Singapore Institute for Clinical Sciences

Abstract Over the past few decades, neuroimaging has become a ubiquitous tool in basic research and clinical studies of the human brain. However, no reference standards currently exist to quantify individual differences in neuroimaging metrics over time, in contrast to growth charts for anthropometric traits such as height and weight 1 . Here we assemble an interactive open resource to benchmark brain morphology derived from any current or future sample of MRI data ( http://www.brainchart.io/ ). With the goal of basing these reference charts on the largest and most inclusive dataset available, acknowledging limitations due to known biases of MRI studies relative to the diversity of the global population, we aggregated 123,984 MRI scans, across more than 100 primary studies, from 101,457 human participants between 115 days post-conception to 100 years of age. MRI metrics were quantified by centile scores, relative to non-linear trajectories 2 of brain structural changes, and rates of change, over the lifespan. Brain charts identified previously unreported neurodevelopmental milestones 3 , showed high stability of individuals across longitudinal assessments, and demonstrated robustness to technical and methodological differences between primary studies. Centile scores showed increased heritability compared with non-centiled MRI phenotypes, and provided a standardized measure of atypical brain structure that revealed patterns of neuroanatomical variation across neurological and psychiatric disorders. In summary, brain charts are an essential step towards robust quantification of individual variation benchmarked to normative trajectories in multiple, commonly used neuroimaging phenotypes.

Extracellular vesicles (EVs), such as exosomes and microvesicles, are released by different cell types and participate in physiological and pathophysiological processes. EVs mediate intercellular communication as cell-derived extracellular signalling organelles that transmit specific information from their cell of origin to their target cells. As a result of these properties, EVs of defined cell types may serve as novel tools for various therapeutic approaches, including (a) anti-tumour therapy, (b) pathogen vaccination, (c) immune-modulatory and regenerative therapies and (d) drug delivery. The translation of EVs into clinical therapies requires the categorization of EV-based therapeutics in compliance with existing regulatory frameworks. As the classification defines subsequent requirements for manufacturing, quality control and clinical investigation, it is of major importance to define whether EVs are considered the active drug components or primarily serve as drug delivery vehicles. For an effective and particularly safe translation of EV-based therapies into clinical practice, a high level of cooperation between researchers, clinicians and competent authorities is essential. In this position statement, basic and clinical scientists, as members of the International Society for Extracellular Vesicles (ISEV) and of the European Cooperation in Science and Technology (COST) program of the European Union, namely European Network on Microvesicles and Exosomes in Health and Disease (ME-HaD), summarize recent developments and the current knowledge of EV-based therapies. Aspects of safety and regulatory requirements that must be considered for pharmaceutical manufacturing and clinical application are highlighted. Production and quality control processes are discussed. Strategies to promote the therapeutic application of EVs in future clinical studies are addressed.

Importance: Depression is the leading cause of mental health-related disease burden and may be reduced by physical activity, but the dose-response relationship between activity and depression is uncertain. Objective: To systematically review and meta-analyze the dose-response association between physical activity and incident depression from published prospective studies of adults. Data Sources: PubMed, SCOPUS, Web of Science, PsycINFO, and the reference lists of systematic reviews retrieved by a systematic search up to December 11, 2020, with no language limits. The date of the search was November 12, 2020. Study Selection: We included prospective cohort studies reporting physical activity at 3 or more exposure levels and risk estimates for depression with 3000 or more adults and 3 years or longer of follow-up. Data Extraction and Synthesis: Data extraction was completed independently by 2 extractors and cross-checked for errors. A 2-stage random-effects dose-response meta-analysis was used to synthesize data. Study-specific associations were estimated using generalized least-squares regression and the pooled association was estimated by combining the study-specific coefficients using restricted maximum likelihood. Main Outcomes and Measures: The outcome of interest was depression, including (1) presence of major depressive disorder indicated by self-report of physician diagnosis, registry data, or diagnostic interviews and (2) elevated depressive symptoms established using validated cutoffs for a depressive screening instrument. Results: Fifteen studies comprising 191 130 participants and 2 110 588 person-years were included. An inverse curvilinear dose-response association between physical activity and depression was observed, with steeper association gradients at lower activity volumes; heterogeneity was large and significant (I2 = 74%; P < .001). Relative to adults not reporting any activity, those accumulating half the recommended volume of physical activity (4.4 marginal metabolic equivalent task hours per week [mMET-h/wk]) had 18% (95% CI, 13%-23%) lower risk of depression. Adults accumulating the recommended volume of 8.8 mMET hours per week had 25% (95% CI, 18%-32%) lower risk with diminishing potential benefits and higher uncertainty observed beyond that exposure level. There were diminishing additional potential benefits and greater uncertainty at higher volumes of physical activity. Based on an estimate of exposure prevalences among included cohorts, if less active adults had achieved the current physical activity recommendations, 11.5% (95% CI, 7.7%-15.4%) of depression cases could have been prevented. Conclusions and Relevance: This systematic review and meta-analysis of associations between physical activity and depression suggests significant mental health benefits from being physically active, even at levels below the public health recommendations. Health practitioners should therefore encourage any increase in physical activity to improve mental health.

