bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reconstructing the history of human impacts on coastal biodiversity in Chile: constraints and opportunities
Authors: Rivadeneira Marcelo M. , Santoro Calogero M. , Marquet Pablo A. 
Published: June 2009

Abstract
Although Chile is at the forefront in evaluating experimentally the importance of human harvesting impacts on coastal biodiversity, there are no evaluations of such impacts on a long‐term historical basis (tens to thousands of years). Different types of archival information (i.e. contemporaneous, archaeological, and palaeontological) were used to carry out a research programme based on the historical assessment of the impacts and intensity of resource extraction on coastal biodiversity along the Chilean coast.
In addition to recent scientific literature, different sources of contemporaneous information (e.g. museum collections, old reports and accounts) can reveal the human impacts observed in the more recent past. Furthermore, the large number of prehistoric shell middens along the entire Chilean coast offer access to ∼11 000 years of history along the entire coast, although the faunal composition, structure, and dynamics of most of them remain largely unstudied.
Finally, the rich and widespread fossil record of some marine groups provides the opportunity to reconstruct the structure and dynamics of benthic communities during different phases of human influence (e.g. pre‐human, prehistoric harvesting, and modern harvesting).
Preliminary comparisons of fossil versus modern bivalve assemblages suggest marked changes in the species composition. Human impacts seem very recent and shifts in the structure of benthic assemblages may have occurred only a few centuries/decades ago.
In contrast, prehistoric harvesting, although intense, was apparently not enough to cause a profound impact on coastal ecosystems. The approach herein envisaged can provide the basis to build a historical baseline to evaluate the human impacts on the coastal biodiversity in the region. Copyright © 2009 John Wiley & Sons, Ltd.
The Relationship Between the Lizard Eye and Associated Bony Features: A Cautionary Note for Interpreting Fossil Activity Patterns
Authors: Hall Margaret I. 
Published: June 2009

AbstractActivity pattern, the time of day when an animal is active, is associated with ecology. There are two major activity patterns: diurnal (awake during the day in a photopic environment) and nocturnal (awake at night in a scotopic environment). Lizards exhibit characteristic eye shapes associated with activity pattern, with scotopic‐adapted lizard eyes optimized for visual sensitivity with large corneal diameters relative to their eye axial lengths, and photopic‐adapted lizards optimized for visual acuity, with larger axial lengths of the eye relative to their corneal diameters. This study: (1) quantifies the relationship between the lizard eye and its associated bony anatomy (the orbit, sclerotic ring, and associated skull widths); (2) investigates how activity pattern is reflected in that bony anatomy; and (3) determines if it is possible to reliably interpret activity pattern for a lizard that does not have the soft tissue available for study, specifically, for a fossil. Knowledge of extinct lizards' activity patterns would be useful in making paleoecological interpretations. Here, 96 scotopic‐ and photopic‐adapted lizard species are analyzed in a phylogenetic context. Although there is a close relationship between the lepidosaur eye and associated bony anatomy, based on these data activity pattern cannot be reliably interpreted for bony‐only specimens, such as a fossil, possibly because of the limited ossification of the lepidosaur skull. Caution should be exercised when utilizing lizard bony anatomy to interpret light‐level adaptation, either for a fossil lizard or as part of an extant phylogenetic bracket to interpret other extinct animals with sclerotic rings, such as dinosaurs. Anat Rec, 292:798–812, 2009. © 2009 Wiley‐Liss, Inc.
Worst‐case optimal control for an electrical drive system with time‐delay
Authors: Gao Yu , Kostyukova Olga , Chong Kil To 
Published: June 2009

AbstractThis paper considers an optimal control developed for an electrical drive system with a DC motor. Since it is a linear control system with input time‐delay subject to unknown but bounded disturbances, we construct a worst‐case feedback control policy, which can guarantee that, for all admissible uncertain disturbances, the real system state should be in a prescribed neighborhood of a desired value at the given final time, and the cost functional takes the best guarantee value. The worst‐case feedback control policy is allowed to be corrected at a given set of correction points between the initial and the final time, which is equivalent to solving a (m‐1)‐level min‐max problem. Since the min‐max problem at each stage does not yield a simple analytical solution, construction of the optimal policy is computationally prohibitive. This is why we consider an approximate control policy which is more convenient for computation. The simulation results illustrate that this proposed approach is feasible. Copyright © 2009 John Wiley and Sons Asia Pte Ltd and Chinese Automatic Control Society
Bayesian modeling of financial returns: A relationship between volatility and trading volume
Authors: Abanto‐Valle Carlos A. , Migon Helio S. , Lopes Hedibert F. 
Published: June 2009

