cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3759189
title: Using VIVO and Other Tools to Achieve a Strategic Vision

description: A globally interconnected research world is the norm. This offers great opportunities for communication and collaboration across fields of research, but it also comes with great challenges, in particular for systems interoperability. Many technology products, systems and tools have been created to help universities and other research organizations meet these challenges while achieving their strategic goals. This is creating a new challenge: a confusing stack of technology for users to assemble into a functional research ecosystem.<br>This panel will explore how one university, Texas A&M, selected and implemented a technology stack and is using it to achieve their strategic plan, “Vision 2020: Creating a Culture of Excellence.” Their stack includes:• VIVO• ORCID• Repositories, Vireo & DSpace • PlumX <br>The panel will discuss the components and the interactions between them, to provide the audience concrete examples of a working, interconnected research ecosystem. <br>Texas A&M will describe its process for defining its technology needs, who was engaged, and the questions that drove decisionmaking. They will describe their current technology stack, and the connections between the components. One cross-platform connector used by Texas A&M is the ORCID ID, which is allowing them to integrate information about researcher works and affiliations across various systems and present this information in their VIVO instance. <br>ORCID will describe how ORCID identifiers are being used at universities to assert researcher affiliation, and how universities may benefit from integrations by publishers and funders. Consortia approaches to implementation and adoption will be discussed, as well as the use of ORCID in federated identity management systems such as eduGAIN, and how ORCID interacts with identifiers for works and organizations. <br>Green open-access institutional repositories are a key component of a research ecosystem. It is the container for the research output conducted at the university. Recent studies have shown that opening up access to research creates more usage and citations for that research. Texas A&M implemented Vireo for theses and dissertations and DSpace for faculty research. <br>How is all of this enabling Texas A&M to measure progress toward its strategic goals? As a component of its tech stack, Texas A&M has integrated PlumX to track research metrics in five categories: usage, captures, mentions, social media and citations. Sometimes this is referred to as altmetrics. This part of the panel will include a discussion of what Texas A&M has discovered by tracking metrics across disciplines including output for the humanities. It will also showcase some other use cases of metrics in institutional repositories, analytics reports and researcher dashboards.
DOI: 10.6084/m9.figshare.3759186
title: Small Molecule Survivin Inhibitor YM155 Displays Potent Activity Against Human Osteosarcoma Cells

description: Survivin is an important oncogenic protein expressed highly in osteosarcoma. Here, we have shown that small molecule inhibitor YM155 potently suppressed survivin expression, inhibited cell growth, and induced apoptosis in osteosarcoma cells. Furthermore, we also showed that knock down of survivin by small interfering RNA strongly inhibited cell viability in two osteosarcoma cell lines, suggesting that suppression of survivin essentially contributes to YM155-mediated anticancer activity in osteosarcoma cells. Collectively, our study suggests that YM155 holds promise for patients with osteosarcoma.
DOI: 10.6084/m9.figshare.3759186.v1
title: Small Molecule Survivin Inhibitor YM155 Displays Potent Activity Against Human Osteosarcoma Cells

description: Survivin is an important oncogenic protein expressed highly in osteosarcoma. Here, we have shown that small molecule inhibitor YM155 potently suppressed survivin expression, inhibited cell growth, and induced apoptosis in osteosarcoma cells. Furthermore, we also showed that knock down of survivin by small interfering RNA strongly inhibited cell viability in two osteosarcoma cell lines, suggesting that suppression of survivin essentially contributes to YM155-mediated anticancer activity in osteosarcoma cells. Collectively, our study suggests that YM155 holds promise for patients with osteosarcoma.
DOI: 10.6084/m9.figshare.3759183
title: ABHD5 interacts with BECN1 to regulate autophagy and tumorigenesis of colon cancer independent of PNPLA2

