cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4174674
title: Supplementary Material for: Virus-Infected Human Mast Cells Enhance Natural Killer Cell Functions

description: Mucosal surfaces are protected from infection by both structural and sentinel cells, such as mast cells. The mast cell's role in antiviral responses is poorly understood; however, they selectively recruit natural killer (NK) cells following infection. Here, the ability of virus-infected mast cells to enhance NK cell functions was examined. Cord blood-derived<b> </b>human mast cells infected with reovirus (Reo-CBMC) and subsequent mast cell products were used for the stimulation of human NK cells. NK cells upregulated the CD69 molecule and cytotoxicity-related genes, and demonstrated increased cytotoxic activity in response to Reo-CBMC soluble products. NK cell interferon (IFN)-γ production was also promoted in the presence of interleukin (IL)-18. In vivo, SCID mice injected with Reo-CBMC in a subcutaneous Matrigel model, could recruit and activate murine NK cells, a property not shared by normal human fibroblasts. Soluble products of Reo-CBMC included IL-10, TNF, type I and type III IFNs. Blockade of the type I IFN receptor abrogated NK cell activation. Furthermore, reovirus-infected mast cells expressed multiple IFN-α subtypes not observed in reovirus-infected fibroblasts or epithelial cells. Our data define an important mast cell IFN response, not shared by structural cells, and a subsequent novel mast cell-NK cell immune axis in human antiviral host defense.
DOI: 10.7910/dvn/v1rjpf/cc920p
title: cbb20160602_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4174674.v1
title: Supplementary Material for: Virus-Infected Human Mast Cells Enhance Natural Killer Cell Functions

description: Mucosal surfaces are protected from infection by both structural and sentinel cells, such as mast cells. The mast cell's role in antiviral responses is poorly understood; however, they selectively recruit natural killer (NK) cells following infection. Here, the ability of virus-infected mast cells to enhance NK cell functions was examined. Cord blood-derived<b> </b>human mast cells infected with reovirus (Reo-CBMC) and subsequent mast cell products were used for the stimulation of human NK cells. NK cells upregulated the CD69 molecule and cytotoxicity-related genes, and demonstrated increased cytotoxic activity in response to Reo-CBMC soluble products. NK cell interferon (IFN)-γ production was also promoted in the presence of interleukin (IL)-18. In vivo, SCID mice injected with Reo-CBMC in a subcutaneous Matrigel model, could recruit and activate murine NK cells, a property not shared by normal human fibroblasts. Soluble products of Reo-CBMC included IL-10, TNF, type I and type III IFNs. Blockade of the type I IFN receptor abrogated NK cell activation. Furthermore, reovirus-infected mast cells expressed multiple IFN-α subtypes not observed in reovirus-infected fibroblasts or epithelial cells. Our data define an important mast cell IFN response, not shared by structural cells, and a subsequent novel mast cell-NK cell immune axis in human antiviral host defense.
DOI: 10.7910/dvn/v1rjpf/ldcdnp
title: cbb20161104_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4174359
title: MaTrace_Global_InData.xlsx

description: Complete set of model data for the MaTrace Global model of metal cycles, published in Resources Conservation and Recycling with the DOI 10.1016/j.resconrec.2016.09.029<br>
DOI: 10.7910/dvn/v1rjpf/4wcdoo
title: cbb20161211_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/nyels1
title: cbb20160222_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/fzmzlo
title: cbb20160814_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/vjqhp0
title: cbb20160909_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/pj7pxa
title: cbb20161117_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/ewpnsh
title: cbb20161212_03.txt.gz

description: :unav
DOI: 10.17608/k6.auckland.4168152
title: Volumetric Characterisation of Contracting Cardiac Trabeculae: Combining Measurement Modalities

description: Data to accompany Chapter 6 of the PhD thesis titled "Volumetric Characterisation of Contracting Cardiac Trabeculae"
DOI: 10.7910/dvn/v1rjpf/rxjzr0
title: cbb20160401_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4168086
title: BIO205 2016 Tut0105 Census 2 Data

description: Data set collected at University of Toronto Mississauga (UTM) campus, following protocol posted at http://www.campusecology.network/protcol/
DOI: 10.7910/dvn/v1rjpf/wkjbhc
title: cbb20161216_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/iy6avy
title: cbb20160713_03.txt.gz

