Reducing Reparameterization Gradient Variance

Optimization with noisy gradients has become ubiquitous in statistics and machine learning. Reparameterization gradients, or gradient estimates computed via the "reparameterization trick," represent a class of noisy gradients often used in Monte Carlo variational inference (MCVI). However, when these gradient estimators are too noisy, the optimization procedure can be slow or fail to converge. One way to reduce noise is to use more samples for the gradient estimate, but this can be computationally expensive. Instead, we view the noisy gradient as a random variable, and form an inexpensive approximation of the generating procedure for the gradient sample. This approximation has high correlation with the noisy gradient by construction, making it a useful control variate for variance reduction. We demonstrate our approach on non-conjugate multi-level hierarchical models and a Bayesian neural net where we observed gradient variance reductions of multiple orders of magnitude (20-2,000x)

High Pressure Insulator-Metal Transition in Molecular Fluid Oxygen

We report the first experimental evidence for a metallic phase in fluid molecular oxygen. Our electrical conductivity measurements of fluid oxygen under dynamic quasi-isentropic compression show that a non-metal/metal transition occurs at 3.4 fold compression, 4500 K and 1.2 Mbar. We discuss the main features of the electrical conductivity dependence on density and temperature and give an interpretation of the nature of the electrical transport mechanisms in fluid oxygen at these extreme conditions.Comment: RevTeX, 4 figure

The Transcription Factor Rfx3 Regulates β-Cell Differentiation, Function, and Glucokinase Expression

OBJECTIVE: Pancreatic islets of perinatal mice lacking the transcription factor Rfx3 exhibit a marked reduction in insulin-producing beta-cells. The objective of this work was to unravel the cellular and molecular mechanisms underlying this deficiency. RESEARCH DESIGN AND METHODS: Immunofluorescence studies and quantitative RT-PCR experiments were used to study the emergence of insulin-positive cells, the expression of transcription factors implicated in the differentiation of beta-cells from endocrine progenitors, and the expression of mature beta-cell markers during development in Rfx3(-/-) and pancreas-specific Rfx3-knockout mice. RNA interference experiments were performed to document the consequences of downregulating Rfx3 expression in Min6 beta-cells. Quantitative chromatin immunoprecipitation (ChIP), ChIP sequencing, and bandshift experiments were used to identify Rfx3 target genes. RESULTS: Reduced development of insulin-positive cells in Rfx3(-/-) mice was not due to deficiencies in endocrine progenitors or beta-lineage specification, but reflected the accumulation of insulin-positive beta-cell precursors and defective beta-cells exhibiting reduced insulin, Glut-2, and Gck expression. Similar incompletely differentiated beta-cells developed in pancreas-specific Rfx3-deficient embryos. Defective beta-cells lacking Glut-2 and Gck expression dominate in Rfx3-deficent adults, leading to glucose intolerance. Attenuated Glut-2 and glucokinase expression, and impaired glucose-stimulated insulin secretion, were also induced by RNA interference-mediated inhibition of Rfx3 expression in Min6 cells. Finally, Rfx3 was found to bind in Min6 cells and human islets to two well-known regulatory sequences, Pal-1 and Pal-2, in the neuroendocrine promoter of the glucokinase gene. CONCLUSIONS: Our results show that Rfx3 is required for the differentiation and function of mature beta-cells and regulates the beta-cell promoter of the glucokinase gene

MARIS: Method for Analyzing RNA following Intracellular Sorting

Transcriptional profiling is a key technique in the study of cell biology that is limited by the availability of reagents to uniquely identify specific cell types and isolate high quality RNA from them. We report a Method for Analyzing RNA following Intracellular Sorting (MARIS) that generates high quality RNA for transcriptome profiling following cellular fixation, intracellular immunofluorescent staining and FACS. MARIS can therefore be used to isolate high quality RNA from many otherwise inaccessible cell types simply based on immunofluorescent tagging of unique intracellular proteins. As proof of principle, we isolate RNA from sorted human embryonic stem cell-derived insulin-expressing cells as well as adult human β cells. MARIS is a basic molecular biology technique that could be used across several biological disciplines.Howard Hughes Medical InstituteHarvard Stem Cell InstituteNational Institutes of Health (U.S.) (grant 2U01DK07247307)National Institutes of Health (U.S.) (grant RL1DK081184)National Institutes of Health (U.S.) (grant 1U01HL10040804

A conceptual framework for interprofessional shared decision making in home care: Protocol for a feasibility study

