bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential dependency network analysis to identify condition-specific topological changes in biological networks
Authors: Zhang Bai , Li Huai , Riggins Rebecca B. , Zhan Ming , Xuan Jianhua , Zhang Zhen , Hoffman Eric P. , Clarke Robert , Wang Yue 
Published: December 2008

AbstractMotivation: Significant efforts have been made to acquire data under different conditions and to construct static networks that can explain various gene regulation mechanisms. However, gene regulatory networks are dynamic and condition-specific; under different conditions, networks exhibit different regulation patterns accompanied by different transcriptional network topologies. Thus, an investigation on the topological changes in transcriptional networks can facilitate the understanding of cell development or provide novel insights into the pathophysiology of certain diseases, and help identify the key genetic players that could serve as biomarkers or drug targets.Results: Here, we report a differential dependency network (DDN) analysis to detect statistically significant topological changes in the transcriptional networks between two biological conditions. We propose a local dependency model to represent the local structures of a network by a set of conditional probabilities. We develop an efficient learning algorithm to learn the local dependency model using the Lasso technique. A permutation test is subsequently performed to estimate the statistical significance of each learned local structure. In testing on a simulation dataset, the proposed algorithm accurately detected all the genes with network topological changes. The method was then applied to the estrogen-dependent T-47D estrogen receptor-positive (ER+) breast cancer cell line datasets and human and mouse embryonic stem cell datasets. In both experiments using real microarray datasets, the proposed method produced biologically meaningful results. We expect DDN to emerge as an important bioinformatics tool in transcriptional network analyses. While we focus specifically on transcriptional networks, the DDN method we introduce here is generally applicable to other biological networks with similar characteristics.Availability: The DDN MATLAB toolbox and experiment data are available at http://www.cbil.ece.vt.edu/software.htm.Contact: yuewang@vt.eduSupplementary information: Supplementary data are available at Bioinformatics online.
How to do (or not to do) … Designing a discrete choice experiment for application in a low-income country
Authors: Mangham Lindsay J , Hanson Kara , McPake Barbara 
Published: December 2008

AbstractUnderstanding the preferences of patients and health professionals is useful for health policy and planning. Discrete choice experiments (DCEs) are a quantitative technique for eliciting preferences that can be used in the absence of revealed preference data. The method involves asking individuals to state their preference over hypothetical alternative scenarios, goods or services. Each alternative is described by several attributes and the responses are used to determine whether preferences are significantly influenced by the attributes and also their relative importance. DCEs are widely used in high-income contexts and are increasingly being applied in low- and middle-income countries to consider a range of policy concerns. This paper aims to provide an introduction to DCEs for policy-makers and researchers with little knowledge of the technique. We outline the stages involved in undertaking a DCE, with an emphasis on the design considerations applicable in a low-income setting.
Platelet Activation by Low Concentrations of Intact Oxidized LDL Particles Involves the PAF Receptor
Authors: Chen Rui , Chen Xi , Salomon Robert G. , McIntyre Thomas M. 
Published: December 2008

Objective—Mitochondrial depolarization aids platelet activation. Oxidized LDL (oxLDL) contains the medium length oxidatively truncated phospholipid hexadecyl azelaoyl-lysoPAF (HAz-LPAF) that disrupts mitochondrial function in nucleated cells, so oxLDL may augment platelet activation.Methods and Results—Flow cytometry showed intact oxLDL particles synergized with subthreshold amounts of soluble agonists to increase intracellular Ca2+, and initiate platelet aggregation and surface expression of activated gpIIb/IIIa and P-selectin. oxLDL also induced aggregation and increased intracellular Ca2+in FURA2-labeled cells by itself at low, although not higher, concentrations. HAz-LPAF, alone and in combination with substimulatory amounts of thrombin, rapidly increased cytoplasmic Ca2+and initiated aggregation. HAz-LPAF depolarized mitochondria in intact platelets, but this required concentrations beyond those that directly activated platelets. An unexpectedly large series of chemically pure truncated phospholipids generated by oxidative fragmentation of arachidonoyl-, docosahexaneoyl-, or linoleoyl alkyl phospholipids were platelet agonists. The PAF receptor, thought to effectively recognize only phospholipids with very shortsn-2 residues, was essential for platelet activation because PAF receptor agonists blocked signaling by all these medium length phospholipids and oxLDL.Conclusions—Intact oxLDL particles activate platelets through the PAF receptor, and the PAF receptor responds to a far wider range of oxidized phospholipids in oxLDL than anticipated.
Allo-restricted CTLs generated by coculturing of PBLs and autologous monocytes loaded with allogeneic peptide/HLA/IgG1-Fc fusion protein
Authors: Weng Xiufang , Lu Shengjun , Zhong Maohua , Liang Zhihui , Shen Guanxin , Chen Jianguo , Wu Xiongwen 
Published: December 2008

