cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4028394
title: Kinetic characterization and fed-batch fermentation for maximal simultaneous production of esterase and protease from <i>Lysinibacillus fusiformis</i> AU01

description: The simultaneous production of intracellular esterase and extracellular protease from the strain <i>Lysinibacillus fusiformis</i> AU01 was studied in detail. The production was performed both under batch and fed-batch modes. The maximum yield of intracellular esterase and protease was obtained under full oxygen saturation at the beginning of the fermentation. The data were fitted to the Luedeking–Piret model and it was shown that the enzyme (both esterase and protease) production was growth associated. A decrease in intracellular esterase and increase in the extracellular esterase were observed during late stationary phase. The appearance of intracellular proteins in extracellular media and decrease in viable cell count and biomass during late stationary phase confirmed that the presence of extracellular esterase is due to cell lysis. Even though the fed-batch fermentation with different feeding strategies showed improved productivity, feeding yeast extract under DO-stat fermentation conditions showed highest intracellular esterase and protease production. Under DO-stat fed-batch cultivation, maximum intracellular esterase activity of 820 × 10<sup>3</sup> U/L and extracellular protease activity of 172 × 10<sup>3</sup> U/L were obtained at the 16th hr. Intracellular esterase and extracellular protease production were increased fivefold and fourfold, respectively, when compared to batch fermentation performed under shake flask conditions.
DOI: 10.7910/dvn/v1rjpf/yjdxyc
title: ykc20170612_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4028394.v2
title: Kinetic characterization and fed-batch fermentation for maximal simultaneous production of esterase and protease from <i>Lysinibacillus fusiformis</i> AU01

description: The simultaneous production of intracellular esterase and extracellular protease from the strain <i>Lysinibacillus fusiformis</i> AU01 was studied in detail. The production was performed both under batch and fed-batch modes. The maximum yield of intracellular esterase and protease was obtained under full oxygen saturation at the beginning of the fermentation. The data were fitted to the Luedeking–Piret model and it was shown that the enzyme (both esterase and protease) production was growth associated. A decrease in intracellular esterase and increase in the extracellular esterase were observed during late stationary phase. The appearance of intracellular proteins in extracellular media and decrease in viable cell count and biomass during late stationary phase confirmed that the presence of extracellular esterase is due to cell lysis. Even though the fed-batch fermentation with different feeding strategies showed improved productivity, feeding yeast extract under DO-stat fermentation conditions showed highest intracellular esterase and protease production. Under DO-stat fed-batch cultivation, maximum intracellular esterase activity of 820 × 10<sup>3</sup> U/L and extracellular protease activity of 172 × 10<sup>3</sup> U/L were obtained at the 16th hr. Intracellular esterase and extracellular protease production were increased fivefold and fourfold, respectively, when compared to batch fermentation performed under shake flask conditions.
DOI: 10.6084/m9.figshare.4028394.v1
title: Kinetic Characterisation and Fed-Batch Fermentation for Maximal Simultaneous Production of Esterase and Protease from <i>Lysinibacillus fusiformis</i> AU01

description: The simultaneous production of intracellular esterase and extracellular protease from the strain <i>Lysinibacillus fusiformis</i> AU01 was studied in detail. The production was carried out both under batch and fedbatch mode. The maximum yield of intracellular esterase and protease was obtained under full oxygen saturation at the beginning of the fermentation. The data was fitted to the Luedeking-Piret model and it was shown that the enzyme (both esterase and protease) production was growth-associated. A decrease in intracellular esterase and increase in the extracellular esterase was observed during late stationary phase. The appearance of intracellular proteins in extracellular media, decrease in viable cell count and decrease in biomass during late stationary phase confirmed that the presence of extracellular esterase is due to cell lysis. Even though the fed-batch fermentation with different feeding strategies showed improved productivity, feeding yeast extract under DO-stat fermentation conditions showed highest intracellular esterase and protease production. Under DO-stat fed-batch cultivation, maximum intracellular esterase activity of 820 × 10<sup>3</sup>U/L and extracellular protease activity of 172 × 10<sup>3</sup>U/L was obtained at the sixteenth hour. Intracellular esterase and extracellular protease production was increased fivefold and fourfold respectively when compared to batch fermentation carried out under shake flask conditions.
DOI: 10.7910/dvn/v1rjpf/rxbo96
title: ykc20170417_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/vamku3
title: ykc20171101_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/ktztyx
title: ykc20161106_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4028361
title: Strain Info and Background Data for EHB Microbial Genetics Manuscript

