cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8247464
title: The results of KEGG annotation

description: The results of KEGG annotation
DOI: 10.6084/m9.figshare.8247470
title: The results of alternative splicing model

description: skipped exon
DOI: 10.6084/m9.figshare.8247476.v1
title: The results of alternative splicing model

description: retained intron
DOI: 10.6084/m9.figshare.8247461
title: The results of KOG annotation

description: The results of KOG annotation
DOI: 10.6084/m9.figshare.8247473.v1
title: The results of alternative splicing model

description: The isoforms of transcripts with alternative splicing
DOI: 10.6084/m9.figshare.8247458
title: The results of NR annotation

description: The results of NR annotation
DOI: 10.6084/m9.figshare.8247464.v1
title: The results of KEGG annotation

description: The results of KEGG annotation
DOI: 10.6084/m9.figshare.8247470.v1
title: The results of alternative splicing model

description: skipped exon
DOI: 10.6084/m9.figshare.8247455
title: The results of NT annotation

description: The results of NT annotation
DOI: 10.6084/m9.figshare.8247461.v1
title: The results of KOG annotation

description: The results of KOG annotation
DOI: 10.6084/m9.figshare.8247452
title: The results of pfam annotation

description: The results of pfam annotation
DOI: 10.6084/m9.figshare.8247458.v1
title: The results of NR annotation

description: The results of NR annotation
DOI: 10.6084/m9.figshare.8247452.v1
title: The results of pfam annotation

description: The results of pfam annotation
DOI: 10.6084/m9.figshare.8247455.v1
title: The results of NT annotation

description: The results of NT annotation
DOI: 10.6084/m9.figshare.8247431
title: DNA methylation, colon cancer and Mediterranean diet: results from the EPIC-Italy cohort

description: The biological mechanisms through which adherence to Mediterranean Diet (MD) protects against colon cancer (CC) are poorly understood. Evidence suggests that chronic inflammation may be implicated in the pathway. Both diet and CC are related to epigenetic regulation. We performed a nested case-control study on 161 pairs from the Italian component of the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort, in which we looked for the methylation signals in DNA extracted from leucocytes associated with both CC and MD in 995 CpGs located in 48 inflammation genes. The DNA methylation signals detected in this analysis were validated in a subgroup of 47 case-control pairs and further replicated (where validated) in 95 new pairs by means of pyrosequencing. Among the CpG sites selected <i>a-priori</i> in inflammation-related genes, seven CpG sites were found to be associated with CC status and with MD, in line with its protective effect. Only two CpG sites (cg17968347-<i>SERPINE1</i> and cg20674490-<i>RUNX3</i>) were validated using bisulphite pyrosequencing and, after replication, we found that DNA methylation of cg20674490-<i>RUNX3</i> may be a potential molecular mediator explaining the protective effect of MD on CC onset. The use of a ‘meet-in-the-middle’ approach to identify the overlap between exposure and predictive markers of disease is innovative in studies on the relationship between diet and cancer, in which exposure assessment is difficult and the mechanisms through which the nutrients exert their protective effect is largely unknown.
DOI: 10.6084/m9.figshare.8247425
title: Additional file: of Application of Work Study to process improvement: Fruit nectar case.

description: Table 6. Observed time for stopwatch time study.
DOI: 10.6084/m9.figshare.8247431.v2
title: DNA methylation, colon cancer and Mediterranean diet: results from the EPIC-Italy cohort

