bluuebunny/crossref_metadata_2025 huggingface dataset:
Priority Research and Management Issues for the Imperiled Great Basin of the Western United States
Authors: Chambers Jeanne C. , Wisdom Michael J.
Published: September 2009

Like many arid and semiarid regions, the Great Basin of the western United States is undergoing major ecological, social, and economic changes that are having widespread detrimental effects on the structure, composition, and function of native ecosystems. The causes of change are highly interactive and include urban, suburban, and exurban growth, past and present land uses, climate change, altered fire regimes, and rapid expansion of invasive species. Cumulative effects include vegetation type conversions, loss of watershed functioning, loss of native species, and diminished economic potential. The diversity and magnitude of issues require consensus on priority issues, and new and innovative research and management approaches that address larger spatial scales and longer time scales than in the past. Primary research coupled with large‐scale assessments and effective monitoring strategies is needed to understand and track the ongoing changes. Prediction and modeling of alternative futures are needed for incorporation into the planning process and use as a basis for adaptive management, and management tools are needed to aid decision‐making and implementation. Historically, research and management in arid and semiarid regions such as the Great Basin have been severely under‐funded and altering current trajectories will require financial resources, political support, and effective policies and institutional mechanisms. Sustaining the ecosystems, resources, and human populations of these regions will require strong collaborative partnerships among research and management organizations to reduce overlap, leverage funds, and increase efficiency. Close involvement of all stakeholders is needed to obtain the needed support for making necessary changes in policies and management activities.
A Landscape Approach for Ecologically Based Management of Great Basin Shrublands
Authors: Wisdom Michael J. , Chambers Jeanne C.
Published: September 2009

Native shrublands dominate the Great Basin of western of North America, and most of these communities are at moderate or high risk of loss from non‐native grass invasion and woodland expansion. Landscape‐scale management based on differences in ecological resistance and resilience of shrublands can reduce these risks. We demonstrate this approach with an example that focuses on maintenance of sagebrush (Artemisia spp.) habitats for Greater Sage‐grouse (Centrocercus urophasianus), a bird species threatened by habitat loss. The approach involves five steps: (1) identify the undesired disturbance processes affecting each shrubland community type; (2) characterize the resistance and resilience of each shrubland type in relation to the undesired processes; (3) assess potential losses of shrublands based on their resistance, resilience, and associated risk; (4) use knowledge from these steps to design a landscape strategy to mitigate the risk of shrubland loss; and (5) implement the strategy with a comprehensive set of active and passive management prescriptions. Results indicate that large areas of the Great Basin currently provide Sage‐grouse habitats, but many areas of sagebrush with low resistance and resilience may be lost to continued woodland expansion or invasion by non‐native annual grasses. Preventing these losses will require landscape strategies that prioritize management areas based on efficient use of limited resources to maintain the largest shrubland areas over time. Landscape‐scale approaches, based on concepts of resistance and resilience, provide an essential framework for successful management of arid and semiarid shrublands and their native species.
Introduction to the Special Section on Alternative Futures for Great Basin Ecosystems
Authors: Fleishman Erica , Chambers Jeanne C. , Wisdom Michael J.
Published: September 2009

Natural and anthropogenic processes are causing extensive and rapid ecological, social, and economic changes in arid and semiarid ecosystems worldwide. Nowhere are these changes more evident than in the Great Basin of the western United States, a region of 400,000 km2 that largely is managed by federal agencies. Major drivers of ecosystems and human demographics of the Great Basin include human population growth, grazing by domestic livestock, extraction of minerals, development and production of energy, changes in fire and other disturbance regimes, and invasion of non‐native annual plants. Exploration of alternative futures may increase the ability of management and policy to maximize the system's resistance and resilience to changes in climate, disturbance regimes, and anthropogenic perturbations. This special section examines the issues facing the Great Basin and then provides examples of approaches to predicting changes in land cover and avifaunal distributions under different management scenarios. Future sustainability of the Great Basin's natural and human systems requires strong, collaborative partnerships among research and management organizations that are capable of obtaining public support and financial resources and developing effective policies and institutional mechanisms.
Evidence for an Interaction Between Age at First Drink and Genetic Influences on DSM‐IV Alcohol Dependence Symptoms
Authors: Agrawal Arpana , Sartor Carolyn E. , Lynskey Michael T. , Grant Julia D. , Pergadia Michele L. , Grucza Richard , Bucholz Kathleen K. , Nelson Elliot C. , Madden Pamela A. F. , Martin Nicholas G. , Heath Andrew C.
Published: September 2009

Background:  Research suggests that individuals who start drinking at an early age are more likely to subsequently develop alcohol dependence. Twin studies have demonstrated that the liability to age at first drink and to alcohol dependence are influenced by common genetic and environmental factors, however, age at first drink may also environmentally mediate increased risk for alcohol dependence. In this study, we examine whether age at first drink moderates genetic and environmental influences, via gene × environment interactions, on DSM‐IV alcohol dependence symptoms.

Methods:  Using data on 6,257 adult monozygotic and dizygotic male and female twins from Australia, we examined the extent to which age at first drink (i) increased mean alcohol dependence symptoms and (ii) whether the magnitude of additive genetic, shared, and nonshared environmental influences on alcohol dependence symptoms varied as a function of decreasing age. Twin models were fitted in Mx.