AbstractThe modified mixture model with Markov switching volatility specification is introduced to analyze the relationship between stock return volatility and trading volume. We propose to construct an algorithm based on Markov chain Monte Carlo simulation methods to estimate all the parameters in the model using a Bayesian approach. The series of returns and trading volume of the British Petroleum stock will be analyzed. Copyright © 2009 John Wiley & Sons, Ltd.
Application of a temperature‐dependent fluorescent dye (Rhodamine B) to the measurement of radiofrequency radiation‐induced temperature changes in biological samples
Authors: Chen Yuen Y. , Wood Andrew W. 
Published: June 2009

AbstractWe have applied a non‐contact method for studying the temperature changes produced by radiofrequency (RF) radiation specifically to small biological samples. A temperature‐dependent fluorescent dye, Rhodamine B, as imaged by laser scanning confocal microscopy (LSCM) was used to do this. The results were calibrated against real‐time temperature measurements from fiber optic probes, with a calibration factor of 3.4% intensity change °C−1 and a reproducibility of ±6%. This non‐contact method provided two‐dimensional and three‐dimensional images of temperature change and distributions in biological samples, at a spatial resolution of a few micrometers and with an estimated absolute precision of around 1.5 °C, with a differential precision of 0.4 °C. Temperature rise within tissue was found to be non‐uniform. Estimates of specific absorption rate (SAR) from absorbed power measurements were greater than those estimated from rate of temperature rise, measured at 1 min intervals, probably because this interval is too long to permit accurate estimation of initial temperature rise following start of RF exposure. Future experiments will aim to explore this. Bioelectromagnetics 30:583–590, 2009. © 2009 Wiley‐Liss, Inc.
Deutung vor der Deutung. Hermeneutische und geschlechtergeschichtliche Aspekte historiographischer Epochenbildung
Authors: Schnicke Falko 
Published: June 2009

AbstractInterpretation before Interpretation. Aspects of Hermeneutics and Gender in Historiographical Periodization. This article focuses on different methods of periodization in modern German historiography. The time models used – as exemplified in studies on the history of biography – fundamentally preshape the represented past in heuristical and gender terms. That manifests itself principally in the fact that several authors, as well as various works by women writers and those excluded from academic circles, are conspicuously absent in certain models. What are ultimately not inconsiderable assumptions often go unacknowledged by the studies' authors, such that the epoch concepts they present are in themselves interpretations before the interpretations they explicitly aim to provide.
The blood platelets contribution to innate host defense – What they have learned from their big brothers
Authors: Zander Dorit M. W. , Klinger Matthias 
Published: June 2009

AbstractBactericidal effects of blood platelets have been known for more than 120 years, but the underlying mechanisms are largely obscure. Keeping in mind structural and functional analogies of platelets to neutrophils, three different mechanisms are thinkable: Engulfment of pathogens, release of microbicidal proteins, and production of reactive oxygen species (ROS). Here, we focus on the release of ROS and a possible contribution of blood plasma and thrombin to the bactericidal effects. Killing of bacteria was evaluated by DNA fluorescence labeling and electron microscopy. Release of ROS by platelets was measured photometrically by cytochrome C and phenol red/peroxidase assays and was further evaluated by topological methods. We found that (i) platelets produce 1500 times less O2– and 4000 times less H2O2 compared to neutrophils, (ii) ROS do not affect the killing rates, and (iii) no local enrichment of ROS was detectable. On the other hand, thrombin and plasma proteins with a molecular mass of >100 kDa are essential for bactericidal effects. We suggest that platelets contribute to the innate host defense by providing a catalytical surface for synthesis of thrombin. In the presence of a heat‐instable plasma protein, thrombin may generate a strong bactericidal complex, which is only effective in close vicinity to the platelet membrane.
Characterization of cell viability during bioprinting processes
Authors: Nair Kalyani , Gandhi Milind , Khalil Saif , Yan Karen Chang , Marcolongo Michele , Barbee Kenneth , Sun Wei 
Published: June 2009

