Computational framework to integrate the effect of antigen recognition on disease epidemiology outcome: multi-scale approach

Human Leukocyte Antigen (HLA) plays an important role, in presenting foreign pathogens to our immune system, there by eliciting early immune responses. HLA genes are highly polymorphic, giving rise to diverse antigen presentation capability. An important factor contributing to enormous variations in individual responses to diseases is differences in their HLA profiles. The heterogeneity in allele specific disease responses decides the overall disease epidemiological outcome. Here we propose an agent based computational framework, capable of incorporating allele specific information, to analyze disease epidemiology. This framework assumes a SIR model to estimate average disease transmission and recovery rate. Using epitope prediction tool, it performs sequence based epitope detection for a given the pathogenic genome and derives an allele specific disease susceptibility index depending on the epitope detection efficiency. The allele specific disease transmission rate, that follows, is then fed to the agent based epidemiology model, to analyze the disease outcome. The methodology presented here has a potential use in understanding how a disease spreads and effective measures to control the disease.

Determinants of self-reported smoking and misclassification during pregnancy, and analysis of optimal cut-off points for urinary cotinine: a cross-sectional study

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Avaliação da qualidade da assistência perinatal : um exercício

A relação da qualidade da prática médica assistencial com os indicadores de saúde tem sido objeto de controvérsia. A possibilidade de avaliar o estado de saúde do recém-nascido em função do cuidado recebido, facilita o estudo desta relação, principalmente na área perinatal onde a expectativa é o nascimento de um bebê saudável ao final de uma gestação sem fatores de riscos acompanhados segundo as normas obstétricas vigentes. Neste estudo, examina-se a adequação do acompanhamento do trabalho de parto em uma maternidade pública do Estado do Rio de Janeiro, sob a ótica de avaliação de qualidade pela abordagem de processos e resultados através de critérios explícitos supondo que os fatores selecionados como componentes do processo de assistência ao trabalho de parto determinariam o resultado. Observa-se tais relações através da metodologia epidemiológica optando por um estudo caso-referente ou um estudo caso-controle, com definição primária da base. Selecionou-se como determinantes da qualidade da prática obstétrica intraparto a duração do trabalho de parto, percepção de alterações durante o trabalho de parto, prontidão para intervenção, número de exames realizados e intervalo entre o último exame e hora do parto. O resultado neonatal adverso caracterizou-se por óbito intra-útero, óbito neonatal e presença de um conjunto de sinais clínicos anormais no período neonatal imediato, com alto valor preditivo para o futuro dano neurológico. O risco de um resultado adverso foi estimado pela razão dos produtos cruzados aodds ratio (OR) numa população de 34 casos e 124 controles. A duração do trabalho de parto maior que doze horas esteve associada a um OR igual a 3,48 (1,28-9,43), idade da gestante, dilatação cervical do colo uterino à admissão e peso ao nascer modificaram o efeito desta associação, que também foi confundida pela paridade e pelo uso da ocitocina contrariando hipótese inicial. A percepção de alterações resultou num OR= 14,73 (4.24-54,27) e, à medida que o tempo de intervenção se prolongava os riscos aumentavam obedecendo a uma tendência linear. Discutem-se as dificuldades de aplicação metodologia epidemiológica ao campo da avaliação da qualidade, essencialmente no que se refere as exigências quantitativas, para garantir precisão e confiabilidade. A observação da interação e o controle do confundimento apontam o cuidado necessário nos trabalhos desta natureza para alcançar consistência e validade.

