Acute limb ischemia as sole initial manifestation of SARS-CoV-2 infection.

We present the case of a patient with acute upper limb ischemia as the sole initial manifestation of severe acute respiratory syndrome associated with coronavirus disease 2 infection, without concomitant respiratory symptoms or pneumonia. Viral infection presumably precipitated the patient's thromboembolic event, causing multifocal vascular occlusions. This case illustrates that coronavirus disease-19 must be considered in the differential diagnosis of patients presenting with signs or symptoms of coagulopathy, even in the absence of respiratory symptoms. We believe that an awareness of the variety of clinical presentations in patients with coronavirus disease-19, particularly extrapulmonary manifestations, is critical for optimal patient management as well as implementation of appropriate infection prevention measures.

Training wheels needed: Lessons in professionalism from a liberal deferral policy.

Learning to self-regulate is an important aspect of professionalism. Thus, in 2015-16, the University of Michigan implemented a learner-centred 'deferral' policy called 'trust and track' in the preclinical phase. This gave students the autonomy to decide whether to attend required experiences, take quizzes and exams on schedule, or submit assignments on time. Surprisingly, quiz and exam deferrals remained relatively stable, but required experience deferrals more than doubled. While late assignments were not specifically tracked, there were multiple reports of assignments being months overdue. Some reasons for deferrals exhibited questionable judgement. Behavioural patterns carried forward, with an unusual spike in deferrals of licensure exams and requests for time off in the clinical phase. Wellness indices did not improve, despite learners having more autonomy and flexibility. It became clear to us that novice learners need clear professional expectations with limits to assist in developing professional behaviours. In 2016-17, we implemented a stricter policy that set clear expectations, established limits, and provided guidance on acceptable reasons to defer. We simultaneously implemented other measures to promote wellness. The moral of the story is that 'training wheels' are needed to help early learners develop the professional behaviours expected of practising physicians.

MIP-MAP: High-Throughput Mapping of Caenorhabditis elegans Temperature-Sensitive Mutants via Molecular Inversion Probes.

Mutants remain a powerful means for dissecting gene function in model organisms such as Caenorhabditis elegans Massively parallel sequencing has simplified the detection of variants after mutagenesis but determining precisely which change is responsible for phenotypic perturbation remains a key step. Genetic mapping paradigms in C. elegans rely on bulk segregant populations produced by crosses with the problematic Hawaiian wild isolate and an excess of redundant information from whole-genome sequencing (WGS). To increase the repertoire of available mutants and to simplify identification of the causal change, we performed WGS on 173 temperature-sensitive (TS) lethal mutants and devised a novel mapping method. The mapping method uses molecular inversion probes (MIP-MAP) in a targeted sequencing approach to genetic mapping, and replaces the Hawaiian strain with a Million Mutation Project strain with high genomic and phenotypic similarity to the laboratory wild-type strain N2 We validated MIP-MAP on a subset of the TS mutants using a competitive selection approach to produce TS candidate mapping intervals with a mean size < 3 Mb. MIP-MAP successfully uses a non-Hawaiian mapping strain and multiplexed libraries are sequenced at a fraction of the cost of WGS mapping approaches. Our mapping results suggest that the collection of TS mutants contains a diverse library of TS alleles for genes essential to development and reproduction. MIP-MAP is a robust method to genetically map mutations in both viable and essential genes and should be adaptable to other organisms. It may also simplify tracking of individual genotypes within population mixtures.

Five Year Clinical Evaluation of Restorations Placed in a Low Shrinkage Stress Composite in UK General Dental Practices.

This paper evaluates the five year clinical evaluation of restorations formed in a low shrinkage stress resin composite material (3M ESPE Filtek Silorane, Seefeld, Germany) and placed in the general dental practices of five members of the PREP Panel, a group of UK practice-based researchers. Results indicated satisfactory performance of the material under evaluation, other than for marginal staining, which affected 60% of the restorations evaluated after five years, albeit with less than 10% of the circumference of the restorations being affected. CLINICAL RELEVANCE: The low shrinkage stress material, Filtek Silorane™, demonstrated good clinical performance in the majority of parameters which were assessed at five years.

