Exploring the effects of demonstration and enactment in facilitating recall of instructions in working memory

Across the lifespan the ability to follow instructions is essential for the successful completion of a multitude of daily activities. This ability will often rely on the storage and processing of information in working memory, and previous research in this domain has found that self-enactment at encoding or observing other-enactment at encoding (demonstration) improves performance at recall. However, no working memory research has directly compared these manipulations. Experiment 1 explored the effects of both self-enactment and demonstration on young adults’ (N=48) recall of action-object instruction sequences (e.g. ‘spin the circle, tap the square’). Both manipulations improved recall, with demonstration providing relatively larger boosts to performance across conditions. More detailed analyses suggested that this improvement was driven by improving the representations of actions, rather than objects, in these action-object sequences. Experiment 2 (N=24) explored this further, removing the objects from the physical environment and comparing partial demonstration (i.e. action-only or object-only) with no or full demonstration. The results showed that partial demonstration only benefitted features that were demonstrated, while full demonstration improved memory for actions, objects and their pairings. Overall these experiments indicate how self-enactment, and particularly demonstration, can benefit verbal recall of instruction sequences through the engagement of visuo-motor processes that provide additional forms of coding to support working memory performance

The validity and reliability of observational assessment tools available to measure fundamental movement skills in school-age children: A systematic review

Background Fundamental Movement Skills (FMS) play a critical role in ontogenesis. Many children have insufficient FMS, highlighting the need for universal screening in schools. There are many observational FMS assessment tools, but their psychometric properties are not readily accessible. A systematic review was therefore undertaken to compile evidence of the validity and reliability of observational FMS assessments, to evaluate their suitability for screening. Methods A pre-search of ‘fundamental movement skills’ OR ‘fundamental motor skills’ in seven online databases (PubMed, Ovid MEDLINE, Ovid Embase, EBSCO CINAHL, EBSCO SPORTDiscus, Ovid PsycINFO and Web of Science) identified 24 assessment tools for school-aged children that: (i) assess FMS; (ii) measure actual motor competence and (iii) evaluate performance on a standard battery of tasks. Studies were subsequently identified that: (a) used these tools; (b) quantified validity or reliability and (c) sampled school-aged children. Study quality was assessed using COnsensus-based Standards for the selection of health Measurement INstruments (COSMIN) checklists. Results Ninety studies were included following the screening of 1863 articles. Twenty-one assessment tools had limited or no evidence to support their psychometric properties. The Test of Gross Motor Development (TGMD, n = 34) and the Movement Assessment Battery for Children (MABC, n = 37) were the most researched tools. Studies consistently reported good evidence for validity, reliability for the TGMD, whilst only 64% of studies reported similarly promising results for the MABC. Twelve studies found good evidence for the reliability and validity of the Bruininks-Oseretsky Test of Motor Proficiency but poor study quality appeared to inflate results. Considering all assessment tools, those with promising psychometric properties often measured limited aspects of validity/reliability, and/or had limited feasibility for large scale deployment in a school-setting. Conclusion There is insufficient evidence to justify the use of any observational FMS assessment tools for universal screening in schools, in their current form

Developing and validating a school-based screening tool of Fundamental Movement Skills (FUNMOVES) using Rasch analysis

Background A large proportion of children are not able to perform age-appropriate fundamental movement skills (FMS). Thus, it is important to assess FMS so that children needing additional support can be identified in a timely fashion. There is great potential for universal screening of FMS in schools, but research has established that current assessment tools are not fit for purpose. Objective To develop and validate the psychometric properties of a FMS assessment tool designed specifically to meet the demands of universal screening in schools. Methods A working group consisting of academics from developmental psychology, public health and behavioural epidemiology developed an assessment tool (FUNMOVES) based on theory and prior evidence. Over three studies, 814 children aged 4 to 11 years were assessed in school using FUNMOVES. Rasch analysis was used to evaluate structural validity and modifications were then made to FUNMOVES activities after each study based on Rasch results and implementation fidelity. Results The initial Rasch analysis found numerous psychometric problems including multidimensionality, disordered thresholds, local dependency, and misfitting items. Study 2 showed a unidimensional measure, with acceptable internal consistency and no local dependency, but that did not fit the Rasch model. Performance on a jumping task was misfitting, and there were issues with disordered thresholds (for jumping, hopping and balance tasks). Study 3 revealed a unidimensional assessment tool with good fit to the Rasch model, and no further issues, once jumping and hopping scoring were modified. Implications The finalised version of FUNMOVES (after three iterations) meets standards for accurate measurement, is free and able to assess a whole class in under an hour using resources available in schools. Thus FUNMOVES has the potential to allow schools to efficiently screen FMS to ensure that targeted support can be provided and disability barriers removed

