One naive T cell, multiple fates in CD8+ T cell differentiation.

The mechanism by which the immune system produces effector and memory T cells is largely unclear. To allow a large-scale assessment of the development of single naive T cells into different subsets, we have developed a technology that introduces unique genetic tags (barcodes) into naive T cells. By comparing the barcodes present in antigen-specific effector and memory T cell populations in systemic and local infection models, at different anatomical sites, and for TCR-pMHC interactions of different avidities, we demonstrate that under all conditions tested, individual naive T cells yield both effector and memory CD8+ T cell progeny. This indicates that effector and memory fate decisions are not determined by the nature of the priming antigen-presenting cell or the time of T cell priming. Instead, for both low and high avidity T cells, individual naive T cells have multiple fates and can differentiate into effector and memory T cell subsets.

Role of the naive and memory CD4+T-cell repertoire in transplantation

Purpose: The exact role of individual T cell-subsets in the development of rejection is not clearly defined. Given their distinct phenotypes, effector functions and trafficking patterns, naïve (CD45RBhiCD44lo) and memory (CD45RBloCD44hi) T cells may play distinct roles in anti-donor immunity after transplantation. Furthermore, only the CD4+CD45RBlo population contains CD4+CD25+ T cells, a subset with suppressive functions playing a major role in the maintenance of peripheral tolerance. The aim of this work was to study the contribution of these individual subsets in alloresponses via the direct and indirect pathways using a murine experimental model. Methods and materials: Purified naïve or memory CD4+ T cells were adoptively transferred into lymphopenic mice undergoing a skin allograft. Donor to recipient MHC combinations were chosen in order to study the direct and the indirect pathways of allorecognition separately. Graft survival and in vivo expansion, effector function and trafficking of the transferred T cells was assessed at different time points after transplantation. Results: We found that the cross-reactive CD4+CD45RBlo memory T-cell pool was heterogeneous and contained cells with regulatory potentials, both in the CD4+CD25+ and CD4+CD25-populations. CD4+ T cells capable of inducing strong primary alloreactive responses in vitro and rejection of a first allograft in vivo were mainly contained within the CD45RBhi naïve CD4+ T-cell compartment. CD4+CD45RBlo T cells proliferated less abundantly to allogeneic stimulation than their naïve counterparts both in vitro and in vivo, and allowed prolonged allograft survival even after the depletion of the CD4+CD25+ subset. Interestingly, CD4+CD25-CD45RBlo T cells were capable of prolonging allograft survival, mainly when the indirect pathway was the only mechanism of allorecognition. The indirect pathway response, which was shown to drive true chronic rejection and contribute to chronic allograft dysfunction, was predominantly mediated by naïve CD4+ T cells. Conclusion: This work provides new insights into the mechanisms that drive allograft rejection and should help develop new clinical immunosuppressive protocols. In particular, our results highlight the importance of selectively targeting individual T-cell subsets to prevent graft rejection but at the same time maintain immune protective responses to common pathogens.

Degeneracy of antigen recognition as the molecular basis for the high frequency of naive A2/Melan-a peptide multimer(+) CD8(+) T cells in humans.

In contrast with the low frequency of most single epitope reactive T cells in the preimmune repertoire, up to 1 of 1,000 naive CD8(+) T cells from A2(+) individuals specifically bind fluorescent A2/peptide multimers incorporating the A27L analogue of the immunodominant 26-35 peptide from the melanocyte differentiation and melanoma associated antigen Melan-A. This represents the only naive antigen-specific T cell repertoire accessible to direct analysis in humans up to date. To get insight into the molecular basis for the selection and maintenance of such an abundant repertoire, we analyzed the functional diversity of T cells composing this repertoire ex vivo at the clonal level. Surprisingly, we found a significant proportion of multimer(+) clonotypes that failed to recognize both Melan-A analogue and parental peptides in a functional assay but efficiently recognized peptides from proteins of self- or pathogen origin selected for their potential functional cross-reactivity with Melan-A. Consistent with these data, multimers incorporating some of the most frequently recognized peptides specifically stained a proportion of naive CD8(+) T cells similar to that observed with Melan-A multimers. Altogether these results indicate that the high frequency of Melan-A multimer(+) T cells can be explained by the existence of largely cross-reactive subsets of naive CD8(+) T cells displaying multiple specificities.

Surveillance of HIV type 1 drug resistance among naive patients from Venezuela.

