Search

Objective: To evaluate the dependability and accuracy of midkine (MK) in the diagnosis of hepatocellular carcinoma (HCC). Methods: PubMed, EMBASE, Web of Science, China Biology Medicine disc and grey literature sources were searched from the date of database inception to January 2019. Two authors (B-H.Z. and B.L.) independently extracted the data and evaluated the study quality using the Quality Assessment of Diagnostic Accuracy Studies-2 tool. The sensitivity, specificity, positive likelihood ratio (LR+) and negative likelihood ratio (LR−) were estimated using a bivariate model. Moreover, hierarchical summary receiver operating characteristic curves were generated. The diagnostic odds ratio (DOR) and area under the curve (AUC) were pooled using a univariate model. Results: Nine articles (11 studies) were included (1941 participants). The bivariate analysis revealed that the sensitivity and specificity of MK for HCC diagnosis were 0.85 (95% CI 0.78–0.91) and 0.83 (95% CI 0.76–0.88), respectively. We also found a LR+ of 5.05 (95% CI 3.33–7.40), a LR− of 0.18 (95% CI 0.11–0.28), a DOR of 31.74 (95% CI 13.98–72.09) and an AUC of 0.91 (95% CI 0.84–0.99). Subgroup analyses showed that MK provided the best efficiency for HCC diagnosis when the cutoff value was greater than 0.5 ng/mL. Conclusions: MK has an excellent diagnostic value for hepatocellular carcinoma. [ABSTRACT FROM AUTHOR]

Superoxide dismutases (SODs), as a family of metalloenzymes related to the removal of reactive oxygen species (ROS), have not previously been investigated at genome-wide level in tea plant. In this study, 10 CsSOD genes were identified in tea plant genome, including 7 Cu/Zn-SODs (CSDs), 2 Fe-SODs (FSDs) and one Mn-SOD (MSD), and phylogenetically classified in three subgroups, respectively. Physico-chemical characteristic, conserved motifs and potential protein interaction analyses about CsSOD proteins were carried out. Exon-intron structures and codon usage bias about CsSOD genes were also examined. Exon-intron structures analysis revealed that different CsSOD genes contained various number of introns. On the basis of the prediction of regulatory miRNAs of CsSODs, a modification 5' RNA ligase-mediated (RLM)-RACE was performed and validated that csn-miR398a-3p-1 directly cleaves CsCSD4. By prediction of cis-acting elements, the expression patterns of 10 CsSOD genes and their regulatory miRNAs were detected under cold, drought, exogenous methyl jasmonate (MeJA) and gibberellin (GA3) treatments. The results showed that most of CsSODs except for CsFSD2 were induced under cold stress and CsCSDs may play primary roles under drought stress; exogenous GA3 and MeJA could also stimulated/inhibited distinct CsSODs at different stages. In addition, we found that csn-miR398a-3p-1 negatively regulated the expression of CsCSD4 may be a crucial regulatory mechanism under cold stress. This study provides a certain basis for the studies about stress resistance in tea plants, even provide insight into comprehending the classification, evolution, diverse functions and influencing factors of expression patterns for CsSOD genes. [ABSTRACT FROM AUTHOR]

Thrips transmit one of the most devastating plant viruses worldwide–tomato spotted wilt tospovirus (TSWV). Tomato spotted wilt tospovirus is a type species in the genus Orthotospovirus and family Tospoviridae. Although there are more than 7,000 thrips species, only nine thrips species are known to transmit TSWV. In this study, we investigated the molecular factors that could affect thrips ability to transmit TSWV. We assembled transcriptomes of a vector, Frankliniella fusca [Hinds], and a non-vector, Frankliniella tritici [Fitch], and performed qualitative comparisons of contigs associated with virus reception, virus infection, and innate immunity. Annotations of F. fusca and F. tritici contigs revealed slight differences across biological process and molecular functional groups. Comparison of virus cell surface receptors revealed that homologs of integrin were present in both species. However, homologs of another receptor, heperan sulfate, were present in F. fusca alone. Contigs associated with virus replication were identified in both species, but a contig involved in inhibition of virus replication (radical s-adenosylmethionine) was only present in the non-vector, F. tritici. Additionally, some differences in immune signaling pathways were identified between vector and non-vector thrips. Detailed investigations are necessary to functionally characterize these differences between vector and non-vector thrips and assess their relevance in orthotospovirus transmission. [ABSTRACT FROM AUTHOR]

Neisseria gonorrhoeae antimicrobial resistance (AMR) surveillance is essential for tracking the emergence and spread of AMR strains in local, national and international populations. This is crucial for developing or refining treatment guidelines. N. gonorrhoeae multiantigen sequence typing (NG-MAST) is beneficial for describing the molecular epidemiology of gonococci at national and international levels. Elucidation of AMR determinants to β-lactam drugs, is a means of monitoring the development of resistance. In Ghana, little is known about the current gonococcal AMR prevalence and no characterization of gonococcal isolates has been previously performed. In this study, gonococcal isolates (n = 44) collected from five health facilities in Ghana from 2012 to 2015, were examined using AMR testing, NG-MAST and sequencing of penA. High rates of resistance were identified to tetracycline (100%), benzylpenicillin (90.9%), and ciprofloxacin (81.8%). One isolate had a high cefixime MIC (0.75 μg/ml). Twenty-eight NG-MAST sequence types (STs) were identified, seventeen of which were novel. The isolate with the high cefixime MIC contained a mosaic penA-34 allele and belonged to NG-MAST ST1407, an internationally spreading multidrug-resistant clone that has accounted for most cefixime resistance in many countries. In conclusion, AMR testing, NG-MAST, and sequencing of the AMR determinant penA, revealed high rates of resistance to tetracycline, benzylpenicillin, and ciprofloxacin; as well as a highly diverse population of N. gonorrhoeae in Ghana. It is imperative to continue with enhanced AMR surveillance and to understand the molecular epidemiology of gonococcal strains circulating in Ghana and other African countries. [ABSTRACT FROM AUTHOR]

Candida auris is an invasive and multidrug-resistant ascomycetous yeast that is under global surveillance. All clinical cases of C. auris infection diagnosed from 1997 to 2019 in Japan were non-invasive and sporadic otitis media cases. In the present study, we performed whole-genome sequencing of seven C. auris strains isolated from patients with otitis media in Japan, all of which belonged to clade II. Comparative genome analysis using the high-quality draft genome sequences JCM 15448T revealed that single nucleotide variations (SNVs), clade-specific accessory genes, and copy number variations (CNVs) were identified in each C. auris clade. A total of 61 genes involved in cell wall and stress response-related functions was absent in clade II, and the pattern of conserved CNVs in each clade was more stable in clade II than in other clades. Our data suggest that the genomic structural diversity is stable in C. auris isolated from each biogeographic location, and Japanese strains isolated from patients with otitis media might belong to an ancestral type of C. auris. One Japanese strain, TWCC 58362, with reduced susceptibility to fluconazole, exhibited no mutation in ergosterol biosynthesis-related genes (ERG). However, TWCC 58362-specific variations, including SNVs, indels, and CNVs were detected, suggesting that gene duplication events in C. auris might contribute to antifungal drug resistance. Taken together, we demonstrated that genomic structural variations in C. auris could correlate to geographical dissemination, epidemiology, lesions in the host, and antifungal resistance. [ABSTRACT FROM AUTHOR]

The spliceosome is a large ribonucleoprotein complex that removes introns from pre-mRNAs. At its functional core lies the essential pre-mRNA processing factor 8 (Prp8) protein. Across diverse eukaryotes, this protein cofactor of RNA catalysis harbors a self-splicing element called an intein. Inteins in Prp8 are extremely pervasive and are found at 7 different sites in various species. Here, we focus on the Prp8 intein from Cryptococcus neoformans (Cne), a human fungal pathogen. We solved the crystal structure of this intein, revealing structural homology among protein splicing sequences in eukaryotes, including the Hedgehog C terminus. Working with the Cne Prp8 intein in a reporter assay, we find that the biologically relevant divalent metals copper and zinc inhibit intein splicing, albeit by 2 different mechanisms. Copper likely stimulates reversible modifications on a catalytically important cysteine, whereas zinc binds at the terminal asparagine and the same critical cysteine. Importantly, we also show that copper treatment inhibits Prp8 protein splicing in Cne. Lastly, an intein-containing Prp8 precursor model is presented, suggesting that metal-induced protein-splicing inhibition would disturb function of both Prp8 and the spliceosome. These results indicate that Prp8 protein splicing can be modulated, with potential functional implications for the spliceosome. [ABSTRACT FROM AUTHOR]

The genus Franciscobasis Machado & Bedê, 2016 is endemic to the Serra da Canastra National Park in Minas Gerais state, Brazil. Two species of Franciscobasis were described simultaneously with the genus description: F. franciscoi and F. sonia, the latter described only from females. Through morphological and molecular analysis, we investigated if F. sonia may represent the young female of F. franciscoi. Resulting data did not present adequate differences between females to characterize them as different species. Therefore, we suggest that F. sonia is a junior synonym of F. franciscoi, and the female of F. franciscoi goes through a complex ontogenetic color change. [ABSTRACT FROM AUTHOR]

