SIFTER search: a web server for accurate phylogeny-based protein function prediction.

We are awash in proteins discovered through high-throughput sequencing projects. As only a minuscule fraction of these have been experimentally characterized, computational methods are widely used for automated annotation. Here, we introduce a user-friendly web interface for accurate protein function prediction using the SIFTER algorithm. SIFTER is a state-of-the-art sequence-based gene molecular function prediction algorithm that uses a statistical model of function evolution to incorporate annotations throughout the phylogenetic tree. Due to the resources needed by the SIFTER algorithm, running SIFTER locally is not trivial for most users, especially for large-scale problems. The SIFTER web server thus provides access to precomputed predictions on 16 863 537 proteins from 232 403 species. Users can explore SIFTER predictions with queries for proteins, species, functions, and homologs of sequences not in the precomputed prediction set. The SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded

lHuman cytotoxic T lymphocytes with reduced sensitivity to Fas-induced apoptosis

Effector-memory T cells expressing Fas (Apo-1/CD95) are switched to an apoptotic program by cross-linking with Fas-ligand (FasL). Consequently, tumors that express FasL can induce apoptosis of infiltrating Fas-positive T lymphocytes and subdue any antitumor host immune response. Since Epstein-Barr virus (EBV)-associated tumors such as Hodgkin lymphoma (HL) and nasopharyngeal carcinoma (NPC) express FasL, we determined whether EBV-specific cytotoxic T lymphocytes (EBV-CTLs) could be modified to resist this evasion strategy. We show that long-term down-modulation of Fas can be achieved in EBV-CTLs by transduction with small interfering RNA (siRNA) encoded in a retrovirus. Modified T cells resisted Fas/FasL-mediated apoptosis compared with control cells and showed minimal cleavage of the caspase3 substrate poly(ADP-ribose) polymerase (PARP) protein after Fas engagement. Prolonged Fas stimulation selected a uniformly Fas(low) and FasL resistant population. Removal of responsiveness to this single death signal had no other discernible effects on EBV-CTLs. In particular, it did not lead to their autonomous growth since the modified EBV-CTLs remained polyclonal, and their survival and proliferation retained dependence on antigen-specific stimulation and on the presence of other physiologic growth signals. EBV-CTLs with knocked down Fas should have a selective functional and survival advantage over unmodified EBV-CTLs in the presence of tumors expressing FasL and may be of value for adoptive cellular therapy. (c) 2005 by The American Society of Hematology

From secondary to primary prevention of progressive renal disease: The case for screening for albuminuria

From secondary to primary prevention of progressive renal disease: The case for screening for albuminuria. Many subjects nowadays present with end-stage renal failure and its attendant cardiovascular complications without known prior renal damage. In this report we review the evidence available to strongly suggest that the present practice of secondary prevention in those with known prior renal disease should be extended to primary prevention for those subjects in the general population who are at risk for progressive renal failure, but who had never suffered from a primary renal disease. We show that such subjects can be detected by screening for albuminuria. Elevated urinary albumin loss is an indicator not only of poor renal, but also of poor cardiovascular prognosis. In addition to diabetic subjects who are at risk for albuminuria, we also show that hypertensive, obese, and smoking subjects are more susceptible. We suggest that therapies that have been shown to lower albumin excretion, such as ACE inhibitors, angiotensin II receptor antagonists, and statins be started early in such patients to prevent them from developing clinical renal disease and its attendant cardiovascular complications

Consequences of wall stiffness for a beta-soft potential

Modifications of the infinite square well E(5) and X(5) descriptions of transitional nuclear structure are considered. The eigenproblem for a potential with linear sloped walls is solved. The consequences of the introduction of sloped walls and of a quadratic transition operator are investigated.Comment: RevTeX 4, 8 pages, as published in Phys. Rev.

An inclusion result for dagger closure in certain section rings of abelian varieties

We prove an inclusion result for graded dagger closure for primary ideals in symmetric section rings of abelian varieties over an algebraically closed field of arbitrary characteristic.Comment: 11 pages, v2: updated one reference, fixed 2 typos; final versio

Automatic correction of hand pointing in stereoscopic depth

In order to examine whether stereoscopic depth information could drive fast automatic correction of hand pointing, an experiment was designed in a 3D visual environment in which participants were asked to point to a target at different stereoscopic depths as quickly and accurately as possible within a limited time window (≤300 ms). The experiment consisted of two tasks: "depthGO" in which participants were asked to point to the new target position if the target jumped, and "depthSTOP" in which participants were instructed to abort their ongoing movements after the target jumped. The depth jump was designed to occur in 20% of the trials in both tasks. Results showed that fast automatic correction of hand movements could be driven by stereoscopic depth to occur in as early as 190 ms.This work was supported by the Grants from the National Natural Science Foundation of China (60970062 and 61173116) and the Doctoral Fund of Ministry of Education of China (20110072110014)

Assessment of the tissue distribution of transplanted human endothelial progenitor cells by radioactive labeling

Background— Transplantation of endothelial progenitor cells (EPCs) improves vascularization and left ventricular function after experimental myocardial ischemia. However, tissue distribution of transplanted EPCs has not yet been monitored in living animals. Therefore, we tested whether radioactive labeling allows us to detect injected EPCs

General theory for integer-type algorithm for higher order differential equations

Based on functional analysis, we propose an algorithm for finite-norm solutions of higher-order linear Fuchsian-type ordinary differential equations (ODEs) P(x,d/dx)f(x)=0 with P(x,d/dx):=[\sum_m p_m (x) (d/dx)^m] by using only the four arithmetical operations on integers. This algorithm is based on a band-diagonal matrix representation of the differential operator P(x,d/dx), though it is quite different from the usual Galerkin methods. This representation is made for the respective CONSs of the input Hilbert space H and the output Hilbert space H' of P(x,d/dx). This band-diagonal matrix enables the construction of a recursive algorithm for solving the ODE. However, a solution of the simultaneous linear equations represented by this matrix does not necessarily correspond to the true solution of ODE. We show that when this solution is an l^2 sequence, it corresponds to the true solution of ODE. We invent a method based on an integer-type algorithm for extracting only l^2 components. Further, the concrete choice of Hilbert spaces H and H' is also given for our algorithm when p_m is a polynomial or a rational function with rational coefficients. We check how our algorithm works based on several numerical demonstrations related to special functions, where the results show that the accuracy of our method is extremely high.Comment: Errors concerning numbering of figures are fixe

Sonoluminescing air bubbles rectify argon

The dynamics of single bubble sonoluminescence (SBSL) strongly depends on the percentage of inert gas within the bubble. We propose a theory for this dependence, based on a combination of principles from sonochemistry and hydrodynamic stability. The nitrogen and oxygen dissociation and subsequent reaction to water soluble gases implies that strongly forced air bubbles eventually consist of pure argon. Thus it is the partial argon (or any other inert gas) pressure which is relevant for stability. The theory provides quantitative explanations for many aspects of SBSL.Comment: 4 page