description: :unav
DOI: 10.17608/k6.auckland.4168152.v3
title: Volumetric Characterisation of Contracting Cardiac Trabeculae: Combining Measurement Modalities

description: Data to accompany Chapter 6 of the PhD thesis titled "Volumetric Characterisation of Contracting Cardiac Trabeculae"
DOI: 10.6084/m9.figshare.4168086.v1
title: BIO205 2016 Tut0105 Census 2 Data

description: Data set collected at University of Toronto Mississauga (UTM) campus, following protocol posted at http://www.campusecology.network/protcol/
DOI: 10.7910/dvn/v1rjpf/605xsy
title: cbb20160211_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4168062
title: Original Project - Insects: Pollinator or Predator?

description: We created our own experiment based on our hypothesis which is as follows; If different colored pan traps are set up in the grasslands and woodlot, then more pollinators will be found in the grassland than the woodlot. Before we began we made the decision to not set up the experiment in the grasslands because we knew for a fact that pollinators would be plenty, as we have seen in past experimental adventures. Our entire experiment takes place in the woodlot, starting from right before the woodlot, where more sunlight and flowers are. We set up four transects of 5 bowls, with alternating colored bowls (yellow, white, blue). We then filled each bowl's bottom with soapy water. The soap has a sweet scent, and we figured would attract insects (specifically pollinators because sweet smell = flowers). Our four transects were about 11.5 feet from one another, as they crept more and more into the woodlot. This would determine the correlation between sunlight and pollinators. Our colored bowls would determine if insects (pollinators to be specific) were attracted to certain colors (in this case, yellow).
DOI: 10.7910/dvn/v1rjpf/nj1axo
title: cbb20160718_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4168044
title: Genome-wide Dam methylation in Escherichia coli during long-term stationary phase

description: h5 files of PacBio SMRT sequencing, aligned to reference genome (ZK126, a derivative of W3110).
DOI: 10.6084/m9.figshare.4168062.v1
title: Original Project - Insects: Pollinator or Predator?

description: We created our own experiment based on our hypothesis which is as follows; If different colored pan traps are set up in the grasslands and woodlot, then more pollinators will be found in the grassland than the woodlot. Before we began we made the decision to not set up the experiment in the grasslands because we knew for a fact that pollinators would be plenty, as we have seen in past experimental adventures. Our entire experiment takes place in the woodlot, starting from right before the woodlot, where more sunlight and flowers are. We set up four transects of 5 bowls, with alternating colored bowls (yellow, white, blue). We then filled each bowl's bottom with soapy water. The soap has a sweet scent, and we figured would attract insects (specifically pollinators because sweet smell = flowers). Our four transects were about 11.5 feet from one another, as they crept more and more into the woodlot. This would determine the correlation between sunlight and pollinators. Our colored bowls would determine if insects (pollinators to be specific) were attracted to certain colors (in this case, yellow).
DOI: 10.7910/dvn/v1rjpf/zzbkwp
title: cbb20160311_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4168029
title: Cizauskas et al 2016 RSOS Figure 1 Data.xlsx

description: Supplemental figure for Cizauskas & Carlson et al. upcoming, Figure 1: a meta-analysis of studies on parasite ecology and climate change
DOI: 10.7910/dvn/v1rjpf/umxdi6
title: cbb20161126_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4168029.v1
title: Cizauskas et al 2016 RSOS Figure 1 Data.xlsx

description: Supplemental figure for Cizauskas & Carlson et al. upcoming, Figure 1: a meta-analysis of studies on parasite ecology and climate change
DOI: 10.7910/dvn/v1rjpf/ruz3im
title: cbb20160506_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/jalfto
title: cbb20160511_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/rfz7fp
title: cbb20161110_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4168014
title: R Source codes

description: The text file contains the R source codes used for analyzing the data use in the publication "Prediction of biomarkers and novel pathways conferring risk to post-traumatic stress disorder" .
DOI: 10.7910/dvn/v1rjpf/nbquon
title: cbb20160414_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4168014.v1
title: R Source codes

