Noncoding RNA gene detection using comparative sequence analysis

BACKGROUND: Noncoding RNA genes produce transcripts that exert their function without ever producing proteins. Noncoding RNA gene sequences do not have strong statistical signals, unlike protein coding genes. A reliable general purpose computational genefinder for noncoding RNA genes has been elusive. RESULTS: We describe a comparative sequence analysis algorithm for detecting novel structural RNA genes. The key idea is to test the pattern of substitutions observed in a pairwise alignment of two homologous sequences. A conserved coding region tends to show a pattern of synonymous substitutions, whereas a conserved structural RNA tends to show a pattern of compensatory mutations consistent with some base-paired secondary structure. We formalize this intuition using three probabilistic "pair-grammars": a pair stochastic context free grammar modeling alignments constrained by structural RNA evolution, a pair hidden Markov model modeling alignments constrained by coding sequence evolution, and a pair hidden Markov model modeling a null hypothesis of position-independent evolution. Given an input pairwise sequence alignment (e.g. from a BLASTN comparison of two related genomes) we classify the alignment into the coding, RNA, or null class according to the posterior probability of each class. CONCLUSIONS: We have implemented this approach as a program, QRNA, which we consider to be a prototype structural noncoding RNA genefinder. Tests suggest that this approach detects noncoding RNA genes with a fair degree of reliability

Connectivity of Markoff mod-p graphs and maximal divisors

Markoff mod-$p$ graphs are conjectured to be connected for all primes $p$. In this paper, we use results of Chen and Bourgain, Gamburd, and Sarnak to confirm the conjecture for all $p > 3.448\cdot10^{392}$. We also provide a method that quickly verifies connectivity for many primes below this bound. In our study of Markoff mod-$p$ graphs we introduce the notion of \emph{maximal divisors} of a number. We prove sharp asymptotic and explicit upper bounds on the number of maximal divisors, which ultimately improves the Markoff graph $p$-bound by roughly 140 orders of magnitude as compared with an approach using all divisors

EVALUACIÓN DE UN SISTEMA DE RIEGO POR GOTEO SOTERRADO EN PLANTACIONES DE MANGO / ASSESSMENT OF AN UNDERGROUND IRRIGATION DRIP SYSTEM IN MANGO PLANTATIONS

El trabajo se llevó a cabo en la unidad empresarial de base (UEB) Frutales Ciego, en la finca Palmarito-I, en plantaciones de mango, con el objetivo de evaluar el sistema de riego por goteo subterráneo, para mejorar la calidad del riego y elevar los rendimientos agrícolas en los sistemas. Se determinó el coeficiente de uniformidad del sistema, obteniendo como resultado un 88 %, lo cual refiere buenas condiciones del mismo. Se evaluó el sistema radicular de las plantaciones mediante la elaboración de una calicata, en la cual se determinó que las raíces activas se concentraban a una profundidad de 10 a 25 cm, con una mayor concentración en las zonas cercanas a los emisores. Mediante la propia calicata, se estudió el comportamiento de la infiltración para determinados valores de tiempo, Lo cual garantiza un mayor aprovechamiento del agua y los fertilizantes empleados en el riego, donde se determinó que, para un riego óptimo, en un tiempo de 4 h, los emisores creaban un bulbo húmedo con una profundidad de 30 cm, los cuales se solapaban entre sí, cubriendo toda la zona de concentración de las raíces activas

