cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4834040
title: Tafamidis delays disease progression in patients with early stage transthyretin familial amyloid polyneuropathy: additional supportive analyses from the pivotal trial

description: <b>Background:</b> Tafamidis, a non-NSAID highly specific transthyretin stabilizer, delayed neurologic disease progression as measured by Neuropathy Impairment Score–Lower Limbs (NIS-LL) in an 18-month, double-blind, placebo-controlled randomized trial in 128 patients with early-stage transthyretin V30M familial amyloid polyneuropathy (ATTRV30M-FAP). The current post hoc analyses aimed to further evaluate the effects of tafamidis in delaying ATTRV30M-FAP progression in this trial. <b>Methods:</b> Pre-specified, repeated-measures analysis of change from baseline in NIS-LL in this trial (ClinicalTrials.gov NCT00409175) was repeated with addition of baseline as covariate and multiple imputation analysis for missing data by treatment group. Change in NIS-LL plus three small-fiber nerve tests (NIS-LL + Σ3) and NIS-LL plus seven nerve tests (NIS-LL + Σ7) were assessed without baseline as covariate. Treatment outcomes over the NIS-LL, Σ3, Σ7, modified body mass index and Norfolk Quality of Life–Diabetic Neuropathy Total Quality of Life Score were also examined using multivariate analysis techniques. <b>Results:</b> Neuropathy progression based on NIS-LL change from baseline to Month 18 remained significantly reduced for tafamidis versus placebo in the baseline-adjusted and multiple imputation analyses. NIS-LL + Σ3 and NIS-LL + Σ7 captured significant treatment group differences. Multivariate analyses provided strong statistical evidence for a superior tafamidis treatment effect. <b>Conclusions:</b> These supportive analyses confirm that tafamidis delays neurologic progression in early-stage ATTRV30M-FAP. <b>Trial registration number:</b> NCT00409175.
DOI: 10.6084/m9.figshare.4834040.v1
title: Tafamidis delays disease progression in patients with early stage transthyretin familial amyloid polyneuropathy: additional supportive analyses from the pivotal trial

description: <b>Background:</b> Tafamidis, a non-NSAID highly specific transthyretin stabilizer, delayed neurologic disease progression as measured by Neuropathy Impairment Score–Lower Limbs (NIS-LL) in an 18-month, double-blind, placebo-controlled randomized trial in 128 patients with early-stage transthyretin V30M familial amyloid polyneuropathy (ATTRV30M-FAP). The current post hoc analyses aimed to further evaluate the effects of tafamidis in delaying ATTRV30M-FAP progression in this trial. <b>Methods:</b> Pre-specified, repeated-measures analysis of change from baseline in NIS-LL in this trial (ClinicalTrials.gov NCT00409175) was repeated with addition of baseline as covariate and multiple imputation analysis for missing data by treatment group. Change in NIS-LL plus three small-fiber nerve tests (NIS-LL + Σ3) and NIS-LL plus seven nerve tests (NIS-LL + Σ7) were assessed without baseline as covariate. Treatment outcomes over the NIS-LL, Σ3, Σ7, modified body mass index and Norfolk Quality of Life–Diabetic Neuropathy Total Quality of Life Score were also examined using multivariate analysis techniques. <b>Results:</b> Neuropathy progression based on NIS-LL change from baseline to Month 18 remained significantly reduced for tafamidis versus placebo in the baseline-adjusted and multiple imputation analyses. NIS-LL + Σ3 and NIS-LL + Σ7 captured significant treatment group differences. Multivariate analyses provided strong statistical evidence for a superior tafamidis treatment effect. <b>Conclusions:</b> These supportive analyses confirm that tafamidis delays neurologic progression in early-stage ATTRV30M-FAP. <b>Trial registration number:</b> NCT00409175.
DOI: 10.6084/m9.figshare.4834031
title: Oostra, Saastamoinen, Zwaan and Wheat 2018. "Strong phenotypic plasticity limits potential for evolutionary responses to climate change". Transcriptome assembly and gene expression data.

