On the Structure and Complexity of Rational Sets of Regular Languages

In a recent thread of papers, we have introduced FQL, a precise specification language for test coverage, and developed the test case generation engine FShell for ANSI C. In essence, an FQL test specification amounts to a set of regular languages, each of which has to be matched by at least one test execution. To describe such sets of regular languages, the FQL semantics uses an automata-theoretic concept known as rational sets of regular languages (RSRLs). RSRLs are automata whose alphabet consists of regular expressions. Thus, the language accepted by the automaton is a set of regular expressions. In this paper, we study RSRLs from a theoretic point of view. More specifically, we analyze RSRL closure properties under common set theoretic operations, and the complexity of membership checking, i.e., whether a regular language is an element of a RSRL. For all questions we investigate both the general case and the case of finite sets of regular languages. Although a few properties are left as open problems, the paper provides a systematic semantic foundation for the test specification language FQL

Proactive Detection of Computer Worms Using Model Checking

Although recent estimates are speaking of 200,000 different viruses, worms, and Trojan horses, the majority of them are variants of previously existing malware. As these variants mostly differ in their binary representation rather than their functionality, they can be recognized by analyzing the program behavior, even though they are not covered by the signature databases of current antivirus tools. Proactive malware detectors mitigate this risk by detection procedures that use a single signature to detect whole classes of functionally related malware without signature updates. It is evident that the quality of proactive detection procedures depends on their ability to analyze the semantics of the binary. In this paper, we propose the use of model checkinga well-established software verification techniquefor proactive malware detection. We describe a tool that extracts an annotated control flow graph from the binary and automatically verifies it against a formal malware specification. To this end, we introduce the new specification language CTPL, which balances the high expressive power needed for malware signatures with efficient model checking algorithms. Our experiments demonstrate that our technique indeed is able to recognize variants of existing malware with a low risk of false positives. © 2006 IEEE

Rabies virus in slaughtered dogs for meat consumption in Ghana: A potential risk for rabies transmission

Dog-mediated rabies is responsible for approximately 60,000 human deaths annually worldwide. Although dog slaughter for human consumption and its potential risk for rabies transmission has been reported, mainly in some parts of Western Africa and South-East Asia, more information on this and factors that influence dog meat consumption is required for a better understanding from places like Ghana where the practice is common. We tested 144 brain tissues from apparently healthy dogs slaughtered for human consumption for the presence of rabies viruses using a Lyssavirus-specific real-Time RT-PCR. Positive samples were confirmed by virus genome sequencing. We also administered questionnaires to 541 dog owners from three regions in Ghana and evaluated factors that could influence dog meat consumption. We interacted with butchers and observed slaughtering and meat preparation procedures. Three out of 144 (2.1%) brain tissues from apparently healthy dogs tested positive for rabies virus RNA. Two of the viruses with complete genomes were distinct from one another, but both belonged to the Africa 2 lineage. The third virus with a partial genome fragment had high sequence identity to the other two and also belonged to the Africa 2 lineage. Almost half of the study participants practiced dog consumption [49% (265/541)]. Males were almost twice (cOR = 1.72, 95% CI (1.17-2.52), p-value = .006) as likely to consume dog meat compared to females. Likewise, the Frafra tribe from northern Ghana [cOR = 825.1, 95% CI (185.3-3672.9), p-value < .0001] and those with non-specific tribes [cOR = 47.05, 95% CI (10.18-217.41), p-value < .0001] presented with higher odds of dog consumption compared to Ewes. The butchers used bare hands in meat preparation. This study demonstrates the presence of rabies virus RNA in apparently healthy dogs slaughtered for human consumption in Ghana and suggests a potential risk for rabies transmission. Veterinary departments and local assemblies are recommended to monitor and regulate this practice

SARS‐CoV‐2 receptor ACE 2 and TMPRSS 2 are primarily expressed in bronchial transient secretory cells

The SARS-CoV-2 pandemic affecting the human respiratory system severely challenges public health and urgently demands for increasing our understanding of COVID-19 pathogenesis, especially host factors facilitating virus infection and replication. SARS-CoV-2 was reported to enter cells via binding to ACE2, followed by its priming by TMPRSS2. Here, we investigate ACE2 and TMPRSS2 expression levels and their distribution across cell types in lung tissue (twelve donors, 39,778 cells) and in cells derived from subsegmental bronchial branches (four donors, 17,521 cells) by single nuclei and single cell RNA sequencing, respectively. While TMPRSS2 is strongly expressed in both tissues, in the subsegmental bronchial branches ACE2 is predominantly expressed in a transient secretory cell type. Interestingly, these transiently differentiating cells show an enrichment for pathways related to RHO GTPase function and viral processes suggesting increased vulnerability for SARS-CoV-2 infection. Our data provide a rich resource for future investigations of COVID-19 infection and pathogenesis

Surveillance of SARS-CoV-2 in Frankfurt am Main from October to December 2020 Reveals High Viral Diversity Including Spike Mutation N501Y in B.1.1.70 and B.1.1.7.

BACKGROUND: International travel is a major driver of the introduction and spread of SARS-CoV-2. AIM: To investigate SARS-CoV-2 genetic diversity in the region of a major transport hub in Germany, we characterized the viral sequence diversity of the SARS-CoV-2 variants circulating in Frankfurt am Main, the city with the largest airport in Germany, from the end of October to the end of December 2020. METHODS: In total, we recovered 136 SARS-CoV-2 genomes from nasopharyngeal swab samples. We isolated 104 isolates that were grown in cell culture and RNA from the recovered viruses and subjected them to full-genome sequence analysis. In addition, 32 nasopharyngeal swab samples were directly sequenced. RESULTS AND CONCLUSION: We found 28 different lineages of SARS-CoV-2 circulating during the study period, including the variant of concern B.1.1.7 (Δ69/70, N501Y). Six of the lineages had not previously been observed in Germany. We detected the spike protein (S) deletion Δ69/Δ70 in 15% of all sequences, a four base pair (bp) deletion (in 2.9% of sequences) and a single bp deletion (in 0.7% of sequences) in ORF3a, leading to ORF3a truncations. In four sequences (2.9%), an amino acid deletion at position 210 in S was identified. In a single sample (0.7%), both a 9 bp deletion in ORF1ab and a 7 bp deletion in ORF7a were identified. One sequence in lineage B.1.1.70 had an N501Y substitution while lacking the Δ69/70 in S. The high diversity of sequences observed over two months in Frankfurt am Main highlights the persisting need for continuous SARS-CoV-2 surveillance using full-genome sequencing, particularly in cities with international airport connections