Hepatitis C virus (HCV) is a major cause of liver cirrhosis and hepatocellular carcinoma. Genotyping of HCV is crucial for successful therapy. To determine the HCV subgenotypes circulating in Palestine and to study the genetic variability of their core, we collected 84 serum samples which had tested positive for anti-HCV antibodies. Thirty-seven of these samples came from hemodialysis patients. Serum samples were subjected to viral RNA isolation and amplification of the HCV core gene. Thirty-three of the samples (39%) tested positive for HCV RNA. The HCV subgenotypes circulating in Palestine included 1a, 3a, and 4a, detected in 38%, 25%, and 22% of the samples, respectively. Furthermore, subgenotype 1b was present in three samples (9%), while the rare subgenotype 4v was present in two samples (6%). We identified a number of substitutions in the retrieved HCV core sequences, such as HCV 1b substitutions R70Q and M91L, which some studies have associated with hepatocellular carcinoma risk and poor virological response. In contrast to two previous studies reporting that HCV genotype 4 was predominant in the Gaza strip (present in just over 70% of samples), genotype 4 was detected in only 31% of the samples in our current study, whereas genotype 1 and 3 were present in 69% of samples. These differences may relate to the fact that many of our samples came from the West Bank and East Jerusalem. The co-circulation of different HCV genotypes and subgenotypes in Palestine suggests that subgenotyping prior to treatment is crucial in Palestinian patients. [ABSTRACT FROM AUTHOR]

The prediction of cell-lines sensitivity to a given set of compounds is a very important factor in the optimization of in-vitro assays. To date, the most common prediction strategies are based upon machine learning or other quantitative structure-activity relationships (QSAR) based approaches. In the present research, we propose and discuss a straightforward strategy not based on any learning modelling but exclusively relying upon the chemical similarity of a query compound to reference compounds with annotated activity against cell lines. We also compare the performance of the proposed method to machine learning predictions on the same problem. A curated database of compounds-cell lines associations derived from ChemBL version 22 was created for algorithm construction and cross-validation. Validation was done using 10-fold cross-validation and testing the models on new data obtained from ChemBL version 25. In terms of accuracy, both methods perform similarly with values around 0.65 across 750 cell lines in 10-fold cross-validation experiments. By combining both methods it is possible to achieve 66% of correct classification rate in more than 26000 newly reported interactions comprising 11000 new compounds. A Web Service implementing the described approaches (both similarity and machine learning based models) is freely available at: . [ABSTRACT FROM AUTHOR]

Early mobilization has been proven to be an effective and safe intervention for preventing complications in mechanically ventilated patients; however, there is currently no unified definition of the optimal mobilization initiation time, hindering widespread clinical implementation. As clinicians are increasingly aware of the benefits of early mobilization, the definition of early mobilization is important. The purpose of this study was to evaluate the effects of different early mobilization initiation times on mechanically ventilated patients and rank these times for practical consideration. The Chinese Biomedical Literature Database, the Chinese Knowledge Infrastructure, Wanfang Data, PubMed, Cochrane Library, Web of Science, and Embase databases, along with grey literature and reference lists, were searched for randomized control trials (RCTs) that evaluated the effects of early mobilization for improving patient outcomes; databases were searched from inception to October 2018. Two authors extracted data independently, using a predesigned Excel form, and assessed the quality of included RCTs according to the Cochrane Handbook (v5.1.0). Data were analyzed using Stata (v13.0) and Review Manager (v5.3.0). A total of 15 RCTs involving 1726 patients and seven mobilization initiation times (which were all compared to usual care) were included in our analysis. Network meta-analysis showed that mechanical ventilation for 48–72 h may be optimal to improve intensive care unit acquired weakness (ICU-AW) and reduce the duration of mechanical ventilation; however, there were no significant differences in length of ICU stay according to mobilization initiation time. The results of this study indicate that initiation of mobilization within 48–72 h of mechanical ventilation may be optimal for improving clinical outcomes for mechanically ventilated patients. [ABSTRACT FROM AUTHOR]

Phosphohexomutase superfamily enzymes catalyze the reversible intramolecular transfer of a phosphoryl moiety on hexose sugars. Bacillus subtilis phosphoglucomutase PgcA catalyzes the reversible interconversion of glucose 6-phosphate (Glc-6-P) and glucose 1-phosphate (Glc-1-P), a precursor of UDP-glucose (UDP-Glc). B. subtilis phosphoglucosamine mutase (GlmM) is a member of the same enzyme superfamily that converts glucosamine 6-phosphate (GlcN-6-P) to glucosamine 1-phosphate (GlcN-1-P), a precursor of the amino sugar moiety of peptidoglycan. Here, we present evidence that B. subtilis PgcA possesses activity as a phosphoglucosamine mutase that contributes to peptidoglycan biosynthesis. This activity was made genetically apparent by the synthetic lethality of pgcA with glmR, a positive regulator of amino sugar biosynthesis, which can be specifically suppressed by overproduction of GlmM. A gain-of-function mutation in a substrate binding loop (PgcA G47S) increases this secondary activity and suppresses a glmR mutant. Our results demonstrate that bacterial phosphoglucomutases may possess secondary phosphoglucosamine mutase activity, and that this dual activity may provide some level of functional redundancy for the essential peptidoglycan biosynthesis pathway. [ABSTRACT FROM AUTHOR]

Recent evidence implicates mononuclear diploid cardiomyocytes as a proliferative and regenerative subpopulation of the postnatal heart. The number of these cardiomyocytes is a complex trait showing substantial natural variation among inbred mouse strains based on the combined influences of multiple polymorphic genes. One gene confirmed to influence this parameter is the cardiomyocyte-specific kinase Tnni3k. Here, we have studied Tnni3k alleles across a number of species. Using a newly-generated kinase-dead allele in mice, we show that Tnni3k function is dependent on its kinase activity. In an in vitro kinase assay, we show that several common human TNNI3K kinase domain variants substantially compromise kinase activity, suggesting that TNNI3K may influence human heart regenerative capacity and potentially also other aspects of human heart disease. We show that two kinase domain frameshift mutations in mice cause loss-of-function consequences by nonsense-mediated decay. We further show that the Tnni3k gene in two species of mole-rat has independently devolved into a pseudogene, presumably associated with the transition of these species to a low metabolism and hypoxic subterranean life. This may be explained by the observation that Tnni3k function in mice converges with oxidative stress to regulate mononuclear diploid cardiomyocyte frequency. Unlike other studied rodents, naked mole-rats have a surprisingly high (30%) mononuclear cardiomyocyte level but most of their mononuclear cardiomyocytes are polyploid; their mononuclear diploid cardiomyocyte level (7%) is within the known range (2–10%) of inbred mouse strains. Naked mole-rats provide further insight on a recent proposal that cardiomyocyte polyploidy is associated with evolutionary acquisition of endothermy. [ABSTRACT FROM AUTHOR]

Background: Previous studies have documented that disordered eating is associated with a wide range of impaired physical and mental health conditions among children and adolescents. The relationship between disordered eating and health-related quality of life (HRQOL) has been predominantly examined in children and adolescents who are overweight or obese or suffer from chronic illnesses. In the last decade, several studies have been conducted to investigate the relationship between disordered eating and HRQOL among school and community children and adolescents. No systematic review or meta-analysis has synthesized the findings from these population-based studies. The purpose of this systematic review and meta-analysis was to synthesize the relationship between disordered eating and HRQOL among the general population of children and adolescents. Methods: We performed a computer search for the English language literature using the databases PUBMED, EMBASE and PSYCINFO to retrieve eligible studies published between 1946 and August 9, 2018. We also searched the relevant articles using PubMed related article search features and manually examined the reference lists of the retrieved full text articles selected from the database search. The association between disordered eating and HRQOL was synthesized using both a qualitative method and a meta-analysis. The review was conducted adhering to the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) guidelines. Results: We identified eight studies that met the inclusion criteria and were included in the final synthesis. The studies included six cross-sectional studies and two longitudinal studies. The systematic review found that disordered eating attitudes and behaviors were associated with lower HRQOL among children and adolescents. Children and adolescents with bulimia nervosa (BN), binge eating disorder (BED), purging disorder (PD) and other eating disorder symptoms had poorer HRQOL than their healthy peers without the eating disorder conditions. The meta-analysis using four out of the eight studies showed that disordered eating was significantly associated with poor psychosocial health and lower overall HRQOL among children and adolescents. Conclusion: The present review reveals that disordered eating behaviors and eating disorders are associated with decreased HRQOL in children and adolescents. More prospective studies are needed to ascertain the directions in the relationship between disordered eating and HRQOL among children and adolescents. The findings of this review suggest that health programs for promoting healthy eating and reducing disordered eating behaviors among school children and adolescents may help to enhance the HRQOL and overall health status of these individuals. [ABSTRACT FROM AUTHOR]

Background: The high chances of getting latent tuberculosis infection (LTBI) among health care workers (HCWs) will an enormous problem in low and upper-middle-income countries. Method: Search strategies were done through both national and international databases include SID, Barakat knowledge network system, Irandoc, Magiran, Iranian national library, web of science, Scopus, PubMed/MEDLINE, OVID, EMBASE, the Cochrane library, and Google Scholar search engine. The Persian and the English languages were used as the filter in national and international databases, respectively. Medical Subject Headings (MeSH) terms was used to controlling comprehensive vocabulary. The search terms were conducted without time limitation till January 01, 2019. Results: The prevalence of LTBI in Iranian’s HCWs, based on the PPD test was 27.13% [CI95%: 18.64–37.7]. The highest prevalence of LTBI in Iranian’s HCWs were estimated 41.4% [CI95%: 25.4–59.5] in the north, and 33.8% [CI95%: 21.1–49.3] in the west. The lowest prevalence of LTBI was evaluated 18.2% [CI95%: 3.4–58.2] in the south of Iran. The prevalence of LTBI in Iranian’s HCWs who had work-experience more than 20 years old were estimated 20.49% [CI95%: 11–34.97]. In the PPD test, the prevalence of LTBI in Iranian’s HCWs who had received the Bacille Calmette–Guérin (BCG) was estimated 15% [CI95%: 3.6–47.73]. While, in the QFT, the prevalence of LTBI in Iranian’s HCWs in non-vaccinated was estimated 25.71% [CI95%: 13.96–42.49]. Conclusions: This meta-analysis shows the highest prevalence of LTBI in Iranian’s HCWs in the north and the west probably due to neighboring countries like Azerbaijan and Iraq, respectively. It seems that Iranian’s HCWs have not received the necessary training to prevent of TB. We also found that BCG was not able to protect Iranian’s HCWs from TB infections, completely. [ABSTRACT FROM AUTHOR]

