bluuebunny/crossref_metadata_2025 huggingface dataset:
Land-Development Dynamics by Morphological Areas: A Case Study of Ribadeo, Northwest Spain
Authors: García Andrés M , Santé Inés , Crecente Rafael , Miranda David
Published: December 2011

The need to understand land-development processes in order to address the problem derived from urban growth led to the implementation of a number of scientific methods aimed at explaining urban-growth patterns. The dynamics that originate these patterns are complex and may vary across space, such that in small areas there may be various processes operating and producing different kinds of growth. Our aim is to use cluster-analysis techniques to identify zones with similar urban-growth patterns in a coastal rural municipality of the northwest of Spain. Then, the processes that originated the different growth patterns identified from the cluster analysis are characterized using logistic regression techniques. The methodology differentiated three clusters (an urban cluster, a rural cluster, and a rural cluster with urban influence) and characterized the underlying dynamics. This proves that the techniques used in this study constitute a straightforward tool to identify and analyze areas with uniform land-development patterns in order to gain deeper knowledge and produce better regulations and zoning for each area.
Hierarchical Representations of Indoor Spaces
Authors: Richter Kai-Florian , Winter Stephan , Santosa Sigit
Published: December 2011

Compared with typical outdoor spaces, indoor spaces are clustered and have a fragmented social structure and diverse groups use the space in different ways, which results in different conceptualizations. Accordingly, these spaces pose many challenges for spatial information systems, amongst them appropriate spatial communication with users as different conceptualizations result in different communication needs. The conceptualizations are hierarchical in nature and, thus, information systems also require hierarchical representations of indoor spaces. In this paper we present a hierarchization process that acounts for different use roles. The hierarchization exploits structural, functional, and organizational dimensions and allows for communicating different aspects of the space in a way tailored to the specific user groups.
Simulating Urban Growth Scenarios Using GIS and Multicriteria Analysis Techniques: A Case Study of the Madrid Region, Spain
Authors: Plata-Rocha Wenseslao , Gómez-Delgado Montserrat , Bosque-Sendra Joaquín
Published: December 2011

Over the last few years, urban expansion has occurred without much control or urban planning, causing both regional and global impacts on the natural ecosystems. This situation has spurred reflection on current planning policies and has also stimulated research into new tools and methodologies for the simulation of alternative territorial scenarios for the future. In this respect, the use of multicriteria evaluation techniques within a GIS environment has proved to be an efficient option for an optimal allocation of land uses. However, those techniques have not been explored thoroughly in the field of future scenario simulation. The aim of our research is to show and to reinforce the possibilities of these techniques in developing three different scenarios of urban growth (business as usual, crisis, and innovation and sustainability). All three scenarios discriminate between three land uses (residential, commercial, and industrial), and have been developed for the Madrid region. The base-line year of these scenarios is 2000 and the time horizon is 2020. In that process, fourteen spatial factors, which encompass environmental, economic, and social issues, have been considered. The results obtained show that some discrepancies exist between the business as usual scenario and European policies for transport and the environment. This situation has an impact on the territory and causes irreversible damage to the environment. The crisis scenario, in contrast, alleviates those pressures, if not because of the application of environmental policies to the planning process, at least because the situation of crisis causes the metropolitan model to change. Finally, innovation has been considered a driver of economic development and good planning practice, the positive effects of which have been highlighted in the third scenario.
Bioturbation by stingrays at Ningaloo Reef, Western Australia
Authors: O'Shea Owen R. , Thums Michele , van Keulen Mike , Meekan Mark
Published: December 2011

Stingrays are an important part of the biomass of the fishes in shallow coastal ecosystems, particularly in inter-reefal areas. In these habitats, they are considered keystone species – modifying physical and biological habitats through their foraging and predation. Here, we quantify the effects of bioturbation by rays on sand flats of Ningaloo Reef lagoon in Western Australia. We measured the daily length, breadth and depth of 108 feeding pits over three 7‐day periods, created by stingrays (Pastinachus atrus, Himantura spp. Taeniura lymma and Urogymnus asperrimus) in Mangrove Bay. Additionally, an area of ~1 km2 of the lagoon at Coral Bay was mapped three times over 18 months, to record patterns of ray and pit presence. Over 21 days at Mangrove Bay, a total of 1.08 m3 of sediment was excavated by rays, equating to a sediment wet weight of 760.8 kg, and 2.42% of the total area sampled, or 0.03% of the whole intertidal zone. We estimate that up to 42% of the soft sediments in our study area would be reworked by stingrays each year. Based on a model predicting the probability of pit presence over time, there was a 40% probability of ray pits persisting for 4 days before being filled in but only a 15% probability of a pit being present after 7 days. Changes in pit volume over time were static, providing evidence for secondary use. Our results imply that rays play an important ecological role creating sheltered habitats for other taxa in addition to the turnover of sediments.
Sustaining cardiovascular absolute risk management in Australian general practice
Authors: Vaidya Ruhie , Pandya Keval V. , Denney-Wilson Elizabeth , Harris Mark
Published: December 2011

