Quantifying the Rise and Fall of Complexity in Closed Systems: The Coffee Automaton

In contrast to entropy, which increases monotonically, the "complexity" or "interestingness" of closed systems seems intuitively to increase at first and then decrease as equilibrium is approached. For example, our universe lacked complex structures at the Big Bang and will also lack them after black holes evaporate and particles are dispersed. This paper makes an initial attempt to quantify this pattern. As a model system, we use a simple, two-dimensional cellular automaton that simulates the mixing of two liquids ("coffee" and "cream"). A plausible complexity measure is then the Kolmogorov complexity of a coarse-grained approximation of the automaton's state, which we dub the "apparent complexity." We study this complexity measure, and show analytically that it never becomes large when the liquid particles are non-interacting. By contrast, when the particles do interact, we give numerical evidence that the complexity reaches a maximum comparable to the "coffee cup's" horizontal dimension. We raise the problem of proving this behavior analytically

The Bioinformatics Links Directory: a Compilation of Molecular Biology Web Servers

The Bioinformatics Links Directory is an online community resource that contains a directory of freely available tools, databases, and resources for bioinformatics and molecular biology research. The listing of the servers published in this and previous issues of Nucleic Acids Research together with other useful tools and websites represents a rich repository of resources that are openly provided to the research community using internet technologies. The 166 servers highlighted in the 2005 Web Server Issue are included in the more than 700 links to useful online resources that are currently contained within the descriptive biological categories of the Bioinformatics Links Directory. This curated listing of bioinformatics resources is available online at the Bioinformatics Links Directory web site, . A complete listing of the 2005 Nucleic Acids Research Web Server Issue servers is available online at the Nucleic Acids web site, , and on the Bioinformatics Links Directory web site,

Oliguria on the Day of Intubation Is Associated With Mortality in Patients With Acute Respiratory Distress Syndrome

To investigate the relationship between oliguric acute kidney injury (AKI) and mortality in patients with acute respiratory distress syndrome (ARDS). DESIGN: Retrospective cohort study. SETTING: This investigation took place at a single-center, tertiary referral multidisciplinary comprehensive healthcare hospital in metropolitan Detroit, Michigan. PATIENTS: Adult patients 18 years old or older hospitalized in the ICU and diagnosed with ARDS on mechanical ventilation. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Three hundred eight patients were included in the final analysis. Risk factors associated with mortality included advanced age (p \u3c 0.001), increased body mass index (p = 0.008), and a history of chronic kidney disease (p = 0.023). Presence of AKI by day 1 of intubation, with elevated creatinine (p = 0.003) and oliguria (p \u3c 0.001), was significantly associated with mortality. On multivariate analysis, advanced age (relative risk [RR], 1.02), urine output on the day of intubation (RR, 0.388), bicarbonate level (RR, 0.948), and Sequential Organ Failure Assessment severity score (RR, 1.09) were independently associated with mortality. A receiver operating characteristic curve identified a threshold urine output on the day of intubation of 0.7 mL/kg/hr (area under the curve, 0.75; p \u3c 0.001) as most closely associated with inpatient mortality (i.e., urine output \u3c 0.7 mL/kg/hr is associated with mortality). CONCLUSIONS: For patients with ARDS, oliguria on the day of intubation was independently associated with increased mortality. Urine output of less than 0.7 mL/kg/hr predicted 80% of inpatient deaths. These findings herald an augmented understanding of the role of urine output in medical decision-making and prognostication

Increased Adherence and Expression of Virulence Genes in a Lineage of Escherichia coli O157:H7 Commonly Associated with Human Infections

Enterohemorrhagic Escherichia coli (EHEC) O157:H7, a food and waterborne pathogen, can be classified into nine phylogenetically distinct lineages, as determined by single nucleotide polymorphism genotyping. One lineage (clade 8) was found to be associated with hemolytic uremic syndrome (HUS), which can lead to kidney failure and death in some cases, particularly young children. Another lineage (clade 2) differs considerably in gene content and is phylogenetically distinct from clade 8, but caused significantly fewer cases of HUS in a prior study. Little is known, however, about how these two lineages vary with regard to phenotypic traits important for disease pathogenesis and in the expression of shared virulence genes.Here, we quantified the level of adherence to and invasion of MAC-T bovine epithelial cells, and examined the transcriptomes of 24 EHEC O157:H7 strains with varying Shiga toxin profiles from two common lineages. Adherence to epithelial cells was >2-fold higher for EHEC O157:H7 strains belonging to clade 8 versus clade 2, while no difference in invasiveness was observed between the two lineages. Whole-genome 70-mer oligo microarrays, which probe for 6088 genes from O157:H7 Sakai, O157:H7 EDL 933, pO157, and K12 MG1655, detected significant differential expression between clades in 604 genes following co-incubation with epithelial cells for 30 min; 186 of the 604 genes had a >1.5 fold change difference. Relative to clade 2, clade 8 strains showed upregulation of major virulence genes, including 29 of the 41 locus of enterocyte effacement (LEE) pathogenicity island genes, which are critical for adherence, as well as Shiga toxin genes and pO157 plasmid-encoded virulence genes. Differences in expression of 16 genes that encode colonization factors, toxins, and regulators were confirmed by qRT-PCR, which revealed a greater magnitude of change than microarrays.These findings demonstrate that the EHEC O157:H7 lineage associated with HUS expresses higher levels of virulence genes and has an enhanced ability to attach to epithelial cells relative to another common lineage