Alternative splicing diversifies mRNA transcripts in human cells. While the spliceosome pairs exons with a high degree of accuracy, the rates of rare aberrant and non-canonical pre-mRNA splicing have not been evaluated at the nucleotide level to determine the quantity and identity of these events across splice junctions. Using ultra-deep sequencing the frequency of aberrant and non-canonical splicing events for three splice junctions flanking exon 7 of SMN1 were determined at single nucleotide resolution. After correction for background noise introduced by PCR amplification and sequencing steps, pre-mRNA splicing was shown to maintain a low overall rate of aberrant and non-canonically spliced events. Several previously unannotated splicing events across 3 exon|intron junctions in SMN1 were identified. Mutations within SMN exon 7 were shown to affect splicing fidelity by modulating RNA secondary structures, by altering the binding site of regulatory proteins and by changing the 5’ splice site strength. Mutations also create a truncated SMN1 exon 7 through the introduction of a de novo non-canonical 5’ splice site. The results from the ultra-deep sequencing approach highlight the impressive fidelity of pre-mRNA splicing and demonstrate that the immediate sequence context around splice sites is the main driving force behind non-canonical splice site pairing. [ABSTRACT FROM AUTHOR]

Background and objective: Trial registration is widely endorsed as it is considered not only to enhance transparency and quality of reporting but also to help safeguard against outcome reporting bias and probably spin, known as specific reporting that could distort the interpretation of results thus mislead readers. We planned to investigate the current registration status of recently published randomized controlled trials (RCTs) of acupuncture, outcome reporting bias in the prospectively registered trials, and the association between trial registration and presence of spin and methodological factors in acupuncture RCTs. Methods: Acupuncture RCTs published in English in recent 5 years (January 2013 to December 2017) were searched in PubMed, Cochrane Central Register of Controlled Trials, and EMBASE. Trial registration records identified in the publications and trial registries were classified into prospectively registered, retrospectively registered, or unregistered. Primary outcomes were identified and the direction of the results was judged as statistically significant (positive) or statistically nonsignificant (negative). We compared registered and published primary outcomes to assess outcome reporting bias and assessed whether discrepancies favored statistically significant outcomes. Frequency and strategies of spin in published reports with statistically nonsignificant results for primary outcomes were then identified. We also analyzed whether the trial registration status was associated with spin and quality of methodological factors. Results: Of the 322 included RCTs, 41.9% (n = 135) were prospectively registered. Among 64 studies that were prospectively registered and specified primary outcomes, 25 trials had the discrepancies between the registered and published primary outcomes and 60% of them (15 trials) favored the statistically significant findings. Among 169 studies that specified primary outcomes, trial registration status was not associated with the direction of results, i.e., statistically significant or not. Spin was identified in 56.4% out of 78 studies with statistically nonsignificant primary outcomes and claiming efficacy with no consideration of statistically nonsignificant primary outcomes was the most common strategy for spin. Trial registration status was not statistically different between studies with and without spin. Conclusion: While trial registration seemed to have improved over time, primary outcomes in registered records and publications were often inconsistent, tending to favor statistically significant findings and spin was common in studies with statistically nonsignificant primary outcomes. Journal editors and researchers in this field should be alerted to still prevalent reporting bias and spin. [ABSTRACT FROM AUTHOR]

Introduction: Epidemic forecasting and prediction tools have the potential to provide actionable information in the midst of emerging epidemics. While numerous predictive studies were published during the 2016–2017 Zika Virus (ZIKV) pandemic, it remains unknown how timely, reproducible, and actionable the information produced by these studies was. Methods: To improve the functional use of mathematical modeling in support of future infectious disease outbreaks, we conducted a systematic review of all ZIKV prediction studies published during the recent ZIKV pandemic using the PRISMA guidelines. Using MEDLINE, EMBASE, and grey literature review, we identified studies that forecasted, predicted, or simulated ecological or epidemiological phenomena related to the Zika pandemic that were published as of March 01, 2017. Eligible studies underwent evaluation of objectives, data sources, methods, timeliness, reproducibility, accessibility, and clarity by independent reviewers. Results: 2034 studies were identified, of which n = 73 met the eligibility criteria. Spatial spread, R0 (basic reproductive number), and epidemic dynamics were most commonly predicted, with few studies predicting Guillain-Barré Syndrome burden (4%), sexual transmission risk (4%), and intervention impact (4%). Most studies specifically examined populations in the Americas (52%), with few African-specific studies (4%). Case count (67%), vector (41%), and demographic data (37%) were the most common data sources. Real-time internet data and pathogen genomic information were used in 7% and 0% of studies, respectively, and social science and behavioral data were typically absent in modeling efforts. Deterministic models were favored over stochastic approaches. Forty percent of studies made model data entirely available, 29% provided all relevant model code, 43% presented uncertainty in all predictions, and 54% provided sufficient methodological detail to allow complete reproducibility. Fifty-one percent of predictions were published after the epidemic peak in the Americas. While the use of preprints improved the accessibility of ZIKV predictions by a median of 119 days sooner than journal publication dates, they were used in only 30% of studies. Conclusions: Many ZIKV predictions were published during the 2016–2017 pandemic. The accessibility, reproducibility, timeliness, and incorporation of uncertainty in these published predictions varied and indicates there is substantial room for improvement. To enhance the utility of analytical tools for outbreak response it is essential to improve the sharing of model data, code, and preprints for future outbreaks, epidemics, and pandemics. [ABSTRACT FROM AUTHOR]

Background: RNA sequencing has been proposed as a means of increasing diagnostic rates in studies of undiagnosed rare inherited disease. Recent studies have reported diagnostic improvements in the range of 7.5–35% by profiling splicing, gene expression quantification and allele specific expression. To-date however, no study has systematically assessed the presence of gene-fusion transcripts in cases of germline disease. Fusion transcripts are routinely identified in cancer studies and are increasingly recognized as having diagnostic, prognostic or therapeutic relevance. Isolated reports exist of fusion transcripts being detected in cases of developmental and neurological phenotypes, and thus, systematic application of fusion detection to germline conditions may further increase diagnostic rates. However, current fusion detection methods are unsuited to the investigation of germline disease due to performance biases arising from their development using tumor, cell-line or in-silico data. Methods: We describe a tailored approach to fusion candidate identification and prioritization in a cohort of 47 undiagnosed, suspected inherited disease patients. We modify an existing fusion transcript detection algorithm by eliminating its cell line-derived filtering steps, and instead, prioritize candidates using a custom workflow that integrates genomic and transcriptomic sequence alignment, biological and technical annotations, customized categorization logic, and phenotypic prioritization. Results: We demonstrate that our approach to fusion transcript identification and prioritization detects genuine fusion events excluded by standard analyses and efficiently removes phenotypically unimportant candidates and false positive events, resulting in a reduced candidate list enriched for events with potential phenotypic relevance. We describe the successful genetic resolution of two previously undiagnosed disease cases through the detection of pathogenic fusion transcripts. Furthermore, we report the experimental validation of five additional cases of fusion transcripts with potential phenotypic relevance. Conclusions: The approach we describe can be implemented to enable the detection of phenotypically relevant fusion transcripts in studies of rare inherited disease. Fusion transcript detection has the potential to increase diagnostic rates in rare inherited disease and should be included in RNA-based analytical pipelines aimed at genetic diagnosis. [ABSTRACT FROM AUTHOR]

Non-invasive fetal electrocardiography (NI-FECG) plays an important role in fetal heart rate (FHR) measurement during the pregnancy. However, despite the large number of methods that have been proposed for adult ECG signal processing, the analysis of NI-FECG remains challenging and largely unexplored. In this study, we propose a prefix tree-based framework, called QRStree, for FHR measurement directly from the abdominal ECG (AECG). The procedure is composed of three stages: Firstly, a preprocessing stage is employed for noise elimination. Secondly, the proposed prefix tree-based method is used for fetal QRS complexes (FQRS) detection. Finally, a correction stage is applied for false positive and false negative correction. The novelty of the framework relies on using the range of FHR to establish the connections between the FQRS. The consecutive FQRS can be considered as strings composed of alphabet items, thus we can use the prefix tree to store them. A vertex of the tree contains an alphabet, thus a path of the tree gives a string. Such that, by storing the connections of the FQRS into the prefix tree structure, the problem of FQRS detection converts to a problem of optimal path selection. Specifically, after selecting the optimal path of the tree, the nodes in the optimal path are collected as detected FQRS. Since the prefix tree can cover every possible combination of the FQRS candidates, it has the potential to reduce the occurrence of miss detections. Results on two different databases show that the proposed method is effective in FHR measurement from single-channel AECG. The focus on single-channel FHR measurement facilitates the long-term monitoring for healthcare at home. [ABSTRACT FROM AUTHOR]

