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Compound heterozygotes occur when different variants at the same locus on both maternal and paternal chromosomes produce a recessive trait. Here we present the tool VarCount for the quantification of variants at the individual level. We used VarCount to characterize compound heterozygous coding variants in patients with epileptic encephalopathy and in the 1000 Genomes Project participants. The Epi4k data contains variants identified by whole exome sequencing in patients with either Lennox-Gastaut Syndrome (LGS) or infantile spasms (IS), as well as their parents. We queried the Epi4k dataset (264 trios) and the phased 1000 Genomes Project data (2504 participants) for recessive variants. To assess enrichment, transcript counts were compared between the Epi4k and 1000 Genomes Project participants using minor allele frequency (MAF) cutoffs of 0.5 and 1.0%, and including all ancestries or only probands of European ancestry. In the Epi4k participants, we found enrichment for rare, compound heterozygous variants in six genes, including three involved in neuronal growth and development – PRTG (p = 0.00086, 1% MAF, combined ancestries), TNC (p = 0.022, 1% MAF, combined ancestries) and MACF1 (p = 0.0245, 0.5% MAF, EU ancestry). Due to the total number of transcripts considered in these analyses, the enrichment detected was not significant after correction for multiple testing and higher powered or prospective studies are necessary to validate the candidacy of these genes. However, PRTG, TNC and MACF1 are potential novel recessive epilepsy genes and our results highlight that compound heterozygous variants should be considered in sporadic epilepsy.
A growing number of studies are revealing that many Milky Way globular clusters possess extended stellar structures beyond their traditional boundaries. Just how ubiquitous these structures are, and how they originate, are key questions to explore. In this contribution, we present a Bayesian technique that we have developed to separate probable members of globular clusters from the dominant Milky Way fore/background at large clustercentric radii and hence facilitate quantitative analyses of these intriguing structures. We demonstrate the promise of our method by showing how it recovers the known extended features around Palomar 5 and NGC 7089.
In experimental and clinical studies, green or black tea consumption has been shown to reduce oxidative stress. However, these studies involved high levels of tea consumption and may not reflect patterns in the general population. Here, we examined the association between black or green tea consumption and oxidative stress in a cross-sectional study of 889 premenopausal US women aged 35–54 years. Tea consumption was measured using the Block-98 FFQ. Urinary 8-iso-PGF2α (F2-IsoP) and 2,3-dinor-5,6-dihydro-15-F2t-isoprostane (15-F2t-IsoP-M) were used as biomarkers of oxidative stress. These compounds were measured by MS and normalised to creatinine. Linear regression was used to calculate the geometric mean differences (GMD) and 95% CI for log-transformed urinary F2-IsoP or 15-F2t-IsoP-M in relation to black or green tea consumption. We further examined whether adjusting for caffeine impacted associations between tea and oxidative stress. Geometric means of urinary F2-IsoP and 15-F2t-IsoP-M were 1·44 (95% CI 1·39, 1·49) and 0·71 (95% CI 0·69, 0·73) ng/mg creatinine, respectively. Overall, green tea consumption was not associated with urinary F2-IsoP or 15-F2t-IsoP-M. High-level black tea consumption (≥5 cups/week compared with 0) was associated with higher 15-F2t-IsoP-M concentrations (adjusted GMD=0·10, 95 % CI 0·02–0.19) but not F2-IsoP. Adjusting for caffeine nullified the association between black tea and 15-F2t-IsoP-M. Our findings do not support the hypothesis that dietary tea consumption is inversely associated with oxidative stress.
Red Supergiant Stars (RSGs) are important probes of stellar and chemical evolution in star-forming environments. They represent the brightest near-IR stellar components of external galaxies and probe the most recent stellar population to provide robust, independent abundance estimates. The Local Group dwarf irregular galaxy, NGC6822, is a reasonably isolated galaxy with an interesting structure and turbulent history. Using RSGs as chemical abundance probes, we estimate metallicities in the central region of NGC6822, finding a suggestion of a metallicity gradient (in broad agreement with nebular tracers), however, this requires further study for confirmation. With intermediate resolution Multi-object spectroscopy (from e.g. KMOS, EMIR, MOSFIRE) combined with state-of-the-art stellar model atmospheres, we demonstrate how RSGs can be used to estimate stellar abundances in external galaxies. In this context, we compare stellar and nebular abundance tracers in NGC 6822 and by combining stellar and nebular tracers we estimate an abundance gradient of −0.18 ± 0.05 dex/kpc.