This study describes the attitudes and practices of patients and GPs 12 months after participating in a trial of absolute cardiovascular risk assessment in general practice. It involved a qualitative design using semistructured interviews with 12 Sydney GPs from the intervention arm of a cluster randomised controlled trial of cardiovascular absolute risk (CVAR) assessment and 15 of their moderate to high risk patients who participated in the assessments. Most GPs had sustained CVAR assessment in their practice, using it primarily to motivate patients to change their behaviour and adhere to management rather than to make decisions about pharmacotherapy or referral. Time was a barrier to its use. Patients who sustained changes to their behaviour had internalised the benefits to their health and received support from family and friends. Those who relapsed attributed this to their own lack of motivation and extrinsic factors. CVAR assessment needs to be incorporated into practice information systems and long-term planned preventive care if it is to be sustained in general practice and have long-term impacts on patient behaviour.
Pannexins in ischemia-induced neurodegeneration
Authors: Bargiotas Panagiotis , Krenz Antje , Hormuzdi Sheriar G. , Ridder Dirk A. , Herb Anne , Barakat Waleed , Penuela Silvia , von Engelhardt Jakob , Monyer Hannah , Schwaninger Markus
Published: December 2011

Pannexin 1 (Px1, Panx1) and pannexin 2 (Px2, Panx2) form large-pore nonselective channels in the plasma membrane of cells and were suggested to play a role in the pathophysiology of cerebral ischemia. To directly test a potential contribution of pannexins in ischemia-related mechanisms, we performed experiments in

Px1
−/−

,

Px2
−/−

, and

Px1
−/−
Px2
−/−

knockout mice. IL-1β release, channel function in astrocytes, and cortical spreading depolarization were not altered in

Px1
−/−
Px2
−/−

mice, indicating that, in contrast to previous concepts, these processes occur normally in the absence of pannexin channels. However, ischemia-induced dye release from cortical neurons was lower, indicating that channel function in

Px1
−/−
Px2
−/−

neurons was impaired. Furthermore,

Px1
−/−
Px2
−/−

mice had a better functional outcome and smaller infarcts than wild-type mice when subjected to ischemic stroke. In conclusion, our data demonstrate that Px1 and Px2 underlie channel function in neurons and contribute to ischemic brain damage.
IgA and IgG antineutrophil cytoplasmic antibody engagement of Fc receptor genetic variants influences granulomatosis with polyangiitis
Authors: Kelley James M. , Monach Paul A. , Ji Chuanyi , Zhou Yebin , Wu Jianming , Tanaka Sumiaki , Mahr Alfred D. , Johnson Sharleen , McAlear Carol , Cuthbertson David , Carette Simon , Davis John C. , Dellaripa Paul F. , Hoffman Gary S. , Khalidi Nader , Langford Carol A. , Seo Phillip , St. Clair E. William , Specks Ulrich , Stone John H. , Spiera Robert F. , Ytterberg Steven R. , Merkel Peter A. , Edberg Jeffrey C. , Kimberly Robert P.
Published: December 2011

Granulomatosis with polyangiitis (Wegener's) is a rare autoimmune neutrophil-mediated vasculitis that can cause renal disease and mucosal manifestations. Antineutrophil cytoplasmic antibodies (ANCA) are present in many patients, vary in level over time, and induce neutrophil activation through engagement with Fc receptors (FcRs). Given roles for FcRs in ANCA-mediated neutrophil activation and IgA antibodies in mucosal immunity, we hypothesized that FcR genetics and previously unappreciated IgA ANCA affect clinical presentation. We assembled a total of 673 patients and 413 controls from two multicenter cohorts, performed ELISA and immunofluorescence assays to determine IgA and IgG ANCA positivity, and used Illumina, TaqMan, or Pyrosequencing to genotype eight haplotype-tagging SNPs in the IgA FcR (FCAR) and to determine NA1/NA2 genotype of FCGR3B, the most prevalent neutrophil IgG FcR. We evaluated neutrophil activation by measuring degranulation marker CD11b with flow cytometry or neutrophil extracellcular trap formation with confocal microscopy. Functional polymorphisms inFCGR3BandFCARdiffered between patient groups stratified by renal involvement. IgA ANCA were found in ∼30% of patients and were less common in patients with severe renal disease. Neutrophil stimulation by IgA or IgG ANCA led to degranulation and neutrophil extracellcular trap formation in a FcR allele-specific manner (IgA:FCARP= 0.008; IgG:FCGR3BP= 0.003). When stimulated with IgA and IgG ANCA together, IgG ANCA induced neutrophil activation was reduced (P= 0.0001). FcR genotypes, IgA ANCA, and IgG ANCA are potential prognostic and therapeutic targets for understanding the pathogenesis and presentation of granulomatosis with polyangiitis (Wegener's).
Estimation of 3D shape from image orientations
Authors: Fleming Roland W. , Holtmann-Rice Daniel , Bülthoff Heinrich H.
Published: December 2011

