bluuebunny/crossref_metadata_2025 huggingface dataset:
The Integrated Use of Models for the Properties and Effects of Chemicals by means of a Structured Workflow
Authors: Bassan Arianna , Worth Andrew P.
Published: January 2008

This paper reviews the applicability of different types of non‐testing methods and in silico tools in the framework of a structured workflow that aids their exploitation for the prediction of properties that contribute to hazard and risk assessments of chemicals. These properties include basic physicochemical properties, metabolic and environmental fate, and ecological and health effects of chemicals. The workflow for the use of methods comprises a structured sequence of operations that integrates the functionalities of a wide array of in silico tools. The workflow could be used for in‐house decision making (e.g. screening the properties of potential drugs and commercial chemicals) as well generating data required in regulatory submissions. The general workflow presented here is intended to broadly applicable to all endpoints and different regulatory frameworks, including the Registration, Evaluation, Authorisation and Restriction of Chemicals (REACH) legislation in the European Union (EU). The general framework can be adapted to meet the needs of specific chemicals, endpoints and regulatory purposes. This review is one of a series of minireviews in this journal.
Low‐lying singlet excited states of isocyanogen
Authors: Ringer Ashley L. , Sherrill C. David , King Rollin A. , Crawford T. Daniel
Published: January 2008

Recent photofragment fluorescence excitation (PHOFEX) spectroscopy experiments have observed the Ã1A″ singlet excited state of isocyanogen (CNCN) for the first time. The observed spectrum is not completely assigned and significant questions remain about the excited states of this system. To provide insight into the energetically accessible excited states of CNCN, optimized geometries, harmonic vibrational frequencies, and excitation energies for the first three singlet excited states are determined using equation‐of‐motion coupled‐cluster theory with singles and doubles (EOM‐CCSD) and correlation‐consistent basis sets. Additionally, excited state coupled‐cluster methods which approximate the contributions from triples (CC3) are utilized to estimate the effect of higher‐order correlation on the energy of each excited state. For the Ã1A″ state, our best estimate for T0 is about 42,200 cm−1, in agreement with the experimentally estimated upper limit for the zero‐point level of 42,523 cm−1. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Potential energy surface and highly excited vibrational lines of NO2 via algebraic approach
Authors: Zheng Yujun , Ding Shiliang
Published: January 2008

The algebraic Hamiltonian of NO2 is optimized using U(4) algebra via fitting to 102 observed vibrational lines. The RMS error of the fitting is 2.39 cm−1. We calculated highly excited vibrational energy levels using this optimized Hamiltonian, and then obtained the potential energy surface for the electronic ground state by using the classical limit of the U(4) algebraic Hamiltonian. We also calculated the dissociation energies, the force constants etc. Our results are in good agreement with the other theoretical results. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Computational Models of a Nano Probe Tip for Static Behaviors
Authors: Feng Shaw C. , Vorburger Theodore V. , Joung Che bong , Dixson Ronald G. , Fu Joseph , Ma Li
Published: January 2008

It is difficult to predict the measurement bias arising from the compliance of the atomic force microscope (AFM) probe. The issue becomes particularly important in this situation where nanometer uncertainties are sought for measurements with dimensional probes composed of flexible carbon nanotubes mounted on AFM cantilevers. We have developed a finite element model for simulating the mechanical behavior of AFM cantilevers with carbon nanotubes attached. Spring constants of both the nanotube and cantilever in two directions are calculated using the finite element method with known Young's moduli of both silicon and multiwall nanotube as input data. Compliance of the nanotube‐attached AFM probe tip may be calculated from the set of spring constants. This paper presents static models that together provide a basis to estimate uncertainties in linewidth measurement using nanotubes. In particular, the interaction between a multiwall nanotube tip and a silicon sample is modeled using the Lennard‐Jones theory. Snap‐in and snap‐out of the probe tip in a scanning mode are calculated by integrating the compliance of the probe and the sample‐tip interacting force model. Cantilever and probe tip deflections and points of contact are derived for both horizontal scanning of a plateau and vertically scanning of a wall. The finite element method and the Lennard‐Jones model provide a means to analyze the interaction of the probe and sample and measurement uncertainty, including actual deflection and the gap between the probe tip and the measured sample surface. SCANNING 30: 47–55, 2008. © 2008 Wiley Periodicals, Inc.
Cytotoxicity of Aggregated Fullerene C60 Particles on CHO and MDCK Cells
Authors: Han Binbing , Karim M. Nazmul
Published: January 2008

