cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3492158
title: RNA- binding protein Stau2 is important for spindle integrity and meiosis progression in mouse oocytes

description: Staufen2 (Stau2) is a double-stranded RNA-binding protein involved in cell fate decision by regulating mRNA transport, mRNA stability, translation, and ribonucleoprotein assembly. Little is known about Stau2 expression and function in mammalian oocytes during meiosis. Herein we report the sub-cellular distribution and function of Stau2 in mouse oocyte meiosis. Western blot analysis revealed high and stable expression of Stau2 in oocytes from germinal vesicle (GV) to metaphase II (MII). Immunofluorescence showed that Stau2 was evenly distributed in oocytes at GV stage, and assembled as filaments after germinal vesicle breakdown (GVBD), particularly, colocalized with spindle at MI and MII. Stau2 was disassembled when microtubules were disrupted with nocodazole, on the other hand, when MTs were stabilized with taxol, Stau2 was not colocalized with the stabilized microtubules, but aggregated around the chromosomes array, indicating Stau2 assembly and colocalization with microtubules require both microtubule integrity and its normal dynamics. During interphase and mitosis of BHK and MEF cells, Stau2 was not distributed on microtubules, but colocalized with <i>cis</i>-Golgi marker GM130, implying its association with Golgi complex but not the spindle in fully differentiated somatic cells. Specific morpholino oligo-mediated Stau2 knockdown disrupted spindle formation, chromosome alignment and microtubule-kinetochore attachment in oocytes. The majority oocytes were arrested at MI stage, with bright MAD1 at kinetochores, indicating activation of spindle assembly checkpoint (SAC). Some oocytes were stranded at telophase I (TI), implying suppressed first polar body extrution. Together these data demonstrate that Stau2 is required for spindle formation and timely meiotic progression in mouse oocytes.
DOI: 10.6084/m9.figshare.3492158.v1
title: RNA- binding protein Stau2 is important for spindle integrity and meiosis progression in mouse oocytes

description: Staufen2 (Stau2) is a double-stranded RNA-binding protein involved in cell fate decision by regulating mRNA transport, mRNA stability, translation, and ribonucleoprotein assembly. Little is known about Stau2 expression and function in mammalian oocytes during meiosis. Herein we report the sub-cellular distribution and function of Stau2 in mouse oocyte meiosis. Western blot analysis revealed high and stable expression of Stau2 in oocytes from germinal vesicle (GV) to metaphase II (MII). Immunofluorescence showed that Stau2 was evenly distributed in oocytes at GV stage, and assembled as filaments after germinal vesicle breakdown (GVBD), particularly, colocalized with spindle at MI and MII. Stau2 was disassembled when microtubules were disrupted with nocodazole, on the other hand, when MTs were stabilized with taxol, Stau2 was not colocalized with the stabilized microtubules, but aggregated around the chromosomes array, indicating Stau2 assembly and colocalization with microtubules require both microtubule integrity and its normal dynamics. During interphase and mitosis of BHK and MEF cells, Stau2 was not distributed on microtubules, but colocalized with <i>cis</i>-Golgi marker GM130, implying its association with Golgi complex but not the spindle in fully differentiated somatic cells. Specific morpholino oligo-mediated Stau2 knockdown disrupted spindle formation, chromosome alignment and microtubule-kinetochore attachment in oocytes. The majority oocytes were arrested at MI stage, with bright MAD1 at kinetochores, indicating activation of spindle assembly checkpoint (SAC). Some oocytes were stranded at telophase I (TI), implying suppressed first polar body extrution. Together these data demonstrate that Stau2 is required for spindle formation and timely meiotic progression in mouse oocytes.
DOI: 10.6084/m9.figshare.3492152
title: BRCA2 mediates centrosome cohesion via an interaction with cytoplasmic dynein

description: BRCA2 is responsible for familial breast and ovarian cancer and has been linked to DNA repair and centrosome duplication. Here we analyzed the mechanism by which the centrosomal localization signal (CLS) of BRCA2 interacts with cytoplasmic dynein 1 to localize BRCA2 to the centrosome. <i>In vitro</i> pull-down assays demonstrated that BRCA2 directly binds to the cytoplasmic dynein 1 light intermediate chain 2. A dominant-negative HA-CLS-DsRed fusion protein, the depletion of dynein by siRNA, and the inactivation of dynein by EHNA, inhibited the localization of BRCA2 at centrosomes and caused the separation of centrosome pairs during the S-phase. The double depletion of BRCA2 and C-Nap1 caused a larger dispersion of centrosome distances than the silencing of C-Nap1. These results suggest that cytoplasmic dynein 1 binds to BRCA2 through the latter's CLS and BRCA2 mediates the cohesion between centrosomes during the S phase, potentially serving as a cell-cycle checkpoint.
DOI: 10.6084/m9.figshare.3492152.v1
title: BRCA2 mediates centrosome cohesion via an interaction with cytoplasmic dynein

