cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7016795
title: Endo N., Ujita, W., et al., Data from: Multiple animal positioning system shows that socially-reared mice influence the social proximity of isolation-reared cagemates

description: Data file set from Endo, N., Ujita, W. et al., Multiple animal positioning system shows socially-reared mice promote social proximity of isolation-reared cagemates. Communications Biology, 2018
DOI: 10.17633/rd.brunel.7016849.v2
title: Performance and Radiation-Tolerance of Honeywell LOHET-II Hall-Effect Sensors

description: MICE, the international Muon Ionization Cooling Experiment, is a project to design, construct, operate and test a cell of a muon ionisation cooling channel that may be used for a future Muon Collider or Neutrino Factory.<br>The object of the MICE experiment is to take a beam of muons created from protons from the ISIS accelerator hitting a titanium target and to show that it is possible to create a narrow intense beam, using detector techniques from particle physics.The MICE Muon Beamline[1] can be set to deliver beams of either positive or negative muons. This is achieved by physically swapping over the current leads for each of the conventional magnet power supplies. Ensuring the actual operating polarity of the beamline is correctly recorded as a manual step was at risk of error or omission.We have deployed a simple system ("POMPOMs", [2]) for monitoring the operating polarity of the two bending magnets by placing in each dipole bore a Honeywell LOHET-II Hall-effect sensor (SS94A1E) that operates past saturation at nominal field strengths, and thus returns one of two well-defined voltages corresponding to the two possible polarities of the magnet.The environment in the experimental hall is monitored by an AKCP securityProbe 5E system integrated into our EPICS-based controls and monitoring system. We read out the beamline polarity sensors using a voltmeter module, and translate the output voltage into a polarity (or alarm) state within EPICS whence it can be accessed by the operators and stored in the output datastream.This spreadsheet contains the data from the LOHET-II sensor initial characterisation, radiation-tolerance testing, and in-situ performance monitoring[3] programmes.<br>1. "The MICE Muon Beam on ISIS and the beam-line instrumentation of the Muon Ionization Cooling Experiment" Journal of Instrumentation (2012). doi:10.1088/1748-0221/7/05/P050092. J.J. Nebrensky and P.M. Hanlet: "POMPOMs: Cost-Efficient Polarity Sensors for the MICE Muon Beamline" TUPD90 at DIPAC'11 - 10th European Workshop on Beam Diagnostics and Instrumentation for Particle Accelerators pp. 518-520 (2011)3. H. Nebrensky: "Routine POMPOM sensor test procedure" (2013)<br>This material forms part of the MICE Miscellaneous data, DOI: 10.17633/rd.brunel.5024885 ( <em>Construction/Beamline/Other/PerformanceAndRadiationToleranceOfHoneywell_LOHET-II_HallEffectSensors.zip</em> ).
DOI: 10.17633/rd.brunel.7016849.v1
title: Performance and Radiation-Tolerance of Honeywell LOHET-II Hall-Effect Sensors

