Showing papers by "University of Georgia published in 2005"
TL;DR: The development, current features, and some directions for future development of the Amber package of computer programs, which contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.
Abstract: We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assisted Model Building with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.
7,672 citations
TL;DR: A comprehensive review is presented on nucleus-independent chem.
Abstract: A comprehensive review is presented on nucleus-independent chem. shift as a criterion for aromaticity. [on SciFinder (R)]
2,463 citations
Book•
19 Sep 2005TL;DR: A review of Monte Carlo methods of computer simulation can be found in this article, where a brief review of other methods of simulation can also be found, as well as a brief introduction to Monte Carlo studies of biological molecules.
Abstract: Preface 1. Introduction 2. Some necessary background 3. Simple sampling Monte Carlo methods 4. Importance sampling Monte Carlo methods 5. More on importance sampling Monte Carlo methods of lattice systems 6. Off-lattice models 7. Reweighting methods 8. Quantum Monte Carlo methods 9. Monte Carlo renormalization group methods 10. Non-equilibrium and irreversible processes 11. Lattice gauge models: a brief introduction 12. A brief review of other methods of computer simulation 13. Monte Carlo simulations at the periphery of physics and beyond 14. Monte Carlo studies of biological molecules 15. Outlook Appendix Index.
2,055 citations
TL;DR: In this paper, a meta-analysis reviewed four categories of predictors of objective and subjective career success: human capital, organizational sponsorship, sociodemographic status, and stable individual differences.
Abstract: Using the contest- and sponsored-mobility perspectives as theoretical guides, this meta-analysis reviewed 4 categories of predictors of objective and subjective career success: human capital, organizational sponsorship, sociodemographic status, and stable individual differences. Salary level and promotion served as dependent measures of objective career success, and subjective career success was represented by career satisfaction. Results demonstrated that both objective and subjective career success were related to a wide range of predictors. As a group, human capital and sociodemographic predictors generally displayed stronger relationships with objective career success, and organizational sponsorship and stable individual differences were generally more strongly related to subjective career success. Gender and time (date of the study) moderated several of the relationships examined.
1,987 citations
TL;DR: A review of 190 work-family studies published in IO/OB journals from 1980 to 2002 is presented in this paper, with a discussion of recurring themes in the literature and the identification of blind spots in the IO/O perspective on work and family.
1,886 citations
University of Maryland, College Park1, University of Michigan2, National Oceanic and Atmospheric Administration3, Monash University, Clayton campus4, Academy of Natural Sciences of Drexel University5, University of Idaho6, University of New Mexico7, United States Geological Survey8, University of Missouri9, University of California, Berkeley10, University of Georgia11
TL;DR: The authors of as mentioned in this paper developed a comprehensive database of >37,000 river restoration projects across the United States, which are intended to enhance water quality, manage riparian zones, improve in-stream habitat, allow fish passage, and stabilize stream banks.
Abstract: The authors of this
Policy Forum
developed a comprehensive database of >37,000 river restoration projects across the United States. Such projects have increased exponentially over the past decade with more than a billion dollars spent annually since 1990. Most are intended to enhance water quality, manage riparian zones, improve in-stream habitat, allow fish passage, and stabilize stream banks. Only 10% of project records document any form of project monitoring, and little if any of this information is either appropriate or available for assessing the ecological effectiveness of restoration activities.
1,693 citations
TL;DR: In this article, the authors show that the loss of foundation tree species changes the local environment on which a variety of other species depend and how this disrupts fundamental ecosystem processes, including rates of decomposition, nutrient fluxes, carbon sequestration, and energy flow.
