Improving High Resolution Histology Image Classification with Deep Spatial Fusion Network

Histology imaging is an essential diagnosis method to finalize the grade and stage of cancer of different tissues, especially for breast cancer diagnosis. Specialists often disagree on the final diagnosis on biopsy tissue due to the complex morphological variety. Although convolutional neural networks (CNN) have advantages in extracting discriminative features in image classification, directly training a CNN on high resolution histology images is computationally infeasible currently. Besides, inconsistent discriminative features often distribute over the whole histology image, which incurs challenges in patch-based CNN classification method. In this paper, we propose a novel architecture for automatic classification of high resolution histology images. First, an adapted residual network is employed to explore hierarchical features without attenuation. Second, we develop a robust deep fusion network to utilize the spatial relationship between patches and learn to correct the prediction bias generated from inconsistent discriminative feature distribution. The proposed method is evaluated using 10-fold cross-validation on 400 high resolution breast histology images with balanced labels and reports 95% accuracy on 4-class classification and 98.5% accuracy, 99.6% AUC on 2-class classification (carcinoma and non-carcinoma), which substantially outperforms previous methods and close to pathologist performance.Comment: 8 pages, MICCAI workshop preceeding

Geometric Multicut: Shortest Fences for Separating Groups of Objects in the Plane

We study the following separation problem: Given a collection of pairwise disjoint coloured objects in the plane with k different colours, compute a shortest “fence” F, i.e., a union of curves of minimum total length, that separates every pair of objects of different colours. Two objects are separated if F contains a simple closed curve that has one object in the interior and the other in the exterior. We refer to the problem as GEOMETRIC k-CUT, as it is a geometric analog to the well-studied multicut problem on graphs. We first give an O(n4log3n)-time algorithm that computes an optimal fence for the case where the input consists of polygons of two colours with n corners in total. We then show that the problem is NP-hard for the case of three colours. Finally, we give a randomised 4/3⋅1.2965-approximation algorithm for polygons and any number of colours

Soft Image Segmentation: On the Clustering of Irregular, Weighted, Multivariate Marked Networks

The contribution exposes and illustrates a general, flexible formalism, together with an associated iterative procedure, aimed at determining soft memberships of marked nodes in a weighted network. Gathering together spatial entities which are both spatially close and similar regarding their features is an issue relevant in image segmentation, spatial clustering, and data analysis in general. Unoriented weighted networks are specified by an ``exchange matrix", determining the probability to select a pair of neighbors. We present a family of membership-dependent free energies, whose local minimization specifies soft clusterings. The free energy additively combines a mutual information, as well as various energy terms, concave or convex in the memberships: within-group inertia, generalized cuts (extending weighted Ncut and modularity), and membership discontinuities (generalizing Dirichlet forms). The framework is closely related to discrete Markov models, random walks, label propagation and spatial autocorrelation (Moran's I), and can express the Mumford-Shah approach. Four small datasets illustrate the theory

Culture-area relation in Axelrod's model for culture dissemination

Axelrod's model for culture dissemination offers a nontrivial answer to the question of why there is cultural diversity given that people's beliefs have a tendency to become more similar to each other's as people interact repeatedly. The answer depends on the two control parameters of the model, namely, the number $F$ of cultural features that characterize each agent, and the number $q$ of traits that each feature can take on, as well as on the size $A$ of the territory or, equivalently, on the number of interacting agents. Here we investigate the dependence of the number $C$ of distinct coexisting cultures on the area $A$ in Axelrod's model -- the culture-area relationship -- through extensive Monte Carlo simulations. We find a non-monotonous culture-area relation, for which the number of cultures decreases when the area grows beyond a certain size, provided that $q$ is smaller than a threshold value $q_c = q_c (F)$ and $F \geq 3$. In the limit of infinite area, this threshold value signals the onset of a discontinuous transition between a globalized regime marked by a uniform culture (C=1), and a completely polarized regime where all $C = q^F$ possible cultures coexist. Otherwise the culture-area relation exhibits the typical behavior of the species-area relation, i.e., a monotonically increasing curve the slope of which is steep at first and steadily levels off at some maximum diversity value

Metarhizium anisopliae Pathogenesis of Mosquito Larvae: A Verdict of Accidental Death

