Eastern Equine Encephalitis Virus Diversity in Massachusetts Patients, 1938-2020.

Eastern equine encephalitis virus (EEEV) is a relatively little-studied alphavirus that can cause devastating viral encephalitis, potentially leading to severe neurological sequelae or death. Although case numbers have historically been low, outbreaks have been increasing in frequency and scale since the 2000 s. It is critical to investigate EEEV evolutionary patterns, especially within human hosts, to understand patterns of emergence, host adaptation, and within-host evolution. To this end, we obtained formalin-fixed paraffin-embedded tissue blocks from discrete brain regions from five contemporary (2004-2020) patients from Massachusetts, confirmed the presence of EEEV RNA by in situ hybridization (ISH) staining, and sequenced viral genomes. We additionally sequenced RNA from scrapings of historical slides made from brain sections of a patient in the first documented EEE outbreak in humans in 1938. ISH staining revealed the presence of RNA in all contemporary samples, and quantification loosely correlated with the proportion of EEEV reads in samples. Consensus EEEV sequences were generated for all six patients, including the sample from 1938; phylogenetic analysis using additional publicly available sequences revealed clustering of each study sample with like sequences from a similar region, whereas an intrahost comparison of consensus sequences between discrete brain regions revealed minimal changes. Intrahost single nucleotide variant (iSNV) analysis of four samples from two patients revealed the presence of tightly compartmentalized, mostly nonsynonymous iSNVs. This study contributes critical primary human EEEV sequences, including a historic sequence as well as novel intrahost evolution findings, contributing substantially to our understanding of the natural history of EEEV infection in humans.

Development and validation of a molecular tool to predict pathologic complete response in esophageal adenocarcinoma.

Pathologic complete response (pCR) to neoadjuvant chemoradiation for locally advanced esophageal adenocarcinoma (EAC) confers significantly improved survival. The ability to infer pCR may spare esophagectomy in some patients. Currently, there are no validated biomarkers of pCR. This study sought to evaluate whether a distinct signature of DNA copy number alterations (CNA) can be predictive of pCR in EAC. Pretreatment biopsies from 38 patients with locally advanced EAC (19 with pCR and 19 with pathologic partial/poor response) were assessed for CNA using OncoScan assay. A novel technique was employed where within every cytogenetic band, the quantity of bases gained by each sample was computed as the sum of gained genomic segment lengths weighted by the surplus copy number of each segment. A threefold cross-validation was used to assess association with pCR or pathologic partial/poor response. Forty patients with locally advanced EAC from The Cancer Genome Atlas (TCGA) constituted an independent validation cohort. Gains in the chromosomal loci 14q11 and 17p11 were preferentially associated with pCR. Average area under the receiver operating characteristic curve (AUC) for predicting pCR was 0.80 among the threefold cross-validation test sets. Using 0.3 megabases as the cutoff that optimizes trade-off between sensitivity (63%) and specificity (89%) in the discovery cohort, similar prediction performance for clinical and radiographic response was demonstrated in the validation cohort from TCGA (sensitivity 61%, specificity 82%). Copy number gains in the 14q11 and 17p11 loci may be useful for prediction of pCR, and, potentially, personalization of esophagectomy in EAC.

Splenic-vasculature involvement is associated with poor prognosis in resected distal pancreatic cancer.

BACKGROUND: Distal pancreatic carcinoma is one of the most lethal cancers largely due to its high incidence of distant metastasis. This study aims to assess the prognostic value of splenic-vasculature involvement in resected distal pancreatic carcinoma. METHODS: In this retrospective study, we collected the clinicopathologic information of 454 patients with pancreatic cancer and performed univariate and multivariate analyses to identify factors associated with progression-free survival (PFS) and overall survival (OS), with an emphasis on the prognostic value of splenic-artery and -vein involvement. RESULTS: Univariate analysis revealed that larger tumor size, non-intraductal papillary mucinous neoplasm (non-IPMN)-associated adenocarcinoma, poor differentiation, stage pT3, nodal metastasis, lymphovascular invasion, perineural invasion, and pathologic and radiographic evidence of splenic-vein invasion were significantly associated with shorter PFS and OS (all P < 0.05). Multivariate analysis confirmed non-IPMN-associated adenocarcinoma, stage pT3, stage pN1-2, and post-operative adjuvant chemotherapy as independent risk factors for both PFS and OS, and larger tumor size and radiographic evidence of splenic-artery invasion as predictors of PFS only. CONCLUSION: Guidelines should be developed for a uniform approach with regard to the examination and reporting of the status of the splenic vasculature when dealing with distal-pancreatic-cancer specimens.