description: BRCA2 is responsible for familial breast and ovarian cancer and has been linked to DNA repair and centrosome duplication. Here we analyzed the mechanism by which the centrosomal localization signal (CLS) of BRCA2 interacts with cytoplasmic dynein 1 to localize BRCA2 to the centrosome. <i>In vitro</i> pull-down assays demonstrated that BRCA2 directly binds to the cytoplasmic dynein 1 light intermediate chain 2. A dominant-negative HA-CLS-DsRed fusion protein, the depletion of dynein by siRNA, and the inactivation of dynein by EHNA, inhibited the localization of BRCA2 at centrosomes and caused the separation of centrosome pairs during the S-phase. The double depletion of BRCA2 and C-Nap1 caused a larger dispersion of centrosome distances than the silencing of C-Nap1. These results suggest that cytoplasmic dynein 1 binds to BRCA2 through the latter's CLS and BRCA2 mediates the cohesion between centrosomes during the S phase, potentially serving as a cell-cycle checkpoint.
DOI: 10.6084/m9.figshare.3492149
title: Conformational dynamics of Peb4 exhibit “mother’s arms” chain model: a molecular dynamics study

description: Peb4 from <i>Campylobacter jejuni</i> is an intertwined dimeric, periplasmic holdase, which also exhibits peptidyl prolyl cis/trans isomerase (PPIase) activity. Peb4 gene deletion alters the outer membrane protein profile and impairs cellular adhesion and biofilm formation for <i>C. jejuni</i>. Earlier crystallographic study has proposed that the PPIase domains are flexible and might form a cradle for holding the substrate and these aspects of Peb4 were explored using sub-microsecond molecular dynamics simulations in solution environment. Our simulations have revealed that PPIase domains are highly flexible and undergo a large structural change where they move apart from each other by 8 nm starting at .5 nm. Further, this large conformational change renders Peb4 as a compact protein with crossed-over conformation, forms a central cavity, which can “cradle” the target substrate. As reported for other chaperone proteins, flexibility of linker region connecting the chaperone and PPIase domains is key to forming the “crossed-over” conformation. The conformational transition of the Peb4 protein from the X-ray structure to the crossed-over conformation follows the “mother’s arms” chain model proposed for the FkpA chaperone protein. Our results offer insights into how Peb4 and similar chaperones can use the conformational heterogeneity at their disposal to perform its much-revered biological function.
DOI: 10.6084/m9.figshare.3492149.v1
title: Conformational dynamics of Peb4 exhibit “mother’s arms” chain model: a molecular dynamics study

description: Peb4 from <i>Campylobacter jejuni</i> is an intertwined dimeric, periplasmic holdase, which also exhibits peptidyl prolyl cis/trans isomerase (PPIase) activity. Peb4 gene deletion alters the outer membrane protein profile and impairs cellular adhesion and biofilm formation for <i>C. jejuni</i>. Earlier crystallographic study has proposed that the PPIase domains are flexible and might form a cradle for holding the substrate and these aspects of Peb4 were explored using sub-microsecond molecular dynamics simulations in solution environment. Our simulations have revealed that PPIase domains are highly flexible and undergo a large structural change where they move apart from each other by 8 nm starting at .5 nm. Further, this large conformational change renders Peb4 as a compact protein with crossed-over conformation, forms a central cavity, which can “cradle” the target substrate. As reported for other chaperone proteins, flexibility of linker region connecting the chaperone and PPIase domains is key to forming the “crossed-over” conformation. The conformational transition of the Peb4 protein from the X-ray structure to the crossed-over conformation follows the “mother’s arms” chain model proposed for the FkpA chaperone protein. Our results offer insights into how Peb4 and similar chaperones can use the conformational heterogeneity at their disposal to perform its much-revered biological function.
DOI: 10.6084/m9.figshare.3492143
title: Tumor mucoso apendicular / Appendiceal mucous tumor

