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Crawling PubMed with web agents for literature search and alerting services

Carvalhal, Carlos; Deusdado, Sérgio; Deusdado, Leonel
Fonte: Universidade de Salamanca Publicador: Universidade de Salamanca
Tipo: Artigo de Revista Científica
ENG
Relevância na Pesquisa
56.1%
In this paper we present ASAP - Automated Search with Agents in PubMed, a web-based service aiming to manage and automate scientific literature search in the PubMed database. The system allows the creation and management of web agents, parameterized thematically and functionally, that crawl the PubMed database autonomously and periodically, aiming to search and retrieve relevant results according the requirements provided by the user. The results, containing the publications list retrieved, are emailed to the agent owner on a weekly basis, during the activity period defined for the web agent. The ASAP service is devoted to help researchers, especially from the field of biomedicine and bioinformatics, in order to increase their productivity, and can be accessed at: http://esa.ipb.pt/~agentes.

Crawling movements of lymphocytes on and beneath fibroblasts in culture

Chang, Tse Wen; Celis, Esteban; Eisen, Herman N.; Solomon, Frank
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em /06/1979 EN
Relevância na Pesquisa
36.4%
Some lymphocytes become highly motile upon immunological stimulation in vivo or in vitro. When introduced into a culture of 3T3 or L cells and followed by live-cell microscopy, some of these lymphocytes were observed to crawl on top of, along the edges of, and preferentially beneath the attached fibroblasts. The crawling could be as rapid as 20 μm/min, easily detectable without a time-lapse device. The striking ability of crawling lymphocytes to penetrate beneath attached 3T3 cells provided a quantitative means to compare the crawling activity of different lymphocyte populations under various conditions. Crawling was diminished by inhibitors of energy metabolism, by agents that disrupt the cytoskeleton, and by absence of Mg2+ and Ca2+, but not of Ca2+ alone. Crawling lymphocytes were virtually absent in normal thymus and spleen cells. They increased greatly in 5-day mixed lymphocyte cultures and in peritoneal exudate lymphocytes taken after mice had been immunized with allogeneic tumor cells. T cells accounted for most of the crawlers. Of two T-cell leukemias tested, R1+ cells were crawlers whereas EL-4 cells were not. The H-2 haplotype of the 3T3 fibroblasts (i.e., whether syngeneic or allogeneic) had no apparent effect on lymphocyte crawling activity. The crawling may relate to the exploration of cell surface antigens by lymphocytes (immune surveillance)...

Dopamine Activates the Motor Pattern for Crawling in the Medicinal Leech

Puhl, Joshua G.; Mesce, Karen A.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 16/04/2008 EN
Relevância na Pesquisa
36.4%
Locomotion in segmented animals is thought to be based on the coupling of “unit burst generators”, but the biological nature of the unit burst generator has been revealed in only a few animal systems. We determined that dopamine (DA), a universal modulator of motor activity, is sufficient to activate fictive crawling in the medicinal leech, and can exert its actions within the smallest division of the animal’s CNS, the segmental ganglion. In the entire isolated nerve cord or in the single ganglion, DA induced slow anti-phasic bursting (ca. 15-second period) of motoneurons known to participate in the two-step elongation-contraction cycle underlying crawling behavior. During each cycle, the dorsal (DE-3) and ventral (VE-4) longitudinal excitor motoneurons fired roughly 180° out of phase from the ventrolateral circular excitor motoneuron (CV), which marks the elongation phase. In many isolated whole nerve cords, DE-3 bursting progressed in an anterior to posterior direction with intersegmental phase delays appropriate for crawling. In the single ganglion, the dorsal (DI-1) and ventral (VI-2) inhibitory longitudinal motoneurons fired out of phase with each DE-3 burst, further confirming that the crawl unit burst generator exists in the single ganglion. All isolated ganglia of the CNS were competent to produce DA-induced robust fictive crawling...