The cytotoxicity of fullerene C60 particles on two mammalian cell lines, i.e. the Chinese hamster ovary (CHO) cells and the Madin‐Darby canine kidney (MDCK) cells, has been investigated. Although innate fullerene particles have a very low solubility in deionized (DI) water, these particles can be dissolved in the tetrahydrofuran (THF) solvent at a great value. Further, the dissolved fullerene particles in the THF solvent could be extracted into a DI water solution at a significantly increased solubility. The formation of fullerene particle aggregates is believed to be the cause of the increased solubility. Results presented here show that once the concentration of the fullerene aggregates reaches a certain level, the cells start to die. The lethal dosage LD50, which is defined as the lowest fullerene concentration that results in a 50% cell death within 24 h, has been determined. Furthermore, the percentage of cell mortality increased with increasing fullerene concentration and incubation time yielding a negative effect on cell viability. These results, illustrated by atomic force microscopy (AFM), dynamic light scattering (DLS) and other microscopic techniques, will help to better understand the side effects of fullerene particles in mammalian cells. SCANNING 30: 000–000, 2008. © 2008 Wiley Periodicals, Inc.
Achieving Precision and Reproducibility for Writing Patterns of n‐alkanethiol Self‐assembled Monolayers with Automated Nanografting
Authors: Ngunjiri Johnpeter N. , Kelley Algernon T. , Lejeune Zorabel M. , Li Jie‐Ren , Lewandowski Brian R. , Serem Wilson K. , Daniels Stephanie L. , Lusker Kathie L. , Garno Jayne C.
Published: January 2008

Nanografting is a high‐precision approach for scanning probe lithography, which provides unique advantages and capabilities for rapidly writing arrays of nanopatterns of thiol self‐assembled monolayers (SAMs). Nanografting is accomplished by force‐ induced displacement of molecules of a matrix SAM, followed immediately by the self‐assembly of n‐alkanethiol ink molecules from solution. The feedback loop used to control the atomic force microscope tip position and displacement enables exquisite control of forces applied to the surface, ranging from pico to nanonewtons. To achieve high‐resolution writing at the nanoscale, the writing speed, direction, and applied force need to be optimized. There are strategies for programing the tip translation, which will improve the uniformity, alignment, and geometries of nanopatterns written using open‐loop feedback control. This article addresses the mechanics of automated nanografting and demonstrates results for various writing strategies when nanografting patterns of n‐alkanethiol SAMs. SCANNING 30: 000–000, 2008. © 2008 Wiley Periodicals, Inc.
Political, religious and occupational identities in context: Placing identity status paradigm in context
Authors: Solomontos‐Kountouri Olga , Hurry Jane
Published: January 2008

This study critically contrasts global identity with domain‐specific identities (political, religious and occupational) and considers context and gender as integral parts of identity. In a cross‐sectional survey, 1038 Greek Cypriot adolescents (449 boys and 589 girls, mean age 16.8) from the three different types of secondary schools (state, state technical and private) and from different SES completed part of the Extended Objective Measure of Ego Identity Status‐2 (EOMEIS‐2). The macro‐context of Greek Cypriot society is used to understand the role of context in adolescents’ identities. Results showed that Greek Cypriot young people were not in the same statuses across their global, political, religious and occupational identities. This heterogeneity in the status of global identity and of each identity domain is partially explained by differences in gender, type of school and SES (socio‐economic status). The fact that identity status is found to be reactive to context suggests that developmental stage models of identity status should place greater emphasis on context.
WEALTH AND INEQUALITY IN 18TH-CENTURY KASTAMONU: ESTIMATIONS FOR THE
MUSLIM MAJORITY
Authors: Ergene Boğaç A. , Berker Ali
Published: January 2008

This paper introduces methods to estimate wealth levels and disparities among
Muslim inhabitants of 18th-century Ottoman Kastamonu. Our sources in this
pursuit are estate inventories of the deceased (sing. tereke) as recorded in Kastamonu court records (sicils), mainly in the first half of the 18th
century (1712-60). By analyzing information provided by these sources through a
variety of quantitative techniques, we measure levels of inequality among
Muslims of Kastamonu and describe the relationship between economic privilege
and social, political, religious, and occupational status as well as gender
identity. Our work outlines the contours of economic stratification in
18th-century Kastamonu and reveals the relative positions of various social
groups within this hierarchy.
POLICING THE COUNTRYSIDE: GENDARMES OF THE LATE 19TH-CENTURY OTTOMAN EMPIRE (1876–1908)
Authors: Özbek Nadir
Published: January 2008

This article lays groundwork for a more systematic history of the Ottoman gendarmerie (jandarma), here with special emphasis on the men in the corps and their working conditions. The gendarmerie, which before 1879 reform the Ottomans calledasakir-i zabtiye, was a provincial paramilitary police organization established by bureaucrats of the Tanzimat state during the 1840s on an ad hoc basis. This force later acquired a more uniform and centralized character, becoming the empire's principal internal security organization. Through this paramilitary police institution, 19th-century Ottoman bureaucrats aimed to extend their authority into the provinces, which at that time could be described as only marginally under Ottoman sovereignty according to contemporary definitions of the term. From the late 18th century on, extending state sovereignty to recognized territorial boundaries emerged as a vital need for most European states as well as the Ottoman Empire. Along with other modern military and civil institutions and modern administrative practices, introducing various types of paramilitary provincial police forces enabled governments in Europe to enhance and extend their authority over territories in which it had been limited. The gendarmerie thus emerged in both Europe and in the Ottoman Empire as integral to modern state formation and its technologies of government. Although acknowledging the Pan-European context of the gendarmerie's emergence and its theoretical ramifications, the present article is concerned more with the Ottoman context within which this police corps was established, evolved, and took on a uniquely Ottoman form.
The Co-ordinating State and the Economy: The Nizamat in Eighteenth-Century Bengal
Authors: MUKHERJEE TILOTTAMA
Published: January 2008

