Type Targeted Testing

We present a new technique called type targeted testing, which translates precise refinement types into comprehensive test-suites. The key insight behind our approach is that through the lens of SMT solvers, refinement types can also be viewed as a high-level, declarative, test generation technique, wherein types are converted to SMT queries whose models can be decoded into concrete program inputs. Our approach enables the systematic and exhaustive testing of implementations from high-level declarative specifications, and furthermore, provides a gradual path from testing to full verification. We have implemented our approach as a Haskell testing tool called TARGET, and present an evaluation that shows how TARGET can be used to test a wide variety of properties and how it compares against state-of-the-art testing approaches

Acceptability of HIV self-sampling kits (TINY vial) among people of black African ethnicity in the UK: a qualitative study

Background: Increasing routine HIV testing among key populations is a public health imperative, so improving access to acceptable testing options for those in need is a priority. Despite increasing targeted distribution and uptake of HIV self-sampling kits (SSKs) among men who have sex with men in the UK, little is known about why targeted SSK interventions for black African users are not as wide-spread or well-used. This paper addresses this key gap, offering insight into why some groups may be less likely than others to adopt certain types of SSK interventions in particular contexts. These data were collected during the development phase of a larger study to explore the feasibility and acceptability of targeted distribution of SSKs to black African people. Methods: We undertook 6 focus groups with members of the public who self-identified as black African (n = 48), 6 groups with specialists providing HIV and social services to black African people (n = 53), and interviews with HIV specialist consultants and policy-makers (n = 9). Framework analysis was undertaken, using inductive and deductive analysis to develop and check themes. Results: We found three valuable components of targeted SSK interventions for this population: the use of settings and technologies that increase choice and autonomy; targeted offers of HIV testing that preserve privacy and do not exacerbate HIV stigma; and ensuring that the specific kit being used (in this case, the TINY vial) is perceived as simple and reliable. Conclusions: This unique and rigorous research offers insights into participants’ views on SSK interventions, offering key considerations when targeting this population.. Given the plethora of HIV testing options, our work demonstrates that those commissioning and delivering SSK interventions will need to clarify (for users and providers) how each kit type and intervention design adds value. Most significantly, these findings demonstrate that without a strong locus of control over their own circumstances and personal information, black African people are less likely to feel that they can pursue an HIV test that is safe and secure. Thus, where profound social inequalities persist, so will inequalities in HIV testing uptake – by any means

Measuring the Effects of a Research-Based Field Experience on Undergraduates and K-12 Teachers

During the summer of 1999, a new type of field course was taught in five of eastern Utah's National Parks and Monuments. It targeted a combination of university undergraduates and K-12 teachers, emphasized development of participants' problem-solving skills, and assessed the effectiveness of several non-traditional teaching methods. The course's primary goal was to teach participants to develop and test their own ideas. The course was also designed to help participants learn to use tools and methods employed by research scientists. A mix of undergraduates and teachers was targeted so that the course could be used to introduce undergraduates to the concept of teaching as a career. Assessments of the course's effectiveness were made on the basis of the achievements of stated outcomes, and by pre-course and post-course testing. Educational levels: Graduate or professional

Targeting The Optimal Design In Randomized Clinical Trials With Binary Outcomes And No Covariate