description: Sequence data, gene expression data, and R script for Oostra et al. 2018. <br><br>Results and methods are described in Oostra et al. 2018 Nature Communications (https://www.nature.com/articles/s41467-018-03384-9). Raw sequencing reads are deposited at NCBI / SRA (BioProject PRJNA376691).<br><br>This fileset contains<br>a) The transcriptome assembly (fasta format)<br>b) raw counts for expression analyses (two separate .cvs files for abdomen and thorax)<br>c) R script for gene expression analyses (text file)<br><br>For any questions or additional data requests please contact Vicencio Oostra at v.oostra@ucl.ac.uk<br>
DOI: 10.6084/m9.figshare.4834049.v1
title: Insights into the human brain proteome: Disclosing the biological meaning of protein networks in cerebrospinal fluid

description: Cerebrospinal fluid (CSF) is an excellent source of biological information regarding the nervous system, once it is in close contact and accurately reflects alterations in this system. Several studies have analyzed differential protein profiles of CSF samples between healthy and diseased human subjects. However, the pathophysiological mechanisms and how CSF proteins relate to diseases are still poorly known. By applying bioinformatics tools, we attempted to provide new insights on the biological and functional meaning of proteomics data envisioning the identification of putative disease biomarkers. Bioinformatics analysis of data retrieved from 99 mass spectrometry (MS)-based studies on CSF profiling highlighted 1985 differentially expressed proteins across 49 diseases. A large percentage of the modulated proteins originate from exosome vesicles, and the majority are involved in either neuronal cell growth, development, maturation, migration, or neurotransmitter-mediated cellular communication. Nevertheless, some diseases present a unique CSF proteome profile, which were critically analyzed in the present study. For instance, 48 proteins were found exclusively upregulated in the CSF of patients with Alzheimer’s disease and are mainly involved in steroid esterification and protein activation cascade processes. A higher number of exclusively upregulated proteins were found in the CSF of patients with multiple sclerosis (76 proteins) and with bacterial meningitis (70 proteins). Whereas in multiple sclerosis, these proteins are mostly involved in the regulation of RNA metabolism and apoptosis, in bacterial meningitis the exclusively upregulated proteins participate in inflammation and antibacterial humoral response, reflecting disease pathogenesis. The exploration of the contribution of exclusively upregulated proteins to disease pathogenesis will certainly help to envision potential biomarkers in the CSF for the clinical management of nervous system diseases.
DOI: 10.6084/m9.figshare.4834031.v1
title: Oostra, Saastamoinen, Zwaan and Wheat 2018. "Strong phenotypic plasticity limits potential for evolutionary responses to climate change". Transcriptome assembly and gene expression data.

description: Sequence data, gene expression data, and R script for Oostra et al. 2018. <br><br>Results and methods are described in Oostra et al. 2018 Nature Communications (https://www.nature.com/articles/s41467-018-03384-9). Raw sequencing reads are deposited at NCBI / SRA (BioProject PRJNA376691).<br><br>This fileset contains<br>a) The transcriptome assembly (fasta format)<br>b) raw counts for expression analyses (two separate .cvs files for abdomen and thorax)<br>c) R script for gene expression analyses (text file)<br><br>For any questions or additional data requests please contact Vicencio Oostra at v.oostra@ucl.ac.uk<br>
DOI: 10.6084/m9.figshare.4834007
title: Trace-element geochemistry of transform-fault serpentinite in high-pressure subduction mélanges (eastern Cuba): implications for subduction initiation

description: The Sierra del Convento and La Corea mélanges (eastern Cuba) are vestiges of a Cretaceous subduction channel in the Caribbean realm. Both mélanges contain blocks of oceanic crust and serpentinite subducted to high pressure within a serpentinite matrix. The bulk composition of serpentinite indicates spinel-harzburgite and -herzolite protoliths. The samples preserve fertile protolith signatures that suggest low melting degrees. High concentration of immobile elements Zr, Th, Nb, and REE contents (from ~0.1 to ~2 CI-chondrite) point to early melt–rock interaction processes before serpentinization took place. Major- and trace-element compositions suggest an oceanic fracture-zone–transform-fault setting. A mild negative Eu anomaly in most samples indicates low-temperature fluid–rock interaction as a likely consequence of seawater infiltration during oceanic serpentinization. A second, more important, serpentinization stage is related to enrichment in U, Pb, Cs, Ba, and Sr due to the infiltration of slab-derived fluids. The mineral assemblages are mainly formed by antigorite, lizardite, and chlorite, with local minor talc, tremolite, anthophyllite, dolomite, brucite, and relict orthopyroxene. The local presence of anthophyllite and the replacements of lizardite by antigorite indicate a metamorphic evolution from the cooling of peridotite/serpentinite at the oceanic context to mild heating and compression in a subduction setting. We propose that serpentinites formed at an oceanic transform-fault setting that was the locus of subduction initiation of the Proto-Caribbean basin below the Caribbean plate during early Cretaceous times. Onset of subduction at the fracture zone allowed the preservation of abyssal transform-fault serpentinites at the upper plate, whereas limited downward drag during mature subduction placed the rocks in the subduction channel where they tectonically mixed with the upward-migrating accreted block of the subducted Proto-Caribbean oceanic crust. Hence, we suggest that relatively fertile serpentinites of high-pressure mélanges were witness to the onset of subduction at an oceanic transform-fault setting.
DOI: 10.6084/m9.figshare.4834007.v1
title: Trace-element geochemistry of transform-fault serpentinite in high-pressure subduction mélanges (eastern Cuba): implications for subduction initiation