Background/Objectives: Maladaptive parenting (including childhood maltreatment, abuse and neglect) has been implicated in the scientific literature exploring the aetiology of personality disorder, particularly borderline personality disorder (BPD). Our primary objective was to summarise the evidence on the relationship between parenting and personality disorder, assisting clinical decision-makers to translate this research into clinical policy and practice. Methods: We conducted an overview of systematic reviews that assessed individuals with personality disorder pathology for experiences of maladaptive parenting, compared to psychiatric or healthy comparisons/controls, and the impact on psychopathological and relational outcomes. Systematic literature searches were conducted in Scopus, Web of Science, MEDLINE, PsycINFO, and by hand in August 2018. Methodological quality was assessed using the CASP systematic review checklist, and results were qualitatively synthesised. A pre-determined protocol was registered in Prospective Register of Systematic Reviews (PROSPERO 2019:CRD42018096177). Results: Of the 312 identified records, 293 abstracts were screened, 36 full-text articles were retrieved and eight systematic reviews met pre-determined criteria for qualitative synthesises. The majority of studies reported outcomes related to BPD (n = 7), and study design, methodology and quality varied. Within the eight systematic reviews there were 211 primary studies, of which 140 (66.35%) met eligibility criteria for inclusion in this overview. Eligible primary studies reported on 121,895 adult, child/adolescent and parent-offspring participants, with most studies focused on borderline personality pathology (n = 100, 71.43%). Study design and methodology also varied for these studies. Overall, five systematic reviews overwhelming found that maladaptive parenting was a psychosocial risk factor for the development of borderline personality pathology, and three studies found that borderline personality pathology was associated with maladaptive parenting, and negative offspring and parenting-offspring outcomes. Conclusions: In light of these findings, we recommend greater emphasis on parenting in clinical practice and the development of parenting interventions for individuals with personality disorder. However, our understanding is limited by the heterogeneity and varying quality of the evidence, and as such, future research utilising more rigorous research methodology is needed. [ABSTRACT FROM AUTHOR]

Introduction: Data on engagement in HIV care from population-based samples in sub-Saharan Africa are limited. The objective of this study was to use double-sampling methods to estimate linkage to HIV care, ART initiation, and mortality among all adults diagnosed with HIV by a comprehensive home-based counseling and testing (HBCT) program in western Kenya. Methods: HBCT was conducted door-to-door from December 2009 to April 2011 in three sub-counties of western Kenya by AMPATH (Academic Model Providing Access to Healthcare). For those identified as HIV-positive, data were merged with electronic medical records to determine engagement with HIV care. A randomly-drawn follow-up sample of 120 adults identified via HBCT who had not linked to care as of June 2015 in Bunyala sub-county were visited by trained fieldworkers to ascertain HIV care engagement and vital status. Double-sampled data were used to generate, via multinomial regression, predicted probabilities of engagement in care and mortality among those whose status could not be ascertained by matching with the electronic medical records in the three catchments. Results: Incorporating information from the double-sampling yielded estimates of prospective linkage to HIV care that ranged from 40–45%. Mortality estimates of those who did not engage in care following HBCT ranged from 12–16%. Among those who linked to care following HBCT, between 72–81% initiated ART. Discussion: In settings without universal national identifiers, rates of linkage to care from community-based programs may be subject to substantial underestimation. Follow-up samples of those with missing information can be used to partially correct this bias, as has been demonstrated previously for mortality among those who were lost-to-care programs. There is a need for harmonized data systems across health systems and programs. [ABSTRACT FROM AUTHOR]

Background: Protease inhibitors (PI) are especially important in salvage therapy. Previous treatment failure with a PI containing regimen may elicit resistance mutations, reducing PI susceptibility and limiting treatment options. The aim of this study was to describe major PI mutations among patients exposed to at least one PI to evaluate predictors of mutation emergence and the impact of subtypes on resistance. Methodology: Partial HIV-1 pol sequences (Sanger Sequencing) from patients exposed to PI with virological failure were genotyped from January 2014 to December 2017. Drug resistance mutations (DRM), antiretroviral susceptibility (GSS) and subtypes, along clinical and laboratory parameters, were evaluated using logistic regression to access the predictors of mutation emergence. Results: In 27.5% (466/1696) of the cases at least one major PI mutations was identified, most commonly M46 (14.7%), V82 (13.8%) and I54 (13.3%). Mutations to NRTI and NNRTI were observed in 69.6% and 59.9%, respectively, of the 1696 sequences. Full activity to darunavir was predicted in 88% (1496/1696), but was only 57% among those with at least one PI-DRM. Subtype C sequences had less major PI-DRMs (10%, 9/87) compared to B (28%, 338/1216) or F (35%, 58/168) (p <0.001) but adjusted analysis suggested that this association is not independent from a shorter treatment time and fewer regimens (OR 0.59, Confidence Interval 95: 0.2–2.5, p = 0.48). Subtype F, together with NRTI mutations and longer time on treatment was associated to presence of PI-DRM, to a lower darunavir GSS and to mutations at codon I50. Conclusions: Among patients with PI-DRM, full activity to darunavir was compromised in almost half of the cases and efforts to detect failure at earlier time are warranted, particularly for HIV-1 subtype F that showed association to the emergence of resistance, with potential impact in protease inhibitors sequencing. Furthermore, NRTI mutations may serve as an indicative of sufficient adherence to allow PI-DRM emergence. [ABSTRACT FROM AUTHOR]

Background: Vector-borne pathogens are a significant public health concern worldwide. Infections with these pathogens, some of which are emerging, are likely under-recognized due to the lack of widely-available laboratory tests. There is an urgent need for further advancement in diagnostic modalities to detect new and known vector-borne pathogens. We evaluated the utility of metagenomic shotgun sequencing (MGS) as a pathogen agnostic approach for detecting vector-borne pathogens from human blood samples. Methods: Residual whole blood samples from patients with known infection with Babesia microti, Borrelia hermsii, Plasmodium falciparum, Mansonella perstans, Anaplasma phagocytophilum or Ehrlichia chaffeensis were studied. Samples underwent DNA extraction, removal of human DNA, whole genome amplification, and paired-end library preparation, followed by sequencing on Illumina HiSeq 2500. Bioinformatic analysis was performed using the Livermore Metagenomics Analysis Toolkit (LMAT), Metagenomic Phylogenetic Analysis (MetaPhlAn2), Genomic Origin Through Taxonomic CHAllenge (GOTTCHA) and Kraken 2. Results: Eight samples were included in the study (2 samples each for P. falciparum and A. phagocytophilum). An average of 27.5 million read pairs was generated per sample (range, 18.3–38.8 million) prior to removal of human reads. At least one of the analytic tools was able to detect four of six organisms at the genus level, and the organism present in five of eight specimens at the species level. Mansonella and Ehrlichia species were not detected by any of the tools; however, mitochondrial cytochrome c oxidase subunit I amino acid sequence analysis suggested the presence of M. perstans genetic material. Conclusions: MGS is a promising tool with the potential to evolve as a non-hypothesis driven diagnostic test to detect vector-borne pathogens, including protozoa and helminths. [ABSTRACT FROM AUTHOR]

Background: Prophages play a significant role in prokaryotic evolution, often altering the function of the cell that they infect via transfer of new genes e.g., virulence or antibiotic resistance factors, inactivation of existing genes or by modifying gene expression. Recently, phage therapy has gathered renewed interest as a promising alternative to control bacterial infections. Cataloging the repertoire of prophages in large collections of species’ genomes is an important initial step in understanding their evolution and potential therapeutic utility. However, current widely-used tools for identifying prophages within bacterial genome sequences are mainly web-based, can have long response times, and do not scale to keep pace with the many thousands of genomes currently being sequenced routinely. Methodology: In this work, we present ProphET, an easy to install prophage predictor to be used in Linux operation system, without the constraints associated with a web-based tool. ProphET predictions rely on similarity searches against a database of prophage genes, taking as input a bacterial genome sequence in FASTA format and its corresponding gene annotation in GFF. ProphET identifies prophages in three steps: similarity search, calculation of the density of prophage genes, and edge refinement. ProphET performance was evaluated and compared with other phage predictors based on a set of 54 bacterial genomes containing 267 manually annotated prophages. Findings and conclusions: ProphET identifies prophages in bacterial genomes with high precision and offers a fast, highly scalable alternative to widely-used web-based applications for prophage detection. [ABSTRACT FROM AUTHOR]

