Functional properties of edible insects: a systematic review.

Consumption of edible insects has been widely suggested as an environmentally sustainable substitute for meat to reduce greenhouse gas emissions. However, the novel research field for edible insects relies on the content of bioactive ingredients and on the ability to induce a functional effect in humans. The goal of this manuscript is to review the available body of evidence on the properties of edible insects in modulating oxidative and inflammatory stress, platelet aggregation, lipid and glucose metabolism and weight control. A search for literature investigating the functional role of edible insects was carried out in the PubMed database using specific keywords. A total of 55 studies, meeting inclusion criteria after screening, were divided on the basis of the experimental approach: in vitro studies, cellular models/ex vivo studies or in vivo studies. In the majority of the studies, insects demonstrated the ability to reduce oxidative stress, modulate antioxidant status, restore the impaired activity of antioxidant enzymes and reduce markers of oxidative damage. Edible insects displayed anti-inflammatory activity reducing cytokines and modulating specific transcription factors. Results from animal studies suggest that edible insects can modulate lipid and glucose metabolism. The limited number of studies focused on the assessment of anti-coagulation activity of edible insects makes it difficult to draw conclusions. More evidence from dietary intervention studies in humans is needed to support the promising evidence from in vitro and animal models about the functional role of edible insect consumption.

Molecular Epidemiology of HIV-1 Subtype B Infection across Florida Reveals Few Large Superclusters with Metropolitan Origin.

Florida is considered an epicenter of HIV in the United States. The U.S. federal plan for Ending the HIV Epidemic (EHE) within 10 years prioritizes seven of Florida's 67 counties for intervention. We applied molecular epidemiology methods to characterize the HIV infection networks in the state and infer whether the results support the EHE. HIV sequences (N = 34,446) and associated clinical/demographic metadata of diagnosed people with HIV (PWH), during 2007 to 2017, were retrieved from the Florida Department of Health. HIV genetic networks were investigated using MicrobeTrace. Associates of clustering were identified through boosted logistic regression. Assortative trait mixing was also assessed. Bayesian phylogeographic methods were applied to evaluate evidence of imported HIV-1 lineages and illustrate spatiotemporal flows within Florida. We identified nine large clusters spanning all seven EHE counties but little evidence of external introductions, suggesting-in the absence of undersampling-an epidemic that evolved independently from the rest of the country or other external influences. Clusters were highly assortative by geography. Most of the sampled infections (82%) did not cluster with others in the state using standard molecular surveillance methods despite satisfactory sequence sampling in the state. The odds of being unclustered were higher among PWH in rural regions, and depending on demographics. A significant number of unclustered sequences were observed in counties omitted from EHE. The large number of missing sequence links may impact timely detection of emerging transmission clusters and ultimately hinder the success of EHE in Florida. Molecular epidemiology may help better understand infection dynamics at the population level and underlying disparities in disease transmission among subpopulations; however, there is also a continuous need to conduct ethical discussions to avoid possible harm of advanced methodologies to vulnerable groups, especially in the context of HIV stigmatization. IMPORTANCE The large number of missing phylogenetic linkages in rural Florida counties and among women and Black persons with HIV may impact timely detection of ongoing and emerging transmission clusters and ultimately hinder the success of epidemic elimination goals in Florida.

Automatic lung segmentation in COVID-19 patients: Impact on quantitative computed tomography analysis.

PURPOSE: To assess the impact of lung segmentation accuracy in an automatic pipeline for quantitative analysis of CT images. METHODS: Four different platforms for automatic lung segmentation based on convolutional neural network (CNN), region-growing technique and atlas-based algorithm were considered. The platforms were tested using CT images of 55 COVID-19 patients with severe lung impairment. Four radiologists assessed the segmentations using a 5-point qualitative score (QS). For each CT series, a manually revised reference segmentation (RS) was obtained. Histogram-based quantitative metrics (QM) were calculated from CT histogram using lung segmentationsfrom all platforms and RS. Dice index (DI) and differences of QMs (ΔQMs) were calculated between RS and other segmentations. RESULTS: Highest QS and lower ΔQMs values were associated to the CNN algorithm. However, only 45% CNN segmentations were judged to need no or only minimal corrections, and in only 17 cases (31%), automatic segmentations provided RS without manual corrections. Median values of the DI for the four algorithms ranged from 0.993 to 0.904. Significant differences for all QMs calculated between automatic segmentations and RS were found both when data were pooled together and stratified according to QS, indicating a relationship between qualitative and quantitative measurements. The most unstable QM was the histogram 90th percentile, with median ΔQMs values ranging from 10HU and 158HU between different algorithms. CONCLUSIONS: None of tested algorithms provided fully reliable segmentation. Segmentation accuracy impacts differently on different quantitative metrics, and each of them should be individually evaluated according to the purpose of subsequent analyses.

