bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid Identification of Probiotic Lactobacillus Biosurfactant Proteins by ProteinChip Tandem Mass Spectrometry Tryptic Peptide Sequencing
Authors: Reid Gregor , Gan Bing Siang , She Yi-Min , Ens Werner , Weinberger Scot , Howard Jeffrey C. 
Published: February 2003

ABSTRACT

A novel ProteinChip-interfaced tandem mass spectrometer was employed to identify collagen binding proteins from biosurfactant produced by
Lactobacillus fermentum
RC-14. On-chip tryptic digestion of the captured collagen binding proteins resulted in rapid sequence identification of five novel tryptic peptide sequences via collision-induced dissociation tandem mass spectrometry.
Effect of Oxidizing Disinfectants (Chlorine, Monochloramine, and Ozone) on
Helicobacter pylori
Authors: Baker Katherine H. , Hegarty John P. , Redmond Brady , Reed Nathan A. , Herson Diane S. 
Published: February 2003

ABSTRACT

The susceptibility of
Helicobacter pylori
to disinfectants was compared to that of
Escherichia coli
.
H. pylori
is more resistant than
E. coli
to chlorine and ozone but not monochloramine.
H. pylori
may be able to tolerate disinfectants in distribution systems and, therefore, may be transmitted by a waterborne route.
Involvement of
glnB, glnZ
, and
glnD
Genes in the Regulation of Poly-3-Hydroxybutyrate Biosynthesis by Ammonia in
Azospirillum brasilense
Sp7
Authors: Sun Jun , Van Dommelen Anne , Van Impe Jan , Vanderleyden Jos 
Published: February 2003

ABSTRACT

The role of three key nitrogen regulatory genes,
glnB
(encoding the P
II
protein),
glnZ
(encoding the P
z
protein), and
glnD
(encoding the GlnD protein), in regulation of poly-3-hydroxybutyrate (PHB) biosynthesis by ammonia in
Azospirillum brasilense
Sp7 was investigated. It was observed that
glnB glnZ
and
glnD
mutants produce substantially higher amounts of PHB than the wild type produces during the active growth phase.
glnB
and
glnZ
mutants have PHB production phenotypes similar to that of the wild type. Our results indicate that the P
II
-P
z
system is apparently involved in nitrogen-dependent regulation of PHB biosynthesis in
A. brasilense
Sp7.
Novel Clade of
Rickettsia
spp. from Leeches
Authors: Kikuchi Yoshitomo , Sameshima Shinya , Kitade Osamu , Kojima Junichi , Fukatsu Takema 
Published: February 2003

ABSTRACT

Intracellular rickettsia-like structures were found in the tissues of a glossiphoniid leech,
Torix tagoi
, by transmission electron microscopy. Diagnostic PCR analysis using specific primers suggested that of the nine glossiphoniid species examined, two species,
T. tagoi
and
Hemicrepsis marginata
, harbored bacteria of the genus
Rickettsia
. A 1.5-kb eubacterial 16S rRNA gene segment obtained from each of these species was amplified by PCR, cloned, and sequenced. Phylogenetic analysis of the 16S rRNA gene demonstrated that the
Rickettsia
species found in the leeches constituted a novel clade that is distinct from the clade of arthropod-associated
Rickettsia
species. In natural populations, 97.7% (43 of 44) of
T. tagoi
leeches and 100% (9 of 9) of
H. marginata
leeches carried
Rickettsia
, suggesting that infection with
Rickettsia
is prevalent in these leeches. This is the first report of
Rickettsia
found in annelids.
Effects of ISSo
2
Insertions in Structural and Regulatory Genes of the Trimethylamine Oxide Reductase of
Shewanella oneidensis
Authors: Bordi Christophe , Iobbi-Nivol Chantal , Méjean Vincent , Patte Jean-Claude 
Published: March 2003

ABSTRACT

We have isolated three
Shewanella oneidensis
mutants specifically impaired in trimethylamine oxide (TMAO) respiration. The mutations arose from insertions of an ISSo
2
element into
torA
,
torR
, and
torS
, encoding, respectively, the TMAO reductase TorA, the response regulator TorR, and the sensor TorS. Although TorA is not the sole enzyme reducing TMAO in
S. oneidensis
, growth analysis showed that it is the main respiratory TMAO reductase. Use of a plasmid-borne
torE
′-
lacZ
fusion confirmed that the TorS-TorR phosphorelay mediates TMAO induction of the
torECAD
operon.
Outer-sphere electron transfer reactions of aqua(5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane-1-acetato) nickel(II) and (III).
Authors: Haines Robert I , Hutchings Dean R 
Published: March 2003