As a leading cause of neonatal sepsis, Streptococcus agalactiae, commonly known as Group B Streptococcus, is a major neonatal pathogen. Current global screening practices employ risk- or culture-based protocols for detection of these organisms. In Western Australia (WA), universal culture-based screening is provided, with subsequent intrapartum antibiotic prophylaxis for all S. agalactiae-positive women during labour. Widespread antibiotic exposure is not ideal and this is one of the factors driving development of vaccines against S. agalactiae. Vaccine candidates have focused on the capsule, surface proteins and pilus types, however, capsule serotypes are known to vary geographically. The aim of this study was to use genome sequencing to gain an understanding of the circulating genotypes in WA, and to assess variations in the associated gene pools. We sequenced 141 antenatal carriage (vaginal/rectal) isolates and 10 neonatal invasive disease isolates from WA. Based on the global PubMLST database, the 151 strains were characterised into 30 sequence types, with clustering of these mainly into clonal complexes 1, 12, 17, 19 and 23. Of the genes encoding eleven surface proteins that were analysed, the most prevalent were fbp, lmb and scpB which were present in ≥ 98% of isolates. A cluster of non-haemolytic isolates, one of which was a neonatal invasive disease isolate, appeared to lack the entire cyl locus. Admixture analysis of population structure revealed evidence of genetic transfer among the WA isolates across structural groups. When compared against the PubMLST S. agalactiae data, WA isolates showed high levels of strain diversity with minimal apparent clustering. This is the first whole genome sequence study of WA S. agalactiae isolates and also represents the first addition of Australian isolate data to PubMLST. This report provides insight into the distribution and diversity of vaccine targets of S. agalactiae within Western Australia, indicating that the most appropriate capsular vaccine for this population would be the proposed pentavalent (Cps Ia, Ib, II, III and V) preparation, whilst vaccines targeting surface proteins should ideally utilise Fbp, Lmb and/or ScpB. [ABSTRACT FROM AUTHOR]

The formation of the sea urchin spicule skeleton requires the participation of hydrogel-forming protein families that regulate mineral nucleation and nanoparticle assembly processes that give rise to the spicule. However, the structure and molecular behavior of these proteins is not well established, and thus our ability to understand this process is hampered. We embarked on a study of sea urchin spicule proteins using a combination of biophysical and bioinformatics techniques. Our biophysical findings indicate that recombinant variants of the two most studied spicule matrix proteins, SpSM50 and SpSM30B/C (S. purpuratus) have a conformational landscape that include a C-terminal random coil/intrinsically disordered MAPQG sequence coupled to a conserved, folded N-terminal C-type lectin-like (CTLL) domain, with SpSM50 > SpSM30B/C with regard to intrinsic disorder. Both proteins possess solvent-accessible unfolded MAQPG sequence regions where Asn, Gln, and Arg residues may be accessible for protein hydrogel interactions with water molecules. Our bioinformatics study included seven other spicule matrix proteins where we note similarities between these proteins and rare, unusual proteins that possess folded and unfolded traits. Moreover, spicule matrix proteins possess three types of sequences: intrinsically disordered, amyloid-like, and folded protein-protein interactive. Collectively these reactive domains would be capable of driving protein assembly and hydrogel formation. Interestingly, three types of global conformations are predicted for the nine member protein set, wherein we note variations in the arrangement of intrinsically disordered and interactive globular domains. These variations may reflect species-specific requirements for spiculogenesis. We conclude that the molecular landscape of spicule matrix protein families enables them to function as hydrogelators, nucleators, and assemblers of mineral nanoparticles. [ABSTRACT FROM AUTHOR]

Background: There have been growing recommendations to include education in multi-disciplinary interventions targeting chronic pain management. However, effects of this strategy on short- and long-term self-management of chronic pain, remain largely unexplored. Objectives: 1. To provide an updated overview of studies that report on the impact of patient education in multi-disciplinary interventions, on self-management of chronic pain; 2. To explore associations between education and chronic pain self-management techniques; and 3. To identify the format and duration of suitable chronic pain interventions targeted at patient self-management. Methods: Design: Narrative systematic literature review of randomised or controlled study designs. Data Sources: PubMed, CINAHL, EMBASE, PsycINFO. Participants: Adult patients with chronic pain of any aetiology participating in multi-disciplinary programs that included education. Main outcome measures: Assessments of level of pain, function, quality of life, self-efficacy, self-management, and any other relevant assessments. Study Appraisal and Synthesis Methods: PRISMA guidelines, Cochrane Risk of Bias tool, and TIDieR model. Results: Database searching identified 485 potential papers. After removal of duplicates, and irrelevant articles by title and abstract, 120 full-text articles were reviewed and 27 studies were included in this systematic review. Studies were predominantly from the United States (n = 8; 29.6%). Over one hundred outcome measures were identified across all studies, with significant variation also observed in terms of how chronic pain duration was defined, and how education was delivered to participants. Overall, positive benefits of education were reported. Conclusions: Education, as part of multi-disciplinary programs, is likely to improve self-management and self-efficacy in people with chronic pain of any aetiology. Heterogeneity in terms of: chronic pain duration; educational resources; healthcare professionals; and outcome measures, were identified as limitations. Further research, in the form of Randomised Controlled Trials addressing these limitations, is recommended. [ABSTRACT FROM AUTHOR]

Aim: To assess the effect of Lactobacillus supplementation on Helicobacter pylori eradication rates and side effects of the triple therapy. Methods: PubMed, Embase, Web of Science and Cochrane Library were searched for articles published up to July, 2019. Review Manager 5.3 and Stata 12.0 were used for statistical analyses. Results: The initial database search resulted in 852 articles. Through exclusion and screening, 11 randomized controlled trials involving a total of 724 patients were finally included in this meta-analysis. The H. pylori elimination rate in the Lactobacillus supplement group was significantly higher than that in the control group (RR 1.16, 95% CI 1.08–1.25, P<0.0001). Subgroup analysis showed that the eradication rates were significantly enhanced in both adults and children group, and no significant difference was detected between Asia and Europe group. In addition, sub-analysis based on duration of Lactobacillus supplementation showed the pooled RRs in the long-term and short-term groups were 1.17 (95%CI 1.06–1.30) and 1.16 (95% CI 1.04–1.30), respectively. Regarding the Lactobacillus strains, the pooled RR was 1.33 (95% CI 1.10–1.62) in the L. casei group, 1.18 (95% CI 1.03–1.34) in the L. reuteri group while 1.02 (95% CI 0.87–1.21) in the Lactobacillus GG group. As for the total side effects, Lactobacillus supplementation significantly reduced the incidence of taste disturbance (RR = 0.36, 95% CI 0.17–0.74, P = 0.005). Conclusions: Lactobacillus supplementation during the treatment of Helicobacter pylori infection can effectively improve the eradication rates, and reduce the incidence of therapy-related taste disturbance. [ABSTRACT FROM AUTHOR]

Background: Detection and pathology analysis of Mycobacterium leprae using skin biopsy tissues are essential for leprosy diagnosis and monitoring response to treatment. Although formalin fixation of patient tissues may not be ideal for molecular studies, biopsy samples are the most accessible material from suspected cases. Therefore, clinical molecular laboratories must be able to utilize formalin-fixed, paraffin-embedded (FFPE) material. Objective: To determine the best molecular method for diagnosing and monitoring leprosy in FFPE specimens, we developed a single-tube nested PCR (STNPCR) (131 bp) and SYBRGreen PCR (101 bp) assay using primers for the M. leprae-specific repetitive element (RLEP) gene and evaluated the results compared to those using previously established RLEP primers (372 bp). Methods: FFPE biopsy samples obtained from 145 leprosy patients (during or after multidrug therapy (MDT)) and patients with 29 other confounding dermatoses were examined by the bacteria index (BI) and by simple PCR, STNPCR, and SYBRGreen PCR using primers amplifying a 372-bp, 131-bp or 101-bp fragment of RLEP, respectively. Results: In leprosy patients receiving MDT, STNPCR showed a highest specificity of 100% and a positive predictive value (PPV) of 100%. For multibacillary (MB), paucibacillary (PB) and all leprosy patients, the highest sensitivities were 91.42%, 39.13%, and 67.92%, negative predictive values (NPVs) were 8.57%, 60.36%, and 32.07%, and the highest accuracies were 93.93%, 62.67%, and 74.81%, respectively, higher than the results of SYBRGreen PCR and simple PCR. For post-MDT leprosy patients, SYBRGreen PCR showed the highest sensitivity of 50.0%, highest specificity of 100%, a PPV of 100%, an NPV of 100% and the highest accuracy of 83.72% for MB patients, which were higher than those of STNPCR and simple PCR. STNPCR showed the highest sensitivity of 26.66% and 34.48%, highest specificity of 100% and 100%, a PPV of 100% and 100%, NPV of 72.50% and 60.21%, and highest accuracy of 75.00% and 67.24% for PB and leprosy patients, respectively, higher than those of SYBRGreen PCR and simple PCR. Conclusions: These findings suggest that STNPCR or SYBRGreen PCR (131-bp and 101-bp fragment amplification, respectively) for RLEP using FFPE specimens performs better as a diagnostic test and for monitoring response to MDT than does simple PCR based on 372-bp fragment amplification. Additionally, STNPCR showed increased sensitivity for PB diagnosis using FFPE specimens, which can be transferred remotely or retrieved from previous leprosy patients. [ABSTRACT FROM AUTHOR]

Context: An estimated 21% of non-U.S.-born persons in the United States have a reactive tuberculin skin test (TST) and are at risk of progressing to TB disease. The effectiveness of strategies by healthcare facilities to improve targeted TB infection testing and linkage to care among this population is unclear. Evidence acquisition: Following Cochrane guidelines, we searched several sources to identify studies that assessed strategies directed at healthcare providers and/or non-U.S.–born patients in U.S. healthcare facilities. Evidence synthesis: Seven studies were eligible. In a randomized controlled trial (RCT), patients with reactive TST who received reminders for follow-up appointments were more likely to attend appointments (risk ratio, RR = 1.05, 95% confidence interval 1.00–1.10), but rates of return in a quasi-RCT study using patient reminders did not significantly differ between study arms (P = 0.520). Patient-provider language concordance in a retrospective cohort study did not increase provider referrals for testing (P = 0.121) or patient testing uptake (P = 0.159). Of three studies evaluating pre and post multifaceted interventions, two increased TB infection testing (from 0% to 77%, p < .001 and RR 2.28, 1.08–4.80) and one increased provider referrals for TST (RR 24.6, 3.5–174). In another pre-post study, electronic reminders to providers increased reading of TSTs (RR 2.84, 1.53–5.25), but only to 25%. All seven studies were at high risk of bias. Conclusions: Multifaceted strategies targeting providers may improve targeted TB infection testing in non-U.S.-born populations visiting U.S. healthcare facilities; uncertainties exist due to low-quality evidence. Additional high-quality studies on this topic are needed. [ABSTRACT FROM AUTHOR]