description: The biological mechanisms through which adherence to Mediterranean Diet (MD) protects against colon cancer (CC) are poorly understood. Evidence suggests that chronic inflammation may be implicated in the pathway. Both diet and CC are related to epigenetic regulation. We performed a nested case-control study on 161 pairs from the Italian component of the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort, in which we looked for the methylation signals in DNA extracted from leucocytes associated with both CC and MD in 995 CpGs located in 48 inflammation genes. The DNA methylation signals detected in this analysis were validated in a subgroup of 47 case-control pairs and further replicated (where validated) in 95 new pairs by means of pyrosequencing. Among the CpG sites selected <i>a-priori</i> in inflammation-related genes, seven CpG sites were found to be associated with CC status and with MD, in line with its protective effect. Only two CpG sites (cg17968347-<i>SERPINE1</i> and cg20674490-<i>RUNX3</i>) were validated using bisulphite pyrosequencing and, after replication, we found that DNA methylation of cg20674490-<i>RUNX3</i> may be a potential molecular mediator explaining the protective effect of MD on CC onset. The use of a ‘meet-in-the-middle’ approach to identify the overlap between exposure and predictive markers of disease is innovative in studies on the relationship between diet and cancer, in which exposure assessment is difficult and the mechanisms through which the nutrients exert their protective effect is largely unknown.
DOI: 10.6084/m9.figshare.8247431.v1
title: DNA methylation, colon cancer and Mediterranean Diet: results from the EPIC-Italy cohort

description: The biological mechanisms through which adherence to Mediterranean Diet (MD) protects against colon cancer (CC) are poorly understood. Evidence suggests that chronic inflammation may be implicated in the pathway. Both diet and CC are related to epigenetic regulation. We performed a nested case control study on 161 pairs from the Italian component of the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort, in which we looked for the methylation signals in DNA extracted from leucocytes associated with both CC and MD in 995 CpGs located in 48 inflammation genes. The DNA methylation signals detected in this analysis were validated in a subgroup of 47 case-control pairs and further replicated (where validated) in 95 new pairs by means of pyrosequencing. Among the CpG sites selected <i>a-priori</i> in inflammation-related genes, 7 CpG sites were found to be associated with CC status and with MD, in line with its protective effect. Only two CpG sites (cg17968347-<i>SERPINE1</i> and cg20674490-<i>RUNX3</i>) were validated using bisulphite pyrosequencing and, after replication, we found that DNA methylation of cg20674490-<i>RUNX3</i> may be a potential molecular mediator explaining the protective effect of MD on CC onset. The use of a “meet-in-the-middle” approach to identify the overlap between exposure and predictive markers of disease is innovative in studies on the relationship between diet and cancer, in which exposure assessment is difficult and the mechanisms through which the nutrients exert their protective effect is largely unknown.
DOI: 10.6084/m9.figshare.8247425.v2
title: Additional file: of Application of Work Study to process improvement: Fruit nectar case.

description: Table 6. Observed time for stopwatch time study.
DOI: 10.6084/m9.figshare.8247425.v1
title: Additional file: of Application of Work Study to process improvement: Fruit nectar case.

description: Figure 6. Observed time for stopwatch time study.
DOI: 10.6084/m9.figshare.8247353
title: SHRIMP U-Pb zircon geochronology and Hf isotope analyses of Middle Permian–early triassic intrusions in southern Manzhouli area, Northeast China: implications for the subduction of Mongol-Okhotsk plate beneath the Erguna massif

description: The results of SHRIMP U-Pb ages and <i>in situ</i> Hf isotope of zircons from three granites in the southern Manzhouli region of northeast China, provide new data to understand the subduction process of Mongol-Okhotsk Plate beneath the Erguna massif. SHRIMP U-Pb zircon geochronology results yield an age of 265.5 Ma (middle Permian) for fine-grained monzogranite. Rocks from the Early–Middle Triassic are mainly granodiorite (247.4 ± 4.6 and 249.3 ± 4.9 Ma), the granites are with SiO<sub>2</sub> = 60.0–77.4 wt.%, Al<sub>2</sub>O<sub>3</sub> = 12.3–16.8wt.% and Na<sub>2</sub>O/K<sub>2</sub>O = 0.7–1.9. Chemically, they are metaluminous to peraluminous and belong to the high-K calc-alkaline series. Enrichments in the large ion lithophile elements (e.g., Rb, Ba, and K) and depletions in the high field strength elements (e.g., Nb, Ta, and Ti) are typical for these rock types. The monzogranite (~265 Ma) and granodiorite (~247 Ma) contain zircons with εHf(t) values of 6.3–8.5 and 5.1–7.9, yielding T<sub>DM2</sub> model ages of 888–752 and 958–774 Ma, respectively. These geochemical and zircon Hf isotopic data indicate that primary magmas for Middle Permian–Early Triassic granites crystallized from primary magmas generated by Neoproterozoic crustal materials, formed in an active continental margin setting. The andesite of the Gegenaobao formation is similar with the Izu–Bonin–Mariana arc, relating to subduction initiation. Based on the characteristics of exposed rocks and zircon U-Pb ages of andesite and granitoid rocks in the study area, we conclude the onset subduction of Mongol-Okhotsk Plate beneath the Erguna massif may occur at early-middle Permian.
DOI: 10.6084/m9.figshare.8247293
title: CRISPR-Cas9 spacer sequence for targeting ldhA gene in Escherichia coli K-12 MG1655

