Post-Acute Care Payment Reform Demonstration: Final Report Volume 4 of 4

This is the Final Report for the Post-Acute Care Payment Reform Demonstration (PAC-PRD), authorized by section 5008 of the Deficit Reduction Act of 2005, Public Law 109-171. The report has 12 sections, which are divided into four volumes: Volume 1: Executive Summary. Volume 2: Sections 1-4 (Section 1: Introduction; Section 2: Underlying Issues of the PAC-PRD Initiating Legislation; Section 3: Developing Standardized Measurement Approaches: The Continuity Assessment Record and Evaluation (CARE); Section 4: Demonstration Methods and Data Collection) Volume 3: Sections 5-6 (Section 5: Framework for Analysis; Section 6: Factors Associated with Hospital Discharge Destination) Volume 4: Sections 7-12; References (Section 7: Outcomes: Hospital Readmissions; Section 8: Outcomes: Functional Status; Section 9: Determinants of Resource Intensity: Methods and Analytic Sample Description; Section 10: Determinants of Resource Intensity: Lessons from the CART Analysis; Section 11: Determinants of Resource Intensity: Multivariate Regression Results; Section 12: Conclusions and Review of Findings; References

Post-Acute Care Payment Reform Demonstration: Final Report Volume 3 of 4

This is the Final Report for the Post-Acute Care Payment Reform Demonstration (PAC-PRD), authorized by section 5008 of the Deficit Reduction Act of 2005, Public Law 109-171. The report has 12 sections, which are divided into four volumes: Volume 1: Executive Summary. Volume 2: Sections 1-4 (Section 1: Introduction; Section 2: Underlying Issues of the PAC-PRD Initiating Legislation; Section 3: Developing Standardized Measurement Approaches: The Continuity Assessment Record and Evaluation (CARE); Section 4: Demonstration Methods and Data Collection) Volume 3: Sections 5-6 (Section 5: Framework for Analysis; Section 6: Factors Associated with Hospital Discharge Destination) Volume 4: Sections 7-12; References (Section 7: Outcomes: Hospital Readmissions; Section 8: Outcomes: Functional Status; Section 9: Determinants of Resource Intensity: Methods and Analytic Sample Description; Section 10: Determinants of Resource Intensity: Lessons from the CART Analysis; Section 11: Determinants of Resource Intensity: Multivariate Regression Results; Section 12: Conclusions and Review of Findings; References

Post-Acute Care Payment Reform Demonstration: Final Report Volume 2 of 4

This is the Final Report for the Post-Acute Care Payment Reform Demonstration (PAC-PRD), authorized by section 5008 of the Deficit Reduction Act of 2005, Public Law 109-171. The report has 12 sections, which are divided into four volumes: Volume 1: Executive Summary. Volume 2: Sections 1-4 (Section 1: Introduction; Section 2: Underlying Issues of the PAC-PRD Initiating Legislation; Section 3: Developing Standardized Measurement Approaches: The Continuity Assessment Record and Evaluation (CARE); Section 4: Demonstration Methods and Data Collection) Volume 3: Sections 5-6 (Section 5: Framework for Analysis; Section 6: Factors Associated with Hospital Discharge Destination) Volume 4: Sections 7-12; References (Section 7: Outcomes: Hospital Readmissions; Section 8: Outcomes: Functional Status; Section 9: Determinants of Resource Intensity: Methods and Analytic Sample Description; Section 10: Determinants of Resource Intensity: Lessons from the CART Analysis; Section 11: Determinants of Resource Intensity: Multivariate Regression Results; Section 12: Conclusions and Review of Findings; References

Post-Acute Care Payment Reform Demonstration: Final Report Volume 1 of 4

This is the Final Report for the Post-Acute Care Payment Reform Demonstration (PAC-PRD), authorized by section 5008 of the Deficit Reduction Act of 2005, Public Law 109-171. The report has 12 sections, which are divided into four volumes: Volume 1: Executive Summary. Volume 2: Sections 1-4 (Section 1: Introduction; Section 2: Underlying Issues of the PAC-PRD Initiating Legislation; Section 3: Developing Standardized Measurement Approaches: The Continuity Assessment Record and Evaluation (CARE); Section 4: Demonstration Methods and Data Collection) Volume 3: Sections 5-6 (Section 5: Framework for Analysis; Section 6: Factors Associated with Hospital Discharge Destination) Volume 4: Sections 7-12; References (Section 7: Outcomes: Hospital Readmissions; Section 8: Outcomes: Functional Status; Section 9: Determinants of Resource Intensity: Methods and Analytic Sample Description; Section 10: Determinants of Resource Intensity: Lessons from the CART Analysis; Section 11: Determinants of Resource Intensity: Multivariate Regression Results; Section 12: Conclusions and Review of Findings; References

