Comprehensive MicroRNA expression profiling identifies novel markers in follicular variant of papillary thyroid carcinoma

BACKGROUND Follicular variant of papillary thyroid carcinoma (FVPTC) shares features of papillary (PTC) and follicular (FTC) thyroid carcinomas on a clinical, morphological, and genetic level. MicroRNA (miRNA) deregulation was extensively studied in PTCs and FTCs. However, very limited information is available for FVPTC. The aim of this study was to assess miRNA expression in FVPTC with the most comprehensive miRNA array panel and to correlate it with the clinicopathological data. METHODS Forty-four papillary thyroid carcinomas (17 FVPTC, 27 classic PTC) and eight normal thyroid tissue samples were analyzed for expression of 748 miRNAs using Human Microarray Assays on the ABI 7900 platform (Life Technologies, Carlsbad, CA). In addition, an independent set of 61 tumor and normal samples was studied for expression of novel miRNA markers detected in this study. RESULTS Overall, the miRNA expression profile demonstrated similar trends between FVPTC and classic PTC. Fourteen miRNAs were deregulated in FVPTC with a fold change of more than five (up/down), including miRNAs known to be upregulated in PTC (miR-146b-3p, -146-5p, -221, -222 and miR-222-5p) and novel miRNAs (miR-375, -551b, 181-2-3p, 99b-3p). However, the levels of miRNA expression were different between these tumor types and some miRNAs were uniquely dysregulated in FVPTC allowing separation of these tumors on the unsupervised hierarchical clustering analysis. Upregulation of novel miR-375 was confirmed in a large independent set of follicular cell derived neoplasms and benign nodules and demonstrated specific upregulation for PTC. Two miRNAs (miR-181a-2-3p, miR-99b-3p) were associated with an adverse outcome in FVPTC patients by a Kaplan-Meier (p < 0.05) and multivariate Cox regression analysis (p < 0.05). CONCLUSIONS Despite high similarity in miRNA expression between FVPTC and classic PTC, several miRNAs were uniquely expressed in each tumor type, supporting their histopathologic differences. Highly upregulated miRNA identified in this study (miR-375) can serve as a novel marker of papillary thyroid carcinoma, and miR-181a-2-3p and miR-99b-3p can predict relapse-free survival in patients with FVPTC thus potentially providing important diagnostic and predictive value.

DYSREGULATION OF MEOX2 FOLLOWING WT1 MUTATION IN KIDNEY DEVELOPMENT AND WILMS TUMORIGENESIS

Wilms tumor (WT) is a childhood tumor of the kidney and a productive model for understanding the role of genetic alteration and interactions in tumorigenesis. The Wilms tumor gene 1 (WT1) is a transcriptional factor and one of the few genes known to have genetic alterations in WT and has been shown be inactivated in 20% of WTs. However, the mechanisms of how WT1 mutations lead to Wilms tumorigenesis and its influence on downstream genes are unknown. Since it has been established that WT1 is a transcriptional regulator, it has been hypothesized that the loss of WT1 leads to the dysregulation of downstream genes, in turn result in the formation of WTs. To identify the dysregulated downstream genes following WT1 mutations, an Affymetrix GeneChip Human Genome Array was previously conducted to assess the differentially expressed genes in the WT1-wildtype human and WT1-mutant human WTs. Approximately 700 genes were identified as being significantly dysregulated. These genes were further prioritized based on their statistical significance, fold change, chromosomal region, spatial pattern of gene expression and known or putative cellular functions. Mesenchyme homeobox 2 (MEOX2) was one of the most significantly upregulated genes in WT1-mutant WT. MEOX2 is known to play a role in cell proliferation, apoptosis, and differentiation. In addition to its biological roles, it is expressed during early kidney development in the condensed mesenchyme similar to WT1. Furthermore, the use of the Match® web-based tool from the BIOBASE Biological Data base identified a significant predicted WT1 binding site within the first intron of MEOX2. The similarity in spatial gene expression in the developing kidney and the significant predicted WT1 binding site found in the first intron of MEOX2 lead to the development of my hypothesis that MEOX2 is upregulated via a WT1-dependent manner. Here as a part of my master’s work, I have validated the Affymetrix GeneChip Human Genome Array data using an independent set of Wilms tumors. MEOX2 remained upregulated in the mutant WT1 Wilms tumor by 41-fold. Wt1 and Meox2 gene expression were assessed in murine newborn kidney; both Wt1 and Meox2 were expressed in the condensed, undifferentiated metanephric mesenchyme. I have shown that the in vivo ablation of Wt1 during embryonic development at embryonic day (E) 13.5 resulted in the slight increase of Meox2 gene expression by two fold. In order to functionally demonstrate the effect of the loss of Wt1 on Meox2 gene expression in undifferentiated metanephric mesenchyme, I have generated a kidney mesenchymal cell line to genetically ablate Wt1 in vitro by adenoviral infection. The ablation of Wt1 in the kidney mesenchymal cell line resulted in the upregulation of Meox2 by 61-fold. Moreover, the upregulation of Meox2 resulted in the significant induction of p21 and Itgb5. In addition to the dysregulation of these genes the ablation of Wt1 in the kidney mesenchymal cells resulted in decrease in cell growth and loss of cellular adherence. However, it is uncertain whether the upregulation of Meox2 caused this particular cellular phenotype. Overall, I have demonstrated that the upregulation of Meox2 is Wt1-dependent during early kidney development.

