Potential Clinical Utility of a Targeted Circulating Tumor DNA Assay in Esophageal Adenocarcinoma.

OBJECTIVE: To explore the clinical utility of circulating tumor DNA (ctDNA) in esophageal adenocarcinoma (EAC) by developing a cost-effective and rapid technique utilising targeted amplicon sequencing. SUMMARY OF BACKGROUND DATA: Emerging evidence suggests that levels of ctDNA in the blood can be used to monitor treatment response and in the detection of disease recurrence in various cancer types. Current staging modalities for EAC such as computerised tomography of the chest/abdomen/pelvis (CT) and positron emission tomography (PET) do not reliably detect occult micro-metastatic disease, the presence of which signifies a poor prognosis. After curative-intent treatment, some patients are still at high risk of recurrent disease, and there is no widely accepted optimal surveillance tool for patients with EAC. METHODS: Sixty-two patients with EAC were investigated for the presence of ctDNA using a tumor-informed approach. We designed a custom targeted amplicon sequencing panel of target specific primers covering mutational foci in 9 of the most commonly mutated genes in EAC. Serial blood samples were taken before and after neoadjuvant treatment (NAT), and during surveillance. RESULTS: Somatic mutations were detected in pre-treatment biopsy samples of 55 out of 62 (89%) EAC patients. Mutations in TP53 (80%) were the most common. Out of these 55 patients, 20 (36%) had detectable ctDNA at baseline. The majority (90%) of patients with detectable ctDNA had either locally advanced tumors, nodal involvement or metastatic disease. In patients with locally advanced tumors, disease free survival (DFS) was more accurately stratified using pre-treatment ctDNA status [HR 4.34 (95% CI 0.93-20.21); P = 0.05] compared to nodal status on PET-CT. In an exploratory subgroup analysis, patients who are node negative but ctDNA positive have inferior DFS [HR 11.71 (95% CI 1.16-118.80) P = 0.04]. In blood samples taken before and following NAT, clearance of ctDNA after NAT was associated with a favourable response to treatment. Furthermore, patients who are ctDNA positive during post-treatment surveillance are at high risk of relapse. CONCLUSIONS: Our study shows that ctDNA has potential to provide additional prognostication over conventional staging investigation such as CT and PET. It may also have clinical utility in the assessment of response to NAT and as a biomarker for the surveillance of recurrent disease.

Uniparental disomy as a mechanism for X-linked chondrodysplasia punctata.

We describe a female infant with X-linked chondrodysplasia punctata (CDPX1) as a result of maternal isodisomy of the X chromosome. Targeted Sanger sequencing and targeted next-generation sequencing of ARSL were used to test for the familial variant. This patient was homozygous for ARSL NM_000047.2: c.1227_1228delinsAT p.(Ser410Cys) familial variant, consistent with a diagnosis of CDPX1. Uniparental disomy is a type of chromosomal variation. Although not necessarily pathogenic, it can cause imprinting disorders and X-linked recessive disorders in females, and be a cause of autosomal recessive conditions when only one parent is a carrier. The patient described highlights that uniparental disomy can be a rare cause of X-linked recessive conditions. This mode of inheritance has not been previously described in this condition.

GRB7 is an oncogenic driver and potential therapeutic target in oesophageal adenocarcinoma.

Efficacious therapeutic approaches are urgently needed to improve outcomes in patients with oesophageal adenocarcinoma (OAC). However, oncogenic drivers amenable to targeted therapy are limited and their functional characterisation is essential. Among few targeted therapies available, anti-human epidermal growth factor receptor 2 (HER2) therapy showed only modest benefit for patients with OAC. Herein, we investigated the potential oncogenic role of growth factor receptor bound protein 7 (GRB7), which is reported to be co-amplified with HER2 (ERBB2) in OAC. GRB7 was highly expressed in 15% of OAC tumours, not all of which could be explained by co-amplification with HER2, and was associated with a trend for poorer overall survival. Knockdown of GRB7 decreased proliferation and clonogenic survival, and induced apoptosis. Reverse phase protein array (RPPA) analyses revealed a role for PI3K, mammalian target of rapamycin (mTOR), MAPK, and receptor tyrosine kinase signalling in the oncogenic action of GRB7. Furthermore, the GRB7 and HER2 high-expressing OAC cell line Eso26 showed reduced cell proliferation upon GRB7 knockdown but was insensitive to HER2 inhibition by trastuzumab. Consistent with this, GRB7 knockdown in vivo with an inducible shRNA significantly inhibited tumour growth in cell line xenografts. HER2 expression did not predict sensitivity to trastuzumab, with Eso26 xenografts remaining refractory to trastuzumab treatment. Taken together, our study provides strong evidence for an oncogenic role for GRB7 in OAC and suggests that targeting GRB7 may be a potential therapeutic strategy for this cancer. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.

