Assessing generalisability of deep learning-based polyp detection and segmentation methods through a computer vision challenge

Polyps are well-known cancer precursors identified by colonoscopy. However, variability in their size, appearance, and location makes the detection of polyps challenging. Moreover, colonoscopy surveillance and removal of polyps are highly operator-dependent procedures and occur in a highly complex organ topology. There exists a high missed detection rate and incomplete removal of colonic polyps. To assist in clinical procedures and reduce missed rates, automated methods for detecting and segmenting polyps using machine learning have been achieved in past years. However, the major drawback in most of these methods is their ability to generalise to out-of-sample unseen datasets from different centres, populations, modalities, and acquisition systems. To test this hypothesis rigorously, we, together with expert gastroenterologists, curated a multi-centre and multi-population dataset acquired from six different colonoscopy systems and challenged the computational expert teams to develop robust automated detection and segmentation methods in a crowd-sourcing Endoscopic computer vision challenge. This work put forward rigorous generalisability tests and assesses the usability of devised deep learning methods in dynamic and actual clinical colonoscopy procedures. We analyse the results of four top performing teams for the detection task and five top performing teams for the segmentation task. Our analyses demonstrate that the top-ranking teams concentrated mainly on accuracy over the real-time performance required for clinical applicability. We further dissect the devised methods and provide an experiment-based hypothesis that reveals the need for improved generalisability to tackle diversity present in multi-centre datasets and routine clinical procedures.

CELLULAR, A Cell Autophagy Imaging Dataset

Cells in living organisms are dynamic compartments that continuously respond to changes in their environment to maintain physiological homeostasis. While basal autophagy exists in cells to aid in the regular turnover of intracellular material, autophagy is also a critical cellular response to stress, such as nutritional depletion. Conversely, the deregulation of autophagy is linked to several diseases, such as cancer, and hence, autophagy constitutes a potential therapeutic target. Image analysis to follow autophagy in cells, especially on high-content screens, has proven to be a bottleneck. Machine learning (ML) algorithms have recently emerged as crucial in analyzing images to efficiently extract information, thus contributing to a better understanding of the questions at hand. This paper presents CELLULAR, an open dataset consisting of images of cells expressing the autophagy reporter mRFP-EGFP-Atg8a with cell-specific segmentation masks. Each cell is annotated into either basal autophagy, activated autophagy, or unknown. Furthermore, we introduce some preliminary experiments using the dataset that can be used as a baseline for future research.

P-272 Automatic Tracking of the ICSI procedure using Deep Learning

Study question

Can deep learning be used to detect and track spermatozoa and the different parts of an ICSI procedure?

Summary answer

Deep learning can be used as a tool to assist and organize the contents of an ICSI procedure.

What is known already

Sperm tracking has been a topic of research and practice for many years, especially in the context of computer-aided sperm analysis (CASA). Recent studies have proposed using deep learning algorithms to track spermatozoa for spermatozoon selection in human and animal samples. One critical part of performing ICSI involves the selection of the “best” spermatozoon for injection, but other parts of the procedure may also be of importance. However, as far as we know, tracking using deep learning has not been applied to the ICSI procedure, where detecting instruments and the oocyte could also be helpful in post-analysis and training.

Study design, size, duration

The study was performed using three anonymized videos of the ICSI procedure. The frames of the videos were manually annotated by data scientists and verified by an embryologist. The annotations were bounding boxes around specific parts of the ICSI procedure, including sperm, pipettes, and the oocyte. We trained a YOLOv5 model on the collected data, where two videos were used for training and one video for validation.

Participants/materials, setting, methods

The videos of the ICSI procedure were captured at 200x magnification with a DeltaPix camera at Fertilitetssenteret in Oslo, Norway. ICSI was performed using a Nikon ECLIPSE TE2000-S microscope connected with Eppendorf TransferMan 4m micromanipulators. The spermatozoa were immobilised in 5 µl Polyvinylpyrrolidone (PVP; CooperSurgical). The videos had a resolution of 1920x1080 and were resized to 640x640 before being processed by the YOLOv5 model. The data will be made public in a later study.

