bluuebunny/crossref_metadata_2025 huggingface dataset:
Introduction to special section on Entropy Properties and Constraints Related to Space Plasma Transport
Authors: Wing Simon , Johnson Jay R.
Published: January 2010

Studies of entropy provide physical insight into space plasma transport, intermittency, turbulence, and information flow in the heliosphere and magnetosphere. Nonconservation of entropy in space plasmas can result from magnetic reconfiguration as well as nonadiabatic processes such as turbulent transport, thermal energy transport due to nonadiabatic particle drifts, energizations, mixing of two or more plasma populations, etc. Examination of entropy properties may provide insight into processes leading to plasma entry across the magnetopause on the dayside and nightside and processes leading to the tail “pressure balance inconsistency” and may provide constraints on which processes are most important in the dynamical transition related to substorms. Moreover, entropy‐based information theory can be used to characterize the dynamics of the magnetosphere. This paper summarizes the special section that highlights state‐of‐the‐art theoretical and observational studies of entropy, the pressure balance inconsistency, and other entropy‐related issues such as those mentioned above.
Effect of unsteady flow on nitrate loss in an oligotrophic, glacial meltwater stream
Authors: Koch Joshua C. , McKnight Diane M. , Baeseman Jenny L.
Published: January 2010

The McMurdo Dry Valleys of Antarctica are among the coldest, driest ecosystems on Earth. During the austral summer, glacial meltwater supports cyanobacterial mat communities in some streams, but they are not ubiquitous. We conducted a nitrate (NO3−) enrichment tracer injection in Huey Creek to quantify NO3− loss in a Dry Valley stream where algal mats would not obscure hyporheic microbial processes. Unsteady streamflow led to diel variability in the tracer concentration and in surface/subsurface water and solute exchange. Subsequently, concentrations of NO3−, nitrite (NO2−), ammonium (NH4+), and dissolved organic carbon (DOC) varied significantly during the injection, with a net loss of NO3−, NO2−, and DOC, and production of nitrous oxide. These mass changes within a reach were often coincident with high streamflows. Reactivity also coincided with the highest DOC concentrations, suggesting that DOC is the primary limitation to heterotrophic microbial activity in the stream. Together, streamflow and DOC availability create the hot spots and hot moments that dominate NO3− reactivity and removal in this polar desert ecosystem. The combination of spatially and temporally variable hyporheic dynamics and solute availability underscore the limitations of common nutrient uptake metrics and transient storage models when unsteady flow conditions exist.
Distinct flavobacterial communities in contrasting water masses of the North Atlantic Ocean
Authors: Gómez-Pereira Paola R , Fuchs Bernhard M , Alonso Cecilia , Oliver Matthew J , van Beusekom Justus E E , Amann Rudolf
Published: January 2010

Members of the class Flavobacteria in the phylum Bacteroidetes are among the most abundant picoplankton in coastal and polar oceans. Their diversity is high in marine waters. However, quantitative information about distribution patterns of flavobacterial clades is scarce. We analyzed the diversity and clade-specific abundances of individual Flavobacteria in different oceanic provinces in the North Atlantic Ocean. Samples were taken along the 30°W meridian between the East Greenland current and the North Atlantic subtropical gyre. Comparative sequence analysis of 16S ribosomal RNA (rRNA) gene libraries revealed high diversity and significant spatial variability within the class Flavobacteria. Published and newly designed oligonucleotide probes were used to enumerate eleven flavobacterial clades by catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH). We found that different provinces harbor distinct flavobacterial communities. Clade DE2 accounted for a substantial fraction of total Flavobacteria only in the Polar Biome (BPLR), whereas the VISION clades VIS1 and VIS4 significantly increased in the Arctic (ARCT) province. Members of the genus Polaribacter were the most abundant clade in all the water masses analyzed, with highest absolute numbers in BPLR and ARCT. We improved the CARD-FISH protocol to quantify the rare clades VIS2, VIS3, VIS5 and VIS6, which were present in abundances below 0.5%. They all showed pronounced regional distribution patterns. Microscopic analysis proved a specific enrichment of Flavobacteria in the phycosphere of nanophytoplankton of BPLR and ARCT. Our results suggest that different marine flavobacterial clades have distinct niches and different life strategies.
Psychosocial Factors and Health Perceptions in Parents and Children Who Are Overweight or Obese
Authors: O'Neil Margaret E. , Shewokis Patricia A. , Falkenstein Kathleen K. , DeLago Cynthia W. , Smith Sinclair A. , Vaughn Nicole A. , Costigan Tracy E.
Published: January 2010

