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hierarchical generative model

Sezin Yüksel, Mario Ziegler, Sebastian Goerke, Uwe Huebner, Karina Weber, Peter Schaaf, Hans-Georg Meyer, Dana Cialla-May, Jürgen Popp
Surface enhanced Raman spectroscopy (SERS) is an attractive tool in analytical sciences due to its high specificity and sensitivity. Since the SERS active substrates are only available as 2D arrays, the fabrication of 3D nanostructures allows for an increased number of hot spots in the focus volume, thus further amplifying the SERS signal. Although a great number of fabrication strategies for powerful SERS substrates exist, the generation of 3D nanostructures with high complexity and periodicity is still challenging...
October 20, 2017: ACS Applied Materials & Interfaces
Yihao Deng, N Rao Chaganty
Archimedean copulas are commonly used in a wide range of statistical models due to their simplicity, manageable analytical expressions, rich choices of generator functions, and other workable properties. However, the exchangeable dependence structure inherent to Archimedean copulas limits its application to familial data, where the dependence among family members is often different. When response variables are binary, modeling the familial associations becomes more challenging due to the stringent constraints imposed on the dependence parameters...
October 17, 2017: Statistics in Medicine
Anaeze C Offodile, L Daniel Muldoon, Faiz Gani, Joseph K Canner, Lisa K Jacobs
BACKGROUND: Diminished use and worse outcomes after immediate breast reconstruction (IBR) have been documented for Medicaid beneficiaries. However, to the authors' knowledge, the contribution of patient clustering at hospitals with a high percentage of Medicaid patients to these inequalities in IBR delivery is unknown. METHODS: A cross-sectional analysis of patients undergoing IBR after mastectomy using the 2007 to 2011 Nationwide Inpatient Sample database was performed...
October 17, 2017: Cancer
Mohamed F Sallam, Chelsea Fizer, Andrew N Pilant, Pai-Yei Whung
Asian tiger and yellow fever mosquitoes (Aedes albopictus and Ae. aegypti) are global nuisances and are competent vectors for viruses such as Chikungunya (CHIKV), Dengue (DV), and Zika (ZIKV). This review aims to analyze available spatiotemporal distribution models of Aedes mosquitoes and their influential factors. A combination of five sets of 3-5 keywords were used to retrieve all relevant published models. Five electronic search databases were used: PubMed, MEDLINE, EMBASE, Scopus, and Google Scholar through 17 May 2017...
October 16, 2017: International Journal of Environmental Research and Public Health
Yassine Ridouane, Gilberto Lopes, Geoffrey Ku, Hasan Masud, Benjamin Haaland
BACKGROUND: Colorectal cancer is common and deadly. First-line treatments for patients with metastatic disease include FOLFIRI and FOLFOX, which have been combined with anti-EGFR or anti-VEGF antibodies to achieve benefit in selected populations. However, optimal therapy remains unclear. RESULTS: Fifteen publications on 10 trials were identified. There was a lack of decisive evidence that FOLFIRI or FOLFOX impact efficacy of either anti-EGFR or anti-VEGF, across mutational status groups...
September 12, 2017: Oncotarget
Lekha Sharma, Rita Kakkar
In this study, hierarchical porous magnesium oxide (Hr-MgO) microspheres have been fabricated from hydromagnesite precursor via a facile precipitation method followed by calcination. The Hr-MgO microspheres consist of several nanosheet building blocks to generate a flower-like architecture. Chlorpyrifos (CPF), a persistent organic pollutant, has been chosen as a model organophosphate pesticide to determine the adsorptive capacities of the fabricated Hr-MgO. The equilibrium adsorption data fits well with the Langmuir isotherm model, having a maximum adsorption capacity of 3974 mg g-1, which is the highest value till date...
October 13, 2017: ACS Applied Materials & Interfaces
Yue Ruan, Les Bluck, James Smith, Adrian Mander, Priya Singh, Michelle Venables
RATIONALE: The doubly labelled water (DLW) method is the reference method for the estimation of free-living total energy expenditure (TEE). In this method, where both (2) H and (18) O are employed, different approaches have been adopted to deal with the non-conformity observed regarding the distribution space for the labels being non-coincident with total body water. However, the method adopted can have a significant effect on the estimated TEE. METHODS: We proposed a Bayesian reasoning approach to modify an assumed prior distribution for the space ratio using experimental data to derive the TEE...