MULTISCALE TWO-DIMENSIONAL MODELING OF A MOTILE SIMPLE-SHAPED CELL*

RUBINSTEIN, B.; JACOBSON, K.; MOGILNER, A.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em //2005 EN
Relevância na Pesquisa
26.25%
Cell crawling is an important biological phenomenon underlying coordinated cell movement in morphogenesis, cancer, and wound healing. In recent decades the process of cell crawling has been experimentally and theoretically dissected into further subprocesses: protrusion of the cell at its leading edge, retraction of the cell body, and graded adhesion. A number of one-dimensional (1-D) models explain successfully a proximal-distal organization and movement of the motile cell. However, more adequate two-dimensional (2-D) models are lacking. We propose a multiscale 2-D computational model of the lamellipodium (motile appendage) of a simply shaped, rapidly crawling fish keratocyte cell. We couple submodels of (i) protrusion and adhesion at the leading edge, (ii) the elastic 2-D lamellipodial actin network, (iii) the actin-myosin contractile bundle at the rear edge, and (iv) the convection-reaction-diffusion actin transport on the free boundary lamellipodial domain. We simulate the combined model numerically using a finite element approach. The simulations reproduce observed cell shapes, forces, and movements and explain some experimental results on perturbations of the actin machinery. This novel 2-D model of the crawling cell makes testable predictions and posits questions to be answered by future modeling.

A Simple 1-D Physical Model for the Crawling Nematode Sperm Cell

Mogilner, A.; Verzi, D. W.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 01/03/2003 EN
Relevância na Pesquisa
36.03%
We develop a one-dimensional physical model of the crawling movement of simple cells: The sperm of a nematode, Ascaris suum. The model is based on the assumptions that polymerization and bundling of the cytoskeletal filaments generate the force for extension at the front, and that energy stored in the gel formed from the filament bundles is subsequently used to produce the contraction that pulls the rear of the cell forward. The model combines the mechanics of protrusion and contraction with chemical control, and shows how their coupling generates stable rapid migration, so that the cell length and velocity regulate to constant values.

Lymphocyte Crawling and Transendothelial Migration Require Chemokine Triggering of High-Affinity LFA-1 Integrin

Shulman, Ziv; Shinder, Vera; Klein, Eugenia; Grabovsky, Valentin; Yeger, Orna; Geron, Erez; Montresor, Alessio; Bolomini-Vittori, Matteo; Feigelson, Sara W.; Kirchhausen, Tomas; Laudanna, Carlo; Shakhar, Guy; Alon, Ronen
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
36.3%
Endothelial chemokines are instrumental for integrin-mediated lymphocyte adhesion and transendothelial migration (TEM). By dissecting how chemokines trigger lymphocyte integrins to support shear-resistant motility on and across cytokine-stimulated endothelial barriers, we found a critical role for high-affinity (HA) LFA-1 integrin in lymphocyte crawling on activated endothelium. Endothelial-presented chemokines triggered HA-LFA-1 and adhesive filopodia at numerous submicron dots scattered underneath crawling lymphocytes. Shear forces applied to endothelial-bound lymphocytes dramatically enhanced filopodia density underneath crawling lymphocytes. A fraction of the adhesive filopodia invaded the endothelial cells prior to and during TEM and extended large subluminal leading edge containing dots of HA-LFA-1 occupied by subluminal ICAM-1. Memory T cells generated more frequent invasive filopodia and transmigrated more rapidly than their naive counterparts. We propose that shear forces exerted on HA-LFA-1 trigger adhesive and invasive filopodia at apical endothelial surfaces and thereby promote lymphocyte crawling and probing for TEM sites.