Abstract: In many forested ecosystems, the architecture and functional ecology of certain tree species define forest structure and their species-specific traits control ecosystem dynamics. Such foundation tree species are declining throughout the world due to introductions and outbreaks of pests and pathogens, selective removal of individual taxa, and over-harvesting. Through a series of case studies, we show that the loss of foundation tree species changes the local environment on which a variety of other species depend; how this disrupts fundamental ecosystem processes, including rates of decomposition, nutrient fluxes, carbon sequestration, and energy flow; and dramatically alters the dynamics of associated aquatic ecosystems. Forests in which dynamics are controlled by one or a few foundation species appear to be dominated by a small number of strong interactions and may be highly susceptible to alternating between stable states following even small perturbations. The ongoing decline of many foundation species provides a set of important, albeit unfortunate, opportunities to develop the research tools, models, and metrics needed to identify foundation species, anticipate the cascade of immediate, short- and long-term changes in ecosystem structure and function that will follow from their loss, and provide options for remedial conservation and management.
1,665 citations
Dalhousie University1, University of Georgia2, Bigelow Laboratory For Ocean Sciences3, Ontario Veterinary College4, New York State Department of Health5, Blaise Pascal University6, Bedford Institute of Oceanography7, University of Louisiana at Lafayette8, Duke University9, Pedagogical University10, Colorado State University11, University of Toronto12, University of Connecticut13, United States Forest Service14, University of Guelph15, Royal Botanic Garden Edinburgh16, Academy of Natural Sciences of Drexel University17, Michigan State University18, University of Copenhagen19, George Mason University20, University of Illinois at Urbana–Champaign21, Saint Petersburg State University22, University of Arkansas23, University of British Columbia24
TL;DR: This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists, and proposes a scheme that is based on nameless ranked systematics.
Abstract: This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists. Whereas the previous revision was primarily to incorporate the results of ultrastructural studies, this revision incorporates results from both ultrastructural research since 1980 and molecular phylogenetic studies. We propose a scheme that is based on nameless ranked systematics. The vocabulary of the taxonomy is updated, particularly to clarify the naming of groups that have been repositioned. We recognize six clusters of eukaryotes that may represent the basic groupings similar to traditional ''kingdoms.'' The multicellular lineages emerged from within monophyletic protist lineages: animals and fungi from Opisthokonta, plants from Archaeplastida, and brown algae from Stramenopiles.
1,620 citations
TL;DR: The importance of design- based research for the development of TELEs is described, principles for implementing design-based research withTELEs are proposed, and future challenges of using this methodology are discussed.
Abstract: During the past decade, design-based research has demonstrated its potential as a methodology suitable to both research and design of technology-enhanced learning environments (TELEs). In this paper, we define and identify characteristics of design-based research, describe the importance of design-based research for the development of TELEs, propose principles for implementing design-based research with TELEs, and discuss future challenges of using this methodology.
1,529 citations
TL;DR: This review describes MGEs, their properties that are important in horizontal gene transfer, and current opportunities to advance MGE genomics.
Abstract: Horizontal genomics is a new field in prokaryotic biology that is focused on the analysis of DNA sequences in prokaryotic chromosomes that seem to have originated from other prokaryotes or eukaryotes. However, it is equally important to understand the agents that effect DNA movement: plasmids, bacteriophages and transposons. Although these agents occur in all prokaryotes, comprehensive genomics of the prokaryotic mobile gene pool or 'mobilome' lags behind other genomics initiatives owing to challenges that are distinct from cellular chromosomal analysis. Recent work shows promise of improved mobile genetic element (MGE) genomics and consequent opportunities to take advantage - and avoid the dangers - of these 'natural genetic engineers'. This review describes MGEs, their properties that are important in horizontal gene transfer, and current opportunities to advance MGE genomics.
1,488 citations
TL;DR: In this paper, the authors propose five criteria for measuring success of river restoration, with emphasis on an ecological perspective, and suggest standards of evaluation for each of the five criteria and provide examples of suitable indicators.
