The Classroom Observation Schedule to Measure Intentional Communication (COSMIC): An observational measure of the intentional communication of children with autism in an unstructured classroom setting

The Classroom Observation Schedule to Measure Intentional Communication (COSMIC) was devised to provide ecologically valid outcome measures for a communication-focused intervention trial. Ninety-one children with autism spectrum disorder aged 6 years 10 months (SD 16 months) were videoed during their everyday snack, teaching and free play activities. Inter-rater reliability was high and relevant items showed significant associations with comparable items from concurrent Autism Diagnostic Observation Schedule – Generic (Lord et al., 2000) assessments. In a subsample of 28 children initial differences in rates of initiations, initiated speech/vocalisation and commenting were predictive of language and communication competence 15 months later. Results suggest that the use of observational measures of intentional communication in natural settings is a valuable assessment strategy for research and clinical practice

Machine speed scaling by adapting methods for convex optimization with submodular constraints

In this paper, we propose a new methodology for the speed-scaling problem based on its link to scheduling with controllable processing times and submodular optimization. It results in faster algorithms for traditional speed-scaling models, characterized by a common speed/energy function. Additionally, it efficiently handles the most general models with job-dependent speed/energy functions with single and multiple machines. To the best of our knowledge, this has not been addressed prior to this study. In particular, the general version of the single-machine case is solvable by the new technique in O(n2) time

Spectroscopic analysis of finite size effects around a Kondo quantum dot

We consider a simple setup in which a small quantum dot is strongly connected to a finite size box. This box can be either a metallic box or a finite size quantum wire.The formation of the Kondo screening cloud in the box strongly depends on the ratio between the Kondo temperature and the box level spacing. By weakly connecting two metallic reservoirs to the quantum dot, a detailed spectroscopic analysis can be performed. Since the transport channels and the screening channels are almost decoupled, such a setup allows an easier access to the measure of finite-size effects associated with the finite extension of the Kondo cloud.Comment: contribution to Les Houches proceeding, ``Quantum magnetism'' 200

Arm rotated medially with supination – the ARMS variant: description of its surgical correction

<p>Abstract</p> <p>Background</p> <p>Patients who have suffered obstetric brachial plexus injury (OBPI) have a high incidence of musculoskeletal complications stemming from the initial nerve injury. The presence of muscle imbalances and contractures leads to typical bony changes affecting the shoulder, including the SHEAR (Scapular Hypoplasia, Elevation and Rotation) deformity. The SHEAR deformity commonly occurs in conjunction with Medial Rotation Contracture (MRC) of the arm. OBPI also causes muscle imbalances at the level of the forearm, that lead to a fixed supination deformity (SD) in a small number of patients. Both MRC and SD will cause severe functional limitations without surgical intervention.</p> <p>Methods</p> <p>Fourteen OBPI patients were diagnosed with MRC of the shoulder and SD of the forearm along with SHEAR deformity during a 16 month study period, with eight patients available to long-term follow-up (age range 2.2 – 18 years). Surgical correction of the MRC was performed as a triangle tilt or humeral osteotomy depending on the age of the child, after which, the patients were treated with a radial osteotomy to correct the fixed supination deformity. Function was assessed using the modified Mallet scale, examination of apparent supination and appearance of the extremity at rest.</p> <p>Results</p> <p>Significant functional improvements were observed in patients with surgical reconstruction. Mallet score increased by an average of 5.2 (p < 0.05). Overall forearm position was not significantly changed from an average of 5° to an average of 34° maximum apparent supination after both shoulder rotation and forearm rotation corrective surgeries.</p> <p>Conclusion</p> <p>The simultaneous presence of two opposing deformities in the same limb will visually offset each other at the level of the wrist and hand, giving the false impression of neutral positioning of the limb. In reality, the neutral-appearing position of the hand indicates a fixed supination posture of the forearm in the face of a medial rotation contracture of the shoulder. Both of these deformities require surgical attention, and the presence of concurrent MRC and SD should be monitored for in OBPI patients.</p

MKEM: a Multi-level Knowledge Emergence Model for mining undiscovered public knowledge