Results:  Risk for alcohol dependence symptoms increased with decreasing age at first drink. Heritable influences on alcohol dependence symptoms were considerably larger in those who reported an age at first drink prior to 13 years of age. In those with later onset of alcohol use, variance in alcohol dependence was largely attributable to nonshared environmental variance (and measurement error). This evidence for unmeasured gene × measured environment interaction persisted even when controlling for the genetic influences that overlapped between age at first drink and alcohol dependence symptoms.

Conclusions:  Early age at first drink may facilitate the expression of genes associated with vulnerability to alcohol dependence symptoms. This is important to consider, not only from a public health standpoint, but also in future genomic studies of alcohol dependence.
Suicide and Alcohol: Do Outlets Play a Role?
Authors: Johnson Fred W. , Gruenewald Paul J. , Remer Lillian G.
Published: September 2009

Background:  The purpose of this study was to determine whether the number of alcohol outlets in local and adjacent areas, in particular bars, was related over time to completed suicide and suicide attempts. There is evidence both from studies of individuals and time series aggregate studies, mostly at the national level, of substantial alcohol involvement in suicide, but no small‐area, longitudinal studies have been carried out. The present study is the first that is both longitudinal and based on a large number of small spatial units, California zip codes, a level of resolution permitting analysis of the relationship between local alcohol access and suicide rates over time.

Method:  Longitudinal data were obtained from 581 consistently defined zip code areas over 6 years (1995–2000) using data from the California Index Locations Database, a geographic information system that contains both population and place information with spatial attributes for the entire state. Measures obtained from each zip code included population characteristics (e.g., median age) and place characteristics (e.g., numbers of retail and alcohol outlets) which were related in separate analyses to (i) suicide mortality and (ii) the number of hospitalizations for injuries caused by suicide attempts. The effect of place characteristics in zip code areas adjacent to each of the 581 local zip codes (spatial lags) was also assessed. Analysis methods were random effects models corrected for spatial autocorrelation.

Results:  Completed suicide rates were higher in zip code areas with greater local and lagged bar densities; and higher in areas with greater local but not lagged off‐premise outlet densities. Whereas completed suicide rates were lower among blacks and Hispanics, completed suicide rates were higher among low income, older whites living in less densely populated areas, that is, rural areas. Rates of suicide attempts were higher in zip code areas with greater local but not lagged bar densities, and higher among low income younger whites living in smaller households and in rural areas. Rates of attempted suicide were also higher among blacks. Completed suicide and suicide attempt rates were lower in zip code areas with greater local restaurant densities; there were no lagged effects for restaurants.

Conclusions:  Bar densities in particular appear related to suicide, meaning, because this is an aggregate‐level spatial analysis, that suicides, both attempted and completed, occur at greater rates in rural community areas with greater bar densities. Because the suicide rate is highest in rural areas, this study suggests that although the number of completed and attempted suicides is no doubt greater in absolute numbers in urban areas, the suicide rate, both completed and attempted, is greater in rural areas, which draws attention, perhaps much needed, to the problems of rural America.
Ethanol Is Self‐Administered Into the Nucleus Accumbens Shell, But Not the Core: Evidence of Genetic Sensitivity
Authors: Engleman Eric A. , Ding Zheng‐Ming , Oster Scott M. , Toalston Jamie E. , Bell Richard L. , Murphy James M. , McBride William J. , Rodd Zachary A.
Published: September 2009

Background: A previous study indicated that selectively bred alcohol‐preferring (P) rats self‐administered ethanol (EtOH) directly into the posterior ventral tegmental area at lower concentrations than Wistar rats. The present study was undertaken to determine involvement of the nucleus accumbens (Acb) with EtOH reinforcement, and a relationship between genetic selection for high alcohol preference and sensitivity of the Acb to the reinforcing effects of EtOH.

Methods: Adult P and Wistar rats were assigned to groups that self‐infused 0 to 300 mg% EtOH into the Acb shell (AcbSh) or Acb Core (AcbC). Rats were placed into 2‐lever (active and inactive) operant chambers and given EtOH for the first 4 sessions (acquisition), artificial cerebrospinal fluid (aCSF) for sessions 5 and 6 (extinction), and EtOH again in session 7 (reinstatement). Responding on the active lever produced a 100‐nl injection of the infusate.

Results: Alcohol‐preferring rats self‐infused 75 to 300 mg% EtOH, whereas Wistar rats reliably self‐infused 100 and 300 mg% EtOH into the AcbSh. Both P and Wistar rats reduced responding on the active lever when aCSF was substituted for EtOH, and reinstated responding in session 7 when EtOH was restored. EtOH was not self‐infused into the AcbC by P or Wistar rats.

