Explore the vast range of titles available.

Abstract We present the Codon Statistics Database, an online database that contains codon usage statistics for all the species with reference or representative genomes in RefSeq (over 15,000). The user can search for any species and access two sets of tables. One set lists, for each codon, the frequency, the Relative Synonymous Codon Usage, and whether the codon is preferred. Another set of tables lists, for each gene, its GC content, Effective Number of Codons, Codon Adaptation Index, and frequency of optimal codons. Equivalent tables can be accessed for (1) all nuclear genes, (2) nuclear genes encoding ribosomal proteins, (3) mitochondrial genes, and (4) chloroplast genes (if available in the relevant assembly). The user can also search for any taxonomic group (e.g., “primates”) and obtain a table comparing all the species in the group. The database is free to access without registration at http://codonstatsdb.unr.edu.

Researchers have studied usable computer security for more than 20 years, and developers have created numerous security interfaces. Here, the authors examine research in this space, starting with a historical look at papers that address two consistent problems: user authentication and email encryption. Drawing from successes and failures within these areas, they study several security systems to determine how important design is to usable security. Their discussion offers guidelines for future system design.

Pathogens differ in their host specificities, with species infecting a unique host (specialist pathogens) and others having a wide host range (generalists). Molecular determinants of pathogen’s host range remain poorly understood. Secreted proteins of generalist pathogens are expected to have a broader range of intermolecular interactions (i.e., higher promiscuity) compared with their specialist counterparts. We hypothesize that this increased promiscuity of generalist secretomes may be based on an elevated content of primitive amino acids and intrinsically disordered regions, as these features are known to increase protein flexibility and interactivity. Here, we measure the proportion of primitive amino acids and percentage of intrinsically disordered residues in secreted, membrane, and cytoplasmic proteins from pathogens with different host specificity. Supporting our prediction, there is a significant general enrichment for primitive amino acids and intrinsically disordered regions in proteins from generalists compared to specialists, particularly among secreted proteins in prokaryotes. Our findings support our hypothesis that secreted proteins' amino acid composition and disordered content influence the pathogens' host range.

Protein evolution in an organism or population is determined by a host of phenomena that affect the overall rate of change in the genome. Selection is thought to have a decreased effect in self-fertilizing plants due to decreased effective population size. Arabidopsis thaliana transitioned to self-fertilization while its congeners A. lyrata and A. halleri have retained obligatory out-crossing. The rate of protein change, measured as the nonsynonymous to synonymous divergence ratio ( dN/dS), showed an increase in evolutionary rate in A. thaliana compared to A. lyrata and A. halleri, likely due to self-fertilization. Preferential codon usage is affected by translational selection, decreasing the rate of synonymous substitution. Preferred codons tend to correspond to the most abundant tRNAs. Codon usage biases differ amongst species and can be different among the tissues of an organism if relative tRNA abundances differ between the different tissues. Previous studies have found that the differences in codon usage biases may also be attributed to GC content and not only to differences in tissue specific protein expression. In the genome of Drosophila melanogaster, I have found that patterns of codon usage are different amongst proteins expressed in different tissues. Using randomized datasets, I show that these differences are always explained by which tissue these genes are expressed in, and are not due to other confounding properties of these proteins, such as GC content, protein length, or protein expression levels.

Thirty years ago, research in designing operating systems to defeat malicious software was very popular. The primary technique was to design and implement a small security kernel that could provide security assurances to the rest of the system. However, as operating systems grew in size throughout the 1980’s and 1990’s, research into security kernels slowly waned. From a security perspective, the story was bleak. Providing security to one of these large operating systems typically required running software within that operating system. This weak security foundation made it relatively easy for attackers to subvert the entire system without detection. The research presented in this thesis aims to reimagine how we design and deploy computer systems. We show that through careful use of virtualization technology, one can effectively isolate the security critical components in a system from malicious software. Furthermore, we can control this isolation to allow the security software a complete view to monitor the running system. This view includes all of the necessary information for implementing useful security applications including the system memory, storage, hardware events, and network traffic. In addition, we show how to perform both passive and active monitoring securely, using this new system architecture. Security applications must be redesigned to work within this new monitoring architecture. The data acquired through our monitoring is typically very low-level and difficult to use directly. In this thesis, we describe work that helps bridge this semantic gap by locating data structures within the memory of a running virtual machine. We also describe work that shows a useful and novel security framework made possible through this new monitoring architecture. This framework correlates human interaction with the system to distinguish legitimate and malicious outgoing network traffic.