description: An Excel spreadsheet displaying strain information, KEGG pathway classification information, and Genome size information for our study on comparative genomics of endohyphal bacteria
DOI: 10.7910/dvn/v1rjpf/a83w5q
title: ykc20170130_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/oa9kap
title: ykc20161120_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4028361.v2
title: Strain Info and Background Data for EHB Microbial Genetics Manuscript

description: An Excel spreadsheet displaying strain information, KEGG pathway classification information, and Genome size information for our study on comparative genomics of endohyphal bacteria
DOI: 10.6084/m9.figshare.4028361.v1
title: Strain Info and Background Data for EHB Microbial Genetics Manuscript

description: An Excel spreadsheet displaying strain information, KEGG pathway classification information, and Genome size information for our study on comparative genomics of endohyphal bacteria
DOI: 10.6084/m9.figshare.4028346
title: YorkU.Forest.Oct05-2016 By Abegail, Antonella, Bethesda, and Natalia

description: Meta Data is in the word doc.
DOI: 10.7910/dvn/v1rjpf/4343s7
title: ykc20160120_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4028346.v1
title: YorkU.Forest.Oct05-2016 By Abegail, Antonella, Bethesda, and Natalia

description: Meta Data is in the word doc.
DOI: 10.7910/dvn/v1rjpf/dfwqvo
title: ykc20160926_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/zgh4wm
title: ykc20170425_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/sen64p
title: ykc20170905_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4028271
title: Stem cells migration during skeletal muscle regeneration - the role of Sdf-1/Cxcr4 and Sdf-1/Cxcr7 axis

description: The skeletal muscle regeneration occurs due to the presence of tissue specific stem cells - satellite cells. These cells, localized between sarcolemma and basal lamina, are bound to muscle fibers and remain quiescent until their activation upon muscle injury. Due to pathological conditions, such as extensive injury or dystrophy, skeletal muscle regeneration is diminished. Among the therapies aiming to ameliorate skeletal muscle diseases are transplantations of the stem cells. In our previous studies we showed that Sdf-1 (stromal derived factor −1) increased migration of stem cells and their fusion with myoblasts <i>in vitro</i>. Importantly, we identified that Sdf-1 caused an increase in the expression of tetraspanin CD9 - adhesion protein involved in myoblasts fusion. In the current study we aimed to uncover the details of molecular mechanism of Sdf-1 action. We focused at the Sdf-1 receptors - Cxcr4 and Cxcr7, as well as signaling pathways induced by these molecules in primary myoblasts, as well as various stem cells - mesenchymal stem cells and embryonic stem cells, i.e. the cells of different migration and myogenic potential. We showed that Sdf-1 altered actin organization <i>via</i> FAK (focal adhesion kinase), Cdc42 (cell division control protein 42), and Rac-1 (Ras-Related C3 Botulinum Toxin Substrate 1). Moreover, we showed that Sdf-1 modified the transcription profile of genes encoding factors engaged in cells adhesion and migration. As the result, cells such as primary myoblasts or embryonic stem cells, became characterized by more effective migration when transplanted into regenerating muscle.
DOI: 10.6084/m9.figshare.4028274
title: Computational methods for direct cell conversion