description: First evolved as a bacterial adaptive immune system, CRISPR-Cas9 has been co-opted to aid genetic engineering of cells. Specifically, CRISPR-Cas9’s endonuclease capability was utilized to generate precise double strand break in DNA, that could be repaired by a repair sequence (e.g., a replacement gene) through homologous recombination. To use CRISPR-Cas9 genome editing capabilities, a guide RNA (gRNA) is needed to guide the Cas9 endonuclease to the specific location in the genome where a change is to be made. Design of the guide RNA sequence requires knowledge of the 20 nucleotide spacer sequence immediately adjacent to the protospacer adjacent motif (PAM) sequence that anchors Cas9 to the DNA strand. Using an in-house MATLAB algorithm that automatically scan the gene of interest for PAM sequence and outputs a list of spacer sequence immediately adjacent to each PAM sequence, a database of CRISPR-Cas9 spacer sequence for the <i>ldhA</i> gene in <i>Escherichia coli</i> K-12 MG1655 was created. Such spacer sequences could be used to target <i>ldhA</i> for genome editing by CRISPR-Cas9. Collectively, using an in-house MATLAB software, a database of spacer sequences that could be used to target <i>ldhA</i> gene of <i>E. coli </i>K-12 MG1655 by CRISPR-Cas9 was created, and could find use in synthetic biology or metabolic engineering studies seeking to either knockdown or knockout the function of <i>ldhA </i>gene that controls the production of lactate during anaerobic metabolism.<br>
DOI: 10.6084/m9.figshare.8247293.v1
title: CRISPR-Cas9 spacer sequence for targeting ldhA gene in Escherichia coli K-12 MG1655

description: First evolved as a bacterial adaptive immune system, CRISPR-Cas9 has been co-opted to aid genetic engineering of cells. Specifically, CRISPR-Cas9’s endonuclease capability was utilized to generate precise double strand break in DNA, that could be repaired by a repair sequence (e.g., a replacement gene) through homologous recombination. To use CRISPR-Cas9 genome editing capabilities, a guide RNA (gRNA) is needed to guide the Cas9 endonuclease to the specific location in the genome where a change is to be made. Design of the guide RNA sequence requires knowledge of the 20 nucleotide spacer sequence immediately adjacent to the protospacer adjacent motif (PAM) sequence that anchors Cas9 to the DNA strand. Using an in-house MATLAB algorithm that automatically scan the gene of interest for PAM sequence and outputs a list of spacer sequence immediately adjacent to each PAM sequence, a database of CRISPR-Cas9 spacer sequence for the <i>ldhA</i> gene in <i>Escherichia coli</i> K-12 MG1655 was created. Such spacer sequences could be used to target <i>ldhA</i> for genome editing by CRISPR-Cas9. Collectively, using an in-house MATLAB software, a database of spacer sequences that could be used to target <i>ldhA</i> gene of <i>E. coli </i>K-12 MG1655 by CRISPR-Cas9 was created, and could find use in synthetic biology or metabolic engineering studies seeking to either knockdown or knockout the function of <i>ldhA </i>gene that controls the production of lactate during anaerobic metabolism.<br>
DOI: 10.6084/m9.figshare.8247215
title: supplemental data for 10% fructose water

description: <b>Supplemental Table 1. Body weight, diet, drink and urine volume in groups subjected with or without 10% fructose water in the WKY rats.</b><b><br></b><b>Supplemental Table 2. Triglycerides, HDL, LDL and total cholesterol levels in the serum in fructose-fed rats.</b><br><br>
DOI: 10.6084/m9.figshare.8247200
title: Test Case Files for Paper "Numerical Modeling of the Saint-Venant Equations: Effects and Adaptions for Bottom Slope Discontinuity"

