The microbiome of pest insects:It is not just bacteria

Insects are associated with multiple microbes that have been reported to influence various aspects of their biology. Most studies in insects, including pest species, focus on the bacterial communities of the microbiome even though the microbiome consists of members of many more kingdoms, which can also have large influence on the life history of insects. In this review, we present some key examples of how the different members of the microbiome, such as bacteria, fungi, viruses, archaea, and protozoa, affect the fitness and behavior of pest insects. Moreover, we argue that interactions within and among microbial groups are abundant and of great importance, necessitating the use of a community approach to study microbial-host interactions. We propose that the restricted focus on bacteria very likely hampers our understanding of the functioning and impact of the microbiome on the biology of pest insects. We close our review by highlighting a few open questions that can provide an in-depth understanding of how other components of the microbiome, in addition to bacteria, might influence host performance, thus contributing to pest insect ecology

Neonatal Mortality Levels for 193 Countries in 2009 with Trends since 1990: A Systematic Analysis of Progress, Projections, and Priorities

Mikkel Oestergaard and colleagues develop annual estimates for neonatal mortality rates and neonatal deaths for 193 countries for 1990 to 2009, and forecasts into the future

Sloan Digital Sky Survey IV: Mapping the Milky Way, Nearby Galaxies, and the Distant Universe

We describe the Sloan Digital Sky Survey IV (SDSS-IV), a project encompassing three major spectroscopic programs. The Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) is observing hundreds of thousands of Milky Way stars at high resolution and high signal-to-noise ratios in the near-infrared. The Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey is obtaining spatially resolved spectroscopy for thousands of nearby galaxies (median $z\sim 0.03$). The extended Baryon Oscillation Spectroscopic Survey (eBOSS) is mapping the galaxy, quasar, and neutral gas distributions between $z\sim 0.6$ and 3.5 to constrain cosmology using baryon acoustic oscillations, redshift space distortions, and the shape of the power spectrum. Within eBOSS, we are conducting two major subprograms: the SPectroscopic IDentification of eROSITA Sources (SPIDERS), investigating X-ray AGNs and galaxies in X-ray clusters, and the Time Domain Spectroscopic Survey (TDSS), obtaining spectra of variable sources. All programs use the 2.5 m Sloan Foundation Telescope at the Apache Point Observatory; observations there began in Summer 2014. APOGEE-2 also operates a second near-infrared spectrograph at the 2.5 m du Pont Telescope at Las Campanas Observatory, with observations beginning in early 2017. Observations at both facilities are scheduled to continue through 2020. In keeping with previous SDSS policy, SDSS-IV provides regularly scheduled public data releases; the first one, Data Release 13, was made available in 2016 July

Sloan Digital Sky Survey IV: Mapping the Milky Way, Nearby Galaxies, and the Distant Universe

We describe the Sloan Digital Sky Survey IV (SDSS-IV), a project encompassing three major spectroscopic programs. The Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) is observing hundreds of thousands of Milky Way stars at high resolution and high signal-to-noise ratios in the near-infrared. The Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey is obtaining spatially resolved spectroscopy for thousands of nearby galaxies (median $z\sim 0.03$). The extended Baryon Oscillation Spectroscopic Survey (eBOSS) is mapping the galaxy, quasar, and neutral gas distributions between $z\sim 0.6$ and 3.5 to constrain cosmology using baryon acoustic oscillations, redshift space distortions, and the shape of the power spectrum. Within eBOSS, we are conducting two major subprograms: the SPectroscopic IDentification of eROSITA Sources (SPIDERS), investigating X-ray AGNs and galaxies in X-ray clusters, and the Time Domain Spectroscopic Survey (TDSS), obtaining spectra of variable sources. All programs use the 2.5 m Sloan Foundation Telescope at the Apache Point Observatory; observations there began in Summer 2014. APOGEE-2 also operates a second near-infrared spectrograph at the 2.5 m du Pont Telescope at Las Campanas Observatory, with observations beginning in early 2017. Observations at both facilities are scheduled to continue through 2020. In keeping with previous SDSS policy, SDSS-IV provides regularly scheduled public data releases; the first one, Data Release 13, was made available in 2016 July

Acceptability of evidence-based neonatal care practices in rural Uganda – implications for programming

