Student academic performance factors affecting matching into first-choice residency and competitive specialties.

BACKGROUND: Although specific specialties and residency programs have investigated student performance factors affecting matching, there is a paucity of information from medical schools. Furthermore, factors contributing to matching into first-choice residency have not been examined. This study aimed to identify academic performance factors affecting matching into first-choice residency and highly competitive specialties. METHODS: The authors conducted a study of 1726 graduates from their institution from 2010 to 2017 and assessed pre-/post-admission academic variables associated with matching into first choice and highly competitive specialties. RESULTS: 53.9% of graduates matched into their first choice. This was associated with passing COMLEX Level 2 CE (p = 0.01), PE (p = 0.02) on first attempt, and higher COMLEX Level 2 CE and USMLE 2 CK scores (p < 0.001 and 0.002; 14.1 and 3.9-point difference in mean scores respectively). Pre-clinical GPA (p = 0.002) and highest MCAT score (p = 0.02) were associated, however differences in means were < 1 point for both. Factors associated with matching into first choice included: MCAT (OR 0.95, 95% CI = (0.92, 0.98)), Level 2 CE score (OR = 1.01, 95% CI = (1.01, 1.02)) and passing Level 2 PE (OR = 3.68, 95% CI = (1.2, 11.28)). 12% of graduates matched into high- and 63% into low-competitiveness specialties. Matching into highly competitive specialties was associated with passing COMLEX Level 1 (p < 0.001), Level 2 CE (p < 0.001), USMLE Step 1 (p < 0.001) and Step 2 CK (p = 0.03) on first attempt. Mean scores of students matching into high- versus low-competitiveness specialties differed as follows: COMLEX Level 1 62.7 points, Level 2 CE 50.5 points, USMLE Step 1 13.6 points, Step 2 CK 7 points (all p < 0.001), as did pre-clinical GPA (2.4 points, p < 0.001). Level 1 score was the strongest predictor for matching into highly competitive specialties (OR = 1.04, 95% CI = (1.02, 1.05)). CONCLUSIONS: Licensing exam performance is important for matching into first-choice residency and into highly competitive specialties. Differences in exam scores were more pronounced for matching into highly competitive specialties than into first choice, with a larger difference in mean scores between students matching into specialties of high versus low competitiveness, than between students matching into their first- versus non first-choice residency. These results may help faculty prepare students and inform curriculum design to improve matching.

Discriminating the effects of Cannabis sativa and Cannabis indica: a web survey of medical cannabis users.

OBJECTIVE: To evaluate the opinions of medical cannabis (MC) users on the effects of Cannabis indica vs. those of Cannabis sativa on conditions and symptoms through an online survey. DESIGN: Survey of 95 non-randomly assigned MC users. A two-sided chi-square test followed by Bonferroni post hoc multiple comparison and Fisher exact test were used to determine correlations. The Cronbach α was used to determine internal consistency. SETTING: Announcements on 13 MC websites with links to SurveyMonkey.com. PARTICIPANTS: Self-identified MC users. INTERVENTION: Web survey. OUTCOME MEASURES: Species effects were compared regarding health symptoms, conditions, purpose, route, and trust in product label. RESULTS: Trust in the purity, the route of administration, or the purpose (recreational vs. medicinal) did not differ between the two species. A preference for C. indica was statistically significant for pain management (p=0.001), helping with sedation (p=0.015), and sleep (p<0.001). C. sativa was preferred for euphoria (p<0.001) and enhancing energy (p=0.022). The conditions reaching statistical significance for C. indica preference were: nonmigraine headaches (p=0.042), glaucoma (p=0.036), neuropathy (p=0.024), spasticity (p=0.048), seizures (p=0.031), insomnia (p<0.001), and joint pain (p=0.048). For C. sativa, no conditions reached significance. The MC websites' descriptions of effects that agreed with the survey results are listed. Some conditions had very few respondents. The internal consistency/reliability (Cronbach α) was adequate for the condition scale but not for the symptom survey. CONCLUSION: In this anonymous Web survey, which had limitations, the two species had different effect associations on symptoms and conditions, possibly because of ingredient differences. Future surveys and subsequent prospective definitive trials are needed to confirm the findings.

Sequencing and comparative genomic analysis of 1227 Felis catus cDNA sequences enriched for developmental, clinical and nutritional phenotypes.

BACKGROUND: The feline genome is valuable to the veterinary and model organism genomics communities because the cat is an obligate carnivore and a model for endangered felids. The initial public release of the Felis catus genome assembly provided a framework for investigating the genomic basis of feline biology. However, the entire set of protein coding genes has not been elucidated. RESULTS: We identified and characterized 1227 protein coding feline sequences, of which 913 map to public sequences and 314 are novel. These sequences have been deposited into NCBI's genbank database and complement public genomic resources by providing additional protein coding sequences that fill in some of the gaps in the feline genome assembly. Through functional and comparative genomic analyses, we gained an understanding of the role of these sequences in feline development, nutrition and health. Specifically, we identified 104 orthologs of human genes associated with Mendelian disorders. We detected negative selection within sequences with gene ontology annotations associated with intracellular trafficking, cytoskeleton and muscle functions. We detected relatively less negative selection on protein sequences encoding extracellular networks, apoptotic pathways and mitochondrial gene ontology annotations. Additionally, we characterized feline cDNA sequences that have mouse orthologs associated with clinical, nutritional and developmental phenotypes. Together, this analysis provides an overview of the value of our cDNA sequences and enhances our understanding of how the feline genome is similar to, and different from other mammalian genomes. CONCLUSIONS: The cDNA sequences reported here expand existing feline genomic resources by providing high-quality sequences annotated with comparative genomic information providing functional, clinical, nutritional and orthologous gene information.