We have studied 65 HIV-1-infected untreated patients recruited in Caracas, Venezuela with TCD4 counts > or =350/microl. The reverse transcriptase and protease sequences of the virus were sequenced, aligned with reference HIV-1 group M strains, and analyzed for drug resistance mutations. Most of the viruses were subtype B genotype in both the protease and RT genomic regions. Five of the 62 virus isolates successfully amplified showed evidence of recombination between protease and RT, with their protease region being non-B while their RT region was derived from subtype B. Four strains were found bearing resistance mutations either to NRTIs, NNRTIs, or PIs. The prevalence of HIV-1 isolates bearing resistance mutations was therefore above the 5% threshold of WHO.

Once-daily dolutegravir versus darunavir plus ritonavir for treatment-naive adults with HIV-1 infection (FLAMINGO): 96 week results from a randomised, open-label, phase 3b study.

BACKGROUND: The primary analysis of the FLAMINGO study at 48 weeks showed that patients taking dolutegravir once daily had a significantly higher virological response rate than did those taking ritonavir-boosted darunavir once daily, with similar tolerability. We present secondary efficacy and safety results analysed at 96 weeks. METHODS: FLAMINGO was a multicentre, open-label, phase 3b, non-inferiority study of HIV-1-infected treatment-naive adults. Patients were randomly assigned (1:1) to dolutegravir 50 mg or darunavir 800 mg plus ritonavir 100 mg, with investigator-selected combination tenofovir and emtricitabine or combination abacavir and lamivudine background treatment. The main endpoints were plasma HIV-1 RNA less than 50 copies per mL and safety. The non-inferiority margin was -12%. If the lower end of the 95% CI was greater than 0%, then we concluded that dolutegravir was superior to ritonavir-boosted darunavir. This trial is registered with ClinicalTrials.gov, number NCT01449929. FINDINGS: Of 595 patients screened, 488 were randomly assigned and 484 included in the analysis (242 assigned to receive dolutegravir and 242 assigned to receive ritonavir-boosted darunavir). At 96 weeks, 194 (80%) of 242 patients in the dolutegravir group and 164 (68%) of 242 in the ritonavir-boosted darunavir group had HIV-1 RNA less than 50 copies per mL (adjusted difference 12·4, 95% CI 4·7-20·2; p=0·002), with the greatest difference in patients with high viral load at baseline (50/61 [82%] vs 32/61 [52%], homogeneity test p=0·014). Six participants (three since 48 weeks) in the dolutegravir group and 13 (four) in the darunavir plus ritonavir group discontinued because of adverse events. The most common drug-related adverse events were diarrhoea (23/242 [10%] in the dolutegravir group vs 57/242 [24%] in the darunavir plus ritonavir group), nausea (31/242 [13%] vs 34/242 [14%]), and headache (17/242 [7%] vs 12/242 [5%]). INTERPRETATION: Once-daily dolutegravir is associated with a higher virological response rate than is once-daily ritonavir-boosted darunavir. Dolutegravir compares favourably in efficacy and safety to a boosted darunavir regimen with nucleoside reverse transcriptase inhibitor background treatment for HIV-1-infected treatment-naive patients. FUNDING: ViiV Healthcare and Shionogi & Co.

Brain ischemia alters platelet ATP diphosphohydrolase and 5'-nucleotidase activities in naive and preconditioned rats

The effects of transient forebrain ischemia, reperfusion and ischemic preconditioning on rat blood platelet ATP diphosphohydrolase and 5'-nucleotidase activities were evaluated. Adult Wistar rats were submitted to 2 or 10 min of single ischemic episodes, or to 10 min of ischemia 1 day after a 2-min ischemic episode (ischemic preconditioning) by the four-vessel occlusion method. Rats submitted to single ischemic insults were reperfused for 60 min and for 1, 2, 5, 10 and 30 days after ischemia; preconditioned rats were reperfused for 60 min 1 and 2 days after the long ischemic episode. Brain ischemia (2 or 10 min) inhibited ATP and ADP hydrolysis by platelet ATP diphosphohydrolase. On the other hand, AMP hydrolysis by 5'-nucleotidase was increased after 2, but not 10, min of ischemia. Ischemic preconditioning followed by 10 min of ischemia caused activation of both enzymes. Variable periods of reperfusion distinctly affected each experimental group. Enzyme activities returned to control levels in the 2-min group. However, the decrease in ATP diphosphohydrolase activity was maintained up to 30 days of reperfusion after 10-min ischemia. 5'-Nucleotidase activity was decreased 60 min and 1 day following 10-min ischemia; interestingly, enzymatic activity was increased after 2 and 5 days of reperfusion, and returned to control levels after 10 days. Ischemic preconditioning cancelled the effects of 10-min ischemia on the enzymatic activities. These results indicate that brain ischemia and ischemic preconditioning induce peripheral effects on ecto-enzymes from rat platelets involved in nucleotide metabolism. Thus, ATP, ADP and AMP degradation and probably the generation of adenosine in the circulation may be altered, leading to regulation of microthrombus formation since ADP aggregates platelets and adenosine is an inhibitor of platelet aggregation.