description: Los tumores mucosos apendiculares tienen baja incidencia y comúnmente se diagnostican en el estudio anatomo-patólogico después de la apendicectomía. Se reporta el caso de una mujer de 41 años de edad, con un cuadro clínico de ocho meses de evolución, caracterizado por dolor abdominal de tipo opresivo, difuso y de gran intensidad en el hemiabdomen inferior, acompañado de náuseas. Después de cinco meses de iniciado este cuadro clínico, se evidenció una masa en la fosa iliaca derecha; el dolor se agudizó e intensificó, y las náuseas continuaron, por lo cual fue remitida al hospital. En los exámenes practicados se observó una masa quística compleja abdomino-pélvica de origen indeterminado, y la tomografía computadorizada de abdomen fue sugestiva de mucocele apendicular. Con estos hallazgos, se optó por el tratamiento quirúrgico por laparotomía, consistente en hemicolectomía derecha, con resección parcial de íleon, epiplectomía, histerectomía y salpigooforectomía bilateral.<br><b>AUTOR: </b><b>Diego Ángeles, Pedro</b>; <b>Vega, Ximena</b>; <b>Palacios, José</b><b>EDITORIAL: </b><b>Asociación Colombiana de Cirugía</b><b>REVISTA: </b><b>Revista Colombiana de Cirugía (rev. colomb. cir.)</b><b>FECHA DE PUBLICACIÓN: MAR 2016</b><b>PDF: Full text / Texto completo</b><b>URL: </b>http://hdl.handle.net/10757/615473<b>ENLACES ADICIONALES: </b>http://www.scielo.org.co/scielo.php?script=sci_arttext&pid=S2011-75822016000100008&lng=es&nrm=iso&tlng=es
DOI: 10.6084/m9.figshare.3492143.v1
title: Tumor mucoso apendicular / Appendiceal mucous tumor

description: Los tumores mucosos apendiculares tienen baja incidencia y comúnmente se diagnostican en el estudio anatomo-patólogico después de la apendicectomía. Se reporta el caso de una mujer de 41 años de edad, con un cuadro clínico de ocho meses de evolución, caracterizado por dolor abdominal de tipo opresivo, difuso y de gran intensidad en el hemiabdomen inferior, acompañado de náuseas. Después de cinco meses de iniciado este cuadro clínico, se evidenció una masa en la fosa iliaca derecha; el dolor se agudizó e intensificó, y las náuseas continuaron, por lo cual fue remitida al hospital. En los exámenes practicados se observó una masa quística compleja abdomino-pélvica de origen indeterminado, y la tomografía computadorizada de abdomen fue sugestiva de mucocele apendicular. Con estos hallazgos, se optó por el tratamiento quirúrgico por laparotomía, consistente en hemicolectomía derecha, con resección parcial de íleon, epiplectomía, histerectomía y salpigooforectomía bilateral.<br><b>AUTOR: </b><b>Diego Ángeles, Pedro</b>; <b>Vega, Ximena</b>; <b>Palacios, José</b><b>EDITORIAL: </b><b>Asociación Colombiana de Cirugía</b><b>REVISTA: </b><b>Revista Colombiana de Cirugía (rev. colomb. cir.)</b><b>FECHA DE PUBLICACIÓN: MAR 2016</b><b>PDF: Full text / Texto completo</b><b>URL: </b>http://hdl.handle.net/10757/615473<b>ENLACES ADICIONALES: </b>http://www.scielo.org.co/scielo.php?script=sci_arttext&pid=S2011-75822016000100008&lng=es&nrm=iso&tlng=es
DOI: 10.6084/m9.figshare.3492098
title: Pico and Nanoplankton Abundance and Carbon Stocks along the Brazilian Bight. PeerJ. Supplementary material. Table S1.

description: <b>Table S1.</b> Raw flow cytometry and environmental data.
DOI: 10.6084/m9.figshare.3492098.v2
title: Pico and Nanoplankton Abundance and Carbon Stocks along the Brazilian Bight. PeerJ. Supplementary material. Table S1.

description: <b>Table S1.</b> Raw flow cytometry and environmental data.
DOI: 10.6084/m9.figshare.3492098.v1
title: Pico and Nanoplankton Abundance and Carbon Stock Dynamics along the Brazilian Bight. PeerJ. Supplementary material. Table S1.

