cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3218851.v1
title: Out of Tibet: an early sheep from the Pliocene of Tibet, <i>Protovis himalayensis</i>, genus and species nov. (Bovidae, Caprini), and origin of Ice Age mountain sheep

description: Modern wild sheep, <i>Ovis</i>, is widespread in the mountain ranges of the Caucasus through Himalaya, Tibetan Plateau, Tianshan-Altai, eastern Siberia, and the Rocky Mountains in North America. In Eurasia, fossil sheep are known at a few Pleistocene sites in North China, eastern Siberia, and western Europe, but are so far absent from the Tibetan Plateau. We describe an extinct sheep, <i>Protovis himalayensis</i>, gen. et sp. nov., from the Pliocene of the Zanda Basin in western Himalaya. Smaller than the living argali, this new form shares with <i>Ovis</i> posterolaterally arched horncores and partially developed sinuses and possesses several transitional characters leading to <i>Ovis. Protovis</i> likely subsisted on C<sub>3</sub> plants, which are the dominant vegetation in the Zanda area during the Pliocene. With the discovery of this new genus and species, we extend the fossil record for the sheep clade into the Pliocene of the Tibetan Plateau, consistent with our previous out-of-Tibet hypothesis. Ancestral sheep in the Pliocene were presumed adapted to high altitude and cold environments, and during the Ice Age, sheep became anatomically modern and dispersed outside of the Tibetan Plateau. Both this new fossil datum and the existing molecular phylogeny suggest that the Tibetan Plateau, possibly including Tianshan-Altai, represents the ancestral home range(s) of mountain sheep and that these basal stocks were the ultimate source of all extant species. Most sheep species survived along their Pleistocene route of dispersal, offering a highly consistent pattern of zoogeography. http://zoobank.org/urn:lsid:zoobank.org:pub:F2AEE746-0A5B-4F40-89B7-8EF0C04F21FD SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP Citation for this article: Wang, X., Q. Li, and G. T. Takeuchi. 2016. Out of Tibet: an early sheep from the Pliocene of Tibet, <i>Protovis himalayensis</i>, gen. et sp. nov. (Bovidae, Caprini), and origin of Ice Age mountain sheep. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2016.1169190.
DOI: 10.6084/m9.figshare.3218857.v1
title: Deciphering the cause of evolutionary variance within intrinsically disordered regions in human proteins

description: Why the intrinsically disordered regions evolve within human proteome has became an interesting question for a decade. Till date, it remains an unsolved yet an intriguing issue to investigate why some of the disordered regions evolve rapidly while the rest are highly conserved across mammalian species. Identifying the key biological factors, responsible for the variation in the conservation rate of different disordered regions within the human proteome, may revisit the above issue. We emphasized that among the other biological features (multifunctionality, gene essentiality, protein connectivity, number of unique domains, gene expression level and expression breadth) considered in our study, the number of unique protein domains acts as a strong determinant that negatively influences the conservation of disordered regions. In this context, we justified that proteins having a fewer types of domains preferably need to conserve their disordered regions to enhance their structural flexibility which in turn will facilitate their molecular interactions. In contrast, the selection pressure acting on the stretches of disordered regions is not so strong in the case of multi-domains proteins. Therefore, we reasoned that the presence of conserved disordered stretches may compensate the functions of multiple domains within a single domain protein. Interestingly, we noticed that the influence of the unique domain number and expression level acts differently on the evolution of disordered regions from that of well-structured ones.
DOI: 10.6084/m9.figshare.3218866.v1
title: 3-Supporting information-Pharm Biol-final.doc

description: In this file, we provide supplemental information that guarantees results discussed in our published work. The DOI of our paper is: 10.1080/13880209.2016.1183683. Once our article has published online, it will be available at the following permanent link:http://dx.doi.org/10.1080/13880209.2016.1183683 .
DOI: 10.6084/m9.figshare.3218866.v3
title: Reduction of Candida tropicalis biofilm by photoactivation of aHeterophyllaea pustulata extract

description: In this file, we provide supplemental information that guarantees results discussed in our published work: Reduction of <i>Candida tropicalis</i> biofilm by photoactivation of a <i>Heterophyllaea pustulata</i> extract. The DOI of our paper is: 10.1080/13880209.2016.1183683. Once our article has published online, it will be available at the following permanent link:http://dx.doi.org/10.1080/13880209.2016.1183683 .
DOI: 10.6084/m9.figshare.3218866.v2
title: Supporting information-Pharm Biol

