Generative discriminative models for multivariate inference and statistical mapping in medical imaging

This paper presents a general framework for obtaining interpretable multivariate discriminative models that allow efficient statistical inference for neuroimage analysis. The framework, termed generative discriminative machine (GDM), augments discriminative models with a generative regularization term. We demonstrate that the proposed formulation can be optimized in closed form and in dual space, allowing efficient computation for high dimensional neuroimaging datasets. Furthermore, we provide an analytic estimation of the null distribution of the model parameters, which enables efficient statistical inference and p-value computation without the need for permutation testing. We compared the proposed method with both purely generative and discriminative learning methods in two large structural magnetic resonance imaging (sMRI) datasets of Alzheimer's disease (AD) (n=415) and Schizophrenia (n=853). Using the AD dataset, we demonstrated the ability of GDM to robustly handle confounding variations. Using Schizophrenia dataset, we demonstrated the ability of GDM to handle multi-site studies. Taken together, the results underline the potential of the proposed approach for neuroimaging analyses.Comment: To appear in MICCAI 2018 proceeding

Initiation and Adequacy of Complementary Feeding

BackgroundInfants and young children are at an increased risk of malnutrition from six months of age onwards, when breast milk alone is no longer sufficient to meet all their nutritional requirements and complementary feeding should be started. Hence this study was undertaken to assess the practices of complementary feeding.Method  This hospital-based cross-sectional study was conducted at two private hospitals – Dr TMA Pai Hospital Udupi and Dr TMA Pai Hospital Karkala and a public hospital, Regional Advanced Paediatric Care Centre, Mangalore, of coastal south India for a two-month period from August 2010 to October 2010. Two-hundred mothers of children between six months and two years attending the paediatric outpatient departments of the above-mentioned hospitals for growth monitoring, immunisation and minor illnesses such as upper respiratory tract infections were selected for the study. The subjects were selected for the study by the order of their arrival to the outpatient department during the study period. ResultsIn the present study 77.5% mothers had started complementary feeding at the recommended time of six months. Only 32% of mothers were giving an adequate quantity of complementary feeds. The association of initiation of complementary feeding with socio-economic status, birth order, place of delivery and maternal education was found to be statistically significant. However the practice of giving an adequate quantity of complementary feeds was significantly associated only with the place of delivery.ConclusionIn the present study, initiation of complementary feeding at the recommended time of six months was seen in the majority of children. However the quantity of complementary feeding was insufficient. Advice about breast feeding and complementary feeding during antenatal check-ups and postnatal visits might improve feeding practices

Large-area ultrathin Te films with substrate-tunable orientation.

Anisotropy in a crystal structure can lead to large orientation-dependent variations of mechanical, optical, and electronic properties. Material orientation control can thus provide a handle to manipulate properties. Here, a novel sputtering approach for 2D materials enables growth of ultrathin (2.5-10 nm) tellurium films with rational control of the crystalline orientation templated by the substrate. The anisotropic Te 〈0001〉 helical chains align in the plane of the substrate on highly oriented pyrolytic graphite (HOPG) and orthogonally to MgO(100) substrates, as shown by polarized Raman spectroscopy and high-resolution electron microscopy. Furthermore, the films are shown to grow in a textured fashion on HOPG, in contrast with previous reports. These ultrathin Te films cover exceptionally large areas (>1 cm2) and are grown at low temperature (25 °C) affording the ability to accommodate a variety of substrates including flexible electronics. They are robust toward oxidation over a period of days and exhibit the non-centrosymmetric P3121 Te structure. Raman signals are acutely dependent on film thickness, suggesting that optical anisotropy persists and is even enhanced at the ultrathin limit. Hall effect measurements indicate orientation-dependent carrier mobility up to 19 cm2 V-1 s-1. These large-area, ultrathin Te films grown by a truly scalable, physical vapor deposition technique with rational control of orientation/thickness open avenues for controlled orientation-dependent properties in semiconducting thin films for applications in electronic and optoelectronic devices.This research was supported by the Air Force Office of Scientific Research grant no. AFOSR-YIP FA9550-17-1-0202 and a 3M Non-Tenured Faculty Award. Elisabeth Bianco acknowledges the support of the National Science Foundation Graduate Research Fellowship under grant no. DGE-1450681. MS acknowledges support from Air Force Office of Scientific Research grant number FA9550-19RYCOR050. This research made use of instruments in the Shared Equipment Authority of Rice University. This research was supported by the Nanoelectronics Branch, Functional Materials Division, Materials and Manufacturing Directorate, Air Force Research Laboratory and made use of instruments in the Materials Characterization Facility in the Materials and Manufacturing Directorate, Air Force Research Laboratory. We thank Dr Dean Brown for performing the FEM modelling and his contributions to Figure S1. EB thanks Dr Krishnamurthy Mahalingam and Dr Brandon Howe for helpful discussions on TEM and growth