Abstract: Summary 1. Increasingly, river managers are turning from hard engineering solutions to ecologically based restoration activities in order to improve degraded waterways. River restoration projects aim to maintain or increase ecosystem goods and services while protecting downstream and coastal ecosystems. There is growing interest in applying river restoration techniques to solve environmental problems, yet little agreement exists on what constitutes a successful river restoration effort. 2. We propose five criteria for measuring success, with emphasis on an ecological perspective. First, the design of an ecological river restoration project should be based on a specified guiding image of a more dynamic, healthy river that could exist at the site. Secondly, the river’s ecological condition must be measurably improved. Thirdly, the river system must be more self-sustaining and resilient to external perturbations so that only minimal follow-up maintenance is needed. Fourthly, during the construction phase, no lasting harm should be inflicted on the ecosystem. Fifthly, both pre- and postassessment must be completed and data made publicly available. 3. Determining if these five criteria have been met for a particular project requires development of an assessment protocol. We suggest standards of evaluation for each of the five criteria and provide examples of suitable indicators. 4. Synthesis and applications . Billions of dollars are currently spent restoring streams and rivers, yet to date there are no agreed upon standards for what constitutes ecologically beneficial stream and river restoration. We propose five criteria that must be met for a river restoration project to be considered ecologically successful. It is critical that the broad restoration community, including funding agencies, practitioners and citizen restoration groups, adopt criteria for defining and assessing ecological success in restoration. Standards are needed because progress in the science and practice of river restoration has been hampered by the lack of agreed upon criteria for judging ecological success. Without well-accepted criteria that are ultimately supported by funding and implementing agencies, there is little incentive for practitioners to assess and report restoration outcomes. Improving methods and weighing the ecological benefits of various restoration approaches require organized national-level reporting systems.
George Washington University1, Seattle Biomed2, University of Washington3, J. Craig Venter Institute4, Karolinska Institutet5, University of California, Los Angeles6, Universidade Federal de Minas Gerais7, Uppsala University8, Centre national de la recherche scientifique9, University of Glasgow10, University of Cambridge11, Federal University of São Paulo12, Children's Hospital Oakland Research Institute13, Johns Hopkins University School of Medicine14, National Research Council15, University of Oxford16, University of London17, University of Massachusetts Amherst18, Oswaldo Cruz Foundation19, University of Buenos Aires20, Central University of Venezuela21, National University of Singapore22, University of Georgia23
TL;DR: Although the Tritryp lack several classes of signaling molecules, their kinomes contain a large and diverse set of protein kinases and phosphatases; their size and diversity imply previously unknown interactions and regulatory processes, which may be targets for intervention.
Abstract: Whole-genome sequencing of the protozoan pathogen Trypanosoma cruzi revealed that the diploid genome contains a predicted 22,570 proteins encoded by genes, of which 12,570 represent allelic pairs. Over 50% of the genome consists of repeated sequences, such as retrotransposons and genes for large families of surface molecules, which include trans-sialidases, mucins, gp63s, and a large novel family (>1300 copies) of mucin-associated surface protein (MASP) genes. Analyses of the T. cruzi, T. brucei, and Leishmania major (Tritryp) genomes imply differences from other eukaryotes in DNA repair and initiation of replication and reflect their unusual mitochondrial DNA. Although the Tritryp lack several classes of signaling molecules, their kinomes contain a large and diverse set of protein kinases and phosphatases; their size and diversity imply previously unknown interactions and regulatory processes, which may be targets for intervention.
Broad Institute1, J. Craig Venter Institute2, Stanford University3, Oregon Health & Science University4, University of Glasgow5, Genetic Information Research Institute6, Institut Universitaire de France7, University of Kentucky8, University of Nebraska–Lincoln9, University of Göttingen10, Pasteur Institute11, University of São Paulo12, Texas A&M University13, Wellcome Trust Sanger Institute14, John Innes Centre15, University of Wisconsin-Madison16, Max Planck Society17, University of Oregon18, University of Nottingham19, Spanish National Research Council20, Ohio State University21, University of Georgia22, Tokyo Institute of Technology23, National Institute of Advanced Industrial Science and Technology24, George Washington University25, University of Manchester26, University of Liverpool27, University of Melbourne28, Karlsruhe Institute of Technology29, University of Idaho30
TL;DR: The aspergilli comprise a diverse group of filamentous fungi spanning over 200 million years of evolution, and a comparative study with Aspergillus fumigatus and As pergillus oryzae, used in the production of sake, miso and soy sauce, provides new insight into eukaryotic genome evolution and gene regulation.