AbstractThe graft-versus-leukemia effect of allogeneic marrow transplantation suggests the dramatic effect of the allogeneic T cell to eradicate malignant disease. Preparation and adoptive transfusion of tumor-specific T cells from HLA-mismatched donors might be expected to circumvent CTL tolerance to the tumor. In this study, a soluble, divalent HLA-A2 molecule was constructed with the Fc part of human IgG1 and was pulsed with a peptide related to melanoma tyrosinase 368–376 [Tyr368–376 (Tyr)] to form the Tyr/HLA-A2 dimer, which allowed loading onto monocytes via interaction of the Fc and FcR. The HLA-A2-negative (HLA-A2-ve) monocytes loaded with the Tyr/HLA-A2 dimer acted as allo-APC with copies of a single allogeneic epitope. After coculture of the HLA-A2-ve PBLs and autologous monocytes loaded with the dimer, CD8+ cells in the coculture show an obvious proliferation and increased frequency of Tyr/HLA-A2 tetramer-stained cells. The sorted Tyr/HLA-A2 tetramer-positive CD8+ cells display an elevated cytotoxic activity against HLA-A2-positive melanoma cells expressing tyrosinase endogenously (i.e., SK-Mel-5) but little against tyrosinase-negative melanoma cells (i.e., A375). The coculture of PBLs and autologous monocytes loaded with allogeneic peptide/HLA complexes offers a novel approach to expand allo-restricted, peptide-specific CTLs, which might be a potential arsenal for treatment of patients with malignant disease, if the tumor-related epitope were defined.
Pivotal Advance: Toll-like receptor regulation of scavenger receptor-A-mediated phagocytosis
Authors: Amiel Eyal , Alonso Anselmo , Uematsu Satoshi , Akira Shizuo , Poynter Matthew E , Berwin Brent 
Published: December 2008

AbstractClass-A scavenger receptors (SR-A) and TLR mediate early immune responses against pathogenic bacteria. SR-A and TLR molecules are expressed on phagocytes and interact with common ligands from Gram-negative and Gram-positive bacteria; however, the contribution of TLR activity to SR-A-mediated phagocytosis has not been assessed directly. Herein, we provide genetic and functional evidence that ligand- and TLR-specific stimuli synergize with SR-A to mediate bacterial phagocytosis. Although complete loss of SR-A (SR-A−/−) is known to impair bacterial clearance, here we identify the first deficiency attributable to SR-A heterozygosity: SR-A+/−TLR4+/− cells and mice are impaired significantly in the clearance of Gram-negative Escherichia coli. This phenotype is specific to the TLR signaling event, as SR-A+/−TLR4+/− cells are not deficient for the clearance of Gram-positive Staphylococcus aureus bacteria, which contain cell-surface TLR2 ligands but lack TLR4 ligands. We demonstrate that this is a global, phagocytic mechanism, regulated independently by multiple TLRs, as analogous to the SR-A+/−TLR4+/− deficit, SR-A+/−TLR2+/− cells are impaired for S. aureus uptake. In support of this, we show that SR-A+/−MyD88+/− cells recapitulate the phagocytosis defect observed in SR-A+/−TLR4+/− cells. These data identify for the first time that TLR-driven innate immune responses, via a MyD88 signaling mechanism, regulate SR-A-dependent phagocytosis of bacteria. These findings provide novel insights into how innate immune cells control SR-A-mediated trafficking and are the first demonstration that subtle changes in the expression of SR-A and TLRs can substantially affect host bacterial clearance.
Retinoic acid regulates Fas-induced apoptosis in Jurkat T cells: reversal of mitogen-mediated repression of Fas DISC assembly
Authors: Engedal Nikolai , Auberger Patrick , Blomhoff Heidi Kiil 
Published: December 2008

