File Fragmentation over an Unreliable Channel

It has been recently discovered that heavy-tailed file completion time can result from protocol interaction even when file sizes are light-tailed. A key to this phenomenon is the RESTART feature where if a file transfer is interrupted before it is completed, the transfer needs to restart from the beginning. In this paper, we show that independent or bounded fragmentation guarantees light-tailed file completion time as long as the file size is light-tailed, i.e., in this case, heavy-tailed file completion time can only originate from heavy-tailed file sizes. If the file size is heavy-tailed, then the file completion time is necessarily heavy-tailed. For this case, we show that when the file size distribution is regularly varying, then under independent or bounded fragmentation, the completion time tail distribution function is asymptotically upper bounded by that of the original file size stretched by a constant factor. We then prove that if the failure distribution has non-decreasing failure rate, the expected completion time is minimized by dividing the file into equal sized fragments; this optimal fragment size is unique but depends on the file size. We also present a simple blind fragmentation policy where the fragment sizes are constant and independent of the file size and prove that it is asymptotically optimal. Finally, we bound the error in expected completion time due to error in modeling of the failure process

Regulation of peptide import through phosphorylation of Ubr1, the ubiquitin ligase of the N-end rule pathway

Substrates of the N-end rule pathway include proteins with destabilizing N-terminal residues. These residues are recognized by E3 ubiquitin ligases called N-recognins. Ubr1 is the N-recognin of the yeast Saccharomyces cerevisiae. Extracellular amino acids or short peptides up-regulate the peptide transporter gene PTR2, thereby increasing the capacity of a cell to import peptides. Cup9 is a transcriptional repressor that down-regulates PTR2. The induction of PTR2 by peptides or amino acids involves accelerated degradation of Cup9 by the N-end rule pathway. We report here that the Ubr1 N-recognin, which conditionally targets Cup9 for degradation, is phosphorylated in vivo at multiple sites, including Ser300 and Tyr277. We also show that the type-I casein kinases Yck1 and Yck2 phosphorylate Ubr1 on Ser300, and thereby make possible (“prime”) the subsequent (presumably sequential) phosphorylations of Ubr1 on Ser296, Ser292, Thr288, and Tyr277 by Mck1, a kinase of the glycogen synthase kinase 3 (Gsk3) family. Phosphorylation of Ubr1 on Tyr277 by Mck1 is a previously undescribed example of a cascade-based tyrosine phosphorylation by a Gsk3-type kinase outside of autophosphorylation. We show that the Yck1/Yck2-mediated phosphorylation of Ubr1 on Ser300 plays a major role in the control of peptide import by the N-end rule pathway. In contrast to phosphorylation on Ser300, the subsequent (primed) phosphorylations, including the one on Tyr277, have at most minor effects on the known properties of Ubr1, including regulation of peptide import. Thus, a biological role of the rest of Ubr1 phosphorylation cascade remains to be identified

Compact medical fluorosensor for minimally invasive tissue characterization

A compact fiber-optic point-measuring fluorosensor fully adapted to clinical studies is described. The system can use two excitation wavelengths, 337 and 405 nm, obtained from a nitrogen laser directly, or after dye laser conversion, respectively. The image intensifier used in the spectrometer can be gated with a variable time delay, allowing also time-resolved spectra to be extracted, with a time resolution of about 4 ns. Moreover, diffusely scattered white light can be spectrally recorded. The system is fully computer controlled enabling short recording times in clinical application, which are illustrated

Proinflammatory Protein Signatures in Cryptogenic and Large Artery Atherosclerosis Stroke

Objectives: The cause of ischemic stroke remains unknown, cryptogenic, in 25% of young and middle‐aged patients. We hypothesized that if atherosclerosis is prominent in cryptogenic stroke, it would have a similar proinflammatory protein signature as large artery atherosclerosis (LAA) stroke. Materials & Methods: Blood was collected in the acute phase and after 3 months from cryptogenic (n = 162) and LAA (n = 73) stroke patients aged 18–69 years and once from age‐matched controls (n = 235). Cryptogenic stroke was divided into Framingham Risk Score (FRS) quartiles to compare low and high risk of atherosclerosis. Plasma concentrations of 25 proteins were analyzed using a Luminex multiplex assay. The discriminating properties were assessed with discriminant analysis and C‐statistics. Results: We identified proteins that separated cryptogenic and LAA stroke from controls (area under the curves, AUCs ≥ 0.85). For both subtypes, RANTES, IL‐4, and IFN‐γ contributed the most at both time points. These associations were independent of risk factors of atherosclerosis. We also identified proteins that separated cryptogenic strokes in the lowest quartile of FRS from those in the highest, and from LAA stroke (AUCs ≥ 0.76), and here eotaxin and MCP‐1 contributed the most. Conclusions: The protein signature separating cases from controls was different from the signature separating cryptogenic stroke with low risk of atherosclerosis from those with high risk and from LAA stroke. This suggests that increased RANTES, IL‐4, and IFN‐γ in stroke may not be primarily related to atherosclerosis, whereas increased eotaxin and MCP‐1 in cryptogenic stroke may be markers of occult atherosclerosis as the underlying cause

