bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microsurgical arterovenous loops and biological templates: A novel in vivo chamber for tissue engineering
Authors: Manasseri Benedetto , Cuccia Giuseppe , Moimas Silvia , D'Alcontres Francesco Stagno , Polito Francesca , Bitto Alessandra , Altavilla Domenica , Squadrito Francesco , Geuna Stefano , Pattarini Lucia , Zentilin Lorena , Collesi Chiara , Puligadda Uday , Giacca Mauro , Colonna Michele Rosario 
Published: September 2007

AbstractBackground: Microsurgical tissue engineering is an emerging topic in regenerative medicine. Here we describe a new microsurgical model of bioengineering in rats based on the use of an arterovenous loop (AV) implanted into a commercially available crosslinked collagen/glycosaminoglycan template. Methods: The microvascular loop was created between the femoral artery and vein and covered by the template folded onto itself. The chamber was isolated from the outside tissue by an outer silicon layer to impede tissue ingrowth. Results: At 1‐month postimplantation, the tissue chamber was found heavily vascularized, as assessed by laser Doppler perfusion analysis. Histological examination showed that the AV loop was integrated into the collagen matrix of the template and that the whole template was filled with a newly formed soft connective tissue. Most interestingly, the whole scaffold was found heavily vascularized, including the formation of a large number of α‐SMA‐positive arterioles. Conclusions: The developed microsurgical chamber provides a highly vascular, isolated tool for in vivo tissue engineering. © 2007 Wiley‐Liss, Inc. Microsurgery, 2007.
Free SCIA/SIEA skin flap: A dual blood supply approach to groin region
Authors: Aydin Mustafa Asim , Nasir Serdar 
Published: September 2007

AbstractFree groin flap donor skin is unequaled in generous skin supply and inconspicuousness. We reliably utilize this region by taking advantage of the dual blood supply from superficial circumlex iliac (SCIA) and superficial inferior epigastric (SIEA) arteries and name the flap “Free SCIA/SIEA skin flap.” The arterial pedicle is selected between SCIA and SIEA according to vascular anatomy which is explored through an incision along the inguinal ligament prior to skin island planning. Among 57 free SCIA/SIEA skin flap transfers, two flap failures occurred; circulatory impairment was restored by taking the patient back to the operating room in four cases; major size discrepancy was noted in one end‐to‐end arterial anastomosis; and no vein grafts were required. Mostly an extended length of skin island is harvested irrespective of wound size in order to utilize the proximal skin as a vascular carrier that compensates for short pedicle. We conclude that, with the current microsurgical expertise, free SCIA/SIEA skin flap is versatile even when the skin quality is considered. © 2007 Wiley‐Liss, Inc. Microsurgery, 2007.
Separating true positive predicted residue contacts from false positive ones in mainly α proteins, using constrained Metropolis MC simulations
Authors: Vicatos Spyridon , Kaznessis Yiannis N. 
Published: September 2007

AbstractWe present a method that significantly improves the accuracy of predicted proximal residue pairs in protein molecules. Computational methods for predicting pairs of amino acids that are distant in the protein sequence but close in the protein 3D structure can benefit attempts to in silico recognize the fold of a protein molecule. Unfortunately, currently available methods suffer from low predictive accuracy. In this work, we use Monte Carlo simulations to fold protein molecules with proximal pair predictions used as additional energy constraints. To test our methods, we study molecules with known tertiary structures. With Monte Carlo, we generate ensembles of structures for each set of residues constraints. The distribution of the root mean square deviation of the folded structures from the known native structure reveals clear information about the accuracy of the constraint sets used. With recursive substitutions of constraints, false positive predictions are identified and filtered out and significant improvements in accuracy are observed. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Extranodal Spreading of Esophageal Squamous Cell Carcinoma: Clinicopathological Characteristics and Prognostic Impact
Authors: Tanabe Tadashi , Kanda Tatsuo , Kosugi Shin‐ichi , Ikeda Yoshiyuki , Makino Shigeto , Komukai Shintaro , Ohashi Manabu , Suzuki Tsutomu , Hatakeyama Katsuyoshi 
Published: September 2007