Mitochondrial Mutation Rate, Spectrum and Heteroplasmy in Caenorhabditis elegans Spontaneous Mutation Accumulation Lines of Differing Population Size.

Mitochondrial genomes of metazoans, given their elevated rates of evolution, have served as pivotal markers for phylogeographic studies and recent phylogenetic events. In order to determine the dynamics of spontaneous mitochondrial mutations in small populations in the absence and presence of selection, we evolved mutation accumulation (MA) lines of Caenorhabditis elegans in parallel over 409 consecutive generations at three varying population sizes of N = 1, 10, and 100 hermaphrodites. The N =1 populations should have a minimal influence of natural selection to provide the spontaneous mutation rate and the expected rate of neutral evolution, whereas larger population sizes should experience increasing intensity of selection. New mutations were identified by Illumina paired-end sequencing of 86 mtDNA genomes across 35 experimental lines and compared with published genomes of natural isolates. The spontaneous mitochondrial mutation rate was estimated at 1.05 × 10-7/site/generation. A strong G/C→A/T mutational bias was observed in both the MA lines and the natural isolates. This suggests that the low G + C content at synonymous sites is the product of mutation bias rather than selection as previously proposed. The mitochondrial effective population size per worm generation was estimated to be 62. Although it was previously concluded that heteroplasmy was rare in C. elegans, the vast majority of mutations in this study were heteroplasmic despite an experimental regime exceeding 400 generations. The frequencies of frameshift and nonsynonymous mutations were negatively correlated with population size, which suggests their deleterious effects on fitness and a potent role for selection in their eradication.

The long-term health impacts of Medicaid and CHIP.

This paper estimates the effect of US public health insurance programs for children on health. Previous work in this area has typically focused on the relationship between current program eligibility and current health. But because health is a stock variable which reflects the cumulative influence of health inputs, it would be preferable to estimate the impact of total program eligibility during childhood on longer-term health outcomes. I provide such estimates by using longitudinal data to construct Medicaid and CHIP eligibility measures that are observed from birth through age 18 and estimating the effect of cumulative program exposure on a variety of health outcomes observed in early adulthood. To account for the endogeneity of program eligibility, I exploit variation in Medicaid and CHIP generosity across states and over time for children of different ages. I find that an additional year of public health insurance eligibility during childhood improves a summary index of adult health by.079 standard deviations, and substantially reduces health limitations, chronic conditions and asthma prevalence while improving self-rated health.

Gene-Environment Interaction in the Intergenerational Transmission of Asthma.

Researchers have found strong linkages between parent and child health, but the mechanisms underlying intergenerational health transmission are not well understood. This paper investigates how the importance of genetic health transmission mechanisms varies by environmental conditions in the case of pediatric asthma, the single most common chronic health condition among American children. Using a sample that includes approximately 2000 adoptees and a large number of similar biological families, I find that the relative importance of genetic transmission differs strongly by socioeconomic status (SES). In high SES families, parent-child asthma associations are approximately 75% weaker among adoptees than biological children, suggesting a dominant role for genetic transmission. In lower SES families, parent-child asthma associations are virtually identical across biological and adoptive children, suggesting a negligible role for genetic transmission. A potential interpretation of this difference is that as environmental conditions affecting asthma improve among higher SES children, an increasingly large share of asthma variation is due to genetics. Copyright © 2016 John Wiley & Sons, Ltd.

Genes and the intergenerational transmission of BMI and obesity.

This paper compares the strength of intergenerational transmission of body mass index (BMI) and obesity in a sample of adoptees relative to a matched sample of biological children with similar observable characteristics. We find that BMI and obesity are strongly correlated among biological parent-child pairs, but there are no significant intergenerational associations in these health traits among adoptive parent-child pairs. The intergenerational elasticity of BMI for children to their parents is 0.2 in the matched biological sample, but indistinguishable from zero for adopted children with a standard error more than three times as large as the coefficient. Under reasonable assumptions, these findings indicate that the intergenerational transmission of BMI and obesity occurs primarily through genetic mechanisms. Additional analyses of transmission rates by parental gender and among step-parents and step-children support this conclusion. The role of determinants of BMI and obesity in the household environment in relation to our findings is discussed. Given the negative consequences of obesity on earnings and other economic measures, our results suggest that the genetic transmission of weight problems contributes substantially to intergenerational persistence in economic outcomes.