One of the main functions of vision is to estimate the 3D shape of objects in our environment. Many different visual cues, such as stereopsis, motion parallax, and shading, are thought to be involved. One important cue that remains poorly understood comes from surface texture markings. When a textured surface is slanted in 3D relative to the observer, the surface patterns appear compressed in the retinal image, providing potentially important information about 3D shape. What is not known, however, is how the brain actually measures this information from the retinal image. Here, we explain how the key information could be extracted by populations of cells tuned to different orientations and spatial frequencies, like those found in the primary visual cortex. To test this theory, we created stimuli that selectively stimulate such cell populations, by “smearing” (filtering) images of 2D random noise into specific oriented patterns. We find that the resulting patterns appear vividly 3D, and that increasing the strength of the orientation signals progressively increases the sense of 3D shape, even though the filtering we apply is physically inconsistent with what would occur with a real object. This finding suggests we have isolated key mechanisms used by the brain to estimate shape from texture. Crucially, we also find that adapting the visual system's orientation detectors to orthogonal patterns causes unoriented random noise to look like a specific 3D shape. Together these findings demonstrate a crucial role of orientation detectors in the perception of 3D shape.
Analysis of Compensatory Responses in Land‐Locked Alewives to Walleye Predation: A Tale of Two Lakes
Authors: Rudstam L. G. , Brooking T. E. , Krueger S. D. , Jackson J. R. , Wetherbee L.
Published: December 2011

We compared one established population (Cayuta Lake) and one expanding population (Canadarago Lake) of landlocked alewives Alosa pseudoharengus to evaluate compensatory responses of alewives to predation by walleyes Sander vitreus. Alewives have been present in Cayuta Lake since at least 1977, and during the years 1995 to 2009 the population ranged from 24,470 fish/ha in 2000 to 3,800 fish/ha in 2007. Alewives were first observed in Canadarago Lake during 1999, and the population remained at low densities (<26 fish/ha) until reaching 370 fish/ha in 2006 and 1,050 fish/ha in 2009. Differences in zooplankton reflected higher planktivory rates in Cayuta Lake than in Canadarago Lake. Density of age‐3 and older walleyes was higher in Canadarago Lake (21–24 fish/ha) than in Cayuta Lake (12–14 fish/ha), despite elevated stocking rates of fingerling walleyes in Cayuta Lake during 2002–2006. Alewife density explained 77–84% of the variation in alewife length at age and 48–84% of the variation in condition (ages 0, 1, and 2) among years and lakes. Alewife length at age under low densities in Canadarago Lake was similar to observations in anadromous populations. Alewife recruitment (number of fall age‐0 recruits/spawner) was higher in Canadarago Lake than in Cayuta Lake. The combined data yielded a Beverton–Holt stock–recruitment curve that rose rapidly at low alewife densities, and 50% of the maximum recruitment was predicted to occur at 400 spawners/ha. Compensatory responses of alewives at low densities include decreased cannibalism and increased growth rates of both adults and age‐0 fish. Compensatory responses should be considered when evaluating the piscivore levels needed to control alewife populations or, conversely, when evaluating the risk of alewife population collapse in response to increased predation rates. Although alewife abundance declined in response to the experimental walleye stocking in Cayuta Lake, we were unable to increase the walleye population sufficiently to decrease alewife recruitment.
Multimetric Fish Indices for Midcontinent (USA) Great Rivers
Authors: Pearson Mark S. , Angradi Ted R. , Bolgrien David W. , Jicha Terri M. , Taylor Debra L. , Moffett Mary F. , Hill Brian H.
Published: December 2011

We developed fish assemblage–based multimetric indices as indicators of ecological conditions for the lower Missouri, impounded upper Mississippi, unimpounded upper Mississippi, and Ohio rivers. Using data from 475 daytime electrofishing samples, we calculated 81 candidate fish metrics. We screened these metrics for their range and their responsiveness to a multimetric stressor gradient that included water chemistry, human disturbance, and landscape‐scale indicators of human disturbance and stress. Each reach‐specific great‐river fish index (GRFIn) included 8–10 nonredundant metrics scored on a continuous scale from 0 to 10 (10 = good). No metrics were common to all four GRFIns; one metric (the number of minnow species) was common to three GRFIns. We determined the least disturbed conditions from the y‐intercepts of the quantile regressions between the GRFIn scores and the corresponding stressor gradients. Ecological condition as indicated by GRFIn score varied among reaches; 44 ± 8% (95% confidence interval around the mean) of the lower Missouri River (by length), 51 ± 20% of the unimpounded upper Mississippi River, 43 ± 8% of the impounded upper Mississippi River, and 39 ± 7% of the Ohio River was most disturbed.
International Trends in Demand for Forensic Mental Health Services
Authors: Jansman-Hart ErikaM. , Seto MichaelC. , Crocker AnneG. , Nicholls ToniaL. , Côté Gilles
Published: December 2011

Deinstitutionalization, changes in both criminal and civil law, and the use of the criminal justice system to manage problematic behavior by individuals with serious mental illnesses have affected the number of people entering forensic mental health systems. This review examines data revealing trends in demand for forensic services in Canada, the United States, and internationally. The number of beds and resources allocated to forensic mental health services has steadily increased not only in Canada, but in other countries across the world. In Canada, the number of new accused entering the system doubled annually from 1992 to 2004. In the United States, the number of individuals found not guilty by reason of insanity (NGRI), forensic beds and forensic expenditures have all increased dramatically in recent years. Furthermore, countries in Western Europe – Austria, Denmark, England, Germany, Ireland, Italy, the Netherlands, Spain and Switzerland – have reported an increase of 110%, on average, in the number of forensic beds between 1990 and 2006. These increases have implications for both forensic and non-forensic mental health services. Suggestions to reduce forensic demand and increase the successful reintegration of forensic clients into the community are discussed.
Referrals to the Washoe County Mental Health Court
Authors: Frailing Kelly
Published: December 2011