AbstractThe effect of the immune regulator vitamin A on T cell death has been poorly characterized. In the present study, we demonstrate that an active metabolite of vitamin A, retinoic acid (RA), promotes cell death in Jurkat leukemic T cells by counteracting mitogen-mediated repression of Fas-induced apoptosis. The effect of RA was dose-dependent, and at the optimal concentration of 1 μM, repression of Fas-induced cell death by the mitogens 12-O-tetradecanoylphorbol 13-acetate (TPA) or Con A was reversed by ∼50% and 30%, respectively. RA promoted apoptosis rather than necrosis, as judged by analysis of cell morphology, mitochondrial membrane depolarization, and DNA fragmentation. TPA-mediated protection from Fas-induced apoptosis is dependent on ERK and NF-κB. However, analyses of ERK and NF-κB activities and expression of target genes indicated that RA-mediated counteraction of the protective effect of TPA did not involve negative crosstalk with ERK or NF-κB survival pathways. RA-induced cell death was accompanied by enhanced cleavage of procaspase-3, -6, and -8, as well as enhanced cleavage of DNA fragmentation factor 45. Interestingly, RA-mediated cleavage of procaspase-8 occurred very early and before any effect of RA could be detected on procaspase-3 cleavage, suggesting that RA might act at the level of the Fas death-inducing signaling complex (DISC). Indeed, DISC immunoprecipitation studies revealed that RA treatment reversed the inhibitory effect of TPA on CH11-induced recruitment and processing of procaspase-8 at the DISC. In conclusion, we have identified a role of RA in abrogating mitogen-mediated repression of Fas DISC assembly, thus enhancing Fas-induced apoptosis in leukemic T cells.
Examples of non-locality
Authors: Baldwin John T. , Shelah Saharon 
Published: December 2008

AbstractWe use κ-free but not Whitehead Abelian groups to construct Abstract Elementary Classes (AEC) which satisfy the amalgamation property but fail various conditions on the locality of Galois-types. We introduce the notion that an AEC admits intersections. We conclude that for AEC which admit intersections, the amalgamation property can have no positive effect on locality: there is a transformation of AEC's which preserves non-locality but takes any AEC which admits intersections to one with amalgamation. More specifically we have: Theorem 5.3. There is an AEC with amalgamation which is not (ℵ0, ℵ1)-tame but is (, ∞)-tame; Theorem 3.3. It is consistent with ZFC that there is an AEC with amalgamation which is not (≤ ℵ2, ≤ ℵ2)-compact.
Selection in the monadic theory of a countable ordinal
Authors: Rabinovich Alexander , Shomrat Amit 
Published: December 2008

AbstractA monadic formula ψ(Y) is a selector for a formula φ(Y) in a structure if there exists a unique subset P of which satisfies ψ and this P also satisfies φ. We show that for every ordinal α ≥ ωω there are formulas having no selector in the structure (α, <). For α ≤ ω1, we decide which formulas have a selector in (α, <) , and construct selectors for them. We deduce the impossibility of a full generalization of the Büchi-Landweber solvability theorem from (ω, <) to (ωω, <). We state a partial extension of that theorem to all countable ordinals. To each formula we assign a selection degree which measures “how difficult it is to select”. We show that in a countable ordinal all non-selectable formulas share the same degree.
Regular ultrafilters and finite square principles
Authors: Kennedy Juliette , Shelah Saharon , Väänänen Jouko 
Published: December 2008

AbstractWe show that many singular cardinals λ above a strongly compact cardinal have regular ultrafilters D that violate the finite square principle introduced in [3]. For such ultrafilters D and cardinals λ there are models of size λ for which Mλ/D is not λ++-universal and elementarily equivalent models M and N of size λ for which Mλ/D and Nλ/D are non-isomorphic. The question of the existence of such ultrafilters and models was raised in [1].
A note on standard systems and ultrafilters
Authors: Engström Fredrik 
Published: December 2008