description: MICE, the international Muon Ionization Cooling Experiment, is a project to design, construct, operate and test a cell of a muon ionisation cooling channel that may be used for a future Muon Collider or Neutrino Factory.<br>The object of the MICE experiment is to take a beam of muons created from protons from the ISIS accelerator hitting a titanium target and to show that it is possible to create a narrow intense beam, using detector techniques from particle physics.The MICE Muon Beamline[1] can be set to deliver beams of either positive or negative muons. This is achieved by physically swapping over the current leads for each of the conventional magnet power supplies. Ensuring the actual operating polarity of the beamline is correctly recorded as a manual step was at risk of error or omission.We have deployed a simple system ("POMPOMs", [2]) for monitoring the operating polarity of the two bending magnets by placing in each dipole bore a Honeywell LOHET-II Hall-effect sensor (SS94A1E) that operates past saturation at nominal field strengths, and thus returns one of two well-defined voltages corresponding to the two possible polarities of the magnet.The environment in the experimental hall is monitored by an AKCP securityProbe 5E system integrated into our EPICS-based controls and monitoring system. We read out the beamline polarity sensors using a voltmeter module, and translate the output voltage into a polarity (or alarm) state within EPICS whence it can be accessed by the operators and stored in the output datastream.This spreadsheet contains the data from the LOHET-II sensor initial characterisation, radiation-tolerance testing, and in-situ performance monitoring[3] programmes.<br>1. "The MICE Muon Beam on ISIS and the beam-line instrumentation of the Muon Ionization Cooling Experiment" Journal of Instrumentation (2012). doi:10.1088/1748-0221/7/05/P050092. J.J. Nebrensky and P.M. Hanlet: "POMPOMs: Cost-Efficient Polarity Sensors for the MICE Muon Beamline" TUPD90 at DIPAC'11 - 10th European Workshop on Beam Diagnostics and Instrumentation for Particle Accelerators pp. 518-520 (2011)3. H. Nebrensky: "Routine POMPOM sensor test procedure" (2013)
DOI: 10.6084/m9.figshare.7016795.v2
title: Endo N., Ujita, W., et al., Data from: Multiple animal positioning system shows that socially-reared mice influence the social proximity of isolation-reared cagemates

description: Data file set from Endo, N., Ujita, W. et al., Multiple animal positioning system shows socially-reared mice promote social proximity of isolation-reared cagemates. Communications Biology, 2018
DOI: 10.6084/m9.figshare.7016795.v1
title: Endo N., Ujita, W., et al., Data from: Multiple animal positioning system shows that socially-reared mice influence the social proximity of isolation-reared cagemates

description: Data file set from Endo, N., Ujita, W. et al., Multiple animal positioning system shows socially-reared mice promote social proximity of isolation-reared cagemates. Communications Biology, 2018
DOI: 10.6084/m9.figshare.7016747
title: In-silico model input data

description: Input data to execute the simulations using FEB3 (<i>Phoebe</i>).
DOI: 10.6084/m9.figshare.7016741
title: Supplementary Material for: Pigment Epithelium-Derived Factor and its Phosphomimetic Mutant Induce JNK-Dependent Apoptosis and P38-Mediated Migration Arrest

description: <b><i>Background/Aims:</i></b> Pigment epithelium-derived factor (PEDF) is a potent endogenous inhibitor of angiogenesis, and a promising anticancer agent. We have previously shown that PEDF can be phosphorylated, and that distinct phosphorylations differentially regulate its physiological functions. We also demonstrated that triple phosphomimetic mutant (EEE-PEDF), has significantly increased antiangiogenic activity, and is much more efficient than WT-PEDF in inhibiting neovascularization and tumor growth. The enhanced antiangiogenic effect was associated with a direct ability to facilitate apoptosis of tumor-residing endothelial cells (EC), and subsequently, disruption of intratumoral vascularization. In the present report, we elucidated the molecular mechanism by which EEE-PEDF exerts more profound effects at the cellular level. <b><i>Methods:</i></b> Here we used Western blotting, as well as <i>in vitro</i> binding, proliferation, apoptosis and migration assays to follow the signaling components responsible for the PEDF and EEE-PEDF effects. <b><i>Results:</i></b> We found that EEE-PEDF suppresses EC proliferation due to caspase-3-dependent apoptosis, and also inhibits migration of the EC much better than WT-PEDF. Although WT-PEDF and EEE-PEDF did not affect proliferation and did not induce apoptosis of cancer cells, these agents efficiently inhibited cancer cell motility, with EEE-PEDF showing stronger effect. The stronger activity of EEE-PEDF was correlated to a better binding to laminin receptors. Furthermore, the proapoptotic and antimigratory activities of WT-PEDF and EEE-PEDF were found respectively regulated by differential activation of two distinct MAPK pathways, namely JNK and p38. We show that JNK and p38 phosphorylation is much higher in cells treated with EEE-PEDF. JNK leads to apoptosis of ECs, while p38 leads to antimigratory effect in both EC and cancer cells. <b><i>Conclusion:</i></b> These results reveal the molecular signaling mechanism by which the phosphorylated PEDF exerts its stronger antiangiogenic, antitumor activities.
DOI: 10.6084/m9.figshare.7016747.v1
title: In-silico model input data

