cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1568358.v1
title: The elicitor-responsive gene for a GRAS family protein, <i>CIGR2</i>, suppresses cell death in rice inoculated with rice blast fungus via activation of a heat shock transcription factor, <i>OsHsf23</i>

description: We show that a rice GRAS family protein, CIGR2, is a <i>bonafide</i> transcriptional activator, and through this function, targets the B-type heat shock protein-encoding gene <i>OsHsf23</i> (Os09g0456800). <i>CIGR2</i> (Os07g0583600) is an <i>N</i>-acetylchitooligosaccharide elicitor-responsive gene whose activity, through the direct transcriptional control of <i>OsHsf23</i>, is required for mediating hypersensitive cell death activation during pathogen infection. RNAi lines of <i>CIGR2</i> and <i>OsHsf23</i> similarly exhibited the higher level of granulation in the epidermal cells of leaf sheath inoculated with an avirulent isolate of rice blast fungus. Interestingly, we did not observe altered levels of resistance, suggesting that CIGR2 suppresses excessive cell death in the incompatible interaction with blast fungus via activation of <i>OsHsf23</i>.
DOI: 10.6084/m9.figshare.1568358.v2
title: The elicitor-responsive gene for a GRAS family protein, <i>CIGR2</i>, suppresses cell death in rice inoculated with rice blast fungus via activation of a heat shock transcription factor, <i>OsHsf23</i>

description: We show that a rice GRAS family protein, CIGR2, is a <i>bonafide</i> transcriptional activator, and through this function, targets the B-type heat shock protein-encoding gene <i>OsHsf23</i> (Os09g0456800). <i>CIGR2</i> (Os07g0583600) is an <i>N</i>-acetylchitooligosaccharide elicitor-responsive gene whose activity, through the direct transcriptional control of <i>OsHsf23</i>, is required for mediating hypersensitive cell death activation during pathogen infection. RNAi lines of <i>CIGR2</i> and <i>OsHsf23</i> similarly exhibited the higher level of granulation in the epidermal cells of leaf sheath inoculated with an avirulent isolate of rice blast fungus. Interestingly, we did not observe altered levels of resistance, suggesting that CIGR2 suppresses excessive cell death in the incompatible interaction with blast fungus via activation of <i>OsHsf23</i>.
DOI: 10.6084/m9.figshare.1568353
title: Registering 2D and 3D imaging data of bone during healing

description: <i>Purpose/Aims of the study</i>: Bone’s hierarchical structure can be visualized using a variety of methods. Many techniques, such as light and electron microscopy generate two-dimensional (2D) images, while micro-computed tomography (µCT) allows a direct representation of the three-dimensional (3D) structure. In addition, different methods provide complementary structural information, such as the arrangement of organic or inorganic compounds. The overall aim of the present study is to answer bone research questions by linking information of different 2D and 3D imaging techniques. A great challenge in combining different methods arises from the fact that they usually reflect different characteristics of the real structure. <i>Materials and methods</i>: We investigated bone during healing by means of µCT and a couple of 2D methods. Backscattered electron images were used to qualitatively evaluate the tissue’s calcium content and served as a position map for other experimental data. Nanoindentation and X-ray scattering experiments were performed to visualize mechanical and structural properties. <i>Results</i>: We present an approach for the registration of 2D data in a 3D µCT reference frame, where scanning electron microscopies serve as a methodic link. Backscattered electron images are perfectly suited for registration into µCT reference frames, since both show structures based on the same physical principles. We introduce specific registration tools that have been developed to perform the registration process in a semi-automatic way. <i>Conclusions</i>: By applying this routine, we were able to exactly locate structural information (e.g. mineral particle properties) in the 3D bone volume. In bone healing studies this will help to better understand basic formation, remodeling and mineralization processes.
DOI: 10.6084/m9.figshare.1568358.v3
title: The elicitor-responsive gene for a GRAS family protein, <i>CIGR2</i>, suppresses cell death in rice inoculated with rice blast fungus via activation of a heat shock transcription factor, <i>OsHsf23</i>