description: In this file, we provide supplemental information that guarantees results discussed in our published work: Reduction of <i>Candida tropicalis</i> biofilm by photo-activation of a <i>Heterophyllaea pustulata</i> extract. The DOI of our paper is: 10.1080/13880209.2016.1183683. Once our article has published online, it will be available at the following permanent link:http://dx.doi.org/10.1080/13880209.2016.1183683 .
DOI: 10.6084/m9.figshare.3218788
title: Changes in Visual Function in the Elderly Population in the United States: 1995–2010

description: <i><b>Purpose</b></i>: To document recent trends in visual function among the United States population aged 70+ years and investigate how the trends can be explained by inter-temporal changes in: (1) population sociodemographic characteristics, and chronic disease prevalence, including eye diseases (compositional changes); and (2) effects of the above factors on visual function (structural changes). <i><b>Methods</b></i>: Data from the 1995 Asset and Health Dynamics among the Oldest Old (AHEAD) and the 2010 Health and Retirement Study (HRS) were merged with Medicare Part B claims in the interview years and the 2 previous years. Decomposition analysis was performed. Respondents from both studies were aged 70+ years. The outcome measure was respondent self-reported visual function on a 6-point scale (from 6 = blind to 1 = excellent). <i><b>Results</b></i>: Overall, visual function improved from slightly worse than good (3.14) in 1995 to slightly better than good (2.98) in 2010. A decline in adverse effects of aging on vision was found. Among the compositional changes were higher educational attainment leading to improved vision, and higher prevalence of such diseases as diabetes mellitus, which tended to lower visual function. However, compared to compositional changes, structural changes were far more important, including decreased adverse effects of aging, diabetes mellitus (when not controlling for eye diseases), and diagnosed glaucoma. <i><b>Conclusion</b></i>: Although the US population has aged and is expected to age further, visual function improved among elderly persons, especially among persons 80+ years, likely reflecting a favorable role of structural changes identified in this study in mitigating the adverse effect of ongoing aging on vision.
DOI: 10.6084/m9.figshare.3218788.v1
title: Changes in Visual Function in the Elderly Population in the United States: 1995–2010

description: <i><b>Purpose</b></i>: To document recent trends in visual function among the United States population aged 70+ years and investigate how the trends can be explained by inter-temporal changes in: (1) population sociodemographic characteristics, and chronic disease prevalence, including eye diseases (compositional changes); and (2) effects of the above factors on visual function (structural changes). <i><b>Methods</b></i>: Data from the 1995 Asset and Health Dynamics among the Oldest Old (AHEAD) and the 2010 Health and Retirement Study (HRS) were merged with Medicare Part B claims in the interview years and the 2 previous years. Decomposition analysis was performed. Respondents from both studies were aged 70+ years. The outcome measure was respondent self-reported visual function on a 6-point scale (from 6 = blind to 1 = excellent). <i><b>Results</b></i>: Overall, visual function improved from slightly worse than good (3.14) in 1995 to slightly better than good (2.98) in 2010. A decline in adverse effects of aging on vision was found. Among the compositional changes were higher educational attainment leading to improved vision, and higher prevalence of such diseases as diabetes mellitus, which tended to lower visual function. However, compared to compositional changes, structural changes were far more important, including decreased adverse effects of aging, diabetes mellitus (when not controlling for eye diseases), and diagnosed glaucoma. <i><b>Conclusion</b></i>: Although the US population has aged and is expected to age further, visual function improved among elderly persons, especially among persons 80+ years, likely reflecting a favorable role of structural changes identified in this study in mitigating the adverse effect of ongoing aging on vision.
DOI: 10.6084/m9.figshare.3218737
title: OH-PRED: prediction of protein hydroxylation sites by incorporating adapted normal distribution bi-profile Bayes feature extraction and physicochemical properties of amino acids

