bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel
Plasmodium vivax dhfr
Alleles from the Indonesian Archipelago and Papua New Guinea: Association with Pyrimethamine Resistance Determined by a
Saccharomyces cerevisiae
Expression System
Authors: Hastings Michele D. , Maguire Jason D. , Bangs Michael J. , Zimmerman Peter A. , Reeder John C. , Baird J. Kevin , Sibley Carol Hopkins 
Published: January 2005

ABSTRACT

In plasmodia, the dihydrofolate reductase (DHFR) enzyme is the target of the pyrimethamine component of sulfadoxine-pyrimethamine (S/P).
Plasmodium vivax
infections are not treated intentionally with antifolates. However, outside Africa, coinfections with
Plasmodium falciparum
and
P. vivax
are common, and
P. vivax
infections are often exposed to S/P. Cloning of the
P. vivax dhfr
gene has allowed molecular comparisons of
dhfr
alleles from different regions. Examination of the
dhfr
locus from a few locations has identified a very diverse set of alleles and showed that mutant alleles of the vivax
dhfr
gene are prevalent in Southeast Asia where S/P has been used extensively. We have surveyed patient isolates from six locations in Indonesia and two locations in Papua New Guinea. We sequenced
P. vivax dhfr
alleles from 114 patient samples and identified 24 different alleles that differed from the wild type by synonymous and nonsynonymous point mutations, insertions, or deletions. Most importantly, five alleles that carried four or more nonsynonymous mutations were identified. Only one of these highly mutant alleles had been previously observed, and all carried the 57L and 117T mutations.
P. vivax
cannot be cultured continuously, so we used a yeast assay system to determine in vitro sensitivity to pyrimethamine for a subset of the alleles. Alleles with four nonsynonymous mutations conferred very high levels of resistance to pyrimethamine. This study expands significantly the total number of novel
dhfr
alleles now identified from
P. vivax
and provides a foundation for understanding how antifolate resistance arises and spreads in natural
P. vivax
populations.
Mutations in the
Pneumocystis jirovecii DHPS
Gene Confer Cross-Resistance to Sulfa Drugs
Authors: Iliades Peter , Meshnick Steven R. , Macreadie Ian G. 
Published: January 2005

ABSTRACT

Pneumocystis jirovecii
is a major opportunistic pathogen that causes
Pneumocystis
pneumonia (PCP) and results in a high degree of mortality in immunocompromised individuals. The drug of choice for PCP is typically sulfamethoxazole (SMX) or dapsone in conjunction with trimethoprim. Drug treatment failure and sulfa drug resistance have been implicated epidemiologically with point mutations in dihydropteroate synthase (DHPS) of
P. jirovecii. P. jirovecii
cannot be cultured in vitro; however, heterologous complementation of the
P. jirovecii
trifunctional folic acid synthesis (PjFAS) genes with an
E. coli DHPS
-disrupted strain was recently achieved. This enabled the evaluation of SMX resistance conferred by
DHPS
mutations. In this study, we sought to determine whether
DHPS
mutations conferred sulfa drug cross-resistance to 15 commonly available sulfa drugs. It was established that the presence of amino acid substitutions (T
517
A or P
519
S) in the DHPS domain of PjFAS led to cross-resistance against most sulfa drugs evaluated. The presence of both mutations led to increased sulfa drug resistance, suggesting cooperativity and the incremental evolution of sulfa drug resistance. Two sulfa drugs (sulfachloropyridazine [SCP] and sulfamethoxypyridazine [SMP]) that had a higher inhibitory potential than SMX were identified. In addition, SCP, SMP, and sulfadiazine (SDZ) were found to be capable of inhibiting the clinically observed drug-resistant mutants. We propose that SCP, SMP, and SDZ should be considered for clinical evaluation against PCP or for future development of novel sulfa drug compounds.
Antistaphylococcal Activity of Dalbavancin, an Experimental Glycopeptide
Authors: Lin Gengrong , Credito Kim , Ednie Lois M. , Appelbaum Peter C. 
Published: January 2005

