Profiling Distributed Virtual Environments by Tracing Causality

Real-time interactive systems such as virtual environments have high performance requirements, and profiling is a key part of the optimisation process to meet them. Traditional techniques based on metadata and static analysis have difficulty following causality in asynchronous systems. In this paper we explore a new technique for such systems. Timestamped samples of the system state are recorded at instrumentation points at runtime. These are assembled into a graph, and edges between dependent samples recovered. This approach minimises the invasiveness of the instrumentation, while retaining high accuracy. We describe how our instrumentation can be implemented natively in common environments, how its output can be processed into a graph describing causality, and how heterogeneous data sources can be incorporated into this to maximise the scope of the profiling. Across three case studies, we demonstrate the efficacy of this approach, and how it supports a variety of metrics for comprehensively bench-marking distributed virtual environments

Cytosolic thioredoxin reductase 1 is required for correct disulfide formation in the ER

Folding of proteins entering the secretory pathway in mammalian cells frequently requires the insertion of disulfide bonds. Disulfide insertion can result in covalent linkages found in the native structure as well as those that are not, so‐called non‐native disulfides. The pathways for disulfide formation are well characterized, but our understanding of how non‐native disulfides are reduced so that the correct or native disulfides can form is poor. Here, we use a novel assay to demonstrate that the reduction in non‐native disulfides requires NADPH as the ultimate electron donor, and a robust cytosolic thioredoxin system, driven by thioredoxin reductase 1 (TrxR1 or TXNRD1). Inhibition of this reductive pathway prevents the correct folding and secretion of proteins that are known to form non‐native disulfides during their folding. Hence, we have shown for the first time that mammalian cells have a pathway for transferring reducing equivalents from the cytosol to the ER, which is required to ensure correct disulfide formation in proteins entering the secretory pathway

Type Ia supernovae with and without blueshifted narrow Na I D lines - how different is their structure?

In studies on intermediate- and high-resolution spectra of Type Ia supernovae (SNe Ia), some objects exhibit narrow Na I D absorptions often blueshifted with respect to the rest wavelength within the host galaxy. The absence of these in other SNe Ia may reflect that the explosions have different progenitors: blueshifted Na I D features might be explained by the outflows of ‘single-degenerate’ systems (binaries of a white dwarf with a non-degenerate companion). In this work, we search for systematic differences among SNe Ia for which the Na I D characteristics have been clearly established in previous studies. We perform an analysis of the chemical abundances in the outer ejecta of 13 ‘spectroscopically normal’ SNe Ia (five of which show blueshifted Na lines), modelling time series of photospheric spectra with a radiative-transfer code. We find only moderate differences between ‘blueshifted-Na’, ‘redshifted-Na’ and ‘no-Na’ SNe Ia, so that we can neither conclusively confirm a ‘one-scenario’ nor a ‘two-scenario’ theory for normal SNe Ia. Yet, some of the trends we see should be further studied using larger observed samples: models for blueshifted-Na SNe tend to show higher photospheric velocities than no-Na SNe, corresponding to a higher opacity of the envelope. Consistently, blueshifted-Na SNe show hints of a somewhat larger iron-group content in the outer layers with respect to the no-Na subsample (and also to the redshifted-Na subsample). This agrees with earlier work where it was found that the light curves of no-Na SNe – often appearing in elliptical galaxies – are narrower, that is, decline more rapidly

Effective Holographic Theories for low-temperature condensed matter systems

The IR dynamics of effective holographic theories capturing the interplay between charge density and the leading relevant scalar operator at strong coupling are analyzed. Such theories are parameterized by two real exponents $(\gamma,\delta)$ that control the IR dynamics. By studying the thermodynamics, spectra and conductivities of several classes of charged dilatonic black hole solutions that include the charge density back reaction fully, the landscape of such theories in view of condensed matter applications is characterized. Several regions of the $(\gamma,\delta)$ plane can be excluded as the extremal solutions have unacceptable singularities. The classical solutions have generically zero entropy at zero temperature, except when $\gamma=\delta$ where the entropy at extremality is finite. The general scaling of DC resistivity with temperature at low temperature, and AC conductivity at low frequency and temperature across the whole $(\gamma,\delta)$ plane, is found. There is a codimension-one region where the DC resistivity is linear in the temperature. For massive carriers, it is shown that when the scalar operator is not the dilaton, the DC resistivity scales as the heat capacity (and entropy) for planar (3d) systems. Regions are identified where the theory at finite density is a Mott-like insulator at T=0. We also find that at low enough temperatures the entropy due to the charge carriers is generically larger than at zero charge density.Comment: (v3): Added discussion on the UV completion of the solutions, and on extremal spectra in the charged case. Expanded discusion on insulating extremal solutions. Many other refinements and corrections. 126 pages. 48 figure

Mechanical compression attenuates normal human bronchial epithelial wound healing