Keeping it together: Mechanisms of intersegmental coordination for a flexible locomotor behavior

Puhl, Joshua G.; Mesce, Karen A.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 10/02/2010 EN
Relevância na Pesquisa
26.34%
The coordination of multiple neural oscillators is key for the generation of productive locomotor movements. In the medicinal leech, we determined that activation and coordination of the segmental crawl oscillators, or unit burst generators, are dependent on signals descending from the cephalic ganglion. In nearly-intact animals, removing descending input (reversibly with a sucrose block) prevented overt crawling, but not swimming. Cephalic depolarization was sufficient for coordination. To determine whether descending signals were necessary for the generation and maintenance of posterior-directed intersegmental phase delays, we induced fictive crawling in isolated whole nerve cords using dopamine (DA) and blocked descending inputs. After blockade, we observed a significant loss of intersegmental coordination. Appropriate phase delays were also absent in DA-treated chains of ganglia. In chains, when one ganglion was removed from its neighbors, crawling in that ganglion emerged robust and stable, underscoring that these oscillators operate best with either all or none of their intersegmental inputs. To study local oscillator coupling, we induced fictive crawling (with DA) in a single oscillator within a chain. Although appropriate intersegmental phase delays were always absent...

The Moving Boundary Node Method: A level set-based, finite volume algorithm with applications to cell motility

Wolgemuth, Charles W.; Zajac, Mark
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 20/09/2010 EN
Relevância na Pesquisa
26.3%
Eukaryotic cell crawling is a highly complex biophysical and biochemical process, where deformation and motion of a cell are driven by internal, biochemical regulation of a poroelastic cytoskeleton. One challenge to building quantitative models that describe crawling cells is solving the reaction-diffusion-advection dynamics for the biochemical and cytoskeletal components of the cell inside its moving and deforming geometry. Here we develop an algorithm that uses the level set method to move the cell boundary and uses information stored in the distance map to construct a finite volume representation of the cell. Our method preserves Cartesian connectivity of nodes in the finite volume representation while resolving the distorted cell geometry. Derivatives approximated using a Taylor series expansion at finite volume interfaces lead to second order accuracy even on highly distorted quadrilateral elements. A modified, Laplacian-based interpolation scheme is developed that conserves mass while interpolating values onto nodes that join the cell interior as the boundary moves. An implicit time-stepping algorithm is used to maintain stability. We use the algoirthm to simulate two simple models for cellular crawling. The first model uses depolymerization of the cytoskeleton to drive cell motility and suggests that the shape of a steady crawling cell is strongly dependent on the adhesion between the cell and the substrate. In the second model...

LFA-1 and Mac-1 define characteristically different intralumenal crawling and emigration patterns for monocytes and neutrophils in situ

Sumagin, Ronen; Prizant, Hen; Lomakina, Elena; Waugh, Richard E; Sarelius, Ingrid H
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
36.46%
To exit blood vessels, lumenally adhered monocytes and neutrophils crawl towards specific locations that support transmigration. Using intravital confocal microscopy of anesthetized mouse cremaster muscle we separately examined the intralumenal crawling of blood monocytes versus neutrophils and determined that CD11a/CD18 (LFA-1) versus CD11b/CD18 (Mac-1) mediated crawling accounted for these differences. In unstimulated venules 58.2±6.1% of all monocytes, but only 13.6±0.9% of all neutrophils were found adhered; TNFα treatment increased the number of adhered monocytes and neutrophils 2- and 3-fold respectively. The majority (~80%) of all adhered leukocytes exhibited intralumenal crawling under both unstimulated and activated conditions. Function blocking antibodies directed against Mac-1 but not LFA-1 significantly attenuated neutrophil crawling in unstimulated and TNFα activated venules, indicating that under both conditions neutrophil crawling is Mac-1 dependent. In contrast, treatment with combinations of Mac-1 and LFA-1 blocking antibodies reveled that both LFA-1 and Mac-1 contribute to monocyte crawling, however the dominant role in mediating monocyte crawling changes from LFA-1 in unstimulated venules to Mac-1 upon inflammation...