This study examined the demographic, mental health, and criminal characteristics of 1,220 referrals to the Washoe County mental health court over a three-year period in order to determine which characteristics were associated with acceptance into the court. Results indicated that those with a thought disorder, a mood disorder, a felony index charge, and a misdemeanor index charge were significantly more likely to be accepted into the mental health court and those with a crime against a person, a crime against the community, and males were significantly less likely to be accepted into the court. A violent current crime and/or criminal history were also associated with rejection from the mental health court. These results have important policy implications for those who are referred to the court but who receive another disposition of their case and for those with violent crimes or criminal histories who are rejected by the court. This research is limited by its focus on one mental health court but does help to fill a void in the mental health court literature and sets the stage for a new focus on what becomes of those rejected from the mental health court.
Is My Test Valid? Guidelines for the Practicing Psychologist for Evaluating the Psychometric Properties of Measures
Authors: Slaney KathleenL. , Storey JenniferE. , Barnes Jordan
Published: December 2011

A general logic for data-based test evaluation based on Slaney and Maraun's (2008) framework is described. On the basis of this framework and other well-known test theoretic results, a set of guidelines is proposed to aid researchers in the assessment of the psychometric properties of the measures they use in their research. The guidelines are organized into eight areas and range from general recommendations, pertaining to understanding different psychometric properties of quantitative measures and at what point in a test evaluation their respective assessments should occur, to clarifications of core psychometric concepts such as factor structure, reliability, coefficient alpha, and dimensionality. Finally, an illustrative example is provided with a data-based test evaluation of the Hare Psychopathy Checklist-Revised (Hare, 1991) as a measure of psychopathic personality disorder in a sample of 384 male offenders serving sentences in a Canadian correctional facility.
Psychopathic Subtypes and Associations with Mental Health Problems in an Incarcerated Sample of Adolescent Boys
Authors: Veen ViolaineC. , Andershed Henrik , Stevens GonnekeW. J. M. , Doreleijers TheoA. H. , Vollebergh WilmaA. M.
Published: December 2011

Research suggests a distinction between high and low anxious psychopathic individuals. However, research on psychopathic subtypes in youth offender populations is largely lacking. Therefore, this study examined psychopathic subtypes in a sample of incarcerated adolescents, and explored the relationship of these subtypes with various (mental health) problems. The Youth Psychopathic traits Inventory was used to measure psychopathic traits in a sample of 299 incarcerated adolescent boys. Related (mental health) problems were measured with, among others, the Youth Self-report. Within a high psychopathic subsample of incarcerated boys, two psychopathic subtypes were identified using Latent Class Analyses: a low anxious-depressed and a high anxious-depressed psychopathic type. Both subtypes showed high scores on psychopathic traits, although high anxious-depressed psychopathic boys scored lower on the affective traits of psychopathy than low anxious-depressed psychopathic boys. High anxious-depressed psychopathic boys reported more mental health problems than non-psychopathic and low anxious-depressed psychopathic boys. This study provided support for the presence of psychopathic subtypes in a sample of incarcerated boys. The characteristics of these two subtypes are generally in line with former descriptions of low anxious and high anxious psychopathic variants.
The Predictive Validity of the Short-Term Assessment of Risk and Treatability (START) in a Secure Forensic Hospital: Risk Factors and Strengths
Authors: Chu ChiMeng , Thomas StuartD. M. , Ogloff JamesR. P. , Daffern Michael
Published: December 2011

There has been an increased interest among researchers and clinicians to understand the violence risk factors that are important in inpatient psychiatric settings, as well as to improve the accuracy of inpatient violence risk assessments. The Short-Term Assessment of Risk and Treatability (START) is a structured violence risk assessment instrument designed to assess multiple risk domains and protective factors that are pertinent to inpatient psychiatric care and treatment. Unlike many structured risk assessment instruments, the START is comprised solely of dynamic factors. Using a sample of 50 inpatients, the present study sought to examine the predictive validity of the START Risk and Strength scales for inpatient aggression in a high-security forensic psychiatric hospital during a 1-month follow-up period. The Risk scale predicted interpersonal violence, verbal threats, and any inpatient aggression, whereas the Strength scale predicted interpersonal violence and any inpatient aggression. The results suggest that short-term inpatient violence risk appraisals using the START are significantly predictive whether risk factors or strengths are considered.
When “Good Enough” Is Just Not Good Enough: Response to Holden and Marjanovic
Authors: Slaney KathleenL. , Storey JenniferE. , Barnes Jordan
Published: December 2011

In this article, we respond to a commentary by Holden and Marjanovic (this issue) on Slaney, Storey, and Barnes’ article “‘Is My Test Valid?’: Guidelines for the Practicing Psychologist for Evaluating the Psychometric Properties of Measures” (this issue). Specifically, we reply to Holden and Marjanovic's claims that our guidelines: endorse a “construct approach” to test evaluation and development, rely too heavily on modern test theoretic methods and as such are too mathematically and technically intractable to be practically useful, and may present too unrealistic a challenge to be used in test development and the evaluation of well-established measures. Finally, we attempt to clarify the major themes that the guidelines described in Slaney, Storey, and Barnes were intended to convey.
Structural and Metric Validity of the Dutch Translation of Psychopathy Checklist: Youth Version (PCL:YV)
Authors: Hillege Sanne , de Ruiter Corine , Smits Niels , van der Baan Hans , Das Jacqueline
Published: December 2011