description: We show that a rice GRAS family protein, CIGR2, is a <i>bonafide</i> transcriptional activator, and through this function, targets the B-type heat shock protein-encoding gene <i>OsHsf23</i> (Os09g0456800). <i>CIGR2</i> (Os07g0583600) is an <i>N</i>-acetylchitooligosaccharide elicitor-responsive gene whose activity, through the direct transcriptional control of <i>OsHsf23</i>, is required for mediating hypersensitive cell death activation during pathogen infection. RNAi lines of <i>CIGR2</i> and <i>OsHsf23</i> similarly exhibited the higher level of granulation in the epidermal cells of leaf sheath inoculated with an avirulent isolate of rice blast fungus. Interestingly, we did not observe altered levels of resistance, suggesting that CIGR2 suppresses excessive cell death in the incompatible interaction with blast fungus via activation of <i>OsHsf23</i>.
DOI: 10.6084/m9.figshare.1568349
title: Association between maternal Group B Streptococcus surface-protein antibody concentrations and invasive disease in their infants

description: Objectives: Group B Streptococcus (GBS) surface-proteins have been shown to be immunogenic and potential vaccine candidates. We aim to determine the association between maternal IgG antibodies to select GBS surface-proteins and invasive GBS disease in their infants. Methods: Using a matched case–control study, maternal antibody levels for GBS-immunogenic bacterial adhesin, fibrinogen-binding protein A and pilus-island (PI) PI-1, PI-2a, PI-2b were compared between infants with invasive GBS disease and well-baby controls. Results: The absolute risk of disease did not differ between cases and colonized controls with increasing antibody concentrations for these surface-proteins. There was, however, a relative risk reduction in invasive disease associated with fibrinogen-binding protein A, with an adjusted odds ratio of 0.04 (95% CI: 0.01–0.69) at antibody levels ≥10,000 AU/ml. Conclusion: We have not demonstrated an association between naturally occurring fibrinogen-binding protein A, GBS-immunogenic bacterial adhesin, and PI surface-protein antibodies and the risk of invasive disease in young infants. These surface-proteins may not be suitable GBS vaccine candidates.
DOI: 10.6084/m9.figshare.1568358.v5
title: The elicitor-responsive gene for a GRAS family protein, <i>CIGR2</i>, suppresses cell death in rice inoculated with rice blast fungus via activation of a heat shock transcription factor, <i>OsHsf23</i>

description: We show that a rice GRAS family protein, CIGR2, is a <i>bonafide</i> transcriptional activator, and through this function, targets the B-type heat shock protein-encoding gene <i>OsHsf23</i> (Os09g0456800). <i>CIGR2</i> (Os07g0583600) is an <i>N</i>-acetylchitooligosaccharide elicitor-responsive gene whose activity, through the direct transcriptional control of <i>OsHsf23</i>, is required for mediating hypersensitive cell death activation during pathogen infection. RNAi lines of <i>CIGR2</i> and <i>OsHsf23</i> similarly exhibited the higher level of granulation in the epidermal cells of leaf sheath inoculated with an avirulent isolate of rice blast fungus. Interestingly, we did not observe altered levels of resistance, suggesting that CIGR2 suppresses excessive cell death in the incompatible interaction with blast fungus via activation of <i>OsHsf23</i>. <i>N</i>-Acetylchitooligosaccharides-responsive <i>CIGR2</i> suppresses cell death of rice in cooperation with <i>OsHsf23</i>.
DOI: 10.6084/m9.figshare.1568353.v1
title: Registering 2D and 3D imaging data of bone during healing

description: <i>Purpose/Aims of the study</i>: Bone’s hierarchical structure can be visualized using a variety of methods. Many techniques, such as light and electron microscopy generate two-dimensional (2D) images, while micro-computed tomography (µCT) allows a direct representation of the three-dimensional (3D) structure. In addition, different methods provide complementary structural information, such as the arrangement of organic or inorganic compounds. The overall aim of the present study is to answer bone research questions by linking information of different 2D and 3D imaging techniques. A great challenge in combining different methods arises from the fact that they usually reflect different characteristics of the real structure.<i>Materials and methods</i>: We investigated bone during healing by means of µCT and a couple of 2D methods. Backscattered electron images were used to qualitatively evaluate the tissue’s calcium content and served as a position map for other experimental data. Nanoindentation and X-ray scattering experiments were performed to visualize mechanical and structural properties.<i>Results</i>: We present an approach for the registration of 2D data in a 3D µCT reference frame, where scanning electron microscopies serve as a methodic link. Backscattered electron images are perfectly suited for registration into µCT reference frames, since both show structures based on the same physical principles. We introduce specific registration tools that have been developed to perform the registration process in a semi-automatic way.<i>Conclusions</i>: By applying this routine, we were able to exactly locate structural information (e.g. mineral particle properties) in the 3D bone volume. In bone healing studies this will help to better understand basic formation, remodeling and mineralization processes.
DOI: 10.6084/m9.figshare.1568358.v4
title: The elicitor-responsive gene for a GRAS family protein, <i>CIGR2</i>, suppresses cell death in rice inoculated with rice blast fungus via activation of a heat shock transcription factor, <i>OsHsf23</i>

