False-positive identifications are a significant problem in metagenomics classification. We present KrakenUniq, a novel metagenomics classifier that combines the fast k-mer-based classification of ...Kraken with an efficient algorithm for assessing the coverage of unique k-mers found in each species in a dataset. On various test datasets, KrakenUniq gives better recall and precision than other methods and effectively classifies and distinguishes pathogens with low abundance from false positives in infectious disease samples. By using the probabilistic cardinality estimator HyperLogLog, KrakenUniq runs as fast as Kraken and requires little additional memory. KrakenUniq is freely available at https://github.com/fbreitwieser/krakenuniq .
Automation inherently removes a certain amount of user control. If perceived as a loss of freedom, users may experience psychological reactance, which is a motivational state that can lead a person ...to engage in behaviors to reassert their freedom. In an online experiment, participants set up and communicated with a hypothetical smart thermostat. Participants read notifications about a change in the thermostat's setting. Phrasing of notifications was altered across three dimensions: strength of authoritative language, deviation of temperature change from preferences, and whether or not the reason for the change was transparent. Authoritative language, temperatures outside the user's preferences, and lack of transparency induced significantly higher levels of reactance. However, when the system presented a temperature change outside of the user's preferences, reactance was mitigated and user acceptance was higher if the thermostat's operations were transparent. Providing justification may be less likely to induce psychological reactance and increase user acceptance. This supports efforts to use behavioral approaches, such as demand response, to increase sustainability and limit the impacts of climate change.
Plant defense compounds occur in floral nectar, but their ecological role is not well understood. We provide evidence that plant compounds pharmacologically alter pollinator behavior by enhancing ...their memory of reward. Honeybees rewarded with caffeine, which occurs naturally in nectar of Coffea and Citrus species, were three times as likely to remember a learned floral scent as were honeybees rewarded with sucrose alone. Caffeine potentiated responses of mushroom body neurons involved in olfactory learning and memory by acting as an adenosine receptor antagonist. Caffeine concentrations in nectar did not exceed the bees' bitter taste threshold, implying that pollinators impose selection for nectar that is pharmacologically active but not repellent. By using a drug to enhance memories of reward, plants secure pollinator fidelity and improve reproductive success.
HIV-related stigma continues to negatively impact the health and well-being of people living with HIV, with deleterious effects on their care, treatment and quality of life. A growing body of ...qualitative research has documented the relationship between HIV-related stigma and health. This review aims to synthesize qualitative evidence that explored the intersections of stigma and health for people with HIV.
A thematic summary was conducted that was guided by the qualitative metasummary technique developed by Sandelowski and Barraso. Literature searches yielded 8,622 references of which 55 qualitative studies were identified that illustrated HIV-related stigma in the context of health.
The metasummary classified qualitative findings into three overarching categories: conceptualizing stigma which identified key dimensions of HIV-related stigma; experiencing stigma which highlighted experiences of stigma in the health context, and managing stigma which described ways in which stigma is avoided or addressed. To better illustrate these connections, the qualitative literature was summarized into the following themes: stigma within health care settings, the role of stigma in caring for one's health, and strategies to address HIV-related stigma in the health context. A number of health care practices were identified--some rooted in institutional practices, others shaped by personal perceptions held by practitioners--that could be stigmatizing or discriminatory towards people with HIV. There existed interconnections between enacted stigma and felt stigma that influenced health care utilization, treatment adherence, and overall health and well-being of people with HIV. Intersectional stigma also emerged as instrumental in the stigma experiences of people living with HIV. A number of strategies to address stigma were identified including social support, education, self-efficacy, resilience activities, and advocacy.
This review of the qualitative evidence indicates that HIV-related stigma within health contexts is a broad social phenomenon that manifests within multiple social spheres, including health care environments. Findings from this review indicate that future stigma research should consider the social structures and societal practices--within and outside of health care environments--that perpetuate and reinforce stigma and discrimination towards people with HIV.