In the present study, the structural validity of the Dutch version of the Psychopathy CheckList: Youth Version (in Dutch: Psychopathie Checklist: Jeugd Versie; PCL:YV; de Ruiter, Kuin, de Vries, & Das, 2002) was examined in adolescent offenders by means of Confirmatory Factor Analysis (CFA) and Item Response Theory (IRT). The PCL:YV item ratings for 269 adolescent males, either admitted to a Dutch juvenile treatment institution or psychologically evaluated upon request of the court, were used to test the fit of different factor models presumed to represent the structure of psychopathy as measured by the PCL-R in adults. The study provides support for a good absolute and relative fit for the 3-factor model, but not for the 4-factor model. Results from IRT analyses demonstrate the highest discriminative value for the affective items in the Dutch adolescent sample. The present findings demonstrate poor discriminative power and age influence on item functioning for most antisocial items of the fourth factor.
An observational 71-year history of seasonally frozen ground changes in the Eurasian high latitudes
Authors: Frauenfeld Oliver W , Zhang Tingjun
Published: December 2011

In recent decades, significant changes have occurred in high-latitude areas, particularly to the cryosphere. Sea ice extent and thickness have declined. In land areas, glaciers and ice sheets are experiencing negative mass balance changes, and there is substantial regional snow cover variability. Subsurface changes are also occurring in northern soils. This study focuses on these changes in the soil thermal regime, specifically the seasonally frozen ground region of Eurasia. We use a database of soil temperatures at 423 stations and estimate the maximum annual soil freezing depth at the 387 sites located on seasonally frozen ground. Evaluating seasonal freeze depth at these sites for 1930–2000 reveals a statistically significant trend of −4.5 cm/decade and a net change of −31.9 cm. Interdecadal variability is also evident such that there was no trend until the late 1960s, after which seasonal freeze depths decreased significantly until the early 1990s. From that point forward, likely through at least 2008, no change is evident. These changes in the soil thermal regime are most closely linked with the freezing index, but also mean annual air temperatures and snow depth. Antecedent conditions from the previous warm season do not appear to play a large role in affecting the subsequent cold season’s seasonal freeze depths. The strong decrease in seasonal freeze depths during the 1970s to 1990s was likely the result of strong atmospheric forcing from the North Atlantic Oscillation during that time period.
Uniform equicontinuity of sequences of measurable operators and non-commutative ergodic theorems
Authors: Litvinov Semyon
Published: December 2011

The notion of uniform equicontinuity in measure at zero for sequences of additive maps from a normed space into the space of measurable operators associated with a semifinite von Neumann algebra is discussed. It is shown that uniform equicontinuity in measure at zero on a dense subset implies the uniform equicontinuity in measure at zero on the entire space, which is then applied to derive some non-commutative ergodic theorems.
Redundancy in metrics describing the composition, structure, and functioning of the North Sea demersal fish community
Authors: Greenstreet Simon P. R. , Fraser Helen M. , Rogers Stuart I. , Trenkel Verena M. , Simpson Stephen D. , Pinnegar John K.
Published: December 2011

Greenstreet, S. P. R., Fraser, H. M., Rogers, S. I., Trenkel, V. M., Simpson, S. D., and Pinnegar, J. K. 2012. Redundancy in metrics describing the composition, structure, and functioning of the North Sea demersal fish community. – ICES Journal of Marine Science, 69: 8–22. Broader ecosystem management objectives for North Sea demersal fish currently focus on restoring community size structure. However, most policy drivers explicitly concentrate on restoring and conserving biodiversity, and it has not yet been established that simply restoring demersal fish size composition will be sufficient to reverse declines in biodiversity and ensure a generally healthy community. If different aspects of community composition, structure, and function vary independently, then to monitor all aspects of community general health will require application of a suite of metrics. This assumes low redundancy among the metrics used in any such suite and implies that addressing biodiversity issues specifically will require explicit management objectives for particular biodiversity metrics. This issue of metric redundancy is addressed, and 15 metrics covering five main attributes of community composition, structure, and function are applied to groundfish survey data. Factor analysis suggested a new interpretation of the metric information and indicated that a minimum suite of seven metrics was necessary to ensure that all changes in the general health of the North Sea demersal fish community were monitored properly. Covariance among size-based and species-diversity metrics was low, implying that restoration of community size structure would not necessarily reverse declines in species diversity.
Quo Vadimus
Authors: Browman Howard I.
Published: December 2011

Browman, H.I. 2012. Quo Vadimus. – ICES Journal of Marine Science, 69: 1–2.
First Report of Zebra Chip Disease and “Candidatus Liberibacter solanacearum” on Potatoes in Idaho
Authors: Crosslin J. M. , Olsen N. , Nolte P.
Published: December 2011