The economy of eighteenth-century Bengal was closely tied to the political, with the indigenous state, theNizamat, maintaining a stake in the success of commercial circuits. TheNizamatplayed a positive role in keeping the structure operative through its patronage and regulating activities. Besides its direct involvement in trade, the article examines the indirect facilitating and co-ordinating role it played, the elaboration of a distinct court culture and the policies it pursued which had a bearing on the health of the economy. The conditions necessary for the functioning of marketing networks—protection of property and enforcement of contract—were maintained. It was a mutually beneficial system with the state with its seat in Murshidabad, the landed élite of the region, and the commercial sector symbiotically tied together.
The Intersection of Students' Perceptions of Instrumentality, Self-Efficacy, and Goal Orientations in an Online Mathematics Course
Authors: Husman Jenefer , Hilpert Jonathan
Published: January 2008

Abstract. The theoretical foundations of this research were Future Time Perspective ( Simons et al., 2004 ) and Expectancy × Value ( Wigfield & Eccles, 2002 ) theories of motivation. The goals of the current study were to better understand (1) the relationship of endogenous perceptions of instrumentality to student self-efficacy, self-regulation, and goal orientation during the semester; (2) the relative influence of endogenous perceptions of instrumentality, self-efficacy, self-regulation, and goal orientation on course performance; (3) the unique contribution of endogenous perceptions of instrumentality, self-efficacy, self-regulation, and goal orientation to course performance; and (4) the potential change in student endogenous perceptions of instrumentality and self-efficacy during the semester of study in relationship to course performance. Four hundred and eighty seven undergraduate students' enrolled in an online introductory algebra course participated in this study. Results indicated that, after controlling for self-efficacy and endogenous perceptions of instrumentality at the beginning of the semester, students' self-regulation, self-efficacy, and endogenous perceptions of instrumentality at the end of the semester predicted 24% of the variance in student course performance. Students' self-reported goal orientations at the beginning of the semester were not related to their course performance.
Are There Gender Differences in Computer Performance? If So, Can Motivation Explain Them?
Authors: Vollmeyer Regina , Imhof Margarete
Published: January 2008

Abstract. Building on previous research which suggests that females are at a disadvantage when working with computers, the current paper investigates possible explanations. We used the cognitive-motivational process model ( Vollmeyer & Rheinberg, 1999 , 2000 ) to explore if motivation can account for the performance differences between male and female students. The model assumes that initial motivation affects strategies and motivation during learning which then influence performance. Male and female students from an introductory statistics class (N = 40), had to solve four statistics tasks with SPSS in 30 minutes. Measurements included initial motivation, functional state (i.e., flow) during task performance, navigation style, and task performance. Results show that males outperform females in terms of time needed for task completion and performance level. Male students displayed more solution-oriented navigation traces than female students. In a tentative exploratory path model, flow-experience and navigation style could be identified as mediating variables. The findings are interpreted in terms of a more effective use of trial-and-error strategies and a preference for tinkering behavior by males.
What Have We Learned About the Link Between Motivation and Learning/Performance?
Authors: Boekaerts Monique
Published: January 2008

Abstract. A brief summary is given of the results reported by the five articles of the special issue. It is explored how each article contributes to our understanding of the motivation-learning/performance link. It is also described how the articles collectively contribute to an increased understanding of the relation between motivation and self-regulated learning. Finally, some of the challenges are addressed that are faced by motivation researcher, focusing mainly on issues that are stimulated by the articles in this special issue, and it is diverged to issues that go beyond the concerns mentioned by the researchers.
Effects of tidal straining on the semidiurnal cycle of dissipation in the Rhine region of freshwater influence: Comparison of model and measurements
Authors: Souza Alejandro J. , Fisher Neil R. , Simpson John H. , Howarth M. John
Published: January 2008

The Rhine region of freshwater influence in the North Sea is a region of the coastal ocean that exhibits strong cross‐shore density gradients interacting with the progressive Kelvin tidal wave which generates mixing. When mixing is low enough to allow stratification to develop, the stratification modifies the tidal currents and generates a strong tidal shear that will strain the density gradients generating a semidiurnal cycle of stratification. Observations of turbulent kinetic energy dissipation ( ) during calm conditions show that the bottom half of the water column has a predominantly M 4 cycle. Higher values of occurring during flood flow are associated with the residual flow in that direction. Following the strong peak in dissipation near the bed, enhanced dissipation is apparent extending up the water column. In the upper part of the water column, shows a predominantly M 2 variation with the maximum occurring at a time when vertical stability is negligible and the effect of tidal straining is to create instability in the water column as the cross‐shore shear forces higher salinity water over fresher water. The inference is that potential energy released by straining is responsible for convective motions and, hence, the enhanced turbulent activity observed. The cycle of stratification and dissipation has been simulated using a one‐dimensional Mellor‐Yamada levels 2 and 2.2 turbulence closure model. The model correctly predicts the amplitude and phase of the stratification. While the model is in qualitative agreement in the description of the dissipation and its variability, the absolute values of appear to be too high.
Late Miocene high and rapid surface uplift and its erosional response in the Andes of central Chile (33°–35°S)
Authors: Farías Marcelo , Charrier Reynaldo , Carretier Sébastien , Martinod Joseph , Fock Andrés , Campbell David , Cáceres Joaquín , Comte Diana
Published: January 2008

