cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9901334.v1
title: Voltage vs. Ligand II: Structural insights of the intrinsic flexibility in cyclic nucleotide-gated channels

description: In the preceding article, we present a flexibility analysis of the voltage-gated ion channel (VGIC) superfamily. In this study, we describe in detail the flexibility profile of the voltage-sensor domain (VSD) and the pore domain (PD) concerning the evolution of 6TM ion channels. In particular, we highlight the role of flexibility in the emergence of CNG channels and describe a significant level of sequence similarity between the archetypical VSD and the TolQ proteins. A highly flexible S4-like segment exhibiting Lys instead Arg for these membrane proteins is reported. Sequence analysis indicates that, in addition to this S4-like segment, TolQ proteins also show similarity with specific motifs in S2 and S3 from typical V-sensors. Notably, S3 flexibility profiles from typical VSDs and S3-like in TolQ proteins are also similar. Interestingly, TolQ from early divergent prokaryotes are comparatively more flexible than those in modern counterparts or true V-sensors. Regarding the PD, we also found that 2TM K<sup>+</sup>-channels in early prokaryotes are considerably more flexible than the ones in modern microbes, and such flexibility is comparable to the one present in CNG channels. Voltage dependence is mainly exhibited in prokaryotic CNG channels whose VSD is rigid whereas the eukaryotic CNG channels are considerably more flexible and poorly V-dependent. The implication of the flexibility present in CNG channels, their sensitivity to cyclic nucleotides and the cation selectivity are discussed. Finally, we generated a structural model of the putative cyclic nucleotide-modulated ion channel, which we coined here as AqK, from the thermophilic bacteria <i>Aquifex aeolicus</i>, one of the earliest diverging prokaryotes known. Overall, our analysis suggests that V-sensors in CNG-like channels were essentially rigid in early prokaryotes but raises the possibility that this module was probably part of a very flexible stator protein of the bacterial flagellum motor complex.
DOI: 10.6084/m9.figshare.9901313.v1
title: Effect of D-ring C-3’ methylation of strigolactone analogs on their transcription regulating activity in rice

description: Strigolactones (SLs) are a well-known class of plant hormones, which are involved in a number of developmental and adaptation processes and mediate different interspecific interactions. In spite of the growing knowledge on SL biosynthesis and signal transduction, effects of structural modifications on the activity and efficiency of SLs and their analogs remain largely elusive. SLs are characterized by the presence of a lactone ring (D-ring) that is connected by an enol ether bridge to a second moiety. In this study, we investigated the effect of additional D-ring methylation of SL analogs on their transcription regulating activity. For this purpose, we compared the SL analogs MP13 and AR8, which differ only by the presence of a methyl group at the C-3ʹ atom in the latter. Transcription regulating activity was determined by quantitative real-time PCR measurement of transcript levels of SL-dependent, feed-back regulated genes in treated wild type and <i>ccd7</i> mutant rice seedlings. Results obtained indicate that C-3ʹ methylation reduces the transcription regulating activity, as shown by the more pronounced suppression of the SL biosynthesis genes <i>DWARF27</i> (<i>D27</i>) and <i>CAROTENOID CLEAVAGE DIOXYGENASES</i> (<i>CCD7</i> and <i>CCD8</i>) and higher induction of the SL signaling repressor gene <i>DWARF53</i> (<i>D53</i>) in MP13 treated seedlings. These results are consistent with a recent study on the biological activities of MP13 and AR8.
DOI: 10.6084/m9.figshare.9901322.v1
title: Smoking and blood DNA methylation: an epigenome-wide association study and assessment of reversibility

description: We conducted a genome-wide association study of blood DNA methylation and smoking, attempted replication of previously discovered associations, and assessed the reversibility of smoking-associated methylation changes. DNA methylation was measured in baseline peripheral blood samples for 5,044 participants in the Melbourne Collaborative Cohort Study. For 1,032 participants, these measures were repeated using blood samples collected at follow-up, a median of 11 years later. A cross-sectional analysis of the association between smoking and DNA methylation and a longitudinal analysis of changes in smoking status and changes in DNA methylation were conducted. We used our cross-sectional analysis to replicate previously reported associations for current (N = 3,327) and former (N = 172) smoking. A comprehensive smoking index accounting for the biological half-life of smoking compounds and several aspects of smoking history was constructed to assess the reversibility of smoking-induced methylation changes. This measure of lifetime exposure to smoking allowed us to detect more associations than comparing current with never smokers. We identified 4,496 cross-sectional associations at P −7, including 3,296 annotated to 1,326 genes that were not previously implicated in smoking-associated DNA methylation changes at this significance threshold. We replicated the majority of previously reported associations (P −7) for current and former smokers. In our data, we observed for former smokers a substantial degree of return to the methylation levels of never smokers, compared with current smokers (median: 74%, IQR = 63-86%), corresponding to small values (median: 2.75, IQR = 1.5–5.25) for the half-life parameter of the comprehensive smoking index. Longitudinal analyses identified 368 sites at which methylation changed upon smoking cessation. Our study demonstrates the usefulness of the comprehensive smoking index to detect associations between smoking and DNA methylation at CpGs across the genome, replicates the vast majority of previously reported associations, and quantifies the reversibility of smoking-induced methylation changes.
DOI: 10.6084/m9.figshare.9901265
title: Metadata record for: Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials

