cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9357047
title: In vitro dimerization of human RIO2 kinase

description: RIO proteins form a conserved family of atypical protein kinases. RIO2 is a serine/threonine protein kinase/ATPase involved in pre-40S ribosomal maturation. Current crystal structures of archaeal and fungal Rio2 proteins report a monomeric form of the protein. Here, we describe three atomic structures of the human RIO2 kinase showing that it forms a homodimer <i>in vitro</i>. Upon self-association, each protomer ATP-binding pocket is partially remodelled and found in an apostate. The homodimerization is mediated by key residues previously shown to be responsible for ATP binding and catalysis. This unusual <i>in vitro</i> protein kinase dimer reveals an intricate mechanism where identical residues are involved in substrate binding and oligomeric state formation. We speculate that such an oligomeric state might be formed also <i>in vivo</i> and might function in maintaining the protein in an inactive state and could be employed during import.
DOI: 10.6084/m9.figshare.9356693
title: Scale.csv

description: Participants' rating for anxiety and avoidance scales for claustrophobia.
DOI: 10.6084/m9.figshare.9357047.v1
title: In vitro dimerization of human RIO2 kinase

description: RIO proteins form a conserved family of atypical protein kinases. RIO2 is a serine/threonine protein kinase/ATPase involved in pre-40S ribosomal maturation. Current crystal structures of archaeal and fungal Rio2 proteins report a monomeric form of the protein. Here, we describe three atomic structures of the human RIO2 kinase showing that it forms a homodimer <i>in vitro</i>. Upon self-association, each protomer ATP-binding pocket is partially remodelled and found in an apostate. The homodimerization is mediated by key residues previously shown to be responsible for ATP binding and catalysis. This unusual <i>in vitro</i> protein kinase dimer reveals an intricate mechanism where identical residues are involved in substrate binding and oligomeric state formation. We speculate that such an oligomeric state might be formed also <i>in vivo</i> and might function in maintaining the protein in an inactive state and could be employed during import.
DOI: 10.6084/m9.figshare.9357011.v1
title: RoomRating.csv

description: Participants' rating for stress, fear and escape in virtual rooms
DOI: 10.6084/m9.figshare.9356666
title: Supplementary Material for: Tofacitinib as Induction and Maintenance Therapy in Japanese Patients with Active Ulcerative Colitis

description: <b><i>Background:</i></b> Tofacitinib is an oral, small molecule Janus kinase inhibitor approved in Japan for the treatment of ulcerative colitis (UC). Differences in the safety profile of tofacitinib in Japanese patients versus the global population, such as a higher risk of herpes zoster, have been reported. <b><i>Objectives:</i></b> We conducted post hoc analyses of tofacitinib treatment in Japanese patients with moderate-to-severe UC in two global phase III studies. <b><i>Methods:</i></b> In OCTAVE Induction 1 (NCT01465763), 62 patients were randomized to placebo or tofacitinib 10 mg twice daily (b.i.d.). In OCTAVE Sustain (NCT01458574), 39 patients with clinical response in OCTAVE Induction 1 were re-randomized to placebo, tofacitinib 5 mg, or 10 mg b.i.d. Efficacy endpoints included: remission (primary endpoint; total Mayo score ≤2; no individual subscore &gt;1; rectal bleeding subscore 0); mucosal healing (Mayo endoscopic subscore ≤1); clinical response (≥30% and ≥3-point decrease from induction study baseline total Mayo score; decrease in rectal bleeding subscore ≥1 or absolute subscore ≤1). Adverse events (AEs) and clinical laboratory parameters were recorded. <b><i>Results:</i></b> At week 8 of OCTAVE Induction 1, 22.4% of patients achieved remission with tofacitinib (placebo, 7.7%). At week 52 of OCTAVE Sustain, 31.3% and 66.7% of patients receiving tofacitinib 5 and 10 mg b.i.d., respectively, achieved remission (placebo, 9.1%). The occurrence of AEs or serious AEs in Japanese patients was generally similar to that in the global study population, with no new or unexpected safety risks observed. <b><i>Conclusions:</i></b> Although patient numbers were small, tofacitinib demonstrated numerically greater efficacy versus placebo among Japanese patients in OCTAVE Induction 1 and OCTAVE Sustain, with a safety profile consistent with that of the global study population.
DOI: 10.6084/m9.figshare.9357083.v1
title: Characterization of novel small RNAs (sRNAs) contributing to the desiccation response of <i>Salmonella enterica</i> serovar Typhimurium

