Update pagine EN descrittive

This commit is contained in:
Samuele E. Locatelli
2020-01-30 15:20:54 +01:00
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<%@ Page Title="" Language="C#" MasterPageFile="~/SiteContained.master" AutoEventWireup="true" CodeBehind="MethodSpecs.aspx.cs" Inherits="WebLCP.MethodSpecs" %>
<asp:Content ID="Content1" ContentPlaceHolderID="MainContent" runat="server">
<div class="card">
<div class="card-header bg-dark text-light">
<div class="row">
<div class="col-9">
<h2>METHODOLOGICAL SPECIFICATION</h2>
</div>
<div class="col-3 text-right p-0">
<img src="../Images/brain.jpg" class="img-fluid" width="128" />
</div>
</div>
</div>
<div class="card-body">
<p>All methodological details can be found in Marizzoni, Ferrari et al. 2019 Neurobiology of Aging <a href="https://doi.org/10.1016/j.neurobiolaging.2019.12.019" target="_blank">https://doi.org/10.1016/j.neurobiolaging.2019.12.019</a>. In brief finite (one dimension) mixture model<sup>1,2</sup>, was applied to the distribution of biomarker in order to detect any subgroup (component). Formally, a mixture model is defined as a weighted sum of random variables (components) belonging to the same family of probability distribution. Each component identifies a cluster and the mixture model procedure allows to produce a probabilistic clustering that quantifies the uncertainty of observations belonging to components of the mixture. In our case, each component belongs to the Gaussian distribution family defined by corresponding parameters mean and standard deviation (SD). The estimation procedure was carried out by Expectation-Maximization algorithm<sup>3</sup>, whereas the number of component and the parametrization of each component (i.e. the best-fit model) was chosen by the Akaike Information Criterion (AIC) and Bayesian Information Criterion (BIC) indexes): lower indexes values indicate best model<sup>4</sup>. The cut-off values for distinguishing the subgroups were defined as the biomarker values for which the Gaussian mixture model assigned equal probability of belonging to two consecutive components.</p>
<p>In order to investigate the effect of covariates in the identifications of subgroups and, thus, cut-offs, an extension of finite mixture model applied to generalized linear model was adopted <sup>5</sup>. With this extension, the components can follow a simple parametric distribution (as for the simple finite mixture model if no risk factors -covariates- are added ) or can be defined by a more complex model as a generalized linear model (if covariates are added). The effect of the covariates on each mixture component were carried out in terms of beta (regression) coefficients (and corresponding pvalues), as well as in terms of the estimated parameters of the component (mean and SD) obtained by taking into account the effect of the covariate. Significant effects of covariates lead to an alteration of the component shape and to the subgroups mixing.</p>
References:
<ol>
<li>
McLAchlan and Peel 2000, “Finite Mixture Models” Wiley&Son, ISBN:9780471006268.
</li>
<li>Fraley and Raftery, 2007, “Model-based Methods of Classification: Using the mclust software in Chemometrics”, Journal of Statistical Software, vol. 18 issue 6.</li>
<li>Dempster, Laird, Rubin, 1977, "Maximum Likelihood from Incomplete Data via the EM Algorithm"; Journal of the Royal Statistical Society, Series B. 39 (1): 138.</li>
<li>Schwarz G, 1978, “Estimating the Dimension of a Model”; The Annals of Statistics, 6, 461464.</li>
<li>Leisch F, 2004; FlexMix: A general framework for finite mixture models and latent class regression in R; Journal of Statistical Software, vol 11, issue 8.</li>
</ol>
</div>
</div>
</asp:Content>
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using System;
using System.Collections.Generic;
using System.Linq;
using System.Web;
using System.Web.UI;
using System.Web.UI.WebControls;
namespace WebLCP
{
public partial class MethodSpecs : System.Web.UI.Page
{
protected void Page_Load(object sender, EventArgs e)
{
}
}
}
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//------------------------------------------------------------------------------
// <generato automaticamente>
// Codice generato da uno strumento.
//
// Le modifiche a questo file possono causare un comportamento non corretto e verranno perse se
// il codice viene rigenerato.