Main results and the role of chance

Mean average precision (mAP) with the threshold of 0.5 (mAP@.5) is the main quantitative parameter measured in the YOLOv5 model. All the experiments were performed using three-fold cross-validation, where we present the average metrics calculated over the three folds. Overall, the method showed an average mAP@.5 of 0.50 across all predicted classes, which means that the method can track the different components with good accuracy. Looking closer at the individual classes, we see that instruments like the holding pipette and ICSI pipette are detected with high accuracy with a mAP@.5 of 0.87 and 0.94, respectively. The oocyte is also easily tracked with a mAP@.5 of 0.92. The first polar body is well detected with a mAP@.5 of 0.65. The model has issues detecting and tracking individual sperm (both outside and within the pipette), where the method achieved a mAP@.5 of 0.46 for tracking sperm outside the pipette and 0.03 for the sperm inside the pipette. The low score of detecting the sperm in the pipette can be explained by the often unclear visibility of the sperm through the pipette and the low number of training samples.

Limitations, reasons for caution

The limited sample size makes the generalizability of the method difficult to determine. A more extensive evaluation is necessary. Moreover, as the currency study focuses on tracking, patient information and clinical outcome were not included in the analysis.

Wider implications of the findings

Deep learning has the potential to aid embryologists to perform successful ICSI through tracking and detection of spermatozoa, pipettes, and the oocyte. This could potentially lead to better internal quality control and teaching possibilities, and hopefully better results.

Trial registration number

not applicable

Visual Sentiment Analysis from Disaster Images in Social Media

The increasing popularity of social networks and users’ tendency towards sharing their feelings, expressions, and opinions in text, visual, and audio content have opened new opportunities and challenges in sentiment analysis. While sentiment analysis of text streams has been widely explored in the literature, sentiment analysis from images and videos is relatively new. This article focuses on visual sentiment analysis in a societally important domain, namely disaster analysis in social media. To this aim, we propose a deep visual sentiment analyzer for disaster-related images, covering different aspects of visual sentiment analysis starting from data collection, annotation, model selection, implementation, and evaluations. For data annotation and analyzing people’s sentiments towards natural disasters and associated images in social media, a crowd-sourcing study has been conducted with a large number of participants worldwide. The crowd-sourcing study resulted in a large-scale benchmark dataset with four different sets of annotations, each aiming at a separate task. The presented analysis and the associated dataset, which is made public, will provide a baseline/benchmark for future research in the domain. We believe the proposed system can contribute toward more livable communities by helping different stakeholders, such as news broadcasters, humanitarian organizations, as well as the general public.

Meta-learning with implicit gradients in a few-shot setting for medical image segmentation

Widely used traditional supervised deep learning methods require a large number of training samples but often fail to generalize on unseen datasets. Therefore, a more general application of any trained model is quite limited for medical imaging for clinical practice. Using separately trained models for each unique lesion category or a unique patient population will require sufficiently large curated datasets, which is not practical to use in a real-world clinical set-up. Few-shot learning approaches can not only minimize the need for an enormous number of reliable ground truth labels that are labour-intensive and expensive, but can also be used to model on a dataset coming from a new population. To this end, we propose to exploit an optimization-based implicit model agnostic meta-learning (iMAML) algorithm under few-shot settings for medical image segmentation. Our approach can leverage the learned weights from diverse but small training samples to perform analysis on unseen datasets with high accuracy. We show that, unlike classical few-shot learning approaches, our method improves generalization capability. To our knowledge, this is the first work that exploits iMAML for medical image segmentation and explores the strength of the model on scenarios such as meta-training on unique and mixed instances of lesion datasets. Our quantitative results on publicly available skin and polyp datasets show that the proposed method outperforms the naive supervised baseline model and two recent few-shot segmentation approaches by large margins. In addition, our iMAML approach shows an improvement of 2%-4% in dice score compared to its counterpart MAML for most experiments.

Rolling Circle Amplification-Coupled Glass Nanopore Counting of Mild Traumatic Brain Injury-Related Salivary miRNAs

Mild traumatic brain injury (mTBI) could be underdiagnosed and underreported due to the delayed onset of symptoms and the conventional subjective assessment. Recent studies have suggested that salivary microRNAs (miRNAs) could be reliable biomarkers for objective mTBI diagnosis. In this work, we demonstrated a rolling circle amplification (RCA)-coupled resistive pulse-counting platform for profiling mTBI-related miRNAs, using easy-to-fabricate large glass nanopores (200 nm diameter). The method relies on the linear and specific elongation of the miRNA to a much larger RCA product, which the large glass nanopore can digitally count with a high signal-to-noise ratio. We developed and validated the RCA assay against let-7a, miR-30e, and miR-21. We demonstrated the quantification capability of this large glass nanopore counting platform for purified miRNAs as well as miRNAs in salivary total RNA background. Finally, we quantitatively evaluated the performance of profiling each individual miRNAs in a mixed analyte. Our results showed that the RCA-coupled large glass nanopore counting provides a promising and accessible alternative toward the clinical diagnosis of mTBI using salivary miRNAs.