description: Noncoding RNA (ncRNA) modulation of gene expression has now been ubiquitously observed across all domains of life. An increasingly apparent role of ncRNAs is to coordinate changes in gene expressions in response to environmental stress. <i>Salmonella enterica</i>, a common food-born pathogen, is known for its striking ability to survive, adapt, and thrive in various unfavorable environments which makes it a particularly difficult pathogen to eliminate as well as an interesting model in which to study ncRNA contributions to cellular stress response. Mounting evidence now suggests that small RNAs (sRNAs) represent key regulators of <i>Salmonella</i> stress adaptation. Approximately 50-500 nucleotides in length, sRNAs regulate gene expression through complementary base pairing with molecular targets and have recently been suggested to outnumber protein coding genes in bacteria. In this work, we employ small RNA transcriptome sequencing to characterize changes in the sRNA profiles of <i>Salmonella</i> in response to desiccation. In all, we identify 102 previously annotated sRNAs significantly differentially expressed during desiccation; and excitingly, 71 novel sRNAs likewise differentially expressed. Small transcript northern blotting and qRT-PCRs confirm the identities and expressions of several of our novel sRNAs, and computational analyses indicate the majority are highly conserved and structurally related to characterized sRNAs. Predicted sRNA targets include several proteins necessary for desiccation survival and this, in part, suggests a role for desiccation-regulated sRNAs in this stress response. Furthermore, we find individual knock-outs of two of the novel sRNAs identified herein, either sRNA1320429 or sRNA3981754, significantly impairs the ability of <i>Salmonella</i> to survive desiccation, confirming their involvements (and suggesting the potential involvements of other sRNAs we identify in this work) in the <i>Salmonella</i> response to desiccation.
DOI: 10.6084/m9.figshare.9356666.v1
title: Supplementary Material for: Tofacitinib as Induction and Maintenance Therapy in Japanese Patients with Active Ulcerative Colitis

description: <b><i>Background:</i></b> Tofacitinib is an oral, small molecule Janus kinase inhibitor approved in Japan for the treatment of ulcerative colitis (UC). Differences in the safety profile of tofacitinib in Japanese patients versus the global population, such as a higher risk of herpes zoster, have been reported. <b><i>Objectives:</i></b> We conducted post hoc analyses of tofacitinib treatment in Japanese patients with moderate-to-severe UC in two global phase III studies. <b><i>Methods:</i></b> In OCTAVE Induction 1 (NCT01465763), 62 patients were randomized to placebo or tofacitinib 10 mg twice daily (b.i.d.). In OCTAVE Sustain (NCT01458574), 39 patients with clinical response in OCTAVE Induction 1 were re-randomized to placebo, tofacitinib 5 mg, or 10 mg b.i.d. Efficacy endpoints included: remission (primary endpoint; total Mayo score ≤2; no individual subscore &gt;1; rectal bleeding subscore 0); mucosal healing (Mayo endoscopic subscore ≤1); clinical response (≥30% and ≥3-point decrease from induction study baseline total Mayo score; decrease in rectal bleeding subscore ≥1 or absolute subscore ≤1). Adverse events (AEs) and clinical laboratory parameters were recorded. <b><i>Results:</i></b> At week 8 of OCTAVE Induction 1, 22.4% of patients achieved remission with tofacitinib (placebo, 7.7%). At week 52 of OCTAVE Sustain, 31.3% and 66.7% of patients receiving tofacitinib 5 and 10 mg b.i.d., respectively, achieved remission (placebo, 9.1%). The occurrence of AEs or serious AEs in Japanese patients was generally similar to that in the global study population, with no new or unexpected safety risks observed. <b><i>Conclusions:</i></b> Although patient numbers were small, tofacitinib demonstrated numerically greater efficacy versus placebo among Japanese patients in OCTAVE Induction 1 and OCTAVE Sustain, with a safety profile consistent with that of the global study population.
DOI: 10.6084/m9.figshare.9355382
title: Supplementary Material for: Randomized Controlled Trial on the Effects of Morning versus Evening Primary Vaccination on Episodes of Hypoxemia and Bradycardia in Very Preterm Infants