Machine learning has shown utility in detecting patterns within large, unstructured, and complex datasets. One of the promising applications of machine learning is in precision medicine, where disease risk is predicted using patient genetic data. However, creating an accurate prediction model based on genotype data remains challenging due to the so-called "curse of dimensionality" (i.e., extensively larger number of features compared to the number of samples). Therefore, the generalizability of machine learning models benefits from feature selection, which aims to extract only the most "informative" features and remove noisy "non-informative," irrelevant and redundant features. In this article, we provide a general overview of the different feature selection methods, their advantages, disadvantages, and use cases, focusing on the detection of relevant features (i.e., SNPs) for disease risk prediction.

Mouse and human dendritic cells (DCs) are composed of functionally specialized subsets, but precise interspecies correlation is currently incomplete. Here, we showed that murine lung and gut lamina propria CD11b+ DC populations were comprised of two subsets: FLT3- and IRF4-dependent CD24(+)CD64(-) DCs and contaminating CSF-1R-dependent CD24(-)CD64(+) macrophages. Functionally, loss of CD24(+)CD11b(+) DCs abrogated CD4+ T cell-mediated interleukin-17 (IL-17) production in steady state and after Aspergillus fumigatus challenge. Human CD1c+ DCs, the equivalent of murine CD24(+)CD11b(+) DCs, also expressed IRF4, secreted IL-23, and promoted T helper 17 cell responses. Our data revealed heterogeneity in the mouse CD11b+ DC compartment and identifed mucosal tissues IRF4-expressing DCs specialized in instructing IL-17 responses in both mouse and human. The demonstration of mouse and human DC subsets specialized in driving IL-17 responses highlights the conservation of key immune functions across species and will facilitate the translation of mouse in vivo findings to advance DC-based clinical therapies.

Dendritic cell (DC)-mediated cross-presentation of exogenous antigens acquired in the periphery is critical for the initiation of CD8(+) T cell responses. Several DC subsets are described in human tissues but migratory cross-presenting DCs have not been isolated, despite their potential importance in immunity to pathogens, vaccines, and tumors and tolerance to self. Here, we identified a CD141(hi) DC present in human interstitial dermis, liver, and lung that was distinct from the majority of CD1c(+) and CD14(+) tissue DCs and superior at cross-presenting soluble antigens. Cutaneous CD141(hi) DCs were closely related to blood CD141(+) DCs, and migratory counterparts were found among skin-draining lymph node DCs. Comparative transcriptomic analysis with mouse showed tissue DC subsets to be conserved between species and permitted close alignment of human and mouse DC subsets. These studies inform the rational design of targeted immunotherapies and facilitate translation of mouse functional DC biology to the human setting.

The electron-transfer process during the oxygen evolution reaction (OER) often either proceeds solely via a metal redox chemistry (adsorbate evolution mechanism (AEM), with metal bands around the Fermi level) or an oxygen redox chemistry (lattice oxygen oxidation mechanism (LOM), with oxygen bands around the Fermi level). Unlike the AEM, the LOM involves oxygen redox chemistry instead of metal redox, which leads to the formation of a direct oxygen-oxygen (OO) bond. As a result, such a process is able to bypass the rate-determining step, that is, OO bonding, in AEM, which highlights the critical advantage of LOM as compared to the conventional AEM. Thus, it has been well reported that LOM-based catalysts are able to demonstrate higher OER activities as compared to AEM-based catalysts. Here, a comprehensive understanding of the oxygen redox in LOM and all documented and possible characterization techniques that can be used to identify the oxygen redox are reviewed. This review will interpret the origins of oxygen redox in the reported LOM-based electrocatalysts and the underlying science of LOM-induced surface reconstruction in transition metal oxides. Finally, perspectives on the future development of LOM electrocatalysts are also provided.

Antimicrobial peptides (AMPs) are promising next generation antibiotics that hold great potential for combating bacterial resistance. AMPs can be both bacteriostatic and bactericidal, induce rapid killing and display a lower propensity to develop resistance than do conventional antibiotics. Despite significant progress in the past 30 years, no peptide antibiotic has reached the clinic yet. Poor understanding of the action mechanisms and lack of rational design principles have been the two major obstacles that have slowed progress. Technological developments are now enabling multidisciplinary approaches including molecular dynamics simulations combined with biophysics and microbiology toward providing valuable insights into the interactions of AMPs with membranes at atomic level. This has led to increasingly robust models of the mechanisms of action of AMPs and has begun to contribute meaningfully toward the discovery of new AMPs. This review discusses the detailed action mechanisms that have been put forward, with detailed atomistic insights into how the AMPs interact with bacterial membranes. The review further discusses how this knowledge is exploited toward developing design principles for novel AMPs. Finally, the current status, associated challenges, and future directions for the development of AMP therapeutics are discussed.