description: Input data to execute the simulations using FEB3 (<i>Phoebe</i>).
DOI: 10.6084/m9.figshare.7016735
title: Discovering Journals Books and Video 2018.xlsx

description: Results of a large scale survey into how readers discover academic journal articles, books and video. The 2018 research, attracted just over 10,000 respondents from all over the world in all sectors, subjects and job roles. The authors have been researching in this area since 2005. Full Report to be published on the 3rd September.
DOI: 10.6084/m9.figshare.12885536.v1
title: R0189_20170925a_videos

description: Rat 0189, skilled reaching data collected on 9/25/2017 in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.7016663
title: Streptococcus pyogenes Causing Skin and Soft Tissue Infections Are Enriched in the Recently Emerged emm89 Clade 3 and Are Not Associated with Abrogation of CovRS - Dataset 2

description: Isolation source, emm type, emm cluster, sequence type, superantigen gene profile, and presence of hasABC locus of 247 Streptococcus pyogenes isolated from invasive infections in Portugal during 2005-2009.
DOI: 10.6084/m9.figshare.7016663.v1
title: Streptococcus pyogenes Causing Skin and Soft Tissue Infections Are Enriched in the Recently Emerged emm89 Clade 3 and Are Not Associated with Abrogation of CovRS - Dataset 2

description: Isolation source, emm type, emm cluster, sequence type, superantigen gene profile, and presence of hasABC locus of 247 Streptococcus pyogenes isolated from invasive infections in Portugal during 2005-2009.
DOI: 10.6084/m9.figshare.7016657
title: Marine sponges (Porifera) from the Bahía San Antonio (North Patagonian Gulfs, Argentina), with additions to the phylogeography of the widely distributed <i>Cliona</i> aff. <i>celata</i> and <i>Hymeniacidon perlevis</i>, and the description of two new species

description: Six sponge species from Bahía San Antonio (north Argentinean Patagonia) are (re)described, including two new species, namely <i>Halichondria (Halichondria) elenae</i> sp. nov. and <i>Clathria (Microciona) saoensis</i> sp. nov., and three new records for the Argentinean coast. <i>Halichondria (H.) elenae</i> sp. nov<i>.</i> is the only yellowish-greenish SW Atlantic <i>Halichondria</i> with oxeas up to 450 µm. The new species’ 18S rRNA blasted with <i>Halichondria bowerbanki</i> from Ireland, but it is argued that co-specificity is unlikely, in view of their rather distinct morphologies. <i>Clathria (M.) saoensis</i> sp. nov<i>.</i> is the only <i>C.</i> (<i>Microciona</i>) in the SW Atlantic, SE Pacific, and (sub)Antarctic regions with smooth (or nearly so) principal megascleres, mostly below 500 µm long, as well as moderately curved toxas, and isochelae of regular non-cleistochelate shape. <i>Cliona</i> aff. <i>celata</i> and <i>Hymeniacidon perlevis</i> had their identifications confirmed by the sequencing of their 28S and 18S rRNA genes, respectively, and mitochondrial CO1. Both of them clustered with previously sequenced specimens from the Temperate North Atlantic, apart from additional samples from SE Brazil, in the case of <i>C.</i> aff. <i>celata</i>, and China and South Korea, in the case of <i>H. perlevis</i>.
DOI: 10.6084/m9.figshare.7016657.v1
title: Marine sponges (Porifera) from the Bahía San Antonio (North Patagonian Gulfs, Argentina), with additions to the phylogeography of the widely distributed <i>Cliona</i> aff. <i>celata</i> and <i>Hymeniacidon perlevis</i>, and the description of two new species

