Project description:The Microbial Database for Activated Sludge (MiDAS) field guide is a freely available online resource linking the identity of abundant and process critical microorganisms in activated sludge wastewater treatment systems to available data related to their functional importance. Phenotypic properties of some of these genera are described, but most are known only from sequence data. The MiDAS taxonomy is a manual curation of the SILVA taxonomy that proposes a name for all genus-level taxa observed to be abundant by large-scale 16?S rRNA gene amplicon sequencing of full-scale activated sludge communities. The taxonomy can be used to classify unknown sequences, and the online MiDAS field guide links the identity to the available information about their morphology, diversity, physiology and distribution. The use of a common taxonomy across the field will provide a solid foundation for the study of microbial ecology of the activated sludge process and related treatment processes. The online MiDAS field guide is a collaborative workspace intended to facilitate a better understanding of the ecology of activated sludge and related treatment processes--knowledge that will be an invaluable resource for the optimal design and operation of these systems.
Project description:Wastewater is increasingly viewed as a resource, with anaerobic digester technology being routinely implemented for biogas production. Characterising the microbial communities involved in wastewater treatment facilities and their anaerobic digesters is considered key to their optimal design and operation. Amplicon sequencing of the 16S rRNA gene allows high-throughput monitoring of these systems. The MiDAS field guide is a public resource providing amplicon sequencing protocols and an ecosystem-specific taxonomic database optimized for use with wastewater treatment facility samples. The curated taxonomy endeavours to provide a genus-level-classification for abundant phylotypes and the online field guide links this identity to published information regarding their ecology, function and distribution. This article describes the expansion of the database resources to cover the organisms of the anaerobic digester systems fed primary sludge and surplus activated sludge. The updated database includes descriptions of the abundant genus-level-taxa in influent wastewater, activated sludge and anaerobic digesters. Abundance information is also included to allow assessment of the role of emigration in the ecology of each phylotype. MiDAS is intended as a collaborative resource for the progression of research into the ecology of wastewater treatment, by providing a public repository for knowledge that is accessible to all interested in these biotechnologically important systems.http://www.midasfieldguide.org.
Project description:BACKGROUND:Relative to their application with adults there is currently little information about the application of preference-based health-related quality of life (HRQL) instruments among populations of young people. The Child Health Utility 9D (CHU9D) is a paediatric-specific generic preference-based HRQL instrument, recently translated and linguistically validated into Danish (CHU9D-DK). The purpose of this study was to investigate the construct validity of the CHU9D-DK in a sample of Danish high school students. METHODS:All students attending a Danish High School were invited to participate in a web-based survey in January 2018 (N?=?272). The survey included the CHU9D-DK, the young adult version of the Pediatric Quality of Life Inventory™ 4.0 Generic Core Scales (PedsQL), self-reported health status, presence/absence of disability/chronic diseases, life satisfaction, and socio-economic questions. CHU9D-DK utility scores were generated by employing the two scoring algorithms developed from adults in the UK and adolescents in Australia, respectively. Internal consistency, reliability and construct validity of the CHU9D-DK instrument were investigated. RESULTS:Two hundred and twenty-eight (84%) students consented to participate and completed the survey. The mean?±?(standard deviation) values of the CHU9D-DK utilities were 0.84 (0.11) when the UK adult algorithm was applied and 0.70 (0.22), when the Australian adolescent algorithm was applied. The mean PedsQL score was 82.32 (13.14). The CHU9D-DK showed good internal consistency reliability (Cronbach's alpha?=?0.803). Higher levels of health status and life satisfaction were significantly associated with higher CHU9D-DK utility scores regardless of which scoring algorithm was applied (p-values <?0.001). Students living with a disability/chronic disease exhibited significantly lower utility scores relative to their healthy peers (p-values <?0.05). Higher socio-economic status (approximated by financial situation and frequency of family vacations) was also associated with higher utility scores (p-values <?0.005). CONCLUSION:The CHU9D-DK demonstrated good psychometric performance overall and shows potential as a valid and reliable instrument for assessing the HRQL of Danish young people. TRIAL REGISTRATION:ClinicalTrials.gov identifier: NCT03391999, Registered 15 October 2017.
