bluuebunny/crossref_metadata_2025 huggingface dataset:
Age validation of walleye pollock (Theragra chalcogramma) from the Gulf of Alaska using the disequilibrium of Pb-210 and Ra-226
Authors: Kastelle Craig R. , Kimura Daniel K.
Published: August 2006

The walleye pollock (Theragra chalcogramma) is a commercially important species in the North Pacific, and harvest quotas are dependent upon accurate determination of ages. The two techniques (called methods A and B) currently used to interpret the growth zone patterns in walleye pollock otoliths were compared. The age distributions from these two techniques differed; method B produced ages twice that of method A. Validation of ages from walleye pollock has not been done previously. Radiometric ageing based on the ratio of Pb-210/Ra-226 was used to evaluate the accuracy of otolith growth zone counts, and it demonstrated that method A, which produced younger ages between 3 and 8 years, was correct. Walleye pollock grow older than the 3–8 year (method A) age range validated in this study. The experimental design was limited to a maximum method A age of 8 years, because available samples did not provide the minimum of 40 fish required for estimating a radiometric age. Our radiometric ageing study on walleye pollock appears to be the first to use the Pb-210/Ra-226 radiometric age-validation method in a boreal fish species where all samples were potentially young, 8 years or less. In previous studies, radiometric ages often approached 100 years. Also, only one presumed year class was used, which was sampled in successive years. Therefore, Ra-226 sample measurements were averaged to provide lower error.
Rapid changes in the level of Kluane Lake in Yukon Territory over the last millennium
Authors: Clague John J. , Luckman Brian H. , Van Dorp Richard D. , Gilbert Robert , Froese Duane , Jensen Britta J.L. , Reyes Alberto V.
Published: August 2006

The level of Kluane Lake, the largest lake in Yukon Territory, was lower than at present during most of the Holocene. The lake rose rapidly in the late seventeenth century to a level 12 m above present, drowning forest and stranding driftwood on a conspicuous high-stand beach, remnants of which are preserved at the south end of the lake. Kluane Lake fell back to near its present level by the end of the eighteenth century and has fluctuated within a range of about 3 m over the last 50 yr. The primary control on historic fluctuations in lake level is the discharge of Slims River, the largest source of water to the lake. We use tree ring and radiocarbon ages, stratigraphy and sub-bottom acoustic data to evaluate two explanations for the dramatic changes in the level of Kluane Lake. Our data support the hypothesis of Hugh Bostock, who suggested in 1969 that the maximum Little Ice Age advance of Kaskawulsh Glacier deposited large amounts of sediment in the Slims River valley and established the present course of Slims River into Kluane Lake. Bostock argued that these events caused the lake to rise and eventually overflow to the north. The overflowing waters incised the Duke River fan at the north end of Kluane Lake and lowered the lake to its present level. This study highlights the potentially dramatic impacts of climate change on regional hydrology during the Little Ice Age in glacierised mountains.
Eurypterida (Chelicerata) from the Welsh Borderlands, England
Authors: TETLIE O. ERIK
Published: August 2006

Eurypterids from the Welsh Borderlands of England are redescribed from most available material. Hughmilleria banksii is here interpreted to represent a new genus. The poorly known Hughmilleria (?) acuminata (Salter, 1859a) is considered a junior synonym of H. banksii. Furthermore, Slimonia? stylops is suspected to be a junior synonym of Salteropterus abbreviatus, although they are not formally synonymized as the location of the only known specimen of S.? stylops is unknown. Morphological differences in carapace shape, eye position, walking leg, genital appendage and telson in H. banksii are noted compared to previous descriptions. A prosomal appendage earlier assigned to H. banksii is here assigned with caution to S. abbreviatus and the reported ‘segments’ in the posterior part of the telson of S. abbreviatus are shown to be cracks. The phylogenetic position of the new genus is inferred to lie between the Hughmilleria and the Slimonia/Salteropterus clades.
Relationship between drug company funding and outcomes of clinical psychiatric research
Authors: KELLY ROBERT E. , COHEN LISA J. , SEMPLE RANDYE J. , BIALER PHILIP , LAU ADAM , BODENHEIMER ALISON , NEUSTADTER ELANA , BARENBOIM ARKADY , GALYNKER IGOR I.
Published: August 2006

Background. Pharmaceutical industry funding of psychiatric research has increased significantly in recent decades, raising the question of a relationship between pharmaceutical company funding of clinical psychiatric studies and the outcomes of those studies. This study examines this relationship.

Method. Abstracts of articles from 1992 and 2002 in four peer-reviewed psychiatric journals were examined. Drug outcomes (n=542) for clinical studies were evaluated and then compared across sponsorship source. Outcome raters were blind to source of sponsorship. The percentage of these studies sponsored by drug companies in 2002 v. 1992 was also compared. In a secondary analysis, the contribution of a series of potentially mediating variables to the relationship between sponsorship source and study outcome was assessed via logistic regression.

Results. The percentage of studies sponsored by drug companies increased from 25% in 1992 to 57% in 2002. Favorable outcomes were significantly more common in studies sponsored by the drug manufacturer (78%) than in studies without industry sponsorship (48%) or sponsored by a competitor (28%). These relationships remained after controlling for the effects of journal, year, drug studied, time since FDA drug approval, diagnosis, sample size, and selected study design variables.