This study examined the relationships among weight status (BMI), health perceptions, and psychosocial characteristics in children, parents, and parent–child dyads. A convenient sample of 114 parent–child dyads participated. All children were overweight or obese. Parents and children completed questionnaires by self‐report or interview. Questionnaires included the Parenting Stress Index–Short Form (PSI), the Parents' Stage of Change (SOC) Questionnaire, and the Pediatric Quality of Life Inventory (PedsQL). Child's mean age was 10.34 years (s.d. = 1.87), mean BMI was 28.13 kg/m2 (s.d. = 5.46), and mean BMI z‐score was 2.17 (s.d. = 0.38). Parent mean age was 37.28 years (s.d. = 12.66) and mean BMI was 34.07 kg/m2 (s.d. = 8.18). Most parents (68.5%) reported that they and their children (70.7%) were African American and many (44.3%) reported that they and their children were Hispanic. Significant correlations included: child health perceptions and child BMI (r = 0.309, P < 0.001) and parent perception of weight and parent BMI (r = 0.691, P < 0.001). For parent–child dyads, one correlation approached significance (child health perceptions and parent stage of change (r = −0.269, P < 0.01). Findings suggest that characteristics of parent–child dyads may be important considerations in the management of childhood obesity.
Selective Alterations Within Executive Functions in Adolescents With Excess Weight
Authors: Verdejo‐García Antonio , Pérez‐Expósito Manuel , Schmidt‐Río‐Valle Jacqueline , Fernández‐Serrano Maria J. , Cruz Francisco , Pérez‐García Miguel , López‐Belmonte Gemma , Martín‐Matillas Miguel , Martín‐Lagos Jose A. , Marcos Ascension , Campoy Cristina
Published: January 2010

Increasing evidence underscores overlapping neurobiological pathways to addiction and obesity. In both conditions, reward processing of preferred stimuli is enhanced, whereas the executive control system that would normally regulate reward‐driven responses is altered. This abnormal interaction can be greater in adolescence, a period characterized by relative immaturity of executive control systems coupled with the relative maturity of reward processing systems. The aim of this study is to explore neuropsychological performance of adolescents with excess weight (n = 27, BMI range 24–51 kg/m2) vs. normal‐weight adolescents (n = 34, BMI range 17–24 kg/m2) on a comprehensive battery of executive functioning tests, including measures of working memory (letter‐number sequencing), reasoning (similarities), planning (zoo map), response inhibition (five‐digit test (FDT)–interference and Stroop), flexibility (FDT–switching and trail‐making test (TMT)), self‐regulation (revised‐strategy application test (R‐SAT)), and decision‐making (Iowa gambling task (IGT)). We also aimed to explore personality traits of impulsivity and sensitivity to reward. Independent sample t‐ and Z Kolmogorov–Smirnov tests showed significant differences between groups on indexes of inhibition, flexibility, and decision‐making (excess‐weight participants performed poorer than controls), but not on tests of working memory, planning, and reasoning, nor on personality measures. Moreover, regression models showed a significant association between BMI and flexibility performance. These results are indicative of selective alterations of particular components of executive functions in overweight adolescents.
Diet‐induced Obesity in Two C57BL/6 Substrains With Intact or Mutant Nicotinamide Nucleotide Transhydrogenase (Nnt) Gene
Authors: Nicholson Anthony , Reifsnyder Peter C. , Malcolm Rachel D. , Lucas Charlotte A. , MacGregor Grant R. , Zhang Weidong , Leiter Edward H.
Published: January 2010

The C57BL/6J (B6/J) male mouse represents a standard for diet‐induced obesity (DIO) and is unique in expressing a loss‐of‐function nicotinamide nucleotide transhydrogenase (Nnt) gene. This mutation was associated with a marked reduction in glucose‐stimulated insulin secretion from B6/J islets in vitro and moderately impaired glucose clearance in vivo. To assess the contribution of this Nnt mutation, we compared DIO responsiveness of Nnt‐mutant B6/J males to Nnt wild‐type C57BL/6NJ (B6/NJ) males over a 14‐week period of feeding a high‐fat (60% of calories) diet. Initial mean body weights at 6 weeks did not distinguish the substrains and both substrains were DIO‐sensitive. However, B6/J males outgained the B6/NJ males, with a significant 3 g higher mean body weight at 20 weeks accompanied by significant increases in both lean and fat mass. Mean nonfasting serum glucose over time was also significantly higher in B6/J males, as was impairment of glucose tolerance assessed at 8 and 20 weeks of age. Serum leptin, but not insulin, was significantly higher in B6/J males over time. Potential contributions of the wild‐type Nnt gene were demonstrable on a lower fat diet (10% of calories) where a significantly greater weight gain over time by B6/NJ males was correlated with a significantly higher serum insulin. In conclusion, DIO developed in response to 60% fat feeding regardless of Nnt allele status. Contribution of the B6/J‐unique Nnt mutation was most evident in response to 10% fat feeding that resulted in reduced serum insulin and weight gain compared to B6/NJ males.
Evaluation of a Comprehensive Care Clinic Model for Children With Brain Tumor and Risk for Hypothalamic Obesity
Authors: Rakhshani Nasimeh , Jeffery Allison S. , Schulte Fiona , Barrera Maru , Atenafu Eshetu G. , Hamilton Jill K.
Published: January 2010

