Design, analysis, tools and applications for programmable high-speed and power-aware 4G processors

Data rate traffic and communication capacity demand have been increased continuously. Therefore, a highly advanced 4G wireless system is required to meet a high demand for modern mobile terminals. For getting a further improvement for 4G communication systems, new paradigms of design, analysis tools and applications for 4G communication processors are necessary. In this paper, some of these new paradigms are discussed. Furthermore, a single-step discrete cosine transform truncation (DCTT) method is proposed for the modeling-simulation in signal integrity verification for high-speed communication processors. ©2011 IEEE.published_or_final_versio

Complications of fixed infrared emitters in computer-assisted total knee arthroplasties

<p>Abstract</p> <p>Background</p> <p>The first stage in the implant of a total knee arthroplasty with computer-assisted surgery is to fasten the emitters to the femur and the tibia. These trackers must be hard-fixed to the bone. The objectives of our study are to evaluate the technical problems and complications of these tracker-pins, the necessary time to fix them to the bone and the possible advantages of a new femoral-fixed tracker-pin.</p> <p>Methods</p> <p>Three hundred and sixty seven tracker-pins were used in one hundred and fifty one computer-assisted total knee replacements. A bicortical screw was used to fix the tracker to the tibia in all cases; in the femur, however, a bicortical tracker was used in 112 cases, while a new device (OrthoLock) with percutaneous fixation pins was employed in the remaining 39.</p> <p>Results</p> <p>Technical problems related to the fixing of the trackers appeared in nine cases (2.5%). The mean surgery time to fix the tracker pin to the tibia was 3 minutes (range 2–7), and 5 minutes in the case of the femoral pin (range: 4–11), although with the new tool it was only three minutes (range 2–4) (p < 0.001). No complications were observed with this new device.</p> <p>Conclusion</p> <p>The incidence of problems and complications with the fixing systems used in knee navigation is very small. The use of a new device with percutaneous pins facilitates the fixing of femoral trackers and decreases the time needed to place them.</p

Simultaneous bilateral total knee and ankle arthroplasty as a single surgical procedure

<p>Abstract</p> <p>Background</p> <p>Simultaneous osteoarthritis (OA) of the ankle joint complicates primary total knee arthroplasty (TKA). In such cases, rehabilitation of TKA is limited by debilitating ankle pain, but varus or valgus ankle arthritis may even compromise placement of knee prosthetic components.</p> <p>Case presentation</p> <p>We present a patient with simultaneous bilateral valgus and patellofemoral OA of the knees and bilateral varus OA of the ankle joints that equally contributed to overall disability. This 63 years old, motivated and otherwise healthy patient was treated by simultaneous bilateral total knee and ankle arthroplasty (quadruple total joint arthroplasty, TJA) during the same anesthesia. Two years outcome showed excellent alignment and function of all four replaced joints. Postoperative time for rehabilitation, back to work (6th week) and hospital stay (12 days) of this special patient was markedly reduced compared to the usual course of separate TJA.</p> <p>Conclusions</p> <p>Simultaneous quadruple TJA in equally disabling OA of bilateral deformed knees and ankles resulted in a better functional outcome and faster recovery compared to the average reported results after TKA and TAA in literature. However, careful preoperative planning, extensive patient education, and two complete surgical teams were considered essential for successful performance. To the best of our knowledge this is the first case report in literature about quadruple major total joint arthroplasty implanted during the same anesthesia in the same patient.</p

Improving gene-set enrichment analysis of RNA-Seq data with small replicates

Deregulated pathways identified from transcriptome data of two sample groups have played a key role in many genomic studies. Gene-set enrichment analysis (GSEA) has been commonly used for pathway or functional analysis of microarray data, and it is also being applied to RNA-seq data. However, most RNA-seq data so far have only small replicates. This enforces to apply the gene-permuting GSEA method (or preranked GSEA) which results in a great number of false positives due to the inter-gene correlation in each gene-set. We demonstrate that incorporating the absolute gene statistic in one-tailed GSEA considerably improves the false-positive control and the overall discriminatory ability of the gene-permuting GSEA methods for RNA-seq data. To test the performance, a simulation method to generate correlated read counts within a gene-set was newly developed, and a dozen of currently available RNA-seq enrichment analysis methods were compared, where the proposed methods outperformed others that do not account for the inter-gene correlation. Analysis of real RNA-seq data also supported the proposed methods in terms of false positive control, ranks of true positives and biological relevance. An efficient R package (AbsFilterG- SEA) coded with C++ (Rcpp) is available from CRAN.open

Biochemical Properties of a Novel Cysteine Protease of Plasmodium vivax, Vivapain-4