Methylation of PITX2, HOXD3, RASSF1 and TDRD1 predicts biochemical recurrence in high-risk prostate cancer

PURPOSE To explore differential methylation of HAAO, HOXD3, LGALS3, PITX2, RASSF1 and TDRD1 as a molecular tool to predict biochemical recurrence (BCR) in patients with high-risk prostate cancer (PCa). METHODS A multiplexed nested methylation-specific PCR was applied to quantify promoter methylation of the selected markers in five cell lines, 42 benign prostatic hyperplasia (BPH) and 71 high-risk PCa tumor samples. Uni- and multivariate Cox regression models were used to assess the importance of the methylation level in predicting BCR. RESULTS A PCa-specific methylation marker HAAO in combination with HOXD3 and a hypomethylation marker TDRD1 distinguished PCa samples (>90 % of tumor cells each) from BPH with a sensitivity of 0.99 and a specificity of 0.95. High methylation of PITX2, HOXD3 and RASSF1, as well as low methylation of TDRD1, appeared to be significantly associated with a higher risk for BCR (HR 3.96, 3.44, 2.80 and 2.85, correspondingly) after correcting for established risk factors. When DNA methylation was treated as a continuous variable, a two-gene model PITX2 × 0.020677 + HOXD3 × 0.0043132 proved to be the best predictor of BCR (HR 4.85) compared with the individual markers. This finding was confirmed in an independent set of 52 high-risk PCa tumor samples (HR 11.89). CONCLUSIONS Differential promoter methylation of HOXD3, PITX2, RASSF1 and TDRD1 emerges as an independent predictor of BCR in high-risk PCa patients. A two-gene continuous DNA methylation model "PITX2 × 0.020677 + HOXD3 × 0.0043132" is a better predictor of BCR compared with individual markers.

Testosterone-to-Estradiol Ratio is Associated with Female Facial Attractiveness

The relationship between facial shape and attractiveness has been extensively studied, yet few studies have investigated the underlying biological factors of an attractive face. Many researchers have proposed a link between female attractiveness and sex hormones, but there is little empirical evidence in support this assumption. In the present study we investigated the relationship between circulating sex hormones and attractiveness. We created prototypes by separately averaging photographs of 15 women with high and low levels of testosterone, estradiol, and testosterone-to-estradiol ratio levels, respectively. An independent set of facial images was then shape transformed toward these prototypes. We paired the resulting images in such a way that one face depicted a female with high hormone level and the other a low hormone level. Fifty participants were asked to choose the more attractive face of each pair. We found that low testosterone-to-estradiol ratio and low testosterone were positively associated with female facial attractiveness. There was no preference for faces with high estradiol levels. In an additional experiment with 36 participants we confirmed that a low testosterone-to-estradiol ratio plays a larger role than low testosterone alone. These results provide empirical evidence that an attractive female face is shaped by interacting effects of testosterone and estradiol.