A comprehensive analysis of classification methods in gastrointestinal endoscopy imaging

Gastrointestinal (GI) endoscopy has been an active field of research motivated by the large number of highly lethal GI cancers. Early GI cancer precursors are often missed during the endoscopic surveillance. The high missed rate of such abnormalities during endoscopy is thus a critical bottleneck. Lack of attentiveness due to tiring procedures, and requirement of training are few contributing factors. An automatic GI disease classification system can help reduce such risks by flagging suspicious frames and lesions. GI endoscopy consists of several multi-organ surveillance, therefore, there is need to develop methods that can generalize to various endoscopic findings. In this realm, we present a comprehensive analysis of the Medico GI challenges: Medical Multimedia Task at MediaEval 2017, Medico Multimedia Task at MediaEval 2018, and BioMedia ACM MM Grand Challenge 2019. These challenges are initiative to set-up a benchmark for different computer vision methods applied to the multi-class endoscopic images and promote to build new approaches that could reliably be used in clinics. We report the performance of 21 participating teams over a period of three consecutive years and provide a detailed analysis of the methods used by the participants, highlighting the challenges and shortcomings of the current approaches and dissect their credibility for the use in clinical settings. Our analysis revealed that the participants achieved an improvement on maximum Mathew correlation coefficient (MCC) from 82.68% in 2017 to 93.98% in 2018 and 95.20% in 2019 challenges, and a significant increase in computational speed over consecutive years.

HyperKvasir, a comprehensive multi-class image and video dataset for gastrointestinal endoscopy

Artificial intelligence is currently a hot topic in medicine. However, medical data is often sparse and hard to obtain due to legal restrictions and lack of medical personnel for the cumbersome and tedious process to manually label training data. These constraints make it difficult to develop systems for automatic analysis, like detecting disease or other lesions. In this respect, this article presents HyperKvasir, the largest image and video dataset of the gastrointestinal tract available today. The data is collected during real gastro- and colonoscopy examinations at Bærum Hospital in Norway and partly labeled by experienced gastrointestinal endoscopists. The dataset contains 110,079 images and 374 videos, and represents anatomical landmarks as well as pathological and normal findings. The total number of images and video frames together is around 1 million. Initial experiments demonstrate the potential benefits of artificial intelligence-based computer-assisted diagnosis systems. The HyperKvasir dataset can play a valuable role in developing better algorithms and computer-assisted examination systems not only for gastro- and colonoscopy, but also for other fields in medicine.

Evaluation of the self-directed format of Walk With Ease in patients with systemic lupus erythematosus: the Walk-SLE Pilot Study

OBJECTIVE

To conduct a proof-of-concept pilot evaluation of the self-directed format of Walk With Ease (WWE), a 6-week walking program developed for adults with arthritis, in patients with systemic lupus erythematosus (SLE).

METHODS

This was a single arm, 6-week pre- and post-evaluation of the self-directed WWE program to assess feasibility, tolerability, safety, acceptability, and effectiveness. Adult patients with physician-diagnosed SLE were recruited to participate during regularly scheduled visits to an academic rheumatology clinic. Self-reported outcomes of pain, stiffness, and fatigue were assessed by visual analog scales (VAS) and the Functional Assessment of Chronic Illness Therapy-Fatigue (FACIT-fatigue) scale at baseline and at completion of the 6-week program. Patients also completed a satisfaction survey at the end of the program. Multivariate linear regression models were used to calculate mean changes between baseline and 6-week follow-up scores, adjusting for covariates. Mean change scores were used to estimate effect sizes (ES).

RESULTS

At 6 weeks, 48 of the 75 recruited participants completed the WWE program. Participants experienced modest improvements in stiffness and fatigue (ES = 0.12 and ES = 0.23, respectively, for VAS scores; ES = 0.16 for FACIT-fatigue score) following the intervention. The majority of participants reported satisfaction with the program (98%) and benefitted from the workbook (96%).

CONCLUSIONS

The self-directed format of WWE appears to reduce stiffness and fatigue in patients with SLE. It also seems to be a feasible and acceptable exercise program to patients with SLE. Larger studies are needed to confirm these findings.