A POROELASTIC MODEL FOR CELL CRAWLING INCLUDING MECHANICAL COUPLING BETWEEN CYTOSKELETAL CONTRACTION AND ACTIN POLYMERIZATION

TABER, L.A.; SHI, Y.; YANG, L.; BAYLY, P.V.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em //2011 EN
Relevância na Pesquisa
36.16%
Much is known about the biophysical mechanisms involved in cell crawling, but how these processes are coordinated to produce directed motion is not well understood. Here, we propose a new hypothesis whereby local cytoskeletal contraction generates fluid flow through the lamellipodium, with the pressure at the front of the cell facilitating actin polymerization which pushes the leading edge forward. The contraction, in turn, is regulated by stress in the cytoskeleton. To test this hypothesis, finite element models for a crawling cell are presented. These models are based on nonlinear poroelasticity theory, modified to include the effects of active contraction and growth, which are regulated by mechanical feedback laws. Results from the models agree reasonably well with published experimental data for cell speed, actin flow, and cytoskeletal deformation in migrating fish epidermal keratocytes. The models also suggest that oscillations can occur for certain ranges of parameter values.

Application of the HeartLander Crawling Robot for Injection of a Thermally Sensitive Anti-Remodeling Agent for Myocardial Infarction Therapy

Chapman, Michael P.; López González, Jose L.; Goyette, Brina E.; Fujimoto, Kazuro L.; Ma, Zuwei; Wagner, William R.; Zenati, Marco A.; Riviere, Cameron N.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em //2010 EN
Relevância na Pesquisa
36.03%
The injection of a mechanical bulking agent into the left ventricular (LV) wall of the heart has shown promise as a therapy for maladaptive remodeling of the myocardium after myocardial infarct (MI). The HeartLander robotic crawler presented itself as an ideal vehicle for minimally-invasive, highly accurate epicardial injection of such an agent. Use of the optimal bulking agent, a thermosetting hydrogel developed by our group, presents a number of engineering obstacles, including cooling of the miniaturized injection system while the robot is navigating in the warm environment of a living patient. We present herein a demonstration of an integrated miniature cooling and injection system in the HeartLander crawling robot, that is fully biocompatible and capable of multiple injections of a thermosetting hydrogel into dense animal tissue while the entire system is immersed in a 37°C water bath.

Integration of crawling waves in an ultrasound imaging system. Part 1: system and design considerations *

Hazard, Christopher; Hah, Zaegyoo; Rubens, Deborah; Parker, Kevin
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
36.16%
An ultrasound system (GE Logiq 9) was modified to produce a synthetic crawling wave using shear wave displacements generated by the radiation force of focused beams formed at the left and the right edge of the region of interest (ROI). Two types of focusing, normal and axicon, were implemented. Baseband (IQ) data was collected to determine the left and right displacements, which were then used to calculate an interference pattern. By imposing a variable delay between the two pushes, the interference pattern moves across the ROI to produce crawling waves. Also temperature and pressure measurements were made to assess the safety issues. The temperature profiles measured in a veal liver along the focal line showed the maximum temperature rise less than 0.8 °C, and the pressure measurements obtained in degassed water and derated by 0.3 dB/cm/MHz demonstrate that the system can operate within FDA safety guidelines.

Integration of crawling waves in an ultrasound imaging System. Part 2: signal processing and applications ☆

Hah, Zaegyoo; Hazard, Chris; Mills, Bradley; Barry, Christopher; Rubens, Deborah; Parker, Kevin
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
36.16%
This paper introduces methods to generate crawling wave interference patterns from the displacement fields generated from radiation force pushes on a GE Logiq 9 scanner. The same transducer and system is providing both the pushing pulses to generate the shear waves and the tracking pulses to measure the displacements. Acoustic power and system limitations result in largely impulsive displacement fields. Measured displacements from pushes on either side of a region of interest (ROI) are used to calculate continuously varying interference patterns. This technique is explained along with a brief discussion of the conventional mechanical source-driven crawling waves for comparison. We demonstrate the method on three example cases: a gelatin based phantom with a cylindrical inclusion, an oil-gelatin phantom, and mouse livers. The oil-gelatin phantom and the mouse livers demonstrate not only shear speed estimation, but the frequency dependence of the shear wave speeds.

