cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1569497.v3
title: What Teachers Should Know About the Bootstrap: Resampling in the Undergraduate Statistics Curriculum

description: Bootstrapping has enormous potential in statistics education and practice, but there are subtle issues and ways to go wrong. For example, the common combination of nonparametric bootstrapping and bootstrap percentile confidence intervals is less accurate than using <i>t</i>-intervals for small samples, though more accurate for larger samples. My goals in this article are to provide a deeper understanding of bootstrap methods—how they work, when they work or not, and which methods work better—and to highlight pedagogical issues. Supplementary materials for this article are available online. [Received December 2014. Revised August 2015]
DOI: 10.6084/m9.figshare.1569495.v2
title: Regulation of the chitin degradation and utilization system by the ChiX small RNA in <i>Serratia marcescens</i> 2170

description: <i>Serratia marcescens</i> 2170 produces three different types of chitinases and chitin-binding protein CBP21. We found that transposon insertion into the 5′ untranslated region (5′ UTR) of <i>chiPQ</i>-<i>ctb</i> led to defective chitinase and CBP21 production. ChiX small RNA possessed the complementary sequence of the 5′ UTRs of the <i>chiPQ</i>-<i>ctb</i> and <i>chiR</i> and repressed the expression of <i>chiP</i> and <i>chiR</i>. ChiX was detected in a medium containing glucose, glycerol, GlcNAc, and (GlcNAc)<sub>2</sub>, but the expression of both <i>chiP</i> and <i>chiR</i> was only observed in a medium containing (GlcNAc)<sub>2</sub>. ∆<i>chiX</i> mutant produced chitinases, CBP21, and chitobiase without induction. <i>chiP</i> transcripts were more abundant than those of <i>chiR</i> or <i>chiX</i> in a medium containing (GlcNAc)<sub>2</sub>. These results suggest that the constitutively expressed ChiX binds to the highly abundant <i>chiP</i> 5′ UTR, thereby leading to the induction of <i>chiR</i> mRNA translation and the subsequent expression of chitinases and CBP21.
DOI: 10.6084/m9.figshare.1569497.v2
title: <b>What Teachers Should Know about the Bootstrap: Resampling in the Undergraduate Statistics Curriculum</b>

description: Bootstrapping has enormous potential in statistics education and practice, but there are subtle issues and ways to go wrong. For example, the common combination of nonparametric bootstrapping and bootstrap percentile confidence intervals is less accurate than using <i>t</i>-intervals for small samples, though more accurate for larger samples. My goals in this article are to provide a deeper understanding of bootstrap methods—how they work, when they work or not, and which methods work better—and to highlight pedagogical issues.
DOI: 10.6084/m9.figshare.1569495.v4
title: Regulation of the chitin degradation and utilization system by the ChiX small RNA in <i>Serratia marcescens</i> 2170

description: <i>Serratia marcescens</i> 2170 produces three different types of chitinases and chitin-binding protein CBP21. We found that transposon insertion into the 5′ untranslated region (5′ UTR) of <i>chiPQ</i>-<i>ctb</i> led to defective chitinase and CBP21 production. ChiX small RNA possessed the complementary sequence of the 5′ UTRs of the <i>chiPQ</i>-<i>ctb</i> and <i>chiR</i> and repressed the expression of <i>chiP</i> and <i>chiR</i>. ChiX was detected in a medium containing glucose, glycerol, GlcNAc, and (GlcNAc)<sub>2</sub>, but the expression of both <i>chiP</i> and <i>chiR</i> was only observed in a medium containing (GlcNAc)<sub>2</sub>. ∆<i>chiX</i> mutant produced chitinases, CBP21, and chitobiase without induction. <i>chiP</i> transcripts were more abundant than those of <i>chiR</i> or <i>chiX</i> in a medium containing (GlcNAc)<sub>2</sub>. These results suggest that the constitutively expressed ChiX binds to the highly abundant <i>chiP</i> 5′ UTR, thereby leading to the induction of <i>chiR</i> mRNA translation and the subsequent expression of chitinases and CBP21.
DOI: 10.6084/m9.figshare.1569495.v3
title: Regulation of the chitin degradation and utilization system by the ChiX small RNA in <i>Serratia marcescens</i> 2170