Abstract: The aspergilli comprise a diverse group of filamentous fungi spanning over 200 million years of evolution. Here we report the genome sequence of the model organism Aspergillus nidulans, and a comparative study with Aspergillus fumigatus, a serious human pathogen, and Aspergillus oryzae, used in the production of sake, miso and soy sauce. Our analysis of genome structure provided a quantitative evaluation of forces driving long-term eukaryotic genome evolution. It also led to an experimentally validated model of mating-type locus evolution, suggesting the potential for sexual reproduction in A. fumigatus and A. oryzae. Our analysis of sequence conservation revealed over 5,000 non-coding regions actively conserved across all three species. Within these regions, we identified potential functional elements including a previously uncharacterized TPP riboswitch and motifs suggesting regulation in filamentous fungi by Puf family genes. We further obtained comparative and experimental evidence indicating widespread translational regulation by upstream open reading frames. These results enhance our understanding of these widely studied fungi as well as provide new insight into eukaryotic genome evolution and gene regulation.
TL;DR: It is concluded that an integrated technology like ERP, which potentially represents a "hard" constraint on human agency, can be resisted and reinvented in use.
Abstract: Recent perspectives on organizational change have emphasized human agency, more than technology or structure, to explain empirical outcomes resulting from the use of information technologies in organizations. Yet, newer technologies such as enterprise resource planning (ERP) systems continue to be associated with the agenda of organizational transformation, largely because they are assumed to constrain human action. We report an interpretive case study of an ERP system after its implementation in a large government agency. Despite the transformation agenda accompanying the new system, users initially chose to avoid using it as much as possible (inertia) and later to work around system constraints in unintended ways (reinvention). We explain the change in enactments with the concept of improvised learning, which was motivated by social influence from project leaders, "power users," and peers. Our results are consistent with arguments regarding the enactment of information technology in organizations and with temporal views of human agency. We conclude that an integrated technology like ERP, which potentially represents a "hard" constraint on human agency, can be resisted and reinvented in use.
TL;DR: New strategies with classic as well as new antioxidants should be implemented in the treatment of diabetes, as it is becoming clear that rather than merely scavenging reactive radicals, a more comprehensive approach aimed at preventing the generation of these reactive species may prove more beneficial.
Abstract: Cardiovascular complications, characterized by endothelial dysfunction and accelerated atherosclerosis, are the leading cause of morbidity and mortality associated with diabetes. There is growing evidence that excess generation of highly reactive free radicals, largely due to hyperglycemia, causes oxidative stress, which further exacerbates the development and progression of diabetes and its complications. Overproduction and/or insufficient removal of these free radicals result in vascular dysfunction, damage to cellular proteins, membrane lipids and nucleic acids. Despite overwhelming evidence on the damaging consequences of oxidative stress and its role in experimental diabetes, large scale clinical trials with classic antioxidants failed to demonstrate any benefit for diabetic patients. As our understanding of the mechanisms of free radical generation evolves, it is becoming clear that rather than merely scavenging reactive radicals, a more comprehensive approach aimed at preventing the generation of these reactive species as well as scavenging may prove more beneficial. Therefore, new strategies with classic as well as new antioxidants should be implemented in the treatment of diabetes.
TL;DR: Recent applications of network thinking to the evolution of networks at the gene and protein level and to the dynamics and stability of communities are reviewed.
Abstract: Although pairwise interactions have always had a key role in ecology and evolutionary biology, the recent increase in the amount and availability of biological data has placed a new focus on the complex networks embedded in biological systems. The increased availability of computational tools to store and retrieve biological data has facilitated wide access to these data, not just by biologists but also by specialists from the social sciences, computer science, physics and mathematics. This fusion of interests has led to a burst of research on the properties and consequences of network structure in biological systems. Although traditional measures of network structure and function have started us off on the right foot, an important next step is to create biologically realistic models of network formation, evolution, and function. Here, we review recent applications of network thinking to the evolution of networks at the gene and protein level and to the dynamics and stability of communities. These studies have provided new insights into the organization and function of biological systems by applying existing techniques of network analysis. The current challenge is to recognize the commonalities in evolutionary and ecological applications of network thinking to create a predictive science of biological networks.