description: The Sierra del Convento and La Corea mélanges (eastern Cuba) are vestiges of a Cretaceous subduction channel in the Caribbean realm. Both mélanges contain blocks of oceanic crust and serpentinite subducted to high pressure within a serpentinite matrix. The bulk composition of serpentinite indicates spinel-harzburgite and -herzolite protoliths. The samples preserve fertile protolith signatures that suggest low melting degrees. High concentration of immobile elements Zr, Th, Nb, and REE contents (from ~0.1 to ~2 CI-chondrite) point to early melt–rock interaction processes before serpentinization took place. Major- and trace-element compositions suggest an oceanic fracture-zone–transform-fault setting. A mild negative Eu anomaly in most samples indicates low-temperature fluid–rock interaction as a likely consequence of seawater infiltration during oceanic serpentinization. A second, more important, serpentinization stage is related to enrichment in U, Pb, Cs, Ba, and Sr due to the infiltration of slab-derived fluids. The mineral assemblages are mainly formed by antigorite, lizardite, and chlorite, with local minor talc, tremolite, anthophyllite, dolomite, brucite, and relict orthopyroxene. The local presence of anthophyllite and the replacements of lizardite by antigorite indicate a metamorphic evolution from the cooling of peridotite/serpentinite at the oceanic context to mild heating and compression in a subduction setting. We propose that serpentinites formed at an oceanic transform-fault setting that was the locus of subduction initiation of the Proto-Caribbean basin below the Caribbean plate during early Cretaceous times. Onset of subduction at the fracture zone allowed the preservation of abyssal transform-fault serpentinites at the upper plate, whereas limited downward drag during mature subduction placed the rocks in the subduction channel where they tectonically mixed with the upward-migrating accreted block of the subducted Proto-Caribbean oceanic crust. Hence, we suggest that relatively fertile serpentinites of high-pressure mélanges were witness to the onset of subduction at an oceanic transform-fault setting.
DOI: 10.6084/m9.figshare.4834004
title: Colin27 high resolution cortical surfaces

description: This data set includes high-resolution (0.5mm) maps of the cerebral cortical surfaces reconstructed from the Colin27 brain atlas [Aubert-Brohe et al., 2006]. The tissue segmentation provided with the atlas was manually edited to merge sub-cortical structures and lateral ventricles with the white matter (WM), then the WM mask was topology-corrected [Bazin et al., 2007] and the WM and cortical gray matter (GM) masks were used to estimate cortical surfaces with the CRUISE algorithm [Han et al., 2004] for the GM/WM boundary (gwb), CSF/GM boundary (cgb), and an average surface (avg) equidistant to both cortical boundaries. Surfaces were reconstructed as levet sets of a signed distance function, and triangular meshes were extracted with the connectivity consistent marching cubes algorithm [Han et al., 2003] and inflated to obtain smooth cortical maps [Tosun et al., 2004]. <br><br>Included here are the left and right cortical segmentations (1=GM, 2=WM), level set surfaces (gwb, cgb, avg) in compressed NIFTI format, and the corresponding extracted and inflated (inf) meshes in VTK ascii format. The NIFTI images are co-aligned with the Colin27 atlas in voxel space, and the surfaces follow the MIPAV mesh space conventions.<br><br>B Aubert-Broche, AC Evans, and DL Collins, “A new improved version of the realistic digital brain phantom,” NeuroImage, vol. 32, no. 1, pp. 138–45, 2006. http://www.ncbi.nlm.nih.gov/pubmed/16750398<br><br>PL Bazin, DL Pham Topology correction of segmented medical images using a fast marching algorithm Computer methods and programs in biomedicine 88 (2), 182-190, 2007<br><br><b>Tosun D</b>, Rettmann ME, Han X, <b>Tao X</b>, Xu C, Resnick SM, Pham DL, Prince JL. Cortical surface segmentation and mapping. Neuroimage. 2004; 23 Suppl 1:S108-18. PMID: 15501080; PMCID: PMC4587756.<br><br>X Han, C Xu, JL Prince A topology preserving level set method for geometric deformable models IEEE Transactions on Pattern Analysis and Machine Intelligence 25 (6), 755-768, 2003<br><br>X Han, DL Pham, D Tosun, ME Rettmann, C Xu, JL Prince CRUISE: cortical reconstruction using implicit surface evolution NeuroImage 23 (3), 997-1012, 2004
DOI: 10.6084/m9.figshare.4833938
title: Procyshyn 2017 GTF2I Oxytocin DataSet from The Williams syndrome prosociality gene GTF2I mediates oxytocin reactivity and social anxiety in a healthy population

