cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8872769
title: Identification of β-catenin target genes in colorectal cancer by interrogating gene fitness screening data

description: β-catenin tends to regulate its target genes, and the dysregulation of Wnt/b-catenin signaling facilitated hallmarks of colorectal cancer (CRC). Identification of β-catenin targets and their potential roles in tumorigenesis has gained increased interest. However, the number of identified targets remains limited. The present study implemented a novel strategy, interrogating gene fitness profiles derived from large-scale RNA interference and CRISPR-CRISPR associated protein 9 screening data to identify β-catenin target genes in CRC cell lines. Using these data sets, we computed pair wise gene fitness similarities, and highlighted a total of 13 genes whose functions were highly correlated with β-catenin. We further demonstrated their altered expressions in CRC, illustrating their potential roles in the progression of CRC. The present study further demonstrated that these targets could be used to predict disease-free survival in CRC. In conclusion, the findings provided novel approaches for the identification of β-catenin targets, which may become prognostic biomarkers or drug targets for the management of CRC.<br>
DOI: 10.6084/m9.figshare.8872787.v1
title: DLBCL of Waldeyer's ring_DATA_2019.6.24.sav

description: DATA_Patients with early stage DLBCL of Waldeyer's ring
DOI: 10.6084/m9.figshare.8872769.v1
title: Identification of β-catenin target genes in colorectal cancer by interrogating gene fitness screening data

description: β-catenin tends to regulate its target genes, and the dysregulation of Wnt/b-catenin signaling facilitated hallmarks of colorectal cancer (CRC). Identification of β-catenin targets and their potential roles in tumorigenesis has gained increased interest. However, the number of identified targets remains limited. The present study implemented a novel strategy, interrogating gene fitness profiles derived from large-scale RNA interference and CRISPR-CRISPR associated protein 9 screening data to identify β-catenin target genes in CRC cell lines. Using these data sets, we computed pair wise gene fitness similarities, and highlighted a total of 13 genes whose functions were highly correlated with β-catenin. We further demonstrated their altered expressions in CRC, illustrating their potential roles in the progression of CRC. The present study further demonstrated that these targets could be used to predict disease-free survival in CRC. In conclusion, the findings provided novel approaches for the identification of β-catenin targets, which may become prognostic biomarkers or drug targets for the management of CRC.<br>
DOI: 10.6084/m9.figshare.8872724
title: PM in Kunming

description: This data has been modified from the RAW data by: The PM10, PM2.5 and PM1 mass concentrations were measured using an environmental dust monitor (Grimm EDM 180-MC, GRIMM Aerosol Technik GmbH & Co. KG) at an interval of 5 min in Kunming.These converted datasets are combined and averaged over 1 hour, and then saved to this file. <br>
DOI: 10.6084/m9.figshare.8872724.v1
title: PM in Kunming

description: This data has been modified from the RAW data by: The PM10, PM2.5 and PM1 mass concentrations were measured using an environmental dust monitor (Grimm EDM 180-MC, GRIMM Aerosol Technik GmbH & Co. KG) at an interval of 5 min in Kunming.These converted datasets are combined and averaged over 1 hour, and then saved to this file. <br>
DOI: 10.6084/m9.figshare.8872718
title: Role of ROCK2 in diabetic kidney disease

description: Supplemental file
DOI: 10.6084/m9.figshare.8872718.v1
title: Role of ROCK2 in diabetic kidney disease

description: Supplemental file
DOI: 10.6084/m9.figshare.8872694
title: Diabetes Self-management and Social Cognitive Factors.dta

description: This is raw data from a cross secional study of 510 people living with diabetes attending the Queen Elizabeth Central Hospital diabetes clinic. Ethical approval for the study was granted by the College of Medicine Research and Ethics Committee (Ref: P.08/17/229). The data were collected between November 2017 and May 2018 using an interviewer administered questionnaire that solicited data on participants demographic and clinical clinical characteristics, five social cognitive theory factors (self-efficacy, outcome expectations, knowledge, social support and barriers to self-management) and self-management (diet, exercise, foot care, medication, self-monitoring of blood glucose and smoking). The data were entered into a Microsoft Access database ten exported into Stata version 14.0 for cleaning and analysis. <br>
DOI: 10.6084/m9.figshare.8872721.v1
title: Gff3 of Nyssa sinensis genome

description: Gff3 of Nyssa sinensis genome
DOI: 10.6084/m9.figshare.8872721.v2
title: The GFF3 file of the Nyssa sinensis genome

description: The GFF3 file of the Nyssa sinensis genome
DOI: 10.6084/m9.figshare.8872694.v2
title: Diabetes Self-management and Social Cognitive Factors.dta