This article is devoted to the asymptotic study of adaptive group sequential designs in the case of randomized clinical trials with binary treatment, binary outcome and no covariate. By adaptive design, we mean in this setting a clinical trial design that allows the investigator to dynamically modify its course through data-driven adjustment of the randomization probability based on data accrued so far, without negatively impacting on the statistical integrity of the trial. By adaptive group sequential design, we refer to the fact that group sequential testing methods can be equally well applied on top of adaptive designs. Prior to collection of the data, the trial protocol specifies the parameter of scientific interest. In the estimation framework, the trial protocol also a priori specifies the confidence level to be used in constructing frequentist confidence intervals for the latter parameter and the related inferential method, which will be based on the maximum likelihood principle. In the testing framework, the trial protocol also a priori specifies the null and alternative hypotheses regarding the latter parameter, the wished type I and type II errors, the rule for determining the maximal statistical information to be accrued, and the frequentist testing procedure, including conditions for early stopping. Furthermore, we assume that the protocol specifies a user-supplied optimal unknown choice of randomization scheme, and we will focus on that randomization scheme which minimizes the asymptotic variance of the maximum likelihood estimator of the parameter of interest. We obtain that, theoretically, the adaptive design converges almost surely to the targeted unknown randomization scheme. In the estimation framework, we obtain that our maximum likelihood estimator of the parameter of interest is a strongly consistent estimator, and it satisfies a central limit theorem. We can estimate its asymptotic variance, which is the same as that it would feature had we known in advance the targeted randomization scheme and independently sampled from it. Consequently, inference can be carried out as if we had resorted to independent and identically distributed (iid) sampling. In the testing framework, we obtain that the multidimensional t-statistics that we would use under iid sampling still converges to the same canonical distribution under adaptive sampling. Consequently, the same group sequential testing can be carried out as if we had resorted to iid sampling. Furthermore, a comprehensive simulation study that we undertake validates the theory. It notably shows in the estimation framework that the confidence intervals we obtain achieve the desired coverage even for moderate sample sizes. In addition, it shows in the testing framework that type I error control at the prescribed level is guaranteed, and that all sampling procedures only suffer from a very slight increase of the type II error. A three-sentence take-home message is: Adaptive designs do learn the targeted optimal design and inference and testing can be carried out under adaptive sampling as they would under the targeted optimal randomization probability iid sampling. In particular, adaptive designs achieve the same efficiency as the fixed oracle design. This is confirmed by a simulation study, at least for moderate or large sample sizes, across a large collection of targeted randomization probabilities

Matriptase regulates c-Met mediated proliferation and invasion in inflammatory breast cancer.

The poor prognosis for patients with inflammatory breast cancer (IBC) compared to patients with other types of breast cancers emphasizes the need to better understand the molecular underpinnings of this disease with the goal of developing effective targeted therapeutics. Dysregulation of matriptase expression, an epithelial-specific member of the type II transmembrane serine protease family, has been demonstrated in many different cancer types. To date, no studies have assessed the expression and potential pro-oncogenic role of matriptase in IBC. We examined the functional relationship between matriptase and the HGF/c-MET signaling pathway in the IBC cell lines SUM149 and SUM190, and in IBC patient samples. Matriptase and c-Met proteins are localized on the surface membrane of IBC cells and their expression is strongly correlated in infiltrating cancer cells and in the cancer cells of lymphatic emboli in patient samples. Abrogation of matriptase expression by silencing with RNAi or inhibition of matriptase proteolytic activity with a synthetic inhibitor impairs the conversion of inactive pro-HGF to active HGF and subsequent c-Met-mediated signaling, leading to efficient impairment of proliferation and invasion of IBC cells. These data show the potential of matriptase inhibitors as a novel targeted therapy for IBC, and lay the groundwork for the development and testing of such drugs

Personal genome testing: Test characteristics to clarify the discourse on ethical, legal and societal issues

Background: As genetics technology proceeds, practices of genetic testing have become more heterogeneous: many different types of tests are finding their way to the public in different settings and for a variety of purposes. This diversification is relevant to the discourse on ethical, legal and societal issues (ELSI) surrounding genetic testing, which must evolve to encompass these differences. One important development is the rise of personal genome testing on the basis of genetic profiling: the testing of multiple genetic variants simultaneously for the prediction of common multifactorial diseases. Currently, an increasing number of companies are offering personal genome tests directly to consumers and are spurring ELSI-discussions, which stand in need of clarification. This paper presents a systematic approach to the ELSI-evaluation of personal genome testing for multifactorial diseases along the lines of its test characteristics. Discussion: This paper addresses four test characteristics of personal genome testing: its being a non-targeted type of testing, its high analytical validity, low clinical validity and problematic clinical utility. These characteristics raise their own specific ELSI, for example: non-targeted genetic profiling poses serious problems for information provision and informed consent. Questions about the quantity and quality of the necessary information, as well as about moral responsibilities with regard to the provision of information are therefore becoming central themes within ELSI-discussions of personal genome testing. Further, the current low level of clinical validity of genetic profiles raises questions concerning societal risks and regulatory requirements, whereas simultaneously it causes traditional ELSI-issues of clinical genetics, such as psychological and health risks, discrimination, and stigmatization, to lose part of their relevance. Also, classic notions of clinical utility are challenged by the newer notion of 'personal utility.' Summary: Consideration of test characteristics is essential to any valuable discourse on the ELSI of personal genome testing for multifactorial diseases. Four key characteristics of the test - targeted/non-targeted testing, analytical validity, clinical validity and clinical utility - together determine the applicability and the relevance of ELSI to specific tests. The paper identifies and discusses four areas of interest for the ELSI-debate on personal genome testing: informational problems, risks, regulatory issues, and the notion of personal utility