Metarhizium anisopliae, a fungal pathogen of terrestrial arthropods, kills the aquatic larvae of Aedes aegypti, the vector of dengue and yellow fever. The fungus kills without adhering to the host cuticle. Ingested conidia also fail to germinate and are expelled in fecal pellets. This study investigates the mechanism by which this fungus adapted to terrestrial hosts kills aquatic mosquito larvae. Genes associated with the M. anisopliae early pathogenic response (proteinases Pr1 and Pr2, and adhesins, Mad1 and Mad2) are upregulated in the presence of larvae, but the established infection process observed in terrestrial hosts does not progress and insecticidal destruxins were not detected. Protease inhibitors reduce larval mortality indicating the importance of proteases in the host interaction. The Ae. aegypti immune response to M. anisopliae appears limited, whilst the oxidative stress response gene encoding for thiol peroxidase is upregulated. Cecropin and Hsp70 genes are downregulated as larval death occurs, and insect mortality appears to be linked to autolysis through caspase activity regulated by Hsp70 and inhibited, in infected larvae, by protease inhibitors. Evidence is presented that a traditional host-pathogen response does not occur as the species have not evolved to interact. M. anisopliae retains pre-formed pathogenic determinants which mediate host mortality, but unlike true aquatic fungal pathogens, does not recognise and colonise the larval host

Choice-Disability and HIV Infection: A Cross Sectional Study of HIV Status in Botswana, Namibia and Swaziland

Interpersonal power gradients may prevent people implementing HIV prevention decisions. Among 7,464 youth aged 15–29 years in Botswana, Namibia and Swaziland we documented indicators of choice-disability (low education, educational disparity with partner, experience of sexual violence, experience of intimate partner violence (IPV), poverty, partner income disparity, willingness to have sex without a condom despite believing partner at risk of HIV), and risk behaviours like inconsistent use of condoms and multiple partners. In Botswana, Namibia and Swaziland, 22.9, 9.1, and 26.1% women, and 8.3, 2.8, and 9.3% men, were HIV positive. Among both women and men, experience of IPV, IPV interacted with age, and partner income disparity interacted with age were associated with HIV positivity in multivariate analysis. Additional factors were low education (for women) and poverty (for men). Choice disability may be an important driver of the AIDS epidemic. New strategies are needed that favour the choice-disabled

Health-related quality of life after vertebral or hip fracture: a seven-year follow-up study

<p>Abstract</p> <p>Background</p> <p>The negative impact of vertebral and hip low-energy fractures on health-related quality-of-life (HRQOL) has been demonstrated previously, but few prospective long-term follow-up studies have been conducted. This study aims to (i) investigate the changes and long-term impact of vertebral or hip fracture and between fracture groups on HRQOL in postmenopausal women prospectively between two and seven years after the inclusion fracture, (ii) compare HRQOL results between fracture and reference groups and (iii) study the relationship between HRQOL and physical performance, spinal deformity index and bone mineral density at seven-year follow-up.</p> <p>Methods</p> <p>Ninety-one women examined two years after a low-energy vertebral or hip fracture were invited to a new examination seven years after the diagnosis. HRQOL was examined using the SF-36 questionnaire and was compared with an age and sex-matched reference group. Physical function was assessed using tests and questionnaires. Bone mineral density was measured. Radiographs of the spine were evaluated using the visual semiquantitative technique. A longitudinal and cross-sectional design was used in this study. Statistical analyses included descriptive statistics, Student's <it>t</it>-tests, ANCOVA, and partial correlation.</p> <p>Results</p> <p>Sixty-seven women participated. In the 42 women (mean age 75.8, SD 4.7) with vertebral fracture as inclusion fracture, bodily pain had deteriorated between two and seven years and might be explained by new fracture. Remaining pronounced reduction of HRQOL was seen in all domains except general health and mental health at seven-year follow-up in women with vertebral fractures compared to the reference group (p < 0.05). All 25 women (mean age 75.0, SD 4.7) with hip fracture as inclusion fracture had no significant changes in HRQOL between two and seven years and did not differ from the reference group regarding HRQOL after seven years. The vertebral group had significantly lower values for bodily pain, vitality, role-emotional function and mental health compared to the hip group. HRQOL showed a positive relationship between physical activity, static balance and handgrip strength.</p> <p>Conclusion</p> <p>The long-term reduction of HRQOL in women with vertebral fracture emerged clearly in this study. The relationships between HRQOL and physical performance in women with vertebral and hip fracture raise questions for more research.</p

The Baker's Yeast Diploid Genome Is Remarkably Stable in Vegetative Growth and Meiosis

Accurate estimates of mutation rates provide critical information to analyze genome evolution and organism fitness. We used whole-genome DNA sequencing, pulse-field gel electrophoresis, and comparative genome hybridization to determine mutation rates in diploid vegetative and meiotic mutation accumulation lines of Saccharomyces cerevisiae. The vegetative lines underwent only mitotic divisions while the meiotic lines underwent a meiotic cycle every ∼20 vegetative divisions. Similar base substitution rates were estimated for both lines. Given our experimental design, these measures indicated that the meiotic mutation rate is within the range of being equal to zero to being 55-fold higher than the vegetative rate. Mutations detected in vegetative lines were all heterozygous while those in meiotic lines were homozygous. A quantitative analysis of intra-tetrad mating events in the meiotic lines showed that inter-spore mating is primarily responsible for rapidly fixing mutations to homozygosity as well as for removing mutations. We did not observe 1–2 nt insertion/deletion (in-del) mutations in any of the sequenced lines and only one structural variant in a non-telomeric location was found. However, a large number of structural variations in subtelomeric sequences were seen in both vegetative and meiotic lines that did not affect viability. Our results indicate that the diploid yeast nuclear genome is remarkably stable during the vegetative and meiotic cell cycles and support the hypothesis that peripheral regions of chromosomes are more dynamic than gene-rich central sections where structural rearrangements could be deleterious. This work also provides an improved estimate for the mutational load carried by diploid organisms

Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa

Background: Climatic and topographic changes function as key drivers in shaping genetic structure and cladogenic radiation in many organisms. Southern Africa has an exceptionally diverse tortoise fauna, harbouring one-third of the world’s tortoise genera. The distribution of Psammobates tentorius (Kuhl, 1820) covers two of the 25 biodiversity hotspots in the world, the Succulent Karoo and Cape Floristic Region. The highly diverged P. tentorius represents an excellent model species for exploring biogeographic and radiation patterns of reptiles in Southern Africa. Results: We investigated genetic structure and radiation patterns against temporal and spatial dimensions since the Miocene in the Psammobates tentorius species complex, using multiple types of DNA markers and niche modelling analyses. Cladogenesis in P. tentorius started in the late Miocene (11.63–5.33 Ma) when populations dispersed from north to south to form two geographically isolated groups. The northern group diverged into a clade north of the Orange River (OR), followed by the splitting of the group south of the OR into a western and an interior clade. The latter divergence corresponded to the intensifcation of the cold Benguela current, which caused western aridifcation and rainfall seasonality. In the south, tectonic uplift and subsequent exhumation, together with climatic fuctuations seemed responsible for radiations among the four southern clades since the late Miocene. We found that each clade occurred in a habitat shaped by diferent climatic parameters, and that the niches difered substantially among the clades of the northern group but were similar among clades of the southern group. Conclusion: Climatic shifts, and biome and geographic changes were possibly the three major driving forces shaping cladogenesis and genetic structure in Southern African tortoise species. Our results revealed that the cladogenesis of the P. tentorius species complex was probably shaped by environmental cooling, biome shifts and topographic uplift in Southern Africa since the late Miocene. The Last Glacial Maximum (LGM) may have impacted the distribution of P. tentorius substantially. We found the taxonomic diversify of the P. tentorius species complex to be highest in the Greater Cape Floristic Region. All seven clades discovered warrant conservation attention, particularly Ptt-B–Ptr, Ptt-A and Pv-

Preoperative biliary drainage for periampullary tumors causing obstructive jaundice; DRainage vs. (direct) OPeration (DROP-trial)

BACKGROUND: Surgery in patients with obstructive jaundice caused by a periampullary (pancreas, papilla, distal bile duct) tumor is associated with a higher risk of postoperative complications than in non-jaundiced patients. Preoperative biliary drainage was introduced in an attempt to improve the general condition and thus reduce postoperative morbidity and mortality. Early studies showed a reduction in morbidity. However, more recently the focus has shifted towards the negative effects of drainage, such as an increase of infectious complications. Whether biliary drainage should always be performed in jaundiced patients remains controversial. The randomized controlled multicenter DROP-trial (DRainage vs. Operation) was conceived to compare the outcome of a 'preoperative biliary drainage strategy' (standard strategy) with that of an 'early-surgery' strategy, with respect to the incidence of severe complications (primary-outcome measure), hospital stay, number of invasive diagnostic tests, costs, and quality of life. METHODS/DESIGN: Patients with obstructive jaundice due to a periampullary tumor, eligible for exploration after staging with CT scan, and scheduled to undergo a "curative" resection, will be randomized to either "early surgical treatment" (within one week) or "preoperative biliary drainage" (for 4 weeks) and subsequent surgical treatment (standard treatment). Primary outcome measure is the percentage of severe complications up to 90 days after surgery. The sample size calculation is based on the equivalence design for the primary outcome measure. If equivalence is found, the comparison of the secondary outcomes will be essential in selecting the preferred strategy. Based on a 40% complication rate for early surgical treatment and 48% for preoperative drainage, equivalence is taken to be demonstrated if the percentage of severe complications with early surgical treatment is not more than 10% higher compared to standard treatment: preoperative biliary drainage. Accounting for a 10% dropout, 105 patients are needed in each arm resulting in a study population of 210 (alpha = 0.95, beta = 0.8). DISCUSSION: The DROP-trial is a randomized controlled multicenter trial that will provide evidence whether or not preoperative biliary drainage is to be performed in patients with obstructive jaundice due to a periampullary tumor