Automated functional classification of experimental and predicted protein structures

BACKGROUND: Proteins that are similar in sequence or structure may perform different functions in nature. In such cases, function cannot be inferred from sequence or structural similarity. RESULTS: We analyzed experimental structures belonging to the Structural Classification of Proteins (SCOP) database and showed that about half of them belong to multi-functional fold families for which protein similarity alone is not adequate to assign function. We also analyzed predicted structures from the LiveBench and the PDB-CAFASP experiments and showed that accurate homology-based functional assignments cannot be achieved approximately one third of the time, when the protein is a member of a multi-functional fold family. We then conducted extended performance evaluation and comparisons on both experimental and predicted structures using our Functional Signatures from Structural Alignments (FSSA) algorithm that we previously developed to handle the problem of classifying proteins belonging to multi-functional fold families. CONCLUSION: The results indicate that the FSSA algorithm has better accuracy when compared to homology-based approaches for functional classification of both experimental and predicted protein structures, in part due to its use of local, as opposed to global, information for classifying function. The FSSA algorithm has also been implemented as a webserver and is available at

A structural annotation resource for the selection of putative target proteins in the malaria parasite

<p>Abstract</p> <p>Background</p> <p>Protein structure plays a pivotal role in elucidating mechanisms of parasite functioning and drug resistance. Moreover, protein structure aids the determination of protein function, which can together with the structure be used to identify novel drug targets in the parasite. However, various structural features in <it>Plasmodium falciparum </it>proteins complicate the experimental determination of protein structures. Limited similarity to proteins in the Protein Data Bank and the shortage of solved protein structures in the malaria parasite necessitate genome-scale structural annotation of <it>P. falciparum </it>proteins. Additionally, the annotation of a range of structural features facilitates the identification of suitable targets for experimental and computational studies.</p> <p>Methods</p> <p>An integrated structural annotation system was developed and applied to <it>P. falciparum</it>, <it>Plasmodium vivax </it>and <it>Plasmodium yoelii</it>. The annotation included searches for sequence similarity, patterns and domains in addition to the following predictions: secondary structure, transmembrane helices, protein disorder, low complexity, coiled-coils and small molecule interactions. Subsequently, candidate proteins for further structural studies were identified based on the annotated structural features.</p> <p>Results</p> <p>The annotation results are accessible through a web interface, enabling users to select groups of proteins which fulfil multiple criteria pertaining to structural and functional features <abbrgrp><abbr bid="B1">1</abbr></abbrgrp>. Analysis of features in the <it>P. falciparum </it>proteome showed that protein-interacting proteins contained a higher percentage of predicted disordered residues than non-interacting proteins. Proteins interacting with 10 or more proteins have a disordered content concentrated in the range of 60–100%, while the disorder distribution for proteins having only one interacting partner, was more evenly spread.</p> <p>Conclusion</p> <p>A series of <it>P. falciparum </it>protein targets for experimental structure determination, comparative modelling and <it>in silico </it>docking studies were putatively identified. The system is available for public use, where researchers may identify proteins by querying with multiple physico-chemical, sequence similarity and interaction features.</p