Bedtime Use of Technology and Associated Sleep Problems in Children

Children comprise one of the largest consumer groups of technology. Sleep is fundamental to optimal functioning during childhood, including health and behavior. The purpose of this study was to explore bedtime electronic use and its impact on 3 health consequences-sleep quantity and quality, inattention, and body mass index. Parents of 234 children, ages 8 to 17 years, were surveyed to quantify hours of technology use (computer, video games, cell phone, and television), hours of sleep, and inattentive behaviors. Using any device at bedtime was associated with a statically significant increased use of multiple forms of technology at bedtime and use in the middle of the night, reducing sleep quantity and quality. Little association was found between technology use and inattention. A statistically significant association was found between bedtime technology use and elevated body mass index. Clinicians should discuss the impact of technology at bedtime to prevent harmful effects of overexposure.

Differential responses of two wetland graminoids to high ammonium at different pH values

Enhanced soil ammonium (NH4+) concentrations in wetlands often lead to graminoid dominance, but species composition is highly variable. Although NH4+ is readily taken up as a nutrient, several wetland species are known to be sensitive to high NH4+ concentrations or even suffer toxicity, particularly at low soil pH. More knowledge about differential graminoid responses to high NH4+ availability in relation to soil pH can help to better understand vegetation changes. The responses of two wetland graminoids, Juncus acutiflorus and Carex disticha, to high (2 mmol·l(-1) ) versus control (20 μmol·l(-1) ) NH4+ concentrations were tested in a controlled hydroponic set up, at two pH values (4 and 6). A high NH4+ concentration did not change total biomass for these species at either pH, but increased C allocation to shoots and increased P uptake, leading to K and Ca limitation, depending on pH treatment. More than 50% of N taken up by C. disticha was invested in N-rich amino acids with decreasing C:N ratio, but only 10% for J. acutiflorus. Although both species appeared to be well adapted to high NH4+ loadings in the short term, C. disticha showed higher classic detoxifying responses that are early warning indicators for decreased tolerance in the long term. In general, the efficient aboveground biomass allocation, P uptake and N detoxification explain the competitive strength of wetland graminoids at the expense of overall biodiversity at high NH4+ loading. In addition, differential responses to enhanced NH4+ affect interspecific competition among graminoids and lead to a shift in vegetation composition.

Type II diabetes increases mitochondrial DNA mutations in the left ventricle of the Goto-Kakizaki diabetic rat

Mitochondrial dysfunction has a significant role in the development of diabetic cardiomyopathy. Mitochondrial oxidant stress has been accepted as the singular cause of mitochondrial DNA (mtDNA) damage as an underlying cause of mitochondrial dysfunction. However, separate from a direct effect on mtDNA integrity, diabetic-induced increases in oxidant stress alter mitochondrial topoisomerase function to propagate mtDNA mutations as a contributor to mitochondrial dysfunction. Both glucose-challenged neonatal cardiomyocytes and the diabetic Goto-Kakizaki (GK) rat were studied. In both the GK left ventricle (LV) and in cardiomyocytes, chronically elevated glucose presentation induced a significant increase in mtDNA damage that was accompanied by decreased mitochondrial function. TTGE analysis revealed a number of base pair substitutions in the 3' end of COX3 from GK LV mtDNA that significantly altered the protein sequence. Mitochondrial topoisomerase DNA cleavage activity in isolated mitochondria was significantly increased in the GK LV compared with Wistar controls. Both hydroxycamptothecin, a topoisomerase type 1 inhibitor, and doxorubicin, a topoisomerase type 2 inhibitor, significantly exacerbated the DNA cleavage activity of isolated mitochondrial extracts indicating the presence of multiple functional topoisomerases in the mitochondria. Mitochondrial topoisomerase function was significantly altered in the presence of H2O2 suggesting that separate from a direct effect on mtDNA, oxidant stress mediated type II diabetes-induced alterations of mitochondrial topoisomerase function. These findings are significant in that the activation/inhibition state of the mitochondrial topoisomerases will have important consequences for mtDNA integrity and the well being of the diabetic myocardium.

Maturity-onset diabetes of the young (MODY): how many cases are we missing?

AIMS/HYPOTHESIS

Maturity-onset diabetes of the young is frequently misdiagnosed as type 1 or type 2 diabetes. A correct diagnosis of MODY is important for determining treatment, but can only be confirmed by molecular genetic testing. We aimed to compare the regional distribution of confirmed MODY cases in the UK and to estimate the minimum prevalence.

