Multiplex Real-Time PCR Assay Using TaqMan Probes for the Identification of Trypanosoma cruzi DTUs in Biological and Clinical Samples

Background: Trypanosoma cruzi has been classified into six Discrete Typing Units (DTUs), designated as TcI–TcVI. In order to effectively use this standardized nomenclature, a reproducible genotyping strategy is imperative. Several typing schemes have been developed with variable levels of complexity, selectivity and analytical sensitivity. Most of them can be only applied to cultured stocks. In this context, we aimed to develop a multiplex Real-Time PCR method to identify the six T. cruzi DTUs using TaqMan probes (MTq-PCR).Methods/Principal Findings: The MTq-PCR has been evaluated in 39 cultured stocks and 307 biological samples from vectors, reservoirs and patients from different geographical regions and transmission cycles in comparison with a multi-locus conventional PCR algorithm. The MTq-PCR was inclusive for laboratory stocks and natural isolates and sensitive for direct typing of different biological samples from vectors, reservoirs and patients with acute, congenital infection or Chagas reactivation. The first round SL-IR MTq-PCR detected 1 fg DNA/reaction tube of TcI, TcII and TcIII and 1 pg DNA/reaction tube of TcIV, TcV and TcVI reference strains. The MTq-PCR was able to characterize DTUs in 83% of triatomine and 96% of reservoir samples that had been typed by conventional PCR methods. Regarding clinical samples, 100% of those derived from acute infected patients, 62.5% from congenitally infected children and 50% from patients with clinical reactivation could be genotyped. Sensitivity for direct typing of blood samples from chronic Chagas disease patients (32.8% from asymptomatic and 22.2% from symptomatic patients) and mixed infections was lower than that of the conventional PCR algorithm.Conclusions/Significance: Typing is resolved after a single or a second round of Real-Time PCR, depending on the DTU. This format reduces carryover contamination and is amenable to quantification, automation and kit production.This work received financial support from the Ministry of Science and Technology of Argentina [PICT 2011-0207 to AGS] and the National Scientific and Technical Research Council in Argentina (CONICET) [PIP 112 2011-010-0974 to AGS]. Work related to evaluation of biological samples was partially sponsored by the Pan-American Health Organization (PAHO) [Small Grants Program PAHO-TDR]; the Drugs and Neglected Diseases Initiative (DNDi, Geneva, Switzerland), Wellcome Trust (London, United Kingdom), SANOFI-AVENTIS (Buenos Aires, Argentina) and the National Council for Science and Technology in Mexico (CONACYT) [FONSEC 161405 to JMR]

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Wat we (niet) weten over het brein van een kind met DCD

Developmental Coordination Disorder (DCD) is een stoornis van de motorische coördinatie zonder duidelijke medisch aanwijsbare oorzaak die niet kan worden verklaard door een verminderde intelligentie. Omwille van het heterogeen klinisch beeld van DCD en de hoge comorbiditeit met ADHD, dyslexie en taalstoornissen kan worden verondersteld dat diverse neurale systemen aan de basis van deze stoornis liggen. Recent onderzoek wijst op de mogelijke betrokkenheid van het cerebellum, de pariëtale cortex, het corpus callosum en/of de basale ganglia (Zwicker, Missiuna & Boyd, 2009). Onderzoek met geavanceerde beeldvormingstechnieken is nodig om beter te begrijpen hoe de neurale structuur en/of het functioneel netwerk van kinderen met DCD afwijkt en hoe deze veranderen als gevolg van ontwikkeling en oefening

Neural underpinnings of impaired predictive motor timing in children with Developmental Coordination Disorder