We address the question of the late Cenozoic geomorphological evolution of the central Chile Andes (33°–35°S), using uplift markers, river incision, previous and new ages of volcanic bodies, and new fission track ages. The uplift markers consist of relicts of high elevated peneplains that evidence >2 km of regional surface uplift lasting ∼2 Ma with variable amount along an E‐W transect. The eastern Coastal Cordillera was uplifted 1.5–2.1 km at 33–34°S and <1 km at 35°S, the western Principal Cordillera was uplifted ∼2 km, and the central eastern Principal Cordillera was uplifted >2.5 at 33°45′S and ∼1.5 km at 34°30′S. Erosional response to uplift was characterized by the retreat of a sharp knickpoint with celerities between 10 and 40 mm a−1. Extrapolation using a stream power law shows that uplift began shortly before 4 Ma or at 10.5–4.6 Ma (7.6 Ma central age) depending on the morphostructural units involved. The first alternative implies simultaneous uplift of the continental margin. The second model (the most reliable one) implies that the uplift affected together the eastern Coastal Cordillera and the Principal Cordillera, while the rest of the western fore arc subsided. This regional uplift can be mostly balanced by crustal thickening resulting from coeval shortening related to the out‐of‐sequence thrusting event in the Principal Cordillera and the uplift of the Frontal Cordillera. Simultaneously, emplacement of the southern edge of the flat slab subduction zone might have partially contributed to this uplift event.
Temporal evolution of the transpolar potential after a sharp enhancement in solar wind dynamic pressure
Authors: Boudouridis A. , Zesta E. , Lyons L. R. , Anderson P. C. , Ridley A. J.
Published: January 2008

Recent studies of ionospheric convection have shown that sudden enhancements in solar wind dynamic pressure have significant effect on the transpolar potential and the coupling efficiency between the solar wind and the terrestrial magnetosphere. Super Dual Auroral Radar Network observations of the dayside convection have demonstrated that the strength of convection correlates well with solar wind dynamic pressure variations, implying an enhancement of dayside reconnection induced by changes in solar wind pressure. At the same time, dynamic pressure increases have been shown to lead to closing of the polar cap, particularly on the nightside, and thus directly drive enhanced tail reconnection. The enhanced dayside and nightside reconnection potentials can both lead to changes in the transpolar potential, but their individual contributions and the balance between the two is not known. We present a case study of the transpolar potential evolution after a long‐lasting solar wind pressure step increase. We show that the potential first rises in response to the increase in pressure, then gradually subsides a few hours later despite the solar wind pressure remaining high. We interpret this behavior in terms of pressure‐driven changes in dayside and nightside reconnection.
Influence of morphology and permafrost dynamics on hyporheic exchange in arctic headwater streams under warming climate conditions
Authors: Zarnetske Jay P. , Gooseff Michael N. , Bowden W. Breck , Greenwald Morgan J. , Brosten Troy R. , Bradford John H. , McNamara James P.
Published: January 2008

We investigated surface‐subsurface (hyporheic) exchange in two morphologically distinct arctic headwater streams experiencing warming (thawing) sub‐channel conditions. Empirically parameterized and calibrated groundwater flow models were used to assess the influence of sub‐channel thaw on hyporheic exchange. Average thaw depths were at least two‐fold greater under the higher‐energy, alluvial stream than under the low‐energy, peat‐lined stream. Alluvial hyporheic exchange had shorter residence times and longer flowpaths that occurred across greater portions of the thawed sediments. For both reaches, the morphologic (longitudinal bed topography) and hydraulic conditions (surface and groundwater flow properties) set the potential for hyporheic flow. Simulations of deeper thaw, as predicted under a warming arctic climate, only influence hyporheic exchange until a threshold depth. This depth is primarily determined by the hydraulic head gradients imposed by the stream morphology. Therefore, arctic hyporheic exchange extent is likely to be independent of greater sub‐stream thaw depths.
An interpretation of Australian rainfall projections
Authors: Shi G. , Ribbe J. , Cai W. , Cowan T.
Published: January 2008

The majority of climate models project a winter rainfall reduction over south‐eastern Australia (SEA), while some show a tendency for a summer rainfall increase. The dynamics for these rainfall changes are not clear. Using outputs from a climate model, we show that a summer rainfall increase is consistent with a large Tasman Sea warming promoting convection, and an upward trend of the Southern Annular Mode (SAM) promoting onshore flows; these processes dominate over a rainfall decrease from an El Niño‐like warming pattern. In winter, similar effects from a Tasman Sea warming and an upward SAM trend operate along Australia's east coast, however, the rain‐reducing impact of an Indian Ocean Dipole‐like warming pattern dominates. In both seasons, the upward SAM trend causes a rainfall reduction over southern Australia. Summer rainfall over north‐western Australia is projected to decrease, due to an unrealistic relationship with the El Niño‐Southern Oscillation. Possible uncertainties are discussed.
Generation of a trigger meander for the 2004 Kuroshio large meander
Authors: Usui Norihisa , Tsujino Hiroyuki , Fujii Yosuke , Kamachi Masafumi
Published: January 2008