Characterization of Drosophila Larval Crawling at the Level of Organism, Segment, and Somatic Body Wall Musculature

Heckscher, Ellie S.; Lockery, Shawn R.; Doe, Chris Q.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 05/09/2012 EN
Relevância na Pesquisa
36.3%
Understanding rhythmic behavior at the developmental and genetic levels has important implications for neurobiology, medicine, evolution, and robotics. We studied rhythmic behavior—larval crawling—in the genetically and developmentally tractable organism, Drosophila melanogaster. We used narrow-diameter channels to constrain behavior to simple, rhythmic crawling. We quantified crawling at the organism, segment, and muscle levels. We showed that Drosophila larval crawling is made up of a series of periodic strides. Each stride consists of two phases. First, while most abdominal segments remain planted on the substrate, the head, tail, and gut translocate; this “visceral pistoning” moves the center of mass. The movement of the center of mass is likely powered by muscle contractions in the head and tail. Second, the head and tail anchor while a body wall wave moves each abdominal segment in the direction of the crawl. These two phases can be observed occurring independently in embryonic stages before becoming coordinated at hatching. During forward crawls, abdominal body wall movements are powered by simultaneous contraction of dorsal and ventral muscle groups, which occur concurrently with contraction of lateral muscles of the adjacent posterior segment. During reverse crawls...

ELASTICITY ESTIMATES FROM IMAGES OF CRAWLING WAVES GENERATED BY MINIATURE SURFACE SOURCES

Partin, Alexander; Hah, Zaegyoo; Barry, Christopher T.; Rubens, Deborah J.; Parker, Kevin J.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
36.03%
We present a surface-based approach to generate shear wave interference patterns, called crawling waves (CrW), within a medium and derive local estimates of biomechanical properties of tissue. In previous experiments, elongated bars operating as vibration sources were used to generate CrW propagation in samples. In the current study, however, a pair of miniature circular vibration sources is applied to the overlying skin to generate the CrW within the medium. The shape and position of the miniature sources make this configuration more applicable for in vivo implementation. A modified ultrasound imaging system is used to display the CrW propagation. A shear speed mapping algorithm is developed using a detailed analysis of the CrW. The proposed setup is applied to several biomaterials including a homogeneous phantom, an inhomogeneous phantom, and ex vivo human liver. The data are analyzed using the mapping algorithm to reveal the biomechanical properties of the biomaterials.

Crawling and Walking Infants Elicit Different Verbal Responses from Mothers

Karasik, Lana; Tamis-LeMonda, Catherine; Adolph, Karen
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
36.03%
We examined mothers’ verbal responses to their crawling or walking infants’ object sharing (i.e., bids). Fifty mothers and their 13-month-olds were observed for 1 hour at home. Infants bid from a stationary position or they bid after carrying the object to their mothers. Mothers responded with affirmations (e.g., “thank you”), descriptions (“red box”), or action directives (“open it”). Infants’ locomotor status and the form of their bids predicted how mothers responded. Mothers of walkers responded with action directives more often than mothers of crawlers. Notably, differences in the responses of mothers of walkers versus those of crawlers were explained by differences in bid form between the two groups of infants. Walkers were more likely to engage in moving bids than crawlers, who typically shared objects from stationary positions. When crawlers displayed moving bids, their mothers offered action directives just as often as did mothers of walkers. Findings illustrate developmental cascades, wherein infants’ locomotor status affects how infants share objects with mothers, which in turn shapes mothers’ verbal responses.