description: The text file contains the R source codes used for analyzing the data use in the publication "Prediction of biomarkers and novel pathways conferring risk to post-traumatic stress disorder" .
DOI: 10.7910/dvn/v1rjpf/puluae
title: cbb20160214_03.txt.gz

description: :unav
DOI: 10.17036/researchdata.aston.ac.uk.00000478
title: Reconsidering Britain’s Soft Power: Lessons from the Perceptions of the Turkish Political Elite
DOI: 10.7910/dvn/v1rjpf/3vpt8p
title: cbb20160830_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/oubduy
title: cbb20160819_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/anewj9
title: cbb20160409_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/shv9cz
title: cbb20160128_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/vsqpz3
title: cbb20160217_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4167804
title: Goodness-of-Fit Assessment in Multidimensional Scaling and Unfolding

description: Judging goodness of fit in multidimensional scaling requires a comprehensive set of diagnostic tools instead of relying on stress rules of thumb. This article elaborates on corresponding strategies and gives practical guidelines for researchers to obtain a clear picture of the goodness of fit of a solution. Special emphasis will be placed on the use of permutation tests. The second part of the article focuses on goodness-of-fit assessment of an important variant of multidimensional scaling called unfolding, which can be applied to a broad range of psychological data settings. Two real-life data sets are presented in order to walk the reader through the entire set of diagnostic measures, tests, and plots. <b>R</b> code is provided as supplementary information that makes the whole goodness-of-fit assessment workflow, as presented in this article, fully reproducible.
DOI: 10.7910/dvn/v1rjpf/6zpshq
title: cbb20160717_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4167804.v2
title: Goodness-of-Fit Assessment in Multidimensional Scaling and Unfolding

description: Judging goodness of fit in multidimensional scaling requires a comprehensive set of diagnostic tools instead of relying on stress rules of thumb. This article elaborates on corresponding strategies and gives practical guidelines for researchers to obtain a clear picture of the goodness of fit of a solution. Special emphasis will be placed on the use of permutation tests. The second part of the article focuses on goodness-of-fit assessment of an important variant of multidimensional scaling called unfolding, which can be applied to a broad range of psychological data settings. Two real-life data sets are presented in order to walk the reader through the entire set of diagnostic measures, tests, and plots. <b>R</b> code is provided as supplementary information that makes the whole goodness-of-fit assessment workflow, as presented in this article, fully reproducible.
DOI: 10.6084/m9.figshare.4167804.v1
title: Goodness-of-Fit Assessment in Multidimensional Scaling and Unfolding

description: Judging goodness of fit in multidimensional scaling requires a comprehensive set of diagnostic tools instead of relying on stress rules of thumb. This article elaborates on corresponding strategies and gives practical guidelines for researchers to obtain a clear picture of the goodness of fit of a solution. Special emphasis will be placed on the use of permutation tests. The second part of the article focuses on goodness-of-fit assessment of an important variant of multidimensional scaling called unfolding, which can be applied to a broad range of psychological data settings. Two real-life data sets are presented in order to walk the reader through the entire set of diagnostic measures, tests, and plots. <b>R</b> code is provided as supplementary information that makes the whole goodness-of-fit assessment workflow, as presented in this article, fully reproducible.
DOI: 10.7910/dvn/v1rjpf/js4gsw
title: cbb20160816_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/psgrzi
title: cbb20160108_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/hlfdo9
title: cbb20160626_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/dlh1nh
title: cbb20160527_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/bxzfxs
title: cbb20161225_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/htqlum
title: cbb20160510_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4165725
title: <i>In silico</i> analysis of candidate proteins sharing homology with <i>Streptococcus agalactiae</i> proteins and their role in male infertility