There are few prevalence studies of suicide attempts and non-suicidal self-harm (NSSH).
We aimed to estimate the prevalence of thoughts of NSSH, suicidal thoughts, NSSH and suicide attempts among 18- to 34-year-olds in Scotland.
We interviewed a representative sample of young adults from across Scotland.
We interviewed 3508 young people; 11.3 and 16.2% reported a lifetime history of suicide attempts and NSSH, respectively. The first episode of NSSH tended to precede the first suicide attempt by about 2 years. Age at onset of NSSH and suicide attempt was younger in females. Earlier age at onset was associated with more frequent NSSH/suicide attempts. Women are significantly more likely to report NSSH and suicide attempts compared with men.
One in nine young people has attempted suicide and one in six has engaged in NSSH. Clinicians should be vigilant, as suicide attempts and NSSH are relatively common.
In ewe lambs, acceleration of growth and accumulation of both muscle and fat leads to earlier sexual maturity and better reproductive performance. The next stage in the development of this theme is to test whether these aspects of growth in young ewes affect milk production in their first lactation and the growth of their first progeny. We studied 75 young Merino ewes that had known phenotypic values for depth of eye muscle (EMD) and fat (FAT), and known Australian Sheep Breeding Values for post-weaning weight (PWT) and depths of eye muscle (PEMD) and fat (PFAT). They lambed for the first time at 1 year of age. Their lambs were weighed weekly from birth to weaning at 10 weeks to determine live weight gain and weaning weight. Progeny birth weight was positively associated with live weight gain and weaning weight (P<0.001). The PWT of the mothers was positively associated with birth weight (P<0.01), live weight gain and weaning weight of the progeny (P<0.05); however, these progeny traits were not influenced by EMD, FAT, PEMD, PFAT of the mothers (P>0.05). The PWT of the sire was positively associated with live weight gain (P<0.05) and weaning weight of the progeny (P<0.01). At around day 20 postpartum, we measured milk production and milk composition (fat, protein, lactose, total solids). Milk production was influenced positively by birth type (single or twin; P<0.05) and negatively by birth weight (P<0.05), but not by mother phenotype or genotype, sire genotype of the mother or the sex of the progeny (P>0.05). The concentrations of fat, protein, lactose and total solids in the milk were not affected by the phenotype or genotype of the mothers or of the sires of the mothers, or by the sex of the progeny (P>0.05). We conclude that selection of young Merino ewes for better growth, and more rapid accumulation of muscle and fat, will lead to progeny that are heavier at birth, grow faster and are heavier at weaning. Moreover, milk production and composition do not seem to be affected by the genetic merit of the mother for post-weaning live weight or PEMD or PFAT. Therefore, Merino ewes can lamb at 1 year of age without affecting the production objectives of the Merino sheep industry.
Plasmodium knowlesi is increasingly recognized as a major cause of malaria in Southeast Asia. Anopheles leucosphyrous group mosquitoes transmit the parasite and natural hosts include long-tailed and pig-tailed macaques. Despite early laboratory experiments demonstrating successful passage of infection between humans, the true role that humans play in P. knowlesi epidemiology remains unclear. The threat posed by its introduction into immunologically naïve populations is unknown despite being a public health priority for this region. A two-host species mathematical model was constructed to analyse this threat. Global sensitivity analysis using Monte Carlo methods highlighted the biological processes of greatest influence to transmission. These included parameters known to be influential in classic mosquito-borne disease models (e.g. vector longevity); however, interesting ecological components that are specific to this system were also highlighted: while local vectors likely have intrinsic preferences for certain host species, how plastic these preferences are, and how this is shaped by local conditions, are key determinants of parasite transmission potential. Invasion analysis demonstrates that this behavioural plasticity can qualitatively impact the probability of an epidemic sparked by imported infection. Identifying key vector sub/species and studying their biting behaviours constitute important next steps before models can better assist in strategizing disease control.