In the last decades, the developmental origins of health and disease (DOHaD) have emerged as a vigorous field combining experimental, clinical, epidemiological and public health research. Its goal is to understand how events in early life shape later morbidity risk, especially of non-communicable chronic diseases. As these diseases become the major cause of morbidity and mortality worldwide, research arising from DOHaD is likely to gain significance to public health and economic development. But action may be hindered by the lack of a firm mechanistic explanation and of a conceptual basis, especially regarding the evolutionary significance of the DOHaD phenomenon. In this article, we provide a succinct historical review of the research into the relationship between development and later disease, consider the evolutionary and developmental significance and discuss the underlying mechanisms of the DOHaD phenomenon. DOHaD should be viewed as a part of a broader biological mechanism of plasticity by which organisms, in response to cues such as nutrition or hormones, adapt their phenotype to environment. These responses may be divided into those for immediate benefit and those aimed at prediction of a future environment: disease occurs in the mismatch between predicted and realized future. The likely mechanisms that enable plasticity involve epigenetic processes, affecting the expression of genes associated with regulatory pathways. There is now evidence that epigenetic marks may be inherited and so contribute to non-genomic heritable disease risk. We end by discussing the global significance of the DOHaD phenomenon and its potential applications for public health purposes.

There are numerous examples in psychology and other disciplines of the enduring effects of early experience on neural function. In this article, we review the emerging evidence for epigenetics as a candidate mechanism for these effects. Epigenetics refers to functionally relevant modifications to the genome that do not involve a change in nucleotide sequence. Such modifications include chemical marks that regulate the transcription of the genome. There is now evidence that environmental events can directly modify the epigenetic state of the genome. Thus studies with rodent models suggest that during both early development and in adult life, environmental signals can activate intracellular pathways that directly remodel the "epigenome," leading to changes in gene expression and neural function. These studies define a biological basis for the interplay between environmental signals and the genome in the regulation of individual differences in behavior, cognition, and physiology.

Gut microbiome has been identified in the past decade as an important factor involved in obesity, but the magnitude of its contribution to obesity and its related comorbidities is still uncertain. Among the vast quantity of factors attributed to obesity, environmental, dietary, lifestyle, genetic, and others, the microbiome has aroused curiosity, and the scientific community has published many original articles. Most of the studies related to microbiome and obesity have been reported based on the associations between microbiota and obesity, and the in-depth study of the mechanisms related has been studied mainly in rodents and exceptionally in humans. Due to the quantity and diverse information published, the need of reviews is mandatory to recapitulate the relevant achievements. In this systematic review, we provide an overview of the current evidence on the association between intestinal microbiota and obesity. Additionally, we analyze the effects of an extreme weight loss intervention such as bariatric surgery on gut microbiota. The review is divided into 2 sections: first, the association of obesity and related metabolic disorders with different gut microbiome profiles, including metagenomics studies, and second, changes on gut microbiome after an extreme weight loss intervention such as bariatric surgery.

In October 2018 a large number of international experts with complementary expertise came together in Taormina to participate in a workshop on occult hepatitis B virus infection (OBI). The objectives of the workshop were to review the existing knowledge on OBI, to identify issues that require further investigation, to highlight both existing controversies and newly emerging perspectives, and ultimately to update the statements previously agreed in 2008. This paper represents the output from the workshop.

The global burden of tuberculosis (TB) morbidity and mortality remains immense. A potential new approach to TB therapy is to augment protective host immune responses. We report that the antidiabetic drug metformin (MET) reduces the intracellular growth of Mycobacterium tuberculosis (Mtb) in an AMPK (adenosine monophosphate-activated protein kinase)-dependent manner. MET controls the growth of drug-resistant Mtb strains, increases production of mitochondrial reactive oxygen species, and facilitates phagosome-lysosome fusion. In Mtb-infected mice, use of MET ameliorated lung pathology, reduced chronic inflammation, and enhanced the specific immune response and the efficacy of conventional TB drugs. Moreover, in two separate human cohorts, MET treatment was associated with improved control of Mtb infection and decreased disease severity. Collectively, these data indicate that MET is a promising candidate host-adjunctive therapy for improving the effective treatment of TB.