<p>Abstract</p> <p>Background</p> <p>Although evidence-based interventions to reach the Millennium Development Goals for Maternal and Neonatal mortality reduction exist, they have not yet been operationalised and scaled up in Sub-Saharan African cultural and health systems. A key concern is whether these internationally recommended practices are acceptable and will be demanded by the target community. We explored the acceptability of these interventions in two rural districts of Uganda.</p> <p>Methods</p> <p>We conducted 10 focus group discussions consisting of mothers, fathers, grand parents and child minders (older children who take care of other children). We also did 10 key informant interviews with health workers and traditional birth attendants.</p> <p>Results</p> <p>Most maternal and newborn recommended practices are acceptable to both the community and to health service providers. However, health system and community barriers were prevalent and will need to be overcome for better neonatal outcomes. Pregnant women did not comprehend the importance of attending antenatal care early or more than once unless they felt ill. Women prefer to deliver in health facilities but most do not do so because they cannot afford the cost of drugs and supplies which are demanded in a situation of poverty and limited male support. Postnatal care is non-existent. For the newborn, delayed bathing and putting nothing on the umbilical cord were neither acceptable to parents nor to health providers, requiring negotiation of alternative practices.</p> <p>Conclusion</p> <p>The recommended maternal-newborn practices are generally acceptable to the community and health service providers, but often are not practiced due to health systems and community barriers. Communities associate the need for antenatal care attendance with feeling ill, and postnatal care is non-existent in this region. Health promotion programs to improve newborn care must prioritize postnatal care, and take into account the local socio-cultural situation and health systems barriers including the financial burden. Male involvement and promotion of waiting shelters at selected health units should be considered in order to increase access to supervised deliveries. Scale-up of the evidence based practices for maternal-neonatal health in Sub-Saharan Africa should follow rapid appraisal and adaptation of intervention packages to address the local health system and socio-cultural situation.</p

Neonatal Mortality and Prevalence of Practices for Newborn Care in a Squatter Settlement of Karachi, Pakistan: A Cross-Sectional Study

Background: During the past two decades there has been a sustained decline in child and infant mortality, however neonatal mortality has remained relatively unchanged. Almost all neonatal deaths (99%) occur in developing countries, where the majority are delivered at homes. Evidence suggests that these deaths could be prevented by simple, inexpensive practices and interventions during the pregnancy, delivery and postnatal period. In Pakistan over the last decade extensive efforts have been made by the international donors and government to implement these practices. However, limited attempts have been made to explore if these efforts have made a difference at the grass root level. This study assessed the burden of neonatal mortality and prevalence of practices for newborn care in a squatter settlement of Karachi, Pakistan.Methodology/Principal Findings: A community based cross-sectional study was performed. A pre-tested structured questionnaire was administered to 565 women who had recently delivered. Information was collected on neonatal morbidity, mortality and practices of women regarding care during pregnancy, child birth and for newborn, till 28th day of birth. Although 70% of women mentioned receiving antenatal care by a skilled provider, only 54.5% had four or more visits. Tetanus toxoid was received by 79% of women while only 56% delivered at a health care facility by a skilled attendant. Newborn care practices like bathing the baby immediately after birth (56%), giving pre-lacteals (79.5%), late initiation of breast feeding (80.3%), application of substances on umbilical cord (58%) and body massage (89%) were common. Most neonates (81.1%) received BCG injection and polio drops after birth. Neonatal mortality rate was 27/1000 live births with the majority of deaths occurring during the first three days of life.Conclusion: Even after years of efforts by government and nongovernmental sector to reduce newborn morbidity and mortality, inadequate antenatal care, home deliveries and unhealthy newborn care practices are highly prevalent. This leads us to important questions of why practices and behaviors have not changed. Who is responsible and what strategies are needed to bring this change

Poor newborn care practices - a population based survey in eastern Uganda

BACKGROUND: Four million neonatal deaths are estimated to occur each year and almost all in low income countries, especially among the poorest. There is a paucity of data on newborn health from sub-Saharan Africa and few studies have assessed inequity in uptake of newborn care practices. We assessed socioeconomic differences in use of newborn care practices in order to inform policy and programming in Uganda. METHODS: All mothers with infants aged 1-4 months (n = 414) in a Demographic Surveillance Site were interviewed. Households were stratified into quintiles of socioeconomic status (SES). Three composite outcomes (good neonatal feeding, good cord care, and optimal thermal care) were created by combining related individual practices from a list of twelve antenatal/essential newborn care practices. Multiple logistic regression analysis was used to identify determinants of each dichotomised composite outcome. RESULTS: There were low levels of coverage of newborn care practices among both the poorest and the least poor. SES and place of birth were not associated with any of the composite newborn care practices. Of newborns, 46% had a facility delivery and only 38% were judged to have had good cord care, 42% optimal thermal care, and 57% were considered to have had adequate neonatal feeding. Mothers were putting powder on the cord; using a bottle to feed the baby; and mixing/replacing breast milk with various substitutes. Multiparous mothers were less likely to have safe cord practices (OR 0.5, CI 0.3 - 0.9) as were mothers whose labour began at night (OR 0.6, CI 0.4 - 0.9). CONCLUSION: Newborn care practices in this setting are low and do not differ much by socioeconomic group. Despite being established policy, most neonatal interventions are not reaching newborns, suggesting a "policy-to-practice gap". To improve newborn survival, newborn care should be integrated into the current maternal and child interventions, and should be implemented at both community and health facility level as part of a universal coverage strategy

