A Bayesian approach to estimating COVID-19 incidence and infection fatality rates.

Naive estimates of incidence and infection fatality rates (IFR) of coronavirus disease 2019 suffer from a variety of biases, many of which relate to preferential testing. This has motivated epidemiologists from around the globe to conduct serosurveys that measure the immunity of individuals by testing for the presence of SARS-CoV-2 antibodies in the blood. These quantitative measures (titer values) are then used as a proxy for previous or current infection. However, statistical methods that use this data to its full potential have yet to be developed. Previous researchers have discretized these continuous values, discarding potentially useful information. In this article, we demonstrate how multivariate mixture models can be used in combination with post-stratification to estimate cumulative incidence and IFR in an approximate Bayesian framework without discretization. In doing so, we account for uncertainty from both the estimated number of infections and incomplete deaths data to provide estimates of IFR. This method is demonstrated using data from the Action to Beat Coronavirus erosurvey in Canada.

MRN findings of lateral antebrachial cutaneous nerve impingement in a collegiate athlete.

Dynamic compression of the lateral antebrachial cutaneous nerve (LABCN) occurs with forearm pronation when the LABCN becomes compressed by the lateral margin of the biceps tendon. LABCN compression is a rare occurrence and is often overlooked as an etiology for forearm pain. While this entity has been described in several case reports in the orthopedic literature, it has not yet been described in radiology literature. We present a case of LABCN compression by the biceps tendon which was suggested by high-resolution magnetic resonance neurography in combination with the clinical findings and was subsequently confirmed and corrected surgically.

A comparison of saline and gadolinium shoulder MR arthrography to arthroscopy.

PURPOSE: Compare the diagnostic performance of saline and gadolinium shoulder magnetic resonance arthrograms (MRA) in the detection of labral and rotator cuff injury compared to arthroscopy. MATERIALS AND METHODS: Consecutive patients who underwent a gadolinium or saline MRA followed by arthroscopy were retrospectively reviewed. The reports were reviewed for injuries. A chi square or Fisher's exact test was performed to compare the MRA and surgery. Kappa values were calculated to correlate diagnosis of tear between MRA and arthroscopy. RESULTS: There were a total of 58 patients included, including 34 gadolinium arthrograms and 24 saline arthrograms. The accuracy of saline MRA was similar compared to gadolinium MRA in the diagnosis of tears of the supraspinatus (accuracy 0.88 vs 0.74, respectively) and infraspinatus (accuracy 0.88 vs 0.65, respectively) tendons and tears of the anterior/anterior inferior, posterior, and superior labrum, (accuracy 0.79 vs 0.76, 0.71 vs 0.62, and 0.58 vs 0.56), and saline vs gadolinium, respectively. Although there was a trend toward overall better saline MRA performance, a statistically significant difference in the accuracy to detect tears was only noted for the infraspinatus tendon. Interobserver agreement for rotator cuff tears was higher for saline than gadolinium MRA. CONCLUSION: Saline MRA was accurate, with no significant differences compared gadolinium arthrograms in the diagnosis of labral and rotator cuff pathology. Given expense, and the potential additional information provided by fluid sensitive sequences over T1 fat-suppressed sequences, consideration should be given to using saline for shoulder MRAs. LEVEL OF EVIDENCE: Level III, Retrospective Cohort Study.

A comprehensive review of the normal, abnormal, and post-operative MRI appearance of the distal biceps brachii.

The biceps brachii myotendinous unit is a common source of shoulder, arm, and elbow pain. Its complex anatomy can present a challenge when interpreting MR images. We discuss the clinical and imaging presentations of injury related to the proximal biceps brachii separately in another manuscript. The purpose of this manuscript is to review the distal biceps anatomy along with pathology and post-operative appearance as seen on MRI.

A comprehensive review of the normal, abnormal, and post-operative MRI appearance of the proximal biceps brachii.

The biceps brachii myotendinous unit, particularly the long head of the biceps tendon and its labral attachment, is a common cause of shoulder and arm pain. Its complex anatomy and normal variations can present a challenge when interpreting MR images. The purpose of this manuscript is to review the proximal biceps anatomy, variants, pathology, and post-operative appearance as seen on MRI. Recent data regarding the accuracy of clinical examination and MRI will be summarized.