// </generato automaticamente>
//------------------------------------------------------------------------------
namespace WebLCP
{
public partial class MethodSpecs
{
}
}
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<nav class="navbar navbar-expand-lg navbar-dark bg-dark text-light">
<a class="navbar-brand" href="Default"><i class="fa fa-object-group" aria-hidden="true"></i> WebLCP</a>
<a class="navbar-brand" href="Default"><i class="fa fa-object-group" aria-hidden="true"></i>WebLCP</a>
<button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarSupportedContent" aria-controls="navbarSupportedContent" aria-expanded="false" aria-label="Toggle navigation">
<span class="navbar-toggler-icon"></span>
</button>
@@ -13,28 +13,28 @@
<a class="nav-link" href="Default"><i class="fa fa-home" aria-hidden="true"></i> Home</a>
</li>
<li runat="server" class='<%# checkPage("JobsList") + " nav-item border border-success" %>' visible='<%# userIsAuth %>'>
<a class="nav-link" href="JobsList"><i class="fa fa-list" aria-hidden="true"></i> Jobs processing</a>
<a class="nav-link" href="JobsList"><i class="fa fa-list" aria-hidden="true"></i>Jobs processing</a>
</li>
<li runat="server" class='<%# checkPage("ComparisonPlot") + " nav-item border border-warning" %>' visible='<%# userIsAuth %>'>
<a class="nav-link" href="ComparisonPlot"><i class="fa fa-chart-area" aria-hidden="true"></i> Comparison Plot</a>
<a class="nav-link" href="ComparisonPlot"><i class="fa fa-chart-area" aria-hidden="true"></i>Comparison Plot</a>
</li>
<li runat="server" class='<%# checkPage("About") + " nav-item" %>'>
<a class="nav-link" href="About"><i class="fa fa-info" aria-hidden="true"></i> Informazioni</a>
<a class="nav-link" href="About"><i class="fa fa-info" aria-hidden="true"></i> About</a>
</li>
<li runat="server" class='<%# checkPage("Contact") + " nav-item" %>'>
<a class="nav-link" href="Contact"><i class="fa fa-users" aria-hidden="true"></i> Contatti</a>
<a class="nav-link" href="Contact"><i class="fa fa-users" aria-hidden="true"></i> Contacts</a>
</li>
<li runat="server" class='<%# checkPage("CondizioniServizio") + " nav-item" %>'>
<a class="nav-link" href="CondizioniServizio"><i class="fa fa-certificate" aria-hidden="true"></i> Condizioni d'uso</a>
<a class="nav-link" href="CondizioniServizio"><i class="fa fa-certificate" aria-hidden="true"></i> Fair Use Condition</a>
</li>
</ul>
<div runat="server" class="form-inline my-2 my-lg-0">
<asp:HyperLink runat="server" ID="hlReset" NavigateUrl="~/reset" CssClass="btn btn-danger text-nowrap" OnClick="return confirm('LOG-OUT utente: sicuro di voler procedere?');" visible='<%# userIsAuth %>'><i class="fa fa-sign-out" ></i> EXIT</asp:HyperLink>
<asp:HyperLink runat="server" ID="hlLogin" NavigateUrl="~/RegisterUser" CssClass="btn btn-success text-nowrap" visible='<%# !userIsAuth %>'><i class="fa fa-sign-in" ></i> LOGIN</asp:HyperLink>
<div runat="server" id="divSearch">
<asp:TextBox runat="server" ID="txtSearch" class="form-control mr-sm-2" type="search" placeholder="Search" aria-label="Search" OnTextChanged="txtSearch_TextChanged" />
<asp:LinkButton runat="server" ID="lbtSearch" class="btn btn-secondary my-2 my-sm-0" type="submit" OnClick="lbtSearch_Click">Search <i class="fa fa-search" aria-hidden="true"></i></asp:LinkButton>
</div>
<asp:HyperLink runat="server" ID="hlReset" NavigateUrl="~/reset" CssClass="btn btn-danger text-nowrap" OnClick="return confirm('LOG-OUT utente: sicuro di voler procedere?');" Visible='<%# userIsAuth %>'><i class="fa fa-sign-out" ></i> EXIT</asp:HyperLink>
<asp:HyperLink runat="server" ID="hlLogin" NavigateUrl="~/RegisterUser" CssClass="btn btn-success text-nowrap" Visible='<%# !userIsAuth %>'><i class="fa fa-sign-in" ></i> LOGIN</asp:HyperLink>
<div runat="server" id="divSearch">
<asp:TextBox runat="server" ID="txtSearch" class="form-control mr-sm-2" type="search" placeholder="Search" aria-label="Search" OnTextChanged="txtSearch_TextChanged" />