Overcoming Educational Challenges and Impact of COVID-19 in a Pathology Residency Program.

Our program in is a 4-year combined anatomic pathology (AP) and clinical pathology (CP) program located in New Hampshire. Prior to the novel coronavirus (COVID-19) pandemic, double-headed sign-outs and multi-headed scope didactic conferences took place daily. On the autopsy service, cases were performed in-house under attending supervision, and forensic cases were performed at the off-site Office of the Medical Examiner. In CP, residents engaged in weekly didactic CP lectures and engaged in in-person resident-attending discussions, laboratory rounds, and direct patient contact on a daily basis. Institutional Universal Guidelines from the Emergency Order from New Hampshire were imposed at the beginning of the pandemic. These included exposure mitigation and employee screening strategies. Changes to resident rotations and didactic sessions, strategies to maintain resident wellness, and the program director perspectives are described. Amid the pandemic, digital pathology, teleconferencing platforms, and social media became important resources for pathology education. Digital platforms allowed groups of people to communicate and watch live presentations while social distancing. In AP, whole slide imaging allowed both attendings and residents to scan slides for personal learning, slide conferences, and didactic learning sessions. Following these measures, we supported the clinical needs of our medical center and learning needs of our residents while enacting social distancing and prevention guidelines early in the pandemic. Although the full impact of COVID-19 on pathology residency programs is still unknown, we incorporated new facets of communication technologies. These were immensely helpful in maintaining social distancing and helping to reduce the spread of disease.

Encapsulated papillary carcinoma with and without frank invasion: Comparison of clinicopathologic features and role of axillary staging.

To investigate clinical and pathologic features of encapsulated papillary carcinomas (EPCs) that may be associated with invasive disease and characterize the axillary staging practices for EPCs at our institution. A pathology database search for cases containing "papillary carcinoma" was performed. Slides were reviewed by two pathologists. Clinicopathological features and axillary staging practices of EPCs with and without invasion were compared. Twenty-five cases of EPCs were identified. Fifteen cases contained a frank invasive tumor (60%), which were all pT1 (0.7 ± 0.56 cm), and the majority were ER-positive, HER2-negative, low-grade IDC-NST. Seventeen patients underwent sentinel lymph node biopsies (SLNB). No nodal metastases were identified. Follow-up was available for 24 patients (mean = 39 ± 29 months); 23 had no NED. Patients that presented with a self-palpated mass (versus screening) were more likely to have an invasive component; however, no pathologic or radiologic features differentiated EPCs with and without frank invasion. Pathologic and radiologic characteristics did not differentiate EPCs with and without frank invasion. EPCs have an excellent prognosis supported by the notable disease-free survival and negative nodal status in our cohort, which supports the notion that patients with EPCs may forgo axillary staging.

Validation of American Joint Committee on Cancer 8th edition of TNM staging in resected distal pancreatic cancer.

BACKGROUND: In order to improve risk stratification and clinical management of the pancreatic ductal adenocarcinoma (PDAC), the American Joint Committee on Cancer (AJCC) has published its eighth edition staging manual. Some major changes have been introduced in the new staging system for both T and N categories. Given the rarity of resectable disease, distal pancreatic cancer is likely underrepresented in the published clinical studies, and how the impact of the staging system actually reflects on to clinical outcomes remain unclear. AIM: To validate the AJCC 8th edition of TNM staging in distal PDAC. METHODS: A retrospective cohort study was performed in seven academic medical centers in the United States. Clinicopathological prognostic factors associated with progression-free survival (PFS) and overall survival (OS) were evaluated through univariate and multivariate analyses. RESULTS: Overall, 454 patients were enrolled in the study, and were divided into 2 subgroups: Invasive intraductal papillary mucinous neoplasms (IPMN) (115 cases) and non-IPMN associated adenocarcinoma (339 cases). Compared to invasive IPMN, non-IPMN associated adenocarcinomas are more common in relatively younger patients, have larger tumor size, are more likely to have positive lymph nodes, and are associated with a higher tumor (T) stage and nodal (N) stage, lymphovascular invasion, perineural invasion, tumor recurrence, and a worse PFS and OS. The cohort was predominantly categorized as stage 3 per AJCC 7th edition staging manual, and it's more evenly distributed based on 8th edition staging manual. T and N staging of both 7th and 8th edition sufficiently stratify PFS and OS in the entire cohort, although dividing into N1 and N2 according to the 8th edition does not show additional stratification. For PDAC arising in IPMN, T staging of the 7th edition and N1/N2 staging of the 8th edition appear to further stratify PFS and OS. For PDAC without an IPMN component, T staging from both versions fails to stratify PFS and OS. CONCLUSION: The AJCC 8th edition TNM staging system provides even distribution for the T staging, however, it does not provide better risk stratification than previous staging system for distal pancreatic cancer.