description: This dataset contains key characteristics about the data described in the Data Descriptor Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br> <br> Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata<br>
DOI: 10.6084/m9.figshare.9901307.v3
title: Immunohistochemical Expression of p53 in Type I and II Epithelial Ovarian Cancer among Sudanese women

description: Immunohistochemical Expression of p53 in Type I and II Epithelial Ovarian Cancer among Sudanese women. In this cross-sectional, hospital-based study a total of 114 paraffin-embedded tissue blocks previously diagnosed as epithelial ovarian cancer were collected from six governmental hospitals in Khartoum state, Sudan, in the period 2013-2016. Immunohistochemistry was performed on tissue microarray slides to measure the protein expression of p53 in the EOC.<br>
DOI: 10.6084/m9.figshare.9901247
title: Supplementary Material for: Levothyroxine Dosage as Predictor of Permanent and Transient Congenital Hypothyroidism: A Multicenter Retrospective Study in Japan

description: <b><i>Background:</i></b> Congenital hypothyroidism (CH) can be divided into 2 types, transient CH (T-CH) and permanent CH (P-CH), depending on the requirement of levothyroxine (LT4) for life-long treatment. Several studies have recently reported that the LT4 dosage is useful for predicting the LT4 requirement, but none of the studies followed their patients to puberty. <b><i>Objective:</i></b> To determine the cutoff value for the LT4 dosage as a predictor of the LT4 requirement after puberty in patients with CH. <b><i>Methods:</i></b> The LT4 dosage and clinical data on 99 patients with CH who were followed at the participating hospitals from the neonatal period to 15 years of age or older were retrospectively analyzed. Based on their LT4 requirement at their last hospital visit, the participants were divided into the P-CH group (<i>n</i> = 75), who were treated with LT4, and the T-CH group (<i>n</i> = 24), who were not. <b><i>Results:</i></b> At age 1 year, a higher LT4 dosage was required for the P-CH group (median 3.75 vs. 2.88 µg/kg/day; <i>p</i> &lt; 0.001). When the LT4 dosage cutoff value at age 1 year was set at 4.79 and 1.74 µg/kg/day, the specificity of P-CH and T-CH (for denying T-CH and P-CH, respectively) was 100 and 97%, respectively. <b><i>Conclusions:</i></b> An LT4 dosage above 4.7 µg/kg/day and below 1.8 µg/kg/day at age 1 year may help predict P-CH and T-CH, respectively.
DOI: 10.6084/m9.figshare.9901265.v2
title: Metadata record for: Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials

description: This dataset contains key characteristics about the data described in the Data Descriptor Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br> <br> Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata<br>
DOI: 10.6084/m9.figshare.9901235
title: Parathethys last gasp in central Asia and late Oligocene accelerated uplift of the Pamirs

description: This dataset composed of chronological constraints of lower Cenozoic sedimentary rocks in the Tajik Basin. Table S3 includes detrital zircon U-Pb geochronologic data for three pilot samples from the PE Section. Table S4 involves detrital monazite U-Pb geochronologic data. Table S5 comprises magnetostratigraphic ChRM-directions for the PE, CD, and WA sections.
DOI: 10.6084/m9.figshare.9901247.v1
title: Supplementary Material for: Levothyroxine Dosage as Predictor of Permanent and Transient Congenital Hypothyroidism: A Multicenter Retrospective Study in Japan