description: Autophagy critically contributes to metabolic reprogramming and chromosomal stability. It has been reported that monoallelic loss of the essential autophagy gene <i>BECN1</i> (encoding BECN1/Beclin 1) promotes cancer development and progression. However, the mechanism by which BECN1 is inactivated in malignancy remains largely elusive. We have previously reported a tumor suppressor role of ABHD5 (abhydrolase domain containing 5), a co-activator of PNPLA2 (patatin like phospholipase domain containing 2) in colorectal carcinoma (CRC). Here we report a noncanonical role of ABHD5 in regulating autophagy and CRC tumorigenesis. ABHD5 directly competes with CASP3 for binding to the cleavage sites of BECN1, and consequently prevents BECN1 from being cleaved by CASP3. ABHD5 deficiency provides CASP3 an advantage to cleave and inactivate BECN1, thus impairing BECN1-induced autophagic flux and augmenting genomic instability, which subsequently promotes tumorigenesis. Notably, clinical data also confirm that ABHD5 proficiency is significantly correlated with the expression levels of BECN1, LC3-II and CASP3 in human CRC tissues. Our findings suggest that ABHD5 possesses a PNPLA2-independent function in regulating autophagy and tumorigenesis, further establishing the tumor suppressor role of ABHD5, and offering an opportunity to develop new approaches aimed at preventing CRC carcinogenesis.
DOI: 10.6084/m9.figshare.3759183.v2
title: ABHD5 interacts with BECN1 to regulate autophagy and tumorigenesis of colon cancer independent of PNPLA2

description: Autophagy critically contributes to metabolic reprogramming and chromosomal stability. It has been reported that monoallelic loss of the essential autophagy gene <i>BECN1</i> (encoding BECN1/Beclin 1) promotes cancer development and progression. However, the mechanism by which BECN1 is inactivated in malignancy remains largely elusive. We have previously reported a tumor suppressor role of ABHD5 (abhydrolase domain containing 5), a co-activator of PNPLA2 (patatin like phospholipase domain containing 2) in colorectal carcinoma (CRC). Here we report a noncanonical role of ABHD5 in regulating autophagy and CRC tumorigenesis. ABHD5 directly competes with CASP3 for binding to the cleavage sites of BECN1, and consequently prevents BECN1 from being cleaved by CASP3. ABHD5 deficiency provides CASP3 an advantage to cleave and inactivate BECN1, thus impairing BECN1-induced autophagic flux and augmenting genomic instability, which subsequently promotes tumorigenesis. Notably, clinical data also confirm that ABHD5 proficiency is significantly correlated with the expression levels of BECN1, LC3-II and CASP3 in human CRC tissues. Our findings suggest that ABHD5 possesses a PNPLA2-independent function in regulating autophagy and tumorigenesis, further establishing the tumor suppressor role of ABHD5, and offering an opportunity to develop new approaches aimed at preventing CRC carcinogenesis.
DOI: 10.6084/m9.figshare.3759183.v1
title: ABHD5 Interacts with BECN1 to Regulate Autophagy and Tumorigenesis of Colon Cancer Independent of PNPLA2

description: Autophagy critically contributes to metabolic reprogramming and chromosomal stability. It has been reported that monoallelic loss of the essential autophagy gene <i>BECN1</i> (encoding BECN1/Beclin1) promotes cancer development and progression. However, the mechanism by which BECN1 is inactivated in malignancy remains largely elusive. We have previously reported a tumor suppressor role of ABHD5 (abhydrolase domain containing 5), a co-activator of PNPLA2 (patatin like phospholipase domain containing 2) in colorectal carcinoma (CRC). Here we report a noncanonical role of ABHD5 in regulating autophagy and CRC tumorigenesis. ABHD5 directly competes with CASP3 for binding to the cleavage sites of BECN1, and consequently prevents BECN1 from being cleaved by CASP3. ABHD5 deficiency provides CASP3 an advantage to cleave and inactivate BECN1, thus impairing BECN1-induced autophagic flux and augmenting genomic instability, which subsequently promotes tumorigenesis. Notably, clinical data also confirm that ABHD5 proficiency is significantly correlated with the expression levels of BECN1, LC3-II and CASP3 in human CRC tissues. Our findings suggest that ABHD5 possesses a PNPLA2-independent function in regulating autophagy and tumorigenesis, further establishing the tumor suppressor role of ABHD5, and offering an opportunity to develop new approaches aimed at preventing CRC carcinogenesis.
DOI: 10.6084/m9.figshare.3759129
title: modzs.gctx: a legacy LINCS L1000 dataset of differential expression signatures

