Self-Determination Theory and Professional Reasoning in Occupational Therapy Students: A Mixed Methods Study

Occupational therapy (OT) education frequently utilizes experiential learning as an effective instructional method to develop professional reasoning in OT students. However, there is little information about the development of professional reasoning. The researchers used a mixed-methods design to determine the extent to which an experiential learning course was effective in supporting professional reasoning ability with thirty-six OT students. Participants were students enrolled in an experiential learning course, which was part of their didactic graduate curriculum. Students attended an assigned setting weekly for sixteen weeks. Researchers collected data using the Self-Assessment of Clinical Reflection and Reasoning (SACRR) as well as reflective journaling. Pre-post scores on the SACRR were analyzed using repeated measures ANOVA and showed a statistically significant increase in self-perceived professional reasoning. The researchers analyzed journals from the perspective of Self-Determination Theory (SDT) using the tenets of competence, relatedness, and autonomy. Students developed professional reasoning along a continuum of competence to relatedness to autonomy. The results show that this progression does not occur in perfect stages or on a defined timeline, and provides novel insights into how the progression occurs. Occupational therapy educators can apply the results to better facilitate student development of professional reasoning. Further research could determine how to best employ SDT in OT education

PubChem3D: Shape compatibility filtering using molecular shape quadrupoles

<p>Abstract</p> <p>Background</p> <p>PubChem provides a 3-D neighboring relationship, which involves finding the maximal shape overlap between two static compound 3-D conformations, a computationally intensive step. It is highly desirable to avoid this overlap computation, especially if it can be determined with certainty that a conformer pair cannot meet the criteria to be a 3-D neighbor. As such, PubChem employs a series of pre-filters, based on the concept of volume, to remove approximately 65% of all conformer neighbor pairs prior to shape overlap optimization. Given that molecular volume, a somewhat vague concept, is rather effective, it leads one to wonder: can the existing PubChem 3-D neighboring relationship, which consists of billions of shape similar conformer pairs from tens of millions of unique small molecules, be used to identify additional shape descriptor relationships? Or, put more specifically, can one place an upper bound on shape similarity using other "fuzzy" shape-like concepts like length, width, and height?</p> <p>Results</p> <p>Using a basis set of 4.18 billion 3-D neighbor pairs identified from single conformer per compound neighboring of 17.1 million molecules, shape descriptors were computed for all conformers. These steric shape descriptors included several forms of molecular volume and shape quadrupoles, which essentially embody the length, width, and height of a conformer. For a given 3-D neighbor conformer pair, the volume and each quadrupole component (Q_x, Q_y, and Q_z) were binned and their frequency of occurrence was examined. Per molecular volume type, this effectively produced three different maps, one per quadrupole component (Q_x, Q_y, and Q_z), of allowed values for the similarity metric, shape Tanimoto (ST) ≥ 0.8.</p> <p>The efficiency of these relationships (in terms of true positive, true negative, false positive and false negative) as a function of ST threshold was determined in a test run of 13.2 billion conformer pairs not previously considered by the 3-D neighbor set. At an ST ≥ 0.8, a filtering efficiency of 40.4% of true negatives was achieved with only 32 false negatives out of 24 million true positives, when applying the separate Q_x, Q_y, and Q_zmaps in a series (Q_xyz). This efficiency increased linearly as a function of ST threshold in the range 0.8-0.99. The Q_xfilter was consistently the most efficient followed by Q_yand then by Q_z. Use of a monopole volume showed the best overall performance, followed by the self-overlap volume and then by the analytic volume.</p> <p>Application of the monopole-based Q_xyzfilter in a "real world" test of 3-D neighboring of 4,218 chemicals of biomedical interest against 26.1 million molecules in PubChem reduced the total CPU cost of neighboring by between 24-38% and, if used as the initial filter, removed from consideration 48.3% of all conformer pairs at almost negligible computational overhead.</p> <p>Conclusion</p> <p>Basic shape descriptors, such as those embodied by size, length, width, and height, can be highly effective in identifying shape incompatible compound conformer pairs. When performing a 3-D search using a shape similarity cut-off, computation can be avoided by identifying conformer pairs that cannot meet the result criteria. Applying this methodology as a filter for PubChem 3-D neighboring computation, an improvement of 31% was realized, increasing the average conformer pair throughput from 154,000 to 202,000 per second per CPU core.</p

