bluuebunny/crossref_metadata_2025 huggingface dataset:
The handmaid's tale: morganatic relationships in early-mediaeval Bavaria
Authors: Hammer Carl I.
Published: November 2008

Malgré la division de principe entre individus légalement libres et non-libres que connaissait la société du haut Moyen Age, il n'en existait pas moins des relations mixtes et des unions entre des membres de ces deux groupes.

Depuis le huitième siècle au moins, on pouvait voir dans certaines de ces unions des mariages valides. L'article cite comme preuve des prescriptions juridiques du haut Moyen Age et s'appuie sur l'étude de 39 contrats bavarois pour décrire comment ces relations se sont constituées ainsi que les réactions aux problémes qu'elles ont suscìtés. Quelle qu'ait été la nature exacte de ces relations, les enfants qui en étaient issus naissaient non-libres et le droit à propriété ou même la liberté du partenaire non-serf pouvaient être remis en cause. Dès la fin du 8e siècle, les Bavarois de statut libre, hommes ou femmes, tentèrent de régler ces difficultés et d'améliorer la condition de leur partenaire et de leur descendance non-libres; toute une série d'arrangements furent trouvés qui intéressèrent en particulier les hommes. Au lOe siècle, la formule la plus courante fut de placer la partie servile du couple sous la dépendance et la protection de l'Eglise, contre une redevance annuelle fixe, le census, qui la libérait de toute autre obligation.
A cuckoo in the nest? The origins of civil registration and state medical statistics in England and Wales
Authors: Higgs Edward
Published: November 2008

On constate une certaine tendance à écrire en termes de religion et de médecine l'histoire de l'instauration de l'état civil ainsi que celle duGeneral Register Officeen Angleterre et Galles en application duRegistration Actde 1836. Nous soutenons dans cet article qu'il est plus fécond d'analyser ces mesures essentiellement en termes d'enregistrement de droits de propriéte; d'autre part les grands débats du XIXe siècle commençant, relatifs à l'assistance aux pauvres, jouèrent aussi un rôle essentiel. On comprend mieux ainsi quelques traits essentiels des données demographiques et médicales publiées dans lesAnnual Reports of the Registrar General.
The devil's children: child witch-trials in early modern Germany
Authors: Walinski-Kiehl Robert S.
Published: November 2008

Cet article s'attache aux procès dont furent l'objet les enfants accusés de sorcellerie dans l'Europe des XVIe et XVIIe siècles, ce mode de persécution de la sorcellerie ayant jusqu'à présent peu retenu l'attention des historiens. On s'attache surtout à l'Allemagne, terrain favori, dans l'Europe de l'époque, de la chasse aux sorcières. Des études de cas ont été menées pour certaines régions (Würzburg, Calw et Bamberg) qui ont permis de définir les caractéristiques majeures des procès en sorcellerie touchant les enfants, du point de vue de plusieurs disciplines, comme la sociologie et la psychologie. L'étude suggère que la mise en jugement des enfants accusés de sorcellerie est à rapprocher des ‘croisades morales’ entreprises par les régimes étatiques pour imposer à leurs sujets une discipline sociale et morale.
The demographic transition in Victorian England and changes in English kinship networks
Authors: Zhao Zhongwei
Published: November 2008

Lorsque l'on étudie le fonctionnement des réseaux de famille et de parenté, la question la plus importante, et pourtant la moins étudiée, est de savoir dans quelle mesure ces systèmes de soutien sont affectés par les conditions démographiques dans le passé. Nous commençons par examiner les changements rapides démographiques intervenus, surtout en matière de mortalité et de fécondité, dans l'Angleterre de l'époque victorienne et rappellons à quel point les cohortes nées dans les années 1851–1855 et 1901–1905 ont pu connaître des conditions démographiques différentes. L'accent est mis sur l'impact que des conditions démographiques modifiées ont pu avoir sur le fonctionnement des réseaux familiaux et le soutien apporté par la parenté. Les modèles de parenté subissent des modifications au cours de la vie, ces changements étant étudiés au niveau des individus, grâce à un programme informatique de simulation, intitulé CAMSIM. Cet exercice de simulation a permis de reconstituer les effets que les modifications de fécondité et de mortalité ont pu entraîner sur le nombre et le type de parents vivants, auxquels un individu peut faire théoriquement appel pour l'aider, è un âge donné.
Lagged cells in alert monkey lateral geniculate nucleus
Authors: SAUL ALAN B.
Published: November 2008

Five lagged cells were recognized by extracellular recording in the lateral geniculate nucleus of an awake, behaving macaque monkey. Previous reports of lagged cells were all in the anesthetized cat. Both parvocellular and magnocellular lagged cells were observed. Response timing was distributed continuously across the population, and both sustained and transient responses were seen in the magnocellular subpopulation. Cortex thus receives signals with a wide range of timing, which can mediate direction selectivity across multiple dimensions.
Therapeutic and prophylactic applications of alphavirus vectors
Authors: Atkins Gregory J. , Fleeton Marina N. , Sheahan Brian J.
Published: November 2008