<p>Abstract</p> <p>Background</p> <p>Shared decision making (SDM) is fundamental to informed consent and client-centered care. So far, SDM frameworks have been limited to the client-physician dyad, even though care is increasingly delivered by interprofessional (IP) teams. IP collaboration is especially essential in home care, one of health care's most rapidly growing areas. This study will assess whether it is possible to practice SDM in IP home care.</p> <p>Methods/Design</p> <p>We will use a qualitative case study and a quantitative survey to capture the macro, meso and micro levels of stakeholders in home care. The case study will follow the knowledge-to-action process framework to evaluate the work of an IP home care team at a Quebec City health center. Sources of data will include one-on-one interviews with patients, family caregivers or surrogates and significant others, and administrators; a focus group of home care health professionals; organizational documents; and government policies and standards. The interview guide for the interviews and the focus group will explore current practices and clinical problems addressed in home care; factors that could influence the implementation of the proposed IP approach to SDM; the face and content validity of the approach; and interventions to facilitate the implementation and evaluation of the approach. The survey will ask 300 health professionals working in home care at the health center to complete a questionnaire based on the Theory of Planned Behaviour that measures their intentions to engage in an IP approach to SDM. We will use our analysis of the individual interviews, the focus group and the survey to elaborate a toolkit for implementing an IP approach to SDM in home care. Finally, we will conduct a pilot study in Alberta to assess the transferability of our findings.</p> <p>Discussion</p> <p>We believe that developing tools to implement IP SDM in home care is essential to strengthening Canada's healthcare system and furthering patient-centered care. This study will contribute to the evaluation of IP SDM delivery models in home care. It will also generate practical, policy-oriented knowledge regarding the barriers and facilitators likely to influence the practice of IP SDM in home care.</p

Interprofessional education through shadowing experiences in multi-disciplinary clinical settings

The World Health Organization has recently added Interprofessional Education (IPE) to its global health agenda recognizing it as a necessary component of all health professionals' education. We suggest mandatory interprofessional shadowing experiences as a mechanism to be used by chiropractic institutions to address this agenda. IPE initiatives of other professions (pharmacy and medicine) are described along with chiropractic. This relative comparison of professions local to our jurisdiction in Ontario, Canada is made so that the chiropractic profession may take note that they are behind other health care providers in implementing IPE

High efficient differentiation of functional hepatocytes from porcine induced pluripotent stem cells

Hepatocyte transplantation is considered to be a promising therapy for patients with liver diseases. Induced pluripotent stem cells (iPSCs) provide an unlimited source for the generation of functional hepatocytes. In this study, we generated iPSCs from porcine ear fibroblasts (PEFs) by overexpressing Sox2, Klf4, Oct4, and c-Myc (SKOM), and developed a novel strategy for the efficient differentiation of hepatocyte-like cells from porcine iPSCs by following the processes of early liver development. The differentiated cells displayed the phenotypes of hepatocytes, exhibited classic hepatocyte-associated bio-functions, such as LDL uptake, glycogen storage and urea secretion, as well as possessed the metabolic activities of cytochrome P-450 (CYP) 3A and 2C. Furthermore, we compared the hepatocyte differentiation efficacy of our protocol with another published method, and the results demonstrated that our differentiation strategy could significantly improve the generation of morphological and functional hepatocyte-like cells from porcine iPSCs. In conclusion, this study establishes an efficient method for in vitro generation of functional hepatocytes from porcine iPSCs, which could represent a promising cell source for preclinical testing of cell-based therapeutics for liver failure and for pharmacological applications. © 2014 Ao et al

INSGFP/w human embryonic stem cells facilitate isolation of in vitro derived insulin-producing cells

AIMS/HYPOTHESIS: We aimed to generate human embryonic stem cell (hESC) reporter lines that would facilitate the characterisation of insulin-producing (INS⁺) cells derived in vitro. METHODS: Homologous recombination was used to insert sequences encoding green fluorescent protein (GFP) into the INS locus, to create reporter cell lines enabling the prospective isolation of viable INS⁺ cells. RESULTS: Differentiation of INS(GFP/w) hESCs using published protocols demonstrated that all GFP⁺ cells co-produced insulin, confirming the fidelity of the reporter gene. INS-GFP⁺ cells often co-produced glucagon and somatostatin, confirming conclusions from previous studies that early hESC-derived insulin-producing cells were polyhormonal. INS(GFP/w) hESCs were used to develop a 96-well format spin embryoid body (EB) differentiation protocol that used the recombinant protein-based, fully defined medium, APEL. Like INS-GFP⁺ cells generated with other methods, those derived using the spin EB protocol expressed a suite of pancreatic-related transcription factor genes including ISL1, PAX6 and NKX2.2. However, in contrast with previous methods, the spin EB protocol yielded INS-GFP⁺ cells that also co-expressed the beta cell transcription factor gene, NKX6.1, and comprised a substantial proportion of monohormonal INS⁺ cells. CONCLUSIONS/INTERPRETATION: INS(GFP/w) hESCs are a valuable tool for investigating the nature of early INS⁺ progenitors in beta cell ontogeny and will facilitate the development of novel protocols for generating INS⁺ cells from differentiating hESCs