Nodal metastases of soft tissue sarcomas: risk factors, imaging findings, and implications.

Soft tissue sarcomas (STS) are malignancies derived from connective tissue, and regional lymph node metastasis (RLNM), while not common, is an important aspect of prognosis and treatment. Various risk factors, in particular the histological subtype, affect the likelihood of nodal involvement, which can be characterized by imaging features such as nodal dimension and morphology. Currently, surveillance and management vary by institution, as concrete societal guidelines have not been established. Common nodal status assessment strategies include physical exam, US CT, MRI, sentinel lymph node biopsy (SLNB) and radical lymphadenectomy. This article summarizes data regarding relevant risk factors of RLNM, imaging features, and any available data regarding surveillance recommendations.

An evaluation of machine learning techniques to predict the outcome of children treated for Hodgkin-Lymphoma on the AHOD0031 trial: A report from the Children's Oncology Group.

In this manuscript we analyze a data set containing information on children with Hodgkin Lymphoma (HL) enrolled on a clinical trial. Treatments received and survival status were collected together with other covariates such as demographics and clinical measurements. Our main task is to explore the potential of machine learning (ML) algorithms in a survival analysis context in order to improve over the Cox Proportional Hazard (CoxPH) model. We discuss the weaknesses of the CoxPH model we would like to improve upon and then we introduce multiple algorithms, from well-established ones to state-of-the-art models, that solve these issues. We then compare every model according to the concordance index and the brier score. Finally, we produce a series of recommendations, based on our experience, for practitioners that would like to benefit from the recent advances in artificial intelligence.

Multiple sporadic schwannomas in a previously radiated field.

Peripheral nerve sheath tumors are a heterogenous group of predominantly benign tumors of neurogenic origin that arise outside of the central nervous system and include schwannomas and neurofibromas. These tumors often occur sporadically, however multiple lesions are generally associated with genetic syndromes such as neurofibromatosis (type 1 and 2) and schwannomatosis, and occasionally these tumors and their malignant variations are associated with a history of radiation treatment. Multiple benign schwannomas in an irradiated field have seldom been reported in the literature. We describe a case of a 49-year-old male with a history of right sided irradiated testicular cancer who presented with 2 histologically confirmed benign schwannomas in the right pelvic wall and right psoas muscle.

Introducing a New High-Resolution Handwritten Digits Data Set with Writer Characteristics.

The contributions in this article are two-fold. First, we introduce a new handwritten digit data set that we collected. It contains high-resolution images of handwritten digits together with various writer characteristics which are not available in the well-known MNIST database. The multiple writer characteristics gathered are a novelty of our data set and create new research opportunities. The data set is publicly available online. Second, we analyse this new data set. We begin with simple supervised tasks. We assess the predictability of the writer characteristics gathered, the effect of using some of those characteristics as predictors in classification task and the effect of higher resolution images on classification accuracy. We also explore semi-supervised applications; we can leverage the high quantity of handwritten digits data sets already existing online to improve the accuracy of various classifications task with noticeable success. Finally, we also demonstrate the generative perspective offered by this new data set; we are able to generate images that mimics the writing style of specific writers. The data set has unique and distinct features and our analysis establishes benchmarks and showcases some of the new opportunities made possible with this new data set. Supplementary Information: The online version contains supplementary material available at 10.1007/s42979-022-01494-2.

A Novel Approach to Determining Tumor Progression Using a Three-Site Pilot Clinical Trial of Spectroscopic MRI-Guided Radiation Dose Escalation in Glioblastoma.

Glioblastoma (GBM) is a fatal disease, with poor prognosis exacerbated by difficulty in assessing tumor extent with imaging. Spectroscopic MRI (sMRI) is a non-contrast imaging technique measuring endogenous metabolite levels of the brain that can serve as biomarkers for tumor extension. We completed a three-site study to assess survival benefits of GBM patients when treated with escalated radiation dose guided by metabolic abnormalities in sMRI. Escalated radiation led to complex post-treatment imaging, requiring unique approaches to discern tumor progression from radiation-related treatment effect through our quantitative imaging platform. The purpose of this study is to determine true tumor recurrence timepoints for patients in our dose-escalation multisite study using novel methodology and to report on median progression-free survival (PFS). Follow-up imaging for all 30 trial patients were collected, lesion volumes segmented and graphed, and imaging uploaded to our platform for visual interpretation. Eighteen months post-enrollment, the median PFS was 16.6 months with a median time to follow-up of 20.3 months. With this new treatment paradigm, incidence rate of tumor recurrence one year from treatment is 30% compared to 60-70% failure under standard care. Based on the delayed tumor progression and improved survival, a randomized phase II trial is under development (EAF211).

