contig was paired with D. rerio sequences and the lowest average e-value was chosen as the annotation. Therefore, more than one R. bonasus contig could be designated with the same D. rerio sequence, allowing for potential redundancy in the de novo R. bonasus transcriptome assembly. The longest open reading frames (ORFs) that were unannotated to D. rerio sequences were annotated by BLASTp using the RefSeq vertebrate protein database (downloaded 4-4-2017). Remaining unannotated contigs were designated by their top forward BLAST hit in D. rerio. For consistency, the same process was used for the little skate (<i>Leucoraja erinacea; Ler</i>) using publicly available stage 31 <i>L. erinacea</i> 100bp PE RNA-seq data (SRA, PRJNA288370)<br>
DOI: 10.7284/118734
title: Gravimeter data collected during research cruise SKQ201510S using a Bell BGM-3 instrument system onboard the platform RV Sikuliaq

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7265579.v2
title: R. bonasus and L. erinacea embryo fin transcriptomes

description: Using bycatch of commercial fisheries, samples from embryos undergoing paired fin development were collected from a wild population of cownose rays (<i>Rhinoptera bonasus; Rbo</i>) in Chesapeake Bay. RNA extractions were made from various fin domains and sequenced on an Illumina HiSeq4000 and Illumina MiSeq. Adapters and low quality sequences from cownose ray data were trimmed from fastq files using the TrimGalore wrapper for Cutadapt and FastQC. Overlapping reads were combined with Flash prior to assembly and orphaned reads were retained. To reduce the impact of genetic variability, data from fin domains of only three individuals were used in the assembly, including: two regions of a stage one embryo (broad anterior pectoral fin region and mid-anterior pectoral fin), one region of a stage seven embryo (clasper) and eight regions of stage three embryos (cephalic lobe, anterior pectoral fin, mid-anterior pectoral fin, mid-pectoral fin, mid-posterior pectoral fin, posterior pectoral fin, zipper region, and pelvic fin). Sequencing with both HiSeq (stage 3 samples, 100bp PE reads) and MiSeq (stage 1 and stage 7 samples, 300 bp PE reads) was conducted to help generate full length transcripts. Abyss was used to assemble contiguous sequences (contigs) from the paired end (PE) and orphaned sequence data with 10 kmer sizes ranging from 25-70 nucleotides. Contigs of 500 nucleotides or greater were summarized according to similarity (e-value &lt; 1e-160) with BLAST+ tools. <br>Using iterative BLAST searches and pairwise alignments, contig sequences with strong e-values (&lt;1e-10) were annotated and used in the final transcriptome. Specifically, initial screening and annotation of contigs was conducted iteratively by best-reciprocal-blast using peptide, coding sequence, and non-coding libraries from Danio rerio (GRCz10) with BLAST+ tools and a minimum e-value threshold of 0.1. Each R. bonasus contig was paired with D. rerio sequences and the lowest average e-value was chosen as the annotation. Therefore, more than one R. bonasus contig could be designated with the same D. rerio sequence, allowing for potential redundancy in the de novo R. bonasus transcriptome assembly. The longest open reading frames (ORFs) that were unannotated to D. rerio sequences were annotated by BLASTp using the RefSeq vertebrate protein database (downloaded 4-4-2017). Remaining unannotated contigs were designated by their top forward BLAST hit in D. rerio. For consistency, the same process was used for the little skate (<i>Leucoraja erinacea; Ler</i>) using publicly available stage 31 <i>L. erinacea</i> 100bp PE RNA-seq data (SRA, PRJNA288370)<br>
DOI: 10.7284/118743
title: Gyrocompass data collected during research cruise SKQ201510S using a Sperry NAVIGAT 2100 instrument system onboard the platform RV Sikuliaq