The outer-sphere oxidation of the nickel(II) complex of the deprotonated pendant-arm macrocycle, 5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane-1-acetate, [NiL1(OH2)]+ by bis-(1,4,7-triazacyclononane)nickel(III), [Ni(tacn)2]3+ has been studied in aqueous perchlorate media. The reaction displays reversible second-order behaviour and the kinetic study reveals the forward and reverse rate constants for the reaction: [Formula: see text] The kinetics show the forward reaction to be acid dependent, a feature that is attributed to protonation of the acetato group of the nickel(II) complex. Using Marcus theory, the self-exchange rate for the [NiL1(OH2)]+/2+ couple has been calculated. The nickel(II/III) electron transfer is a reversible one electron process with E° = 1.04 V (vs. S.H.E.). The formation of the authentic nickel(III) product has been confirmed by esr spectroscopy. The kinetics of reduction of the [NiL1(OH2)]2+ species by Fe2+(aq) exhibits a second-order rate law, the reaction being independent of acid. Using the calculated self-exchange rate for the nickel complex, its reaction with Fe2+(aq) has been examined in terms of an inner- versus outer-sphere mechanism. Key words: nickel(III), pendant-arm macrocycles, hexaaquairon(II), outer sphere, kinetics, Marcus theory.
COMPARISON OF HEURISTICS FOR ONE-TO-ALL AND ALL-TO-ALL COMMUNICATIONS IN PARTIAL MESHES
Authors: FRAIGNIAUD PIERRE , VIAL SANDRINE 
Published: February 2003

Broadcasting (one-to-all) and gossiping (all-to-all) are two major communication paradigms that were considered from both practical and theoretical points of view. Indeed, such communication patterns frequently appear in parallel programming, and therefore are included in most of the communication libraries (e.g., MPI or PVM). Also, broadcasting and gossiping times of graphs are important parameters yielding lots of fundamental results. For most of the communication models, the corresponding decision problems are NP-complete in general. Therefore, in this paper, we consider broadcasting and gossiping heuristics. We study the performances of several heuristics applied to partial meshes, that is to connected subgraphs of the mesh. This choice of topology is motivated by the fact that a regularly connected multicomputer can be shared by many users, each of them dealing with an irregular sub-topology of the original network. The result of our comparison is that, although they were defined for arbitrary topologies, the matching-based heuristics offer the best performances for partial meshes compared to sophisticated heuristics defined specifically for these networks (we derive a new heuristic for this class of topologies), or for graphs with [Formula: see text]-diameter. Since matching-based heuristics are simple, and do not require intensive computation, they appear to be the best candidates to solve broadcasting and gossiping problems in multi-user mesh architectures.
SHARED MEMORY VERSUS MESSAGE PASSING FOR ITERATIVE SOLUTION OF SPARSE, IRREGULAR PROBLEMS
Authors: CHONG FREDERIC T. , AGARWAL ANANT 
Published: February 2003

The benefits of hardware support for shared memory versus those for message passing are difficult to evaluate without an in-depth study of real applications on a common platform. We evaluate the communication mechanisms of the MIT Alewife machine, a multiprocessor which provides integrated cache-coherent shared memory, massage passing, and DMA. We perform this evaluation with "best-effort" implementations which solve several sparse, irregular benchmark problems with a preconditioned conjugate gradient sparse matrix solver (ICCG). We find that machines with fast global memory operations do not need message passing or bulk transfer to suport our irregular problems. This is primarily due to three reasons. First, a 5-to-1 ratio between global and local cache misses makes memory copies in bulk communication expensive relati to communication via shared memory. Second, although message passing has synchronization semantics superior to shared memory for data-driven computation, efficient shared memory can overcome this handicap by using global read-modify-writes to change from the traditional owner-computers model to a producer-computes model. Third, bulk transfers can result in high processor idle times in irregular applications.
OPTIMALITY AND SELF-STABILIZATION IN ROOTED TREE NETWORKS
Authors: PETIT FRANCK , VILLAIN VINCENT 
Published: February 2003