A patient-specific approach for quantitative and automatic analysis of computed tomography images in lung disease: Application to COVID-19 patients.

PURPOSE: Quantitative metrics in lung computed tomography (CT) images have been widely used, often without a clear connection with physiology. This work proposes a patient-independent model for the estimation of well-aerated volume of lungs in CT images (WAVE). METHODS: A Gaussian fit, with mean (Mu.f) and width (Sigma.f) values, was applied to the lower CT histogram data points of the lung to provide the estimation of the well-aerated lung volume (WAVE.f). Independence from CT reconstruction parameters and respiratory cycle was analysed using healthy lung CT images and 4DCT acquisitions. The Gaussian metrics and first order radiomic features calculated for a third cohort of COVID-19 patients were compared with those relative to healthy lungs. Each lung was further segmented in 24 subregions and a new biomarker derived from Gaussian fit parameter Mu.f was proposed to represent the local density changes. RESULTS: WAVE.f resulted independent from the respiratory motion in 80% of the cases. Differences of 1%, 2% and up to 14% resulted comparing a moderate iterative strength and FBP algorithm, 1 and 3 mm of slice thickness and different reconstruction kernel. Healthy subjects were significantly different from COVID-19 patients for all the metrics calculated. Graphical representation of the local biomarker provides spatial and quantitative information in a single 2D picture. CONCLUSIONS: Unlike other metrics based on fixed histogram thresholds, this model is able to consider the inter- and intra-subject variability. In addition, it defines a local biomarker to quantify the severity of the disease, independently of the observer.

Brain tissue transcriptomic analysis of SIV-infected macaques identifies several altered metabolic pathways linked to neuropathogenesis and poly (ADP-ribose) polymerases (PARPs) as potential therapeutic targets.

Despite improvements in antiretroviral therapy, human immunodeficiency virus type 1 (HIV-1)-associated neurocognitive disorders (HAND) remain prevalent in subjects undergoing therapy. HAND significantly affects individuals' quality of life, as well as adherence to therapy, and, despite the increasing understanding of neuropathogenesis, no definitive diagnostic or prognostic marker has been identified. We investigated transcriptomic profiles in frontal cortex tissues of Simian immunodeficiency virus (SIV)-infected Rhesus macaques sacrificed at different stages of infection. Gene expression was compared among SIV-infected animals (n = 11), with or without CD8+ lymphocyte depletion, based on detectable (n = 6) or non-detectable (n = 5) presence of the virus in frontal cortex tissues. Significant enrichment in activation of monocyte and macrophage cellular pathways was found in animals with detectable brain infection, independently from CD8+ lymphocyte depletion. In addition, transcripts of four poly (ADP-ribose) polymerases (PARPs) were up-regulated in the frontal cortex, which was confirmed by real-time polymerase chain reaction. Our results shed light on involvement of PARPs in SIV infection of the brain and their role in SIV-associated neurodegenerative processes. Inhibition of PARPs may provide an effective novel therapeutic target for HIV-related neuropathology.

Cost-Effectiveness of a Statewide Pre-Exposure Prophylaxis Program for Gay, Bisexual, and Other Men Who Have Sex with Men.

Pre-exposure prophylaxis (PrEP) is an effective tool for preventing HIV infection among men who have sex with men (MSM), but its cost-effectiveness has varied across settings. Using an agent-based model, we projected the cost-effectiveness of a statewide PrEP program for MSM in Rhode Island over the next decade. In the absence of PrEP, the model predicted an average of 830 new HIV infections over ten years. Scaling up the existing PrEP program to cover 15% of MSM with ten or more partners each year could reduce the number of new HIV infections by 33.1% at a cost of $184,234 per quality-adjusted life-year (QALY) gained. Expanded PrEP use among MSM at high risk for HIV infection has the potential to prevent a large number of new HIV infections but the high drug-related costs may limit the cost-effectiveness of this intervention.

Emergence of recombinant Mayaro virus strains from the Amazon basin.