Development of a PCR assay to detect papillomavirus infection in the snow leopard.

BACKGROUND: Papillomaviruses (PVs) are a group of small, non-encapsulated, species-specific DNA viruses that have been detected in a variety of mammalian and avian species including humans, canines and felines. PVs cause lesions in the skin and mucous membranes of the host and after persistent infection, a subset of PVs can cause tumors such as cervical malignancies and head and neck squamous cell carcinoma in humans. PVs from several species have been isolated and their genomes have been sequenced, thereby increasing our understanding of the mechanism of viral oncogenesis and allowing for the development of molecular assays for the detection of PV infection. In humans, molecular testing for PV DNA is used to identify patients with persistent infections at risk for developing cervical cancer. In felids, PVs have been isolated and sequenced from oral papillomatous lesions of several wild species including bobcats, Asian lions and snow leopards. Since a number of wild felids are endangered, PV associated disease is a concern and there is a need for molecular tools that can be used to further study papillomavirus in these species. RESULTS: We used the sequence of the snow leopard papillomavirus UuPV1 to develop a PCR strategy to amplify viral DNA from samples obtained from captive animals. We designed primer pairs that flank the E6 and E7 viral oncogenes and amplify two DNA fragments encompassing these genes. We detected viral DNA for E6 and E7 in genomic DNA isolated from saliva, but not in paired blood samples from snow leopards. We verified the identity of these PCR products by restriction digest and DNA sequencing. The sequences of the PCR products were 100% identical to the published UuPV1 genome sequence. CONCLUSIONS: We developed a PCR assay to detect papillomavirus in snow leopards and amplified viral DNA encompassing the E6 and E7 oncogenes specifically in the saliva of animals. This assay could be utilized for the molecular investigation of papillomavirus in snow leopards using saliva, thereby allowing the detection of the virus in the anatomical site where oral papillomatous lesions develop during later stages of infection and disease development.

Abnormal gene expression in cerebellum of Npc1-/- mice during postnatal development.

Niemann-Pick Type C (NPC) disease is an autosomal recessive neurodegenerative disorder with abnormal lipid storage as the major cellular pathologic hallmark. Genetic analyses have identified mutations in NPC1 gene in the great majority of cases, while mutations in NPC2 account for the remainders. Yet little is known regarding the cellular mechanisms responsible for NPC pathogenesis, especially for neurodegeneration, which is the usual cause of death. To identify critical steps that could account for the pathological manifestations of the disease in one of the most affected brain structures, we performed global gene expression analysis in the cerebellum from 3-week old Npc1+/+ and Npc1-/- mice with two different microarray platforms (Agilent and Illumina). Differentially expressed genes identified by both microarray platforms were then subjected to KEGG pathway analysis. Expression of genes in six pathways was significantly altered in Npc1-/- mice; functionally, these signaling pathways belong to the following three categories: (1) steroid and terpenoid biosynthesis, (2) immune response, and (3) cell adhesion/motility. In addition, the expression of several proteins involved in lipid transport was significantly altered in Npc1-/- mice. Our results provide novel molecular insight regarding the mechanisms of pathogenesis in NPC disease and reveal potential new therapeutic targets.

Saliva as an alternative source of high yield canine genomic DNA for genotyping studies.

BACKGROUND: The domestic dog presents an attractive model system for the study of the genetic basis of disease. The development of resources such as the canine genome sequence and SNP genotyping platforms has allowed for the implementation of canine genetic studies. Successful implementation of such studies depends not only on the quality of individual DNA samples, but also on the number of samples obtained. The latter can be maximized using a non-invasive DNA collection method that can increase study participation. We compared the DNA yield and quality obtained from blood and buccal swabs to those obtained using a non-invasive saliva collection kit (Oragene *ANIMAL kit). We also assessed the success rate of PCR amplification and genotyping accuracy of DNA isolated using these collection methods. FINDINGS: Comparison of DNA yields from matched saliva, blood and buccal swab samples showed that yields from saliva were significantly higher than those from blood (p = 0.0198) or buccal swabs (p = 0.0008). Electrophoretic analysis revealed that blood and saliva produced higher quality DNA than buccal swabs. In addition, a 1.1-kb PCR fragment was successfully amplified using the paired DNA samples and genotyping by PCR-RFLP yielded identical results. CONCLUSION: We demonstrate that DNA yields from canine saliva are higher than those from blood or buccal swabs. The quality of DNA extracted from saliva is sufficient for successful amplification of a 1.1-kb fragment and for accurate SNP genotyping by PCR-RFLP. We conclude that saliva presents a non-invasive alternative source of high quantities of canine genomic DNA suitable for genotyping studies.