Background: Portugal has one of the most severe HIV-1 epidemics in Western Europe. Two subtypes circulate in parallel since the beginning of the epidemic. Comparing their transmission patterns and its association with transmitted drug resistance (TDR) is important to pinpoint transmission hotspots and to develop evidence-based treatment guidelines. Methods: Demographic, clinical and genomic data were collected from 3599 HIV-1 naive patients between 2001 and 2014. Sequences obtained from drug resistance testing were used for subtyping, TDR determination and transmission clusters (TC) analyses. Results: In Portugal, transmission of subtype B was significantly associated with young males, while transmission of subtype G was associated with older heterosexuals. In Portuguese originated people, there was a decreasing trend both for prevalence of subtype G and for number of TCs in this subtype. The active TCs that were identified (i.e. clusters originated after 2008) were associated with subtype B-infected males residing in Lisbon. TDR was significantly different when comparing subtypes B (10.8% [9.5–12.2]) and G (7.6% [6.4–9.0]) (p = 0.001). Discussion: TC analyses shows that, in Portugal, the subtype B epidemic is active and fueled by young male patients residing in Lisbon, while transmission of subtype G is decreasing. Despite similar treatment rates for both subtypes in Portugal, TDR is significantly different between subtypes. [ABSTRACT FROM AUTHOR]

Serum components of sepsis patients vary with the severity of infection, the resulting inflammatory response, per individual, and even over time. Tracking these changes is crucial in properly treating sepsis. Hence, several blood-derived biomarkers have been studied for their potential in assessing sepsis severity. However, the classical approach of selecting individual biomarkers is problematic in terms of accuracy and efficiency. We therefore present a novel approach for detecting biomarkers using longitudinal proteomics data. This does not require a predetermined set of proteins and can therefore reveal previously unknown related proteins. Our approach involves examining changes over time of both protein abundance and post-translational modifications in serum, using two-dimensional gel electrophoresis (2D-PAGE). 2D-PAGE was conducted using serum from n = 20 patients, collected at five time points, starting from the onset of sepsis. Changes in protein spots were examined using 49 spots for which the signal intensity changed by at least two-fold over time. These were then screened for significant spikes or dips in intensity that occurred exclusively in patients with adverse outcome. Individual level variation was handled by a mixed effects model. Finally, for each time transition, partial correlations between spots were estimated through a Gaussian graphical model (GGM) based on the ridge penalty. Identifications of spots of interest by tandem mass spectrometry revealed that many were either known biomarkers for inflammation (complement components), or had previously been suggested as biomarkers for kidney failure (haptoglobin) or liver failure (ceruloplasmin). The latter two are common complications in severe sepsis. In the GGM, many of the tightly connected spots shared known biological functions or even belonged to the same protein; including hemoglobin chains and acute phase proteins. Altogether, these results suggest that our screening method can successfully identify biomarkers for disease states and cluster biologically related proteins using longitudinal proteomics data derived from 2D-PAGE. [ABSTRACT FROM AUTHOR]

Background: Pulmonary embolism (PE) is correlated with increased mortality among patients with lung cancer (LC). The characteristics of patients with LC presenting with PE have not been fully established, and our meta-analysis aims to comprehensively investigate the clinical characteristics associated with PE in patients with LC to help physicians identify PE earlier in these patients. Methods: Multiple databases were searched, including PubMed, EMBASE, Cochrane Library, China National Knowledge Infrastructure and Wanfang. Odds ratios (ORs) and weighted mean differences (WMDs) with 95% confidence intervals (95% CIs) were used as effect measures for dichotomous and continuous variables, respectively. Moreover, Egger’s test, Begg’s test and a sensitivity analysis were performed to assess the publication bias and reliability of the articles. Results: In total, 16 studies were included in our meta-analysis. The results indicated that history of chronic obstructive pulmonary disease (OR = 2.59, 95% CI: 1.09, 6.15; P = 0.03), adenocarcinoma (OR = 2.28, 95% CI: 1.88, 2.77; P < 0.01), advanced tumour stage (TNM III-IV vs. I-II, OR = 2.38, 95% CI: 1.99, 2.86; P < 0.01), history of central venous catheter (OR = 1.95, 95% CI: 1.36, 2.78; P < 0.01), history of chemotherapy (OR = 2.32, 95% CI: 1.80, 2.99, P < 0.01), high levels of D-dimer (WMD = 4.31, 95% CI: 2.53, 6.10; P < 0.01) and carcinoembryonic antigen (WMD = 10.30, 95% CI: 9.95, 10.64; P < 0.01) and a low level of partial pressure of oxygen (WMD = -25.97, 95% CI: -31.31, -20.62; P < 0.01) were clinical features of LC patients with PE compared to those without PE. Conclusions: These results reveal that LC patients with PE have specific clinical features, including but not limited to several cancer- and treatment-related factors, that may help their early identification. [ABSTRACT FROM AUTHOR]

The gut microbial community structure of adult Thrips tabaci collected from 10 different agro-climatically diverse locations of India was characterized by using the Illumina MiSeq platform to amplify the V3 region of the 16S rRNA gene of bacteria present in the sampled insects. Analyses were performed to study the bacterial communities associated with Thrips tabaci in India. The complete bacterial metagenome of T. tabaci was comprised of 1662 OTUs of which 62.25% belong to known and 37.7% of unidentified/unknown bacteria. These OTUs constituted 21 bacterial phyla of 276 identified genera. Phylum Proteobacteria was predominant, followed by Actinobacteria, Firmicutes, Bacteroidetes and Cyanobacteria. Additionally, the occurrence of the reproductive endosymbiont, Wolbachia was detected at two locations (0.56%) of the total known OTUs. There is high variation in diversity and species richness among the different locations. Alpha-diversity metrics indicated the higher gut bacterial diversity at Bangalore and lowest at Rahuri whereas higher bacterial species richness at T. tabaci samples from Imphal and lowest at Jhalawar. Beta diversity analyses comparing bacterial communities between the samples showed distinct differences in bacterial community composition of T. tabaci samples from different locations. This paper also constitutes the first record of detailed bacterial communities associated with T. tabaci. The location-wise variation in microbial metagenome profile of T. tabaci suggests that bacterial diversity might be governed by its population genetic structure, environment and habitat. [ABSTRACT FROM AUTHOR]

The Epstein-Barr virus (EBV) induces B-cell proliferation with high efficiency through expression of latent proteins and microRNAs. This process takes place in vivo soon after infection, presumably to expand the virus reservoir, but can also induce pathologies, e.g. an infectious mononucleosis (IM) syndrome after primary infection or a B-cell lymphoproliferation in immunosuppressed individuals. In this paper, we investigated the growth characteristics of EBV-infected B-cells isolated from transplant recipients or patients with IM. We found that these cells grew and withstood apoptosis at highly variable rates, suggesting that the expansion rate of the infected B-cells widely varies between individuals, thereby influencing the size of the B-cell reservoir and the ability to form tumors in infected individuals. All viruses investigated were type 1 and genetically close to western strains. EBV-infected B-cells expressed the transforming EBV latent genes and microRNAs (miRNAs) at variable levels. We found that the B-cell growth rates positively correlated with the BHRF1 miRNA levels. Comparative studies showed that infected B-cells derived from transplant recipients with iEBVL on average expressed higher levels of EBV miR-BHRF1 miRNAs and grew more rapidly than B-cells from IM patients, suggesting infection by more transforming viruses. Altogether, these findings suggest that EBV infection has a highly variable impact on the B-cell compartment that probably reflects the genetic diversity of both the virus and the host. It also demonstrates the unexpected finding that B-cells from different individuals can grow at different speed under the influence of the same virus infection. [ABSTRACT FROM AUTHOR]

Introduction: The prevalence of bacteremia caused by Gram negative non-fermentative (GNNF) bacteria has been increasing globally over the past decade. Many studies have investigated their epidemiology but focus on the common GNNF including Pseudomonas aeruginosa and Acinetobacter baumannii. Knowledge of the uncommon GNNF bacteremias is very limited. This study explores invasive bloodstream infection GNNF isolates that were initially unidentified after testing with standard microbiological techniques. All isolations were made during laboratory-based surveillance activities in two rural provinces of Thailand between 2006 and 2014. Methods: A subset of GNNF clinical isolates (204/947), not identified by standard manual biochemical methodologies were run on the BD Phoenix automated identification and susceptibility testing system. If an organism was not identified (12/204) DNA was extracted for whole genome sequencing (WGS) on a MiSeq platform and data analysis performed using 3 web-based platforms: Taxonomer, CGE KmerFinder and One Codex. Results: The BD Phoenix automated identification system recognized 92% (187/204) of the GNNF isolates, and because of their taxonomic complexity and high phenotypic similarity 37% (69/187) were only identified to the genus level. Five isolates grew too slowly for identification. Antimicrobial sensitivity (AST) data was not obtained for 93/187 (50%) identified isolates either because of their slow growth or their taxa were not in the AST database associated with the instrument. WGS identified the 12 remaining unknowns, four to genus level only. Conclusion: The GNNF bacteria are of increasing concern in the clinical setting, and our inability to identify these organisms and determine their AST profiles will impede treatment. Databases for automated identification systems and sequencing annotation need to be improved so that opportunistic organisms are better covered. [ABSTRACT FROM AUTHOR]