AbstractBackgroundMicroscopic cancer spreading to extranodal connective tissues (extranodal spreading: ENS) is occasionally found in resected specimens from patients with esophageal squamous cell carcinoma (SCC), but the prognostic impact of ENS remains unclear. The aims of this study were to elucidate the prognostic impact of ENS to help determine the most suitable management for the patients with ENS.MethodsWe histologically re‐evaluated 7,349 lymph nodes obtained from 171 patients with SCC of the thoracic esophagus who underwent potentially curable resection between 1992 and 2003. We defined ENS as microscopic penetration of tumor cells from metastatic lymph nodes or tumor cell dissemination into extranodal connective tissues.ResultsExtranodal spreading was found in 37 (21.6%) patients, and it had a significant relationship with diameter and depth of the tumor, lymphatic and venous invasion, intramural metastasis, and number of metastatic nodes. Patients who were ENS positive were at higher risk of recurrence, and their overall survival rate was lower than that for ENS‐negative patients. Furthermore, recurrent risk was higher and overall survival rate was lower in ENS‐positive patients than in ENS‐negative patients when they had 1–3 metastatic nodes, but recurrent risk and overall survival rate of the patients with 4 or more metastatic nodes were very similar in ENS‐positive and ENS‐negative patients.ConclusionsThe present findings suggest that in SCC of the thoracic esophagus, the presence of ENS increases recurrent risk and reduces the overall survival of the patients with 1–3 metastatic nodes. Patients showing ENS should be managed in the same way as patients with 4 or more metastatic nodes.
The effects of maternal inflammation on neuronal development: possible mechanisms
Authors: Jonakait G. Miller 
Published: September 2007

AbstractThat maternal inflammation adversely affects fetal brain development is well established. Less well understood are the mechanisms that account for neurodevelopmental disorders arising from maternal inflammation. This review seeks to begin an examination of possible sites and mechanisms of action whereby inflammatory cytokines – produced by the mother or by the fetal brain – could impact the developing fetus. We focus first on the placenta where cytokines maintain the immunological environment that prevents maternal rejection of the fetus. Following a brief examination of placental transfer of maternal cytokines, the focus turns on embryonic microglia, early and ubiquitous residents of the developing brain. Finally, a more intense examination of interleukin‐6 (IL‐6) and bone morphogenetic proteins (BMPs) provides examples of glial‐ or maternal‐derived cytokines that are known to have profound effects on developing systems and that could, if dysregulated, have undesirable consequences for brain development.
Application of magnetic resonance imaging in animal models of perinatal hypoxic‐ischemic cerebral injury
Authors: Lodygensky Gregory A. , Inder Terrie E. , Neil Jeffrey J. 
Published: September 2007

AbstractBrain injury occurring in the perinatal period is an important etiology of subsequent neurodevelopmental disabilities. Magnetic resonance imaging (MRI) is a tool that is used to evaluate the nature of brain injury in the human infant. MRI techniques have also been applied to various animal models of perinatal injury. The most commonly used model is the immature rat, but there have also been imaging studies in mice, rabbit kits and piglets. The studies have been carried out using MR systems of various magnetic field strengths, ranging from 1.5 to 11.7 tesla (T), with applications for quantification of infarct volume, T1 measurements, T2 measurements, proton and phosphorus spectroscopy and diffusion imaging. The MR findings are then related to histopathology and, in a few cases, behavioral evaluations. There is also a growing number of studies utilizing MRI in evaluating the efficacy of neuroprotective treatments, such as hypothermia.
Postnatal changes in 5HT and NK1 receptors in rat trigeminal motor nucleus and surroundings
Authors: Tanaka‐Gomi Nami , Yasuda Kouichi , Nakamura Masaaki , Hasumi‐Nakayama Yoko , Umemura Tetsuhiro , Tanaka Susumu , Furusawa Kiyofumi 
Published: September 2007

AbstractOur previous study showed that developmental changes to serotonin and substance P coexist in the trigeminal motor nucleus (Vmo), dorsolateral subnucleus (Vmo.dl), ventromedial subnucleus (Vmo.vm) and the area within 300 μm surrounding Vmo (SVmo). This occurred in rats from embryonic day (E)19 to postnatal day (P)70, with density of these terminals peaking at P7 in these three areas. The present study examined postnatal development of serotonergic 1A receptor (5HT1A receptor) and substance P receptor (NK1 receptor) expression in Vmo and SVmo in rats from E19 to P70. No significant changes in percentages of 5HT1A and NK1 receptor‐expressing cells were seen between E19 and P70 by immunohistochemical study or in situ hybridization. In a real‐time PCR study, quantities of 5HT1A and NK1 receptor expression peaked at P7, indicating that expression of these receptors was maximized in each neuronal cell body in the Vmo and SVmo at P7. This result corresponds with postnatal changes in serotonin/substance P‐coexisting terminals found in our previous study. Furthermore, 5HT1A and NK1 receptors displayed very similar patterns of expression, which may support the hypothesis that potentiation of serotonin and substance P are involved in excitability regulating trigeminal motor functions, including mastication and breathing.
Log-linear model-based multifactor dimensionality reduction method to detect gene–gene interactions
Authors: Yeoun Lee Seung , Chung Yujin , Elston Robert C. , Kim Youngchul , Park Taesung 
Published: September 2007