Alphavirus vectors are high-level, transient expression vectors for therapeutic and prophylactic use. These positive-stranded RNA vectors, derived from Semliki Forest virus, Sindbis virus and Venezuelan equine encephalitis virus, multiply and are expressed in the cytoplasm of most vertebrate cells, including human cells. Part of the genome encoding the structural protein genes, which is amplified during a normal infection, is replaced by a transgene. Three types of vector have been developed: virus-like particles, layered DNA–RNA vectors and replication-competent vectors. Virus-like particles contain replicon RNA that is defective since it contains a cloned gene in place of the structural protein genes, and thus are able to undergo only one cycle of expression. They are produced by transfection of vector RNA, and helper RNAs encoding the structural proteins. Layered DNA–RNA vectors express the Semliki Forest virus replicon from a cDNA copy via a cytomegalovirus promoter. Replication-competent vectors contain a transgene in addition to the structural protein genes. Alphavirus vectors are used for three main applications: vaccine construction, therapy of central nervous system disease, and cancer therapy.
Determination of Carotenoids in Yellow Maize, the Effects of Saponification and Food Preparations
Authors: Muzhingi  , Yeum  , Russell  , Johnson  , Qin  , Tang
Published: November 2008

Maize is an important staple food consumed by millions of people in many countries. Yellow maize naturally contains carotenoids which not only provide provitamin A carotenoids but also xanthophylls, which are known to be important for eye health. This study was aimed at 1) evaluating the effect of saponification during extraction of yellow maize carotenoids, 2) determining the major carotenoids in 36 genotypes of yellow maize by high-performance liquid chromatography with a C30 column, and 3) determining the effect of cooking on the carotenoid content of yellow maize. The major carotenoids in yellow maize were identified as all-trans lutein, cis-isomers of lutein, all-trans zeaxanthin, α- and β-cryptoxanthin, all-trans β-carotene, 9-cis β-carotene, and 13-cis β-carotene. Our results indicated that carotenoid extraction without saponification showed a significantly higher yield than that obtained using saponification. Results of the current study indicate that yellow maize is a good source of provitamin A carotenoids and xanthophylls. Cooking by boiling yellow maize at 100° C for 30 minutes increased the carotenoid concentration, while baking at 450° F for 25 minutes decreased the carotenoid concentrations by almost 70% as compared to the uncooked yellow maize flour.
Vitamin E Inadequacy Observed in a Group of 2- to 6-Year-Old Children Living in Kwangju, Republic of Korea
Authors: Giraud  , Kim  , Cho  , Driskell
Published: November 2008

Studies on the vitamin E status of Korean children are lacking. Dietary intakes and plasma concentrations of tocopherols of healthy 2- to 6-year-olds living in Kwangju, Republic of Korea, were determined and their vitamin E status evaluated. Subjects included 66 girls and 65 boys, with 21–32 subjects per age group. Subjects’ intakes were recorded by a trained interviewer for foods eaten at preschool/kindergarten; otherwise, three consecutive 24-hour food recalls were obtained from parents. Plasma tocopherol concentrations were determined using high-performance liquid chromatography. Intakes of energy and total monounsaturated and polyunsaturated fats were significantly different (p < 0.05) among age groups, not gender, with 2- and 3-year-olds having lower intakes. Alpha- and γ-tocopherol intakes were similar by age and gender. Sixty-seven percent consumed less than the Korean Adequate Intakes for vitamin E, and 77% had α-tocopherol intakes less than USA/Canadian Estimated Average Requirements. Plasma α-tocopherol concentrations, but not γ-tocopherol, were significantly higher (p < 0.05) for 2-year-olds. Two-thirds of subjects had plasma α-tocopherol concentrations less than 12 μmol/L, which is indicative of vitamin E inadequacy in adults; guidelines for children do not exist. Many of the Korean children had inadequate intakes and likely inadequate plasma concentrations of vitamin E.
Vitamin A and Vitamin E Isoforms Stability and Peroxidation Potential of All-In-One Admixtures for Parenteral Nutrition
Authors: Guidetti  , Sforzini  , Bersani  , Corsini  , Grossi  , Zolezzi  , Fasano  , Pironi
Published: November 2008

Background: In all-in-one admixtures (AIOs), vitamins can be degraded and lipid can be peroxidized by light exposure, oxygen action, and multiple chemical interactions. Aim: We investigated the impact of three commercial lipid emulsions and two multivitamin preparations on vitamin A and vitamin E chemical stability and lipid peroxidation potential of AIOs. Methods: A soybean oil (Soy), soybean/medium-chain triacylglycerol oil (MCT), and olive/soybean oil (Olive)-based emulsion (all 20%), and a lyophilized (Lyo) and emulsified (Emu) multivitamin compounds, were tested. Two AIOs for each lipid emulsion were prepared, the former with Lyo and the latter with Emu. The concentrations of retinol palmitate, α-γ-δ-tocopherol, and malondialdehyde were analyzed in AIOs, immediately (T0) and 24 hours (T24) after compounding. Results: Retinol palmitate, and α- and γ-tocopherol were more stable in MCT-AIOs than in both Soy-AIOs and Olive-AIOs (p < 0.013; p < 0.001 respectively). Furthermore α-tocopherol was more stable in Lyo-AIOs than in Emu-AIOs (p < 0.004). Malondialdehyde (MDA) increased differently among the admixtures; however the concentrations were similar in all AIOs at T24. Conclusions: The differences in retinol palmitate stability were due both to lipid emulsions per se and to interaction between lipid emulsions and multivitamin preparations. The α-γ-tocopherol stability depended on both lipid emulsions and multivitamin preparations. In tested AIOs there was a different degradation rate of fat-soluble vitamins to keep the same lipid peroxidation level, since MDA concentrations at T24 were similar among AIOs.
Design and rationale of a randomized, double-blind, placebo-controlled phase III study for autologous bone marrow cell transplantation in critical limb ischemia: the BONe Marrow Outcomes Trial in Critical Limb Ischemia (BONMOT-CLI)
Authors: Amann  , Lüdemann  , Rückert  , Lawall  , Liesenfeld  , Schneider  , Schmidt-Lucke
Published: November 2008

