bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fire Ecology and Conservation in the High Tropical Andes: Observations from Northern Ecuador
Authors: Keating Philip L 
Published: April 2007

The upper montane zone of the Ecuadorian Andes includes a diverse mixture of forest, páramo (tropical alpine vegetation), and agricultural lands. These areas have been occupied by humans for at least 7,000 years, and it is likely that repeated anthropogenic disturbances, especially fires, have altered the vegetation frequently. More than twelve major protected areas have been established in the highland region, but greater knowledge of disturbance ecology must be acquired before appropriate environmental management schemes can be implemented. This article reviews recent findings concerning the fire ecology of páramo communities within the Cotacachi-Cayapas Ecological Reserve and on Cerro Imbabura, an adjacent peak in northern Ecuador. After summarizing the environmental history of the region, the relationships among contemporary fire regimes, conservation practice and various attitudes toward páramo are discussed. Utilizing field observations from both protected and unprotected páramos, I demonstrate that fires are most likely not reducing species diversity, and that fire suppression is not an effective management policy. The "pristine myth" that provides a basis for some conservation efforts is evaluated, and recommendations for more effective conservation policies are made. 	La zona de la alta montaña de los Andes ecuatorianos incluye una mezcla diversa de bosques, páramos (vegetación alpina tropical) y tierras agrícolas. Estas áreas han sido ocupadas por el hombre durante por lo menos 7,000 años y, es probable, que disturbios antropogénicos repetidos -especialmente incendios- hayan cambiado la vegetación muchas veces. Más de doce áreas mayores protegidas han sido establecidas en la región alta, pero un conocimiento mayor de la ecología de los disturbios debe ser adquirido antes de que un sistema de manejo ambiental apropiado pueda ser implementado. Este artículo revisará los hallazgos recientes alrededor de la ecología de disturbios de las comunidades del páramo de la Reserva Ecológica Cotacachi-Cayapas y del Cerro Imbabura, un pico adyacente, en el norte de Ecuador. Después de describir la historia ambiental, serán discutidas las relaciones entre las prácticas de conservación y las varias actitudes hacia el páramo. Utilizando observaciones basadas en el trabajo de campo, serán comparados los impactos de incendios en los páramos protegidos y no-protegidos. Demuestro que es muy probable que los incendios no reduzcan la diversidad de especies y que la supresión de incendios no es muy efectiva como política de manejo. El "mito de pristinismo," que provee una base para algunos esfuerzos de conservación, será evaluado y se ofrecen recomendaciones para unas políticas de conservación más efectivas.
Identifying and Assessing Tropical Montane Forests on the Eastern Flank of the Ecuadorian Andes
Authors: Keese James , Mastin Thomas , Yun David 
Published: April 2007

The forests of the mountain tropics comprise one of the most unique and bio-diverse of all vegetation regions, but they are also among the most threatened. Threats include colonization, road building, habitat fragmentation, logging, livestock pasturing, and agriculture. However, large areas of tropical montane forest on the eastern flank of the Andes Mountains of Ecuador remain intact, at least for now. This research uses Landsat 7 ETM+ satellite data and field study to identify land covers and land uses between Sangay and Podocarpus National Parks in Ecuador and to identify a potential conservation corridor between the two parks. The analysis reveals that eighty-eight percent of the study area remains in forest or highland tundra (páramo). However, there are three significant breaks in connectivity, and the adjacent areas of the upland valleys and Amazon Basin colonization zone are largely cleared, suggesting that deforestation pressures will intensify in the future. The results of this study demonstrate the benefits and drawbacks of moderate resolution satellite data for identifying, mapping, and monitoring land cover in less developed countries. GIS is also used to analyze relationships between roads, slope, and deforestation. Potential actions by government, NGOs, and local communities are suggested. 	Los boques de la sierra tropical incluyen una de las más singulares y bio-diversas de todas las regiones de vegetación, pero éstas también se encuentran dentro del grupo más amenazado. Las amenazas incluyen la colonización, construcción de caminos, fragmentación del hábitat, deforestación, pastoreo de ganadería, y agricultura. Sin embargo, hasta ahora por lo menos, todavía existen grandes áreas de bosque de montaña al lado este de los Andes ecuatorianos. Este estudio utiliza datos del satélite Landsat 7 ETM+ e investigaciones de campo para identificar la cobertura y uso de la tierra entre los parques nacionales Sangay y Podocarpus de Ecuador, también para identificar un posible corredor de conservación entre los dos parques. El análisis demuestra que el ochenta y ocho por ciento de la zona de estudio se mantiene como bosque o páramo. Sin embargo, existen tres grandes rupturas en la conectividad y en las zonas de colonización de los valles altos y de la cuenca amazónica donde no quedan bosques. Este patrón representa el efecto a futuro de lo que pudiera pasar con la continuación de la deforestación. Los resultados resaltan los beneficios y dificultades del uso de datos de satélites de resolución moderada para identificar, mapear y monitorear la cobertura de la tierra en países menos-desarrollados. SIG también puede ser muy útil para analizar las relaciones entre caminos, la topografía y la deforestación. El estudio ofrece sugerencias de posibles acciones gubernamentales, de las ONGs y de las comunidades locales.
The Forests Are Bleeding: How Land Use Change Is Creating a New Fire Regime in the Ecuadorian Amazon
Authors: Messina Joseph P , Cochrane Mark A 
Published: April 2007

