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variational inference

Cristina Drugan, Tudor C Drugan, Paula Grigorescu-Sido, Ioana Naşcu
Chitotriosidase, an enzyme secreted by activated macrophages, is widely used as a biomarker for therapeutic monitoring and patient follow-up in Gaucher disease (GD), a lysosomal disorder caused by an inherited deficiency of glucocerebrosidase. We analyzed the long-term evolution of chitotriosidase aiming to establish an accurate model that describes the influence of enzyme replacement therapy (ERT) and the impact of several covariates. A total of 55 patients with non-neuronopathic (type 1) GD were followed for almost 17 years (during a maximum of 7...
March 20, 2017: Scandinavian Journal of Clinical and Laboratory Investigation
Isabelle Veissier, Marie-Madeleine Mialon, Karen Helle Sloth
Biological rhythms are an essential regulator of life. There is evidence that circadian rhythm of activity is disrupted under chronic stress in animals and humans, and it may also be less marked during diseases. Here we investigated whether a detectable circadian rhythm of activity exists in dairy cows in commercial settings using a real-time positioning system. We used CowView (GEA Farm Technologies) to regularly record the individual positions of 350 cows in a Danish dairy farm over 5 mo and to infer the cows' activity (resting, feeding, in alley)...
March 16, 2017: Journal of Dairy Science
Graham D Farquhar, Florian A Busch
Mitochondrial respiration often appears to be inhibited in the light when compared with measurements in the dark. This inhibition is inferred from the response of the net CO2 assimilation rate (A) to absorbed irradiance (I), changing slope around the light compensation point (Ic ). We suggest a model that provides a plausible mechanistic explanation of this 'Kok effect'. The model uses the mathematical description of photosynthesis developed by Farquhar, von Caemmerer and Berry; it involves no inhibition of respiration rate in the light...
April 2017: New Phytologist
Otso Ovaskainen, Gleb Tikhonov, Anna Norberg, F Guillaume Blanchet, Leo Duan, David Dunson, Tomas Roslin, Nerea Abrego
Community ecology aims to understand what factors determine the assembly and dynamics of species assemblages at different spatiotemporal scales. To facilitate the integration between conceptual and statistical approaches in community ecology, we propose Hierarchical Modelling of Species Communities (HMSC) as a general, flexible framework for modern analysis of community data. While non-manipulative data allow for only correlative and not causal inference, this framework facilitates the formulation of data-driven hypotheses regarding the processes that structure communities...
March 20, 2017: Ecology Letters
Yajuan Cao, Hua Yin, Hui Peng, Shaoyu Tang, Guining Lu, Zhi Dang
Aerobic biodegradation of 2,2',4,4'-tetrabrominated diphenyl ether (BDE-47) by Phanerochaete chrysosporium in the presence of Cd(2+) was investigated in this study. The results showed that P. chrysosporium could effectively degrade BDE-47, and its extracellular enzyme played an important role in the process of decomposition. BDE-47 biodegradation by fungi was more tolerant than extracellular enzyme in the presence of Cd(2+). Also, both of the activity of two typical enzymes, MnP and LiP, descended with ascended Cd(2+) concentration...
March 18, 2017: Environmental Science and Pollution Research International
Janna M Andronowski, Amy Z Mundorff, Isaac V Pratt, Jon M Davoren, David M L Cooper
Molecular human identification has conventionally focused on DNA sampling from dense, weight-bearing cortical bone tissue, typically from femora or tibiae. A comparison of skeletal elements from three contemporary individuals demonstrated that elements with high quantities of cancellous bone yielded nuclear DNA at the highest rates, suggesting that preferentially sampling cortical bone may be suboptimal (Mundorff & Davoren, 2014). Despite these findings, the reason for the differential DNA yields between cortical and cancellous bone tissues remains unknown...
March 6, 2017: Forensic Science International. Genetics
I H Saleh, A A Abdel-Halim
This study investigated the radioactivity behavior of (7)Be in surface soil, airborne and deposited dust along Alexandria region in Egypt. The results obtained were used to predict scavenging processes of (7)Be from surface soil to infer soil erosion and land vulnerable to accelerated sea-level rise. The areal activity concentrations of (7)Be in surface soil were investigated in 30 undisturbed sites and (7)Be inventories were determined via deposited dust in 10 locations. Results of the former were found to be ranged from 78 Bq/m(2) to 104 Bq/m(2)...