On Channel Failures, File Fragmentation Policies, and Heavy-Tailed Completion Times

It has been recently discovered that heavy-tailed completion times can result from protocol interaction even when file sizes are light-tailed. A key to this phenomenon is the use of a restart policy where if the file is interrupted before it is completed, it needs to restart from the beginning. In this paper, we show that fragmenting a file into pieces whose sizes are either bounded or independently chosen after each interruption guarantees light-tailed completion time as long as the file size is light-tailed; i.e., in this case, heavy-tailed completion time can only originate from heavy-tailed file sizes. If the file size is heavy-tailed, then the completion time is necessarily heavy-tailed. For this case, we show that when the file size distribution is regularly varying, then under independent or bounded fragmentation, the completion time tail distribution function is asymptotically bounded above by that of the original file size stretched by a constant factor. We then prove that if the distribution of times between interruptions has nondecreasing failure rate, the expected completion time is minimized by dividing the file into equal-sized fragments; this optimal fragment size is unique but depends on the file size. We also present a simple blind fragmentation policy where the fragment sizes are constant and independent of the file size and prove that it is asymptotically optimal. Both these policies are also shown to have desirable completion time tail behavior. Finally, we bound the error in expected completion time due to error in modeling of the failure process

Circulating granulocyte colony-stimulating factor and functional outcome after ischemic stroke: an observational study

Objectives: While granulocyte colony-stimulating factor (G-CSF) has shown beneficial effects in experimental ischemic stroke (IS), these effects have not been reproduced clinically. Small-to-medium-sized observational studies have reported varying associations for G-CSF with stroke severity and post-stroke functional outcome, prompting their investigation in a larger study. Methods: Endogenous serum G-CSF (S-GCSF) was measured in the acute phase and after 3 months in patients with IS (N = 435; 36% females; mean age, 57 years) from the Sahlgrenska Academy Study on Ischemic Stroke (SAHLSIS). Stroke severity was scored according to the National Institutes of Health Stroke Scale (NIHSS), and the modified Rankin Scale (mRS) assessed functional outcomes at 3-month and 2-year post-stroke. Correlation and logistic regression analyses with confounder adjustments assessed the relationships. Results: The acute S-GCSF level was 23% higher than at 3-month post-stroke (p < 0.001). Acute G-CSF correlated weakly with stroke severity quintiles (r = 0.12, p = 0.013) and with high-sensitivity C-reactive protein (r = 0.29, p < 0.001). The association between S-GCSF (as quintiles, q) and poor functional outcome at 3 months (mRS 3–6; S-GCSF-q5 vs. S-GCSF-q1, age- and sex-adjusted odds ratio: 4.27, 95% confidence interval: 1.82–9.99; p = 0.001) withstood adjustment for cardiovascular risk factors and stroke subtype, but not additional correction for stroke severity. Post-stroke changes in S-GSCF and absolute 3-month S-GCSF were not associated with 3-month or 2-year functional outcomes. Discussion: Early post-stroke S-GCSF is increased in severe IS and associated with 3-month poor functional outcomes. The change in S-GCSF and the 3-month S-GCSF appear to be less-important, and S-GCSF likely reflects inflammation in large infarctions

Plasma pyroglutamate-modified amyloid beta differentiates amyloid pathology

INTRODUCTION: Pyroglutamate‐modified amyloid β (Aβ_{pE3}) could be a biomarker for Aβ plaque pathology in the brain. An ultra‐high‐sensitive assay is needed for detecting Aβ_{pE3-40}. METHODS: mmunomagnetic reduction was used for quantification of Aβ_{pE3-40} in plasma from 46 participants. The concentrations of Aβ_{pE3-40} of these subjects were compared with 18F‐florbetapir positron emission tomography (PET) images. RESULTS: Aβ_{pE3-40} concentration was 44.1 ± 28.2 fg/mL in PET‐ (n = 28) and 91.6 ± 54.6 fg/mL in PET+ (n = 18; P < .05). The cutoff value of Aβ_{pE3-40} for discriminating PET‐ from PET+ was 55.5 fg/mL, resulting in a sensitivity of 83.3%, a specificity of 71.4%. The concentration of Aβ_{pE3-40} showed a moderate correlation (r = 0.437) with PET standardized uptake value ratio. DISCUSSION: We did not enroll pre‐clinical AD subject with normal cognition but Aβ PET+. It would be an important issue to explore the feasibility of using Aβ_{pE3-40} for screening pre‐clinical subjects. CONCLUSION: These results reveal the feasibility of detecting Aβ pathology using quantification of a plaque‐derived Aβ molecule in plasma