A dysfunction in predictive motor timing is put forward to underlie DCD-related motor problems. Predictive timing allows for the pre-selection of motor programmes (except ‘program’ in computers) in order to decrease processing load and facilitate reactions. Using functional magnetic resonance imaging (fMRI), this study investigated the neural correlates of motor timing in DCD (n = 17) and typically developing children (n = 17). The task involved motor responses to sequences of visual stimuli with predictive or unpredictive interstimulus intervals (ISIs). DCD children responded with a smaller reaction time (RT) advantage to predictive ISIs compared to typically developing children. Typically developing children exhibited higher activation in the right dorsolateral prefrontal cortex (DLPFC) and right inferior frontal gyrus (IFG) for responses at unpredictive as opposed to predictive ISIs, whereas activations in DCD children were non-differentiable. Moreover, DCD children showed less activation than typically developing children in the right DLPFC, the left posterior cerebellum (crus I) and the right temporo-parietal junction (TPJ) for this contrast. Notably, activation in the right temporo-parietal junction (TPJ) positively correlated with RT as an indicator of processing load in both groups. These data indicate that motor performance in DCD children requires extra processing demands due to impaired predictive encoding

Brain connectomics of visual-motor deficits in children with developmental coordination disorder

Objective: To extend preliminary findings on associated white matter deficits and structural connectivity in children with developmental coordination disorder ( DCD ). Study design: Diffusion magnetic resonance imaging-based tractography was used to identify abnormal microstructural properties of specific sensorimotor white matter tracts in 21 children with DCD between 8 and 10 years of age and 20 age- and sex-matched typically developing controls. Graph theoretical analyses were applied to evaluate whole brain connectomics. Associations were also calculated between the tractography/connectome results and visual-motor performance, as measured with the Beery-Buktenica Developmental Test of Visual Motor Integration. Results: Significant positive correlations were obtained between visual-motor trace scores and fractional anisotropy ( FA ) in the retrolenticular limb of the internal capsule within the group with DCD. Moreover, lower FA in sensorimotor tracts and altered structural connectivity were observed for children with DCD. Compared with controls, subjects with DCD showed decreases in clustering coefficient, and global and local efficiency, suggesting weaker structural network segregation and integration. The degree of decreased global efficiency was significantly associated with poor visual-motor tracing outcomes, above and beyond FA reductions. Specifically, nodal efficiency at the cerebellar lobule VI and right parietal superior gyrus were found significant predictors to discriminate between children with DCD and those with typical development. Conclusions: Specific white matter alterations and network topology features associate with visual-motor deficits and DCD diagnosis indicating the clinical potential of diffusion magnetic resonance imaging-based metrics for diagnosing DCD

Deficient motor timing in children with neurofibromatosis type 1

Neurofibromatosis type 1 (NF1) is one of the most common single-gene disorders affecting fine and visual-motor skills. This case–control study investigated motor timing as a possible related performance deficit in children with NF1. A visual-motor reaction time (VRT) test was administered in 20 NF1 children (mean age 9 years 7 months) and 20 age- and gender-matched typically developing (TD) children. Copying and tracing performance were evaluated using the Beery-Buktenica Developmental Test of Visual-Motor Integration (Beery VMI). Children with NF1 responded with an increased reaction time (RT) to temporally predictive stimuli compared to TD children, whereas RT at unpredictive stimuli did not differ between groups. Motor timing indexed by the RT decrease at predictive stimuli significantly associated with the Beery VMI copy and tracing outcomes. Deficient motor timing as an actual symptom may add to further research on the pathogenesis of NF1-associated motor impairment and the development of more effective treatment

Effectiveness of a self-regulated remedial program for handwriting difficulties

Background: Handwriting difficulties may have pervasive effects on a child's school performance. I Can! is a remedial handwriting program with a focus on self-regulated learning and applying motor learning principles combined with a behavioural approach. It is developed for typically developing children with handwriting problems. Objective: The study aim was to evaluate the program's effectiveness. Materials and methods: Thirty-one children aged 7-8 year participated in a cross-over study. Handwriting quality and speed were repeatedly assessed by means of the Systematic Screening of Handwriting Difficulties test. Difficulties addressed were fluency in letter formation, fluency in letter connections, letter height, regularity of letter height, space between words, and line path. Results: Mixed model analysis revealed improved quality of writing and speed for all children but significantly more improvement in handwriting quality for the children participating in the program. Although writing speed improved over time, no additional effects of the program occurred. Conclusions and significance: I Can!' is found to be an effective instructive program to ameliorate handwriting quality in typically developing children with handwriting difficulties. The program's success was by a therapy burst of only 7 weeks focusing on the child's self-regulated learning capacities, within an individualized education plan according to their needs and goals