description: We show that a rice GRAS family protein, CIGR2, is a <i>bonafide</i> transcriptional activator, and through this function, targets the B-type heat shock protein-encoding gene <i>OsHsf23</i> (Os09g0456800). <i>CIGR2</i> (Os07g0583600) is an <i>N</i>-acetylchitooligosaccharide elicitor-responsive gene whose activity, through the direct transcriptional control of <i>OsHsf23</i>, is required for mediating hypersensitive cell death activation during pathogen infection. RNAi lines of <i>CIGR2</i> and <i>OsHsf23</i> similarly exhibited the higher level of granulation in the epidermal cells of leaf sheath inoculated with an avirulent isolate of rice blast fungus. Interestingly, we did not observe altered levels of resistance, suggesting that CIGR2 suppresses excessive cell death in the incompatible interaction with blast fungus via activation of <i>OsHsf23</i>.
DOI: 10.6084/m9.figshare.1568349.v1
title: Association between maternal Group B Streptococcus surface-protein antibody concentrations and invasive disease in their infants

description: Objectives: Group B Streptococcus (GBS) surface-proteins have been shown to be immunogenic and potential vaccine candidates. We aim to determine the association between maternal IgG antibodies to select GBS surface-proteins and invasive GBS disease in their infants. Methods: Using a matched case–control study, maternal antibody levels for GBS-immunogenic bacterial adhesin, fibrinogen-binding protein A and pilus-island (PI) PI-1, PI-2a, PI-2b were compared between infants with invasive GBS disease and well-baby controls. Results: The absolute risk of disease did not differ between cases and colonized controls with increasing antibody concentrations for these surface-proteins. There was, however, a relative risk reduction in invasive disease associated with fibrinogen-binding protein A, with an adjusted odds ratio of 0.04 (95% CI: 0.01–0.69) at antibody levels ≥10,000 AU/ml. Conclusion: We have not demonstrated an association between naturally occurring fibrinogen-binding protein A, GBS-immunogenic bacterial adhesin, and PI surface-protein antibodies and the risk of invasive disease in young infants. These surface-proteins may not be suitable GBS vaccine candidates.
DOI: 10.6084/m9.figshare.1568349.v2
title: Association between maternal Group B Streptococcus surface-protein antibody concentrations and invasive disease in their infants

description: Objectives: Group B Streptococcus (GBS) surface-proteins have been shown to be immunogenic and potential vaccine candidates. We aim to determine the association between maternal IgG antibodies to select GBS surface-proteins and invasive GBS disease in their infants. Methods: Using a matched case–control study, maternal antibody levels for GBS-immunogenic bacterial adhesin, fibrinogen-binding protein A and pilus-island (PI) PI-1, PI-2a, PI-2b were compared between infants with invasive GBS disease and well-baby controls. Results: The absolute risk of disease did not differ between cases and colonized controls with increasing antibody concentrations for these surface-proteins. There was, however, a relative risk reduction in invasive disease associated with fibrinogen-binding protein A, with an adjusted odds ratio of 0.04 (95% CI: 0.01–0.69) at antibody levels ≥10,000 AU/ml. Conclusion: We have not demonstrated an association between naturally occurring fibrinogen-binding protein A, GBS-immunogenic bacterial adhesin, and PI surface-protein antibodies and the risk of invasive disease in young infants. These surface-proteins may not be suitable GBS vaccine candidates.
DOI: 10.6084/m9.figshare.1568349.v4
title: Association between maternal Group B Streptococcus surface-protein antibody concentrations and invasive disease in their infants

description: Objectives: Group B Streptococcus (GBS) surface-proteins have been shown to be immunogenic and potential vaccine candidates. We aim to determine the association between maternal IgG antibodies to select GBS surface-proteins and invasive GBS disease in their infants. Methods: Using a matched case–control study, maternal antibody levels for GBS-immunogenic bacterial adhesin, fibrinogen-binding protein A and pilus-island (PI) PI-1, PI-2a, PI-2b were compared between infants with invasive GBS disease and well-baby controls. Results: The absolute risk of disease did not differ between cases and colonized controls with increasing antibody concentrations for these surface-proteins. There was, however, a relative risk reduction in invasive disease associated with fibrinogen-binding protein A, with an adjusted odds ratio of 0.04 (95% CI: 0.01–0.69) at antibody levels ≥10,000 AU/ml. Conclusion: We have not demonstrated an association between naturally occurring fibrinogen-binding protein A, GBS-immunogenic bacterial adhesin, and PI surface-protein antibodies and the risk of invasive disease in young infants. These surface-proteins may not be suitable GBS vaccine candidates.
DOI: 10.6084/m9.figshare.1568349.v3
title: Association between maternal Group B Streptococcus surface-protein antibody concentrations and invasive disease in their infants