Conclusions: The present results indicate that the AcbSh, but not AcbC, is a neuroanatomical structure that mediates the reinforcing actions of EtOH. The data also suggest that, compared to Wistar rats, the AcbSh of P rats is more sensitive to the reinforcing effects of EtOH.
Polymorphisms of the IL‐1 Gene Complex Are Associated With Alcohol Dependence in Spanish Caucasians: Data From an Association Study
Authors: Saiz Pilar A. , Garcia‐Portilla Maria P. , Florez Gerardo , Corcoran Paul , Arango Celso , Morales Blanca , Leza Juan C. , Alvarez Sandra , Díaz Eva M. , Alvarez Victoria , Coto Eliecer , Nogueiras Luis , Bobes Julio
Published: September 2009

Background:  There is growing evidence for involvement of pro‐inflammatory cytokines in alcohol dependence. The aim of this study was to investigate whether 4 functionally relevant polymorphisms of the interleukin‐1 (IL‐1) and tumor necrosis factor‐alpha genes were associated with alcohol dependence and with measures of clinical severity and treatment outcome.

Methods:  Two hundred alcohol‐dependent (AD) patients and 420 healthy controls from the same Spanish Caucasian population were genotyped using standard methods. Baseline and 6‐month assessments included alcohol intake, addiction severity, and biomarkers of alcohol intake.

Results:  Alcohol‐dependent patients showed an excess of IL‐1α−889 C/T [50.8% vs. 39.3%, χ2 (df) = 7.30 (2), uncorrected p = 0.026, corrected p = 0.104] and IL‐1RA (86 bp)n A1/A1 genotypes [64.8% vs. 50.8%, χ2 (df) = 12.65 (3), corrected p = 0.020]. The A1/A1 excess was associated with alcohol dependence only in men [69.9% vs. 49.5%, χ2 (df) = 15.72 (2), corrected p < 0.001]. Six‐month clinical and hematological outcome measures did not vary by genotype of the 4 polymorphisms. Haplotype analysis revealed an excess of the IL‐1α−889 C/IL‐1β +3953 C/IL‐1RA A2 haplotype in the control group compared with AD patients [20.0% vs. 14.1%, χ2 (df) = 7.25 (1), p = 0.007; odds ratio (OR) = 0.64, 95% confidence interval (CI) = 0.46–0.89] and in the abstainers after 6 months of treatment compared with nonabstinent patients [14.7% vs. 6.2%, χ2 (df) = 5.65 (1), p = 0.017; OR = 2.56, 95% CI = 1.15–5.62].

Conclusions:  Our findings provide further tentative evidence of the role of IL‐1 in alcohol dependence as well as evidence that the nature of the associations may be direct, gender‐specific, or involve haplotype effects. However, findings from single association studies constitute tentative knowledge and must be interpreted carefully and precise replication is required.
The Retention of Cast Metal Dowels Fabricated by Direct and Indirect Techniques
Authors: Al‐Omari Wael M. , Zagibeh Ayman M.
Published: September 2009

Purpose: To explore the effect of fabrication technique, cement type, and cementation procedure on retention of cast metal dowels.

Methods and Materials: Eighty intact single‐rooted teeth were selected. The clinical crown was removed at the cementoenamel junction level. Each root was prepared to receive a cast metal dowel of 10‐mm length and 1.45 mm in diameter. The 80 specimens were divided into two major groups of 40 based on fabrication technique (direct and indirect). Each group was further divided into four subgroups of ten based on the cement type (zinc phosphate and glass ionomer), and cementation procedure (with and without lentulo spiral). The dowels were subjected to a constantly increasing tensile force, in a universal Instron testing machine, at crosshead speed of 5 mm/min until failure.

Results: The most significant factor to affect retention was the cementation procedure, as cementation with lentulo spiral produced greater retention than cementation without the use of lentulo spiral (p < 0.05); however, there seems to be a close interaction between fabrication technique, cement type, and cementation procedure (p= 0.051). The least retentive group was the one fabricated by direct technique, cemented with zinc phosphate without the use of lentulo spiral.

Conclusion: Fabrication technique does not affect retention of cast dowels, except when zinc phosphate was the luting agent and placed in the canal space without using a lentulo spiral. The cementation procedure had a significant effect on retention; thus, it is recommended that cementation should be done using the lentulo spiral.
Segmentation and Estimation for SNP Microarrays: A Bayesian Multiple Change‐Point Approach
Authors: Tai Yu Chuan , Kvale Mark N. , Witte John S.
Published: September 2009

Summary High‐density single‐nucleotide polymorphism (SNP) microarrays provide a useful tool for the detection of copy number variants (CNVs). The analysis of such large amounts of data is complicated, especially with regard to determining where copy numbers change and their corresponding values. In this article, we propose a Bayesian multiple change‐point model (BMCP) for segmentation and estimation of SNP microarray data. Segmentation concerns separating a chromosome into regions of equal copy number differences between the sample of interest and some reference, and involves the detection of locations of copy number difference changes. Estimation concerns determining true copy number for each segment. Our approach not only gives posterior estimates for the parameters of interest, namely locations for copy number difference changes and true copy number estimates, but also useful confidence measures. In addition, our algorithm can segment multiple samples simultaneously, and infer both common and rare CNVs across individuals. Finally, for studies of CNVs in tumors, we incorporate an adjustment factor for signal attenuation due to tumor heterogeneity or normal contamination that can improve copy number estimates.
Modeling Complex Phenotypes: Generalized Linear Models Using Spectrogram Predictors of Animal Communication Signals
Authors: Holan Scott H. , Wikle Christopher K. , Sullivan‐Beckers Laura E. , Cocroft Reginald B.
Published: September 2009

