Recurrence of non-muscle invasive bladder carcinoma after transurethral resection with hexaminolevulinate photodynamic diagnosis or regular cystoscopy.

OBJECTIVES: To compare the recurrence of non-muscle invasive bladder carcinoma (NMIBC) after transurethral resection employing cystoscopy with hexaminolevulinate-based photodynamic diagnosis (PDD) or with standard white light. PATIENTS AND METHODS: We included patients with newly suspected NMIBC in this retrospective cohort study and compared those undergoing transurethral resection by white light cystoscopy (WLC) (2008-2010) and PDD (2010-2012). All patients were treated following established criteria for good quality resection. The primary outcome was the difference in the recurrence rate after 60 months' follow-up, but we also stratified recurrence by risk groups, as set by the European Organization for Research and Treatment of Cancer. The mean recurrence-free survival was compared between the cohorts. Odds ratios or hazard ratios are reported with their 95% confidence intervals. RESULTS: The WLC and PDD cohorts comprised 124 and 91 subjects, respectively. There were no significant differences in recurrence rates between the cohorts at 6 months (recurrence rate 9/123; 7.3%), 12 months (17/118; 14.4%) or 60 months (39/102; 38.2%), with odds ratios of 1.23 (CI 0.48-3.25), 1.32 (CI 0.67-2.62) and 1.12 (CI 0.70-1.79), in favour of WLC, respectively. Further analysis showed no significant effect of PDD on either recurrence by risk group or on mean recurrence-free survival (hazard ratio, 1.12 [CI 0.70-1.79]). CONCLUSION: We found no relevant differences in the recurrence of NMIBC after the introduction of PDD with hexaminolevulinate compared to standard WLC when used for transurethral resection in our single institution.

Development and feasibility of a telemedicine tool for patients with recurrent urinary tract infection: myRUTIcoach.

INTRODUCTION AND HYPOTHESIS: Patients with recurrent urinary tract infection (rUTI) have limited knowledge of preventive strategies to lower the risk of UTI. We aimed to develop and test the feasibility of an eHealth system for women with rUTI, named myRUTIcoach, and explored the facilitators and barriers related to its adoption. METHODS: We developed myRUTIcoach in a structured iterative process and tested its feasibility among 25 women with rUTI over 2 months. Subsequent questionnaires covered satisfaction, accessibility, and experiences with myRUTIcoach. A random selection of participants and relevant stakeholders took part in semi-structured interviews to explore adoption. Data were analyzed and elaborated using inductive and deductive approaches using the Non-adoption, Abandonment, Spread, Scale-up, and Sustainability (NASSS) framework. RESULTS: MyRUTIcoach was not only widely accepted but also facilitated communication with health care professionals (HCPs) and contributed to greater knowledge of rUTI. Women graded the system a mean of 8.0 (±0.6) out of 10, with 89% stating that they would recommend it to others. Patients indicated that self-management skills were the major facilitators and barriers related to adoption, whereas HCPs stated that the disconnect between myRUTIcoach and electronic health care records (EHRs) was the major barrier. CONCLUSIONS: This research describes the development and testing of myRUTIcoach for women with rUTI. Patients and HCPs reported high satisfaction and compliance with myRUTIcoach. However, adoption by the intended users is complex and influenced by all examined domains of the NASSS framework. We have already improved linkage to EHRs, but further optimization to meet patient needs may improve the effectiveness of this self-management tool for rUTI.

The Patient Pathway for Men with Chronic Urinary Retention: Treatments, Complications, and Consequences.

