Covering line graphs with equivalence relations

An equivalence graph is a disjoint union of cliques, and the equivalence number $\mathit{eq}(G)$ of a graph $G$ is the minimum number of equivalence subgraphs needed to cover the edges of $G$. We consider the equivalence number of a line graph, giving improved upper and lower bounds: $\frac 13 \log_2\log_2 \chi(G) < \mathit{eq}(L(G)) \leq 2\log_2\log_2 \chi(G) + 2$. This disproves a recent conjecture that $\mathit{eq}(L(G))$ is at most three for triangle-free $G$; indeed it can be arbitrarily large. To bound $\mathit{eq}(L(G))$ we bound the closely-related invariant $\sigma(G)$, which is the minimum number of orientations of $G$ such that for any two edges $e,f$ incident to some vertex $v$, both $e$ and $f$ are oriented out of $v$ in some orientation. When $G$ is triangle-free, $\sigma(G)=\mathit{eq}(L(G))$. We prove that even when $G$ is triangle-free, it is NP-complete to decide whether or not $\sigma(G)\leq 3$.Comment: 10 pages, submitted in July 200

A morphological study of the glomerular lesions in chronic nephritis in the dog

Renal disease is of major importance in the dog, in terms of both morbidity and mortality. However, while the last two decades have seen great advances in the knowledge of Human and certain experimental animal nephropathies, very few in depth investigations of canine renal diseases have been published. In particular, despite the prominence of glomerular injury in many canine nephropathies, this process has largely been ignored. In Part 1 of this thesis, the literature on the most important canine nephropathies*viz; interstitial nephritis, glomerulonephritis, amyloidosis and suppurative nephropathies, was reviewed. An attempt was made to highlight the most important gaps in our knowledge with particular reference to pathogenesis of the lesions and morphological Changes in the glomeruli. The most common cause of renal failure in the dog is Chronic interstitial nephritis. In Part 2 of this thesis the first detailed combined light, electron and immunofluorescence microscopic study was carried out on this nephropathy as it is described in Britain. In addition, elution studies were performed to investigate further the immunopathology of the kidney. The diagnosis of chronic interstitial nephritis was found to cover a heterogeneous group of dogs. Of the 30 cases studied, 24 were probably the result of previous L. canicola infection. The remaining 6 cases appeared less likely to have resulted from L. canicola infection, but no positive evidence emerged to implicate another cause. However all 30 cases were alike in respect of immunopathology; neither autoantibodies nor immune complex deposition played a role in the severe renal scarring that characterized these cases. Recently a morphologically similar nephropathy, chronic glomerulonephritis, has been described in the dog. 10 cases were studied with the same techniques as listed above, and included in Part 2 of this thesis, for a comparative evaluation. In contrast to chronic interstitial nephritis, chronic glomerulonephritis is an immunologically mediated nephropathy. In all cases widespread deposits of immunoglobulin and bound complement were present in the glomeruli. In 9 cases granular deposits were found, a pattern highly suggestive of the involvement of immune complexes. In the remaining case linear deposits were present along the capillary walls a pattern suggestive of the presence of anti-glomerular basement membrane antibodies, but this was not confirmed by the elution studies. Despite this difference in aetiology, both nephropathies were Characterized by the Same progressive scarring and obliteration of the glomeruli. This process was described in detail in Part 2 of this thesis for the first time in the dog. The major components of this process were found to be a) thickening, wrinkling and duplication of both glomerular and capsular basement membranes, b) expansion of the mesangial cells and matrix, c) the deposition of fibrin obliterating capillaries and leading to the formation of capsular adhesions, d) the formation of collagen particularly in the urinary space. Fibrin deposition appeared to play a major role in the progression of glomerular scarring. This concept has been supported by studies on several experimental animal models, but none of this work had ever been carried out on the dog or the results applied to canine nephropathies. Therefore, Part 3 of this thesis was devoted to a combined light, electron and immunofluorescence microscopic study of two experimental canine nephropathies characterized by fibrin deposition in the glomeruli. In the first, a transient period of glomerular thrombosis, resulting from disseminated intravascular coagulation induced by Liquoid (sodium polyanetholsulphonate) injection, was followed by mild focal glomerular scarring. In the second, severe diffuse glomerular scarring followed a prolonged period of extensive fibrin deposition induced by nephrotoxic serum containing anti-glomerular basement membrane antibodies. Thus in both experimental immunological and non-immunological nephropathies glomerular scarring, similar to that encountered in both chronic interstitial nephritis and chronic glomerulonephritis, followed the deposition of fibrin in the glomeruli. This gave credibility to the view that fibrin deposition plays an important role in the progression of glomerular injury and obsolescence in chronic nephropathies of the dog