The objectives of this study were to evaluate outcomes of a comprehensive care clinic (CCC) for children with hypothalamic obesity due to treatment for brain tumors by assessing weight parameters; health‐related quality of life (HRQoL); and perception of health status, disease burden, care satisfaction, and physical activity. Thirty‐nine patients (16 males) were reviewed. While attending the CCC the median %weight gain and percent ideal body weight (%IBW) of patients was lower (8.5%/year (range −3 to −14) and −4%/year (141.7–34), respectively) than the median %weight gain and %IBW (21.4% (15.8−32.0) and 19.9% (−18.7 to 149.2)) while treated in standard care. Rate of increase in %BMI slowed (4.5 kg/m2 %/year (−17.8 to 8.4) vs. 8.4 kg/m2 %/year (−3.1 to 28.1)) in patients attending the clinic compared to their before treatment in standard care. There was no change in blood pressure, fasting glucose, triglycerides or low‐density lipoprotein cholesterol, and a significant increase in high‐density lipoprotein cholesterol (1.09 ± 0.33 to 1.24 ± 0.04). After attending the CCC for a year, significant increases for child reported total HRQoL (63.7 ± 18.4–71.3 ± 13.3; P < 0.017), physical functioning (65.3 ± 15.9–69.5 ± 15.9; P < 0.045) and school functioning (61.1 ± 21.0–71.1 ± 16.5; P < 0.051) were found. Parents reported no significant change in HRQoL over the same period. Parents had significantly improved responses in areas of coordination of health care and understanding of their child's disease. Patients attending the CCC gained less weight while attending the clinic and exhibited improved HRQoL. Parents noticed improvements in various areas of their child's medical care.
Shear stress activates Akt during vascular smooth muscle cell reorientation
Authors: Rice Kevin M. , Kakarla Sunil K. , Mupparaju Sriram P. , Paturi Satyanarayana , Katta Anjaiah , Wu Miaozong , Harris Robert T. , Blough Eric R.
Published: January 2010

Vascular intervention procedures can lead to endothelial damage and expose the underlying VSMCs (vascular smooth muscle cells) to shear stress. Although shear stress has been implicated in the proliferation and migration of VSMCs, the molecular mechanism(s) underlying these events are not well understood. In the present study, we examined the effect of shear stress on VSMC reorientation and the activation of Akt (also called protein kinase B) pathway signalling. Cells were subjected to a shear of 9.8 dynes/cm2 (1 dyne=10−5 N) for 0 min, 5 min, 15 min, 30 min, 1 h, 4 h and 24 h. Shear stress caused the VSMCs to realign at an angle that was ∼45 ° relative to the shear force vector after 24 h. Immunoblotting demonstrated that the phosphorylations of Akt and Akt‐related signalling proteins [mTOR (mammalian target of rapamycin), PTEN (phosphatase and tensin homologue deleted on chromosome 10) and p70S6k (p70 S6‐kinase)] were increased after shear stimulation. These results indicate that the activation of the Akt pathway signalling is closely correlated with shear‐induced VSMC reorientation.
Characterization of non-cytosolic hexokinase activity in white skeletal muscle from goldfish (Carassius auratus L.) and the effect of cold acclimation
Authors: dos Santos Reinaldo Sousa , Diniz Luan Pereira , Galina Antonio , da-Silva Wagner Seixas
Published: January 2010

HK (hexokinase) is an enzyme involved in the first step in the glucose metabolism pathway, converting glucose into G6P (glucose 6-phosphate). Owing to the importance of skeletal muscle for fish swimming and acclimation processes, we used goldfish (Carassius auratus L.) white muscle in order to investigate subcellular distribution and kinetics of HK. In this study, we report that HK activity is predominantly localized in the mitochondrial fraction [NC-HK (non-cytosolic HK)] in goldfish white muscle. Studies of the kinetic parameters revealed that the Km (Michaelis–Menten constant) for glucose was 0.41±0.03 mM and that for mannose was 3-fold lower, whereas the affinity for fructose was too low to be measured. The Km for ATP was 0.88±0.05 mM, whereas no activity was observed when either GTP or ITP was used as a phosphate donor. A moderate inhibition (20–40%) was found for ADP and AMP. Similar to mammalian HK, G6P and glucose analogues were able to promote an inhibition of between 85 and 100% of activity. Here, we found that acclimation of goldfish at 5°C promoted a 2.5-fold increase in NC-HK compared with its counterpart acclimated at 25°C. However, cytosolic HK activity was not altered after thermal acclimation. In summary, our results suggest that the goldfish has a constitutive NC-HK that shows some similarities to mammalian HK-II and, curiously, may play a role in the broad metabolic changes required during the cold acclimation process.
Light changes the atmospheric reactivity of soot
Authors: Monge Maria Eugenia , D’Anna Barbara , Mazri Linda , Giroir-Fendler Anne , Ammann Markus , Donaldson D. J. , George Christian
Published: January 2010

Soot particles produced by incomplete combustion processes are one of the major components of urban air pollution. Chemistry at their surfaces lead to the heterogeneous conversion of several key trace gases; for example NO
2
interacts with soot and is converted into HONO, which rapidly photodissociates to form OH in the troposphere. In the dark, soot surfaces are rapidly deactivated under atmospheric conditions, leading to the current understanding that soot chemistry affects tropospheric chemical composition only in a minor way. We demonstrate here that the conversion of NO
2
to HONO on soot particles is drastically enhanced in the presence of artificial solar radiation, and leads to persistent reactivity over long periods. Soot photochemistry may therefore be a key player in urban air pollution.
Structure of intact
Thermus thermophilus
V-ATPase by cryo-EM reveals organization of the membrane-bound V
O
motor
Authors: Lau Wilson C. Y. , Rubinstein John L.
Published: January 2010