Conclusions. These data indicate an association between pharmaceutical industry funding of clinical studies and positive outcomes of those studies. Further research is needed to elucidate the mechanisms underlying this relationship.
Caffeine intake, toxicity and dependence and lifetime risk for psychiatric and substance use disorders: an epidemiologic and co-twin control analysis
Authors: KENDLER KENNETH S. , MYERS JOHN , O. GARDNER CHARLES
Published: August 2006

Background. Although caffeine is the most commonly used psychoactive substance and often produces symptoms of toxicity and dependence, little is known, especially in community samples, about the association between caffeine use, toxicity and dependence and risk for common psychiatric and substance use disorders.

Method. Assessments of lifetime maximal caffeine use and symptoms of caffeine toxicity and dependence were available on over 3600 adult twins ascertained from the population-based Virginia Twin Registry. Lifetime histories of major depression (MD), generalized anxiety disorder (GAD) and panic disorder, alcohol dependence, adult antisocial behavior and cannabis and cocaine abuse/dependence were obtained at personal interview. Logistic regression analyses in the entire sample and within monozygotic (MZ) twin pairs were conducted in SAS.

Results. In the entire sample, measures of maximal caffeine use, heavy caffeine use, and caffeine-related toxicity and dependence were significantly and positively associated with all seven psychiatric and substance use disorders. However, within MZ twin pairs, controlling for genetic and family environmental factors, these associations, while positive, were all non-significant. These results were similar when excluding twins who denied regular caffeine use.

Conclusions. Maximal lifetime caffeine intake and caffeine-associated toxicity and dependence are moderately associated with risk for a wide range of psychiatric and substance use disorders. Analyses of these relationships within MZ twin pairs suggest that most of the observed associations are not causal. Rather, familial factors, which are probably in part genetic, predispose to both caffeine intake, toxicity and dependence and the risk for a broad array of internalizing and externalizing disorders.
Face affect recognition deficits in personality-disordered offenders: association with psychopathy
Authors: DOLAN MAIREAD , FULLAM RACHAEL
Published: August 2006

Background. There is a limited literature examining face affect recognition in offenders. In line with the Integrated Emotion Systems (IES) model, existing studies suggest a psychopathy-related deficit in sad/fear recognition. However, many of these studies have small samples, and few include a healthy control group in order to examine the contribution of criminality.

Method. We compared the performance of male criminals with dissocial (antisocial) personality disorder (PD group) and healthy male IQ-matched controls, on a morphed face affect-processing task and examined the relationship between psychopathy (assessed using the Psychopathy Checklist: Screening Version, PCL: SV), score and performance on this task in the PD sample.

Results. The PD group had a specific deficit in the recognition of sad facial affect that was present even at 100% expression intensity. This deficit could not be attributed to impulsive responding as the PD group generally had longer mean reaction times than healthy controls. Within the PD group, those with high scores on the PCL: SV were less accurate than low scorers at classifying sad facial affect. There was also a significant negative correlation between total psychopathy score and sad affect recognition accuracy. There were no specific relationships between affect recognition and the subcomponents of psychopathy.

Conclusions. The findings suggest that criminality/antisocial personality may be associated with a deficit in the recognition of aversive cues in others, and that this deficit is more severe in psychopathic offenders. The findings lend further support to the IES model.
Hybrid velocity/force control for robot navigation in compliant unknown environments
Authors: Palejiya Dushyant , Tanner Herbert G.
Published: August 2006

We combine a “hybrid” force-/position-control scheme with a potential field approach into a novel method for collision recovery and navigation in unknown environments. It can be implemented both on manipulators and mobile robots. The use of force sensors allows us to locally sense the environment and design a dynamic control law. Multiple Lyapunov functions are used to establish asymptotic stability of the closed-loop system. The switching conditions and stability criteria are established under reasonable assumptions on the type of obstacles present in the environment. Extensive simulation results are presented to illustrate the system behavior under the designed control scheme, and verify its stability, collision recovery, and navigation properties.
New visibility-based path-planning approach for covert robotic navigation
Authors: Marzouqi Mohamed S. , Jarvis Ray A.
Published: August 2006

A new promising approach for visibility-sensitive path-planning problems is presented. The paper focuses on covert navigation where a mobile robot needs to plan a stealthy path to approach a designated destination in a cluttered environment. The aim is to minimize the robot's exposure to hostile sentries within the same environment. The approach can be adapted to work with different levels of initial knowledge the robot may have about both the environment map and the sentries' locations. The approach depends on estimating a cost value at each free-space location that presents the risk of being seen by any sentry. Based on the distance transform algorithm methodology, the minimum visibility–distance cost to a goal is calculated at each cell in the grid-based environment map. Moving along the steepest descent trajectory from any starting point generates an optimal covert path to a goal. The approach has been evaluated with both simulated and physical experiments. A number of test cases are presented. In each case, a path with considerable covertness, compared to a short path to the same destination, is generated. In addition to covert navigation, the approach is introduced briefly as a potential solution for other visibility-based path-planning problems.
Physiological and subjective responses to articulated robot motion
Authors: Kulić Dana , Croft Elizabeth
Published: August 2006