Summary A major goal of evolutionary biology is to understand the dynamics of natural selection within populations. The strength and direction of selection can be described by regressing relative fitness measurements on organismal traits of ecological significance. However, many important evolutionary characteristics of organisms are complex, and have correspondingly complex relationships to fitness. Secondary sexual characteristics such as mating displays are prime examples of complex traits with important consequences for reproductive success. Typically, researchers atomize sexual traits such as mating signals into a set of measurements including pitch and duration, in order to include them in a statistical analysis. However, these researcher‐defined measurements are unlikely to capture all of the relevant phenotypic variation, especially when the sources of selection are incompletely known. In order to accommodate this complexity we propose a Bayesian dimension‐reduced spectrogram generalized linear model that directly incorporates representations of the entire phenotype (one‐dimensional acoustic signal) into the model as a predictor while accounting for multiple sources of uncertainty. The first stage of dimension reduction is achieved by treating the spectrogram as an “image” and finding its corresponding empirical orthogonal functions. Subsequently, further dimension reduction is accomplished through model selection using stochastic search variable selection. Thus, the model we develop characterizes key aspects of the acoustic signal that influence sexual selection while alleviating the need to extract higher‐level signal traits a priori. This facet of our approach is fundamental and has the potential to provide additional biological insight, as is illustrated in our analysis.
On Efficiency of Constrained Longitudinal Data Analysis Versus Longitudinal Analysis of Covariance
Authors: Lu Kaifeng
Published: September 2009

Summary:  In randomized clinical trials, measurements are often collected on each subject at a baseline visit and several post‐randomization time points. The longitudinal analysis of covariance in which the postbaseline values form the response vector and the baseline value is treated as a covariate can be used to evaluate the treatment differences at the postbaseline time points. Liang and Zeger (2000, Sankhyā: The Indian Journal of Statistics, Series B 62, 134–148) propose a constrained longitudinal data analysis in which the baseline value is included in the response vector together with the postbaseline values and a constraint of a common baseline mean across treatment groups is imposed on the model as a result of randomization. If the baseline value is subject to missingness, the constrained longitudinal data analysis is shown to be more efficient for estimating the treatment differences at postbaseline time points than the longitudinal analysis of covariance. The efficiency gain increases with the number of subjects missing baseline and the number of subjects missing all postbaseline values, and, for the pre–post design, decreases with the absolute correlation between baseline and postbaseline values.
Cutaneous myoepithelioma with a plexiform pattern of growth: a case report
Authors: Franklin Gillian , Chen Sheng , Sznyter Laura A. , Morgenstern Nora
Published: September 2009

Cutaneous myoepithelioma, a recently recognized, rare but well‐characterized entity, is comprised solely of myoepithelial cells. In this report, we describe a cutaneous myoepithelioma with a plexiform pattern of growth in the scapular region of a 58‐year‐old woman.
Movements of Murray cod (Maccullochella peelii peelii) in a large Australian lowland river
Authors: Koehn J. D. , McKenzie J. A. , O’Mahony D. J. , Nicol S. J. , O’Connor J. P. , O’Connor W. G.
Published: September 2009

Abstract – This study of Murray cod (Maccullochella peelii peelii) movements in a large lowland river in south‐eastern Australia indicated that the species was not sedentary, but undertook complex movements that followed a seasonal pattern. While there were sedentary periods with limited home ranges and high site fidelity, Murray cod also under took larger movements for considerable portions of the year coinciding with its spawning schedule. This generally comprised movements (up to 130 km) from a home location in late winter and early spring to a new upstream position, followed by a rapid downstream migration typically back to the same river reach. Timing of movements was not synchronous amongst individuals and variation in the scale of movements was observed between individuals, fish size, original location and years.
Immune reconstitution inflammatory syndrome after highly active antiretroviral therapy: a review
Authors: Tsang CSP , Samaranayake LP
Published: September 2009

Oral Diseases (2010) 16, 248–256

The use of highly active antiretroviral therapy (HAART) in the management of human immunodeficiency virus (HIV) restores immune responses against pathogens and has greatly decreased mortality. However, in about 25% to 35% of patients receiving HAART, the reconstituted immune system leads to a pathological inflammatory response, commonly known as immune reconstitution inflammatory syndrome (IRIS), which causes substantial short‐term morbidity or even mortality. Although we have gleaned some knowledge on IRIS in the past few years, a number of unanswered questions remain. In this review, we discuss the definition, diagnostic criteria, pathogenesis, risk factors, clinical spectrum including oral manifestations, and management of IRIS.
Morphometric analysis of the cranial cavity and caudal cranial fossa in the dog: a computerized tomographic study
Authors: García‐Real Isabel , Kass Philip H. , Sturges Beverly K. , Wisner Erik R.
Published: September 2009

This investigation was initiated to develop a reliable and simple computerized tomography (CT) method for evaluating the morphometry of the cranial cavity (CC) and caudal cranial fossa in the dog. We obtained linear, area, and volume measurements of the entire CC and the caudal fossa compartment in 24 dogs, using transverse and reformatted sagittal and dorsal CT images. The ratios between the CC and the caudal fossa volumes were calculated, as were the ratios between the CC and caudal fossa midsagittal (MS) areas. There were statistically significant correlations between absolute volume data and certain linear measurements, a positive correlation between volume ratio and weight, and significant differences in absolute volume values and volume ratio between males and females. The volume ratio, MS area, and certain linear measurements included in this study can be considered as accurate parameters to evaluate the relative size of the CC to caudal fossa in the dog. Such quantitative measures may be useful in systematically characterizing Chiari‐type malformations and other developmental anomalies in the dog.
Romantic Federalism: Atlantic Republican Literature between Cosmopolitanism and Confederation
Authors: Von Morzé Leonard
Published: September 2009