Comparison of adoption agency breed identification and DNA breed identification of dogs.

Governmental and other agencies may require dog caregivers (owners) to provide breed identification of their dogs. This study compares breed identification by adoption agencies with identification by DNA analysis in 20 dogs of unknown parentage. Of the 20 dogs who had been adopted from 17 different locations, the study identified 16 dogs as having (or probably having) 1 or 2 specific breed(s) in their ancestry. DNA analysis of these dogs indicated that 25% (4/16) did in fact contain genetic evidence of an adoption agency's identified breed as one of the predominant breeds in a dog's ancestry. DNA analysis did not detect all specified breeds in 14 of these dogs. That is, 87.5% of the dogs identified by an adoption agency as having specific breeds in their ancestry did not have all of those breeds detected by DNA analysis. The discrepancies between opinions of adoption agencies and identification by DNA analysis suggest that it would be worthwhile to reevaluate the reliability of breed identification as well as the justification of current public and private policies pertaining to specific dog breeds.

Kaposi's sarcoma-associated herpesvirus/human herpesvirus 8 RTA reactivates murine gammaherpesvirus 68 from latency.

Murine gammaherpesvirus 68 (MHV-68), Kaposi's sarcoma-associated herpesvirus (HHV-8), and Epstein-Barr virus (EBV) are all members of the gammaherpesvirus family, characterized by their ability to establish latency in lymphocytes. The RTA protein, conserved in all gammaherpesviruses, is known to play a critical role in reactivation from latency. Here we report that HHV-8 RTA, not EBV RTA, was able to induce MHV-68 lytic viral proteins and DNA replication and processing and produce viable MHV-68 virions from latently infected cells at levels similar to those for MHV-68 RTA. HHV-8 RTA was also able to activate two MHV-68 lytic promoters, whereas EBV RTA was not. In order to define the domains of RTA responsible for their functional differences in viral promoter activation and initiation of the MHV-68 lytic cycle, chimeric RTA proteins were constructed by exchanging the N-terminal and C-terminal domains of the RTA proteins. Our data suggest that the species specificity of MHV-68 RTA resides in the N-terminal DNA binding domain.

Detecting tissue-specific regulation of alternative splicing as a qualitative change in microarray data.

Alternative splicing has recently emerged as a major mechanism of regulation in the human genome, occurring in perhaps 40-60% of human genes. Thus, microarray studies of functional regulation could, in principle, be extended to detect not only the changes in the overall expression of a gene, but also changes in its splicing pattern between different tissues. However, since changes in the total expression of a gene and changes in its alternative splicing can be mixed in complex ways among a set of samples, separating these effects can be difficult, and is essential for their accurate assessment. We present a simple and general approach for distinguishing changes in alternative splicing from changes in expression, based on detecting systematic anti-correlation between the log-ratios of two different samples versus a pool containing both samples. We have tested this analysis method on microarray data for five human tissues, generated using a standard microarray platform and experimental protocols shown previously to be sensitive to alternative splicing. Our automatic analysis was able to detect a wide variety of tissue-specific alternative splicing events, such as exon skipping,mutually exclusive exons, alternative 3' and alternative 5' splicing, alternative initiation and alternative termination, all of which were validated by independent reverse-transcriptase PCR experiments, with validation rates of 70-85%. Our analysis method also enables hierarchical clustering of genes and samples by the level of similarity to their alternative splicing patterns, revealing patterns of tissue-specific regulation that are distinct from those obtained by hierarchical clustering of gene expression from the same microarray data. Our data and analysis source code are available from http://www.bioinformatics.ucla.edu/ASAP.

The DNA architectural protein HMGB1 displays two distinct modes of action that promote enhanceosome assembly.

HMGB1 (also called HMG-1) is a DNA-bending protein that augments the affinity of diverse regulatory proteins for their DNA sites. Previous studies have argued for a specific interaction between HMGB1 and target proteins, which leads to cooperative binding of the complex to DNA. Here we propose a different model that emerged from studying how HMGB1 stimulates enhanceosome formation by the Epstein-Barr viral activator Rta on a target gene, BHLF-1. HMGB1 stimulates binding of individual Rta dimers to multiple sites in the enhancer. DNase I and hydroxyl radical footprinting, electrophoretic mobility shift assays, and immobilized template assays failed to reveal stable binding of HMGB1 within the complex. Furthermore, mutational analysis failed to identify a specific HMGB1 target sequence. The effect of HMGB1 on Rta could be reproduced by individual HMG domains, yeast HMO1, or bacterial HU. These results, combined with the effects of single-amino-acid substitutions within the DNA-binding surface of HMGB1 domain A, argue for a mechanism whereby DNA-binding and bending by HMGB1 stimulate Rta-DNA complex formation in the absence of direct interaction with Rta or a specific HMGB1 target sequence. The data contrast with our analysis of HMGB1 action on another BHLF-1 regulatory protein called ZEBRA. We discuss the two distinct modes of HMGB1 action on a single regulatory region and propose how HMGB1 can function in diverse contexts.