AbstractMotivation: The identification and characterization of susceptibility genes that influence the risk of common and complex diseases remains a statistical and computational challenge in genetic association studies. This is partly because the effect of any single genetic variant for a common and complex disease may be dependent on other genetic variants (gene–gene interaction) and environmental factors (gene–environment interaction). To address this problem, the multifactor dimensionality reduction (MDR) method has been proposed by Ritchie et al. to detect gene–gene interactions or gene–environment interactions. The MDR method identifies polymorphism combinations associated with the common and complex multifactorial diseases by collapsing high-dimensional genetic factors into a single dimension. That is, the MDR method classifies the combination of multilocus genotypes into high-risk and low-risk groups based on a comparison of the ratios of the numbers of cases and controls. When a high-order interaction model is considered with multi-dimensional factors, however, there may be many sparse or empty cells in the contingency tables. The MDR method cannot classify an empty cell as high risk or low risk and leaves it as undetermined.Results: In this article, we propose the log-linear model-based multifactor dimensionality reduction (LM MDR) method to improve the MDR in classifying sparse or empty cells. The LM MDR method estimates frequencies for empty cells from a parsimonious log-linear model so that they can be assigned to high-and low-risk groups. In addition, LM MDR includes MDR as a special case when the saturated log-linear model is fitted. Simulation studies show that the LM MDR method has greater power and smaller error rates than the MDR method. The LM MDR method is also compared with the MDR method using as an example sporadic Alzheimer's disease.Contact: tspark@stats.snu.ac.kr
IGG: A tool to integrate GeneChips for genetic studies
Authors: Li M.-X. , Jiang L. , Ho S.-L. , Song Y.-Q. , Sham P.-C. 
Published: September 2007

AbstractSummary: To facilitate genetic studies using high-throughput genotyping technologies, we have developed an open source tool to integrate genotype data across the Affymetrix and Illumina platforms. It can efficiently integrate a large amount of data from various GeneChips, add genotypes of the HapMap Project into a specific project, flexibly trim and export the integrated data with different formats of popular genetic analysis tools, and highly control the quality of genotype data. Furthermore, this tool has sufficiently simplified its usage through its user-friendly graphic interface and is independent of third-party databases. IGG has successfully been applied to a genome-wide linkage scan in a Charcot-Marie-Tooth disease pedigree by integrating three types of GeneChips and HapMap project genotypes.Availability: http://bioinfo.hku.hk/iggweb (version 0.9).Contact: limx54@yahoo.com and songy@hku.hk
EGEETomo: a user-friendly, fault-tolerant and grid-enabled application for 3D reconstruction in electron tomography
Authors: Bilbao-Castro J. R. , García I. , Fernández J. J. 
Published: September 2007

AbstractSummary: Electron tomography is the leading technique to elucidate the structure of complex biological specimens. Due to the resolution needs, huge reconstructions are required. Grid computing has the potential to face the significant computational demands involved. However, there are a number of key issues, such as stability or difficult user-grid interaction, that currently preclude fully exploitation of its potential. EGEETomo is a user-friendly application that facilitates the interaction with the grid for the non-specialized user and automates job submission and supervision. In addition, EGEETomo is supplied with an automated fault recovery mechanism, which is key to make all the work transparent to the user. EGEETomo significantly accelerates tomographic reconstruction by exploiting the computational resources in the EGEE grid with minimal user intervention.Availability: http://www.ace.ual.es/~jrbcast/EGEETomo.tar.gzContact: jrbcast@ace.ual.es or jose@ace.ual.es
Graph-based consensus clustering for class discovery from gene expression data
Authors: Yu Zhiwen , Wong Hau-San , Wang Hongqiang 
Published: September 2007