This paper describes the implementation and validation of a fuzzy inference engine for estimating human affective state in real-time, using robot motions as the stimulus. The inference engine was tested with 36 subjects. To the authors' knowledge, this paper reports the first such trial that measures affective response to human-scale physical robot motions for a statistically significant population. The results demonstrate that affective state arousal can be detected using physiological signals and the inference engine. Comparison of results between the two planners shows that subjects report less anxiety and surprise with the safe planner.
Discernment between deliberate and natural infectious disease outbreaks
Authors: DEMBEK Z. F. , KORTEPETER M. G. , PAVLIN J. A.
Published: August 2006

Public health authorities should be vigilant to the potential for outbreaks deliberately caused by biological agents (bioterrorism). Such events require a rapid response and incorporation of non-traditional partners for disease investigation and outbreak control. The astute application of infectious disease epidemiological principles can promote an enhanced index of suspicion for such events. We discuss epidemiological indicators that should be considered during outbreak investigations, and also examine their application during bioterrorism incidents, an accidental release of an agent, outbreaks of infections that were alleged to have been deliberately initiated, and a model scenario. The Grunow & Finke epidemiological assessment tool is used to examine these historical events and the model scenario. The results received from this analysis, coupled with an understanding of epidemiological clues to unnatural events, and knowledge of how to manage such events, can aid in the improved response and resolution of epidemics.
Hepatitis C virus infection among injecting drug users in Scotland: a review of prevalence and incidence data and the methods used to generate them
Authors: ROY K. M. , HUTCHINSON S. J. , WADD S. , TAYLOR A. , CAMERON S. O. , BURNS S. , MOLYNEAUX P. , MCINTYRE P. G. , GOLDBERG D. J.
Published: August 2006

It is estimated that of 50000 persons in Scotland (1% of the county's population), infected with the hepatitis C virus (HCV), around 90% injected drugs. This paper reviews data on the prevalence and incidence of HCV, and the methods used to generate such information, among injecting drug users (IDUs), in Scotland. The prevalence estimate for HCV among IDUs in Scotland as a whole (44% in 2000), is comparable with those observed in many European countries. Incidence rates ranged from 11·9 to 28·4/100 person-years. The data have shaped policy to prevent infection among IDUs and have informed predictions of the number of HCV-infected IDUs who will likely progress to, and require treatment and care for, severe HCV-related liver disease. Although harm reduction interventions, in particular needle and syringe exchanges and methadone maintenance therapy, reduced the transmission of HCV among IDUs during the early to mid-1990s, incidence in many parts of the country remains high. The prevention of HCV among IDUs continues to be one of Scotland's major public health challenges.
Estimation of European wild boar relative abundance and aggregation: a novel method in epidemiological risk assessment
Authors: ACEVEDO P. , VICENTE J. , HÖFLE U. , CASSINELLO J. , RUIZ-FONS F. , GORTAZAR C.
Published: August 2006

Wild boars are important disease reservoirs. It is well known that abundance estimates are needed in wildlife epidemiology, but the expense and effort required to obtain them is prohibitive. We evaluated a simple method based on the frequency of faecal droppings found on transects (FBII), and developed a spatial aggregation index, based on the runs test statistic. Estimates were compared with hunting data, and with porcine circovirus and Aujeszky's disease virus seroprevalences and Mycobacterium tuberculosis complex and Metastrongylus spp. prevalence. The FBII and the aggregation index were correlated with the hunting index, but both of the former estimates correlated better than the latter with the disease prevalences. Hence, at least in habitats with high wild boar densities, the FBII combined with the aggregation index constitutes a cheap and reliable alternative for wild boar abundance estimation that can be used for epidemiological risk assessment, even outside the hunting season and in areas with no available data on hunting activities.
Risk factors for typhoid fever in a slum in Dhaka, Bangladesh
Authors: RAM P. K. , NAHEED A. , BROOKS W. A. , HOSSAIN M. A. , MINTZ E. D. , BREIMAN R. F. , LUBY S. P.
Published: August 2006

We systematically investigated risk factors for typhoid fever in Kamalapur, a poor urban area of Bangladesh, to inform targeted public health measures for its control. We interviewed patients with typhoid fever and two age-matched controls per case about exposures during the 14 days before the onset of illness. The municipal water supply was used by all 41 cases and 81of 82 controls. In multivariate analysis, drinking unboiled water at home was a significant risk factor [adjusted odds ratio (aOR) 12·1, 95% CI 2·2–65·6]. Twenty-three (56%) cases and 21 (26%) controls reported that water from the primary source was foul-smelling (aOR 7·4, 95% CI 2·1–25·4). Eating papaya was associated with illness (aOR 5·2, 95% CI 1·2–22·2). Using a latrine for defecation was significantly protective (aOR 0·1, 95% CI 0·02–0·9). Improved chlorination of the municipal water supply or disinfecting drinking water at the household level may dramatically reduce the risk of typhoid fever in Kamalapur. The protective effect of using latrines, particularly among young children, should be investigated further.
Cooling of the West Spitsbergen Current: Isopycnal diffusion by topographic vorticity waves
Authors: Nilsen Frank , Gjevik Bjørn , Schauer Ursula
Published: August 2006

