Internal and External Bitstream Relocation for Partial Dynamic Reconfiguration

The research described in this paper shows how the runtime relocation of a reconfigurable component can be obtained using a system component that is able to update the bitstream information, moving the reconfigurable module in the desired position. This scenario defines the so-called partial bitstream relocation activity. This paper proposes a relocation filter that can be implemented both as a hardware and a software component. The former is hosted in the static part of the reconfigurable architecture, while the latter is made to be run on the processor placed on the field-programmable gate array (FPGA). The proposed approach has also been validated over different FPGAs, i.e., Virtex II Pro, Virtex 4, and Virtex 5, proposing a runtime relocation support that can be customized to meet all the different constraints associated with these different target architectures.     

Chlordanes in the indoor and outdoor air of three U.S. cities

Indoor and outdoor concentrations of six chlordane components (trans-chlordane, cis-chlordane, trans-nonachlor, cis-nonachlor, oxychlordane, and MC5) were measured at 157 residences, all of which were inhabited by nonsmoking individuals, in three urban areas during June 1999-May 2000. The analyses were conducted on a subset of 48 h integrated samples collected in Los Angeles County, CA, Houston, TX, and Elizabeth, NJ within the Relationship of Indoor, Outdoor, and Personal Air (RIOPA) study. Both particle-bound (PM2.5; quartz fiber filter) and vapor-phase (PUF sorbant) chlordane concentrations were separately measured by GC/EI MS after solvent extraction. The outdoor (gas + particle) total chlordane (trans-chlordane + cis-chlordane + trans-nonachlor + cis-nonachlor) concentrations ranged from 0.036 to 4.27 ng m(-3) in Los Angeles County, from 0.008 to 11.00 ng m(-3) in Elizabeth, and from 0.062 to 1.77 ng m(-3) in Houston. The corresponding indoor total chlordane concentrations ranged from 0.037 to 112.0 ng m(-3) in Los Angeles County, from 0.260 to 31.80 ng m(-3) in Elizabeth, and from 0.410 to 38.90 ng m(-3) in Houston study homes. Geometric mean concentrations were higher in indoor air than outdoor air (1.98 vs 0.58 ng m(-3) in CA; 1.30 vs 0.17 ng m(-3) in NJ; 4.18 vs 0.28 ng m(-3) in TX), which suggests there are significant indoor sources of chlordane species in a subset of homes in each of the three cities. Calculated source strengths relate to home age, with the highest apparent indoor source strengths occurring in unattached single-family homes built during the period from 1945 to 1959. Principle indoor sources of chlordanes likely include volatilization from residues of indoor application of chlordanes and infiltration from subsurface and foundation application of chlordane-containing termiticides during home construction.     

Source proximity and outdoor-residential VOC concentrations: results from the RIOPA study

Ambient volatile organic compound concentrations outside residences were measured in Elizabeth, New Jersey as part of the Relationship of Indoor, Outdoor, and Personal A:r (RIOPA) study to assess the influence of proximity of the residences to known ambient emissions sources. The closest distances between the outdoor samplers and emission sources were determined using Geographic Information Systems (GIS)techniques. Multiple regression models were developed for residential ambient concentrations of aromatic hydrocarbons (BTEX), methyl tert butyl ether (MTBE), and tetrachloroethylene (PCE). The natural log transformed ambient concentrations of BTEX were inversely associated with distances to major roadways with high traffic densities and gasoline stations, atmospheric stability, temperature, and wind speed. Ambient MTBE levels were associated with inverse distance to gas stations and interstate highways. Residential ambient PCE concentration was inversely associated with distance to dry cleaning facilities, atmospheric stability, temperature, wind speed, and relative humidity. The linear regression models that include proximity to emission sources and meteorological variables explained 16-45% of the overall variation of ambient residential VOC concentrations. Meteorological conditions, especially atmospheric stability and temperature, explained 60-90% of the total variation in the regression models. The residential ambient air concentrations were 1.5-4 times higher than the urban background levels outside homes very close (<50 m) to ambient emission sources where approximately 7% of the population live. However, the relative increase of risk for disease is small and variations in air concentration in the background urban atmosphere are greater than those from the proximity to roadways.     