A generation process of a small meander southeast of Kyushu, which triggered the subsequent Kuroshio large meander in 2004, has been investigated using an ocean data assimilation and prediction system. The assimilation result reveals that the small meander is the most developed one since 1993. A cyclonic eddy propagating westward from the Kuroshio recirculation (KR) and a disturbance from the East China Sea (ESC) that accompanies a high potential vorticity (high‐PV) anomaly play important roles for the generation of the small meander. The cyclonic eddy triggers an initial cyclonic anomaly southeast of Kyushu. When the high‐PV anomaly passes through the Tokara Strait, a large positive vorticity is generated because the stretching of the water column is enhanced. The positive vorticity is brought in the cyclonic anomaly and accumulates there. As a result, the small meander is generated. From two sensitivity experiments an occurrence condition is determined by the cyclonic eddy from the KR by triggering the initial small‐scale meander, and the disturbance from the ECS contributes to the horizontal scale of the small meander. Tracing back the disturbance further to the upstream region of the Kuroshio, it is revealed that the disturbance is a frontal wave with a large horizontal scale generated by collision between a strong anticyclonic eddy and the Kuroshio east of Taiwan. The frontal wave propagates along the Kuroshio accompanying high‐PV generated around the continental shelf edge by viscosity. Thus the large frontal wave could contribute to the generation of the developed trigger meander by transporting a larger amount of high‐PV anomaly to the Tokara Strait.
Possible representation errors in inversions of satellite CO2 retrievals
Authors: Corbin Katherine D. , Denning A. Scott , Lu Lixin , Wang Jih‐Wang , Baker Ian T.
Published: January 2008

Owing to global spatial sampling and sheer data volume, satellite CO2 concentrations can be used in inverse models to enhance our understanding of the carbon cycle. Using column measurements to represent a transport model grid column may introduce spatial, local clear‐sky, and temporal sampling errors into inversions: the footprint is smaller than a grid cell, total column concentrations are only retrieved in clear skies, and the mixing ratios are only sampled at one time. To investigate these errors, we used a coupled ecosystem‐atmosphere cloud‐resolving model to create CO2 fields over fine (∼1° × 1°) and coarse (∼4° × 4°) grid columns from 1 km2 and 25 km2 pixels that utilized explicit microphysics. We performed two simulations in August 2001: one in central North America and one in the Brazilian Amazon. Differences between satellite and grid column concentrations were calculated by subtracting the domain mean column concentration from 10‐km‐wide simulated satellite measurements. Spatial and local clear‐sky errors were less than 0.5 ppm for the fine grid column; however, these errors became large and biased over the coarse grid column in North America. To avoid these errors, transport models should be run at high resolution. Using satellite measurements to represent bimonthly averages created large (>1 ppm) errors for all cases. The errors were negatively biased (approximately −0.4 ppm) in the North American simulation, indicating that inverse models cannot use satellite measurements to represent temporal averages. Simulated representation errors did not arise because of differences in ecosystem metabolism in cloudy versus sunny conditions; rather, they reflected large‐scale CO2 gradients in midlatitudes that were organized along frontal boundaries and masked under regional cloud cover. Such boundaries were not found in the dry‐season tropical simulation presented here and may be less prevalent in the tropics in general. To avoid incurring errors, inversions must accurately model synoptic‐scale atmospheric transport and CO2 concentrations must be assimilated at the time and place observed.
Addressing equifinality and uncertainty in eutrophication models
Authors: Arhonditsis George B. , Perhar Gurbir , Zhang Weitao , Massos Evangelia , Shi Molu , Das Argho
Published: January 2008

Large simulation models of eutrophication processes are commonly used to aid scientific understanding and to guide management decisions. Confidence in models for these purposes depends on uncertainty in model equations (structural uncertainty) and on effects of input uncertainties (model parameters, initial conditions, and forcing functions) on model outputs. Our objective herein is to illustrate two strategies, a generalized likelihood uncertainty estimation (GLUE) approach combined with a simple Monte Carlo sampling scheme and a Bayesian methodological framework along with Markov Chain Monte Carlo (MCMC) simulations, for elucidating the propagation of uncertainty in the high‐dimensional parameter spaces of mechanistic eutrophication models. We examine the ability of the two approaches to offer insights into the degree of information about model inputs that the data contain, to quantify the correlation structure among parameter estimates, and to obtain predictions along with uncertainty bounds for modeled output variables. Our analysis is based on a four‐state‐variable (phosphate‐detritus‐phytoplankton‐zooplankton) model and the mesotrophic Lake Washington (Washington State, United States) as a case study. Scientific knowledge, expert judgment, and observational data were used to formulate prior probability distributions and characterize the uncertainty pertaining to 14 model parameters. Despite the conceptual differences for addressing model equifinality, that is, wide ranges of parameter values subject to complex multivariate relationships that result in plausible observed behaviors and produce equivalently accurate predictions, we found that the two strategies provided fairly consistent estimates of the posterior parameter correlation structure and output uncertainty. Nonetheless, our analysis also shows that MCMC can more efficiently quantify the joint probability distribution of model parameters and make inference about this distribution. The latter finding can be explained by the basic idea underlying the MCMC methodology, that is, the configuration of a Markov process whose stationary distribution approximates the joint posterior distribution of all the stochastic model nodes; as a result, Monte Carlo samples are not drawn from the prior parameter space, and problems of wide or highly correlated prior distributions can be overcome. Finally, our study stresses the lack of perfect simulators of natural system dynamics and introduces two statistical formulations that can explicitly account for the discrepancy between mathematical models and environmental systems.
Social Phobia in an Outpatient Alcohol and Drug Treatment Sample
Authors: Adamson Simon J. , Sellman J. Douglas , Robertson Paul J.
Published: January 2008