In this paper, we consider arbitrary tree networks where every processor, except one, called the root, executes the same program. We show that, to design a depth-first token circulation protocol in such networks, it is necessary to have at least [Formula: see text] configurations, where n is the number of processors in the network and Δi is the degree of processor pi. We then propose a depth-first token circulation algorithm which matches the above minimal number of configurations. We show that the proposed algorithm is self-stabilizing, i.e., the system eventually recovers itself to a legitimate state after any perturbation modifying the state of the processors. Hence, the proposed algorithm is optimal in terms of the number of configurations and no extra cost is involved in making it stabilizing.
A NOTE ON THE IMPLEMENTATION OF REPLICATION-BASED GARBAGE COLLECTION FOR MULTITHREADED APPLICATIONS AND MULTIPROCESSOR ENVIRONMENTS
Authors: AZAGURY ALAIN , KOLODNER ELLIOT K. , PETRANK EREZ 
Published: February 2003

Replication-based incremental garbage collection is one of the more appealing concurrent garbage collection algorithms known today. It allows continuous operation of the application (the mutator) with very short pauses for garbage collection. There is a growing need for such garbage collectors suitable for a multithreaded environments such as the Java Virtual Machine. Furthermore, it is desirable to construct collectors that also work on multiprocessor computers. We begin by pointing out an important, yet subtle point, which arises when implementing the replication-based garbage collector for a multithreaded environment. We first show that a simple and natural implementation of the algorithm may lead to an incorrect behavior of multithreaded applications. We then show that another simple and natural implementation eliminates the problem completely. Thus, the contribution of this part is in stressing this warning to future implementors. Next, we address the effects of the memory coherence model on this algorithm. We show that even when the algorithm is properly implemented with respect to our first observation, a problem might still arise when a multiprocessor system is used. Adopting a naive solution to this problem results in very frequent (and expensive) synchronization. We offer a slight modification to the algorithm which eliminates the problem and requires little synchronization.
A FUZZY OBJECT-BASED DATA MODEL FOR IMPERFECT SPATIAL INFORMATION INTEGRATING EXACT OBJECTS AND FIELDS
Authors: BORDOGNA GLORIA , CHIESA SERGIO 
Published: February 2003

In this contribution a fuzzy object-based data model for imperfect spatial information is proposed within the formal framework of fuzzy set theory and possibility theory. The proposal integrates the two opposite views of geographic entities seen as either exact objects or continuous fields in current Geographic Information Systems. By assuming a Fuzzy Object-Oriented Data modelling approach new data types for representing geographic entities characterized by either unsharp boundaries or indeterminate boundaries and relationships are defined.Linguistic qualifiers are adopted both to express the extent by which an element of the spatial domain satisfies a gradual property, and to identify regions with indeterminate boundaries.
UNCERTAINTY AND TERM SELECTION IN TEXT CATEGORIZATION
Authors: PETERS CHARLES M. E. E. , KOSTER CORNELIS H. A. 
Published: February 2003

This paper discusses the notion of Uncertainty, which has a prominent place in the theory and experimental practice of modern Physics. It argues that the awareness of Uncertainty may also be of tremendous importance to the field of Information Retrieval, and in particular Text Categorization. As an application of Uncertainty in Text Categorization, a new criterion for Term Selection is described, which is based on the Uncertainty in Term Frequency across categories. This criterion allows to distinguish between low-quality (or "noisy") and high-quality ("stiff") terms. We describe an experiment investigating the effect of eliminating noisy and stiff terms in the context of text classification. In the experiment we applied the Rocchio and Winnow classification algorithms to a collection of newspaper items, a mono-classified subset of the well-known Reuters 21578 corpus. This investigation shows that both the local elimination of noisy terms and the global elimination of stiff terms can be used for Term Selection in Text Categorization.
Docosahexaenoic acid enhances arsenic trioxide–mediated apoptosis in arsenic trioxide–resistant HL-60 cells
Authors: Sturlan Sanda , Baumgartner Melanie , Roth Erich , Bachleitner-Hofmann Thomas 
Published: March 2003