Violência entre parceiros íntimos nos primeiros cinco meses de pós-parto em usuárias de unidades básicas de saúde do Rio de Janeiro

A Violência entre Parceiros Íntimos (VPI) tem sido reconhecida como um importante problema de saúde pública e um fator de risco para agravos a saúde de mulheres e crianças. Os serviços de saúde desempenham importante papel na detecção precoce da VPI, especialmente em momentos da vida nos quais se preconiza o atendimento sistematizado, como na gestação e primeira infância. Esta dissertação tem como objetivo principal estimar a probabilidade de ocorrência de Violência Física entre Parceiros Íntimos (VFPI) durante a gestação e/ou pós-parto em população atendida em Unidades Básicas de Saúde (UBS), segundo diferentes características sócio-econômicas e demográficas da clientela. Trata-se de um estudo transversal, realizado com usuárias de 5 UBS da cidade do Rio de Janeiro no ano de 2007. Foram entrevistadas 811 mães de crianças de até cinco meses de idade, que não possuíam nenhuma contra-indicação formal para a amamentação e que relataram ter tido pelo menos uma relação amorosa um mês ou mais durante a gestação ou no período do pós-parto. Condições socioeconômicas e demográficas e relativas aos hábitos de vida do casal foram consideradas como potenciais preditores de violência. Utilizou-se a versão em português da CTS2 para identificar as situações de VPI. A variável de desfecho foi analisada em três níveis: ausência de VFPI, presença de VFPI no período da gestação ou do pós-parto e presença de VFPI em ambos os períodos. Utilizou-se um modelo logito-multinomial para as projeções de prevalências segundo os descritores selecionados. Os fatores que mais aumentaram a probabilidade de ocorrência de violência durante a gestação e/ou nos primeiros cinco meses de vida da criança foram: idade materna < 20 anos, escolaridade materna inferior ao 2 grau completo, ter 2 ou mais filhos menores de cinco anos, tabagismo materno, uso inadequado de álcool pela mãe e/ou companheiro, uso de drogas pela mãe e/ou companheiro e percepção materna sobre a saúde do bebê aquém da esperada. Entre mães com todas estas características, a estimativa de prevalência projetada de VFPI na gestação e/ou no pós-parto chegou a 96,4%, sendo 59,4% a estimativa de ocorrência em apenas um dos dois períodos e 37% em ambos. Por outro lado, a probabilidade de ocorrência de VFPI cai a 3,6% em famílias sem estas características. Os resultados indicam que a presença de certas características da criança e de sua família aumenta enormemente a probabilidade de ocorrência de VFPI, devendo ser levadas em consideração ao se estabelecer estratégias de intervenção que visem à detecção precoce e uma efetiva intervenção.

Changes of urinary steroid conjugates and gonadotropin excretion in the menstrual cycle and pregnancy in the Yunnan snub-nosed monkey (Rhinopithecus bieti)

The Yunnan snub-nosed monkey (Rhinopithecus bieti) is one of the most endangered species in the world, and it is endemic to China. According to our knowledge, there was no information on reproduction for this species. The present study was designed to und

Dopaminergic and Non-Dopaminergic Value Systems in Conditioning and Outcome-Specific Revaluation

Animals are motivated to choose environmental options that can best satisfy current needs. To explain such choices, this paper introduces the MOTIVATOR (Matching Objects To Internal Values Triggers Option Revaluations) neural model. MOTIVATOR describes cognitiveemotional interactions between higher-order sensory cortices and an evaluative neuraxis composed of the hypothalamus, amygdala, and orbitofrontal cortex. Given a conditioned stimulus (CS), the model amygdala and lateral hypothalamus interact to calculate the expected current value of the subjective outcome that the CS predicts, constrained by the current state of deprivation or satiation. The amygdala relays the expected value information to orbitofrontal cells that receive inputs from anterior inferotemporal cells, and medial orbitofrontal cells that receive inputs from rhinal cortex. The activations of these orbitofrontal cells code the subjective values of objects. These values guide behavioral choices. The model basal ganglia detect errors in CS-specific predictions of the value and timing of rewards. Excitatory inputs from the pedunculopontine nucleus interact with timed inhibitory inputs from model striosomes in the ventral striatum to regulate dopamine burst and dip responses from cells in the substantia nigra pars compacta and ventral tegmental area. Learning in cortical and striatal regions is strongly modulated by dopamine. The model is used to address tasks that examine food-specific satiety, Pavlovian conditioning, reinforcer devaluation, and simultaneous visual discrimination. Model simulations successfully reproduce discharge dynamics of known cell types, including signals that predict saccadic reaction times and CS-dependent changes in systolic blood pressure.