OBJECTIVE: To explore the treatment options for chronic urinary retention (CUR) in men, including treatment-related complications and consequences. METHODS: This retrospective cohort study included male patients diagnosed with a non-neurogenic, symptomatic and/or high-risk, CUR >150 mL in a large Dutch non-academic teaching hospital. Data for treatments, complications, and consequences (eg, diagnostics, additional treatments, and hospital contact) were recorded and incidence rate ratios (IRRs) were calculated. RESULTS: We enrolled 177 patients (median age, 77 years; range, 44-94) with a median follow-up of 68 months (range, 1-319) during which they had a median of 8 events (range, 1-51). Most patients initially received a urethral catheter (74%) and some form of catheterization as their final treatment (87%). Compared with non-surgical cases, catheterization was more likely to be stopped after de-obstructive prostate surgery (IRR, 4.18; P < 0.001). Urinary tract infection (IRR, 3.68; P < 0.001) and macroscopic hematuria (IRR, 5.35; P < 0.001) were more common with catheterization, but post-renal problems were more likely in patients with no catheterization (IRR, 25.36; P < 0.001). The lowest chance of complication was with clean intermittent catheterization, and complications were usually managed in outpatient (77%) or emergency (6%) departments, rather than by admission (17%). CONCLUSION: Most patients require catheterization for CUR, with clean intermittent catheterization preferred due to its comparatively lower complication risk. De-obstructive prostate surgery increases the chance of stopping catheterization and may be considered in suitable cases.

Influence of environmental factors on the tropical peatlands diazotrophic communities from the Southern Brazilian Atlantic Rain Forest.

The tropical peatlands of southern Brazil are essential for the maintenance of the Atlantic Rain Forest, one of the 25 hotspots of biodiversity in the world. Although diazotrophic micro-organisms are essential for the maintenance of this nitrogen limited ecosystem, so far studies have focused only on micro-organisms involved in the carbon cycle. In this work, peat samples were collected from three tropical peatland regions during dry and rainy seasons and their chemical and microbial characteristics were evaluated. Our results showed that the structure of the diazotrophic communities in the Brazilian tropical peatlands differs in the evaluated seasons. The abundance of the genus Bradyrhizobium showed to be affected by rainfall and peat pH. Despite the shifts of the nitrogen-fixing population in the tropical peatland caused by seasonality it showed to be constantly dominated by α-Proteobacteria followed by Cyanobacteria. In addition, more than 50% of nifH gene sequences have not been classified, indicating the necessity for more studies in tropical peatland, since the reduction of N supply in the peatlands stimulates the recalcitrant organic matter decomposition performed by peatland micro-organisms, influencing the C stock.

Scrotal necrosis after cobra (Naja annulifera) envenomation.

A 47-year-old man received a snouted cobra (Naja annulifera) snake bite to his genitals while on holiday in South Africa. His penis and scrotum were noted to be swollen, deep purple in color, and painful on hospital admission. Scrotal necrosis was diagnosed, and he received multiple doses of a non-specific snake venom antiserum and broad-spectrum antibiotics. Although no neurological sequelae developed, he did require hemodialysis due to acute kidney injury. After stabilizing, he was repatriated to the Netherlands for further treatment and has since made a full recovery.

Assessment and treatment of recurrent urinary tract infections in women: development of a questionnaire based on a qualitative study of patient expectations in secondary care.

BACKGROUND: To develop a questionnaire to facilitate the inventorying of women's expectations for the assessment and treatment of recurrent urinary tract infection (UTI) in secondary care. METHODS: Semi-structured interviews were conducted among women with recurrent UTI referred to our urology department. The interviews were conducted by one interviewer, recorded, transcribed verbatim, and analyzed thematically by two researchers. We first developed 35 questions to identify potential themes, and we then tested them among women with and without recurrent UTI. Changes were made according to the feedback received. RESULTS: Six interviews were conducted before saturation was reached. Thematic analysis identified three themes: patient pathway, personal knowledge, and social implications. All respondents had received multiple antibiotic courses but no prophylactic antibiotic therapy, and although all were aware of some preventive measures, they wanted more information about their disease. However, some women were afraid to access information for fear of what they might learn. Recurrent UTI also significantly affected the daily lives all respondents. Some women expressed fears over frequent antibiotic use, and others felt that there must be something wrong with their body to have so many UTIs. Women expected the urologist to provide an explanation and to start adequate therapy for their recurrent UTI. We created a 32-item questionnaire based on these themes CONCLUSION: This study not only developed a questionnaire for use when assessing patient expectations of recurrent UTI management in secondary care but also provided novel insights into the thoughts, opinions, and expectations of women who are referred.