Background: Critical limb ischemia (CLI) is the end-stage of peripheral artery disease. Only about two thirds of patients with CLI can be revascularised, one third progresses to leg amputation with high associated morbidity and mortality. Therapeutic angiogenesis with bone marrow cells has shown promising improvement in less severe stages of peripheral ischemia. Our study evaluates the therapeutic value of bone marrow cell induced angiogenesis and arteriogenesis in severe, limb-threatening ischemia. Patients and methods: the BONe Marrow Outcome Trial in Critical Limb Ischemia (BONMOT-CLI) is a investigator-initiated, double-blinded, 1:1 randomized, placebo-controlled multi-centre study at 4 sites in Germany. Only patients with no option for revascularisation or after failed revascularisation will be included. A total of 90 patients is to be included. One arm with 45 subjects will be treated with a concentrate of autologous bone marrow cells which will be injected at 40 sites into the ischemic limb. In the placebo arm, study subjects will undergo a sham bone marrow punction and 40 saline injections. At three months, a combined primary endpoint of major amputation or persisting critical limb ischemia (no clinical or perfusion improvement) will be evaluated. Secondary endpoints are death, changes in perfusion, quality of life, walking distance, minor amputations, wound healing, collateral density and cancer incidence. Post-study follow-up is up to two years. Conclusions: The results of this first randomized placebo-controlled trial for autologous bone marrow cell therapy in CLI will clarify the value of this new therapeutic modality in a patient population with no other alternatives except major amputation.
Acute ischaemia of the leg following accidental intra-arterial injection of dissolved flunitrazepam tablets
Authors: Leifert  , Bossaller  , Uhl
Published: November 2008

Accidental intra-arterial injection of drugs is a sporadic complication in i.v. drug addicts. A 22-year-old drug-abuser injected flunitrazepam tablets dissolved in tap water into her left femoral artery and presented with clinical signs of acute ischaemia of the left leg. Severe rhabdomyolysis developed within 5 hours after the injection. Selective arterial catheter angiography showed an acute occlusion of the posterior tibial artery. Combination therapy with i.a. urokinase, i.a. prostaglandines and i.v. anticoagulation resulted in re-opening of the obstructed distal artery and complete cessation of symptoms.
Capsule endoscopy findings in congenital afibrinogenemia-associated angiopathy
Authors: Katsinelos  , Vasiliadis  , Soufleris  , Chatzimavroudis  , Zavos  , Paroutoglou  , Katsinelos  , Papaziogas  , Kountouras
Published: November 2008

Congenital afibrinogenemia is a rare genetic disorder characterized by the complete absence of functional fibrinogen. We report a 22-year-old female who developed nephrogenic arterial hypertension and intestinal ischemia due to congenital afibrinogenemia-associated angiopathy of large abdominal arteries. We describe, for the first time, the capsule findings and discuss the pathophysiology of this unusual condition.
The origin of conical mounds at the mouth of Chasma Boreale
Authors: Warner Nicholas H. , Farmer Jack D.
Published: November 2008

One‐hundred and six isolated conical mound landforms were identified proximal to the north polar cap of Mars at the mouth of Chasma Boreale. Five unique morphologies were identified including moderately sloped (4°–6°) cratered mound forms including two mounds of Abalos Colles, flat‐topped moderately sloped (4°–6°) polygonal mound forms, steeper (6–13°) conical mound forms, subdued mound forms with low‐angle slopes (0.5–3°), and small (<2 km diameter) clustered conical forms with low‐ to moderate‐angle (1–5°) flank slopes. From first‐order relationships between flank slope and the volcano productivity index (volume/diameter ratio), 16 mounds were found to be morphologically similar to terrestrial low‐angle basaltic shield volcanoes. Thirteen mounds exhibit summit craters that range in depth (d) to diameter (D) ratio from 1:9 to 1:320. The circularity and d/D ratios of mound summit craters are consistent with highly modified northern plains impact craters. Image analysis of shield‐like mounds reveals morphologic characteristics inconsistent with pristine volcanic landforms for most features. Horizontal flank layering (10–100 m thick), polygonal map‐view morphology, topographic relationships, and spatial association with retreating polar scarps suggest that mound forms at the mouth of Chasma Boreale represent remnants of a once thicker, more continuous sequence of near‐polar layered material. Evidence for northward scarp retreat is visible along Rupes Tenuis, a sinuous scarp located west of Chasma Boreale. Along this scarp, a single ∼100‐m‐thick resistant cap unit (part of the Early Amazonian age Rupes Tenuis unit) is being undermined by aeolian erosion, solar ablation, and mass wasting. Remnants of the cap unit rest along the scarp margin and in places form small conical mound clusters at the base of the scarp. Fracture controlled retreat of the scarp is visible along the eastern portion of Rupes Tenuis and along the Escorial crater remnant mesa where small tongue‐like promontories have been sculpted into the cap unit. Isolation of these irregularities by scarp retreat has formed several volcanic‐like scarp and mesa proximal mounds. Mound forms located closest to the retreating Rupes Tenuis scarp above 78°N were found to be the steepest and tallest mound landforms in the region. Mounds located distal to Rupes Tenuis were found to be broad and subdued. This observation is consistent with long‐term retreat of a once more extensive Rupes Tenuis scarp and long‐term modification of isolated conical remnants.
Late Pliocene‐early Pleistocene 100‐ka problem
Authors: Nie Junsheng , King John , Fang Xiaomin
Published: November 2008