description: <i>Serratia marcescens</i> 2170 produces three different types of chitinases and chitin-binding protein CBP21. We found that transposon insertion into the 5′ untranslated region (5′ UTR) of <i>chiPQ</i>-<i>ctb</i> led to defective chitinase and CBP21 production. ChiX small RNA possessed the complementary sequence of the 5′ UTRs of the <i>chiPQ</i>-<i>ctb</i> and <i>chiR</i> and repressed the expression of <i>chiP</i> and <i>chiR</i>. ChiX was detected in a medium containing glucose, glycerol, GlcNAc, and (GlcNAc)<sub>2</sub>, but the expression of both <i>chiP</i> and <i>chiR</i> was only observed in a medium containing (GlcNAc)<sub>2</sub>. ∆<i>chiX</i> mutant produced chitinases, CBP21, and chitobiase without induction. <i>chiP</i> transcripts were more abundant than those of <i>chiR</i> or <i>chiX</i> in a medium containing (GlcNAc)<sub>2</sub>. These results suggest that the constitutively expressed ChiX binds to the highly abundant <i>chiP</i> 5′ UTR, thereby leading to the induction of <i>chiR</i> mRNA translation and the subsequent expression of chitinases and CBP21.
DOI: 10.6084/m9.figshare.1569476.v2
title: Confidence Bands for ROC Curves With Serially Dependent Data

description: We propose serial correlation-robust asymptotic confidence bands for the receiver operating characteristic (ROC) curve and its functional, viz., the area under ROC curve (AUC), estimated by quasi-maximum likelihood in the binormal model. Our simulation experiments confirm that this new method performs fairly well in finite samples, and confers an additional measure of robustness to nonnormality. The conventional procedure is found to be markedly undersized in terms of yielding empirical coverage probabilities lower than the nominal level, especially when the serial correlation is strong. An example from macroeconomic forecasting demonstrates the importance of accounting for serial correlation when the probability forecasts for real GDP declines are evaluated using ROC. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1569472.v1
title: RAB24 facilitates clearance of autophagic compartments during basal conditions

description: RAB24 belongs to a family of small GTPases and has been implicated to function in autophagy. Here we confirm the intracellular localization of RAB24 to autophagic vacuoles with immuno electron microscopy and cell fractionation, and show that prenylation and guanine nucleotide binding are necessary for the targeting of RAB24 to autophagic compartments. Further, we show that RAB24 plays a role in the maturation and/or clearance of autophagic compartments under nutrient-rich conditions, but not during short amino acid starvation. Quantitative electron microscopy shows an increase in the numbers of late autophagic compartments in cells silenced for <i>RAB24</i>, and mRFP-GFP-LC3 probe and autophagy flux experiments indicate that this is due to a hindrance in their clearance. Formation of autophagosomes is shown to be unaffected by <i>RAB24</i>-silencing with siRNA. A defect in aggregate clearance in the absence of RAB24 is also shown in cells forming polyglutamine aggregates. This study places RAB24 function in the termination of the autophagic process under nutrient-rich conditions.
DOI: 10.6084/m9.figshare.1569469
title: Opinions of Japanese and American ALS caregivers regarding tracheostomy with invasive ventilation (TIV)

description: Our objective was to learn more about possible factors contributing to the higher rates of tracheostomy with invasive ventilation (TIV) for ALS patients in Japan compared with the United States by eliciting attitudes of caregivers of ALS patients in both countries. One hundred and fifty-four American caregivers from five, geographically-distributed ALS clinics and 66 Japanese caregivers from six sites in Japan completed questionnaires regarding TIV. Results showed that 33% of American caregivers were in favor of TIV for their family member compared to 53% of Japanese caregivers; 44% of American and 37% of Japanese caregivers were undecided; and 22% of American and 10% of Japanese caregivers were opposed (<i>p</i>
DOI: 10.6084/m9.figshare.1569472.v2
title: RAB24 facilitates clearance of autophagic compartments during basal conditions

description: RAB24 belongs to a family of small GTPases and has been implicated to function in autophagy. Here we confirm the intracellular localization of RAB24 to autophagic vacuoles with immuno electron microscopy and cell fractionation, and show that prenylation and guanine nucleotide binding are necessary for the targeting of RAB24 to autophagic compartments. Further, we show that RAB24 plays a role in the maturation and/or clearance of autophagic compartments under nutrient-rich conditions, but not during short amino acid starvation. Quantitative electron microscopy shows an increase in the numbers of late autophagic compartments in cells silenced for <i>RAB24</i>, and mRFP-GFP-LC3 probe and autophagy flux experiments indicate that this is due to a hindrance in their clearance. Formation of autophagosomes is shown to be unaffected by <i>RAB24</i>-silencing with siRNA. A defect in aggregate clearance in the absence of RAB24 is also shown in cells forming polyglutamine aggregates. This study places RAB24 function in the termination of the autophagic process under nutrient-rich conditions.
DOI: 10.6084/m9.figshare.1569472
title: RAB24 facilitates clearance of autophagic compartments during basal conditions