We investigate the heat budget in the West Spitsbergen Current on the basis of theoretical considerations and current meter data across the slope at 78.83°N between September 1997 and September 1998. The dispersion relation for topographically trapped waves along the West Spitsbergen Slope with a barotropic along‐slope velocity is calculated by use of an idealized numerical model. Signal processing and coherence calculations of the current meter data show that barotropic vorticity waves with enhanced energy at the diurnal period exist along the slope. A wave length of 32 km is given by the dispersion relation for the 24‐hour period and a corresponding second mode with a 35‐hour period. Coherence calculations and complex demodulations of the current meter time series confirm the spatial and temporal variations given by the dispersion relation. The eddy characteristics of the first two modes are used to estimate the heat loss of the warm core of the West Spitsbergen Current by isopycnal eddy diffusion. We present the first isopycnal heat loss estimates obtained through dynamical considerations of the West Spitsbergen Current and compare them with earlier diagnostic estimates for the mean heat loss in the subsurface layers. Within the standard errors we estimate the heat flux to be O(1000) W/m2 throughout the year except for the summer months June–July. If the 9798 heat flux time series are representative for the subsurface layer between 100 and 500 m depth, the heat loss is on the same order of magnitude as the mean winter value of 1050 W/m2 from earlier diagnostic estimates.
Satellite observations of sea surface temperature and sea surface wind coupling in the Japan Sea
Authors: Shimada Teruhisa , Kawamura Hiroshi
Published: August 2006

We investigate ocean‐atmosphere coupling in the Japan Sea by using microwave satellite measurements of sea surface temperature (SST) and sea surface wind from 1 June 2002 to 31 December 2004. First, it is observed that instantaneous wind speeds are modified by SST front meanders in widespread areas in the Japan Sea. Increased/reduced wind speeds are found over warmer/colder water. Then, we compute SST and wind speed anomalies by spatial high‐pass filtering in order to present their time evolution along 132°E. SST and wind speed anomalies are negatively correlated off Vladivostok (>41°N) in winter. This is consistent with the interpretation that there is large turbulent heat flux loss due to the wind speed maximum off Vladivostok or the gap exit region of the northwesterly wind jet. However, except for this region in winter, we find strong positive correlation between SST and wind speed anomalies throughout the year at any latitudes. Wind speed anomalies are linearly related to SST anomalies. Meanwhile, we identify two pairs of positive and negative SST anomaly bands in the time‐space structure of the Japan Sea and compare the band locations with meridional SST gradient magnitude. As a result, the two boundaries of the SST anomaly bands are associated with the Polar Front and the Tsushima Warm Current front. Additionally, it is found that discontinuous SST anomaly patches correspond to oceanic eddies. These results lead to the conclusion that sea surface winds over the Japan Sea come under the influence of those SST frontal systems.
Radiative transfer modeling of the effect of mineralogy on some empirical methods for estimating iron concentration from multispectral imaging of the Moon
Authors: Lucey Paul G.
Published: August 2006

Several empirical models for deriving FeO concentration from multispectral imaging of the Moon are tested using model spectra of lunar soil. The spectra are computed from a radiative transfer model based on the work of Bruce Hapke and cover the system plagioclase‐orthopyroxene‐clinopyroxene‐olivine‐ilmenite, and vary the Mg number and maturity over lunar relevant ranges. The high degree of correlation between measured and spectrally estimated FeO when applied to lunar soils returned by Apollo provides constraints on the abundance of certain rock types, and these constraints are consistent with geochemical mixing models. Good FeO estimates are yielded for mixtures of plagioclase, clinopyroxene, and ilmenite by all the algorithms. It is found that all spectral algorithms show large errors in the presence of significant olivine and significant errors in the presence of ferroan orthopyroxene. The best performance is shown by the LeMouelic et al. (2002) algorithm that is also insensitive to topographic shading in the absence of ilmenite. Previously noted differences between spectrally derived FeO and that derived by other techniques are all consistent with reported mineralogical differences.
Magnetotelluric imaging of crustal magma storage beneath the Mesozoic crystalline mountains in a nonvolcanic region, northeast Japan
Authors: Umeda Koji , Asamori Koichi , Negi Tateyuki , Ogawa Yasuo
Published: August 2006

Mesozoic crystalline mountains (Iide Mountains) in a nonvolcanic region of the Northeast Japan Arc were imaged by wide‐band magnetotelluric soundings. A two‐dimensional model shows that an anomalous conductive body (<10 Ωm) is clearly visible beneath the Iide Mountains. The conductor widens with increasing depth and extends from the near‐surface down to the base of the crust and perhaps into the upper mantle. The location of the conductive body correlates with high‐temperature hot springs with high 3He/4He ratio, thinning of the brittle seismogenic layer, and anomalies of low seismic velocity. We conclude that the conductor reflects the presence of partial melts in the crust, related to renewed magmatism in the present‐day subduction system.
Modeling the response to changes in tropospheric methane concentration: Application to the Permian‐Triassic boundary
Authors: Lamarque J.‐F. , Kiehl J. T. , Shields C. A. , Boville B. A. , Kinnison D. E.
Published: August 2006