Learning from Seller Experiements in Online Markets

The internet has dramatically reduced the cost of varying prices, dis- plays and information provided to consumers, facilitating both active and passive experimentation. We document the prevalence of targeted pricing and auction design variation on eBay, and identify hundreds of thousands of experiments con- ducted by sellers across a wide array of retail products. We show how this type of data can be used to address questions about consumer behavior and market outcomes, and provide illustrative results on price dispersion, the frequency of over-bidding, the choice of reserve prices, ?buy now?options and other auction design parameters, and on consumer sensitivity to shipping fees. We argue that leveraging the experiments of market participants takes advantage of the scale and heterogeneity of online markets and can be a powerful approach for testing and measurement.

Outcomes of patients with advanced cancer and KRAS mutations in phase I clinical trials.

BackgroundKRAS mutation is common in human cancer. We assessed the clinical factors, including type of KRAS mutation and treatment, of patients with advanced cancer and tumor KRAS mutations and their association with treatment outcomes.MethodsPatients referred to the Phase I Clinic for treatment who underwent testing for KRAS mutations were analyzed.ResultsOf 1,781 patients, 365 (21%) had a KRAS mutation. The G12D mutation was the most common mutation (29%). PIK3CA mutations were found in 24% and 10% of patients with and without KRAS mutations (p<0.0001). Of 223 patients with a KRAS mutation who were evaluable for response, 56 were treated with a MEK inhibitor-containing therapy and 167 with other therapies. The clinical benefit (partial response and stable disease lasting ≥6 months) rates were 23% and 9%, respectively, for the MEK inhibitor versus other therapies (p=0.005). The median progression-free survival (PFS) was 3.3 and 2.2 months, respectively (p=0.09). The respective median overall survival was 8.4 and 7.0 months (p=0.38). Of 66 patients with a KRAS mutation and additional alterations, higher rates of clinical benefit (p=0.04), PFS (p=0.045), and overall survival (p=0.02) were noted in patients treated with MEK inhibitor-containing therapy (n=9) compared to those treated with targeted therapy matched to the additional alterations (n=24) or other therapy (n=33).ConclusionsMEK inhibitors in patients with KRAS-mutated advanced cancer were associated with higher clinical benefit rates compared to other therapies. Therapeutic strategies that include MEK inhibitors or novel agents combined with other targeted therapies or chemotherapy need further investigation

A targeted gene panel that covers coding, non-coding and short tandem repeat regions improves the diagnosis of patients with neurodegenerative diseases

Genetic testing for neurodegenerative diseases (NDs) is highly challenging because of genetic heterogeneity and overlapping manifestations. Targeted-gene panels (TGPs), coupled with next-generation sequencing (NGS), can facilitate the profiling of a large repertoire of ND-related genes. Due to the technical limitations inherent in NGS and TGPs, short tandem repeat (STR) variations are often ignored. However, STR expansions are known to cause such NDs as Huntington\u27s disease and spinocerebellar ataxias type 3 (SCA3). Here, we studied the clinical utility of a custom-made TGP that targets 199 NDs and 311 ND-associated genes on 118 undiagnosed patients. At least one known or likely pathogenic variation was found in 54 patients; 27 patients demonstrated clinical profiles that matched the variants; and 16 patients whose original diagnosis were refined. A high concordance of variant calling were observed when comparing the results from TGP and whole-exome sequencing of four patients. Our in-house STR detection algorithm has reached a specificity of 0.88 and a sensitivity of 0.82 in our SCA3 cohort. This study also uncovered a trove of novel and recurrent variants that may enrich the repertoire of ND-related genetic markers. We propose that a combined comprehensive TGPs-bioinformatics pipeline can improve the clinical diagnosis of NDs