TL;DR: Representatives of the Roseobacter clade stand out as representing one of the most readily cultivated of the major marine lineages, and are serving as the foundation for an improved understanding of marine bacterial ecology and physiology.
Abstract: Despite the overwhelming bacterial diversity present in the world's oceans, the majority of recognized marine bacteria fall into as few as nine major clades ([36][1]), many of which have yet to be cultivated in the laboratory Molecular-based approaches targeting 16S rRNA genes demonstrate that the
TL;DR: A key target of the LIF self-renewal pathway is identified by showing that STAT3 directly regulates the expression of the Myc transcription factor, which is crucial for regulation of Myc activity in ES cells and therefore in promoting self-Renewal.
Abstract: Murine ES cells can be maintained as a pluripotent, self-renewing population by LIF/STAT3-dependent signaling. The downstream effectors of this pathway have not been previously defined. In this report, we identify a key target of the LIF self-renewal pathway by showing that STAT3 directly regulates the expression of the Myc transcription factor. Murine ES cells express elevated levels of Myc and following LIF withdrawal, Myc mRNA levels collapse and Myc protein becomes phosphorylated on threonine 58 (T58), triggering its GSK3beta dependent degradation. Maintained expression of stable Myc (T58A) renders self-renewal and maintenance of pluripotency independent of LIF. By contrast, expression of a dominant negative form of Myc antagonizes self-renewal and promotes differentiation. Transcriptional control by STAT3 and suppression of T58 phosphorylation are crucial for regulation of Myc activity in ES cells and therefore in promoting self-renewal. Together, our results establish a mechanism for how LIF and STAT3 regulate ES cell self-renewal and pluripotency.
Posted Content•
TL;DR: In this paper, the authors develop a corporate governance framework, provide a broad overview of recent corporate governance research, and place each of the Special Issue papers within the context of this framework.
Abstract: I develop a corporate governance framework, provide a broad overview of recent corporate governance research, and place each of the Special Issue papers within the context of this framework The papers in the issue contribute to our understanding of a wide range of governance topics including: the role of antitakeover measures, board structure, capital market governance, compensation and incentives, debt and agency costs, director and officer labor markets, fraud, lawsuits, ownership structure, and regulation In short, the papers span almost every aspect of governance systems
TL;DR: This work reports how the vibrational spectrum of protonated water clusters evolves in the size range from 2 to 11 water molecules, revealing the pronounced spectral impact of subtle changes in the hydration environment.
Abstract: The ease with which the pH of water is measured obscures the fact that there is presently no clear molecular description for the hydrated proton. The mid-infrared spectrum of bulk aqueous acid, for example, is too diffuse to establish the roles of the putative Eigen (H 3 O + ) and Zundel (H 5 O 2 + ) ion cores. To expose the local environment of the excess charge, we report how the vibrational spectrum of protonated water clusters evolves in the size range from 2 to 11 water molecules. Signature bands indicating embedded Eigen or Zundel limiting forms are observed in all of the spectra with the exception of the three- and five-membered clusters. These unique species display bands appearing at intermediate energies, reflecting asymmetric solvation of the core ion. Taken together, the data reveal the pronounced spectral impact of subtle changes in the hydration environment.
TL;DR: A multispecies viral analysis would provide needed information for controlling pollution by source, determining human health risks based on assessments of human virus loading and exposure, and determining potential risks to production animal health and could indicate the potential for the presence of other zoonotic pathogens.
Abstract: Waterborne enteric viruses threaten both human and animal health. These pathogens are host specific and cause a wide range of diseases and symptoms in humans or other animals. While considerable research has documented the risk of enteric viruses to human health from contact with contaminated water, the current bacterial indicator-based methods for evaluation of water quality are often ineffectual proxies for pathogenic viruses. Additionally, relatively little work has specifically investigated the risk of waterborne viruses to animal health, and this risk currently is not addressed by routine water quality assessments. Nonetheless, because of their host specificity, enteric viruses can fulfill a unique role both for assessing health risks and as measures of contamination source in a watershed, yet the use of animal, as well as human, host-specific viruses in determining sources of fecal pollution has received little attention. With improved molecular detection assays, viruses from key host groups can be targeted directly using PCR amplification or hybridization with a high level of sensitivity and specificity. A multispecies viral analysis would provide needed information for controlling pollution by source, determining human health risks based on assessments of human virus loading and exposure, and determining potential risks to production animal health and could indicate the potential for the presence of other zoonotic pathogens. While there is a need to better understand the prevalence and environmental distribution of nonhuman enteric viruses, the development of improved methods for specific and sensitive detection will facilitate the use of these microbes for library-independent source tracking and water quality assessment tools.