description: This is raw data from a cross secional study of 510 people living with diabetes attending the Queen Elizabeth Central Hospital diabetes clinic. Ethical approval for the study was granted by the College of Medicine Research and Ethics Committee (Ref: P.08/17/229). The data were collected between November 2017 and May 2018 using an interviewer administered questionnaire that solicited data on participants demographic and clinical clinical characteristics, five social cognitive theory factors (self-efficacy, outcome expectations, knowledge, social support and barriers to self-management) and self-management (diet, exercise, foot care, medication, self-monitoring of blood glucose and smoking). The data were entered into a Microsoft Access database ten exported into Stata version 14.0 for cleaning and analysis. <br>
DOI: 10.6084/m9.figshare.8872694.v1
title: diabetes self-management and social cogtive factors.dta

description: This is raw data from a cross secional study of 510 people living with diabetes attending the Queen Elizabeth Central Hospital diabetes clinic. Ethical approval for the study was granted by the College of Medicine Research and Ethics Committee (Ref: P.08/17/229). The data were collected between November 2017 and May 2018 using an interviewer administered questionnaire that solicited data on participants demographic and clinical clinical characteristics, five social cognitive theory factors (self-efficacy, outcome expectations, knowledge, social support and barriers to self-management) and self-management (diet, exercise, foot care, medication, self-monitoring of blood glucose and smoking). The data were entered into a Microsoft Access database ten exported into Stata version 14.0 for cleaning and analysis. <br>
DOI: 10.6084/m9.figshare.8872700.v1
title: Chromosome-scale genome assembly of Nyssa sinensis

description: Chromosome-scale genome assembly of Nyssa sinensis
DOI: 10.6084/m9.figshare.8872721.v3
title: The GFF3 file of the Nyssa sinensis genome

description: The GFF3 file of the Nyssa sinensis genome
DOI: 10.6084/m9.figshare.8872700.v2
title: Chromosome-level assembly of the Nyssa sinensis genome

description: Chromosome-level assembly of the Nyssa sinensis genome
DOI: 10.6084/m9.figshare.8872721.v4
title: A chromosome-level genome assembly of the Chinese tupelo Nyssa sinensis

description: The GFF3 file of the Nyssa sinensis genome
DOI: 10.6084/m9.figshare.8872700.v3
title: A chromosome-level genome assembly of the Chinese tupelo Nyssa sinensis

description: Chromosome-level assembly of the Nyssa sinensis genome
DOI: 10.6084/m9.figshare.8872646
title: GitHub repo for Spencer et al. 2019, Oly carryover effects

description: GitHub repository for manuscript, <i>Carry-over effects of temperature and pCO<sub>2</sub> across multiple Olympia oyster populations.</i><i><br></i>To view in GitHub: https://github.com/RobertsLab/Paper-oly-adult-oa<i><br></i><b>Abstract</b><b><br></b>Impacts of adult exposure to elevated winter temperature and altered carbonate chemistry on reproduction and offspring viability were examined in the Olympia oyster (Ostrea lurida). Three distinct populations of adult, hatchery-reared O. lurida, plus an additional cohort spawned from one of the populations, were sequentially exposed to elevated temperature (+4°C, at 10°C), followed by elevated pCO2 (+2204 µatm, at 3045 µatm) during winter months. Male gametes were more developed after elevated temperature exposure and less developed after high pCO2 exposure, but there was no impact on female gametes or sex ratios. Oysters previously exposed to elevated winter temperature released larvae earlier, regardless of pCO2 exposure. Those exposed to elevated winter temperature as a sole treatment produced more larvae per day, but when oysters were also exposed to high pCO2 there was no effect. These combined results indicate that elevated winter temperature accelerates O. lurida spermatogenesis, resulting in earlier larval release and increased production, with elevated pCO2 exposure negating effects of elevated temperature. Offspring were reared in common conditions for one year, then deployed in four bays for three months. Offspring of parents exposed to elevated pCO2 had higher survival rates in two of the four bays, which had distinct environmental conditions. This carryover effect demonstrates that parental conditions can have substantial ecologically relevant impacts that should be considered when predicting impacts of environmental change. <br>
DOI: 10.6084/m9.figshare.8872598
title: Improving grain yield, stress-resilience, and quality of bread wheat using state-of-the-art genomics

description: CIMMYT wheat genotyping data<br>
DOI: 10.6084/m9.figshare.8872646.v1
title: GitHub repo for Spencer et al. 2019, Oly carryover effects

