Differentiated sex chromosomes in mammals and other vertebrates evolved independently but in strikingly similar ways. Vertebrates with differentiated sex chromosomes share the problems of the unequal ...expression of the genes borne on sex chromosomes, both between the sexes and with respect to autosomes. Dosage compensation of genes on sex chromosomes is surprisingly variable - and can even be absent - in different vertebrate groups. Systems that compensate for different gene dosages include a wide range of global, regional and gene-by-gene processes that differ in their extent and their molecular mechanisms. However, many elements of these control systems are similar across distant phylogenetic divisions and show parallels to other gene silencing systems. These dosage systems cannot be identical by descent but were probably constructed from elements of ancient silencing mechanisms that are ubiquitous among vertebrates and shared throughout eukaryotes.
Recognizing lines of unconstrained handwritten text is a challenging task. The difficulty of segmenting cursive or overlapping characters, combined with the need to exploit surrounding context, has ...led to low recognition rates for even the best current recognizers. Most recent progress in the field has been made either through improved preprocessing or through advances in language modeling. Relatively little work has been done on the basic recognition algorithms. Indeed, most systems rely on the same hidden Markov models that have been used for decades in speech and handwriting recognition, despite their well-known shortcomings. This paper proposes an alternative approach based on a novel type of recurrent neural network, specifically designed for sequence labeling tasks where the data is hard to segment and contains long-range bidirectional interdependencies. In experiments on two large unconstrained handwriting databases, our approach achieves word recognition accuracies of 79.7 percent on online data and 74.1 percent on offline data, significantly outperforming a state-of-the-art HMM-based system. In addition, we demonstrate the network's robustness to lexicon size, measure the individual influence of its hidden layers, and analyze its use of context. Last, we provide an in-depth discussion of the differences between the network and HMMs, suggesting reasons for the network's superior performance.
Sex chromosomes—particularly the human Y—have been a source of fascination for decades because of their unique transmission patterns and their peculiar cytology. The outpouring of genomic data ...confirms that their atypical structure and gene composition break the rules of genome organization, function, and evolution. The X has been shaped by dosage differences to have a biased gene content and to be subject to inactivation in females. The Y chromosome seems to be a product of a perverse evolutionary process that does not select the fittest Y, which may cause its degradation and ultimate extinction.
There is growing concern that the way that soils are used often results in their degradation, giving rise to significant costs, both to direct users of soils and to society as a whole. This paper ...develops and uses an approach to derive the total economic cost of soil degradation in England and Wales. An estimate was made of degradation costs at the national scale for dominant combinations of land cover and soils, defined as ‘soilscapes’. An ecosystem services framework was used to assess how degradation affects the capacity of soils to support a range of ‘final goods’, distinguishing between on-site and off-site costs, and market and non-market effects. Quantifiable soil degradation costs ranged between £0.9 bn and £1.4 bn per year, with a central estimate of £1.2 bn, mainly linked to loss of organic content of soils (47% of total cost), compaction (39%) and erosion (12%). Eighty percent of costs occur off-site and, as such, are often of limited concern to those whose actions may be causing soil degradation. The findings confirm that control of soil degradation has implications for a number of key policy areas such as flood risk management and climate change mitigation.
Polygenic sex determination (PSD) is defined as the determination of sexual phenotype by the combined action of two or more genes at independently inherited loci in one individual.PSD should not be ...ascribed to multiple alleles at the same sex determination (SD) locus that may be polymorphic in the population, elements of a common biochemical pathway, and to multiple sex chromosomes that are polymorphic in a population, or neo-sex chromosomes or sex chromosome chains when sexual development of the individuum is triggered by one SD locus.A consistent nomenclature that adheres to accepted definitions of genes and alleles is recommended.Evolutionary theory predicts that PSD is an unstable state.Documented cases of PSD are rare. Those examined are best explained by transitionary stages during sex chromosome turnover or aberrant situations in hybrids between species with different sex chromosomes.
Genetic sex determination (SD) in most vertebrates is controlled by a single master sex gene, which ensures a 1:1 sex ratio. However, more complex systems abound, and several have been ascribed to polygenic SD (PSD), in which many genes at different loci interact to produce the sexual phenotype. Here we examine claims for PSD in vertebrates, finding that most constitute transient states during sex chromosome turnover, or aberrant systems in species hybrids. To avoid confusion about terminology, we propose a consistent nomenclature for genetic SD systems.