description: <b>Table S1.</b> Raw flow cytometry and environmental data.
DOI: 10.6084/m9.figshare.3492068
title: respiratory atmospheric observations Greek 1 2004.xls

description: This data set dates from 2004. It is a 10 column excel spread sheet. This data set contains daily health condition data on hospital admission of young children with in the Athens Greece urbanized area. The data set also contains atmospheric measures of aerosol atmospheric optical thickness. The columns are 1) Julian date, 2) total daily count of asthma hospital admissions, 3)weighted daily average count to accommodated capacitance of asthma expression 4) measured AOT values of first pixel in over urbanized area 5) measured AOT of second pixel over urbanized area (in the event of more than one pixel in area) 6)measured AOT of third pixel over urbanized area (in the event of more than two pixel in area) 7) measured AOT of fourth pixel over urbanized area (in the event of more than three pixel in area), 8) count of pixels in urbanized area, 9) weighted 10 day AOT incidence, and column 10 is a draft column of preliminary correlations of various date ranges between incidence counts and AOT value measures. The correlation date ranges in column 10 are indicated in the excel expression in the column 10
DOI: 10.6084/m9.figshare.3492068.v1
title: respiratory atmospheric observations Greek 1 2004.xls

description: This data set dates from 2004. It is a 10 column excel spread sheet. This data set contains daily health condition data on hospital admission of young children with in the Athens Greece urbanized area. The data set also contains atmospheric measures of aerosol atmospheric optical thickness. The columns are 1) Julian date, 2) total daily count of asthma hospital admissions, 3)weighted daily average count to accommodated capacitance of asthma expression 4) measured AOT values of first pixel in over urbanized area 5) measured AOT of second pixel over urbanized area (in the event of more than one pixel in area) 6)measured AOT of third pixel over urbanized area (in the event of more than two pixel in area) 7) measured AOT of fourth pixel over urbanized area (in the event of more than three pixel in area), 8) count of pixels in urbanized area, 9) weighted 10 day AOT incidence, and column 10 is a draft column of preliminary correlations of various date ranges between incidence counts and AOT value measures. The correlation date ranges in column 10 are indicated in the excel expression in the column 10
DOI: 10.6084/m9.figshare.3491951
title: test-data.zip

description: Test data set for MetaGen.
DOI: 10.6084/m9.figshare.3491945
title: Alignments.zip

description: This zipfile contains the sequence alignments used for the phylogenetic trees in the publication "Draft genome sequences of eight bacteria isolated from the indoor environment: Staphylococcus capitis strain H36, S. capitis strain H65, S. cohnii strain H62, S. hominis strain H69, Microbacterium sp. strain H83, Mycobacterium iranicum strain H39, Plantibacter sp. strain H53, and Pseudomonas oryzihabitans strain H72"<br>
DOI: 10.6084/m9.figshare.3491924
title: Spectral Data Files for reproducing Figure 3 and Figure S1

description: There are eight datasets (four for Figure 3 and four for Figure S1) and each dataset consists of three comma separated files. 1) SpectralData (zipped): Numeric matrix where rows are the samples and the columns are the spectral variables.2) SampleInfo: Metadata for the samples where binary vectors for cohorts, phases and QC samples are given. First row includes the headers of the columns.3) VariableInfo: Metadata for the variables where NMR chemical shifts in ppm are given. First row includes the header of the column.
DOI: 10.6084/m9.figshare.3491924.v2
title: Spectral Data Files for reproducing Figure 3 and Figure S1

description: There are eight datasets (four for Figure 3 and four for Figure S1) and each dataset consists of three comma separated files. 1) SpectralData (zipped): Numeric matrix where rows are the samples and the columns are the spectral variables.2) SampleInfo: Metadata for the samples where binary vectors for cohorts, phases and QC samples are given. First row includes the headers of the columns.3) VariableInfo: Metadata for the variables where NMR chemical shifts in ppm are given. First row includes the header of the column.
DOI: 10.6084/m9.figshare.3491924.v1
title: Spectral Data Files for reproducing Figure 3 and Figure S1

description: There are eight datasets (four for Figure 3 and four for Figure S1) and each dataset consists of three comma separated files. 1) SpectralData (zipped): Numeric matrix where rows are the samples and the columns are the spectral variables.2) SampleInfo: Metadata for the samples where binary vectors for cohorts, phases and QC samples are given. First row includes the headers of the columns.3) VariableInfo: Metadata for the variables where NMR chemical shifts in ppm are given. First row includes the header of the column.
DOI: 10.6084/m9.figshare.3491873.v1
title: CUAHSIworkshopdata

description: This is the dataset prepared for CUAHSI workshop
DOI: 10.6084/m9.figshare.3491825
title: LPFG.jpg

description: Layout of LPG
DOI: 10.6084/m9.figshare.3491825.v1
title: LPFG.jpg

description: Layout of LPG
DOI: 10.6084/m9.figshare.3491726
title: Enriched housing reduces disesase susceptibility.xlsx