In September 2011, potato (Solanum tuberosum L.) tubers graded in a packing facility in south-central Idaho were observed with internal discolorations suggestive of zebra chip disease (ZC). Symptoms were observed in 1 to 2% of tubers of cv. Russet Norkotah and included brown spots and streaks especially in and near the vascular tissue. Some tubers also showed a dark and sunken stolon attachment typical of ZC (1). Initially, tissue samples were taken from seven symptomatic tubers and tested by PCR for “Candidatus Liberibacter solanacearum”, the bacterium associated with ZC. Primers specific for the 16S rDNA (primers CLipoF [4] and OI2c [3]) and the outer membrane protein (OMB 1482f and 2086r) (2) were used. Six of these samples were positive for the bacterium. The amplified 16S rDNA and OMB products from two symptomatic tubers of cv. Russet Norkotah were cloned and three clones of each were sequenced. The 16S sequences (1,071 bp; GenBank Accession Nos. JN848755 and JN848756) from the two tubers varied by one nucleotide and had 99 to 100% sequence identity to numerous “Ca. L. solanacearum” sequences in GenBank (e.g., Accession Nos. HM246509, FJ957897, and EU935004). Sequences of the two OMB clones (605 bp; GenBank Accession Nos. JN848757 and JN848758) had 97% sequence identity to the two “Ca. L. solanacearum” OMB sequences in GenBank (Accession Nos. CP002371 and FJ914617). Six of eight additional symptomatic field-collected cv. Russet Norkotah tubers corresponding to tubers collected in the packing facility were also positive for “Ca. L. solanacearum” by PCR. Additional severely symptomatic tubers of cvs. Russet Burbank, Yukon Gold, and raw cut French fries of Ranger Russet produced in south-central Idaho were subsequently tested by PCR and were found to be positive for “Ca. L. solanacearum” as well. On the basis of the symptoms, specific PCR amplification with two distinct primer pairs and DNA sequence analysis, zebra chip disease caused by “Ca. L. solanacearum” was determined to be present in Idaho. This disease has caused significant economic damage to potatoes in many regions, including Texas, Mexico, Central America, and New Zealand (1). Idaho is the largest potato-producing state in the United States, with over 150,000 ha planted this year, and therefore, ZC potentially poses a significant risk to agriculture in this state.

References: (1) J. M. Crosslin et al. Online publication. doi:10.1094/PHP-2010-0317-01-RV, Plant Health Progress, 2010. (2) J. M. Crosslin et al. Southwest. Entomol. 36:125, 2011. (3) S. Jagoueix et al. Mol. Cell. Probes 10:43, 1996. (4) G. A. Secor. Plant Dis. 93:574, 2009.
Real estate ads in Emei music frog vocalizations: female preference for calls emanating from burrows
Authors: Cui Jianguo , Tang Yezhong , Narins Peter M.
Published: December 2011

During female mate choice, both the male's phenotype and resources (e.g. his nest) contribute to the chooser's fitness. Animals other than humans are not known to advertise resource characteristics to potential mates through vocal communication; although in some species of anurans and birds, females do evaluate male qualities through vocal communication. Here, we demonstrate that calls of the male Emei music frog (
Babina dauchina
), vocalizing from male-built nests, reflect nest structure information that can be recognized by females. Inside-nest calls consisted of notes with energy concentrated at lower frequency ranges and longer note durations when compared with outside-nest calls. Centre frequencies and note durations of the inside calls positively correlate with the area of the burrow entrance and the depth of the burrow, respectively. When given a choice between outside and inside calls played back alternately, more than 70 per cent of the females (33/47) chose inside calls. These results demonstrate that males of this species faithfully advertise whether or not they possess a nest to potential mates by vocal communication, which probably facilitates optimal mate selection by females. These results revealed a novel function of advertisement calls, which is consistent with the wide variation in both call complexity and social behaviour within amphibians.
Optimized nanoscale composite behaviour in limpet teeth
Authors: Lu Dun , Barber Asa H.
Published: December 2011

Limpet teeth are striking examples of a biological fibrous nanocomposite consisting of goethite mineral within a polymeric chitin matrix. The mechanical function of limpet teeth is critically dependent on the efficient composite behaviour of goethite, formed as distinct discontinuous nanofibres, reinforcing the matrix. The mechanical properties of discrete volumes from a limpet tooth measured using atomic force microscopy indicate how the tooth structure can be approximated as a short fibre-reinforced composite. Short fibre composite analysis reveals how the goethite nanofibres have a length optimized for the transfer of stress from the matrix to fibre and highlight how this limpet tooth structure is efficient in a mechanical load-bearing function.
Particle-wave duality: a dichotomy between symmetry and asymmetry
Authors: Vaccaro Joan A.
Published: December 2011

Symmetry plays a central role in many areas of modern physics. Here, we show that it also underpins the dual particle and wave nature of quantum systems. We begin by noting that a classical point particle breaks translational symmetry, whereas a wave with uniform amplitude does not. This provides a basis for associating particle nature with asymmetry and wave nature with symmetry. We derive expressions for the maximum amount of classical information we can have about the symmetry and asymmetry of a quantum system with respect to an arbitrary group. We find that the sum of the information about the symmetry (wave nature) and the asymmetry (particle nature) is bounded by

, where
D
is the dimension of the Hilbert space. The combination of multiple systems is shown to exhibit greater symmetry and thus a more wavelike character. In particular, a class of entangled systems is shown to be capable of exhibiting wave-like symmetry as a whole while exhibiting particle-like asymmetry internally. We also show that superdense coding can be viewed as being essentially an interference phenomenon involving wave-like symmetry with respect to the group of Pauli operators.
Broken baby Skyrmions
Authors: Jäykkä Juha , Speight Martin , Sutcliffe Paul
Published: December 2011

The baby Skyrme model is a (2+1)-dimensional analogue of the Skyrme model, in which baryons are described by topological solitons. We introduce a version of the baby Skyrme model in which the global
O
(3) symmetry is broken to the dihedral group
D