The age of democratic revolution in the Atlantic world (1776–1815) was marked by writing whose politics have been described as both patriotic and universalist. Far from reflecting a simple contradiction in revolutionary republicanism, these two strains reflect the simultaneous development of federalist and cosmopolitan discourses in the late Enlightenment and early Romanticism. This essay argues that we need a paradoxical conception of ‘Romantic federalism’ to account for transatlantic republican discourse in this period. Romantic federalism, in this essay’s account, facilitated both an ethnological interest in human diversity and a universalist understanding of popular sovereignty. The essay first takes as its case studies an anonymous visionary pamphlet, entitledThe Golden Age; Constantin‐François Volney’s best‐known work,The Ruins; and the literary legacy of Anacharsis Cloots, the ‘Orator of the Human Race’. The essay concludes with a review of recent literary studies of both federalism and nationalism, and suggests ways that overemphasis on the nation form has led to neglect not only of republicanism but also of imperialism.
Literary Criticism’s Road Scholars at the American Century’s Turn
Authors: Larson Lars Erik
Published: September 2009

Literary scholarship’s spatial turn has produced a number of studies exploring the site of the road and its automobile culture. This article surveys seven monographs published between 1996 and 2007 that analyze works of American fiction and nonfiction for their representation of highway narratives. These works (by Ronald Primeau, Roger Casey, Kris Lackey, Rowland Sherrill, Deborah Paes de Barros, Katie Mills, and Deborah Clarke) explore the genre’s rendering of mobility, identity, and politics on the 20th‐century’s roads of America. The essay compares these analyses for their critical methods and offers a sense of what work remains in the ongoing study of road narratives.
Donor and acceptor substrate selectivity among plant glycoside hydrolase family 32 enzymes
Authors: Van den Ende Wim , Lammens Willem , Van Laere André , Schroeven Lindsey , Le Roy Katrien
Published: September 2009

Plant family 32 glycoside hydrolase enzymes include hydrolases (cell wall invertases, fructan exohydrolases, vacuolar invertases) and fructosyltransferases. These enzymes are very similar at the molecular and structural levels but are functionally different. Understanding the basis of the functional diversity in this family is a challenging task. By combining structural and site‐directed mutagenesis data, Asp239 in AtcwINV1 was identified as an amino acid critical for binding and stabilizing sucrose. Plant fructan exohydrolases lack such an Asp239 equivalent. Substitution of Asp239 led to the loss of invertase activity, while its introduction in fructan exohydrolases increased invertase activity. Some fructan exohydrolases are inhibited by sucrose. The difference between the inhibitor (fructan exohydrolase) and the substrate (invertase) binding configurations of sucrose can be explained by the different orientation of Trp82. Furthermore, the evolutionary hydrolase/transferase transition could be mimicked and the difference between S‐type fructosyltransferases (sucrose as donor) and F‐type fructosyltransferases (fructan as donor) could be unravelled.
Drainage ditch–aquifer interaction with special reference to surface water salinity in the Thurne catchment, Norfolk, UK
Authors: Simpson Trevor , Holman Ian P. , Rushton Ken
Published: September 2009

Open drainage ditches located in low permeability material can interact with an underlying aquifer, especially if the drains almost or totally penetrate through to the aquifer. This interaction can be represented by drain coefficients incorporated in regional groundwater models. The drain coefficients depend on both the vertical distance from the base of the drain to the aquifer and the hydraulic conductivities of the low permeability deposits and the underlying aquifer. In a case study of drained marshes in the Thurne catchment in Norfolk, UK, drains with a water level below ordnance datum (OD) draw in saline water from the coast and freshwater from recharge areas. Pathlines, derived from a regional groundwater model analysis, explain the salinities measured in drains. In addition a series of vertical section numerical model solutions are used to develop general guidance on the selection of drain coefficients.
Instream Flow Science For Sustainable River Management1
Authors: Petts Geoffrey E
Published: September 2009

Abstract:  Concerns for water resources have inspired research developments to determine the ecological effects of water withdrawals from rivers and flow regulation below dams, and to advance tools for determining the flows required to sustain healthy riverine ecosystems. This paper reviews the advances of this environmental flows science over the past 30 years since the introduction of the Instream Flow Incremental Methodology. Its central component, Physical HABitat SIMulation, has had a global impact, internationalizing the e‐flows agenda and promoting new science. A global imperative to set e‐flows, including an emerging trend to set standards at the regional scale, has led to developments of hydrological and hydraulic approaches but expert judgment remains a critical element of the complex decision‐making process around water allocations. It is widely accepted that river ecosystems are dependent upon the natural variability of flow (the flow regime) that is typical of each hydro‐climatic region and upon the range of habitats found within each channel type within each region. But as the sophistication of physical (hydrological and hydraulic) models has advanced emerging biological evidence to support those assumptions has been limited. Empirical studies have been important to validate instream flow recommendations but they have not generated transferable relationships because of the complex nature of biological responses to hydrological change that must be evaluated over decadal time‐scales. New models are needed to incorporate our evolving knowledge of climate cycles and morphological sequences of channel development but most importantly we need long‐term research involving both physical scientists and biologists to develop new models of population dynamics that will advance the biological basis for 21st Century e‐flow science.
Return to the River: Environmental Flow Policy in the United States and Canada1
Authors: MacDonnell Lawrence J.
Published: September 2009