description: <b><i>Background:</i></b> Congenital hypothyroidism (CH) can be divided into 2 types, transient CH (T-CH) and permanent CH (P-CH), depending on the requirement of levothyroxine (LT4) for life-long treatment. Several studies have recently reported that the LT4 dosage is useful for predicting the LT4 requirement, but none of the studies followed their patients to puberty. <b><i>Objective:</i></b> To determine the cutoff value for the LT4 dosage as a predictor of the LT4 requirement after puberty in patients with CH. <b><i>Methods:</i></b> The LT4 dosage and clinical data on 99 patients with CH who were followed at the participating hospitals from the neonatal period to 15 years of age or older were retrospectively analyzed. Based on their LT4 requirement at their last hospital visit, the participants were divided into the P-CH group (<i>n</i> = 75), who were treated with LT4, and the T-CH group (<i>n</i> = 24), who were not. <b><i>Results:</i></b> At age 1 year, a higher LT4 dosage was required for the P-CH group (median 3.75 vs. 2.88 µg/kg/day; <i>p</i> &lt; 0.001). When the LT4 dosage cutoff value at age 1 year was set at 4.79 and 1.74 µg/kg/day, the specificity of P-CH and T-CH (for denying T-CH and P-CH, respectively) was 100 and 97%, respectively. <b><i>Conclusions:</i></b> An LT4 dosage above 4.7 µg/kg/day and below 1.8 µg/kg/day at age 1 year may help predict P-CH and T-CH, respectively.
DOI: 10.6084/m9.figshare.9901307.v2
title: Immunohistochemical Expression of p53 in Type I and II Epithelial Ovarian Cancer among Sudanese women

description: hosbital based cross sectional study conducted in six govermental hosbitals in sudanese women affected with ovarian cancer
DOI: 10.6084/m9.figshare.9901229
title: Supplementary Material for: Cheek Microbial Communities Vary in Young Children with Atopic Dermatitis in China

description: <b><i>Background:</i></b> Atopic dermatitis (AD) is a chronic, recurrent skin condition with recently increased incidence in younger children. AD development has been correlated with the skin microbiome, and <i>Staphylococcus aureus</i> enrichment causes significant increases in skin lesions. <b><i>Objective:</i></b> Our objectives were to compare the microbial diversity of the cheek skin of children with or without AD aged 0–1 years in China, and to determine whether 4 types of skin-isolated bacteria could inhibit <i>S. aureus</i> in vitro. <b><i>Methods:</i></b> The skin microbial samples of cheek skin of children were sequenced by 16S rRNA V1-V2 region. Four skin isolated bacterial fermentation supernatants were tested for effects on <i>S. aureus</i> growth, membrane formation, and induction of cytokine secretion from HaCaT cells. <b><i>Results:</i></b> Bacterial diversity decreased significantly in skin with severe AD compared to healthy skin (<i>p</i> &lt; 0.01). Seven phyla had content &gt;1%, 4 of which differed in AD (<i>p</i> &lt; 0.05). 38 genera had content &gt;1%, 15 differed (<i>p</i> &lt; 0.05). Differences in 8 species were observed (<i>p</i> &lt; 0.05). In vitro antibacterial and cellular experiments showed that <i>S. aureus</i> growth, biofilm formation, and induction of interleukin (IL)-1α and IL-6 secretion from HaCaT cells were significantly inhibited by <i>Klebsiella oxytoca</i>, <i>Kocuria rhizophila</i>, and <i>Staphylococcus epidermidis</i> culture supernatants (<i>p</i> &lt; 0.05). <b><i>Conclusion:</i></b> Skin microbiome changes in children varied with age and with AD. There were complex interactions between skin isolated bacteria and <i>S. aureus</i> which could inhibit <i>S. aureus</i> growth and biofilm formation in vitro, suggesting that these microorganisms could be used in AD treatment.
DOI: 10.6084/m9.figshare.9901265.v1
title: Metadata record for: Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials

description: This dataset contains key characteristics about the data described in the Data Descriptor Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.9901229.v1
title: Supplementary Material for: Cheek Microbial Communities Vary in Young Children with Atopic Dermatitis in China