Mayaro virus (MAYV), causative agent of Mayaro Fever, is an arbovirus transmitted by Haemagogus mosquitoes. Despite recent attention due to the identification of several cases in South and Central America and the Caribbean, limited information on MAYV evolution and epidemiology exists and represents a barrier to prevention of further spread. We present a thorough spatiotemporal evolutionary study of MAYV full-genome sequences collected over the last sixty years within South America and Haiti, revealing recent recombination events and adaptation to a broad host and vector range, including Aedes mosquito species. We employed a Bayesian phylogeography approach to characterize the emergence of recombinants in Brazil and Haiti and report evidence in favor of the putative role of human mobility in facilitating recombination among MAYV strains from geographically distinct regions. Spatiotemporal characteristics of recombination events and the emergence of this previously neglected virus in Haiti, a known hub for pathogen spread to the Americas, warrants close monitoring of MAYV infection in the immediate future.

Computer-Aided Optimization of Combined Anti-Retroviral Therapy for HIV: New Drugs, New Drug Targets and Drug Resistance.

BACKGROUND: Resistance to antiretroviral drugs is a complex and evolving area with relevant implications in the treatment of human immunodeficiency virus (HIV) infection. Several rules, algorithms and full-fledged computer programs have been developed to assist the HIV specialist in the choice of the best patient-tailored therapy. METHODS: Experts' rules and statistical/machine learning algorithms for interpreting HIV drug resistance, along with their program implementations, were retrieved from PubMed and other on-line resources to be critically reviewed in terms of technical approach, performance, usability, update, and evolution (i.e. inclusion of novel drugs or expansion to other viral agents). RESULTS: Several drug resistance prediction algorithms for the nucleotide/nucleoside/non-nucleoside reverse transcriptase, protease and integrase inhibitors as well as coreceptor antagonists are currently available, routinely used, and have been validated thoroughly in independent studies. Computer tools that combine single-drug genotypic/phenotypic resistance interpretation and optimize combination antiretroviral therapy have been also developed and implemented as web applications. Most of the systems have been updated timely to incorporate new drugs and few have recently been expanded to meet a similar need in the Hepatitis C area. Prototype systems aiming at predicting virological response from both virus and patient indicators have been recently developed but they are not yet being routinely used. CONCLUSION: Computing HIV genotype to predict drug susceptibility in vitro or response to combination antiretroviral therapy in vivo is a continuous and productive research field, translating into successful treatment decision support tools, an essential component of the management of HIV patients.

Postoperative Pain Surveys in Italy from 2006 and 2012: (POPSI and POPSI-2).

OBJECTIVE: Despite established standards, effective treatments, and evidence-based guidelines, postoperative pain control in Italy and other parts of the world remains suboptimal. Pain control has been recognized as a fundamental human right. Effective treatments exist to control postsurgical pain. Inadequate postoperative analgesia may prolong the length of hospital stays and may adversely impact outcomes. MATERIALS AND METHODS: The same multiple-choice survey administered at the SIAARTI National Congress in Perugia in 2006 (n=588) was given at the SIAARTI National Congress in Naples, Italy in 2012 (n=635). The 2012 survey was analysed and compared to the 2006 results. RESULTS: Postoperative pain control in Italy was less than optimal in 2006 and showed no substantial improvements in 2012. Geographical distinctions were evident with certain parts of Italy offering better postoperative pain control than other. Fewer than half of hospitals represented had an active Acute Pain Service (APS) and only about 10% of postsurgical patients were managed according to evidence-based guidelines. For example, elastomeric pumps for continuous IV infusion are commonly used in Italy, although patient-controlled analgesia systems are recommended in the guidelines. The biggest obstacles to optimal postoperative pain control reported by respondents could be categorized as organizational, cultural, and economic. CONCLUSIONS: There is considerable room for improvement in postoperative pain control in Italy, specifically in the areas of clinical education, evidence-based treatments, better equipment, and implementation of active APS departments in more hospitals. Two surveys taken six years apart in Italy reveal, with striking similarity, that there are many unmet needs in postoperative pain control and that Italy still falls below European standards for postoperative pain control.

Evolution pathways of IgE responses to grass and mite allergens throughout childhood.