AbstractRecent reports indicate a broad spectrum of antileukemic activity for arsenic trioxide (As2O3) due to its ability to induce apoptosis via intracellular production of reactive oxygen species (ROS). Despite its potent apoptotic mechanism, As2O3 is not equally effective in all leukemic cells, which has prompted a search for agents enhancing As2O3 efficacy. Recently, evidence has been gathered that the polyunsaturated fatty acid docosahexaenoic acid (DHA) may sensitize tumor cells to ROS-inducing anticancer agents. The aim of our investigation was to evaluate whether DHA enhances As2O3-mediated apoptosis in As2O3-resistant HL-60 cells. While 1 μM As2O3 or 25 μM DHA reduced cell viability to 85.8% ± 2.9% and 69.2% ± 3.6%, combined treatment with As2O3 and DHA reduced viability to 13.0% ± 9.9% with a concomitant increase of apoptosis. Apoptotic cell death was preceded by collapse of the mitochondrial membrane potential, increased expression of proapoptotic B-cell lymphoma protein-2–associated X protein (Bax), and caspase-3 activation. Importantly, the combined effect of As2O3 and DHA was associated with increased production of intracellular ROS and toxic lipid peroxidation products and was abolished by the antioxidant vitamin E or when oleic acid (a nonperoxidizable fatty acid) was used in place of DHA. Intracellular ROS and toxic lipid peroxidation products most likely constitute the key mediators contributing to the combined effect of As2O3 and DHA. Our data provide the first evidence that DHA may help to extend the therapeutic spectrum of As2O3 and suggest that the combination of As2O3 and DHA could be more broadly applied in leukemia therapy.
Major mutations in calf-1 and calf-2 domains of glycoprotein IIb in patients with Glanzmann thrombasthenia enable GPIIb/IIIa complex formation, but impair its transport from the endoplasmic reticulum to the Golgi apparatus
Authors: Rosenberg Nurit , Yatuv Rivka , Sobolev Vladimir , Peretz Hava , Zivelin Ariella , Seligsohn Uri 
Published: March 2003

AbstractThe crystal structure of integrin αvβ3 comprises 3 regions of contact between αv and β3. The main contact on αv is located in the β-propeller while calf-1 and calf-2 domains contribute minor interfaces. Whether or not contacts between calf-1 and calf-2 domains of glycoprotein (GP) IIb (αIIb) and GPIIIa (β3) play a role in GPIIb/IIIa complex formation has not been established. In this study we analyzed the effects of 2 naturally occurring mutations in calf-1 and calf-2 domains on GPIIb/IIIa complex formation, its processing, and transport to the cell membrane. The mutations investigated were a deletion-insertion in exon 25 located in calf-2 and an in-frame skipping of exon 20 located in calf-1. Mutated GPIIb cDNAs were cotransfected in baby hamster kidney cells with normal GPIIIa (β3) cDNA. Analysis by flow cytometry failed to demonstrate detectable amounts of GPIIb or GPIIb/IIIa complex on the surface of cells transfected with each mutation, but immunohistochemical staining revealed their intracellular presence. GPIIb was mainly demonstrable as pro-GPIIb by immunoprecipitation of cell lysates expressing each mutation. Differential immunofluorescence staining of GPIIb and cellular organelles suggested that most altered complexes were located in the endoplasmic reticulum. Homology modeling of normal GPIIb based on the αvβ3 crystal structure revealed similar contacts between αv and β3 and between αIIb and β3. Introduction of the mutations into the model yielded partial disruption of the normal contacts in the corresponding domains. These data suggest that despite partial disruption of calf-1 or calf-2 domain, GPIIb/IIIa complex is formed but its transport from the endoplasmic reticulum is impaired.
Phosphatidylserine externalization in sickle red blood cells: associations with cell age, density, and hemoglobin F
Authors: Yasin Zahida , Witting Scott , Palascak Mary B. , Joiner Clinton H. , Rucknagel Donald L. , Franco Robert S. 
Published: March 2003