October 13, 2017: Rapid Communications in Mass Spectrometry: RCM
Leonie Korn, Daniel Rüschen, Niklas Zander, Steffen Leonhardt, Marian Walter
Classically, mock circulatory loops only simulate mechanical properties of the circulation. To connect the hydraulic world with electrophysiology, we present a real-time electrical activity model of the heart and show how to integrate this model into a real-time mock loop simulation. The model incorporates a predefined conduction pathway and a simplified volume conductor to solve the bidomain equations and the forward problem of electrocardiography, resulting in a physiological simulation of the electrocardiogram (ECG) at arbitrary electrode positions...
October 12, 2017: Artificial Organs
Jian'an Jia, Xiaotao Liang, Shipeng Chen, Hui Wang, Huiming Li, Meng Fang, Xin Bai, Ziyi Wang, Mengmeng Wang, Shanfeng Zhu, Fengzhu Sun, Chunfang Gao
In order to investigate if deletion patterns of the preS region can predict liver disease advancement, the preS region of the hepatitis B virus (HBV) genome in 45 chronic hepatitis B (CHB) and 94 HBV-related hepatocellular carcinoma (HCC) patients was sequenced by next-generation sequencing (NGS) and the percentages of nucleotide deletion in the preS region were analysed. Hierarchical clustering and heatmaps based on deletion percentages of preS revealed different deletion patterns between CHB and HCC patients...
October 12, 2017: Journal of General Virology
Lingyun Luo, Ling Tong, Xiaoxi Zhou, Jose L V Mejino, Chunping Ouyang, Yongbin Liu
Organizing the descendants of a concept under a particular semantic relationship may be rather arbitrarily carried out during the manual creation processes of large biomedical terminologies, resulting in imbalances in relationship granularity. This work aims to propose scalable models towards systematically evaluating the granularity balance of semantic relationships. We first utilize "parallel concepts set (PCS)" and two features (the length and the strength) of the paths between PCSs to design the general evaluation models, based on which we propose eight concrete evaluation models generated by two specific types of PCSs: single concept set and symmetric concepts set...
October 4, 2017: Journal of Biomedical Informatics
V R Dharnidharka, A S Naik, D A Axelrod, M A Schnitzler, Z Zhang, S Bae, D L Segev, D C Brennan, T Alhamad, R Ouseph, N N Lam, M Nazzal, H Randall, B L Kasiske, M McAdams-Demarco, K L Lentine
To assess factors that influence the choice of induction regimen in contemporary kidney transplantation, we examined center-identified, national transplant registry data for 166,776 US recipients (2005-2014). Bi-level hierarchical models were constructed, wherein use of each regimen was compared pairwise with use of interleukin-2 receptor blocking antibodies (IL2rAb). Overall, 81.8% of patients received induction, including thymoglobulin (TMG, 46.0%), IL2rAb (21.9%), alemtuzumab (ALEM, 12.5%), and other agents (1...
October 7, 2017: Transplant International: Official Journal of the European Society for Organ Transplantation
Duccio Piovani, Carlos Molinero, Alan Wilson
Characterising road networks has been the focus of a large body of research due to it being the main driver of activities in an urban ecosystem and the structuring factor in the dynamics of the city. One of these activities, and one with the largest economical impact in a city, is retail dynamics and its evolution. Therefore, the mathematical modeling of the location of retail activities and of the emergence of clustering in retail centers has as well generated a large number of works. Despite these two interwoven components strongly depending on one another and their fundamental importance in understanding cities, little work has been done in order to compare their local and global properties...
2017: PloS One
Luciana Inés Oklander, Carolina Isabel Miño, Gabriela Fernández, Mariela Caputo, Daniel Corach
Black-and-gold howler monkeys Alouatta caraya, are arboreal primates, inhabitants of Neotropical forests, highly susceptible to the yellow fever virus, considered early 'sentinels' of outbreaks, and thus, of major epidemiological importance. Currently, anthropogenic habitat loss and modifications threatens their survival. Habitat modification can prevent, reduce or change dispersal behavior, which, in turn, may influence patterns of gene flow. We explored past and contemporary levels of genetic diversity, elucidated genetic structure and identified its possible drivers, in ten populations (n = 138) located in the southernmost distribution range of the species in South America, in Argentina and Paraguay...