An inflamed necrotic appendix epiploicum with immediate contact to a non-inflamed appendix vermiformis: a case report

<p>Abstract</p> <p>Introduction</p> <p>Epiploic appendagitis is a rare cause of focal abdominal pain which, depending on its localisation, can mimic a variety of abdominal diseases. We describe a patient with an inflamed necrotic appendix epiploicum with immediate contact to a non-inflamed appendix vermiformis mimicking acute appendicitis. Considering the rare localization, this is the first report of this kind in the literature.</p> <p>Case presentation</p> <p>We present the case of a 50-year-old Caucasian man who presented with classic signs of acute appendicitis. On clinical exam, McBurney and Blumberg signs were positive. Additionally he had fever, leucocytosis (12/nl) and a slight increase in C-reactive protein (1 mg/dl). Based on the clinical presentation, the patient was taken to the operating room to perform an appendicectomy. Surprisingly, we found an inflamed necrotic appendix epiploicum, located immediately on a non-inflamed appendix vermiformis, which was ligated and excised.</p> <p>Conclusion</p> <p>This case report demonstrates that epiploic appendagitis can mimic acute appendicitis on clinical exam and should be considered in the broad spectrum of abdominal disease presenting with right lower quadrant pain.</p

Predicting cell types and genetic variations contributing to disease by combining GWAS and epigenetic data

Genome-wide association studies (GWASs) identify single nucleotide polymorphisms (SNPs) that are enriched in individuals suffering from a given disease. Most disease-associated SNPs fall into non-coding regions, so that it is not straightforward to infer phenotype or function; moreover, many SNPs are in tight genetic linkage, so that a SNP identified as associated with a particular disease may not itself be causal, but rather signify the presence of a linked SNP that is functionally relevant to disease pathogenesis. Here, we present an analysis method that takes advantage of the recent rapid accumulation of epigenomics data to address these problems for some SNPs. Using asthma as a prototypic example; we show that non-coding disease-associated SNPs are enriched in genomic regions that function as regulators of transcription, such as enhancers and promoters. Identifying enhancers based on the presence of the histone modification marks such as H3K4me1 in different cell types, we show that the location of enhancers is highly cell-type specific. We use these findings to predict which SNPs are likely to be directly contributing to disease based on their presence in regulatory regions, and in which cell types their effect is expected to be detectable. Moreover, we can also predict which cell types contribute to a disease based on overlap of the disease-associated SNPs with the locations of enhancers present in a given cell type. Finally, we suggest that it will be possible to re-analyze GWAS studies with much higher power by limiting the SNPs considered to those in coding or regulatory regions of cell types relevant to a given disease

Bianchi Type-II String Cosmological Models in Normal Gauge for Lyra's Manifold with Constant Deceleration Parameter

The present study deals with a spatially homogeneous and anisotropic Bianchi-II cosmological models representing massive strings in normal gauge for Lyra's manifold by applying the variation law for generalized Hubble's parameter that yields a constant value of deceleration parameter. The variation law for Hubble's parameter generates two types of solutions for the average scale factor, one is of power-law type and other is of the exponential form. Using these two forms, Einstein's modified field equations are solved separately that correspond to expanding singular and non-singular models of the universe respectively. The energy-momentum tensor for such string as formulated by Letelier (1983) is used to construct massive string cosmological models for which we assume that the expansion ($\theta$) in the model is proportional to the component $\sigma^{1}_{~1}$ of the shear tensor $\sigma^{j}_{i}$. This condition leads to $A = (BC)^{m}$, where A, B and C are the metric coefficients and m is proportionality constant. Our models are in accelerating phase which is consistent to the recent observations. It has been found that the displacement vector $\beta$ behaves like cosmological term $\Lambda$ in the normal gauge treatment and the solutions are consistent with recent observations of SNe Ia. It has been found that massive strings dominate in the decelerating universe whereas strings dominate in the accelerating universe. Some physical and geometric behaviour of these models are also discussed.Comment: 24 pages, 10 figure

A computational framework to emulate the human perspective in flow cytometric data analysis