Health assessments and screening tools for adults experiencing homelessness: a systematic review.

BACKGROUND: Homelessness is increasing globally. It results in poorer physical and mental health than age matched people living in permanent housing. Better information on the health needs of people experiencing homelessness is needed to inform effective resourcing, planning and service delivery by government and care organisations. The aim of this review was to identify assessment tools that are valid, reliable and appropriate to measure the health status of people who are homeless. METHODS: Data sources: A systematic literature search was conducted in PubMed (and Medline), PsychInfo, Scopus, CINAHL and ERIC from database inception until September 2018. Key words used were homeless, homelessness, homeless persons, vagrancy, health status, health, health issues, health assessment and health screening. The protocol was registered with PROSPERO. The National Health and Medical Research Council of Australia (NHMRC) hierarchy of evidence was applied; methodological quality of included articles was assessed using the McMaster critical appraisal tools and psychometric properties of the tools were appraised using the International Centre for Allied Health Evidence Ready Reckoner. RESULTS: Diverse tools and measures (N = 71) were administered within, and across the reviewed studies (N = 37), with the main focus being on general health, oral health and nutrition. Eleven assessment tools in 13 studies had evidence of appropriate psychometric testing for the target population in domains of quality of life and health status, injury, substance use, mental health, psychological and cognitive function. Methodological quality of articles and tools were assessed as moderate to good. No validated tools were identified to assess oral health, chronic conditions, anthropometry, demography, nutrition, continence, functional decline and frailty, or vision and hearing. However, assessments of physical constructs (such as oral health, anthropometry, vision and hearing) could be applied to homeless people on a presumption of validity, because the constructs would be measured with clinical indicators in the same manner as people living in permanent dwellings. CONCLUSIONS: This review highlighted the need to develop consistent and comprehensive health assessment tools validated with, and tailored for, adults experiencing homelessness.

Effects of ketamine on brain function during response inhibition.

INTRODUCTION: The uncompetitive N-methyl-D-aspartate (NMDA) receptor (NMDAR) antagonist ketamine has been proposed to model symptoms of psychosis. Inhibitory deficits in the schizophrenia spectrum have been reliably reported using the antisaccade task. Interestingly, although similar antisaccade deficits have been reported following ketamine in non-human primates, ketamine-induced deficits have not been observed in healthy human volunteers. METHODS: To investigate the effects of ketamine on brain function during an antisaccade task, we conducted a double-blind, placebo-controlled, within-subjects study on n = 15 healthy males. We measured the blood oxygen level dependent (BOLD) response and eye movements during a mixed antisaccade/prosaccade task while participants received a subanesthetic dose of intravenous ketamine (target plasma level 100 ng/ml) on one occasion and placebo on the other occasion. RESULTS: While ketamine significantly increased self-ratings of psychosis-like experiences, it did not induce antisaccade or prosaccade performance deficits. At the level of BOLD, we observed an interaction between treatment and task condition in somatosensory cortex, suggesting recruitment of additional neural resources in the antisaccade condition under NMDAR blockage. DISCUSSION: Given the robust evidence of antisaccade deficits in schizophrenia spectrum populations, the current findings suggest that ketamine may not mimic all features of psychosis at the dose used in this study. Our findings underline the importance of a more detailed research to further understand and define effects of NMDAR hypofunction on human brain function and behavior, with a view to applying ketamine administration as a model system of psychosis. Future studies with varying doses will be of importance in this context.

A case of spontaneous urinary bladder rupture secondary to urinary retention due to an urethral stricture.

A spontaneous, non-traumatic, urinary bladder rupture is a rare condition. We describe a case of a 23-year-old male with a spontaneous bladder rupture secondary to urinary retention, due to an urethral stricture. He presented to the emergency department with voiding difficulties, severe abdominal pain and renal failure. Abdominal ultrasound revealed large amounts of ascites. After an unsuccessful attempt to place a Foley catheter a cystoscopy was performed which showed an urethral stricture. On CT-cystogram an intra-peritoneal bladder rupture was diagnosed and the patient underwent laparoscopic repair of the bladder wall. The postoperative course was uneventful.