Why governments cannot afford Codentify to support their track and trace solutions.

BACKGROUND: In anticipation of the Protocol to Eliminate Illicit Trade in Tobacco Products (ITP) entering into force in 2018, there is a growing demand for information on track and trace (T&T) solutions for tobacco products. This article contrasts the efficacy of Codentify from the perspective of authentication with that of material-based multilayered security technologies. METHOD: To calculate the probability of detecting one fraudulent pack under Codentify, we relied on a modified Bernoulli trial experiment with independent repeated sampling without replenishment. The probability is calculated using a multinomial distribution formula adjusted for the fact that both legitimate and non-legitimate packs may be sold in the market. RESULTS: In a relatively small market, a law enforcement authority would have to inspect over 27 000 (almost 31 000) packs per week to have a 90% (95%) certainty that it did not miss a fraudulent pack under the Codentify system. A material based T&T solution would require only 45 (59) pack inspections a week to have the same level of confidence. CONCLUSIONS: This study demonstrates the inefficiency of Codentify compared to other solutions that incorporate material-based security features. Signatories to the ITP should reject Codentify due to both its low efficacy and its clear violation of the ITP's requirement that T&T shall not be performed by or delegated to the tobacco industry or its front groups.

Reward-based contextual learning supported by anterior cingulate cortex.

The anterior cingulate cortex (ACC) is commonly associated with cognitive control and decision making, but its specific function is highly debated. To explore a recent theory that the ACC learns the reward values of task contexts (Holroyd & McClure in Psychological Review, 122, 54-83, 2015; Holroyd & Yeung in Trends in Cognitive Sciences, 16, 122-128, 2012), we recorded the event-related brain potentials (ERPs) from participants as they played a novel gambling task. The participants were first required to select from among three games in one "virtual casino," and subsequently they were required to select from among three different games in a different virtual casino; unbeknownst to them, the payoffs for the games were higher in one casino than in the other. Analysis of the reward positivity, an ERP component believed to reflect reward-related signals carried to the ACC by the midbrain dopamine system, revealed that the ACC is sensitive to differences in the reward values associated with both the casinos and the games inside the casinos, indicating that participants learned the values of the contexts in which rewards were delivered. These results highlight the importance of the ACC in learning the reward values of task contexts in order to guide action selection.

Alcohol related mental imagery: The effects of a priming dose in at risk drinkers.

OBJECTIVES: Drug related mental imagery is proposed to play a central role in addictive behaviour. However, little is known about such cognition or how it is pharmacologically modulated. Here, we test theoretical predictions of the 'elaborated intrusion' theory by comparing neutral with alcohol related mental imagery, and examine the effects of low dose alcohol on phenomenological aspects of this imagery. METHODS: Alcohol related and neutral imagery was assessed after at risk drinkers (n = 40) consumed alcohol (0.3 g/kg) or placebo, in a crossover design. Sensory and visuospatial qualities of imagery, along with associated craving, positive affect and 'mind wandering' were assessed. RESULTS: Alcohol related mental imagery was rated as more vivid and sensorially rich, effects that were larger following the priming dose of alcohol. In addition, mind wandering was substantially lower during alcohol versus neutral imagery, especially after alcohol consumption. First person perspective was more prevalent for alcohol imagery after alcohol, although the Drink × Imagery type interaction did not reach statistical significance. However, first person imagery was associated with higher levels of craving during alcohol related imagery. CONCLUSIONS: Alcohol related mental imagery differs phenomenologically from neutral imagery on a number of dimensions. Priming with alcohol may enable cognitive elaboration by biasing the output of controlled cognitive processing towards enhanced sensory elaboration and increased attention to alcohol related cognition. These feedforward effects may be involved in focusing cognitive and behavioural resources on alcohol acquisition/consumption through the elaboration and rehearsal of relevant goals and plans.

