Long-read sequencing technologies have substantially improved the assemblies of many isolate bacterial genomes as compared to fragmented short-read assemblies. However, assembling complex metagenomic ...datasets remains difficult even for state-of-the-art long-read assemblers. Here we present metaFlye, which addresses important long-read metagenomic assembly challenges, such as uneven bacterial composition and intra-species heterogeneity. First, we benchmarked metaFlye using simulated and mock bacterial communities and show that it consistently produces assemblies with better completeness and contiguity than state-of-the-art long-read assemblers. Second, we performed long-read sequencing of the sheep microbiome and applied metaFlye to reconstruct 63 complete or nearly complete bacterial genomes within single contigs. Finally, we show that long-read assembly of human microbiomes enables the discovery of full-length biosynthetic gene clusters that encode biomedically important natural products.
Recent advances in molecular approaches and DNA sequencing have greatly progressed the field of ecology and allowed for the study of complex communities in unprecedented detail. Next generation ...sequencing (NGS) can reveal powerful insights into the diversity, composition, and dynamics of cryptic organisms, but results may be sensitive to a number of technical factors, including molecular practices used to generate amplicons, sequencing technology, and data processing. Despite the popularity of some techniques over others, explicit tests of the relative benefits they convey in molecular ecology studies remain scarce. Here we tested the effects of PCR replication, sequencing depth, and sequencing platform on ecological inference drawn from environmental samples of soil fungi. We sequenced replicates of three soil samples taken from pine biomes in North America represented by pools of either one, two, four, eight, or sixteen PCR replicates with both 454 pyrosequencing and Illumina MiSeq. Increasing the number of pooled PCR replicates had no detectable effect on measures of α- and β-diversity. Pseudo-β-diversity - which we define as dissimilarity between re-sequenced replicates of the same sample - decreased markedly with increasing sampling depth. The total richness recovered with Illumina was significantly higher than with 454, but measures of α- and β-diversity between a larger set of fungal samples sequenced on both platforms were highly correlated. Our results suggest that molecular ecology studies will benefit more from investing in robust sequencing technologies than from replicating PCRs. This study also demonstrates the potential for continuous integration of older datasets with newer technology.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Objectives. This study investigated the relationships between job characteristics and coping in predicting levels of anxiety and depression in nurses. The study was based on current theories of ...occupational stress, and predictors included job demands, social support, decision authority and skill discretion control, effort, over‐commitment, rewards, and ways of coping. It was predicted that job demands, extrinsic effort, over‐commitment, and negative coping behaviours would be positively associated with depression and anxiety, and social support, rewards, decision authority, skill discretion control, and positive coping would be negatively associated with depression and anxiety.
Methods. Participants were 870 nurses, who responded to a bulk mail sent randomly to 4,000 nurses from the south of England.
Results. The results showed that job demands, extrinsic effort, and over‐commitment were associated with higher levels of anxiety and depression. Social support, rewards, and skill discretion were negatively associated with mental health problems. Few interactions were found between the variables. Coping behaviours significantly added to the explanation of variance in anxiety and depression outcomes, over and above the use of demand–control–support, and effort–reward factors alone.
Conclusion. The results from the study demonstrated the importance of coping factors in work‐stress research, in accordance with the multi‐factorial premise of transactional stress models. It is argued that multi‐factor research is needed to help develop effective organizational interventions.
Background Although peanut oral immunotherapy (OIT) has been conclusively shown to cause desensitization, it is currently unknown whether clinical protection persists after stopping therapy. ...Objective Our primary objective was to determine whether peanut OIT can induce sustained unresponsiveness after withdrawal of OIT. Methods We conducted a pilot clinical trial of peanut OIT at 2 US centers. Subjects age 1 to 16 years were recruited and treated for up to 5 years with peanut OIT. The protocol was modified over time to permit dose increases to a maximum of 4000 mg/d peanut protein. Blood was collected at multiple time points. Clinical end points were measured with 5000-mg double-blinded, placebo-controlled food challenges once specific criteria were met. Results Of the 39 subjects originally enrolled, 24 completed the protocol and had evaluable outcomes. Twelve (50%) of 24 successfully passed a challenge 1 month after stopping OIT and achieved sustained unresponsiveness. Peanut was added to the diet. At baseline and the time of challenge, such subjects had smaller skin test results, as well as lower IgE levels specific for peanut, Ara h 1, and Ara h 2 and lower ratios of peanut-specific IgE/total IgE compared with subjects not passing. There were no differences in peanut IgG4 levels or functional activity at the end of the study. Conclusions This is the first demonstration of sustained unresponsiveness after peanut OIT, occurring in half of subjects treated for up to 5 years. OIT favorably modified the peanut-specific immune response in all subjects completing the protocol. Smaller skin test results and lower allergen-specific IgE levels were predictive of successful outcome.