Objective: To examine characteristics of patients with social phobia (SP) in alcohol and drug treatment settings and to identify features distinguishing this group from patients with and without other psychiatric conditions.

Method: A random sample of 105 patients completing an initial assessment at two outpatient alcohol and drug treatment services were assessed and agreed to a 9 month follow-up interview, completed by n=102 (97%). At baseline the Composite International Diagnostic Interview (CIDI) was administered. Current diagnoses at baseline were used to separate the sample into those with SP (n=33), other current psychiatric disorders (OPD, n=40), and those with no current psychiatric diagnosis other than a substance use disorder (NPD, n=29). The novel methodology used in this study compared the SP group first to the NPD group to see if SP was associated with a different presentation, and then compared the SP group to the OPD group to see if any identified differences were associated with SP per se or psychopathology generally. The three groups were compared on demographic, current clinical, and past treatment utilization variables at baseline, while follow-up data were used to compare the groups on treatment outcome and treatment utilization.

Results: The SP group did not differ from either group in a systematic way. What differences did emerge tended to show a difference between OPD and NPD, with SP intermediate between the two, or that SP and OPD together were different from NPD.

Conclusions: Despite the relatively small sample size, these findings suggest that in substance use disorder treatment settings, patients with coexisting SP do not represent a distinctly high-needs or at-risk group in the broader context of patient populations, for which coexisting psychiatric diagnoses are the norm rather than the exception.
Clozapine Use in a Forensic Population in a New South Wales Prison Hospital
Authors: Martin Adam , O'Driscoll Colmán , Samuels Anthony
Published: January 2008

Objective: To document and measure various parameters and outcomes in patients prescribed clozapine in a forensic psychiatric setting.

Method: A retrospective file review was conducted on patients prescribed clozapine. Parameters and outcomes were recorded and compared against a group prescribed other antipsychotics, matched for sex and diagnosis.

Results: Patients prescribed clozapine had higher rates of substance misuse syndromes and comorbidity when compared to patients prescribed other antipsychotics. Clozapine was found to be effective in treatment of psychosis. High rates of adverse effects were noted. Discontinuation of clozapine for a variety of reasons was common.

Conclusion: Patients identified as treatment resistant who are prescribed clozapine are often more complex in the pattern of illness and subsequent needs. Clozapine is effective in the treatment of psychosis in this forensic service. Its benefits need to be balanced against the potential for adverse effects and problems ensuring adherence. Regular, objective monitoring of clinical and adverse effects would aid patient safety, clinical decision-making and future research.
Microanatomy of Early Devonian book lungs
Authors: Kamenz Carsten , Dunlop Jason A , Scholtz Gerhard , Kerp Hans , Hass Hagen
Published: January 2008

The book lungs of an exceptionally preserved fossil arachnid (Trigonotarbida) from the Early Devonian (approx. 410 Myr ago) Rhynie cherts of Scotland were studied using a non-destructive imaging technique. Our three-dimensional modelling of fine structures, based on assembling successive images made at different focal planes through the translucent chert matrix, revealed for the first time fossil trabeculae: tiny cuticular pillars separating adjacent lung lamellae and creating a permanent air space. Trabeculae thus show unequivocally that trigonotarbids were fully terrestrial and that the microanatomy of the earliest known lungs is indistinguishable from that in modern Arachnida. A recurrent controversy in arachnid evolution is whether the similarity between the book lungs of Pantetrapulmonata (i.e. spiders, trigonotarbids, etc.) and those of scorpions is a result of convergence. Drawing on comparative studies of extant taxa, we have identified explicit characters (trabeculae, spines on the lamellar edge) shared by living and fossil arachnid respiratory organs, which support the hypothesis that book lungs were derived from a single, common, presumably terrestrial, ancestor.
The economics of altruistic punishment and the maintenance of cooperation
Authors: Egas Martijn , Riedl Arno
Published: January 2008