A new deformable model for analysis of X-ray CT images in preclinical studies of mice for polycystic kidney disease

This paper describes the application of a new probabilistic shape and appearance model (PSAM) algorithm to the task of detecting polycystic kidney disease (PKD) in X-ray computed tomography images of laboratory mice. The genetically engineered PKD mouse is a valuable animal model that can be used to develop new treatments for kidney-related problems in humans. PSAM is a statistical-based deformable model that improves upon existing point distribution models for boundary-based object segmentation. This new deformable model algorithm finds the optimal boundary position using an objective function that has several unique characteristics. Most importantly, the objective function includes both global shape and local gray-level characteristics, so optimization occurs with respect to both pieces of information simultaneously. PSAM is employed to segment the mouse kidneys and then texture measurements are applied within kidney boundaries to detect PKD. The challenges associated with the segmentation non-rigid organs along with the availability of a priori information led to the choice of a trainable, deformable model for this application. In 103 kidney images that were analyzed as part of a preclinical animal study, the mouse kidneys and spine were segmented with an average error of 2.4 pixels per boundary point. In all 103 cases, the kidneys were successfully segmented at a level where PKD could be detected using mean-of-local-variance texture measurements within the located boundary.     

Identification of Clostridium beijerinckii, Cl. butyricum, Cl. sporogenes, Cl. tyrobutyricum isolated from silage, raw milk and hard cheese by a multiplex PCR assay

Late blowing, caused by the outgrowth of clostridial spores present in raw milk and originating from silage, can create considerable product loss, especially in the production of hard and semi-hard cheeses. The conventional method for the isolation of Clostridium spp. from cheeses with late-blowing symptoms is very complicated and the identification of isolates is problematic. The aim of this work was the development of a multiplex PCR method for the detection of the main dairy-related clostridia such as: Cl. beijerinckii, Cl. butyricum, Cl. sporogenes, Cl. tyrobutyricum. Samples derived from silage, raw milk and hard cheese were analysed by the most probable number (MPN) enumeration. Forty-four bacterial strains isolated from gas positive tubes were used to check the reliability of the multiplex PCR assay. The specificity of the primers was tested by individually analysing each primer pair and the primer pair combined in the multiplex PCR. It was interesting to note that the samples not identified by the multiplex PCR assay were amplified by V2-V3 16S rRNA primer pair and the sequencing revealed the aligned 16S rRNA sequences to be Paenibacillus and Bacillus spp. This new molecular assay provides a simple promising alternative to traditional microbiological methods for a rapid, sensitive detection of clostridia in dairy products.     

Development of a pentaplex PCR assay for the simultaneous detection of Streptococcus thermophilus, Lactobacillus delbrueckii subsp. bulgaricus, L. delbrueckii subsp. lactis, L. helveticus, L. fermentum in whey starter for Grana Padano cheese

A pentaplex PCR assay for the rapid, selective and simultaneous detection of Lactobacillus helveticus, L. delbrueckii subsp. lactis, L. delbrueckii subsp. bulgaricus, Streptococcus thermophilus, and L. fermentum, was developed. The target sequences were a group of genes coding for beta-galactosidase production (S. thermophilus and L. delbrueckii subsp. bulgaricus), for cell-enveloped associated proteinase synthesis (L. helveticus), for dipeptide transport system production (L. delbrueckii subsp. lactis) and for arginine-ornithine antiporter protein production (L. fermentum). The analytical specificity of the assay was evaluated with 5 reference strains and 140 lactic acid bacterial strains derived from raw milk cheeses and belonging to the Lactobacillus, Streptococcus, Lactococcus and Enterococcus genera. The identification limit for each target strain was 10³ CFU/ml. This new molecular assay was used to investigate the LAB population by direct extraction of DNA from the 12 whey cultures for Grana Padano. The pentaplex PCR assay revealed a good correspondence with microbiological analyses and allowed to identify even minor LAB community members which, can be out-competed in vitro by numerically more abundant microbial species.     