BACKGROUND: Little is known about longitudinal patterns of the development of IgE to distinct allergen components. OBJECTIVE: We sought to investigate the evolution of IgE responses to allergenic components of timothy grass and dust mite during childhood. METHODS: In a population-based birth cohort (n = 1184) we measured IgE responses to 15 components from timothy grass and dust mite in children with available samples at 3 time points (ages 5, 8, and 11 years; n = 235). We designed a nested, 2-stage latent class analysis to identify cross-sectional sensitization patterns at each follow-up and their longitudinal trajectories. We then ascertained the association of longitudinal trajectories with asthma, rhinitis, eczema, and lung function in children with component data for at least 2 time points (n = 534). RESULTS: Longitudinal latent class analysis revealed 3 grass sensitization trajectories: (1) no/low sensitization; (2) early onset; and (3) late onset. The early-onset trajectory was associated with asthma and diminished lung function, and the late-onset trajectory was associated with rhinitis. Four longitudinal trajectories emerged for mite: (1) no/low sensitization; (2) group 1 allergens; (3) group 2 allergens; and (3) complete mite sensitization. Children in the complete mite sensitization trajectory had the highest odds ratios (ORs) for asthma (OR, 7.15; 95% CI, 3.80-13.44) and were the only group significantly associated with comorbid asthma, rhinitis, and eczema (OR, 5.91; 95% CI, 2.01-17.37). Among children with wheezing, those in the complete mite sensitization trajectory (but not other longitudinal mite trajectories) had significantly higher risk of severe exacerbations (OR, 3.39; 95% CI, 1.62-6.67). CONCLUSIONS: The nature of developmental longitudinal trajectories of IgE responses differed between grass and mite allergen components, with temporal differences (early vs late onset) dominant in grass and diverging patterns of IgE responses (group 1 allergens, group 2 allergens, or both) in mite. Different longitudinal patterns bear different associations with clinical outcomes, which varied by allergen.

A look inside the association codeine-paracetamol: clinical pharmacology supports analgesic efficacy.

Acute and chronic pain often requires a multimodal approach. Combination therapy reduces the number of individual daily administrations and improves patient's compliance with the prescribed analgesic treatment. Despite the association codeine/paracetamol is one of the most widely used central analgesic, the exact mechanism of action, particularly of paracetamol, is still object of pharmacological research. Recent findings showed that paracetamol may act through cerebral cyclo-oxygenase, descending opioidergic inhibitory pathways, serotonin pathway, and the endocannabinoid system; while codeine activity seems to related not only to its conversion to morphine, as previously known, but also by itself and through its metabolites, such as norcodeine (NORC) and codeine-6-glucuronide (C-6-G). The addition of codeine to paracetamol significantly improves the analgesic action and reduces the number needed to treat (NNT) from 5 to 2.3-3.1. Recent warnings about the risk of its metabolism related to CYP450 and its genetic variability in general population should be mainly considered when the association is used in paediatric patients undergoing tonsillectomy and/or adenoidectomy procedures for obstructive sleep apnoea syndrome (OSAS). In adults, the association codeine/paracetamol has been shown to be effective and safe in different settings: acute pain, trauma patients, and chronic nociceptive pain.

Flavanols, proanthocyanidins and antioxidant activity changes during cocoa (Theobroma cacao L.) roasting as affected by temperature and time of processing.

The effect of roasting on the content of flavanols and proanthocyanidins and on the antioxidant activity of cocoa beans was investigated. Cocoa beans were roasted at three temperatures (125, 135 and 145 °C), for different times, to reach moisture contents of about 2 g 100 g(-1). Flavanols and proanthocyanidins were determined, and the antioxidant activity was tested by total phenolic index (TPI), ferric reducing antioxidant power (FRAP) and total radical trapping antioxidant parameter (TRAP) methods. The rates of flavanol and total proanthocyanidin loss increased with roasting temperatures. Moisture content of the roasted beans being equal, high temperature-short time processes minimised proanthocyanidins loss. Moisture content being equal, the average roasting temperature (135 °C) determined the highest TPI and FRAP values and the highest temperature (145 °C) determined the lowest TPI values. Moisture content being equal, low temperature-long time roasting processes maximised the chain-breaking activity, as determined by the TRAP method.

Italian Intersociety Recommendations on pain management in the emergency setting (SIAARTI, SIMEU, SIS 118, AISD, SIARED, SICUT, IRC).

