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    • Software/Code (127818)
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127818 results

A man-machine model

Contributors: Chang Liu

Date: 2019-11-30

... This database supports the paper titled as "A man-machine model: pattern recognition and forecasts for complex structures supervised by multi-model ensembles"

Files:

  • Software/Code(2)
  • Tabular Data

Monitoring the prolonged TNF stimulation in space and time with topological-functional networks

Contributors: Christoforos Nikolaou

Date: 2019-11-30

... In this work we monitor the prolonged TNF stimulation of mouse synovial fibroblasts in space and time through a combination of functional and topological analyses. We introduce a novel concept in the form of bipartite functional/positional networks that capture the interaction between genome organization and the functional footprint of a given regulatory program. By implementing this approach in a time-dependent gene expression experiment we are able to dissect the complex cellular response to a cytokine trigger. We treated synovial fibroblasts in culture for 1, 3, 6, 24 hours to a final point of 7 days with TNF. Control cultures that were grown for the same period without TNF were used as controls. RNA was extracted and RNASeq was performed on a Solexa NextSeq Platform in triplicates. Mapping was performed with BowTie and differential expression was calculated with Cufflinks/CuffDiff (Langmead and Salzberg, 2012; Trapnell et al., 2012;). The differential expression files were used for analysis with abs(log 2 (FC)) 1500 were found to be differentially expressed in at least one timepoint. They were clustered in 8 groups depending on their relative gene expression in time. Functional analysis was performed with gProfiler for each of the 8 clusters. We analyzed gene expression in linear genomic space through an implementation of the "breakpoints" R function, which uses a Chow test to define significant differences between adjacent linear models in time series data. We used differential gene expression as the time series data and defined sets of ~300 domains of consistent gene expression in each time point, which we termed Domains of Focal Deregulation. We then selected a subset of DFDs from each timepoint on the basis of high/low mean scores of differential expression as the most prominent in terms of gene deregulation and created bipartite positional/functional bipartite networks through a functional enrichment analysis of the genes contained in each DFD. Comparison of the bipartite networks monitors the progression of TNF stimulation, which appears to take place through two distinct transition points. A first, at 3h with a large expansion of inflammatory and immune-related functions and second, at 24h which is marked by immune-related functions being shut down and replaced by pathways associated with development and cell adhesion.

Files:

  • Software/Code(32)
  • Tabular Data(11)
  • Unknown File Type

Tabulated results for automatically controlled angiogenic inhibition therapy based on sliding mode technique

Contributors: Ozgur R Doruk

Date: 2019-11-30

... A sliding mode based inhibitory agent injection law is derived using the angiogenic inhibition model of cancer progression which describes the variation of the tumor and supporting vasculature volumes in targeted molecular therapies. The data set present the most important results that indicate the performance of the closed-loop treatment. Each column represents the current value of the related parameter. The first six parameters are the PID sliding surface and sliding mode dynamical constants. These are the proportional gain (Kp), integral gain (Ki), D derivative gain (Kd), the constant \eta, \gamma and the sigmoid slope parameter 'c'. The remaining are the desired final value of the tumor volume (r), the actual final value of the tumor volume (x1(infty)) and supporting vasculature volume (x2(infty)), maximum value of the inhibitory agent administration rate (umax), final value of the inhibitory agent rate (u(infty)) and the setup time which is the duration required to decrease the tumor volume to to 1% of its initial level. The results are obtained from a small C program. The developments are made by MATLAB.

Files:

  • Text
  • Software/Code

Data for: Using the negative control design with a prenatal exposure subject to assortative mating

Contributors: Paul Madley-Dowd, Jon Heron, Stan Zammit, Dheeraj Rai

Date: 2019-11-29

... The following files simulate the data and run all models. Each do file takes arguments "nobs" and "effsize" to define the number of observations and effectsize - neg_contout_datsim (continuous outcome with no paternal effect) - neg_contout_datsim2 (continuous outcome with paternal effect) - neg_contr_datsim.do (binary outcome) Each of these uses "progs.do" to run the bootstrapping of the confidence interval of the difference in maternal and paternal effect estimates The separate datasets for each sample size and effect size are compiled into a single dataset using "compile_results.do". Statistics across simulations are calculated using the following files: - sim_cont_ready.do (continuous outcome with no paternal effect) - sim_cont_ready2.do (continuous outcome with paternal effect) - sim_bin_ready.do (binary outcome) The final datasets are included as the following .csv files: - neg_cont_simout (bias and other statistics for continuous outcome) - neg_cont_difs (mean and bootstrapped 95% CI of difference in estimates for continuous outcome) - neg_cont_simout (bias and other statistics for continuous outcome with paternal effect) - neg_cont_difs (mean and bootstrapped 95% CI of difference in estimates for continuous outcome with paternal effect) - neg_bin_simout (mean and bootstrapped 95% CI of difference in estimates for binary outcome) - neg_bin_difs (mean and bootstrapped 95% CI of difference in estimates for binary outcome)