TL;DR: The results indicate that the coordinated release of 2-AG and anandamide in the periaqueductal grey matter might mediate opioid-independent stress-induced analgesia, and identify monoacylglycerol lipase as a previously unrecognized therapeutic target.
Abstract: Acute stress suppresses pain by activating brain pathways that engage opioid or non-opioid mechanisms. Here we show that an opioid-independent form of this phenomenon, termed stress-induced analgesia, is mediated by the release of endogenous marijuana-like (cannabinoid) compounds in the brain. Blockade of cannabinoid CB(1) receptors in the periaqueductal grey matter of the midbrain prevents non-opioid stress-induced analgesia. In this region, stress elicits the rapid formation of two endogenous cannabinoids, the lipids 2-arachidonoylglycerol (2-AG) and anandamide. A newly developed inhibitor of the 2-AG-deactivating enzyme, monoacylglycerol lipase, selectively increases 2-AG concentrations and, when injected into the periaqueductal grey matter, enhances stress-induced analgesia in a CB1-dependent manner. Inhibitors of the anandamide-deactivating enzyme fatty-acid amide hydrolase, which selectively elevate anandamide concentrations, exert similar effects. Our results indicate that the coordinated release of 2-AG and anandamide in the periaqueductal grey matter might mediate opioid-independent stress-induced analgesia. These studies also identify monoacylglycerol lipase as a previously unrecognized therapeutic target.
TL;DR: In this article, the authors examined functional characteristics of 6 tributaries of the Chattahoochee River near Atlanta, Georgia, USA, whose catchments differed in degree of urbanization.
Abstract: Ecologists have described an urban stream syndrome with attributes such as elevated nutrients and contaminants, increased hydrologic flashiness, and altered biotic assemblages. Ecosystem function probably also varies with extent of urbanization, although there are few stream networks in which this prediction has been studied. We examined functional characteristics of 6 tributaries of the Chattahoochee River near Atlanta, Georgia, USA, whose catchments differed in degree of urbanization. We conducted short-term NH4- and PO4-addition experiments to measure nutrient uptake velocity, which is the rate at which a nutrient moves through the water column toward the benthos. Both NH4 and soluble reactive P uptake velocities decreased as indicators of urbanization (i.e., % of catchment covered by high-intensity urban development) increased. The amount of fine benthic organic matter (FBOM) also decreased with increasing urbanization, and uptake velocities were directly related to FBOM. Uptake velocities wer...
TL;DR: This model focuses at the subunit level of the organization and includes intermediate benefits through which ERP's overall subunit impact occurs (in this case at the plant level).
Abstract: We present a model of the organizational impacts of enterprise resource planning (ERP) systems once the system has gone live and the "shake-out" phase has occurred. Organizational information processing theory states that performance is influenced by the level of fit between information processing mechanisms and organizational context. Two important elements of this context are interdependence and differentiation among subunits of the organization. Because ERP systems include data and process integration, the theory suggests that ERP will be a relatively better fit when interdependence is high and differentiation is low. Our model focuses at the subunit level of the organization (business function or location, such as a manufacturing plant) and includes intermediate benefits through which ERP's overall subunit impact occurs (in our case at the plant level). ERP customization and the amount of time since ERP implementation are also included in the model. The resulting causal model is tested using a questionnaire survey of 111 manufacturing plants. The data support the key assertions in the model.
TL;DR: In this paper, the authors used grounded theory to build a framework to address two questions: (a) which UTTO's structures and licensing strategies are most conducive to new venture formation; and (b) how are the various UTTOs' structures and license strategies correlated with each other.