METHODS

UK referrals for genetic testing in 2,072 probands and 1,280 relatives between 1996 and 2009 were examined by region, country and test result. Referral rate and prevalence were calculated using UK Census 2001 figures.

RESULTS

MODY was confirmed in 1,177 (35%) patients, with HNF1A (52%) and GCK mutations (32%) being most frequent in probands confirmed with MODY. There was considerable regional variation in proband referral rates (from <20 per million in Wales and Northern Ireland to >50 per million for South West England and Scotland) and patients diagnosed with MODY (5.3 per million in Northern Ireland, 48.9 per million in South West England). Referral rates and confirmed cases were highly correlated (r = 0.96, p < 0.0001). The minimum prevalence of MODY was estimated to be 108 cases per million.

CONCLUSIONS/INTERPRETATION

Assuming this minimal prevalence throughout the UK then >80% of MODY is not diagnosed by molecular testing. The marked regional variation in the prevalence of confirmed MODY directly results from differences in referral rates. This could reflect variation in awareness of MODY or unequal access to genetic testing. Increased referral for diagnostic testing is required if the majority of MODY patients are to have the genetic diagnosis necessary for optimal treatment.

Conformational diversity of short DNA duplex

Two 25 base-pair cDNA strands are encapsulated within an optically trapped nanodroplet, and we observe the kinetics of their hybridization in dynamic equilibrium via single-molecule fluorescence resonance energy transfer (FRET) as a function of temperature and of the solution's NaCl concentration. We have observed the duplex unfolding and refolding, and we have observed quasistable partially unfolded states under low salinity conditions. Furthermore, our measurements reveal that, even in conditions under which the duplex is stable, it undergoes conformational fluctuations in solution.

The effects of plant traits and phylogeny on soil-to-plant transfer of 99Tc

Assessments of the behaviour of (99)Tc in terrestrial environments necessitate predicting soil-to-plant transfer. An experiment with 116 plant taxa showed that (99)Tc transfer to plants was positively related to plant dry weight but negatively related to % dry matter and age at exposure. Activities of (99)Tc analysed by hierarchical ANOVA coded with an angiosperm phylogeny revealed significant effects, with 55% of the variance between species explained at the Ordinal level and above. Monocots had significantly lower transfer of (99)Tc than Eudicots, within which Caryophyllales > Solanales > Malvales > Brassicales > Asterales > Fabales. There was a significant phylogenetic signal in soil-to-plant transfer of (99)Tc. This phylogenetic signal is used to suggest that, for example, a nominal Tc Transfer Factor of 5 could be adjusted to 2.3 for Monocots and 5.3 for Eudicots.

Exercise training enhanced myocardial endothelial nitric oxide synthase (eNOS) function in diabetic Goto-Kakizaki (GK) rats

BACKGROUND

Different mechanisms of diabetic-induced NO dysfunction have been proposed and central to most of them are significant changes in eNOS function as the rate-limiting step in NO bioavailability. eNOS exists in both monomeric and dimeric conformations, with the dimeric form catalyzing the synthesis of nitric oxide, while the monomeric form catalyzes the synthesis of superoxide (O2-). Diabetic-induced shifts to decrease the dimer:monomer ratio is thought to contribute to the degradation of nitric oxide (NO) bioavailability. Exercise has long been useful in the management of diabetes. Although exercise-induced increases expression of eNOS has been reported, it is unclear if exercise may alter the functional coupling of eNOS.

METHODS

To investigate this question, Goto-Kakizaki rats (a model of type II diabetes) were randomly assigned to a 9-week running program (train) or sedentary (sed) groups.

RESULTS

Exercise training significantly (p < .05) increased plantaris muscle cytochrome oxidase, significantly improved glycosylated hemoglobin (sed: 7.33 +/- 0.56%; train: 6.1 +/- 0.18%), ad improved insulin sensitivity. Exercise increased both total eNOS expression and the dimer:monomer ratio in the left ventricle LV (sed: 11.7 +/- 3.2%; train: 41.4 +/- 4.7%). Functional analysis of eNOS indicated that exercise induced significant increases in nitric oxide (+28%) production and concomitant decreases in eNOS-dependent superoxide (-12%) production. This effect was observed in the absence of tetrahydrobiopterin (BH4), but not in the presence of exogenous BH4. Exercise training also significantly decreased NADPH-dependent O2- activity.