description: Demographic data, anxiety score, oxytocin measurements, GTF2I genotyping data
DOI: 10.6084/m9.figshare.4833941
title: Data from Modulation of the composite face effect by unintended emotion cues

description: This file contains the data for each of the studies
DOI: 10.6084/m9.figshare.4833941.v1
title: Data from Modulation of the composite face effect by unintended emotion cues

description: This file contains the data for each of the studies
DOI: 10.6084/m9.figshare.4833938.v1
title: Procyshyn 2017 GTF2I Oxytocin DataSet from The Williams syndrome prosociality gene GTF2I mediates oxytocin reactivity and social anxiety in a healthy population

description: Demographic data, anxiety score, oxytocin measurements, GTF2I genotyping data
DOI: 10.6084/m9.figshare.4833872
title: Data from: Dynamic species classification of microorganisms across time, abiotic and biotic environments - a sliding window approach

description: The following datasets were used for the analyses presented in the publication called "Dynamic species classification of microorganisms across time, abiotic and biotic environments --- a sliding window approach".<br>Mixed models and figure 5:* Logistic regression across temperature and species richness (LR_all_class_data.csv)* Four datasets for the logistic regressions using subsets of species, temperatures, time and number of trajectories(LR_[sp, temp, ws, trjs]_data.csv)<br>Comparing automatic and manual counts & Figure 6:* The comparison between the RF classifier and manual identification (Automatic_RF_id.csv & Manual_id.csv)* The comparison between RF, NB and SVM classifier and manual identifications (NB_SVM_RF_id.csv & Manual_id.csv)
DOI: 10.6084/m9.figshare.4833872.v1
title: Data from: Dynamic species classification of microorganisms across time, abiotic and biotic environments - a sliding window approach

description: The following datasets were used for the analyses presented in the publication called "Dynamic species classification of microorganisms across time, abiotic and biotic environments --- a sliding window approach".<br>Mixed models and figure 5:* Logistic regression across temperature and species richness (LR_all_class_data.csv)* Four datasets for the logistic regressions using subsets of species, temperatures, time and number of trajectories(LR_[sp, temp, ws, trjs]_data.csv)<br>Comparing automatic and manual counts & Figure 6:* The comparison between the RF classifier and manual identification (Automatic_RF_id.csv & Manual_id.csv)* The comparison between RF, NB and SVM classifier and manual identifications (NB_SVM_RF_id.csv & Manual_id.csv)
DOI: 10.6084/m9.figshare.4833806
title: Biphonal calls in Atlantic spotted dolphins (<i>Stenella frontalis</i>): bitonal and burst-pulse whistles