Files:

  • Tabular Data(6)
  • Software/Code(8)

The immune landscape of uterine leiomyosarcomas

Contributors: Marco Manzoni, Maddalena M Bolognesi, Asier Antoranz, Mario Faretta, Francesca M Bosisio, Giorgio Cattoretti

Date: 2019-11-29

... Personalized immune intervention to release and redirect the T cells against a tumor has shown substantial progress in aggressive tumors such as melanoma and lung cancer, despite the fact that predictors of sustained response are still unclear. Data on less common histotypes are scanty. Among soft tissue sarcomas, uterine leiomyosarcomas (ULMS) have a dire prognosis, yet therapeutic advances are needed in order to improve the actual treatment. Immune checkpoint inhibitor therapy has been applied to exceptionally few cases, of which the immune cell composition was not examined in detail. We analyzed in situ the inflammatory infiltrate of 21 untreated ULMS in high-dimensional, single cell phenotyping on routinely processed tissue, directed at the characterization of lymphoid cells and macrophages. T-lymphoid cells displayed a composite phenotype common to all tumors, suggestive of antigen-exposure; in about half of the cases containing sufficient lymphocytes, we found evidence of exhaustion and a CD8+ TCF7+ phenotype, this latter associated with T-cell reactivation. To the contrary, myelomonocytic cells had case-specific individual combinations of phenotypes and subsets. We identified five distinct monocyte-macrophage cell types: histiocytes, phagocytes, tumor-associated macrophages, inflammatory monocytes and myelomonocytic cells of undefined phenotype. Immunosuppressive molecules (TIM3, B7H3, VISTA, PD1, PDL1) were heterogeneously expressed in inflammatory and endothelial cells. The heterogeneity and phenotype of the monocyte-macrophage population may represents a challenge for which we provide an initial understanding.

Files:

  • Tabular Data(45)
  • Image(48)
  • Software/Code(2)
  • Unknown File Type
  • File Set

Data for: Analysis of a DNA mixture case involving Romani reference populations

Contributors: Julia Mortera, Francesco Dotto, Laura Baldasarri, Vincenzo Pascali

Date: 2019-11-29

... Data files in R .rda format containing the 7 DNA mixtures B1-B7 and the main persons of interest A and B.

Files:

  • Software/Code(9)

L2 WTC and L2MSS Dataset

Contributors: Semih Ekin

Date: 2019-11-29

... This data was prepared to understand the tertiary level students’ L2 willingness to communicate (L2WTC) levels inside and outside the classroom. It also included some important variables which were L2 motivational self-system (ideal L2 self, ought-to L2 self, language learning experience), vision, imagery capacity, and intended effort etc. By exploring what affects L2WTC inside and outside the classroom, the data can reveal important aspects of communication preferences of L2 learners in an EFL context.

Files:

  • Software/Code(2)

Data for: An iterative linear procedure using frequency-dependent soil parameters for site response analyses

Contributors: romain meite, Connor Hayden, Russell Green, Christopher McGann, Liam Wotherspoon

Date: 2019-11-29

... The data files contain the numerical code implemented to generate the strain amplitude spectrum required in the proposed frequency-dependent equivalent linear method.

Files:

  • Unknown File Type(5)
  • Software/Code(8)
  • Text

Data for: Panic attack provocation in panic disorder patients with a computer simulation

Contributors: Rafael Freire, Antonio E Nardi, Renan Martins, Mariana Cabo, Rafael Ferreira-Garcia

Date: 2019-11-28

... Panic attack provocation in panic disorder patients with a computer simulation

Files:

  • Software/Code(2)
  • Document(2)

Shiraz Women's Healthy Ageing Cohort Project(SWHACP©)

Contributors: Abdolrahim Asadollahi, PhD, MSC., GGCP

Date: 2019-11-28

... The attached data-set is a comprehensive and expanded study on women's health and ageing in the city of Shiraz in mid-2019. The statistical population includes all elderly women over 60 years of age living in Shiraz, southern Iran. The sample includes 9117 elderly female and data was collected over the years 2017 till now.

Files:

  • Software/Code
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