Learning Topic Models and Latent Bayesian Networks Under Expansion Constraints

Unsupervised estimation of latent variable models is a fundamental problem central to numerous applications of machine learning and statistics. This work presents a principled approach for estimating broad classes of such models, including probabilistic topic models and latent linear Bayesian networks, using only second-order observed moments. The sufficient conditions for identifiability of these models are primarily based on weak expansion constraints on the topic-word matrix, for topic models, and on the directed acyclic graph, for Bayesian networks. Because no assumptions are made on the distribution among the latent variables, the approach can handle arbitrary correlations among the topics or latent factors. In addition, a tractable learning method via $\ell_1$ optimization is proposed and studied in numerical experiments.Comment: 38 pages, 6 figures, 2 tables, applications in topic models and Bayesian networks are studied. Simulation section is adde

General methods for designing single-mode planar photonic crystal waveguides in hexagonal lattice structures

We systematically investigate and compare general methods of designing single mode photonic crystal waveguides in a two-dimensional hexagonal lattice of air holes in a dielectric material. We apply the rather general methods to dielectric-core hexagonal lattice photonic crystals since they have not been widely explored before. We show that it is possible to obtain single mode guiding in a limited portion of the photonic bandgap of hexagonal lattice structures. We also compare the potentials of different photonic crystal lattices for designing single-mode waveguides and conclude that triangular lattice structures are the best choice

Parentage verification and identity test of Ghezel sheep using microsatillate markers

The Ghezel sheep is a fat tail high weight Iranian breed which is raised in the North-west of Iran. To design an efficient improvement program and genetic evaluation system for this indigenous breed, accurate estimates of the population genetic parameters is per-required and all pedigrees and relationships should be correctly recorded. Otherwise, it can produce biased evaluations when pedigrees contain errors and procedures utilize information from relatives. The pedigree and genotype data of Ghezel sheep were examined for errors. Parentage control has been performed by amplification of microsatellites. Mean heterozygosities, mean polymorphism index content (PIC) and mean number of alleles per loci were 0.50, 0.43 and 3.71, respectively. Mendelian errors were found following the pedigree corrections. Alleles at the following seven microsatellite loci were identified: BM4307, CSSM004, BM415, RM029, INRA49, BM3205 and OarFCB5. The pedigree was considered incorrect in 6 (12%) out of all the evaluated progeny, as their genotype did not match their parents. The present findings attest to the usefulness of the investigated microsatellites for parentage control in Ghezel sheep.Key words: Ghezel sheep, microsatellites, genotyping errors, progeny test

Shelf-life of apples coated with whey protein concentrate-gellan gum edible coatings

ABSTRACT: Edible coatings made from whey protein concentrate (WPC) and gellan gum (G) were investigated for their capacity to preserve the quality of Malus domestica cv Golab apples. WPC and gellan gum coatings at different concentrations plasticized with glycerol (Gly) were tested. Postharvest storage quality condition testes included weight loss, color and texture changes, titratable acidity and soluble solids content and consumer acceptance. The results indicated that WPC-gellan-coated fruits were rated highest for taste, glossiness, colour and overall acceptability and were lowest for weight loss in this study. Results also showed no significant difference in soluble solids content and titratable acidity between control and the coated apples after 4 weeks at 4°C

Investigating the Influence of Penetration Length of Cut-off Wall on its Dynamic Interaction with Core and Foundation of Earth Dam

Seepage and flow of water in the soil is one of the most important issue and effective elements in designing embankment dams. One of the methods to control seepage in alluvial foundation of earth dams is to use a plastic concrete cutoff-wall. For better seepage control, the cutoff-wall extends inside the clayey core as the one of common method of connection of cut-off wall and the core. Due to the stiffness difference of the core material and cutoff-wall, and also due to geological situation, physical and mechanical properties of rock and foundation, interaction of core and foundation with cut-off wall in different static and dynamic load cases is very considerable. Failure of cut-off wall occurs in cut-off wall and core joint.  So the study of their interaction, especially during an earthquake is very important. Karkheh dam cut-off wall with an area of about 150000 m2 is chosen for this study. FLAC software has been used to study the effect of cutoff-wall penetration length variation, inside the clay core of Karkheh earth dam under dynamic loading.  In numerical analysis of Karkheh earth dam model, all construction stages and seepage through dam are modelled. The model is first calibrated according to the results obtained from the dam instrumentations. After calibrating, according to available seismic studies of region, a suitable acceleration was selected and applied to the model. In this research, in order to find the optimum length, the effect of 0, 5, 10, 15 and 20 meters penetration length of cut-off wall in aforementioned conditions has been investigated. The results of the numerical study showed that the horizontal displacement and the maximum shear strain in the cutoff-wall is occurred adjacent to the clay core and the interface of core and foundation is a critical point for the cut-off wall, and also the stress in cut off wall joint increases with the elongation of penetration depth of the wall

Apolipoprotein A1 as a novel anti-implantation biomarker in polycystic ovary syndrome: A case-control study

