cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1571351
title: The C-terminal domains of human neurofibromin and its budding yeast homologs Ira1 and Ira2 regulate the metaphase to anaphase transition

description: The human tumor suppressor neurofibromin contains a cysteine and serine-rich domain/Ras-GTPase activating protein domain (CSRD/RasGAP) and a C-terminal domain (CTD). Domain studies of neurofibromin suggest it has other functions in addition to being a RasGAP, but the mechanisms underlying its tumor suppressor activity are not well understood. The budding yeast <i>Saccharomyces cerevisiae</i> is a good model system for studying neurofibromin function because it possesses Ira1 and Ira2, which are homologous to human neurofibromin in both sequence and function. We found that overexpression of CTD or a neurofibromin CTD-homologous domain (CHD) of Ira1/2 in budding yeast delayed degradation of the securin protein Pds1, whereas overexpression of CSRD/RasGAP did not affect Pds1 degradation. We also found that when CTD or CHD was overexpressed, the number of cells in metaphase was higher than in the control. These results demonstrate that CTD and CHD function in the metaphase to anaphase transition. In addition, Δ<i>ira1</i>Δ<i>ira2</i> cells bypassed mitotic arrest in response to spindle damage, indicating that Ira1 and Ira2 may be involved in the spindle assembly checkpoint (SAC). However, Δ<i>ira1</i>Δ<i>ira2</i>Δ<i>mad2</i> cells are more sensitive to spindle damage than Δ<i>mad2</i> or Δ<i>ira1</i>Δ<i>ira2</i> cells are, suggesting that Ira1/2 and Mad2 function in different pathways. Overexpression of CTD but not CSRD/RasGAP partially rescued the hypersensitivity of Δ<i>ira1</i>Δ<i>ira2</i>Δ<i>mad2</i> cells to microtubule-destabilizing drugs, indicating a role for CTD in the SAC pathway. Taken together, independently of RasGAP activity, the C-terminal domains of neurofibromin, Ira1, and Ira2 regulate the metaphase to anaphase transition in a Mad2-independent fashion.
DOI: 10.6084/m9.figshare.1571349.v1
title: <i>Fucci2a:</i> A bicistronic cell cycle reporter that allows Cre mediated tissue specific expression in mice

description: Markers of cell cycle stage allow estimation of cell cycle dynamics in cell culture and during embryonic development. The Fucci system incorporates genetically encoded probes that highlight G1 and S/G2/M phases of the cell cycle allowing live imaging. However the available mouse models that incorporate Fucci are beset by problems with transgene inactivation, varying expression level, lack of conditional potential and/or the need to maintain separate transgenes—there is no transgenic mouse model that solves all these problems. To address these shortfalls we re-engineered the Fucci system to create 2 bicistronic Fucci variants incorporating both probes fused using the <i>Thosea asigna</i> virus 2A (T2A) self cleaving peptide. We characterize these variants in stable 3T3 cell lines. One of the variants (termed Fucci2a) faithfully recapitulated the nuclear localization and cell cycle stage specific florescence of the original Fucci system. We go on to develop a conditional mouse allele (<i>R26Fucci2aR</i>) carefully designed for high, inducible, ubiquitous expression allowing investigation of cell cycle status in single cell lineages within the developing embryo. We demonstrate the utility of <i>R26Fucci2aR</i> for live imaging by using high resolution confocal microscopy of <i>ex vivo</i> lung, kidney and neural crest development. Using our 3T3 system we describe and validate a method to estimate cell cycle times from relatively short time-lapse sequences that we then apply to our neural crest data. The Fucci2a system and the <i>R26Fucci2aR</i> mouse model are compelling new tools for the investigation of cell cycle dynamics in cell culture and during mouse embryonic development.
DOI: 10.6084/m9.figshare.1570986
title: A Programming Framework for Physics

description: The fundamental difficulty with scientific software is that the existing languages are either<br>too general-purpose and too low-level, or both. Thus, physics equations are entangled with the<br>way they are implemented, even to low level details such as grid structure, cache optimization,<br>etc. Because everything is coupled, it is difficult for the various scientific communities to adapt to<br>algorithm or hardware advances. More importantly, it means that researchers cannot specialize<br>as easily. Everyone must understand physics, software engineering, and computer science to a<br>to a very deep level, and the learning process, especially for students, is much more arduous<br>than it needs to be.<br>In principle, it should be possible to independently specify (1) the scientific equations to be<br>solved; (2) the type of grids; (3) the type of numerical methods, e.g. time integrators, elliptic<br>solvers; (4) the intended execution platform (desktop, accelerated cluster, etc.); (5) performance<br>goals, e.g. as fast as possible, minimum cost, etc.
DOI: 10.6084/m9.figshare.1570979
title: Bounds on transient instability for complex ecosystems - dataset