Abstract Type 2 diabetes (T2D) is a heterogeneous disease that develops through diverse pathophysiological processes 1,2 and molecular mechanisms that are often specific to cell type 3,4 . Here, to characterize the genetic contribution to these processes across ancestry groups, we aggregate genome-wide association study data from 2,535,601 individuals (39.7% not of European ancestry), including 428,452 cases of T2D. We identify 1,289 independent association signals at genome-wide significance ( P &lt; 5 × 10 −8 ) that map to 611 loci, of which 145 loci are, to our knowledge, previously unreported. We define eight non-overlapping clusters of T2D signals that are characterized by distinct profiles of cardiometabolic trait associations. These clusters are differentially enriched for cell-type-specific regions of open chromatin, including pancreatic islets, adipocytes, endothelial cells and enteroendocrine cells. We build cluster-specific partitioned polygenic scores 5 in a further 279,552 individuals of diverse ancestry, including 30,288 cases of T2D, and test their association with T2D-related vascular outcomes. Cluster-specific partitioned polygenic scores are associated with coronary artery disease, peripheral artery disease and end-stage diabetic nephropathy across ancestry groups, highlighting the importance of obesity-related processes in the development of vascular outcomes. Our findings show the value of integrating multi-ancestry genome-wide association study data with single-cell epigenomics to disentangle the aetiological heterogeneity that drives the development and progression of T2D. This might offer a route to optimize global access to genetically informed diabetes care.

Malnutrition is associated with poor clinical outcomes among hospitalized patients. However, studies linking malnutrition with poor clinical outcomes in the intensive care unit (ICU) often have conflicting findings due in part to the inappropriate diagnosis of malnutrition. We primarily aimed to determine whether malnutrition diagnosed by validated nutrition assessment tools such as the Subjective Global Assessment (SGA) or Mini Nutritional Assessment (MNA) is independently associated with poorer clinical outcomes in the ICU and if the use of nutrition screening tools demonstrate a similar association. PubMed, CINAHL, Scopus, and Cochrane Library were systematically searched for eligible studies. Search terms included were synonyms of malnutrition, nutritional status, screening, assessment, and intensive care unit. Eligible studies were case-control or cohort studies that recruited adults in the ICU; conducted the SGA, MNA, or used nutrition screening tools before or within 48 hours of ICU admission; and reported the prevalence of malnutrition and relevant clinical outcomes including mortality, length of stay (LOS), and incidence of infection (IOI). Twenty of 1168 studies were eligible. The prevalence of malnutrition ranged from 38% to 78%. Malnutrition diagnosed by nutrition assessments was independently associated with increased ICU LOS, ICU readmission, IOI, and the risk of hospital mortality. The SGA clearly had better predictive validity than the MNA. The association between malnutrition risk determined by nutrition screening was less consistent. Malnutrition is independently associated with poorer clinical outcomes in the ICU. Compared with nutrition assessment tools, the predictive validity of nutrition screening tools were less consistent.