Background: Women with polycystic ovary syndrome have lower pregnancy rates, possibly due to the decreased uterine receptivity. Successful implantation depends on protein networks that are essential for cross-talk between the embryo and endometrium. Apolipoprotein A1 has been proposed as a putative anti-implantation factor. In this study, we evaluated apolipoprotein A1 expression in human endometrial tissues. Materials and Methods: Endometrial apolipoprotein A1 messenger RNA (mRNA) and protein expression were investigated using quantitative real-time polymerase chain reaction (PCR) and Western blot. The distribution of apolipoprotein A1 was also detected by immunostaining. Samples were obtained from 10 patients with polycystic ovary syndrome and 15 healthy fertile women in the proliferative (on day 2 or day 3 before ovulation, n = 7) and secretory (on days 3-5 after ovulation, n = 8) phases. Results: Endometrial apolipoprotein A1 expression was upregulated in patients with polycystic ovary syndrome compared to normal subjects. However, apolipoprotein A1 expression in the proliferative phase was significantly higher than in the luteal phase (P value < 0.05). Conclusion: It seems that differentially expressed apolipoprotein A1 negatively affects endometrial receptivity in patients with polycystic ovary syndrome. The results showed that apolipoprotein A1 level significantly changes in the human endometrium during the menstrual cycle with minimum expression in the secretory phase, coincident with the receptive phase (window of implantation). Further studies are required to clarify the clinical application of this protein. © 2015 Journal of Research in Medical Sciences

Comparing high-resolution gridded precipitation data with satellite rainfall estimates of TRMM_3B42 over Iran

To evaluate satellite rainfall estimates of Tropical Rain Measurement Mission (TRMM) level 3 output (3B42) (TRMM_3B42) over Iran (20&deg;–45&deg; N, 40&deg;–65&deg; E), we compared these data with high-resolution gridded precipitation datasets (0.25&deg;&times;0.25&deg; latitude/longitude) based on rain gauges (Iran Synoptic gauges Version 0902 (IS0902)). Spatial distribution of mean annual and mean seasonal rainfall in both IS0902 and TRMM_3B42 from 1998 to 2006 shows two main rainfall patterns along the Caspian Sea and over the Zagros Mountains. Scatter plots of annual average rainfall from IS0902 versus TRMM_3B42 for each 0.25&deg;&times;0.25&deg; grid cell over the entire country (25&deg;–40&deg; N, 45&deg;–60&deg; E), along the Caspian Sea (35&deg;–40&deg; N, 48&deg;–56&deg; E), and over the Zagros Mountains (28&deg;–37&deg; N, 46&deg;–55&deg; E) were derived. For the entire country, the Caspian Sea region, and the Zagros Mountains, TRMM_3B42 underestimates mean annual precipitation by 0.17, 0.39, and 0.15 mm day^&minus;1, respectively, and the mean annual rainfall spatial correlation coefficients are 0.77, 0.57, and 0.75, respectively. The mean annual precipitation temporal correlation coefficient for IS0902 and TRMM_3B42 is ~0.8 in the area along the Zagros Mountains, and ~0.6 in the Caspian Sea and desert regions

A panel of cultivate specific marker based on polymorphisms at microsatellite markers for Iranian cultivated Almonds (Prunus dulcis).

Molecular markers developed for Prunus also offer a powerful tool to study the evolution of the genome, and for understanding of genome structure and determinants of genetic diversity. Two hundred eighty almond genotypes/cultivars from different origins distributed throughout Iran besides some foreign cultivars and their hybrids with Iranian ones were collected. Microsatellite analysis was carried out using 9 pair flanking SSR sequences previously cloned and sequenced specifically in almond. The total number of detected alleles was 152 (9 to 20 alleles per locus with an average of 16.87). The mean PIC value of the polymorphic loci wasrelatively high (0.81) and the mean value for He was 0.83, so that we were able to distinguish 98% of the genotypes using 5 loci. Incluster analysis, the genotypes were divided into 2 major groups, foreign cultivars and Iranian almond genotypes. Principal coordinate analysis based on Shared Allele method indicated proper distribution of the studied markers through the genome. Some specific markers were recorded among the germ plasm which can be used efficiently in rapid and precise identification of the related genotypes and also in breeding programs through MAS. Genotypes were coded using our suggested coding method for genotype molecular identification

Digestion of rice straw and oil palm fronds by microflora from rumen and termite bacteria, in vitro.

The digestion and Volatile Fatty Acid (VFA) production from rice straw and oil palm fronds by cellulolytic bacteria isolated from the termite Coptotermes curvignathus were investigated. The bacteria were Acinetobacter strain Raminalimon, Enterobacter aerogenes strain Razmin C, Enterobacter cloacae strain Razmin B, Bacillus cereus strain Razmin A and Chryseobacterium kwangyangense strain Cb. Acinetobacter strain Raminalimon is an aerobic bacterium, while the other species are facultative anaerobes. There were significant differences (p<0.05) among the bacteria for Dry Matter (DM) lost and acetic acid production from rice straw and Acinetobacter strain Raminalimon showed the highest activity. The facultative bacteria C. kwangyangense strain Cb (cfu mL(-1) 231 x 10(-6), OD: 0.5), E. cloacae (cfu mL(-1) 68 x 10(-7), OD: 0.5) and E. aerogenes (cfu mL(-1) 33 x 10(-7), OD: 0.5) were used for digestion study with the rumen fluid microflora. The in vitro gas production technique was applied for the comparative study and the parameters measured were pH, gas (volume), dry matter lost, acetic acid, propionic acid and butyric acid concentrations. pH was not significantly (p<0.05) different among the five treatments. The bacterium C. kwangyangense strain Cb showed the highest activity (p<0.05) for DM lost, acetic acid, propionic acid and butyric acid production from rice straw when compared to the other bacterial activities. There was no significance (p<0.05) difference between the three bacteria for the dry matter lost of oil palm fronds but the production of Volatile Fatty Acids (VFA) was significantly (p<0.05) high in the treatment which was inoculated with C. kwangyangense strain Cb. The Gen Bank NCBI/EMBL accession numbers for the bacterial strains are EU332791, EU305608, EU305609, EU294508 and EU169201