bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extracellular matrix functions during neuronal migration and lamination in the mammalian central nervous system
Authors: Franco Santos J. , Müller Ulrich 
Published: July 2011

AbstractExtracellular matrix (ECM) glycoproteins are expressed in the central nervous system (CNS) in complex and developmentally regulated patterns. The ECM provides a number of critical functions in the CNS, contributing both to the overall structural organization of the CNS and to control of individual cells. At the cellular level, the ECM affects its functions by a wide range of mechanisms, including providing structural support to cells, regulating the activity of second messenger systems, and controlling the distribution and local concentration of growth and differentiation factors. Perhaps the most well known role of the ECM is as a substrate on which motile cells can migrate. Genetic, cell biological, and biochemical studies provide strong evidence that ECM glycoproteins such as laminins, tenascins, and proteoglycans control neuronal migration and positioning in several regions of the developing and adult brain. Recent findings have also shed important new insights into the cellular and molecular mechanisms by which reelin regulates migration. Here we will summarize these findings, emphasizing the emerging concept that ECM glycoproteins promote different modes of neuronal migration such as radial, tangential, and chain migration. We also discuss several studies demonstrating that mutations in ECM glycoproteins can alter neuronal positioning by cell nonautonomous mechanisms that secondarily affect migrating neurons. © 2011 Wiley Periodicals, Inc. Develop Neurobiol 71: 889‐900, 2011
Understanding ecohydrological connectivity in savannas: a system dynamics modelling approach
Authors: Miller Gretchen R. , Cable Jessica M. , McDonald Alyson K. , Bond Barbara , Franz Trenton E. , Wang Lixin , Gou Si , Tyler Anna P. , Zou Chris B. , Scott Russell L. 
Published: July 2011

ABSTRACTEcohydrological connectivity is a system level property that results from the linkages in the networks of water transport through ecosystems, by which feedbacks and other emergent system behaviours may be generated. We created a system dynamics model that represents primary ecohydrological networks to examine how connectivity between ecosystem components impacts ecosystem processes. Here, we focused on the savanna ecosystems, although the analyses may be expanded to other ecosystem types in the future. To create the model, a set of differential equations representing ecohydrological processes was programmed into the dynamic solver Vensim. Stocks of water storage (e.g. atmospheric and soil moisture) were linked by flows [e.g. precipitation and evapotranspiration (ET)] that were in turn dynamically controlled by the amount of water stored. Precipitation was forced stochastically, and soil moisture and potential ET controlled actual ET. The model produced extended, probabilistic time series of stocks and flows, including precipitation, soil moisture, runoff, transpiration, and groundwater recharge. It was used to describe the behaviour of several previously studied savanna ecosystems in North America and Africa. The model successfully reproduced seasonal patterns of soil moisture dynamics and ET at the California site. It also demonstrated more complex, system level behaviours, such as multiyear persistence of drought and synergistic or antagonistic responses to disconnection of system components. Future improvements to the model will focus on capturing other important aspects of long‐term system behaviour, such as changes in physiology or phenology, and spatial heterogeneity, such as the patchwork nature of savannas. Copyright © 2011 John Wiley & Sons, Ltd.
Influence of fructose and oxygen gradients on fed‐batch recombinant protein production using Bacillus megaterium
Authors: Korneli Claudia , David Florian , Godard Thibault , Franco‐Lara Ezequiel 
Published: July 2011

AbstractBacillus megaterium expressing a variant of the green fluorescent protein (GFP) was used to investigate the influence of gradients in dissolved oxygen (DO) and fructose concentration on biomass and product formation. For this purpose, several fed‐batch experiments with DO as feed control parameter were performed using suboptimal and optimal adjusted control parameters. In a first approach, suboptimal DO‐feeding was reached by varying randomly the controller output between 10 and 20% of the maximal pumping capacity. This led to fluctuations in DO between 20 and 80% and to substrate gradients around 3 g/L. GFP formation thereby was decreased. In a second approach, an optimal feeding profile was realized using a PI‐control with a constant controller output of 20% was used. Thereby no gradients in substrate concentration, but low‐amplitude and high‐frequency oscillations in the DO concentration were obtained, leading to increased GFP formation. In a final experimental approach, large‐scale conditions were emulated in a two‐compartment scale‐down system consisting of a 3.7‐L stirred tank reactor and a 0.7‐L non‐stirred vessel. DO‐based feeding was applied with the measurement in the 3.7‐L bioreactor and feeding in the small vessel. This setup led to a fairly constant gradient of 20% between both vessels, which also resulted in a decreased GFP productivity.
A novel interface‐tracking method based on Lagrangian particles for deformation analysis of a red blood cell in a capillary
Authors: Li Hua , Ye Ting , Lam K. Y. 
Published: July 2011