A machine learning algorithm for simulating immunohistochemistry: development of SOX10 virtual IHC and evaluation on primarily melanocytic neoplasms.

Immunohistochemistry (IHC) is a diagnostic technique used throughout pathology. A machine learning algorithm that could predict individual cell immunophenotype based on hematoxylin and eosin (H&E) staining would save money, time, and reduce tissue consumed. Prior approaches have lacked the spatial accuracy needed for cell-specific analytical tasks. Here IHC performed on destained H&E slides is used to create a neural network that is potentially capable of predicting individual cell immunophenotype. Twelve slides were stained with H&E and scanned to create digital whole slide images. The H&E slides were then destained, and stained with SOX10 IHC. The SOX10 IHC slides were scanned, and corresponding H&E and IHC digital images were registered. Color-thresholding and machine learning techniques were applied to the registered H&E and IHC images to segment 3,396,668 SOX10-negative cells and 306,166 SOX10-positive cells. The resulting segmentation was used to annotate the original H&E images, and a convolutional neural network was trained to predict SOX10 nuclear staining. Sixteen thousand three hundred and nine image patches were used to train the virtual IHC (vIHC) neural network, and 1,813 image patches were used to quantitatively evaluate it. The resulting vIHC neural network achieved an area under the curve of 0.9422 in a receiver operator characteristics analysis when sorting individual nuclei. The vIHC network was applied to additional images from clinical practice, and was evaluated qualitatively by a board-certified dermatopathologist. Further work is needed to make the process more efficient and accurate for clinical use. This proof-of-concept demonstrates the feasibility of creating neural network-driven vIHC assays.

Fine needle aspiration of malignant melanoma with myxoid features: A case report with molecular analysis.

Malignant melanoma with myxoid features (MMM) is a rare melanoma variant in which tumor cells are embedded within a basophilic myxoid stroma. The stromal matrix is composed of acidic mucopolysaccharides, which are thought to be produced by mesenchymal stromal cells in response to melanoma invasion. Interestingly, this myxoid matrix is more often seen in metastasis from a primary tumor that does not have a myxoid stroma. The diagnosis of MMM on fine needle aspiration (FNA) can be confused with other myxoid tumors. Herein, we present a case of MMM diagnosed by FNA of a peri-auricular lymph node in an 89-year-old man with a history of resected malignant melanoma. We describe the clinical, cytohistological, and immunohistochemical findings, and present the unique molecular alterations that were identified. We also discuss the differential diagnosis and potential diagnostic pitfalls associated with MMM.

Melanocytic aggregates with unique morphology associated with regression of basal cell carcinoma.

BACKGROUND: Spontaneous regression of basal cell carcinomas (BCC) is a well-documented phenomenon. In practice, we have observed melanocytic aggregates associated with BCC at various stages of regression showing unique morphologic features. METHODS: Fourteen cases featuring melanocytic aggregates were retrospectively identified through a pathology database search. Clinical and histopathologic features were systematically evaluated, and additional immunohistochemical studies were performed. Melanocyte density within tumor nodules was compared to a group of control BCCs. RESULTS: All cases showed BCC at various stages of regression with associated melanocytic aggregates, as highlighted by Melan-A and SOX10 immunostains. Three of 14 cases (21.4%) had only dermal melanocytic nests, while 11 (78.6%) had both junctional and dermal nests. The melanocytic aggregates all had similar asymmetrical architecture and lacked maturation. The melanocytes were small, uniform, bland, and had minimal cytoplasm. Their nuclei were overlapping and hyperchromatic, and had inconspicuous nucleoli. None of the melanocytic aggregates stained for BRAFV600E by immunohistochemistry. No patient developed a recurrent or metastatic melanocytic lesion (median follow-up 42 months). Melanocyte density was higher in the case series than in the control BCCs (P = 0.0008). CONCLUSION: We described the unique morphology of melanocytic aggregates associated with BCC regression.

Modelling permafrost thickness in Great Britain over glacial cycles.