description: Leukocytospermia is a physiologic condition defined as human semen with a leukocyte count of &gt;1 x 10<sup>6</sup> cells/ml that is often correlated with male infertility. Moreover, bacteriospermia has been associated with leukocytospermia ultimately leading to male infertility. We have found that semen samples with &gt;1 x 10<sup>6</sup>/ml leukocytes and/or bacteriospermia have oxidative predominance as evidenced by augmented protein carbonyl and lipid peroxidation status of the semen which is implicated in sperm dysfunction. It has been reported that <i>Streptococcus agalactiae</i> is present in bacteriospermic samples. Previous research has shown that human leukocyte antigen beta chain paralog (HLA-DRB) alleles interact best with the infected sperm cells rather than the non-infected cells. Little is known about the interaction of major histocompatibility complex (MHC) present on leukocytes with the sperm upon bacterial infection and how it induces an immunological response which we have addressed by epitope mapping. Therefore, we examined MHC class II derived bacterial peptides which might have human sperm-related functional aspects. Twenty-two <i>S. agalactiae</i> proteins were obtained from PUBMED protein database for our study. Protein sequences with more than two accession numbers were aligned using CLUSTAL Omega to check their conservation pattern. Each protein sequence was then analyzed for T-cell epitope prediction against HLA-DRB alleles using the immune epitope database (IEDB) analysis tool. Out of a plethora of peptides obtained from this analysis, peptides corresponding to proteins of interest such as DNA binding response regulator, hyaluronate lyase and laminin binding protein were screened against the human proteome using Blastp. Interestingly, we have found bacterial peptides sharing homology with human peptides deciphering some of the important sperm functions. Antibodies raised against these probable bacterial antigens of fertility will not only help us understand the mechanism of leukocytospermia/bacteriospermia induced male factor infertility but also open new avenues for immunocontraception. <b>Abbreviations</b>: AA: amino acid; ASA: antisperm antibodies; GBS: group B streptococcus; HLA: human leukocyte antigen; HAS3: hyaluronan synthase 3: IEDB: immune epitope database; MAPO2: O<sup>6</sup>–methylguanine–induced apoptosis 2; MHC: major histocompatibility complex; ROS: reactive oxygen species; Rosbin1: round spermatid basic protein 1; <i>S. agalactiae: Streptococcus agalactiae;</i>SA: sperm antigen; SPATA17: spermatogenesis associated protein17; SPNR: spermatid perinuclear RNA binding protein; TEX15: testis-expressed sequence 15 protein; TOPAZ: testis– and ovary-specific PAZ domain–containing protein; TPABP: testis-specific poly–A binding protein; TPAP: testis–specific poly(A) polymerase; WHO: World Health Organization
DOI: 10.7910/dvn/v1rjpf/rrkerl
title: cbb20160509_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4165725.v1
title: <i>In silico</i> analysis of candidate proteins sharing homology with <i>Streptococcus agalactiae</i> proteins and their role in male infertility

description: Leukocytospermia is a physiologic condition defined as human semen with a leukocyte count of &gt;1 x 10<sup>6</sup> cells/ml that is often correlated with male infertility. Moreover, bacteriospermia has been associated with leukocytospermia ultimately leading to male infertility. We have found that semen samples with &gt;1 x 10<sup>6</sup>/ml leukocytes and/or bacteriospermia have oxidative predominance as evidenced by augmented protein carbonyl and lipid peroxidation status of the semen which is implicated in sperm dysfunction. It has been reported that <i>Streptococcus agalactiae</i> is present in bacteriospermic samples. Previous research has shown that human leukocyte antigen beta chain paralog (HLA-DRB) alleles interact best with the infected sperm cells rather than the non-infected cells. Little is known about the interaction of major histocompatibility complex (MHC) present on leukocytes with the sperm upon bacterial infection and how it induces an immunological response which we have addressed by epitope mapping. Therefore, we examined MHC class II derived bacterial peptides which might have human sperm-related functional aspects. Twenty-two <i>S. agalactiae</i> proteins were obtained from PUBMED protein database for our study. Protein sequences with more than two accession numbers were aligned using CLUSTAL Omega to check their conservation pattern. Each protein sequence was then analyzed for T-cell epitope prediction against HLA-DRB alleles using the immune epitope database (IEDB) analysis tool. Out of a plethora of peptides obtained from this analysis, peptides corresponding to proteins of interest such as DNA binding response regulator, hyaluronate lyase and laminin binding protein were screened against the human proteome using Blastp. Interestingly, we have found bacterial peptides sharing homology with human peptides deciphering some of the important sperm functions. Antibodies raised against these probable bacterial antigens of fertility will not only help us understand the mechanism of leukocytospermia/bacteriospermia induced male factor infertility but also open new avenues for immunocontraception. <b>Abbreviations</b>: AA: amino acid; ASA: antisperm antibodies; GBS: group B streptococcus; HLA: human leukocyte antigen; HAS3: hyaluronan synthase 3: IEDB: immune epitope database; MAPO2: O<sup>6</sup>–methylguanine–induced apoptosis 2; MHC: major histocompatibility complex; ROS: reactive oxygen species; Rosbin1: round spermatid basic protein 1; <i>S. agalactiae: Streptococcus agalactiae;</i>SA: sperm antigen; SPATA17: spermatogenesis associated protein17; SPNR: spermatid perinuclear RNA binding protein; TEX15: testis-expressed sequence 15 protein; TOPAZ: testis– and ovary-specific PAZ domain–containing protein; TPABP: testis-specific poly–A binding protein; TPAP: testis–specific poly(A) polymerase; WHO: World Health Organization
DOI: 10.7910/dvn/v1rjpf/ade9hl
title: cbb20160114_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4165683
title: lagleads424v3a.xlsx