Little is known about the 100‐ka ice volume cycles immediately before 1 Ma except that they are coherent with the 100‐ka eccentricity cycles. Here we show that ice volume and ocean circulation change/global carbon mass balance are phase‐locked and highly coupled regarding amplitude envelopes at the 100‐ka band, but neither is phase‐locked to and amplitude‐coupled to the 100‐ka eccentricity orbital forcing signal between 3‐1 Ma. We describe this phasing and amplitude mismatch at the 100‐ka band between 3‐1 Ma between eccentricity forcing and paleo‐ice volume records as the “late Pliocene‐early Pleistocene 100‐ka problem.” A free 100‐ka oscillation internal to our climate system, especially those related to oscillations of atmospheric CO2 concentration, operating on an Earth characterized by a high‐inertia deep thermohaline ocean that can store carbon and heat, might hold the key for the “late Pliocene‐early Pleistocene 100‐ka problem.”
Spatiotemporal correlations of earthquakes in the continuum limit of the one‐dimensional Burridge‐Knopoff model
Authors: Mori Takahiro , Kawamura Hikaru
Published: November 2008

Spatiotemporal correlations of the one‐dimensional spring‐block (Burridge‐Knopoff) model of earthquakes, either with or without the viscosity term, are studied by means of numerical computer simulations. The continuum limit of the model is examined by systematically investigating the model properties by varying the block‐size parameter a toward a → 0. The Kelvin viscosity term is introduced so that the model dynamics possesses a sensible continuum limit. In the presence of the viscosity term, many of the properties of the original discrete BK model are kept qualitatively unchanged even in the continuum limit, although the size of minimum earthquakes gets smaller as a gets smaller. One notable exception is the existence/nonexistence of the doughnutlike quiescence prior to the mainshock. Although large events of the original discrete BK model accompany seismic acceleration together with a doughnutlike quiescence just before the mainshock, the spatial range of the doughnutlike quiescence becomes narrower as a gets smaller, and in the continuum limit, the doughnutlike quiescence might vanish altogether. The doughnutlike quiescence observed in the discrete BK model is then a phenomenon closely related to the short‐length cutoff scale of the model.
Variability of sea ice simulations assessed with RGPS kinematics
Authors: Kwok R. , Hunke E. C. , Maslowski W. , Menemenlis D. , Zhang J.
Published: November 2008

Sea ice drift and deformation from coupled ice‐ocean models are compared with high‐resolution ice motion from the RADARSAT Geophysical Processor System (RGPS). In contrast to buoy drift, the density and extent of the RGPS coverage allows a more extensive assessment and understanding of model simulations at spatial scales from ∼10 km to near basin scales and from days to seasonal timescales. This work illustrates the strengths of the RGPS data set as a basis for examining model ice drift and its gradients. As it is not our intent to assess relative performance, we have selected four models with a range of attributes and grid resolution. Model fields are examined in terms of ice drift, export, deformation, deformation‐related ice production, and spatial deformation patterns. Even though the models are capable of reproducing large‐scale drift patterns, variability among model behavior is high. When compared to the RGPS kinematics, the characteristics shared by the models are (1) ice drift along coastal Alaska and Siberia is slower, (2) the skill in explaining the time series of regional divergence of the ice cover is poor, and (3) the deformation‐related volume production is consistently lower. Attribution of some of these features to specific causes is beyond our current scope because of the complex interplay between model processes, parameters, and forcing. The present work suggests that high‐resolution ice drift observations, like those from the RGPS, would be essential for future model developments, improvements, intercomparisons, and especially for evaluation of the small‐scale behavior of models with finer grid spacing.
Integration of a prognostic sea surface skin temperature scheme into weather and climate models
Authors: Brunke Michael A. , Zeng Xubin , Misra Vasubandhu , Beljaars Anton
Published: November 2008

A prognostic skin sea surface temperature (SST) algorithm is included in the Community Atmosphere Model (CAM3.1). With this algorithm, the model produces a mean diurnal cycle of <0.5 K over most oceanic regions and >0.5 K primarily in tropical and subtropical oceans of the summer hemisphere with isolated areas of >2 K. The diurnal cycle in air temperature is substantially increased over regions with large skin SST diurnal cycles, and the enhanced diurnal cycle agrees better with the TAO buoy data over the equatorial Pacific. There is also a significant effect on the diurnal cycle in precipitation particularly in the increased hourly maximum precipitation over the Bay of Bengal and the western Pacific in boreal summer. These changes to the diurnal cycle in SST affect the seasonal climatologies in the model with improved seasonal mean precipitation mainly in the tropics following similar patterns to the hourly maximum precipitation rates. The near‐surface flow across the Indian subcontinent is also increased during the summer monsoon resulting in higher seasonal precipitation over the Bay of Bengal.
Multiple‐point geostatistics for modeling subsurface heterogeneity: A comprehensive review
Authors: Hu L. Y. , Chugunova T.
Published: November 2008