CONCLUSION

Exercise-induced increased eNOS dimerization resulted in an increased coupling of the enzyme to facilitate production of NO at the expense of ROS generation. This shift that could serve to decrease diabetic-related oxidative stress, which should serve to lessen diabetic-related complications.

Impact of platinum group metals on the environment: a toxicological, genotoxic and analytical chemistry study

Recent studies show particles of Platinum Group Metals (PGMs); primarily platinum, palladium and rhodium; released from automobile catalytic converters are being deposited alongside roadways. This deposition is leading to increasing concentrations of PGMs in the environment, raising concerns about the environmental impact and toxicity of these elements in living organisms. The objective of this study was to determine how PGMs alter the patterns of growth, development, and physiology by studying the toxicological and genotoxic effects of these metals. Two vastly different species were used as models: plant-a wild wetland common Sphagnum moss, and animal-6-week old rats Sprague-Dawley. Both species were exposed, in controlled environments, to different concentrations of the PGMs. Toxicological and genotoxic effects were determined by assessment of plant growth, animal survival and pathology, and influence on DNA in both models. Our results on the uptake of PGMs by Sphagnum showed significant decreases in plant length and biomass as PGM concentration increased. Histological and pathological analysis of the animal model revealed vacuolization, eosinophil inclusion bodies in adrenal glands, shrinkage of glomeruli in the kidney, and enlargement of white pulp in the spleen. In both models, DNA damage was detected. Chemical analysis using ICP-AES atomic absorption demonstrated accumulation of PGMs in plant tissues at all PGM levels, proportional to concentration.

Acetylated sialic acid residues and blood group antigens localise within the epithelium in microvillous atrophy indicating internal accumulation of the glycocalyx

BACKGROUND

Microvillous atrophy, a disorder of intractable diarrhoea in infancy, is characterised by the intestinal epithelial cell abnormalities of abnormal accumulation of periodic acid-Schiff (PAS) positive secretory granules within the apical cytoplasm and the presence of microvillous inclusions. The identity of the PAS positive material is not known, and the aim of this paper was to further investigate its composition.

METHODS

Formaldehyde fixed sections were stained with alcian blue/PAS to identify the acidic or neutral nature of the material, phenylhydrazine blocking was employed to stain specifically for sialic acid, and saponification determined the presence of sialic acid acetylation. The specificity of sialic acid staining was tested by digestion with mild sulphuric acid. Expression of blood group related antigens was tested immunochemically.

RESULTS

Alcian blue/PAS staining identified a closely apposed layer of acidic material on the otherwise neutral (PAS positive) brush border in controls. In microvillous atrophy, a triple layer was seen with an outer acidic layer, an unstained brush border region, and accumulation within the epithelium of a neutral glycosubstance that contained acetylated sialic acid. Blood group antigens were detected on the brush border, in mucus, and within goblet cells in controls. In microvillous atrophy they were additionally expressed within the apical cytoplasm of epithelial cells mirroring the PAS abnormality. Immuno electron microscopy localised expression to secretory granules.

CONCLUSIONS

A neutral, blood group antigen positive, glycosubstance that contains acetylated sialic acid accumulates in the epithelium in microvillous atrophy. Previous studies have demonstrated that the direct and indirect constitutive pathways are intact in this disorder and it is speculated that the abnormal staining pattern reflects accumulation of glycocalyx related material.

Roles for Fis and YafK in biofilm formation by enteroaggregative Escherichia coli

Enteroaggregative Escherichia coli (EAEC) forms thick biofilms on the intestinal mucosa. Here, we show that most EAEC strains form a biofilm on glass or plastic surfaces when grown in cell culture medium with high sugar and osmolarity. Biofilm-forming ability in two prototype EAEC strains required aggregative adherence fimbriae (AAF), although many other EAEC strains that do not express AAF also developed biofilms under these conditions. Ten thousand transposon mutants of EAEC strain 042 were isolated, and 100 were found to be deficient in biofilm formation. Of these, 93 were either deficient in in vitro growth or mapped to genes known to be required for AAF/II expression. Of the seven remaining insertions, five mapped to one of two unsuspected loci. Two insertions involved the E. coli chromosomal fis gene, a DNA-binding protein that is involved in growth phase-dependent regulation. Using reverse transcription-polymerase chain reaction (RT-PCR), we determined that the effect of fis was at the level of transcription of the AAF/II activator aggR. Biofilm formation also required the product of the yafK gene, which is predicted to encode a secreted 28 kDa protein. The yafK product is required for transcription of AAF/II-encoding genes. Our data do not suggest a role for type 1 fimbriae or motility in biofilm formation. EAEC appears to form a novel biofilm, which may be mediated solely by AAF and may reflect its interactions with the intestinal mucosa.