Resultados de la Cirugía Refractiva en la Provincia de Villa Clara

A descriptive prospective and longitudinal study was conducted in a total of 145 eyes of patients who were seen at the doctor’s office in order to be operated on for a refractive defect. A total of 111 eyes were operated on with LASIK and 34 with LASEK + MC. There was a predominance of females between 20 and 29 years of age. The most common refractive error was compound myopic astigmatism. The visual results to the present are significant because the patients have achieved an uncorrected visual acuity between 20/25 and 20/20. The most common complication found was superficial punctate keratitis. In the case of LASEK, mitomycin C was used in patients with high myopia, and haze has been prevented, thus improving the quality of life of these patients.Se realizó un estudio descriptivo prospectivo y longitudinal en un total de 145 ojos de pacientes que acudieron a consulta para ser operados por algún defecto refractivo. Un total de 111 ojos fueron intervenidos por LASIK y 34 por LASEK+MC. Predominó  el sexo femenino en edades entre 20–29 años. El defecto refractivo más frecuente fue el astigmatismo miópico compuesto, los resultados visuales hasta la fecha son significativos -cuando los aquejados logran una agudeza visual sin corrección entre 20/25 y 20/20-. La complicación más encontrada fue la queratitis punteada superficial. En el caso del LASEK se usó mitomicina C en pacientes con altas miopías y se ha podido evitar el Haze, lo que mejora la calidad de vida de éstos

Resultados de la Cirugía Refractiva en Villa Clara

Objective: to describe the results of refractive surgery in Villa Clara province. Method: a descriptive, prospective and longitudinal study was conducted in a total of 145 eyes of patients who were seen at the doctor’s office in order to be operated on for a refractive error. Results: a total of 111 eyes were operated on with LASIK and 34 with LASEK. There was a predominance of female patients between 20 and 29 years of age. The most common refractive error was compound myopic astigmatism. The visual results to the present are significant because the patients have achieved a visual acuity without optical correction between 0.8 and 1.0. Conclusions: the implementation of refractive surgery in Villa Clara has had encouraging results.Objetivo: describir los resultados de la Cirugía Refractiva en la Provincia de Villa Clara. Método: se realizó un estudio descriptivo prospectivo y longitudinal en un total de 145 ojos de pacientes que acudieron a consulta para ser operados por algún defecto refractivo. Resultados: un total de 111 ojos fueron intervenidos por LASIK y 34 por LASEK, predominó el sexo femenino en edades entre 20-29 años, el defecto refractivo más frecuente fue el astigmatismo miópico compuesto, los resultados visuales hasta la fecha son significativos una vez que los pacientes han logrado una agudeza visual sin corrección entre 0.8 y 1.0 y la complicación más encontrada fue la queratitis punteada superficial. Conclusiones: la realización de la intervención quirúrgica refractiva en Villa Clara ha tenido resultados alentadores

Epidemiología de la toxoplasmosis ocular en pacientes del municipio Machiques de Perijá, Venezuela. Agosto 2004 - julio 2005

A cross-sectional descriptive study of all the patients suffering from ocular toxoplasmosis treated at the Ophthalmology Services of the Machiques de Perija municipality in the state of Zulia , Venezuela , from August 2004 to July 30, 2004, was carried out. The objective of the study was to determine the epidemiologic aspects of the patients suffering from this condition. The universe of study was formed by 1132 patients treated in the consulting room and presenting as the main symptom a visual deficit. The sample included 67 patients whose visual defect was related to the clinical ophthalmologic diagnosis of ocular toxoplasmosis. The most affected age group was between 30 and 44 years of age, mostly males. Most of the patients lived in houses in poor condition; most of them lived with dogs and cats (32). More than half of the patients used to eat poorly cooked meats. The majority of the patients presenting a predominance of cicatricial plaques in the macular area were diagnosed with congenital toxoplasmosis. On the other hand, there were more active plaques and plaques of peripheral localization in those patients presenting acquired toxoplasmosis. The most common associated ophthalmologic illness was posterior uveitis. More than half of the patients remained with a vision lower than 0.01.Se realizó un estudio descriptivo transversal de todos los pacientes atendidos con el diagnóstico de toxoplasmosis ocular que asistieron a la Consulta de Oftalmología del municipio Machiques de Perijá en el Estado Zulia, Venezuela, en el período comprendido desde el primero de agosto de 2004 al 30 de julio del año 2005 con el objetivo de determinar aspectos epidemiológicos de los pacientes con esta enfermedad. De los 1 132 pacientes que fueron atendidos en consulta por presentar como síntoma fundamental el defecto visual, en 67 enfermos se diagnosticó toxoplasmosis ocular; el grupo de edad más afectado resultó ser el de 30 a 44 años, con predilección por el sexo masculino; primaron las viviendas con malas condiciones y un alto número de pacientes (32) convivían con perros o gatos; se encontró que más de la mitad de los enfermos eran consumidores de carnes mal cocidas; se realizó un mayor diagnóstico de toxoplasmosis congénita entre los enfermos en lo que predominaron las placas cicatrizales en área macular; contrariamente encontramos mayor número de placas activas y de localización periférica en la toxoplasmosis adquirida; la enfermedad oftalmológica asociada más frecuente fue la uveítis posterior; más de la mitad de los pacientes quedaron con una visión inferir a 0.01