SUMMARYA novel efficient interface‐tracking method is developed to gain an insight into the interface in a multiphase or multifluid system, called the modified particle binary level set (MPBLS) method, in which the binary level set function is defined to distinguish the different phases or fluids and further modified by Lagrangian particles scattered along the interface for achieving higher accuracy. The validation of the MPBLS method is carried out first by simulating the free motion of a red blood cell (RBC) in the rotating, shear and Poiseuille flows, respectively. Subsequently, further validations are performed by comparing with the experimental and numerical results published previously. As one of important applications, the MPBLS method is employed to investigate the deformation behaviors of RBCs with different shapes in a capillary. The simulations show that the healthy RBC gradually changes the geometric shape from a biconcave to a steady parachute shape. It is thus guaranteed that the RBC successfully traverses through the smaller capillaries compared with undeformed RBC. However, the unhealthy RBC with the circular or elliptical shape has different deformation behaviors, in which the steady parachute shape is much less concave at the rear and more convex in the front. Copyright © 2011 John Wiley & Sons, Ltd.
Implicit preconditioned high‐order compact scheme for the simulation of the three‐dimensional incompressible Navier–Stokes equations with pseudo‐compressibility method
Authors: Qian ZhanSen , Zhang JingBai 
Published: July 2011

SUMMARYThis paper combines the pseudo‐compressibility procedure, the preconditioning technique for accelerating the time marching for stiff hyperbolic equations, and high‐order accurate central compact scheme to establish the code for efficiently and accurately solving incompressible flows numerically based on the finite difference discretization. The spatial scheme consists of the sixth‐order compact scheme and 10th‐order numerical filter operator for guaranteeing computational stability. The preconditioned pseudo‐compressible Navier–Stokes equations are marched temporally using the implicit lower–upper symmetric Gauss–Seidel time integration method, and the time accuracy is improved by the dual‐time step method for the unsteady problems. The efficiency and reliability of the present procedure are demonstrated by applications to Taylor decaying vortices phenomena, double periodic shear layer rolling‐up problem, laminar flow over a flat plate, low Reynolds number unsteady flow around a circular cylinder at Re = 200, high Reynolds number turbulence flow past the S809 airfoil, and the three‐dimensional flows through two 90°curved ducts of square and circular cross sections, respectively. It is found that the numerical results of the present algorithm are in good agreement with theoretical solutions or experimental data. Copyright © 2011 John Wiley & Sons, Ltd.
Neural mechanisms underlying the grouping effect in short‐term memory
Authors: Kalm Kristjan , Davis Matthew H. , Norris Dennis 
Published: July 2011

AbstractDividing auditory sequence into groups, or imposing rhythmic, tonal, or spatial structure during presentation, improves recall performance. Several competing computational models have been proposed to account for these effects, but little is known about the neural correlates of grouping and hence the representations that encode grouped sequences. The present study used functional magnetic resonance imaging (fMRI) to compare the auditory encoding of grouped and ungrouped lists of sub‐span (six letters) and supra‐span (nine letters) length in an immediate serial recall (ISR) task. Analysis of activation revealed an extensive premotor and prefrontal network, which was significantly less active when short‐term memory (STM) span was exceeded during encoding. Only primary auditory cortex showed an increase in activation when memory span was exceeded. Comparison of activation for grouped and ungrouped lists showed that during the subspan phase bilateral planum temporale showed less activation for grouped stimuli, while during the supra‐span phase supramarginal and inferior parietal areas were more active for grouped lists. The magnitude of both temporal and parietal activations predicted enhanced recall of grouped lists. Thus neural signatures of grouping seem to reflect more structured processing in parietal areas instead of reliance on perceptual‐auditory processing in temporal regions. Hum Brain Mapp, 2011. © 2011 Wiley‐Liss, Inc.
Cortical thickness is linked to executive functioning in adulthood and aging
Authors: Burzynska Agnieszka Z. , Nagel Irene E. , Preuschhof Claudia , Gluth Sebastian , Bäckman Lars , Li Shu‐Chen , Lindenberger Ulman , Heekeren Hauke R. 
Published: July 2011