Positional targets for lingual consonants defined using electromagnetic articulography.

The study examined the positional targets for lingual consonants defined using a point-parameterized approach with Wave (NDI, Waterloo, ON, Canada). The overall goal was to determine which consonants had unique tongue positions with respect to other consonants. Nineteen talkers repeated vowel-consonant-vowel (VCV) syllables that included consonants /t, d, s, z, , k, g/ in symmetrical vowel contexts /i, u, a/, embedded in a carrier phrase. Target regions for each consonant, characterized in terms of x,y,z tongue positions at the point of maximum tongue elevation, were extracted. Distances and overlaps were computed between all consonant pairs and compared to the distances and overlaps of their contextual targets. Cognates and postalveolar homorganics were found to share the location of their target regions. On average, alveolar stops showed distinctively different target regions than alveolar fricatives, which in turn showed different target region locations than the postalveolar consonants. Across talker variability in target locations was partially explained by differences in habitual speaking rate and hard palate characteristics.

Refractory occipital scalp pruritus treated with computed tomography-guided greater occipital nerve ablation.

Greater occipital nerve blocks and thermal ablations have been widely discussed as an efficacious treatment strategy for multiple difficult to treat conditions, including occipital neuralgia, migraines, and cervicogenic headaches. Nerve blocks have also recently been presented as a method of treating neuropathic itch in the upper extremities, where pruritus occurs without visible dermatologic manifestations. We report a case of refractory occipital scalp pruritus in a patient who had excellent although time-limited response to greater occipital nerve blocks but achieved durable symptom control with CT-guided greater occipital nerve ablation.

Capturing spatial dependence of COVID-19 case counts with cellphone mobility data.

Spatial dependence is usually introduced into spatial models using some measure of physical proximity. When analysing COVID-19 case counts, this makes sense as regions that are close together are more likely to have more people moving between them, spreading the disease. However, using the actual number of trips between each region may explain COVID-19 case counts better than physical proximity. In this paper, we investigate the efficacy of using telecommunications-derived mobility data to induce spatial dependence in spatial models applied to two Spanish communities' COVID-19 case counts. We do this by extending Besag York Mollié (BYM) models to include both a physical adjacency effect, alongside a mobility effect. The mobility effect is given a Gaussian Markov random field prior, with the number of trips between regions as edge weights. We leverage modern parametrizations of BYM models to conclude that the number of people moving between regions better explains variation in COVID-19 case counts than physical proximity data. We suggest that this data should be used in conjunction with physical proximity data when developing spatial models for COVID-19 case counts.

Retrospective study of non-natural manners of death in Ontario: Effects of the COVID-19 pandemic and related public health measures.