<asp:LinkButton runat="server" ID="lbtSearch" class="btn btn-secondary my-2 my-sm-0" type="submit" OnClick="lbtSearch_Click">Search <i class="fa fa-search" aria-hidden="true"></i></asp:LinkButton>
</div>
</div>
</div>
@@ -42,9 +42,21 @@
<asp:UpdateProgress ID="updProgress" runat="server" DynamicLayout="true" DisplayAfter="5">
<ProgressTemplate>
<div class="d-flex">
<div class="progress w-100" style="height:0.5em">
<div class="progress-bar progress-bar-striped progress-bar-animated" style="width: 80%"></div>
</div>
<div class="progress w-100" style="height: 0.5em">
<div class="progress-bar progress-bar-striped progress-bar-animated" style="width: 80%"></div>
</div>
</div>
</ProgressTemplate>
</asp:UpdateProgress>
</asp:UpdateProgress>
<div class="container">
<div class="row mt-1 mb-0">
<div class="col">
<img src="../Images/logoAlzheimerAssociation.png" class="img-fluid" width="256" />
</div>
<div class="col text-right">
<img src="../Images/logoIRCSS.png" class="img-fluid" width="128" />
<br />
<b>IRCCS</b> Istituto Centro San Giovanni di Dio Fatebenefratelli Brescia
</div>
</div>
</div>
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<%@ Control Language="C#" AutoEventWireup="true" CodeBehind="mod_about.ascx.cs" Inherits="WebLCP.WUC.mod_about" %>
<h2>About Page.</h2>
<h3>Descrizione del sito / progetto.</h3>
<p>Questa è l'area da usare per le informazioni addizionali.</p>
<div class="card">
<div class="card-header bg-dark text-light">
<div class="row">
<div class="col-9">
<h2>PROJECT DESCRIPTION</h2>
</div>
<div class="col-3 text-right p-0">
<img src="../Images/brain.jpg" class="img-fluid" width="128" />
</div>
</div>
</div>
<div class="card-body">
<p>The project aims at detecting the presence of any cut-offs in AD biomarkers distribution that allows to classify subject/patients in terms of prognostic evaluation. In particular, the main target is to provide a free, user-friendly on-line interface of an ad-hoc developed algorithm that evaluates the effects of genetic/demographic AD-related factors (APOE, age and sex) on the detected biomarker cut-offs. The idea is to allow people non-familiar with the R package to use this powerful instrument for improving the disease understanding and to create a platform for collaboration of different centers and researchers.</p>
<p>
This on-line software is an open and user-friendly tool for:
</p>
<ol>
<li>extracting any data-driven cut-off of quantitative biomarker (i.e. continuous variable) and
</li>
<li>evaluating the effect of APOE, age and sex on cut-offs estimation (Marizzoni, Ferrari, et al. 2019; <a href="https://doi.org/10.1016/j.neurobiolaging.2019.12.019" target="_blank">https://doi.org/10.1016/j.neurobiolaging.2019.12.019</a>).
</li>
</ol>
<p>
The cut-off extraction is based on finite Gaussian mixture model approach that allows to produce a probabilistic clustering/classification of the data into any subgroups (defined by the components of the mixture distribution) of the overall population. The effect of APOE, age and sex on cut-offs values was estimated by applying an extension of finite mixture model applied to a generalized linear model (more details are reported
<asp:HyperLink runat="server" NavigateUrl="~/MethodSpecs">here.</asp:HyperLink>)
</p>
</div>
</div>
@@ -1,17 +1,29 @@
<%@ Control Language="C#" AutoEventWireup="true" CodeBehind="mod_condizioniServizio.ascx.cs" Inherits="WebLCP.WUC.mod_condizioniServizio" %>
<div class="card">
<div class="card-header">
<h3>Condizioni d'uso</h3>
<div class="card-header bg-dark text-light">
<div class="row">
<div class="col-9">
<h2>FAIR USE CONDITION</h2>
</div>
<div class="col-3 text-right p-0">
<img src="../Images/brain.jpg" class="img-fluid" width="128" />
</div>
</div>
</div>
<div class="card-body">
Qui vanno riportare le condizioni d'uso del servizio erogato... ad esempio
This site is for biomarker data investigation purpose only, and it aims to evaluate the methodology proposed in our research.