The time-resolved transcriptome of C. elegans.

We generated detailed RNA-seq data for the nematode Caenorhabditis elegans with high temporal resolution in the embryo as well as representative samples from post-embryonic stages across the life cycle. The data reveal that early and late embryogenesis is accompanied by large numbers of genes changing expression, whereas fewer genes are changing in mid-embryogenesis. This lull in genes changing expression correlates with a period during which histone mRNAs produce almost 40% of the RNA-seq reads. We find evidence for many more splice junctions than are annotated in WormBase, with many of these suggesting alternative splice forms, often with differential usage over the life cycle. We annotated internal promoter usage in operons using SL1 and SL2 data. We also uncovered correlated transcriptional programs that span >80 kb. These data provide detailed annotation of the C. elegans transcriptome.

Remarkably Divergent Regions Punctuate the Genome Assembly of the Caenorhabditis elegans Hawaiian Strain CB4856.

The Hawaiian strain (CB4856) of Caenorhabditis elegans is one of the most divergent from the canonical laboratory strain N2 and has been widely used in developmental, population, and evolutionary studies. To enhance the utility of the strain, we have generated a draft sequence of the CB4856 genome, exploiting a variety of resources and strategies. When compared against the N2 reference, the CB4856 genome has 327,050 single nucleotide variants (SNVs) and 79,529 insertion-deletion events that result in a total of 3.3 Mb of N2 sequence missing from CB4856 and 1.4 Mb of sequence present in CB4856 but not present in N2. As previously reported, the density of SNVs varies along the chromosomes, with the arms of chromosomes showing greater average variation than the centers. In addition, we find 61 regions totaling 2.8 Mb, distributed across all six chromosomes, which have a greatly elevated SNV density, ranging from 2 to 16% SNVs. A survey of other wild isolates show that the two alternative haplotypes for each region are widely distributed, suggesting they have been maintained by balancing selection over long evolutionary times. These divergent regions contain an abundance of genes from large rapidly evolving families encoding F-box, MATH, BATH, seven-transmembrane G-coupled receptors, and nuclear hormone receptors, suggesting that they provide selective advantages in natural environments. The draft sequence makes available a comprehensive catalog of sequence differences between the CB4856 and N2 strains that will facilitate the molecular dissection of their phenotypic differences. Our work also emphasizes the importance of going beyond simple alignment of reads to a reference genome when assessing differences between genomes.

Isolation of specific neurons from C. elegans larvae for gene expression profiling.

BACKGROUND: The simple and well-described structure of the C. elegans nervous system offers an unprecedented opportunity to identify the genetic programs that define the connectivity and function of individual neurons and their circuits. A correspondingly precise gene expression map of C. elegans neurons would facilitate the application of genetic methods toward this goal. Here we describe a powerful new approach, SeqCeL (RNA-Seq of C. elegans cells) for producing gene expression profiles of specific larval C. elegans neurons. METHODS AND RESULTS: We have exploited available GFP reporter lines for FACS isolation of specific larval C. elegans neurons for RNA-Seq analysis. Our analysis showed that diverse classes of neurons are accessible to this approach. To demonstrate the applicability of this strategy to rare neuron types, we generated RNA-Seq profiles of the NSM serotonergic neurons that occur as a single bilateral pair of cells in the C. elegans pharynx. These data detected >1,000 NSM enriched transcripts, including the majority of previously known NSM-expressed genes. SIGNIFICANCE: This work offers a simple and robust protocol for expression profiling studies of post-embryonic C. elegans neurons and thus provides an important new method for identifying candidate genes for key roles in neuron-specific development and function.

Genetic mechanisms in the intergenerational transmission of health.