Simplifying the Development, Use and Sustainability of HPC Software

Developing software to undertake complex, compute-intensive scientific processes requires a challenging combination of both specialist domain knowledge and software development skills to convert this knowledge into efficient code. As computational platforms become increasingly heterogeneous and newer types of platform such as Infrastructure-as-a-Service (IaaS) cloud computing become more widely accepted for HPC computations, scientists require more support from computer scientists and resource providers to develop efficient code and make optimal use of the resources available to them. As part of the libhpc stage 1 and 2 projects we are developing a framework to provide a richer means of job specification and efficient execution of complex scientific software on heterogeneous infrastructure. The use of such frameworks has implications for the sustainability of scientific software. In this paper we set out our developing understanding of these challenges based on work carried out in the libhpc project.Comment: 4 page position paper, submission to WSSSPE13 worksho

www.springerreference.com/docs/html/chapterdbid/60497.html Mechanical Computing: The Computational Complexity of Physical Devices

- Mechanism: A machine or part of a machine that performs a particular task computation: the use of a computer for calculation.- Computable: Capable of being worked out by calculation, especially using a computer.- Simulation: Used to denote both the modeling of a physical system by a computer as well as the modeling of the operation of a computer by a mechanical system; the difference will be clear from the context. Definition of the Subject Mechanical devices for computation appear to be largely displaced by the widespread use of microprocessor-based computers that are pervading almost all aspects of our lives. Nevertheless, mechanical devices for computation are of interest for at least three reasons: (a) Historical: The use of mechanical devices for computation is of central importance in the historical study of technologies, with a history dating back thousands of years and with surprising applications even in relatively recent times. (b) Technical &amp; Practical: The use of mechanical devices for computation persists and has not yet been completely displaced by widespread use of microprocessor-based computers. Mechanical computers have found applications in various emerging technologies at the micro-scale that combine mechanical functions with computational and control functions not feasible by purely electronic processing. Mechanical computers also have been demonstrated at the molecular scale, and may also provide unique capabilities at that scale. The physical designs for these modern micro and molecular-scale mechanical computers may be based on the prior designs of the large-scale mechanical computers constructed in the past. (c) Impact of Physical Assumptions on Complexity of Motion Planning, Design, and Simulation: The study of computation done by mechanical devices is also of central importance in providing lower bounds on the computational resources such as time and/or space required to simulate a mechanical syste

The benzodiazepine class of compounds as a potential for the treatment of cutaneous leishmaniasis

Cutaneous leishmaniasis is endemic in over 70 countries in the tropics and neotropics. Several Leishmania species are the causative agent of this form of the disease and are transmitted to humans and animals by a bite of a phlebotomies sandfly. Antileishmanial drugs including antimonials, Amphotericin B, pentamidine, paromomycin, allupurinol and miltefosine have been the treatment of choice over recent years. However, toxicity, difficulty of administration and emergence of resistance have limited the number of chemotherapeutic options available hence underlying the urgency for the identification of new classes of compounds with antileishmanial activity. The benzodiazepine class of compounds whose core structure entails the fusion of a benzene and diazepine ring have been used over the past 50 years as psychoactive drugs in the treatment of anxiety, insomnia and as an anticonvulsants. The aim of this study was to explore the antileishmanial effects of this class of compounds on stationary phase promastigotes of old and new world Leishmania species (L. aethiopica, L. major, L. tropica and L. mexicana) using the 3-(4,5-dimethylthiazol+2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium(MTS) assay for assessing parasite viability. An array of compounds with modifications brought about at the benzene and diazepine structures were tested over a range of concentrations over a 24-hour period for all species mentioned above. The three most active compounds (RRP223, RRP262 and RRP 199) displayed a different range of activity with inhibition of parasite growth at micromolar range in all 4 species. These findings implicate selective activity and demonstrate Leishmanicidal potential in the benzodiazepine class of compounds