Gene expression and proliferation biomarkers for antidepressant treatment resistance.

The neurotrophic hypothesis of depression suggests an association between effects on neuroplasticity and clinical response to antidepressant drug therapy. We studied individual variability in antidepressant drug effects on cell proliferation in lymphoblastoid cell lines (LCLs) from n=25 therapy-resistant patients versus n=25 first-line therapy responders from the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study. Furthermore, the variability in gene expression of genes associated with cell proliferation was analyzed for tentative candidate genes for prediction of individual LCL donor's treatment response. Cell proliferation was quantified by EdU (5-ethynyl-2'-deoxyuridine) assays after 21-day incubation of LCLs with fluoxetine (0.5 ng µl-1) and citalopram (0.3 ng µl-1) as developed and described earlier. Gene expression of a panel of candidate genes derived from genome-wide expression analyses of antidepressant effects on cell proliferation of LCLs from the Munich Antidepressant Response Signature (MARS) study was analyzed by real-time PCR. Significant differences in in vitro cell proliferation effects were detected between the group of LCLs from first-line therapy responders and LCLs from treatment-resistant patients. Gene expression analysis of the candidate gene panel revealed and confirmed influence of the candidate genes ABCB1, FZD7 and WNT2B on antidepressant drug resistance. The potential of these genes as tentative biomarkers for antidepressant drug resistance was confirmed. In vitro cell proliferation testing may serve as functional biomarker for individual neuroplasticity effects of antidepressants.

An audit of the quality of online immunisation information available to Australian parents.

BACKGROUND: The Internet is increasingly a source of health information for parents, who use the Internet alongside health care providers for immunisation information. Concerns have been raised about the reliability of online immunisation information, however to date there has been no audit of the quality or quantity of what is available to Australian parents. The objective of this study was to address this gap by simulating a general online search for immunisation information, and assessing the quality and quantity of the web sites returned by the search. METHODS: We used Google trends to identify the most common immunisation search terms used in Australia. The ten most common terms were entered into five search engines and the first ten non-commercial results from each search collated. A quality assessment tool was developed using the World Health Organization Global Advisory Committee on Vaccine Safety (GACVS) criteria for assessing the quality of vaccine safety web sites, and used to assess and score the quality of the sites. RESULTS: Seven hundred web pages were identified, of which 514 were duplicates, leaving 186 pages from 115 web sites which were audited. Forty sites did not include human immunisation information, or presented personal opinion about individuals, and were not scored. Of the 75 sites quality scored, 65 (87%) were supportive of immunisation, while 10 (13%) were not supportive. The overall mean quality score was 57/100 (range 14/100 to 92/100). When stratified by pro and anti-vaccination stance, the average quality score for pro-vaccine sites was 61/100, while the average score for anti-vaccine sites was 30/100. Pro-vaccine information could be divided into three content groups: generalist overview with little detail; well-articulated and understandable detail; and lengthy and highly technical explanations. The main area found to be lacking in pro-vaccine sites was lack of transparent authorship. CONCLUSION: Our findings suggest a need for information which is easily found, transparently authored, well-referenced, and written in a way that is easily understood.

Proliferation rates and gene expression profiles in human lymphoblastoid cell lines from patients with depression characterized in response to antidepressant drug therapy.

