The Welfare Consequences and Efficacy of Training Pet Dogs with Remote Electronic Training Collars in Comparison to Reward Based Training

This study investigated the welfare consequences of training dogs in the field with manually operated electronic devices (e-collars). Following a preliminary study on 9 dogs, 63 pet dogs referred for recall related problems were assigned to one of three Groups: Treatment Group A were trained by industry approved trainers using e-collars; Control Group B trained by the same trainers but without use of e-collars; and Group C trained by members of the Association of Pet Dog Trainers, UK again without e-collar stimulation (n = 21 for each Group). Dogs received two 15 minute training sessions per day for 4–5 days. Training sessions were recorded on video for behavioural analysis. Saliva and urine were collected to assay for cortisol over the training period. During preliminary studies there were negative changes in dogs'' behaviour on application of electric stimuli, and elevated cortisol post-stimulation. These dogs had generally experienced high intensity stimuli without pre-warning cues during training. In contrast, in the subsequent larger, controlled study, trainers used lower settings with a pre-warning function and behavioural responses were less marked. Nevertheless, Group A dogs spent significantly more time tense, yawned more often and engaged in less environmental interaction than Group C dogs. There was no difference in urinary corticosteroids between Groups. Salivary cortisol in Group A dogs was not significantly different from that in Group B or Group C, though Group C dogs showed higher measures than Group B throughout sampling. Following training 92% of owners reported improvements in their dog''s referred behaviour, and there was no significant difference in reported efficacy across Groups. Owners of dogs trained using e-collars were less confident of applying the training approach demonstrated. These findings suggest that there is no consistent benefit to be gained from e-collar training but greater welfare concerns compared with positive reward based training.     

Interhemispheric functional differences in prefrontal cortex of monkeys

Monkeys had nonpolarizable electrodes implanted bilaterally in prefrontal (principal sulcus), precentral, and occipital cortex. They were trained on a spatial delayed-response (DR) task (8-sec intratrial delay), while cortical potentials were recorded. Three groups of monkeys were trained to 90% criterion: (A) 4 monkeys with only the right hand (the left wrist was attached to the testing chair); (B) 2 monkeys with only the left hand; and (C) 2 monkeys with the left and right hands on alternate sessions. Intermanual transfer tests were then given. Averaged steady potential (SP) shifts of several seconds duration were found in prefrontal cortex during cue presentation and the early portion of the intratrial delay and from the precentral area during the choice response. Evaluations of these SP shift magnitudes indicated: (1) Training with only one hand resulted in substantially larger SP shifts in the prefrontal and precentral areas contralateral to the responding hand; (2) alternate hand training resulted in somewhat larger prefrontal SP shifts in the right hemisphere; (3) intermanual transfer had marked effects on the precentral SP shifts, with larger magnitudes in the hemisphere contralateral to the responding hand, but had little effect on the magnitudes of both prefrontal SP shifts. (4) Subsequent training of Group C monkeys with only one hand resulted in greater SP shifts in the prefrontal area contralateral to the responding hand and in decreased SP shifts in the ipsilateral prefrontal area; and (5) additional intermanual transfer tests had no effects on SP shift magnitudes from both prefrontal areas. These findings indicate a dissociation in interhemispheric functions between the precentral and prefrontal cortical areas, with the former implicated in motor organization for the contralateral limb, and the latter in mediation of mnemonic processes, primarily in one hemisphere. This hemispheric specialization is affected by the hand-training procedure, but other endogenous or experiential factors may be involved.     