In one particular legal opinion, a judge compared construction, in its complexity and risk, to the management of a battle. The majority of the designer's influence lies in the pre-construction work of design and documentation, which forms the very basis of the construction project. Given that construction tends to be adversarial even in the best of circumstances, the architectural and engineering design must strive to provide the contractor the clearest instructions possible regarding the intent of the designer. Although perfection of construction documents is nearly impossible to achieve, in no circumstances should the documents themselves be allowed to provide the basis for conflict, confusion on the construction site, and eventual litigation. This paper seeks to distill a relatively complicated body of law into some central principles useful to the architect and engineer in everyday practice. This paper introduces the principles and then illustrate their application through three case studies.

Motivation: Most amino acids can be encoded by a set of synonymous codons. Often, for any given amino acid, certain codons are significantly more used than others, a phenomenon known as codon usage bias. The genomes of different species differ in the frequencies at which they use each codon (e.g., a codon that is highly used in one species may be lowly used in another species). In addition, within any given genome, genes differ in their degree of codon bias, with highly expressed genes being more likely to use preferred codons. Knowing the codons that are preferred by a certain genome, and the amount of codon bias exhibited by each gene, has multiple applications (e.g., in heterologous expression, gene prediction, or phylogenetic inference). Results: We have developed the Codon Statistics Database, an online database that contains codon usage statistics for all the species with reference or representative genomes in RefSeq. The user can search for any species and access two sets of tables. One set lists, for each codon, the frequency, the Relative Synonymous Codon Usage (RSCU), and whether the codon is preferred. Another set of tables lists, for each gene, its GC content, Effective Number of Codons (ENC), Codon Adaptation Index (CAI), and frequency of optimal codons (Fop). Equivalent tables can be accessed for 1) all nuclear genes, 2) nuclear genes encoding ribosomal proteins, 3) mitochondrial genes and 4) chloroplastic genes (if available in the relevant assembly). The user can also search for any taxonomic group (e.g., \"primates\") and obtain a table comparing all the species in the group. Availability: The database is free to access without registration at http://codonstatsdb.unr.edu. Competing Interest Statement The authors have declared no competing interest.

Modern virtualized service infrastructures expose attack vectors that enable attacks of high severity, such as attacks targeting hypervisors. A malicious user of a guest VM (virtual machine) may execute an attack against the underlying hypervisor via hypercalls, which are software traps from a kernel of a fully or partially paravirtualized guest VM to the hypervisor. The exploitation of a vulnerability of a hypercall handler may have severe consequences such as altering hypervisor's memory, which may result in the execution of malicious code with hypervisor privilege. Despite the importance of vulnerabilities of hypercall handlers, there is not much publicly available information on them. This significantly hinders advances towards securing hypercall interfaces. In this work, we provide in-depth technical information on publicly disclosed vulnerabilities of hypercall handlers. Our vulnerability analysis is based on reverse engineering the released patches fixing the considered vulnerabilities. For each analyzed vulnerability, we provide background information essential for understanding the vulnerability, and information on the vulnerable hypercall handler and the error causing the vulnerability. We also show how the vulnerability can be triggered and discuss the state of the targeted hypervisor after the vulnerability has been triggered.

There is one thing one wants after an all-day hike: Hot food and lots of it. Payne discusses cookware for fast cooking and simple cleanup that won't destroy one's budget.