TL;DR: Differences in the activity of mechanisms for retrotransposon regulation or deletion generation between species could explain current genome size variation without any requirement for natural selection to act on this trait, although the results do not preclude selection as a contributing factor.
TL;DR: Analytical methods are used to show that ignoring the latent period or making the common assumption of exponentially distributed latent and infectious periods always results in underestimating the basic reproductive ratio of an infection from outbreak data.
Abstract: Background Mathematical models have become invaluable management tools for epidemiologists, both shedding light on the mechanisms underlying observed dynamics as well as making quantitative predictions on the effectiveness of different control measures. Here, we explain how substantial biases are introduced by two important, yet largely ignored, assumptions at the core of the vast majority of such models.
Methods and Findings First, we use analytical methods to show that (i) ignoring the latent period or (ii) making the common assumption of exponentially distributed latent and infectious periods (when including the latent period) always results in underestimating the basic reproductive ratio of an infection from outbreak data. We then proceed to illustrate these points by fitting epidemic models to data from an influenza outbreak. Finally, we document how such unrealistic a priori assumptions concerning model structure give rise to systematically overoptimistic predictions on the outcome of potential management options.
Conclusion This work aims to highlight that, when developing models for public health use, we need to pay careful attention to the intrinsic assumptions embedded within classical frameworks.
TL;DR: Evidence is examined to support both theories of interhemispheric communication and the possibility remains that the corpus callosum can serve both an inhibitory and excitatory influence on the contralateral hemisphere.
Abstract: The corpus callosum is the major neural pathway that connects homologous cortical areas of the two cerebral hemispheres. The nature of how that interhemispheric connection is manifested is the topic of this review; specifically, does the corpus callosum serve to communicate an inhibitory or excitatory influence on the contralateral hemisphere? Several studies take the position that the corpus callosum provides the pathway through which a hemisphere or cortical area can inhibit the other hemisphere or homologous cortical area in order to facilitate optimal functional capacity. Other studies suggest that the corpus callosum integrates information across cerebral hemispheres and thus serves an excitatory function in interhemispheric communication. This review examines these two contrasting theories of interhemispheric communication. Studies of callosotomies, callosal agenesis, language disorders, theories of lateralization and hemispheric asymmetry, and comparative research are critically considered. The available research, no matter how limited, primarily supports the notion that the corpus callosum serves a predominantly excitatory function. There is evidence, however, to support both theories and the possibility remains that the corpus callosum can serve both an inhibitory and excitatory influence on the contralateral hemisphere.
TL;DR: A pattern of repeat-mediated chromosomal rearrangement, and high coadaptation of both male genes and cis-regulatory sequences emerges as important themes of genome divergence between these species of Drosophila.
Abstract: We have sequenced the genome of a second Drosophila species, Drosophila pseudoobscura, and compared this to the genome sequence of Drosophila melanogaster, a primary model organism. Throughout evolution the vast majority of Drosophila genes have remained on the same chromosome arm, but within each arm gene order has been extensively reshuffled, leading to a minimum of 921 syntenic blocks shared between the species. A repetitive sequence is found in the A pseudoobscura genome at many junctions between adjacent syntenic blocks. Analysis of this novel repetitive element family suggests that recombination between offset elements may have given rise to many paracentric inversions, thereby contributing to the shuffling of gene order in the D. pseudoobscura lineage. Based on sequence similarity and synteny, 10,516 putative orthologs have been identified as a core gene set conserved over 25-55 million years (Myr) since the pseudoobscura/melanogaster divergence. Genes expressed in the testes had higher amino acid sequence divergence than the genome-wide average, consistent with the rapid evolution of sex-specific proteins. Cis-regulatory sequences are more conserved than random and nearby sequences between the species-but the difference is slight, suggesting that the evolution of cis-regulatory elements is flexible. Overall, a pattern of repeat-mediated chromosomal rearrangement, and high coadaptation of both male genes and cis-regulatory sequences emerges as important themes of genome divergence between these species of Drosophila.