Staged induction of HIV-1 glycan–dependent broadly neutralizing antibodies

A preventive HIV-1 vaccine should induce HIV-1–specific broadly neutralizing antibodies (bnAbs). However, bnAbs generally require high levels of somatic hypermutation (SHM) to acquire breadth, and current vaccine strategies have not been successful in inducing bnAbs. Because bnAbs directed against a glycosylated site adjacent to the third variable loop (V3) of the HIV-1 envelope protein require limited SHM, the V3-glycan epitope is an attractive vaccine target. By studying the cooperation among multiple V3-glycan B cell lineages and their coevolution with autologous virus throughout 5 years of infection, we identify key events in the ontogeny of a V3-glycan bnAb. Two autologous neutralizing antibody lineages selected for virus escape mutations and consequently allowed initiation and affinity maturation of a V3-glycan bnAb lineage. The nucleotide substitution required to initiate the bnAb lineage occurred at a low-probability site for activation-induced cytidine deaminase activity. Cooperation of B cell lineages and an improbable mutation critical for bnAb activity defined the necessary events leading to breadth in this V3-glycan bnAb lineage. These findings may, in part, explain why initiation of V3-glycan bnAbs is rare, and suggest an immunization strategy for inducing similar V3-glycan bnAbs

Multi-scale Inference of Interaction Rules in Animal Groups Using Bayesian Model Selection

Inference of interaction rules of animals moving in groups usually relies on an analysis of large scale system behaviour. Models are tuned through repeated simulation until they match the observed behaviour. More recent work has used the fine scale motions of animals to validate and fit the rules of interaction of animals in groups. Here, we use a Bayesian methodology to compare a variety of models to the collective motion of glass prawns (Paratya australiensis). We show that these exhibit a stereotypical ‘phase transition’, whereby an increase in density leads to the onset of collective motion in one direction. We fit models to this data, which range from: a mean-field model where all prawns interact globally; to a spatial Markovian model where prawns are self-propelled particles influenced only by the current positions and directions of their neighbours; up to non-Markovian models where prawns have ‘memory’ of previous interactions, integrating their experiences over time when deciding to change behaviour. We show that the mean-field model fits the large scale behaviour of the system, but does not capture fine scale rules of interaction, which are primarily mediated by physical contact. Conversely, the Markovian self-propelled particle model captures the fine scale rules of interaction but fails to reproduce global dynamics. The most sophisticated model, the non-Markovian model, provides a good match to the data at both the fine scale and in terms of reproducing global dynamics. We conclude that prawns' movements are influenced by not just the current direction of nearby conspecifics, but also those encountered in the recent past. Given the simplicity of prawns as a study system our research suggests that self-propelled particle models of collective motion should, if they are to be realistic at multiple biological scales, include memory of previous interactions and other non-Markovian effects

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

The rural Prehospital Acute Stroke Triage (PAST) trial protocol: a controlled trial for rapid facilitated transport of rural acute stroke patients to a regional stroke centre

Rationale Access to intravenous thrombolysis for acute ischaemic stroke is limited worldwide, particularly in regional and rural areas including in Australia. We are testing the effectiveness of a new rural Prehospital Acute Stroke Triage protocol that includes prehospital assessment and rapid transport of patients from a rural catchment to the major stroke centre in Newcastle, NSW, Australia. The local district hospitals within the rural catchment do not have the capability or infrastructure to deliver acute stroke thrombolysis. The trial has relevance to stroke clinicians, health service managers and planners responsible for rural populations. Aims: To implement a system of rapid prehospital assessment and facilitated transport that will significantly increase stroke thrombolysis rates to 10% of ischaemic stroke cases in the rural catchment. Validate an eight-point modified National Institutes of Health Stroke Scale for use by paramedics in the prehospital setting to assess patients’ potential eligibility for stroke thrombolysis. Design: The joint project between the John Hunter Hospital Acute Stroke Team and the Ambulance Service of NSW will use a prospective cohort with an historical control group. Tools and protocols have been developed and education undertaken for ambulance field and operations centre personnel. These include a cut-down eight-item National Institutes of Health Stroke Scale (Hunter NIHSS-8) score to be used in the field by paramedics and a transport decision matrix to expedite transport for a suspected stroke patient (road or road plus air transport). Outcomes: The primary outcome measure will be the rate of intravenous tissue plasminogen activator delivery for those who suffer an ischaemic stroke following protocol implementation, in comparison with historical rates over a corresponding period prior to implementation, for residents within the catchment. Sixty cases are required in the postimplementation time epoch to demonstrate a statistically significant absolute increase in thrombolysis rates for ischaemic strokes from <1% to 10%, (power of 80%, α error of 0·05). The major secondary outcome will be inter-rater reliability of the Hunter NIHSS-8