Imbalance of naive and memory T lymphocytes with sustained high cellular activation during the first year of life from uninfected children born to HIV-1-infected mothers on HAART

The immune consequences of in utero HIV exposure to uninfected children whose mothers were submitted to highly active antiretroviral therapy (HAART) during gestation are not well defined. We evaluated 45 HIV-exposed uninfected (ENI) neonates and 45 healthy unexposed control (CT) neonates. All HIV-infected mothers received HAART during pregnancy, and the viral load at delivery was <50 copies/mL for 56.8%. Twenty-three ENI neonates were further evaluated after 12 months and compared to 23 unexposed healthy age-matched infants. Immunophenotyping was performed by flow cytometry in cord and peripheral blood. Cord blood lymphocyte numbers did not differ between groups. However, ENI neonates had a lower percentage of naive T cells than CT neonates (CD4+, 76.6 vs 83.1%, P < 0.001; CD8+, 70.9 vs 79.6%, P = 0.003) and higher percentages of central memory T cells than CT neonates (CD4+, 13.9 vs 8.7%, P < 0.001; CD8+, 8.6 vs 4.8%, P = 0.001). CD38 mean fluorescence intensity of T cells was higher in ENI neonates (CD4+, 62.2 vs 52.1, P = 0.007; CD8+, 47.7 vs 35.3, P < 0.001). At 12 months, ENI infants still had higher mean fluorescence intensity of CD38 on T cells (CD4+, 34.2 vs 23.3, P < 0.001; CD8+, 26.8 vs 19.4, P = 0.035). Despite effective maternal virologic control at delivery, HIV-exposed uninfected children were born with lower levels of naive T cells. Immune activation was present at birth and remained until at least 12 months of age, suggesting that in utero exposure to HIV causes subtle immune abnormalities.

COMBINED FEATURE EXTRACTION TECHNIQUES AND NAIVE BAYES CLASSIFIER FOR SPEECH RECOGNITION

Speech processing and consequent recognition are important areas of Digital Signal Processing since speech allows people to communicate more natu-rally and efficiently. In this work, a speech recognition system is developed for re-cognizing digits in Malayalam. For recognizing speech, features are to be ex-tracted from speech and hence feature extraction method plays an important role in speech recognition. Here, front end processing for extracting the features is per-formed using two wavelet based methods namely Discrete Wavelet Transforms (DWT) and Wavelet Packet Decomposition (WPD). Naive Bayes classifier is used for classification purpose. After classification using Naive Bayes classifier, DWT produced a recognition accuracy of 83.5% and WPD produced an accuracy of 80.7%. This paper is intended to devise a new feature extraction method which produces improvements in the recognition accuracy. So, a new method called Dis-crete Wavelet Packet Decomposition (DWPD) is introduced which utilizes the hy-brid features of both DWT and WPD. The performance of this new approach is evaluated and it produced an improved recognition accuracy of 86.2% along with Naive Bayes classifier.

Improving Multi-class Text Classification with Naive Bayes

There are numerous text documents available in electronic form. More and more are becoming available every day. Such documents represent a massive amount of information that is easily accessible. Seeking value in this huge collection requires organization; much of the work of organizing documents can be automated through text classification. The accuracy and our understanding of such systems greatly influences their usefulness. In this paper, we seek 1) to advance the understanding of commonly used text classification techniques, and 2) through that understanding, improve the tools that are available for text classification. We begin by clarifying the assumptions made in the derivation of Naive Bayes, noting basic properties and proposing ways for its extension and improvement. Next, we investigate the quality of Naive Bayes parameter estimates and their impact on classification. Our analysis leads to a theorem which gives an explanation for the improvements that can be found in multiclass classification with Naive Bayes using Error-Correcting Output Codes. We use experimental evidence on two commonly-used data sets to exhibit an application of the theorem. Finally, we show fundamental flaws in a commonly-used feature selection algorithm and develop a statistics-based framework for text feature selection. Greater understanding of Naive Bayes and the properties of text allows us to make better use of it in text classification.