AbstractLet (M,)⊨ ACA0be such that, the collection of all unbounded sets in, admits a definable complete ultrafilter and letTbe a theory extending first order arithmetic coded insuch thatMthinksTis consistent. We prove that there is an end-extensionN⊨TofMsuch that the subsets ofMcoded inNare precisely those in. As a special case we get that any Scott set with a definable ultrafilter coding a consistent theoryTextending first order arithmetic is the standard system of a recursively saturated model ofT.
Internal consistency for embedding complexity
Authors: Friedman Sy-David , Thompson Catherine 
Published: December 2008

AbstractIn a previous paper with M. Džamonja, class forcings were given which fixed the complexity (a universality covering number) for certain types of structures of size λ together with the value of 2λ for every regular λ. As part of a programme for examining when such global results can be true in an inner model, we build generics for these class forcings.
Scott's problem for Proper Scott sets
Authors: Gitman Victoria 
Published: December 2008

AbstractSome 40 years ago, Dana Scott proved that every countable Scott set is the standard system of a model of PA. Two decades later, Knight and Nadel extended his result to Scott sets of sizeω1. Here, I show that assuming the Proper Forcing Axiom (PFA), every A-proper Scott set is the standard system of a model of PA. I define that a Scott setis proper if the quotient Boolean algebra/Fin is a proper partial order and A-proper ifis additionally arithmetically closed. I also investigate the question of the existence of proper Scott sets.
The 116 reducts of (ℚ, <, a)
Authors: Junker Markus , Ziegler Martin 
Published: December 2008

AbstractThis article aims to classify those reducts of expansions of (ℚ, <) by unary predicates which eliminate quantifiers, and in particular to show that, up to interdefinability, there are only finitely many for a given language. Equivalently, we wish to classify the closed subgroups of Sym(ℚ) containing the group of all automorphisms of (ℚ, <) fixing setwise certain subsets. This goal is achieved for expansions by convex predicates, yielding expansions by constants as a special case, and for the expansion by a dense, co-dense predicate. Partial results are obtained in the general setting of several dense predicates.
Classifying model-theoretic properties
Authors: Conidis Chris J. 
Published: December 2008

AbstractIn 2004 Csima, Hirschfeldt, Knight, and Soare [1] showed that a set A ≤T 0′ is nonlow2 if and only if A is prime bounding, i.e., for every complete atomic decidable theory T, there is a prime model computable in A. The authors presented nine seemingly unrelated predicates of a set A, and showed that they are equivalent for sets. Some of these predicates, such as prime bounding, and others involving equivalence structures and abelian p-groups come from model theory, while others involving meeting dense sets in trees and escaping a given function come from pure computability theory.As predicates of A, the original nine properties are equivalent for sets; however, they are not equivalent in general. This article examines the (degree-theoretic) relationship between the nine properties. We show that the nine properties fall into three classes, each of which consists of several equivalent properties. We also investigate the relationship between the three classes, by determining whether or not any of the predicates in one class implies a predicate in another class.
Perfect trees and elementary embeddings
Authors: Friedman Sy-David , Thompson Katherine 
Published: December 2008

AbstractAn important technique in large cardinal set theory is that of extending an elementary embedding j: M → N between inner models to an elementary embedding j* : M[G] → N[G*] between generic extensions of them. This technique is crucial both in the study of large cardinal preservation and of internal consistency. In easy cases, such as when forcing to make the GCH hold while preserving a measurable cardinal (via a reverse Easton iteration of α-Cohen forcing for successor cardinals α), the generic G* is simply generated by the image of G. But in difficult cases, such as in Woodin's proof that a hypermeasurable is sufficient to obtain a failure of the GCH at a measurable, a preliminary version of G* must be constructed (possibly in a further generic extension of M[G]) and then modified to provide the required G*. In this article we use perfect trees to reduce some difficult cases to easy ones, using fusion as a substitute for distributivity. We apply our technique to provide a new proof of Woodin's theorem as well as the new result that global domination at inaccessibles (the statement that d(κ) is less than 2κ for inaccessible κ, where d(κ) is the dominating number at κ) is internally consistent, given the existence of 0#.
Strong cut-elimination in sequent calculus using Klop's ι-translation and perpetual reductions
Authors: Sørensen Morten Heine , Urzyczyn PaweŁ 
Published: December 2008