Nonalcoholic steatohepatitis (NASH) is a serious liver disease associated with obesity. Characterized by metabolic syndrome, hepatic steatosis, and liver inflammation, NASH is believed to be under ...the influence of the gut microflora. Here, the composition of gut bacterial communities of NASH, obese, and healthy children was determined by 16S ribosomal RNA pyrosequencing. In addition, peripheral blood ethanol was analyzed to monitor endogenous ethanol production of patients and healthy controls. UniFrac‐based principle coordinates analysis indicated that most of the microbiome samples clustered by disease status. Each group was associated with a unique pattern of enterotypes. Differences were abundant at phylum, family, and genus levels between healthy subjects and obese patients (with or without NASH), and relatively fewer differences were observed between obese and the NASH microbiomes. Among those taxa with greater than 1% representation in any of the disease groups, Proteobacteria, Enterobacteriaceae, and Escherichia were the only phylum, family and genus types exhibiting significant difference between obese and NASH microbiomes. Similar blood‐ethanol concentrations were observed between healthy subjects and obese non‐NASH patients, but NASH patients exhibited significantly elevated blood ethanol levels. Conclusions: The increased abundance of alcohol‐producing bacteria in NASH microbiomes, elevated blood‐ethanol concentration in NASH patients, and the well‐established role of alcohol metabolism in oxidative stress and, consequently, liver inflammation suggest a role for alcohol‐producing microbiota in the pathogenesis of NASH. We postulate that the distinct composition of the gut microbiome among NASH, obese, and healthy controls could offer a target for intervention or a marker for disease. (HEPATOLOGY 2013)
Pathogenesis of nonalcoholic steatohepatitis Liu, Wensheng; Baker, Robert D.; Bhatia, Tavleen ...
Cellular and molecular life sciences : CMLS,
05/2016, Letnik:
73, Številka:
10
Journal Article
Recenzirano
Nonalcoholic steatohepatitis (NASH) is a severe form of nonalcoholic fatty liver disease and a risk factor for cirrhosis and hepatocellular carcinoma. The pathological features of NASH include ...steatosis, hepatocyte injury, inflammation, and various degrees of fibrosis. Steatosis reflects disordered lipid metabolism. Insulin resistance and excessive fatty acid influx to the liver are two important contributing factors. Steatosis is also likely associated with lipotoxicity and cellular stresses such as oxidative stress and endoplasmic reticulum stress, which result in hepatocyte injury. Inflammation and fibrosis are frequently triggered by various signals such as proinflammatory cytokines and chemokines, released by injuried hepatocytes and activated Kupffer cells. Although much progress has been made, the pathogenesis of NASH is not fully elucidated. The purpose of this review is to discuss the current understanding of NASH pathogenesis, mainly focusing on factors contributing to steatosis, hepatocyte injury, inflammation, and fibrosis.
Although deep learning has revolutionized protein structure prediction, almost all experimentally characterized de novo protein designs have been generated using physically based approaches such as ...Rosetta. Here, we describe a deep learning-based protein sequence design method, ProteinMPNN, that has outstanding performance in both in silico and experimental tests. On native protein backbones, ProteinMPNN has a sequence recovery of 52.4% compared with 32.9% for Rosetta. The amino acid sequence at different positions can be coupled between single or multiple chains, enabling application to a wide range of current protein design challenges. We demonstrate the broad utility and high accuracy of ProteinMPNN using x-ray crystallography, cryo-electron microscopy, and functional studies by rescuing previously failed designs, which were made using Rosetta or AlphaFold, of protein monomers, cyclic homo-oligomers, tetrahedral nanoparticles, and target-binding proteins.
We review recent findings and hypotheses on the roles of gut microbiome in the pathogenesis of nonalcoholic fatty liver diseases (NAFLD). Microbial metabolites and cell components contribute to the ...development of hepatic steatosis and inflammation, key components of nonalcoholic steatohepatitis (NASH), the severe form of NAFLD. Altered gut microbiome can independently cause obesity, the most important risk factor for NAFLD. This capability is attributed to short-chain fatty acids (SCFAs), major gut microbial fermentation products. SCFAs account for a large portion of caloric intake of the host, and they enhance intestinal absorption by activating GLP-2 signaling. However, elevated SCFAs may be an adaptive measure to suppress colitis, which could be a higher priority than imbalanced calorie intake. The microbiome of NASH patients features an elevated capacity for alcohol production. The pathomechanisms for alcoholic steatohepatitis may apply to NASH. NAFLD/NASH is associated with elevated Gram-negative microbiome and endotoxemia. However, many NASH patients exhibited normal serum endotoxin indicating that endotoxemia is not required for the pathogenesis of NASH. These observations suggest that microbial intervention may benefit NAFLD/NASH patients. However, very limited effects were observed using traditional probiotic species. Novel probiotic therapy based on NAFLD/NASH specific microbial composition represents a promising future direction.
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