The current therapy success of depressive disorders remains in need of improvement due to low response rates and a delay in symptomatic improvement. Reliable functional biomarkers would be necessary to predict the individual treatment outcome. On the basis of the neurotrophic hypothesis of antidepressant's action, effects of antidepressant drugs on proliferation may serve as tentative individual markers for treatment efficacy. We studied individual differences in antidepressant drug effects on cell proliferation and gene expression in lymphoblastoid cell lines (LCLs) derived from patients treated for depression with documented clinical treatment outcome. Cell proliferation was characterized by EdU (5-ethynyl-2'-deoxyuridine) incorporation assays following a 3-week incubation with therapeutic concentrations of fluoxetine. Genome-wide expression profiling was conducted by microarrays, and candidate genes such as betacellulin-a gene involved in neuronal stem cell regeneration-were validated by quantitative real-time PCR. Ex vivo assessment of proliferation revealed large differences in fluoxetine-induced proliferation inhibition between donor LCLs, but no association with clinical response was observed. Genome-wide expression analyses followed by pathway and gene ontology analyses identified genes with different expression before vs after 21-day incubation with fluoxetine. Significant correlations between proliferation and gene expression of WNT2B, FZD7, TCF7L2, SULT4A1 and ABCB1 (all involved in neurogenesis or brain protection) were also found. Basal gene expression of SULT4A1 (P=0.029), and gene expression fold changes of WNT2B by ex vivo fluoxetine (P=0.025) correlated with clinical response and clinical remission, respectively. Thus, we identified potential gene expression biomarkers eventually being useful as baseline predictors or as longitudinal targets in antidepressant therapy.

Which Back Pain Patients Benefit From Multidisciplinary Pain Management? A Comparative Cost Analysis Using Claims Data of Statutory Health Insurance.

Aim: Multidisciplinary pain therapy (MPT) is considered as best practice for treating patients with chronical back pain. Several studies showed the cost effectiveness of interdisciplinary treatment. The aim of the present study is to identify patient characteristics that, under condition of MMT, can be associated with favourable cost trajectories after intervention. We assume that an improved health status leads to less health care utilisation. Furthermore, we aim at identifying those patients with back pain without MPT for whom we can expect favourable cost trajectories. Methods: On the basis of pseudonymised claims data of a nationwide health insurance, we identified MMT back pain patients as well as a control group of back pain patients without MMT. Using comparative cost analysis (costs insensitive to indication), we determined those MMT patients for whom the cumulated total costs per patient for the two postinterventional years were lower than the mean cumulated total costs of the control group. By means of a CART analysis, we identified statistically significant characteristics (profiles) associated with these favourable cost trajectories. Additionally, we quantified control group patients with the same profiles. Results: The study population comprised 1 252 patients with specific back pain and 767 patients with pain due to spinal disc conditions who received MPT. Compared to the control group, total post-therapy costs (insensitive to indication) of MPT patients were higher. For roughly half of MPT patients per pain type, we could identify favourable cost trajectories as per definition. These patients mainly displayed lower levels of pain intensity, no pain-related hospitalisation, and less (mental) co-morbidity in the year preceding the intervention. These profiles concerned to 58-65% of back pain patients without MPT. Conclusion: The developed methodology enables identification of back pain patients likely to benefit from MPT. The study points out the need for patient individual pain management and underlines the importance of early-stage integration of patients into multidisciplinary pain management programmes.

Effects of ketamine on brain function during smooth pursuit eye movements.

The uncompetitive NMDA receptor antagonist ketamine has been proposed to model symptoms of psychosis. Smooth pursuit eye movements (SPEM) are an established biomarker of schizophrenia. SPEM performance has been shown to be impaired in the schizophrenia spectrum and during ketamine administration in healthy volunteers. However, the neural mechanisms mediating SPEM impairments during ketamine administration are unknown. In a counter-balanced, placebo-controlled, double-blind, within-subjects design, 27 healthy participants received intravenous racemic ketamine (100 ng/mL target plasma concentration) on one of two assessment days and placebo (intravenous saline) on the other. Participants performed a block-design SPEM task during functional magnetic resonance imaging (fMRI) at 3 Tesla field strength. Self-ratings of psychosis-like experiences were obtained using the Psychotomimetic States Inventory (PSI). Ketamine administration induced psychosis-like symptoms, during ketamine infusion, participants showed increased ratings on the PSI dimensions cognitive disorganization, delusional thinking, perceptual distortion and mania. Ketamine led to robust deficits in SPEM performance, which were accompanied by reduced blood oxygen level dependent (BOLD) signal in the SPEM network including primary visual cortex, area V5 and the right frontal eye field (FEF), compared to placebo. A measure of connectivity with V5 and FEF as seed regions, however, was not significantly affected by ketamine. These results are similar to the deviations found in schizophrenia patients. Our findings support the role of glutamate dysfunction in impaired smooth pursuit performance and the use of ketamine as a pharmacological model of psychosis, especially when combined with oculomotor biomarkers. Hum Brain Mapp 37:4047-4060, 2016. © 2016 Wiley Periodicals, Inc.