<p>Abstract</p> <p>Background</p> <p>Since Swanson proposed the Undiscovered Public Knowledge (UPK) model, there have been many approaches to uncover UPK by mining the biomedical literature. These earlier works, however, required substantial manual intervention to reduce the number of possible connections and are mainly applied to disease-effect relation. With the advancement in biomedical science, it has become imperative to extract and combine information from multiple disjoint researches, studies and articles to infer new hypotheses and expand knowledge.</p> <p>Methods</p> <p>We propose MKEM, a Multi-level Knowledge Emergence Model, to discover implicit relationships using Natural Language Processing techniques such as Link Grammar and Ontologies such as Unified Medical Language System (UMLS) MetaMap. The contribution of MKEM is as follows: First, we propose a flexible knowledge emergence model to extract implicit relationships across different levels such as molecular level for gene and protein and Phenomic level for disease and treatment. Second, we employ MetaMap for tagging biological concepts. Third, we provide an empirical and systematic approach to discover novel relationships.</p> <p>Results</p> <p>We applied our system on 5000 abstracts downloaded from PubMed database. We performed the performance evaluation as a gold standard is not yet available. Our system performed with a good precision and recall and we generated 24 hypotheses.</p> <p>Conclusions</p> <p>Our experiments show that MKEM is a powerful tool to discover hidden relationships residing in extracted entities that were represented by our Substance-Effect-Process-Disease-Body Part (SEPDB) model. </p

Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe

Shigella are human-adapted Escherichia coli that have gained the ability to invade the human gut mucosa and cause dysentery1,2, spreading efficiently via low-dose fecal-oral transmission3,4. Historically, S. sonnei has been predominantly responsible for dysentery in developed countries, but is now emerging as a problem in the developing world, apparently replacing the more diverse S. flexneri in areas undergoing economic development and improvements in water quality4-6. Classical approaches have shown S. sonnei is genetically conserved and clonal7. We report here whole-genome sequencing of 132 globally-distributed isolates. Our phylogenetic analysis shows that the current S. sonnei population descends from a common ancestor that existed less than 500 years ago and has diversified into several distinct lineages with unique characteristics. Our analysis suggests the majority of this diversification occurred in Europe, followed by more recent establishment of local pathogen populations in other continents predominantly due to the pandemic spread of a single, rapidly-evolving, multidrug resistant lineage

“Excellence R Us”: university research and the fetishisation of excellence

The rhetoric of “excellence” is pervasive across the academy. It is used to refer to research outputs as well as researchers, theory and education, individuals and organisations, from art history to zoology. But does “excellence” actually mean anything? Does this pervasive narrative of “excellence” do any good? Drawing on a range of sources we interrogate “excellence” as a concept and find that it has no intrinsic meaning in academia. Rather it functions as a linguistic interchange mechanism. To investigate whether this linguistic function is useful we examine how the rhetoric of excellence combines with narratives of scarcity and competition to show that the hypercompetition that arises from the performance of “excellence” is completely at odds with the qualities of good research. We trace the roots of issues in reproducibility, fraud, and homophily to this rhetoric. But we also show that this rhetoric is an internal, and not primarily an external, imposition. We conclude by proposing an alternative rhetoric based on soundness and capacity-building. In the final analysis, it turns out that that “excellence” is not excellent. Used in its current unqualified form it is a pernicious and dangerous rhetoric that undermines the very foundations of good research and scholarship

The IGF1 small dog haplotype is derived from Middle Eastern grey wolves

<p>Abstract</p> <p>Background</p> <p>A selective sweep containing the insulin-like growth factor 1 (<it>IGF1</it>) gene is associated with size variation in domestic dogs. Intron 2 of <it>IGF1 </it>contains a SINE element and single nucleotide polymorphism (SNP) found in all small dog breeds that is almost entirely absent from large breeds. In this study, we surveyed a large sample of grey wolf populations to better understand the ancestral pattern of variation at <it>IGF1 </it>with a particular focus on the distribution of the small dog haplotype and its relationship to the origin of the dog.</p> <p>Results</p> <p>We present DNA sequence data that confirms the absence of the derived small SNP allele in the intron 2 region of <it>IGF1 </it>in a large sample of grey wolves and further establishes the absence of a small dog associated SINE element in all wild canids and most large dog breeds. Grey wolf haplotypes from the Middle East have higher nucleotide diversity suggesting an origin there. Additionally, PCA and phylogenetic analyses suggests a closer kinship of the small domestic dog <it>IGF1 </it>haplotype with those from Middle Eastern grey wolves.</p> <p>Conclusions</p> <p>The absence of both the SINE element and SNP allele in grey wolves suggests that the mutation for small body size post-dates the domestication of dogs. However, because all small dogs possess these diagnostic mutations, the mutations likely arose early in the history of domestic dogs. Our results show that the small dog haplotype is closely related to those in Middle Eastern wolves and is consistent with an ancient origin of the small dog haplotype there. Thus, in concordance with past archeological studies, our molecular analysis is consistent with the early evolution of small size in dogs from the Middle East.</p> <p>See associated opinion by Driscoll and Macdonald: <url>http://jbiol.com/content/9/2/10</url></p

Diets containing sea cucumber (Isostichopus badionotus) meals are hypocholesterolemic in young rats

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