description: Directed cell conversion (or transdifferentiation) of one somatic cell-type to another can be achieved by ectopic expression of a set of transcription factors. Since the experimental identification of transcription factors for transdifferentiation is extremely time-consuming and expensive, there are still relatively few transdifferentiations achieved in comparison to the number of human cell-types. However, the growing volume of transcriptional data available and the recent introduction of data-driven algorithmic approaches that predict factors for transdifferentiation holds great promise for accelerating this field. Here we review those computational methods whose in-silico predictions have been experimentally validated, highlighting differences and similarities. Our analysis reveals that the factors predicted by each method tend to be different due to varying source cells used, gene expression quantification and algorithmic steps. We show these differences have an impact on the regulatory influences downstream, with some methods favoring transcription factors regulating developmental progression and others favoring factors regulating mature cell processes. These computational approaches offer a starting point to predict and test novel factors for transdifferentiation. We argue that collecting high-quality gene expression data from single-cells or pure cell-populations across a broader set of cell-types would be necessary to improve the quality and consistency of the in-silico predictions.
DOI: 10.6084/m9.figshare.4028271.v1
title: Stem cells migration during skeletal muscle regeneration - the role of Sdf-1/Cxcr4 and Sdf-1/Cxcr7 axis

description: The skeletal muscle regeneration occurs due to the presence of tissue specific stem cells - satellite cells. These cells, localized between sarcolemma and basal lamina, are bound to muscle fibers and remain quiescent until their activation upon muscle injury. Due to pathological conditions, such as extensive injury or dystrophy, skeletal muscle regeneration is diminished. Among the therapies aiming to ameliorate skeletal muscle diseases are transplantations of the stem cells. In our previous studies we showed that Sdf-1 (stromal derived factor −1) increased migration of stem cells and their fusion with myoblasts <i>in vitro</i>. Importantly, we identified that Sdf-1 caused an increase in the expression of tetraspanin CD9 - adhesion protein involved in myoblasts fusion. In the current study we aimed to uncover the details of molecular mechanism of Sdf-1 action. We focused at the Sdf-1 receptors - Cxcr4 and Cxcr7, as well as signaling pathways induced by these molecules in primary myoblasts, as well as various stem cells - mesenchymal stem cells and embryonic stem cells, i.e. the cells of different migration and myogenic potential. We showed that Sdf-1 altered actin organization <i>via</i> FAK (focal adhesion kinase), Cdc42 (cell division control protein 42), and Rac-1 (Ras-Related C3 Botulinum Toxin Substrate 1). Moreover, we showed that Sdf-1 modified the transcription profile of genes encoding factors engaged in cells adhesion and migration. As the result, cells such as primary myoblasts or embryonic stem cells, became characterized by more effective migration when transplanted into regenerating muscle.
DOI: 10.7910/dvn/v1rjpf/kpltwk
title: ykc20161201_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/k39m2q
title: ykc20161209_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4028226
title: Systematic literature review shows that appetite rating does not predict energy intake

description: Ratings of appetite are commonly used to assess appetite modification following an intervention. Subjectively rated appetite is a widely employed proxy measure for energy intake (EI), measurement of which requires greater time and resources. However, the validity of appetite as a reliable predictor of EI has not yet been reviewed systematically. This literature search identified studies that quantified both appetite ratings and EI. Outcomes were predefined as: (1) agreement between self-reported appetite scores and EI; (2) no agreement between self-reported appetitescores and EI. The presence of direct statistical comparison between the endpoints, intervention type and study population were also recorded. 462 papers were included in this review. Appetite scores failed to correspond with EI in 51.3% of the total studies. Only 6% of all studies evaluated here reported a direct statistical comparison between appetite scores and EI. χ<sup>2</sup> analysis demonstrated that any relationship between EI and appetite was independent of study type stratification by age, gender or sample size. The very substantive corpus reviewed allows us to conclude that self-reported appetite ratings of appetite do not reliably predict EI. Caution should be exercised when drawing conclusions based from self-reported appetite scores in relation to prospective EI.
DOI: 10.7910/dvn/v1rjpf/80oqkq
title: ykc20160313_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/m0z2uy
title: ykc20160318_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4028226.v2
title: Systematic literature review shows that appetite rating does not predict energy intake