description: GitHub repository for manuscript, <i>Carry-over effects of temperature and pCO<sub>2</sub> across multiple Olympia oyster populations.</i>
DOI: 10.6084/m9.figshare.8872646.v2
title: GitHub repo for Spencer et al. 2019, Oly carryover effects

description: GitHub repository for manuscript, <i>Carry-over effects of temperature and pCO<sub>2</sub> across multiple Olympia oyster populations.</i>
DOI: 10.6084/m9.figshare.8872598.v2
title: Improving grain yield, stress-resilience, and quality of bread wheat using state-of-the-art genomics

description: CIMMYT wheat genotyping data<br>
DOI: 10.6084/m9.figshare.8872598.v1
title: Improving grain yield, stress-resilience, and quality of bread wheat using state-of-the-art genomics

description: CIMMYT wheat genotyping data<br>
DOI: 10.6084/m9.figshare.8872514
title: grid.11984.35

description: Network Graphs for institution grid.11984.35 created for "What Does a University Look Like?" poster
DOI: 10.6084/m9.figshare.8872463
title: grid.1035.7

description: Network Graph Files for grid.1035.7, for "What Does a University Look Like?" Project
DOI: 10.6084/m9.figshare.8872514.v1
title: grid.11984.35

description: Network Graphs for institution grid.11984.35 created for "What Does a University Look Like?" poster
DOI: 10.6084/m9.figshare.8872376
title: Input files for PCA, Structure and DAPC

description: Input files for PCA, Structure and DAPCData from: More than the eye can see: genomic insights into the drivers of genetic differentiation in Royal/Macaroni penguins across the Southern Ocean<br>
DOI: 10.6084/m9.figshare.8872361
title: 15 Ribosomal Protein Phylogenetic Tree

description: A phylogenetic tree of 484 representative genomes (at 98% ANI) using 15 ribosomal proteins.
DOI: 10.6084/m9.figshare.8872358
title: Vcf and population map of macaroni and royal penguins populations

description: Vcf and population map of macaroni and royal penguins populationsData from: More than the eye can see: genomic insights into the drivers of genetic differentiation in Royal/Macaroni penguins across the Southern Ocean<br>
DOI: 10.6084/m9.figshare.8872361.v1
title: 15 Ribosomal Protein Phylogenetic Tree

description: A phylogenetic tree of 484 representative genomes (at 98% ANI) using 15 ribosomal proteins.
DOI: 10.6084/m9.figshare.8872376.v1
title: Input file for Structure, PCA and DAPC

description: Input file for PCA, Structure and DAPC
DOI: 10.6084/m9.figshare.8872358.v1
title: Populaltion map and vcf file

description: Vcf and population map of macaroni and royal penguins populations
DOI: 10.6084/m9.figshare.8872376.v2
title: Data from: More than the eye can see: genomic insights into the drivers of genetic differentiation in Royal/Macaroni penguins across the Southern Ocean

description: Input file for PCA, Structure and DAPC
DOI: 10.6084/m9.figshare.8872358.v2
title: Data from: More than the eye can see: genomic insights into the drivers of genetic differentiation in Royal/Macaroni penguins across the Southern Ocean

description: Vcf and population map of macaroni and royal penguins populations
DOI: 10.6084/m9.figshare.8872253
title: Nascimento et al. Relative prolixity Dataset 1 CC0

description: The extent to which researchers follow the recommendation write introduction sections as short and informative as possible is unknown. Although it is evident that many authors do not follow this recommendation, the extent to which researchers follow it is unknown. Here, we investigated the degree of relative prolixity among 101 journals with different CiteScore™ classified in the ‘Pharmaceutical Science’ category. We recorded the number of characters (including spaces), paragraphs and citations in their introduction sections. Based on these data, relative prolixity was calculated as the ratio between the number of characters and the number of citations contained in the introductory section of original articles.
DOI: 10.6084/m9.figshare.8872229
title: get_dz.Rda

description: Loads R object containing info on phylogenetic specificity of parasites on definitive hosts (time saver to running raw code chunk)
DOI: 10.6084/m9.figshare.8872253.v1
title: Nascimento et al. Relative prolixity Dataset 1 CC0

description: The extent to which researchers follow the recommendation write introduction sections as short and informative as possible is unknown. Although it is evident that many authors do not follow this recommendation, the extent to which researchers follow it is unknown. Here, we investigated the degree of relative prolixity among 101 journals with different CiteScore™ classified in the ‘Pharmaceutical Science’ category. We recorded the number of characters (including spaces), paragraphs and citations in their introduction sections. Based on these data, relative prolixity was calculated as the ratio between the number of characters and the number of citations contained in the introductory section of original articles.
DOI: 10.6084/m9.figshare.8871956
title: get_fMpd.Rda