description: Objectives: Group B Streptococcus (GBS) surface-proteins have been shown to be immunogenic and potential vaccine candidates. We aim to determine the association between maternal IgG antibodies to select GBS surface-proteins and invasive GBS disease in their infants. Methods: Using a matched case–control study, maternal antibody levels for GBS-immunogenic bacterial adhesin, fibrinogen-binding protein A and pilus-island (PI) PI-1, PI-2a, PI-2b were compared between infants with invasive GBS disease and well-baby controls. Results: The absolute risk of disease did not differ between cases and colonized controls with increasing antibody concentrations for these surface-proteins. There was, however, a relative risk reduction in invasive disease associated with fibrinogen-binding protein A, with an adjusted odds ratio of 0.04 (95% CI: 0.01–0.69) at antibody levels ≥10,000 AU/ml. Conclusion: We have not demonstrated an association between naturally occurring fibrinogen-binding protein A, GBS-immunogenic bacterial adhesin, and PI surface-protein antibodies and the risk of invasive disease in young infants. These surface-proteins may not be suitable GBS vaccine candidates.
DOI: 10.6084/m9.figshare.1568337.v1
title: Combined evaluation of lc3b puncta and hmgb1 expression predicts residual risk of relapse after adjuvant chemotherapy in breast cancer

description: ABSTRACTIn spite of adjuvant chemotherapy, a significant fraction of patients with localized breast cancer (BC) relapse after optimal treatment. We determined the occurrence of cytoplasmic MAP1LC3B/LC3B (microtubule-associated protein 1 light chain 3B)-positive puncta, as well as the presence of nuclear HMGB1 (high mobility group box 1) in cancer cells within surgical BC specimens by immunohistochemistry, first in a test cohort (152 patients) and then in a validation cohort of localized BC patients who all received adjuvant anthracycline-based chemotherapy (1646 patients). Cytoplasmic LC3B<sup>+</sup> puncta inversely correlated with the intensity of SQSTM1 staining, suggesting that a high percentage cells with LC3B<sup>+</sup> puncta reflects autophagic flux. After setting optimal thresholds in the test cohort, cytoplasmic LC3B<sup>+</sup> puncta and nuclear HMGB1 were scored as positive in 27.2% and 28.6% of the tumors, respectively, in the validation cohort, while 8.7% were considered as double positive. LC3B<sup>+</sup> puncta or HMGB1 expression alone did not constitute independent prognostic factors for metastasis-free survival (MFS) in multivariate analyses. However, the combined positivity for LC3B<sup>+</sup> puncta and nuclear HMGB1 constituted an independent prognostic factor significantly associated with prolonged MFS (hazard ratio: 0.49 95% confidence interval [0.26-0.89]; <i>P</i>=0.02), and improved breast cancer specific survival (hazard ratio: 0.21 95% confidence interval [0.05-0.85]; <i>P</i>=0.029). Subgroup analyses revealed that within patients with poor-prognosis BC, HMGB1<sup>+ </sup>LC3B<sup>+</sup> double-positive tumors had a better prognosis than BC that lacked one or both of these markers. Altogether, these results suggest that the combined positivity for LC3B<sup>+</sup> puncta and nuclear HMGB1 is a positive predictor for longer BC survival.
DOI: 10.6084/m9.figshare.1568337.v2
title: Combined evaluation of LC3B puncta and HMGB1 expression predicts residual risk of relapse after adjuvant chemotherapy in breast cancer

