cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c56688v6w
title: MassIVE MSV000092539 - Essential role of MFSD1-GLMP-GIMAP5 in lymphocyte survival and liver homeostasis
title: In this study, we detected three alleles that caused lymphopenia, splenomegaly, progressive liver pathology and extramedullary hematopoiesis (EMH), resulting from N-ethyl-N-nitrosourea (ENU)-induced mutations in the major facilitator superfamily domain containing 1 protein (Mfsd1) which encodes a lysosomal membrane-bound solute carrier protein with no previously described function in immunity. By proteomic analysis, we identified MFSD1 functions together with GLMP (glycosylated lysosomal membrane protein), and GIMAP5 (GTPase of immunity-associated protein 5). Germ line knock alleles of MFSD1, GLMP, and GIMAP5 were generated in mice and confirmed occurrence of lymphopenia, liver pathology, EMH, and lipid deposition in the bone marrow and liver of each strain. We found that the interaction of MFSD1 and GLMP with GIMAP5 is essential to maintain normal GIMAP5 expression that is critical to support lymphocyte development and liver homeostasis that suppresses EMH. These findings provide new insight into the mechanism of how MFSD1-GLMP-GIMAP5 complex functions together to regulate immunity and liver homeostasis that were previously unknown.
DOI: 10.6084/m9.figshare.23795880
title: Ioduria_consumo_diario.sav

description: A cross-sectional study, 199 women were evaluated on three different days of their first trimester of pregnancy.
DOI: 10.6084/m9.figshare.23795880.v1
title: Ioduria_consumo_diario.sav

description: A cross-sectional study, 199 women were evaluated on three different days of their first trimester of pregnancy.
DOI: 10.13140/rg.2.2.31806.46404
title: 17 FF IN 1971 WAR AS SEEN BY COLONEL MOHAMMAD UMAR KIRMANI
DOI: 10.13140/rg.2.2.15029.24805
title: 17 FF IN 1971 WAR AS SEEN BY COLONEL MOHAMMAD UMAR KIRMANI
DOI: 10.6084/m9.figshare.21493544
title: In vitro effects of different fungicides (botanicals, chemicals, and bio-agents) on mycelial growth of <i>Sclerotium rolfsii</i> causing betel vine (<i>Piper betle</i> L) foot rot disease in Bangladesh

description: <i>Sclerotium rolfsii</i> Sacc causing foot rot disease which is one of the major limiting factor for betelvine cultivation in Bangladesh. In this study, we have evaluated the antifungal activity of medicinal plant extracts, chemical fungicides, and antagonistic fungal isolates on mycelial growth of <i>Sclerotium rolfsii</i>. Among the tested medicinal plants, the highest percent inhibition was exhibited by leaf extracts of <i>Datura metel</i> and <i>Lowsonia inermis</i> L. in all three solvents (aqueous; ethanol and acetone) and concentrations. The chemicals fungicides - Bavistin DF (Carbendazim) and Dithane M-45 (Mancozeb), effectively inhibited the growth of the <i>S. rolfsii</i>. However, at lower concentrations, other tested fungicides were found to be less effective. Among the six biological control agents, <i>Trichoderma harzianum</i> showed the highest percent inhibition of radial growth of <i>S. rolfsii</i>. The secondary metabolites of <i>T. harzianum</i> and <i>T. viride</i> significantly reduced the mycelial growth of <i>S. rolfsii.</i>
DOI: 10.6084/m9.figshare.21493544.v1
title: In vitro effects of different fungicides (botanicals, chemicals, and bio-agents) on mycelial growth of <i>Sclerotium rolfsii</i> causing betel vine (<i>Piper betle</i> L) foot rot disease in Bangladesh