Like other countries, the UK has opted for deep geological disposal for the long-term, safe management of higher-activity radioactive waste. However, a site and a geological environment have yet to be identified to host a geological disposal facility. In considering its long-term safety functionality, it is necessary to consider natural processes, such as permafrost development, that have the potential to alter the geological environment over the time-scale of glacial-interglacial cycles. We applied a numerical model to simulate the impact of long-term climatic variability on groundwater flow and permafrost dynamics in two contrasting geological settings in Great Britain: (i) higher strength rocks (HSR) overlain by higher permeability sandstones with a high topographic gradient (GS1); (ii) a mixed sedimentary sequence of high and low permeability rocks resting on igneous HSR with a very low topographic gradient (GS2). We evaluated the sensitivity of simulated permafrost thickness to a variety of climatic and subsurface conditions. Uncertainty in the scaling of the surface temperature time-series, 10-25 °C below present day temperature, has the largest impact on maximum permafrost thickness, PFmax, compared to other variables. However, considering plausible parameter ranges for UK settings, PFmax is up to twice as sensitive to changes in thermal conductivity and geothermal heat flux than to changes in porosity. Heat advection only affects modelled PFmax for high hydraulic conductivity rocks and if permafrost is considered to be relatively permeable. Whilst local differences in permafrost thickness of tens of meters, caused by variations in heat advection, are of minor importance over glacial-interglacial cycles, heat advection can be important in the development of taliks and the maintenance of a more active groundwater flow system. We conclude that it is likely to be important to simulate the effect of heat advection on coupled permafrost and groundwater flow systems in settings containing higher permeability lithological sequences.

Automated Detection of Celiac Disease on Duodenal Biopsy Slides: A Deep Learning Approach.

CONTEXT: Celiac disease (CD) prevalence and diagnosis have increased substantially in recent years. The current gold standard for CD confirmation is visual examination of duodenal mucosal biopsies. An accurate computer-aided biopsy analysis system using deep learning can help pathologists diagnose CD more efficiently. SUBJECTS AND METHODS: In this study, we trained a deep learning model to detect CD on duodenal biopsy images. Our model uses a state-of-the-art residual convolutional neural network to evaluate patches of duodenal tissue and then aggregates those predictions for whole-slide classification. We tested the model on an independent set of 212 images and evaluated its classification results against reference standards established by pathologists. RESULTS: Our model identified CD, normal tissue, and nonspecific duodenitis with accuracies of 95.3%, 91.0%, and 89.2%, respectively. The area under the receiver operating characteristic curve was >0.95 for all classes. CONCLUSIONS: We have developed an automated biopsy analysis system that achieves high performance in detecting CD on biopsy slides. Our system can highlight areas of interest and provide preliminary classification of duodenal biopsies before review by pathologists. This technology has great potential for improving the accuracy and efficiency of CD diagnosis.

Superficial malignant peripheral nerve sheath tumor with overlying intradermal melanocytic nevus mimicking spindle cell melanoma.

Malignant peripheral nerve sheath tumors are rare soft tissue sarcomas with histological and immunohistochemical similarities to spindle cell melanoma. Although spindle cell melanoma is significantly more common, both tumors may express S100 and lack staining for HMB-45, Melan-A or MITF. Here we present a case of superficial malignant peripheral nerve sheath tumor with diffuse S100 positivity arising in a subtle neurofibroma in close proximity to an intradermal melanocytic nevus. This configuration had led to prior misdiagnosis as a desmoplastic melanoma arising in the nevus and to sentinel lymph node biopsy. Identification of the background neurofibroma, as well as CD34 positivity raised consideration of a low grade malignant peripheral nerve sheath tumor, which was confirmed via observation of Schwannian differentiation on electron microscopy. The importance of distinguishing these two tumors is stressed owing to the difference in management.

Surgeon Awareness of Operating Room Supply Costs.

BACKGROUND: The extent to which surgeons understand costs associated with expensive operative procedures remains unclear. The goal of the study was to better understand surgeon cost awareness of operating room supplies and implants. METHODS: This was a cross-sectional study of faculty (n = 24) and trainees (fellow and residents, n = 27) in the Department of Otolaryngology. Participants completed surveys to assess opinions on importance of cost and ease in accessing cost data and were asked to estimate the costs of operating room (OR) supplies and implants. Estimates within 20% of actual cost were considered correct. Analyses were stratified into faculty and trainee surgeons. RESULTS: Cost estimates varied widely, with a low percentage of correct estimations (25% for faculty, 12% for trainees). Surgeons tended to underestimate the cost of high-cost items (55%) and overestimate the cost of low-cost items (77%). Attending surgeons were more accurate at correctly estimating costs within their own subspecialty (33% vs 16%, P < .001). Self-rated cost knowledge and years in practice did not correlate with cost accuracy (P < .05). CONCLUSIONS: A majority of surgeons were unable to correctly estimate the costs of items/implants used in their OR. An opportunity exists to improve the mechanisms by which cost data are fed back to physicians to help promote value-based decision making.