Project description:The antibacterial activities of DK-507k, a novel quinolone, were compared with those of other quinolones: ciprofloxacin, gatifloxacin, levofloxacin, moxifloxacin, sitafloxacin, and garenoxacin (BMS284756). DK-507k was as active as sitafloxacin and was as active as or up to eightfold more active than gatifloxacin, moxifloxacin, and garenoxacin against Streptococcus pneumoniae, methicillin-susceptible and methicillin-resistant Staphylococcus aureus, and coagulase-negative staphylococci. DK-507k was as active as or 4-fold more active than garenoxacin and 2- to 16-fold more active than gatifloxacin and moxifloxacin against ciprofloxacin-resistant strains of S. pneumoniae, including clinical isolates and in vitro-selected mutants with known mutations. DK-507k inhibited all ciprofloxacin-resistant strains of S. pneumoniae at 1 microg/ml. A time-kill assay with S. pneumoniae showed that DK-507k was more bactericidal than gatifloxacin and moxifloxacin. The activities of DK-507k against most members of the family Enterobacteriaceae were comparable to those of ciprofloxacin and equal to or up to 32-fold higher than those of gatifloxacin, levofloxacin, moxifloxacin, and garenoxacin. DK-507k was fourfold less active than sitafloxacin and ciprofloxacin against Pseudomonas aeruginosa, while it was two to four times more potent than levofloxacin, gatifloxacin, moxifloxacin, and garenoxacin against P. aeruginosa. In vivo, intravenous treatment with DK-507k was more effective than that with gatifloxacin and moxifloxacin against systemic infections caused by S. aureus, S. pneumoniae, and P. aeruginosa in mice. In a mouse model of pneumonia due to penicillin-resistant S. pneumoniae, DK-507k administered subcutaneously showed dose-dependent efficacy and eliminated the bacteria from the lungs, whereas gatifloxacin and moxifloxacin had no significant efficacy. Oral treatment with DK-507k was slightly more effective than that with ciprofloxacin in a rat model of foreign body-associated urinary tract infection caused by a P. aeruginosa isolate for which the MIC of DK-507k was fourfold higher than that of ciprofloxacin. Oral administration of DK-507k to rats achieved higher peak concentrations in serum and higher concentrations in cumulative urine than those achieved with ciprofloxacin. These data indicate the potential advantages of DK-507k over other quinolones for the treatment of a wide range of community-acquired infections.
Project description:This study used a rat contact lens (CL) model to test if high- versus low-Dk lens wear caused changes in (1) conjunctival Langerhans cell (LC) number or location; (2) Bcl-2 expression; and (3) infection risk.Female, Lewis rats wore a high- or low-Dk CL continuously for 2 weeks. Afterward, corneas were harvested and processed for ADPase activity to identify LCs, for immunostaining and for real time-polymerase chain reaction. Contact lens-wearing rats also were challenged with Pseudomonas aeruginosa by placing a bacterial-soaked CL on the eye followed by topical delivery of bacteria. After 48 hrs, slit lamp examination and real time-polymerase chain reaction were used to evaluate the corneal response.Conjunctival LC were significantly increased after low- versus high-Dk CL wear (P<0.0001). In contrast, conjunctival LC in non-lens wearing rats was not significantly different from the high-Dk lens wearing group. Bcl-2 mRNA levels were significantly decreased in low- versus high-Dk CL wearing rats, while Bax, FasL, caspase 3, and caspase 9 levels were unchanged. Immunostaining for Bcl-2 showed fewer positively stained epithelial cells in the low- versus high-Dk lens wearing group. After bacterial challenge, 30% of low- versus none of the high-Dk CL wearing corneas became infected and showed increased mRNA levels for several proinflammatory cytokines/chemokines, inducible nitric oxide synthase and matrix metalloproteinase-9.Low- versus high-Dk or non-CL wear led to an increased number of conjunctival LC, decreased Bcl-2 levels, and increased the risk of bacterial infection.
Project description:Statistical parametric maps formed via voxel-wise mass-univariate tests, such as the general linear model, are commonly used to test hypotheses about regionally specific effects in neuroimaging cross-sectional studies where each subject is represented by a single image. Despite being informative, these techniques remain limited as they ignore multivariate relationships in the data. Most importantly, the commonly employed local Gaussian smoothing, which is important for accounting for registration errors and making the data follow Gaussian distributions, is usually chosen in an ad hoc fashion. Thus, it is often suboptimal for the task of detecting group differences and correlations with non-imaging variables. Information mapping techniques, such as searchlight, which use pattern classifiers to exploit multivariate information and obtain more powerful statistical maps, have become increasingly popular in recent years. However, existing methods may lead to important interpretation errors in practice (i.e., misidentifying a cluster as informative, or failing to detect truly informative voxels), while often being computationally expensive. To address these issues, we introduce a novel efficient multivariate statistical framework for cross-sectional studies, termed MIDAS, seeking highly sensitive and specific voxel-wise brain maps, while leveraging the power of regional discriminant analysis. In MIDAS, locally linear discriminative learning is applied to estimate the pattern that best discriminates between two groups, or predicts a variable of interest. This pattern is equivalent to local filtering by an optimal kernel whose coefficients are the weights of the linear discriminant. By composing information from all neighborhoods that contain a given voxel, MIDAS produces a statistic that collectively reflects the contribution of the voxel to the regional classifiers as well as the discriminative power of the classifiers. Critically, MIDAS efficiently assesses the statistical significance of the derived statistic by analytically approximating its null distribution without the need for computationally expensive permutation tests. The proposed framework was extensively validated using simulated atrophy in structural magnetic resonance imaging (MRI) and further tested using data from a task-based functional MRI study as well as a structural MRI study of cognitive performance. The performance of the proposed framework was evaluated against standard voxel-wise general linear models and other information mapping methods. The experimental results showed that MIDAS achieves relatively higher sensitivity and specificity in detecting group differences. Together, our results demonstrate the potential of the proposed approach to efficiently map effects of interest in both structural and functional data.
