Increased predominance of HIV-1 CRF01_AE and its recombinants in the Philippines.

The growth rate of new HIV infections in the Philippines was the fastest of any countries in the Asia-Pacific region between 2010 and 2016. To date, HIV-1 subtyping results in the Philippines have been determined by characterizing only partial viral genome sequences. It is not known whether recombination occurs in the majority of unsequenced genome regions. Near-full-length genome (NFLG) sequences were obtained by amplifying two overlapping half genomes from plasma samples collected between 2015 and 2017 from 23 newly diagnosed infected individuals in the Philippines. Phylogenetic analysis showed that the newly characterized sequences were CRF01_AE (14), subtype B (3), CRF01/B recombinants (5) and a CRF01/CRF07/B recombinant (1). All 14 CRF01_AE formed a tight cluster, suggesting that they were derived from a single introduction. The time to the most recent common ancestor (tMRCA) for CRF01_AE in the Philippines was 1995 (1992-1998), about 10-15 years later than that of CRF01_AE in China and Thailand. All five CRF01/B recombinants showed distinct recombination patterns, suggesting ongoing recombination between the two predominant circulating viruses. The identification of partial CRF07_BC sequences in one CRF01/CRF07/B recombinant, not reported previously in the Philippines, indicated that CRF07_BC may have been recently introduced into that country from China, where CRF07_BC is prevalent. Our results show that the major epidemic strains may have shifted to an increased predominance of CRF01_AE and its recombinants, and that other genotypes such as CRF07_BC may have been introduced into the Philippines.

How Prepared Are They? Pediatric Boot Camps and Intern Performance.

OBJECTIVE: To determine whether participation in a pediatric boot camp during medical school was associated with higher intern performance. Secondary objectives were to determine whether participation in general boot camps, pediatric subinternships or pediatric electives was associated with higher performance. METHODS: Intern surveys and faculty performance assessments during early internship were collected from a convenience sample of pediatric residency programs. Interns completed a survey regarding participation in medical school boot camps, pediatric subinternships and pediatric electives. Faculty assessed intern performance on selected Milestone-based subcompetencies on a 5-point scale following each intern's initial inpatient rotation and results were compared between groups. RESULTS: Seventeen pediatric residency programs participated. Two hundred eighty-seven interns completed the survey (69%), and faculty completed assessments on 71% of these interns. Of interns with complete faculty assessments (n = 198), 25% participated in 5 or more days of pediatric boot camp, 30% in general boot camp, and 45% in no boot camp. There were no educationally significant associations between participation in 5 or more days of pediatric boot camp, general boot camp, subinternships, or electives and intern performance. Interns completing at least 10 days of pediatric boot camp (n = 25) had slightly higher ratings for incorporating feedback and engaging in help-seeking behavior during June and July only. CONCLUSIONS: Participation in pediatric boot camps, general boot camps, pediatric subinternships or electives was not associated with substantially higher intern performance as measured by selected Milestone subcompetencies. Pediatric educators should carefully consider boot camp curricula and anticipated outcomes associated with boot camp participation.

Dynamics and differential proliferation of transposable elements during the evolution of the B and A genomes of wheat.

Transposable elements (TEs) constitute >80% of the wheat genome but their dynamics and contribution to size variation and evolution of wheat genomes (Triticum and Aegilops species) remain unexplored. In this study, 10 genomic regions have been sequenced from wheat chromosome 3B and used to constitute, along with all publicly available genomic sequences of wheat, 1.98 Mb of sequence (from 13 BAC clones) of the wheat B genome and 3.63 Mb of sequence (from 19 BAC clones) of the wheat A genome. Analysis of TE sequence proportions (as percentages), ratios of complete to truncated copies, and estimation of insertion dates of class I retrotransposons showed that specific types of TEs have undergone waves of differential proliferation in the B and A genomes of wheat. While both genomes show similar rates and relatively ancient proliferation periods for the Athila retrotransposons, the Copia retrotransposons proliferated more recently in the A genome whereas Gypsy retrotransposon proliferation is more recent in the B genome. It was possible to estimate for the first time the proliferation periods of the abundant CACTA class II DNA transposons, relative to that of the three main retrotransposon superfamilies. Proliferation of these TEs started prior to and overlapped with that of the Athila retrotransposons in both genomes. However, they also proliferated during the same periods as Gypsy and Copia retrotransposons in the A genome, but not in the B genome. As estimated from their insertion dates and confirmed by PCR-based tracing analysis, the majority of differential proliferation of TEs in B and A genomes of wheat (87 and 83%, respectively), leading to rapid sequence divergence, occurred prior to the allotetraploidization event that brought them together in Triticum turgidum and Triticum aestivum, <0.5 million years ago. More importantly, the allotetraploidization event appears to have neither enhanced nor repressed retrotranspositions. We discuss the apparent proliferation of TEs as resulting from their insertion, removal, and/or combinations of both evolutionary forces.