Generalization of Auditory Sensory and Cognitive Learning in Typically Developing Children

Despite the well-established involvement of both sensory (“bottom-up”) and cognitive (“top-down”) processes in literacy, the extent to which auditory or cognitive (memory or attention) learning transfers to phonological and reading skills remains unclear. Most research has demonstrated learning of the trained task or even learning transfer to a closely related task. However, few studies have reported “far-transfer” to a different domain, such as the improvement of phonological and reading skills following auditory or cognitive training. This study assessed the effectiveness of auditory, memory or attention training on far-transfer measures involving phonological and reading skills in typically developing children. Mid-transfer was also assessed through untrained auditory, attention and memory tasks. Sixty 5- to 8-year-old children with normal hearing were quasi-randomly assigned to one of five training groups: attention group (AG), memory group (MG), auditory sensory group (SG), placebo group (PG; drawing, painting), and a control, untrained group (CG). Compliance, mid-transfer and far-transfer measures were evaluated before and after training. All trained groups received 12 x 45-min training sessions over 12 weeks. The CG did not receive any intervention. All trained groups, especially older children, exhibited significant learning of the trained task. On pre- to post-training measures (test-retest), most groups exhibited improvements on most tasks. There was significant mid-transfer for a visual digit span task, with highest span in the MG, relative to other groups. These results show that both sensory and cognitive (memory or attention) training can lead to learning in the trained task and to mid-transfer learning on a task (visual digit span) within the same domain as the trained tasks. However, learning did not transfer to measures of language (reading and phonological awareness), as the PG and CG improved as much as the other trained groups. Further research is required to investigate the effects of various stimuli and lengths of training on the generalization of sensory and cognitive learning to literacy skills.     

A New Approach to Improving Healthcare Personnel Influenza Immunization Programs: A Randomized Controlled Trial

Background

Healthcare personnel influenza immunization rates remain sub-optimal. Following multiple studies and expert consultations, the “Successful Influenza Immunization Programs for Healthcare Personnel: A Guide for Program Planners” was produced. This trial assessed the impact of the Guide with facilitation in improving healthcare personnel influenza immunization rates in Canadian healthcare organizations.

Methods

A sample of 26 healthcare organizations across six Canadian provinces (ON, MB, NS, BC, SK, NL) was randomized to Intervention (n=13) or Control groups (n=13). Baseline influenza immunization rates were obtained for 2008–2009; the study groups were followed over two subsequent influenza seasons. The Intervention group received the Guide, facilitation support through workshops for managers and ongoing support. The Control groups conducted programs as usual. The Groups were compared using their reported influenza healthcare personnel influenza immunization rates and scores from a program assessment questionnaire.

Findings

Twenty-six organizations agreed to participate. 35% (9/26) of sites were acute care hospitals, 19% (5/26) continuing care, long-term care organizations or nursing homes, and 46% (12/26) were mixed acute care hospitals and long-term care or regional health authorities. The median rate of influenza immunization among healthcare personnel for the Intervention group was 43%, 44%, and 51% at three points in time respectively, and in the Control group: 62%, 57%, and 55% respectively. No significant differences were observed between the groups at the three points in time. However, there was a 7% increase in the median rates between the Baseline Year and Year Two in the Intervention group, and a 6% decrease in the Control group over the same time period, which was statistically significant (0.071 versus -0.058, p < 0.001).

Interpretation

This pragmatic randomized trial of the Guide with facilitation of its implementation improved healthcare personnel immunization rates, but these rates continued to be sub-optimal and below rates achievable in programs requiring personnel to be immunized.

Trial Registration

ClinicalTrials.gov NCT01207518     

Molecular Pathology of Rare Bleeding Disorders (RBDs) in India: A Systematic Review

Background

Though rare in occurrence, patients with rare bleeding disorders (RBDs) are highly heterogeneous and may manifest with severe bleeding diathesis. Due to the high rate of consanguinity in many caste groups, these autosomal recessive bleeding disorders which are of rare occurrence in populations across the world, may not be as rare in India.

Objectives

To comprehensively analyze the frequency and nature of mutations in Indian patients with RBDs.

