Chromosome-Aware Phylogenomics of Assassin Bugs (Hemiptera: Reduvioidea) Elucidates Ancient Gene Conflict.

Though the phylogenetic signal of loci on sex chromosomes can differ from those on autosomes, chromosomal-level genome assemblies for nonvertebrates are still relatively scarce and conservation of chromosomal gene content across deep phylogenetic scales has therefore remained largely unexplored. We here assemble a uniquely large and diverse set of samples (17 anchored hybrid enrichment, 24 RNA-seq, and 70 whole-genome sequencing samples of variable depth) for the medically important assassin bugs (Reduvioidea). We assess the performance of genes based on multiple features (e.g., nucleotide vs. amino acid, nuclear vs. mitochondrial, and autosomal vs. X chromosomal) and employ different methods (concatenation and coalescence analyses) to reconstruct the unresolved phylogeny of this diverse (∼7,000 spp.) and old (>180 Ma) group. Our results show that genes on the X chromosome are more likely to have discordant phylogenies than those on autosomes. We find that the X chromosome conflict is driven by high gene substitution rates that impact the accuracy of phylogenetic inference. However, gene tree clustering showed strong conflict even after discounting variable third codon positions. Alternative topologies were not particularly enriched for sex chromosome loci, but spread across the genome. We conclude that binning genes to autosomal or sex chromosomes may result in a more accurate picture of the complex evolutionary history of a clade.

Concordance Analysis of the 23-Gene Expression Signature (myPath Melanoma) With Fluorescence In Situ Hybridization Assay and Single Nucleotide Polymorphism Array in the Analysis of Challenging Melanocytic Lesions: Results From an Academic Medical Center.

BACKGROUND: Fluorescence in situ hybridization (FISH) and single nucleotide polymorphism (SNP) arrays are well-established molecular tests for the analysis of challenging melanocytic lesions. A 23-gene expression signature (GES), marketed as myPath Melanoma, is a recently introduced molecular test that categorizes melanocytic lesions as "benign," "malignant," and "indeterminate." There are few studies on the concordance between FISH, SNP, and GES in the analysis of melanocytic lesions. METHODS: A single-institution retrospective analysis of 61 contiguous cases of challenging melanocytic lesions with molecular analysis by 2 or more techniques. The primary objective was to determine the intertest agreement, which was calculated as percent agreement. A secondary objective was to determine the combined-test performance, that is, the frequency of obtaining a successful test (a test with an abnormal or normal, benign or malignant result) when 2 or more molecular tests were performed. RESULTS: Of the 61 cases, 58 cases were submitted for analysis using the GES assay, 44 cases were submitted for FISH analysis, and 21 cases were submitted for SNP array analysis. Percent agreement between GES and FISH array was 50.9% (18/34), which improved to 69.7% (18/23) when indeterminate/equivocal results were excluded. Similarly, percent agreement between GES and SNP array was 57.1% (8/14); this improved to 77.8% (7/9) when indeterminate/equivocal results were excluded. In 44% of cases submitted for GES and FISH and in 39% of cases submitted for GES and SNP, one test was successful and the other was not. CONCLUSION: For challenging melanocytic lesions, the choice of a molecular test is consequential as the GES assay correlated with FISH and SNP arrays approximately only half of the time. This improved when cases with indeterminate/equivocal results were excluded from the calculations. The combined-test analysis supports the utility of conducting more than one molecular test, as this increased the odds of obtaining a successful test.

Kikuchi-Fujimoto disease preceded by lupus erythematosus panniculitis: do these findings together herald the onset of systemic lupus erythematosus?

Kikuchi-Fujimoto disease (KFD), also known as histiocytic necrotizing lymphadenitis, is a rare disorder that must be distinguished from systemic lupus erythematosus (SLE). Although a minority of patients with KFD develop SLE, most patients have a self-limited disease. Importantly, KFD can have skin manifestations resembling cutaneous lupus. Therefore, the diagnosis of SLE should be predicated on a complete rheumatologic workup and not on the constellation of skin disease and lymphadenitis. Nonetheless, as our exceedingly rare case illustrates, patients who do not initially meet diagnostic criteria for SLE require dermatologic follow-up. We present a young adult woman who had a remote history of KFD and later presented with combined features of discoid lupus and lupus erythematosus panniculitis (LEP). On subsequent rheumatologic workup, she fulfilled criteria for SLE. We discuss the differential diagnosis of both KFD and LEP and emphasize how strong communication among dermatologists and other healthcare providers is essential in the management of patients with KFD.

A demonstration of unsupervised machine learning in species delimitation.