description: In order to perform the plots, simply load AllData.mat into matlab and run plotall.m.
DOI: 10.6084/m9.figshare.1570986.v1
title: A Programming Framework for Physics

description: The fundamental difficulty with scientific software is that the existing languages are either<br>too general-purpose and too low-level, or both. Thus, physics equations are entangled with the<br>way they are implemented, even to low level details such as grid structure, cache optimization,<br>etc. Because everything is coupled, it is difficult for the various scientific communities to adapt to<br>algorithm or hardware advances. More importantly, it means that researchers cannot specialize<br>as easily. Everyone must understand physics, software engineering, and computer science to a<br>to a very deep level, and the learning process, especially for students, is much more arduous<br>than it needs to be.<br>In principle, it should be possible to independently specify (1) the scientific equations to be<br>solved; (2) the type of grids; (3) the type of numerical methods, e.g. time integrators, elliptic<br>solvers; (4) the intended execution platform (desktop, accelerated cluster, etc.); (5) performance<br>goals, e.g. as fast as possible, minimum cost, etc.
DOI: 10.6084/m9.figshare.1570979.v2
title: Bounds on transient instability for complex ecosystems - dataset

description: In order to perform the plots, simply load AllData.mat into matlab and run plotall.m.
DOI: 10.6084/m9.figshare.1570969
title: EDI3 links choline metabolism to integrin expression, cell adhesion and spreading

description: Endometrial carcinoma differential 3 (EDI3) was the first member of the glycerophosphodiesterase (GDE) protein family shown to be associated with cancer. Our initial work demonstrated that endometrial and ovarian cancer patients with primary tumors overexpressing EDI3 had a higher risk of developing metastasis and decreased survival. Further analysis indicated that EDI3 cleaves glycerophosphocholine to choline and glycerol-3-phosphate, increases the levels of active PKC, and enhances the migratory activity of tumor cells. Despite these initial findings, EDI3 remained mainly uncharacterized. Therefore, to obtain an overview of processes in which EDI3 may be involved, gene array analysis was performed using MCF-7 breast cancer cells after EDI3 knockdown compared with a non-targeting control siRNA. Several biological motifs were altered, including an enrichment of genes involved in integrin-mediated signaling. More specifically, silencing of EDI3 in MCF-7 and OVCAR-3 cells was associated with reduced expression of the key receptor subunit integrin β1, leading to decreased cell attachment and spreading accompanied by delayed formation of cell protrusions. To confirm these results, we stably overexpressed EDI3 in MCF-7 cells which led to elevated integrin β1 expression associated with enhanced cell attachment and spreading - two processes critical for metastasis. In conclusion, our data provide further insight into the role of EDI3 during cancer progression.
DOI: 10.6084/m9.figshare.1570979.v1
title: Bounds on transient instability for complex ecosystems

description: In order to perform the plots, simply load AllData.mat into matlab and run plotall.m.
DOI: 10.6084/m9.figshare.1570969.v1
title: EDI3 links choline metabolism to integrin expression, cell adhesion and spreading

description: Endometrial carcinoma differential 3 (EDI3) was the first member of the glycerophosphodiesterase (GDE) protein family shown to be associated with cancer. Our initial work demonstrated that endometrial and ovarian cancer patients with primary tumors overexpressing EDI3 had a higher risk of developing metastasis and decreased survival. Further analysis indicated that EDI3 cleaves glycerophosphocholine to choline and glycerol-3-phosphate, increases the levels of active PKC, and enhances the migratory activity of tumor cells. Despite these initial findings, EDI3 remained mainly uncharacterized. Therefore, to obtain an overview of processes in which EDI3 may be involved, gene array analysis was performed using MCF-7 breast cancer cells after EDI3 knockdown compared with a non-targeting control siRNA. Several biological motifs were altered, including an enrichment of genes involved in integrin-mediated signaling. More specifically, silencing of EDI3 in MCF-7 and OVCAR-3 cells was associated with reduced expression of the key receptor subunit integrin β1, leading to decreased cell attachment and spreading accompanied by delayed formation of cell protrusions. To confirm these results, we stably overexpressed EDI3 in MCF-7 cells which led to elevated integrin β1 expression associated with enhanced cell attachment and spreading - two processes critical for metastasis. In conclusion, our data provide further insight into the role of EDI3 during cancer progression.
DOI: 10.6084/m9.figshare.1570957
title: Code for "Neural sequence generation using spatiotemporal patterns of inhibition", PLOS Comp Bio