AbstractBioprinting is an emerging technology in the field of tissue engineering and regenerative medicine. The process consists of simultaneous deposition of cells, biomaterial and/or growth factors under pressure through a micro‐scale nozzle. Cell viability can be controlled by varying the parameters like pressure and nozzle diameter. The process itself can be a very useful tool for evaluating an in vitro cell injury model. It is essential to understand the cell responses to process‐induced mechanical disturbances because they alter cell morphology and function. We carried out analysis and quantification of the degree of cell injury induced by bioprinting process. A parametric study with different process parameters was conducted to analyze and quantify cell injury as well as to optimize the parameters for printing viable cells. A phenomenological model was developed correlating the percentage of live, apoptotic and necrotic cells to the process parameters. This study incorporates an analytical formulation to predict the cell viability through the system as a function of the maximum shear stress in the system. The study shows that dispensing pressure has a more significant effect on cell viability than the nozzle diameter. The percentage of live cells is reduced significantly (by 38.75%) when constructs are printed at 40 psi compared to those printed at 5 psi.
Imaging ion flux and ion homeostasis in blood stage malaria parasites
Authors: Rohrbach Petra 
Published: June 2009

AbstractThe steady‐state regulation of intracellular levels of essential ions and ionic gradients is critical for almost all functions within a cell. Thus, it is not surprising to find that ions have been shown to play an important role in numerous parasitic processes, such as invasion, development and possibly drug resistance mechanisms. Live cell imaging has become a widespread technique to visualize and quantify several of these processes, including pH and Ca2+ homeostasis, in an effort to better understand the biology and physiology of cells. This is now also the case for many human pathogens. The aim of this review is to emphasize the importance of this technique and provide an overview of what we have learned so far, using the malaria parasite Plasmodium falciparum as a paradigm.
Probing vocal fold fibroblast response to hyaluronan in 3D contexts
Authors: Munoz‐Pinto Dany J. , Jimenez‐Vergara Andrea Carolina , Gelves L. Marcela , McMahon Rebecca E. , Guiza‐Arguello Viviana , Hahn Mariah S. 
Published: June 2009

AbstractA number of treatments are being investigated for vocal fold (VF) scar, including designer implants. The aim of the present study was to validate a 3D model system for probing the effects of various bioactive moieties on VF fibroblast (VFF) behavior toward rational implant design. We selected poly(ethylene glycol) diacrylate (PEGDA) hydrogels as our base‐scaffold due to their broadly tunable material properties. However, since cells encapsulated in PEGDA hydrogels are generally forced to take on rounded/stellate morphologies, validation of PEGDA gels as a 3D VFF model system required that the present work directly parallel previous studies involving more permissive scaffolds. We therefore chose to focus on hyaluronan (HA), a polysaccharide that has been a particular focus of the VF community. Toward this end, porcine VFFs were encapsulated in PEGDA hydrogels containing consistent levels of high M w HA (${\rm HA}_{{\rm H}{M}_{\rm W} } $), intermediate Mw HA (${\rm HA}_{{\rm I}{M}_{\rm W} } $), or the control polysaccharide, alginate, and cultured for 7 and 21 days. ${\rm HA}_{{\rm H}{M}_{\rm W} } $ promoted sustained increases in active ERK1/2 relative to ${\rm HA}_{{\rm I}{M}_{\rm W} } $ . Furthermore, VFFs in ${\rm HA}_{{\rm I}{M}_{\rm W} } $ gels displayed a more myofibroblast‐like phenotype, higher elastin production, and greater protein kinase C (PkC) levels at day 21 than VFFs in ${\rm HA}_{{\rm H}{M}_{\rm W} } $ and alginate gels. The present results are in agreement with a previous 3D study of VFF responses to ${\rm HA}_{{\rm I}{M}_{\rm W} } $ relative to alginate in collagen‐based scaffolds permissive of cell elongation, indicating that PEGDA hydrogels may serve as an effective 3D model system for probing at least certain aspects of VFF behavior. Biotechnol. Bioeng. 2009; 104: 821–831 © 2009 Wiley Periodicals, Inc.
Model identification in presence of incomplete information by generalized principal component analysis: Application to the common and differential responses of Escherichia coli to multiple pulse perturbations in continuous, high‐biomass density culture
Authors: Guebel Daniel V. , Cánovas Manuel , Torres Néstor V. 
Published: June 2009