Albedos and diameters of three Mars Trojan asteroids

We observed the Mars Trojan asteroids (5261) Eureka and (101429) 1998 VF31 and the candidate Mars Trojan 2001 FR127 at 11.2 and 18.1 microns using Michelle on the Gemini North telescope. We derive diameters of 1.28, 0.78, and <0.52 km, respectively, with corresponding geometric visible albedos of 0.39, 0.32, and >0.14. The albedos for Eureka and 1998 VF31 are consistent with the taxonomic classes and compositions (S(I)/angritic and S(VII)/achrondritic, respectively) and implied histories presented in a companion paper by Rivkin et al. Eureka's surface likely has a relatively high thermal inertia, implying a thin regolith that is consistent with predictions and the small size that we derive.Comment: Icarus, in press. See companion paper 0709.1925 by Rivkin et al; two minor typos fixe

Performance of Common Analysis Methods for Detecting Low-Frequency Single Nucleotide Variants in Targeted Next-Generation Sequence Data

Next-generation sequencing (NGS) is becoming a common approach for clinical testing of oncology specimens for mutations in cancer genes. Unlike inherited variants, cancer mutations may occur at low frequencies because of contamination from normal cells or tumor heterogeneity and can therefore be challenging to detect using common NGS analysis tools, which are often designed for constitutional genomic studies. We generated high-coverage (>1000×) NGS data from synthetic DNA mixtures with variant allele fractions (VAFs) of 25% to 2.5% to assess the performance of four variant callers, SAMtools, Genome Analysis Toolkit, VarScan2, and SPLINTER, in detecting low-frequency variants. SAMtools had the lowest sensitivity and detected only 49% of variants with VAFs of approximately 25%; whereas the Genome Analysis Toolkit, VarScan2, and SPLINTER detected at least 94% of variants with VAFs of approximately 10%. VarScan2 and SPLINTER achieved sensitivities of 97% and 89%, respectively, for variants with observed VAFs of 1% to 8%, with >98% sensitivity and >99% positive predictive value in coding regions. Coverage analysis demonstrated that >500× coverage was required for optimal performance. The specificity of SPLINTER improved with higher coverage, whereas VarScan2 yielded more false positive results at high coverage levels, although this effect was abrogated by removing low-quality reads before variant identification. Finally, we demonstrate the utility of high-sensitivity variant callers with data from 15 clinical lung cancers

Failure to deactivate the default mode network indicates a possible endophenotype of autism.

BACKGROUND: Reduced activity during cognitively demanding tasks has been reported in the default mode network in typically developing controls and individuals with autism. However, no study has investigated the default mode network (DMN) in first-degree relatives of those with autism (such as siblings) and it is not known whether atypical activation of the DMN is specific to autism or whether it is also present in unaffected relatives. Here we use functional magnetic resonance imaging to investigate the pattern of task-related deactivation during completion of a visual search task, the Embedded Figures Task, in teenagers with autism, their unaffected siblings and typically developing controls. FINDINGS: We identified striking reductions in deactivation during the Embedded Figures Task in unaffected siblings compared to controls in brain regions corresponding to the default mode network. Adolescents with autism and their unaffected siblings similarly failed to deactivate regions, including posterior cingulate and bilateral inferior parietal cortex. CONCLUSIONS: This suggests that a failure to deactivate these regions is a functional endophenotype of autism, related to familial risk for the condition shared between individuals with autism and their siblings.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Structural Racism in the United States: A Report to the U.N. Committee for the Elimination of Racial Discrimination on the occasion of its review of the Periodic Report of the United States of America

As a signatory to the Convention on the Elimination of Racial Discrimination (CERD), 1 the United States is under an obligation to condemn and pursue a policy of eliminating racial discrimination, in all its forms (art. 2, ¶1). The U.S. has not taken seriously the duty under Article 2 of CERD to affirmatively address racial discrimination. Instead, the U.S. has rationalized racial discriminatory effects as not covered by U.S. law. Sometimes these effects are caused by explicit government polices. At other times they are caused by private actors. Frequently, it is a combination of both. The Convention defines racial discrimination (art. 1, ¶1) to mean distinctions, exclusions, restrictions or preferences based on race which have “the purpose or effect” of nullifying or impairing the recognition, enjoyment or exercise, on an equal footing, of human rights and fundamental freedoms in any field of public life. CERD’s definition of discrimination is unequivocal: effects and racially disparate outcomes caused by individual action or government practices or policies, singularly or collectively, are of primary concern. Contrary to CERD, U.S. law defines racial discrimination more narrowly in at least two critical respects. First, with few exceptions U.S. law narrowly defines cognizable racial discrimination by requiring evidence of intent to discriminate. Section II demonstrates that such a requirement is contrary to the framework of CERD and does not reflect the real-world operation of discriminatory behavior in contemporary American society