cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3980184.v1
title: HDLEC siRNA migration primary screen images

description: Images from high content genome-wide siRNA screen of lymphatic endothelial cell migration<br><br><b>File names:</b><br>Each folder is named according to the following convention:<br><br>(YYMMDD)(initials)(celltype)_(dharmacon plate #)(VCFG library freeze version 'A' or 'C')_(screen plate #)(technical rep 'A' or 'B')_(t00 or t24)<br><br>eg. 110131SWLEC_11024A_001A_t00<br><br>Each folder contains 96x 16-bit TIF images (ie from one plate) labelled with plate number and 'Well_A01' through to 'Well_H12', followed by the gene targeted by siRNA.<br><br>16-bit TIF images require specialised image analysis software to open correctly, such as the freely available ImageJ package.<br><br><b>Plate layout:</b><br>For detailed mapping of siRNA layout, please see Pubchem entry AID1159578 which includes migration data for the screen.<br><br><br><br>
DOI: 10.7910/dvn/v1rjpf/jhvv9c
title: snk20160419_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/gsrjrm
title: snk20160202_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/j6b3jl
title: snk20150213_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3980145
title: Discussing practical applications for altmetrics: social media profiles for African, European and North American publications

description: Study presented by Rodrigo Costas at the 3:AM conference, Bucharest, 28th - 29th September 2016
DOI: 10.6084/m9.figshare.3980136
title: External Knowledge Sourcing Data

description: This study addresses two research questions: does external knowledge sourcing lead to market performance and how does external knowledge sourcing interact with a firm’s different innovation activities to enhance market performance.
DOI: 10.7910/dvn/v1rjpf/vpt5bv
title: snk20151027_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/co65tw
title: snk20150805_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.12912146.v1
title: Matrisome genes and their category..xlsx

description: Matrisome genes and their category
DOI: 10.7910/dvn/v1rjpf/xoed2t
title: snk20151020_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3980136.v1
title: External Knowledge Sourcing Data.xlsx

description: This study addresses two research questions: does external knowledge sourcing lead to market performance and how does external knowledge sourcing interact with a firm’s different innovation activities to enhance market performance.
DOI: 10.7910/dvn/v1rjpf/pdovef
title: snk20150824_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3980121
title: Supplementary data from Characterizing the reproduction number of epidemics with early subexponential growth dynamics

description: Early estimates of the transmission potential of emerging and re-emerging infections are increasingly used to inform public health authorities on the level of risk posed by outbreaks. Existing methods to estimate the reproduction number generally assume exponential growth in case incidence in the first few disease generations, before susceptible depletion sets in. In reality, outbreaks can display subexponential (i.e. polynomial) growth in the first few disease generations, owing to clustering in contact patterns, spatial effects, inhomogeneous mixing, reactive behaviour changes or other mechanisms. Here, we introduce the <i>generalized</i> growth model to characterize the early growth profile of outbreaks and estimate the effective reproduction number, with no need for explicit assumptions about the shape of epidemic growth. We demonstrate this phenomenological approach using analytical results and simulations from mechanistic models, and provide validation against a range of empirical disease datasets. Our results suggest that subexponential growth in the early phase of an epidemic is the rule rather the exception. Mechanistic simulations show that slight modifications to the classical susceptible–infectious–removed model, result in subexponential growth, and in turn a rapid decline in the reproduction number within three to five disease generations. For empirical outbreaks, the generalized-growth model consistently outperforms the exponential model for a variety of directly and indirectly transmitted diseases datasets (pandemic influenza, measles, smallpox, bubonic plague, cholera, foot-and-mouth disease, HIV/AIDS and Ebola) with model estimates supporting subexponential growth dynamics. The rapid decline in effective reproduction number predicted by analytical results and observed in real and synthetic datasets within three to five disease generations contrasts with the expectation of invariant reproduction number in epidemics obeying exponential growth. The generalized-growth concept also provides us a compelling argument for the unexpected extinction of certain emerging disease outbreaks during the early ascending phase. Overall, our approach promotes a more reliable and data-driven characterization of the early epidemic phase, which is important for accurate estimation of the reproduction number and prediction of disease impact.
DOI: 10.6084/m9.figshare.3980121.v1
title: Supplementary data from Characterizing the reproduction number of epidemics with early subexponential growth dynamics