Modern lifestyles and nutritional transition have given rise to an emerging epidemic of obesity and type 2 diabetes in developed and developing countries.1,2 In general, metabolic compromise is seen in South Asians at relatively lower levels of obesity compared with Europeans, with Chinese having an intermediate relationship, suggesting that the patterns of development of obesity and metabolic function in different Asian populations merits focused investigation.3 The prevalence of type 2 diabetes in Singapore has increased from 1.9% in 1975 to 11.2% in 2010, and is now one of the highest in the developed world.4 The three major Singaporean ethnic groups, Chinese, Malays and Indians, appear to have distinct susceptibilities leading to differing metabolic risk.5 Such differences may be genetic, developmental or cultural in origin. The pathways leading to insulin resistance, obesity and related traits are complex and derive from an interplay of genomic and environmental factors operating over the lifespan, including during early development.6 Environmental cues such as maternal nutrition can have important effects on foetal gene expression and have been shown to influence developmental plasticity7 via epigenetic processes.8 In recent years, major epigenetic pathways involving histone and DNA modifications have been unravelled and more technological tools developed to study their function.9,10 It has recently been reported that it may be of value to measure epigenetic changes in DNA derived from foetal tissues at birth, such as umbilical cord.11 Hence, we wished to examine whether specific epigenetic marks have utility as biomarkers for identifying babies that are ‘programmed’ in utero to develop obesity or non-communicable diseases later in life.11,12 A set of epigenetic biomarkers would allow clinical intervention at early stages in individuals at risk, thereby enabling prevention of obesity and metabolic diseases.13 The Growing Up in Singapore Towards healthy Outcomes (GUSTO) study comprises one of the most carefully phenotyped parent-offspring cohorts with a particular focus on epigenetic observations and detailed study in the first years of life, enabling examination of the potential roles of foetal, developmental and epigenetic factors in pathways to disease. The primary objective of the GUSTO cohort study is to evaluate the role of influences operating during early development, affecting pathways to metabolic compromise and altered body composition. Secondary objectives are: To identify maternal determinants of the offspring’s epigenetic state and associations with other indices of early life experience that may influence growth and body composition. To evaluate risk factors and potential epigenetic biomarkers for allergic disorders. To evaluate the predictors of retinal vasculature development in utero and during postnatal life, and to determine relationships between early life factors and early refractive error development, including the potential role of epigenetic processes. To understand pre- and postnatal influences on individual differences in neurocognitive and emotional development and their relation to somatic growth and metabolic health. The GUSTO study recruited pregnant women aged 18 years and above, attending their first trimester antenatal dating ultrasound scan clinic at Singapore’s two major public maternity units, namely National University Hospital (NUH) and KK Women's and Children's Hospital (KKH) between June 2009 and September 2010. The participants approached were Singapore citizens or permanent residents who were of Chinese, Malay or Indian ethnicity with homogeneous parental ethnic background and who had the intention of eventually delivering in NUH or KKH and residing in Singapore for the next 5 years. Mothers receiving chemotherapy, psychotropic drugs or who had type I diabetes mellitus were excluded. Only women who agreed to donate birth tissues including cord, placenta and cord blood at delivery were included. Informed written consent was obtained from each participant. We screened 3751 families, of which 2034 met eligibility criteria. The reasons for the ineligibility of 1717 families are listed in Supplementary Table 1 (available as Supplementary data at IJE online). Ineligibility was principally due to an intention to deliver outside the two study hospitals or not to remain in Singapore for the next 5 years, booking beyond the first trimester, or non-homogeneous parental ethnic background. Of the 1247 women (response rate 61.3%) recruited, 1162 conceived naturally and 85 conceived through in vitro fertilisation (IVF). At baseline, 55.9% were Chinese, 26.1% Malay and 18.0% Indian. Mean maternal age at recruitment was 30.6 years (range: 18–46 years). The ethnic background of those not recruited differed somewhat [61.3% Chinese, 14.2% Malay and 24.5% Indian (P = 0.042 compared with responders)], with a similar mean age of 31.5 years [range: 18–48 years (P = 0.085)]. A total of 1176 babies were born. The first baby was born on 30 November 2009 and the last baby was born on 1 May 2011. Figure 1 shows the flow chart of the progress of participants through the study. Progress of the GUSTO study The women returned to the hospital at 19–21, 26–28 and 32–34 weeks of gestation for ultrasound scans to assess gestational age and foetal growth. Detailed interviews were conducted in the clinic at recruitment and at 26–28 weeks gestation. Birth tissues were obtained at delivery and anthropometric measurements of the newborn made within 24 h of birth. During infancy, the babies are examined at home at 3 weeks, 3 months and 3-monthly thereafter until 15 months of age. The children are then seen at the study clinic at 18, 24 and 36 months. Further follow-up is planned for later childhood. The current attrition rate is 12.7%, with most participants having withdrawn before or soon after delivery. During pregnancy, 70 participants (5.6%) dropped out primarily for the following reasons: (i) lost to follow-up (n = 15, 1.2%); (ii) family disapproval (n = 10, 0.8%); (iii) personal reasons (n = 36, 2.9%); and (iv) inconvenience (n = 7, 0.6%). After delivery, 88 participants (n = 7.1%) withdrew voluntarily because of personal or family circumstances. Families continuing in the study have a similar ethnicity profile to those recruited but, in keeping with most birth cohort studies, tend to have slightly higher household monthly income, maternal age and educational attainment (Supplementary Table 2, available as Supplementary data at IJE online). Table 1 specifies the information collected at each study visit. Data collected at each stage of the GUSTO birth cohort study ‘s' indicates that a subset of the participants underwent the measures at this timepoint. Data collected at each stage of the GUSTO birth cohort study ‘s' indicates that a subset of the participants underwent the measures at this timepoint. At the recruitment visit (<14 weeks) and at 26–28 weeks of gestation, questionnaires were administered to the women to capture demographic, socio-economic, lifestyle, maternal well-being, obstetric and medical history data. Anthropometric measurements included skin fold thicknesses and mid upper arm circumference, performed at 26–28 weeks of gestation. Pulse wave analysis was measured to derive the maternal central aortic systolic pressure, radial augmentation index and a range of other indices from the radial pulse. Autorefraction and fundus photography were conducted to assess changes in the mothers’ retinal vessel diameters during pregnancy. Routine antenatal clinical and laboratory data were abstracted from the hospital case notes, including measurements of weight, blood pressure, full blood count and urine dipstick. Maternal well-being was assessed using the Edinburgh Postnatal Depression Scale which has been validated in Singapore women.14,15 The State-Trait Anxiety Inventory and Beck Depression Inventory were also administered in conjunction with the Pittsburgh Sleep Quality Index. A series of questionnaires was used to assess maternal childbearing attitudes and social support. Maternal well-being and postnatal affective state were assessed 3 months after delivery and reassessed at the 12-, 24- and 36-month visits. Interviewer-administered questionnaires and prospective 3-day diaries were administered at 26–28 weeks of gestation to assess maternal dietary intakes and patterns. Patterns of maternal diet during the confinement period have unique Asian characteristics and were determined at 3 weeks postpartum. The confinement period is practised by major Asian ethnic groups for about 30 days immediately following delivery, when women are confined to their homes and observe a broad set of restrictions on their diet and activities.15 Blood was collected for an oral glucose tolerance test at 26–28 weeks of gestation and analyses of other biochemical markers. Hair samples were collected for toxicology screening (exposure to lead, metals) and to determine steroid levels. Buccal swabs were collected for DNA to investigate the role of epigenetic processes. Intrauterine growth parameters, namely foetal biparietal diameter, head and abdominal circumferences and femur and humerus lengths, were assessed by ultrasonography at 11–12, 19–21, 26–28 and 32–34 weeks of gestation. Scans were conducted in a standard manner at both hospitals by trained ultrasonographers. After delivery, all routinely recorded birth data including birthweight, gestational age and neonatal problems were abstracted from the case notes. A key feature of the GUSTO study is the collection of body fat measures on all infants. Within the first 24 h after delivery, body composition of the neonate was assessed by anthropometry. Subsequently the percentages of neonatal fat and fat-free mass were assessed