Gastric cancer: diagnosis, risk factors, treatment and life issues

Gastric cancer is the sixth most common malignancy in the UK. It is responsible for over 9000 deaths annually in the UK. Distal gastric cancer has a decreasing incidence, but proximal gastric cancer continues to increase. Gastroscopy remains the gold standards for accurate diagnosis. Early diagnosis is essential, but symptoms and signs are often mistaken for other less serious diseases. Major surgery is the only proven treatment, but 5-year survival rates postoperatively are only 34%, and many people will continue to suffer side-effects of the surgery. Open access gastroscopy and health promotion may be the best chance of detecting this disease early enough so that it is treated successfully.

Delayed, spontaneous hypothermia reduces neuronal damage after asphyxial cardiac arrest in rats

OBJECTIVE

Core temperature is reduced spontaneously after asphyxial cardiac arrest in rats. To determine whether spontaneous hypothermia influences neurologic damage after asphyxial arrest, we compared neurologic outcome in rats permitted to develop spontaneous hypothermia vs. rats managed with controlled normothermia.

INTERVENTIONS

Male Sprague-Dawley rats were asphyxiated for 8 mins and resuscitated. After extubation, a cohort of rats was managed with controlled normothermia (CN) by placement in a servo-controlled incubator set to maintain rectal temperature at 37.4 degrees C for 48 hrs. CN rats were compared with permissive hypothermia (PH) rats that were returned to an ambient temperature environment after extubation. Rats were killed at either 72 hrs (PH72hr, n = 14; CN72hr, n = 9) or 6 wks (PH6wk, n = 6, CN6wk, n = 6) after resuscitation. PH72 rats were historic controls for the CN72 rats, whereas PH6 and CN6 rats were randomized and studied contemporaneously.

MEASUREMENTS

A clinical neurodeficit score (NDS) was determined daily. A pathologist blinded to group scored 40 hematoxylin and eosin -stained brain regions for damage by using a 5-point scale (0 = none, 5 = severe). Quantitative analysis of CA1 hippocampus injury was performed by counting normal-appearing neurons in a defined subsection of CA1.

MAIN RESULTS

Mean rectal temperatures measured in the PH6wk rats (n = 6) were 36.9, 34.8, 35.5, 36.7, and 37.4 degrees C at 2, 8, 12, 24, and 36 hrs, respectively. Mortality rate (before termination) was lower in PH compared with CN (0/20 vs. 7/15; p < .005). PH demonstrated a more favorable progression of NDS (p = .04) and less weight loss (p < .005) compared with CN. Median histopathology scores were lower (less damage) in PH72hr vs. CN72hr for temporal cortex (0 vs. 2.5), parietal cortex (0 vs. 2), thalamus (0 vs. 3), CA1 hippocampus (1.5 vs. 4.5), CA2 hippocampus (0 vs. 3.5), subiculum (0 vs. 4), and cerebellar Purkinje cell layer (2 vs. 4) (all p < .05). There was almost complete loss of normal-appearing CA1 neurons in CN72hr rats (6 +/- 2 [mean +/- SD] normal neurons compared with 109 +/- 12 in naïve controls). In contrast, PH72hr rats demonstrated marked protection (97 +/- 23 normal-appearing neurons) that was still evident, although attenuated, at 6 wks (42 +/- 24 normal-appearing neurons, PH6wk).

CONCLUSION

Rats resuscitated from asphyxial cardiac arrest develop delayed, mild to moderate, prolonged hypothermia that is neuroprotective.

Enterohaemorrhagic Escherichia coli O157:H7 target Peyer's patches in humans and cause attaching/effacing lesions in both human and bovine intestine

BACKGROUND

Enterohaemorrhagic Escherichia coli (EHEC) constitute a significant risk to human health worldwide, and infections, particularly with serogroup O157:H7, are associated with consumption of a variety of food and water vehicles, particularly food of bovine origin. EHEC cause acute gastroenteritis, bloody diarrhoea, and haemorrhagic colitis; up to 10% of cases develop severe complications, including the haemolytic uraemic syndrome, with a 5% case fatality. A virulence characteristic of enteropathogenic E coli, the attaching/effacing lesion, is considered to be important in EHEC. However, although EHEC produce this lesion on cultured human cells, this has not been demonstrated on human intestinal mucosal surfaces. In addition, the initial site(s) of colonisation of EHEC in humans is not known.