description: EEG processed data containing averaged and standard deviation of phase values and coherence analysis of individuals engaged in simple task activities (finger movement).<br>
DOI: 10.7910/dvn/v1rjpf/4tkqax
title: cbb20161012_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4165659
title: Persistence to anti-cancer treatments in the stationary to proliferating transition

description: The heterogeneous responses of clonal cancer cells to treatment is understood to be caused by several factors, including stochasticity, cell-cycle dynamics, and different micro-environments. In a tumor, cancer cells may encounter fluctuating conditions and transit from a stationary culture to a proliferating state, for example this may occur following treatment. Here, we undertake a quantitative evaluation of the response of single cancerous lymphoblasts (L1210 cells) to various treatments administered during this transition. Additionally, we developed an experimental system, a “Mammalian Mother Machine,” that tracks the fate of thousands of mammalian cells over several generations under transient exposure to chemotherapeutic drugs. Using our developed system, we were able to follow the same cell under repeated treatments and continuously track many generations. We found that the dynamics of the transition between stationary and proliferative states are highly variable and affect the response to drug treatment. Using cell-cycle markers, we were able to isolate a subpopulation of persister cells with distinctly higher than average survival probability. The higher survival rate encountered with cell-cycle phase specific drugs was associated with a significantly longer time-till-division, and was reduced by a non cell-cycle specific drug. Our results suggest that the variability of transition times from the stationary to the proliferating state may be an obstacle hampering the effectiveness of drugs and should be taken into account when designing treatment regimens.
DOI: 10.6084/m9.figshare.4165683.v1
title: lagleads424v3a.xlsx

description: EEG processed data containing averaged and standard deviation of phase values and coherence analysis of individuals engaged in simple task activities (finger movement).<br>
DOI: 10.7910/dvn/v1rjpf/ukxgg7
title: cbb20160618_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4165659.v2
title: Persistence to anti-cancer treatments in the stationary to proliferating transition

description: The heterogeneous responses of clonal cancer cells to treatment is understood to be caused by several factors, including stochasticity, cell-cycle dynamics, and different micro-environments. In a tumor, cancer cells may encounter fluctuating conditions and transit from a stationary culture to a proliferating state, for example this may occur following treatment. Here, we undertake a quantitative evaluation of the response of single cancerous lymphoblasts (L1210 cells) to various treatments administered during this transition. Additionally, we developed an experimental system, a “Mammalian Mother Machine,” that tracks the fate of thousands of mammalian cells over several generations under transient exposure to chemotherapeutic drugs. Using our developed system, we were able to follow the same cell under repeated treatments and continuously track many generations. We found that the dynamics of the transition between stationary and proliferative states are highly variable and affect the response to drug treatment. Using cell-cycle markers, we were able to isolate a subpopulation of persister cells with distinctly higher than average survival probability. The higher survival rate encountered with cell-cycle phase specific drugs was associated with a significantly longer time-till-division, and was reduced by a non cell-cycle specific drug. Our results suggest that the variability of transition times from the stationary to the proliferating state may be an obstacle hampering the effectiveness of drugs and should be taken into account when designing treatment regimens.
DOI: 10.7910/dvn/v1rjpf/8ggbv2
title: cbb20160918_03.txt.gz

description: :unav