Virtual reality gaming in the rehabilitation of the upper extremities post-stroke.

BACKGROUND: Occurrences of strokes often result in unilateral upper limb dysfunction. Dysfunctions of this nature frequently persist and can present chronic limitations to activities of daily living. METHODS: Research into applying virtual reality gaming systems to provide rehabilitation therapy have seen resurgence. Themes explored in stroke rehab for paretic limbs are action observation and imitation, versatility, intensity and repetition and preservation of gains. Fifteen articles were ultimately selected for review. The purpose of this literature review is to compare the various virtual reality gaming modalities in the current literature and ascertain their efficacy. RESULTS: The literature supports the use of virtual reality gaming rehab therapy as equivalent to traditional therapies or as successful augmentation to those therapies. While some degree of rigor was displayed in the literature, small sample sizes, variation in study lengths and therapy durations and unequal controls reduce generalizability and comparability. CONCLUSIONS: Future studies should incorporate larger sample sizes and post-intervention follow-up measures.

Migrating Tundra Peregrine Falcons accumulate polycyclic aromatic hydrocarbons along Gulf of Mexico following Deepwater Horizon oil spill.

Monitoring internal crude oil exposure can assist the understanding of associated risks and impacts, as well as the effectiveness of restoration efforts. Under the auspices of a long-term monitoring program of Tundra Peregrine Falcons (Falco peregrinus tundrius) at Assateague (Maryland) and South Padre Islands (Texas), we measured the 16 parent (unsubstituted) polycyclic aromatic hydrocarbons (PAHs), priority pollutants identified by the United States Environmental Protection Agency and components of crude oil, in peripheral blood cells of migrating Peregrine Falcons from 2009 to 2011. The study was designed to assess the spatial and temporal trends of crude oil exposure associated with the 2010 Deepwater Horizon (DWH) oil spill which started 20 April 2010 and was capped on 15 July of that year. Basal PAH blood distributions were determined from pre-DWH oil spill (2009) and unaffected reference area sampling. This sentinel species, a predator of shorebirds and seabirds during migration, was potentially exposed to residual oil from the spill in the northern Gulf of Mexico. Results demonstrate an increased incidence (frequency of PAH detection and blood concentrations) of PAH contamination in 2010 fall migrants sampled along the Texas Gulf Coast, declining to near basal levels in 2011. Kaplan-Meier peak mean ∑PAH blood concentration estimates varied with age (Juveniles-16.28 ± 1.25, Adults-5.41 ± 1.10 ng/g, wet weight) and PAHs detected, likely attributed to the discussed Tundra Peregrine natural history traits. Increased incidence of fluorene, pyrene and anthracene, with the presence of alkylated PAHs in peregrine blood suggests an additional crude oil source after DWH oil spill. The analyses of PAHs in Peregrine Falcon blood provide a convenient repeatable method, in conjunction with ongoing banding efforts, to monitoring crude oil contamination in this avian predator.

The use of genetics for the management of a recovering population: temporal assessment of migratory peregrine falcons in North America.