Explaining the evolution and maintenance of cooperation among unrelated individuals is one of the fundamental problems in biology and the social sciences. Recent findings suggest that altruistic punishment is an important mechanism maintaining cooperation among humans. We experimentally explore the boundaries of altruistic punishment to maintain cooperation by varying both the cost and the impact of punishment, using an exceptionally extensive subject pool. Our results show that cooperation is only maintained if conditions for altruistic punishment are relatively favourable: low cost for the punisherandhigh impact on the punished. Our results indicate that punishment is strongly governed by its cost-to-impact ratio and that its effect on cooperation can be pinned down to one single variable: the threshold level of free-riding that goes unpunished. Additionally, actual pay-offs are the lowest when altruistic punishment maintains cooperation, because the pay-off destroyed through punishment exceeds the gains from increased cooperation. Our results are consistent with the interpretation that punishment decisions come from an amalgam of emotional response and cognitive cost–impact analysis and suggest that altruistic punishment alone can hardly maintain cooperation under multi-level natural selection. Uncovering the workings of altruistic punishment as has been done here is important because it helps predicting under which conditions altruistic punishment is expected to maintain cooperation.
Genetic diversity within honeybee colonies increases signal production by waggle-dancing foragers
Authors: Mattila Heather R , Burke Kelly M , Seeley Thomas D
Published: January 2008

Recent work has demonstrated considerable benefits of intracolonial genetic diversity for the productivity of honeybee colonies: single-patriline colonies have depressed foraging rates, smaller food stores and slower weight gain relative to multiple-patriline colonies. We explored whether differences in the use of foraging-related communication behaviour (waggle dances and shaking signals) underlie differences in foraging effort of genetically diverse and genetically uniform colonies. We created three pairs of colonies; each pair had one colony headed by a multiply mated queen (inseminated by 15 drones) and one colony headed by a singly mated queen. For each pair, we monitored the production of foraging-related signals over the course of 3 days. Foragers in genetically diverse colonies had substantially more information available to them about food resources than foragers in uniform colonies. On average, in genetically diverse colonies compared with genetically uniform colonies, 36% more waggle dances were identified daily, dancers performed 62% more waggle runs per dance, foragers reported food discoveries that were farther from the nest and 91% more shaking signals were exchanged among workers each morning prior to foraging. Extreme polyandry by honeybee queens enhances the production of worker–worker communication signals that facilitate the swift discovery and exploitation of food resources.
Counter-intuitive developmental plasticity induced by host quality
Authors: Röder Gregory , Rahier Martine , Naisbit Russell E
Published: January 2008

Adaptation to different hosts plays a central role in the evolution of specialization and speciation in phytophagous insects and parasites, and our ability to experimentally rank hosts by their quality is critical to research to understand these processes. Here we provide a counter-intuitive example in which growth is faster on poor quality hosts. The leaf beetles
Oreina elongata
and
Oreina cacaliae
share their host plant with the rust
Uromyces cacaliae
. Larvae reared on infected
Adenostyles alliariae
show reduced growth rate, reduced maximum weight and longer development time. However, they normally respond adaptively to the rust's mid-season arrival. When switched during development from healthy to infected leaves, larvae accelerate growth and reduce development time, but pupate at lower body weight. In this novel plant–insect–fungus interaction, infection forms the cue to trade off life-history traits in order to complete development within the brief alpine summer. It represents a novel mode of developmental plasticity, which is likely to be found in other host–parasite systems whenever host quality deteriorates due to multiple infection or ageing. This phenotypic plasticity would modify competition after co-infection and the mutual selection imposed by hosts and parasites, and creates a paradoxical negative correlation between growth rate and environmental quality.
Calcium signalling during neural induction inXenopus laevisembryos
Authors: Moreau Marc , Néant Isabelle , Webb Sarah E , Miller Andrew L , Leclerc Catherine
Published: January 2008

InXenopus, experiments performed with isolated ectoderm suggest that neural determination is a ‘by default’ mechanism, which occurs when bone morphogenetic proteins (BMPs) are antagonized by extracellular antagonists, BMP being responsible for the determination of epidermis. However, Ca2+imaging of intactXenopusembryos reveals patterns of Ca2+transients which are generated via the activation of dihydropyridine-sensitive Ca2+channels in the dorsal ectoderm but not in the ventral ectoderm. These increases in the concentration of intracellular Ca2+([Ca2+]i) appear to be necessary and sufficient to orient the ectodermal cells towards a neural fate as increasing the [Ca2+]iartificially results in neuralization of the ectoderm. We constructed a subtractive cDNA library between untreated and caffeine-treated ectoderms (to increase [Ca2+]i) and then identified early Ca2+-sensitive target genes expressed in the neural territories. One of these genes, an arginine methyltransferase, controls the expression of the early proneural gene, Zic3. Here, we discuss the evidence for the existence of an alternative model to the ‘by default’ mechanism, where Ca2+plays a central regulatory role in the expression ofZic3, an early proneural gene, and in epidermal determination which only occurs when the Ca2+-dependent signalling pathways are inactive.
Understanding how morphogens work
Authors: Smith J.C , Hagemann A , Saka Y , Williams P.H
Published: January 2008

In this article, we describe the mechanisms by which morphogens in theXenopusembryo exert their long-range effects. Our results are consistent with the idea that signalling molecules such as activin and the nodal-related proteins traverse responding tissue not by transcytosis or by cytonemes but by movement through the extracellular space. We suggest, however, that additional experiments, involving real-time imaging of morphogens, are required for a real understanding of what influences signalling range and the shape of a morphogen gradient.
Evidence of frequent recombination among human adenoviruses
Authors: Lukashev Alexander N. , Ivanova Olga E. , Eremeeva Tatiana P. , Iggo Richard D.
Published: January 2008