description: Matlab code used in: Cannon J, Kopell N, Gardner T, Markowitz J Neural sequence generation using spatiotemporal patterns of inhibition. PLOS Computational Biology
DOI: 10.6084/m9.figshare.1570940
title: Psychology data on the effects of study schedules on category-member classification: Dataset

description: Subjects (<i>N</i> = 100) studied a series of 6 natural exemplars (birds) from each of 12 different categories (families). Birds were presented in one of 4 ways: (1) blocked by category; (2) intermixed; (3) first blocked, then intermixed; or (4) first intermixed, then blocked. Following study, subjects judged the likelihood that they would be able to classify new birds belonging to families that had been studied earlier. Last, subjects were asked to classify 6 new birds from each of 12 studied families. The data were collected in the laboratory and are stored using <i>fig</i><i>share</i> in an Excel file alongside an annotation file. The data can inform future investigations of the way that individuals learn natural concepts and categories.
DOI: 10.6084/m9.figshare.1570462
title: Effect of conductive substrate (working electrode) on the morphology of electrodeposited Cu2O

description: Cu2O thin fims were electrodeposited from a Cu(II) acetate solution containing 0.02 M<br>Copper(II) acetate (Cu(OAc)2) and 0.1 Msodium acetate (NaOAc) at pH 5.6, using three<br>different working conductive electrodes with approximately the same square resistance<br>-indium doped tin oxide glass (ITO/Glass), florine-doped tin oxide glass (FTO/Glass), and<br>Indium doped tin oxide Polyethylene terephthalate (ITO/PET)—under identical conditions<br>using a common growth condition. The Cu2O thin fims werecharacterized by means<br>ofscanning electron microscopy (SEM), x-raydiffraction (XRD),current density versus<br>growth time for Cu2O fims, and electrochemical impedance spectroscopy (EIS). The results<br>showed that the choice of substratematerials hasa crucial role in controlling of Cu2O growth.<br>The charge transfer resistance (Rct) of FTO/Glass-Cu2O exhibits the lowest value; this<br>means that FTO/Glass-Cu2O possess the highest electron transfer effiiency.All Cu2O fims<br>showed n-type semiconductor characteristic with charge carrier densities varying between<br>1.4 × 1018–1.2 × 1019 cm−3.
DOI: 10.6084/m9.figshare.1570888
title: A five-factor biomarker profile obtained week 4–12 of treatment for improved prognostication in metastatic renal cell carcinoma: Results from DARENCA study 2

description: <i>Background</i>: Several biomarkers of treatment efficacy have been associated with a better prognosis in patients with metastatic renal cell carcinoma (mRCC). The prognostic significance of biomarkers in the early treatment phase is unclear. <i>Material and methods</i>: In a complete national cohort of mRCC patients receiving first-line tyrosine kinase inhibitors (TKI) or interleukin-2 based immunotherapy (IT) from 2006 to 2010, overall survival (OS) was analysed for baseline International mRCC Database Consortium (IMDC) classification factors and on-treatment time-dependent biomarkers obtained day 1 each cycle week 4–12 after treatment initiation with multivariate analysis and bootstrap validation. <i>Results</i>: A total of 735 patients received first-line TKI (59%) or IT (41%). Median OS was overall 14.0 months and 33.4, 18.5, and 5.8 months for baseline IMDC favourable, intermediate, and poor risk groups, respectively (<i>p</i> p ≤ 0.04). Concordance (C)-index for IMDC classification alone was 0.625 (95% CI 0.59–0.66) and combined with the five-factor biomarker profile 0.683 (95% CI 0.64–0.72). For patients with good (3–5 factors) and poor (0–2 factors) biomarker profile median OS were 23.5 and 9.6 months, respectively (<i>p</i> p p p = 0.112). <i>Conclusion</i>: On-treatment hypertension, neutropenia, thrombocytopenia, LDH below 1.5 times upper level of normal, and normal sodium, obtained week 4–12 of treatment, are independent biomarkers of favourable outcome in mRCC, independent of treatment type.
DOI: 10.6084/m9.figshare.1570940.v4
title: Psychology data from a natural concept study schedule project: Dataset