description: Hydroxylation of proline or lysine residues in proteins is a common post-translational modification event, and such modifications are found in many physiological and pathological processes. Nonetheless, the exact molecular mechanism of hydroxylation remains under investigation. Because experimental identification of hydroxylation is time-consuming and expensive, bioinformatics tools with high accuracy represent desirable alternatives for large-scale rapid identification of protein hydroxylation sites. In view of this, we developed a supporter vector machine-based tool, OH-PRED, for the prediction of protein hydroxylation sites using the adapted normal distribution bi-profile Bayes feature extraction in combination with the physicochemical property indexes of the amino acids. In a jackknife cross validation, OH-PRED yields an accuracy of 91.88% and a Matthew’s correlation coefficient (MCC) of 0.838 for the prediction of hydroxyproline sites, and yields an accuracy of 97.42% and a MCC of 0.949 for the prediction of hydroxylysine sites. These results demonstrate that OH-PRED increased significantly the prediction accuracy of hydroxyproline and hydroxylysine sites by 7.37 and 14.09%, respectively, when compared with the latest predictor PredHydroxy. In independent tests, OH-PRED also outperforms previously published methods.
DOI: 10.6084/m9.figshare.3218728
title: Understanding Editing Behaviors in Multilingual Wikipedia

description: Multilingualism is common offline, but we have a more limited understanding of the ways multilingualism is displayed online and the roles that multilinguals play in the spread of content between speakers of different languages. We take a computational approach to studying multilingualism using one of the largest usergenerated content platforms, Wikipedia. We study multilingualism by collecting and analyzing a large dataset of the content written by multilingual editors of the English, German, and Spanish editions of Wikipedia. This dataset contains over two million paragraphs edited by over 15,000 multilingual users from July 8 to August 9, 2013. We analyze these multilingual editors in terms of their engagement, interests, and language proficiency in their primary and non-primary (secondary) languages and find that the English edition of Wikipedia displays different dynamics from the Spanish and German editions. Users primarily editing the Spanish and German editions make more complex edits than users who edit these editions as a second language. In contrast, users editing the English edition as a second language make edits that are just as complex as the edits by users who primarily edit the English edition. In this way, English serves a special role bringing together content written by multilinguals from many language editions. Nonetheless, language remains a formidable hurdle to the spread of content: we find evidence for a complexity barrier whereby editors are less likely to edit complex content in a second language. In addition, we find that multilinguals are less engaged and show lower levels of language proficiency in their second languages. We also examine the topical interests of multilingual editors and find that there is no significant difference between primary and non-primary editors in each language.<br>
DOI: 10.6084/m9.figshare.3218737.v1
title: OH-PRED: prediction of protein hydroxylation sites by incorporating adapted normal distribution bi-profile Bayes feature extraction and physicochemical properties of amino acids

description: Hydroxylation of proline or lysine residues in proteins is a common post-translational modification event, and such modifications are found in many physiological and pathological processes. Nonetheless, the exact molecular mechanism of hydroxylation remains under investigation. Because experimental identification of hydroxylation is time-consuming and expensive, bioinformatics tools with high accuracy represent desirable alternatives for large-scale rapid identification of protein hydroxylation sites. In view of this, we developed a supporter vector machine-based tool, OH-PRED, for the prediction of protein hydroxylation sites using the adapted normal distribution bi-profile Bayes feature extraction in combination with the physicochemical property indexes of the amino acids. In a jackknife cross validation, OH-PRED yields an accuracy of 91.88% and a Matthew’s correlation coefficient (MCC) of 0.838 for the prediction of hydroxyproline sites, and yields an accuracy of 97.42% and a MCC of 0.949 for the prediction of hydroxylysine sites. These results demonstrate that OH-PRED increased significantly the prediction accuracy of hydroxyproline and hydroxylysine sites by 7.37 and 14.09%, respectively, when compared with the latest predictor PredHydroxy. In independent tests, OH-PRED also outperforms previously published methods.
DOI: 10.6084/m9.figshare.3218728.v1
title: Understanding Editing Behaviors in Multilingual Wikipedia