BACKGROUND: The effects of the COVID-19 pandemic on non-natural manners of death in Ontario is not known. Understanding the indirect consequences of the pandemic and related public health measures (i.e. lockdown) fills a vital need to inform best practice in public health and guide policy decisions. METHODS: The Office of the Chief Coroner and the Ontario Forensic Pathology Service (OCC-OFPS) investigate sudden and unexpected deaths in the province of Ontario. The number of homicides, suicides, and accidental deaths (non-natural deaths=77,655) were extracted from the centralized Coroner's Information System database (total deaths=197,966), across four provincially defined stages of lockdown related to the COVID-19 pandemic (March 17 to December 31, 2020), and crude rates (per 100,000 people) were compared to the previous eleven years. FINDINGS: There was no major change to the rate of homicides during 2020 compared to 2009-2019 (RR 1⋅1, 95% CI 0⋅95-1⋅2; p=0⋅19; estimated annual effect=21 more deaths in 2020). The rate of suicides also did not show an overall major change in 2020 (RR 1⋅02, 95% CI 0⋅96-1⋅1; p=0⋅50; estimated annual effect=27 more deaths in 2020). However, during the first stage of lockdown (Stage 0), there was a decrease in the rate of suicides compared to all combinations of recent years from 2013 onwards (RRs 0⋅82-0⋅86, combined 95% CI 0⋅69-0⋅99; max p=0⋅039; estimated effect of 30 less deaths in Stage 0). There was an excess of over 1,500 accidental drug-related deaths that occurred during 2020 (RR 2⋅5, 95% CI 2⋅4-2⋅7; p<0⋅001). This finding held up to 'interrupted time series' robustness testing, indicating that 2020 had substantially more drug-related deaths, even when accounting for the linear increasing trend over time. Although motor vehicle collision associated fatalities appeared to decrease slightly in 2020 (RR 0⋅89, 95% CI 0⋅81-0⋅96; p=0⋅0039; estimated annual effect of 78 less deaths), we could not conclude any lockdown-associated effect, particularly when compared to 2019 (RR 0⋅26, 95% CI 0⋅75-1⋅1; p=0⋅26). INTERPRETATION: In Ontario, the short-term effects of the COVID-19 pandemic did not greatly increase homicide or suicide rates, nor decrease motor vehicle collision fatality rates; however, the longer-term impact of the pandemic remains to be elucidated and ongoing vigilance is warranted in the event that other trends emerge. Accidental drug-related fatalities substantially increased during all stages of the lockdown, marking an urgent need for consideration in policy. These results highlight the vital role of death investigation systems in providing high quality and timely data to inform public health recommendations.

Subduing the influence of PCR inhibitors on amplifying aged, degraded, and low copy number DNA: PCR enhancer cocktail-p and rescue PCR.

PCR inhibitors are a formidable problem to the study of aged, degraded, and/or low copy number DNA. As a result, there is a need to find alternate methods that ameliorate the efficacy of PCR. In this study, we attempted to use genetic methods to identify the species of salmonid (Oncorhynchus spp.) remains recovered from archaeological sites along the Feather River located in northern California, United States. In the process of doing so, we compared the efficacy of a PCR enhancer cocktail called "PEC-P" and a reagent rich PCR recipe called "rescue PCR" over standard PCR. Across all treatments (full concentration and 1:10 dilute eluates subjected to standard PCR, PEC-P, and rescue PCR) species identification was possible for 74 of 93 archaeological fish specimens (79.6%). Overall, six of the 93 samples (6.5%) consistently yielded species identification across all treatments. The species of ten specimens (10.8%) were uniquely identified from amplicons produced with either PEC-P or rescue PCR or both. Notably, the species of seven samples (7.5%) were uniquely identified with standard PCR over the alternative treatments. Considering both full concentration and 1:10 dilute eluates (N = 186), standard PCR performed as well as PEC-P (p = 0.1451) and rescue (p = 0.6753). Yet, considering results from full concentration eluates alone (N = 93), PEC-P (60.2%) outperformed both standard PCR (44.1%; p = 0.0277) and rescue PCR (40.9%; p = 0.0046). Stochasticity observed in our study cautions us against choosing a "best" performing method of those explored here and suggests their respective potentials to improve success may be sample dependent. When working with samples compromised by PCR inhibitors, it is useful to have alternative methodologies for subduing the problem. Both PEC-P and rescue PCR represent useful alternative methods for the study of aged, degraded, and/or low copy number DNA samples compromised by PCR inhibitors.

A probable prehistoric case of meningococcal disease from San Francisco Bay: Next generation sequencing of Neisseria meningitidis from dental calculus and osteological evidence.

Next Generation Sequencing (NGS) of ancient dental calculus samples from a prehistoric site in San Francisco Bay, CA-SCL-919, reveals a wide range of potentially pathogenic bacteria. One older adult woman, in particular, had high levels of Neisseria meningitidis and low levels of Haemophilus influenzae, species that were not observed in the calculus from three other individuals. Combined with the presence of incipient endocranial lesions and pronounced meningeal grooves, we interpret this as an ancient case of meningococcal disease. This disease afflicts millions around the globe today, but little is known about its (pre)history. With additional sampling, we suggest NGS of calculus offers an exciting new window into the evolutionary history of these bacterial species and their interactions with humans.