description: <b><i>Background:</i></b> Atopic dermatitis (AD) is a chronic, recurrent skin condition with recently increased incidence in younger children. AD development has been correlated with the skin microbiome, and <i>Staphylococcus aureus</i> enrichment causes significant increases in skin lesions. <b><i>Objective:</i></b> Our objectives were to compare the microbial diversity of the cheek skin of children with or without AD aged 0–1 years in China, and to determine whether 4 types of skin-isolated bacteria could inhibit <i>S. aureus</i> in vitro. <b><i>Methods:</i></b> The skin microbial samples of cheek skin of children were sequenced by 16S rRNA V1-V2 region. Four skin isolated bacterial fermentation supernatants were tested for effects on <i>S. aureus</i> growth, membrane formation, and induction of cytokine secretion from HaCaT cells. <b><i>Results:</i></b> Bacterial diversity decreased significantly in skin with severe AD compared to healthy skin (<i>p</i> &lt; 0.01). Seven phyla had content &gt;1%, 4 of which differed in AD (<i>p</i> &lt; 0.05). 38 genera had content &gt;1%, 15 differed (<i>p</i> &lt; 0.05). Differences in 8 species were observed (<i>p</i> &lt; 0.05). In vitro antibacterial and cellular experiments showed that <i>S. aureus</i> growth, biofilm formation, and induction of interleukin (IL)-1α and IL-6 secretion from HaCaT cells were significantly inhibited by <i>Klebsiella oxytoca</i>, <i>Kocuria rhizophila</i>, and <i>Staphylococcus epidermidis</i> culture supernatants (<i>p</i> &lt; 0.05). <b><i>Conclusion:</i></b> Skin microbiome changes in children varied with age and with AD. There were complex interactions between skin isolated bacteria and <i>S. aureus</i> which could inhibit <i>S. aureus</i> growth and biofilm formation in vitro, suggesting that these microorganisms could be used in AD treatment.
DOI: 10.6084/m9.figshare.9901235.v1
title: Parathethys last gasp in central Asia and late Oligocene accelerated uplift of the Pamirs

description: This dataset composed of chronological constraints of lower Cenozoic sedimentary rocks in the Tajik Basin. Table S3 includes detrital zircon U-Pb geochronologic data for three pilot samples from the PE Section. Table S4 involves detrital monazite U-Pb geochronologic data. Table S5 comprises magnetostratigraphic ChRM-directions for the PE, CD, and WA sections.
DOI: 10.6084/m9.figshare.9901181
title: Supplementary Material for: Clinical and Humoral Determinants of Congestion in Heart Failure: Potential Role of Adiponectin

description: <b><i>Background:</i></b> Some patients with heart failure (HF) are more prone to systemic congestion than others. The goal of this study was to identify clinical and humoral factors linked to congestion and its prognostic impact in HF patients. <b><i>Methods:</i></b> A total of 371 advanced HF patients underwent physical examination, echocardiography, right heart catheterization, blood samplings, and Minnesota Living with HF Questionnaire. Subjects were followed-up for adverse events (death, urgent transplantation, or assist device implantation without heart transplantation). <b><i>Results:</i></b> Thirty-one percent of patients were classified as prone to congestion. During a median follow-up of 1,093 days, 159 (43%) patients had an adverse event. In the Cox analysis, the congestion-prone (CP) status was associated with a 43% higher event risk. The CP status was strongly (<i>p</i> ˂ 0.001) associated with body weight loss, right ventricular dysfunction (RVD), dilated inferior vena cava (IVC), diuretics, and beta-blockers prescription and the majority of tested hormones in the univariate analysis. In the multivariate analysis, the only independent variables associated with the CP status were adiponectin, albumin, IVC diameter, and RVD. Adiponectin by itself was predictive of adverse events. In a multivariate model, CP status was no longer predictive of adverse events, in contrast to adiponectin. <b><i>Conclusions:</i></b> CP patients experienced more severe symptoms and had shorter survival. Potential role of adiponectin, a new independent predictor of CP status, should be further examined.
DOI: 10.6084/m9.figshare.9901181.v1
title: Supplementary Material for: Clinical and Humoral Determinants of Congestion in Heart Failure: Potential Role of Adiponectin

description: <b><i>Background:</i></b> Some patients with heart failure (HF) are more prone to systemic congestion than others. The goal of this study was to identify clinical and humoral factors linked to congestion and its prognostic impact in HF patients. <b><i>Methods:</i></b> A total of 371 advanced HF patients underwent physical examination, echocardiography, right heart catheterization, blood samplings, and Minnesota Living with HF Questionnaire. Subjects were followed-up for adverse events (death, urgent transplantation, or assist device implantation without heart transplantation). <b><i>Results:</i></b> Thirty-one percent of patients were classified as prone to congestion. During a median follow-up of 1,093 days, 159 (43%) patients had an adverse event. In the Cox analysis, the congestion-prone (CP) status was associated with a 43% higher event risk. The CP status was strongly (<i>p</i> ˂ 0.001) associated with body weight loss, right ventricular dysfunction (RVD), dilated inferior vena cava (IVC), diuretics, and beta-blockers prescription and the majority of tested hormones in the univariate analysis. In the multivariate analysis, the only independent variables associated with the CP status were adiponectin, albumin, IVC diameter, and RVD. Adiponectin by itself was predictive of adverse events. In a multivariate model, CP status was no longer predictive of adverse events, in contrast to adiponectin. <b><i>Conclusions:</i></b> CP patients experienced more severe symptoms and had shorter survival. Potential role of adiponectin, a new independent predictor of CP status, should be further examined.
DOI: 10.6084/m9.figshare.9901118
title: Mångberg tree-ring data