BACKGRAUND: Pain is the primary reason for admission to the Emergency Department (ED). However, the management of pain in this setting is often inadequate because of opiophagia, fear of excessive sedation, and fear of compromising an adequate clinical assessment. METHODS: An intersociety consensus conference was held in 2010 on the assessment and treatment of pain in the emergency setting. This report is the Italian Intersociety recommendations on pain management in the emergency department setting. RESULTS: The list of level A recommendations includes: 1) use of IV acetaminophen for opioid sparing properties and reduction of opioid related adverse events; 2) ketamine-midazolam combination preferred over fentanyl-midazolam fentanyl-propofol in pediatric patients; 3) boluses of ketamine IV (particularly in the population under the age of 2 years and over the age of 13) can lead to impairment of the upper airways, including the onset of laryngospasm, requiring specific expertise and skills for administration; 4) the use of ketamine increases the potential risk of psychomotor agitation, which can happen in up to 30% of adult patients (this peculiar side effect can be significantly reduced by concomitant systemic use of benzodiazepines); 5) for shoulder dislocations and fractures of the upper limbs, the performance of brachial plexus block reduces the time spent in ED compared to sedation; 6) pain relief and the use of opioids in patients with acute abdominal pain do not increase the risk of error in the diagnostic and therapeutic pathway in adults; 7) in newborns, the administration of sucrose reduces behavioural responses to blood sampling from a heel puncture; 8) in newborns, breastfeeding or formula feeding during the procedure reduces the measures of distress; 9) in pediatric patients, non-pharmacological techniques such as distraction, hypnosis and cognitive-behavioural interventions reduce procedural pain caused by the use of needles; 10) in pediatric patients, preventive application of eutectic mixtures of prilocaine and lidocaine allows arterial and venous samples to be taken in optimum conditions; 11) in pediatric patients, the combination of hypnotics (midazolam) and N2O is effective for procedural pain, but may be accompanied by loss of consciousness. CONCLUSION: The diagnostic-therapeutic pathway of pain management in emergency should be implemented, through further interdisciplinary trials, in order to improve the EBM level of specific guidelines.

[Paracetamol-codeine, an always actual choice for the treatment of pain]. / Paracetamolo-codeina, una scelta sempre attuale per il trattamento del dolore.

Acute pain of mild to moderate intensity is one of the problems most frequently encountered in primary care and emergency medicine and is a major reason of request for visit by patients. In recent years the focus has been more on the treatment of chronic pain, perhaps ignoring the negative impact of acute pain on quality of life and functional status of the patient, despite a growing number of evidence indicating the need to treat optimally also acute pain to avoid it prolongs in time. The remarkable progress achieved in the understanding of the physiological mechanisms of the nociceptive stimulus, as well as those common to biochemical inflammation and acute pain, highlighted the active and complex role of central nervous system in the genesis and maintenance of pain that from acute, if not promptly and adequately treated, can become chronic. In this article, after a brief introduction on the most recent advances on the transition from acute to chronic pain, we have focused on paracetamol, an analgesic drug widely used for over a century for its demonstrated efficacy and tolerability. Paracetamol that, thanks to a complex and not yet fully defined mechanism of action, certainly localized in the central nervous system, can have a significant role in the early treatment of acute pain aimed to reduce the risk of chronicization. Pharmacokinetic parameters and pharmacodynamic studies are outlined, as well as the latest acquisitions in terms of metabolism of this drug and the risks related to its misuse. Are also discussed the recommendations issued by scientific societies and recent articles that indicate paracetamol as the drug of first choice for mild to moderate pain in various clinical settings, such as post-operative pain, post-traumatic and osteoarticular diseases, alone or in association with weak opioids, in particular with codeine. Most recent findings about metabolism and analgesic effect of codeine and its metabolites are highlighted, and how, in combination with acetaminophen, there is an increase in analgesic efficacy without increasing side effects, offering the chance of obtaining a better pain control.

Can multiple SNP testing in BRCA2 and BRCA1 female carriers be used to improve risk prediction models in conjunction with clinical assessment?