description: Ratings of appetite are commonly used to assess appetite modification following an intervention. Subjectively rated appetite is a widely employed proxy measure for energy intake (EI), measurement of which requires greater time and resources. However, the validity of appetite as a reliable predictor of EI has not yet been reviewed systematically. This literature search identified studies that quantified both appetite ratings and EI. Outcomes were predefined as: (1) agreement between self-reported appetite scores and EI; (2) no agreement between self-reported appetitescores and EI. The presence of direct statistical comparison between the endpoints, intervention type and study population were also recorded. 462 papers were included in this review. Appetite scores failed to correspond with EI in 51.3% of the total studies. Only 6% of all studies evaluated here reported a direct statistical comparison between appetite scores and EI. χ<sup>2</sup> analysis demonstrated that any relationship between EI and appetite was independent of study type stratification by age, gender or sample size. The very substantive corpus reviewed allows us to conclude that self-reported appetite ratings of appetite do not reliably predict EI. Caution should be exercised when drawing conclusions based from self-reported appetite scores in relation to prospective EI.
DOI: 10.7910/dvn/v1rjpf/6qrans
title: ykc20170930_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4028226.v1
title: Systematic Literature Review Shows That Appetite Rating Does Not Predict Energy Intake

description: Ratings of appetite are commonly used to assess appetite modification following an intervention. Subjectively rated appetite is a widely employed proxy measure for energy intake (EI), measurement of which requires greater time and resources. However, the validity of appetite as a reliable predictor of EI has not yet been reviewed systematically. This literature search identified studies that quantified both appetite ratings and EI. Outcomes were pre-defined as: 1) agreement between self-reported appetite scores and EI; 2) no agreement between self-reported appetite scores and EI. The presence of direct statistical comparison between the endpoints, intervention type and study population were also recorded. 462 papers were included in this review. Appetite scores failed to correspond with EI in 51.3% of the total studies. Only 6% of all studies evaluated here reported a direct statistical comparison between appetite scores and EI. χ<sup>2</sup> analysis demonstrated that any relationship between EI and appetite was independent of study type stratification by age, gender or sample size. The very substantive corpus reviewed allows us to conclude that self-reported appetite ratings of appetite do not reliably predict EI. Caution should be exercised when drawing conclusions based from self-reported appetite scores in relation to prospective EI.
DOI: 10.6084/m9.figshare.4028208
title: Health-related quality of life 24 months after sustaining a minor musculoskeletal injury in a road traffic crash: A prospective cohort study

description: <b>Objectives</b>: A better understanding of the long-term factors that independently predict poorer quality of life following mild to moderate musculoskeletal injuries is needed. We aimed to establish the predictors of quality of life (including sociodemographic, health, psychosocial, and pre-injury factors) 24 months after a noncatastrophic road traffic injury. <b>Methods</b>: In a prospective cohort study of 252 participants with mild/moderate injury sustained in a road traffic crash, quality of life was measured 24 months following the baseline survey. A telephone-administered questionnaire obtained information on various potential explanatory variables. Health-related quality of life was measured using the European Quality of Life–5 Dimensions (EQ-5D) and Medical Outcomes Survey Short Form–12 (SF-12). Multivariable linear regression analyses determined the associations between explanatory variables and quality of life measures. <b>Results</b>: Mean SF-12 physical component summary (PCS) and mental component summary (MCS) scores increased by 7.3 and 2.5 units, respectively, from baseline to 24-month follow-up. Each 10-year increase in baseline age was independently associated with 3.1-unit (<i>P</i> &lt; .001) and 1.5-unit (<i>P</i> = .001) decrease in EQ Visual Analogue Scale (VAS) and SF-12 PCS scores at follow-up, respectively. Poor/fair compared to excellent pre-injury health was associated with a 0.16-, 21.3-, and 11.5-unit decrease in EQ-5D summary (<i>P</i> = .03), VAS scores (<i>P</i> = .001), and SF-12 PCS scores (<i>P</i> &lt; .001), respectively. Baseline pain severity ratings and pain catastrophizing scores were inversely associated with 24-month EQ VAS scores (both <i>P</i> &lt; .001). Each unit increase in baseline pain score (<i>P</i> = .001) and pain catastrophizing score (<i>P</i> = .02) was associated with a 1.0- and 4.6-unit decrease in SF-12 MCS scores at 24 months, respectively. Other observed predictors of quality of life measures (EQ-5D summary and/or VAS scores and/ or SF-12 MCS) included marital status, smoking, hospital admission, pre-injury health (anxiety/depression and chronic illness), and whiplash injury. <b>Conclusion</b>: Sociodemographic indicators, pre-injury health, and biopsychosocial correlates were independently associated with health-related quality of life 24 months following a noncatastrophic road traffic crash injury.
DOI: 10.7910/dvn/v1rjpf/fszjz1
title: ykc20171122_03.txt.gz