description: modzs.gctx contains a probe (rows) × signature (columns) matrix of differential expression z-scores from the LINCS L1000 project. The file uses a compressed binary encoding that can be read using the `cmap/l1ktools` drivers.<br>modzs.gctx is an input for the dhimmel/lincs repository, but is too large to be uploaded to GitHub. dhimmel/lincs extracts signatures from modzs.gctx to compute consensus signatures for perturbagens. Consensus signatures from dhimmel/lincs are available at https://doi.org/bp22 as user-friendly TSV files. modzs.gctx is uploaded for reproducibility of dhimmel/lincs and longterm preservation. Users who need raw LINCS L1000 data are encouraged to use the Broad Production Data hosted on GEO rather than the legacy modzs.gctx file.<br>I (Daniel Himmelstein) originally retrieved modzs.gctx from the following path on the L1000 C3 Cloud (c3.lincscloud.org): /xchip/cogs/data/build/a2y13q1/modzs.gctx. However, the original hosting is no longer operating. Therefore, I am uploading this file to figshare.<br>I am choosing a CC BY license with the requirement to attribute the LINCS L1000 Team at the Broad Institute. However, users should note that the licensing of modzs.gctx is murky. The Broad license (https://git.io/vieCF) states that data files cannot be redistributed, which conflicts the NIH LINCS Data Release Policy. See https://doi.org/bfmn for more information.
DOI: 10.6084/m9.figshare.3759126
title: subject1.mat

description: EEG recorded during a visual task where Subject1 had to make a 2 Alternative Forced Choice decision. This data is to be used as an example with artifact correction software, artscreenEEG.<br>
DOI: 10.6084/m9.figshare.3759075
title: Survival analysis of two versions of a database

description: Diffuse intrinsic pontine tumors (DIPG) are the brain tumors that have the highest mortality in the age group of children and adolescents (0-18 years). Children with a median age of 7 years are the most affected, with no difference of gender. [1] There is no effective curative treatment. Most of these gliomas arise in the ventral region of the pons and their growth pattern is infiltrative, affecting most or virtually all of the cross diameter of the pons. As a rule, they does not form a contrast-enhanced tumor mass and have no precise limits on magnetic resonance imaging. [2](excerpt)
DOI: 10.6084/m9.figshare.3759075.v2
title: Survival analysis of two versions of a database

description: Diffuse intrinsic pontine tumors (DIPG) are the brain tumors that have the highest mortality in the age group of children and adolescents (0-18 years). Children with a median age of 7 years are the most affected, with no difference of gender. [1] There is no effective curative treatment. Most of these gliomas arise in the ventral region of the pons and their growth pattern is infiltrative, affecting most or virtually all of the cross diameter of the pons. As a rule, they does not form a contrast-enhanced tumor mass and have no precise limits on magnetic resonance imaging. [2](excerpt)
DOI: 10.6084/m9.figshare.3759075.v1
title: Survival analysis of two versions of a database

description: Diffuse intrinsic pontine tumors (DIPG) are the brain tumors that have the highest mortality in the age group of children and adolescents (0-18 years). Children with a median age of 7 years are the most affected, with no difference of gender. [1] There is no effective curative treatment. Most of these gliomas arise in the ventral region of the pons and their growth pattern is infiltrative, affecting most or virtually all of the cross diameter of the pons. As a rule, they does not form a contrast-enhanced tumor mass and have no precise limits on magnetic resonance imaging. [2](excerpt)
DOI: 10.6084/m9.figshare.3758988
title: Toxicological and ecotoxicological properties of gas-to-liquid (GTL) products. 1. Mammalian toxicology