Validation of the National Institutes of Health stroke scale-8 to detect large vessel occlusion in ischemic stroke

Background Patients with acute ischemic stroke and large vessel occlusion (LVO) may benefit from prehospital identification and transfer to a center offering endovascular therapy. Aims We aimed to assess the accuracy of an existing 8-item stroke scale (National Institutes of Health Stroke Scale-8 [NIHSS-8]) for identification of patients with acute stroke with LVO. Methods We retrospectively calculated NIHSS-8 scores in a population of consecutive patients with presumed acute stroke assessed by emergency medical services (EMS). LVO was identified on admission computed tomography angiography. Accuracy to identify LVO was calculated using receiver operating characteristics analysis. We used weighted Cohen's kappa statistics to assess inter-rater reliability for the NIHSS-8 score between the EMS and the hospital stroke team on a prospectively evaluated subgroup. Results Of the 551 included patients, 381 had a confirmed ischemic stroke and 136 patients had an LVO. NIHSS scores were significantly higher in patients with LVO (median 18; interquartile range 14-22). The NIHSS-8 score reliably predicted the presence of LVO (area under the receiver operating characteristic curve.82). The optimum NIHSS-8 cutoff of 8 or more had a sensitivity of.81, specificity of.75, and Youden index of.56 for prediction of LVO. The EMS and the stroke team reached substantial agreement (κ =.69). Conclusions Accuracy of the NIHSS-8 to identify LVO in a population of patients with suspected acute stroke is comparable to existing prehospital stroke scales. The scale can be performed by EMS with reasonable reliability. Further validation in the field is needed to assess accuracy of the scale to identify patients with LVO eligible for endovascular treatment in a prehospital setting

Soroprevalência de anticorpos contra vírus herpes simples 1-2 no Brasil Seroprevalencia de anticuerpos contra virus herpes simples 1-2 en Brasil Seroprevalence of herpes simplex 1-2 antibodies in Brazil