description: :unav
DOI: 10.5281/zenodo.4013737
title: KALIv2: calibration and validation experiment results

description: The presented .zip archive consists of calibration and validation results we obtained while investigating the effect of calibration data length on the performance of different hydrological models. For more information, please visit our GitHub repository at https://github.com/hydrogo/KALIv2.
DOI: 10.6084/m9.figshare.4028208.v2
title: Health-related quality of life 24 months after sustaining a minor musculoskeletal injury in a road traffic crash: A prospective cohort study

description: <b>Objectives</b>: A better understanding of the long-term factors that independently predict poorer quality of life following mild to moderate musculoskeletal injuries is needed. We aimed to establish the predictors of quality of life (including sociodemographic, health, psychosocial, and pre-injury factors) 24 months after a noncatastrophic road traffic injury. <b>Methods</b>: In a prospective cohort study of 252 participants with mild/moderate injury sustained in a road traffic crash, quality of life was measured 24 months following the baseline survey. A telephone-administered questionnaire obtained information on various potential explanatory variables. Health-related quality of life was measured using the European Quality of Life–5 Dimensions (EQ-5D) and Medical Outcomes Survey Short Form–12 (SF-12). Multivariable linear regression analyses determined the associations between explanatory variables and quality of life measures. <b>Results</b>: Mean SF-12 physical component summary (PCS) and mental component summary (MCS) scores increased by 7.3 and 2.5 units, respectively, from baseline to 24-month follow-up. Each 10-year increase in baseline age was independently associated with 3.1-unit (<i>P</i> &lt; .001) and 1.5-unit (<i>P</i> = .001) decrease in EQ Visual Analogue Scale (VAS) and SF-12 PCS scores at follow-up, respectively. Poor/fair compared to excellent pre-injury health was associated with a 0.16-, 21.3-, and 11.5-unit decrease in EQ-5D summary (<i>P</i> = .03), VAS scores (<i>P</i> = .001), and SF-12 PCS scores (<i>P</i> &lt; .001), respectively. Baseline pain severity ratings and pain catastrophizing scores were inversely associated with 24-month EQ VAS scores (both <i>P</i> &lt; .001). Each unit increase in baseline pain score (<i>P</i> = .001) and pain catastrophizing score (<i>P</i> = .02) was associated with a 1.0- and 4.6-unit decrease in SF-12 MCS scores at 24 months, respectively. Other observed predictors of quality of life measures (EQ-5D summary and/or VAS scores and/ or SF-12 MCS) included marital status, smoking, hospital admission, pre-injury health (anxiety/depression and chronic illness), and whiplash injury. <b>Conclusion</b>: Sociodemographic indicators, pre-injury health, and biopsychosocial correlates were independently associated with health-related quality of life 24 months following a noncatastrophic road traffic crash injury.
DOI: 10.7910/dvn/v1rjpf/hh6yrm
title: ykc20170814_03.txt.gz

description: :unav
DOI: 10.5281/zenodo.4013736
title: KALIv2: calibration and validation experiment results

description: The presented .zip archive consists of calibration and validation results we obtained while investigating the effect of calibration data length on the performance of different hydrological models. For more information, please visit our GitHub repository at https://github.com/hydrogo/KALIv2.