We discuss model experiments valid for the Permian‐Triassic boundary in which we explore the impact of changes in tropospheric methane concentration. For scenarios relevant to methane clathrate release, we consider surface methane concentration with values up to 5000 times its preindustrial concentration. We employ a comprehensive three‐dimensional tropospheric‐stratospheric model with chemistry that allows for the feedbacks between chemistry and climate. We show that stratospheric ozone starts collapsing for methane surface concentrations on the order of 1000 times their preindustrial concentration. At 5000 times, more than half of the total ozone column has disappeared. As a result a large rise (up to a factor of 7) in surface UV‐B radiation is found. Other chemical consequences include a rise in CO and ozone surface concentrations; although becoming very large (up to 17 ppmv for CO), neither seems to reach lethal values according to present‐day life forms. Finally, we show that tropospheric OH does not collapse for any of the scenarios; a corollary of this is a finite methane lifetime (45 years at the most). As a result, if methane were to increase significantly enough over a short period, the associated UV‐B increase and/or deterioration of surface conditions could provide an explanation for the landmass extinction at the Permian‐Triassic boundary.
Stress and the suppression of subordinate reproduction in cooperatively breeding meerkats
Authors: Young Andrew J. , Carlson Anne A. , Monfort Steven L. , Russell Andrew F. , Bennett Nigel C. , Clutton-Brock Tim
Published: August 2006

In many animal societies, dominant individuals monopolize reproduction, but the tactics they employ to achieve this are poorly understood. One possibility is that aggressive dominants render their subordinates infertile by inducing chronic physiological “stress.” However, this hypothesis has been discarded largely for cooperatively breeding species, where reproductive monopolies are often extreme. Here we provide strong support for the stress-related suppression hypothesis in a cooperative mammal, the meerkat (
Suricata suricatta
). When pregnant, dominant females subject some subordinate females to escalating aggression, culminating in temporary evictions from the group. While evicted, subordinate females suffer chronic elevation of their glucocorticoid adrenal hormone levels, reproductive down-regulation (reduced pituitary sensitivity to gonadotropin-releasing hormone), reduced conception rates, and increased abortion rates. Rather than constantly harassing all subordinate females, dominants only become aggressive when pregnant themselves (when subordinate reproduction would otherwise conflict with their own) and target those females with whom reproductive conflict is most likely (older, pregnant, and more distantly related females). Our findings suggest that dominant female meerkats employ stressful evictions to suppress reproduction among their probable competitors, when attempting to breed themselves. Given the lack of evidence for stress-related suppression in other cooperative breeders to date, it is clear that social stress alone cannot account for the reproductive failure of subordinates across such societies. However, our findings raise the possibility that, in some cooperative breeders at least, dominants may employ stress-related suppression as a backup mechanism to guard against lapses in reproductive restraint by their subordinates.
Sex- and clock-controlled expression of the
neuropeptide F
gene in
Drosophila
Authors: Lee Gyunghee , Bahn Jae Hoon , Park Jae H.
Published: August 2006

Drosophila
neuropeptide F (NPF), a homolog of vertebrate neuropeptide Y, functions in feeding and coordination of behavioral changes in larvae and in modulation of alcohol sensitivity in adults, suggesting diverse roles for this peptide. To gain more insight into adult-specific NPF neuronal functions, we studied how
npf
expression is regulated in the adult brain. Here, we report that
npf
expression is regulated in both sex-nonspecific and male-specific manners. Our data show that male-specific
npf
(ms-
npf
) expression is controlled by the
transformer
(
tra
)-dependent sex-determination pathway. Furthermore,
fruitless
, one of the major genes functioning downstream of
tra
, is apparently an upstream regulator of ms-
npf
transcription. Males lacking ms-
npf
expression (through

tra
F

-mediated feminization) or
npf
-ablated male flies display significantly reduced male courtship activity, suggesting that one function of ms-
npf
neurons is to modulate
fruitless
-regulated sexual behavior. Interestingly, one of the ms-
npf
neuronal groups belongs to the previously defined clock-controlling dorsolateral neurons. Such ms-
npf
expression in the dorsolateral neurons is absent in arrhythmic

Clock
Jrk

and

cycle
02

mutants, suggesting that
npf
is under dual regulation by circadian and sex-determining factors. Based on these data, we propose that NPF also plays a role in clock-controlled sexual dimorphism in adult
Drosophila
.
Interstellar H
3
+
Authors: Oka Takeshi
Published: August 2006

Protonated molecular hydrogen, H
3
+
, is the simplest polyatomic molecule. It is the most abundantly produced interstellar molecule, next only to H
2
, although its steady state concentration is low because of its extremely high chemical reactivity. H
3
+
is a strong acid (proton donor) and initiates chains of ion-molecule reactions in interstellar space thus leading to formation of complex molecules. Here, I summarize the understandings on this fundamental species in interstellar space obtained from our infrared observations since its discovery in 1996 and discuss the recent observations and analyses of H
3
+
in the Central Molecular Zone near the Galatic center that led to a revelation of a vast amount of warm and diffuse gas existing in the region.
The galactic cosmic ray ionization rate
Authors: Dalgarno A.
Published: August 2006