description: Subjects (<em>N</em> = 100) studied a series of 6 natural exemplars (birds) belonging to 12 different categories (families). Birds were presented either: (1) blocked by category, (2) intermixed, (3) first blocked, then intermixed, or (4) first intermixed, then blocked. Following study, subjects judged the likelihood that they would be able to classify new birds belonging to studied families. Last, subjects were asked to classify 6 new birds belonging to studied families. The data were collected in the laboratory and are stored using Figshare in an Excel file. The data can inform future investigations of the way that individuals learn natural categories.
DOI: 10.6084/m9.figshare.1570888.v1
title: A five-factor biomarker profile obtained week 4–12 of treatment for improved prognostication in metastatic renal cell carcinoma: Results from DARENCA study 2

description: <i>Background</i>: Several biomarkers of treatment efficacy have been associated with a better prognosis in patients with metastatic renal cell carcinoma (mRCC). The prognostic significance of biomarkers in the early treatment phase is unclear. <i>Material and methods</i>: In a complete national cohort of mRCC patients receiving first-line tyrosine kinase inhibitors (TKI) or interleukin-2 based immunotherapy (IT) from 2006 to 2010, overall survival (OS) was analysed for baseline International mRCC Database Consortium (IMDC) classification factors and on-treatment time-dependent biomarkers obtained day 1 each cycle week 4–12 after treatment initiation with multivariate analysis and bootstrap validation. <i>Results</i>: A total of 735 patients received first-line TKI (59%) or IT (41%). Median OS was overall 14.0 months and 33.4, 18.5, and 5.8 months for baseline IMDC favourable, intermediate, and poor risk groups, respectively (<i>p</i> p ≤ 0.04). Concordance (C)-index for IMDC classification alone was 0.625 (95% CI 0.59–0.66) and combined with the five-factor biomarker profile 0.683 (95% CI 0.64–0.72). For patients with good (3–5 factors) and poor (0–2 factors) biomarker profile median OS were 23.5 and 9.6 months, respectively (<i>p</i> p p p = 0.112). <i>Conclusion</i>: On-treatment hypertension, neutropenia, thrombocytopenia, LDH below 1.5 times upper level of normal, and normal sodium, obtained week 4–12 of treatment, are independent biomarkers of favourable outcome in mRCC, independent of treatment type.
DOI: 10.6084/m9.figshare.1569882
title: Efeitos da inibição da NOS II sensível a aminoguanidina nas respostas comportamentais tipo ansiedade em zebrafishes adultos (Danio rerio)

description: Efeitos da inibição da NOS II sensível a aminoguanidina nas respostas comportamentais tipo ansiedade em zebrafishes adultos (Danio rerio). 1 Suellen de Nazaré da Silva, 2 Laís do Socorro Rodrigues, 3 Rhayra Xavier do Carmo, 4 Caio Maximino, 5 Monica Gomes Lima, 6 Anderson Manoel Herculano 1,2,3,4 Laboratório de Neurociências e Comportamento, Universidade do Estado do Pará, Marabá/PA 5 Instituto de Estudos em Saúde e Biológicas, Universidade Federal do Sul e Sudeste do Pará, Marabá/PA 6 Laboratório de Neurofarmacologia Experimental, Universidade Federal do Pará, Belém/PA Objetivo: Estudar o papel da NOS-2 na sensibilização das respostas comportamentais a substância de alarme (SA) em zebrafish. Metodologia e resultados: 40 paulistinhas adultos (longfin) foram expostos à SA, e tratados com aminoguanidina (AG, 5mg/kg) e L-NAME (5mg/kg) 30 min após estresse. Após 24 horas, foram testados no teste de preferência claro/escuro. Os procedimentos foram autorizados pela CEUA da UFPA (Parecer 213-14) A AG bloqueou o efeito da SA no tempo no branco (F(1,26)=5,783, p = 0,0236), avaliação de risco (F(1, 26) = 6,992, p = 0,0137), e na tigmotaxia (F(1, 26) = 4,914, p = 0,0356), mas não no nado errático (F(1, 26) = 19,14, p = 0,0002). O L-NAME bloqueou os efeitos da SA no tempo no branco (F(3, 39) = 3.377, p = 0.0278), duração das entradas (F(3, 39) = 2,777, p = 0,00539) e avaliação de risco (H3 = 8.362, p = 0.0391), mas não no nado errático (H3 = 11.15, p = 0.0109) ou na tigmotaxia (F[3, 39] = 12.76, p &lt; 0.0001). Conclusão: A SA produz sensibilização às respostas de nado errático, avaliação de risco, tigmotaxia e tempo branco no teste claro/escuro. A NOS-2 participa da sensibilização da tigmotaxia, e outras isoformas também podem participar da sensibilização da escototaxia e avaliação de risco.
DOI: 10.6084/m9.figshare.1570181
title: Data from Painting et al. 2015 Multiple exaggerated weapon morphs: a novel form of polymorphism in harvestmen

