Performance of HBsAg point-of-care tests for detection of diagnostic escape-variants in clinical samples

BACKGROUND Hepatitis B viruses (HBV) harboring mutations in the a-determinant of the Hepatitis B surface antigen (HBsAg) are associated with reduced reactivity of HBsAg assays. OBJECTIVES To evaluate the sensitivity and specificity of three HBsAg point-of-care tests for the detection of HBsAg of viruses harboring HBsAg mutations. STUDY DESIGN A selection of 50 clinical plasma samples containing HBV with HBsAg mutations was used to evaluate the performance of three HBsAg point-of-care tests (Vikia(®), bioMérieux, Marcy-L'Étoile, France. Alere Determine HBsAg™, Iverness Biomedical Innovations, Köln, Germany. Quick Profile™, LumiQuick Diagnostics, California, USA) and compared to the ARCHITECT HBsAg Qualitative(®) assay (Abbott Laboratories, Sligo, Ireland). RESULTS The sensitivity of the point-of-care tests ranged from 98% to 100%. The only false-negative result occurred using the Quick Profile™ assay with a virus harboring a D144A mutation. CONCLUSIONS The evaluated point-of-care tests revealed an excellent sensitivity in detecting HBV samples harboring HBsAg mutations.

n-fatty acids of shale partings in the Franciscan bedded cherts

Normal saturated fatty acid (n-fatty acid) in marine sediments from coastal and pelagic environments were analyzed. The coastal sediments contain both short-chained n-fatty acids with carbon numbers from 12 to 18 and long-chained acids from 22 to 32, whereas the pelagic sediments contain predominantly short-chained acids. The relative abundance of short-chained to long-chained n-fatty acids, expressed by the molar ratio C16/C26, can be an indicator to assess the depositional environment of sedimentary rocks. The ratio of long-chained n-fatty acids (C22-C32) to the total n-fatty acids also has the potential to discriminate sedimentary environments. The indicators based on the n-fatty acids were applied to the Franciscan bedded cherts. The result shows that the bedded cherts had deposited in continuous environments from the pelagic to the coastal. This is in harmony with the same inference based on major, trace and rare earth elements and normal paraffins.

Temperature and photoperiod effects on sex determination in Leuresthes tenuis (fish)

In some gonochoristic species, sex is influenced not only by genotype at conception but also by the environment that offspring experience during early ontogeny (termed environmental sex determination or ESD). ESD is thought to be adaptive when seasonal variations in environmental conditions provide a sex-specific fitness advantage. In vertebrates, temperature is the most common determinant of sex, and seasonal variation in temperature serves as a temporal cue of environmental quality such as length of the growing season. Some environments, however, lack strong seasonal temperature fluctuations and other cues, particularly photoperiod, may provide a more reliable indicator of the environment offspring enter. We tested this hypothesis by rearing the offspring of the California grunion (Leuresthes tenuis, Ayres), which experiences low seasonal temperature variation in nature, under common garden conditions at three temperature and two photoperiod treatments. Our experiments revealed that both temperature and photoperiod significantly affected sex ratios in L. tenuis. More females were produced at cooler temperatures and longer day lengths, which is consistent with female biased sex ratios early in the breeding season, and likely adaptive through increased female size and fecundity. To our knowledge, this is the first documented case of photoperiod-dependent sex determination in a gonochoristic vertebrate.

Seawater carbonate chemistry and processes during experiments with crabs Chionoecetes tanneri and Cancer magister, 2007

Rising levels of atmospheric carbon dioxide could be curbed by large-scale sequestration of CO2 in the deep sea. Such a solution requires prior assessment of the impact of hypercapnic, acidic seawater on deep-sea fauna. Laboratory studies were conducted to assess the short-term hypercapnic tolerance of the deep-sea Tanner crab Chionoecetes tanneri, collected from 1000 m depth in Monterey Canyon off the coast of central California, USA. Hemolymph acid- base parameters were monitored over 24 h of exposure to seawater equilibrated with ~1% CO2 (seawater PCO2 ~6 torr or 0.8 kPa, pH 7.1), and compared with those of the shallow-living Dungeness crab Cancer magister. Short-term hypercapnia-induced acidosis in the hemolymph of Chionoecetes tanneri was almost uncompensated, with a net 24 h pH reduction of 0.32 units and a net bicarbonate accumulation of only 3 mM. Under simultaneous hypercapnia and hypoxia, short-term extracellular acidosis in Chionoecetes tanneri was completely uncompensated. In contrast, Cancer magister fully recovered its hemolymph pH over 24 h of hypercapnic exposure by net accumulation of 12 mM bicarbonate from the surrounding medium. The data support the hypothesis that deep-sea animals, which are adapted to a stable environment and exhibit reduced metabolic rates, lack the short-term acid-base regulatory capacity to cope with the acute hypercapnic stress that would accompany large-scale CO2 sequestration. Additionally, the data indicate that sequestration in oxygen-poor areas of the ocean would be even more detrimental to deep-sea fauna.