AbstractMotivation: Consensus clustering, also known as cluster ensemble, is one of the important techniques for microarray data analysis, and is particularly useful for class discovery from microarray data. Compared with traditional clustering algorithms, consensus clustering approaches have the ability to integrate multiple partitions from different cluster solutions to improve the robustness, stability, scalability and parallelization of the clustering algorithms. By consensus clustering, one can discover the underlying classes of the samples in gene expression data.Results: In addition to exploring a graph-based consensus clustering (GCC) algorithm to estimate the underlying classes of the samples in microarray data, we also design a new validation index to determine the number of classes in microarray data. To our knowledge, this is the first time in which GCC is applied to class discovery for microarray data. Given a pre specified maximum number of classes (denoted as Kmax in this article), our algorithm can discover the true number of classes for the samples in microarray data according to a new cluster validation index called the Modified Rand Index. Experiments on gene expression data indicate that our new algorithm can (i) outperform most of the existing algorithms, (ii) identify the number of classes correctly in real cancer datasets, and (iii) discover the classes of samples with biological meaning.Availability: Matlab source code for the GCC algorithm is available upon request from Zhiwen Yu.Contact: yuzhiwen@cs.cityu.edu.hk and cshswong@cityu.edu.hkSupplementary information: Supplementary data are available at Bioinformatics online.
CIRCADIAN CLOCK ASSOCIATED1 Transcript Stability and the Entrainment of the Circadian Clock in Arabidopsis
Authors: Yakir Esther , Hilman Dror , Hassidim Miriam , Green Rachel M. 
Published: September 2007

Abstract
The circadian clock is an endogenous mechanism that generates rhythms with an approximately 24-h period and enables plants to predict and adapt to daily and seasonal changes in their environment. These rhythms are generated by molecular oscillators that in Arabidopsis (Arabidopsis thaliana) have been shown to consist of interlocking feedback loops involving a number of elements. An important characteristic of circadian oscillators is that they can be entrained by daily environmental changes in light and temperature. Previous work has shown that one possible entrainment point for the Arabidopsis oscillator is the light-mediated regulation of expression of one of the oscillator genes, CIRCADIAN CLOCK ASSOCIATED1 (CCA1). In this article, we have used transgenic plants with constitutive CCA1 expression to show that light also regulates CCA1 transcript stability. Our experiments show that CCA1 messenger RNA is relatively stable in the dark and in far-red light but has a short half-life in red and blue light. Furthermore, using transgenic plants expressing chimeric CCA1 constructs, we demonstrate that the instability determinants in CCA1 transcripts are probably located in the coding region. We suggest that the combination of light regulation of CCA1 transcription and CCA1 messenger RNA degradation is important for ensuring that the Arabidopsis circadian oscillator is accurately entrained by environmental changes.
Transcription Factor RAP2.2 and Its Interacting Partner SINAT2: Stable Elements in the Carotenogenesis of Arabidopsis Leaves
Authors: Welsch Ralf , Maass Dirk , Voegel Tanja , DellaPenna Dean , Beyer Peter 
Published: September 2007

AbstractThe promoter of phytoene synthase, the first specific enzyme of carotenoid biosynthesis, shows two main regulatory regions: a G-box-containing region located near the TATA box, and a TATA box distal region containing the cis-acting element ATCTA, which mediates strong basal promoter activity. This second element was also present in the promoter of phytoene desaturase, the next step of the carotenoid pathway, suggesting a common regulatory mechanism. In this work, we demonstrate that AtRAP2.2, a member of the APETALA2 (AP2)/ethylene-responsive element-binding protein transcription factor family, binds to the ATCTA element. In Arabidopsis (Arabidopsis thaliana) leaves, AtRAP2.2 transcript and protein levels were tightly controlled as indicated by unchanged transcript and protein levels in T-DNA insertion mutants in the AtRAP2.2 promoter and 5′ untranslated region and the lack of change in AtRAP2.2 protein levels in lines strongly overexpressing the AtRAP2.2 transcript. Homozygous loss-of-function mutants could not be obtained for the AtRAP2.2 5′ untranslated region T-DNA insertion line indicating a lethal phenotype. In AtRAP2.2 overexpression lines, modest changes in phytoene synthase and phytoene desaturase transcripts were only observed in root-derived calli, which consequently showed a reduction in carotenoid content. The RING finger protein SEVEN IN ABSENTIA OF ARABIDOPSIS2 (SINAT2) was identified as an AtRAP2.2 interaction partner using a two-hybrid approach. The structure of SINAT2 and related proteins of Arabidopsis show homology to the SEVEN IN ABSENTIA protein of Drosophila that is involved in proteasome-mediated regulation in a variety of developmental processes. The action of SINAT2 may explain the recalcitrance of AtRAP2.2 protein levels to change by altering AtRAP2.2 transcription.
Vitamer Levels, Stress Response, Enzyme Activity, and Gene Regulation of Arabidopsis Lines Mutant in the Pyridoxine/Pyridoxamine 5′-Phosphate Oxidase (PDX3) and the Pyridoxal Kinase (SOS4) Genes Involved in the Vitamin B6 Salvage Pathway
Authors: González Eugenia , Danehower David , Daub Margaret E. 
Published: September 2007