Land use and cover of the Northeastern Ecuadorian Amazon has changed significantly over the last 40 years. These well-documented changes are slowly modifying the physical environment of the region from one dominated by the classic humid tropics to one more reminiscent of the eastern Amazon basin with cyclical moisture and temperature gradients, consequent emergent fire regimes and persistent deforestation. This paper discusses the causes of local land use and cover change, the remote sensing and sampling methods employed that led to the discovery of burned areas, and presents a physical climatology of diffusion and convection to explain the presence of burned areas in the traditionally fire immune humid tropical Ecuadorian Amazon. 	En los últimos 40 años la cobertura de la tierra en el noreste del Amazonas ecuatoriano ha cambiado significativamente. Estos ampliamente documentados cambios están modificando lentamente el ambiente físico de la región transformándolo de tropical húmedo clásico a un ambiente más parecido al de la cuenca oriental del Amazonas, con cambios cíclicos de humedad y temperatura acompañados de regimenes de incendios emergentes y deforestación persistentes. El presente artículo analiza: (i) las causas de cambio en la cobertura y uso de la tierra, y (ii) los métodos de muestreo y de teledetección utilizados en el proceso de descubrimiento de áreas quemadas. También presenta una climatología física de difusión y convección como posible explicación a la presencia de áreas quemadas en regiones como el Amazonas ecuatoriano, una region que tradicionalmente ha sido considerada como tropical húmeda e inmune a incendios.
Estimating the Number of Ancestral Lineages Using a Maximum-Likelihood Method Based on Rejection Sampling
Authors: Blum Michael G B , Rosenberg Noah A 
Published: April 2007

AbstractEstimating the number of ancestral lineages of a sample of DNA sequences at time t in the past can be viewed as a variation on the problem of estimating the time to the most recent common ancestor. To estimate the number of ancestral lineages, we develop a maximum-likelihood approach that takes advantage of a prior model of population demography, in addition to the molecular data summarized by the pattern of polymorphic sites. The method relies on a rejection sampling algorithm that is introduced for simulating conditional coalescent trees given a fixed number of ancestral lineages at time t. Computer simulations show that the number of ancestral lineages can be estimated accurately, provided that the number of mutations that occurred since time t is sufficiently large. The method is applied to 986 present-day human sequences located in hypervariable region 1 of the mitochondrion to estimate the number of ancestral lineages of modern humans at the time of potential admixture with the Neanderthal population. Our estimates support a view that the proportion of the modern population consisting of Neanderthal contributions must be relatively small, less than ∼5%, if the admixture happened as recently as 30,000 years ago.
Ancestry Influences the Fate of Duplicated Genes Millions of Years After Polyploidization of Clawed Frogs (Xenopus)
Authors: Evans Ben J 
Published: April 2007

