Performance modelling of wormhole-routed hypercubes with bursty traffice and finite buffers

An open queueing network model (QNM) is proposed for wormhole-routed hypercubes with finite buffers and deterministic routing subject to a compound Poisson arrival process (CPP) with geometrically distributed batches or, equivalently, a generalised exponential (GE) interarrival time distribution. The GE/G/1/K queue and appropriate GE-type flow formulae are adopted, as cost-effective building blocks, in a queue-by-queue decomposition of the entire network. Consequently, analytic expressions for the channel holding time, buffering delay, contention blocking and mean message latency are determined. The validity of the analytic approximations is demonstrated against results obtained through simulation experiments. Moreover, it is shown that the wormholerouted hypercubes suffer progressive performance degradation with increasing traffic variability (burstiness)

Presaging critical residues in protein interfaces-web server (PCRPi-W):a web server to chart hot spots in protein interfaces

BACKGROUND: It is well established that only a portion of residues that mediate protein-protein interactions (PPIs), the so-called hot spot, contributes the most to the total binding energy, and thus its identification is an important and relevant question that has clear applications in drug discovery and protein design. The experimental identification of hot spots is however a lengthy and costly process, and thus there is an interest in computational tools that can complement and guide experimental efforts. PRINCIPAL FINDINGS: Here, we present Presaging Critical Residues in Protein interfaces-Web server (http://www.bioinsilico.org/PCRPi), a web server that implements a recently described and highly accurate computational tool designed to predict critical residues in protein interfaces: PCRPi. PRCPi depends on the integration of structural, energetic, and evolutionary-based measures by using Bayesian Networks (BNs). CONCLUSIONS: PCRPi-W has been designed to provide an easy and convenient access to the broad scientific community. Predictions are readily available for download or presented in a web page that includes among other information links to relevant files, sequence information, and a Jmol applet to visualize and analyze the predictions in the context of the protein structure

PCRPi, Presaging Critical Residues in Protein interfaces, a new computational tool to chart hot spots in protein interfaces

Protein–protein interactions (PPIs) are ubiquitous in Biology, and thus offer an enormous potential for the discovery of novel therapeutics. Although protein interfaces are large and lack defining physiochemical traits, is well established that only a small portion of interface residues, the so-called hot spot residues, contribute the most to the binding energy of the protein complex. Moreover, recent successes in development of novel drugs aimed at disrupting PPIs rely on targeting such residues. Experimental methods for describing critical residues are lengthy and costly; therefore, there is a need for computational tools that can complement experimental efforts. Here, we describe a new computational approach to predict hot spot residues in protein interfaces. The method, called Presaging Critical Residues in Protein interfaces (PCRPi), depends on the integration of diverse metrics into a unique probabilistic measure by using Bayesian Networks. We have benchmarked our method using a large set of experimentally verified hot spot residues and on a blind prediction on the protein complex formed by HRAS protein and a single domain antibody. Under both scenarios, PCRPi delivered consistent and accurate predictions. Finally, PCRPi is able to handle cases where some of the input data is either missing or not reliable (e.g. evolutionary information)

LMO2 is required for TAL1 DNA binding activity and initiation of definitive haematopoiesis at the haemangioblast stage

LMO2 is a bridging factor within a DNA binding complex and is required for definitive haematopoiesis to occur. The developmental stage of the block in haematopoietic specification is not known. We show that Lmo2-/- mouse embryonic stem cells differentiated to Flk-1+ haemangioblasts, but less efficiently to haemogenic endothelium, which only produced primitive haematopoietic progenitors. Genome-wide approaches indicated that LMO2 is required at the haemangioblast stage to position the TAL1/LMO2/LDB1 complex to regulatory elements that are important for the establishment of the haematopoietic developmental program. In the absence of LMO2, the target site recognition of TAL1 is impaired. The lack of LMO2 resulted in altered gene expression levels already at the haemangioblast stage, with transcription factor genes accounting for ∼15% of affected genes. Comparison of Lmo2-/- with Tal1-/- Flk-1+ cells further showed that TAL1 was required to initiate or sustain Lmo2 expression

Smart nanocrystals of artemether: fabrication, characterization, and comparative in vitro and in vivo antimalarial evaluation

YesArtemether (ARTM) is a very effective antimalarial drug with poor solubility and consequently low bioavailability. Smart nanocrystals of ARTM with particle size of 161±1.5 nm and polydispersity index of 0.172±0.01 were produced in <1 hour using a wet milling technology, Dena® DM-100. The crystallinity of the processed ARTM was confirmed using differential scanning calorimetry and powder X-ray diffraction. The saturation solubility of the ARTM nanocrystals was substantially increased to 900 µg/mL compared to the raw ARTM in water (145.0±2.3 µg/mL) and stabilizer solution (300.0±2.0 µg/mL). The physical stability studies conducted for 90 days demonstrated that nanocrystals stored at 2°C-8°C and 25°C were very stable compared to the samples stored at 40°C. The nanocrystals were also shown to be stable when processed at acidic pH (2.0). The solubility and dissolution rate of ARTM nanocrystals were significantly increased (P<0.05) compared to those of its bulk powder form. The results of in vitro studies showed significant antimalarial effect (P<0.05) against Plasmodium falciparum and Plasmodium vivax. The IC50 (median lethal oral dose) value of ARTM nanocrystals was 28- and 54-fold lower than the IC50 value of unprocessed drug and 13- and 21-fold lower than the IC50 value of the marketed tablets, respectively. In addition, ARTM nanocrystals at the same dose (2 mg/kg) showed significantly (P<0.05) higher reduction in percent parasitemia (89%) against P. vivax compared to the unprocessed (27%), marketed tablets (45%), and microsuspension (60%). The acute toxicity study demonstrated that the LD50 value of ARTM nanocrystals is between 1,500 mg/kg and 2,000 mg/kg when given orally. This study demonstrated that the wet milling technology (Dena® DM-100) can produce smart nanocrystals of ARTM with enhanced antimalarial activities

A crucial role for the ubiquitously expressed transcription factor Sp1 at early stages of hematopoietic specification

Mammalian development is regulated by the interplay of tissue-specific and ubiquitously expressed transcription factors, such as Sp1. Sp1 knockout mice die in utero with multiple phenotypic aberrations, but the underlying molecular mechanism of this differentiation failure has been elusive. Here, we have used conditional knockout mice as well as the differentiation of mouse ES cells as a model with which to address this issue. To this end, we examine