description: Gas-to-liquid (GTL) products are synthetic hydrocarbons produced from natural gas using a Fischer–Tropsch process. This process yields a synthetic crude oil that consists of saturated hydrocarbons, primarily linear alkanes, with increasing amounts of branched (methyl-groups) alkanes as the chains get longer. In addition, small amounts of cycloalkanes (branched cyclopentanes and cyclohexanes) may be formed as the polymerization reaction prolongs. This synthetic crude can subsequently be refined to a range of products very similar to petroleum refining. However, in contrast to their petroleum-derived analogs, GTL products are essentially free of unsaturated or aromatic constituents and also no sulfur-, oxygen-, or nitrogen-containing constituents are present. From a regulatory perspective, GTL products are new substances which require extensive testing to assess their hazardous properties. As a consequence, a wide range of GTL products, covering the entire portfolio of GTL products, have been tested over the past few years in a wide variety of toxicological studies, including reproductive and prenatal development toxicity studies. This review provides an overview of the hazardous properties of the various GTL products. In general, the data collected on GTL products provide strong proof that they exert minimal health effects. In addition, these data provide supporting evidence for what is known on the mechanisms of mammalian toxicology of their petroleum-derived analogs. In the few cases where adverse effects were found for the GTL substances, these were usually less severe than the adverse effects observed with their petroleum-derived analogs.
DOI: 10.6084/m9.figshare.3758988.v1
title: Toxicological and ecotoxicological properties of gas-to-liquid (GTL) products. 1. Mammalian toxicology

description: Gas-to-liquid (GTL) products are synthetic hydrocarbons produced from natural gas using a Fischer–Tropsch process. This process yields a synthetic crude oil that consists of saturated hydrocarbons, primarily linear alkanes, with increasing amounts of branched (methyl-groups) alkanes as the chains get longer. In addition, small amounts of cycloalkanes (branched cyclopentanes and cyclohexanes) may be formed as the polymerization reaction prolongs. This synthetic crude can subsequently be refined to a range of products very similar to petroleum refining. However, in contrast to their petroleum-derived analogs, GTL products are essentially free of unsaturated or aromatic constituents and also no sulfur-, oxygen-, or nitrogen-containing constituents are present. From a regulatory perspective, GTL products are new substances which require extensive testing to assess their hazardous properties. As a consequence, a wide range of GTL products, covering the entire portfolio of GTL products, have been tested over the past few years in a wide variety of toxicological studies, including reproductive and prenatal development toxicity studies. This review provides an overview of the hazardous properties of the various GTL products. In general, the data collected on GTL products provide strong proof that they exert minimal health effects. In addition, these data provide supporting evidence for what is known on the mechanisms of mammalian toxicology of their petroleum-derived analogs. In the few cases where adverse effects were found for the GTL substances, these were usually less severe than the adverse effects observed with their petroleum-derived analogs.
DOI: 10.6084/m9.figshare.3756768
title: Quantifying activity through repository mining: the case of Moose

description: An analysis of a software library written in Perl, Moose, and how it shows some features, maybe all, of self-organized criticality.<br>You can obtain the data files and the R Markdown file also http://github.com/JJ/literaturame<br>
DOI: 10.6084/m9.figshare.3756600
title: Spreadsheet of sources: Gamification of Software Testing - an MLR

description: The sources used in the paper and the analysis results (raw data). <br><br>Mäntylä, M. V., Smolander, K. Gamification of Software Testing - an MLR, In Proceedings of The 17th International Conference on Product-Focused Software Process Improvement PROFES, 22th – 24th November 2016, Trondheim, Norway <br>
DOI: 10.6084/m9.figshare.3756600.v1
title: Gamification of Software Testing - an MLR (Profes 2016 paper online sources and analysis)

description: The sources used in the paper and the analysis results (raw data). <br><br>Mäntylä, M. V., Smolander, K. Gamification of Software Testing - an MLR, In Proceedings of Home Important Dates Timetable Workshops Call for Papers Committee Venue Contact The 17th International Conference on Product-Focused Software Process Improvement PROFES, 22th – 24th November 2016, Trondheim, Norway <br>
DOI: 10.6084/m9.figshare.3756594
title: Economic Risk Factors of FGM and its impact on Fertility and the Marriage Market