description: Early estimates of the transmission potential of emerging and re-emerging infections are increasingly used to inform public health authorities on the level of risk posed by outbreaks. Existing methods to estimate the reproduction number generally assume exponential growth in case incidence in the first few disease generations, before susceptible depletion sets in. In reality, outbreaks can display subexponential (i.e. polynomial) growth in the first few disease generations, owing to clustering in contact patterns, spatial effects, inhomogeneous mixing, reactive behaviour changes or other mechanisms. Here, we introduce the <i>generalized</i> growth model to characterize the early growth profile of outbreaks and estimate the effective reproduction number, with no need for explicit assumptions about the shape of epidemic growth. We demonstrate this phenomenological approach using analytical results and simulations from mechanistic models, and provide validation against a range of empirical disease datasets. Our results suggest that subexponential growth in the early phase of an epidemic is the rule rather the exception. Mechanistic simulations show that slight modifications to the classical susceptible–infectious–removed model, result in subexponential growth, and in turn a rapid decline in the reproduction number within three to five disease generations. For empirical outbreaks, the generalized-growth model consistently outperforms the exponential model for a variety of directly and indirectly transmitted diseases datasets (pandemic influenza, measles, smallpox, bubonic plague, cholera, foot-and-mouth disease, HIV/AIDS and Ebola) with model estimates supporting subexponential growth dynamics. The rapid decline in effective reproduction number predicted by analytical results and observed in real and synthetic datasets within three to five disease generations contrasts with the expectation of invariant reproduction number in epidemics obeying exponential growth. The generalized-growth concept also provides us a compelling argument for the unexpected extinction of certain emerging disease outbreaks during the early ascending phase. Overall, our approach promotes a more reliable and data-driven characterization of the early epidemic phase, which is important for accurate estimation of the reproduction number and prediction of disease impact.
DOI: 10.7910/dvn/v1rjpf/mj3u17
title: snk20161009_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3980109
title: PowerPoint Slides for: Use of Extended-Release Calcifediol to Treat Secondary Hyperparathyroidism in Stages 3 and 4 Chronic Kidney Disease

description: <i>Background/Aims:</i> Vitamin D insufficiency and secondary hyperparathyroidism (SHPT) are associated with increased morbidity and mortality in chronic kidney disease (CKD) and are poorly addressed by current treatments. The present clinical studies evaluated extended-release (ER) calcifediol, a novel vitamin D prohormone repletion therapy designed to gradually correct low serum total 25-hydroxyvitamin D, improve SHPT control and minimize the induction of CYP24A1 and FGF23. <i>Methods:</i> Two identical multicenter, randomized, double-blind, placebo-controlled studies enrolled subjects from 89 US sites. A total of 429 subjects, balanced between studies, with stage 3 or 4 CKD, SHPT and vitamin D insufficiency were randomized 2:1 to receive oral ER calcifediol (30 or 60 µg) or placebo once daily at bedtime for 26 weeks. Most subjects (354 or 83%) completed dosing, and 298 (69%) entered a subsequent open-label extension study wherein ER calcifediol was administered without interruption for another 26 weeks. <i>Results:</i> ER calcifediol normalized serum total 25-hydroxyvitamin D concentrations (&gt;30 ng/ml) in &gt;95% of per-protocol subjects and reduced plasma intact parathyroid hormone (iPTH) by at least 10% in 72%. The proportion of subjects receiving ER calcifediol who achieved iPTH reductions of ≥30% increased progressively with treatment duration, reaching 22, 40 and 50% at 12, 26 and 52 weeks, respectively. iPTH lowering with ER calcifediol was independent of CKD stage and significantly greater than with placebo. ER calcifediol had inconsequential impact on serum calcium, phosphorus, FGF23 and adverse events. <i>Conclusion:</i> Oral ER calcifediol is safe and effective in treating SHPT and vitamin D insufficiency in CKD.
DOI: 10.7910/dvn/v1rjpf/wsmmkb
title: snk20161219_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/kilt5s
title: snk20151016_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/zay2vo
title: snk20150915_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/tk15ux
title: snk20150104_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/atndq0
title: snk20160305_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/qx93xc
title: snk20160405_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3980079
title: README from Quantifying trace element and isotope fluxes at the ocean-sediment boundary: a review