Abstract:  This paper provides an overview and summary of United States and Canadian federal, state, and provincial laws that offer some form of legal protection for environmental flows. Special attention is given to the new “second generation” law established in Texas and to ways western states are beginning to encourage transactions that help restore dewatered streams. Progress in the eastern states and some Canadian provinces to provide environmental flow protection is addressed. Based on this review, this paper presents recommended elements of a “model” environmental flow policy.
Estimating Gear Tooth Surface Geometry by Means of the Vibration Measurement: Distinction of the Vibration Characteristics of Gears With Tooth Surface Form Error
Authors: Ratanasumawong Chanat , Matsumura Shigeki , Tatsuno Tetsuo , Houjoh Haruo
Published: September 2009

Tooth surface measurement is an important way to verify the quality of produced gears. To reduce inspection time and cost, only a few tooth profiles and traces on some teeth are inspected. Measured data are not likely representatives of all gear teeth because errors may occur in assembly procedure and affect tooth contact condition. Frequently, tooth surface measuring data cannot show contact condition and used to predict gear vibration accurately. Field inspection method whose measured results relate directly to the meshing condition is required. This paper derives the relationship between meshing vibration components and the common gear tooth surface geometries of helical gears. The tooth surface geometries considered here are lead crowning, profile convex, pressure angle error, and bias-in modification. The polar plot representation, which plots meshing components in a complex plane, is proposed here to distinguish vibration characteristics of gears with various tooth surface forms. It is found that the vector of the second order of meshing component is valuable for classifying the type of tooth surface geometry.
Kinematic Geometry of Circular Surfaces With a Fixed Radius Based on Euclidean Invariants
Authors: Cui Lei , Wang Delun , Dai Jian S.
Published: September 2009

A circular surface with a fixed radius can be swept out by moving a circle with its center following a curve, which acts as the spine curve. Based on a system of Euclidean invariants, the paper identifies those circular surfaces taking lines of curvature as generating circles and further explores the properties of the principal curvatures and Gaussian curvature of the tangent circular surfaces. The paper then applies the study to mechanism analysis by proving the necessary and sufficient condition for a circular surface to be generated by a serially connected C′R, HR, or RR mechanism, where C′ joint can be visualized as a special H joint with a variable pitch of one degree of freedom. Following the analysis, this paper reveals for the first time the relationship between the invariants of a circular surface and the commonly used D-H parameters of C′R, HR, and RR mechanisms.
Recombinant Sindbis Virus Vectors Designed To Express Protective Antigen of
Bacillus anthracis
Protect Animals from Anthrax and Display Synergy with Ciprofloxacin
Authors: Thomas John M. , Moen Scott T. , Gnade Bryan T. , Vargas-Inchaustegui Diego A. , Foltz Sheri M. , Suarez Giovanni , Heidner Hans W. , König Rolf , Chopra Ashok K. , Peterson Johnny W.
Published: September 2009

Recombinant Sindbis viruses were engineered to express alternative forms of the protective antigen (PA) of
Bacillus anthracis
. The recombinant viruses induced PA-specific immunoglobulin G and neutralizing antibodies in Swiss Webster mice. Vaccination with the recombinant viruses induced immunity that offered some protection from a lethal Ames strain spore challenge and synergized the protective effects of ciprofloxacin.
A Novel 5-Lipoxygenase-Activating Protein Inhibitor, AM679, Reduces Inflammation in the Respiratory Syncytial Virus-Infected Mouse Eye
Authors: Musiyenko Alla , Correa Lucia , Stock Nicholas , Hutchinson John H. , Lorrain Daniel S. , Bain Gretchen , Evans Jilly F. , Barik Sailen
Published: September 2009

Respiratory syncytial virus (RSV) is an important cause of viral respiratory disease in children, and RSV bronchiolitis has been associated with the development of asthma in childhood. RSV spreads from the eye and nose to the human respiratory tract. Correlative studies of humans and direct infection studies of BALB/c mice have established the eye as a significant pathway of entry of RSV to the lung. At the same time, RSV infection of the eye produces symptoms resembling allergic conjunctivitis. Cysteinyl leukotrienes (CysLTs) are known promoters of allergy and inflammation, and the first step in their biogenesis from arachidonic acid is catalyzed by 5-lipoxygenase (5-LO) in concert with the 5-LO-activating protein (FLAP). We have recently developed a novel compound, AM679, which is a topically applied and potent inhibitor of FLAP. Here we show with the BALB/c mouse eye RSV infection model that AM679 markedly reduced the RSV-driven ocular pathology as well as the synthesis of CysLTs in the eye. In addition, AM679 decreased the production of the Th2 cell cytokine interleukin-4 but did not increase the viral load in the eye or the lung. These results suggest that FLAP inhibitors may be therapeutic for RSV-driven eye disease and possibly other inflammatory eye indications.
Clinical and Resistance Consequences of Misquantification of Plasma and Cerebrospinal Fluid Human Immunodeficiency Virus Type 1 (HIV-1) RNA in Samples from an HIV-1 Subtype G-Infected Patient
Authors: Delaugerre Constance , Denis Blandine , Peytavin Gilles , Palmer Pierre , Mourez Thomas , Le Goff Jerôme , Molina Jean-Michel , Simon François
Published: September 2009

