49,554 research outputs found
Thermodynamic framework to assess low abundance DNA mutation detection by hybridization
The knowledge of genomic DNA variations in patient samples has a high and increasing value for human diagnostics in its broadest sense. Although many methods and sensors to detect or quantify these variations are available or under development, the number of underlying physico-chemical detection principles is limited. One of these principles is the hybridization of sample target DNA versus nucleic acid probes. We introduce a novel thermodynamics approach and develop a framework to exploit the specific detection capabilities of nucleic acid hybridization, using generic principles applicable to any platform. As a case study, we detect point mutations in the KRAS oncogene on a microarray platform. For the given platform and hybridization conditions, we demonstrate the multiplex detection capability of hybridization and assess the detection limit using thermodynamic considerations; DNA containing point mutations in a background of wild type sequences can be identified down to at least 1% relative concentration. In order to show the clinical relevance, the detection capabilities are confirmed on challenging formalin-fixed paraffin-embedded clinical tumor samples. This enzyme-free detection framework contains the accuracy and efficiency to screen for hundreds of mutations in a single run with many potential applications in molecular diagnostics and the field of personalised medicine
Inference of Population History using Coalescent HMMs: Review and Outlook
Studying how diverse human populations are related is of historical and
anthropological interest, in addition to providing a realistic null model for
testing for signatures of natural selection or disease associations.
Furthermore, understanding the demographic histories of other species is
playing an increasingly important role in conservation genetics. A number of
statistical methods have been developed to infer population demographic
histories using whole-genome sequence data, with recent advances focusing on
allowing for more flexible modeling choices, scaling to larger data sets, and
increasing statistical power. Here we review coalescent hidden Markov models, a
powerful class of population genetic inference methods that can effectively
utilize linkage disequilibrium information. We highlight recent advances, give
advice for practitioners, point out potential pitfalls, and present possible
future research directions.Comment: 12 pages, 2 figure
Test Case Purification for Improving Fault Localization
Finding and fixing bugs are time-consuming activities in software
development. Spectrum-based fault localization aims to identify the faulty
position in source code based on the execution trace of test cases. Failing
test cases and their assertions form test oracles for the failing behavior of
the system under analysis. In this paper, we propose a novel concept of
spectrum driven test case purification for improving fault localization. The
goal of test case purification is to separate existing test cases into small
fractions (called purified test cases) and to enhance the test oracles to
further localize faults. Combining with an original fault localization
technique (e.g., Tarantula), test case purification results in better ranking
the program statements. Our experiments on 1800 faults in six open-source Java
programs show that test case purification can effectively improve existing
fault localization techniques
SlowFuzz: Automated Domain-Independent Detection of Algorithmic Complexity Vulnerabilities
Algorithmic complexity vulnerabilities occur when the worst-case time/space
complexity of an application is significantly higher than the respective
average case for particular user-controlled inputs. When such conditions are
met, an attacker can launch Denial-of-Service attacks against a vulnerable
application by providing inputs that trigger the worst-case behavior. Such
attacks have been known to have serious effects on production systems, take
down entire websites, or lead to bypasses of Web Application Firewalls.
Unfortunately, existing detection mechanisms for algorithmic complexity
vulnerabilities are domain-specific and often require significant manual
effort. In this paper, we design, implement, and evaluate SlowFuzz, a
domain-independent framework for automatically finding algorithmic complexity
vulnerabilities. SlowFuzz automatically finds inputs that trigger worst-case
algorithmic behavior in the tested binary. SlowFuzz uses resource-usage-guided
evolutionary search techniques to automatically find inputs that maximize
computational resource utilization for a given application.Comment: ACM CCS '17, October 30-November 3, 2017, Dallas, TX, US
A survey of cost-sensitive decision tree induction algorithms
The past decade has seen a significant interest on the problem of inducing decision trees that take account of costs of misclassification and costs of acquiring the features used for decision making. This survey identifies over 50 algorithms including approaches that are direct adaptations of accuracy based methods, use genetic algorithms, use anytime methods and utilize boosting and bagging. The survey brings together these different studies and novel approaches to cost-sensitive decision tree learning, provides a useful taxonomy, a historical timeline of how the field has developed and should provide a useful reference point for future research in this field
Designing antibiotic cycling strategies by determining and understanding local adaptive landscapes
The evolution of antibiotic resistance among bacteria threatens our continued
ability to treat infectious diseases. The need for sustainable strategies to
cure bacterial infections has never been greater. So far, all attempts to
restore susceptibility after resistance has arisen have been unsuccessful,
including restrictions on prescribing [1] and antibiotic cycling [2,3]. Part of
the problem may be that those efforts have implemented different classes of
unrelated antibiotics, and relied on removal of resistance by random loss of
resistance genes from bacterial populations (drift). Here, we show that
alternating structurally similar antibiotics can restore susceptibility to
antibiotics after resistance has evolved. We found that the resistance
phenotypes conferred by variant alleles of the resistance gene encoding the TEM
{\beta}-lactamase (blaTEM) varied greatly among 15 different {\beta}-lactam
antibiotics. We captured those differences by characterizing complete adaptive
landscapes for the resistance alleles blaTEM-50 and blaTEM-85, each of which
differs from its ancestor blaTEM-1 by four mutations. We identified pathways
through those landscapes where selection for increased resistance moved in a
repeating cycle among a limited set of alleles as antibiotics were alternated.
Our results showed that susceptibility to antibiotics can be sustainably
renewed by cycling structurally similar antibiotics. We anticipate that these
results may provide a conceptual framework for managing antibiotic resistance.
This approach may also guide sustainable cycling of the drugs used to treat
malaria and HIV
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