description: Biphonation, the simultaneous production of two sounds by a single animal, is found in the vocalizations of a range of mammalian species. Its prevalence suggests it plays an important role in acoustic communication. Concurrent vocal and behavioural recordings were made of Atlantic spotted dolphins (<i>Stenella frontalis</i>) off Bimini, The Bahamas. The occurrence of two types of biphonal signals is reported: burst-pulse whistles with combined tonal and burst-pulse elements, and bitonal whistles. Biphonal whistles are rarely described in reports of dolphin acoustic repertoires, but were common in these dolphins: of all whistles analysed (<i>n</i> = 1211), 26.84% were burst-pulse whistles and 4.71% were bitonal whistles. A subset of whistles (<i>n</i> = 397) were attributed to dolphins of specific age classes, and used to compare prevalence of biphonation across age. Biphonation occurred in 61.54% of sexually mature and 48.32% of sexually immature dolphins’ whistles. Sexually immature dolphins emitted more burst-pulse whistles than older dolphins: 44.13% of sexually immature dolphins’ whistles were burst-pulse whistles, while 15.38% of adult whistles were burst-pulse whistles. Bitonal whistle production was more prevalent in sexually mature dolphins: 41.03% of adult whistles were bitonal, while only 4.19% of sexually immature dolphins’ whistles were bitonal. The prevalence of a biphonal component in specific repeated, stereotyped whistle contours suggests that these acoustic features could be important components of contact calls, or signature whistles. The biphonal components of spotted dolphin whistles may serve to convey additional information as to identity, age or other factors to conspecifics.
DOI: 10.6084/m9.figshare.4833809
title: Impact of different educational interventions on psychosocial well-being of women with a positive high-risk human papillomavirus and normal cervical cytology: a randomised trial

description: <b>Introduction:</b> The aim of this study was to compare the effect of two educational interventions on the psychosocial well-being of Hong Kong Chinese women who have a positive high-risk human papillomavirus (HPV) test and normal cervical cytology. <b>Methods:</b> Participants were randomised into either leaflet group, in which a written HPV factsheet was provided; or counselling group, in which a didactic HPV presentation in person in addition to the factsheet was provided. Women’s psychological conditions were assessed by self-administered questionnaires at pre, post (within one week) and 6 months after the educational interventions. Main outcome measures were psychosocial well-being (cervical cancer worry, anxiety and depression, screening-related anxieties, HPV-related shame) and knowledge of cervical screening and HPV. <b>Results:</b> Data from 121 women (52 in leaflet group; 69 in counselling group) were analysed. There was no significant difference in the psychosocial well-being between the two groups at alltime points. Irrespective of the two educational interventions, cervical cancer worry and anxiety decreased over time. The counselling group had a significantly higher score in knowledge of cervical screening and HPV compared with leaflet group (mean score 4.65 ± 0.19 versus 3.71 ± 0.23, <i>p</i> = 0.002) at post-educational intervention, but there was no significant difference (mean score 4.14 ± 0.22 versus 3.58 ± 0.24, <i>p</i> = 0.084) at 6 months. <b>Discussion:</b> Both educational interventions were comparable in relieving adverse HPV-related psychosocial effects. Combination of counselling and leaflet were more effective than leaflet only in improving women’s knowledge on cervical screening and HPV soon after educational interventions but the benefit was not apparent after 6 months.
DOI: 10.6084/m9.figshare.4833803
title: <i>In silico</i> prediction of drug resistance due to S247R mutation of Influenza H1N1 neuraminidase protein

description: We present here <i>in silico</i> studies on antiviral drug resistance due to a novel mutation of influenza A/H1N1 neuraminidase (NA) protein. Influenza A/H1N1 virus was responsible for a recent pandemic and is currently circulating among the seasonal influenza strains. M2 and NA are the two major viral proteins related to pathogenesis in humans and have been targeted for drug designing. Among them, NA is preferred because the ligand-binding site of NA is highly conserved between different strains of influenza virus. Different mutations of the NA active site residues leading to drug resistance or susceptibility of the virus were studied earlier. We report here a novel mutation (S247R) in the NA protein that was sequenced earlier from the nasopharyngeal swab from Sri Lanka and Thailand in the year 2009 and 2011, respectively. Another mutation (S247N) was already known to confer resistance to oseltamivir. We did a comparative study of these two mutations vis-a-vis the drug-sensitive wild type NA to understand the mechanism of drug resistance of S247N and to predict the probability of the novel S247R mutation to become resistant to the currently available drugs, oseltamivir and zanamivir. We performed molecular docking- and molecular dynamics-based analysis of both the mutant proteins and showed that mutation of S247R affects drug binding to the protein by positional displacement due to altered active site cavity architecture, which in turn reduces the affinity of the drug molecules to the NA active site. Our analysis shows that S247R may have high probability of being resistant.