The chemistry that occurs in the interstellar medium in response to cosmic ray ionization is summarized, and a review of the ionization rates that have been derived from measurements of molecular abundances is presented. The successful detection of large abundances of H
3
+
in diffuse clouds and the recognition that dissociative recombination of H
3
+
is fast has led to an upward revision of the derived ionization rates. In dense clouds the molecular abundances are sensitive to the depletion of carbon monoxide, atomic oxygen, nitrogen, water, and metals and the presence of large molecules and grains. Measurements of the relative abundances of deuterated species provide information about the ion removal mechanisms, but uncertainties remain. The models, both of dense and diffuse clouds, that are used to interpret the observations may be seriously inadequate. Nevertheless, it appears that the ionization rates differ in dense and diffuse clouds and in the intercloud medium.
Chemistry in low-mass protostellar and protoplanetary regions
Authors: van Dishoeck Ewine F.
Published: August 2006

When interstellar clouds collapse to form new stars and planets, the surrounding gas and dust become part of the infalling envelopes and rotating disks, thus providing the basic material from which new solar systems are formed. Instrumentation to probe the chemistry in low-mass star-forming regions has only recently become available. The results of a systematic program to study the abundances in solar-mass protostellar and protoplanetary regions are presented. Surveys at submillimeter and infrared wavelengths reveal a rich chemistry, including simple and complex (organic) gases, ices, polycyclic aromatic hydrocarbons, and silicates. Each of these species traces different aspects of the physical and chemical state of the objects as they evolve from deeply embedded protostars to pre-main sequence stars with planet-forming disks. Quantitative information on temperatures, densities, and abundances is obtained through molecular excitation and radiative transfer models as well as from analysis of solid-state line profiles. The chemical characteristics are dominated by freeze-out in the coldest regions and ice evaporation in the warmer zones. In the surface layers of disks, UV radiation controls the chemistry. The importance of complementary laboratory experiments and calculations to obtain basic molecular data is emphasized.
The chemistry in circumstellar envelopes of evolved stars: Following the origin of the elements to the origin of life
Authors: Ziurys Lucy M.
Published: August 2006

Mass loss from evolved stars results in the formation of unusual chemical laboratories: circumstellar envelopes. Such envelopes are found around carbon- and oxygen-rich asymptotic giant branch stars and red supergiants. As the gaseous material of the envelope flows from the star, the resulting temperature and density gradients create a complex chemical environment involving hot, thermodynamically controlled synthesis, molecule “freeze-out,” shock-initiated reactions, and photochemistry governed by radical mechanisms. In the circumstellar envelope of the carbon-rich star IRC+10216, >50 different chemical compounds have been identified, including such exotic species as C
8
H, C
3
S, SiC
3
, and AlNC. The chemistry here is dominated by molecules containing long carbon chains, silicon, and metals such as magnesium, sodium, and aluminum, which makes it quite distinct from that found in molecular clouds. The molecular composition of the oxygen-rich counterparts is not nearly as well explored, although recent studies of VY Canis Majoris have resulted in the identification of HCO
+
, SO
2
, and even NaCl in this object, suggesting chemical complexity here as well. As these envelopes evolve into planetary nebulae with a hot, exposed central star, synthesis of molecular ions becomes important, as indicated by studies of NGC 7027. Numerous species such as HCO
+
, HCN, and CCH are found in old planetary nebulae such as the Helix. This “survivor” molecular material may be linked to the variety of compounds found recently in diffuse clouds. Organic molecules in dense interstellar clouds may ultimately be traced back to carbon-rich fragments originally formed in circumstellar shells.
Crystallography on curved surfaces
Authors: Vitelli Vincenzo , Lucks J. B. , Nelson D. R.
Published: August 2006

We study static and dynamical properties that distinguish 2D crystals constrained to lie on a curved substrate from their flat-space counterparts. A generic mechanism of dislocation unbinding in the presence of varying Gaussian curvature is presented in the context of a model surface amenable to full analytical treatment. We find that glide diffusion of isolated dislocations is suppressed by a binding potential of purely geometrical origin. Finally, the energetics and biased diffusion dynamics of point defects such as vacancies and interstitials are explained in terms of their geometric potential.
A codon deletion confers resistance to herbicides inhibiting protoporphyrinogen oxidase
Authors: Patzoldt William L. , Hager Aaron G. , McCormick Joel S. , Tranel Patrick J.
Published: August 2006

Herbicides that act by inhibiting protoporphyrinogen oxidase (PPO) are widely used to control weeds in a variety of crops. The first weed to evolve resistance to PPO-inhibiting herbicides was
Amaranthus tuberculatus
, a problematic weed in the midwestern United States that previously had evolved multiple resistances to herbicides inhibiting two other target sites. Evaluation of a PPO-inhibitor-resistant
A. tuberculatus
biotype revealed that resistance was a (incompletely) dominant trait conferred by a single, nuclear gene. Three genes predicted to encode PPO were identified in
A. tuberculatus
. One gene from the resistant biotype, designated
PPX2L
, contained a codon deletion that was shown to confer resistance by complementation of a
hemG
mutant strain of
Escherichia coli
grown in the presence and absence of the PPO inhibitor lactofen.
PPX2L
is predicted to encode both plastid- and mitochondria-targeted PPO isoforms, allowing a mutation in a single gene to confer resistance to two herbicide target sites. Unique aspects of the resistance mechanism include an amino acid deletion, rather than a substitution, and the dual-targeting nature of the gene, which may explain why resistance to PPO inhibitors has been rare.
Competitive recruitment of the periplasmic translocation portal TolB by a natively disordered domain of colicin E9
Authors: Loftus Steven R. , Walker Daniel , Maté Maria J. , Bonsor Daniel A. , James Richard , Moore Geoffrey R. , Kleanthous Colin
Published: August 2006