AbstractIn a previous report we described a multivariate approach to discriminate between the different response mechanisms operating in Escherichia coli when a steady, continuous culture of these bacteria was perturbed by a glycerol pulse (Guebel et al., 2009, Biotechnol Bioeng 102: 910–922). Herein, we present a procedure to extend this analysis when multiple, spaced pulse perturbations (glycerol, fumarate, acetate, crotonobetaine, hypersaline plus high‐glycerol basal medium and crotonobetaine plus hypersaline basal medium) are being assessed. The proposed method allows us to identify not only the common responses among different perturbation conditions, but to recognize the specific response for a given stimulus even when the dynamics of the perturbation is unknown. Components common to all conditions are determined first by Generalized Principal Components Analysis (GPCA) upon a set of covariance matrices. A metrics is then built to quantify the similitude distance. This is based on the degree of variance extraction achieved for each variable along the GPCA deflation processes by the common factors. This permits a cluster analysis, which recognizes several compact sub‐sets containing only the most closely related responsive groups. The GPCA is then run again but is restricted to the groups in each sub‐set. Finally, after the data have been exhaustively deflated by the common sub‐set factors, the resulting residual matrices are used to determine the specific response factors by classical principal component analysis (PCA). The proposed method was validated by comparing its predictions with those obtained when the dynamics of the perturbation was determined. In addition, it showed to have a better performance than the obtained with other multivariate alternatives (e.g., orthogonal contrasts based on direct GPCA, Tucker‐3 model, PARAFAC, etc.). Biotechnol. Bioeng. 2009; 104: 785–795 © 2009 Wiley Periodicals, Inc.
The effect of Bcl‐2, YAMA, and XIAP over‐expression on apoptosis and adenovirus production in HEK293 cell line
Authors: Sandhu Kalbinder Singh , Al‐Rubeai Mohamed 
Published: June 2009

AbstractMany viruses induce cell death and lysis as part of their replication and dissemination strategy, and in many cases features of apoptosis are observed. Attempts have been made to further increase productivity by prolonging cell survival via the over‐expression of anti‐apoptotic genes. Here, we extend the study to investigate the association between virus replication and apoptosis, pertinent to large‐scale vector production for gene therapy. Infection of an HEK293 cell line with a replication defective type‐5‐adenovirus expressing a GFP reporter (Ad5GFP) resulted in rapid decline in viability associated with increased virus titer. The over‐expression of bcl‐2 resulted in improved cell resistance to apoptosis and prolonged culture duration, but reduced virus specific and total productivity. In contrast, the over‐expression of pro‐caspase‐3 (Yama/CPP32/apopain) resulted in reduced cell survival but increased virus productivity. The treatment of infected cells with caspase inhibitors support the preposition that caspase‐3 dependent apoptosis, and to a lesser degree caspase‐9 dependent apoptosis, represent important steps in virus production, thus implicating the intrinsic apoptosis pathway in the production of adenovirus from HEK293 cells. The suppression of apoptosis by the over‐expression of XIAP (inhibitors of caspase family cell death proteases) further shows that caspase‐mediated activation plays an important role in virus infection and maturation. Biotechnol. Bioeng. 2009; 104: 752–765 © 2009 Wiley Periodicals, Inc.
Shear stress magnitude and duration modulates matrix composition and tensile mechanical properties in engineered cartilaginous tissue
Authors: Gemmiti Christopher V. , Guldberg Robert E. 
Published: June 2009