Characterization of Human Endogenous Retrovirus (HERV) expression within the transcriptomic landscape using RNA-seq is complicated by uncertainty in fragment assignment because of sequence similarity. We present Telescope, a computational software tool that provides accurate estimation of transposable element expression (retrotranscriptome) resolved to specific genomic locations. Telescope directly addresses uncertainty in fragment assignment by reassigning ambiguously mapped fragments to the most probable source transcript as determined within a Bayesian statistical model. We demonstrate the utility of our approach through single locus analysis of HERV expression in 13 ENCODE cell types. When examined at this resolution, we find that the magnitude and breadth of the retrotranscriptome can be vastly different among cell types. Furthermore, our approach is robust to differences in sequencing technology, and demonstrates that the retrotranscriptome has potential to be used for cell type identification. We compared our tool with other approaches for quantifying TE expression, and found that Telescope has the greatest resolution, as it estimates expression at specific TE insertions rather than at the TE subfamily level. Telescope performs highly accurate quantification of the retrotranscriptomic landscape in RNA-seq experiments, revealing a differential complexity in the transposable element biology of complex systems not previously observed. Telescope is available at . [ABSTRACT FROM AUTHOR]

Cancer driver genes, i.e., oncogenes and tumor suppressor genes, are involved in the acquisition of important functions in tumors, providing a selective growth advantage, allowing uncontrolled proliferation and avoiding apoptosis. It is therefore important to identify these driver genes, both for the fundamental understanding of cancer and to help finding new therapeutic targets or biomarkers. Although the most frequently mutated driver genes have been identified, it is believed that many more remain to be discovered, particularly for driver genes specific to some cancer types. In this paper, we propose a new computational method called LOTUS to predict new driver genes. LOTUS is a machine-learning based approach which allows to integrate various types of data in a versatile manner, including information about gene mutations and protein-protein interactions. In addition, LOTUS can predict cancer driver genes in a pan-cancer setting as well as for specific cancer types, using a multitask learning strategy to share information across cancer types. We empirically show that LOTUS outperforms five other state-of-the-art driver gene prediction methods, both in terms of intrinsic consistency and prediction accuracy, and provide predictions of new cancer genes across many cancer types. [ABSTRACT FROM AUTHOR]

Open data science and algorithm development competitions offer a unique avenue for rapid discovery of better computational strategies. We highlight three examples in computational biology and bioinformatics research in which the use of competitions has yielded significant performance gains over established algorithms. These include algorithms for antibody clustering, imputing gene expression data, and querying the Connectivity Map (CMap). Performance gains are evaluated quantitatively using realistic, albeit sanitized, data sets. The solutions produced through these competitions are then examined with respect to their utility and the prospects for implementation in the field. We present the decision process and competition design considerations that lead to these successful outcomes as a model for researchers who want to use competitions and non-domain crowds as collaborators to further their research. [ABSTRACT FROM AUTHOR]

Background: Referral networks are critical in the timely delivery of surgical care, particularly for populations residing in rural areas who have limited access to specialist services. However, in low- and middle-income countries (LMICs) referral networks are often undermined by systemic inefficiencies. If equitable access to essential surgical services is to be achieved, sound evidence is needed to ensure efficient patient care pathways. The aim of this scoping review was to investigate current knowledge regarding inter-hospital surgical referral systems in LMICs to identify the main obstacles to their functioning and to critically assess proposed solutions. Methods: MEDLINE, EMBASE and Global Health databases and grey literature were systematically searched to identify relevant studies. The search generated 2261 unique records, of which 14 studies were selected for inclusion in the review. The narrative synthesis of retrieved data is based on a conceptual framework developed though a thematic analysis approach. Results: Multiple shortages in surgical infrastructure, equipment and personnel, as well as gaps in surgical and decision-making skills of clinicians at sending hospitals, act as obstacles to safe and appropriate referrals. Comprehensive protocols for surgical referrals are lacking in most LMICs and established patient pathways, when in place, are not correctly followed. Interventions to improve coordination and communication between different level facilities may enhance efficiency of referral pathways. Strengthening capacity of referring hospitals to manage more surgical conditions locally could improve outcomes, decrease the need for referral and reduce the burden on tertiary facilities. Discussion: The field of surgical referrals is still an uncharted territory and the limited empirical evidence available is of low quality. Developing strategies for assessing functionality and effectiveness of referral systems in surgery is essential to improve access, coverage and quality of services in resource-limited settings, as well as overall health systems performance. [ABSTRACT FROM AUTHOR]

Clostridium difficile (Cd) infection (CDI) typically occurs after antibiotic usage perturbs the gut microbiota. Mucosa-associated invariant T cells (MAIT) are found in the gut and their development is dependent on Major histocompatibility complex-related protein 1 (MR1) and the host microbiome. Here we were interested in determining whether the absence of MR1 impacts resistance to CDI. To this end, wild-type (WT) and MR1-/- mice were treated with antibiotics and then infected with Cd spores. Surprisingly, MR1-/- mice exhibited resistance to Cd colonization. 16S rRNA gene sequencing of feces revealed inherent differences in microbial composition. This colonization resistance was transferred from MR1-/- to WT mice via fecal microbiota transplantation, suggesting that MR1-dependent factors influence the microbiota, leading to CDI susceptibility. [ABSTRACT FROM AUTHOR]

Background: In Citrus spp., gibberellic acid (GA) has been proposed to improve different processes related to crop cycle and yield. Accordingly, many studies have been published about how GA affects flowering and fruiting. Nevertheless, some such evidence is contradictory and the use of GA applications by farmers are still confusing and lack the expected results. Purpose: This review aims to collate, present, analyze and synthesize the most relevant empirical evidence to answer the following questions: (i) how does gibberellic acid act on flowering and fruiting of citrus trees?; (ii) why is all this knowledge sometimes not correctly used by farmers to solve yield problems relating to flowering and fruit set? Methods: An extensive literature search to obtain a large number of records about the topic was done. Searches were done in five databases: WoS, Scopus, Google Academics, PubMed and Scielo. The search string used was "Gibberellic acid" AND "Citrus". Records were classified into 11 groups according to the development process they referred to and initial data extraction was done. Records related with flowering and fruit set were drawn, and full texts were screened. Fifty-eight full text records were selected for the final data extraction. Results: Selected studies were published from 1959 to 2017 and were published mainly in Spain, USA, Brazil and Japan. Twelve species were studied, and Citrus sinensis, C. reticulata and C. unshiu were the principal ones. Most publications with pre-flowering treatments agreed that GA decreases flowering, while only 3 out of 18 did not observe any effect. In most of these studies, the effect on fruit set and yield was not evaluated. Studies with treatments at full bloom or some weeks later mostly reported increased fruit set. However, these increases did not imply higher yields. The results on yield were highly erratic as we found increases, decreases, no effects or variable effects. Conclusions: Despite some limitations, the action of GA related to cell division and growth, stimulating the sink ability of the organ and discouraging its abscission, has been clearly established through reviewed studies. GA applications before flowering counteract the floral induction caused by stress reducing flowering. However, on adult trees under field conditions, reducing flowering by applying GA would be difficult because it would be necessary to previously estimate the natural floral induction of trees. During flowering and fruit set, many problems may arise that limit production. Only when the problem is lack of fruit set stimulus can GA applications improve yields. However, much evidence suggests that the main factor-limiting yield would be carbohydrate availability rather than GA levels. GA applications increased fruit set (often transiently), but this increase did not mean improved yields. [ABSTRACT FROM AUTHOR]

Trade involving elasmobranch products in Bangladesh is a four-decade-long practice in large scale and there is little understanding of its impact on species composition, population, and subsequent conservation. Capacity for monitoring and identification is lacking in landing and shark processing centres. A rapid survey and collection of tissue samples were performed in three landings and nine shark processing centres between 2016 and 2017 in the south-eastern coastal region of Bangladesh. Sequencing for a 707-bp fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene was used to assess the taxonomic status and species composition from 71 elasmobranch tissue samples collected from the shark processing centre only. Good quality COI sequences were obtained for 34 specimens representing 21 species—the majority of which are threatened with extinction. A total of ten species of sharks (Carcharhinus brevipinna, C. amboinensis, C. leucas, C. sorrah, C. amblyrhynchoides, Chiloscyllium burmensis, Galeocerdo cuvier, Rhincodon typus, Scoliodon laticaudus, and Sphyrna lewini), eleven species of rays (Aetomylaeus maculatus, Gymnura poecilura, Mobula mobular, M. kuhlii, Neotrygon indica, Pateobatis uarnacoides, Rhinoptera javanica, and R. jayakari), including three species of guitarfish (Glaucostegus granulatus, G. obtusus, and G. typus), were identified. Four species (14.7% of samples) were found to be listed in the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) in Appendix II. Sixteen species (59% of the specimens) were threatened with extinction according to IUCN Red List, whereas 41% were data deficient or not assessed. The results have important implications for the management of regional fisheries and the conservation of elasmobranchs as they 1) represent a preliminary understanding of elasmobranch diversity in trade; 2) depict a lack of awareness and monitoring; and 3) demonstrate a need for urgent monitoring and regulation of elasmobranch trade in Bangladesh. [ABSTRACT FROM AUTHOR]

