The DIY Data Collecting Computer Project: Integrating the Scholarship of Teaching and Learning and Scholarship of Community Engagement

This poster highlights an innovative STEM project focused on two goals: (1) reducing the cost of computer-based measuring devices, and (2) the implementation of these devices in middle school classrooms. The first phase of the project -- creating the DIY Data Collecting Computer -- was a collaborative effort between computer science and science teacher education faculty and their students. Single-board computers, including the Raspberry Pi and Arduino Uno, were used as the basis for the data collecting computer. In the second phase, the university team worked with middle school teachers and administrators to implement a multi-day unit in which eighth grade students built the computer in a technology elective class. Once created, these computers were used by the students as measuring devices in their physical science class. Multi-level collaborative effort was involved throughout, with cross-departmental university collaboration, university and middle school collaboration, and finally, cross-subject middle school collaboration

Multiversion Concurrency with Bounded Delay and Precise Garbage Collection

In this paper we are interested in bounding the number of instructions taken to process transactions. The main result is a multiversion transactional system that supports constant delay (extra instructions beyond running in isolation) for all read-only transactions, delay equal to the number of processes for writing transactions that are not concurrent with other writers, and lock-freedom for concurrent writers. The system supports precise garbage collection in that versions are identified for collection as soon as the last transaction releases them. As far as we know these are first results that bound delays for multiple readers and even a single writer. The approach is particularly useful in situations where read-transactions dominate write transactions, or where write transactions come in as streams or batches and can be processed by a single writer (possibly in parallel). The approach is based on using functional data structures to support multiple versions, and an efficient solution to the Version Maintenance (VM) problem for acquiring, updating and releasing versions. Our solution to the VM problem is precise, safe and wait-free (PSWF). We experimentally validate our approach by applying it to balanced tree data structures for maintaining ordered maps. We test the transactional system using multiple algorithms for the VM problem, including our PSWF VM algorithm, and implementations with weaker guarantees based on epochs, hazard pointers, and read-copy-update. To evaluate the functional data structure for concurrency and multi-versioning, we implement batched updates for functional tree structures and compare the performance with state-of-the-art concurrent data structures for balanced trees. The experiments indicate our approach works well in practice over a broad set of criteria

Decision-making among experts in advanced Hodgkin Lymphoma.

BACKGROUND In the treatment of advanced Hodgkin Lymphoma (aHL), based on guidelines a multitude of treatment options are available. The availability of PET guided decision-making and new therapeutic agents increase the complexity of the decision-making process. METHODS Thirteen experts of Swiss university and cantonal hospitals in Switzerland were asked to describe their institutional decision-making practice in aHL. Variables influencing the decision-making process were identified, standardized and converted into decision trees for analysis of consent and discrepancies. The algorithms of all participating experts were analyzed with the objective consensus methodology. RESULTS Four decision criteria (age, fertility preservation, fitness, interim PET) and 12 unique treatment regimens were identified. Consensus for the treatment of aHL for young and fit, as well as for older patients without comorbidity was found. Large heterogeneity was identified with use of a variety of different regimens for unfit patients with aHL and for young female patients with a desire of fertility preservation. CONCLUSION Four major decision criteria were identified allowing the representation of expert's approach to first-line treatment of aHL. Among Swiss experts, consensus for a PET guided curative treatment of aHL was identified. The use of a multitude of treatment regimens was observed for older and comorbid (unfit) aHL patients, highlighting the need for clinical trials and recommendations for this group of patients

Inhibition of lipid oxidation increases glucose metabolism and enhances 2-deoxy-2-[¹⁸F]fluoro-D-glucose uptake in prostate cancer mouse xenografts