description: In spite of adjuvant chemotherapy, a significant fraction of patients with localized breast cancer (BC) relapse after optimal treatment. We determined the occurrence of cytoplasmic MAP1LC3B/LC3B (microtubule-associated protein 1 light chain 3B)-positive puncta, as well as the presence of nuclear HMGB1 (high mobility group box 1) in cancer cells within surgical BC specimens by immunohistochemistry, first in a test cohort (152 patients) and then in a validation cohort of localized BC patients who all received adjuvant anthracycline-based chemotherapy (1646 patients). Cytoplasmic LC3B<sup>+</sup> puncta inversely correlated with the intensity of SQSTM1 staining, suggesting that a high percentage cells of LC3B<sup>+</sup> puncta reflects increased autophagic flux. After setting optimal thresholds in the test cohort, cytoplasmic LC3B<sup>+</sup> puncta and nuclear HMGB1 were scored as positive in 27.2% and 28.6% of the tumors, respectively, in the validation cohort, while 8.7% were considered as double positive. LC3B<sup>+</sup> puncta or HMGB1 expression alone did not constitute independent prognostic factors for metastasis-free survival (MFS) in multivariate analyses. However, the combined positivity for LC3B<sup>+</sup> puncta and nuclear HMGB1 constituted an independent prognostic factor significantly associated with prolonged MFS (hazard ratio: 0.49 95% confidence interval [0.26–0.89]; <i>P</i> = 0.02), and improved breast cancer specific survival (hazard ratio: 0.21 95% confidence interval [0.05–0.85]; <i>P</i> = 0.029). Subgroup analyses revealed that within patients with poor-prognosis BC, HMGB1<sup>+</sup> LC3B<sup>+</sup> double-positive tumors had a better prognosis than BC that lacked one or both of these markers. Altogether, these results suggest that the combined positivity for LC3B<sup>+</sup> puncta and nuclear HMGB1 is a positive predictor for longer BC survival.
DOI: 10.6084/m9.figshare.1568332
title: An Adaptive, Automatic Multiple-Case Deletion Technique for Detecting Influence in Regression

description: Critical to any regression analysis is the identification of observations that exert a strong influence on the fitted regression model. Traditional regression influence statistics such as Cook's distance and DFFITS, each based on deleting single observations, can fail in the presence of multiple influential observations if these influential observations “mask” one another, or if other effects such as “swamping” occur. Masking refers to the situation where an observation reveals itself as influential only after one or more other observations are deleted. Swamping occurs when points that are not actually outliers/influential are declared to be so because of the effects on the model of other unusual observations. One computationally expensive solution to these problems is the use of influence statistics that delete multiple rather than single observations. In this article, we build on previous work to produce a computationally feasible algorithm for detecting an unknown number of influential observations in the presence of masking. An important difference between our proposed algorithm and existing methods is that we focus on the data that remain after observations are deleted, rather than on the deleted observations themselves. Further, our approach uses a novel confirmatory step designed to provide a secondary assessment of identified observations. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1568337.v3
title: Combined evaluation of LC3B puncta and HMGB1 expression predicts residual risk of relapse after adjuvant chemotherapy in breast cancer

description: In spite of adjuvant chemotherapy, a significant fraction of patients with localized breast cancer (BC) relapse after optimal treatment. We determined the occurrence of cytoplasmic MAP1LC3B/LC3B (microtubule-associated protein 1 light chain 3B)-positive puncta, as well as the presence of nuclear HMGB1 (high mobility group box 1) in cancer cells within surgical BC specimens by immunohistochemistry, first in a test cohort (152 patients) and then in a validation cohort of localized BC patients who all received adjuvant anthracycline-based chemotherapy (1646 patients). Cytoplasmic LC3B<sup>+</sup> puncta inversely correlated with the intensity of SQSTM1 staining, suggesting that a high percentage cells of LC3B<sup>+</sup> puncta reflects increased autophagic flux. After setting optimal thresholds in the test cohort, cytoplasmic LC3B<sup>+</sup> puncta and nuclear HMGB1 were scored as positive in 27.2% and 28.6% of the tumors, respectively, in the validation cohort, while 8.7% were considered as double positive. LC3B<sup>+</sup> puncta or HMGB1 expression alone did not constitute independent prognostic factors for metastasis-free survival (MFS) in multivariate analyses. However, the combined positivity for LC3B<sup>+</sup> puncta and nuclear HMGB1 constituted an independent prognostic factor significantly associated with prolonged MFS (hazard ratio: 0.49 95% confidence interval [0.26–0.89]; <i>P</i> = 0.02), and improved breast cancer specific survival (hazard ratio: 0.21 95% confidence interval [0.05–0.85]; <i>P</i> = 0.029). Subgroup analyses revealed that within patients with poor-prognosis BC, HMGB1<sup>+</sup> LC3B<sup>+</sup> double-positive tumors had a better prognosis than BC that lacked one or both of these markers. Altogether, these results suggest that the combined positivity for LC3B<sup>+</sup> puncta and nuclear HMGB1 is a positive predictor for longer BC survival.