Methods

Pubmed search was used (www.pubmed.com) to explore the published literature from India on RBDs using the key words “rare bleeding disorders”, “mutations”, “India”, “fibrinogen”, “afibrinogenemia”, “factor II deficiency”, “prothrombin” “factor VII deficiency”, “factor V deficiency”, “factor X deficiency”, “factor XI deficiency”, “combined factor V and VIII deficiency”, “factor XIII deficiency”, “Bernard Soulier syndrome” and “Glanzmanns thrombasthenia” in different combinations. A total of 60 relevant articles could be retrieved. The distribution of mutations from India was compared with that of the world literature by referring to the Human Gene Mutation Database (HGMD) (www.hgmd.org).

Results

Taken together, 181 mutations in 270 patients with different RBDs have been reported from India. Though the types of mutations reported from India and their percentage distribution with respect to the world data are largely similar, yet much higher percentage of small deletions, duplication mutations, insertions, indels were observed in this analysis. Besides the identification of novel mutations and polymorphisms, several common mutations have also been reported, which will allow to develop a strategy for mutation screening in Indian patients with RBDs.

Conclusion

There is a need for a consortium of Institutions working on the molecular pathology of RBDs in India. This will facilitate a quicker and cheaper diagnosis of RBDs besides its utility in first trimester prenatal diagnosis of the affected families.     

Prediction and Analysis of Quorum Sensing Peptides Based on Sequence Features

Quorum sensing peptides (QSPs) are the signaling molecules used by the Gram-positive bacteria in orchestrating cell-to-cell communication. In spite of their enormous importance in signaling process, their detailed bioinformatics analysis is lacking. In this study, QSPs and non-QSPs were examined according to their amino acid composition, residues position, motifs and physicochemical properties. Compositional analysis concludes that QSPs are enriched with aromatic residues like Trp, Tyr and Phe. At the N-terminal, Ser was a dominant residue at maximum positions, namely, first, second, third and fifth while Phe was a preferred residue at first, third and fifth positions from the C-terminal. A few motifs from QSPs were also extracted. Physicochemical properties like aromaticity, molecular weight and secondary structure were found to be distinguishing features of QSPs. Exploiting above properties, we have developed a Support Vector Machine (SVM) based predictive model. During 10-fold cross-validation, SVM achieves maximum accuracy of 93.00%, Mathew’s correlation coefficient (MCC) of 0.86 and Receiver operating characteristic (ROC) of 0.98 on the training/testing dataset (T^200p+200n). Developed models performed equally well on the validation dataset (V^20p+20n). The server also integrates several useful analysis tools like “QSMotifScan”, “ProtFrag”, “MutGen” and “PhysicoProp”. Our analysis reveals important characteristics of QSPs and on the basis of these unique features, we have developed a prediction algorithm “QSPpred” (freely available at: http://crdd.osdd.net/servers/qsppred).     

The 2015 Bioinformatics Open Source Conference (BOSC 2015)

The Bioinformatics Open Source Conference (BOSC) is organized by the Open Bioinformatics Foundation (OBF), a nonprofit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Since its inception in 2000, BOSC has provided bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results, and software. BOSC is run as a two-day special interest group (SIG) before the annual Intelligent Systems in Molecular Biology (ISMB) conference. BOSC 2015 took place in Dublin, Ireland, and was attended by over 125 people, about half of whom were first-time attendees. Session topics included “Data Science;” “Standards and Interoperability;” “Open Science and Reproducibility;” “Translational Bioinformatics;” “Visualization;” and “Bioinformatics Open Source Project Updates”. In addition to two keynote talks and dozens of shorter talks chosen from submitted abstracts, BOSC 2015 included a panel, titled “Open Source, Open Door: Increasing Diversity in the Bioinformatics Open Source Community,” that provided an opportunity for open discussion about ways to increase the diversity of participants in BOSC in particular, and in open source bioinformatics in general. The complete program of BOSC 2015 is available online at http://www.open-bio.org/wiki/BOSC_2015_Schedule.Open in a separate window     

Effect of a musical intervention on tolerance and efficacy of non-invasive ventilation in the ICU: study protocol for a randomized controlled trial (MUSique pour l’Insuffisance Respiratoire Aigue - Mus-IRA)