description: Text file description of the contents of the Aluminium model output file
DOI: 10.7910/dvn/v1rjpf/5prtmr
title: snk20150219_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/mswroc
title: snk20160205_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3980079.v1
title: README from Quantifying trace element and isotope fluxes at the ocean-sediment boundary: a review

description: Text file description of the contents of the Aluminium model output file
DOI: 10.6084/m9.figshare.3980073
title: Aluminium model output from Quantifying trace element and isotope fluxes at the ocean-sediment boundary: a review

description: Supplemenatry file (Al_model_output_PTA.mat) contains output data of optimized Aluminum (Al) cycle model presented in Homoky et al (2016), Quantifying trace element and isotope fluxes at the ocean-sediment boundary - a review, Phil. Trans. Royal Soc. A.
DOI: 10.7910/dvn/v1rjpf/o9tm7f
title: snk20161214_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3980073.v1
title: Aluminium model output from Quantifying trace element and isotope fluxes at the ocean-sediment boundary: a review

description: Supplemenatry file (Al_model_output_PTA.mat) contains output data of optimized Aluminum (Al) cycle model presented in Homoky et al (2016), Quantifying trace element and isotope fluxes at the ocean-sediment boundary - a review, Phil. Trans. Royal Soc. A.
DOI: 10.7910/dvn/v1rjpf/xx3tem
title: snk20151002_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3980064
title: Global Database from Neodymium in the oceans: a global database, a regional comparison and implications for palaeoceanographic research

description: The neodymium (Nd) isotopic composition of seawater has been used extensively to reconstruct ocean circulation on a variety of timescales. However, dissolved neodymium concentrations and isotopes do not always behave conservatively, and quantitative deconvolution of this non-conservative component can be used to detect trace metal inputs and isotopic exchange at ocean–sediment interfaces. In order to facilitate such comparisons for historical datasets, we here provide an extended global database for Nd isotopes and concentrations in the context of hydrography and nutrients. Since 2010, combined datasets for a large range of trace elements and isotopes are collected on international GEOTRACES section cruises, alongside classical nutrient and hydrography measurements. Here, we take a first step towards exploiting these datasets by comparing high-resolution Nd sections for the western and eastern North Atlantic in the context of hydrography, nutrients and aluminium (Al) concentrations. Evaluating those data in tracer–tracer space reveals that North Atlantic seawater Nd isotopes and concentrations generally follow the patterns of advection, as do Al concentrations. Deviations from water mass mixing are observed locally, associated with the addition or removal of trace metals in benthic nepheloid layers, exchange with ocean margins (i.e. boundary exchange) and/or exchange with particulate phases (i.e. reversible scavenging). We emphasize that the complexity of some of the new datasets cautions against a quantitative interpretation of individual palaeo Nd isotope records, and indicates the importance of spatial reconstructions for a more balanced approach to deciphering past ocean changes.
DOI: 10.7910/dvn/v1rjpf/p3srpp
title: snk20150810_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3980064.v1
title: Global Database from Neodymium in the oceans: a global database, a regional comparison and implications for palaeoceanographic research