AIMS

To assess the association of EHEC O157:H7 with paediatric and bovine intestine using in vitro organ culture and determine if attaching/effacing lesions occur.

METHODS

Ultrastructural analysis of in vitro intestinal organ cultures of human small and large intestine was used to investigate adhesion of O157:H7 EHEC to intestinal surfaces. Bovine intestinal organ culture was used to examine the pathology produced by the same EHEC strain in cattle.

RESULTS

The study showed that EHEC O157:H7 adhered to human intestinal mucosa. Binding and attaching/effacing lesion formation of O157:H7 in humans was restricted to follicle associated epithelium of Peyer's patches. The same strain caused attaching/effacing lesions on bovine mucosa.

CONCLUSIONS

O157:H7 targets follicle associated epithelium in humans where it causes attaching/effacing lesions. The same human isolate can cause attaching/effacing lesions in cattle, indicating that similar pathogenic mechanisms operate across human and bovine species

Involvement of the enteroaggregative Escherichia coli plasmid-encoded toxin in causing human intestinal damage

Enteroaggregative Escherichia coli (EAEC) strains have been shown to adhere to human intestinal tissue in an in vitro organ culture (IVOC) model, and certain strains manifest mucosal toxicity. We have recently described the EAEC plasmid-encoded toxin (Pet), a member of a specific serine protease subclass of the autotransporter proteins. When injected into rat ileal loops, Pet both elicited fluid accumulation and had cytotoxic effects on the mucosa. Furthermore, the Pet protein caused rises in short circuit current from rat jejunal tissue mounted in a Ussing chamber and rounding of intestinal epithelial cells in culture. We therefore hypothesized that the mucosal pathology induced by EAEC strains in the IVOC model was related to expression of the Pet protein. Here, we have examined the effects of EAEC strain 042 and its isogenic pet mutant in the IVOC model. 042-infected colonic explants exhibited dilation of crypt openings, increased cell rounding, development of prominent intercrypt crevices, and absence of apical mucus plugs. Colonic tissue incubated with the pet mutant exhibited significantly fewer mucosal abnormalities both subjectively and as quantitated morphometrically by measurement of crypt aperture diameter. Mucosal effects were restored upon complementation of the pet mutation in trans. Interestingly, we found that the ability of 042 to damage T84 cells was not dependent upon Pet. The data suggest that the Pet toxin is active on the human intestinal mucosa but that EAEC may have other mechanisms of eliciting mucosal damage.

Interactions of buprenorphine and selective dopamine receptor antagonists in the rat nucleus accumbens

1. Extracellular recording of spontaneously active nucleus accumbens neurons was employed to characterize interactions of the mixed opioid buprenorphine and selective dopamine receptor antagonists. 2. Buprenorphine caused depression of single-unit activity at all doses tested but evoked facilitation only at low doses. 3. In experiments with the D1 antagonist SCH 23390, buprenorphine-induced depression was consistently blocked, but facilitation was unaffected. 4. Conversely, the D2 antagonist eticlopride blocked buprenorphine-induced facilitation, though it was ineffective against depression.

Generation of Escherichia coli intimin derivatives with differing biological activities using site-directed mutagenesis of the intimin C-terminus domain

Intimins, encoded by eae genes, are outer membrane proteins involved in attaching-effacing (A/E) lesion formation and host cell invasion by pathogenic bacteria, including enteropathogenic Escherichia coli (EPEC) and Citrobacter rodentium. A series of intimins, harbouring specific mutations close to the C-terminus, were constructed using pCVD438, which encodes the eae gene from EPEC strain E2348/69. These mutant plasmids were introduced into EPEC strain CVD206 and C. rodentium strain DBS255, which both contain deletion mutations in their eae genes. CVD206, CVD206(pCVD438) and CVD206(pCVD438) derivatives were assessed for their ability to promote A/E lesion formation or invasion of HEp-2 cells and to induce A/E lesions on fresh human intestinal in vitro organ cultures (IVOC). The pathogenicity of C. rodentium DBS255 harbouring these plasmid derivatives was also studied in mice. Here, we report that intimin-mediated A/E lesion formation can be segregated from intimin-mediated HEp-2 cell invasion. Moreover, adherence to IVOC, EPEC-induced microvillus elongation and colonization of the murine intestine by C. rodentium were also modulated by the modified intimins.