description: Multilingualism is common offline, but we have a more limited understanding of the ways multilingualism is displayed online and the roles that multilinguals play in the spread of content between speakers of different languages. We take a computational approach to studying multilingualism using one of the largest usergenerated content platforms, Wikipedia. We study multilingualism by collecting and analyzing a large dataset of the content written by multilingual editors of the English, German, and Spanish editions of Wikipedia. This dataset contains over two million paragraphs edited by over 15,000 multilingual users from July 8 to August 9, 2013. We analyze these multilingual editors in terms of their engagement, interests, and language proficiency in their primary and non-primary (secondary) languages and find that the English edition of Wikipedia displays different dynamics from the Spanish and German editions. Users primarily editing the Spanish and German editions make more complex edits than users who edit these editions as a second language. In contrast, users editing the English edition as a second language make edits that are just as complex as the edits by users who primarily edit the English edition. In this way, English serves a special role bringing together content written by multilinguals from many language editions. Nonetheless, language remains a formidable hurdle to the spread of content: we find evidence for a complexity barrier whereby editors are less likely to edit complex content in a second language. In addition, we find that multilinguals are less engaged and show lower levels of language proficiency in their second languages. We also examine the topical interests of multilingual editors and find that there is no significant difference between primary and non-primary editors in each language.<br>
DOI: 10.6084/m9.figshare.3218725
title: Dynamic polygonal spreading of a droplet on a lyophilic pillar-arrayed surface

description: We experimentally investigated the dynamic polygonal spreading of droplets on lyophilic pillar-arrayed substrates. When deposited on lyophilic rough surfaces, droplets adopt dynamic evolutions of projected shapes from initial circles to final bilayer polygons. These dynamic processes are distinguished in two regimes on the varied substrates. The bilayer structure of a droplet, induced by micropillars on the surface, was explained by the interaction between the fringe (liquid in the space among the micropillars) and the bulk (upper liquid). The evolution of polygonal shapes, following the symmetry of the pillar-arrayed surface, was analysed by the competition effects of excess driving energy and resistance which were induced by micropillars with increasing solid surface area fraction. Though the anisotropic droplets spread in different regimes, they obey the same scaling law <i>S</i> ~ <i>t</i><sup>2/3</sup> (<i>S</i> being the wetted area and <i>t</i> being the spreading time), which is derived from the molecular kinetic theory. These results may expand our knowledge of the liquid dynamics on patterned surfaces and assist surface design in practical applications.
DOI: 10.6084/m9.figshare.3218725.v1
title: Dynamic polygonal spreading of a droplet on a lyophilic pillar-arrayed surface

description: We experimentally investigated the dynamic polygonal spreading of droplets on lyophilic pillar-arrayed substrates. When deposited on lyophilic rough surfaces, droplets adopt dynamic evolutions of projected shapes from initial circles to final bilayer polygons. These dynamic processes are distinguished in two regimes on the varied substrates. The bilayer structure of a droplet, induced by micropillars on the surface, was explained by the interaction between the fringe (liquid in the space among the micropillars) and the bulk (upper liquid). The evolution of polygonal shapes, following the symmetry of the pillar-arrayed surface, was analysed by the competition effects of excess driving energy and resistance which were induced by micropillars with increasing solid surface area fraction. Though the anisotropic droplets spread in different regimes, they obey the same scaling law <i>S</i> ~ <i>t</i><sup>2/3</sup> (<i>S</i> being the wetted area and <i>t</i> being the spreading time), which is derived from the molecular kinetic theory. These results may expand our knowledge of the liquid dynamics on patterned surfaces and assist surface design in practical applications.
DOI: 10.6084/m9.figshare.3213319
title: Supplementary Material for: Improved (4 Plus 2) Rituximab Protocol for Severe Cases of Mixed Cryoglobulinemia: A 6-Year Observational Study