description: Six sponge species from Bahía San Antonio (north Argentinean Patagonia) are (re)described, including two new species, namely <i>Halichondria (Halichondria) elenae</i> sp. nov. and <i>Clathria (Microciona) saoensis</i> sp. nov., and three new records for the Argentinean coast. <i>Halichondria (H.) elenae</i> sp. nov<i>.</i> is the only yellowish-greenish SW Atlantic <i>Halichondria</i> with oxeas up to 450 µm. The new species’ 18S rRNA blasted with <i>Halichondria bowerbanki</i> from Ireland, but it is argued that co-specificity is unlikely, in view of their rather distinct morphologies. <i>Clathria (M.) saoensis</i> sp. nov<i>.</i> is the only <i>C.</i> (<i>Microciona</i>) in the SW Atlantic, SE Pacific, and (sub)Antarctic regions with smooth (or nearly so) principal megascleres, mostly below 500 µm long, as well as moderately curved toxas, and isochelae of regular non-cleistochelate shape. <i>Cliona</i> aff. <i>celata</i> and <i>Hymeniacidon perlevis</i> had their identifications confirmed by the sequencing of their 28S and 18S rRNA genes, respectively, and mitochondrial CO1. Both of them clustered with previously sequenced specimens from the Temperate North Atlantic, apart from additional samples from SE Brazil, in the case of <i>C.</i> aff. <i>celata</i>, and China and South Korea, in the case of <i>H. perlevis</i>.
DOI: 10.6084/m9.figshare.11530785
title: supp2_tables_evaluation of lncRNA identification tools.xlsx

description: Supplementary tables S1-S16
DOI: 10.6084/m9.figshare.7016450
title: Supplementary Material for: Increased Mortality Rate after Hospitalization Among Chronic Hemodialysis Patients: A Prospective Cohort Study

description: <b><i>Background/Aims:</i></b> Hemodialysis patients are at high risk of hospitalization and their condition may worsen with repeated hospitalization. The aim of this study was to evaluate the impact of the cumulative number of hospitalizations on post-discharge mortality. <b><i>Methods:</i></b> This study was a prospective cohort study. We examined 3,359 adult patients on hemodialysis for at least 90 days who participated in the Japanese Dialysis Outcomes and Practice Patterns Study phases 3 and 4 (2005–2012). The patients hospitalized within 3 months before enrollment were excluded. The main exposure was the time-varying cumulative number of hospitalizations during the follow-up period. Hazard ratios (HRs) for all-cause mortality rate after discharge were estimated by time-dependent Cox regressions after adjusting for potential confounders. <b><i>Results:</i></b> The median follow-up time was 2.7 years, and 873 (26%) patients experienced at least 1 hospitalization during follow-up. The hospitalization rate was 0.23 per person-year and the mortality rate was 0.036 per person-year. The HR and 95% CI for post-discharge mortality increased as the cumulative number of hospitalizations increased: once, 1.41 (0.99–2.00); and twice or more, 2.27 (1.59–3.23). The cause-specific hospitalization categories, “infectious disease” and “cancer,” affected post-discharge mortality HRs in a similar manner: 2.41(1.32–4.41) and 2.70 (1.23–5.93), respectively. <b><i>Conclusion:</i></b> A higher cumulative number of hospitalizations is associated with increased post-discharge mortality in chronic hemodialysis patients. The cause-specific hospitalizations category of “infectious disease” showed an impact on mortality similar to that of hospitalization for “cancer.” Therefore, physicians should pay more attention to reducing preventable hospitalizations.
DOI: 10.6084/m9.figshare.7016453
title: Supplementary Material for: Long Noncoding RNA Lnc-SEMT Modulates IGF2 Expression by Sponging miR-125b to Promote Sheep Muscle Development and Growth