March 14, 2017: Journal of Environmental Radioactivity
Guor-Cheng Fang, Yu-Cheng Chen, Chaur-Tsuen Lo, Meng-Hsien Cho, Yuan-Jie Zhuang, Kai-Hsiang Tsai, Chao-Yang Huang, You-Fu Xiao
The concentrations of particulates and metallic elements that were bound to total suspended particulates in ambient air at Long Cyuan Elementary School (LCYES), Lung Ching Elementary School (LCHES) and Long Shan Primary School (LSPS) sampling sites in the Longjing area were measured. Significant difference tests were conducted at LSPS, LCYES and LCHES sites. Finally, carcinogenic and non-carcinogenic risk values for LSPS, LCYES and LCHES sites in the Longjing district were evaluated. The results show that the most average particulate and metallic element concentrations were highest in October, November, January, February, March, April, August, and September The average particulate and metallic element concentrations at LCHES were higher than at the other sampling sites...
March 16, 2017: Environmental Geochemistry and Health
Jon Slate
The genetic architecture of a trait usually refers to the number and magnitude of loci that explain phenotypic variation. A description of genetic architecture can help us to understand how genetic variation is maintained, how traits have evolved and how phenotypes might respond to selection. However, linkage mapping and association studies can suffer from problems of bias, especially when conducted in natural populations where the opportunity to perform studies with very large sample sizes can be limited. In this issue of Molecular Ecology, Li and colleagues perform an association study of brain traits in ninespine sticklebacks Pungitius pungitius...
March 2017: Molecular Ecology
Samuel P C Brand, Matt J Keeling
It is a long recognized fact that climatic variations, especially temperature, affect the life history of biting insects. This is particularly important when considering vector-borne diseases, especially in temperate regions where climatic fluctuations are large. In general, it has been found that most biological processes occur at a faster rate at higher temperatures, although not all processes change in the same manner. This differential response to temperature, often considered as a trade-off between onward transmission and vector life expectancy, leads to the total transmission potential of an infected vector being maximized at intermediate temperatures...
March 2017: Journal of the Royal Society, Interface
Zhenhua Yu, Ao Li, Minghui Wang
BACKGROUND: Copy number alterations (CNA) and loss of heterozygosity (LOH) represent a large proportion of genetic structural variations of cancer genomes. These aberrations are continuously accumulated during the procedure of clonal evolution and patterned by phylogenetic branching. This invariably results in the emergence of multiple cell populations with distinct complement of mutational landscapes in tumor sample. With the advent of next-generation sequencing technology, inference of subclonal populations has become one of the focused interests in cancer-associated studies, and is usually based on the assessment of combinations of somatic single-nucleotide variations (SNV), CNA and LOH...
March 15, 2017: BMC Medical Genomics
C Ahlstrom, P Muellner, S E F Spencer, S Hong, A Saupe, A Rovira, C Hedberg, A Perez, U Muellner, J Alvarez
Salmonella enterica is a global health concern because of its widespread association with foodborne illness. Bayesian models have been developed to attribute the burden of human salmonellosis to specific sources with the ultimate objective of prioritizing intervention strategies. Important considerations of source attribution models include the evaluation of the quality of input data, assessment of whether attribution results logically reflect the data trends and identification of patterns within the data that might explain the detailed contribution of different sources to the disease burden...
March 13, 2017: Zoonoses and Public Health
Thomas Marcussen, Andrea S Meseguer
The cosmopolitan genus Geranium L. (Geraniaceae) consists of c. 350 species distributed in temperate habitats worldwide, with most of its diversity concentrated in the Mediterranean region. Unlike other genera in Geraniaceae, the species of Geranium present contrasting seed discharge syndromes, i.e. the 'Erodium-type' (ET), the 'carpel-projection type' (CP), the 'seed-ejection type' (SE), and the 'inoperative type' (IT), which have been used to delimit major groups within the genus. However, phylogenetic relationships within Geranium are unknown and so is the evolution of the different seed discharge mechanisms...
March 10, 2017: Molecular Phylogenetics and Evolution
Motoharu Sonogashira, Takuya Funatomi, Masaaki Iiyama, Michihiko Minoh
Image restoration is a fundamental problem in the field of image processing. The key objective of image restoration is to recover clean images from images degraded by noise and blur. Recently, a family of new statistical techniques called variational Bayes (VB) has been introduced to image restoration, which enables us to automatically tune parameters that control restoration. While information from one image is often insufficient for high-quality restoration, however, current state-of-theart methods of image restoration via VB approaches use only a single degraded image to recover a clean image...