Structural and functional annotation of the porcine immunome

Background: The domestic pig is known as an excellent model for human immunology and the two species share many pathogens. Susceptibility to infectious disease is one of the major constraints on swine performance, yet the structure and function of genes comprising the pig immunome are not well-characterized. The completion of the pig genome provides the opportunity to annotate the pig immunome, and compare and contrast pig and human immune systems.[br/] Results: The Immune Response Annotation Group (IRAG) used computational curation and manual annotation of the swine genome assembly 10.2 (Sscrofa10.2) to refine the currently available automated annotation of 1,369 immunity-related genes through sequence-based comparison to genes in other species. Within these genes, we annotated 3,472 transcripts. Annotation provided evidence for gene expansions in several immune response families, and identified artiodactyl-specific expansions in the cathelicidin and type 1 Interferon families. We found gene duplications for 18 genes, including 13 immune response genes and five non-immune response genes discovered in the annotation process. Manual annotation provided evidence for many new alternative splice variants and 8 gene duplications. Over 1,100 transcripts without porcine sequence evidence were detected using cross-species annotation. We used a functional approach to discover and accurately annotate porcine immune response genes. A co-expression clustering analysis of transcriptomic data from selected experimental infections or immune stimulations of blood, macrophages or lymph nodes identified a large cluster of genes that exhibited a correlated positive response upon infection across multiple pathogens or immune stimuli. Interestingly, this gene cluster (cluster 4) is enriched for known general human immune response genes, yet contains many un-annotated porcine genes. A phylogenetic analysis of the encoded proteins of cluster 4 genes showed that 15% exhibited an accelerated evolution as compared to 4.1% across the entire genome.[br/] Conclusions: This extensive annotation dramatically extends the genome-based knowledge of the molecular genetics and structure of a major portion of the porcine immunome. Our complementary functional approach using co-expression during immune response has provided new putative immune response annotation for over 500 porcine genes. Our phylogenetic analysis of this core immunome cluster confirms rapid evolutionary change in this set of genes, and that, as in other species, such genes are important components of the pig’s adaptation to pathogen challenge over evolutionary time. These comprehensive and integrated analyses increase the value of the porcine genome sequence and provide important tools for global analyses and data-mining of the porcine immune response

Interaction between Red Meat Intake and NAT2 Genotype in Increasing the Risk of Colorectal Cancer in Japanese and African Americans

Heterocyclic aromatic amines formed in cooked meat may be an underlying mechanism for the red meat-colorectal cancer (CRC) association. These compounds require bioactivaction by N-acetyltransferase 2 (NAT2). An interaction effect between red meat consumption and NAT2 in increasing CRC risk has been inconsistently reported in whites. We investigated this interaction in two populations in which the high-activity rapid NAT2 phenotype is 10- and 2-fold more common than in whites. We meta-analyzed four studies of Japanese (2,217 cases, 3,788 controls) and three studies of African Americans (527 cases, 4,527 controls). NAT2 phenotype was inferred from an optimized seven-SNP genotyping panel. Processed and total red meat intakes were associated with an increased CRC risk in Japanese and in both ethnic groups combined (P’s ≤ 0.002). We observed an interaction between processed meat intake and NAT2 in Japanese (P = 0.04), African Americans (P = 0.02), and in both groups combined (P = 0.006). The association of processed meat with CRC was strongest among individuals with the rapid NAT2 phenotype (combined analysis, OR for highest vs. lowest quartile: 1.62, 95% CI: 1.28–2.05; Ptrend = 8.0×10−5), intermediate among those with the intermediate NAT2 phenotype (1.29, 95% CI: 1.05–1.59; Ptrend = 0.05) and null among those with the slow phenotype (Ptrend = 0.45). A similar interaction was found for NAT2 and total red meat (Pinteraction = 0.03). Our findings support a role for NAT2 in modifying the association between red meat consumption and CRC in Japanese and African Americans

Livestock 2.0 – genome editing for fitter, healthier, and more productive farmed animals

Abstract The human population is growing, and as a result we need to produce more food whilst reducing the impact of farming on the environment. Selective breeding and genomic selection have had a transformational impact on livestock productivity, and now transgenic and genome-editing technologies offer exciting opportunities for the production of fitter, healthier and more-productive livestock. Here, we review recent progress in the application of genome editing to farmed animal species and discuss the potential impact on our ability to produce food

Analyses of pig genomes provide insight into porcine demography and evolution

For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ∼1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model