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7265582.v1
title: Modelling cost-effectiveness of tenofovir for prevention of mother to child transmission of hepatitis B virus infection in South Africa

description: We developed a decision-analytic model that assessed the cost-effectiveness of three possible HBV PMTCT approaches in pregnancy; <b>S1</b>: no PMTCT intervention; <b>S2:</b>screening and antiviral prophylaxis for all women who test HBsAg-positive; <b>S3</b>: screening of all women for HBsAg, followed by HBeAg testing and antiviral prophylaxis for women who are HBsAg-positive and HBeAg-positive. We compared use of standard laboratory assays with a point of care test for HBsAg. Our outcome was cost per HBV infection avoided and the analysis followed a healthcare perspective.We populated our model with data from South Africa.
DOI: 10.6084/m9.figshare.7265579.v1
title: Ler_transcriptome.fa

description: Using bycatch of commercial fisheries, samples from embryos undergoing paired fin development were collected from a wild population of cownose rays (<i>Rhinoptera bonasus; Rbo</i>) in Chesapeake Bay. RNA extractions were made from various fin domains and sequenced on an Illumina HiSeq4000 and Illumina MiSeq. Adapters and low quality sequences from cownose ray data were trimmed from fastq files using the TrimGalore wrapper for Cutadapt and FastQC. Overlapping reads were combined with Flash prior to assembly and orphaned reads were retained. To reduce the impact of genetic variability, data from fin domains of only three individuals were used in the assembly, including: two regions of a stage one embryo (broad anterior pectoral fin region and mid-anterior pectoral fin), one region of a stage seven embryo (clasper) and eight regions of stage three embryos (cephalic lobe, anterior pectoral fin, mid-anterior pectoral fin, mid-pectoral fin, mid-posterior pectoral fin, posterior pectoral fin, zipper region, and pelvic fin). Sequencing with both HiSeq (stage 3 samples, 100bp PE reads) and MiSeq (stage 1 and stage 7 samples, 300 bp PE reads) was conducted to help generate full length transcripts. Abyss was used to assemble contiguous sequences (contigs) from the paired end (PE) and orphaned sequence data with 10 kmer sizes ranging from 25-70 nucleotides. Contigs of 500 nucleotides or greater were summarized according to similarity (e-value &lt; 1e-160) with BLAST+ tools. <br>Using iterative BLAST searches and pairwise alignments, contig sequences with strong e-values (&lt;1e-10) were annotated and used in the final transcriptome. Specifically, initial screening and annotation of contigs was conducted iteratively by best-reciprocal-blast using peptide, coding sequence, and non-coding libraries from Danio rerio (GRCz10) with BLAST+ tools and a minimum e-value threshold of 0.1. Each R. bonasus contig was paired with D. rerio sequences and the lowest average e-value was chosen as the annotation. Therefore, more than one R. bonasus contig could be designated with the same D. rerio sequence, allowing for potential redundancy in the de novo R. bonasus transcriptome assembly. The longest open reading frames (ORFs) that were unannotated to D. rerio sequences were annotated by BLASTp using the RefSeq vertebrate protein database (downloaded 4-4-2017). Remaining unannotated contigs were designated by their top forward BLAST hit in D. rerio. For consistency, the same process was used for the little skate (<i>Leucoraja erinacea; Ler</i>) using publicly available stage 31 <i>L. erinacea</i> 100bp PE RNA-seq data (SRA, PRJNA288370)<br>
DOI: 10.7284/118744
title: Gyrocompass data collected during research cruise SKQ201510S using a Sperry NAVIGAT 2100 instrument system onboard the platform RV Sikuliaq

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7265564
title: Bridging the gaps: using an NHP model to predict single dose radiation absorption in humans

