bluuebunny/crossref_metadata_2025 huggingface dataset:
Vascular Endothelial Growth Factor Is Required for Coronary Collateral Growth in the Rat
Authors: Toyota Eiji , Warltier David C. , Brock Tommy , Ritman Erik , Kolz Christopher , O’Malley Peter , Rocic Petra , Focardi Marta , Chilian William M.
Published: October 2005

Background—

The goal of this study was to determine whether the expression of vascular endothelial growth factor (VEGF) is critical for coronary collateral growth. Previous studies have provided an association between coronary collateral growth and VEGF, but none have allowed determination of a causal role.

Methods and Results—

We measured coronary collateral growth in rats subjected to repetitive episodes of myocardial ischemia (RI; one 40-second occlusion every 20 minutes for 2 hours 40 minutes, followed by 5 hours 20 minutes of rest, with this 8-hour cycle repeated 3 times per day for 10 days). Collateral growth was measured from blood flow (radioactive microspheres), visualization of arterial-arterial anastomoses (x-ray micro-CT), and maintenance of function during complete coronary occlusion in 3 groups of animals: sham (received instrumentation but no RI), experimental (subjected to RI), and anti–vascular endothelial growth factor (RI+anti-VEGF 0.6 mg/100 g per day) to block the endogenous actions of VEGF. In the 3 groups, native collateral flow (measurement for RI or sham protocol) averaged 0.2 to 0.3 mL · min
−1
· g
−1
of tissue. In the sham group, collateral flow did not increase during the protocol. Collateral flow in the control RI group increased by ≈6-fold to 1.63 mL · min
−1
· g
−1
tissue, but in the anti-VEGF group, collateral flow did not increase after the RI protocol (0.22 mL · min
−1
· g
−1
). In acute experiments, collateral flow was unchanged during vasodilation with dipyridamole, indicating the increases in collateral flow are due to collateral growth and not vasodilation. X-ray micro-CT analysis revealed a 3-fold increase (versus sham group) in the number of arterial-arterial anastomoses per heart after RI, which was prevented by treatment with anti-VEGF. The growth of the collateral circulation was functional in the RI group because complete coronary occlusion did not induce any untoward effects on hemodynamics or arrhythmias. In the sham or anti-VEGF groups, coronary occlusion at the end of the protocol induced many arrhythmias and deterioration of function.

Conclusions—

From these results, we conclude that the expression of VEGF is critical to the growth of coronary collaterals.
No Replication of Association Between Estrogen Receptor α Gene Polymorphisms and Susceptibility to Myocardial Infarction in a Large Sample of Patients of European Descent
Authors: Koch Werner , Hoppmann Petra , Pfeufer Arne , Mueller Jakob C. , Schömig Albert , Kastrati Adnan
Published: October 2005

Background—

The effects of estrogen on blood vessels are partly due to changes in vascular cell gene expression and protein synthesis that are mediated by estrogen receptors. In previous association studies, the −397T/C (rs2234693) and −351A/G (rs9340799) single nucleotide polymorphisms in the estrogen receptor α gene (
ESR1
) have been implicated in the risk of coronary atherosclerosis and myocardial infarction. To test these findings, we examined the relationship of the polymorphisms to myocardial infarction in a large sample of white patients and control individuals of predominantly European descent.

Methods and Results—

The case group included 3657 patients with myocardial infarction, and the control group comprised 1211 individuals with angiographically normal coronary arteries and without signs or symptoms of myocardial infarction. TaqMan assays were used for the determination of genotypes. Genotype distributions of the −397T/C and −351A/G polymorphisms were not significantly different between the control and patient groups (
P
≥0.85). The frequencies of haplotypes defined by the −397T/C and −351A/G polymorphisms were similar in the control group and the patient group (
P
=0.42). In addition, the distributions of haplotype-defined genotypes (diplotypes) were not significantly different between the control group and the patient group (
P
=0.81). Separate analyses in women and men did not reveal sex-related associations of specific genotypes or haplotypes of the polymorphisms with myocardial infarction (
P
≥0.25).

Conclusions—

The results indicate that the −397T/C and −351A/G polymorphisms of
ESR1
or haplotypes based on these polymorphisms are not associated with myocardial infarction in a white population.
Comparing Knowledge Sources for Nominal Anaphora Resolution
Authors: Markert Katja , Nissim Malvina
Published: September 2005