Project description:To understand microbial community functional structures of activated sludge in wastewater treatment plants (WWTPs) and the effects of environmental factors on their structure, 12 activated sludge samples were collected from four WWTPs in Beijing. GeoChip 4.2 was used to determine the microbial functional genes involved in a variety of biogeochemical processes. The results showed that, for each gene category, such as egl, amyA, nir, ppx, dsrA sox and benAB, there were a number of microorganisms shared by all 12 samples, suggestive of the presence of a core microbial community in the activated sludge of four WWTPs. Variance partitioning analyses (VPA) showed that a total of 53% of microbial community variation can be explained by wastewater characteristics (25%) and operational parameters (23%), respectively. This study provided an overall picture of microbial community functional structures of activated sludge in WWTPs and discerned the linkages between microbial communities and environmental variables in WWTPs. Four full-scale wastewater treatment systems located in Beijing were investigated. Triplicate samples were collected in each site.
Project description:BACKGROUND: Animal pigmentation has received much attention in evolutionary biology research due to its strong implications for adaptation and speciation. However, apart from a few cases the genetic changes associated with these evolutionary processes remain largely unknown. The Midas cichlid fish from Central America are an ideal model system for investigating pigmentation traits that may also play a role in speciation. Most Midas cichlids maintain their melanophores and exhibit a grayish (normal) color pattern throughout their lives. A minority of individuals, however, undergo color change and exhibit a distinctive gold or even white coloration in adulthood. The ontogenetic color change in the Midas cichlids may also shed light on the molecular mechanisms underlying pigmentation disorders in humans. RESULTS: Here we use next-generation sequencing (Illumina) RNAseq analyses to compare skin transcriptome-wide expression levels in three distinct stages of color transformation in Midas cichlids. cDNA libraries of scale tissue, for six biological replicates of each group, were generated and sequenced using Illumina technology. Using a combination of three differential expression (DE) analyses we identified 46 candidate genes that showed DE between the color morphs. We find evidence for two key DE patterns: a) genes involved in melanosomal pathways are up-regulated in normally pigmented fish; and b) immediate early and inflammatory response genes were up-regulated in transitional fish, a response that parallels some human skin disorders such as melanoma formation and psoriasis. One of the DE genes segregates with the gold phenotype in a genetic cross and might be associated with incipient speciation in this highly "species-rich" lineage of cichlids. CONCLUSIONS: Using transcriptomic analyses we successfully identified key expression differences between different color morphs of Midas cichlid fish. These differentially expressed genes have important implications for our understanding of the molecular mechanisms underlying speciation in this lineage of extremely young species since they mate strongly assortatively, and new species may arise by sexual selection due to this color polymorphism. Some of the human orthologues of the genes identified here may also be involved in pigmentation differences and diseases and therefore provide genetic markers for the detection of human pigmentation disorders.
Project description:The Migraine Disability Assessment (MIDAS) is a brief questionnaire and measures headache-related disability. This study aimed to translate and cross-culturally adapt the original English version of the MIDAS to German and to test its reliability.The standardized translation process followed international guidelines. The pre-final version was tested for clarity and comprehensibility by 34 headache sufferers. Test-retest reliability of the final version was quantified by 36 headache patients completing the MIDAS twice with an interval of 48 h. Reliability was determined by intraclass correlation coefficients and internal consistency by Cronbach's ?.All steps of the translation process were followed, documented and approved by the developer of the MIDAS. The expert committee discussed in detail the complex phrasing of the questions that refer to one to another, especially exclusion of headache-days from one item to the next. The German version contains more active verb sentences and prefers the perfect to the imperfect tense. The MIDAS scales intraclass correlation coefficients ranged from 0.884 to 0.994 and was 0.991 (95% CI: 0.982-0.995) for the MIDAS total score. Cronbach's ? for the MIDAS as a whole was 0.69 at test and 0.67 at retest.The translation process was challenged by the comprehensibility of the questionnaire. The German version of the MIDAS is a highly reliable instrument for assessing headache related disability with moderate internal consistency. Provided validity testing of the German MIDAS is successful, it can be recommended for use in clinical practice as well as in research.