Differential Micro RNA Expression in PBMC from Multiple Sclerosis Patients

Differences in gene expression patterns have been documented not only in Multiple Sclerosis patients versus healthy controls but also in the relapse of the disease. Recently a new gene expression modulator has been identified: the microRNA or miRNA. The aim of this work is to analyze the possible role of miRNAs in multiple sclerosis, focusing on the relapse stage. We have analyzed the expression patterns of 364 miRNAs in PBMC obtained from multiple sclerosis patients in relapse status, in remission status and healthy controls. The expression patterns of the miRNAs with significantly different expression were validated in an independent set of samples. In order to determine the effect of the miRNAs, the expression of some predicted target genes of these were studied by qPCR. Gene interaction networks were constructed in order to obtain a co-expression and multivariate view of the experimental data. The data analysis and later validation reveal that two miRNAs (hsa-miR-18b and hsa-miR-599) may be relevant at the time of relapse and that another miRNA (hsa-miR-96) may be involved in remission. The genes targeted by hsa-miR-96 are involved in immunological pathways as Interleukin signaling and in other pathways as wnt signaling. This work highlights the importance of miRNA expression in the molecular mechanisms implicated in the disease. Moreover, the proposed involvement of these small molecules in multiple sclerosis opens up a new therapeutic approach to explore and highlight some candidate biomarker targets in MS

Estudio de la permeabilidad y de la resistencia a tracción en hormigones precomprimidos

Entre los requisitos que deben cumplir las estructuras se debe garantizar que estas posean la durabilidad necesaria para permanecer en servicio a lo largo de todo el periodo de vida útil para el que han sido proyectadas. Para conseguir este objetivo las normativas han ido incorporando prescripciones para el diseño del hormigón, en base a distintas clases de exposición dependiendo del origen y magnitud de la agresividad exterior. En ambientes con una elevada agresividad, una de las comprobaciones que debe cumplir el hormigón es que tenga una permeabilidad inferior a los valores máximos fijados según la clase de exposición, y que en caso de considerar como ensayo de referencia el de penetración de agua, analiza el frente de penetración limitando las profundidades de penetración media y máxima. Adicionalmente a las condiciones de diseño según el tipo de ambiente, principalmente basadas en la dosificación del hormigón en términos de la relación agua/cemento y el mínimo contenido de cemento y el recubrimiento de las armaduras, durante la vida en servicio las estructuras pueden están solicitadas por distintas acciones imprevistas que pueden provocar cambios en la microestructura interna del hormigón que modifican su permeabilidad y resistencia, y por tanto pueden alterar la durabilidad inicialmente prevista. Es conocido el efecto de cansancio del hormigón cuando está solicitado por cargas de compresión mantenidas en el tiempo, provocando bajas en su resistencia debido al incremento de la microfisuración. Dada la relación entre la permeabilidad y la microfisuración del hormigón, es previsible el aumento de la permeabilidad en hormigones que han sido precomprimidos durante un periodo largo de tiempo. Los estudios de la permeabilidad en hormigones previamente comprimidos se han realizado analizando periodos de tiempo de compresión cortos que no permiten evaluar el efecto del cansancio sobre la permeabilidad. La presente tesis doctoral investiga la permeabilidad y resistencia a tracción en hormigones que previamente han sido comprimidos en carga mantenida durante distintos plazos de tiempo, al objeto de conocer su evolución en base al tiempo de precompresión. La investigación se apoya en el estudio de otras dos variables como son el tipo de hormigón de acuerdo a su dosificación según el tipo de ambiente considerando una agresividad baja, media o alta, y el grado de compresión aplicado respecto de su carga última de rotura. En los resultados del plan experimental desarrollado se ha obtenido que la permeabilidad presenta un incremento significante con el tiempo de precompresión, que dependiendo del valor inicial de la permeabilidad que tiene el hormigón puede provocar que hormigones que previamente satisfacen las limitaciones de permeabilidad pasen a incumplirlas, pudiendo afectar a su durabilidad. También se confirma la influencia del tiempo de precompresión sobre la resistencia a tracción obteniendo bajas de resistencia importantes en los casos pésimos ensayados, que deben ser tenidas en consideración en tanto afectan a la capacidad resistente del hormigón como a otros aspectos fundamentales como el anclaje de las armaduras en el hormigón armado y pretensado. One of the requirements that structures must meet is to guarantee their durability to remain in service throughout all the working life period for which they have been designed. To achieve this goal, building standards and codes have included specifications for the design of concrete structures, based on different exposure classes depending on the environmental conditions and their origin and magnitude. In severe aggressive environments, one of the specifications the concrete must meet is to have a permeability lower than the maximum values set for a certain exposure class. If this parameter is referenced to water penetration on specimens, then the average and maximum depths of front penetration are analyzed. In addition to the design conditions depending on the exposure class, which regulate the dosage of concrete in terms of the water/cement ratio, minimum samples that have been pre-compressed for a long period of time. Previous studies on permeability have been carried on pre-compressed concrete elements analyzing short periods of time. However, they have not studied the effects of compression forces on concrete in the long term. This Thesis investigates permeability and tensile strength of concrete samples that have been previously compressed under loads applied for different periods of time. The goal is to understand its evolution based on the time exposed to compression. The research variables also include the type of concrete according to the dosage used - depending on the environmental exposure it will have low, medium or high aggressiveness-, and the amount of compression applied in relation to its failure load. Results of the experimental tests showed that permeability increases significantly over the time of pre-compression. Depending on the initial value of permeability, this change could make the concrete not meet the original permeability restrictions and therefore affect its durability. These investigations also confirmed the influence of time of pre-compression in tensile strength, where some cases showed a significant decrease of resistance. These issues must be taken into consideration as they affect the bearing capacity of the material and other key features such as the anchoring of steel bars in reinforced and pre-stressed concrete. amount of cement content and the minimum concrete cover of the steel bars, during their working life structures may be subject to various unforeseen actions. As a result, the concrete’s internal microstructure might be affected, changing its permeability and resistance, and possibly altering the original specified durability. It is a known fact that when concrete is loaded in compression maintained over a long time, its resistance to compression forces is diminished due to the increase in micro-cracking. Considering the relationship between permeability and microcracking of concrete, an increase in permeability may be expected in concrete