description: <i>Sclerotium rolfsii</i> Sacc causing foot rot disease which is one of the major limiting factor for betelvine cultivation in Bangladesh. In this study, we have evaluated the antifungal activity of medicinal plant extracts, chemical fungicides, and antagonistic fungal isolates on mycelial growth of <i>Sclerotium rolfsii</i>. Among the tested medicinal plants, the highest percent inhibition was exhibited by leaf extracts of <i>Datura metel</i> and <i>Lowsonia inermis</i> L. in all three solvents (aqueous; ethanol and acetone) and concentrations. The chemicals fungicides - Bavistin DF (Carbendazim) and Dithane M-45 (Mancozeb), effectively inhibited the growth of the <i>S. rolfsii</i>. However, at lower concentrations, other tested fungicides were found to be less effective. Among the six biological control agents, <i>Trichoderma harzianum</i> showed the highest percent inhibition of radial growth of <i>S. rolfsii</i>. The secondary metabolites of <i>T. harzianum</i> and <i>T. viride</i> significantly reduced the mycelial growth of <i>S. rolfsii.</i>
DOI: 10.6084/m9.figshare.23792301
title: Raw Data files associated with Figure 5 in RBL2 represses the transcriptional activity of Multicilin to inhibit multiciliogenesis

description: <b>Immunoprecipitation, immunoblotting analysis, and silver staining</b>For identifying interacting proteins of FLAG-tagged Multicilin by MASS analysis, MEFs were infected by pAd/CMV/V5 vector encoding 3xFLAG-Multicilin, NLS-6xmyc-E2f4ΔCt-VP16-T2A-Multicilin, and NLS-6xmyc-E2f4WT-T2A-Multicilin. Non-infected MEFs were used as the negative control. Two days after infection, the non-infected MEFs or infected MEFs were lysed in lysis buffer (50mM HEPES-KOH [pH 7.5], 500NaCl, 5mM EDTA [pH 8.0]), 2% Triton, DNase I (10ug/ml)) by incubation on ice for 20min. Lysates were cleared by centrifugation at 12,000 rpm for 20 min at 4 °C, then precleared by incubation with Protein G agarose (Invitrogen #20397) agitating for 1hr at 4°C. Spun-down beads were incubated with FLAG M2 agarose (Sigma #A2220) agitating for 2.5 hours at 4°C. The beads were washed twice with wash buffer (1:1 mix of 50mM HEPES and Lysis buffer), washed with lysis buffer twice, then washed twice again with wash buffer. Spun-down beads were incubated with 40uL of FLAG peptide (500ng/mL) for bound protein elution overnight at 4°C. Elutes were subjected to protein sampling for further immunoblot analysis and silver staining. Eluted protein samples and experimental protein lysates were subjected to SDS-PAGE and transferred to a PVDF membrane that was then blocked with 0.5% casein blocker (#161-0783, Bio-Rad) in PBS for 30 min followed by incubation with the indicated primary antibodies overnight at 4 °C in 0.1% Tween-20 in blocking buffer. After extensive washing in 0.1% Tween-20 in PBS, the blots were incubated with Alexa 680 or 800-conjugated anti- mouse or rabbit secondary antibodies (Invitrogen, A21058, A21076, A32735) for 45 min at room temperature, washed with 0.1% Tween-20 in PBS, and imaged using Odyssey (LI-COR). Silver staining was performed with Pierce Silver Stain Kit (Thermo #24612) based on the manufacturer’s instructions.
DOI: 10.3886/e193004
title: Adult Misclassified EL Study

description: The workspace includes the retrospective interview protocol used with adult former English learners. The participants were 104 adults who responded to Twitter, Facebook, or email recruitment to participate in an in-depth retrospective interview about being misclassified as learning English in the United States. Retrospective interviews of adults meant that the interviews covered their entire K-12 experience and facilitated the recruitment of ethnoracially diverse participants with varied life experiences who were educated in different parts of the US. IRB protocols and confidentiality prevent me from sharing the entire interview transcripts generated from this research. <br>
DOI: 10.3886/e193004v1
title: Adult Misclassified EL Study