description: Data set belonging to the article : Enriched housing reduces disease susceptibility to co-infection with Porcine Reproductive and Respiratory Virus (PRRSV) and <i>Actinobacillus</i> <i>pleuropneumoniae</i> (<i>A. pleuropneumoniae</i>) in young pigs
DOI: 10.6084/m9.figshare.3491714
title: S1 Figure from the paper "Genetic drift, not life history or RNAi, determine long term evolution of transposable elements"

description: <b>S1 Figure:</b> Correlation between TE loads and genome assembly statistics. The correlation between TE loads and the N50 length, the genome assembly length and the genome size.
DOI: 10.6084/m9.figshare.3491714.v2
title: S1 Figure from the paper "Genetic drift, not life history or RNAi, determine long term evolution of transposable elements"

description: <b>S1 Figure:</b> Correlation between TE loads and genome assembly statistics. The correlation between TE loads and the N50 length, the genome assembly length and the genome size.
DOI: 10.6084/m9.figshare.3491714.v1
title: Nematoda TE MS, S1 Figure

description: <b>S1 Figure:</b> Correlation between TE loads and genome assembly statistics. The correlation between TE loads and the N50 length, the genome assembly length and the genome size.
DOI: 10.6084/m9.figshare.3491690
title: Jekyll posts with a DOI number

description: The next step in the publishing of this _open clinical trial notebook_ is to get a _DOI_ (Digital Object Identifier) for each post. DOIs are [persistent interoperable identifiers], internet uniform resource locators (URL) with the characteristic of being persistent and not subject to 'link rot'. This makes them useful for identification and citation of academic material. A not-for-profit organization, the [International DOI Foundation] is the governance and management body for the Registration Agencies that provides DOI numbers.
DOI: 10.6084/m9.figshare.3491690.v1
title: Jekyll posts with a DOI number

description: The next step in the publishing of this _open clinical trial notebook_ is to get a _DOI_ (Digital Object Identifier) for each post. DOIs are [persistent interoperable identifiers], internet uniform resource locators (URL) with the characteristic of being persistent and not subject to 'link rot'. This makes them useful for identification and citation of academic material. A not-for-profit organization, the [International DOI Foundation] is the governance and management body for the Registration Agencies that provides DOI numbers.
DOI: 10.6084/m9.figshare.3491663
title: Image inventory.xlsx

description: Inventory of image file names
DOI: 10.6084/m9.figshare.3491615
title: Supplementary Material for: Photochemotherapy of Cutaneous Graft-versus-Host Disease May Reduce Concomitant Visceral Disease

description: <i>Background:</i> Photochemotherapy may be used to treat cutaneous graft-versus-host disease (GvHD). Animal models show that in the days after photochemotherapy and antigen provocation, cells with an antigen-specific suppressive phenotype are elicited in the lymphoid organs. In GvHD, host antigens are present not only in the skin treated by photochemotherapy but also in the visceral tissues. <i>Objective:</i> The aim of this paper was to evaluate the effect on visceral acute GvHD (aGvHD) of photochemotherapy of the skin. <i>Methods:</i> We retrospectively evaluated 33 patients with aGvHD of the skin, the liver, and/or the gastrointestinal tract treated with photochemotherapy for their aGvHD of the skin and did a long-term follow-up of 10 years on survival. <i>Results:</i> The complete response (CR) to photochemotherapy was 39%, the complete and partial response was 64% and the 6-month survival was 64%. Total body irradiation (TBI) before hematopoietic stem cell transplantation predisposed for CR of aGvHD of the liver and the gastrointestinal tract (p = 0.045). In the TBI group, the accumulated dose (numbers of treatments) for CR of visceral aGvHD increased with the body surface area affected by disease, from 8 (min-max: 5-14) for skin disease stage 1 to 10.5 (6-33) for stage 2 and 13 (11-21) for stage 3 (p = 0.04). Skin disease stage 1 showed a trend to be associated with CR in visceral disease at 28, 56, and 100 days (p = 0.07). Overall CR in visceral disease predicted a better 10-year overall survival (p = 0.0036). Finally, after TBI aGvHD of the gastrointestinal tract without anti-thymocyte globulin (ATG), clearance of T cells and dendritic cells responded better than aGvHD of the liver and aGvHD of the gastrointestinal tract with ATG (p = 0.01). <i>Conclusion:</i> Photochemotherapy after ionizing irradiation regulates the cell-mediated immunity in the viscera, and the systemic efficacy increases when the skin itself is less affected by disease. ATG modulates the regulatory effect of the gastrointestinal tract.