using bioelectrical impedance analysis (BIA) and PEA POD non-invasive air-displacement plethysmography. Many of the babies (n = 388) underwent whole body magnetic resonance imaging (MRI), including brain and eye imaging, at age 7–10 days and a small number at 6 weeks (n = 30) and 6 months(n = 50) to document adipose tissue distribution and organ size. Abdominal adipose tissue is segmented and quantified as superficial subcutaneous, deep subcutaneous and internal depots. Infant formula feeding and breastfeeding patterns, including brands of formula milks, volume, duration, partial vs exclusive breastfeeding and expressed vs direct breast milk, have been ascertained to analyse relations with outcome measures. The infant’s weaning diet has been assessed using 3-day food diaries and interview-administered questionnaires at ages 6, 9 and 12 months, with portion size picture guides customized for this age group. The toddler’s diet is assessed further at 15, 18, 24 and 36 months of age using food diaries and interview-administered food frequency and preferences questionnaires. Serial anthropometric measures of early growth trajectories and BIA are made in the child’s home by trained observers. Health status (including oral health) of the child is recorded via interviews at each visit. In addition, any interim illnesses including infections and respiratory diseases are recorded and the relevant case notes traced from the hospital if necessary. Atopic dermatitis, allergic rhinitis, asthma and food allergy symptoms are monitored for the development of allergic outcomes.16 Skin prick testing using relevant allergens is carried out as clinically indicated and at ages 18 and 36 months. Cycloplegic autorefraction is performed on the child at age 36 months to measure refractive error. Facial imitation tests and electroencephalography were conducted within 24 h after delivery to assess their potential value as measures of cognitive development in the neonatal period. A subset of the participants (n = 532) have undergone extensive neurocognitive phenotyping including electroencephalography and eye tracking, at 6, 18 and 36 months of age, and were administered the Bayley Scales of Infant and Toddler Development at the 24-months visit. The majority are regularly assessed for developmental milestones in areas of cognition, behaviour, language and gross and fine motor skills at each visit until 36 months of age. Rinsed umbilical cord, cord blood and placenta were obtained at delivery by trained personnel to enable investigation of epigenetic processes. Breast-milk samples were collected at 3 weeks, 3 and 6 months after delivery in breastfeeding mothers. For the children, stools specimens are collected from birth up to 24 months of age to assess evolution of gut microbiota. Buccal swabs are collected at each visit for DNA analysis. Nasal swabs for cytology smears and molecular studies for respiratory viruses are taken where indicated and at the regular visits. Buccal swabs are collected from the fathers at the 24-months visit. The primary hypothesis to be evaluated is that the in utero and early life environments influence the epigenome, which in turn influences patterns of growth, body composition and development in infancy and childhood. Biological specimens such as umbilical cord and buccal swabs from infants taken longitudinally are analysed by genome-wide methodologies for RNA expression and DNA methylation characterization. Methods to survey the latter include the Illumina Infinium Methylation human 450 K bead array,17,18 a bead-based technology for genome-wide methylation analysis, as well as reduced representation bisulfite sequencing (RRBS) and other next-generation sequencing methodologies.19,20 Candidate marks are technically repeated and statistically validated in larger specimen numbers by pyrosequencing (Qiagen) and Sequenom (Sequenom)-based technologies for DNA methylation, and quantitative real-time reverse transcription polymerase chain reaction (RT-PCR) for gene expression studies. Gene expression and DNA methylation data are analysed, processed and integrated with genotype and clinical data at the pathway, gene and base level. Associations of epigenetic marks with clinical data are discovered via multivariate analysis controlling for false discovery rate. Pathway and network analysis is used to enrich for true positives and to build mechanistic hypotheses that can be tested in model systems. At recruitment, 58.5% of the mothers had completed GCE A levels or polytechnic education and 46.3% were expecting their first child. The mean self-reported pre-pregnancy BMI of GUSTO mothers was 22.7 kg/m2 (SD = 4.5); however, 25.3% were overweight and 12.5% were obese prior to pregnancy. In all, 7.9% of the women scored above 15 on the Edinburgh Depression Scale (EPDS) administered at 26 weeks’ gestational age, suggesting they could be suffering from a depressive illness; 2.3% of women smoked; and 1.6% of women consumed alcohol during pregnancy. Elevated blood pressure, greater pre-pregnancy and pregnancy BMI were found to be associated with a range of adverse retinal arteriolar changes in pregnant women, suggesting an effect of maternal obesity and blood pressure on the microcirculation.21,22 As the cohort’s youngest offspring was born in May 2011, analyses are now possible. Early conclusions from the neonatal imaging and molecular studies have been reached. Among Chinese, Malay and Indian neonates, brain morphological shape and white matter microstructure differences, especially anatomical variations in the spinal-cerebellar and cortical-striatal-thalamic neural circuits associated with sensorimotor functions, were observed using MRI and diffusion tensor imaging.23 Sexual dimorphism of the basal ganglia and thalamus during neonatal period has been found which differs from that found in older children and adults, suggesting that regionally distinct patterns of postnatal brain development between males and females are due to ongoing neurodevelopmental processes after birth.24 DNA from GUSTO umbilical cords shows good agreement between Illumina Infinium Methylation human 450 K bead array and RRBS.25 We have found that the umbilical cord transcriptome is substantially influenced by gestational age even within the normal range. The effect of gestational age is far stronger than that of birthweight even when extreme birthweights are studied (Figure 2). The RNA expression changes dependent on gestational age are enriched in signal transduction pathways, such as Hedgehog and cytokine signalling.26 Variation in the transcriptomics data is associated with gestational age. Principal component analysis using the RNA expression microarray data across a range of birthweights (1698–4151 g) and gestational ages (35–41 weeks) returned principal component 1 (x-axis) which has a significant correlation with gestational age (y-axis) of the samples (P = 0.05, R = 0.55). Samples are classified into high birthweight group (>3700 g) in orange; low birthweight group (<2500 g) in green; normal birthweight and gestational age less than or equal to 37 weeks in blue; or normal birthweight and gestational age more than 37 weeks in red.26 There is a paucity of high-quality data on foetal and early life outcomes in Asian populations. The GUSTO study helps fill this gap with recruitment in the first trimester and tracking of development, growth and other parameters throughout the antenatal period, birth and the first 3 years of life, providing new insights into development in the early part of the human life course. Monitoring of infant growth is undertaken at more frequent time-points than in many other studies. This is further complemented by the assessment of body composition using multiple measurement methods including anthropometry, MRI, BIA and the PEA POD. At birth, body composition has been assessed and epigenetic biomarkers in perinatal tissues is being analysed in an Asian population, providing an important opportunity to investigate the developmental pathways underlying variable disease risk in the three major ethnic groups. Serial postnatal buccal swabs are also collected to capture epigenetic changes in relation to environmental exposures. During recruitment, the eligibility criteria were designed to allow examination of differences between ethnically homogeneous groups, to enable detailed characterization from early pregnancy onwards in two maternity hospitals and to maximize long term follow-up; as Singapore is a cosmopolitan city with interracial marriages and global mobility, only 54.2% met these criteria. The response rate of 61.3% (1247 families can rise to and we evaluated the ethnic background and age of those recruited and not The ethnic background differed between these two groups as we had planned to the recruitment with a higher of Malays than The mean ages were in studies such as GUSTO is and we that in all studies, may from the relationships We that home visit and other measures attrition through multiple including frequent with the The three distinct ethnic groups, Chinese, Malays and Indians, in the Singaporean population, allow to examine associations between genomic and This is important given the high about the in metabolic diseases in emerging as well as developed Asian is designed to and in Singapore in with to this important in the of principal principal and GUSTO has a focused on information for the at information is also available on the of the on to which is as Singapore This is by the on to by the National and administered by the National is by the Singapore for is by the National for Health through the We the GUSTO study group and all clinical and The of all participants is The GUSTO study group and K of and have for at by nutritional are part of an that has from and