The natively disordered N-terminal 83-aa translocation (T) domain of E group nuclease colicins recruits OmpF to a colicin-receptor complex in the outer membrane (OM) as well as TolB in the periplasm ofEscherichia coli, the latter triggering translocation of the toxin across the OM. We have identified the 16-residue TolB binding epitope in the natively disordered T-domain of the nuclease colicin E9 (ColE9) and solved the crystal structure of the complex. ColE9 folds into a distorted hairpin within a canyon of the six-bladed β-propeller of TolB, using two tryptophans to bolt the toxin to the canyon floor and numerous intramolecular hydrogen bonds to stabilize the bound conformation. This mode of binding enables colicin side chains to hydrogen-bond TolB residues in and around the channel that runs through the β-propeller and that constitutes the binding site of peptidoglycan-associated lipoprotein (Pal). Pal is a globular binding partner of TolB, and their association is known to be important for OM integrity. The structure is therefore consistent with translocation models wherein the colicin disrupts the TolB–Pal complex causing local instability of the OM as a prelude to toxin import. Intriguingly, Ca2+ions, which bind within the β-propeller channel and switch the surface electrostatics from negative to positive, are needed for the negatively charged T-domain to bind TolB with an affinity equivalent to that of Pal and competitively displace it. Our study demonstrates that natively disordered proteins can compete with globular proteins for binding to folded scaffolds but that this can require cofactors such as metal ions to offset unfavorable interactions.
Eastern North America as an independent center of plant domestication
Authors: Smith Bruce D.
Published: August 2006

The status of eastern North America as an independent center of plant domestication has recently been called into question by a number of genetic and archaeological studies, which suggest that the region may not have witnessed the independent domestication of local crop plants, but rather may have been on the receiving end of domesticated crop plants introduced from Mexico. Here, I provide a synthesis of the currently available archaeological and genetic evidence from both eastern North America and Mexico regarding the spatial and temporal context of initial domestication of the four plant species identified as potential eastern North American domesticates: marshelder (
Iva annua
), chenopod (
Chenopodium berlandieri
), squash (
Cucurbita pepo
), and sunflower (
Helianthus annuus
). Genetic and archaeological evidence provides strong support for the independent domestication of all four of these plant species in the eastern United States and reconfirms the region as one of the world’s independent centers of domestication.
End-to-end distance distributions and intrachain diffusion constants in unfolded polypeptide chains indicate intramolecular hydrogen bond formation
Authors: Möglich Andreas , Joder Karin , Kiefhaber Thomas
Published: August 2006

Characterization of the unfolded state is essential for the understanding of the protein folding reaction. We performed time-resolved FRET measurements to gain information on the dimensions and the internal dynamics of unfolded polypeptide chains. Using an approach based on global analysis of data obtained from two different donor–acceptor pairs allowed for the determination of distance distribution functions and diffusion constants between the chromophores. Results on a polypeptide chain consisting of 16 Gly-Ser repeats between the FRET chromophores reveal an increase in the average end-to-end distance from 18.9 to 39.2 Å between 0 and 8 M GdmCl. The increase in chain dimensions is accompanied by an increase in the end-to-end diffusion constant from (3.6 ± 1.0) × 10−7cm2s−1in water to (14.8 ± 2.5) × 10−7cm2s−1in 8 M GdmCl. This finding suggests that intrachain interactions in water exist even in very flexible chains lacking hydrophobic groups, which indicates intramolecular hydrogen bond formation. The interactions are broken upon denaturant binding, which leads to increased chain flexibility and longer average end-to-end distances. This finding implies that rapid collapse of polypeptide chains during refolding of denaturant-unfolded proteins is an intrinsic property of polypeptide chains and can, at least in part, be ascribed to nonspecific intramolecular hydrogen bonding. Despite decreased intrachain diffusion constants, the conformational search is accelerated in the collapsed state because of shorter diffusion distances. The measured distance distribution functions and diffusion constants in combination with Szabo–Schulten–Schulten theory were able to reproduce experimentally determined rate constants for end-to-end loop formation.
Osteogenic differentiation of mouse adipose-derived adult stromal cells requires retinoic acid and bone morphogenetic protein receptor type IB signaling
Authors: Wan Derrick C. , Shi Yun-Ying , Nacamuli Randall P. , Quarto Natalina , Lyons Karen M. , Longaker Michael T.
Published: August 2006