N

. It is found that the single soliton in this theory is composed of
N
partons that are topologically confined. The case
N
=3 is studied in some detail and multi-soliton solutions are computed and related to polyiamonds, which are plane figures composed of equilateral triangles joined by common edges. It is shown that the solitons may be viewed as pieces of a doubly periodic soliton lattice. It is proved, for a general baby Skyrme model on a general torus, that the condition that the energy of a soliton lattice is critical with respect to variations of the torus is equivalent to the field satisfying a virial relation and being, in a precise sense, conformal on average. An alternative model with
D
3
symmetry is also introduced, which has an exact explicit soliton lattice solution. Soliton solutions are computed and compared in the two
D
3
theories. Some comments are made regarding the extension of these ideas to the Skyrme model.
Selection for mitonuclear co-adaptation could favour the evolution of two sexes
Authors: Hadjivasiliou Zena , Pomiankowski Andrew , Seymour Robert M. , Lane Nick
Published: December 2011

Mitochondria are descended from free-living bacteria that were engulfed by another cell between one and a half to two billion years ago. A redistribution of DNA led to most genetic information being lost or transferred to a large central genome in the nucleus, leaving a residual genome in each mitochondrion. Oxidative phosphorylation, the most critical function of mitochondria, depends on the functional compatibility of proteins encoded by both the nucleus and mitochondria. We investigate whether selection for adaptation between the nuclear and mitochondrial genomes (mitonuclear co-adaptation) could, in principle, have promoted uniparental inheritance of mitochondria and thereby the evolution of two mating types or sexes. Using a mathematical model, we explore the importance of the radical differences in ploidy levels, sexual and asexual modes of inheritance, and mutation rates of the nucleus and mitochondria. We show that the major features of mitochondrial inheritance, notably uniparental inheritance and bottlenecking, enhance the co-adaptation of mitochondrial and nuclear genes and therefore improve fitness. We conclude that, under a wide range of conditions, selection for mitonuclear co-adaptation favours the evolution of two distinct mating types or sexes in sexual species.
Brood parasite eggs enhance egg survivorship in a multiply parasitized host
Authors: Gloag Ros , Fiorini Vanina D. , Reboreda Juan C. , Kacelnik Alex
Published: December 2011

Despite the costs to avian parents of rearing brood parasitic offspring, many species do not reject foreign eggs from their nests. We show that where multiple parasitism occurs, rejection itself can be costly, by increasing the risk of host egg loss during subsequent parasite attacks. Chalk-browed mockingbirds (Mimus saturninus) are heavily parasitized by shiny cowbirds (Molothrus bonariensis), which also puncture eggs in host nests. Mockingbirds struggle to prevent cowbirds puncturing and laying, but seldom remove cowbird eggs once laid. We filmed cowbird visits to nests with manipulated clutch compositions and found that mockingbird eggs were more likely to escape puncture the more cowbird eggs accompanied them in the clutch. A Monte Carlo simulation of this ‘dilution effect’, comparing virtual hosts that systematically either reject or accept parasite eggs, shows that acceptors enjoy higher egg survivorship than rejecters in host populations where multiple parasitism occurs. For mockingbirds or other hosts in which host nestlings fare well in parasitized broods, this benefit might be sufficient to offset the fitness cost of rearing parasite chicks, making egg acceptance evolutionarily stable. Thus, counterintuitively, high intensities of parasitism might decrease or even reverse selection pressure for host defence via egg rejection.
Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in Drosophila
Authors: Khodor Yevgenia L. , Rodriguez Joseph , Abruzzi Katharine C. , Tang Chih-Hang Anthony , Marr Michael T. , Rosbash Michael
Published: December 2011

To determine the prevalence of cotranscriptional splicing in Drosophila, we sequenced nascent RNA transcripts from Drosophila S2 cells as well as from Drosophila heads. Eighty-seven percent of the introns assayed manifest >50% cotranscriptional splicing. The remaining 13% are cotranscriptionally spliced poorly or slowly, with ∼3% being almost completely retained in nascent pre-mRNA. Although individual introns showed slight but statistically significant differences in splicing efficiency, similar global levels of splicing were seen from both sources. Importantly, introns with low cotranscriptional splicing efficiencies are present in the same primary transcript with efficiently spliced introns, indicating that splicing is intron-specific. The analysis also indicates that cotranscriptional splicing is less efficient for first introns, longer introns, and introns annotated as alternative. Finally, S2 cells expressing the slow RpII215C4 mutant show substantially less intron retention than wild-type S2 cells.
Mechanisms and functions of Tet protein-mediated 5-methylcytosine oxidation
Authors: Wu Hao , Zhang Yi
Published: December 2011

Ten-eleven translocation 1–3 (Tet1–3) proteins have recently been discovered in mammalian cells to be members of a family of DNA hydroxylases that possess enzymatic activity toward the methyl mark on the 5-position of cytosine (5-methylcytosine [5mC]), a well-characterized epigenetic modification that has essential roles in regulating gene expression and maintaining cellular identity. Tet proteins can convert 5mC into 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) through three consecutive oxidation reactions. These modified bases may represent new epigenetic states in genomic DNA or intermediates in the process of DNA demethylation. Emerging biochemical, genetic, and functional evidence suggests that Tet proteins are crucial for diverse biological processes, including zygotic epigenetic reprogramming, pluripotent stem cell differentiation, hematopoiesis, and development of leukemia. Insights into how Tet proteins contribute to dynamic changes in DNA methylation and gene expression will greatly enhance our understanding of epigenetic regulation of normal development and human diseases.
Macrophages and cathepsin proteases blunt chemotherapeutic response in breast cancer
Authors: Shree Tanaya , Olson Oakley C. , Elie Benelita T. , Kester Jemila C. , Garfall Alfred L. , Simpson Kenishana , Bell-McGuinn Katherine M. , Zabor Emily C. , Brogi Edi , Joyce Johanna A.
Published: December 2011