<br />
<br />
In particular
<ul>
<li>I dati utente sono impiegati solo per motivi strettamente indispensabili all'erogazione del servizio</li>
<li>Le elaborazioni sono effettuate su dati che sono anonimizzati all'origine (prima dell'invio sulla piattaforma) e tale anonimizzazione è responsabilità di chi usufruisce del servizio</li>
<li>Non sono raccolte statistiche se non quelle necessarie a determinare il fair use del servizio stesso (nome utente, numero job richiesti, tempi di elaborazione)</li>
<li>input data must be anonymized before upload and provided in the format described in the DB_INPUT file specification of the Job manager menu.
</li>
<li>usage log data will be archived for statistical and for fair use evaluation (username + job name + date-time of execution)
</li>
<li>acquired statistical data will be kept only for computational related issues
</li>
</ul>
</div>
</div>
</div>
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<%@ Control Language="C#" AutoEventWireup="true" CodeBehind="mod_contacts.ascx.cs" Inherits="WebLCP.WUC.mod_contacts" %>
<h2>Contatti</h2>
<h3>Questa è la pagina dei contatti.</h3>
Andrebbero suddivisi tra
<ul>
<li>amministrativo (se c'è)</li>
<li>scientifico (algoritmo)</li>
<li>tecnico (noi)</li>
</ul>
lascio di default un esempio di contatto microsoft "lorem ipsum"...
<hr />
<div class="card">
<div class="card-header bg-dark text-light">
<div class="row">
<div class="col-9">
<h2>CONTACTS</h2>
</div>
<div class="col-3 text-right p-0">
<img src="../Images/brain.jpg" class="img-fluid" width="128" />
</div>
</div>
</div>
<div class="card-body">
<address>
One Microsoft Way<br />
Redmond, WA 98052-6399<br />
<abbr title="Phone">P:</abbr>
425.555.0100
</address>
<h5>IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia</h5>
<hr />
<dl class="row">
<dt class="col-sm-3">Administrative Support</dt>
<dd class="col-sm-9"><a href="mailto:lcavaliere@fatebenefratelli.eu">lcavaliere@fatebenefratelli.eu</a></dd>
<dt class="col-sm-3">Scientific Support</dt>
<dd class="col-sm-9"><a href="mailto:mmarizzoni@fatebenefratelli.eu">mmarizzoni@fatebenefratelli.eu</a><br />
<a href="mailto:cferrari@fatebenefratelli.eu">cferrari@fatebenefratelli.eu</a>
</dd>
</dl>
<br />
<h5>Steamware</h5>
<hr />
<dl class="row">
<dt class="col-sm-3">Technical Support</dt>
<dd class="col-sm-9"><a href="mailto:info@steamware.net">info@steamware.net</a></dd>
</dl>
</div>
</div>
<address>
<strong>Support:</strong> <a href="mailto:Support@example.com">Support@example.com</a><br />
<strong>Marketing:</strong> <a href="mailto:Marketing@example.com">Marketing@example.com</a>
</address>
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<%@ Control Language="C#" AutoEventWireup="true" CodeBehind="mod_home.ascx.cs" Inherits="WebLCP.WUC.mod_home" %>
<div class="row">
<div class="col">
<img src="../Images/logoAlzheimerAssociation.png" class="img-fluid" width="256" />
<div class="card">
<div class="card-header bg-dark text-light">
<div class="row">
<div class="col-9">
<h2>The dark side of APOE:</h2>
<h4>unravelling amyloid-independent effects in Alzheimers Diesease (AD)</h4>
</div>
<div class="col-3 text-right p-0">
<img src="../Images/brain.jpg" class="img-fluid" width="128" />
</div>
</div>
</div>
<div class="col text-right">
<img src="../Images/logoIRCSS.png" class="img-fluid" width="128" />
<div class="card-body">
<div class="titoloViola">
</div>
<br />
<b>IRCCS</b> Istituto Centro San Giovanni di Dio Fatebenefratelli Brescia
</div>
</div>
<div class="jumbotron">
<div class="titoloViola">
<h1>The dark side of APOE:</h1>
<h3>Unravelling amyloid-independent effects in Alzheimers Diesease (AD)</h3>
</div>
<br />
<p>
This project will be carried out by the Laboratory of Alzheimers Neuroimaging and Epidemiolog (LANE) and the Unit of Statistics of the IRCCS Fatebenefratelli in Brescia, Italy. The two units have a well-established expertise in AD biomarkers scientific investigation and analyses.