On Reasoning with RDF Statements about Statements using Singleton Property Triples

The Singleton Property (SP) approach has been proposed for representing and querying metadata about RDF triples such as provenance, time, location, and evidence. In this approach, one singleton property is created to uniquely represent a relationship in a particular context, and in general, generates a large property hierarchy in the schema. It has become the subject of important questions from Semantic Web practitioners. Can an existing reasoner recognize the singleton property triples? And how? If the singleton property triples describe a data triple, then how can a reasoner infer this data triple from the singleton property triples? Or would the large property hierarchy affect the reasoners in some way? We address these questions in this paper and present our study about the reasoning aspects of the singleton properties. We propose a simple mechanism to enable existing reasoners to recognize the singleton property triples, as well as to infer the data triples described by the singleton property triples. We evaluate the effect of the singleton property triples in the reasoning processes by comparing the performance on RDF datasets with and without singleton properties. Our evaluation uses as benchmark the LUBM datasets and the LUBM-SP datasets derived from LUBM with temporal information added through singleton properties

The PubChem chemical structure sketcher

PubChem is an important public, Web-based information source for chemical and bioactivity information. In order to provide convenient structure search methods on compounds stored in this database, one mandatory component is a Web-based drawing tool for interactive sketching of chemical query structures. Web-enabled chemical structure sketchers are not new, being in existence for years; however, solutions available rely on complex technology like Java applets or platform-dependent plug-ins. Due to general policy and support incident rate considerations, Java-based or platform-specific sketchers cannot be deployed as a part of public NCBI Web services. Our solution: a chemical structure sketching tool based exclusively on CGI server processing, client-side JavaScript functions, and image sequence streaming. The PubChem structure editor does not require the presence of any specific runtime support libraries or browser configurations on the client. It is completely platform-independent and verified to work on all major Web browsers, including older ones without support for Web2.0 JavaScript objects

Reaction Data in PubChem

A presentation at the enviPathPlus workshop (held online) on "Reaction Data in PubChem". Presented by E. Schymanski on behalf of all authors. See slides for details and many hyperlinks - thanks to Kathrin Fenner for the opportunity

New records of ant species from Yunnan, China

published_or_final_versio

Complete Genome Sequence of Clostridium estertheticum DSM 8809, a Microbe Identified in Spoiled Vacuum Packed Beef

peer-reviewedBlown pack spoilage (BPS) is a major issue for the beef industry. Etiological agents of BPS involve members of a group of Clostridium species, including Clostridium estertheticum which has the ability to produce gas, mostly carbon dioxide, under anaerobic psychotrophic growth conditions. This spore-forming bacterium grows slowly under laboratory conditions, and it can take up to 3 months to produce a workable culture. These characteristics have limited the study of this commercially challenging bacterium. Consequently information on this bacterium is limited and no effective controls are currently available to confidently detect and manage this production risk. In this study the complete genome of C. estertheticum DSM 8809 was determined by SMRT® sequencing. The genome consists of a circular chromosome of 4.7 Mbp along with a single plasmid carrying a potential tellurite resistance gene tehB and a Tn3-like resolvase-encoding gene tnpR. The genome sequence was searched for central metabolic pathways that would support its biochemical profile and several enzymes contributing to this phenotype were identified. Several putative antibiotic/biocide/metal resistance-encoding genes and virulence factors were also identified in the genome, a feature that requires further research. The availability of the genome sequence will provide a basic blueprint from which to develop valuable biomarkers that could support and improve the detection and control of this bacterium along the beef production chain