description: RAB24 belongs to a family of small GTPases and has been implicated to function in autophagy. Here we confirm the intracellular localization of RAB24 to autophagic vacuoles with immuno electron microscopy and cell fractionation, and show that prenylation and guanine nucleotide binding are necessary for the targeting of RAB24 to autophagic compartments. Further, we show that RAB24 plays a role in the maturation and/or clearance of autophagic compartments under nutrient-rich conditions, but not during short amino acid starvation. Quantitative electron microscopy shows an increase in the numbers of late autophagic compartments in cells silenced for <i>RAB24</i>, and mRFP-GFP-LC3 probe and autophagy flux experiments indicate that this is due to a hindrance in their clearance. Formation of autophagosomes is shown to be unaffected by <i>RAB24</i>-silencing with siRNA. A defect in aggregate clearance in the absence of RAB24 is also shown in cells forming polyglutamine aggregates. This study places RAB24 function in the termination of the autophagic process under nutrient-rich conditions.
DOI: 10.6084/m9.figshare.1569472.v4
title: RAB24 facilitates clearance of autophagic compartments during basal conditions

description: RAB24 belongs to a family of small GTPases and has been implicated to function in autophagy. Here we confirm the intracellular localization of RAB24 to autophagic vacuoles with immuno electron microscopy and cell fractionation, and show that prenylation and guanine nucleotide binding are necessary for the targeting of RAB24 to autophagic compartments. Further, we show that RAB24 plays a role in the maturation and/or clearance of autophagic compartments under nutrient-rich conditions, but not during short amino acid starvation. Quantitative electron microscopy shows an increase in the numbers of late autophagic compartments in cells silenced for <i>RAB24</i>, and mRFP-GFP-LC3 probe and autophagy flux experiments indicate that this is due to a hindrance in their clearance. Formation of autophagosomes is shown to be unaffected by <i>RAB24</i>-silencing with siRNA. A defect in aggregate clearance in the absence of RAB24 is also shown in cells forming polyglutamine aggregates. This study places RAB24 function in the termination of the autophagic process under nutrient-rich conditions.
DOI: 10.6084/m9.figshare.1569469.v2
title: Opinions of Japanese and American ALS caregivers regarding tracheostomy with invasive ventilation (TIV)

description: Our objective was to learn more about possible factors contributing to the higher rates of tracheostomy with invasive ventilation (TIV) for ALS patients in Japan compared with the United States by eliciting attitudes of caregivers of ALS patients in both countries. One hundred and fifty-four American caregivers from five, geographically-distributed ALS clinics and 66 Japanese caregivers from six sites in Japan completed questionnaires regarding TIV. Results showed that 33% of American caregivers were in favor of TIV for their family member compared to 53% of Japanese caregivers; 44% of American and 37% of Japanese caregivers were undecided; and 22% of American and 10% of Japanese caregivers were opposed (<i>p</i>
DOI: 10.6084/m9.figshare.1569467
title: ATG5-knockout mutants of Physcomitrella provide a platform for analyzing the involvement of autophagy in senescence processes in plant cells

description: Autophagy is a pathway in which a cell degrades part of its cytoplasm in vacuoles or lysosomes. To identify the physiological functions of autophagy in plants, we disrupted <i>ATG5</i>, an autophagy-related gene, in <i>Physcomitrella</i>, and confirmed that <i>atg5</i> mutants are deficient in the process of autophagy. On carbon or nitrogen starvation medium, <i>atg5</i> colonies turned yellow earlier than the wild-type (WT) colonies, showing that <i>Physcomitrella atg5</i> mutants, like yeast and <i>Arabidopsis</i>, are sensitive to nutrient starvation. In the dark, even under nutrient-sufficient conditions, colonies turned yellow and the net degradation of chlorophyll and Rubisco protein occurred together with the upregulation of several senescence-associated genes. Yellowing reactions were inhibited by the protein synthesis inhibitor cycloheximide, suggesting that protonemal colonies undergo dark-induced senescence like the green leaves of higher plants. Such senescence responses in the dark occurred earlier in <i>atg5</i> colonies than WT colonies. The sugar content was almost the same between WT and <i>atg5</i> colonies, indicating that the early-senescence phenotype of <i>atg5</i> is not explained by sugar deficiency. However, the levels of 7 amino acids showed significantly different alteration between <i>atg5</i> and WT in the dark: 6 amino acids, particularly arginine and alanine, were much more deficient in the <i>atg5</i> mutants, irrespective of the early degradation of Rubisco protein. On nutrient-sufficient medium supplemented with casamino acids, the early-senescence phenotype was slightly moderated. We propose that the early-senescence phenotype in <i>atg5</i> mutants is partly explained by amino acid imbalance because of the lack of cytoplasmic degradation by autophagy in <i>Physcomitrella</i>.
DOI: 10.6084/m9.figshare.1569472.v3
title: RAB24 facilitates clearance of autophagic compartments during basal conditions