We compare two ways of obtaining lexical knowledge for antecedent selection in other-anaphora and definite noun phrase coreference. Specifically, we compare an algorithm that relies on links encoded in the manually created lexical hierarchy WordNet and an algorithm that mines corpora by means of shallow lexico-semantic patterns. As corpora we use the British National Corpus (BNC), as well as the Web, which has not been previously used for this task. Our results show that (a) the knowledge encoded in WordNet is often insufficient, especially for anaphor' antecedent relations that exploit subjective or context-dependent knowledge; (b) for other-anaphora, the Web-based method outperforms the WordNet-based method; (c) for definite NP coreference, the Web-based method yields results comparable to those obtained using WordNet over the whole data set and outperforms the WordNet-based method on subsets of the data set; (d) in both case studies, the BNC-based method is worse than the other methods because of data sparseness. Thus, in our studies, the Web-based method alleviated the lexical knowledge gap often encountered in anaphora resolution and handled examples with context-dependent relations between anaphor and antecedent. Because it is inexpensive and needs no hand-modeling of lexical knowledge, it is a promising knowledge source to integrate into anaphora resolution systems.
Large-Scale Induction and Evaluation of Lexical Resources from the Penn-II and Penn-III Treebanks
Authors: O'Donovan Ruth , Burke Michael , Cahill Aoife , Genabith Josef van , Way Andy
Published: September 2005

We present a methodology for extracting subcategorization frames based on an automatic lexical-functional grammar (LFG) f-structure annotation algorithm for the Penn-II and Penn-III Treebanks. We extract syntactic-function-based subcategorization frames (LFG semantic forms) and traditional CFG category-based subcategorization frames as well as mixed function/category-based frames, with or without preposition information for obliques and particle information for particle verbs. Our approach associates probabilities with frames conditional on the lemma, distinguishes between active and passive frames, and fully reflects the effects of long-distance dependencies in the source data structures. In contrast to many other approaches, ours does not predefine the subcategorization frame types extracted, learning them instead from the source data. Including particles and prepositions, we extract 21,005 lemma frame types for 4,362 verb lemmas, with a total of 577 frame types and an average of 4.8 frame types per verb. We present a large-scale evaluation of the complete set of forms extracted against the full COMLEX resource. To our knowledge, this is the largest and most complete evaluation of subcategorization frames acquired automatically for English.
Sentence Fusion for Multidocument News Summarization
Authors: Barzilay Regina , McKeown Kathleen R.
Published: September 2005

A system that can produce informative summaries, highlighting common information found in many online documents, will help Web users to pinpoint information that they need without extensive reading. In this article, we introduce sentence fusion, a novel text-to-text generation technique for synthesizing common information across documents. Sentence fusion involves bottom-up local multisequence alignment to identify phrases conveying similar information and statistical generation to combine common phrases into a sentence. Sentence fusion moves the summarization field from the use of purely extractive methods to the generation of abstracts that contain sentences not found in any of the input documents and can synthesize information across sources.
The Effect of NMDA Receptors on Gain Modulation
Authors: Berends Michiel , Maex Reinoud , Schutter Erik De
Published: September 2005

The ability of individual neurons to modulate the gain of their input-output function is important for information processing in the brain. In a recent study (Mitchell & Silver, 2003), shunting inhibition was found to modulate the gain of cerebellar granule cells subjected to simulated currents through AMPA receptor synapses. Here we investigate the effect on gain modulation resulting from adding the currents mediated by NMDA receptors to a compartmental model of the granule cell. With only AMPA receptors, the changes in gain induced by shunting inhibition decreased gradually with the average firing rate of the afferent mossy fibers. With NMDA receptors present, this decrease was more rapid, therefore narrowing the bandwidth of mossy fiber firing rates available for gain modulation. The deterioration of gain modulation was accompanied by a reduced variability of the input current and saturation of NMDA receptors. However, when the output of the granule cell was plotted as a function of the average input current instead of the input firing frequency, both models showed very similar response curves and comparable gain modulation. We conclude that NMDA receptors do not directly impair gain control by shunting inhibition, but the effective bandwidth decreases as a consequence of the increased total charge transfer.
Learning Curves for Stochastic Gradient Descent in Linear Feedforward Networks
Authors: Werfel Justin , Xie Xiaohui , Seung H. Sebastian
Published: September 2005

Gradient-following learning methods can encounter problems of implementation in many applications, and stochastic variants are sometimes used to overcome these difficulties. We analyze three online training methods used with a linear perceptron: direct gradient descent, node perturbation, and weight perturbation. Learning speed is defined as the rate of exponential decay in the learning curves. When the scalar parameter that controls the size of weight updates is chosen to maximize learning speed, node perturbation is slower than direct gradient descent by a factor equal to the number of output units; weight perturbation is slower still by an additional factor equal to the number of input units. Parallel perturbation allows faster learning than sequential perturbation, by a factor that does not depend on network size. We also characterize how uncertainty in quantities used in the stochastic updates affects the learning curves. This study suggests that in practice, weight perturbation may be slow for large networks, and node perturbation can have performance comparable to that of direct gradient descent when there are few output units. However, these statements depend on the specifics of the learning problem, such as the input distribution and the target function, and are not universally applicable.
A Robust Information Clustering Algorithm
Authors: Song Qing
Published: September 2005