The eubacterium
Thermus thermophilus
uses a macromolecular assembly closely related to eukaryotic V-ATPase to produce its supply of ATP. This simplified V-ATPase offers several advantages over eukaryotic V-ATPases for structural analysis and investigation of the mechanism of the enzyme. Here we report the structure of the complex at ∼16 
Å
resolution as determined by single particle electron cryomicroscopy (cryo-EM). The resolution of the map and our use of cryo-EM, rather than negative stain EM, reveals detailed information about the internal organization of the assembly. We could separate the map into segments corresponding to subunits A and B, the threefold pseudosymmetric C-subunit, a central rotor consisting of subunits D and F, the L-ring, the stator subcomplex consisting of subunits I, E, and G, and a micelle of bound detergent. The architecture of the V
O
region shows a remarkably small area of contact between the I-subunit and the ring of L-subunits and is consistent with a two half-channel model for proton translocation. The arrangement of structural elements in V
O
gives insight into the mechanism of torque generation from proton translocation.
dbTEU: a protein database of trace element utilization
Authors: Zhang Yan , Gladyshev Vadim N.
Published: January 2010

Summary: Biological trace elements are required for numerous biological processes and by all organisms. We describe a database, dbTEU (DataBase of Trace Element Utilization), that features known transporters and user proteins for five trace elements (copper, molybdenum, nickel, cobalt and selenium) and represents sequenced organisms from the three domains of life. The manually curated dbTEU currently includes ∼16 500 proteins from >700 organisms, and offers interactive trace element, protein, organism and sequence search and browse tools.

Availability and Implementation: dbTEU is freely available at http://gladyshevlab.bwh.harvard.edu/trace_element/

Contact:  vgladyshev@rics.bwh.harvard.edu
GWAS Analyzer: integrating genotype, phenotype and public annotation data for genome-wide association study analysis
Authors: Fong Christine , Ko Dennis C. , Wasnick Michael , Radey Matthew , Miller Samuel I. , Brittnacher Mitchell
Published: January 2010

Motivation: Genome-wide association studies are beginning to elucidate how our genetic differences contribute to susceptibility and severity of disease. While computational tools have previously been developed to support various aspects of genome-wide association studies, there is currently a need for informatics solutions that facilitate the integration of data from multiple sources.

Results: Here we present GWAS Analyzer, a database driven web-based tool that integrates genotype and phenotype data, association analysis results and genomic annotations from multiple public resources. GWAS Analyzer contains features for browsing these interrelated data, exploring phenotypic values by family or genotype, and filtering association results based on multiple criteria. The utility of the tool has been demonstrated by a genome-wide association study of human in vitro susceptibility to bacterial infection. GWAS Analyzer facilitated management of large sets of phenotype and genotype data, analysis of phenotypic variation and heritability, and most importantly, generation of a refined set of candidate single nucleotide polymorphisms (SNPs). The tool revealed a SNP that was experimentally validated to be associated with increased cell death among Salmonella infected HapMap cell lines.

Availability:  http://www.nwrce.org/gwas-analyzer

Contact:  mbrittna@u.washington.edu

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Xper2: introducing e-taxonomy
Authors: Ung Visotheary , Dubus Guillaume , Zaragüeta-Bagils René , Vignes-Lebbe Régine
Published: January 2010

Motivation: Computer Aided Identification systems provide users with the resources to relate morpho-anatomic observations with taxa names and to subsequently access other knowledge about the organisms. They have the ability to manage descriptive data and make identifications through interactive keys. They are essential for both authors and users of biodiversity information. Xper2 version 2.0 is one of the most user-friendly tools in its category and provides a complete environment dedicated to taxonomic management.

Availability: Xper2 software can be freely downloaded at http://lis-upmc.snv.jussieu.fr/lis/?q=en/resources/softwares/xper2

Contact:  visotheary.riviere-ung@snv.jussieu.fr
A linked separable–ADAPT VPA assessment model for western horse mackerel (Trachurus trachurus), accounting for realized fecundity as a function of fish weight
Authors: De Oliveira José A. A. , Darby Chris D. , Roel Beatriz A.
Published: January 2010

De Oliveira, J. A. A., Darby, C. D., and Roel, B. A. 2010. A linked separable–ADAPT VPA assessment model for western horse mackerel (Trachurus trachurus), accounting for realized fecundity as a function of fish weight. – ICES Journal of Marine Science, 67: 916–930. The western horse mackerel stock covers a large area of the Northeast Atlantic and is characterized by the sporadic occurrence of strong year classes. The only fishery-independent data available for its assessments are the estimates of total annual egg production from triennial egg surveys. Horse mackerel are indeterminate spawners, so a direct conversion of total annual egg production to spawning-stock biomass using prespawning-season estimates of fecundity is not viable. There is also evidence that potential fecundity per kg spawning female increases with fish weight. A linked separable–ADAPT VPA (SAD) model was developed that combines data on total catch, catch-at-age, and total annual egg production with data on potential and realized fecundity to provide population estimates for western horse mackerel. The model accounts for potential fecundity as a function of fish weight and for the development of a targeted fishery on the strong 1982 year class. Simulations confirm that the SAD model is able to reproduce population estimates without bias under a range of scenarios, except where there is a trend in realized fecundity. This underscores the need for improved information on realized fecundity, or alternatively the need to develop management plans that are robust to this source of uncertainty.
Breakdown of Host Resistance by Independent Evolutionary Lineages of Beet necrotic yellow vein virus Involves a Parallel C/U Mutation in Its p25 Gene
Authors: Acosta-Leal Rodolfo , Bryan Becky K. , Smith Jessica T. , Rush Charles M.
Published: January 2010