BACKGROUND: Several single nucleotide polymorphisms (SNPs) at different loci have been associated with breast cancer susceptibility, accounting for around 10% of the familial component. Recent studies have found direct associations between specific SNPs and breast cancer in BRCA1/2 mutation carriers. Our aim was to determine whether validated susceptibility SNP scores improve the predictive ability of risk models in comparison/conjunction to other clinical/demographic information. METHODS: Female BRCA1/2 carriers were identified from the Manchester genetic database, and included in the study regardless of breast cancer status or age. DNA was extracted from blood samples provided by these women and used for gene and SNP profiling. Estimates of survival were examined with Kaplan-Meier curves. Multivariable Cox proportional hazards models were fit in the separate BRCA datasets and in menopausal stages screening different combinations of clinical/demographic/genetic variables. Nonlinear random survival forests were also fit to identify relevant interactions. Models were compared using Harrell's concordance index (1 - c-index). RESULTS: 548 female BRCA1 mutation carriers and 523 BRCA2 carriers were identified from the database. Median Kaplan-Meier estimate of survival was 46.0 years (44.9-48.1) for BRCA1 carriers and 48.9 (47.3-50.4) for BRCA2. By fitting Cox models and random survival forests, including both a genetic SNP score and clinical/demographic variables, average 1 - c-index values were 0.221 (st.dev. 0.019) for BRCA1 carriers and 0.215 (st.dev. 0.018) for BRCA2 carriers. CONCLUSIONS: Random survival forests did not yield higher performance compared to Cox proportional hazards. We found improvement in prediction performance when coupling the genetic SNP score with clinical/demographic markers, which warrants further investigation.

Baseline CD4+ T cell counts correlates with HIV-1 synonymous rate in HLA-B*5701 subjects with different risk of disease progression.

HLA-B*5701 is the host factor most strongly associated with slow HIV-1 disease progression, although risk of progression may vary among patients carrying this allele. The interplay between HIV-1 evolutionary rate variation and risk of progression to AIDS in HLA-B*5701 subjects was studied using longitudinal viral sequences from high-risk progressors (HRPs) and low-risk progressors (LRPs). Posterior distributions of HIV-1 genealogies assuming a Bayesian relaxed molecular clock were used to estimate the absolute rates of nonsynonymous and synonymous substitutions for different set of branches. Rates of viral evolution, as well as in vitro viral replication capacity assessed using a novel phenotypic assay, were correlated with various clinical parameters. HIV-1 synonymous substitution rates were significantly lower in LRPs than HRPs, especially for sets of internal branches. The viral population infecting LRPs was also characterized by a slower increase in synonymous divergence over time. This pattern did not correlate to differences in viral fitness, as measured by in vitro replication capacity, nor could be explained by differences among subjects in T cell activation or selection pressure. Interestingly, a significant inverse correlation was found between baseline CD4+ T cell counts and mean HIV-1 synonymous rate (which is proportional to the viral replication rate) along branches representing viral lineages successfully propagating through time up to the last sampled time point. The observed lower replication rate in HLA-B*5701 subjects with higher baseline CD4+ T cell counts provides a potential model to explain differences in risk of disease progression among individuals carrying this allele.

Spatiotemporal dynamics of simian immunodeficiency virus brain infection in CD8+ lymphocyte-depleted rhesus macaques with neuroAIDS.

Despite the success of combined antiretroviral therapy in controlling viral replication in human immunodeficiency virus (HIV)-infected individuals, HIV-associated neurocognitive disorders, commonly referred to as neuroAIDS, remain a frequent and poorly understood complication. Infection of CD8(+) lymphocyte-depleted rhesus macaques with the SIVmac251 viral swarm is a well-established rapid disease model of neuroAIDS that has provided critical insight into HIV-1-associated neurocognitive disorder onset and progression. However, no studies so far have characterized in depth the relationship between intra-host viral evolution and pathogenesis in this model. Simian immunodeficiency virus (SIV) env gp120 sequences were obtained from six infected animals. Sequences were sampled longitudinally from several lymphoid and non-lymphoid tissues, including individual lobes within the brain at necropsy, for four macaques; two animals were sacrificed at 21 days post-infection (p.i.) to evaluate early viral seeding of the brain. Bayesian phylodynamic and phylogeographic analyses of the sequence data were used to ascertain viral population dynamics and gene flow between peripheral and brain tissues, respectively. A steady increase in viral effective population size, with a peak occurring at ~50-80 days p.i., was observed across all longitudinally monitored macaques. Phylogeographic analysis indicated continual viral seeding of the brain from several peripheral tissues throughout infection, with the last migration event before terminal illness occurring in all macaques from cells within the bone marrow. The results strongly supported the role of infected bone marrow cells in HIV/SIV neuropathogenesis. In addition, our work demonstrated the applicability of Bayesian phylogeography to intra-host studies in order to assess the interplay between viral evolution and pathogenesis.