description: <b><i>Background/Aims:</i></b> Long noncoding RNAs (lncRNAs) are RNA transcripts that are more than 200 nt long but have little protein-coding potential. Within the last few years, thousands of lncRNAs have been identified and their functions in biological processes have begun to be understood. Although many studies havebegun to examine the functions of many noncoding RNAs, very little is known about the functions of long noncoding (lncRNA) function of livestock production and molecular mechanisms of their functions are still lackingrelated to livestock production. <b><i>Methods:</i></b> Expression of sheep enhanced muscularityTranscript lncRNA (lnc-SEMT) and miR-125b were examined in sheep using quantitative reverse-transcription polymerase chain reaction. Expression of <i>Myod</i> (myogenic determination factor), <i>Myog</i> (myoglobin) and Insulin-like growth factor 2 (IGF2)were examined by Western Blot.Luciferase reporter assays were performedto confirm the relationship between lnc-SEMT and miR-125b. <b><i>Results:</i></b> Here, we identified a novel lnc-SEMT that promote sheep myoblast differentiation <i>in vitro</i> and enhanced sheep muscularity <i>in vivo</i>. Functional analyses showed that lnc-SEMT accelerates sheep myoblast differentiation <i>in vitro</i>. lnc-SEMT transgenic sheep exhibit a muscle hypertrophy phenotype characterized by increased body weight, and increased the number of muscle fibers indicating that lnc-SEMT play an important role in the regulation of skeletal muscle differentiation <i>in vivo</i>. Our results show that lnc-SEMT acts as a molecular sponge by antagonizing miR-125b to control IGF2 protein labundance <i>in vitro</i> and <i>in vivo</i>. <b><i>Conclusion:</i></b> In brief, lnc-SEMT is the first example of a lncRNA could be a useful candidate for improving biological growth traits such as skeletal muscle production in sheep.
DOI: 10.6084/m9.figshare.7016450.v1
title: Supplementary Material for: Increased Mortality Rate after Hospitalization Among Chronic Hemodialysis Patients: A Prospective Cohort Study

description: <b><i>Background/Aims:</i></b> Hemodialysis patients are at high risk of hospitalization and their condition may worsen with repeated hospitalization. The aim of this study was to evaluate the impact of the cumulative number of hospitalizations on post-discharge mortality. <b><i>Methods:</i></b> This study was a prospective cohort study. We examined 3,359 adult patients on hemodialysis for at least 90 days who participated in the Japanese Dialysis Outcomes and Practice Patterns Study phases 3 and 4 (2005–2012). The patients hospitalized within 3 months before enrollment were excluded. The main exposure was the time-varying cumulative number of hospitalizations during the follow-up period. Hazard ratios (HRs) for all-cause mortality rate after discharge were estimated by time-dependent Cox regressions after adjusting for potential confounders. <b><i>Results:</i></b> The median follow-up time was 2.7 years, and 873 (26%) patients experienced at least 1 hospitalization during follow-up. The hospitalization rate was 0.23 per person-year and the mortality rate was 0.036 per person-year. The HR and 95% CI for post-discharge mortality increased as the cumulative number of hospitalizations increased: once, 1.41 (0.99–2.00); and twice or more, 2.27 (1.59–3.23). The cause-specific hospitalization categories, “infectious disease” and “cancer,” affected post-discharge mortality HRs in a similar manner: 2.41(1.32–4.41) and 2.70 (1.23–5.93), respectively. <b><i>Conclusion:</i></b> A higher cumulative number of hospitalizations is associated with increased post-discharge mortality in chronic hemodialysis patients. The cause-specific hospitalizations category of “infectious disease” showed an impact on mortality similar to that of hospitalization for “cancer.” Therefore, physicians should pay more attention to reducing preventable hospitalizations.
DOI: 10.6084/m9.figshare.11530785.v3
title: supp2_tables_evaluation of lncRNA identification tools.xlsx

description: Supplementary tables S1-S16
DOI: 10.6084/m9.figshare.11530785.v2
title: supp2_tables_evaluation of lncRNA identification tools.xlsx