Breakdown of sugar beet Rz1-mediated resistance against Beet necrotic yellow vein virus (BNYVV) infection was previously found, by reverse genetics, to be caused by a single mutation in its p25 gene. The possibility of alternative breaking mutations, however, has not been discarded. To explore the natural diversity of BNYVV in the field and its effects on overcoming Rz1, wild-type (WT) and resistance-breaking (RB) p25 genes from diverse production regions of North America were characterized. The relative titer of WT p25 was inversely correlated with disease expression in Rz1 plants from Minnesota and California. In Minnesota, the predominant WT p25 encoded the A67C68 amino acid signature whereas, in California, it encoded A67L68. In both locations, these WT signatures were associated with asymptomatic BNYVV infections of Rz1 cultivars. Further analyses of symptomatic resistant plants revealed that, in Minnesota, WT A67C68 was replaced by V67C68 whereas, in California, WT A67L68 was replaced by V67L68. Therefore, V67 was apparently critical in overcoming Rz1 in both pathosystems. The greater genetic distances between isolates from different geographic regions rather than between WT and RB from the same location indicate that the underlying C to U transition originated independently in both BNYVV lineages.
Turgid female toads give males the slip: a new mechanism of female mate choice in the Anura
Authors: Bruning Bas , Phillips Benjamin L. , Shine Richard
Published: January 2010

In many anuran species, males vocalize to attract females but will grasp any female that comes within reach and retain their hold unless displaced by a rival male. Thus, female anurans may face strong selection to repel unwanted suitors, but no mechanism is known for doing so. We suggest that a defensive trait (the ability to inflate the body to ward off attack) has been co-opted for this role: by inflating their bodies, females are more difficult for males to grasp and hence, it is easier for another male to displace an already amplexed rival. Inflating a model female cane toad (Bufo marinus) strongly reduced a male's ability to maintain amplexus; and females who were experimentally prevented from inflating their bodies experienced no successful takeovers from rival males, in contrast to control females. Thus, the ability of a female cane toad to inflate her body may allow her to manipulate the outcome of male–male competition. This overlooked mechanism of anuran mate choice may reflect a common evolutionary pattern, whereby females co-opt defensive traits for use in sexual selection.
Deep-ocean origin of the freshwater eels
Authors: Inoue Jun G. , Miya Masaki , Miller Michael J. , Sado Tetsuya , Hanel Reinhold , Hatooka Kiyotaka , Aoyama Jun , Minegishi Yuki , Nishida Mutsumi , Tsukamoto Katsumi
Published: January 2010

Of more than 800 species of eels of the order Anguilliformes, only freshwater eels (genus
Anguilla
with 16 species plus three subspecies) spend most of their lives in freshwater during their catadromous life cycle. Nevertheless, because their spawning areas are located offshore in the open ocean, they migrate back to their specific breeding places in the ocean, often located thousands of kilometres away. The evolutionary origin of such enigmatic behaviour, however, remains elusive because of the uncertain phylogenetic position of freshwater eels within the principally marine anguilliforms. Here, we show strong evidence for a deep oceanic origin of the freshwater eels, based on the phylogenetic analysis of whole mitochondrial genome sequences from 56 species representing all of the 19 anguilliform families. The freshwater eels occupy an apical position within the anguilliforms, forming a highly supported monophyletic group with various oceanic midwater eel species. Moreover, reconstruction of the growth habitats on the resulting tree unequivocally indicates an origination of the freshwater eels from the midwater of the deep ocean. This shows significant concordance with the recent collection of mature adults of the Japanese eel in the upper midwater of the Pacific, suggesting that they have retained their evolutionary origin as a behavioural trait in their spawning areas.
Tool use by wild New Caledonian crowsCorvus moneduloidesat natural foraging sites
Authors: Bluff Lucas A. , Troscianko Jolyon , Weir Alex A. S. , Kacelnik Alex , Rutz Christian
Published: January 2010

New Caledonian crowsCorvus moneduloidesuse tools made from sticks or leaf stems to ‘fish’ woodboring beetle larvae from their burrows in decaying wood. Previous research on this behaviour has been confined to baited sites, leaving its ecological context and significance virtually unexplored. To obtain detailed observations of natural, undisturbed tool use, we deployed motion-triggered video cameras at seven larva-fishing sites. From 1797 camera hours of surveillance over 111 days, we recorded 317 site visits by at least 14 individual crows. Tool use was observed during 150 site visits. Our video footage revealed notable variation in foraging success among identifiable crows. Two nutritionally independent, immature crows spent considerable time using tools, but were much less successful than local adults, highlighting the potential role of individual and social learning in the acquisition of tool-use proficiency. During systematic surveys of larva-fishing sites, we collected 193 tools that crows had left inserted in larva burrows. Comparing these tools with the holes in which they were found, and with raw materials available around logs, provides evidence for tool selectivity by New Caledonian crows under natural conditions. Taken together, these two complementary lines of investigation provide, to our knowledge, the first quantitative description of larva fishing by wild crows in its full ecological context.
Pattern mimicry of host eggs by the common cuckoo, as seen through a bird's eye
Authors: Stoddard Mary Caswell , Stevens Martin
Published: January 2010