For two decades, the Hopi Cultural Preservation Office has worked with archaeologists to co-create knowledge about the past and document contemporary values associated with heritage sites. Much of this work has been accomplished within the framework of research mandated by the National Historic Preservation Act and National Environmental Policy Act. Here we describe a case study that illustrates the processes of this community-based participatory research, including research design, implementation of fieldwork, peer review of research findings, and reporting. The case study is a project conducted in 2014 by the Hopi Tribe in partnership with Anthropological Research, LLC, to investigate traditional cultural properties associated with an Arizona Public Service Company transmission line. The Hopi Tribe’s collaborative research with archaeologists provides intellectual benefits for the management of archaeological resources and the humanistic and scientific understanding of the past.
To examine the association between women’s empowerment in agriculture and nutritional status among children under 2 years of age in rural Nepal.
Cross-sectional survey of 4080 households conducted in 2012. Data collected included: child and maternal anthropometric measurements; child age and sex; maternal age, education, occupation and empowerment in agriculture; and household size, number of children, religion, caste and agro-ecological zone. Associations between the Women’s Empowerment in Agriculture Index (WEAI)’s Five Domains of Empowerment (5DE) sub-index and its ten component indicators and child length-for-age Z-scores (LAZ) and weight-for-length Z-scores (WLZ) were estimated, using ordinary least-squares regression models, with and without adjustments for key child, maternal and household level covariates.
Two hundred and forty rural communities across sixteen districts of Nepal.
Children under 24 months of age and their mothers (n 1787).
The overall WEAI 5DE was positively associated with LAZ (β=0·20, P=0·04). Three component indicators were also positively associated with LAZ: satisfaction with leisure time (β=0·27, P<0·01), access to and decisions regarding credit (β=0·20, P=0·02) and autonomy in production (β=0·10, P=0·04). No indicator of women’s empowerment in agriculture was associated with WLZ.
Women’s empowerment in agriculture, as measured by the WEAI 5DE and three of its ten component indicators, was significantly associated with LAZ, highlighting the potential role of women’s empowerment in improving child nutrition in Nepal. Additional studies are needed to determine whether interventions to improve women’s empowerment will improve child nutrition.
In most countries, male pigs are physically castrated soon after birth to reduce the risk of boar taint and to avoid behaviours such as fighting and mounting. However, entire male pigs are more feed efficient and deposit less fat than barrows. In addition, many animal welfare organizations are lobbying for a cessation of castration, with a likelihood that this could lead to inferior pork unless an alternative method is used to control boar taint. An alternative to physical castration is immunization against gonadotrophin releasing factor (GnRF) which allows producers to capitalize on the superior feed efficiency and carcass characteristics of boars without the risk of boar taint. From a physiological perspective, immunized pigs are entire males until shortly after the second dose, typically given 4 to 6 weeks before slaughter. Following full immunization, there is a temporary suppression of testicular function and a hormonal status that resembles that of a barrow. Nutrient requirements will be different in these two phases, before and after full immunization. Given that there have been few published studies comparing the lysine requirements of entire males and barrows in contemporary genotypes, it is useful to use gilt requirements as a benchmark. A series of meta-analyses comparing anti-GnRF immunized boars and physical castrates and use of nutritional models suggest that the lysine requirement of entire males before the second immunization is 5% higher than for gilts, from 25 to 50 kg BW, and by 8% from 50 to 95 kg. Given that the penalty in growth performance for having inadequate dietary lysine is greater in males than in gilts or barrows, it is important to ensure that lysine requirements are met to obtain the maximum benefits of entire male production during this phase. After the second immunization, the lysine requirement of immunized males decreases and may become more like that of barrows. In addition, a consistent effect of full immunization is a marked increase in voluntary feed intake from about 10 days after the second dose. Putting these together, the estimated lysine requirement, expressed in terms of diet composition, falls to 94% of the gilt level. Although general principles can be described now, further research is needed to fully define the lysine requirements of immunized boars. It is important that the temporal pattern of tissue deposition rates and feed intake be explored to be incorporated into models to predict nutrient requirements over the period of rapidly changing metabolism.