Genome stability is a prerequisite for the production and use of adenoviruses for therapy of genetic diseases and cancer. To test the premise that the adenoviral genome is stable, the phylogenetic relationships of 16 adenovirus C (AdC) field isolates were studied in four genome regions: hexon, fiber, polymerase and E1A. The phylogenetic relationships in the fiber gene concurred with those in the hexon region. In contrast, the non-structural regions had marks of frequent recombination, to the point that an isolate of one serotype could contain non-structural proteins that were identical to the genes from a different serotype. Our results suggest that recombination among circulating adenoviruses is very frequent and plays an important role in shaping the phylogenetic relationships of adenovirus genomes. Analysis of the available complete genome sequences of AdB, AdC and AdD species showed that recombination shuffles genome fragments within a species, but not between species. One of the AdC field isolates possessed the fiber gene of AdC type 6, but a hexon gene that was distinct from all AdC serotypes. This strain could not be typed unambiguously in a neutralization test and might represent a novel serotype of AdC. Comparison of the right end (nt 18838–33452) of this isolate with that of the ATCC Ad6 strain showed clear evidence of multiple recombination events.
Evaluation of drugs for treatment of prion infections of the central nervous system
Authors: Riemer Constanze , Burwinkel Michael , Schwarz Anja , Gültner Sandra , Mok Simon W. F. , Heise Ines , Holtkamp Nikola , Baier Michael
Published: January 2008

Prion diseases are fatal and at present there are neither cures nor therapies available to delay disease onset or progression in humans. Inspired in part by therapeutic approaches in the fields of Alzheimer's disease and amyotrophic lateral sclerosis, we tested five different drugs, which are known to efficiently pass through the blood–brain barrier, in a murine prion model. Groups of intracerebrally prion-challenged mice were treated with the drugs curcumin, dapsone, ibuprofen, memantine and minocycline. Treatment with antibiotics dapsone and minocycline had no therapeutic benefit. Ibuprofen-treated mice showed severe adverse effects, which prevented assessment of therapeutic efficacy. Mice treated with low- but not high-dose curcumin and mice treated with memantine survived infections significantly longer than untreated controls (P<0.01). These results encourage further research efforts to improve the therapeutic effect of these drugs.
Hepatitis C virus proteins interfere with the activation of chemokine gene promoters and downregulate chemokine gene expression
Authors: Sillanpää Maarit , Kaukinen Pasi , Melén Krister , Julkunen Ilkka
Published: January 2008

The hepatitis C virus (HCV) non-structural (NS) 3/4A protein complex inhibits the retinoic acid inducible gene I (RIG-I) pathway by proteolytically cleaving mitochondria-associated CARD-containing adaptor protein Cardif, and this leads to reduced production of beta interferon (IFN-β). This study examined the expression of CCL5 (regulated upon activation, normal T-cell expressed and secreted, or RANTES), CXCL8 (interleukin 8) and CXCL10 (IFN-γ-activated protein 10, or IP-10) chemokine genes in osteosarcoma cell lines that inducibly expressed NS3/4A, NS4B, core-E1-E2-p7 and the entire HCV polyprotein. Sendai virus (SeV)-induced production of IFN-β, CCL5, CXCL8 and CXCL10 was downregulated by the NS3/4A protein complex and by the full-length HCV polyprotein. Expression of NS3/4A and the HCV polyprotein reduced the binding of interferon regulatory factors (IRFs) 1 and 3 and, to a lesser extent, nuclear factor (NF)-κB (p65/p50) to their respective binding elements on the CXCL10 promoter during SeV infection. Furthermore, binding of IRF1 and IRF3 to the interferon-stimulated response element-like element, and of c-Jun and phosphorylated c-Jun to the activator protein 1 element of the CXCL8 promoter, was reduced when NS3/4A and the HCV polyprotein were expressed. In cell lines expressing NS3/4A and the HCV polyprotein, the subcellular localization of mitochondria was changed, and this was kinetically associated with the partial degradation of endogenous Cardif. These results indicate that NS3/4A alone or as part of the HCV polyprotein disturbs the expression of IRF1- and IRF3-regulated genes, as well as affecting mitogen-activated protein kinase kinase- and NF-κB-regulated genes.
Transcripts encoding the nanovirus master replication initiator proteins are terminally redundant
Authors: Grigoras Ioana , Timchenko Tatiana , Gronenborn Bruno
Published: January 2008

The multicomponent single-stranded DNA plant nanoviruses encode unique master replication initiator (Rep) proteins. We have mapped the 5′ and 3′ termini of the corresponding polyadenylated mRNAs from faba bean necrotic yellows virus (FBNYV) and subterranean clover stunt virus and found that these are terminally redundant by up to about 160 nt. Moreover, the origin of viral DNA replication is transcribed into RNA that is capable of folding into extended secondary structures. Other nanovirus genome components, such as the FBNYV DNA encoding the protein Clink or an FBNYV DNA encoding a non-essential para-Rep protein, are not transcribed in such a unique fashion. Thus, terminally redundant mRNAs and the resulting transcription of the replication origin appear to be restricted to nanovirus master Rep DNAs. We speculate that this may be a way to regulate the expression of the essential master Rep protein.