Cuckoo–host interactions provide classical examples of coevolution. Cuckoos place hosts under selection to detect and reject foreign eggs, while host defences result in the evolution of host-egg mimicry in cuckoos. Despite a long history of research, egg pattern mimicry has never been objectively quantified, and so its coevolution with host defences has not been properly assessed. Here, we use digital image analysis and modelling of avian vision to quantify the level of pattern mimicry in eight host species of the common cuckoo
Cuculus canorus
and their respective cuckoo host-races. We measure a range of pattern attributes, including marking size, diversity in size, contrast, coverage and dispersion. This new technique reveals hitherto unnoticed sophistication in egg pattern mimicry. We show that various features of host egg pattern are mimicked by the eggs of their respective cuckoo host-races, and that cuckoos have evolved better pattern mimicry for host species that exhibit stronger egg rejection. Pattern differs relatively more between eggs of different host species than between their respective cuckoo host-races. We suggest that cuckoos may have more ‘average’ markings in order to be able to use subsidiary hosts. Our study sheds new light on cuckoo–host coevolution and illustrates a new technique for quantifying animal markings with respect to the relevant animal visual system.
The energetic basis of acoustic communication
Authors: Gillooly James F. , Ophir Alexander G.
Published: January 2010

Animals produce a tremendous diversity of sounds for communication to perform life's basic functions, from courtship and parental care to defence and foraging. Explaining this diversity in sound production is important for understanding the ecology, evolution and behaviour of species. Here, we present a theory of acoustic communication that shows that much of the heterogeneity in animal vocal signals can be explained based on the energetic constraints of sound production. The models presented here yield quantitative predictions on key features of acoustic signals, including the frequency, power and duration of signals. Predictions are supported with data from nearly 500 diverse species (e.g. insects, fishes, reptiles, amphibians, birds and mammals). These results indicate that, for all species, acoustic communication is primarily controlled by individual metabolism such that call features vary predictably with body size and temperature. These results also provide insights regarding the common energetic and neuromuscular constraints on sound production, and the ecological and evolutionary consequences of producing these sounds.
Fluorescence Resonance Energy Transfer-Sensitized Emission of Yellow Cameleon 3.60 Reveals Root Zone-Specific Calcium Signatures in Arabidopsis in Response to Aluminum and Other Trivalent Cations
Authors: Rincón-Zachary Magaly , Teaster Neal D. , Sparks J. Alan , Valster Aline H. , Motes Christy M. , Blancaflor Elison B.
Published: January 2010

Fluorescence resonance energy transfer-sensitized emission of the yellow cameleon 3.60 was used to study the dynamics of cytoplasmic calcium ([Ca2+]cyt) in different zones of living Arabidopsis (Arabidopsis thaliana) roots. Transient elevations of [Ca2+]cyt were observed in response to glutamic acid (Glu), ATP, and aluminum (Al3+). Each chemical induced a [Ca2+]cyt signature that differed among the three treatments in regard to the onset, duration, and shape of the response. Glu and ATP triggered patterns of [Ca2+]cyt increases that were similar among the different root zones, whereas Al3+ evoked [Ca2+]cyt transients that had monophasic and biphasic shapes, most notably in the root transition zone. The Al3+-induced [Ca2+]cyt increases generally started in the maturation zone and propagated toward the cap, while the earliest [Ca2+]cyt response after Glu or ATP treatment occurred in an area that encompassed the meristem and elongation zone. The biphasic [Ca2+]cyt signature resulting from Al3+ treatment originated mostly from cortical cells located at 300 to 500 μ m from the root tip, which could be triggered in part through ligand-gated Glu receptors. Lanthanum and gadolinium, cations commonly used as Ca2+ channel blockers, elicited [Ca2+]cyt responses similar to those induced by Al3+. The trivalent ion-induced [Ca2+]cyt signatures in roots of an Al3+-resistant and an Al3+-sensitive mutant were similar to those of wild-type plants, indicating that the early [Ca2+]cyt changes we report here may not be tightly linked to Al3+ toxicity but rather to a general response to trivalent cations.
Prolonged responses in patients with MDS and CMML treated with azacitidine and etanercept
Authors: Scott Bart L. , Ramakrishnan Aravind , Storer Barry , Becker Pamela S. , Petersdorf Steve , Estey Elihu H. , Deeg H.Joachim
Published: January 2010

Combination therapy with azacitidine and etanercept was hypothesized to lead to improved responses in myelodysplastic syndrome (MDS) patients. Thirty‐two patients with MDS/chronic myelomonocytic leukaemia were treated with azacitidine + etanercept; 30 completed at least three therapy cycles. At 3 months, nine patients had achieved complete response (CR), two had partial response, 10 had marrow CRs, seven had stable disease, two patients had haematological improvement without marrow response and two patients had disease progression. The overall response rate was 72%; median duration of response was not reached at 2 years. Marrow response rates and duration were improved with azacitidine + etanercept compared to azacitidine alone.
Inter‐population variation in seed longevity for two invasive weeds: Chrysanthemoides monilifera ssp. monilifera (boneseed) and ssp. rotundata (bitou bush)
Authors: SCHOEMAN J , BUCKLEY Y M , CHERRY H , LONG R L , STEADMAN K J
Published: January 2010

Schoeman J, Buckley YM, Cherry H, Long RL & Steadman KJ (2010). Inter‐population variation in seed longevity for two invasive weeds: Chrysanthemoides monilifera ssp. monilifera (boneseed) and ssp. rotundata (bitou bush). Weed Research50, 67–75.

