Explainable Disease Classification via weakly-supervised segmentation

Deep learning based approaches to Computer Aided Diagnosis (CAD) typically pose the problem as an image classification (Normal or Abnormal) problem. These systems achieve high to very high accuracy in specific disease detection for which they are trained but lack in terms of an explanation for the provided decision/classification result. The activation maps which correspond to decisions do not correlate well with regions of interest for specific diseases. This paper examines this problem and proposes an approach which mimics the clinical practice of looking for an evidence prior to diagnosis. A CAD model is learnt using a mixed set of information: class labels for the entire training set of images plus a rough localisation of suspect regions as an extra input for a smaller subset of training images for guiding the learning. The proposed approach is illustrated with detection of diabetic macular edema (DME) from OCT slices. Results of testing on on a large public dataset show that with just a third of images with roughly segmented fluid filled regions, the classification accuracy is on par with state of the art methods while providing a good explanation in the form of anatomically accurate heatmap /region of interest. The proposed solution is then adapted to Breast Cancer detection from mammographic images. Good evaluation results on public datasets underscores the generalisability of the proposed solution

Deep Learning Method for Mandibular Canal Segmentation in Dental Cone Beam Computed Tomography Volumes

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Harnessing Uncertainty in Radiotherapy Auto-Segmentation Quality Assurance

One of the key contributions of this study is the reappropriation of standard DL outputs as a quality indicator to identify cases that clinicians should review further. The authors achieve this by applying an empirically derived threshold to the softmax output of their DL network, computing the mean of the thresholded score map (termed the HiS metric), and correlating it with standard geometric quality indices. When juxtaposed with a mean entropy — a commonly used measure of model output uncertainty — HiS consistently demonstrated a stronger correlation with the geometric indices, suggesting its superior ability to stratify cases needing additional review. We applaud the authors\u27 efforts for their novel contributions and would like to note some potential caveats that could pave the way for future research directions

After colonic surgery: The lived experience of participating in a fast-track programme

Postoperative recovery can be accelerated and hospitalization reduced through fast-track programmes. However, documented knowledge is limited and primarily focusing on a medical perspective whereas the patients' perspective lacks documentation. This study describes the lived experience of participating in a fast-track programme after colonic surgery. Sixteen patients were interviewed twice. The interviews were analysed using a descriptive phenomenological approach. Participating in a fast-track programme is characterized by a process where patients experience how the daily regimen works both with them and against them. To succeed in the overall goal of recovering fast according to the evidence-based care plan involves facing dilemmas and mobilizing courage and will to follow the regimen. Support from the professionals is crucial. The participants had a strong desire to comply and regain health; but this role of being a good and cooperative patient had a built-in asymmetric power relationship favouring the professionals' expectations. The complexities of this power relationship were related to both patient factors and contextual factors, e.g. the daily regimen and hospital norms. Although patient participation in care is an accepted ideal, it is demanding and difficult to accomplish. More studies on fast-track programmes are needed, with special attention to patient autonomy and partnership

Can sacrificial feeding areas protect aquatic plants from herbivore grazing? Using behavioural ecology to inform wildlife management

Effective wildlife management is needed for conservation, economic and human well-being objectives. However, traditional population control methods are frequently ineffective, unpopular with stakeholders, may affect non-target species, and can be both expensive and impractical to implement. New methods which address these issues and offer effective wildlife management are required. We used an individual-based model to predict the efficacy of a sacrificial feeding area in preventing grazing damage by mute swans (Cygnus olor) to adjacent river vegetation of high conservation and economic value. The accuracy of model predictions was assessed by a comparison with observed field data, whilst prediction robustness was evaluated using a sensitivity analysis. We used repeated simulations to evaluate how the efficacy of the sacrificial feeding area was regulated by (i) food quantity, (ii) food quality, and (iii) the functional response of the forager. Our model gave accurate predictions of aquatic plant biomass, carrying capacity, swan mortality, swan foraging effort, and river use. Our model predicted that increased sacrificial feeding area food quantity and quality would prevent the depletion of aquatic plant biomass by swans. When the functional response for vegetation in the sacrificial feeding area was increased, the food quantity and quality in the sacrificial feeding area required to protect adjacent aquatic plants were reduced. Our study demonstrates how the insights of behavioural ecology can be used to inform wildlife management. The principles that underpin our model predictions are likely to be valid across a range of different resource-consumer interactions, emphasising the generality of our approach to the evaluation of strategies for resolving wildlife management problems

Electric field-navigated transcranial magnetic stimulation for chronic tinnitus: a randomized, placebo-controlled study