Are oral health-related self-efficacy, knowledge and fatalism indicators for non-toothbrush ownership in a homeless population?

AIM: To determine if the social cognitive theory (SCT)-constructs of oral health-related efficacy, knowledge and fatalism were indicators of non-toothbrush ownership in a metropolitan-based homeless population in Australia. METHODS: Self-report data were collected from a convenience sample of 248 homeless participants located in Adelaide, Australia. Log binomial regression was used to estimate the strength of the association of the SCT constructs efficacy, knowledge and fatalism with the frequency of non-ownership of a toothbrush before and after adjusting for selected characteristics and associated factors. RESULTS: Of the study population (aged 17-78 years, 79% male) just over one-fifth (21%) did not own a toothbrush. In an unadjusted model, low self-efficacy (PR = 1.18) and low knowledge (1.27) were indicators for non-toothbrush ownership. These relationships were attenuated by 5.2% and 3.2% respectively after adjusting for social determinants, health factors, substance use and dental service utilisation-related factors, but remained statistically significant in the final model. CONCLUSIONS: Poor oral health-related self-efficacy and knowledge were both indicators for non-ownership of a toothbrush among a homeless population. This relationship held even after adjustment for relevant social and behavioural factors. Fatalism was not an indicator for non-toothbrush ownership in this population.

Association of Common Polymorphisms in the Nicotinic Acetylcholine Receptor Alpha4 Subunit Gene with an Electrophysiological Endophenotype in a Large Population-Based Sample.

Variation in genes coding for nicotinic acetylcholine receptor (nAChR) subunits affect cognitive processes and may contribute to the genetic architecture of neuropsychiatric disorders. Single nucleotide polymorphisms (SNPs) in the CHRNA4 gene that codes for the alpha4 subunit of alpha4/beta2-containing receptors have previously been implicated in aspects of (mostly visual) attention and smoking-related behavioral measures. Here we investigated the effects of six synonymous but functional CHRNA4 exon 5 SNPs on the N100 event-related potential (ERP), an electrophysiological endophenotype elicited by a standard auditory oddball. A total of N = 1,705 subjects randomly selected from the general population were studied with electroencephalography (EEG) as part of the German Multicenter Study on nicotine addiction. Two of the six variants, rs1044396 and neighboring rs1044397, were significantly associated with N100 amplitude. This effect was pronounced in females where we also observed an effect on reaction time. Sequencing of the complete exon 5 region in the population sample excluded the existence of additional/functional variants that may be responsible for the observed effects. This is the first large-scale population-based study investigation the effects of CHRNA4 SNPs on brain activity measures related to stimulus processing and attention. Our results provide further evidence that common synonymous CHRNA4 exon 5 SNPs affect cognitive processes and suggest that they also play a role in the auditory system. As N100 amplitude reduction is considered a schizophrenia-related endophenotype the SNPs studied here may also be associated with schizophrenia outcome measures.

Genetic Geostatistical Framework for Spatial Analysis of Fine-Scale Genetic Heterogeneity in Modern Populations: Results from the KORA Study.