Seed longevity has a major influence on the success of weed management and eradication programmes. A correlation between responses to a controlled aging test performed at 45°C, 60% relative humidity (RH) and seed persistence in the field has recently been suggested. Here we investigated whether collections of differing quality of two closely related invasive weeds, Chrysanthemoides monilifera ssp. monilifera and ssp. rotundata (boneseed and bitou bush, respectively), had different seed longevity using the controlled aging test. Chrysanthemoides monilifera ssp. monilifera fruits were collected from across five Australian states, and C. monilifera ssp. rotundata from one state, covering their invasive ranges. Seed quality was assessed visually and using tetrazolium staining, and a series of germination tests established appropriate germination conditions. The controlled aging test was run for a subset of collections. Chrysanthemoides monilifera ssp. rotundata seeds died more quickly (time to lose 50% viability, P50 = 16 days) than the C. monilifera ssp. monilifera collections (P50 = 47 days) when aged at 45°C and 60% RH. This difference was significant even considering the large differences in longevity between C. monilifera ssp. monilifera populations (P50 = 35–61 days; probably due to differences in maturity at collection). Based on a published correlation, we predict that mature C. monilifera ssp. monilifera may have a long‐lived (>3 years) seed bank and C. monilifera ssp. rotundata may have a transient (<1 year) seed bank. This suggests the two sub‐species should be considered separately when designing effective control measures.
Breeding spring wheat for improved allelopathic potential
Authors: BERTHOLDSSON N‐O
Published: January 2010

Bertholdsson N‐O (2010). Breeding spring wheat for improved allelopathic potential. Weed Research50, 49–57.

It is becoming apparent that allelopathy plays a significant role in the competitive ability of cereals against weeds; barley, wheat and rice cultivars with high allelopathic activity have been identified. However, direct breeding efforts to improve allelopathy have to date only been reported in rice. In this study, a breeding programme in spring wheat (Triticum aestivum) was evaluated to determine the efficiency of selection of allelopathy and the ability of breeding lines to suppress weeds in the field. The material used originated from a cross between a Swedish cultivar with low allelopathic activity and a Tunisian cultivar with high allelopathic activity. Allelopathic activity was measured as growth inhibition of perennial ryegrass (Lolium perenne) roots when grown together with the wheat cultivars on agar. For screening of F2 populations, a single plant bioassay was used for the first time. In the F6 and F7 generations, three breeding lines with an average improved allelopathy of 20% and one line with an unimproved allelopathy activity, but with the same phenotype as the high allelopathic lines, were tested together with the low allelopathic Swedish parent. The main result from the field study was a 19% average reduction of weed biomass for the high allelopathic lines, but no significant reduction of the low allelopathic breeding line. Early shoot length and early crop biomass (stages 37–39, Zadoks scale) and straw length of the high allelopathic lines were not significantly different from the Swedish parent. A negative effect was that grain yield was reduced by 9% in the high allelopathic lines. It is suggested that the reduced biomass of weeds in plots planted with the highly allelopathic wheat lines is related to differences in allelopathic activity and not differences in plant growth.
Occurrence and pathogenicity of Neofusicoccum parvum and N. mangiferae on ornamental Tibouchina species
Authors: Heath R. N. , Roux J. , Slippers B. , Drenth A. , Pennycook S. R. , Wingfield B. D. , Wingfield M. J.
Published: January 2010

Species in the Botryosphaeriaceae are important canker pathogens of woody plants, including Eucalyptus spp. The recent discovery of the Eucalyptus pathogen, Chrysoporthe austroafricana, on ornamental Tibouchina trees raised the question as to whether Tibouchina spp. might be alternative hosts for other Eucalyptus pathogens. Therefore, the aim of this study was to consider whether species of the Botryosphaeriaceae occurring on Eucalyptus spp. might also occur on ornamental Tibouchina spp. Isolations were made from Tibouchina trees in South Africa, New Zealand and Australia. Isolates were identified using morphological characteristics and DNA‐based techniques. Neofusicoccum parvum and N. mangiferae were identified from the samples. Pathogenicity trials on T. urvilleana showed that both species are pathogenic to this host.
Serological Detection of Cymbidium mosaic and Odontoglossum ringspot viruses in Orchids with Polyclonal Antibodies Produced Against Their Recombinant Coat Proteins
Authors: Rani Pooja , Pant Rajendra Prasad , Jain Rakesh Kumar
Published: January 2010

Cymbidium mosaic and Odontoglossum ringspot viruses infecting orchids were identified by coat protein (CP) properties. The Cymbidium mosaic virus (CymMV) CP gene is 672 nt long, potentially encoding 223 amino acids (aa). The Odontoglossum ringspot virus (ORSV) CP gene is 477 nt long, potentially encoding 158 aa. The CP gene of CymMV and ORSV isolates originating from different locations was highly conserved both at the nucleotide and amino acid levels (94–100%). Polyclonal antibodies against CymMV and ORSV were separately produced using bacterially expressed recombinant CP as immunogens. Antisera to CymMV (titre 1 : 2000) and ORSV (titre 1 : 250) detected the viruses by direct antigen‐coated enzyme‐linked immunosorbent assay (DAC‐ELISA) in orchid samples collected from Sikkim, India. Survey results indicated the prevalence of mixed infection of CymMV and ORSV in Cymbidium spp. The immunoreagents we developed will be useful for virus indexing in orchid certification programmes.
The political battlefield: negotiating space to protect indigenous and traditional knowledge under capitalism
Authors: Busingye Janice , Keim Wiebke
Published: January 2010