Vav1 is Essential for Mechanotactic Crawling and Migration of Neutrophils out of the Inflamed Microvasculature

Phillipson, Mia; Heit, Bryan; Parsons, Sean A.; Petri, Björn; Mullaly, Sarah C.; Colarusso, Pina; Gower, R. Michael; Neely, Gregory; Simon, Scott I.; Kubes, Paul
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 01/06/2009 EN
Relevância na Pesquisa
36.34%
Mac-1 dependent crawling is a new step in the leukocyte recruitment cascade which follows LFA-1 dependent adhesion and precedes emigration. Neutrophil adhesion via LFA-1 has been shown to induce cytoskeletal reorganization through Vav1-dependent signaling, and the current study investigates the role of Vav1 in the leukocyte recruitment process in vivo with particular attention to the events immediately downstream of LFA-1 dependent adhesion. Intravital and spinning-disk-confocal microscopy was used to investigate intravascular crawling in relation to endothelial junctions in vivo in wild-type (WT) and Vav1−/− mice. Adherent WT neutrophils almost immediately began crawling perpendicular to or against blood flow via Mac-1 until they reached an endothelial junction where they often changed direction. This pattern of perpendicular, mechanotactic crawling was recapitulated in vitro when shear was applied. In sharp contrast, the movement of Vav1−/− neutrophils was always in the direction of flow, and appeared more passive as if the cells were dragged in the direction of flow in vivo and in vitro. More than 80% of Vav1−/− neutrophils moved independent of Mac-1 and could be detached with LFA-1 antibodies. An inability to release the uropod was frequently noted for Vav1−/− neutrophils...

The Costs and Benefits of Development: The Transition From Crawling to Walking

Adolph, Karen E.; Tamis-LeMonda, Catherine S.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 02/12/2014 EN
Relevância na Pesquisa
36.3%
The transition from crawling to walking requires infants to relinquish their status as experienced, highly skilled crawlers in favor of being inexperienced, lowskilled walkers. Yet infants willingly undergo this developmental transition, despite incurring costs of shaky steps, frequent falls, and inability to gauge affordances for action in their new upright posture. Why do infants persist with walking when crawling serves the purpose of independent mobility? In this article, we present an integrative analysis of the costs and benefits associated with crawling and walking that challenges prior assumptions, and reveals deficits of crawling and benefits of upright locomotion that were previously overlooked. Inquiry into multiple domains of development reveals that the benefits of persisting with walking outweigh the costs: Compared to crawlers, walking infants cover more space more quickly, experience richer visual input, access and play more with distant objects, and interact in qualitatively new ways with caregivers.

Transport of a 1D viscoelastic actin–myosin strip of gel as a model of a crawling cell

Larripa, Kamila; Mogilner, Alex
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 01/12/2006 EN
Relevância na Pesquisa
36.03%
Cell crawling is an important biological phenomenon because it underlies coordinated cell movement in morphogenesis, cancer and wound healing. This phenomenon is based on protrusion at the cell's leading edge, retraction at the rear, contraction and graded adhesion powered by the dynamics of actin and myosin protein networks. A few one-dimensional models successfully explain an anteroposterior organization of the motile cell, but don't sufficiently explore the viscoelastic nature of the actin-myosin gel. We develop and numerically solve a model of a treadmilling strip of viscoelastic actin-myosin gel. The results show that the strip translocates steadily as a traveling pulse, without changing length, and that protein densities, velocities and stresses become stationary. The simulations closely match the observed forces, movements and protein distributions in the living cell.

Training profoundly retarded children to stop crawling1

O'Brien, F.; Azrin, N. H.; Bugle, C.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em //1972 EN
Relevância na Pesquisa
26.25%
Many profoundly retarded children continue to crawl even though they can walk. Crawling and walking were viewed as two alternative response modes, both reinforced by movement. Children choose the one mode that is easier and faster for them. A training program was designed to increase the ease and speed of walking relative to that of crawling, and consisted of restraint-for-crawling and priming-of-walking. With the program, four retarded children reduced crawling and began to walk instead. When training was discontinued, two children with moderate walking impairment continued to walk rather than crawl. Two children with severe impairment of walking, however, required the occasional use of the restraint procedure to maintain walking as the dominant mode of locomotion. The program was easily administered, required little time, and was effective for all four children.