Aiming to investigate fine-scale patterns of genetic heterogeneity in modern humans from a geographic perspective, a genetic geostatistical approach framed within a geographic information system is presented. A sample collected for prospective studies in a small area of southern Germany was analyzed. None indication of genetic heterogeneity was detected in previous analysis. Socio-demographic and genotypic data of German citizens were analyzed (212 SNPs; n = 728). Genetic heterogeneity was evaluated with observed heterozygosity (H O ). Best-fitting spatial autoregressive models were identified, using socio-demographic variables as covariates. Spatial analysis included surface interpolation and geostatistics of observed and predicted patterns. Prediction accuracy was quantified. Spatial autocorrelation was detected for both socio-demographic and genetic variables. Augsburg City and eastern suburban areas showed higher H O values. The selected model gave best predictions in suburban areas. Fine-scale patterns of genetic heterogeneity were observed. In accordance to literature, more urbanized areas showed higher levels of admixture. This approach showed efficacy for detecting and analyzing subtle patterns of genetic heterogeneity within small areas. It is scalable in number of loci, even up to whole-genome analysis. It may be suggested that this approach may be applicable to investigate the underlying genetic history that is, at least partially, embedded in geographic data.

Biosom: gene synonym analysis by self-organizing map.

There are several guidelines for gene nomenclature, but they are not always applied to the names of newly identified genes. The lack of standardization in naming genes generates inconsistent databases with errors such as genes with the same function and different names, genes with different functions and the same name, and use of an abbreviated name. This paper presents a methodology for predicting synonyms in a given gene nomenclature, thereby detecting and minimizing naming redundancy and inconsistency and facilitating the annotation of new genes and data mining in public databases. To identify gene synonyms, i.e., gene ambiguity, the methodology proposed begins by grouping genes according to their names using a Kohonen self-organizing map artificial neural network. Afterwards, it identifies the groups generated employing the Matrix-U technique. The employment of such techniques allows one to infer the synonyms of genes, to predict probable hypothetical gene names and to point out possible errors in a database record. Many mistakes related to gene nomenclature were detected in this research, demonstrating the importance of predicting synonyms. The methodology developed is applicable for describing hypothetical, putative and other types of genes without a known function. Moreover, it can also indicate a possible function for genes after grouping them.

Quantitative assessment of protein function prediction programs.

Fast prediction of protein function is essential for high-throughput sequencing analysis. Bioinformatic resources provide cheaper and faster techniques for function prediction and have helped to accelerate the process of protein sequence characterization. In this study, we assessed protein function prediction programs that accept amino acid sequences as input. We analyzed the classification, equality, and similarity between programs, and, additionally, compared program performance. The following programs were selected for our assessment: Blast2GO, InterProScan, PANTHER, Pfam, and ScanProsite. This selection was based on the high number of citations (over 500), fully automatic analysis, and the possibility of returning a single best classification per sequence. We tested these programs using 12 gold standard datasets from four different sources. The gold standard classification of the databases was based on expert analysis, the Protein Data Bank, or the Structure-Function Linkage Database. We found that the miss rate among the programs is globally over 50%. Furthermore, we observed little overlap in the correct predictions from each program. Therefore, a combination of multiple types of sources and methods, including experimental data, protein-protein interaction, and data mining, may be the best way to generate more reliable predictions and decrease the miss rate.

Microbial community and performance of slaughterhouse wastewater treatment filters.

The performance of anaerobic filter bioreactors (AFs) is influenced by the composition of the substrate, support medium, and the microbial species present in the sludge. In this study, the efficiency of a slaughterhouse effluent treatment using three AFs containing different support media was tested, and the microbial diversity was investigated by amplified ribosomal DNA restriction analysis and 16S rRNA gene sequencing. The physicochemical analysis of the AF systems tested suggested their feasibility, with rates of chemical oxygen demand removal of 72±8% in hydraulic retention times of 1 day. Analysis of pH, alkalinity, volatile acidity, total solids, total volatile solids, total Kjeldahl nitrogen, and the microbial community structures indicated high similarity among the three AFs. The composition of prokaryotic communities showed a prevalence of Proteobacteria (27.3%) and Bacteroidetes (18.4%) of the Bacteria domain and Methanomicrobiales (36.4%) and Methanosarcinales (35.3%) of the Archaea domain. Despite the high similarity of the microbial communities among the AFs, the reactor containing pieces of clay brick as a support medium presented the highest richness and diversity of bacterial and archaeal operational taxonomic units.