Zoonotic disease research in East Africa

Abstract Background The East African region is endemic with multiple zoonotic diseases and is one of the hotspots for emerging infectious zoonotic diseases with reported multiple outbreaks of epidemic diseases such as Ebola, Marburg and Rift Valley Fever. Here we present a systematic assessment of published research on zoonotic diseases in the region and thesis research in Kenya to understand the regional research focus and trends in publications, and estimate proportion of theses research transitioning to peer-reviewed journal publications. Methods We searched PubMed, Google Scholar and African Journals Online databases for publications on 36 zoonotic diseases identified to have occurred in the East Africa countries of Burundi, Ethiopia, Kenya, Tanzania, Rwanda and Uganda, for the period between 1920 and 2017. We searched libraries and queried online repositories for masters and PhD theses on these diseases produced between 1970 and 2016 in five universities and two research institutions in Kenya. Results We identified 771 journal articles on 22, and 168 theses on 21 of the 36 zoonotic diseases investigated. Research on zoonotic diseases increased exponentially with the last 10 years of our study period contributing more than half of all publications 460 (60%) and theses 102 (61%) retrieved. Endemic diseases were the most studied accounting for 656 (85%) and 150 (89%) of the publication and theses studies respectively, with publications on epidemic diseases associated with outbreaks reported in the region or elsewhere. Epidemiological studies were the most common study types but limited to cross-sectional studies while socio-economics were the least studied. Only 11% of the theses research transitioned to peer-review publications, taking an average of 2.5 years from theses production to manuscript publication. Conclusion Our findings demonstrate increased attention to zoonotic diseases in East Africa but reveal the need to expand the scope, focus and quality of studies to adequately address the public health, social and economic threats posed by zoonoses

Atypical glandular cells in conventional cervical smears: Incidence and follow-up

BACKGROUND: Atypical glandular cells on cervical smears are often associated with clinically significant uterine lesions. The frequency and accuracy of AGC-NOS (i.e. atypical glandular cells, not otherwise specified) diagnoses, regardless of the gland cell type or the degree of suspicion, and their outcome were investigated. METHODS: From January 1, 1990 to December 31, 1999 a total of 261 patients had an AGC-NOS diagnosis made by conventional cervical Papanicolaou smear interpretation representing 0.05% of all Pap-smears analyzed at the national level. 191 (73.2%) patients had a subsequent histological examination, 8 samples were not representative by origin and were excluded. RESULTS: Out of 183 AGC-NOS diagnosed, 56.3% (103/183) were associated with tissue-proven precancerous and/or cancerous lesions, 44% being of endocervical and 56% of endometrial origin. 75% of all AGC-patients were asymptomatic. 66.7% (6/9) of the patients with subsequent invasive endocervical adenocarcinoma (AC) and 56% (28/50) of those patients with invasive endometrial AC were without clinical symptoms. 3 patients out of 9 with an invasive endocervical AC were 35 years of age or less. 10.1% and 12.3% of all 'new' tissue-proven invasive endocervical or endometrial AC respectively recorded by the national Morphologic Tumour Registry (MTR) were first identified by a cytological AGC-NOS diagnosis. CONCLUSION: Our findings emphasize the importance of the cytological AGC-category even in the absence of a precise origin or cell type specification. 56% of the AGC-diagnoses being associated with significant cancerous or precancerous conditions, a complete and careful evaluation is required

RSpred, a set of Hidden Markov Models to detect and classify the RIFIN and STEVOR proteins of Plasmodium falciparum