We focus on the scenario of robust information clustering (RIC) based on the minimax optimization of mutual information (MI). The minimization of MI leads to the standard mass-constrained deterministic annealing clustering, which is an empirical risk-minimization algorithm. The maximization of MI works out an upper bound of the empirical risk via the identification of outliers (noisy data points). Furthermore, we estimate the real risk VC-bound and determine an optimal cluster number of the RIC based on the structural risk-minimization principle. One of the main advantages of the minimax optimization of MI is that it is a nonparametric approach, which identifies the outliers through the robust density estimate and forms a simple data clustering algorithm based on the square error of the Euclidean distance.
Incremental Online Learning in High Dimensions
Authors: Vijayakumar Sethu , D'Souza Aaron , Schaal Stefan
Published: September 2005

Locally weighted projection regression (LWPR) is a new algorithm for incremental nonlinear function approximation in high-dimensional spaces with redundant and irrelevant input dimensions. At its core, it employs nonparametric regression with locally linear models. In order to stay computationally efficient and numerically robust, each local model performs the regression analysis with a small number of univariate regressions in selected directions in input space in the spirit of partial least squares regression. We discuss when and how local learning techniques can successfully work in high-dimensional spaces and review the various techniques for local dimensionality reduction before finally deriving the LWPR algorithm. The properties of LWPR are that it (1) learns rapidly with second-order learning methods based on incremental training, (2) uses statistically sound stochastic leave-one-out cross validation for learning without the need to memorize training data, (3) adjusts its weighting kernels based on only local information in order to minimize the danger of negative interference of incremental learning, (4) has a computational complexity that is linear in the number of inputs, and (5) can deal with a large number of—possibly redundant—inputs, as shown in various empirical evaluations with up to 90 dimensional data sets. For a probabilistic interpretation, predictive variance and confidence intervals are derived. To our knowledge, LWPR is the first truly incremental spatially localized learning method that can successfully and efficiently operate in very high-dimensional spaces.
Information Geometry of Interspike Intervals in Spiking Neurons
Authors: Ikeda Kazushi
Published: September 2005

An information geometrical method is developed for characterizing or classifying neurons in cortical areas, whose spike rates fluctuate in time. Under the assumption that the interspike intervals of a spike sequence of a neuron obey a gamma process with a time-variant spike rate and a fixed shape parameter, we formulate the problem of characterization as a semiparametric statistical estimation, where the spike rate is a nuisance parameter. We derive optimal criteria from the information geometrical viewpoint when certain assumptions are added to the formulation, and we show that some existing measures, such as the coefficient of variation and the local variation, are expressed as estimators of certain functions under the same assumptions.
A Systematic, Reliable Approach to Play Assessment in Preschoolers
Authors: Kelly-Vance Lisa , Ryalls Brigette Oliver
Published: October 2005

Play assessment is gaining attention as a measure of the developing skills of young children. The procedures and methods of coding child behaviours vary considerably across researchers and practitioners. Because of this, definitive statements about the use of play assessment cannot be made without further research. The present study is an attempt to report a set of standardized procedures for play assessment along with an empirically based coding scheme (PIECES). The reliability of this system of play assessment is also investigated. High inter-observer reliability was found along with moderate test-retest correlations for both the typically developing ( r = 0.48) and exceptional ( r = 0.58) children. Thus, this version of play assessment holds promise as an observation system for intervention and progress monitoring in early childhood. The authors stress that more research is needed in this area before play assessment can either be used in early childhood or discounted as an inappropriate tool.
Parents’ Experiences of Their Rights in the Implementation of Inclusive Education in South Africa
Authors: Engelbrecht Petra , Oswald Marietjie , Swart Estelle , Kitching Ansie , Eloff Irma
Published: October 2005

Parental involvement was a driving and decisive factor in the development of inclusive education worldwide. In South Africa parents also became the advocates of the inclusive education movement in the 1990s, paving the way for parents to be involved in the decision-making process regarding the school placement of their children with disabilities. The purpose of this article is to focus on the way in which equity, individual rights and freedom of choice manifest itself in the implementation of inclusive education with specific reference to the way in which parents experience it. Results indicate that the inclusion of a child into mainstream education is a challenging and dynamic process that starts with the parents’ decision to place their child in a mainstream setting. In spite of legislation and the desires of parents, the development of inclusive educational practises in South Africa does not always reflect the values of equity and individual rights. Failure to establish collaborative and trusting relationships between teachers, parents and professionals poses a major challenge and can have a serious impact on the outcomes of inclusive education.
Between Global and Local: Eight European Works Councils in Retrospect and Prospect
Authors: Huzzard Tony , Docherty Peter
Published: October 2005

This article reports on case studies of eight Swedish-based European Works Councils (EWCs) with a particular focus on impacts and outcomes. Three issues are explored: (1) the benefits of EWCs from both employee and management perspectives; (2) whether the EWCs have evolved as genuine forums for information, consultation and negotiation; and (3) the effects of EWCs on industrial relations systems - specifically whether their evolution signals a unified, convergent mode of industrial relations engagement at the European level. The authors conclude that there are few prospects for convergence or transnational bargaining, and that distinct national practices will persist, not only because of opposition from employers but also, and perhaps surprisingly, because of opposition from union quarters in Scandinavia.
A Community-Based Program to Encourage Patients’ Attention to Their Own Diabetes Care
Authors: Polonsky William H. , Zee Julia , Yee Martha Ah , Crosson Mary Ann , Jackson Richard A.
Published: October 2005

Purpose

The authors evaluated the ability of a brief educational program to enhance patients’ self-care behavior and their familiarity with the meaning and utility of 5 of the major clinical tests in diabetes (A1C, blood pressure, low-density lipoprotein [LDL] cholesterol, microalbumin, and the dilated eye examination).