description: The neodymium (Nd) isotopic composition of seawater has been used extensively to reconstruct ocean circulation on a variety of timescales. However, dissolved neodymium concentrations and isotopes do not always behave conservatively, and quantitative deconvolution of this non-conservative component can be used to detect trace metal inputs and isotopic exchange at ocean–sediment interfaces. In order to facilitate such comparisons for historical datasets, we here provide an extended global database for Nd isotopes and concentrations in the context of hydrography and nutrients. Since 2010, combined datasets for a large range of trace elements and isotopes are collected on international GEOTRACES section cruises, alongside classical nutrient and hydrography measurements. Here, we take a first step towards exploiting these datasets by comparing high-resolution Nd sections for the western and eastern North Atlantic in the context of hydrography, nutrients and aluminium (Al) concentrations. Evaluating those data in tracer–tracer space reveals that North Atlantic seawater Nd isotopes and concentrations generally follow the patterns of advection, as do Al concentrations. Deviations from water mass mixing are observed locally, associated with the addition or removal of trace metals in benthic nepheloid layers, exchange with ocean margins (i.e. boundary exchange) and/or exchange with particulate phases (i.e. reversible scavenging). We emphasize that the complexity of some of the new datasets cautions against a quantitative interpretation of individual palaeo Nd isotope records, and indicates the importance of spatial reconstructions for a more balanced approach to deciphering past ocean changes.
DOI: 10.7910/dvn/v1rjpf/nuuglq
title: snk20160722_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/xnrmbw
title: snk20150227_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/m6esdu
title: snk20150522_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/cmpbns
title: snk20160624_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/cz9xup
title: snk20151118_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/kmz7gm
title: snk20160107_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/ddrl3x
title: snk20150316_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/zbxhb2
title: snk20150322_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/mtv78p
title: snk20151009_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.12912149
title: Attention-figshare-Datas.xlsx

description: <b>Abstract</b><b>Introduction:</b> Compassion focused-imagery (CFI), one of the psychological interventions of compassion-focused therapy, is receiving increasing attention. It is a therapeutic tool that targets the process of self-criticism by prompting individuals to imagine themselves as compassionate or to imagine receiving compassion from an ideal compassionate other. This research examines the role of self-criticism in the attentional processing of emotional stimuli, namely, critical and compassionate facial expressions. It is hypothesized that the activation of positive social emotions through CFI plays a role in broadening attention in the processing of emotional stimuli. <b>Method:</b> The McEwan Faces stimulus set, which includes critical, neutral and compassionate faces, was used to create an attentional bias task called the dot probe task. The processing of emotional faces was assessed before and after exposure to either CFI or neutral imagery, controlling for the process of sensory integration (<i>n </i>= 80). <b>Results:</b> Before the imagery task, participants tended to look away from critical faces, and their level of self-criticism played a role. Both types of imagery significantly reduced the bias away from critical faces when the stimuli were presented for 1200 ms. This effect was reversed in the neutral condition for participants with high levels of self-criticism but not in the CFI condition. <b>Discussion:</b> Interestingly, self-criticism impacts the attentional treatment of critical faces and the effect of imagery entailing sensory integration on this treatment. CFI seems to preserve this effect for participants with high levels of self-criticism, possibly due to the activation of positive social emotions.
DOI: 10.7910/dvn/v1rjpf/pmn9ts
title: snk20150314_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/adywol
title: snk20150914_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3979998
title: Fig.4 The effect of the prestress from vdW interaction for the helical nanowires.xls from The vibration of the nanosprings affected by van der Waals interactions

description: Raw data for figure 4
DOI: 10.7910/dvn/v1rjpf/grued1
title: snk20150404_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3979998.v1
title: Fig.4 The effect of the prestress from vdW interaction for the helical nanowires.xls from The vibration of the nanosprings affected by van der Waals interactions

description: Raw data for figure 4
DOI: 10.7910/dvn/v1rjpf/vbcjoe
title: snk20160715_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3979992
title: Table S1-S5 from Positive selection of the TRIM family regulatory region in primate genomes