Knowledge has increasingly become an essential resource in the global economy, hence the capitalist tendency to regard it as a form of capital and as a motor for innovation and profit. Like any other capitalist commodity, conflicts over the ownership and use of various types of knowledge have arisen, thereby calling for legal protection. Nation‐states as well as inter‐state organisms are developing these legal frameworks in order to regulate the conflicts between different social actors. Consequently, thinking on knowledge and power has evolved to include the protection of knowledge from those who seek to gain control of it through the acquisition of legal rights, for instance, intellectual property (IP) rights. In many commercialised industrialised countries, legal frameworks have already been developed to protect IP. These include patents and copyrights as well as other trademarks, database rights and so on. However, in many developing countries with a weak technological base and less commercialisation IP protection mechanisms have not yet become firmly established. This is happening even though they have genetic resources and traditional knowledge that are of value to them and to the world at large. The protection of indigenous knowledge has existed as long as the knowledge itself, but the recognition of such mechanisms has been tightly controlled by stronger powers. In this article we argue that, whatever local communities choose to do to protect their indigenous knowledge, in the context of the current IP regime and the power of commercially driven global actors, the concept of traditional or indigenous knowledge itself becomes political. If the traditionality of knowledge can be reasonably questioned from an epistemological point of view, it would seem possible to claim rights and recognition for local communities in a highly controversial and economically relevant international arena.
The east–west advancement flap (horizontal advancement flap) to repair a defect on the nose ala
Authors: Ascari‐Raccagni A , Dondas A , Righini MG , Trevisan G
Published: January 2010

Background  The repair of an alar nasal defect is a frequent challenge for dermatologic surgeons for reasons of the high rate of non‐melanoma cancers in the area.

Objective  Our aim was to describe the use of an east–west cheek‐based flap (horizontal advancement flap) to repair a surgical defect on the nose ala.

Methods  Benefits and limits of this surgical procedure are evaluated.

Result  The resulting S‐shaped scar was well‐camouflaged among the natural skin lines (melolabial fold and melonasal junction). No architectural distortion of the nose resulted from the procedure.

Conclusion  In selected patients with small‐to‐medium‐size defects of the nasal ala, the horizontal advancement flap is a simple, reliable and aesthetic reconstruction option.
Distribution and expression of CD200 in the rat respiratory system under normal and endotoxin‐induced pathological conditions
Authors: Jiang‐Shieh Ya‐Fen , Chien Hsiung‐Fei , Chang Chiu‐Yun , Wei Tsui‐Shan , Chiu Mei‐Miao , Chen Hui‐Min , Wu Ching‐Hsiang
Published: January 2010

In vivo and in vitro studies have clearly demonstrated that signaling mediated by the interaction of CD200 and its cognate receptor, CD200R, results in an attenuation of inflammatory or autoimmune responses through multiple mechanisms. The present results have shown a differential expression of CD200 in the respiratory tract of intact rats. Along the respiratory passage, CD200 was specifically distributed at the bronchiolar epithelia with intense CD200 immunoreactivity localized at the apical surface of some ciliated epithelial cells; only a limited expression was detected on the Clara cells extending into the alveolar duct. In the alveolar septum, double immunofluorescence showed intense CD200 immunolabeling on the capillary endothelia. A moderate CD200 labeling was observed on the alveolar type II epithelial cells. It was, however, absent in the alveolar type I epithelial cells and the alveolar macrophages. Immunoelectron microscopic study has revealed a specific distribution of CD200 on the luminal front of the thin portion of alveolar endothelia. During endotoxemia, the injured lungs showed a dose‐ and time‐dependent decline of CD200 expression accompanied by a vigorous infiltration of immune cells, some of them expressing ionized calcium binding adapter protein 1 or CD200. Ultrastructural examination further showed that the marked reduction of CD200 expression was mainly attributable to the loss of alveolar endothelial CD200. It is therefore suggested that CD200 expressed by different lung cells may play diverse roles in immune homeostasis of normal lung, in particular, the molecules on alveolar endothelia that may control regular recruitment of immune cells via CD200‐CD200R interaction. Additionally, it may contribute to intense infiltration of immune cells following the loss or inefficiency of CD200 under pathological conditions.
Mast cells in the amphibian brain during development
Authors: Pinelli Claudia , Santillo Alessandra , Baccari Gabriella Chieffi , Monteforte Rossella , Rastogi Rakesh K.
Published: January 2010

This is the first descriptive study of ontogenesis and anatomical distribution of mast cells in the developing brain of three different amphibian species. In the toad and the green frog, mast cells are preferentially located in: (i) the meningeal lining (pia mater), (ii) the choroid plexuses, both anterior and posterior, and (iii) the neuropil, in close association with the epithelial cell lining of blood vessels. It is only in the perennially aquatic African clawed frog that mast cells never appear inside brain ventricles and within the neuropil. Mast cells first become identifiable in brain of different species in different stages of development. While there are differences in the number of mast cells in different species at different stages of development, the number nearly doubles in all three species during the transition from pro‐metamorphic stage of larval development to the peak of metamorphic climax. Furthermore, the number of mast cells is comparatively higher in the toad and remarkably lower in the fully aquatic Xenopus laevis, in which species the first appearance of identifiable mast cells during larval development occurs much later than in equivalent stages of development of the toad and the green frog. The secretory nature of mast cells can be assumed by the presence of cytoplasmic granules, which may show species‐specific texture. Further experimental analyses are required to unveil the usefulness of mast cells in the amphibian brain.