AbstractExecutive functions that are dependent upon the frontal‐parietal network decline considerably during the course of normal aging. To delineate neuroanatomical correlates of age‐related executive impairment, we investigated the relation between cortical thickness and executive functioning in 73 younger (20–32 years) and 56 older (60–71 years) healthy adults. Executive functioning was assessed using the Wisconsin Card Sorting Test (WCST). Cortical thickness was measured at each location of the cortical mantle using surface‐based segmentation procedures on high‐resolution T1‐weighted magnetic resonance images. For regions involved in WCST performance, such as the lateral prefrontal and parietal cortices, we found that thicker cortex was related to higher accuracy. Follow‐up ROI‐based analyses revealed that these associations were stronger in older than in younger adults. Moreover, among older adults, high and low performers differed in cortical thickness within regions generally linked to WCST performance. Our results indicate that the structural cortical correlates of executive functioning largely overlap with previously identified functional patterns. We conclude that structural preservation of relevant brain regions is associated with higher levels of executive performance in old age, and underscore the need to consider the heterogeneity of brain aging in relation to cognitive functioning. Hum Brain Mapp, 2011. © 2011 Wiley‐Liss, Inc.
Clinicopathologic analysis and predictive factors for distant metastases in patients with head and neck squamous cell carcinomas
Authors: Coca‐Pelaz Andrés , Rodrigo Juan P. , Suárez Carlos 
Published: July 2011

AbstractBackgroundThe recognition of patients at high risk for the development of distant metastasis (DM) is required to recognize a subset of patients who may benefit from systemic therapy.MethodsIn a retrospective analysis of patients treated between 1995 and 2006, 443 patients with surgically treated primary head and neck squamous cell carcinoma were included. The frequency and clinicopathologic risk factors for DM were evaluated.ResultsA total of 60 patients (13.5%) developed DM. In a univariate analysis, tumor site (pharynx), pN classification (pN2–N3), differentiation grade (poorly differentiated), disease stage (stage IV), number (3 or more nodes), and site (bilateral nodes) of nodal metastasis were found to be significantly associated with the risk of DM. In a multivariate analysis, the only significant risk factors were the differentiation grade and the number and site of nodal metastasis.ConclusionsPatients with pharyngeal poorly differentiated tumors, with multiple or bilateral nodal metastases, are at greater risk of DM and should be considered for systemic therapy. © 2011 Wiley Periodicals, Inc. Head Neck, 2011
Secondary tracheoesophageal puncture and myotomy—A novel outpatient technique
Authors: Duvdevani Shay I. , Talmi Yoav P. , Horowitz Zeev , Wolf Michael , Bedrin Lev 
Published: July 2011

AbstractBackgroundThe purpose of this study was to show a novel technique for secondary tracheoesophageal puncture (TEP) and myotomy in patients who previously underwent total laryngectomy.MethodsFifteen patients underwent secondary TEP and 3 patients underwent myotomy. In 1 patient, both myotomy and TEP were done concurrently. A Foley catheter is nasally inserted into the esophagus with the patient under local anesthesia and the catheter balloon is inflated at the site of the planned procedure. The myotomy is performed over the inflated balloon for esophageal posterior wall protection and a voice prosthesis is inserted in a small incision made by the physician. When only myotomy is performed, the muscles over the mucosa are incised. A voice test is performed immediately.ResultsAll patients exhibited good voice rehabilitation. One patient who had a myotomy had a penetration of the pharyngeal mucosa with immediate closure and no sequelae.ConclusionOutpatient Foley catheter–guided myotomy and secondary TEP are simple, safe, time saving, and cost‐effective procedures. © 2011 Wiley Periodicals, Inc. Head Neck, 2012
Recurrent episodes of asystole from carotid sinus hypersensitivity triggered by positioning for head and neck surgery
Authors: Truong Angela T. , Sturgis Erich M. , Rozner Marc A. , Truong Dam‐Thuy 
Published: July 2011