description: RAB24 belongs to a family of small GTPases and has been implicated to function in autophagy. Here we confirm the intracellular localization of RAB24 to autophagic vacuoles with immuno electron microscopy and cell fractionation, and show that prenylation and guanine nucleotide binding are necessary for the targeting of RAB24 to autophagic compartments. Further, we show that RAB24 plays a role in the maturation and/or clearance of autophagic compartments under nutrient-rich conditions, but not during short amino acid starvation. Quantitative electron microscopy shows an increase in the numbers of late autophagic compartments in cells silenced for <i>RAB24</i>, and mRFP-GFP-LC3 probe and autophagy flux experiments indicate that this is due to a hindrance in their clearance. Formation of autophagosomes is shown to be unaffected by <i>RAB24</i>-silencing with siRNA. A defect in aggregate clearance in the absence of RAB24 is also shown in cells forming polyglutamine aggregates. This study places RAB24 function in the termination of the autophagic process under nutrient-rich conditions.
DOI: 10.6084/m9.figshare.1569465
title: Impulse oscillometry in acute and stable asthmatic children: a comparison with spirometry

description: <i>Objective</i>: Lung function tests have attracted interest for the diagnosis and follow-up of childhood asthma in recent years. For patients who cannot perform forced expiratory maneuvers, impulse oscillometry (IOS), performed during spontaneous breathing, may be an alternative tool. <i>Methods</i>: Thirty-five acute, 107 stable asthmatic and 103 healthy children who presented to our clinic performed IOS followed by spirometry before and after salbutamol inhalation. The mean baseline and reversibility of IOS and spirometry parameters were compared between the groups. Correlation analyses were undertaken within the asthmatics, and the healthy controls separately. To distinguish the three groups, the sensitivity and specificity of baseline and reversibility values of IOS and spirometry were computed. When spirometry was taken as the gold standard, the discriminating performance of IOS to detect the airway obstruction and reversibility was investigated. <i>Results</i>: The mean absolute values of Zrs, R5, R5−R20, X5, X10, X15, Fres, AX, and all spirometric parameters, and the mean reversibility values of R5, R10, Fres, AX and forced expiratory volume in one second were different between the groups and the highest area under curve values to discriminate the groups was obtained from area of reactance (AX) and ΔAX. Zrs, all resistance (including R5−R20) and reactance parameters, Fres and AX were correlated with at least one spirometric parameter. Spirometric reversibility was detected by ≤−22.34 and ≤−39.05 cut-off values of ΔR5 and ΔAX, respectively. <i>Conclusions</i>: IOS has shown a highly significant association with spirometric indices and reversibility testing. It may be a substitute for spirometry in children who fail to perform forced expiratory maneuvers.
DOI: 10.6084/m9.figshare.1569462
title: SRSF3 and hnRNP H1 regulate a splicing hotspot of <i>HER2</i> in breast cancer cells