description: <b><i>Background:</i></b> Hypoxemia and bradycardia occur frequently in preterm infants, but are incompletely understood. They are more prevalent during infections and following immunization. Data on adults suggested an increased immune response if subjects slept following vaccination, suggesting an interaction between circadian rhythm and the immune system. Whether this holds true for preterm infants with their less well-established circadian rhythm is unclear. <b><i>Objective:</i></b> Do infants born at 26–30 weeks’ gestation and having received their first routine hexavalent vaccination in the morning have a lower cardiorespiratory event rate (CER) after vaccination than those receiving it in the evening? <b><i>Methods:</i></b> Twenty-six infants were randomized to an evening versus morning vaccination group in a pilot and main study with 10 and 16 participants, respectively. Pulse oximeter saturation, actigraphy, and rectal temperature were obtained for 24 h before and after vaccination. Blood samples for vaccination titers were taken before vaccination and during a follow-up examination in our outpatient clinic; another blood sample was taken 24 h after vaccination to determine inflammatory markers. <b><i>Results:</i></b> Vaccination led to an increase in CER in both groups, but there was no difference in CER between the morning and evening groups. Vaccination titers for <i>Bordetella pertussis</i> were increased in both groups, with no difference in inflammatory markers 24 h after vaccination. Body temperature increased in both groups after vaccination. Participants in the evening group slept longer after vaccination. <b><i>Conclusions:</i></b> We did not identify a difference in CER between morning and evening vaccination but could confirm increased body temperatures and vaccination titers following vaccination.
DOI: 10.6084/m9.figshare.9355382.v1
title: Supplementary Material for: Randomized Controlled Trial on the Effects of Morning versus Evening Primary Vaccination on Episodes of Hypoxemia and Bradycardia in Very Preterm Infants

description: <b><i>Background:</i></b> Hypoxemia and bradycardia occur frequently in preterm infants, but are incompletely understood. They are more prevalent during infections and following immunization. Data on adults suggested an increased immune response if subjects slept following vaccination, suggesting an interaction between circadian rhythm and the immune system. Whether this holds true for preterm infants with their less well-established circadian rhythm is unclear. <b><i>Objective:</i></b> Do infants born at 26–30 weeks’ gestation and having received their first routine hexavalent vaccination in the morning have a lower cardiorespiratory event rate (CER) after vaccination than those receiving it in the evening? <b><i>Methods:</i></b> Twenty-six infants were randomized to an evening versus morning vaccination group in a pilot and main study with 10 and 16 participants, respectively. Pulse oximeter saturation, actigraphy, and rectal temperature were obtained for 24 h before and after vaccination. Blood samples for vaccination titers were taken before vaccination and during a follow-up examination in our outpatient clinic; another blood sample was taken 24 h after vaccination to determine inflammatory markers. <b><i>Results:</i></b> Vaccination led to an increase in CER in both groups, but there was no difference in CER between the morning and evening groups. Vaccination titers for <i>Bordetella pertussis</i> were increased in both groups, with no difference in inflammatory markers 24 h after vaccination. Body temperature increased in both groups after vaccination. Participants in the evening group slept longer after vaccination. <b><i>Conclusions:</i></b> We did not identify a difference in CER between morning and evening vaccination but could confirm increased body temperatures and vaccination titers following vaccination.
DOI: 10.6084/m9.figshare.9354152
title: Field investigation data during and after the super typhoon

description: The data include: (1)Field investigation data at stations V1 and V2 during the super typhoon,including the tidal, wave, current velocity, river discharge, suspended sediment concentration(SSC).(2)fluid mud thickness along the channel, as well as the depth of mud layer with density of 1050kg/m3 and 1235kg/m3 .(3) vertical distribution of mud density at four stations.
DOI: 10.6084/m9.figshare.9354152.v1
title: Field investigation data during and after the super typhoon

description: The data include: (1)Field investigation data at stations V1 and V2 during the super typhoon,including the tidal, wave, current velocity, river discharge, suspended sediment concentration(SSC).(2)fluid mud thickness along the channel, as well as the depth of mud layer with density of 1050kg/m3 and 1235kg/m3 .(3) vertical distribution of mud density at four stations.
DOI: 10.6084/m9.figshare.9353432
title: Tracking changes in Jain devotional singing