This paper uses a sample of adoptees to study the genetic mechanisms underlying intergenerational associations in chronic health conditions. I begin by estimating baseline intergenerational models with a sample of approximately 125,000 parent-child pairs, and find that children with a parent who has a specific chronic health condition are at least 100% more likely to have the same condition themselves. To assess the role of genetic mechanisms in generating these strong correlations, I estimate models using a sample of approximately 2400 adoptees, and find that genetic transmission accounts for only 20-30% of the baseline associations. As falsification tests, I repeat this exercise using health measures with externally established levels of genetic determination (height and chicken pox), and the results suggest that comparisons of biological and adopted children are a valid method of isolating genetic effects in this sample. Finally, to corroborate these adoptee-based estimates, I examine health correlations among monozygotic twins, which provide an upper bound estimate of genetic influences, and find a similarly modest role for genetic transmission. I conclude that intergenerational health transmission is an important hindrance to overall socioeconomic mobility, but that the majority of transmission occurs through environmental factors or gene-environment interactions, leaving scope for interventions to effectively mitigate health persistence.

Diagnostic yield of array comparative genomic hybridization in adults with autism spectrum disorders.

PURPOSE: Array comparative genomic hybridization is available for the evaluation of autism spectrum disorders. The diagnostic yield of testing is 5-18% in children with developmental disabilities, including autism spectrum disorders and multiple congenital anomalies. The yield of array comparative genomic hybridization in the adult autism spectrum disorder population is unknown. METHODS: We performed a retrospective chart review for 40 consecutive patients referred for genetic evaluation of autism from July 2009 through April 2012. Four pediatric patients were excluded. Medical history and prior testing were reviewed. Clinical genetic evaluation and testing were offered to all patients. RESULTS: The study population comprised 36 patients (age range 18-45, mean 25.3 years). An autism spectrum disorder diagnosis was confirmed in 34 of 36 patients by medical record review. One patient had had an abnormal karyotype; none had prior array comparative genomic hybridization testing. Of the 23 patients with autism who underwent array comparative genomic hybridization, 2 of 23 (8.7%) had pathogenic or presumed pathogenic abnormalities and 2 of 23 (8.7%) had likely pathogenic copy-number variants. An additional 5 of 23 (22%) of autism patients had variants of uncertain significance without subclassification. CONCLUSION: Including one patient newly diagnosed with fragile X syndrome, our data showed abnormal or likely pathogenic findings in 5 of 24 (21%) adult autism patients. Genetic reevaluation in adult autism patients is warranted.

The million mutation project: a new approach to genetics in Caenorhabditis elegans.

We have created a library of 2007 mutagenized Caenorhabditis elegans strains, each sequenced to a target depth of 15-fold coverage, to provide the research community with mutant alleles for each of the worm's more than 20,000 genes. The library contains over 800,000 unique single nucleotide variants (SNVs) with an average of eight nonsynonymous changes per gene and more than 16,000 insertion/deletion (indel) and copy number changes, providing an unprecedented genetic resource for this multicellular organism. To supplement this collection, we also sequenced 40 wild isolates, identifying more than 630,000 unique SNVs and 220,000 indels. Comparison of the two sets demonstrates that the mutant collection has a much richer array of both nonsense and missense mutations than the wild isolate set. We also find a wide range of rDNA and telomere repeat copy number in both sets. Scanning the mutant collection for molecular phenotypes reveals a nonsense suppressor as well as strains with higher levels of indels that harbor mutations in DNA repair genes and strains with abundant males associated with him mutations. All the strains are available through the Caenorhabditis Genetics Center and all the sequence changes have been deposited in WormBase and are available through an interactive website.

Racial disparities in the cognition-health relationship.

This paper investigates how the association between cognitive achievement and self-rated health in middle age differs by race, and attempts to explain these differences. The role of cognition in health determination has received only limited empirical attention, and even less is known about how race may affect this relationship. Using data from the NLSY, I find that while Whites with higher cognitive achievement scores tend to report substantially better general health, this relationship is far weaker or wholly absent among Blacks. Further tests suggest that about 35% of this racial difference can be explained by behavioral decisions during adulthood, and that another portion of the disparity may trace back to prenatal and early childhood experiences. The paper closes by noting that its results are broadly consistent with explanations of the racial health gap that emphasize entrenched forms of racial discrimination.