description: The workspace includes the retrospective interview protocol used with adult former English learners. The participants were 104 adults who responded to Twitter, Facebook, or email recruitment to participate in an in-depth retrospective interview about being misclassified as learning English in the United States. Retrospective interviews of adults meant that the interviews covered their entire K-12 experience and facilitated the recruitment of ethnoracially diverse participants with varied life experiences who were educated in different parts of the US. IRB protocols and confidentiality prevent me from sharing the entire interview transcripts generated from this research. <br>
DOI: 10.25345/c52f7k21p
title: MassIVE MSV000092540 - Essential role of MFSD1-GLMP-GIMAP5 in lymphocyte survival and liver homeostasis
title: In this study, we detected three alleles that caused lymphopenia, splenomegaly, progressive liver pathology and extramedullary hematopoiesis (EMH), resulting from N-ethyl-N-nitrosourea (ENU)-induced mutations in the major facilitator superfamily domain containing 1 protein (Mfsd1) which encodes a lysosomal membrane-bound solute carrier protein with no previously described function in immunity. By proteomic analysis, we identified MFSD1 functions together with GLMP (glycosylated lysosomal membrane protein), and GIMAP5 (GTPase of immunity-associated protein 5). Germ line knock alleles of MFSD1, GLMP, and GIMAP5 were generated in mice and confirmed occurrence of lymphopenia, liver pathology, EMH, and lipid deposition in the bone marrow and liver of each strain. We found that the interaction of MFSD1 and GLMP with GIMAP5 is essential to maintain normal GIMAP5 expression that is critical to support lymphocyte development and liver homeostasis that suppresses EMH. These findings provide new insight into the mechanism of how MFSD1-GLMP-GIMAP5 complex functions together to regulate immunity and liver homeostasis that were previously unknown.
DOI: 10.6084/m9.figshare.23792301.v1
title: Raw Data files associated with Figure 5 in RBL2 represses the transcriptional activity of Multicilin to inhibit multiciliogenesis

description: <b>Immunoprecipitation, immunoblotting analysis, and silver staining</b>For identifying interacting proteins of FLAG-tagged Multicilin by MASS analysis, MEFs were infected by pAd/CMV/V5 vector encoding 3xFLAG-Multicilin, NLS-6xmyc-E2f4ΔCt-VP16-T2A-Multicilin, and NLS-6xmyc-E2f4WT-T2A-Multicilin. Non-infected MEFs were used as the negative control. Two days after infection, the non-infected MEFs or infected MEFs were lysed in lysis buffer (50mM HEPES-KOH [pH 7.5], 500NaCl, 5mM EDTA [pH 8.0]), 2% Triton, DNase I (10ug/ml)) by incubation on ice for 20min. Lysates were cleared by centrifugation at 12,000 rpm for 20 min at 4 °C, then precleared by incubation with Protein G agarose (Invitrogen #20397) agitating for 1hr at 4°C. Spun-down beads were incubated with FLAG M2 agarose (Sigma #A2220) agitating for 2.5 hours at 4°C. The beads were washed twice with wash buffer (1:1 mix of 50mM HEPES and Lysis buffer), washed with lysis buffer twice, then washed twice again with wash buffer. Spun-down beads were incubated with 40uL of FLAG peptide (500ng/mL) for bound protein elution overnight at 4°C. Elutes were subjected to protein sampling for further immunoblot analysis and silver staining. Eluted protein samples and experimental protein lysates were subjected to SDS-PAGE and transferred to a PVDF membrane that was then blocked with 0.5% casein blocker (#161-0783, Bio-Rad) in PBS for 30 min followed by incubation with the indicated primary antibodies overnight at 4 °C in 0.1% Tween-20 in blocking buffer. After extensive washing in 0.1% Tween-20 in PBS, the blots were incubated with Alexa 680 or 800-conjugated anti- mouse or rabbit secondary antibodies (Invitrogen, A21058, A21076, A32735) for 45 min at room temperature, washed with 0.1% Tween-20 in PBS, and imaged using Odyssey (LI-COR). Silver staining was performed with Pierce Silver Stain Kit (Thermo #24612) based on the manufacturer’s instructions.
DOI: 10.6084/m9.figshare.23792301.v2
title: Raw Data files associated with Figure 5 in RBL2 represses the transcriptional activity of Multicilin to inhibit multiciliogenesis

