sscMap: An extensible Java application for connecting small-molecule drugs using gene-expression signatures

Background
Connectivity mapping is a process to recognize novel pharmacological and toxicological properties in small molecules by comparing their gene expression signatures with others in a database. A simple and robust method for connectivity mapping with increased specificity and sensitivity was recently developed, and its utility demonstrated using experimentally derived gene signatures.

Results
This paper introduces sscMap (statistically significant connections' map), a Java application designed to undertake connectivity mapping tasks using the recently published method. The software is bundled with a default collection of reference gene-expression profiles based on the publicly available dataset from the Broad Institute Connectivity Map 02, which includes data from over 7000 Affymetrix microarrays, for over 1000 small-molecule compounds, and 6100 treatment instances in 5 human cell lines. In addition, the application allows users to add their custom collections of reference profiles and is applicable to a wide range of other 'omics technologies.

Conclusion
The utility of sscMap is two fold. First, it serves to make statistically significant connections between a user-supplied gene signature and the 6100 core reference profiles based on the Broad Institute expanded dataset. Second, it allows users to apply the same improved method to custom-built reference profiles which can be added to the database for future referencing. The software can be freely downloaded from http://purl.oclc.org/NET/sscMap

JVM-based Techniques for Improving Java Observability

Observability measures the support of computer systems to accurately capture, analyze, and present (collectively observe) the internal information about the systems. Observability frameworks play important roles for program understanding, troubleshooting, performance diagnosis, and optimizations. However, traditional solutions are either expensive or coarse-grained, consequently compromising their utility in accommodating today’s increasingly complex software systems. New solutions are emerging for VM-based languages due to the full control language VMs have over program executions. Existing such solutions, nonetheless, still lack flexibility, have high overhead, or provide limited context information for developing powerful dynamic analyses. In this thesis, we present a VM-based infrastructure, called marker tracing framework (MTF), to address the deficiencies in the existing solutions for providing better observability for VM-based languages. MTF serves as a solid foundation for implementing fine-grained low-overhead program instrumentation. Specifically, MTF allows analysis clients to: 1) define custom events with rich semantics ; 2) specify precisely the program locations where the events should trigger; and 3) adaptively enable/disable the instrumentation at runtime. In addition, MTF-based analysis clients are more powerful by having access to all information available to the VM. To demonstrate the utility and effectiveness of MTF, we present two analysis clients: 1) dynamic typestate analysis with adaptive online program analysis (AOPA); and 2) selective probabilistic calling context analysis (SPCC). In addition, we evaluate the runtime performance of MTF and the typestate client with the DaCapo benchmarks. The results show that: 1) MTF has acceptable runtime overhead when tracing moderate numbers of marker events; and 2) AOPA is highly effective in reducing the event frequency for the dynamic typestate analysis; and 3) language VMs can be exploited to offer greater observability.

An examination of the utility of the AUDIT in people with schizophrenia

Objective: To examine the reliability and validity of the Alcohol Use Disorders Identification Test (AUDIT) compared to a structured diagnostic interview, the Composite international Diagnostic Interview (CIDI; 12-month version) in psychiatric patients with a diagnosis of schizophrenia. Method: Patients (N = 71, 53 men) were interviewed using the CIDI (Alcohol Misuse Section; 12-month version) and then completed the AUDIT. Results: The CIDI identified 32.4% of the sample as having an alcohol use disorder. Of these, 5 (7.0%) met diagnostic criteria for harmful use of alcohol, 1 (1.4%) met diagnostic criteria for alcohol abuse and 17 (23.9%) met diagnostic criteria for alcohol dependence. The AUDIT was found to have good internal reliability (coefficient = 0.85). An AUDIT cutoff of greater than or equal to 8 had a sensitivity of 87% and specificity of 90% in detecting CIDI-diagnosed alcohol disorders. All items except Item 9 contributed significantly to discriminant validity. Conclusions: The findings replicate and extend previous findings of high rates of alcohol use disorders in people with severe mental illness. The AUDIT was found to be reliable and valid in this sample and can be used with confidence as a screening instrument for alcohol use disorders in people with schizophrenia.

The utility and challenges of using ICD codes in child maltreatment research : a review of existing literature

Objective: The objectives of this article are to explore the extent to which the International Statistical Classification of Diseases and Related Health Problems (ICD) has been used in child abuse research, to describe how the ICD system has been applied and to assess factors affecting the reliability of ICD coded data in child abuse research.----- Methods: PubMed, CINAHL, PsychInfo and Google Scholar were searched for peer reviewed articles written since 1989 that used ICD as the classification system to identify cases and research child abuse using health databases. Snowballing strategies were also employed by searching the bibliographies of retrieved references to identify relevant associated articles. The papers identified through the search were independently screened by two authors for inclusion, resulting in 47 studies selected for the review. Due to heterogeneity of studies metaanalysis was not performed.----- Results: This paper highlights both utility and limitations of ICD coded data. ICD codes have been widely used to conduct research into child maltreatment in health data systems. The codes appear to be used primarily to determine child maltreatment patterns within identified diagnoses or to identify child maltreatment cases for research.----- Conclusions: A significant impediment to the use of ICD codes in child maltreatment research is the under-ascertainment of child maltreatment by using coded data alone. This is most clearly identified and, to some degree, quantified, in research where data linkage is used. Practice Implications: The importance of improved child maltreatment identification will assist in identifying risk factors and creating programs that can prevent and treat child maltreatment and assist in meeting reporting obligations under the CRC.

The Autistic Behavioural Indicators Instrument (ABII) : development and instrument utility in discriminating autistic disorder from speech and language impairment and typical development

The Autistic Behavioural Indicators Instrument (ABII) is an 18-item instrument developed to identify children with Autistic Disorder (AD) based on the presence of unique autistic behavioural indicators. The ABII was administered to 20 children with AD, 20 children with speech and language impairment (SLI) and 20 typically developing (TD) children aged 2-6 years. Results indicated that the ABII discriminated children diagnosed with AD from those diagnosed with SLI and those who were TD, based on the presence of specific social attention, sensory, and behavioural symptoms. A combination of symptomology across these domains correctly classified 100% of children with and without AD. The paper concludes that the ABII shows considerable promise as an instrument for the early identification of AD.