Microbial community composition in fresh water at different stations

Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes was used to investigate the phylogenetic composition of bacterioplankton communities in several freshwater and marine samples. An average of about 50% of the cells were detected by probes for the domains Bacteria and Archaea. Cells were concentrated from water samples (1 to 100 ml) on white polycarbonate filters (diameter, 47 mm; pore size, 0.2 mm; type GTTP 4700 [Millipore, Eschborn, Germany]) by applying a vacuum of <25 kPa. They were subsequently fixed by covering the filter with 3 ml of a freshly prepared, phosphate-buffered saline (pH 7.2)-4% paraformaldehyde (Sigma, Deisenhofen, Germany) solution for 30 min at room temperature. Airdried filters are ready for hybridization and can be stored at 220°C or room temperature for several months without showing apparent changes. Probes BET42a, GAM42a, and PLA886 were used with competitor oligonucleotides as described previously amongst others in Manz et al., (1992; doi:10.1016/S0723-2020(11)80121-9). The filters were transferred to a vial containing 50 ml of prewarmed (48°C) washing solution (70 mM NaCl, 20 mM Tris-HCl [pH 7.4], 5 mM EDTA, 0.01% sodium dodecyl sulfate) and incubated freely floating without shaking at 48°C for 15 min. The filter sections were dried on Whatman 3M paper (Whatman Ltd., Maidstone, United Kingdom) and covered with 50 ml of DAPI solution (1 mg/ml in distilled water filtered through at 0.2-mm filter) for 5 min at room temperature in the dark. For each sample and probe, more than 500 cells were enumerated; for the DAPI examination, more than 1,500 cells were counted per sample. All probe-specific cell counts are presented as the percentage of cells visualized by DAPI. The mean abundances and standard deviations were calculated from the counts of 10 to 20 randomly chosen fields on each filter section. All counts were corrected by subtracting the counts obtained with the negative control NON338. Mean and standard deviation were calculated from the counts of 10 to 20 randomly chosen fields on each filter section.

A Fast Reconfigurable 2D HW Core Architecture on FPGAs for Evolvable Self- Adaptive Systems

Modern FPGAs with Dynamic and Partial Reconfiguration (DPR) feature allow the implementation of complex, yet flexible, hardware systems. Combining this flexibility with evolvable hardware techniques, real adaptive systems, able to reconfigure themselves according to environmental changes, can be envisaged. In this paper, a highly regular and modular architecture combined with a fast reconfiguration mechanism is proposed, allowing the introduction of dynamic and partial reconfiguration in the evolvable hardware loop. Results and use case show that, following this approach, evolvable processing IP Cores can be built, providing intensive data processing capabilities, improving data and delay overheads with respect to previous proposals. Results also show that, in the worst case (maximum mutation rate), average reconfiguration time is 5 times lower than evaluation time.

Multipath Reflectivity Estimation in Urban Environments for Synthetic Aperture Radar Images

Synthetic Aperture Radar (SAR) images a target region reflectivity function in the multi-dimensional spatial domain of range and cross-range. SAR synthesizes a large aperture radar in order to achieve a finer azimuth resolution than the one provided by any on-board real antenna. Conventional SAR techniques assume a single reflection of transmitted waveforms from targets. Nevertheless, today¿s new scenes force SAR systems to work in urban environments. Consequently, multiple-bounce returns are added to directscatter echoes. We refer to these as ghost images, since they obscure true target image and lead to poor resolution. By analyzing the quadratic phase error (QPE), this paper demonstrates that Earth¿s curvature influences the defocusing degree of multipath returns. In addition to the QPE, other parameters such as integrated sidelobe ratio (ISLR), peak sidelobe ratio (PSLR), contrast (C) and entropy (E) provide us with the tools to identify direct-scatter echoes in images containing undesired returns coming from multipath.

Implementation of multiple specialization in logic programs

We study the múltiple specialization of logic programs based on abstract interpretation. This involves in general generating several versions of a program predícate for different uses of such predícate, making use of information obtained from global analysis performed by an abstract interpreter, and finally producing a new, "multiply specialized" program. While the topic of múltiple specialization of logic programs has received considerable theoretical attention, it has never been actually incorporated in a compiler and its effects quantified. We perform such a study in the context of a parallelizing compiler and show that it is indeed a relevant technique in practice. Also, we propose an implementation technique which has the same power as the strongest of the previously proposed techniques but requires little or no modification of an existing abstract interpreter.

A simulation study of or- and independent and-parallelism

Although studies of a number of parallel implementations of logic programming languages are now available, the results are difficult to interpret due to the multiplicity of factors involved, the effect of each of which is difficult to sepárate. In this paper we present the results of a highlevel simulation study of or- and independent and-parallelism with a wide selection of Prolog programs that aims to facilítate this separation. We hope this study will be instrumental in better understanding and comparing results from actual implementations, as shown by an example in the paper. In addition, the paper examines some of the issues and tradeoffs associated with the combination of and- and or-parallelism and proposes reasonable solutions based on the simulation data.