AbstractCartilage tissue‐engineering strategies aim to produce a functional extracellular matrix similar to that of the native tissue. However, none of the myriad approaches taken have successfully generated a construct possessing the structure, composition, and mechanical properties of healthy articular cartilage. One possible approach to modulating the matrix composition and mechanical properties of engineered tissues is through the use of bioreactor‐driven mechanical stimulation. In this study, we hypothesized that exposing scaffold‐free cartilaginous tissue constructs to 7 days of continuous shear stress at 0.001 or 0.1 Pa would increase collagen deposition and tensile mechanical properties compared to that of static controls. Histologically, type II collagen staining was evident in all construct groups, while a surface layer of type I collagen increased in thickness with increasing shear stress magnitude. The areal fraction of type I collagen was higher in the 0.1‐Pa group (25.2 ± 2.2%) than either the 0.001‐Pa (13.6 ± 3.8%) or the static (7.9 ± 1.5%) group. Type II collagen content, as assessed by ELISA, was also higher in the 0.1‐Pa group (7.5 ± 2.1%) compared to the 0.001‐Pa (3.0 ± 2.25%) or static groups (3.7 ± 3.2%). Temporal gene expression analysis showed a flow‐induced increase in type I and type II collagen expression within 24 h of exposure. Interestingly, while the 0.1‐Pa group showed higher collagen content, this group retained less sulfated glycosaminoglycans in the matrix over time in bioreactor culture. Increases in both tensile Young's modulus and ultimate strength were observed with increasing shear stress, yielding constructs possessing a modulus of nearly 5 MPa and strength of 1.3 MPa. This study demonstrates that shear stress is a potent modulator of both the amount and type of synthesized extracellular matrix constituents in engineered cartilaginous tissue with corresponding effects on mechanical function. Biotechnol. Bioeng. 2009; 104: 809–820 © 2009 Wiley Periodicals, Inc.
Interactive engagement with embodied agents: an empirically validated framework
Authors: van Vugt H. C. , Hoorn J. F. , Konijn E. A. 
Published: June 2009

AbstractThis paper presents an empirically tested theoretical framework to explain user engagement and end‐user satisfaction with interactive agents. Such a framework is not only important from a scientific point of view; application designers may find a set of dos and don'ts that help them create more satisfying embodied agents in different task domains and social settings. From a multidisciplinary perspective, we have conducted a series of experiments to verify underlying mechanisms in the processes of interacting and engaging with embodied agents in various task domains. Our results show that the most commonly held views are not always tenable; sometimes other factors provide better explanations for liking an embodied agent or end‐user satisfaction. For example, it is not realism but rather affordances and ethics that are key for understanding user responses, and a beautiful design is not always the most preferable. From our results, guidelines for designers and future research are reflected upon. Copyright © 2009 John Wiley & Sons, Ltd.
Angular momentum guided motion concatenation
Authors: Shum Hubert P. H. , Komura Taku , Yadav Pranjul 
Published: June 2009

AbstractIn this paper, we propose a new method to concatenate two dynamic full‐body motions such as punches, kicks, and flips by using the angular momentum as a cue. Through the observation of real humans, we have identified two patterns of angular momentum that make the transition of such motions efficient. Based on these observations, we propose a new method to concatenate two full‐body motions in a natural manner. Our method is useful for applications where dynamic, full‐body motions are required, such as 3D computer games and animations. Copyright © 2009 John Wiley & Sons, Ltd.
Malonyl carba(dethia)‐ and Malonyl oxa(dethia)‐coenzyme A as Tools for Trapping Polyketide Intermediates
Authors: Tosin Manuela , Spiteller Dieter , Spencer Jonathan B. 
Published: June 2009

AbstractCaught in a trap. In this study trapped polyketide species (see figure) were off‐loaded from a type III PKS by novel nonhydrolyzable malonyl coenzyme A analogues in which a methylene group or an oxygen atom replaces the sulfur atom of malonyl‐CoA. This strategy allows the straightforward characterisation of intermediates of polyketide biosynthesis by LC‐HR‐ESI‐MS/MS and provides valuable insights on the mechanism and timing of polyketide formation.magnified imageIn order to study intermediates in polyketide biosynthesis two nonhydrolyzable malonyl coenzyme A analogues were synthesised by a chemoenzymatic route. In these analogues the sulfur atom of CoA was replaced either by a methylene group (carbadethia analogue) or by an oxygen atom (oxadethia analogue). These malonyl‐CoA analogues were found to compete with the natural extender unit malonyl‐CoA and to trap intermediates from stilbene synthase, a type III polyketide synthase (PKS). From the reaction of stilbene synthase with its natural phenylpropanoid substrates, diketide, triketide and tetraketide species were successfully off‐loaded and characterised by LC‐MS. Moreover, the reactivity of the nonhydrolyzable analogues offers insights into the flexibility of substrate alignment in the PKS active site for efficient malonyl decarboxylation and condensation.