Background: Airway narrowing associated with chronic asthma results in the transmission of injurious compressive forces to the bronchial epithelium and promotes the release of pro-inflammatory mediators and the denudation of the bronchial epithelium. While the individual effects of compression or denudation are well characterized, there is no data to elucidate how these cells respond to the application of mechanical compression in the presence of a compromised epithelial layer. Methods: Accordingly, differentiated normal human bronchial epithelial cells were exposed to one of four conditions: 1) unperturbed control cells, 2) single scrape wound only, 3) static compression (6 hours of 30 cmH(2)O), and 4) 6 hours of static compression after a scrape wound. Following treatment, wound closure rate was recorded, media was assayed for mediator content and the cytoskeletal network was fluorescently labeled. Results: We found that mechanical compression and scrape injury increase TGF-beta 2 and endothelin-1 secretion, while EGF content in the media is attenuated with both injury modes. The application of compression after a pre-existing scrape wound augmented these observations, and also decreased PGE(2) media content. Compression stimulated depolymerization of the actin cytoskeleton and significantly attenuated wound healing. Closure rate was partially restored with the addition of exogenous PGE(2), but not EGF. Conclusion: Our results suggest that mechanical compression reduces the capacity of the bronchial epithelium to close wounds, and is, in part, mediated by PGE(2) and a compromised cytoskeleton

Pathomechanisms of ulnar ligament lesions of the wrist in a cadaveric distal radius fracture model

Background and purpose: Mechanisms of injury to ulnar sided ligaments, stabilizing the distal radioulnar joint and the ulna to the carpus, associated with dorsally displaced distal radius fractures are poorly described. We investigated the injury patterns in a human cadaver fracture model. Methods: Fresh frozen human cadaver arms were used. A dorsal open wedge osteotomy was made in the distal radius. In 8 specimens pressure was applied to the palm with the wrist in dorsiflexion and ulnar sided stabilizing structures subsequently severed. Dorsal angulation was measured on digitized radiographs. In 8 more specimens the triangular fibrocartilage complex was forced into rupture by axially loading the forearm with the wrist in dorsiflexion. The ulnar side was dissected and injuries were recorded. Results: Intact ulnar soft tissues limited the dorsal angulation of the distal radius fragment to a median of 32o (16-34o). A combination of bending and shearing of the distal radius fragment was needed to create TFCC injuries. Both palmar and dorsal injuries were observed simultaneously in 6/8 specimens. Interpretation: A TFCC injury can be expected when dorsal angulation of a distal radius fracture exceeds 32o. The extensor carpi ulnaris subsheath may be a functionally integral part of the TFCC. Both dorsal and palmar structures can tear simultaneously. These findings may have implications for reconstruction of ulnar sided soft tissue injuries

Systematic review and meta-analysis of the diagnostic accuracy of ultrasonography for deep vein thrombosis

Background Ultrasound (US) has largely replaced contrast venography as the definitive diagnostic test for deep vein thrombosis (DVT). We aimed to derive a definitive estimate of the diagnostic accuracy of US for clinically suspected DVT and identify study-level factors that might predict accuracy. Methods We undertook a systematic review, meta-analysis and meta-regression of diagnostic cohort studies that compared US to contrast venography in patients with suspected DVT. We searched Medline, EMBASE, CINAHL, Web of Science, Cochrane Database of Systematic Reviews, Cochrane Controlled Trials Register, Database of Reviews of Effectiveness, the ACP Journal Club, and citation lists (1966 to April 2004). Random effects meta-analysis was used to derive pooled estimates of sensitivity and specificity. Random effects meta-regression was used to identify study-level covariates that predicted diagnostic performance. Results We identified 100 cohorts comparing US to venography in patients with suspected DVT. Overall sensitivity for proximal DVT (95% confidence interval) was 94.2% (93.2 to 95.0), for distal DVT was 63.5% (59.8 to 67.0), and specificity was 93.8% (93.1 to 94.4). Duplex US had pooled sensitivity of 96.5% (95.1 to 97.6) for proximal DVT, 71.2% (64.6 to 77.2) for distal DVT and specificity of 94.0% (92.8 to 95.1). Triplex US had pooled sensitivity of 96.4% (94.4 to 97.1%) for proximal DVT, 75.2% (67.7 to 81.6) for distal DVT and specificity of 94.3% (92.5 to 95.8). Compression US alone had pooled sensitivity of 93.8 % (92.0 to 95.3%) for proximal DVT, 56.8% (49.0 to 66.4) for distal DVT and specificity of 97.8% (97.0 to 98.4). Sensitivity was higher in more recently published studies and in cohorts with higher prevalence of DVT and more proximal DVT, and was lower in cohorts that reported interpretation by a radiologist. Specificity was higher in cohorts that excluded patients with previous DVT. No studies were identified that compared repeat US to venography in all patients. Repeat US appears to have a positive yield of 1.3%, with 89% of these being confirmed by venography. Conclusion Combined colour-doppler US techniques have optimal sensitivity, while compression US has optimal specificity for DVT. However, all estimates are subject to substantial unexplained heterogeneity. The role of repeat scanning is very uncertain and based upon limited data

Identification of diarrheagenic Escherichia coli isolated from infants and children in Dar es Salaam, Tanzania