description: Ring width measurements from pine (Pinus sylvestris).<br>Mångberg area.<br>Lat: 60°51'N Long: 14°35'E<br>http://www.mangberg.se/<br>
DOI: 10.6084/m9.figshare.9901118.v1
title: Mångberg tree-ring data

description: Ring width measurements from pine (Pinus sylvestris).<br>Mångberg area.<br>Lat: 60°51'N Long: 14°35'E<br>http://www.mangberg.se/<br>
DOI: 10.6084/m9.figshare.9901061
title: Region of Difference

description: RD analysis based on RD-Analyzer on MDRTB from Malaysia
DOI: 10.6084/m9.figshare.9901064
title: Table S1 and Table S2

description: Table S1: U-Pb isotopic data for zircon grains from the Neoproterozoic meta-sedimentary rocks in the Chinese Central Tianshan Block<br>Table S2: Lu-Hf isotopic data for zircon grains from the Neoproterozoic meta-sedimentay rocks in the Chinese Central Tianshan Block
DOI: 10.6084/m9.figshare.9901046
title: NPC1L1-25hydroxycholesterol Complex

description: Varios sterols binding to NPC1L11) NPC1L1-25-hydroxycholesterol Complex.pdb<br>2) MMPBSA output from trajectory analysis3) Decompose analysis from trajectory analysis4) trajectory analysis: Backbone RMSD, B-factor, Gyration
DOI: 10.6084/m9.figshare.9901061.v2
title: Region of Difference

description: RD analysis based on RD-Analyzer on MDRTB from Malaysia
DOI: 10.6084/m9.figshare.9901028
title: Supplementary Material for: Elevated Serum Uric Acid and Self-Reported Heart Failure in US Adults: 2007–2016 National Health and Nutrition Examination Survey

description: <b><i>Introduction:</i></b> There is limited evidence examining the relationship between elevated serum uric acid (sUA) concentration and heart failure (HF) in United States (US) adults. The aim of the present study was to examine the association(s) between elevated sUA and HF using a nationally representative sample of US adults. <b><i>Methods:</i></b> The final sample with complete data for this analysis (<i>n</i> = 17,349) included men and women aged ≥40 years who participated in the 2007–2016 National Health and Nutrition Examination Survey. Self-reported diagnosis of HF was assessed via interview. Elevated sUA was defined as values &gt;6.0 mg/dL for women and &gt;7.2 mg/dL for men. Multivariable gender-stratified logistic regression was utilized to examine the odds of self-reported HF. <b><i>Results:</i></b> The estimated prevalence of HF was 3.9 and 3.4% among men and women, respectively. Age-adjusted analysis revealed significantly increased odds of HF in men (OR 2.79; 95% CI 2.15–3.84, <i>p</i> &lt; 0.01) and women (OR 3.24; 95% CI 2.37–4.44, <i>p</i> &lt; 0.01) with elevated sUA. This relationship remained statistically significant following adjustment for age, race, education, income, alcohol consumption, smoking status, blood pressure, diabetes, physical activity level, cholesterol, creatinine level, and body mass index in men (OR 1.70; 95% CI 1.13–2.57 <i>p</i> &lt; 0.05) and women (OR 1.74; 95% CI 1.18–2.58, <i>p</i> &lt; 0.05). <b><i>Conclusions:</i></b> In a representative sample of US adults, having an elevated sUA concentration was associated with significantly increased odds of HF when compared to adults with normal sUA.
DOI: 10.6084/m9.figshare.9901046.v2
title: NPC1L1-25hydroxycholesterol Complex

description: Varios sterols binding to NPC1L11) NPC1L1-25-hydroxycholesterol Complex.pdb<br>2) MMPBSA output from trajectory analysis3) Decompose analysis from trajectory analysis4) trajectory analysis: Backbone RMSD, B-factor, Gyration