Genomic instability in human cancer: molecular insights and opportunities for therapeutic attack and prevention through diet and nutrition

Genomic instability can initiate cancer, augment progression, and influence the overall prognosis of the affected patient. Genomic instability arises from many different pathways, such as telomere damage, centrosome amplification, epigenetic modifications, and DNA damage from endogenous and exogenous sources, and can be perpetuating, or limiting, through the induction of mutations or aneuploidy, both enabling and catastrophic. Many cancer treatments induce DNA damage to impair cell division on a global scale but it is accepted that personalized treatments, those that are tailored to the particular patient and type of cancer, must also be developed. In this review, we detail the mechanisms from which genomic instability arises and can lead to cancer, as well as treatments and measures that prevent genomic instability or take advantage of the cellular defects caused by genomic instability. In particular, we identify and discuss five priority targets against genomic instability: (1) prevention of DNA damage; (2) enhancement of DNA repair; (3) targeting deficient DNA repair; (4) impairing centrosome clustering; and, (5) inhibition of telomerase activity. Moreover, we highlight vitamin D and B, selenium, carotenoids, PARP inhibitors, resveratrol, and isothiocyanates as priority approaches against genomic instability. The prioritized target sites and approaches were cross validated to identify potential synergistic effects on a number of important areas of cancer biology

Survey of Period Variations of Superhumps in SU UMa-Type Dwarf Novae. II: The Second Year (2009-2010)

As an extension of the project in Kato et al. (2009, arXiv:0905.1757), we collected times of superhump maxima for 61 SU UMa-type dwarf novae mainly observed during the 2009-2010 season. The newly obtained data confirmed the basic findings reported in Kato et al. (2009): the presence of stages A-C, as well as the predominance of positive period derivatives during stage B in systems with superhump periods shorter than 0.07 d. There was a systematic difference in period derivatives for systems with superhump periods longer than 0.075 d between this study and Kato et al. (2009). We suggest that this difference is possibly caused by the relative lack of frequently outbursting SU UMa-type dwarf novae in this period regime in the present study. We recorded a strong beat phenomenon during the 2009 superoutburst of IY UMa. The close correlation between the beat period and superhump period suggests that the changing angular velocity of the apsidal motion of the elliptical disk is responsible for the variation of superhump periods. We also described three new WZ Sge-type objects with established early superhumps and one with likely early superhumps. We also suggest that two systems, VX For and EL UMa, are WZ Sge-type dwarf novae with multiple rebrightenings. The O-C variation in OT J213806.6+261957 suggests that the frequent absence of rebrightenings in very short-Porb objects can be a result of sustained superoutburst plateau at the epoch when usual SU UMa-type dwarf novae return to quiescence preceding a rebrightening. We also present a formulation for a variety of Bayesian extension to traditional period analyses.Comment: 63 pages, 77 figures, 1 appendix, Accepted for publication in PASJ, data correctio