Knowledge of the immunological events necessary to control hepatitis B virus (HBV) infection has accelerated in recent years, but their translation towards therapeutic strategies able to achieve a durable HBV suppression has been challenging. The scenario of how HBV deals with the host immunity is presented and used to discuss how the immune response can be harnessed to potentially achieve infection control.

BACKGROUND: Maternal care is associated with long-term effects on behavior and epigenetic programming of the NR3C1 (GLUCOCORTICOID RECEPTOR) gene in the hippocampus of both rats and humans. In the rat, these effects are reversed by cross-fostering, demonstrating that they are defined by epigenetic rather than genetic processes. However, epigenetic changes at a single gene promoter are unlikely to account for the range of outcomes and the persistent change in expression of hundreds of additional genes in adult rats in response to differences in maternal care. METHODOLOGY/PRINCIPAL FINDINGS: We examine here using high-density oligonucleotide array the state of DNA methylation, histone acetylation and gene expression in a 7 million base pair region of chromosome 18 containing the NR3C1 gene in the hippocampus of adult rats. Natural variations in maternal care are associated with coordinate epigenetic changes spanning over a hundred kilobase pairs. The adult offspring of high compared to low maternal care mothers show epigenetic changes in promoters, exons, and gene ends associated with higher transcriptional activity across many genes within the locus examined. Other genes in this region remain unchanged, indicating a clustered yet specific and patterned response. Interestingly, the chromosomal region containing the protocadherin-α, -β, and -γ (Pcdh) gene families implicated in synaptogenesis show the highest differential response to maternal care. CONCLUSIONS/SIGNIFICANCE: The results suggest for the first time that the epigenetic response to maternal care is coordinated in clusters across broad genomic areas. The data indicate that the epigenetic response to maternal care involves not only single candidate gene promoters but includes transcriptional and intragenic sequences, as well as those residing distantly from transcription start sites. These epigenetic and transcriptional profiles constitute the first tiling microarray data set exploring the relationship between epigenetic modifications and RNA expression in both protein coding and non-coding regions across a chromosomal locus in the mammalian brain.