One major challenge to delimiting species with genetic data is successfully differentiating population structure from species-level divergence, an issue exacerbated in taxa inhabiting naturally fragmented habitats. Many fields of science are now using machine learning, and in evolutionary biology supervised machine learning has recently been used to infer species boundaries. These supervised methods require training data with associated labels. Conversely, unsupervised machine learning (UML) uses inherent data structure and does not require user-specified training labels, potentially providing more objectivity in species delimitation. In the context of integrative taxonomy, we demonstrate the utility of three UML approaches (random forests, variational autoencoders, t-distributed stochastic neighbor embedding) for species delimitation in an arachnid taxon with high population genetic structure (Opiliones, Laniatores, Metanonychus). We find that UML approaches successfully cluster samples according to species-level divergences and not high levels of population structure, while model-based validation methods severely over-split putative species. UML offers intuitive data visualization in two-dimensional space, the ability to accommodate various data types, and has potential in many areas of systematic and evolutionary biology. We argue that machine learning methods are ideally suited for species delimitation and may perform well in many natural systems and across taxa with diverse biological characteristics.

A diagnostically-challenging case of melanoma ex blue nevus with comprehensive molecular analysis, including the 23-gene expression signature (myPath melanoma).

Melanoma ex blue nevus (MEBN) is a rare, aggressive, and potentially lethal neoplasm. Distinguishing MEBN from an atypical cellular blue nevus can be very challenging. We report a diagnostically difficult case of MEBN with lymph node metastases, in which single nucleotide polymorphism array and fluorescence in situ hybridization were used to arrive at the correct diagnosis. It was also analyzed by the recently-introduced proprietary 23-gene expression signature test. To the best of our knowledge, this is the second reported case of MEBN analyzed by the 23-gene expression signature, which provided a false-negative result. More studies are needed to assess the sensitivity and specificity of this test in various melanocytic proliferations.

Cutaneous manifestations of systemic viral diseases in neonates: an update.

PURPOSE OF REVIEW: Dermatologic findings may be the first signs of a neonatal viral infection. This review provides an update of the diagnostic features and therapies for selected viral illnesses [herpes simplex virus (HSV), varicella zoster virus, enterovirus, and Zika virus] that present with cutaneous manifestations in the neonate. RECENT FINDINGS: HSV DNA polymerase chain reaction of plasma and cerebrospinal fluid, routinely used in the diagnosis of neonatal HSV, may have expanded utility in assessing prognosis and acyclovir therapeutic efficacy. Maternal antiviral suppressive therapy may alter the clinical appearance of congenital HSV, resulting in delayed diagnosis and treatment. VariZIG, a varicella zoster immune globulin, is a US Food and Drug Administration approved form of prophylaxis for varicella. The Centers for Disease Control and Prevention has expanded the period of VariZIG eligibility for preterm infants, a group particularly susceptible to severe varicella infection. For severe neonatal enterovirus sepsis, the results of a randomized, double-blind, placebo-controlled trial of pleconaril, a viral capsid inhibitor, suggest that this compound is an effective therapy. Human Parechovirus type 3, a strain within a newly formed viral genus, has a similar, and potentially underestimated, clinical presentation to enterovirus sepsis. However, a distinctive erythematous palmoplantar rash may be specific to human Parechovirus type 3 infection. Perinatal Zika virus infection in the neonate may present with a nonspecific macular and papular rash. As this rash is not specific, obtaining a maternal travel history and, if appropriate, requesting additional diagnostic testing are critical for early diagnosis. SUMMARY: Neonatal rashes may be harmless and transient, whereas others may reflect the presence of a severe systemic illness. Recognizing key cutaneous features of viral-associated rashes may aid in the prompt and accurate diagnosis and treatment of neonatal viral illnesses.

Comparing Whole Slide Imaging and Light Microscopy to Identify Tumor in en face Frozen Sections.

OBJECTIVE: To assess accuracy of whole slide imaging (WSI) in the interpretation of permanent and frozen sections in surgical pathology and the identification of tumors in cutaneous en face frozen sections. METHODS: Twenty glass slides containing cutaneous en face frozen sections were selected from twenty cases of keratinocyte carcinomas treated with Mohs micrographic surgery. Ten slides contained tumor and ten did not. A blinded dermatologic surgeon used traditional light microscopy (LM) to assess physical slides for tumor presence and type, while noting the confidence (scale 1-10) and time (min) in making the determination. After a seven-day washout period, the surgeon repeated this process using WSI of the same slides, each de-identified and scanned at 20x using the Aperio AT2 (Leica Biosystems). RESULTS: Percent agreement between LM and WSI was 100%, with Cohen's kappa of 1.0. The average time taken to determine tumor presence was significantly greater using WSI than LM. Similarly, the surgeon was significantly more confident using LM than WSI. CONCLUSION: This proof-of-concept study suggests that diagnostic concordance is excellent between LM and WSI in the evaluation of Mohs frozen sections. However, WSI was cumbersome to use, not ergonomic, and required significantly more time.

Production Processes for Creating Educational Videos.