For more than half a century, geostatistics has been developed and has increasingly been used for modeling subsurface heterogeneity. Traditionally, geostatistical simulations are based on a random function model defined according to the specificities of the geological formation under investigation. Unlike traditional geostatistics, multiple‐point (MP) geostatistics avoids the explicit definition of a random function but directly infers the necessary multivariate distributions from training images. This confers on MP geostatistics a potential applicability to any geological environment, provided that there is a training image representative of the geological heterogeneity and that the essential features of this training image can be characterized by statistics defined on a limited point configuration. This paper presents a comprehensive review of MP geostatistics. If the principle of MP geostatistics is straightforward and attractive, its industrial applicability largely depends on the implementation methods. The use of a search tree for storing MP statistics is a great step that made MP geostatistics actually applicable in industry. In the meantime, other methods such as multiple grids and image postprocessing are introduced and allow enhancing the reproduction of patterns observed in training images. Because of the sequential procedure, MP simulations can easily honor local hard data. There are methods available for constraining MP simulations to target global statistics (facies proportions) and also for integrating spatial auxiliary constraints that can tremendously improve the spatial features of MP simulations. Furthermore, both the gradual deformation method and the probability perturbation method are compatible with MP geostatistics and allow integrating hydrodynamic data into MP simulations. More recent developments of MP geostatistics include sequentially simulating patterns instead of points and using different geological scenarios (training images) for dynamic data inversion.
Estimating transmissivity fields and their influence on flow and transport: The case of Champagne mounts
Authors: Renard F. , Jeannée N.
Published: November 2008

This paper presents a flexible and general methodology that combines hydrogeological and geostatistical modeling techniques to estimate a set of transmissivity fields and their influence on flow and transport. The methodology may be applied to any case with only hydraulic head observations, even if most of them are concentrated inside a small part of the entire domain of interest. It is applied here to the case of the Champagne chalk aquifer (France), where it is shown to be very efficient. The methodology is decomposed in three independent parts. First, a reference head distribution is constructed by kriging in order to constrain the inverse problem. As hydraulic heads and elevations are correlated, a smoothed digital elevation model is used as external drift. The inverse problem is then solved by using a simplified pilot point method with an efficient and easy‐to‐use minimization algorithm. Finally, geostatistical simulations combined with flow simulations lead to a set of acceptable transmissivity fields. The induced uncertainty is evaluated by calculating tracer concentrations, pointing out areas where flow behavior is uncertain and where new borings would be advantageously drilled.
CD40 regulates human dendritic cell‐derived IL‐7 production that, in turn, contributes to CD8+ T‐cell antigen‐specific expansion
Authors: Carreno Beatriz M , Becker‐Hapak Michelle , Linette Gerald P
Published: November 2008

CD40L (CD154) expressed on activated CD4+ T cells has been shown to provide CD40+ dendritic cells (DCs), a critical signal for establishing CD8+ T‐cell immunity. CD40L–CD40 interaction leads to DC maturation with IL‐12 production and upregulation of various costimulatory molecules. In this study, we show that CD40 engagement provides a unique maturation signal for human monocyte‐derived DCs to upregulate IL‐7 production. Other inducers of DC maturation, such as TLR 4 and TLR 7/8 agonist, fail to induce IL‐7 upregulation. Neutralization of IL‐7 activity in human CD8+ T‐cell cultures stimulated with CMV pp65‐NLV peptide‐pulsed mature DCs (mDCs) leads to a reduction in antigen‐specific CD8+ T‐cell yields suggesting a role for mDC‐derived IL‐7 during T‐cell receptor (TCR) activation. Furthermore, IL‐7 signaling requires a temporal coordination with TCR activation for maximal antigen‐specific T‐cell yields. These results show that CD40 signals regulate DC‐derived IL‐7 production that, in turn, may instruct CD8+ T cells at the time of TCR engagement for survival leading to an increased expansion of antigen‐specific T cells.
Solution structure and catalytic mechanism of human protein histidine phosphatase 1
Authors: Gong Weibin , Li Yifei , Cui Gaofeng , Hu Jicheng , Fang Huaming , Jin Changwen , Xia Bin
Published: November 2008

Protein histidine phosphorylation exists widely in vertebrates, and it plays important roles in signal transduction and other cellular functions. However, knowledge about eukaryotic PHPT (protein histidine phosphatase) is still very limited. To date, only one vertebrate PHPT has been discovered, and two crystal structures of hPHPT1 (human PHPT1) have been solved. However, these two structures gave different ligand-binding sites and co-ordination patterns. In the present paper, we have solved the solution structures of hPHPT1 in both Pi-free and Pi-bound states. Through comparison of the structures, along with a mutagenesis study, we have determined the active site of hPHPT1. In contrast with previous results, our results indicate that the active site is located between helix α1 and loop L5. His53 was identified to be the catalytic residue, and the NH groups of residues His53, Ala54 and Ala96 and the OH group of Ser94 should act as anchors of Pi or substrate by forming H-bonds with Pi. On the basis of our results, a catalytic mechanism is proposed for hPHPT1: the imidazole ring of His53 serves as a general base to activate a water molecule, and the activated water would attack the substrate as a nucleophile in the catalysis; the positively charged side chain of Lys21 can help stabilize the transition state. No similar catalytic mechanism can be found in the EzCatDB database.
Integrating simulation of architectural development and source - sink behaviour of peach trees by incorporating Markov chains and physiological organ function submodels into L-PEACH
Authors: Lopez Gerardo , Favreau Romeo R. , Smith Colin , Costes Evelyne , Prusinkiewicz Przemyslaw , DeJong Theodore M.
Published: November 2008