The expression and regulation of pregnancy-specific glycoproteins in the mouse

Pregnancy-Specific Glycoproteins (PSG) are the most abundant fetally expressed proteins in the maternal bloodstream at term. This multigene family are immunoglobulin superfamily members and are predominantly expressed in the syncytiotrophoblast of human placenta and in giant cells and spongiotrophoblast of rodent placenta. PSGs are encoded by seventeen genes in the mouse and ten genes in the human. Little is known about the function of this gene family, although they have been implicated in immune modulation and angiogenesis through the induction of cytokines such as IL-10 and TGFβ1 in monocytes, and more recently, have been shown to inhibit the platelet-fibrinogen interaction. I provide new information concerning the evolution of the murine Psg genomic locus structure and organisation, through the discovery of a recent gene inversion event of Psg22 within the major murine Psg cluster. In addition to this, I have performed an examination of the expression patterns of individual Psg genes in placental and non-placental tissues. This study centres on Psg22, which is the most abundant murine Psg transcript detected in the first half of pregnancy. A novel alternative splice variant transcript of Psg22 lacking the protein N1-domain was discovered, and similar to the full length isoform induces TGFβ1 in macrophage and monocytic cell lines. The identification of a bidirectional antisense long non-coding RNA transcript directly adjacent to Psg22 and its associated active local chromatin conformation, suggests an interesting epigenetic gene-specific regulatory mechanism that may be responsible for the high level of Psg22 expression relative to the other Psg family members upon trophoblast giant cell differentiation

Vitamin D status and requirements during pregnancy and lactation

Vitamin D deficiency during pregnancy, lactation, and early infancy has been widely reported. Current understanding of vitamin D metabolism during pregnancy and lactation is incomplete, and to date, experimental data to support vitamin D requirements for these life stages are scarce. There is a shortage of nationally representative data and appropriate reference ranges for serum 25-hydroxyvitamin D (25OHD) during pregnancy, lactation and infancy, including in umbilical cord blood. This thesis described concentrations of total 25OHD and individual metabolites including 25OHD3, 25OHD2, and 3-epi-25OHD3 at 15 weeks’ gestation in a large seasonally balanced pregnancy cohort study (n 1768), carried out in Cork, Ireland (52oN). The prevalence of low 25OHD concentrations in pregnant women was higher than published reports in other Caucasian women, and was highest among non-users of vitamin D-containing supplements during winter. A longitudinal pregnancy study was included which suggested gestational stages had an impact on the total serum 25OHD concentration. This thesis incorporated a randomized controlled trial carried out among 100 women across 3 intervention groups using 20 μg/day of vitamin D3 with or without 500 mg calcium, or placebo, over 12-weeks of lactation to investigate the vitamin D requirement for lactating mothers and the vitamin D content of human milk. A daily intake of 25 μg/day was suggested to meet the requirement of lactating women to maintain a 25OHD levels above 50 nmol/L in 97.5% of the population at 52oN all year around. However, vitamin D content in human milk did not increase in response to supplementation. Serum 25OHD concentration has been used as a predictor of a number of health outcomes. This thesis reported large differences in serum 25OHD concentrations using different methods in 86 umbilical cord samples. The need for international standardization of serum 25OHD measurements was re-emphasized in this thesis.