Asynchronous video-based educational resources allow for increased course material engagement. In today's climate, educators are encouraged to create videos for online instruction but are typically given limited production guidance. Few formal resources exist to guide educators for high-quality video production in a non-studio setting. This article is a how-to guide for producing videos using widely available primary resources through three steps: preproduction, production, and postproduction. During preproduction, educators consider style and project scope, including the "what, how, and why" of the content. For production, we have provided information on the set, light, sounds, and video equipment needed for optimizing video production in a non-studio setting. Finally, during postproduction, the educator considers how to combine and edit the video as well as organize content. Overall, this article is an approachable guide to help educators begin their low-budget video-production journeys.

A stable phylogenomic classification of Travunioidea (Arachnida, Opiliones, Laniatores) based on sequence capture of ultraconserved elements.

Molecular phylogenetics has transitioned into the phylogenomic era, with data derived from next-generation sequencing technologies allowing unprecedented phylogenetic resolution in all animal groups, including understudied invertebrate taxa. Within the most diverse harvestmen suborder, Laniatores, most relationships at all taxonomic levels have yet to be explored from a phylogenomics perspective. Travunioidea is an early-diverging lineage of laniatorean harvestmen with a Laurasian distribution, with species distributed in eastern Asia, eastern and western North America, and south-central Europe. This clade has had a challenging taxonomic history, but the current classification consists of ~77 species in three families, the Travuniidae, Paranonychidae, and Nippononychidae. Travunioidea classification has traditionally been based on structure of the tarsal claws of the hind legs. However, it is now clear that tarsal claw structure is a poor taxonomic character due to homoplasy at all taxonomic levels. Here, we utilize DNA sequences derived from capture of ultraconserved elements (UCEs) to reconstruct travunioid relationships. Data matrices consisting of 317-677 loci were used in maximum likelihood, Bayesian, and species tree analyses. Resulting phylogenies recover four consistent and highly supported clades; the phylogenetic position and taxonomic status of the enigmatic genus Yuria is less certain. Based on the resulting phylogenies, a revision of Travunioidea is proposed, now consisting of the Travuniidae, Cladonychiidae, Paranonychidae (Nippononychidae is synonymized), and the new family Cryptomastridae Derkarabetian & Hedin, fam. n., diagnosed here. The phylogenetic utility and diagnostic features of the intestinal complex and male genitalia are discussed in light of phylogenomic results, and the inappropriateness of the tarsal claw in diagnosing higher-level taxa is further corroborated.

Dead Tumor Cells Expressing Infectious Salmon Anemia Virus Fusogenic Protein Favor Antigen Cross-Priming In Vitro.

Antigen cross-presentation is a crucial step in the assembly of an antitumor immune response leading to activation of naïve CD8 T cells. This process has been extensively used in clinical trials, in which dendritic cells generated in vitro are loaded with tumor antigens and then autotransplanted to the patients. Recently, the use of autologous transplant of dendritic cells fused with dying tumor cells has demonstrated good results in clinical studies. In this work, we generated a similar process in vivo by treating mice with dead tumor cells [cell bodies (CBs)] expressing the fusogenic protein of the infectious salmon anemia virus (ISAV). ISAV fusion protein retains its fusogenic capability when is expressed on mammalian cells in vitro and the CBs expressing it facilitates DCs maturation, antigen transfer by antigen-presenting cells, and increase cross-presentation by DCs in vitro. Additionally, we observed in the melanoma model that CBs with or without ISAV fusion protein reduce tumor growth in prophylactic treatment; however, only ISAV expressing CBs showed an increase CD4 and CD8 cells in spleen. Overall, our results suggest that CBs could be used as a complement with other type of strategies to amplify antitumor immune response.

Dual-mode crystal-bound and X-type passivation of quantum dots.

In this report, we present a new path to the control of quantum dot surface chemistry that can lead to a better understanding of nanoscale interfaces and the development of improved photocatalysts. Control of the synthetic methodology leads to QDs that are concomitantly ligated by crystal-bound organics at the surface anion sites and small X-type ligands on the surface cation sites.

Taxonomic revision of Plyomydas Wilcox & Papavero, 1971 with the description of two new species and its transfer to Mydinae (Insecta: Diptera: Mydidae)

ABSTRACT The monotypic Neotropical Mydidae genus Plyomydas Wilcox & Papavero, 1971, to date confined to coastal Peru, is reviewed. Two new species, Plyomydas adelphe sp. nov. and Plyomydas phalaros sp. nov., are described from mid-elevational western Argentina, which extends the distribution of the genus considerably. Distribution, occurrence in biodiversity hotspots sensu Conservation International, and seasonal incidence are discussed. Descriptions/re-descriptions, photographs, illustrations, and identification keys are provided and made openly accessible in data depositories to support future studies of the included taxa. Plyomydas is transferred from the Leptomydinae to the Mydinae: Messiasiini based on the absence of acanthophorite spines on abdominal tergite 10 in females and the presence of vein M3 + M4 terminating in the costal vein C. Leptomydinae is therefore restricted to the Northern Hemisphere with the exception of Hessemydas Kondratieff, Carr & Irwin, 2005 known from Madagascar. Messiasia notospila (Wiedemann, 1828) is compared to Plyomydas species.