<p>
This project will be carried out by the Laboratory of Alzheimers Neuroimaging and Epidemiolog (LANE) and the Unit of Statistics of the IRCCS Fatebenefratelli in Brescia, Italy. The two units have a well-established expertise in AD biomarkers scientific investigation and analyses.
The project aims at detecting the presence of any cut-offs in AD biomarkers distribution that allows to classify subject/patients in terms of prognostic evaluation.
</p>
This tool:
</p>
This tool:
<ul>
<li>provides finite Gaussian mixture model output: i.e. identify sub-populations and cut-off values for each biomarker distribution taking or not into account the genetic and demographic variables effects;</li>
<li>handles several jobs (i.e. input data file) simultaneously for each user (the jobs are processed in batch and an email is sent to the user when the execution of jobs is completed);</li>
<li>produces two different output file for each job (Results file with model estimation text output; Results plot with output plots -densities and scatterplots- of unadjusted and adjusted cut-offs);</li>
<li>allows to display and export simultaneously selected output plot of different jobs.</li>
</ul>
<br />
<br />
<b>How to cite:</b>
<div>Marizzoni M., Ferrari C., et al. CSF cut-offs for MCI due to AD depend on APOEε4 carrier status Neurobiology of Aging, 2019 <a target="_blank" href="https://doi.org/10.1016/j.neurobiolaging.2019.12.019">https://doi.org/10.1016/j.neurobiolaging.2019.12.019</a></div>
</div>
<div class="card-footer">
<b>How to cite:</b>
<div>Marizzoni M., Ferrari C., et al. CSF cut-offs for MCI due to AD depend on APOEε4 carrier status Neurobiology of Aging, 2019 <a target="_blank" href="https://doi.org/10.1016/j.neurobiolaging.2019.12.019">https://doi.org/10.1016/j.neurobiolaging.2019.12.019</a></div>
</div>
</div>
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<Content Include="favicon.ico" />
<Content Include="fonts\fontawesome-webfont.svg" />
<Content Include="Global.asax" />
<Content Include="Images\brain.jpg" />
<Content Include="Images\logoAlzheimerAssociation.png" />
<Content Include="Images\logoIRCSS.png" />
<Content Include="Images\WIP.png" />
<Content Include="JobsList.aspx" />
<Content Include="jumper.aspx" />
<Content Include="login.aspx" />
<Content Include="MethodSpecs.aspx" />
<Content Include="mongocrypt.dll" />
<Content Include="RegisterUser.aspx" />
<Content Include="reset.aspx" />
@@ -504,6 +507,13 @@
<Compile Include="login.aspx.designer.cs">
<DependentUpon>login.aspx</DependentUpon>
</Compile>
<Compile Include="MethodSpecs.aspx.cs">
<DependentUpon>MethodSpecs.aspx</DependentUpon>
<SubType>ASPXCodeBehind</SubType>
</Compile>
<Compile Include="MethodSpecs.aspx.designer.cs">
<DependentUpon>MethodSpecs.aspx</DependentUpon>
</Compile>
<Compile Include="Properties\AssemblyInfo.cs" />
<Compile Include="RegisterUser.aspx.cs">
<DependentUpon>RegisterUser.aspx</DependentUpon>