BackgroundNon-invasive ventilation (NIV) tolerance is a key factor of NIV success. Hence, numerous sedative pharmacological or non-pharmacological strategies have been assessed to improve NIV tolerance. Music therapy in various health care settings has shown beneficial effects. In invasively ventilated critical care patients, encouraging results of music therapy on physiological parameters, anxiety, and agitation have been reported. We hypothesize that a musical intervention improves NIV tolerance in comparison to conventional care. We therefore question the potential benefit of a receptive music session administered to patients by trained caregivers (“musical intervention”) to enhance acceptance and tolerance of NIV.Methods/designWe conduct a prospective, three-center, open-label, three-arm randomized trial involving patients in the intensive care unit (ICU) who require NIV, as assessed by the treating physician. Participants are allocated to a “musical intervention” arm (“musical intervention” applied during all NIV sessions), to a “sensory deprivation” arm (sight and hearing isolation during all NIV sessions), or to the control group. The primary endpoint is the change in respiratory comfort (measured with a digital visual scale) before the initiation and after 30 minutes of the first NIV session. The evaluation of the primary endpoint is performed blindly from the treatment group. Secondary endpoints include changes in respiratory and cardiovascular parameters during NIV sessions, the percentage of patients requiring endotracheal intubation, day-90 anxiety/depression and health-related quality of life, post-trauma stress induced by NIV, and the overall assessment of NIV.The follow-up for each participant is 90 days. We expect to randomize a total of 99 participants.DiscussionAs music intervention is a simple and easy-to-implement non-pharmacological technique, efficacious in reducing anxiety in critically ill patients, it appeared logical to assess its efficacy in NIV, one of the most stressful techniques used in the ICU. Patient centeredness was crucial in choosing the outcomes assessed.

Trial registration

ClinicalTrials.gov: {"type":"clinical-trial","attrs":{"text":"NCT02265458","term_id":"NCT02265458"}}NCT02265458. Registered on 25 August 2014.

Electronic supplementary material

The online version of this article (doi:10.1186/s13063-016-1574-z) contains supplementary material, which is available to authorized users.     

AntiAngioPred: A Server for Prediction of Anti-Angiogenic Peptides

The process of angiogenesis is a vital step towards the formation of malignant tumors. Anti-angiogenic peptides are therefore promising candidates in the treatment of cancer. In this study, we have collected anti-angiogenic peptides from the literature and analyzed the residue preference in these peptides. Residues like Cys, Pro, Ser, Arg, Trp, Thr and Gly are preferred while Ala, Asp, Ile, Leu, Val and Phe are not preferred in these peptides. There is a positional preference of Ser, Pro, Trp and Cys in the N terminal region and Cys, Gly and Arg in the C terminal region of anti-angiogenic peptides. Motif analysis suggests the motifs “CG-G”, “TC”, “SC”, “SP-S”, etc., which are highly prominent in anti-angiogenic peptides. Based on the primary analysis, we developed prediction models using different machine learning based methods. The maximum accuracy and MCC for amino acid composition based model is 80.9% and 0.62 respectively. The performance of the models on independent dataset is also reasonable. Based on the above study, we have developed a user-friendly web server named “AntiAngioPred” for the prediction of anti-angiogenic peptides. AntiAngioPred web server is freely accessible at http://clri.res.in/subramanian/tools/antiangiopred/index.html (mirror site: http://crdd.osdd.net/raghava/antiangiopred/).     