BACKGROUND: Our ability to monitor populations or species that were once threatened or endangered and in the process of recovery is enhanced by using genetic methods to assess overall population stability and size over time. This can be accomplished most directly by obtaining genetic measures from temporally-spaced samples that reflect the overall stability of the population as given by changes in genetic diversity levels (allelic richness and heterozygosity), degree of population differentiation (F(ST) and D(EST)), and effective population size (N(e)). The primary goal of any recovery effort is to produce a long-term self-sustaining population, and these genetic measures provide a metric by which we can gauge our progress and help make important management decisions. METHODOLOGY/PRINCIPAL FINDINGS: The peregrine falcon in North America (Falco peregrinus tundrius and anatum) was delisted in 1994 and 1999, respectively, and its abundance will be monitored by the species Recovery Team every three years until 2015. Although the United States Fish and Wildlife Service makes a distinction between tundrius and anatum subspecies, our genetic results based on eleven microsatellite loci suggest limited differentiation that can be attributed to an isolation by distance relationship and warrant no delineation of these two subspecies in its northern latitudinal distribution from Alaska through Canada into Greenland. Using temporal samples collected at Padre Island, Texas during migration (seven temporal time periods between 1985-2007), no significant differences in genetic diversity or significant population differentiation in allele frequencies between time periods were observed and were indistinguishable from those obtained from tundrius/anatum breeding locations throughout their northern distribution. Estimates of harmonic mean N(e) were variable and imprecise, but always greater than 500 when employing multiple temporal genetic methods. CONCLUSIONS/SIGNIFICANCE: These results, including those from simulations to assess the power of each method to estimate N(e), suggest a stable or growing population, which is consistent with ongoing field-based monitoring surveys. Therefore, historic and continuing efforts to prevent the extinction of the peregrine falcon in North America appear successful with no indication of recent decline, at least from the northern latitude range-wide perspective. The results also further highlight the importance of archiving samples and their use for continual assessment of population recovery and long-term viability.

Wintering area DDE source to migratory white-faced ibis revealed by satellite telemetry and prey sampling.

Locations of contaminant exposure for nesting migratory species are difficult to fully understand because of possible additional sources encountered during migration or on the wintering grounds. A portion of the migratory white-faced ibis (Plegadis chihi) nesting at Carson Lake, Nevada continues to be exposed to dichloro-diphenyldichloro-ethylene (DDE) with no change, which is unusual, observed in egg concentrations between 1985 and 2000. About 45-63% of the earliest nesting segment shows reduced reproductive success correlated with elevated egg concentrations of >4 microg/g wet weight (ww). Local prey (primarily earthworms) near nests contained little DDE so we tracked the migration and wintering movements of 20 adult males during 2000-2004 to determine the possible source. At various wintering sites, we found a correlation (r (2) = 0.518, P = 0.0125, N = 11) between DDE in earthworm composites and DDE in blood plasma of white-faced ibis wintering there, although the plasma was collected on their breeding grounds soon after arrival. The main source of DDE was wintering areas in the Mexicali Valley of Baja California Norte, Mexico, and probably the adjacent Imperial Valley, California, USA. This unusual continuing DDE problem for white-faced ibis is associated with: the long-term persistence in soil of DDE; the earthworms' ability to bioconcentrate DDE from soil; the proclivity of white-faced ibis to feed on earthworms in agricultural fields; the species's extreme sensitivity to DDE in their eggs; and perhaps its life history strategy of being a "capital breeder". We suggest surveying and sampling white-faced ibis eggs at nesting colonies, especially at Carson Lake, to monitor the continuing influence of DDE.

Intake rates and the functional response in shorebirds (Charadriiformes) eating macro-invertebrates.