The cattle rumen has a diverse microbial ecosystem that is essential for the host to digest plant material. Extremes in body weight (BW) gain in mice and humans have been associated with different ...intestinal microbial populations. The objective of this study was to characterize the microbiome of the cattle rumen among steers differing in feed efficiency. Two contemporary groups of steers (n=148 and n=197) were fed a ration (dry matter basis) of 57.35% dry-rolled corn, 30% wet distillers grain with solubles, 8% alfalfa hay, 4.25% supplement, and 0.4% urea for 63 days. Individual feed intake (FI) and BW gain were determined. Within contemporary group, the four steers within each Cartesian quadrant were sampled (n=16/group) from the bivariate distribution of average daily BW gain and average daily FI. Bacterial 16S rRNA gene amplicons were sequenced from the harvested bovine rumen fluid samples using next-generation sequencing technology. No significant changes in diversity or richness were indicated, and UniFrac principal coordinate analysis did not show any separation of microbial communities within the rumen. However, the abundances of relative microbial populations and operational taxonomic units did reveal significant differences with reference to feed efficiency groups. Bacteroidetes and Firmicutes were the dominant phyla in all ruminal groups, with significant population shifts in relevant ruminal taxa, including phyla Firmicutes and Lentisphaerae, as well as genera Succiniclasticum, Lactobacillus, Ruminococcus, and Prevotella. This study suggests the involvement of the rumen microbiome as a component influencing the efficiency of weight gain at the 16S level, which can be utilized to better understand variations in microbial ecology as well as host factors that will improve feed efficiency.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
This paper examines impacts of childhood health on socioeconomic status (SES) outcomes observed during adulthood: levels and trajectories of education, family income, household wealth, individual ...earnings, and labor supply. The analysis is conducted using panel data that collect these SES measures using a sample who were originally children and are now well into their adult years. Since all siblings are in the panel, unmeasured family and neighborhood background effects can be controlled for. With the exception of education, poor childhood health has a quantitatively large effect on all of these outcomes. Moreover, these estimated effects are larger when unobserved family effects are controlled.
•N95 respirators are equivalent to type 3 face masks in preventing infection transmission.•Proper donning and doffing is critical for safe use of PPE.•Face shields should be used only in combination ...with lower face protection.•High volume evacuation helps to limit the production of aerosolized particles at the source.
With the 2019 emergence of coronavirus disease 19 (colloquially called COVID-19) came renewed public concern about airborne and aerosolized virus transmission. Accompanying this concern were many conflicting dialogues about which forms of personal protective equipment best protect dental health care practitioners and their patients from viral exposure. In this comprehensive review we provide a thorough and critical assessment of face masks and face shields, some of the most frequently recommended personal safeguards against viral infection.
We begin by describing the function and practicality of the most common mask types used in dentistry: procedural masks, surgical masks, and filtering respirator facemasks (also called N95s). This is followed by a critical assessment of mask use based on a review of published evidence in three key domains: the degree to which each mask type is shown to protect against airborne and aerosolized disease, the reported likelihood for non-compliance among mask users, and risk factors associated with both proper and improper mask use. We use this information to conclude our review with several practical, evidence-based recommendations for mask use in dental and dental educational clinics.
Summary Background Very-low-birth-weight (VLBW, <1500 g birth weight) infants are at high risk for both early- and late-onset sepsis. Prior studies have observed a predominance of Gram-negative ...organisms as a cause of early-onset sepsis and Gram-positive organisms as a cause of late-onset sepsis. These reports are limited to large, academic neonatal intensive care units (NICUs) and may not reflect findings in other units. The purpose of this study was to determine the risk factors for sepsis, the causative organisms, and mortality following infection in a large and diverse sample of NICUs. Methods We analysed the results of all cultures obtained from VLBW infants admitted to 313 NICUs from 1997 to 2010. Results Over 108,000 VLBW infants were admitted during the study period. Early-onset sepsis occurred in 1032 infants, and late-onset sepsis occurred in 12,204 infants. Gram-negative organisms were the most commonly isolated pathogens in early-onset sepsis, and Gram-positive organisms were most commonly isolated in late-onset sepsis. Early- and late-onset sepsis were associated with increased risk of death controlling for other confounders (odds ratio 1.45 95% confidence interval CI 1.21,1.73, and OR 1.30 95%CI 1.21, 1.40, respectively). Conclusions This is the largest report of sepsis in VLBW infants to date. Incidence for early-onset sepsis and late-onset sepsis has changed little over this 14-year period, and overall mortality in VLBW infants with early- and late-onset sepsis is higher than in infants with negative cultures.
Trees and forests provide a wide variety of ecosystem services in addition to timber, food, and other provisioning services. New approaches to pest and disease management are needed that take into ...account these multiple services and the different stakeholders they benefit, as well as the likelihood of greater threats in the future resulting from globalization and climate change. These considerations will affect priorities for both basic and applied research and how trade and phytosanitary regulations are formulated.
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