In pediatric burns the use of systemic antibiotic prophylaxis is a standard procedure in some burn centers, though its beneficial effect on the infectious complications is debated. The present meta-analysis aimed at determining whether systemic antibiotic prophylaxis prevents infectious complications in pediatric patients with burn injuries. We searched the PubMed, EMBASE, and Cochrane Library databases from inception to August 2019. We included 6 studies, in which event rates of infectious complications were reported in children with burn injuries receiving or not receiving systemic antibiotic prophylaxis. We found that the overall odds ratio (OR) of developing an infection (including local and systemic) was not different between the groups (OR = 1.35; 95% CI, 0.44, 4.18). The chances for systemic infectious complications alone were also not different between antibiotic-treated and non-treated patients (OR = 0.74; 95% CI, 0.38, 1.45). Based on the age, affected total body surface area, and country income level, we did not find any subgroup that benefited from the prophylaxis. Our findings provide quantitative evidence for the inefficacy of systemic antibiotic prophylaxis in preventing infections in pediatric burns. To validate our conclusion, multinational, randomized trials in a diverse population of children with burn injuries are warranted. [ABSTRACT FROM AUTHOR]

Phytoplasmas are insect-transmitted bacterial pathogens that colonize a wide range of plant species, including vegetable and cereal crops, and herbaceous and woody ornamentals. Phytoplasma-infected plants often show dramatic symptoms, including proliferation of shoots (witch’s brooms), changes in leaf shapes and production of green sterile flowers (phyllody). Aster Yellows phytoplasma Witches’ Broom (AY-WB) infects dicots and its effector, secreted AYWB protein 11 (SAP11), was shown to be responsible for the induction of shoot proliferation and leaf shape changes of plants. SAP11 acts by destabilizing TEOSINTE BRANCHED 1-CYCLOIDEA-PROLIFERATING CELL FACTOR (TCP) transcription factors, particularly the class II TCPs of the CYCLOIDEA/TEOSINTE BRANCHED 1 (CYC/TB1) and CINCINNATA (CIN)-TCP clades. SAP11 homologs are also present in phytoplasmas that cause economic yield losses in monocot crops, such as maize, wheat and coconut. Here we show that a SAP11 homolog of Maize Bushy Stunt Phytoplasma (MBSP), which has a range primarily restricted to maize, destabilizes specifically TB1/CYC TCPs. SAP11MBSP and SAP11AYWB both induce axillary branching and SAP11AYWB also alters leaf development of Arabidopsis thaliana and maize. However, only in maize, SAP11MBSP prevents female inflorescence development, phenocopying maize tb1 lines, whereas SAP11AYWB prevents male inflorescence development and induces feminization of tassels. SAP11AYWB promotes fecundity of the AY-WB leafhopper vector on A. thaliana and modulates the expression of A. thaliana leaf defence response genes that are induced by this leafhopper, in contrast to SAP11MBSP. Neither of the SAP11 effectors promote fecundity of AY-WB and MBSP leafhopper vectors on maize. These data provide evidence that class II TCPs have overlapping but also distinct roles in regulating development and defence in a dicot and a monocot plant species that is likely to shape SAP11 effector evolution depending on the phytoplasma host range. [ABSTRACT FROM AUTHOR]

Auxin is a major developmental regulator in plants and the acquisition of a transcriptional response to auxin likely contributed to developmental innovations at the time of water-to-land transition. Auxin Response Factors (ARFs) Transcription Factors (TFs) that mediate auxin-dependent transcriptional changes are divided into A, B and C evolutive classes in land plants. The origin and nature of the first ARF proteins in algae is still debated. Here, we identify the most ‘ancient’ ARF homologue to date in the early divergent charophyte algae Chlorokybus atmophyticus, CaARF. Structural modelling combined with biochemical studies showed that CaARF already shares many features with modern ARFs: it is capable of oligomerization, interacts with the TOPLESS co-repressor and specifically binds Auxin Response Elements as dimer. In addition, CaARF possesses a DNA-binding specificity that differs from class A and B ARFs and that was maintained in class C ARF along plants evolution. Phylogenetic evidence together with CaARF biochemical properties indicate that the different classes of ARFs likely arose from an ancestral proto-ARF protein with class C-like features. The foundation of auxin signalling would have thus happened from a pre-existing hormone-independent transcriptional regulation together with the emergence of a functional hormone perception complex. [ABSTRACT FROM AUTHOR]

Telomeres are nucleo-protein structures that protect the ends of eukaryotic chromosomes. They are not completely synthesized during DNA replication and are elongated by specific mechanisms. The structure of the telomeres and the elongation mechanism have not been determined in Dictyostelium discoideum. This organism presents extrachromosomal palindromic elements containing two copies of the rDNA, also present at the end of the chromosomes. In this article the structure of the terminal region of the rDNA is shown to consist of repetitions of the A(G)n sequence where the number of Gs is variable. These repeats extend as a 3’ single stranded region. The G-rich region is preceded by four tandem repetitions of two different DNA motifs. D. discoideum telomere reverse transcriptase homologous protein (TERTHP) presented RNase-sensitive enzymatic activity and was required to maintain telomere structure since terthp-mutant strains presented reorganizations of the DNA terminal regions. These modifications were different in several terthp-mutants and changed with their prolonged culture and subcloning. However, the terthp gene is not essential for D. discoideum proliferation. Telomeres could be maintained in terthp-mutant strains by homologous recombination mechanisms such as ALT (Alternative Lengthening of Telomeres) or HAATI (heterochromatin amplification-mediated and telomerase-independent). In agreement with this hypothesis, the expression of mRNAs coding for several proteins involved in homologous recombination was induced in terthp-mutant strains. Extrachromosomal rDNA could serve as substrate in these DNA homologous recombination reactions. [ABSTRACT FROM AUTHOR]

Neuronal defense against oxidative damage is mediated primarily by the glutathione redox system. Traditionally considered a mechanism to protect proteins from irreversible oxidation, mounting evidence supports a role for protein S-glutathionylation in cell signaling in response to changes in intracellular redox status. Here we determined the specific sites on the actin binding protein cofilin that undergo S-glutathionylation. In addition, we show that S-glutathionylation of cofilin reduces its capacity to depolymerize F-actin. We further describe an assay to determine the S-glutathionylation of target proteins in brain tissue from behaving rodents. Using this technique, we show that cofilin in the rat nucleus accumbens undergoes S-glutathionylation during 15-minutes of cued cocaine seeking in the absence of cocaine. Our findings demonstrate that cofilin S-glutathionylation is increased in response to cocaine-associated cues and that increased cofilin S-glutathionylation reduces cofilin-dependent depolymerization of F-actin. Thus, S-glutathionylation of cofilin may serve to regulate actin cycling in response to drug-conditioned cues. [ABSTRACT FROM AUTHOR]

Around the world, pansies are one of the most popular garden flowers, but they are generally sensitive to high temperatures, and this limits the practicality of planting them during the warmest days of the year. However, a few pansy germplasms with improved heat tolerance have been discovered or bred, but the mechanisms of their heat resistance are not understood. In this study, we investigated the transcript profiles of a heat-tolerant pansy inbred line, DFM16, in response to high temperatures using RNAseq. Approximately 55.48 Gb of nucleotide data were obtained and assembled into 167,576 unigenes with an average length of 959 bp, of which, 5,708 genes were found to be differentially expressed after heat treatments. Real-time qPCR was performed to validate the expression profiles of the selected genes. Nine metabolic pathways were found to be significantly enriched, in the analysis of the differentially expressed genes. Several potentially interesting genes that encoded putative transcription regulators or key components involving heat shock protein (HSP), heat shock transcription factors (HSF), and antioxidants biosynthesis, were identified. These genes were highlighted to indicate their significance in response to heat stress and will be used as candidate genes to improve pansy heat-tolerance in the future. [ABSTRACT FROM AUTHOR]

The Best Possible Self (BPS) exercise promotes a positive view of oneself in the best possible future, after working hard towards it. Since the first work that attempted to examine the benefits of this intervention in 2001, studies on the BPS have grown exponentially and, currently, this is one of the most widely used Positive Psychology Interventions. However, little is yet known about its overall effectiveness in increasing wellbeing outcomes. Thus, the aim of this meta-analysis is to shed light on this question. A systematic literature search was conducted, and 29 studies (in 26 articles) met the inclusion criteria of empirically testing the intervention and comparing it to a control condition. In addition, BPS was compared to gratitude interventions in some of the included studies. A total of 2,909 participants were involved in the analyses. The outcome measures were wellbeing, optimism, depressive symptoms, and positive and negative affect. Results showed that the BPS is an effective intervention to improve wellbeing (d+ = .325), optimism (d+ = .334) and positive affect (d+ = .511) comparing to controls. Small effect sizes were obtained for negative affect and depressive symptoms. Moderator analyses did not show statistically significant results for wellbeing, except for a trend towards significance in the age of the participants (years) and the magnitude of the intervention (total minutes of practice). In addition, the BPS was found to be more beneficial for positive and negative affect than gratitude interventions (d+ = .326 and d+ = .485, respectively). These results indicate that the BPS can be considered a valuable Positive Psychology Intervention to improve clients’ wellbeing, and it seems that it might be more effective for older participants and with shorter practices (measured as total minutes of practice). [ABSTRACT FROM AUTHOR]