description: Over the last two and a half decades of research in the Śvetāmbar Mūrtipūjak Jain community in Pune, Maharashtra, I have been in a unique position to track changes in the ways that Jain devotional singing is performed. In order to discuss some observations I have made over these decades, I chose to track some notable consistencies and changes help illuminate the impact of socio-economic conditions on religious practices and musicality of the performances in the region. This chapter will contextualize the performance of one particular stavan, <i>Śrī Śankheśvar Pārśvanāthnu Stavan</i>, also known as ‘<i>Antarajāmī Suṇ Alavesara</i>,’ and examine how three performances of this <i>stavan</i> illustrate changes in the ways Jains perform devotional music over the last twenty-five years.
DOI: 10.6084/m9.figshare.9353432.v1
title: Tracking changes in Jain devotional singing

description: Over the last two and a half decades of research in the Śvetāmbar Mūrtipūjak Jain community in Pune, Maharashtra, I have been in a unique position to track changes in the ways that Jain devotional singing is performed. In order to discuss some observations I have made over these decades, I chose to track some notable consistencies and changes help illuminate the impact of socio-economic conditions on religious practices and musicality of the performances in the region. This chapter will contextualize the performance of one particular stavan, <i>Śrī Śankheśvar Pārśvanāthnu Stavan</i>, also known as ‘<i>Antarajāmī Suṇ Alavesara</i>,’ and examine how three performances of this <i>stavan</i> illustrate changes in the ways Jains perform devotional music over the last twenty-five years.
DOI: 10.6084/m9.figshare.9352838
title: Prediction failure blocks the use of local semantic context

description: Before accumulation of recent experimental evidence, prediction was thought to be too prone to failure and thus too costly for language comprehension. Although prediction is now widely assumed, questions about the costs of prediction failure and recovery still remain. An event-related potentials study using highly constraining Italian sentence contexts addressed these questions. It manipulated how predictive local contexts were for target nouns after cueing comprehenders to the status of global sentential predictions with article gender congruence. Predictive local contexts reduced target noun N400 amplitude when the preceding article’s gender was congruent with global predictions, but not when gender was incongruent. This suggests that prediction failure impeded the facilitative use of local context for target nouns. Predictive local contexts following gender incongruence also elicited a broader late frontal positivity on target nouns, suggesting further recovery difficulties. Prediction failures, therefore, are not cost-free, and recovery from these failures requires further consideration.
DOI: 10.6084/m9.figshare.9352838.v1
title: Prediction failure blocks the use of local semantic context

description: Before accumulation of recent experimental evidence, prediction was thought to be too prone to failure and thus too costly for language comprehension. Although prediction is now widely assumed, questions about the costs of prediction failure and recovery still remain. An event-related potentials study using highly constraining Italian sentence contexts addressed these questions. It manipulated how predictive local contexts were for target nouns after cueing comprehenders to the status of global sentential predictions with article gender congruence. Predictive local contexts reduced target noun N400 amplitude when the preceding article’s gender was congruent with global predictions, but not when gender was incongruent. This suggests that prediction failure impeded the facilitative use of local context for target nouns. Predictive local contexts following gender incongruence also elicited a broader late frontal positivity on target nouns, suggesting further recovery difficulties. Prediction failures, therefore, are not cost-free, and recovery from these failures requires further consideration.
DOI: 10.6084/m9.figshare.9351293
title: Speech production abilities of 4- to 5-year-old children with and without a history of late talking: The tricky tyrannosaurus

description: <i>Purpose:</i> Research on the speech production abilities of children with a history of late talking (HLT) is limited. We compared 4- to 5-year-old children with and without a HLT on a routine speech assessment and a single-word polysyllable assessment. <i>Method:</i> The two speech assessments were administered to 13 children with a HLT (4;4–5;9 years) and 11 children with a history of typical development (HTD) (4;1–5;10 years). Data were analysed using descriptive and inferential statistics. <i>Result:</i> The HLT group had significantly poorer speech accuracy than the HTD group on both the routine speech and polysyllable assessments. The HLT group also showed a significantly higher percentage occurrence of consonant omissions on both speech assessments compared to the HTD group. Descriptive analysis of participants’ polysyllable productions indicated that the HLT group showed a higher percentage occurrence of a range of error types compared to the HTD group. <i>Conclusion:</i> By 4–5 years of age, children who were late to talk had speech production abilities that were significantly poorer than their peers who were not late to talk, suggesting continued underlying differences.
DOI: 10.6084/m9.figshare.9351632
title: SACRED PLAY