<p>Abstract</p> <p>Background</p> <p>Relatively few studies have been done in Tanzania to detect and classify diarrheagenic <it>Escherichia coli </it>(DEC) strains among children with diarrhea. This study aimed at investigating DEC among children in Dar es Salaam aged less than five years hospitalized due to acute/persistent diarrhea.</p> <p>Methods</p> <p>DEC were isolated from stool samples collected from two hundred and eighty children with acute/persistent diarrhea at Muhimbili National Hospital and Ilala and Mwananyamala Municipal Hospitals in Dar es Salaam. A multiplex PCR system method was used to detect a species specific gene for <it>E.coli </it>and ten different virulence genes for detection of five pathogroups of DEC namely enteroaggregative- (EAEC), enteropathogenic- (EPEC), enterotoxigenic- (ETEC), enteroinvasive- (EIEC) and enterohemorghagic- <it>Escherichia coli </it>(EHEC).</p> <p>Results</p> <p>Sixty-four patients (22.9%) harbored DEC. Forty-one of them (14.6%) were categorized as EAEC. Most of the EAEC (82.9%) were classified as typical EAEC possessing the <it>aggR </it>gene, and 92.6% carried the <it>aat </it>gene. Isolates from thirteen patients were EPEC (4.6%) and most of these (92.3%) were typical EPEC with both <it>eae </it>and <it>bfpA </it>genes. Ten isolates were identified as ETEC (3.6%) with only the heat stable toxin; either <it>st1a </it>or <it>st1b </it>but not both. Age wise, EAEC and EPEC were significantly more prevalent among the age group 0–6 months (p < 0.05). Genes for EHEC (<it>stx</it>₁and <it>stx</it>₂) and EIEC <it>(ial</it>) were not detected in this study group.</p> <p>Conclusion</p> <p>The results show a high proportion of DEC among Tanzanian children with diarrhea, with typical EAEC and typical EPEC predominating. The use of primers for both variants of ST1 (st1a and st1b) increased the sensitivity for detection of ETEC strains.</p

Filaggrin Genotype Determines Functional and Molecular Alterations in Skin of Patients with Atopic Dermatitis and Ichthyosis Vulgaris

BACKGROUND: Several common genetic and environmental disease mechanisms are important for the pathophysiology behind atopic dermatitis (AD). Filaggrin (FLG) loss-of-function is of great significance for barrier impairment in AD and ichthyosis vulgaris (IV), which is commonly associated with AD. The molecular background is, however, complex and various clusters of genes are altered, including inflammatory and epidermal-differentiation genes. OBJECTIVE: The objective was to study whether the functional and molecular alterations in AD and IV skin depend directly on FLG loss-of-function, and whether FLG genotype determines the type of downstream molecular pathway affected. METHODS AND FINDINGS: Patients with AD/IV (n = 43) and controls (n = 15) were recruited from two Swedish outpatient clinics and a Swedish AD family material with known FLG genotype. They were clinically examined and their medical history recorded using a standardized questionnaire. Blood samples and punch biopsies were taken and trans-epidermal water loss (TEWL) and skin pH was assessed with standard techniques. In addition to FLG genotyping, the STS gene was analyzed to exclude X-linked recessive ichthyosis (XLI). Microarrays and quantitative real-time PCR were used to compare differences in gene expression depending on FLG genotype. Several different signalling pathways were altered depending on FLG genotype in patients suffering from AD or AD/IV. Disease severity, TEWL and pH follow FLG deficiency in the skin; and the number of altered genes and pathways are correlated to FLG mRNA expression. CONCLUSIONS: We emphasize further the role of FLG in skin-barrier integrity and the complex compensatory activation of signalling pathways. This involves inflammation, epidermal differentiation, lipid metabolism, cell signalling and adhesion in response to FLG-dependent skin-barrier dysfunction

Observational and Physical Classification of Supernovae

This chapter describes the current classification scheme of supernovae (SNe). This scheme has evolved over many decades and now includes numerous SN Types and sub-types. Many of these are universally recognized, while there are controversies regarding the definitions, membership and even the names of some sub-classes; we will try to review here the commonly-used nomenclature, noting the main variants when possible. SN Types are defined according to observational properties; mostly visible-light spectra near maximum light, as well as according to their photometric properties. However, a long-term goal of SN classification is to associate observationally-defined classes with specific physical explosive phenomena. We show here that this aspiration is now finally coming to fruition, and we establish the SN classification scheme upon direct observational evidence connecting SN groups with specific progenitor stars. Observationally, the broad class of Type II SNe contains objects showing strong spectroscopic signatures of hydrogen, while objects lacking such signatures are of Type I, which is further divided to numerous subclasses. Recently a class of super-luminous SNe (SLSNe, typically 10 times more luminous than standard events) has been identified, and it is discussed. We end this chapter by briefly describing a proposed alternative classification scheme that is inspired by the stellar classification system. This system presents our emerging physical understanding of SN explosions, while clearly separating robust observational properties from physical inferences that can be debated. This new system is quantitative, and naturally deals with events distributed along a continuum, rather than being strictly divided into discrete classes. Thus, it may be more suitable to the coming era where SN numbers will quickly expand from a few thousands to millions of events.Comment: Extended final draft of a chapter in the "SN Handbook". Comments most welcom