description: <br><strong><em>Background:</em></strong> In a prospective, single-center open study, we evaluated the very long-term effects of rituximab (RTX) administered to patients with severe mixed cryoglobulinemia (MC). <b><i>Methods:</i></b> RTX was administered to 31 patients with MC (type II in 29 cases and type III in 2) with diffuse membranoproliferative glomerulonephritis (16 cases), peripheral neuropathy (26) and large skin ulcers (7). All but 4 patients had serum anti-hepatitis C virus antibodies. RTX was administered at a dose of 375 mg/m<sup>2</sup>, according to a ‘4 + 2' protocol (days 1, 8, 15 and 22 plus 1 dose 1 and 2 months later). No other immunosuppressive drugs were added. Response was evaluated over a very long-term follow-up (mean 72.47 months, range 30-148). <b><i>Results:</i></b> Complete remission of pretreatment active manifestations was observed in all cases of purpuric lesions and non-healing vasculitic ulcers, and in 80% of the peripheral neuropathies. Cryoglobulinemic nephropathy significantly improved during follow-up, starting from the 2nd month after RTX (serum creatinine from 2.1 ± 1.7 to 1.5 ± 1.6 mg/dl, p ≤ 0.05; 24-hour proteinuria from 2.3 ± 2.1 to 0.9 ± 1.9 g/24 h, p ≤ 0.05). Improvement of cryoglobulinemic serological hallmarks, such as cryocrit and low complement C4, were observed. No clinically relevant side effects were recorded. Re-induction with RTX was carried out in 9 relapsed patients after a mean of 31.1 months (12-54), again with beneficial effects. The survival rate was 75% at 6 years and the probability of remaining symptom-free for 10 years without any therapy was of about 60% after a single ‘4 + 2' infusion cycle, while the probability of living symptom-free 5 years after relapsing was 80% if given the same treatment. <b><i>Conclusion:</i></b> In this open, prospective study, RTX appeared to be very effective and safe in the treatment of the most severe cases of MC.
DOI: 10.6084/m9.figshare.3218569
title: S1_megablast_results_reanalysis_Rivera-Perez2015.zip

description: Megablast results of data from Rivera-Perez et al. 2015 (PLoS One), showing all suggested 'retrovirus' hits are from human sources.
DOI: 10.6084/m9.figshare.3218713.v2
title: nets induce the production of IL-1

description: supporting data
DOI: 10.6084/m9.figshare.3208942
title: Modulation of the Nrf2 signalling pathway in Hct116 colon carcinoma cells by baicalein and its methylated derivative negletein

description: <b>Context:</b> Baicalein is a major compound in extracts derived from <i>Scutellaria baicalensis</i> Georgi (Lamiaceae) which are used in the Traditional Chinese Medicine for the treatment of inflammatory and gastrointestinal diseases. This flavonoid is an activator of the Nrf2 signalling pathway but the molecular mechanism is not clearly established. <b>Objective:</b> We investigated the molecular mode of baicalein-mediated Nrf2-activation in Hct116 cells by the analysis of proteasomal activity, radical-scavenging activity and the comparison with baicalein derivatives. <b>Materials and methods:</b> The radical-scavenging activity (TEAC, DCF) up to 25 μM, cytotoxicity (MTT assay, 48 h) up to 100 μM, proteasomal activity and the Nrf2-activation (luciferase assay, ubiquitinylation, western blot, Ser40-phosphorylation; incubation for 1 or 4 h) by concentrations up to 40 or 50 μM of the compounds were analysed in Hct116 human colon carcinoma cells. <b>Results:</b> No change in the ubiquitinylation of Nrf2, proteasomal activity and transcription of the <i>NRF2</i> gene were detectable. Baicalein decreased the phosphorylation of Nrf2 (IC<sub>50-</sub>value approximately 20 μM) suggesting an inhibitory effect of the flavonoid on protein kinases. Since the activation of the Nrf2 pathway by baicalein might be also due to redox-activity of the compound, we investigated the effects of methylated baicalein derivatives oroxylin A, negeletein and baicaleintrimethylether. Oroxylin A and negletein showed a comparable redox-active potential, but only negletein (50 μM, 4 h) was able to activate Nrf2. <b>Conclusion:</b> This result confirms the hypothesis that baicalein, a component of extracts derived from <i>Baical Skullcap</i>, causes an activation of Nrf2 independent of a modulation of the cellular redox potential.
DOI: 10.6084/m9.figshare.3209908
title: The dataset for study "Structural Alterations of Segmented Macular Inner Layers in Aquaporin4-Antibody-Positive Optic Neuritis Patients in a Chinese Population "

description: Data base suppoort results of the study "Structural Alterations of Segmented Macular Inner Layers in Aquaporin4-Antibody-Positive Optic Neuritis Patients in a Chinese Population ". It mainly includes perpapillary retinal nerve fiber layer thickness and inner macular segmented layers OCT measurements in AQP4-Ab negative and positive ON cohorts and healthy controls for 0-2 months, 2-4 months, 4-6 months and more than 6 months.