description: <b>Immunoprecipitation, immunoblotting analysis, and silver staining</b>For identifying interacting proteins of FLAG-tagged Multicilin by MASS analysis, MEFs were infected by pAd/CMV/V5 vector encoding 3xFLAG-Multicilin, NLS-6xmyc-E2f4ΔCt-VP16-T2A-Multicilin, and NLS-6xmyc-E2f4WT-T2A-Multicilin. Non-infected MEFs were used as the negative control. Two days after infection, the non-infected MEFs or infected MEFs were lysed in lysis buffer (50mM HEPES-KOH [pH 7.5], 500NaCl, 5mM EDTA [pH 8.0]), 2% Triton, DNase I (10ug/ml)) by incubation on ice for 20min. Lysates were cleared by centrifugation at 12,000 rpm for 20 min at 4 °C, then precleared by incubation with Protein G agarose (Invitrogen #20397) agitating for 1hr at 4°C. Spun-down beads were incubated with FLAG M2 agarose (Sigma #A2220) agitating for 2.5 hours at 4°C. The beads were washed twice with wash buffer (1:1 mix of 50mM HEPES and Lysis buffer), washed with lysis buffer twice, then washed twice again with wash buffer. Spun-down beads were incubated with 40uL of FLAG peptide (500ng/mL) for bound protein elution overnight at 4°C. Elutes were subjected to protein sampling for further immunoblot analysis and silver staining. Eluted protein samples and experimental protein lysates were subjected to SDS-PAGE and transferred to a PVDF membrane that was then blocked with 0.5% casein blocker (#161-0783, Bio-Rad) in PBS for 30 min followed by incubation with the indicated primary antibodies overnight at 4 °C in 0.1% Tween-20 in blocking buffer. After extensive washing in 0.1% Tween-20 in PBS, the blots were incubated with Alexa 680 or 800-conjugated anti- mouse or rabbit secondary antibodies (Invitrogen, A21058, A21076, A32735) for 45 min at room temperature, washed with 0.1% Tween-20 in PBS, and imaged using Odyssey (LI-COR). Silver staining was performed with Pierce Silver Stain Kit (Thermo #24612) based on the manufacturer’s instructions.
DOI: 10.25345/c5xp6vd6p
title: MassIVE MSV000092541 - SARS-CoV-2 Nsp15 endoribonuclease
title: The emergence of SARS-CoV-2, the causative agent of COVID-19, has resulted in the largest pandemic in recent history. Current therapeutic strategies to mitigate this disease have focused on the development of vaccines and on drugs that inhibit the viral 3CL protease or RNA-dependent RNA polymerase enzymes. A less- explored and potentially complementary drug target is Nsp15, a uracil-specific RNA endonuclease that shields coronaviruses and other nidoviruses from mammalian innate immune defenses. Here, we perform a high-throughput screen of over 100,000 small molecules to identify Nsp15 inhibitors. We characterize the potency, mechanism, selectivity, and predicted binding mode of five lead compounds. We show that one of these, IPA-3, is a covalent inhibitor that modifies two key Cys residues (Cys291 and Cys293) within the catalytic core of Nsp15 that are implicated in activity. Moreover, we demonstrate that three of these inhibitors (Hexachlorophene, IPA-3, and CID5675221) block SARS-CoV-2 replication in cells at subtoxic doses. This study provides a pipeline for the identification of Nsp15 inhibitors, and pinpoints lead compounds for further development against COVID-19 and related coronavirus infections.
DOI: 10.15468/dl.g8ew9r
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query: { "TaxonKey" : [ "is Scilla ciliata Baker" ] } The dataset includes 0 records from 0 constituent datasets:
DOI: 10.6084/m9.figshare.23795949
title: Raw Data files associated with Figure 6 in RBL2 represses the transcriptional activity of Multicilin to inhibit multiciliogenesis.