As field determinations take much effort, it would be useful to be able to predict easily the coefficients describing the functional response of free-living predators, the function relating food intake rate to the abundance of food organisms in the environment. As a means easily to parameterise an individual-based model of shorebird Charadriiformes populations, we attempted this for shorebirds eating macro-invertebrates. Intake rate is measured as the ash-free dry mass (AFDM) per second of active foraging; i.e. excluding time spent on digestive pauses and other activities, such as preening. The present and previous studies show that the general shape of the functional response in shorebirds eating approximately the same size of prey across the full range of prey density is a decelerating rise to a plateau, thus approximating the Holling type II ('disc equation') formulation. But field studies confirmed that the asymptote was not set by handling time, as assumed by the disc equation, because only about half the foraging time was spent in successfully or unsuccessfully attacking and handling prey, the rest being devoted to searching.A review of 30 functional responses showed that intake rate in free-living shorebirds varied independently of prey density over a wide range, with the asymptote being reached at very low prey densities (<150/m-2). Accordingly, most of the many studies of shorebird intake rate have probably been conducted at or near the asymptote of the functional response, suggesting that equations that predict intake rate should also predict the asymptote.A multivariate analysis of 468 'spot' estimates of intake rates from 26 shorebirds identified ten variables, representing prey and shorebird characteristics, that accounted for 81% of the variance in logarithm-transformed intake rate. But four-variables accounted for almost as much (77.3%), these being bird size, prey size, whether the bird was an oystercatcher Haematopus ostralegus eating mussels Mytilus edulis, or breeding. The four variable equation under-predicted, on average, the observed 30 estimates of the asymptote by 11.6%, but this discrepancy was reduced to 0.2% when two suspect estimates from one early study in the 1960s were removed. The equation therefore predicted the observed asymptote very successfully in 93% of cases. We conclude that the asymptote can be reliably predicted from just four easily measured variables. Indeed, if the birds are not breeding and are not oystercatchers eating mussels, reliable predictions can be obtained using just two variables, bird and prey sizes. A multivariate analysis of 23 estimates of the half-asymptote constant suggested they were smaller when prey were small but greater when the birds were large, especially in oystercatchers. The resulting equation could be used to predict the half-asymptote constant, but its predictive power has yet to be tested. As well as predicting the asymptote of the functional response, the equations will enable research workers engaged in many areas of shorebird ecology and behaviour to estimate intake rate without the need for conventional time-consuming field studies, including species for which it has not yet proved possible to measure intake rate in the field.

Chronic hypoxia up-regulates expression of adenosine A1 receptors in DDT1-MF2 cells.

As the first step to understand how chronic hypoxia might regulate smooth muscle function in health and disease, we have employed an established immortalised cell model of smooth muscle, DDT1-MF2 cells, to address the hypothesis that adenosine A1 receptor density is modulated by O2 availability. Maximal specific binding (Bmax) of the selective adenosine A1 receptor antagonist, [3H]-DPCPX, to cell membranes increased 3.5-fold from 0.48 +/- 0.02 pmol/mg to 1.7 +/- 0.5 pmol/mg protein after 16 hr of hypoxia and this effect was not accompanied by any statistically significant changes in either binding affinity (0.84 +/- 0.2 nM vs. 1.2 +/- 0.3 nM) or Hill coefficient (1.1 +/- 0.1 vs. 0.99 +/- 0.03). Hypoxia-evoked increases in membrane receptor density were paralleled in intact DDT1-MF2 cells. In addition, the increase in [3H]-DPCPX binding to intact cells was inhibited by co-incubation during hypoxia with the translational inhibitor cycloheximide, the transcriptional blocker actinomycin D and the NFkappaB inhibitor sulphasalazine. Together, these data show that adenosine A1 receptor density is modulated, at least in part, by O2-dependent activation of the transcription factor NFkappaB and adds to the list of processes dynamically regulated by ambient oxygen availability. Since hypoxia is an initiating factor in acute renal failure, similar changes in transcription may account for up-regulation of adenosine A1 receptors noted previously in the renal vasculature of rats with acute renal failure.

Alternative learning environments: what do they contribute to professional development of medical students?

Special study modules provide opportunities for students to develop lifelong learning skills and develop areas of interest. The GMC also recommends opportunities to study topics not included in the core medical curriculum. This paper reports the evaluation of modules based within alternative learning environments developed to provide students with experiences outside traditional medical, scientific or academic cultures. The attachment was highly rated as contributing to professional development, provided novel learning experiences, and was stimulating for both students and supervisors. All students achieved new skills that they felt were pertinent to their personal development. Assessment was by standardized pro forma, including generic transferable skills and module specific outcomes. Whilst overall assessment grades were comparable to similar course components, unease amongst both students and supervisors was expressed reflecting anxieties in the diversity of workloads and assessment. Attempts to standardize assessment across the diversity of modules did not reduce anxieties and potentially detracted from the learning experiences.