Background: In recent years, intense research efforts have focused on developing methods for automated flow cytometric data analysis. However, while designing such applications, little or no attention has been paid to the human perspective that is absolutely central to the manual gating process of identifying and characterizing cell populations. In particular, the assumption of many common techniques that cell populations could be modeled reliably with pre-specified distributions may not hold true in real-life samples, which can have populations of arbitrary shapes and considerable inter-sample variation. &lt;p/&gt;Results: To address this, we developed a new framework flowScape for emulating certain key aspects of the human perspective in analyzing flow data, which we implemented in multiple steps. First, flowScape begins with creating a mathematically rigorous map of the high-dimensional flow data landscape based on dense and sparse regions defined by relative concentrations of events around modes. In the second step, these modal clusters are connected with a global hierarchical structure. This representation allows flowScape to perform ridgeline analysis for both traversing the landscape and isolating cell populations at different levels of resolution. Finally, we extended manual gating with a new capacity for constructing templates that can identify target populations in terms of their relative parameters, as opposed to the more commonly used absolute or physical parameters. This allows flowScape to apply such templates in batch mode for detecting the corresponding populations in a flexible, sample-specific manner. We also demonstrated different applications of our framework to flow data analysis and show its superiority over other analytical methods. &lt;p/&gt;Conclusions: The human perspective, built on top of intuition and experience, is a very important component of flow cytometric data analysis. By emulating some of its approaches and extending these with automation and rigor, flowScape provides a flexible and robust framework for computational cytomics

Genomic evolution and transcriptional changes in the evolution of prostate cancer into neuroendocrine and ductal carcinoma types

Prostate cancer is typically of acinar adenocarcinoma type but can occasionally present as neuroendocrine and/or ductal type carcinoma. These are associated with clinically aggressive disease, and the former often arises on a background of androgen deprivation therapy, although it can also arise de novo. Two prostate cancer cases were sequenced by exome capture from archival tissue. Case 1 was de novo small cell neuroendocrine carcinoma and ductal adenocarcinoma with three longitudinal samples over 5 years. Case 2 was a single time point after the development of treatment-related neuroendocrine prostate carcinoma. Case 1 showed whole genome doubling in all samples and focal amplification of AR in all samples except the first time point. Phylogenetic analysis revealed a common ancestry for ductal and small cell carcinoma. Case 2 showed 13q loss (involving RB1) in both adenocarcinoma and small cell carcinoma regions, and 3p gain, 4p loss, and 17p loss (involving TP53) in the latter. By using highly curated samples, we demonstrate for the first time that small-cell neuroendocrine and ductal prostatic carcinoma can have a common ancestry. We highlight whole genome doubling in a patient with prostate cancer relapse, reinforcing its poor prognostic nature

A transcriptomic snapshot of early molecular communication between Pasteuria penetrans and Meloidogyne incognita

© The Author(s). 2018Background: Southern root-knot nematode Meloidogyne incognita (Kofoid and White, 1919), Chitwood, 1949 is a key pest of agricultural crops. Pasteuria penetrans is a hyperparasitic bacterium capable of suppressing the nematode reproduction, and represents a typical coevolved pathogen-hyperparasite system. Attachment of Pasteuria endospores to the cuticle of second-stage nematode juveniles is the first and pivotal step in the bacterial infection. RNA-Seq was used to understand the early transcriptional response of the root-knot nematode at 8 h post Pasteuria endospore attachment. Results: A total of 52,485 transcripts were assembled from the high quality (HQ) reads, out of which 582 transcripts were found differentially expressed in the Pasteuria endospore encumbered J2 s, of which 229 were up-regulated and 353 were down-regulated. Pasteuria infection caused a suppression of the protein synthesis machinery of the nematode. Several of the differentially expressed transcripts were putatively involved in nematode innate immunity, signaling, stress responses, endospore attachment process and post-attachment behavioral modification of the juveniles. The expression profiles of fifteen selected transcripts were validated to be true by the qRT PCR. RNAi based silencing of transcripts coding for fructose bisphosphate aldolase and glucosyl transferase caused a reduction in endospore attachment as compared to the controls, whereas, silencing of aspartic protease and ubiquitin coding transcripts resulted in higher incidence of endospore attachment on the nematode cuticle. Conclusions: Here we provide evidence of an early transcriptional response by the nematode upon infection by Pasteuria prior to root invasion. We found that adhesion of Pasteuria endospores to the cuticle induced a down-regulated protein response in the nematode. In addition, we show that fructose bisphosphate aldolase, glucosyl transferase, aspartic protease and ubiquitin coding transcripts are involved in modulating the endospore attachment on the nematode cuticle. Our results add new and significant information to the existing knowledge on early molecular interaction between M. incognita and P. penetrans.Peer reviewedFinal Published versio