Neogene radiolarian datum levels in the equatorial Indian and Pacific Oceans

Fifty radiolarian events of early Pleistocene and Neogene age were identified in an E-W transect of equatorial DSDP sites, extending from the Gulf of Panama to the western Pacific and eastern Indian Oceans. Our objective was to document the degree of synchroneity or time-transgressiveness of stratigraphically-useful datum levels from this geologic time interval. We restricted our study to low latitudes within which morphological variations of individual taxa are minimal, the total assemblage diversity remains high, and stratigraphic continuity is well-documented by an independent set of criteria. Each of the five sites chosen (503, 573, 289/586, 214) was calibrated to an "absolute" time scale, using a multiple of planktonic foraminiferal, nannofossil, and diatom datum levels which have been independently correlated to the paleomagnetic polarity time scale in piston core material. With these correlations we have assigned "absolute" ages to each radiolarian event, with a precision of 0.1-0.2 m.y. and an accuracy of 0.2-0.4 m.y. On this basis we have classified each of the events as either: (a) synchronous (range of ages <0.4 m.y.); (b) time-transgressive (i.e., range of ages >1.0 m.y.); and (c) not resolvable (range of ages 0.4-1.0 m.y.). Our results show that, among the synchronous datum levels, a large majority (15 out of 19) are last occurrences. Among those events which are clearly time-transgressive, most are first appearances (10 out of 13). In many instances taxa appear to evolve first in the Indian Ocean, and subsequently in the western and eastern Pacific Ocean. This pattern is particularly unexpected in view of the strong east-to-west zonal flow in equatorial latitudes. Three of the time-transgressive events have been used to define zonal boundaries: the first appearances of Spongaster pentas, Diartus hughesi, and D. petterssoni. Our results suggest that biostratigraphic non-synchroneity may be substantial (i.e., greater than 1 m.y.) within a given latitudinal zone; one would expect this effect to be even more pronounced across oceanographic and climatic gradients. We anticipate that the extent of diachroneity may be comparable for diatom, foraminiferal, and nannofossil datum levels as well. If this proves true, global "time scales" may need to be re-formulated on the basis of a smaller number of demonstrably synchronous events.