Sex determination in animals is amazingly plastic. Vertebrates display contrasting strategies ranging from complete genetic control of sex (genotypic sex determination) to environmentally determined ...sex (for example, temperature-dependent sex determination). Phylogenetic analyses suggest frequent evolutionary transitions between genotypic and temperature-dependent sex determination in environmentally sensitive lineages, including reptiles. These transitions are thought to involve a genotypic system becoming sensitive to temperature, with sex determined by gene-environment interactions. Most mechanistic models of transitions invoke a role for sex reversal. Sex reversal has not yet been demonstrated in nature for any amniote, although it occurs in fish and rarely in amphibians. Here we make the first report of reptile sex reversal in the wild, in the Australian bearded dragon (Pogona vitticeps), and use sex-reversed animals to experimentally induce a rapid transition from genotypic to temperature-dependent sex determination. Controlled mating of normal males to sex-reversed females produces viable and fertile offspring whose phenotypic sex is determined solely by temperature (temperature-dependent sex determination). The W sex chromosome is eliminated from this lineage in the first generation. The instantaneous creation of a lineage of ZZ temperature-sensitive animals reveals a novel, climate-induced pathway for the rapid transition between genetic and temperature-dependent sex determination, and adds to concern about adaptation to rapid global climate change.
Purpose
Cognitive impairment after critical illness is common and debilitating. We developed a cognitive therapy program for critically ill patients and assessed the feasibility and safety of ...administering combined cognitive and physical therapy early during a critical illness.
Methods
We randomized 87 medical and surgical ICU patients with respiratory failure and/or shock in a 1:1:2 manner to three groups: usual care, early once-daily physical therapy, or early once-daily physical therapy plus a novel, progressive, twice-daily cognitive therapy protocol. Cognitive therapy included orientation, memory, attention, and problem-solving exercises, and other activities. We assessed feasibility outcomes of the early cognitive plus physical therapy intervention. At 3 months, we also assessed cognitive, functional, and health-related quality of life outcomes. Data are presented as median (interquartile range) or frequency (%).
Results
Early cognitive therapy was a delivered to 41/43 (95 %) of cognitive plus physical therapy patients on 100 % (92–100 %) of study days beginning 1.0 (1.0–1.0) day following enrollment. Physical therapy was received by 17/22 (77 %) of usual care patients, by 21/22 (95 %) of physical therapy only patients, and 42/43 (98 %) of cognitive plus physical therapy patients on 17 % (10–26 %), 67 % (46–87 %), and 75 % (59–88 %) of study days, respectively. Cognitive, functional, and health-related quality of life outcomes did not differ between groups at 3-month follow-up.
Conclusions
This pilot study demonstrates that early rehabilitation can be extended beyond physical therapy to include cognitive therapy. Future work to determine optimal patient selection, intensity of treatment, and benefits of cognitive therapy in the critically ill is needed.
Humans, mice, and even kangaroos have an XX female:XY male system of sex determination, in which the Y harbors a male-dominant sex-determining gene SRY. Birds have the opposite, ZZ males and ZW ...females, and may use a dosage-sensitive Z-borne gene. Other reptiles have genetic sex but no visible sex chromosomes, or determine sex by temperature of egg incubation. How can we make sense of so much variation? How do systems change in evolution? Studies of some unlikely animals-platypus and dragon lizards, frogs and fish-confirm that evolutionary transitions have occurred between TSD and GSD systems, between XY and ZW systems, and even between male and female heterogametic systems. Here I explore nonmodel systems that offer some new perspectives on some venerable questions of sex and sex chromosomes.
How temperature determines sex remains unknown. A recent hypothesis proposes that conserved cellular mechanisms (calcium and redox; 'CaRe' status) sense temperature and identify genes and regulatory ...pathways likely to be involved in driving sexual development. We take advantage of the unique sex determining system of the model organism, Pogona vitticeps, to assess predictions of this hypothesis. P. vitticeps has ZZ male: ZW female sex chromosomes whose influence can be overridden in genetic males by high temperatures, causing male-to-female sex reversal. We compare a developmental transcriptome series of ZWf females and temperature sex reversed ZZf females. We demonstrate that early developmental cascades differ dramatically between genetically driven and thermally driven females, later converging to produce a common outcome (ovaries). We show that genes proposed as regulators of thermosensitive sex determination play a role in temperature sex reversal. Our study greatly advances the search for the mechanisms by which temperature determines sex.