2017: PloS One
Natal Santos da Silva, Eduardo A Undurraga, Elis Regina da Silva Ferreira, Cássia Fernanda Estofolete, Maurício Lacerda Nogueira
In Brazil, the incidence of hospitalization due to dengue, as an indicator of severity, has drastically increased since 1998. The objective of our study was to identify risk factors associated with subsequent hospitalization related to dengue. We analyzed 7613 dengue confirmed via serology (ELISA), non-structural protein 1, or polymerase chain reaction amplification. We used a hierarchical framework to generate a multivariate logistic regression based on a variety of risk variables. This was followed by multiple statistical analyses to assess hierarchical model accuracy, variance, goodness of fit, and whether or not this model reliably represented the population...
September 28, 2017: Acta Tropica
Dvir Kleper, Noa Saka
The present study explored the construct validity of the Psychometric Entrance Test (PET) for higher education in Israel, as represented by the factorial structure of the scholastic aptitudes it measures, and focused on whether the test presents a single measure of overall ability or a measure of the fields of knowledge that are being tested. In Study 1, we used Exploratory Factor Analysis to generate hypotheses regarding the factorial structure of the test. In Study 2, Confirmatory Factor Analysis was carried out to compare competing models that were constructed based on theoretical considerations and the results of Study 1...
2017: Journal of Applied Measurement
Jillian Pine, Ann M Steffen
OBJECTIVES: The present study used Pearlin, Mullan, Semple & Skaff's (1990) caregiving stress process model as a framework to examine the comparative influence of two stressors: (a) intergenerational ambivalence as a unified construct and (b) dyadic strain, which is one isolated component of intergenerational ambivalence. METHODS: Participants were 120 women providing healthcare and medication assistance to an earlier generation family member with physical and/or cognitive impairments...
July 28, 2017: Clinical Gerontologist
Tzach Auman, Ariel D Chipman
Our understanding of the genetics of arthropod body plan development originally stems from work on Drosophila melanogaster from the late 1970s and onward. In Drosophila, there is a relatively detailed model for the network of gene interactions that proceeds in a sequential-hierarchical fashion to define the main features of the body plan. Over the years, we have a growing understanding of the networks involved in defining the body plan in an increasing number of arthropod species. It is now becoming possible to tease out the conserved aspects of these networks and to try to reconstruct their evolution...
September 1, 2017: Integrative and Comparative Biology
Andreas Antoniades, Loukianos Spyrou, David Martin-Lopez, Antonio Valentin, Gonzalo Alarcon, Saeid Sanei, Clive Cheong Took
Detection algorithms for electroencephalography (EEG) data, especially in the field of interictal epileptiform discharge (IED) detection, have traditionally employed handcrafted features which utilised specific characteristics of neural responses. Although these algorithms achieve high accuracy, mere detection of an IED holds little clinical significance. In this work, we consider deep learning for epileptic subjects to accommodate automatic feature generation from intracranial EEG data, while also providing clinical insight...
September 22, 2017: IEEE Transactions on Neural Systems and Rehabilitation Engineering
Duanchen Sun, Yinliang Liu, Xiang-Sun Zhang, Ling-Yun Wu
BACKGROUND: High-throughput experimental techniques have been dramatically improved and widely applied in the past decades. However, biological interpretation of the high-throughput experimental results, such as differential expression gene sets derived from microarray or RNA-seq experiments, is still a challenging task. Gene Ontology (GO) is commonly used in the functional enrichment studies. The GO terms identified via current functional enrichment analysis tools often contain direct parent or descendant terms in the GO hierarchical structure...
September 21, 2017: BMC Systems Biology
Kieu Trinh Do, Maik Pietzner, David Jnp Rasp, Nele Friedrich, Matthias Nauck, Thomas Kocher, Karsten Suhre, Dennis O Mook-Kanamori, Gabi Kastenmüller, Jan Krumsiek
The identification of phenotype-driven network modules in complex, multifluid metabolomics data poses a considerable challenge for statistical analysis and result interpretation. This is the case for phenotypes with only few associations ('sparse' effects), but, in particular, for phenotypes with a large number of metabolite associations ('dense' effects). Herein, we postulate that examining the data at different layers of resolution, from metabolites to pathways, will facilitate the interpretation of modules for both the sparse and the dense cases...
2017: NPJ Systems Biology and Applications
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