description: <b>Immunoprecipitation, immunoblotting analysis, and silver staining</b>For identifying interacting proteins of FLAG-tagged Multicilin by MASS analysis, MEFs were infected by pAd/CMV/V5 vector encoding 3xFLAG-Multicilin, NLS-6xmyc-E2f4ΔCt-VP16-T2A-Multicilin, and NLS-6xmyc-E2f4WT-T2A-Multicilin. Non-infected MEFs were used as the negative control. Two days after infection, the non-infected MEFs or infected MEFs were lysed in lysis buffer (50mM HEPES-KOH [pH 7.5], 500NaCl, 5mM EDTA [pH 8.0]), 2% Triton, DNase I (10ug/ml)) by incubation on ice for 20min. Lysates were cleared by centrifugation at 12,000 rpm for 20 min at 4 °C, then precleared by incubation with Protein G agarose (Invitrogen #20397) agitating for 1hr at 4°C. Spun-down beads were incubated with FLAG M2 agarose (Sigma #A2220) agitating for 2.5 hours at 4°C. The beads were washed twice with wash buffer (1:1 mix of 50mM HEPES and Lysis buffer), washed with lysis buffer twice, then washed twice again with wash buffer. Spun-down beads were incubated with 40uL of FLAG peptide (500ng/mL) for bound protein elution overnight at 4°C. Elutes were subjected to protein sampling for further immunoblot analysis and silver staining. Eluted protein samples and experimental protein lysates were subjected to SDS-PAGE and transferred to a PVDF membrane that was then blocked with 0.5% casein blocker (#161-0783, Bio-Rad) in PBS for 30 min followed by incubation with the indicated primary antibodies overnight at 4 °C in 0.1% Tween-20 in blocking buffer. After extensive washing in 0.1% Tween-20 in PBS, the blots were incubated with Alexa 680 or 800-conjugated anti- mouse or rabbit secondary antibodies (Invitrogen, A21058, A21076, A32735) for 45 min at room temperature, washed with 0.1% Tween-20 in PBS, and imaged using Odyssey (LI-COR). Silver staining was performed with Pierce Silver Stain Kit (Thermo #24612) based on the manufacturer’s instructions.
DOI: 10.6084/m9.figshare.23795949.v1
title: Raw Data files associated with Figure 6 in RBL2 represses the transcriptional activity of Multicilin to inhibit multiciliogenesis.

description: <b>Immunoprecipitation, immunoblotting analysis, and silver staining</b>For identifying interacting proteins of FLAG-tagged Multicilin by MASS analysis, MEFs were infected by pAd/CMV/V5 vector encoding 3xFLAG-Multicilin, NLS-6xmyc-E2f4ΔCt-VP16-T2A-Multicilin, and NLS-6xmyc-E2f4WT-T2A-Multicilin. Non-infected MEFs were used as the negative control. Two days after infection, the non-infected MEFs or infected MEFs were lysed in lysis buffer (50mM HEPES-KOH [pH 7.5], 500NaCl, 5mM EDTA [pH 8.0]), 2% Triton, DNase I (10ug/ml)) by incubation on ice for 20min. Lysates were cleared by centrifugation at 12,000 rpm for 20 min at 4 °C, then precleared by incubation with Protein G agarose (Invitrogen #20397) agitating for 1hr at 4°C. Spun-down beads were incubated with FLAG M2 agarose (Sigma #A2220) agitating for 2.5 hours at 4°C. The beads were washed twice with wash buffer (1:1 mix of 50mM HEPES and Lysis buffer), washed with lysis buffer twice, then washed twice again with wash buffer. Spun-down beads were incubated with 40uL of FLAG peptide (500ng/mL) for bound protein elution overnight at 4°C. Elutes were subjected to protein sampling for further immunoblot analysis and silver staining. Eluted protein samples and experimental protein lysates were subjected to SDS-PAGE and transferred to a PVDF membrane that was then blocked with 0.5% casein blocker (#161-0783, Bio-Rad) in PBS for 30 min followed by incubation with the indicated primary antibodies overnight at 4 °C in 0.1% Tween-20 in blocking buffer. After extensive washing in 0.1% Tween-20 in PBS, the blots were incubated with Alexa 680 or 800-conjugated anti- mouse or rabbit secondary antibodies (Invitrogen, A21058, A21076, A32735) for 45 min at room temperature, washed with 0.1% Tween-20 in PBS, and imaged using Odyssey (LI-COR). Silver staining was performed with Pierce Silver Stain Kit (Thermo #24612) based on the manufacturer’s instructions.
DOI: 10.25345/c5t14v062
title: MassIVE MSV000092538 - Essential role of MFSD1-GLMP-GIMAP5 in lymphocyte survival and liver homeostasis
title: In this study, we detected three alleles that caused lymphopenia, splenomegaly, progressive liver pathology and extramedullary hematopoiesis (EMH), resulting from N-ethyl-N-nitrosourea (ENU)-induced mutations in the major facilitator superfamily domain containing 1 protein (Mfsd1) which encodes a lysosomal membrane-bound solute carrier protein with no previously described function in immunity. By proteomic analysis, we identified MFSD1 functions together with GLMP (glycosylated lysosomal membrane protein), and GIMAP5 (GTPase of immunity-associated protein 5). Germ line knock alleles of MFSD1, GLMP, and GIMAP5 were generated in mice and confirmed occurrence of lymphopenia, liver pathology, EMH, and lipid deposition in the bone marrow and liver of each strain. We found that the interaction of MFSD1 and GLMP with GIMAP5 is essential to maintain normal GIMAP5 expression that is critical to support lymphocyte development and liver homeostasis that suppresses EMH. These findings provide new insight into the mechanism of how MFSD1-GLMP-GIMAP5 complex functions together to regulate immunity and liver homeostasis that were previously unknown.
DOI: 10.48577/jpl.1uhzfy
title: Experimental Characterization of the Pyridine:Acetylene Co-crystal and Implications for Titan’s Surface