Pregnancy-specific glycoprotein function, conservation and receptor investigation

Pregnancy-specific glycoproteins (PSGs) are highly glycosylated secreted proteins encoded by multi-gene families in some placental mammals. They are carcinoembryonic antigen (CEA) family and immunoglobulin (Ig) superfamily members. PSGs are immunomodulatory, and have been demonstrated to possess antiplatelet and pro-angiogenic properties. Low serum levels of these proteins have been correlated with adverse pregnancy outcomes. Objectives: Main research goals of this thesis were: 1). To attempt to replicate previously reported cytokine responses to PSG-treatment of immune cells and subsequently to investigate functionally important amino acids within PSG1. 2). To determine whether candidate receptor, integrin αvβ3, was a binding partner for PSG1 and to investigate whether PSG1 possessed functionality in a leukocyte-endothelial interaction assay. 3). To determine whether proteins generated from recently identified putative PSG genes in the horse shared functional properties with PSGs from other species. Outcomes: 1). Sequential domain deletion of PSG1 as well as mutation of conserved residues within the PSG1 Ndomain did not affect PSG1-induced TGF-β1. The investigated response was subsequently found to be the result of latent TGF-β1 contaminating the recombinant protein. Protein further purified by SEC to remove this showed no induction of TGF-β1. The most N-terminal glycosylation site was demonstrated to have an important role in PSG N domain secretion. PSG1 attenuated LPS-induced IL-6 and TNF-α. Investigations into signalling underpinning this proved inconclusive. 2). Integrin αvβ3 was identified as a novel PSG1 receptor mediating an as yet unknown function. Preliminary investigations into a role for PSGs as inhibitors of leukocyte endothelial interactions showed no effect by PSG1. 3). Horse PSG protein, CEACAM49, was shown to be similarly contaminated by latent TGF-β1 particle and once removed did not demonstrate TGF-β1 release. Interestingly horse PSG did show anti-platelet properties through inhibition of the plateletfibrinogen interaction as previously published for mouse and human PSGs.

Cesarean section and rate of subsequent stillbirth, miscarriage and ectopic pregnancy: a Danish register-based cohort study

Background: With cesarean section rates increasing worldwide, clarity regarding negative effects is essential. This study aimed to investigate the rate of subsequent stillbirth, miscarriage, and ectopic pregnancy following primary cesarean section, controlling for confounding by indication. Methods and Findings: We performed a population-based cohort study using Danish national registry data linking various registers. The cohort included primiparous women with a live birth between January 1, 1982, and December 31, 2010 (n = 832,996), with follow-up until the next event (stillbirth, miscarriage, or ectopic pregnancy) or censoring by live birth, death, emigration, or study end. Cox regression models for all types of cesarean sections, sub-group analyses by type of cesarean, and competing risks analyses for the causes of stillbirth were performed. An increased rate of stillbirth (hazard ratio [HR] 1.14, 95% CI 1.01, 1.28) was found in women with primary cesarean section compared to spontaneous vaginal delivery, giving a theoretical absolute risk increase (ARI) of 0.03% for stillbirth, and a number needed to harm (NNH) of 3,333 women. Analyses by type of cesarean section showed similarly increased rates for emergency (HR 1.15, 95% CI 1.01, 1.31) and elective cesarean (HR 1.11, 95% CI 0.91, 1.35), although not statistically significant in the latter case. An increased rate of ectopic pregnancy was found among women with primary cesarean overall (HR 1.09, 95% CI 1.04, 1.15) and by type (emergency cesarean, HR 1.09, 95% CI 1.03, 1.15, and elective cesarean, HR 1.12, 95% CI 1.03, 1.21), yielding an ARI of 0.1% and a NNH of 1,000 women for ectopic pregnancy. No increased rate of miscarriage was found among women with primary cesarean, with maternally requested cesarean section associated with a decreased rate of miscarriage (HR 0.72, 95% CI 0.60, 0.85). Limitations include incomplete data on maternal body mass index, maternal smoking, fertility treatment, causes of stillbirth, and maternally requested cesarean section, as well as lack of data on antepartum/intrapartum stillbirth and gestational age for stillbirth and miscarriage. Conclusions: This study found that cesarean section is associated with a small increased rate of subsequent stillbirth and ectopic pregnancy. Underlying medical conditions, however, and confounding by indication for the primary cesarean delivery account for at least part of this increased rate. These findings will assist women and health-care providers to reach more informed decisions regarding mode of delivery.