The Completed SDSS-IV extended Baryon Oscillation Spectroscopic Survey: Measurement of the BAO and growth rate of structure of the luminous red galaxy sample from the anisotropic power spectrum between redshifts 0.6 and 1.0

We analyse the clustering of the Sloan Digital Sky Survey IV extended Baryon Oscillation Spectroscopic Survey Data Release 16 luminous red galaxy sample (DR16 eBOSS LRG) in combination with the high redshift tail of the Sloan Digital Sky Survey III Baryon Oscillation Spectroscopic Survey Data Release 12 (DR12 BOSS CMASS).We measure the redshift space distortions (RSD) and also extract the longitudinal and transverse baryonic acoustic oscillation (BAO) scale from the anisotropic power spectrum signal inferred from 377 458 galaxies between redshifts 0.6 and 1.0, with the effective redshift of zeff = 0.698 and effective comoving volume of 2.72 Gpc3. After applying reconstruction, we measure the BAO scale and infer DH(zeff)/rdrag = 19.30 ± 0.56 and DM(zeff)/rdrag = 17.86 ± 0.37. When we perform an RSD analysis on the pre-reconstructed catalogue on the monopole, quadrupole, and hexadecapole we find, DH(zeff)/rdrag = 20.18 ± 0.78, DM(zeff)/rdrag = 17.49 ± 0.52 and fσ8(zeff) = 0.454 ± 0.046. We combine both sets of results along with the measurements in configuration space and report the following consensus values: DH(zeff)/rdrag = 19.77 ± 0.47, DM(zeff)/rdrag = 17.65 ± 0.30 and fσ8(zeff) = 0.473 ± 0.044, which are in full agreement with the standard CDM and GR predictions. These results represent the most precise measurements within the redshift range 0.6 ≤ z ≤ 1.0 and are the culmination of more than 8 yr of SDSS observations

Scanning and filling : ultra-dense SNP genotyping combining genotyping-by-sequencing, SNP array and whole-genome resequencing data

Genotyping-by-sequencing (GBS) represents a highly cost-effective high-throughput genotyping approach. By nature, however, GBS is subject to generating sizeable amounts of missing data and these will need to be imputed for many downstream analyses. The extent to which such missing data can be tolerated in calling SNPs has not been explored widely. In this work, we first explore the use of imputation to fill in missing genotypes in GBS datasets. Importantly, we use whole genome resequencing data to assess the accuracy of the imputed data. Using a panel of 301 soybean accessions, we show that over 62,000 SNPs could be called when tolerating up to 80% missing data, a five-fold increase over the number called when tolerating up to 20% missing data. At all levels of missing data examined (between 20% and 80%), the resulting SNP datasets were of uniformly high accuracy (96– 98%). We then used imputation to combine complementary SNP datasets derived from GBS and a SNP array (SoySNP50K). We thus produced an enhanced dataset of >100,000 SNPs and the genotypes at the previously untyped loci were again imputed with a high level of accuracy (95%). Of the >4,000,000 SNPs identified through resequencing 23 accessions (among the 301 used in the GBS analysis), 1.4 million tag SNPs were used as a reference to impute this large set of SNPs on the entire panel of 301 accessions. These previously untyped loci could be imputed with around 90% accuracy. Finally, we used the 100K SNP dataset (GBS + SoySNP50K) to perform a GWAS on seed oil content within this collection of soybean accessions. Both the number of significant marker-trait associations and the peak significance levels were improved considerably using this enhanced catalog of SNPs relative to a smaller catalog resulting from GBS alone at 20% missing data. Our results demonstrate that imputation can be used to fill in both missing genotypes and untyped loci with very high accuracy and that this leads to more powerful genetic analyses