AbstractPhosphatidylserine (PS) is normally confined to the cytoplasmic leaflet of the red blood cell (RBC) membrane, but some sickle RBCs expose PS in the outer leaflet (PS+ cells). This study examined the relationships among PS externalization, fetal hemoglobin content, hydration state, and cell age. Sickle RBCs exhibit a wide range of PS externalization. Those with low-level exposure (type 1 PS+) include many young transferrin-receptor-positive (TfR+) cells. This is not specific for sickle cell disease because many nonsickle TfR+ cells are also PS+. RBCs with higher PS exposure (type 2 PS+) appear to be more specific for sickle cell disease. Their formation is most likely sickling dependent because type 2 PS+ dense sickle cells have a lower percentage of fetal hemoglobin (HbF) than PS- cells in the same density fraction (1.7 vs 2.9; n = 8; P &lt; .01). In vivo experiments using biotin-labeled sickle cells showed a sharp decrease in the percentage of circulating, labeled PS+ cells in the first 24 hours after reinfusion. This decrease was confined to type 1 PS+ cells and was thus consistent with the reversal of PS exposure in very young cells. As the labeled cells aged in the circulation, the percentages of type 1 and type 2 PS+ cells increased. These studies indicate that PS externalization in sickle cells may be low level, as observed in many immature cells, or high level, which is associated with dehydration and appears to be more specific for sickle RBCs. (Blood. 2003;102: 365-370)
Telomerase and telomere length in multiple myeloma: correlations with disease heterogeneity, cytogenetic status, and overall survival
Authors: Wu Kai-Da , Orme Lisa M. , Shaughnessy John , Jacobson Joth , Barlogie Bart , Moore Malcolm A. S. 
Published: March 2003

AbstractWe have investigated the significance of telomerase activity (TA) and telomere length (TL) in multiple myeloma (MM). The analyses were undertaken on CD138+ MM cells isolated from the marrow of 183 patients either at diagnosis or in relapse. There was heterogeneity in telomerase expression; 36% of the patients had TA levels comparable to those detected in normal plasma cells, and 13% of patients had levels 1- to 4-fold greater than in a neuroblastoma cell line control. The TL of MM cells was significantly shorter than that of the patients' own leukocytes; in 25% of patients, the TL measured less than 4.0 kbp. Analysis of TL distribution indicated selective TA-mediated stabilization of shorter telomeres when mean TL fell below 5.5 kbp. Unusually long (10.8-15.0 kbp) telomeres were observed in 7 patients, and low TA was observed in 5 of 7 patients, suggesting the operation of a TA-independent pathway of telomere stabilization. A strong negative correlation existed between TA and TL or platelet count. TL negatively correlated with age and with interleukin-6 (IL-6) and β2-microglobulin levels. Various cytogenetic abnormalities, including those associated with poor prognosis, strongly correlated with TA and, to a lesser extent, with short TL. High TA and short TL defined a subgroup of patients with poor prognosis. At 1 year the survival rate in patients with TA levels lower than 25% of neuroblastoma control and TL greater than 5.5 kbp was 82%, whereas in patients with higher TA and shorter TL the survival rate was 63% (P = .004). The 2-year survival rate for patients with TA levels lower than 25% was 81%, and it was 52% in those with higher TA levels (P &lt;.0001).
Involvement of a CD47-dependent pathway in platelet adhesion on inflamed vascular endothelium under flow
Authors: Lagadec Patricia , Dejoux Olivier , Ticchioni Michel , Cottrez Françoise , Johansen Mette , Brown Eric J. , Bernard Alain 
Published: March 2003

AbstractResting platelet adhesion to inflammatory vascular endothelium is thought to play a causal role in secondary thrombus formation or microcirculatory disturbance after vessel occlusion. However, though adhesion receptors involved in platelet-matrix interactions have been extensively studied, the molecular mechanisms involved in platelet-endothelium interactions are incompletely characterized and have been mainly studied under static conditions. Using human platelets or platelets from wild-type and CD47–/– mice in whole blood, we demonstrated that at low shear rate, CD47 expressed on human and mouse platelets significantly contributes to platelet adhesion on tumor necrosis factor-α (TNF-α)–stimulated vascular endothelial cells. Using the CD47 agonist peptide 4N1K and blocking monoclonal antibodies (mAbs), we showed that CD47 binds the cell-binding domain (CBD) of endothelial thrombospondin-1 (TSP-1), inducing activation of the platelet αIIbβ3 integrin that in turn becomes able to link the endothelial receptors intercellular adhesion molecule 1 (ICAM-1) and αvβ3. Platelet CD36 and GPIbα are also involved because platelet incubation with blocking mAbs directed against each of these 2 receptors significantly decreased platelet arrest. Given that anti-CD47 treatment of platelets did not further decrease the adhesion of anti-CD36–treated platelets and CD36 is a TSP-1 receptor, it appears that CD36/TSP-1 interaction could trigger the CD47-dependent pathway. Overall, CD47 antagonists may be potentially useful to inhibit platelet adhesion on inflamed endothelium.