description: Supplementary tables S1-S15
DOI: 10.6084/m9.figshare.7016411
title: Supplementary Material for: tRNA-Derived Fragments as Novel Predictive Biomarkers for Trastuzumab-Resistant Breast Cancer

description: <b><i>Background/Aims:</i></b> Resistance to trastuzumab remains a common challenge to HER-2 positive breast cancer. Up until now, the underlying mechanism of trastuzumab resistance is still unclear. tRNA-derived small non-coding RNAs, a new class of small non-coding RNA (sncRNAs), have been observed to play an important role in cancer progression. However, the relationship between tRNA-derived fragments and trastuzumab resistance is still unknown. <b><i>Methods:</i></b> We detected the levels of tRNA-derived fragments expression in normal breast epithelial cell lines, trastuzumab-sensitive and -resistant breast cancer cell lines using high-throughput sequencing. qRT-PCR was conducted to validate the differentially expressed fragments in serums from trastuzumab-sensitive and -resistant patients. A receiver operating characteristic (ROC) curve analysis was performed to evaluate the power of specific tRNA-derived fragments. Progression-free survival (PFS) was analyzed using Cox-regression. <b><i>Results:</i></b> Our sequence results showed that tRNA-derived fragments were differentially expressed in the HBL-100, SKBR3, and JIMT-1 cell lines. tRF-30-JZOYJE22RR33 and tRF-27-ZDXPHO53KSN were found significantly upregulated in trastuzumab-resistant patients compared to sensitive individuals, and the ROC analysis showed that tRF-30-JZOYJE22RR33 and tRF-27-ZDXPHO53KSN were correlated with trastuzumab resistance. In a multivariate analysis, higher levels of tRF-30-JZOYJE22RR33 and tRF-27-ZDXPHO53KSN expression were associated with significantly shorter PFS in patients with metastatic HER-2 positive breast cancer. <b><i>Conclusion:</i></b> Our results suggest that tRF-30-JZOYJE22RR33 and tRF-27-ZDXPHO53KSN play important roles in trastuzumab resistance. Patients with high levels of tRF-30-JZOYJE22RR33 and tRF-27-ZDXPHO53KSN expression benefitted less from trastuzumab-based therapy than those that express lower-levels of these molecules. tRF-30-JZOYJE22RR33 and tRF-27-ZDXPHO53KSN may be potential biomarkers and intervention targets in the clinical treatment of trastuzumab-resistant breast cancer.
DOI: 10.6084/m9.figshare.7016390
title: Supplementary Material for: MACUSTAR: Development and Clinical Validation of Functional, Structural, and Patient-Reported Endpoints in Intermediate Age-Related Macular Degeneration

description: <b><i>Purpose:</i></b> Currently, no outcome measures are clinically validated and accepted as clinical endpoints by regulatory agencies for drug development in intermediate age-related macular degeneration (iAMD). The MACUSTAR Consortium, a public-private research group funded by the European Innovative Medicines Initiative intends to close this gap. <b><i>Procedures:</i></b> Development of study protocol and statistical analysis plan including predictive modelling of multimodal endpoints based on a review of the literature and expert consensus. <b><i>Results:</i></b> This observational study consists of a cross-sectional and a longitudinal part. Functional outcome measures assessed under low contrast and low luminance have the potential to detect progression of visual deficit within iAMD and to late AMD. Structural outcome measures will be multimodal and investigate topographical relationships with function. Current patient-reported outcome measures (PROMs) are not acceptable to regulators and may not capture the functional deficit specific to iAMD with needed precision, justifying development of novel PROMs for iAMD. The total sample size will be <i>n</i> = 750, consisting mainly of subjects with iAMD (<i>n</i> = 600). <b><i>Conclusions:</i></b> As clinical endpoints currently accepted by regulators cannot detect functional loss or patient-relevant impact in iAMD, we will clinically validate novel candidate endpoints for iAMD.