The Overlap of Small Molecule and Protein Binding Sites within Families of Protein Structures

Protein–protein interactions are challenging targets for modulation by small molecules. Here, we propose an approach that harnesses the increasing structural coverage of protein complexes to identify small molecules that may target protein interactions. Specifically, we identify ligand and protein binding sites that overlap upon alignment of homologous proteins. Of the 2,619 protein structure families observed to bind proteins, 1,028 also bind small molecules (250–1000 Da), and 197 exhibit a statistically significant (p<0.01) overlap between ligand and protein binding positions. These “bi-functional positions”, which bind both ligands and proteins, are particularly enriched in tyrosine and tryptophan residues, similar to “energetic hotspots” described previously, and are significantly less conserved than mono-functional and solvent exposed positions. Homology transfer identifies ligands whose binding sites overlap at least 20% of the protein interface for 35% of domain–domain and 45% of domain–peptide mediated interactions. The analysis recovered known small-molecule modulators of protein interactions as well as predicted new interaction targets based on the sequence similarity of ligand binding sites. We illustrate the predictive utility of the method by suggesting structural mechanisms for the effects of sanglifehrin A on HIV virion production, bepridil on the cellular entry of anthrax edema factor, and fusicoccin on vertebrate developmental pathways. The results, available at http://pibase.janelia.org, represent a comprehensive collection of structurally characterized modulators of protein interactions, and suggest that homologous structures are a useful resource for the rational design of interaction modulators.     

Ensuring the quality and specificity of preregistrations

Researchers face many, often seemingly arbitrary, choices in formulating hypotheses, designing protocols, collecting data, analyzing data, and reporting results. Opportunistic use of “researcher degrees of freedom” aimed at obtaining statistical significance increases the likelihood of obtaining and publishing false-positive results and overestimated effect sizes. Preregistration is a mechanism for reducing such degrees of freedom by specifying designs and analysis plans before observing the research outcomes. The effectiveness of preregistration may depend, in part, on whether the process facilitates sufficiently specific articulation of such plans. In this preregistered study, we compared 2 formats of preregistration available on the OSF: Standard Pre-Data Collection Registration and Prereg Challenge Registration (now called “OSF Preregistration,” http://osf.io/prereg/). The Prereg Challenge format was a “structured” workflow with detailed instructions and an independent review to confirm completeness; the “Standard” format was “unstructured” with minimal direct guidance to give researchers flexibility for what to prespecify. Results of comparing random samples of 53 preregistrations from each format indicate that the “structured” format restricted the opportunistic use of researcher degrees of freedom better (Cliff’s Delta = 0.49) than the “unstructured” format, but neither eliminated all researcher degrees of freedom. We also observed very low concordance among coders about the number of hypotheses (14%), indicating that they are often not clearly stated. We conclude that effective preregistration is challenging, and registration formats that provide effective guidance may improve the quality of research.

Researchers face many, often seemingly arbitrary choices in formulating hypotheses, designing protocols, collecting data, analyzing data, and reporting results. A study of two formats of preregistration available on the OSF reveals that the opportunistic use of researcher degrees of freedom aimed at obtaining statistical significance is restricted by using more extensive preregistration guidelines; however, these guidelines should be further improved.     

A Preliminary Investigation of Individual Differences in Subjective Responses to D-Amphetamine,Alcohol, and Delta-9-Tetrahydrocannabinol Using a Within-Subjects Randomized Trial

Polydrug use is common, and might occur because certain individuals experience positive effects from several different drugs during early stages of use. This study examined individual differences in subjective responses to single oral doses of d-amphetamine, alcohol, and delta-9-tetrahydrocannabinol (THC) in healthy social drinkers. Each of these drugs produces feelings of well-being in at least some individuals, and we hypothesized that subjective responses to these drugs would be positively correlated. We also examined participants’ drug responses in relation to personality traits associated with drug use. In this initial, exploratory study, 24 healthy, light drug users (12 male, 12 female), aged 21–31 years, participated in a fully within-subject, randomized, counterbalanced design with six 5.5-hour sessions in which they received d-amphetamine (20mg), alcohol (0.8 g/kg), or THC (7.5 mg), each paired with a placebo session. Participants rated the drugs’ effects on both global measures (e.g. feeling a drug effect at all) and drug-specific measures. In general, participants’ responses to the three drugs were unrelated. Unexpectedly, “wanting more” alcohol was inversely correlated with “wanting more” THC. Additionally, in women, but not in men, “disliking” alcohol was negatively correlated with “disliking” THC. Positive alcohol and amphetamine responses were related, but only in individuals who experienced a stimulant effect of alcohol. Finally, high trait constraint (or lack of impulsivity) was associated with lower reports of liking alcohol. No personality traits predicted responses across multiple drug types. Generally, these findings do not support the idea that certain individuals experience greater positive effects across multiple drug classes, but instead provide some evidence for a “drug of choice” model, in which individuals respond positively to certain classes of drugs that share similar subjective effects, and dislike other types of drugs.