The formation and fate of internal waves in the South China Sea.

Internal gravity waves, the subsurface analogue of the familiar surface gravity waves that break on beaches, are ubiquitous in the ocean. Because of their strong vertical and horizontal currents, and the turbulent mixing caused by their breaking, they affect a panoply of ocean processes, such as the supply of nutrients for photosynthesis, sediment and pollutant transport and acoustic transmission; they also pose hazards for man-made structures in the ocean. Generated primarily by the wind and the tides, internal waves can travel thousands of kilometres from their sources before breaking, making it challenging to observe them and to include them in numerical climate models, which are sensitive to their effects. For over a decade, studies have targeted the South China Sea, where the oceans' most powerful known internal waves are generated in the Luzon Strait and steepen dramatically as they propagate west. Confusion has persisted regarding their mechanism of generation, variability and energy budget, however, owing to the lack of in situ data from the Luzon Strait, where extreme flow conditions make measurements difficult. Here we use new observations and numerical models to (1) show that the waves begin as sinusoidal disturbances rather than arising from sharp hydraulic phenomena, (2) reveal the existence of >200-metre-high breaking internal waves in the region of generation that give rise to turbulence levels >10,000 times that in the open ocean, (3) determine that the Kuroshio western boundary current noticeably refracts the internal wave field emanating from the Luzon Strait, and (4) demonstrate a factor-of-two agreement between modelled and observed energy fluxes, which allows us to produce an observationally supported energy budget of the region. Together, these findings give a cradle-to-grave picture of internal waves on a basin scale, which will support further improvements of their representation in numerical climate predictions.

Chemoprophylaxis for venous thromboembolism in otolaryngology.

IMPORTANCE: Venous thromboembolism (VTE) causes significant morbidity and mortality in surgical patients. Despite strong evidence that thromboprophylaxis reduces the incidence VTE, guidelines for prophylaxis in otolaryngology are not well established. Key to the development of VTE prophylaxis recommendations are effective VTE risk stratification and evaluation of the benefits and harms of prophylaxis. OBJECTIVE: To evaluate the effectiveness and safety of VTE chemoprophylaxis among a population of otolaryngology patients stratified by risk. DESIGN, SETTING, AND PARTICIPANTS: Retrospective cohort study of 3498 adult patients admitted for otolaryngologic surgery at a single-institution academic tertiary care medical center between September 1, 2003, and June 30, 2010. INTERVENTIONS: Patients were stratified into 2 groups based on whether they received VTE chemoprophylaxis. MAIN OUTCOMES AND MEASURES: Incidence of VTE and bleeding-related complications within 30 days after surgery. RESULTS: Of 1482 patients receiving VTE chemoprophylaxis, 18 (1.2%) developed a VTE compared with 27 of 2016 patients (1.3%) who did not receive prophylaxis (P = .75). Patients with Caprini VTE risk scores greater than 7 were less likely to have a VTE with perioperative chemoprophylaxis (5.3% vs 10.4%; P = .06). Of patients with VTE chemoprophylaxis, 3.5% developed a bleeding complication compared with 1.2% of patients without prophylaxis (P < .001). Bleeding complications were associated with concomitant use of antiplatelet medications and chemoprophylaxis. Among patients undergoing free tissue transfer, chemoprophylaxis significantly decreased the incidence of VTE (2.1% vs 7.7%; P = .002) and increased bleeding complications (11.9% vs 4.5%; P = .01). In all other patients, VTE chemoprophylaxis did not significantly influence the likelihood of VTE (1.0% vs 0.6%; P = .12) or bleeding (1.5% vs 0.9%; P = .15). CONCLUSIONS AND RELEVANCE: Effectiveness and safety of VTE chemoprophylaxis differed between patient subgroups, defined by Caprini risk score and by procedure. Effectiveness was most evident in patients with high Caprini risk scores and microvascular free tissue reconstruction. Bleeding complications were associated with VTE chemoprophylaxis administered in close proximity to potent antiplatelet therapy. The Caprini risk assessment model appears to be an effective tool to stratify otolaryngology patients by risk for VTE. Patients undergoing free tissue reconstruction merit further study before developing recommendations for VTE prophylaxis because of their higher risk of both VTE and bleeding.