On the Maximum Number of Linearly Independent Cycles and Paths in a Network

Central to network tomography is the problem of identifiability, the ability to identify internal network characteristics uniquely from end-to-end measurements. This problem is often underconstrained even when internal network characteristics such as link delays are modeled as additive constants. While it is known that the network topology can play a role in determining the extent of identifiability, there is a lack in the fundamental understanding of being able to quantify it for a given network. In this paper, we consider the problem of identifying additive link metrics in an arbitrary undirected network using measurement nodes and establishing paths/cycles between them. For a given placement of measurement nodes, we define and derive the ``link rank'' of the network-the maximum number of linearly independent cycles/paths that may be established between the measurement nodes. We achieve this in linear time. The link rank helps quantify the exact extent of identifiability in a network. We also develop a quadratic time algorithm to compute a set of cycles/paths that achieves the maximum rank.

Fast distributed approximation algorithms for vertex cover and set cover in anonymous networks

We present a distributed algorithm that finds a maximal edge packing in O(Δ + log* W) synchronous communication rounds in a weighted graph, independent of the number of nodes in the network; here Δ is the maximum degree of the graph and W is the maximum weight. As a direct application, we have a distributed 2-approximation algorithm for minimum-weight vertex cover, with the same running time. We also show how to find an f-approximation of minimum-weight set cover in O(f2k2 + fk log* W) rounds; here k is the maximum size of a subset in the set cover instance, f is the maximum frequency of an element, and W is the maximum weight of a subset. The algorithms are deterministic, and they can be applied in anonymous networks.

Gate commutated thyristor with voltage independent maximum controllable current

In this letter, we use a novel 3-D model, earlier calibrated with experimental results on standard gate commutated thyristors (GCTs), with the aim to explain the physics behind the high-power technology (HPT) GCT, to investigate what impact this design would have on 24 mm diameter GCTs, and to clarify the mechanisms that limit safe switching at different dc-link voltages. The 3-D simulation results show that the HPT design can increase the maximum controllable current in 24 mm diameter devices beyond the realm of GCT switching, known as the hard-drive limit. It is proposed that the maximum controllable current becomes independent of the dc-link voltage for the complete range of operating voltage. © 1980-2012 IEEE.

Predicting Growth of Panicum maximum: An Adaptation of the CROPGRO-Perennial Forage Model

Warm-season grasses are economically important for cattle production in tropical regions and tools to aid in management and research on these forages would be highly beneficial both in research and the industry. This research was conducted to adapt the CROPGRO-Perennial Forage model to simulate growth of the tropical species guineagrass (Panicum maximum Jacq. cv. 'Tanzania') and to describe model adaptation for this species. To develop the CROPGRO parameters for this species, we began with values and relationships reported in the literature. Some parameters and relationships were calibrated by comparison with observed growth, development, dry matter accumulation, and partitioning during a 17-mo experiment with Tanzania guineagrass in Piracicaba, SP, Brazil. Compared with starting parameters for palisadegrass [Brachiaria brizantha (A. Rich.) Stapf. cv. 'Xaraes'], dormancy effects of the perennial forage model had to be minimized, partitioning to storage tissue or root decreased, and partitioning to leaf and stem increased to provide for more leaf and stem growth and less root. Parameters affecting specific leaf area and senescence of plant tissues were improved. After these changes were made to the model, biomass accumulation was better simulated, mean predicted herbage yield was 6576 kg ha(-1), averaged across 11 regrowth cycles of 35 (summer) or 63 d (winter), with a RMSE of 494 kg ha(-1) (Willmott's index of agreement d = 0.985, simulated/observed ratio = 1.014). The model also gave good predictions against an independent data set, with similar RMSE, ratio, and d. The results of the adaptation suggest that the CROPGRO model is an efficient tool to integrate physiological aspects of guineagrass and can be used to simulate growth.

A Variable Neighborhood Search Approach for Solving the Maximum Set Splitting Problem

This paper presents a Variable neighbourhood search (VNS) approach for solving the Maximum Set Splitting Problem (MSSP). The algorithm forms a system of neighborhoods based on changing the component for an increasing number of elements. An efficient local search procedure swaps the components of pairs of elements and yields a relatively short running time. Numerical experiments are performed on the instances known in the literature: minimum hitting set and Steiner triple systems. Computational results show that the proposed VNS achieves all optimal or best known solutions in short times. The experiments indicate that the VNS compares favorably with other methods previously used for solving the MSSP. ACM Computing Classification System (1998): I.2.8.