Trial Registration

ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT02485158","term_id":"NCT02485158"}}NCT02485158     

Improving Executive Functioning in Children with ADHD: Training Multiple Executive Functions within the Context of a Computer Game. A Randomized Double-Blind Placebo Controlled Trial

Introduction

Executive functions (EFs) training interventions aimed at ADHD-symptom reduction have yielded mixed results. Generally, these interventions focus on training a single cognitive domain (e.g., working memory [WM], inhibition, or cognitive-flexibility). However, evidence suggests that most children with ADHD show deficits on multiple EFs, and that these EFs are largely related to different brain regions. Therefore, training multiple EFs might be a potentially more effective strategy to reduce EF-related ADHD symptoms.

Methods

Eighty-nine children with a clinical diagnosis of ADHD (aged 8–12) were randomized to either a full-active-condition where visuospatial WM, inhibition and cognitive-flexibility were trained, a partially-active-condition where inhibition and cognitive-flexibility were trained and the WM-training task was presented in placebo-mode, or to a full placebo-condition. Short-term and long-term (3-months) effects of this gamified, 25-session, home-based computer-training were evaluated on multiple outcome domains.

Results

During training compliance was high (only 3% failed to meet compliance criteria). After training, only children in the full-active condition showed improvement on measures of visuospatial short-term-memory (STM) and WM. Inhibitory performance and interference control only improved in the full-active- and the partially-active condition. No Treatment-condition x Time interactions were found for cognitive-flexibility, verbal WM, complex-reasoning, nor for any parent-, teacher-, or child-rated ADHD behaviors, EF-behaviors, motivational behaviors, or general problem behaviors. Nonetheless, almost all measures showed main Time-effects, including the teacher-ratings.

Conclusions

Improvements on inhibition and visuospatial STM and WM were specifically related to the type of treatment received. However, transfer to untrained EFs and behaviors was mostly nonspecific (i.e., only interference control improved exclusively in the two EF training conditions). As such, in this multiple EF-training, mainly nonspecific treatment factors – as opposed to the specific effects of training EFs—seem related to far transfer effects found on EF and behavior.

Trial Registration

trialregister.nl NTR2728. Registry name: improving executive functioning in children with ADHD: training executive functions within the context of a computer game; registry number: NTR2728.     

Automatic Assignment of Prokaryotic Genes to Functional Categories Using Literature Profiling

In the last years, there was an exponential increase in the number of publicly available genomes. Once finished, most genome projects lack financial support to review annotations. A few of these gene annotations are based on a combination of bioinformatics evidence, however, in most cases, annotations are based solely on sequence similarity to a previously known gene, which was most probably annotated in the same way. As a result, a large number of predicted genes remain unassigned to any functional category despite the fact that there is enough evidence in the literature to predict their function. We developed a classifier trained with term-frequency vectors automatically disclosed from text corpora of an ensemble of genes representative of each functional category of the J. Craig Venter Institute Comprehensive Microbial Resource (JCVI-CMR) ontology. The classifier achieved up to 84% precision with 68% recall (for confidence≥0.4), F-measure 0.76 (recall and precision equally weighted) in an independent set of 2,220 genes, from 13 bacterial species, previously classified by JCVI-CMR into unambiguous categories of its ontology. Finally, the classifier assigned (confidence≥0.7) to functional categories a total of 5,235 out of the ∼24 thousand genes previously in categories “Unknown function” or “Unclassified” for which there is literature in MEDLINE. Two biologists reviewed the literature of 100 of these genes, randomly picket, and assigned them to the same functional categories predicted by the automatic classifier. Our results confirmed the hypothesis that it is possible to confidently assign genes of a real world repository to functional categories, based exclusively on the automatic profiling of its associated literature. The LitProf - Gene Classifier web server is accessible at: www.cebio.org/litprofGC.     