AbstractBackgroundWe present a case report of a patient with recurrent thyroid carcinoma, previously treated with surgery and radiotherapy, who developed asystolic episodes on 2 occasions as the result of positioning of the neck in hyperextension for head and neck surgery.Methods and ResultsIn carotid sinus hypersensitivity (CSH), the carotid sinus reflex is greatly exaggerated, resulting in profound bradycardia and asystole. Predisposing risk factors for the development of CSH in this patient included history of previously treated head and neck cancer and the presence of tight surgical scars. His negative cardiovascular history, the time sequence between neck positioning and asystole, and the fact that asystole recurred during the second surgery strongly suggest that CSH was precipitated by hyperextension of the neck during positioning.ConclusionsA heightened awareness of this syndrome, close monitoring, and preparedness for timely diagnosis and management are essential for a successful outcome. © 2011 Wiley Periodicals, Inc. Head Neck, 2013
Involvement of Th2 cytokines in the mouse model of flutamide‐induced acute liver injury
Authors: Higuchi Satonori , Kobayashi Masanori , Yano Azusa , Tsuneyama Koichi , Fukami Tatsuki , Nakajima Miki , Yokoi Tsuyoshi 
Published: July 2011

ABSTRACTDrug‐induced liver injury is a growing concern for pharmaceutical companies and patients because numerous drugs have been linked to hepatotoxicity and it is the most common reason for a drug to be withdrawn. Flutamide rarely causes liver dysfunction in humans, and immune allergic reactions have been suggested in some cases. In this study, we investigated the mechanisms of flutamide‐induced liver injury in BALB/c mice. Plasma alanine aminotransferase and aspartate aminotransferase levels were significantly increased 3, 6 and 9 h after flutamide (1500 mg kg−1, p.o.) administration. The biomarker for oxidative stress was not changed, but Th2‐dominant immune‐related factors, such as interleukin (IL)‐4, IL‐5, STAT6 and GATA‐binding protein (GATA)‐3, were induced in flutamide‐administered mice. The pre‐administration of monoclonal‐IL‐4 antibody suppressed the hepatotoxicity of flutamide. In addition, we investigated the effect of 13,14‐dihydro‐15‐keto‐PGD2 (DK‐PGD2; 10 µg per mouse, i.p.) administration on flutamide‐induced acute liver injury. Coadministration of DK‐PGD2 and flutamide resulted in a significant increase in alanine aminotransferase and a remarkable increase of macrophage inflammatory protein‐2. In conclusion, we demonstrated that flutamide‐induced acute liver injury is mediated by Th2‐dominant immune responses in mice. Copyright © 2011 John Wiley & Sons, Ltd.
GPU‐accelerated atom and dynamic bond visualization using hyperballs: A unified algorithm for balls, sticks, and hyperboloids
Authors: Chavent Matthieu , Vanel Antoine , Tek Alex , Levy Bruno , Robert Sophie , Raffin Bruno , Baaden Marc 
Published: July 2011

AbstractRay casting on graphics processing units (GPUs) opens new possibilities for molecular visualization. We describe the implementation and calculation of diverse molecular representations such as licorice, ball‐and‐stick, space‐filling van der Waals spheres, and approximated solvent‐accessible surfaces using GPUs. We introduce HyperBalls, an improved ball‐and‐stick representation replacing tubes, linking the atom spheres by hyperboloids that can smoothly connect them. This type of depiction is particularly useful to represent dynamic phenomena, such as the evolution of noncovalent bonds. It is furthermore well suited to represent coarse‐grained models and spring networks. All these representations can be defined by a single general algebraic equation that is adapted for the ray‐casting technique and is well suited for execution on the GPU. Using GPU capabilities, this implementation can routinely, accurately, and interactively render molecules ranging from a few atoms up to huge macromolecular assemblies with more than 500,000 particles. In simple cases, based only on spheres, we have been able to display up to two million atoms smoothly. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Ab initio molecular dynamics of protonated water clusters by integrated multicenter molecular‐orbital method
Authors: Udagawa Taro , Sakai Shogo 
Published: July 2011