Methods

Adults with type 1 or type 2 diabetes were invited to attend a free, 90-minute, small-group workshop about diabetes care, which included on-site metabolic testing that provided patients with immediate results and personalized feedback to understand those results. In total, 221 individuals with diabetes participated and completed baseline and 3-month follow-up questionnaires.

Results

From baseline to 3 months, participants reported significant improvement in following recommendations for meal planning (P < .001), regular exercise (P < .002), and blood glucose monitoring (P < .05) and a significant rise in test awareness for A1C, blood pressure, LDL cholesterol, and microalbumin (in all cases, P < .001).

Conclusions

A brief educational intervention appeared effective in encouraging patients toward better self-management and more regular metabolic testing and to become more aware of their own test results. Future research should aim to replicate and extend these findings in a randomized controlled trial.
'Masculinity-Femininity: An Exception to a Famous Dictum?'
Authors: Constantinople Anne
Published: October 2005

The major tests of masculinity-femininity (M-F) in adults are reviewed with special attention to the ways in which their construction and use reflect three untested assumptions about the nature of the M-F construct: (a) that it is best defined in terms of sex differences in item responses; (b) that it is a single bipolar dimension ranging from extreme masculinity at one end to extreme femininity at the other; and (c) that it is unidimensional in nature and can be adequately measured by a single score. Evidence which questions the validity of these assumptions and, therefore, of the tests of M-F is presented, with the conclusion that further theoretical and empirical work is necessary in all aspects of the problem.
Philosophical foundations of computer simulation validation
Authors: Klein Esther E. , Herskovitz Paul J.
Published: October 2005

Innovations in information technology (IT) have been responsible for the rapid growth of computer simulation, which in turn has encouraged IT innovation. However, there is a striking contrast between the technological sophistication that drives and is driven by computer simulation and the rudimentary, underdeveloped state of theory underpinning the simulation endeavor. This article attempts to provide computer simulation with a theoretical framework by the application of philosophy of science to simulation validation. The authors discuss the key elements of Popper’s theory of falsification and explore how simulation validation is in fact anchored to Popper’s theory. Moreover, this article suggests that a Popperian perspective encourages the review of a validated model’s continuing validity, thereby potentially leading to the construction of a new, improved model. Finally, we contrast Popper’s falsificationist philosophy of science with Quine’s philosophical system of holism and early-period Putnam’s scientific realism, both of which discourage the building of better models.
Enhancing environmental awareness: Ecological and economic effects of food consumption
Authors: Hansmann Ralf , Scholz Roland W. , Francke Carl-Johan A. C. , Weymann Martin
Published: October 2005

The authors developed SIMULME, an Internet-based simulation game of the environmental and economic consequences of food consumption, to improve environmental knowledge, attitudes, and behaviors of individuals. The game was first applied with 215 pupils divided into 12 classes. Six classes were taught the consequences of food consumption using the learning game (experimental condition) and 6 using a standard lecture (control condition). Positive changes in environmental attitudes concerning nutrition behavior were more marked in the experimental than in the control condition. An additional experiment tested the game’s effects on subsequent buying behavior. After playing the game (experimental) or not (control), participants entered the nutrition section of the online shop of the Swiss retailer Coop with the possibility of winning a purchase worth CHF 40. The consumption pattern of those who played SIMULME was ecologically more positive than that of the control participants. Aspects of game validity and game design are discussed with respect to the effectiveness of games for environmental education.
Ready-to-use-simulation: THE SLIPPERY SLOPE©
Authors: Teach Richard D. , Christensen Sandra L. , Schwartz Robert G.
Published: October 2005

The purpose of THE SLIPPERY SLOPE© is to expose participants to a complex process of how individuals and firms deal with ethical issues in business. This experiential game is being developed as a response to continued corporate unethical and often illegal decision making, coupled with perceptions that there is increased cheating in schools across the United States.
Teaching autonomy
Authors: Railton Diane , Watson Paul
Published: October 2005

A key factor in the transition to university is the enculturation of new students into both the discipline they are studying and effective study practices. Most significantly, students, whatever their chosen discipline, must learn to become autonomous learners. Too often this process is either left to chance or seen as a natural attribute of the higher education learning system rather than a particular skill that must be learnt and can be taught. In this article we discuss one particular approach to designing ‘structured autonomy’ into a first year core media studies module. We argue that the notion of autonomy needs to be considered as a central component of learning, teaching and assessment strategies and, moreover, that an integrated approach towards these factors has the additional benefit of contributing towards a more holistic first year experience for students.
Academic achievement
Authors: Maclellan Effie
Published: October 2005