description: Viral selection pressure has acted on restriction factors that play an important role in innate immune system by inhibiting the replication of viruses during primate evolution. Tripartite motif-containing (TRIM) family members are some of these restriction factors. It is becoming increasingly clear that gene expression differences, rather than protein-coding regions changes, could play a vital role in the anti-retroviral immune mechanism. Increasingly, recent studies have created genome-scale catalogues of DNase I hypersensitive sites (DHSs), which demark potentially functional regulatory DNA. To improve our understanding of the molecular evolution mechanism of antiviral differences between species, we leveraged 14 130 DHSs derived from 145 cell types to characterize the regulatory landscape of the TRIM region. Subsequently, we compared the alignments of the DHSs across six primates and found 375 DHSs that are conserved in non-human primates but exhibit significantly accelerated rates of evolution in the human lineage (haDHSs). Furthermore, we discovered 31 human-specific potential transcription factor motifs within haDHSs, including the <i>KROX</i> and <i>SP1</i>, that both interact with <i>HIV-1</i>. Importantly, the corresponding haDHS was correlated with antiviral factor <i>TRIM23</i>. Thus, our results suggested that some viruses may contribute, through regulatory DNA differences, to organismal evolution by mediating TRIM gene expression to escape immune surveillance.
DOI: 10.6084/m9.figshare.3979989
title: Fig.6 The effect of the number (n) of the helical nanowires.xls from The vibration of the nanosprings affected by van der Waals interactions

description: Raw data for figure 6
DOI: 10.6084/m9.figshare.3979992.v1
title: Table S1-S5 from Positive selection of the TRIM family regulatory region in primate genomes

description: Viral selection pressure has acted on restriction factors that play an important role in innate immune system by inhibiting the replication of viruses during primate evolution. Tripartite motif-containing (TRIM) family members are some of these restriction factors. It is becoming increasingly clear that gene expression differences, rather than protein-coding regions changes, could play a vital role in the anti-retroviral immune mechanism. Increasingly, recent studies have created genome-scale catalogues of DNase I hypersensitive sites (DHSs), which demark potentially functional regulatory DNA. To improve our understanding of the molecular evolution mechanism of antiviral differences between species, we leveraged 14 130 DHSs derived from 145 cell types to characterize the regulatory landscape of the TRIM region. Subsequently, we compared the alignments of the DHSs across six primates and found 375 DHSs that are conserved in non-human primates but exhibit significantly accelerated rates of evolution in the human lineage (haDHSs). Furthermore, we discovered 31 human-specific potential transcription factor motifs within haDHSs, including the <i>KROX</i> and <i>SP1</i>, that both interact with <i>HIV-1</i>. Importantly, the corresponding haDHS was correlated with antiviral factor <i>TRIM23</i>. Thus, our results suggested that some viruses may contribute, through regulatory DNA differences, to organismal evolution by mediating TRIM gene expression to escape immune surveillance.
DOI: 10.6084/m9.figshare.3979989.v1
title: Fig.6 The effect of the number (n) of the helical nanowires.xls from The vibration of the nanosprings affected by van der Waals interactions

description: Raw data for figure 6
DOI: 10.7910/dvn/v1rjpf/uhwuqh
title: snk20160729_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/vxgbd4
title: snk20160824_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/7nwput
title: snk20150719_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3979974
title: Fig.7 The vibration of the helical carbon nanotubes.xls from The vibration of the nanosprings affected by van der Waals interactions

description: Raw data for figure 7
DOI: 10.6084/m9.figshare.3979974.v1
title: Fig.7 The vibration of the helical carbon nanotubes.xls from The vibration of the nanosprings affected by van der Waals interactions

description: Raw data for figure 7
DOI: 10.7910/dvn/v1rjpf/dh21b6
title: snk20161220_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/nqvblb
title: snk20151019_03.txt.gz

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DOI: 10.6084/m9.figshare.3979962
title: Fig.5 The effect of the stiffness k for the helical nanowires.xls from The vibration of the nanosprings affected by van der Waals interactions

description: Raw data for figure 5
DOI: 10.7910/dvn/v1rjpf/r1axa1
title: snk20161113_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3979962.v1
title: Fig.5 The effect of the stiffness k for the helical nanowires.xls from The vibration of the nanosprings affected by van der Waals interactions

description: Raw data for figure 5
DOI: 10.7910/dvn/v1rjpf/cogt5e
title: snk20160214_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/gfuayo
title: snk20160325_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/felg3e
title: snk20161221_03.txt.gz

description: :unav