AbstractAllopolyploid species form through the fusion of two differentiated genomes and, in the earliest stages of their evolution, essentially all genes in the nucleus are duplicated. Because unique mutations occur in each ancestor prior to allopolyploidization, duplicate genes in these species potentially are not interchangeable, and this could influence their genetic fates. This study explores evolution and expression of a simple duplicated complex—a heterodimer between RAG1 and RAG2 proteins in clawed frogs (Xenopus). Results demonstrate that copies of RAG1 degenerated in different polyploid species in a phylogenetically biased fashion, predominately in only one lineage of closely related paralogs. Surprisingly, as a result of an early deletion of one RAG2 paralog, it appears that in many species RAG1/RAG2 heterodimers are composed of proteins that were encoded by unlinked paralogs. If the tetraploid ancestor of extant species of Xenopus arose through allopolyploidization and if recombination between paralogs was rare, then the genes that encode functional RAG1 and RAG2 proteins in many polyploid species were each ultimately inherited from different diploid progenitors. These observations are consistent with the notion that ancestry can influence the fate of duplicate genes millions of years after duplication, and they uncover a dimension of natural selection in allopolyploid genomes that is distinct from other genetic phenomena associated with polyploidization or segmental duplication.
The Early Developmental Gene Semaphorin 5c Contributes to Olfactory Behavior in Adult Drosophila
Authors: Rollmann Stephanie M , Yamamoto Akihiko , Goossens Tim , Zwarts Liesbeth , Callaerts-Végh Zsuzsanna , Callaerts Patrick , Norga Koenraad , Mackay Trudy F C , Anholt Robert R H 
Published: April 2007

Abstract
Behaviors are complex traits influenced by multiple pleiotropic genes. Understanding the mechanisms that give rise to complex behaviors requires an understanding of how variation in transcriptional regulation shapes nervous system development and how variation in brain structure influences an organism's ability to respond to its environment. To begin to address this problem, we used olfactory behavior in Drosophila melanogaster as a model and showed that a hypomorphic transposon-mediated mutation of the early developmental gene Semaphorin-5c (Sema-5c) results in aberrant behavioral responses to the repellant odorant benzaldehyde. We fine mapped this effect to the Sema-5c locus using deficiency mapping, phenotypic reversion through P-element excision, and transgenic rescue. Morphometric analysis of this Sema-5c allele reveals subtle neuroanatomical changes in the brain with a reduction in the size of the ellipsoid body. High-density oligonucleotide expression microarrays identified 50 probe sets with altered transcriptional regulation in the Sema-5c background and quantitative complementation tests identified epistatic interactions between nine of these coregulated genes and the transposon-disrupted Sema-5c gene. Our results demonstrate how hypomorphic mutation of an early developmental gene results in genomewide transcriptional consequences and alterations in brain structure accompanied by profound impairment of adult behavior.
No Evidence for Absence of Paternal mtDNA in Male Progeny From Pair Matings of the Mussel Mytilus galloprovincialis
Authors: Theologidis Ioannis , Saavedra Carlos , Zouros Eleftherios 
Published: April 2007

Abstract
The claim that a Mytilus galloprovincialis male failed to transmit mtDNA to its sons in controlled crosses is shown to be false. At present there is no evidence for mussel males lacking a paternal mtDNA. This makes unlikely the hypothesis that maternal genomes may become paternally transmitted by invading the germ line of males that lack a paternal genome.
Wavelet-Based Parametric Functional Mapping of Developmental Trajectories With High-Dimensional Data
Authors: Zhao Wei , Li Hongying , Hou Wei , Wu Rongling 
Published: April 2007