Human immunodeficiency virus (HIV) load is the main marker used to monitor antiviral treatment efficacy and resistance. We report a case of underquantification of HIV type 1 (HIV-1) RNA in plasma and cerebrospinal fluid from an HIV-1 subtype G-infected woman, leading to delayed diagnosis of HIV encephalitis and to the emergence of drug resistance.
Molecular and Phenotypic Characteristics of Methicillin-Resistant and Vancomycin-Intermediate
Staphylococcus aureus
Isolates from Patients with Septic Arthritis
Authors: Wang Wei-Yao , Lee Shih-Yi , Chiueh Tzong-Shi , Lu Jang-Jih
Published: September 2009

Staphylococcus aureus
is one of the most common pathogens in community- and hospital-associated infections and frequently causes severe and intractable infections in osteoarticular tissues.
S. aureus
isolates that are resistant to methicillin (meticillin) (MRSA isolates) and intermediately resistant to vancomycin (VISA isolates) have emerged. In this report, we described two patients, one female and one male, diagnosed with septic arthritis due to
S. aureus
infections. A total of 13 MRSA isolates were obtained from these two patients. All but one isolate belonged to the VISA group. All seven isolates from the female patient were determined to be community associated, multilocus sequence type (MLST) 59, and staphylococcal cassette chromosome
mecA
(SCC
mec
) type IV; had direct repeat units (DRUs) of nine repeats; were
spa
type t437; and were susceptible to sulfa and quinolone antibiotics. The other six isolates, from the male patient, were determined to be hospital associated, MLST 239, and SCC
mec
type III; had DRUs of 14 repeats; were
spa
type t037; and were resistant to sulfa and quinolone antibiotics. All 13 MRSA isolates were in
agr
group I, were
pvl
negative, and showed no evidence of any association between vancomycin resistance and autolysis.
Antigenemia in Patients with Mediterranean Visceral Leishmaniasis
Authors: Ferrua Bernard , Rol Nicolas , Michel Grégory , Marty Pierre
Published: September 2009

Antigenemia in patients with Mediterranean visceral leishmaniasis (MVL) due to
Leishmania infantum
was retrospectively assessed by sandwich enzyme-linked immunosorbent assay (ELISA). Circulating
Leishmania
antigens, partially in free form, were in evidence in 53% of serum samples from immunocompetent individuals with MVL. Following successful therapy, antigenemia decline as measured by ELISA was more pronounced than antibody decrease.
Foot-and-Mouth Disease Virus Antigen Detection Enzyme-Linked Immunosorbent Assay Using Multiserotype-Reactive Monoclonal Antibodies
Authors: Morioka Kazuki , Fukai Katsuhiko , Yoshida Kazuo , Yamazoe Reiko , Onozato Hiroyuki , Ohashi Seiichi , Tsuda Tomoyuki , Sakamoto Kenichi
Published: September 2009

Monoclonal antibody (MAb)-based sandwich direct enzyme-linked immunosorbent assay (MSD-ELISA) methods that can detect foot-and-mouth disease virus (FMDV) antigens, both multiserotype (MSD-ELISA/MS) (for O, A, C, and Asia 1) and single-serotype (MSD-ELISA/SS) (for O, A, and Asia 1, specifically), were developed. MAb 1H5 was used as an antigen-trapping antibody that reacted with all seven serotypes of FMDV. The MAbs 71F2, 70C4, 16C6, and 7C2 were used as peroxidase-labeled detecting antibodies for multiple serotypes (O, A, C, and Asia 1), type O, type A, and type Asia 1, respectively, in both MSD-ELISA/MS and MSD-ELISA/SS. Our MSD-ELISAs showed high specificity. They produced a very low background of negative samples (buffer, plasma, and saliva) and were able to detect FMDV antigens from clinical samples (plasma and saliva), with results correlating with those of real-time reverse transcription-PCR. In terms of sensitivity, the MSD-ELISAs showed higher optical density values against each diluted serotype antigen than the indirect sandwich ELISA method, which is currently recommended in the manual of the World Organization for Animal Health. The sensitivity and specificity of the MSD-ELISAs seem to be sufficient for the antigenic diagnosis of FMDV.
Two Distinct Clones of Methicillin-Resistant
Staphylococcus aureus
(MRSA) with the Same USA300 Pulsed-Field Gel Electrophoresis Profile: a Potential Pitfall for Identification of USA300 Community-Associated MRSA
Authors: Larsen Anders Rhod , Goering Richard , Stegger Marc , Lindsay Jodi A. , Gould Katherine A. , Hinds Jason , Sørum Marit , Westh Henrik , Boye Kit , Skov Robert
Published: September 2009