description: Overexpression of the oncogene HER2 occurs in 20–30% of invasive breast cancer and is associated with poor prognosis. A number of different splice variants of HER2 have been identified which produce functionally different proteins. Previously these splice variants have been investigated separately, but in the present study we collectively look at the expression and regulation of a group of HER2 splice variants produced by a splicing hotspot. Initial investigation in a cohort of tumor samples showed large variations in HER2 variant expression between patient samples. RNA interference studies identified 2 splicing factors involved in the regulation of splicing within this region, hnRNP H1 and SRSF3. siRNA targeting hnRNP H1 increases levels of X5 and the oncogenic variant Δ16HER2. Furthermore RNA chromatography assays demonstrated binding of hnRNP H1 to RNA in this region. Additionally the proto-oncogene SRSF3 was also identified as an important regulator of splicing with SRSF3 knockdown resulting in changes in all the splice variants located at the hotspot. Most notably knockdown of SRSF3 resulted in a switch from the oncogenic Δ16HER2 to p100 which inhibits cell proliferation. Binding of SRSF3 to RNA within this region was also demonstrated by RNA chromatography and more specifically 2 SRSF3 binding sites were identified within exon 15. SRSF3 and hnRNP H1 are the first splicing factors identified which regulate the production of these functionally distinct HER2 splice variants and therefore maybe important for the regulation of HER2 signaling.
DOI: 10.6084/m9.figshare.1569465.v1
title: Impulse oscillometry in acute and stable asthmatic children: a comparison with spirometry

description: <i>Objective</i>: Lung function tests have attracted interest for the diagnosis and follow-up of childhood asthma in recent years. For patients who cannot perform forced expiratory maneuvers, impulse oscillometry (IOS), performed during spontaneous breathing, may be an alternative tool. <i>Methods</i>: Thirty-five acute, 107 stable asthmatic and 103 healthy children who presented to our clinic performed IOS followed by spirometry before and after salbutamol inhalation. The mean baseline and reversibility of IOS and spirometry parameters were compared between the groups. Correlation analyses were undertaken within the asthmatics, and the healthy controls separately. To distinguish the three groups, the sensitivity and specificity of baseline and reversibility values of IOS and spirometry were computed. When spirometry was taken as the gold standard, the discriminating performance of IOS to detect the airway obstruction and reversibility was investigated. <i>Results</i>: The mean absolute values of Zrs, R5, R5−R20, X5, X10, X15, Fres, AX, and all spirometric parameters, and the mean reversibility values of R5, R10, Fres, AX and forced expiratory volume in one second were different between the groups and the highest area under curve values to discriminate the groups was obtained from area of reactance (AX) and ΔAX. Zrs, all resistance (including R5−R20) and reactance parameters, Fres and AX were correlated with at least one spirometric parameter. Spirometric reversibility was detected by ≤−22.34 and ≤−39.05 cut-off values of ΔR5 and ΔAX, respectively. <i>Conclusions</i>: IOS has shown a highly significant association with spirometric indices and reversibility testing. It may be a substitute for spirometry in children who fail to perform forced expiratory maneuvers.
DOI: 10.6084/m9.figshare.1569467.v1
title: <i>ATG5</i>-knockout mutants of <i>Physcomitrella</i> provide a platform for analyzing the involvement of autophagy in senescence processes in plant cells

description: Autophagy is a pathway in which a cell degrades part of its cytoplasm in vacuoles or lysosomes. To identify the physiological functions of autophagy in plants, we disrupted <i>ATG5</i>, an autophagy-related gene, in <i>Physcomitrella</i>, and confirmed that <i>atg5</i> mutants are deficient in the process of autophagy. On carbon or nitrogen starvation medium, <i>atg5</i> colonies turned yellow earlier than the wild-type (WT) colonies, showing that <i>Physcomitrella atg5</i> mutants, like yeast and <i>Arabidopsis</i>, are sensitive to nutrient starvation. In the dark, even under nutrient-sufficient conditions, colonies turned yellow and the net degradation of chlorophyll and Rubisco protein occurred together with the upregulation of several senescence-associated genes. Yellowing reactions were inhibited by the protein synthesis inhibitor cycloheximide, suggesting that protonemal colonies undergo dark-induced senescence like the green leaves of higher plants. Such senescence responses in the dark occurred earlier in <i>atg5</i> colonies than WT colonies. The sugar content was almost the same between WT and <i>atg5</i> colonies, indicating that the early-senescence phenotype of <i>atg5</i> is not explained by sugar deficiency. However, the levels of seven amino acids showed significantly different alteration between <i>atg5</i> and WT in the dark: six amino acids, particularly arginine and alanine, were much more deficient in the <i>atg5</i> mutants, irrespective of the early degradation of Rubisco protein. On nutrient-sufficient medium supplemented with casamino acids, the early-senescence phenotype was slightly moderated. We propose that the early-senescence phenotype in <i>atg5</i> mutants is partly explained by amino acid imbalance because of the lack of cytoplasmic degradation by autophagy in <i>Physcomitrella</i>.