The motivation of students is an important issue in higher education, particularly in the context of the increasing diversity of student populations. A social-cognitive perspective assumes motivation to be dynamic, context-sensitive and changeable, thereby rendering it to be a much more differentiated construct than previously understood. This complexity may be perplexing to tutors who are keen to develop applications to improve academic achievement. One application that is within the control of the tutor, at least to some extent, is the use of praise. Using psychological literature, the article argues that in motivating students, the tutor is not well served by relying on simplistic and common sense understandings of the construct of praise and that effective applications of praise are mediated by students’ goal orientations, which of themselves may be either additive or interactive composites of different objectives and different contexts.
Managing the transition into higher education
Authors: Laing Christopher , Robinson Alan , Johnston Veronique
Published: October 2005

In helping students manage the transition into higher education, there must be (i) an understanding of the needs and expectations of the students, and (ii) a process that inducts the students into the needs and expectations of higher education. This premise underpins the on-line Spiral Induction Programme (onSIP) developed at Southampton Institute. onSIP consists of various on-line activities designed to help students take responsibility for their own learning; feedback from these activities enables both staff and students to identify if and what additional support is required. The intention was to provide a real-time analysis and indication of those students who may be ‘at risk’, allowing for the appropriate targeting of timely support. Initial results indicate a positive reaction by the students to onSIP. In addition, the predictive feedback from onSIP demonstrates a good correlation with the end-of-year outcomes for a cohort of technology students at Southampton Institute.
Navigating justice in practice
Authors: Cribb Alan , Gewirtz Sharon
Published: October 2005

This article is an attempt to make an empirical contribution to a more grounded model of thinking about justice. It focuses on the work of one practitioner working in an inner-London local education authority with a remit relating to the achievement of ‘African-Caribbean’ students. In describing the challenges that she faces in the course of her work and how she responds to them, we want to illuminate the contribution that this kind of practice-focused analysis can make to understandings of what social justice is, how tensions in social justice arise, and how they might be responded to.
Human agency and the curriculum
Authors: Alexander Hanan A.
Published: October 2005

It is generally supposed that a curriculum should engage students with worthwhile knowledge, which requires an understanding of what it means for something to be worthwhile: a substantive conception of the good. Yet a number of influential curriculum theories deny or undermine one or another aspect of the key assumption upon which a meaningful account of the good depends - that people are the agents of their own beliefs, desires and actions. This renders a significant encounter between the curriculum and substantive ethics highly problematic. In this article I explore the meeting between curriculum and human agency in four seminal curriculum theories, and offer a framework to engage the curriculum with this key concept of substantive ethics.
Functional analysis of HGF/MET signaling and aberrant HGF-activator expression in diffuse large B-cell lymphoma
Authors: Tjin Esther P. M. , Groen Richard W. J. , Vogelzang Irma , Derksen Patrick W. B. , Klok Melanie D. , Meijer Helen P. , van Eeden Susanne , Pals Steven T. , Spaargaren Marcel
Published: September 2005

Inappropriate activation of MET, the receptor tyrosine kinase for hepatocyte growth factor (HGF), has been implicated in tumorigenesis. Although we have previously shown that HGF/MET signaling controls survival and proliferation of multiple myeloma (MM), its role in the pathogenesis of other B-cell malignancies has remained largely unexplored. Here, we have examined a panel of 110 B-cell malignancies for MET expression, which, apart from MM (48%), was found to be largely confined to diffuse large B-cell lymphomas (DLBCLs) (30%). No amplification of the MET gene was found; however, mutational analysis revealed 2 germ-line missense mutations: R1166Q in the tyrosine kinase domain in 1 patient, and R988C in the juxtamembrane domain in 4 patients. The R988C mutation has recently been shown to enhance tumorigenesis. In MET-positive DLBCL cells, HGF induces MEK-dependent activation of ERK and PI3K-dependent phosphorylation of PKB, GSK3, and FOXO3a. Furthermore, HGF induces PI3K-dependent α4β1 integrin-mediated adhesion to VCAM-1 and fibronectin. Within the tumor microenvironment of DLBCL, HGF is provided by macrophages, whereas DLBCL cells themselves produce the serine protease HGF activator (HGFA), which autocatalyzes HGF activation. Taken together, these data indicate that HGF/MET signaling, and secretion of HGFA by DLBCL cells, contributes to lymphomagenesis in DLBCL. (Blood. 2006;107:760-768)
Redundant roles of VEGF-B and PlGF during selective VEGF-A blockade in mice
Authors: Malik Ajay K. , Baldwin Megan E. , Peale Franklin , Fuh Germaine , Liang Wei-Ching , Lowman Henry , Meng Gloria , Ferrara Napoleone , Gerber Hans-Peter
Published: September 2005