Advances in endophenotyping schizophrenia

The search for the genetic architecture of schizophrenia has employed multiple, often converging strategies. One such strategy entails the use of tracing the heritability and neurobiology of endophenotypes. Endophenotypes are quantifiable traits not visible to the eye, which are thought to reflect an intermediate place on the path from genes to disorder. Endophenotype abnormalities in domains such as neurophysiology or neurocognition occur in schizophrenia patients as well as their clinically “unaffected” relatives, and reflect polymorphisms in the DNA of schizophrenia spectrum subjects which create vulnerability to developing schizophrenia. By identifying the single nucleotide polymorphisms (SNPs) associated with endophenotypes in schizophrenia, psychiatric neuroscientists can select new strong inference based molecular targets for the treatment of schizophrenia.     

Diagnostic performance of a Recombinant Polymerase Amplification Test—Lateral Flow (RPA-LF) for cutaneous leishmaniasis in an endemic setting of Colombia

BackgroundControl of cutaneous leishmaniasis by public health systems in the Americas relies on case identification and treatment. Point-of-care diagnostics that can be performed by health workers within or near affected communities could effectively bring the health system to the resource-limited sites providing early diagnosis and treatment, reducing morbidity and the burden of disease.Methodology/principal findingsA cross-sectional study was undertaken to evaluate the diagnostic test performance of Isothermal Recombinase Polymerase Amplification (RPA) targeting Leishmania kinetoplast DNA, coupled with a lateral flow (LF) immunochromatographic strip, in a field setting and a laboratory reference center. Minimally invasive swab and FTA filter paper samples were obtained by community health workers and highly trained technicians from ulcerated lesions of > 2 weeks’ evolution from 118 patients’ ≥ 2 years of age in the municipality of Tumaco, Nariño. Extracted DNA was processed by RPA-LF at a reference center or in a primary health facility in the field. Evaluation was based on a composite “gold standard” that included microscopy, culture, biopsy and real-time polymerase chain reaction detection of Leishmania 18S rDNA. Standard of care routine diagnostic tests were explored as comparators.Sensitivity and specificity of RPA-LF in the reference lab scenario were 87% (95%CI 74–94) and 86% (95%CI 74–97), respectively. In the field scenario, the sensitivity was 75% (95%CI 65–84) and specificity 89% (95%CI 78–99). Positive likelihood ratios in both scenarios were higher than 6 while negative likelihood ratios ranged to 0.2–0.3 supporting the usefulness of RPA-LF to rule-in and potentially to rule-out infection.Conclusions/significanceThe low complexity requirements of RPA-LF combined with non-invasive sampling support the feasibility of its utilization by community health workers with the goal of strengthening the diagnostic capacity for cutaneous leishmaniasis in Colombia.Trial registrationClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT04500873","term_id":"NCT04500873"}}NCT04500873.     

Genome sequence of the Lebeckia ambigua-nodulating “Burkholderia sprentiae” strain WSM5005T

“Burkholderia sprentiae” strain WSM5005^T is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated in Australia from an effective N₂-fixing root nodule of Lebeckia ambigua collected in Klawer, Western Cape of South Africa, in October 2007. Here we describe the features of “Burkholderia sprentiae” strain WSM5005^T, together with the genome sequence and its annotation. The 7,761,063 bp high-quality-draft genome is arranged in 8 scaffolds of 236 contigs, contains 7,147 protein-coding genes and 76 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program.