Fast Predictive Image Registration

We present a method to predict image deformations based on patch-wise image appearance. Specifically, we design a patch-based deep encoder-decoder network which learns the pixel/voxel-wise mapping between image appearance and registration parameters. Our approach can predict general deformation parameterizations, however, we focus on the large deformation diffeomorphic metric mapping (LDDMM) registration model. By predicting the LDDMM momentum-parameterization we retain the desirable theoretical properties of LDDMM, while reducing computation time by orders of magnitude: combined with patch pruning, we achieve a 1500x/66x speed up compared to GPU-based optimization for 2D/3D image registration. Our approach has better prediction accuracy than predicting deformation or velocity fields and results in diffeomorphic transformations. Additionally, we create a Bayesian probabilistic version of our network, which allows evaluation of deformation field uncertainty through Monte Carlo sampling using dropout at test time. We show that deformation uncertainty highlights areas of ambiguous deformations. We test our method on the OASIS brain image dataset in 2D and 3D

The pathology of familial breast cancer: The pre-BRCA1/BRCA2 era - historical perspectives

A proportion of breast carcinomas develop as a result of a genetic predispostion to the disease. Prior to cloning of the BRCA1 and BRCA2 genes a limited number of studies were carried out to identify specific histopathological characteristics of hereditary breast cancer. These studies are the subject of this review. The main finding was the association of the (atypical) medullary type of breast cancer with a family history; the most important caveat being that medullary breast cancer is found more frequently in young patients. In view of the frequent bilateral occurrence of lobular cancer, this histologic type is also likely to be associated with a predisposing genetic defect. Future investigations will have to test this hypothesis. In addition to mutations in the BRCA1 and BRCA2 genes, there are as yet unidentified genetic defects predisposing to breast cancer development, and histopathology may well help in identifying these genes in the future

Adatom Fe(III) on the hematite surface: Observation of a key reactive surface species

The reactivity of a mineral surface is determined by the variety and population of different types of surface sites (e.g., step, kink, adatom, and defect sites). The concept of "adsorbed nutrient" has been built into crystal growth theories, and many other studies of mineral surface reactivity appeal to ill-defined "active sites." Despite their theoretical importance, there has been little direct experimental or analytical investigation of the structure and properties of such species. Here, we use ex-situ and in-situ scanning tunneling microcopy (STM) combined with calculated images based on a resonant tunneling model to show that observed nonperiodic protrusions and depressions on the hematite (001) surface can be explained as Fe in an adsorbed or adatom state occupying sites different from those that result from simple termination of the bulk mineral. The number of such sites varies with sample preparation history, consistent with their removal from the surface in low pH solutions

Mellin Amplitudes for Dual Conformal Integrals

Motivated by recent work on the utility of Mellin space for representing conformal correlators in $AdS$/CFT, we study its suitability for representing dual conformal integrals of the type which appear in perturbative scattering amplitudes in super-Yang-Mills theory. We discuss Feynman-like rules for writing Mellin amplitudes for a large class of integrals in any dimension, and find explicit representations for several familiar toy integrals. However we show that the power of Mellin space is that it provides simple representations even for fully massive integrals, which except for the single case of the 4-mass box have not yet been computed by any available technology. Mellin space is also useful for exhibiting differential relations between various multi-loop integrals, and we show that certain higher-loop integrals may be written as integral operators acting on the fully massive scalar $n$-gon in $n$ dimensions, whose Mellin amplitude is exactly 1. Our chief example is a very simple formula expressing the 6-mass double box as a single integral of the 6-mass scalar hexagon in 6 dimensions.Comment: 29+7 page

R^4 counterterm and E7(7) symmetry in maximal supergravity

The coefficient of a potential R^4 counterterm in N=8 supergravity has been shown previously to vanish in an explicit three-loop calculation. The R^4 term respects N=8 supersymmetry; hence this result poses the question of whether another symmetry could be responsible for the cancellation of the three-loop divergence. In this article we investigate possible restrictions from the coset symmetry E7(7)/SU(8), exploring the limits as a single scalar becomes soft, as well as a double-soft scalar limit relation derived recently by Arkani-Hamed et al. We implement these relations for the matrix elements of the R^4 term that occurs in the low-energy expansion of closed-string tree-level amplitudes. We find that the matrix elements of R^4 that we investigated all obey the double-soft scalar limit relation, including certain non-maximally-helicity-violating six-point amplitudes. However, the single-soft limit does not vanish for this latter set of amplitudes, which suggests that the E7(7) symmetry is broken by the R^4 term.Comment: 33 pages, typos corrected, published versio

Nanotube Action between Human Mesothelial Cells Reveals Novel Aspects of Inflammatory Responses

A well-known role of human peritoneal mesothelial cells (HPMCs), the resident cells of the peritoneal cavity, is the generation of an immune response during peritonitis by activation of T-cells via antigen presentation. Recent findings have shown that intercellular nanotubes (NTs) mediate functional connectivity between various cell types including immune cells - such as T-cells, natural killer (NK) cells or macrophages - by facilitating a spectrum of long range cell-cell interactions. Although of medical interest, the relevance of NT-related findings for human medical conditions and treatment, e.g. in relation to inflammatory processes, remains elusive, particularly due to a lack of appropriate in vivo data. Here, we show for the first time that primary cultures of patient derived HPMCs are functionally connected via membranous nanotubes. NT formation appears to be actin cytoskeleton dependent, mediated by the action of filopodia. Importantly, significant variances in NT numbers between different donors as a consequence of pathophysiological alterations were observable. Furthermore, we show that TNF-α induces nanotube formation and demonstrate a strong correlation of NT connectivity in accordance with the cellular cholesterol level and distribution, pointing to a complex involvement of NTs in inflammatory processes with potential impact for clinical treatment

