I am using JPA with Hibernate 3 and Spring 3.5. 
I am unable to make JPA/hibernate refresh to changes made in database in the backend outside of hibernate (via direct queries).
I am using EHCache , and second level caching. Following are the key configuration items:

&lt;bean id="dataSource" class="com.mchange.v2.c3p0.ComboPooledDataSource"&gt;
    &lt;!-- key properties pulled from prop file --&gt;        
    &lt;property name="driverClass" value="${dataSource.driverClassName}"/&gt;
    &lt;property name="jdbcUrl" value="${dataSource.url}"/&gt;
    &lt;property name="user" value="${dataSource.username}"/&gt;
    &lt;property name="password" value="${dataSource.password}"/&gt;
    &lt;property name="maxPoolSize" value="50"/&gt;
    &lt;property name="maxIdleTime" value="14400"/&gt;
    &lt;property name="checkoutTimeout" value="5000"/&gt;
    &lt;property name="idleConnectionTestPeriod" value="60"/&gt;
    &lt;property name="preferredTestQuery" value="select 1"/&gt;
    &lt;property name="maxAdministrativeTaskTime" value="300"/&gt;
    &lt;property name="numHelperThreads" value="10"/&gt;
&lt;/bean&gt;

&lt;!-- We are Using JPA --&gt;
&lt;bean id="entityManagerFactory" class="org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean"&gt;
    &lt;property name="dataSource" ref="dataSource"/&gt;
    &lt;property name="persistenceXmlLocation" value="classpath:persistence.xml"/&gt;
    &lt;property name="jpaProperties"&gt;
        &lt;props&gt;
            &lt;prop key="hibernate.dialect"&gt;org.hibernate.dialect.MySQL5InnoDBDialect&lt;/prop&gt;
            &lt;prop key="hibernate.show_sql"&gt;true&lt;/prop&gt;
            &lt;prop key="hibernate.format_sql"&gt;true&lt;/prop&gt;
            &lt;prop key="hibernate.use_sql_comments"&gt;false&lt;/prop&gt;
            &lt;prop key="hibernate.hbm2ddl.auto"&gt;update&lt;/prop&gt;
            &lt;prop key="hibernate.generate_statistics"&gt;true&lt;/prop&gt;
            &lt;prop key="hibernate.cache.region.factory_class"&gt;net.sf.ehcache.hibernate.EhCacheRegionFactory&lt;/prop&gt;
            &lt;prop key="hibernate.cache.use_query_cache"&gt;true&lt;/prop&gt;
            &lt;prop key="hibernate.cache.use_second_level_cache"&gt;true&lt;/prop&gt;
            &lt;prop key="hibernate.cache.use_structured_entries"&gt;true&lt;/prop&gt;
            &lt;prop key="hibernate.cache.generate_statistics"&gt;true&lt;/prop&gt;
        &lt;/props&gt;
    &lt;/property&gt;
    &lt;property name="jpaVendorAdapter"&gt;
        &lt;bean class="org.springframework.orm.jpa.vendor.HibernateJpaVendorAdapter"/&gt;
    &lt;/property&gt;
&lt;/bean&gt;


I am also using JpaTransactionManager with Propagation=REQUIRED for all methods interacting with entities.

Please advice. 


Question: Results with and without interaction
Answer: The interaction means the effect to X in the response Y is different in the categories defined by the Group variable. 
Sometime it is useful to do a stratified analysis, by Groups, where you analysis the effect of X in Y in each group. You should see the effects are different. You could present these stratified analysis and show the P-value of the interaction for justify the stratification.