Objective: Repetitive transcranial magnetic stimulation (rTMS) may alleviate tinnitus. We evaluated effects of electric field (E-field) navigated rTMS targeted according to tinnitus pitch. No controlled studies have investigated anatomically accurate E-field-rTMS for tinnitus. Design: Effects of E-field-rTMS were evaluated in a prospective randomised placebo-controlled 6-month follow-up study on parallel groups. Patients received 10 sessions of 1Hz rTMS or placebo targeted to the left auditory cortex corresponding to tonotopic representation of tinnitus pitch. Effects were evaluated immediately after treatment and at 1, 3 and 6 months. Primary outcome measures were visual analogue scores (VAS 0-100) for tinnitus intensity, annoyance and distress, and the Tinnitus Handicap Inventory (THI). Study sample: Thirty-nine patients (mean age 50.3 years). Results: The mean tinnitus intensity (F-3=15.7, p<0.0001), annoyance (F-3=8.8, p=0.0002), distress (F-3=9.1, p=0.0002) and THI scores (F-4=13.8, p<0.0001) decreased in both groups over time with non-significant differences between the groups. After active rTMS, 42% and 37% of the patients showed excellent response at 1 and 3 months against 15% and 10% in the placebo group (p=0.082 and p=0.065). Conclusions: Despite the significant effects of rTMS on tinnitus, differences between active and placebo groups remained non-significant, due to large placebo-effect and wide inter-individual variation

"Am I really ready to go home?" : a qualitative study of patients' experience of early discharge following an Enhanced Recovery Programme for Liver Resection Surgery

This qualitative data demonstrates some of the complexities of patients' expectations and experiences of the ERP. Whilst patients generally experience the ERP positively, they also have concerns about the process. The study highlights areas where additional support may be needed for patients enrolled in ERPs and discharged early

A multilocus assay reveals high nucleotide diversity and limited differentiation among Scandinavian willow grouse (Lagopus lagopus)

<p>Abstract</p> <p>Background</p> <p>There is so far very little data on autosomal nucleotide diversity in birds, except for data from the domesticated chicken and some passerines species. Estimates of nucleotide diversity reported so far in birds have been high (~10^-3) and a likely explanation for this is the generally higher effective population sizes compared to mammals. In this study, the level of nucleotide diversity has been examined in the willow grouse, a non-domesticated bird species from the order Galliformes, which also holds the chicken. The willow grouse (<it>Lagopus lagopus</it>) has an almost circumpolar distribution but is absent from Greenland and the north Atlantic islands. It primarily inhabits tundra, forest edge habitats and sub-alpine vegetation. Willow grouse are hunted throughout its range, and regionally it is a game bird of great cultural and economical importance.</p> <p>Results</p> <p>We sequenced 18 autosomal protein coding loci from approximately 15–18 individuals per population. We found a total of 127 SNP's, which corresponds to 1 SNP every 51 bp. 26 SNP's were amino acid replacement substitutions. Total nucleotide diversity (<it>π</it>_<it>t</it>) was between 1.30 × 10^-4and 7.66 × 10^-3(average <it>π</it>_{<it>t </it>}= 2.72 × 10^-3± 2.06 × 10^-3) and silent nucleotide diversity varied between 4.20 × 10^-4and 2.76 × 10^-2(average <it>π</it>_{<it>S </it>}= 9.22 × 10^-3± 7.43 × 10^-4). The synonymous diversity is approximately 20 times higher than in humans and two times higher than in chicken. Non-synonymous diversity was on average 18 times lower than the synonymous diversity and varied between 0 and 4.90 × 10^-3(average <it>π</it>_{<it>a </it>}= 5.08 × 10^-4± 7.43 × 10³), which suggest that purifying selection is strong in these genes. <it>F</it>_STvalues based on synonymous SNP's varied between -5.60 × 10^-4and 0.20 among loci and revealed low levels of differentiation among the four localities, with an overall value of <it>F</it>_ST= 0.03 (95% CI: 0.006 – 0.057) over 60 unlinked loci. Non-synonymous SNP's gave similar results. Low levels of linkage disequilibrium were observed within genes, with an average r²= 0.084 ± 0.110, which is expected for a large outbred population with no population differentiation. The mean per site per generation recombination parameter (ρ) was comparably high (0.028 ± 0.018), indicating high recombination rates in these genes.</p> <p>Conclusion</p> <p>We found unusually high levels of nucleotide diversity in the Scandinavian willow grouse as well as very little population structure among localities with up to 1647 km distance. There are also low levels of linkage disequilibrium within the genes and the population recombination rate is high, which is indicative of an old panmictic population, where recombination has had time to break up any haplotype blocks. The non-synonymous nucleotide diversity is low compared with the silent, which is in agreement with effective purifying selection, possibly due to the large effective population size.</p