Studies to quantify genetic variation in cassava germplasm, available within the national breeding programmes in Africa, have been limited. Here, we report on the nature and extent of genetic variation that exists within 1401 cassava varieties from seven countries: Tanzania (270 genotypes); Uganda (268); Kenya (234); Rwanda (184); Democratic Republic of Congo (DRC; 177); Madagascar (186); Mozambique (82). The vast majority of these genotypes do not exist within a formal germplasm conservation initiative and were derived from farmers' fields and National Agricultural Research Systems breeding programmes. Genotypes were assayed using 26 simple sequence repeat markers. Moderate genetic variation was observed with evidence of a genetic bottleneck in the region. Some differentiation was observed among countries in both cultivars and landraces. Euclidean distance revealed the pivotal position of Tanzanian landraces in the region, and STRUCTURE analysis revealed subtle and fairly complex relationships among cultivars and among landraces and cultivars analysed together. This is likely to reflect original germplasm introductions, gene flow including farmer exchanges, disease pandemics, past breeding programmes and the introduction of cultivars from the International Institute of Tropical Agriculture – Nigeria. Information generated from this study will be useful to justify and guide a regional cassava genetic resource conservation strategy, to identify gaps in cassava diversity in the region and to guide breeding strategies.
The reproductive efficiency of the entire sheep flock could be improved if ewe lambs go through puberty early and produce their first lamb at 1 year of age. The onset of puberty is linked to the attainment of critical body mass, and therefore we tested whether it would be influenced by genetic selection for growth rate or for rate of accumulation of muscle or fat. We studied 136 Merino ewe lambs with phenotypic values for depth of eye muscle (EMD) and fat (FAT) and Australian Sheep Breeding Values at post-weaning age (200 days) for live weight (PWT), eye muscle depth (PEMD) and fat depth (PFAT). First oestrus was detected with testosterone-treated wethers and then entire rams as the ewes progressed from 6 to 10 months of age. Blood concentrations of leptin and IGF-I were measured to test whether they were related to production traits and reproductive performance (puberty, fertility and reproductive rate). In total, 97% of the lambs reached first oestrus at average weight 39.4 ± 0.4 kg (mean ± s.e.m.) and age 219 days (range 163 to 301). Age at first oestrus decreased with increases in values for PWT (P < 0.001), and concentrations of IGF-I (P < 0.05) and leptin (P < 0.01). The proportion of ewe lambs that achieved puberty was positively related with increases in values for EMD (P < 0.01), FAT (P < 0.05) or PWT (P < 0.01), and 75% of the ewe lambs were pregnant at average weight 44.7 ± 0.5 kg and age 263 days (range 219 to 307). Ewe lambs that were heavier at the start of mating were more fertile (P < 0.001) and had a higher reproductive rate (P < 0.001). Fertility and reproductive rate were positively correlated with increases in values for EMD (P < 0.01), FAT (P < 0.05), PWT (P < 0.01) and leptin concentration (P < 0.01). Fertility, but not reproductive rate, increased as values for PFAT increased (P < 0.05). Leptin concentration increased with increases in values for EMD (P < 0.001), FAT (P < 0.001), PWT (P < 0.001), PEMD (P < 0.05) and PFAT (P < 0.05). Many of these relationships became non-significant when PWT or live weight was added to the statistical model. We conclude that selection for genetic potential for growth can accelerate the onset of puberty and increase fertility and reproductive rate of Merino ewe lambs. The metabolic hormones, IGF-I and leptin, might act as a physiological link between the growing tissues and the reproductive axis.
InGaN epilayers have been investigated for use in photovoltaic solar cells for the past years. At present, almost all photovoltaic device structures reported have exhibited very low short circuit currents and thus very low solar conversion efficiency. This phenomenon has been attributed to point and extended defect chemistry in InGaN epilayers (e.g. vacancies, misfit dislocations, and V-defects), as well as to spinodal decomposition of the strained InGaN wurtzite lattice system. These defects become more dominant for higher indium concentration InGaN epilayers needed for multijunction photovoltaic device structures. In this work, we will report on the growth and characterization of indium-rich InGaN epilayers that have been grown by novel MOCVD growth technology, including the growth at superatmospheric reactor pressures.