description: This dataset provides Raman spectra and XRD pattern data for the pyridine-acetylene co-crystal experiments presented in the manuscript. Specifically, the data covers figures 1-4 and 6-8 of the manuscript.
DOI: 10.5281/zenodo.7226610
title: Code Review Visualization: An Exploratory Study of Collaboration, Expertise, and Workload

description: Dataset for Code Review Visualization: An Exploratory Study of Collaboration, Expertise, and Workload
DOI: 10.5281/zenodo.7874726
title: Integrating Visual Aids to Enhance the Code Reviewer Selection Process Replication Package

description: Modern Code Review (MCR) is an integral part of a software development strategy that accelerates product quality by identifying defects, code smells, and other harmful practices. However, assigning appropriate reviewers to evaluate changed code during the review process remains challenging. While automated tools for reviewer assignments have limited impact in practice, the process often relies on manual investigation of project histories to retrieve knowledge of team members and their activities. Therefore, in this study, we present an approach to automatically assemble developers' information and visualize it meaningfully, which helps to choose appropriate reviewers. First, we propose three metrics that measure developers' collaboration, reviewers' expertise, and reviewers' workload and visualize them through networks. Second, we perform a case study of three popular open-source projects, where we compute and visualize each developers' information according to the proposed metrics. Finally, we conducted two online surveys to assess the developers' perceptions of the proposed visual benefits. The results show that the proposed method can assist in identifying relevant reviewers and be immensely helpful to new developers. Additionally, survey respondents expressed reliance on the efficacy of the visual aids in workload balancing and reducing review time.
DOI: 10.5281/zenodo.7226609
title: Integrating Visual Aids to Enhance the Code Reviewer Selection Process Replication Package

description: Modern Code Review (MCR) is an integral part of a software development strategy that accelerates product quality by identifying defects, code smells, and other harmful practices. However, assigning appropriate reviewers to evaluate changed code during the review process remains challenging. While automated tools for reviewer assignments have limited impact in practice, the process often relies on manual investigation of project histories to retrieve knowledge of team members and their activities. Therefore, in this study, we present an approach to automatically assemble developers' information and visualize it meaningfully, which helps to choose appropriate reviewers. First, we propose three metrics that measure developers' collaboration, reviewers' expertise, and reviewers' workload and visualize them through networks. Second, we perform a case study of three popular open-source projects, where we compute and visualize each developers' information according to the proposed metrics. Finally, we conducted two online surveys to assess the developers' perceptions of the proposed visual benefits. The results show that the proposed method can assist in identifying relevant reviewers and be immensely helpful to new developers. Additionally, survey respondents expressed reliance on the efficacy of the visual aids in workload balancing and reducing review time.