Molecular Fingerprint of BMD Patients Lacking a Portion in the Rod Domain of Dystrophin

BMD is characterized by a marked heterogeneity of gene mutations resulting in many abnormal dystrophin proteins with different expression and residual functions. The smaller dystrophin molecules lacking a portion around exon 48 of the rod domain, named the D8 region, are related to milder phenotypes. The study aimed to determine which proteins might contribute to preserving muscle function in these patients. Patients were subdivided, based on the absence or presence of deletions in the D8 region, into two groups, BMD1 and BMD2. Muscle extracts were analyzed by 2-D DIGE, label-free LC-ESI-MS/MS, and Ingenuity pathway analysis (IPA). Increased levels of proteins typical of fast fibers and of proteins involved in the sarcomere reorganization characterize BMD2. IPA of proteomics datasets indicated in BMD2 prevalence of glycolysis and gluconeogenesis and a correct flux through the TCA cycle enabling them to maintain both metabolism and epithelial adherens junction. A 2-D DIGE analysis revealed an increase of acetylated proteoforms of moonlighting proteins aldolase, enolase, and glyceraldehyde-3-phosphate dehydrogenase that can target the nucleus promoting stem cell recruitment and muscle regeneration. In BMD2, immunoblotting indicated higher levels of myogenin and lower levels of PAX7 and SIRT1/2 associated with a set of proteins identified by proteomics as involved in muscle homeostasis maintenance.     

Sequence determinants for hnRNP I protein nuclear localization

hnRNP I, also referred to as polypyrimidine tract binding protein, is one of the proteins associated with nascent pre-mRNA in the heterogeneous nuclear ribonucleoprotein (hnRNP) complexes. As for all karyophilic proteins, the nuclear import of hnRNP proteins requires specific sequence determinants that in many instances differ from the canonical import signal. In order to identify the sequences responsible for the nuclear localization, various hnRNP I portions were fused to a reporter protein (bacterial chloramphenicol acetyl transferase) and used in transient transfection assay. By this approach we identified a 60-amino-acid sequence located at the amino terminus of hnRNP I (designated NLD-I) that is both necessary and sufficient for nuclear localization. NLD-I represents a novel bipartite type of nuclear localization signal that bears no resemblance to other nuclear localization determinants so far identified in hnRNP proteins.     

Detection of human immunodeficiency virus type 1 (HIV-1) RNA in pools of sera negative for antibodies to HIV-1 and HIV-2

A total of 234 pools were prepared from 10,692 consecutive serum samples negative for antibodies to human immunodeficiency virus type 1 (HIV-1) and HIV-2 collected at five virological laboratories (average pool size, 45 serum samples). Pools were screened for the presence of HIV-1 RNA by a modified commercial assay (Amplicor HIV-1 Monitor test) which included an additional polyethylene glycol (PEG) precipitation step prior to purification of viral RNA (PEG Amplicor assay). The sensitivity of this assay for HIV-1 RNA detection in individual serum samples within pools matches that of standard commercial assays for individual serum samples, i.e., 500 HIV-1 RNA copies per ml. Five pools were identified as positive, and each one contained one antibody-negative, HIV-1 RNA-positive serum sample, corresponding to an average of 1 infected sample per 2,138 serum samples. Retrospective analysis revealed that the five HIV-1 RNA-positive specimens originated from individuals who had symptomatic primary HIV-1 infection at the time of sample collection and who were also positive for p24 antigenemia. We next assessed the possibility of performing the prepurification step by high-speed centrifugation (50,000 x g for 80 min) of 1.5-ml pools containing 25 microl of 60 individual serum samples, of which only 1 contained HIV-1 RNA (centrifugation Amplicor assay). The sensitivity of this assay also matches the sensitivities of standard commercial assays for HIV-1 RNA detection in individual serum samples. The results demonstrate that both assays with pooled sera can be applied to the screening of large numbers of serum samples in a time- and cost-efficient manner.     

Uncertainties in quantization-noise estimates for analog-to-digitalconverters

Estimates of quantization noise, obtained by stimulating an ideal analog-to-digital converter with a sine wave contained in the input range, are affected by an appreciable uncertainty, which may affect SNR and ENB specifications, especially in the case of low resolution devices. The uncertainty can be eliminated, when possible, by the use of an input sine wave bringing the converter into saturation. The different effects of additive noise on the noise estimates obtained by the various test procedures are also discussed, showing, in particular, that quantization noise may be overestimated by histogram testing with a nonsaturating input sine wave. Therefore, any noise specification should clearly make reference to the test signal parameters and to the instrumentation characteristics