Unsupervised joint PoS tagging and stemming for agglutinative languages

This is an accepted manuscript of an article published by Association for Computing Machinery (ACM) in ACM Transactions on Asian and Low-Resource Language Information Processing on 25/01/2019, available online: https://doi.org/10.1145/3292398 The accepted version of the publication may differ from the final published version.The number of possible word forms is theoretically infinite in agglutinative languages. This brings up the out-of-vocabulary (OOV) issue for part-of-speech (PoS) tagging in agglutinative languages. Since inflectional morphology does not change the PoS tag of a word, we propose to learn stems along with PoS tags simultaneously. Therefore, we aim to overcome the sparsity problem by reducing word forms into their stems. We adopt a Bayesian model that is fully unsupervised. We build a Hidden Markov Model for PoS tagging where the stems are emitted through hidden states. Several versions of the model are introduced in order to observe the effects of different dependencies throughout the corpus, such as the dependency between stems and PoS tags or between PoS tags and affixes. Additionally, we use neural word embeddings to estimate the semantic similarity between the word form and stem. We use the semantic similarity as prior information to discover the actual stem of a word since inflection does not change the meaning of a word. We compare our models with other unsupervised stemming and PoS tagging models on Turkish, Hungarian, Finnish, Basque, and English. The results show that a joint model for PoS tagging and stemming improves on an independent PoS tagger and stemmer in agglutinative languages.This research is supported by the Scientific and Technological Research Council of Turkey (TUBITAK) with the project number EEEAG-115E464.Published versio

Pneumococcal carriage in sub-Saharan Africa--a systematic review.

BACKGROUND: Pneumococcal epidemiology varies geographically and few data are available from the African continent. We assess pneumococcal carriage from studies conducted in sub-Saharan Africa (sSA) before and after the pneumococcal conjugate vaccine (PCV) era. METHODS: A search for pneumococcal carriage studies published before 2012 was conducted to describe carriage in sSA. The review also describes pneumococcal serotypes and assesses the impact of vaccination on carriage in this region. RESULTS: Fifty-seven studies were included in this review with the majority (40.3%) from South Africa. There was considerable variability in the prevalence of carriage between studies (I-squared statistic = 99%). Carriage was higher in children and decreased with increasing age, 63.2% (95% CI: 55.6-70.8) in children less than 5 years, 42.6% (95% CI: 29.9-55.4) in children 5-15 years and 28.0% (95% CI: 19.0-37.0) in adults older than 15 years. There was no difference in the prevalence of carriage between males and females in 9/11 studies. Serotypes 19F, 6B, 6A, 14 and 23F were the five most common isolates. A meta-analysis of four randomized trials of PCV vaccination in children aged 9-24 months showed that carriage of vaccine type (VT) serotypes decreased with PCV vaccination; however, overall carriage remained the same because of a concomitant increase in non-vaccine type (NVT) serotypes. CONCLUSION: Pneumococcal carriage is generally high in the African continent, particularly in young children. The five most common serotypes in sSA are among the top seven serotypes that cause invasive pneumococcal disease in children globally. These serotypes are covered by the two PCVs recommended for routine childhood immunization by the WHO. The distribution of serotypes found in the nasopharynx is altered by PCV vaccination

Pothead or pot smoker? a taxometric investigation of cannabis dependence

BACKGROUND: Taxometric methods were used to discern the latent structure of cannabis dependence. Such methods help determine if a construct is categorical or dimensional. Taxometric analyses (MAXEIG and MAMBAC) were conducted on data from 1,474 cannabis-using respondents to the 2001–2002 National Epidemiologic Survey on Alcohol and Related Conditions (NESARC). Respondents answered questions assessing DSM-IV criteria for cannabis dependence. RESULTS: Both taxometric methods provided support for a dimensional structure of cannabis dependence. CONCLUSION: Although the MAMBAC results were not entirely unequivocal, the majority of evidence favored a dimensional structure of cannabis dependence

Histone deacetylases as new therapy targets for platinum-resistant epithelial ovarian cancer

Introduction: In developed countries, ovarian cancer is the fourth most common cancer in women. Due to the nonspecific symptomatology associated with the disease many patients with ovarian cancer are diagnosed late, which leads to significantly poorer prognosis. Apart from surgery and radiotherapy, a substantial number of ovarian cancer patients will undergo chemotherapy and platinum based agents are the mainstream first-line therapy for this disease. Despite the initial efficacy of these therapies, many women relapse; therefore, strategies for second-line therapies are required. Regulation of DNA transcription is crucial for tumour progression, metastasis and chemoresistance which offers potential for novel drug targets. Methods: We have reviewed the existing literature on the role of histone deacetylases, nuclear enzymes regulating gene transcription. Results and conclusion: Analysis of available data suggests that a signifant proportion of drug resistance stems from abberant gene expression, therefore HDAC inhibitors are amongst the most promising therapeutic targets for cancer treatment. Together with genetic testing, they may have a potential to serve as base for patient-adapted therapies