Vascular endothelial growth factor-A (VEGF-A) and its 2 transmembrane tyrosine-kinase receptors, VEGFR-1 and VEGFR-2, constitute a ligand-receptor signaling system that is crucial for developmental angiogenesis. VEGF-B and placental growth factor (PlGF) activate VEGFR-1 selectively, however, mice lacking either ligand display only minor developmental defects. We hypothesized that the relative contributions of VEGF-B and PlGF to VEGFR-1 signaling may be masked in the presence of VEGF-A, which is abundantly expressed during postnatal development. To test this hypothesis, neonatal or adult mice were treated with a monoclonal antibody (G6-23-IgG) blocking murine VEGF-A or a soluble VEGFR-1 receptor IgG chimeric construct [mFlt(1-3)-IgG], which neutralizes VEGF-A, VEGF-B, and PlGF. Both compounds attenuated growth and survival of neonatal mice to similar extents and the pathophysiologic alterations, including a reduction in organ size and vascularization, changes in gene expression, and hematologic end points, were essentially indistinguishable. In adult mice, we observed only minor changes in response to treatment, which were similar between both anti-VEGF compounds. In conclusion, our findings suggest that PlGF and VEGF-B do not compensate during conditions of VEGF-A blockade, suggesting a minor role for compensatory VEGFR-1 signaling during postnatal development and vascular homeostasis in adults. The absence of compensatory VEGFR-1 signaling by VEGF-B and PlGF may have important implications for the development of anticancer strategies targeting the VEGF ligand/receptor system.
Deletion of the core region of 5′ HS2 of the mouse β-globin locus control region reveals a distinct effect in comparison with human β-globin transgenes
Authors: Hu Xiao , Bulger Michael , Bender M. A. , Fields Jennifer , Groudine Mark , Fiering Steven
Published: September 2005

The β-globin locus control region (LCR) is a large DNA element that is required for high-level expression of β-like globin genes from the endogenous mouse locus or in transgenic mice carrying the human β-globin locus. The LCR encompasses 6 DNaseI hypersensitive sites (HSs) that bind transcription factors. These HSs each contain a core of a few hundred base pairs (bp) that has most of the functional activity and exhibits high interspecies sequence homology. Adjoining the cores are 500- to 1000-bp “flanks” with weaker functional activity and lower interspecies homology. Studies of human β-globin transgenes and of the endogenous murine locus show that deletion of an entire HS (core plus flanks) moderately suppresses expression. However, human transgenes in which only individual HS core regions were deleted showed drastic loss of expression accompanied by changes in chromatin structure. To address these disparate results, we have deleted the core region of 5′HS2 from the endogenous murine β-LCR. The phenotype was similar to that of the larger 5′HS2 deletion, with no apparent disruption of chromatin structure. These results demonstrate that the greater severity of HS core deletions in comparison to full HS deletions is not a general property of the β-LCR. (Blood. 2006;107:821-826)
Inducible platelet-derived growth factor D-chain expression by angiotensin II and hydrogen peroxide involves transcriptional regulation by Ets-1 and Sp1
Authors: Liu Mary Yanxia , Eyries Melanie , Zhang Chunyan , Santiago Fernando S. , Khachigian Levon M.
Published: September 2005

Platelet-derived growth factor D-chain (PDGF-D) is the newest member of the PDGF family of mitogens and chemoattractants expressed in a wide variety of cell types, including vascular smooth muscle cells (SMCs). The molecular mechanisms regulating PDGF-D transcription are not known. Primer extension analysis mapped a single transcriptional start site to the ccAGCGC motif with several potential Ets motifs located upstream. Ets-1, but not Ets-1 bearing only the DNA-binding domain, activates the PDGF-D promoter and mRNA expression in SMCs. Ets site D3 (–470GGAT–467) is singly required for basal and Ets-1–inducible PDGF-D promoter-dependent expression. D3 supports the interaction of endogenous and recombinant Ets-1 and Sp1. Sp1, like Ets-1, induces PDGF-D transcription and mRNA expression, which is blocked by mutant Ets-1. H2O2 stimulates Ets-1, but not Sp1, and activates D3-dependent PDGF-D transcription. Ets-1 and Sp1 siRNA block peroxide-inducible PDGF-D expression. Angiotensin II (ATII) induction of PDGF-D and Ets-1 was blocked by prior incubation of the cells with PEG-catalase, but not BSA, indicating that ATII-inducible Ets-1 and PDGF-D expression is mediated via H2O2. Thus, 2 separate trans-acting factors regulate PDGF-D transcription, alone and in response to oxidative stress.
Elevated levels of homocysteine compromise blood-brain barrier integrity in mice
Authors: Kamath Atul F. , Chauhan Anil K. , Kisucka Janka , Dole Vandana S. , Loscalzo Joseph , Handy Diane E. , Wagner Denisa D.
Published: September 2005