AbstractThe biological and statistical advantages of functional mapping result from joint modeling of the mean-covariance structures for developmental trajectories of a complex trait measured at a series of time points. While an increased number of time points can better describe the dynamic pattern of trait development, significant difficulties in performing functional mapping arise from prohibitive computational times required as well as from modeling the structure of a high-dimensional covariance matrix. In this article, we develop a statistical model for functional mapping of quantitative trait loci (QTL) that govern the developmental process of a quantitative trait on the basis of wavelet dimension reduction. By breaking an original signal down into a spectrum by taking its averages (smooth coefficients) and differences (detail coefficients), we used the discrete Haar wavelet shrinkage technique to transform an inherently high-dimensional biological problem into its tractable low-dimensional representation within the framework of functional mapping constructed by a Gaussian mixture model. Unlike conventional nonparametric modeling of wavelet shrinkage, we incorporate mathematical aspects of developmental trajectories into the smooth coefficients used for QTL mapping, thus preserving the biological relevance of functional mapping in formulating a number of hypothesis tests at the interplay between gene actions/interactions and developmental patterns for complex phenotypes. This wavelet-based parametric functional mapping has been statistically examined and compared with full-dimensional functional mapping through simulation studies. It holds great promise as a powerful statistical tool to unravel the genetic machinery of developmental trajectories with large-scale high-dimensional data.
Mutations in Cytochrome c Oxidase Subunit VIa Cause Neurodegeneration and Motor Dysfunction in Drosophila
Authors: Liu Wensheng , Gnanasambandam Radhakrishnan , Benjamin Jeffery , Kaur Gunisha , Getman Patricia B , Siegel Alan J , Shortridge Randall D , Singh Satpal 
Published: April 2007

AbstractMitochondrial dysfunction is involved in many neurodegenerative disorders in humans. Here we report mutations in a gene (designated levy) that codes for subunit VIa of cytochrome c oxidase (COX). The mutations were identified by the phenotype of temperature-induced paralysis and showed the additional phenotypes of decreased COX activity, age-dependent bang-induced paralysis, progressive neurodegeneration, and reduced life span. Germ-line transformation using the levy+ gene rescued the mutant flies from all phenotypes including neurodegeneration. The data from levy mutants reveal a COX-mediated pathway in Drosophila, disruption of which leads to mitochondrial encephalomyopathic effects including neurodegeneration, motor dysfunction, and premature death. The data present the first case of a mutation in a nuclear-encoded structural subunit of COX that causes mitochondrial encephalomyopathy rather than lethality, whereas several previous attempts to identify such mutations have not been successful. The levy mutants provide a genetic model to understand the mechanisms underlying COX-mediated mitochondrial encephalomyopathies and to explore possible therapeutic interventions.
Origin and Evolution of Human microRNAs From Transposable Elements
Authors: Piriyapongsa Jittima , Mariño-Ramírez Leonardo , Jordan I King 
Published: April 2007

Abstract
We sought to evaluate the extent of the contribution of transposable elements (TEs) to human microRNA (miRNA) genes along with the evolutionary dynamics of TE-derived human miRNAs. We found 55 experimentally characterized human miRNA genes that are derived from TEs, and these TE-derived miRNAs have the potential to regulate thousands of human genes. Sequence comparisons revealed that TE-derived human miRNAs are less conserved, on average, than non-TE-derived miRNAs. However, there are 18 TE-derived miRNAs that are relatively conserved, and 14 of these are related to the ancient L2 and MIR families. Comparison of miRNA vs. mRNA expression patterns for TE-derived miRNAs and their putative target genes showed numerous cases of anti-correlated expression that are consistent with regulation via mRNA degradation. In addition to the known human miRNAs that we show to be derived from TE sequences, we predict an additional 85 novel TE-derived miRNA genes. TE sequences are typically disregarded in genomic surveys for miRNA genes and target sites; this is a mistake. Our results indicate that TEs provide a natural mechanism for the origination miRNAs that can contribute to regulatory divergence between species as well as a rich source for the discovery of as yet unknown miRNA genes.
Genetic Mapping of Developmental Instability: Design, Model and Algorithm
Authors: Wu Jiasheng , Zhang Bo , Cui Yuehua , Zhao Wei , Xu Li'an , Huang Minren , Zeng Yanru , Zhu Jun , Wu Rongling 
Published: April 2007