description: <b>Purpose:</b> Design and characterization of a radiation biodosimetry device are complicated by the fact that the requisite data are not available in the intended use population, namely humans exposed to a single, whole-body radiation dose. Instead, one must turn to model systems. We discuss our studies utilizing healthy, unexposed humans, human bone marrow transplant patients undergoing total body irradiation (TBI), non-human primates subjected to the same irradiation regimen received by the human TBI patients and NHPs given a single, whole-body dose of ionizing radiation. <b>Materials and Methods:</b> We use Bayesian linear mixed models to characterize the association between NHP and human expression patterns in radiation response genes when exposed to a common exposure regimen and across exposure regimens within the same species. <b>Results:</b> We show that population average differences in expression of our radiation response genes from one to another model system are comparable to typical differences between two randomly sampled members of a given model system and that these differences are smaller, on average, for linear combinations of the probe data and for the model-based combinations employed for dose prediction as part of a radiation biodosimetry device. <b>Conclusions:</b> Our analysis suggests that dose estimates based on our gene list will be accurate when applied to humans who have received a single, whole-body exposure to ionizing radiation.
DOI: 10.7284/118735
title: INS (Inertial Navigation System) data collected during research cruise SKQ201510S using a Kongsberg Seapath 320+ instrument system onboard the platform RV Sikuliaq

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7265564.v1
title: Bridging the gaps: using an NHP model to predict single dose radiation absorption in humans

description: <b>Purpose:</b> Design and characterization of a radiation biodosimetry device are complicated by the fact that the requisite data are not available in the intended use population, namely humans exposed to a single, whole-body radiation dose. Instead, one must turn to model systems. We discuss our studies utilizing healthy, unexposed humans, human bone marrow transplant patients undergoing total body irradiation (TBI), non-human primates subjected to the same irradiation regimen received by the human TBI patients and NHPs given a single, whole-body dose of ionizing radiation. <b>Materials and Methods:</b> We use Bayesian linear mixed models to characterize the association between NHP and human expression patterns in radiation response genes when exposed to a common exposure regimen and across exposure regimens within the same species. <b>Results:</b> We show that population average differences in expression of our radiation response genes from one to another model system are comparable to typical differences between two randomly sampled members of a given model system and that these differences are smaller, on average, for linear combinations of the probe data and for the model-based combinations employed for dose prediction as part of a radiation biodosimetry device. <b>Conclusions:</b> Our analysis suggests that dose estimates based on our gene list will be accurate when applied to humans who have received a single, whole-body exposure to ionizing radiation.
DOI: 10.7284/118745
title: Meteorological Station data collected during research cruise SKQ201510S using a Vaisala WXT520 instrument system onboard the platform RV Sikuliaq

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/118731
title: Multibeam Echosounder data collected during research cruise SKQ201510S using a Kongsberg EM302 instrument system onboard the platform RV Sikuliaq

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/118732
title: Multibeam Echosounder data collected during research cruise SKQ201510S using a Kongsberg EM710 instrument system onboard the platform RV Sikuliaq

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/118746
title: Radiometer data collected during research cruise SKQ201510S using a RMR Co. PRP instrument system onboard the platform RV Sikuliaq

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/118747
title: Radiometer data collected during research cruise SKQ201510S using a Biospherical QSR-2150 instrument system onboard the platform RV Sikuliaq

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/118736
title: Rain Gauge data collected during research cruise SKQ201510S using a OSI ORG-815 instrument system onboard the platform RV Sikuliaq

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7265462
title: Additional file 6: of Tracking key virulence loci encoding aerobactin and salmochelin siderophore synthesis in Klebsiella pneumoniae

description: Representative Enterobacterales genome sequences included in iro and iuc phylogenetic analysis. (CSV 6 kb)
DOI: 10.7284/118739
title: Rain Gauge data collected during research cruise SKQ201510S using a RM Young 50202 instrument system onboard the platform RV Sikuliaq

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7265462.v1
title: Additional file 6: of Tracking key virulence loci encoding aerobactin and salmochelin siderophore synthesis in Klebsiella pneumoniae

description: Representative Enterobacterales genome sequences included in iro and iuc phylogenetic analysis. (CSV 6 kb)
DOI: 10.6084/m9.figshare.7265459
title: Additional file 5: of Tracking key virulence loci encoding aerobactin and salmochelin siderophore synthesis in Klebsiella pneumoniae

description: Salmochelin sequence types (SmSTs) and corresponding alleles. (TXT 1 kb)