Elevated levels of plasma homocysteine (Hcy) correlate with increased risk of cardiovascular and Alzheimer diseases. We studied the effect of elevated Hcy on the blood-brain barrier (BBB) to explore the possibility of a vascular link between the 2 diseases. On a hyperhomocysteinemic diet, cystathionine beta-synthase (Cbs)–heterozygous mice develop hyperhomocysteinemia. Intravital microscopy analysis of the mesenteric venules showed that leukocyte rolling velocity was markedly decreased and numbers of adherent cells were increased in the mutant mice. This was due at least in part to increased expression of P-selectin. BBB permeability was measured by Evans blue dye permeation and was found to be 25% greater in the Cbs+/– cortex compared with wild-type controls. Our study suggests an important toxic effect of elevated Hcy on brain microvessels and implicates Hcy in the disruption of the BBB.
Amphotericin B blunts erythropoietin response to hypoxia by reinforcing FIH-mediated repression of HIF-1
Authors: Yeo Eun-Jin , Ryu Ji-Hye , Cho Young-Suk , Chun Yang-Sook , Huang L. Eric , Kim Myung-Suk , Park Jong-Wan
Published: September 2005

Amphotericin B (AmB) is widely used for treating severe systemic fungal infections. However, long-term AmB treatment is invariably associated with adverse effects such as anemia. The erythropoietin (EPO) suppression by AmB has been proposed to contribute to the development of anemia. However, the mechanism whereby EPO is suppressed remains obscure. In this study, we investigated the possibility that AmB inhibits the transcription of the EPO gene by inactivating HIF-1, which is a known key transcription factor and regulator of EPO expression. EPO mRNA levels were markedly attenuated by AmB treatment both in rat kidneys and in Hep3B cells. AmB inactivated the transcriptional activity of HIF-1α, but did not affect the expression or localization of HIF-1 subunits. Moreover, AmB was found to specifically repress the C-terminal transactivation domain (CAD) of HIF-1α, and this repression by AmB required Asn803, a target site of the factor-inhibiting HIF-1 (FIH); moreover, this repressive effect was reversed by FIH inhibitors. Furthermore, AmB stimulated CAD-FIH interaction and inhibited the p300 recruitment by CAD. We propose that this mechanism underlies the unexplained anemia associated with AmB therapy.
PKC412 inhibits in vitro growth of neoplastic human mast cells expressing the D816V-mutated variant of KIT: comparison with AMN107, imatinib, and cladribine (2CdA) and evaluation of cooperative drug effects
Authors: Gleixner Karoline V. , Mayerhofer Matthias , Aichberger Karl J. , Derdak Sophia , Sonneck Karoline , Böhm Alexandra , Gruze Alexander , Samorapoompichit Puchit , Manley Paul W. , Fabbro Doriano , Pickl Winfried F. , Sillaber Christian , Valent Peter
Published: September 2005

In most patients with systemic mastocytosis (SM), including aggressive SM and mast cell leukemia (MCL), neoplastic cells express the oncogenic KIT mutation D816V. KIT D816V is associated with constitutive tyrosine kinase (TK) activity and thus represents an attractive drug target. However, imatinib and most other TK inhibitors fail to block the TK activity of KIT D816V. We show that the novel TK-targeting drugs PKC412 and AMN107 counteract TK activity of D816V KIT and inhibit the growth of Ba/F3 cells with doxycycline-inducible expression of KIT D816V as well as the growth of primary neoplastic mast cells and HMC-1 cells harboring this KIT mutation. PKC412 was a superior agent with median inhibitory concentration (IC50) values of 50 to 250 nM without differences seen between HMC-1 cells exhibiting or lacking KIT D816V. By contrast, AMN107 exhibited more potent effects in KIT D816V- HMC-1 cells. Corresponding results were obtained with Ba/F3 cells exhibiting wild-type or D816V-mutated KIT. The growth-inhibitory effects of PKC412 and AMN107 on HMC-1 cells were associated with induction of apoptosis and down-regulation of CD2 and CD63. PKC412 was found to cooperate with AMN107, imatinib, and cladribine (2CdA) in producing growth inhibition in HMC-1, but synergistic drug interactions were observed only in cells lacking KIT D816V. Together, PKC412 and AMN107 represent promising novel agents for targeted therapy of SM. (Blood. 2006;107: 752-759)
The definition of anemia: what is the lower limit of normal of the blood hemoglobin concentration?
Authors: Beutler Ernest , Waalen Jill
Published: September 2005

The diagnosis of anemia is an important aspect of the practice of hematology. The first step is to decide whether the patient is, in fact, anemic. Unless earlier blood counts are available, and they often are not, the physician must make his or her decision on the basis of the population distribution of hemoglobin values. How likely is it that the patient's hemoglobin value lies below the normal distribution; that is, “the lower limit”?
Methodological modifications on quantification of phosphatidylethanol in blood from humans abusing alcohol, using high-performance liquid chromatography and evaporative light scattering detection
Authors: Aradottir Steina , Olsson Bo L
Published: September 2005

Background

Phosphatidylethanol (PEth) is an abnormal phospholipid formed slowly in cell membranes by a transphosphatidylation reaction from phosphatidylcholine in the presence of ethanol and catalyzed by the enzyme phospholipase D. PEth in blood is a promising new marker of ethanol abuse depending on the high specificity and sensitivity of this marker. None of the biological markers used in clinical routine at the present time are sensitive and specific enough for the diagnosis of alcohol abuse.