Includes bibliographic references.PURPOSE: Prostate cancer (PCa) is the second most common cause of cancer-related death among men in the United States. Due to the lipid-driven metabolic phenotype of Pca, imaging with 2-deoxy-2-[¹⁸F]fluoro-D-glucose ([¹⁸F]FDG) is suboptimal, since tumors tend to have low avidity for glucose. PROCEDURES: We have used the fat oxidation inhibitor etomoxir (2-[6-(4-chlorophenoxy)-hexyl]oxirane-2-carboxylate) that targets carnitine-palmitoyl-transferase-1 (CPT-1) to increase glucose uptake in PCa cell lines. Small hairpin RNA specific for CPT1A was used to confirm the glycolytic switch induced by etomoxir in vitro. Systemic etomoxir treatment was used to enhance [¹⁸F]FDG-positron emission tomography ([¹⁸F]FDG-PET) imaging in PCa xenograft mouse models in 24 h. RESULTS: PCa cells significantly oxidize more of circulating fatty acids than benign cells via CPT-1 enzyme, and blocking this lipid oxidation resulted in activation of the Warburg effect and enhanced [¹⁸F]FDG signal in PCa mouse models. CONCLUSIONS: Inhibition of lipid oxidation plays a major role in elevating glucose metabolism of PCa cells, with potential for imaging enhancement that could also be extended to other cancers

Aberrant phase separation and nucleolar dysfunction in rare genetic diseases

Thousands of genetic variants in protein-coding genes have been linked to disease. However, the functional impact of most variants is unknown as they occur within intrinsically disordered protein regions that have poorly defined functions1-3. Intrinsically disordered regions can mediate phase separation and the formation of biomolecular condensates, such as the nucleolus4,5. This suggests that mutations in disordered proteins may alter condensate properties and function6-8. Here we show that a subset of disease-associated variants in disordered regions alter phase separation, cause mispartitioning into the nucleolus and disrupt nucleolar function. We discover de novo frameshift variants in HMGB1 that cause brachyphalangy, polydactyly and tibial aplasia syndrome, a rare complex malformation syndrome. The frameshifts replace the intrinsically disordered acidic tail of HMGB1 with an arginine-rich basic tail. The mutant tail alters HMGB1 phase separation, enhances its partitioning into the nucleolus and causes nucleolar dysfunction. We built a catalogue of more than 200,000 variants in disordered carboxy-terminal tails and identified more than 600 frameshifts that create arginine-rich basic tails in transcription factors and other proteins. For 12 out of the 13 disease-associated variants tested, the mutation enhanced partitioning into the nucleolus, and several variants altered rRNA biogenesis. These data identify the cause of a rare complex syndrome and suggest that a large number of genetic variants may dysregulate nucleoli and other biomolecular condensates in humans.© 2023. The Author(s)

Deconstructive Aporias: Quasi-Transcendental and Normative

This paper argues that Derrida’s aporetic conclusions regarding moral and political concepts, from hospitality to democracy, can only be understood and accepted if the notion of différance and similar infrastructures are taken into account. This is because it is the infrastructures that expose and commit moral and political practices to a double and conflictual (thus aporetic) future: the conditional future that projects horizonal limits and conditions upon the relation to others, and the unconditional future without horizons of anticipation. The argument thus turns against two kinds of interpretation: the first accepts normative unconditionality in ethics but misses its support by the infrastructures. The second rejects unconditionality as a normative commitment precisely because the infrastructural support for unconditionality seems to rule out that it is normatively required. In conclusion, the article thus reconsiders the relation between a quasi-transcendental argument and its normative implications, suggesting that Derrida avoids the naturalistic fallacy

The Gene Ontology in 2010: extensions and refinements

The Gene Ontology (GO) Consortium (http://www.geneontology.org) (GOC) continues to develop, maintain and use a set of structured, controlled vocabularies for the annotation of genes, gene products and sequences. The GO ontologies are expanding both in content and in structure. Several new relationship types have been introduced and used, along with existing relationships, to create links between and within the GO domains. These improve the representation of biology, facilitate querying, and allow GO developers to systematically check for and correct inconsistencies within the GO. Gene product annotation using GO continues to increase both in the number of total annotations and in species coverage. GO tools, such as OBO-Edit, an ontology-editing tool, and AmiGO, the GOC ontology browser, have seen major improvements in functionality, speed and ease of use.This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by Oxford University Press. The published article can be found at: http://nar.oxfordjournals.org/