A cost-effective strategy for nonoscillatory convection without clipping

Clipping of narrow extrema and distortion of smooth profiles is a well known problem associated with so-called high resolution nonoscillatory convection schemes. A strategy is presented for accurately simulating highly convective flows containing discontinuities such as density fronts or shock waves, without distorting smooth profiles or clipping narrow local extrema. The convection algorithm is based on non-artificially diffusive third-order upwinding in smooth regions, with automatic adaptive stencil expansion to (in principle, arbitrarily) higher order upwinding locally, in regions of rapidly changing gradients. This is highly cost effective because the wider stencil is used only where needed-in isolated narrow regions. A recently developed universal limiter assures sharp monotonic resolution of discontinuities without introducing artificial diffusion or numerical compression. An adaptive discriminator is constructed to distinguish between spurious overshoots and physical peaks; this automatically relaxes the limiter near local turning points, thereby avoiding loss of resolution in narrow extrema. Examples are given for one-dimensional pure convection of scalar profiles at constant velocity

Coordinating Tissue Regeneration Through Transforming Growth Factorâ β Activated Kinase 1 Inactivation and Reactivation

Aberrant wound healing presents as inappropriate or insufficient tissue formation. Using a model of musculoskeletal injury, we demonstrate that loss of transforming growth factorâ β activated kinase 1 (TAK1) signaling reduces inappropriate tissue formation (heterotopic ossification) through reduced cellular differentiation. Upon identifying increased proliferation with loss of TAK1 signaling, we considered a regenerative approach to address insufficient tissue production through coordinated inactivation of TAK1 to promote cellular proliferation, followed by reactivation to elicit differentiation and extracellular matrix production. Although the current regenerative medicine paradigm is centered on the effects of drug treatment (â drug onâ ), the impact of drug withdrawal (â drug offâ ) implicit in these regimens is unknown. Because current TAK1 inhibitors are unable to phenocopy genetic Tak1 loss, we introduce the dualâ inducible COmbinational Sequential Inversion ENgineering (COSIEN) mouse model. The COSIEN mouse model, which allows us to study the response to targeted drug treatment (â drug onâ ) and subsequent withdrawal (â drug offâ ) through genetic modification, was used here to inactivate and reactivate Tak1 with the purpose of augmenting tissue regeneration in a calvarial defect model. Our study reveals the importance of both the â drug onâ (Creâ mediated inactivation) and â drug offâ (Flpâ mediated reactivation) states during regenerative therapy using a mouse model with broad utility to study targeted therapies for disease. Stem Cells 2019;37:766â 778Manipulating transforming growth factor βâ activated kinase 1 for cell and scaffold free tissue regeneration using a dualâ inducible Combinational Sequential Inversion Engineering mouse model.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/149573/1/stem2991_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149573/2/stem2991.pd

Genomic characterization of malignant progression in neoplastic pancreatic cysts

Intraductal papillary mucinous neoplasms (IPMNs) and mucinous cystic neoplasms (MCNs) are non-invasive neoplasms that are often observed in association with invasive pancreatic cancers, but their origins and evolutionary relationships are poorly understood. In this study, we analyze 148 samples from IPMNs, MCNs, and small associated invasive carcinomas from 18 patients using whole exome or targeted sequencing. Using evolutionary analyses, we establish that both IPMNs and MCNs are direct precursors to pancreatic cancer. Mutations in SMAD4 and TGFBR2 are frequently restricted to invasive carcinoma, while RNF43 alterations are largely in non-invasive lesions. Genomic analyses suggest an average window of over three years between the development of high-grade dysplasia and pancreatic cancer. Taken together, these data establish non-invasive IPMNs and MCNs as origins of invasive pancreatic cancer, identifying potential drivers of invasion, highlighting the complex clonal dynamics prior to malignant transformation, and providing opportunities for early detection and intervention

Mapping genetic variations to three- dimensional protein structures to enhance variant interpretation: a proposed framework