description: Test cases for paper "Numerical Modeling of the Saint-Venant Equations: Effects and Adaptions for Bottom Slope Discontinuity", submitted to Water Resources Research
DOI: 10.6084/m9.figshare.8247215.v1
title: supplemental data for 10% fructose water

description: <b>Supplemental Table 1. Body weight, diet, drink and urine volume in groups subjected with or without 10% fructose water in the WKY rats.</b><b><br></b><b>Supplemental Table 2. Triglycerides, HDL, LDL and total cholesterol levels in the serum in fructose-fed rats.</b><br><br>
DOI: 10.6084/m9.figshare.8247200.v2
title: Test Case Files for Paper "Numerical Modeling of the Saint-Venant Equations: Effects and Adaptions for Bottom Slope Discontinuity"

description: Test cases for paper "Numerical Modeling of the Saint-Venant Equations: Effects and Adaptions for Bottom Slope Discontinuity", submitted to Water Resources Research
DOI: 10.6084/m9.figshare.8247200.v1
title: Test Case Files for Paper "Numerical Modeling of the Saint-Venant Equations: Effects and Adaptions for Bottom Slope Discontinuity"

description: Test cases for paper "Numerical Modeling of the Saint-Venant Equations: Effects and Adaptions for Bottom Slope Discontinuity", submitted to Water Resources Research
DOI: 10.15131/shef.data.8247131
title: UK (LSE) (Makerspaces in the Early Years)

description: The project focused on visits to three museums in Silicon Valley, USA in 2017.Field site A was a museum makerspace located in Marin, at the northern end of the San Francisco Bay. Many parents had high economic and cultural capital. The age range for children at this makerspace was three-to-ten. Field site B was a makerspace located in San Jose, a mixed ethnicity city, at the Southern end of Silicon Valley. While there was a wide range, the target age for this makerspace was six-to-nine-year olds. Field site C was a makerspace located across the bay from San Francisco in Berkeley, California. Although there was a range the target range for visitors were children aged four or five.Each museum makerspace was visited three to five times, for several hours per visit.Interviews were conducted with facilitators and families at each makerspace.Interviews were completed during each visit first with senior museum staff followed by families that agreed to speak with once given an information sheet and consent form.
DOI: 10.15131/shef.data.8247110
title: Norway (Makerspaces in the Early Years)

description: The project in Norway was undertaken with a museum and a kindergarten.Participants included (a) a team of researchers, including five educational researchers with different experience and focus but sharing a concern with the design andunderstanding of technology-enhanced spaces for learning; (b) a team of three museum curators and educators who have a specific responsibility for developing science enquiry experiences for young children in the science museum; (c) and four kindergarten educators from a kindergarten in the Oslo area, along with a group of twenty kindergarten children between 5 and 6 years old. The participatory designprocess involved design meetings, as well as observations in the science museum and the kindergarten. In addition, interviews were conducted with museum and kindergarten educators during the process. The workshops were recorded using traditional zoom-lens cameras, as well as wide-angle action cameras, to ensure adequately capturing embodied interaction in both the design and the designed spaces. The team started by observing an existing activity in the museum. Then, they arranged a design meeting with museum staff where the goal was to design a makingactivity. After that, children were observed involved in arts-based activities in the kindergarten and engaging in a new making activity in the museum. Three exploratory design meetings with partners in the project were also held as part of the research study.
DOI: 10.15131/shef.data.8247119
title: Romania (Makerspaces in the Early Years)

description: The Romanian projects took place in three different schools in Bucharest. The schools served diverse socioeconomic communities. At least six workshops were offered at each school to 10 children. The design of the workshops included many layers of simultaneous activities on the principle of modularity. Each session lasted for 2–3 hours, during which children were able to engage in maker activities, includingcoding. The data collected were field notes and video data, both video data collected by adults, and Go-Pro cameras worn by children.
DOI: 10.15131/shef.data.8247119.v2
title: Romania (Makerspaces in the Early Years)