Comparison of subcellular partitioning, distribution, and internal speciation of Cu between Cu-tolerant and naive populations of Dendrodrilus rubidus Savigny

When considering contaminated site ecology and ecological risk assessment a key question is whether organisms that appear unaffected by accumulation of contaminants are tolerant or resistant to those contaminants. A population of Dendrodrilus rubidus Savigny earthworms from the Coniston Copper Mines, an area of former Cu mining, exhibit increased tolerance and accumulation of Cu relative to a nearby non-Cu exposed population. Distribution of total Cu between different body parts (posterior, anterior, body wall) of the two populations was determined after a 14 day exposure to 250 mg Cu kg(-1) in Cu-amended soil. Cu concentrations were greater in Coniston earthworms but relative proportions of Cu in different body parts were the same between populations. Cu speciation was determined using extended X-ray absorption fine structure spectroscopy (EXAFS). Cu was coordinated to 0 atoms in the exposure soil but to S atoms in the earthworms. There was no difference in this speciation between the different earthworm populations. In another experiment earthworms were exposed to a range of Cu concentrations (200-700 mg Cu kg(-1)). Subcellular partitioning of accumulated Cu was determined. Coniston earthworms accumulated more Cu but relative proportions of Cu in the different fractions (cytosol > granular > tissue fragments, cell membranes, and intact cells) were the same between populations. Results suggest that Coniston D. rubidus are able to survive in the Cu-rich Coniston Copper Mines soil through enlargement of the same Cu storage reservoirs that exist in a nearby non-Cu exposed population.

The use of cues to convergence and accommodation in naive, uninstructed participants

A remote haploscopic video refractor was used to assess vergence and accommodation responses in a group of 32 emmetropic, orthophoric, symptom free, young adults naïve to vision experiments in a minimally instructed setting. Picture targets were presented at four positions between 2 m and 33 cm. Blur, disparity and looming cues were presented in combination or separately to asses their contributions to the total near response in a within-subjects design. Response gain for both vergence and accommodation reduced markedly whenever disparity was excluded, with much smaller effects when blur and proximity were excluded. Despite the clinical homogeneity of the participant group there were also some individual differences.

Memory versus naive T-cell migration

Our established understanding of lymphocyte migration suggests that naive and memory T cells travel throughout the body via divergent pathways; naive T cells circulate between blood and lymph whereas memory T cells additionally migrate through non-lymphoid organs. Evidence is now gradually emerging which suggests such disparate pathways between naive and memory T cells may not strictly be true, and that naive T cells gain access to the non-lymphoid environment in numbers approaching that of memory T cells. We discuss here the evidence for naive T-cell traffic into the non-lymphoid environment, compare and contrast this movement with what is known of memory T cells, and finally discuss the functional importance of why naive T cells might access the parenchymal tissues.

Ventilatory frequency indicates visual recognition of an allopatric predator in naive Nile tilapia

Perceiving a possible predator may promote physiological changes to support prey 'fight or flight'. In this case, an increase in ventilatory frequency (VF) may be expected, because this is a way to improve oxygen uptake for escape tasks. Therefore, changes in VF may be used as a behavioral tool to evaluate visual recognition of a predator threat. Thus, we tested the effects of predator visual exposure on VF in the fish Nile tilapia, Oreochromis niloticus. For this, we measured tilapia VF before and after the presentation of three stimuli: an aquarium with a harmless fish or a predator or water (control). Nile tilapia VF increased significantly in the group visually exposed to a predator compared with the other two, which were similar to each other. Hence, we conclude that Nile tilapia may recognize an allopatric predator; consequently VF is an effective tool to indicate visual recognition of predator threat in fish. (C) 2002 Elsevier B.V. B.V. All rights reserved.

Plasma cortisol in first episode drug-naive mania: Differential levels in euphoric versus irritable mood

Background: Dysregulation of HPA axis has been widely described in subjects with bipolar disorder (BD), including changes in cortisol levels during mood episodes and euthymia. However, most of the studies were done with medicated BD patients with variable length of illness, which was shown to interfere on peripheral cortisol levels. Therefore, the present study aims to evaluate plasma cortisol levels in drug-naive BD subjects during the first manic episode, as well as investigate the relationship between plasma cortisol levels and manic symptomatology. Methods: Twenty-six drug-naive patients were enrolled meeting criteria for a first manic episode in bipolar I disorder. Severity of mania was assessed using the Young Mania Rating Scale (YMRS). The control group included 27 healthy subjects matched by age and gender. Cortisol was quantified using a direct radioimmunoassay. Results: Plasma cortisol levels were decreased during first manic episode compared to healthy controls. Higher cortisol levels were positively associated with the presence of irritability (dysphoria), while elated mania showed lower cortisol levels compared to controls. Limitation: Data including larger samples are lacking. Conclusion: Higher cortisol in dysphoric mania compared to predominantly elated/euphoric mania may indicate a clinical and neurobiological polymorphic phenomenon, potentially involving a higher biological sensitivity to stress in the presence of irritable mood. The present findings highlight the importance to add a dimensional approach to the traditional categorical diagnosis for future neurobiological studies in BD. (C) 2011 Elsevier B.V. All rights reserved.