<p>Abstract</p> <p>Background</p> <p>Many parasites use multicopy protein families to avoid their host's immune system through a strategy called antigenic variation. RIFIN and STEVOR proteins are variable surface antigens uniquely found in the malaria parasites <it>Plasmodium falciparum </it>and <it>P. reichenowi</it>. Although these two protein families are different, they have more similarity to each other than to any other proteins described to date. As a result, they have been grouped together in one Pfam domain. However, a recent study has described the sub-division of the RIFIN protein family into several functionally distinct groups. These sub-groups require phylogenetic analysis to sort out, which is not practical for large-scale projects, such as the sequencing of patient isolates and meta-genomic analysis.</p> <p>Results</p> <p>We have manually curated the <it>rif </it>and <it>stevor </it>gene repertoires of two <it>Plasmodium falciparum </it>genomes, isolates DD2 and HB3. We have identified 25% of mis-annotated and ~30 missing <it>rif </it>and <it>stevor </it>genes. Using these data sets, as well as sequences from the well curated reference genome (isolate 3D7) and field isolate data from Uniprot, we have developed a tool named RSpred. The tool, based on a set of hidden Markov models and an evaluation program, automatically identifies STEVOR and RIFIN sequences as well as the sub-groups: A-RIFIN, B-RIFIN, B1-RIFIN and B2-RIFIN. In addition to these groups, we distinguish a small subset of STEVOR proteins that we named STEVOR-like, as they either differ remarkably from typical STEVOR proteins or are too fragmented to reach a high enough score. When compared to Pfam and TIGRFAMs, RSpred proves to be a more robust and more sensitive method. We have applied RSpred to the proteomes of several <it>P. falciparum </it>strains, <it>P. reichenowi, P. vivax</it>, <it>P. knowlesi </it>and the rodent malaria species. All groups were found in the <it>P. falciparum </it>strains, and also in the <it>P. reichenowi </it>parasite, whereas none were predicted in the other species.</p> <p>Conclusions</p> <p>We have generated a tool for the sorting of RIFIN and STEVOR proteins, large antigenic variant protein groups, into homogeneous sub-families. Assigning functions to such protein families requires their subdivision into meaningful groups such as we have shown for the RIFIN protein family. RSpred removes the need for complicated and time consuming phylogenetic analysis methods. It will benefit both research groups sequencing whole genomes as well as others working with field isolates. RSpred is freely accessible via <url>http://www.ifm.liu.se/bioinfo/</url>.</p

Whole genome sequencing to investigate the emergence of clonal complex 23 Neisseria meningitidis serogroup Y disease in the United States

In the United States, serogroup Y, ST-23 clonal complex Neisseria meningitidis was responsible for an increase in meningococcal disease incidence during the 1990s. This increase was accompanied by antigenic shift of three outer membrane proteins, with a decrease in the population that predominated in the early 1990s as a different population emerged later in that decade. To understand factors that may have been responsible for the emergence of serogroup Y disease, we used whole genome pyrosequencing to investigate genetic differences between isolates from early and late N. meningitidis populations, obtained from meningococcal disease cases in Maryland in the 1990s. The genomes of isolates from the early and late populations were highly similar, with 1231 of 1776 shared genes exhibiting 100% amino acid identity and an average πN = 0.0033 and average πS = 0.0216. However, differences were found in predicted proteins that affect pilin structure and antigen profile and in predicted proteins involved in iron acquisition and uptake. The observed changes are consistent with acquisition of new alleles through horizontal gene transfer. Changes in antigen profile due to the genetic differences found in this study likely allowed the late population to emerge due to escape from population immunity. These findings may predict which antigenic factors are important in the cyclic epidemiology of meningococcal disease

Species by Environment Interactions Affect Pyrrolizidine Alkaloid Expression in Senecio jacobaea, Senecio aquaticus, and Their Hybrids

We examined the effects of water and nutrient availability on the expression of the defense pyrrolizidine alkaloids (PAs) in Senecio jacobaea and S. aquaticus. Senecio jacobaea, and S. aquaticus are adapted to different natural habitats, characterized by differing abiotic conditions and different selection pressures from natural enemies. We tested if PA concentration and diversity are plastic over a range of water and nutrient treatments, and also whether such plasticity is dependent on plant species. We also tested the hypothesis that hybridization may contribute to PA diversity within plants, by comparing PA expression in parental species to that in artificially generated F1 hybrids, and also in later generation natural hybrids between S. jacobaea and S. aquaticus. We showed that total PA concentration in roots and shoots is not dependent on species, but that species determines the pattern of PA diversification. Pyrrolizidine alkaloid diversity and concentration are both dependent on environmental factors. Hybrids produce a putatively novel PA, and this PA is conserved in natural hybrids, that are backcrossed to S. jacobaea. Natural hybrids that are backcrossed several times to S. jacobaea are with regard to PA diversity significantly different from S. jacobaea but not from S. aquaticus, while F1 hybrids are in all cases more similar to S. jacobaea. These results collectively suggest that PA diversity is under the influence of natural selection