Abstract
PDX3 and SALT OVERLY SENSITIVE4 (SOS4), encoding pyridoxine/pyridoxamine 5′-phosphate oxidase and pyridoxal kinase, respectively, are the only known genes involved in the salvage pathway of pyridoxal 5′-phosphate in plants. In this study, we determined the phenotype, stress responses, vitamer levels, and regulation of the vitamin B6 pathway genes in Arabidopsis (Arabidopsis thaliana) plants mutant in PDX3 and SOS4. sos4 mutant plants showed a distinct phenotype characterized by chlorosis and reduced plant size, as well as hypersensitivity to sucrose in addition to the previously noted NaCl sensitivity. This mutant had higher levels of pyridoxine, pyridoxamine, and pyridoxal 5′-phosphate than the wild type, reflected in an increase in total vitamin B6 observed through HPLC analysis and yeast bioassay. The sos4 mutant showed increased activity of PDX3 as well as of the B6 de novo pathway enzyme PDX1, correlating with increased total B6 levels. Two independent lines with T-DNA insertions in the promoter region of PDX3 (pdx3-1 and pdx3-2) had decreased PDX3 activity. Both also had decreased activity of PDX1, which correlated with lower levels of total vitamin B6 observed using the yeast bioassay; however, no differences were noted in levels of individual vitamers by HPLC analysis. Both pdx3 mutants showed growth reduction in vitro and in vivo as well as an inability to increase growth under high light conditions. Increased expression of salvage and some of the de novo pathway genes was observed in both the pdx3 and sos4 mutants. In all mutants, increased expression was more dramatic for the salvage pathway genes.
TheArabidopsisBEL1-LIKE HOMEODOMAIN Proteins SAW1 and SAW2 Act Redundantly to RegulateKNOXExpression Spatially in Leaf Margins
Authors: Kumar Ravi , Kushalappa Kumuda , Godt Dietmute , Pidkowich Mark S. , Pastorelli Sandro , Hepworth Shelley R. , Haughn George W. 
Published: September 2007

AbstractIn Arabidopsis thaliana, the BEL1-like TALE homeodomain protein family consists of 13 members that form heterodimeric complexes with the Class 1 KNOX TALE homeodomain proteins, including SHOOTMERISTEMLESS (STM) and BREVIPEDICELLUS (BP). The BEL1-like protein BELLRINGER (BLR) functions together with STM and BP in the shoot apex to regulate meristem identity and function and to promote correct shoot architecture. We have characterized two additional BEL1-LIKE HOMEODOMAIN (BLH) proteins, SAWTOOTH1 (BLH2/SAW1) and SAWTOOTH2 (BLH4/SAW2) that, in contrast with BLR, are expressed in lateral organs and negatively regulate BP expression. saw1 and saw2 single mutants have no obvious phenotype, but the saw1 saw2 double mutant has increased leaf serrations and revolute margins, indicating that SAW1 and SAW2 act redundantly to limit leaf margin growth. Consistent with this hypothesis, overexpression of SAW1 suppresses overall growth of the plant shoot. BP is ectopically expressed in the leaf serrations of saw1 saw2 double mutants. Ectopic expression of Class 1 KNOX genes in leaves has been observed previously in loss-of-function mutants of ASYMMETRIC LEAVES (AS1). Overexpression of SAW1 in an as1 mutant suppresses the as1 leaf phenotype and reduces ectopic BP leaf expression. Taken together, our data suggest that BLH2/SAW1 and BLH4/SAW2 establish leaf shape by repressing growth in specific subdomains of the leaf at least in part by repressing expression of one or more of the KNOX genes.