L-PEACH is an L-system-based functional–structural model for simulating architectural growth and carbohydrate partitioning among individual organs in peach (Prunus persica (L.) Batsch) trees. The original model provided a prototype for how tree architecture and carbon economy could be integrated, but did not simulate peach tree architecture realistically. Moreover, evaluation of the functional characteristics of the individual organs and the whole tree remained a largely open issue. In the present study, we incorporated Markovian models into L-PEACH to improve the architecture of the simulated trees. The model was also calibrated to grams of carbohydrate, and tools for systematically displaying quantitative outputs and evaluating the behaviour of the model were developed. The use of the Markovian model concept to model tree architecture in L-PEACH reproduced tree behaviour and responses to management practices visually similar to trees in commercial orchards. The new architectural model along with several improvements in the carbohydrate-partitioning algorithms derived from the model evaluation significantly improved the results related to carbon allocation, such as organ growth, carbohydrate assimilation, reserve dynamics and maintenance respiration. The model results are now consistent within the modelled tree structure and are in general agreement with observations of peach trees growing under field conditions.
An automated procedure for estimating the leaf area index (LAI) of woodland ecosystems using digital imagery, MATLAB programming and its application to an examination of the relationship between remotely sensed and field measurements of LAI
Authors: Fuentes Sigfredo , Palmer Anthony R. , Taylor Daniel , Zeppel Melanie , Whitley Rhys , Eamus Derek
Published: November 2008

Leaf area index (LAI) is one of the most important variables required for modelling growth and water use of forests. Functional–structural plant models use these models to represent physiological processes in 3-D tree representations. Accuracy of these models depends on accurate estimation of LAI at tree and stand scales for validation purposes. A recent method to estimate LAI from digital images (LAID) uses digital image capture and gap fraction analysis (Macfarlane et al. 2007b) of upward-looking digital photographs to capture canopy LAID (cover photography). After implementing this technique in Australian evergreen Eucalyptus woodland, we have improved the method of image analysis and replaced the time consuming manual technique with an automated procedure using a script written in MATLAB 7.4 (LAIM). Furthermore, we used this method to compare MODIS LAI values with LAID values for a range of woodlands in Australia to obtain LAI at the forest scale. Results showed that the MATLAB script developed was able to successfully automate gap analysis to obtain LAIM. Good relationships were achieved when comparing averaged LAID and LAIM (LAIM = 1.009 – 0.0066 LAID; R2 = 0.90) and at the forest scale, MODIS LAI compared well with LAID (MODIS LAI = 0.9591 LAID – 0.2371; R2 = 0.89). This comparison improved when correcting LAID with the clumping index to obtain effective LAI (MODIS LAI = 1.0296 LAIe + 0.3468; R2 = 0.91). Furthermore, the script developed incorporates a function to connect directly a digital camera, or high resolution webcam, from a laptop to obtain cover photographs and LAI analysis in real time. The later is a novel feature which is not available on commercial LAI analysis softwares for cover photography. This script is available for interested researchers.
Spray deposition on plant surfaces: a modelling approach
Authors: Dorr Gary , Hanan Jim , Adkins Steve , Hewitt Andrew , O'Donnell Chris , Noller Barry
Published: November 2008

For pesticides to effectively manage pests, they must first be deposited on the target (typically a plant surface) in a manner in which the active ingredient(s) can be readily taken up by the target organism. A plant architectural model that enables the location of various plant components in 3-D space combined with a particle trajectory model has been used to study the interception of spray droplets by various vegetative elements. Results from the simulation are compared with wind tunnel studies of glyphosate deposition on cotton (Gossypium hirsutum L. var. Sicala), sow thistle (Sonchus oleraceus L.) and wild oats (Avena ludoviciana Durieu). An air induction flat fan nozzle (AI110015 at 500 kPa pressure) and an extended range flat fan nozzle (XR11002 at 280 kPa pressure) were predicted to have similar glyphosate deposition on cotton and sow thistle plants, whereas the extended range nozzle resulted in higher deposit on wild oats. Spray deposition (µg cm−2) on wild oat plants at the 5-leaf stage was more than double the amount of deposition on sow thistle or wild oat plants at the 2-leaf stage. The model was in good agreement with the experimental data except that it tended to over predict deposition on sow thistle plants.
Evaluation of a turbid medium model to simulate light interception by walnut trees (hybrid NG38×RA and Juglans regia) and sorghum canopies (Sorghum bicolor) at three spatial scales
Authors: Combes Didier , Chelle Michaël , Sinoquet Hervé , Varlet-Grancher Claude
Published: November 2008