AbstractDevelopmental instability or noise, defined as the phenotypic imprecision of an organism in the face of internal or external stochastic disturbances, has been thought to play an important role in shaping evolutionary processes and patterns. The genetic studies of developmental instability have been based on fluctuating asymmetry (FA) that measures random differences between the left and the right sides of bilateral traits. In this article, we frame an experimental design characterized by a spatial autocorrelation structure for determining the genetic control of developmental instability for those traits that cannot be bilaterally measured. This design allows the residual environmental variance of a quantitative trait to be dissolved into two components due to permanent and random environmental factors. The degree of developmental instability is quantified by the relative proportion of the random residual variance to the total residual variance. We formulate a mixture model to estimate and test the genetic effects of quantitative trait loci (QTL) on the developmental instability of the trait. The genetic parameters including the QTL position, the QTL effects, and spatial autocorrelations are estimated by implementing the EM algorithm within the mixture model framework. Simulation studies were performed to investigate the statistical behavior of the model. A live example for poplar trees was used to map the QTL that control root length growth and its developmental instability from cuttings in water culture.
Association of microalbuminuria and the urine albumin-to-creatinine ratio with systemic disease in cats
Authors: Whittemore Jacqueline C. , Miyoshi Zona , Jensen Wayne A. , Radecki Steven V. , Lappin Michael R. 
Published: April 2007

Abstract
Objective—To determine the diagnostic usefulness of semiquantitative and quantitative microalbuminuria assays and urine albumin-to-creatinine (UAC) ratio for detecting disease in cats.
Design—Prospective study.
Animals—441 cats evaluated at a veterinary teaching hospital.
Procedures—Urine samples from cats for which a complete medical record was available were included. Urine dipstick results, urine protein-to-creatinine ratios (cutoffs, 0.1 and 0.4), semiquantitative and quantitative microalbuminuria assay results (cutoff, 1 mg/dL), and UAC ratio values (cutoffs, 100 and 200 mg/g) were determined. Clinical diagnoses determined within 3 months of enrollment were recorded. Sensitivity and specificity were determined with disease status used as the standard. The influences of clinical diagnosis, sex, age, serum urea nitrogen and creatinine concentrations, blood pressure, bacterial urine culture results, rectal temperature, pyuria, hematuria, and bacteriuria were evaluated by means of logistic regression.
Results—Of 441 cats that were eligible for inclusion, 40 were healthy and 401 had ≥ 1 disease. Results of logistic regression indicated that significant associations existed for age, presence of disease, presence of urinary tract disease, azotemia, hematuria, and pyuria and results of 1 or both of the microalbuminuria assays.
Conclusions and Clinical Relevance—Microalbuminuria was associated with underlying disease. Sensitivity and specificity of the microalbuminuria assays for detection of systemic disease were superior to those of other tests. Microalbuminuria testing in conjunction with other screening procedures may increase identification of occult disease. A prospective study evaluating the predictive values of screening tests with and without microalbuminuria determination is needed to validate this recommendation.
Measurement of serum antinuclear antibody titer in dogs with and without systemic lupus erythematosus: 120 cases (1997–2005)
Authors: Smee Nicole M. , Harkin Kenneth R. , Wilkerson Melinda J. 
Published: April 2007

Abstract
Objective—To determine serum antinuclear antibody (ANA) titers in dogs with systemic lupus erythematosus (SLE) and in dogs with related clinical and clinicopathologic findings.
Design—Retrospective case series.
Animals—120 dogs.
Procedures—Information that was evaluated included signalment, clinical signs, results of routine laboratory testing, ANA titer, and diagnosis.
Results—The most common clinical signs were arthralgia, myalgia, and stiffness (n = 41 [34.2%]); the most common clinicopathologic abnormality was thrombocytopenia (30 [25%]). Serum ANA titer was < 160 (seronegative) in 89 dogs (74.2%), 160 in 14 dogs (11.7%), 320 in 5dogs (4.2%), and ≥ 640 in 12 dogs (10%). Immune-mediated disease was confirmed in 40 dogs, 18 of which fulfilled the criteria for a definitive or probable diagnosis of SLE. Only 1 of 47 dogs with no major signs compatible with SLE had immune-mediated disease, compared with 26 of 57 dogs with 1 major sign and 13 of 16 dogs with ≥ 2 major signs.
Conclusions and Clinical Relevance—Results suggested that measurement of ANA titer was not a useful diagnostic test in dogs without any major clinical or clinicopathologic abnormalities suggestive of SLE. In contrast, there was a good chance that results of the ANA assay would be positive and that the dog would be found to have immune-mediated disease if at least 2 major signs were evident. Findings suggest that it would be reasonable to limit the use of the ANA assay to those dogs that have at least 1 major sign compatible with a diagnosis of SLE.