AbstractThere is a simple technique, due to Dragalin. for proving strong cut-elimination for intuitionistic sequent calculus, but the technique is constrained to certain choices of reduction rules, preventing equally natural alternatives. We consider such a natural, alternative set of reduction rules and show that the classical technique is inapplicable. Instead we develop another approach combining two of our favorite tools—Klop's ι-translation and perpetual reductions.These tools are of independent interest and have proved useful in a variety of settings; it is therefore natural to investigate, as we do here, what they have to offer the field of sequent calculus.
The modal logic of affine planes is not finitely axiomatisable
Authors: Hodkinson Ian , Hussain Altaf 
Published: December 2008

AbstractWe consider a modal language for affine planes, with two sorts of formulas (for points and lines) and three modal boxes. To evaluate formulas, we regard an affine plane as a Kripke frame with two sorts (points and lines) and three modal accessibility relations, namely the point-line and line-point incidence relations and the parallelism relation between lines. We show that the modal logic of affine planes in this language is not finitely axiomatisable.
On a result of Szemerédi
Authors: Jones Albin L. 
Published: December 2008

AbstractWe provide a short proof that if κ is a regular cardinal with κ < c, thenfor any ordinal α < min{, κ}. In particular,for any ordinal α < . This generalizes an unpublished result of E. Szemerédi that Martin's axiom implies thatfor any cardinal κ with κ < c.
Construction d'un groupe dans les structures C-minimales
Authors: Maalouf Fares 
Published: December 2008

AbstractWe will study some aspects of the local structure of models of certain C-minimal theories. We will prove (theorem 19) that, in a sufficiently saturated C-minimal structure in which the algebraic closure has the exchange property and which is locally modular, we can construct an infinite type-definable group around any non trivial point (a term to be defined later).
On Skolemization in constructive theories
Authors: Baaz Matthias , Iemhoff Rosalie 
Published: December 2008

AbstractIn this paper a method for the replacement, in formulas, of strong quantifiers by functions is introduced that can be considered as an alternative to Skolemization in the setting of constructive theories. A constructive extension of intuitionistic predicate logic that captures the notions of preorder and existence is introduced and the method, orderization, is shown to be sound and complete with respect to this logic. This implies an analogue of Herbrand's theorem for intuitionistic logic. The orderization method is applied to the constructive theories of equality and groups.
The degree spectra of homogeneous models
Authors: Lange Karen 
Published: December 2008

AbstractMuch previous study has been done on the degree spectra of prime models of a complete atomic decidable theory. Here we study the analogous questions for homogeneous models. We say a countable model has a d-basis if the types realized in are all computable and the Turing degree d can list -indices for all types realized in . We say has a d-decidable copy if there exists a model ≅ such that the elementary diagram of is d-computable. Goncharov, Millar, and Peretyat'kin independently showed there exists a homogeneous with a 0-basis but no decidable copy.We prove that any homogeneous with a 0′-basis has a low decidable copy. This implies Csima's analogous result for prime models. In the case where all types of the theory T are computable and is a homogeneous model with a 0-basis, we show has copies decidable in every nonzero degree. A degree d is 0-homogeneous bounding if any automorphically nontrivial homogeneous with a 0-basis has a d-decidable copy. We show that the nonlow2 degrees are 0-homogeneous bounding.
Aronszajn lines and the club filter
Authors: Moore Justin Tatch 
Published: December 2008

AbstractThe purpose of this note is to demonstrate that a weak form of club guessing on ω1implies the existence of an Aronszajn line with no Countryman suborders. An immediate consequence is that the existence of a five element basis for the uncountable linear orders does not follow from the forcing axiom for ω-proper forcings.
Motives for perfect PAC fields with pro-cyclic Galois group
Authors: Halupczok Immanuel 
Published: December 2008

AbstractDenef and Loeser denned a map from the Grothendieck ring of sets definable in pseudo-finite fields to the Grothendieck ring of Chow motives, thus enabling to apply any cohomological invariant to these sets. We generalize this to perfect, pseudo algebraically closed fields with pro-cyclic Galois group.In addition, we define some maps between different Grothendieck rings of definable sets which provide additional information, not contained in the associated motive. In particular we infer that the map of Denef-Loeser is not injective.