A Critical Examination of the X-Wind Model for Chondrule and Calcium-rich, Aluminum-rich Inclusion Formation and Radionuclide Production

Meteoritic data, especially regarding chondrules and calcium-rich, aluminum-rich inclusions (CAIs), and isotopic evidence for short-lived radionuclides (SLRs) in the solar nebula, potentially can constrain how planetary systems form. Intepretation of these data demands an astrophysical model, and the "X-wind" model of Shu et al. (1996) and collaborators has been advanced to explain the origin of chondrules, CAIs and SLRs. It posits that chondrules and CAIs were thermally processed < 0.1 AU from the protostar, then flung by a magnetocentrifugal outflow to the 2-3 AU region to be incorporated into chondrites. Here we critically examine key assumptions and predictions of the X-wind model. We find a number of internal inconsistencies: theory and observation show no solid material exists at 0.1 AU; particles at 0.1 AU cannot escape being accreted into the star; particles at 0.1 AU will collide at speeds high enough to destroy them; thermal sputtering will prevent growth of particles; and launching of particles in magnetocentrifugal outflows is not modeled, and may not be possible. We also identify a number of incorrect predictions of the X-wind model: the oxygen fugacity where CAIs form is orders of magnitude too oxidizing; chondrule cooling rates are orders of magnitude lower than those experienced by barred olivine chondrules; chondrule-matrix complementarity is not predicted; and the SLRs are not produced in their observed proportions. We conclude that the X-wind model is not relevant to chondrule and CAI formation and SLR production. We discuss more plausible models for chondrule and CAI formation and SLR production.Comment: Accepted for publication in The Astrophysical Journa

The Chlamydia effector TarP mimics the mammalian leucine-aspartic acid motif of paxillin to subvert the focal adhesion kinase during invasion

Host cell signal transduction pathways are often targets of bacterial pathogens, especially during the process of invasion when robust actin remodeling is required. We demonstrate that the host cell focal adhesion kinase (FAK) was necessary for the invasion by the obligate intracellular pathogen Chlamydia caviae. Bacterial adhesion triggered the transient recruitment of FAK to the plasma membrane to mediate a Cdc42- and Arp2/3-dependent actin assembly. FAK recruitment was via binding to a domain within the virulence factor TarP that mimicked the LD2 motif of the FAK binding partner paxillin. Importantly, bacterial two-hybrid and quantitative imaging assays revealed a similar level of interaction between paxillin-LD2 and TarP-LD. The conserved leucine residues within the L(D/E)XLLXXL motif were essential to the recruitment of FAK, Cdc42, p34Arc, and actin to the plasma membrane. In the absence of FAK, TarP-LD-mediated F-actin assembly was reduced, highlighting the functional relevance of this interaction. Together, the data indicate that a prokaryotic version of the paxillin LD2 domain targets the FAK signaling pathway, with TarP representing the first example of an LD-containing Type III virulence effector

Operational Research in Education

Operational Research (OR) techniques have been applied, from the early stages of the discipline, to a wide variety of issues in education. At the government level, these include questions of what resources should be allocated to education as a whole and how these should be divided amongst the individual sectors of education and the institutions within the sectors. Another pertinent issue concerns the efficient operation of institutions, how to measure it, and whether resource allocation can be used to incentivise efficiency savings. Local governments, as well as being concerned with issues of resource allocation, may also need to make decisions regarding, for example, the creation and location of new institutions or closure of existing ones, as well as the day-to-day logistics of getting pupils to schools. Issues of concern for managers within schools and colleges include allocating the budgets, scheduling lessons and the assignment of students to courses. This survey provides an overview of the diverse problems faced by government, managers and consumers of education, and the OR techniques which have typically been applied in an effort to improve operations and provide solutions

Multiple Mutations in Heterogeneous Miltefosine-Resistant Leishmania major Population as Determined by Whole Genome Sequencing

Leishmania spp. are parasitic protozoa responsible for a spectrum of diseases known as leishmaniasis. There are few drugs available for the treatment of these diseases, and miltefosine is the first oral drug used in treatment of visceral leishmaniasis, a form of the disease that can be lethal if not treated. In this study, we seek to understand the mechanism of action and identify targets of the drug by generating promastigote mutants highly resistant to miltefosine. Two independent mutants were submitted to short read whole genome sequencing. Genome analysis of these mutants has permitted us to identify point mutations in three genes (P-type ATPase, pyridoxal kinase and α-adaptin like protein) that were also present in other independent miltefosine resistant mutants. Some of the new genes identified here could be useful as potential markers for miltefosine resistance in Leishmania. Moreover, our approach has permitted us to highlight that resistance can be highly heterogeneous at the population level with individual clones derived from this population differing both in terms of genotypes but also susceptibility phenotypes. This may have practical applications while studying resistance