OBJETIVO: Estimar a soroprevalência de anticorpos por vírus herpes simples (HSV-1 e HSV-2) e analisar fatores associados no Brasil. MÉTODOS: Estudo transversal realizado entre 1996 e 1997 em 1.090 indivíduos com idade entre um e 40 anos da população geral, em quatro diferentes regiões geográficas no Brasil. Foram analisadas amostras sangüíneas para detecção de anticorpos para HSV-1 e HSV-2 com teste tipo-específico Elisa. Foram descritas freqüências e proporções, comparadas entre grupos utilizando o teste de Fisher bilateral exato. Foi realizada análise de regressão logística para avaliar influência das variáveis sociodemográficas e histórico de DST, sobre a soroprevalência de HSV-1 e/ou HSV-2. RESULTADOS: As soroprevalências de anticorpos para HSV-1 e HSV-2, ajustadas por idade, foram 67,2% e 11,3% respectivamente, sem diferença quanto ao sexo e maiores na Região Norte. As soroprevalências aumentaram com a idade, e para HSV-2 o maior aumento ocorreu na adolescência e entre adultos jovens. Indivíduos soropositivos para HSV-1 apresentaram maior risco de serem positivos para HSV-2 (15,7%) quando comparados com os negativos para HSV-1 (4,7%). Na análise multivariada, o histórico de DST aumentou significativamente (OR=3,2) a probabilidade de soropositividade para HSV-2. CONCLUSÕES: As soroprevalências para HSV-1 e para HSV-2 variam com a idade e entre as regiões do Brasil. História pregressa de DST é importante fator de risco para aquisição de infecção por HSV-2.<br>OBJETIVO: Estimar la seroprevalencia de anticuerpos por virus herpes simples (HSV-1 y HSV-2) en diferentes áreas geográficas en Brasil y analizar factores asociados. MÉTODOS: Estudio transversal realizado entre 1996 y 1997 con individuos de la población en general en cuatro diferentes áreas geográficas en Brasil y estratificados por edad (de uno a 40 años) y sexo, de los cuales 1.090 fueron incluidos en el análisis final. Fueron analizadas muestras de sangre para detección de anticuerpos para HSV-1 y HSV-2 con prueba tipo-específica ELISA gG1-gG2. Fueron descritas frecuencias y proporciones y comparadas entre grupos utilizando la prueba de Fisher bilateral exacta. Fue realizado análisis de regresión logística para evaluar influencia de las variables edad, sexo, geografía, grupo económico, histórico de DST, seropositividad para anti-HSV-1 o anti-HSV-2 e interacciones de cualquiera de esos factores sobre la seroprevalencia de HSV-1 y/o HSV-2. RESULTADOS: La tasa de seroprevalencia de anticuerpos para HSV-1 ajustada por edad fue de 67,2%, sin diferencia con relación al sexo, siendo mayor en la Región Norte. Las seroprevalencias aumentaron con la edad, y para HSV-2, hube un aumento significativo en la adolescencia y entre adultos jóvenes. Individuos seropositivos para HSV-1 presentaron mayor riesgo de ser positivos para HSV-2 (15,7%) cuando se compararon con los negativos para HSV-1 (4,7%). En el análisis multivariado, el histórico de DST aumentó significativamente (OR=3,2) la probabilidad de seropositividad para HSV-2. CONCLUSIONES: Las seroprevalencias para HSV-1 y para HSV-2 varían con la edad y presentan diferencias significativas entre las regiones de Brasil. Historia anterior de DST es importante factor de riesgo para adquisición de infección por HSV-2.<br>OBJECTIVE: To estimate the seroprevalence of HSV-1 and HSV-2 antibodies in Brazil and to analyze factors associated. METHODS: Cross-sectional study including subjects aged 1-40 years from the general population in four different geographical areas in Brazil between 1996 and 1997. All subjects were stratified by age and gender and 1,090 of them were included in the final analysis. Blood samples were tested for HSV-1 and HSV-2 antibodies by type-specific (gG1 and gG2) ELISA. Frequencies and proportions were described and compared among groups using two-sided Fisher's exact test. A logistic regression analysis was performed to assess the influence of the variables age, gender, geographical area, socioeconomic condition, past history of STD, seropositivity for anti-HSV-1 or anti-HSV-2 and interactions of any of these factors on the seroprevalence of HSV-1 and/or HSV-2. RESULTS: The age-adjusted seroprevalences of HSV-1 and HSV-2 antibodies were 67.2% and 11.3%, respectively, without sex differences and being higher in the North region. Seroprevalences increased with age and, for HSV-2 infection, the higher increase was observed among adolescents and young adults. Subjects who tested positive for HSV-1 were more likely to also test positive for HSV-2 (15.7%) compared to HSV-1 negative subjects (4.7%). In the multivariate analysis past history of STD significantly (OR=3.2) increased the likelihood of HSV-2 infection whereas socioeconomic condition did not affect the results. CONCLUSIONS: HSV-1 and HSV-2 seroprevalences vary with age and among Brazilian regions. Past history of STD is a major risk factor for HSV-2 infection