description: Documentation of interview content.
DOI: 10.6084/m9.figshare.9351293.v1
title: Speech production abilities of 4- to 5-year-old children with and without a history of late talking: The tricky tyrannosaurus

description: <i>Purpose:</i> Research on the speech production abilities of children with a history of late talking (HLT) is limited. We compared 4- to 5-year-old children with and without a HLT on a routine speech assessment and a single-word polysyllable assessment. <i>Method:</i> The two speech assessments were administered to 13 children with a HLT (4;4–5;9 years) and 11 children with a history of typical development (HTD) (4;1–5;10 years). Data were analysed using descriptive and inferential statistics. <i>Result:</i> The HLT group had significantly poorer speech accuracy than the HTD group on both the routine speech and polysyllable assessments. The HLT group also showed a significantly higher percentage occurrence of consonant omissions on both speech assessments compared to the HTD group. Descriptive analysis of participants’ polysyllable productions indicated that the HLT group showed a higher percentage occurrence of a range of error types compared to the HTD group. <i>Conclusion:</i> By 4–5 years of age, children who were late to talk had speech production abilities that were significantly poorer than their peers who were not late to talk, suggesting continued underlying differences.
DOI: 10.6084/m9.figshare.9351632.v1
title: SACRED PLAY

description: Documentation of interview content.
DOI: 10.6084/m9.figshare.9350918
title: Additional file 1: of Impact of on-site clinical genetics consultations on diagnostic rate in children and young adults with autism spectrum disorder

description: Table S1. List of 439 known intellectual disability/ASD genes or candidate genes tested by panel resequencing. (XLSX 196 kb)
DOI: 10.6084/m9.figshare.9350918.v1
title: Additional file 1: of Impact of on-site clinical genetics consultations on diagnostic rate in children and young adults with autism spectrum disorder

description: Table S1. List of 439 known intellectual disability/ASD genes or candidate genes tested by panel resequencing. (XLSX 196 kb)
DOI: 10.6084/m9.figshare.9350897
title: Additional file 7 of Discovery of stroke-related blood biomarkers from gene expression network models

description: : miRNA:mRNA target predictions â a complete list of statistically significant associations between log FC in miRNAs and mRNA log FC in the 6 network-central predictor genes, including the confidence scores. (TXT 29 kb)
DOI: 10.6084/m9.figshare.9350888
title: Additional file 6 of Discovery of stroke-related blood biomarkers from gene expression network models

description: : Diseases associated with variants or differential expression of the 6 predictive network-central genes with a gene-disease association (GDA) or variant-disease association (VDA) scoreâ &gt;â 0.001 according to DisGeNet. (TXT 1 kb)
DOI: 10.6084/m9.figshare.9350885
title: Additional file 5 of Discovery of stroke-related blood biomarkers from gene expression network models

description: : DAVID enrichment clusters for the genes with statistically significant FC between stroke and control (S5A), as well as for Hamming distance d ≤ 1 neighborhoods for each of the network-central predictor genes: S5B – ID3, S5C – MBTPS1, S5D – NOG, S5E – SFXN2, S5F – BMX, S5G – SLC22A1. (7Z 17 kb)
DOI: 10.6084/m9.figshare.9350888.v1
title: Additional file 6 of Discovery of stroke-related blood biomarkers from gene expression network models

description: : Diseases associated with variants or differential expression of the 6 predictive network-central genes with a gene-disease association (GDA) or variant-disease association (VDA) scoreâ &gt;â 0.001 according to DisGeNet. (TXT 1 kb)
DOI: 10.6084/m9.figshare.9350885.v1
title: Additional file 5 of Discovery of stroke-related blood biomarkers from gene expression network models

description: : DAVID enrichment clusters for the genes with statistically significant FC between stroke and control (S5A), as well as for Hamming distance d ≤ 1 neighborhoods for each of the network-central predictor genes: S5B – ID3, S5C – MBTPS1, S5D – NOG, S5E – SFXN2, S5F – BMX, S5G – SLC22A1. (7Z 17 kb)
DOI: 10.6084/m9.figshare.9350876
title: Additional file 4 of Discovery of stroke-related blood biomarkers from gene expression network models

description: : This file contains a complete list of Hamming distance dâ =â 1 neighborhoods for the 6 predictive network-central genes, for both the control (non-stroke) and stroke gene expression networks. (TXT 9 kb)