The microenvironment is known to critically modulate tumor progression, yet its role in regulating treatment response is poorly understood. Here we found increased macrophage infiltration and cathepsin protease levels in mammary tumors following paclitaxel (Taxol) chemotherapy. Cathepsin-expressing macrophages protected against Taxol-induced tumor cell death in coculture, an effect fully reversed by cathepsin inhibition and mediated partially by cathepsins B and S. Macrophages were also found to protect against tumor cell death induced by additional chemotherapeutics, specifically etoposide and doxorubicin. Combining Taxol with cathepsin inhibition in vivo significantly enhanced efficacy against primary and metastatic tumors, supporting the therapeutic relevance of this effect. Additionally incorporating continuous low-dose cyclophosphamide dramatically impaired tumor growth and metastasis and improved survival. This study highlights the importance of integrated targeting of the tumor and its microenvironment and implicates macrophages and cathepsins in blunting chemotherapeutic response.
Rare versus common variants in pharmacogenetics: SLCO1B1 variation and methotrexate disposition
Authors: Ramsey Laura B. , Bruun Gitte H. , Yang Wenjian , Treviño Lisa R. , Vattathil Selina , Scheet Paul , Cheng Cheng , Rosner Gary L. , Giacomini Kathleen M. , Fan Yiping , Sparreboom Alex , Mikkelsen Torben S. , Corydon Thomas J. , Pui Ching-Hon , Evans William E. , Relling Mary V.
Published: December 2011

Methotrexate is used to treat autoimmune diseases and malignancies, including acute lymphoblastic leukemia (ALL). Inter-individual variation in clearance of methotrexate results in heterogeneous systemic exposure, clinical efficacy, and toxicity. In a genome-wide association study of children with ALL, we identified SLCO1B1 as harboring multiple common polymorphisms associated with methotrexate clearance. The extent of influence of rare versus common variants on pharmacogenomic phenotypes remains largely unexplored. We tested the hypothesis that rare variants in SLCO1B1 could affect methotrexate clearance and compared the influence of common versus rare variants in addition to clinical covariates on clearance. From deep resequencing of SLCO1B1 exons in 699 children, we identified 93 SNPs, 15 of which were non-synonymous (NS). Three of these NS SNPs were common, with a minor allele frequency (MAF) >5%, one had low frequency (MAF 1%–5%), and 11 were rare (MAF <1%). NS SNPs (common or rare) predicted to be functionally damaging were more likely to be found among patients with the lowest methotrexate clearance than patients with high clearance. We verified lower function in vitro of four SLCO1B1 haplotypes that were associated with reduced methotrexate clearance. In a multivariate stepwise regression analysis adjusting for other genetic and non-genetic covariates, SLCO1B1 variants accounted for 10.7% of the population variability in clearance. Of that variability, common NS variants accounted for the majority, but rare damaging NS variants constituted 17.8% of SLCO1B1's effects (1.9% of total variation) and had larger effect sizes than common NS variants. Our results show that rare variants are likely to have an important effect on pharmacogenetic phenotypes.
Phototropins But Not Cryptochromes Mediate the Blue Light-Specific Promotion of Stomatal Conductance, While Both Enhance Photosynthesis and Transpiration under Full Sunlight
Authors: Boccalandro Hernán E. , Giordano Carla V. , Ploschuk Edmundo L. , Piccoli Patricia N. , Bottini Rubén , Casal Jorge J.
Published: December 2011

Leaf epidermal peels of Arabidopsis (Arabidopsis thaliana) mutants lacking either phototropins 1 and 2 (phot1 and phot2) or cryptochromes 1 and 2 (cry1 and cry2) exposed to a background of red light show severely impaired stomatal opening responses to blue light. Since phot and cry are UV-A/blue light photoreceptors, they may be involved in the perception of the blue light-specific signal that induces the aperture of the stomatal pores. In leaf epidermal peels, the blue light-specific effect saturates at low irradiances; therefore, it is considered to operate mainly under the low irradiance of dawn, dusk, or deep canopies. Conversely, we show that both phot1 phot2 and cry1 cry2 have reduced stomatal conductance, transpiration, and photosynthesis, particularly under the high irradiance of full sunlight at midday. These mutants show compromised responses of stomatal conductance to irradiance. However, the effects of phot and cry on photosynthesis were largely nonstomatic. While the stomatal conductance phenotype of phot1 phot2 was blue light specific, cry1 cry2 showed reduced stomatal conductance not only in response to blue light, but also in response to red light. The levels of abscisic acid were elevated in cry1 cry2. We conclude that considering their effects at high irradiances cry and phot are critical for the control of transpiration and photosynthesis rates in the field. The effects of cry on stomatal conductance are largely indirect and involve the control of abscisic acid levels.