Plasmodium vivax affects hundreds of millions each year and results in severe morbidity and mortality. Plasmodial cysteine proteases (CPs) play crucial roles during the progression of malaria since inhibition of these molecules impairs parasite growth. These CPs might be targeted for new antimalarial drugs. We characterized a novel P. vivax CP, vivapain-4 (VX-4), which appeared to evolve differentially among primate Plasmodium species. VX-4 showed highly unique substrate preference depending on surrounding micro-environmental pH. It effectively hydrolyzed benzyloxycarbonyl-Leu-Arg-4-methyl-coumaryl-7-amide (Z-Leu-Arg-MCA) and Z-Phe-Arg-MCA at acidic pH and Z-Arg-Arg-MCA at neutral pH. Three amino acids (Ala90, Gly157 and Glu180) that delineate the S2 pocket were found to be substituted in VX-4. Alteration of Glu180 abolished hydrolytic activity against Z-Arg-Arg-MCA at neutral pH, indicating Glu180 is intimately involved in the pH-dependent substrate preference. VX-4 hydrolyzed actin at neutral pH and hemoglobin at acidic pH, and participated in plasmepsin 4 activation at neutral/acidic pH. VX-4 was localized in the food vacuoles and cytoplasm of the erythrocytic stage of P. vivax. The differential substrate preferences depending on pH suggested a highly efficient mechanism to enlarge biological implications of VX-4, including hemoglobin degradation, maturation of plasmepsin, and remodeling of the parasite architecture during growth and development of P. vivax

Identification of an OsPR10a promoter region responsive to salicylic acid

Orysa sativa pathogenesis-related protein 10a (OsPR10a) was induced by pathogens, salicylic acid (SA), jasmonic acid (JA), ethephon, abscisic acid (ABA), and NaCl. We tried to analyze the OsPR10a promoter to investigate the transcriptional regulation of OsPR10a by SA. We demonstrated the inducibility of OsPR10a promoter by SA using transgenic Arabidopsis carrying OsPR10a:GFP as well as by transient expression assays in rice. To further identify the promoter region responsible for its induction by SA, four different deletions of the OsPR10a promoter were made, and their activities were measured by transient assays. The construct containing 687-bp OsPR10a promoter from its start codon exhibited a six-fold increase of induction compared to the control in response to SA. Mutation in the W-box like element 1 (WLE 1) between 687 and 637-bp from TGACA to TGAAA completely abolished induction of the OsPR10a promoter by SA, indicating that the WLE 1 between −687 and −637 of OsPR10a promoter is important in SA-mediated OsPR10a expression. We show for the first time that the W-box like element plays a role in SA mediated PR gene expression

Selected heterozygosity at cis-regulatory sequences increases the expression homogeneity of a cell population in humans

Background: Examples of heterozygote advantage in humans are scarce and limited to protein-coding sequences. Here, we attempt a genome-wide functional inference of advantageous heterozygosity at cis-regulatory regions. Results: The single-nucleotide polymorphisms bearing the signatures of balancing selection are enriched in active cis-regulatory regions of immune cells and epithelial cells, the latter of which provide barrier function and innate immunity. Examples associated with ancient trans-specific balancing selection are also discovered. Allelic imbalance in chromatin accessibility and divergence in transcription factor motif sequences indicate that these balanced polymorphisms cause distinct regulatory variation. However, a majority of these variants show no association with the expression level of the target gene. Instead, single-cell experimental data for gene expression and chromatin accessibility demonstrate that heterozygous sequences can lower cell-to-cell variability in proportion to selection strengths. This negative correlation is more pronounced for highly expressed genes and consistently observed when using different data and methods. Based on mathematical modeling, we hypothesize that extrinsic noise from fluctuations in transcription factor activity may be amplified in homozygotes, whereas it is buffered in heterozygotes. While high expression levels are coupled with intrinsic noise reduction, regulatory heterozygosity can contribute to the suppression of extrinsic noise. Conclusions: This mechanism may confer a selective advantage by increasing cell population homogeneity and thereby enhancing the collective action of the cells, especially of those involved in the defense systems in humansope

Significant Effects of Antiretroviral Therapy on Global Gene Expression in Brain Tissues of Patients with HIV-1-Associated Neurocognitive Disorders

Antiretroviral therapy (ART) has reduced morbidity and mortality in HIV-1 infection; however HIV-1-associated neurocognitive disorders (HAND) persist despite treatment. The reasons for the limited efficacy of ART in the brain are unknown. Here we used functional genomics to determine ART effectiveness in the brain and to identify molecular signatures of HAND under ART. We performed genome-wide microarray analysis using Affymetrix U133 Plus 2.0 Arrays, real-time PCR, and immunohistochemistry in brain tissues from seven treated and eight untreated HAND patients and six uninfected controls. We also determined brain virus burdens by real-time PCR. Treated and untreated HAND brains had distinct gene expression profiles with ART transcriptomes clustering with HIV-1-negative controls. The molecular disease profile of untreated HAND showed dysregulated expression of 1470 genes at p<0.05, with activation of antiviral and immune responses and suppression of synaptic transmission and neurogenesis. The overall brain transcriptome changes in these patients were independent of histological manifestation of HIV-1 encephalitis and brain virus burdens. Depending on treatment compliance, brain transcriptomes from patients on ART had 83% to 93% fewer dysregulated genes and significantly lower dysregulation of biological pathways compared to untreated patients, with particular improvement indicated for nervous system functions. However a core of about 100 genes remained similarly dysregulated in both treated and untreated patient brain tissues. These genes participate in adaptive immune responses, and in interferon, cell cycle, and myelin pathways. Fluctuations of cellular gene expression in the brain correlated in Pearson's formula analysis with plasma but not brain virus burden. Our results define for the first time an aberrant genome-wide brain transcriptome of untreated HAND and they suggest that antiretroviral treatment can be broadly effective in reducing pathophysiological changes in the brain associated with HAND. Aberrantly expressed transcripts common to untreated and treated HAND may contribute to neurocognitive changes defying ART