AbstractTo analyze large‐scale cluster systems theoretically, we recently developed an “integrated multicenter molecular‐orbital” (IMiC‐MO) method. This method calculates the force of an entire system by dividing the system into small regions. We used the method to analyze the effect of cluster size and the process of hydrogen bond network (HBN) growth to form H+(H2O)n (n = 9, 17, and 33) clusters. Our simulations reveal that H3O+ and water molecules in the first solvation shell function take an important role to grow the HBN. In addition, the number of hydrogen donors in each water molecule is strongly related to the shape of the HBN. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Role of endoscopic sonography in the diagnosis of a fish bone perforation of the gastric wall resulting in a submucosal pseudotumor
Authors: Huang Ching‐Hsiu , Chiang Ching‐Chung , Yan Yuan‐Horng , Tsai Tsung‐Jung , Chen Chi‐Yi 
Published: July 2011

AbstractWe report the case of a 72‐year‐old woman with a fish bone‐induced granulation tissue in the gastric wall that was initially diagnosed as a submucosal tumor by panendoscopy. High‐frequency endoscopic ultrasonography identified the linear calcified fish bone embedded in a heterogeneous mass. © 2011 Wiley Periodicals, Inc. J Clin Ultrasound 2011
Investigating genotype–phenotype influences on the development of type 1 diabetes
Authors: Peakman Mark 
Published: July 2011

AbstractThe identification of genes associated with type 1 diabetes has provided important clues to the nature of the pathogenesis of the disease. Currently, this information is encapsulated in several putative mechanisms through which islet autoimmunity might arise and become converted into a malignant autoimmune disease leading to diabetes. One of these mechanisms involves the immune response to viruses, including the human enteroviruses.The link between polymorphisms, splice variants, and deletions, in the interferon induced with helicase C domain 1 gene IFIH1 (which acts as a viral sensing gene), and diabetes has reinforced the “aberrant immune response to virus” pathway for the development of diabetes [Nejentev et al., 2009].In order to understand how such pathways might operate in type 1 diabetes, we have taken the approach of selecting subjects with polarized genotypes (homozygous susceptibility vs. homozygous protection) for type 1 diabetes‐associated SNPs and examining the immunological phenotypes associated with these variants.These studies indicate that with a careful design of assays that examine effects highly proximal to the genes of interest, it is possible to identify immunological phenotypes influenced by type 1 diabetes‐associated polymorphic gene variants. J. Med. Virol. 83:1671–1671, 2011. © 2011 Wiley‐Liss, Inc.
Prevalence of JC polyomavirus genomic sequences from the large t‐antigen and non‐coding control regions among bulgarian patients with primary brain tumors
Authors: Tsekov Iliya , Ferdinandov Dilyan , Bussarsky Ventzeslav , Hristova Svetlana , Kalvatchev Zlatko 
Published: July 2011

AbstractA total of 111 fresh brain biopsies from patients with primary brain tumors were examined for JC polyomavirus sequences from the Large T antigen encoding region (LT) and the viral non‐coding control region (NCCR). SYBR Green and TaqMan real‐time polymerase chain reaction assays were used. In the glioblastoma group of 39 patients 48.7% were positive for LT sequences. Among the astrocytoma group (19 patients) and the oligodendroglioma group (12 patients) 31.6% and 33.3% were also positive. The prevalence of LT genomic sequences among the other groups was as follows: in 2 out of 3 oligoastrocytomas; in 3 out 5 gangliogliomas; in 2 out of 5 meduloblastomas; in 1 out 3 pineocytomas; and in none of the tested 5 ependimomas. All positive samples had a late threshold cycle that varied from 36 to 49, indicative of very low starting viral number. Only 21 of all the 111 samples were positive for NCCR. Low copy number in range of 10–1,000 was present. Notably, only 8 of all NCCR positive specimens were also LT positive. It might be suggested that the disproportion between the results for LT and NCCR is either due to clonally integrated LT fragments, with loss of genetic material, or changes in the NCCR. The latter would alter the productive course of the infection and may establish a premise for continuous interaction of viral regulatory proteins with cell molecules that are responsible for the control of the cell cycle. This may lead subsequently to malignant transformation. J. Med. Virol. 83:1608–1613, 2011. © 2011 Wiley‐Liss, Inc.