A randomised control trial of a self-management program for people with a chronic illness from Vietnamese, Chinese, Italian and Greek backgrounds.

OBJECTIVE: This study investigated the effectiveness of the Chronic Disease Self-management Program (CDSMP) when delivered to for people from Vietnamese, Chinese, Italian and Greek backgrounds living in Victoria, Australia. METHOD: The CDSMP was administered to 320 people with chronic illnesse(es) in selected low income areas in the State of Victoria, Australia. At 6 months, they were compared with randomised wait-list control subjects (n=154) using analyses of covariance. RESULTS: Participants in the intervention group had significantly better outcomes on energy, exercise, symptom management, self-efficacy, general health, pain, fatigue and health distress. There were no significant effects for health services utilisation. Interactions across language groups were observed with the Vietnamese and Chinese speaking participants gaining greater benefit. CONCLUSION: Self-management programs can be successfully implemented with culturally and linguistically diverse populations in Australia. Further research is needed to evaluate long-term outcomes; explore effects on service utilisation; and to determine whether the benefits obtained from participating in a self-management program can be maintained. PRACTICE IMPLICATIONS: Self-management programs should be considered for people from culturally and linguistically diverse backgrounds. Care also needs to be taken in designing recruitment strategies to minimize withdrawal rates and to ensure harder to reach people are given encouragement to participate.

Fast Dissemination of New HIV-1 CRF02/A1 Recombinants in Pakistan.

A number of HIV-1 subtypes are identified in Pakistan by characterization of partial viral gene sequences. Little is known whether new recombinants are generated and how they disseminate since whole genome sequences for these viruses have not been characterized. Near full-length genome (NFLG) sequences were obtained by amplifying two overlapping half genomes or next generation sequencing from 34 HIV-1-infected individuals in Pakistan. Phylogenetic tree analysis showed that the newly characterized sequences were 16 subtype As, one subtype C, and 17 A/G recombinants. Further analysis showed that all 16 subtype A1 sequences (47%), together with the vast majority of sequences from Pakistan from other studies, formed a tight subcluster (A1a) within the subtype A1 clade, suggesting that they were derived from a single introduction. More in-depth analysis of 17 A/G NFLG sequences showed that five shared similar recombination breakpoints as in CRF02 (15%) but were phylogenetically distinct from the prototype CRF02 by forming a tight subcluster (CRF02a) while 12 (38%) were new recombinants between CRF02a and A1a or a divergent A1b viruses. Unique recombination patterns among the majority of the newly characterized recombinants indicated ongoing recombination. Interestingly, recombination breakpoints in these CRF02/A1 recombinants were similar to those in prototype CRF02 viruses, indicating that recombination at these sites more likely generate variable recombinant viruses. The dominance and fast dissemination of new CRF02a/A1 recombinants over prototype CRF02 suggest that these recombinant have more adapted and may become major epidemic strains in Pakistan.

Comparative organization of wheat homoeologous group 3S and 7L using wheat-rice synteny and identification of potential markers for genes controlling xanthophyll content in wheat.

EST and genomic DNA sequencing efforts for rice and wheat have provided the basis for interpreting genome organization and evolution. In this study we have used EST and genomic sequencing information and a bioinformatic approach in a two-step strategy to align portions of the wheat and rice genomes. In the first step, wheat ESTs were used to identify rice orthologs and it was shown that wheat 3S and rice 1 contain syntenic units with intrachromosomal rearrangements. Further analysis using anchored rice contiguous sequences and TBLASTX alignments in a second alignment step showed interruptions by orthologous genes that map elsewhere in the wheat genome. This indicates that gene content and order is not as conserved as large chromosomal blocks as previously predicted. Similarly, chromosome 7L contains syntenic units with rice 6 and 8 but is interrupted by combinations of intrachromosomal and interchromosomal rearrangements involving syntenic units and single gene orthologs from other rice chromosome groups. We have used the rice sequence annotations to identify genes that can be used to develop markers linked to biosynthetic pathways on 3BS controlling xanthophyll production in wheat and thus involved in determining flour colour.