Challenges in interpreting allergen microarrays in relation to clinical symptoms: a machine learning approach.

BACKGROUND: Identifying different patterns of allergens and understanding their predictive ability in relation to asthma and other allergic diseases is crucial for the design of personalized diagnostic tools. METHODS: Allergen-IgE screening using ImmunoCAP ISAC(®) assay was performed at age 11 yrs in children participating a population-based birth cohort. Logistic regression (LR) and nonlinear statistical learning models, including random forests (RF) and Bayesian networks (BN), coupled with feature selection approaches, were used to identify patterns of allergen responses associated with asthma, rhino-conjunctivitis, wheeze, eczema and airway hyper-reactivity (AHR, positive methacholine challenge). Sensitivity/specificity and area under the receiver operating characteristic (AUROC) were used to assess model performance via repeated validation. RESULTS: Serum sample for IgE measurement was obtained from 461 of 822 (56.1%) participants. Two hundred and thirty-eight of 461 (51.6%) children had at least one of 112 allergen components IgE > 0 ISU. The binary threshold >0.3 ISU performed less well than using continuous IgE values, discretizing data or using other data transformations, but not significantly (p = 0.1). With the exception of eczema (AUROC~0.5), LR, RF and BN achieved comparable AUROC, ranging from 0.76 to 0.82. Dust mite, pollens and pet allergens were highly associated with asthma, whilst pollens and dust mite with rhino-conjunctivitis. Egg/bovine allergens were associated with eczema. CONCLUSIONS: After validation, LR, RF and BN demonstrated reasonable discrimination ability for asthma, rhino-conjunctivitis, wheeze and AHR, but not for eczema. However, further improvements in threshold ascertainment and/or value transformation for different components, and better interpretation algorithms are needed to fully capitalize on the potential of the technology.

Challenges in identifying asthma subgroups using unsupervised statistical learning techniques.

RATIONALE: Unsupervised statistical learning techniques, such as exploratory factor analysis (EFA) and hierarchical clustering (HC), have been used to identify asthma phenotypes, with partly consistent results. Some of the inconsistency is caused by the variable selection and demographic and clinical differences among study populations. OBJECTIVES: To investigate the effects of the choice of statistical method and different preparations of data on the clustering results; and to relate these to disease severity. METHODS: Several variants of EFA and HC were applied and compared using various sets of variables and different encodings and transformations within a dataset of 383 children with asthma. Variables included lung function, inflammatory and allergy markers, family history, environmental exposures, and medications. Clusters and original variables were related to asthma severity (logistic regression and Bayesian network analysis). MEASUREMENTS AND MAIN RESULTS: EFA identified five components (eigenvalues ≥ 1) explaining 35% of the overall variance. Variations of the HC (as linkage-distance functions) did not affect the cluster inference; however, using different variable encodings and transformations did. The derived clusters predicted asthma severity less than the original variables. Prognostic factors of severity were medication usage, current symptoms, lung function, paternal asthma, body mass index, and age of asthma onset. Bayesian networks indicated conditional dependence among variables. CONCLUSIONS: The use of different unsupervised statistical learning methods and different variable sets and encodings can lead to multiple and inconsistent subgroupings of asthma, not necessarily correlated with severity. The search for asthma phenotypes needs more careful selection of markers, consistent across different study populations, and more cautious interpretation of results from unsupervised learning.

Empirical validation of viral quasispecies assembly algorithms: state-of-the-art and challenges.

Next generation sequencing (NGS) is superseding Sanger technology for analysing intra-host viral populations, in terms of genome length and resolution. We introduce two new empirical validation data sets and test the available viral population assembly software. Two intra-host viral population 'quasispecies' samples (type-1 human immunodeficiency and hepatitis C virus) were Sanger-sequenced, and plasmid clone mixtures at controlled proportions were shotgun-sequenced using Roche's 454 sequencing platform. The performance of different assemblers was compared in terms of phylogenetic clustering and recombination with the Sanger clones. Phylogenetic clustering showed that all assemblers captured a proportion of the most divergent lineages, but none were able to provide a high precision/recall tradeoff. Estimated variant frequencies mildly correlated with the original. Given the limitations of currently available algorithms identified by our empirical validation, the development and exploitation of additional data sets is needed, in order to establish an efficient framework for viral population reconstruction using NGS.