Circulating levels of vascular endothelial growth factor and post-stroke long-term functional outcome

OBJECTIVES: Vascular endothelial growth factor (VEGF) acts in angiogenesis and neuroprotection, although the beneficial effects on experimental ischemic stroke (IS) have not been replicated in clinical studies. We investigated serum VEGF (s-VEGF) in the acute stage (baseline) and 3 months post-stroke in relation to stroke severity and functional outcome. METHODS: The s-VEGF and serum high-sensitivity C-reactive protein (hs-CRP) concentrations were measured in patients enrolled in the Sahlgrenska Academy Study on Ischemic Stroke (SAHLSIS) at the acute time-point (median 4 days, N=492, 36% female; mean age, 57 years) and at 3 months post-stroke (N=469). Baseline stroke severity was classified according to the National Institutes of Health Stroke Scale (NIHSS) and functional outcomes (3 months and 2 years) were evaluated using the modified Rankin Scale (mRS), dichotomized into good (mRS 0-2) and poor (mRS 3-6) outcomes. Multivariable logistic regression analyses were adjusted for covariates. RESULTS: The baseline s-VEGF did not correlate with stroke severity but correlated moderately with hs-CRP (r=0.17, p<0.001). The baseline s-VEGF was 39.8% higher in total anterior cerebral infarctions than in lacunar cerebral infarctions. In binary logistic regression analysis, associations with 3-month functional outcome were non-significant. However, an association between the 3-month s-VEGF and poor 2-year outcome withstood adjustments for age, sex, cardiovascular covariates, and stroke severity (per ten-fold increase in s-VEGF, odds ratio [OR], 2.56, 95% confidence interval [CI] 1.12-5.82) or hs-CRP (OR 2.53, CI 1.15-5.55). CONCLUSIONS: High 3-month s-VEGF is independently associated with poor 2-year functional outcome but not with 3-month outcome

Gravastar energy conditions revisited

We consider the gravastar model where the vacuum phase transition between the de Sitter interior and the Schwarzschild or Schwarzschild-de Sitter exterior geometries takes place at a single spherical delta-shell. We derive sharp analytic bounds on the surface compactness (2m/r) that follow from the requirement that the dominant energy condition (DEC) holds at the shell. In the case of Schwarzschild exterior, the highest surface compactness is achieved with the stiff shell in the limit of vanishing (dark) energy density in the interior. In the case of Schwarzschild-de Sitter exterior, in addition to the gravastar configurations with the shell under surface pressure, gravastar configurations with vanishing shell pressure (dust shells), as well as configurations with the shell under surface tension, are allowed by the DEC. Respective bounds on the surface compactness are derived for all cases. We also consider the speed of sound on the shell as derived from the requirement that the shell is stable against the radial perturbations. The causality requirement (sound speed not exceeding that of light) further restricts the space of allowed gravastar configurations.Comment: LaTeX/IOP-style, 16 pages, 2 figures, changes wrt v1: motivation for eq. (6) clarified, several referecnes added (to appear in Class. Quantum Grav.

Translational Medicine and Patient Safety in Europe:TRANSFoRm - Architecture for the Learning Health System in Europe

The Learning Health System (LHS) describes linking routine healthcare systems directly with both research translation and knowledge translation as an extension of the evidence-based medicine paradigm, taking advantage of the ubiquitous use of electronic health record (EHR) systems. TRANSFoRm is an EU FP7 project that seeks to develop an infrastructure for the LHS in European primary care. Methods. The project is based on three clinical use cases, a genotype-phenotype study in diabetes, a randomised controlled trial with gastroesophageal reflux disease, and a diagnostic decision support system for chest pain, abdominal pain, and shortness of breath. Results. Four models were developed (clinical research, clinical data, provenance, and diagnosis) that form the basis of the projects approach to interoperability. These models are maintained as ontologies with binding of terms to define precise data elements. CDISC ODM and SDM standards are extended using an archetype approach to enable a two-level model of individual data elements, representing both research content and clinical content. Separate configurations of the TRANSFoRm tools serve each use case. Conclusions. The project has been successful in using ontologies and archetypes to develop a highly flexible solution to the problem of heterogeneity of data sources presented by the LHS