description: Female Genital Mutilation is widespread in sub- Saharan Africa despite being illegal in many countries. It has been shown in previous research that female genital mutilation occurs due to long standing tradition which creates difficulty in the elimination of the practice. In any case, the effects of mutilation can have long lasting effects on future demographics through impacts on future fertility and marriage markets. This study looks to identify socio-economic risk factors that can increase the risk of circumcision of respondent first daughters in Senegal suing Demographic Health Survey data. Marriage Markets are affected through a number of channels due to the existence of female genital mutilation. For example, circumcision is associated with preparation for marriage reducing the age of marriages within populations. Furthermore, female circumcision can be used as a mechanism of control for women under the male dominated household, causing circumcision status to effect potential value on the marriage market assuming men supposedly make rational decisions when choosing a wife. Additionally, the practice can have negative impacts on female health, leading to the assumption that fertility will be negatively affected. Literature on the subject of female circumcision is growing, however few address the issue in relation to economic theories of circumcision. Likewise, much of the quantitative literature on female circumcision disregard the severity of circumcision. This paper attempts to link the severity of circumcision to fertility impacts through measurement of birth parity spacing and total births.The Demographic Health Survey provides a wealth of data needed for this type of research data. DHS allows us to use important measures of economic, health and demographics that can be used for government intervention on a range of issues. In regards to FGM, the Senegal: Standard DHS 2010-2011 provides extensive data on socio-demographic, reproduction, marriage, sexual activity and FGM. <br>
DOI: 10.6084/m9.figshare.3756594.v1
title: Economic Risk Factors of FGM and its impact on Fertility and the Marriage Market

description: Female Genital Mutilation is widespread in sub- Saharan Africa despite being illegal in many countries. It has been shown in previous research that female genital mutilation occurs due to long standing tradition which creates difficulty in the elimination of the practice. In any case, the effects of mutilation can have long lasting effects on future demographics through impacts on future fertility and marriage markets. This study looks to identify socio-economic risk factors that can increase the risk of circumcision of respondent first daughters in Senegal suing Demographic Health Survey data. Marriage Markets are affected through a number of channels due to the existence of female genital mutilation. For example, circumcision is associated with preparation for marriage reducing the age of marriages within populations. Furthermore, female circumcision can be used as a mechanism of control for women under the male dominated household, causing circumcision status to effect potential value on the marriage market assuming men supposedly make rational decisions when choosing a wife. Additionally, the practice can have negative impacts on female health, leading to the assumption that fertility will be negatively affected. Literature on the subject of female circumcision is growing, however few address the issue in relation to economic theories of circumcision. Likewise, much of the quantitative literature on female circumcision disregard the severity of circumcision. This paper attempts to link the severity of circumcision to fertility impacts through measurement of birth parity spacing and total births.The Demographic Health Survey provides a wealth of data needed for this type of research data. DHS allows us to use important measures of economic, health and demographics that can be used for government intervention on a range of issues. In regards to FGM, the Senegal: Standard DHS 2010-2011 provides extensive data on socio-demographic, reproduction, marriage, sexual activity and FGM. <br>
DOI: 10.6084/m9.figshare.3756573.v1
title: Introductory Presentation for Using a Pencilfish to Write Whales Workshop

description: The introductory presentation given by Anna Zivian for the Using a Pencilfish to Write Whales science-poetry workshop at the International Marine Conservation Congress #4 in St John's Newfoundland, Canada, 2016.
DOI: 10.6084/m9.figshare.3756564
title: The effect of microablative fractional CO<sub>2</sub> laser on vaginal flora of postmenopausal women

description: <b>Objectives:</b> To assess the effect of microablative fractional CO<sub>2</sub> laser (MFCO<sub>2</sub>-Laser) therapy on the vaginal microenvironment of postmenopausal women. <b>Methods:</b> Three laser therapies at monthly intervals were applied in postmenopausal women with moderate to severe symptoms of genitourinary syndrome of menopause, pH of vaginal fluid &gt;4.5 and superficial epithelial cells on vaginal smear &lt;5%. Vaginal fluid pH values, fresh wet mount microscopy, Gram stain and aerobic and anaerobic cultures were evaluated at baseline and 1 month after each subsequent therapy. Nugent score and Hay-Ison criteria were used to evaluate vaginal flora. <b>Results:</b> Fifty-three women (mean age 57.2 ± 5.4 years) participated and completed this study. MFCO<sub>2</sub>-Laser therapy increased <i>Lactobacillus</i> (<i>p</i> p p Lactobacillus changed from 30% initially to 79% after the last treatment. Clinical signs and symptoms of bacterial vaginosis, aerobic vaginitis or candidiasis did not appear in any participant. <b>Conclusion:</b> MFCO<sub>2</sub>-Laser therapy is a promising treatment for improving the vaginal health of postmenopausal women by helping repopulate the vagina with normally existing <i>Lactobacillus species</i> and reconstituting the normal flora to premenopausal status.