The method for PEth analysis includes lipid extraction of whole blood, a one-hour HPLC separation of lipids and ELSD (evaporative light scattering) detection of PEth.

Results

Methodological improvements are presented which comprise a simpler extraction procedure, the use of phosphatidylbutanol as internal standard and a new algorithm for evaluation of unknown samples. It is further demonstrated that equal test results are obtained with blood collected in standard test tubes with EDTA as with the previously used heparinized test tubes. The PEth content in blood samples is stable for three weeks in the refrigerator.

Conclusion

Methodological changes make the method more suitable for routine laboratory use, lower the limit of quantification (LOQ) and improve precision.
An analysis of extensible modelling for functional genomics data
Authors: Jones Andrew R , Paton Norman W
Published: September 2005

Background

Several data formats have been developed for large scale biological experiments, using a variety of methodologies. Most data formats contain a for allowing extensions to encode unanticipated data types. Extensions to data formats are important because the experimental methodologies tend to be fairly diverse and rapidly evolving, which hinders the creation of formats that will be stable over time.

Results

In this paper we review the data formats that exist in functional genomics, some of which have become de facto or de jure standards, with a particular focus on how each domain has been modelled, and how each format allows extensions. We describe the tasks that are frequently performed over data formats and analyse how well each task is supported by a particular modelling structure.

Conclusion

From our analysis, we make recommendations as to the types of modelling structure that are most suitable for particular types of experimental annotation. There are several standards currently under development that we believe could benefit from systematically following a set of guidelines.
SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution
Authors: Pang Andy , Smith Andrew D , Nuin Paulo AS , Tillier Elisabeth RM
Published: September 2005

Background

General protein evolution models help determine the baseline expectations for the evolution of sequences, and they have been extensively useful in sequence analysis and for the computer simulation of artificial sequence data sets.

Results

We have developed a new method of simulating protein sequence evolution, including insertion and deletion (indel) events in addition to amino-acid substitutions. The simulation generates both the simulated sequence family and a true sequence alignment that captures the evolutionary relationships between amino acids from different sequences. Our statistical model for indel evolution is based on the empirical indel distribution determined by Qian and Goldstein. We have parameterized this distribution so that it applies to sequences diverged by varying evolutionary times and generalized it to provide flexibility in simulation conditions. Our method uses a Monte-Carlo simulation strategy, and has been implemented in a C++ program named Simprot.

Conclusion

Simprot will be useful for testing methods of analysis of protein sequence families particularly alignment methods, phylogenetic tree building, detection of recombination and horizontal gene transfer, and homology detection, where knowing the true course of sequence evolution is essential.
RLIP76, a non-ABC transporter, and drug resistance in epilepsy
Authors: Awasthi Sanjay , Hallene Kerri L , Fazio Vince , Singhal Sharad S , Cucullo Luca , Awasthi Yogesh C , Dini Gabriele , Janigro Damir
Published: September 2005

Background

Permeability of the blood-brain barrier is one of the factors determining the bioavailability of therapeutic drugs and resistance to chemically different antiepileptic drugs is a consequence of decreased intracerebral accumulation. The ABC transporters, particularly P-glycoprotein, are known to play a role in antiepileptic drug extrusion, but are not by themselves sufficient to fully explain the phenomenon of drug-resistant epilepsy. Proteomic analyses of membrane protein differentially expressed in epileptic foci brain tissue revealed the frequently increased expression of RLIP76/RALBP1, a recently described non-ABC multi-specific transporter. Because of a significant overlap in substrates between P-glycoprotein and RLIP76, present studies were carried out to determine the potential role of RLIP76 in AED transport in the brain.

Results

RLIP76 was expressed in brain tissue, preferentially in the lumenal surface of endothelial cell membranes. The expression was most prominent in blood brain barrier tissue from excised epileptic foci. Saturable, energy-dependent, anti-gradient transport of both phenytoin and carbamazepine were demonstrated using recombinant RLIP76 reconstituted into artificial membrane liposomes. Immunotitration studies of transport activity in crude membrane vesicles prepared from whole-brain tissue endothelium showed that RLIP76 represented the dominant transport mechanism for both drugs. RLIP76-/-knockout mice exhibited dramatic toxicity upon phenytoin administration due to decreased drug extrusion mechanisms at the blood-brain barrier.

Conclusion

We conclude that RLIP76 is the predominant transporter of AED in the blood brain barrier, and that it may be a transporter involved in mechanisms of drug-resistant epilepsy.