Conservation practitioners have long recognized ecological connectivity as a global priority for preserving biodiversity and ecosystem function. In the early years of conservation science, ecologists ...extended principles of island biogeography to assess connectivity based on source patch proximity and other metrics derived from binary maps of habitat. From 2006 to 2008, the late Brad McRae introduced circuit theory as an alternative approach to model gene flow and the dispersal or movement routes of organisms. He posited concepts and metrics from electrical circuit theory as a robust way to quantify movement across multiple possible paths in a landscape, not just a single least‐cost path or corridor. Circuit theory offers many theoretical, conceptual, and practical linkages to conservation science. We reviewed 459 recent studies citing circuit theory or the open‐source software Circuitscape. We focused on applications of circuit theory to the science and practice of connectivity conservation, including topics in landscape and population genetics, movement and dispersal paths of organisms, anthropogenic barriers to connectivity, fire behavior, water flow, and ecosystem services. Circuit theory is likely to have an effect on conservation science and practitioners through improved insights into landscape dynamics, animal movement, and habitat‐use studies and through the development of new software tools for data analysis and visualization. The influence of circuit theory on conservation comes from the theoretical basis and elegance of the approach and the powerful collaborations and active user community that have emerged. Circuit theory provides a springboard for ecological understanding and will remain an important conservation tool for researchers and practitioners around the globe.
Aplicaciones de la Teoría de Circuitos a la Conservación y a la Ciencia de la Conectividad
Resumen
Quienes practican la conservación han reconocido durante mucho tiempo que la conectividad ecológica es una prioridad mundial para la preservación de la biodiversidad y el funcionamiento del ecosistema. Durante los primeros años de la ciencia de la conservación los ecólogos difundieron los principios de la biografía de islas para evaluar la conectividad con base en la proximidad entre el origen y el fragmento, así como otras medidas derivadas de los mapas binarios de los hábitats. Entre 2006 y 2008 el fallecido Brad McRae introdujo la teoría de circuitos como una estrategia alternativa para modelar el flujo génico y la dispersión o las rutas de movimiento de los organismos. McRae propuso conceptos y medidas de la teoría de circuitos eléctricos como una manera robusta para cuantificar el movimiento a lo largo de múltiples caminos posibles en un paisaje, no solamente a lo largo de un camino o corredor de menor costo. La teoría de circuitos ofrece muchos enlaces teóricos, conceptuales y prácticos con la ciencia de la conservación. Revisamos 459 estudios recientes que citan la teoría de circuitos o el software de fuente abierta Circuitscape. Nos enfocamos en las aplicaciones de la teoría de circuitos a la ciencia y a la práctica de la conservación de la conectividad, incluyendo temas como la genética poblacional y del paisaje, movimiento y caminos de dispersión de los organismos, barreras antropogénicas de la conectividad, comportamiento ante incendios, flujo del agua, y servicios ambientales. La teoría de circuitos probablemente tenga un efecto sobre la ciencia de la conservación y quienes la practican por medio de una percepción mejorada de las dinámicas del paisaje, el movimiento animal, y los estudios de uso de hábitat, y por medio del desarrollo de nuevas herramientas de software para el análisis de datos y su visualización. La influencia de la teoría de circuitos sobre la conservación viene de la base teórica y la elegancia de la estrategia y de las colaboraciones fuertes y la comunidad activa de usuarios que han surgido recientemente. La teoría de circuitos proporciona un trampolín para el entendimiento ecológico y seguirá siendo una importante herramienta de conservación para los investigadores y practicantes en todo el mundo.
摘要
保护实践者长期以来一直将生态连接度视为保护生物多样性和生态系统功能的当务之急。在保护科学发展早期, 生态学家将岛屿生物地理学的原理进行扩展, 基于源斑块邻近度和其它来自二元生境图的指标来评估连接度。2006 年到2008 年, 已故的Brad McRae 引入了电路理论, 作为模拟基因流和生物体扩散或移动路径的新方法。他用电路理论中的概念和指标开发了一种稳健的方法来量化景观中多种可能的移动路径, 而这不只是一条最低成本的路径或廊道。电路理论为保护科学提供了许多理论、概念和实践方面的联系。我们综述了近期引用电路理论或是开源软件Circuitscape的459 项研究, 重点关注电路理论在连接度保护科学与实践中的应用, 包括景观和种群遗传学、生物体运动和扩散路径、连接度的人为障碍、火灾、水流和生态系统服务等问题。电路理论通过帮助理解景观动力学、动物移动和生境利用研究, 以及开发新的数据分析和可视化软件工具, 影响着保护科学和实践者。电路理论对保护的影响来自于该方法的理论基础和优雅性, 以及现已出现的强大的合作队伍和活跃的用户群体。电路理论为生态学理解提供了跳板, 并将继续作为全球研究人员和实践者的重要保护工具。翻译: 胡怡思; 审校: 聂永刚
Article impact statement: Uses of circuit theory to understand connectivity have had a durable and global impact on conservation science and practice.
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