description: Loads R object containing info on definitive hosts phylogenetic diet specificity on intermediate hosts (time saver to running raw code chunk)
DOI: 10.6084/m9.figshare.8872229.v1
title: get_dz.Rda

description: Loads R object containing info on phylogenetic specificity of parasites on definitive hosts (time saver to running raw code chunk)
DOI: 10.6084/m9.figshare.8871956.v1
title: get_fMpd.Rda

description: Loads R object containing info on definitive hosts phylogenetic diet specificity on intermediate hosts (time saver to running raw code chunk)
DOI: 10.6084/m9.figshare.8870804
title: Coregonus clupeaformis 5'-COI DNA barcode sequences

description: 5'-COI DNA barcode multiple sequence alignment for lake whitefish (Coregonus clupeaformis) used in Phillips et. al (submitted)
DOI: 10.6084/m9.figshare.8870798
title: Mechanical properties of the shoulder and pectoralis major in women undergoing breast-conserving surgery with either axillary dissection and breast and regional nodal radiotherapy or sentinel node surgery and breast radiotherapy only - Full Dataset

description: Shoulder Stiffness Data:<br>Participant ID<br>Group <i>(1 =ALND + Breast/Nodal RT; 2 = SNB + Breast RT; 3 = Healthy Controls)</i>Activation<i>(0 = 0% MVC -e.g. at rest; 1 = -10% MVC; 2 = 10% MVC)</i>Direction<i>(0 = Vertical Plane; 1 = Horizontal Plane)</i>Shoulder Stiffness (Units: Nm/rad)<br>Muscle Stiffness and RT Data:Participant ID<br>Group <i>(1 =ALND + Breast/Nodal RT; 2 = SNB + Breast RT; 3 = Healthy Controls)</i>Activation<i>(0 = 0% MVC -e.g. at rest; 1 = 10% MVC in Vertical Direction; 2 = 10% MVC in Horizontal Direction)</i>PM_Muscle<i>(0 = Sternocostal Region of Pectoralis Major; 1 = Clavicular </i><i>Region of Pectoralis Major</i><i>)</i>Shear Wave Velocity (Units: m/s)Mean_RT_Dose (Units: Gy)V40_RT_Dose (Units: normalized to percentage)Note: There is no RT data for healthy controls as these participants did not undergo cancer treatment.<br><br>
DOI: 10.6084/m9.figshare.8870804.v1
title: Coregonus clupeaformis 5'-COI DNA barcode sequences

description: 5'-COI DNA barcode multiple sequence alignment for lake whitefish (Coregonus clupeaformis) used in Phillips et. al (submitted)
DOI: 10.6084/m9.figshare.8870798.v1
title: Mechanical properties of the shoulder and pectoralis major in women undergoing breast-conserving surgery with either axillary dissection and breast and regional nodal radiotherapy or sentinel node surgery and breast radiotherapy only - Full Dataset

description: Shoulder Stiffness Data:<br>Participant ID<br>Group <i>(1 =ALND + Breast/Nodal RT; 2 = SNB + Breast RT; 3 = Healthy Controls)</i>Activation<i>(0 = 0% MVC -e.g. at rest; 1 = -10% MVC; 2 = 10% MVC)</i>Direction<i>(0 = Vertical Plane; 1 = Horizontal Plane)</i>Shoulder Stiffness (Units: Nm/rad)<br>Muscle Stiffness and RT Data:Participant ID<br>Group <i>(1 =ALND + Breast/Nodal RT; 2 = SNB + Breast RT; 3 = Healthy Controls)</i>Activation<i>(0 = 0% MVC -e.g. at rest; 1 = 10% MVC in Vertical Direction; 2 = 10% MVC in Horizontal Direction)</i>PM_Muscle<i>(0 = Sternocostal Region of Pectoralis Major; 1 = Clavicular </i><i>Region of Pectoralis Major</i><i>)</i>Shear Wave Velocity (Units: m/s)Mean_RT_Dose (Units: Gy)V40_RT_Dose (Units: normalized to percentage)Note: There is no RT data for healthy controls as these participants did not undergo cancer treatment.<br><br>
DOI: 10.6084/m9.figshare.8870705
title: PLOS-ONE 2019 DATA.xlsx

description: The result of the online experiment evaluating the effectiveness of the proposed method of adaptive trust calibration.
DOI: 10.6084/m9.figshare.8870705.v1
title: PLOS-ONE 2019 DATA.xlsx

description: The result of the online experiment evaluating the effectiveness of the proposed method of adaptive trust calibration.
DOI: 10.6084/m9.figshare.8870600
title: Ready-to-use single tube quadruplex PCR for differential identification of mutton, chicken, pork and beef in processed meat samples