Analysis of methicillin-resistant
Staphylococcus aureus
(MRSA) characterized as USA300 by pulsed-field gel electrophoresis identified two distinct clones. One was similar to community-associated USA300 MRSA (ST8-IVa, t008, and Panton-Valentine leukocidin positive). The second (ST8-IVa, t024, and PVL negative) had different molecular characteristics and epidemiology, suggesting independent evolution. We recommend
spa
typing and/or PCR to discriminate between the two clones.
Characterization of
fHbp
,
nhba
(
gna2132
),
nadA
,
porA
, Sequence Type (ST), and Genomic Presence of IS
1301
in Group B Meningococcal ST269 Clonal Complex Isolates from England and Wales
Authors: Lucidarme Jay , Comanducci Maurizio , Findlow Jamie , Gray Stephen J. , Kaczmarski Edward B. , Guiver Malcolm , Kugelberg Elisabeth , Vallely Pamela J. , Oster Philipp , Pizza Mariagrazia , Bambini Stefania , Muzzi Alessandro , Tang Christoph M. , Borrow Ray
Published: September 2009

Highly effective glycoconjugate vaccines exist against four of the five major pathogenic groups of meningococci: A, C, W-135, and Y. An equivalent vaccine against group B meningococci (menB) has remained elusive due to the poorly immunogenic capsular polysaccharide. A promising alternative, the investigational recombinant menB (rMenB)- outer membrane vesicle (OMV) vaccine, contains fHBP, NHBA (previously GNA2132), NadA, and outer membrane vesicles (OMVs) from the New Zealand MeNZB vaccine. MenB currently accounts for 90% of meningococcal disease in England and Wales, where the multilocus sequence type (ST) 269 (ST269) clonal complex (cc269) has recently expanded to account for a third of menB cases. To assess the potential cc269 coverage of the rMenB-OMV vaccine, English and Welsh cc269 isolates from the past decade were genetically characterized with respect to fHBP, NHBA, and NadA. All of the isolates harbored
fHbp
and
nhba
alleles, while 98% of the cc269 isolates were devoid of
nadA
. Subvariant profiling of
fHbp
,
nhba
, and
porA
against STs revealed the presence of two broadly distinct and well-defined clusters of isolates, centered around ST269 and ST275, respectively. An additional molecular marker, insertion sequence IS
1301
, was found to be present in 100% and <2% of isolates of the respective clusters. On the basis of the genetic data, the potential rMenB-OMV coverage of cc269 in England and Wales is high (up to 100%) within both clusters. Expression studies and serum bactericidal antibody assays will serve to enhance predictions of coverage and will augment ongoing studies regarding the significance of IS
1301
within the ST269 cluster.
Non-
spa
-Typeable Clinical
Staphylococcus aureus
Strains Are Naturally Occurring Protein A Mutants
Authors: Baum Cathrin , Haslinger-Löffler Bettina , Westh Henrik , Boye Kit , Peters Georg , Neumann Claudia , Kahl Barbara C.
Published: September 2009

Staphylococcus aureus
is a major human pathogen responsible for increasing the prevalence of community- and hospital-acquired infections. Protein A (SpA) is a key virulence factor of
S. aureus
and is highly conserved. Sequencing of the variable-number tandem-repeat region of SpA (
spa
typing) provides a rapid and reliable method for epidemiological studies. Rarely, non-
spa
-typeable
S. aureus
strains are encountered. The reason for this is not known. In this study, we characterized eight non-
spa
-typeable bacteremia isolates. Sequencing of the entire
spa
locus was successful for five strains and revealed various mutations of
spa
, all of which included a deletion of immunoglobulin G binding domain C, in which the upper primer for
spa
typing is located, while two strains were truly
spa
negative. This is the first report demonstrating that nontypeability of
S. aureus
by
spa
sequencing is due either to mutation or to a true deficiency of
spa
.
Evidence of Pathogenic Subgroups among Atypical Enteropathogenic
Escherichia coli
Strains
Authors: Scaletsky Isabel C. A. , Aranda Katia R. S. , Souza Tamara B. , Silva Neusa P. , Morais Mauro B.
Published: September 2009

We describe the characterization of 126 atypical enteropathogenic
Escherichia coli
(aEPEC) isolates from 1,749 Brazilian children. Classic aEPEC strains were more frequently found in children with diarrhea than in controls (
P
< 0.001), showing their importance as acute diarrhea agents in our country. Only aEPEC strains carrying either the
ehxA
or
paa
gene were significantly associated with diarrhea.
Airway Obstruction Is Increased in
Pneumocystis
-Colonized Human Immunodeficiency Virus-Infected Outpatients
Authors: Morris Alison , Alexander Travis , Radhi Saba , Lucht Lorrie , Sciurba Frank C. , Kolls Jay K. , Srivastava Ruma , Steele Chad , Norris Karen A.
Published: September 2009

We investigated the relationship of
Pneumocystis
colonization, matrix metalloprotease levels in sputum, and airway obstruction in a cohort of human immunodeficiency virus (HIV)-infected outpatients.
Pneumocystis
-colonized subjects had worse obstruction of airways and higher levels of matrix metalloprotease-12 in sputa, suggesting that
Pneumocystis
colonization may be important in HIV-associated chronic obstructive pulmonary disease.