description: This is an excel spreadsheet with all the measurement data from the individual male <em>Pantopsalis cheliferoides </em>harvestmen used in the current study published in Scientific Reports, available at http://dx.doi.org/10.1038/srep16368
DOI: 10.6084/m9.figshare.1570940.v5
title: Psychology data from an experiment on the effects of study schedules on classification of category members: Dataset

description: Subjects (<em>N</em> = 100) studied a series of 6 natural exemplars (birds) belonging to 12 different categories (families). Birds were presented either: (1) blocked by category, (2) intermixed, (3) first blocked, then intermixed, or (4) first intermixed, then blocked. Following study, subjects judged the likelihood that they would be able to classify new birds belonging to studied families. Last, subjects were asked to classify 6 new birds belonging to studied families. The data were collected in the laboratory and are stored using Figshare in an Excel file. The data can inform future investigations of the way that individuals learn natural categories.
DOI: 10.6084/m9.figshare.1570346
title: Outcome of patients with systemic diseases admitted to the medical intensive care unit of a tertiary referral hospital: a single-centre retrospective study

description: <b>Objectives</b>: Systemic diseases form a rare heterogeneous group of diseases, with important morbidity caused by disease evolution and/or treatment. We describe the clinical features and outcome of patients with these diseases admitted to a referral hospital intensive care unit (ICU). <b>Method</b>: We conducted a retrospective case review of all patients with systemic diseases (n = 86) admitted to the medical ICU of Leuven University Hospital between May 2007 and September 2012. <b>Results</b>: The most frequent diagnoses were systemic vasculitis (n = 31), sarcoidosis (n = 15), systemic sclerosis (n = 9), and systemic lupus erythematosus (SLE) (n = 7). The main reason for admission was infection (60%), followed by disease-related organ failure (48%). Respiratory failure was the most common organ dysfunction. The mean APACHE II (Acute Physiology and Chronic Health Evaluation II) score was 28 ± 10. Mortality was 19% during ICU admission, 39% during hospital stay, and 58% at the end of follow-up. Death was caused by infection in the majority of cases (56%), and by evolution of the underlying disease in 32%. Only age and APACHE II score were associated with mortality. <b>Conclusions</b>: The mortality of patients with systemic diseases admitted to an ICU is high, both during their stay in the ICU and afterwards. Age and APACHE II score, but not infection or immunosuppressive therapy, were associated with mortality.
DOI: 10.6084/m9.figshare.1570346.v1
title: Outcome of patients with systemic diseases admitted to the medical intensive care unit of a tertiary referral hospital: a single-centre retrospective study

description: <b>Objectives</b>: Systemic diseases form a rare heterogeneous group of diseases, with important morbidity caused by disease evolution and/or treatment. We describe the clinical features and outcome of patients with these diseases admitted to a referral hospital intensive care unit (ICU). <b>Method</b>: We conducted a retrospective case review of all patients with systemic diseases (n = 86) admitted to the medical ICU of Leuven University Hospital between May 2007 and September 2012. <b>Results</b>: The most frequent diagnoses were systemic vasculitis (n = 31), sarcoidosis (n = 15), systemic sclerosis (n = 9), and systemic lupus erythematosus (SLE) (n = 7). The main reason for admission was infection (60%), followed by disease-related organ failure (48%). Respiratory failure was the most common organ dysfunction. The mean APACHE II (Acute Physiology and Chronic Health Evaluation II) score was 28 ± 10. Mortality was 19% during ICU admission, 39% during hospital stay, and 58% at the end of follow-up. Death was caused by infection in the majority of cases (56%), and by evolution of the underlying disease in 32%. Only age and APACHE II score were associated with mortality. <b>Conclusions</b>: The mortality of patients with systemic diseases admitted to an ICU is high, both during their stay in the ICU and afterwards. Age and APACHE II score, but not infection or immunosuppressive therapy, were associated with mortality.
DOI: 10.6084/m9.figshare.1570358
title: Tumor bed variation during multi-lumen balloon-based accelerated partial breast irradiation: implication of surgical clips

description: Tumor bed variation during multi-lumen balloon-based accelerated partial breast irradiation: implication of surgical clips