Light is one of the most important components to be included in functional–structural plant models that simulate the biophysical processes, such as photosynthesis, evapotranspiration and photomorphogenesis, involved in plant growth and development. In general, in these models, light is treated using a turbid medium approach in which radiation attenuation is described by the Beer–Lambert law. In the present study, we assessed the hypothesis of leaf random dispersion in the Beer–Lambert law at the whole-canopy, horizontal-layer and local scales. We compared two calculation methods of radiation attenuation: a 3D turbid medium model using the Beer–Lambert law and the other based on a projective method. The two models were compared by applying the calculations to two walnut trees and two sorghum canopies, which have contrasting structural characteristics. The structures of these canopies were measured in 3D to take into account the arrangement and orientation features of the plant elements. The assumptions made by the Beer–Lambert law allowed adequate simulation of light interception in a structure with little overlapping at the horizontal-layer and whole-canopy scales. At the local scale, discrepancies between the turbid medium model and the model based on a virtual plant were reduced with an adequate choice of structural parameters, such as the leaf inclination distribution function.
Dissecting external effects on logistic-based growth: equations, analytical solutions and applications
Authors: Seleznyova Alla N.
Published: November 2008

Characteristic growth patterns of individual organs are, to a large extent, determined by genetic factors, but can also be affected by intra-plant competition for resources and by environmental conditions. The current study proposes a dynamical system for modelling this dual control for logistic-based growth. The state of the system is defined by two state variables: size (s), and developmental age (α). The intrinsic properties of the system are represented by the potential relative growth rate as a function of α. This formulation allows dissection of the external effects on the system dynamics into two components: one that changes the duration of growth without affecting the final size and one that affects the final size without much effect on the duration. The former component determines the relationship between α and time, while the latter determines the effect on the system trajectory, s(α). The presented dynamical system is simpler and has a wider range of potential applications than the system proposed by Thornley and France (2005) for modelling logistic growth under resource limitation. The current approach can be also useful in ecology and in comparative studies of different genotypes and their responses to environmental conditions.
Peptide antisense nanoparticles
Authors: Patel Pinal C. , Giljohann David A. , Seferos Dwight S. , Mirkin Chad A.
Published: November 2008

We have designed a heterofunctionalized nanoparticle conjugate consisting of a 13-nm gold nanoparticle (Au NP) containing both antisense oligonucleotides and synthetic peptides. The synthesis of this conjugate is accomplished by mixing thiolated oligonucleotides and cysteine-terminated peptides with gold nanoparticles in the presence of salt, which screens interactions between biomolecules, yielding a densely functionalized nanomaterial. By controlling the stoichiometry of the components in solution, we can control the surface loading of each biomolecule. The conjugates are prepared easily and show perinuclear localization and an enhanced gene regulation activity when tested in a cellular model. This heterofunctionalized structure represents a new strategy for preparing nanomaterials with potential therapeutic applications.
Focal adhesion proteins connect IgE receptors to the cytoskeleton as revealed by micropatterned ligand arrays
Authors: Torres Alexis J. , Vasudevan Lavanya , Holowka David , Baird Barbara A.
Published: November 2008

Patterned surfaces that present specific ligands in spatially defined arrays are used to examine structural linkages between clustered IgE receptors (IgE-FcεRI) and the cytoskeleton in rat basophilic leukemia (RBL) mast cells. We showed with fluorescence microscopy that cytoskeletal F-actin concentrates in the same regions as cell surface IgE-FcεRI that bind to the micrometer-size patterned ligands. However, the proteins mediating these cytoskeletal connections and their functional relevance were not known. We now show that whereas the adaptor proteins ezrin and moesin do not detectably concentrate with the array of clustered IgE-FcεRI, focal adhesion proteins vinculin, paxillin, and talin, which are known to link F-actin with integrins, accumulate in these regions on the same time scale as F-actin. Moreover, colocalization of these focal adhesion proteins with clustered IgE-FcεRI is enhanced after addition of fibronectin-RGD peptides. Significantly, the most prominent rat basophilic leukemia cell integrin (α5) avoids the patterned regions occupied by the ligands and associates preferentially with exposed regions of the silicon substrate. Thus, spatial separation provided by the patterned surface reveals that particular focal adhesion proteins, which connect to the actin cytoskeleton, associate with ligand-cross-linked IgE-FcεRI, independently of integrins. We investigated the functional role of one of these proteins, paxillin, in IgE-FcεRI-mediated signaling by using small interfering RNA. From these results, we determine that paxillin reduces stimulated phosphorylation of the FcεRI β subunit but enhances stimulated Ca2+release from intracellular stores. The results suggest that paxillin associated with clustered IgE-FcεRI has a net positive effect on FcεRI signaling.
Linking global turnover of species and environments
Authors: Buckley Lauren B. , Jetz Walter
Published: November 2008