description: A reliable and sensitive identification method is required to tackle food adulteration mainly in meat production. We developed a dry reagent based ready-to-use single tube quadruplex PCR assay for accurate identification of chicken, mutton, beef and pork. The assay was found to be specific and reproducible. Thermo-stability studies of lyophilized PCR master mix were conducted at different temperature and time intervals, which revealed significant stability for 75 days at 4°C and for 60 days at 25°C. The developed assay was shown to be sensitive down to 16 pg DNA per reaction and the detection limit was found to be 0.01% (w/w) of each species. Furthermore, this method has been applied to the analysis of 68 commercial meat products and the results indicated that nine samples contained non-declared meat components. This dry reagent-based quadruplex PCR assay can be utilized to monitor various processed food products and also to maintain quality control in food industries mainly in the resource-limited settings.
DOI: 10.6084/m9.figshare.8870684
title: Physico-chemical stability of co-formulation of PEGylated human amylin with insulin

description: Since the discovery of amylin no combined formulation with insulin has been made available. Amylin or its triple proline analog pramlintide are not compatible in solution with insulin. The drug candidate hAmy-PEG5k is a novel monoPEGylated amylin derivative with improved physicochemical properties and retained similar pharmacological activity compared to free amylin and pramlintide. We have investigated the short- and long-term physicochemical compatibility of hAmy-PEG5k co-formulated with slow-acting human insulin analogs glargine or detemir. While human amylin promptly aggregates over a large range of pH, and both free and in the presence of regular, glargine or detemir insulin, the hAmy-PEG5k analog is stable at these conditions as shown by Thioflavin T (ThT) binding assay. When hAmy-PEG5k (100 or 500 µg/mL) was added to the commercial formulations of either insulin glargine or detemir (95 IU/mL), the combinations remained stable after 6 months stored at 4 °C, as probed by ThT, dynamic light scattering (DLS) measurements and high performance liquid chromatography (HPLC) analyses, confirming the absence of amyloid fibers, minor aggregation products or loss of material. These results suggest hAmy-PEG5k and the insulin analogs glargine and detemir are physicochemically compatible and are candidate ready-to-use fixed-dose combinations.
DOI: 10.6084/m9.figshare.8870600.v1
title: Ready-to-use single tube quadruplex PCR for differential identification of mutton, chicken, pork and beef in processed meat samples

description: A reliable and sensitive identification method is required to tackle food adulteration mainly in meat production. We developed a dry reagent based ready-to-use single tube quadruplex PCR assay for accurate identification of chicken, mutton, beef and pork. The assay was found to be specific and reproducible. Thermo-stability studies of lyophilized PCR master mix were conducted at different temperature and time intervals, which revealed significant stability for 75 days at 4°C and for 60 days at 25°C. The developed assay was shown to be sensitive down to 16 pg DNA per reaction and the detection limit was found to be 0.01% (w/w) of each species. Furthermore, this method has been applied to the analysis of 68 commercial meat products and the results indicated that nine samples contained non-declared meat components. This dry reagent-based quadruplex PCR assay can be utilized to monitor various processed food products and also to maintain quality control in food industries mainly in the resource-limited settings.
DOI: 10.6084/m9.figshare.8870684.v1
title: Physico-chemical stability of co-formulation of PEGylated human amylin with insulin

description: Since the discovery of amylin no combined formulation with insulin has been made available. Amylin or its triple proline analog pramlintide are not compatible in solution with insulin. The drug candidate hAmy-PEG5k is a novel monoPEGylated amylin derivative with improved physicochemical properties and retained similar pharmacological activity compared to free amylin and pramlintide. We have investigated the short- and long-term physicochemical compatibility of hAmy-PEG5k co-formulated with slow-acting human insulin analogs glargine or detemir. While human amylin promptly aggregates over a large range of pH, and both free and in the presence of regular, glargine or detemir insulin, the hAmy-PEG5k analog is stable at these conditions as shown by Thioflavin T (ThT) binding assay. When hAmy-PEG5k (100 or 500 µg/mL) was added to the commercial formulations of either insulin glargine or detemir (95 IU/mL), the combinations remained stable after 6 months stored at 4 °C, as probed by ThT, dynamic light scattering (DLS) measurements and high performance liquid chromatography (HPLC) analyses, confirming the absence of amyloid fibers, minor aggregation products or loss of material. These results suggest hAmy-PEG5k and the insulin analogs glargine and detemir are physicochemically compatible and are candidate ready-to-use fixed-dose combinations.