The translation of personal genomics to precision medicine depends on the accurate interpretation of the multitude of genetic variants observed for each individual. However, even when genetic variants are predicted to modify a protein, their functional implications may be unclear. Many diseases are caused by genetic variants affecting important protein features, such as enzyme active sites or interaction interfaces. The scientific community has catalogued millions of genetic variants in genomic databases and thousands of protein structures in the Protein Data Bank. Mapping mutations onto three-dimensional (3D) structures enables atomic-level analyses of protein positions that may be important for the stability or formation of interactions; these may explain the effect of mutations and in some cases even open a path for targeted drug development. To accelerate progress in the integration of these data types, we held a two-day Gene Variation to 3D (GVto3D) workshop to report on the latest advances and to discuss unmet needs. The overarching goal of the workshop was to address the question: what can be done together as a community to advance the integration of genetic variants and 3D protein structures that could not be done by a single investigator or laboratory? Here we describe the workshop outcomes, review the state of the field, and propose the development of a framework with which to promote progress in this arena. The framework will include a set of standard formats, common ontologies, a common application programming interface to enable interoperation of the resources, and a Tool Registry to make it easy to find and apply the tools to specific analysis problems. Interoperability will enable integration of diverse data sources and tools and collaborative development of variant effect prediction methods

Applying accreditation standards in a self-evaluation process: The experience of Educational Development Center of Tehran University of Medical Sciences

Introduction: Educational Development Centers (EDCs), as the coordinator in education development in Medical Sciences universities, in order to improve their quality should evaluate their activities. In spite of remarkable performance of Tehran University of Medical Sciences (TUMS) EDC in previous national rankings, but it faces many challenges and problems. This paper provided the process, results and lessons learned from a self-evaluation experience conducted at TUMS EDC based on accreditation standards. Method: The present study is an Institutional self-evaluation study based on the national accreditation standards of EDCs (2012). Data were gathered using an open-ended questionnaire developed on the basis of the SWOT format. A directional content analysis applied to analyze the data. Results: In total, 84 point of strengths, 87 weaknesses, 15 opportunities, 24 threats and also 99 recommendations for quality improvement were reported. The most important strengths of the center were the existence of an established mechanism regarding research process in education and scholarship of education, holding various faculty development courses and training standardized patient. The most important weaknesses were the lack of specified procedures in some areas such as monitoring the planning and reviewing of educational programs in the field of educational programs and evaluation of empowerment courses. Conclusion: The present evaluation results will be useful in directing future policies of TUMS EDC such as revising its strategic planning. We hope that the current experience can be helpful for administrators in EDCs in the Ministry of Health and Medical Education and also other Medical Sciences Universities

Evaluation of T helper17 as skeletal homeostasis factor in peripheral blood mononuclear cells and T helper cells of end-stage renal disease cases with impaired parathyroid hormone

Background Chronic renal failure is mainly connected with high and low parathyroid hormone (PTH) levels and immunological impairments. The present study aimed to evaluate T helper 17 (Th17) cells as a crucial modulator of the immune system and skeletal homeostasis in hemodialysis patients with impaired intact PTH (iPTH).Methods In this research, blood samples were taken from ESRD patients with high (> 300 pg/mL), normal (150-300 pg/mL), and low (< 150 pg/mL) serum intact parathyroid hormone (iPTH( levels (n = 30 in each group). The frequency of Th17 (CD4(+) IL17(+)) cells was evaluated by flow cytometry in each group. The expression levels of Th17 cell-related master transcription factors, cytokines in peripheral blood mononuclear cells (PBMC), and Th cells, and the level of the mentioned cytokines were determined in the supernatant of PBMCs.Results The number of Th17 cells remarkably increased in subjects with high iPTH against low and normal iPTH. Also, ROR?t and STAT3 levels were significantly higher in high iPTH ESRD patients than in other groups in the expression of mRNA and protein levels. These findings are confirmed by evaluating the IL-17 and IL-23 in the supernatant of cultured PBMCs and isolated Th cells.Conclusion Our findings indicated that increased serum PTH levels in hemodialysis cases may be involved in increasing the differentiation of CD4 + cells to Th17 cells in PBMC