The sensory experience of eating is an important determinant of food intake control, often attributed to the positive hedonic response associated with certain sensory cues. However, palatability is just one aspect of the sensory experience. Sensory cues based on a food's sight, smell, taste and texture are operational before, during and after an eating event. The focus of this review is to look beyond palatability and highlight recent advances in our understanding of how certain sensory characteristics can be used to promote better energy intake control. We consider the role of visual and odour cues in identifying food in the near environment, guiding food choice and memory for eating, and highlight the ways in which tastes and textures influence meal size and the development of satiety after consumption. Considering sensory characteristics as a functional feature of the foods and beverages we consume provides the opportunity for research to identify how sensory enhancements might be combined with energy reduction in otherwise palatable foods to optimize short-term energy intake regulation in the current food environment. Moving forward, the challenge for sensory nutritional science will be to assess the longer-term impact of these principles on weight management.

Chronic hepatitis C virus (HCV) infection is a leading cause of liver disease. Liver inflammation underlies infection-induced fibrosis, cirrhosis and liver cancer but the processes that promote hepatic inflammation by HCV are not defined. We provide a systems biology analysis with multiple lines of evidence to indicate that interleukin-1β (IL-1β) production by intrahepatic macrophages confers liver inflammation through HCV-induced inflammasome signaling. Chronic hepatitis C patients exhibited elevated levels of serum IL-1β compared to healthy controls. Immunohistochemical analysis of healthy control and chronic hepatitis C liver sections revealed that Kupffer cells, resident hepatic macrophages, are the primary cellular source of hepatic IL-1β during HCV infection. Accordingly, we found that both blood monocyte-derived primary human macrophages, and Kupffer cells recovered from normal donor liver, produce IL-1β after HCV exposure. Using the THP-1 macrophage cell-culture model, we found that HCV drives a rapid but transient caspase-1 activation to stimulate IL-1β secretion. HCV can enter macrophages through non-CD81 mediated phagocytic uptake that is independent of productive infection. Viral RNA triggers MyD88-mediated TLR7 signaling to induce IL-1β mRNA expression. HCV uptake concomitantly induces a potassium efflux that activates the NLRP3 inflammasome for IL-1β processing and secretion. RNA sequencing analysis comparing THP1 cells and chronic hepatitis C patient liver demonstrates that viral engagement of the NLRP3 inflammasome stimulates IL-1β production to drive proinflammatory cytokine, chemokine, and immune-regulatory gene expression networks linked with HCV disease severity. These studies identify intrahepatic IL-1β production as a central feature of liver inflammation during HCV infection. Thus, strategies to suppress NLRP3 or IL-1β activity could offer therapeutic actions to reduce hepatic inflammation and mitigate disease.