Patterns of species turnover are central to the geography of biodiversity and resulting challenges for conservation, but at broad scales remain relatively little understood. Here, we take a first spatially-explicitly and global perspective to link the spatial turnover of species and environments. We compare how major groups of vertebrate ectotherms (amphibians) and endotherms (birds) respond to spatial environmental gradients. We find that high levels of species turnover occur regardless of environmental turnover rates, but environmental turnover provides a lower bound for species turnover. This lower bound increases more steeply with environmental turnover in tropical realms. While bird and amphibian turnover rates are correlated, the rate of amphibian turnover is four times steeper than bird rates. This is the same factor by which average geographic ranges of birds are larger than those of amphibians. Narrow-ranged birds exhibit rapid rates of species turnover similar to those for amphibians, while wide-ranged birds largely drive the aggregate patterns of avian turnover. We confirm a strong influence of the environment on species turnover that is mediated by range sizes and regional history. In contrast to geographic patterns of species richness, we find that the turnover in one group (amphibians) is a much better predictor for the turnover in another (birds) than is environment. This result confirms the role of amphibian sensitivity to environmental conditions for patterns of turnover and supports their value as a surrogate group. This spatially-explicit analysis of environmental turnover provides understanding for conservation planning in changing environments.
Identification of reptilian genes encoding hair keratin-like proteins suggests a new scenario for the evolutionary origin of hair
Authors: Eckhart Leopold , Valle Luisa Dalla , Jaeger Karin , Ballaun Claudia , Szabo Sandra , Nardi Alessia , Buchberger Maria , Hermann Marcela , Alibardi Lorenzo , Tschachler Erwin
Published: November 2008

The appearance of hair is one of the main evolutionary innovations in the amniote lineage leading to mammals. The main components of mammalian hair are cysteine-rich type I and type II keratins, also known as hard α-keratins or “hair keratins.” To determine the evolutionary history of these important structural proteins, we compared the genomic loci of the human hair keratin genes with the homologous loci of the chicken and of the green anole lizard
Anolis carolinenis
. The genome of the chicken contained one type II hair keratin-like gene, and the lizard genome contained two type I and four type II hair keratin-like genes. Orthology of the latter genes and mammalian hair keratins was supported by gene locus synteny, conserved exon–intron organization, and amino acid sequence similarity of the encoded proteins. The lizard hair keratin-like genes were expressed most strongly in the digits, indicating a role in claw formation. In addition, we identified a novel group of reptilian cysteine-rich type I keratins that lack homologues in mammals. Our data show that cysteine-rich α-keratins are not restricted to mammals and suggest that the evolution of mammalian hair involved the co-option of pre-existing structural proteins.
Antimicrobial strategies in burying beetles breeding on carrion
Authors: Rozen D. E. , Engelmoer D. J. P. , Smiseth P. T.
Published: November 2008

Rich and ephemeral resources, such as carrion, are a source of intense interspecific competition among animal scavengers and microbial decomposers. Janzen [Janzen DH (1977)
Am Nat
111:691–713] hypothesized that microbes should be selected to defend such resources by rendering them unpalatable or toxic to animals, and that animals should evolve counterstrategies of avoidance or detoxification. Despite the ubiquity of animal-microbe competition, there are few tests of Janzen's hypothesis, in particular with respect to antimicrobial strategies in animals. Here, we use the burying beetle
Nicrophorus vespilloides
, a species that obligately breeds on carcasses of small vertebrates, to investigate the role of parental care and avoidance as antimicrobial strategies. We manipulated competition between beetle larvae and microbes by providing beetles with either fresh carcasses or old ones that had reached advanced putrefaction. We found evidence for a strong detrimental effect of microbial competition on beetle reproductive success and larval growth. We also found that parental care can largely compensate for these negative effects, and that when given a choice between old and fresh carcasses, parents tended to choose to rear their broods on the latter. We conclude that parental care and carcass avoidance can function as antimicrobial strategies in this species. Our findings extend the range of behavioral counterstrategies used by animals during competition with microbes, and generalize the work of Janzen to include competition between microbes and insects that rely on carrion as an obligate resource for breeding and not just as an opportunistic meal.
Polyphosphate-dependent synthesis of ATP and ADP by the family-2 polyphosphate kinases in bacteria
Authors: Nocek Boguslaw , Kochinyan Samvel , Proudfoot Michael , Brown Greg , Evdokimova Elena , Osipiuk Jerzy , Edwards Aled M. , Savchenko Alexei , Joachimiak Andrzej , Yakunin Alexander F.
Published: November 2008

Inorganic polyphosphate (polyP) is a linear polymer of tens or hundreds of phosphate residues linked by high-energy bonds. It is found in all organisms and has been proposed to serve as an energy source in a pre-ATP world. This ubiquitous and abundant biopolymer plays numerous and vital roles in metabolism and regulation in prokaryotes and eukaryotes, but the underlying molecular mechanisms for most activities of polyP remain unknown. In prokaryotes, the synthesis and utilization of polyP are catalyzed by 2 families of polyP kinases, PPK1 and PPK2, and polyphosphatases. Here, we present structural and functional characterization of the PPK2 family. Proteins with a single PPK2 domain catalyze polyP-dependent phosphorylation of ADP to ATP, whereas proteins containing 2 fused PPK2 domains phosphorylate AMP to ADP. Crystal structures of 2 representative proteins, SMc02148 from
Sinorhizobium meliloti
and PA3455 from
Pseudomonas aeruginosa
, revealed a 3-layer α/β/α sandwich fold with an α-helical lid similar to the structures of microbial thymidylate kinases, suggesting that these proteins share a common evolutionary origin and catalytic mechanism. Alanine replacement mutagenesis identified 9 conserved residues, which are required for activity and include the residues from both Walker A and B motifs and the lid. Thus, the PPK2s represent a molecular mechanism, which potentially allow bacteria to use polyP as an intracellular energy reserve for the generation of ATP and survival.