description: The Romanian projects took place in three different schools in Bucharest. The schools served diverse socioeconomic communities. At least six workshops were offered at each school to 10 children. The design of the workshops included many layers of simultaneous activities on the principle of modularity. Each session lasted for 2–3 hours, during which children were able to engage in maker activities, includingcoding. The data collected were field notes and video data, both video data collected by adults, and Go-Pro cameras worn by children.
DOI: 10.15131/shef.data.8247131.v2
title: UK (LSE) (Makerspaces in the Early Years)

description: The project focused on visits to three museums in Silicon Valley, USA in 2017.Field site A was a museum makerspace located in Marin, at the northern end of the San Francisco Bay. Many parents had high economic and cultural capital. The age range for children at this makerspace was three-to-ten. Field site B was a makerspace located in San Jose, a mixed ethnicity city, at the Southern end of Silicon Valley. While there was a wide range, the target age for this makerspace was six-to-nine-year olds. Field site C was a makerspace located across the bay from San Francisco in Berkeley, California. Although there was a range the target range for visitors were children aged four or five.Each museum makerspace was visited three to five times, for several hours per visit.Interviews were conducted with facilitators and families at each makerspace.Interviews were completed during each visit first with senior museum staff followed by families that agreed to speak with once given an information sheet and consent form.
DOI: 10.6084/m9.figshare.8247104
title: vHIT Normal Study data

description: The data sheet of publication 'The human vestibulo-ocular reflex and saccades: normal subjects and the effect of age' by Pogson, et al. (2019), doi: 10.1152/jn.00847.2018. <br><br>This data sheet follows 'tidy data' principles, with one column per variable and one row per observation, reading from left to right. <br>
DOI: 10.15131/shef.data.8247110.v2
title: Norway (Makerspaces in the Early Years)

description: The project in Norway was undertaken with a museum and a kindergarten.Participants included (a) a team of researchers, including five educational researchers with different experience and focus but sharing a concern with the design andunderstanding of technology-enhanced spaces for learning; (b) a team of three museum curators and educators who have a specific responsibility for developing science enquiry experiences for young children in the science museum; (c) and four kindergarten educators from a kindergarten in the Oslo area, along with a group of twenty kindergarten children between 5 and 6 years old. The participatory designprocess involved design meetings, as well as observations in the science museum and the kindergarten. In addition, interviews were conducted with museum and kindergarten educators during the process. The workshops were recorded using traditional zoom-lens cameras, as well as wide-angle action cameras, to ensure adequately capturing embodied interaction in both the design and the designed spaces. The team started by observing an existing activity in the museum. Then, they arranged a design meeting with museum staff where the goal was to design a makingactivity. After that, children were observed involved in arts-based activities in the kindergarten and engaging in a new making activity in the museum. Three exploratory design meetings with partners in the project were also held as part of the research study.
DOI: 10.15131/shef.data.8247119.v1
title: Romania

description: The Romanian projects took place in three different schools in Bucharest. The schools served diverse socioeconomic communities. At least six workshops were offered at each school to 10 children. The design of the workshops included many layers of simultaneous activities on the principle of modularity. Each session lasted for 2–3 hours, during which children were able to engage in maker activities, includingcoding. The data collected were field notes and video data, both video data collected by adults, and Go-Pro cameras worn by children.
DOI: 10.15131/shef.data.8247131.v1
title: UK (LSE)

description: The project focused on visits to three museums in Silicon Valley, USA in 2017.Field site A was a museum makerspace located in Marin, at the northern end of the San Francisco Bay. Many parents had high economic and cultural capital. The age range for children at this makerspace was three-to-ten. Field site B was a makerspace located in San Jose, a mixed ethnicity city, at the Southern end of Silicon Valley. While there was a wide range, the target age for this makerspace was six-to-nine-year olds. Field site C was a makerspace located across the bay from San Francisco in Berkeley, California. Although there was a range the target range for visitors were children aged four or five.Each museum makerspace was visited three to five times, for several hours per visit.Interviews were conducted with facilitators and families at each makerspace.Interviews were completed during each visit first with senior museum staff followed by families that agreed to speak with once given an information sheet and consent form.