Although the multilineage potential of human adipose-derived adult stromal cells (ADAS) has been well described, few published studies have investigated the biological and molecular mechanisms underlying osteogenic differentiation of mouse ADAS. We report here that significant osteogenesis, as determined by gene expression and histological analysis, is induced only when mouse ADAS are cultured in the presence of retinoic acid with or without recombinant human bone morphogenetic protein (BMP)-2 supplementation. Furthermore, a dynamic expression profile for the BMP receptor (BMPR) isoform IB was observed, with dramatic up-regulation during osteogenesis. Western blot analysis revealed that retinoic acid enhanced levels of BMPR-IB protein during the first 7 days of osteogenic differentiation and that RNAi-mediated suppression of BMPR-IB dramatically impaired the ability of ADAS to form bone
in vitro
. In contrast, absence of BMPR-IA did not significantly diminish ADAS osteogenesis. Our data therefore demonstrate that the osteogenic commitment of multipotent mouse ADAS requires retinoic acid, which enhances expression of the critical BMPR-IB isoform.
Permanent carbon dioxide storage in deep-sea sediments
Authors: House Kurt Zenz , Schrag Daniel P. , Harvey Charles F. , Lackner Klaus S.
Published: August 2006

Stabilizing the concentration of atmospheric CO
2
may require storing enormous quantities of captured anthropogenic CO
2
in near-permanent geologic reservoirs. Because of the subsurface temperature profile of terrestrial storage sites, CO
2
stored in these reservoirs is buoyant. As a result, a portion of the injected CO
2
can escape if the reservoir is not appropriately sealed. We show that injecting CO
2
into deep-sea sediments <3,000-m water depth and a few hundred meters of sediment provides permanent geologic storage even with large geomechanical perturbations. At the high pressures and low temperatures common in deep-sea sediments, CO
2
resides in its liquid phase and can be denser than the overlying pore fluid, causing the injected CO
2
to be gravitationally stable. Additionally, CO
2
hydrate formation will impede the flow of CO
2
(l) and serve as a second cap on the system. The evolution of the CO
2
plume is described qualitatively from the injection to the formation of CO
2
hydrates and finally to the dilution of the CO
2
(aq) solution by diffusion. If calcareous sediments are chosen, then the dissolution of carbonate host rock by the CO
2
(aq) solution will slightly increase porosity, which may cause large increases in permeability. Karst formation, however, is unlikely because total dissolution is limited to only a few percent of the rock volume. The total CO
2
storage capacity within the 200-mile economic zone of the U.S. coastline is enormous, capable of storing thousands of years of current U.S. CO
2
emissions.
Infant brains detect arithmetic errors
Authors: Berger Andrea , Tzur Gabriel , Posner Michael I.
Published: August 2006

A current debate is whether increased looking time in infancy is related to violation of expectations. In this study, 6- to 9-month-old infants’ brain activity was analyzed during presentation of correct and incorrect solutions to simple arithmetic equations [(e.g., presentation of 1 + 1; one doll on a TV monitor, with another doll added from behind a screen, followed by a solution of 2 (correct) or 1 (incorrect)]. Infants looked longer at incorrect solutions than at correct ones. Event-related potentials, time-locked to the presentation of the solution, also differed between conditions, with greater negative activity for the incorrect solution condition. Spectral analysis showed a similar pattern to that of adults observing correct and incorrect arithmetical equations. These findings show (
i
) that the brain network involved in error detection can be identified in infancy and (
ii
) that this network can support an association between looking time and violation of expectations.
Interstellar chemistry
Authors: Klemperer William
Published: August 2006

In the past half century, radioastronomy has changed our perception and understanding of the universe. In this issue of PNAS, the molecular chemistry directly observed within the galaxy is discussed. For the most part, the description of the molecular transformations requires specific kinetic schemes rather than chemical thermodynamics. Ionization of the very abundant molecular hydrogen and atomic helium followed by their secondary reactions is discussed. The rich variety of organic species observed is a challenge for complete understanding. The role and nature of reactions involving grain surfaces as well as new spectroscopic observations of interstellar and circumstellar regions are topics presented in this special feature.
Broad-spectrum biofilm inhibition by a secreted bacterial polysaccharide
Authors: Valle Jaione , Da Re Sandra , Henry Nelly , Fontaine Thierry , Balestrino Damien , Latour-Lambert Patricia , Ghigo Jean-Marc
Published: August 2006

The development of surface-attached biofilm bacterial communities is considered an important source of nosocomial infections. Recently, bacterial interference via signaling molecules and surface active compounds was shown to antagonize biofilm formation, suggesting that nonantibiotic molecules produced during competitive interactions between bacteria could be used for biofilm reduction. Hence, a better understanding of commensal/pathogen interactions within bacterial community could lead to an improved control of exogenous pathogens. To reveal adhesion or growth-related bacterial interference, we investigated interactions between uropathogenic and commensal
Escherichia coli
in mixed
in vitro
biofilms. We demonstrate here that the uropathogenic strain CFT073 and all
E. coli
expressing group II capsules release into their environment a soluble polysaccharide that induces physicochemical surface alterations, which prevent biofilm formation by a wide range of Gram-positive and Gram-negative bacteria. We show that the treatment of abiotic surfaces with group II capsular polysaccharides drastically reduces both initial adhesion and biofilm development by important nosocomial pathogens. These findings identify capsular polymers as antiadhesion bacterial interference molecules, which may prove to be of significance in the design of new strategies to limit biofilm formation on medical in dwelling devices.