March 6, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
Ke He, Hong-Yi Liu, Yun-Fa Ge, Shao-Ying Wu, Qiu-Hong Wan
Major histocompatibility complex (MHC) is a good marker system for geographical genetics since they are functional genes in the immune system that are likely to affect the fitness of the individual, and the survival and evolutionary potential of a population in a changing environment. Golden pheasant (Chrysolophus pictus) is a wild Phasianidae distributed in central and north China. In this study, we used a locus-specific genotyping technique for MHC IIB genes of golden pheasant. Combining with microsatellites (simple sequence repeat, SSR) and mitochondrial DNA (mtDNA) D-loop region, we investigated the demographic history and illuminate genetic structure of this bird in detail...
March 7, 2017: Molecular Phylogenetics and Evolution
Hung Manh Nguyen, Hien Van Hoang, Loan Thi Ho
The present study was performed to reveal the morphological characteristics and molecular phylogenetic position of Platynosomum fastosum Kossack, 1910. A total 167 specimens of P. fastosum were collected in 8 (4.9%) out of 163 sets of gall-bladders and bile ducts of cats. The number of worms was 1-105 per infected cat. This species was characterized by having a long and slender body, slightly larger ventral sucker than the oral sucker, indistinct prepharynx, small pharynx, short esophagus, bifurcation midway between 2 suckers, and ceca extending to the posterior end of the body...
February 2017: Korean Journal of Parasitology
Cong-Hui Yang, Peng-Cheng Yang, Su-Fang Zhang, Zhi-Yong Shi, Le Kang, Ai-Bing Zhang
Cuticular proteins (CPs) are vital components of the insects' cuticle that support movement and protect insect from adverse environmental conditions. The CPs exist in a large number and diversiform structures, thus, the accurate annotation is the first step to interpreting their roles in insect growth. The rapid development of sequencing technology has simplified the access to the information on protein sequences, especially for non-model species. Dendrolimus punctatus is a Lepidopteran defoliator, and its periodic outbreaks cause severe damage to the coniferous forests...
March 8, 2017: Insect Biochemistry and Molecular Biology
Anmin Yin, Xiaochen Wang, Christ Glorieux, Quan Yang, Feng Dong, Fei He, Yanlong Wang, Jan Sermeus, Tom Van der Donck, Xuedao Shu
A photoacoustic, laser ultrasonics based approach in an Impulsive Stimulated Scattering (ISS) implementation was used to investigate the texture in polycrystalline metal plates. The angular dependence of the 'polycrystalline' surface acoustic wave (SAW) velocity measured along regions containing many grains was experimentally determined and compared with simulated results that were based on the angular dependence of the 'single grain' SAW velocity within single grains and the grain orientation distribution...
February 24, 2017: Ultrasonics
Kimberly F McManus, Angela M Taravella, Brenna M Henn, Carlos D Bustamante, Martin Sikora, Omar E Cornejo
The human DARC (Duffy antigen receptor for chemokines) gene encodes a membrane-bound chemokine receptor crucial for the infection of red blood cells by Plasmodium vivax, a major causative agent of malaria. Of the three major allelic classes segregating in human populations, the FY*O allele has been shown to protect against P. vivax infection and is at near fixation in sub-Saharan Africa, while FY*B and FY*A are common in Europe and Asia, respectively. Due to the combination of strong geographic differentiation and association with malaria resistance, DARC is considered a canonical example of positive selection in humans...
March 10, 2017: PLoS Genetics
Osamu Miura, Gen Kanaya, Shizuko Nakai, Hajime Itoh, Satoshi Chiba, Wataru Makino, Tomohiro Nishimura, Shigeaki Kojima, Jotaro Urabe
Natural disturbances often destroy local populations and can considerably affect the genetic properties of these populations. The 2011 Tohoku Earthquake Tsunami greatly damaged local populations of various coastal organisms, including the mud snail Batillaria attramentaria, which was an abundant macroinvertebrate on the tidal flats in the Tohoku region. To evaluate the impact of the tsunami on the ecology and population genetic properties of these snails, we monitored the density, shell size, and microsatellite DNA variation of B...
March 10, 2017: Scientific Reports
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