PubChem3D: Diversity of shape

<p>Abstract</p> <p>Background</p> <p>The shape diversity of 16.4 million biologically relevant molecules from the PubChem Compound database and their 1.46 billion diverse conformers was explored as a function of molecular volume.</p> <p>Results</p> <p>The diversity of shape space was investigated by determining the shape similarity threshold to achieve a maximum on the count of reference shapes per unit of conformer volume. The rate of growth in shape space, as represented by a decreasing shape similarity threshold, was found to be remarkably smooth as a function of volume. There was no apparent correlation between the count of conformers per unit volume and their diversity, meaning that a single reference shape can describe the shape space of many chemical structures. The ability of a volume to describe the shape space of lesser volumes was also examined. It was shown that a given volume was able to describe 40-70% of the shape diversity of lesser volumes, for the majority of the volume range considered in this study.</p> <p>Conclusion</p> <p>The relative growth of shape diversity as a function of volume and shape similarity is surprisingly uniform. Given the distribution of chemicals in PubChem versus what is theoretically synthetically possible, the results from this analysis should be considered a conservative estimate to the true diversity of shape space.</p

PubChem3D: Similar conformers

<p>Abstract</p> <p>Background</p> <p>PubChem is a free and open public resource for the biological activities of small molecules. With many tens of millions of both chemical structures and biological test results, PubChem is a sizeable system with an uneven degree of available information. Some chemical structures in PubChem include a great deal of biological annotation, while others have little to none. To help users, PubChem pre-computes "neighboring" relationships to relate similar chemical structures, which may have similar biological function. In this work, we introduce a "Similar Conformers" neighboring relationship to identify compounds with similar 3-D shape and similar 3-D orientation of functional groups typically used to define pharmacophore features.</p> <p>Results</p> <p>The first two diverse 3-D conformers of 26.1 million PubChem Compound records were compared to each other, using a shape Tanimoto (ST) of 0.8 or greater and a color Tanimoto (CT) of 0.5 or greater, yielding 8.16 billion conformer neighbor pairs and 6.62 billion compound neighbor pairs, with an average of 253 "Similar Conformers" compound neighbors per compound. Comparing the 3-D neighboring relationship to the corresponding 2-D neighboring relationship ("Similar Compounds") for molecules such as caffeine, aspirin, and morphine, one finds unique sets of related chemical structures, providing additional significant biological annotation. The PubChem 3-D neighboring relationship is also shown to be able to group a set of non-steroidal anti-inflammatory drugs (NSAIDs), despite limited PubChem 2-D similarity.</p> <p>In a study of 4,218 chemical structures of biomedical interest, consisting of many known drugs, using more diverse conformers per compound results in more 3-D compound neighbors per compound; however, the overlap of the compound neighbor lists per conformer also increasingly resemble each other, being 38% identical at three conformers and 68% at ten conformers. Perhaps surprising is that the average count of conformer neighbors per conformer increases rather slowly as a function of diverse conformers considered, with only a 70% increase for a ten times growth in conformers per compound (a 68-fold increase in the conformer pairs considered).</p> <p>Neighboring 3-D conformers on the scale performed, if implemented naively, is an intractable problem using a modest sized compute cluster. Methodology developed in this work relies on a series of filters to prevent performing 3-D superposition optimization, when it can be determined that two conformers cannot possibly be a neighbor. Most filters are based on Tanimoto equation volume constraints, avoiding incompatible conformers; however, others consider preliminary superposition between conformers using reference shapes.</p> <p>Conclusion</p> <p>The "Similar Conformers" 3-D neighboring relationship locates similar small molecules of biological interest that may go unnoticed when using traditional 2-D chemical structure graph-based methods, making it complementary to such methodologies. The computational cost of 3-D similarity methodology on a wide scale, such as PubChem contents, is a considerable issue to overcome. Using a series of efficient filters, an effective throughput rate of more than 150,000 conformers per second per processor core was achieved, more than two orders of magnitude faster than without filtering.</p