ABSTRACT
Dalbavancin, tested against 146 staphylococci, was more potent than other drugs tested, with an MIC at which 50% of staphylococci were inhibited of 0.03 μg/ml and an MIC at which 90% of staphylococci were inhibited of 0.06 μg/ml by microdilution. For all strains, MICs of vancomycin, linezolid, ranbezolid, oritavancin, daptomycin, and quinupristin-dalfopristin were ≤4.0 μg/ml. Dalbavancin was bactericidal at four times the MIC against all six strains tested.
Plasmid-Mediated Quinolone Resistance in Isolates Obtained in German Intensive Care Units
Authors: Jonas Daniel , Biehler Klaus , Hartung Doris , Spitzmüller Bettina , Daschner Franz D. 
Published: January 2005

ABSTRACT

Screening of 703 isolates of
Enterobacteriaceae
, obtained from 34 German intensive care units (ICUs), revealed
qnr
-positive, integron-containing isolates of
Enterobacter
sp. and
Citrobacter freundii
from four patients in 2 German ICUs. This is one of the first reports of
qnr
-positive strains obtained from patients in Europe.
Simple Fibroblast-Based Assay To Test the Pyrazinamide Susceptibility of
Mycobacterium tuberculosis
Authors: Takii Takemasa , Hamasaki Sonomi , Hirano Kazue , Abe Chiyoji , Onozaki Kikuo 
Published: January 2005

ABSTRACT

A simple fibroblast-based assay (SFA) was found to be efficient in evaluating the susceptibilities of clinical isolates of
Mycobacterium tuberculosis
to pyrazinamide (PZA). Forty-five clinical isolates were examined. The MICs of PZA for susceptible strains in an SFA were between 3.13 and 12.5 μg/ml, and the MICs of PZA for resistant strains were more than 100 μg/ml.
Combination Therapy with Amphotericin B Lipid Complex and Caspofungin Acetate of Disseminated Zygomycosis in Diabetic Ketoacidotic Mice
Authors: Spellberg Brad , Fu Yue , Edwards John E. , Ibrahim Ashraf S. 
Published: January 2005

ABSTRACTWe studied the combination of amphotericin B lipid complex (ABLC) and caspofungin in mice with disseminatedRhizopus oryzae. Combination therapy improved survival compared to that of mice given monotherapy and that of untreated controls (P< 0.05) but did not improve organ clearance. In addition, prophylactic combination therapy was not more effective than prophylactic ABLC alone.
Dissemination of Sulfonamide Resistance Genes (
sul1
,
sul2
, and
sul3
) in Portuguese
Salmonella enterica
Strains and Relation with Integrons
Authors: Antunes Patrícia , Machado Jorge , Sousa João Carlos , Peixe Luísa 
Published: January 2005

ABSTRACT

In 200 sulfonamide-resistant Portuguese
Salmonella
isolates, 152
sul1
, 74
sul2
, and 14
sul3
genes were detected. Class 1 integrons were always associated with
sul
genes, including
sul3
alone in some isolates. The
sul3
gene has been identified in isolates from different sources and serotypes, which also carried a class 1 integron with
aadA
and
dfrA
gene cassettes.
Stability of Fluoroquinolone Resistance in
Streptococcus pneumoniae
Clinical Isolates and Laboratory-Derived Mutants
Authors: Smith-Adam Heather J. , Nichol Kimberly A. , Hoban Daryl J. , Zhanel George G. 
Published: January 2005

ABSTRACT

The stability of fluoroquinolone resistance in
Streptococcus pneumoniae
was evaluated in laboratory-derived mutants and clinical isolates. Isolates with various genotypes and phenotypes were subcultured for 20 days on antibiotic-free media and were monitored by E-tests to identify any alterations in resistance. Fluoroquinolone resistance mechanisms, whether efflux or chromosomally mediated, remained stable in both clinical and laboratory-derived mutants.
Selected Arylpiperazines Are Capable of Reversing Multidrug Resistance in
Escherichia coli
Overexpressing RND Efflux Pumps
Authors: Bohnert Jürgen A. , Kern Winfried V. 
Published: January 2005

ABSTRACT

Several arylpiperazines capable of reversing multidrug resistance (MDR) in
Escherichia coli
overexpressing
acrAB
and
acrEF
but not in pump-deficient mutant strains were identified. 1-(1-Naphthylmethyl)-piperazine, one of the more active compounds, enhanced susceptibility to fluoroquinolones and other agents and increased the intracellular concentration of levofloxacin and ethidium bromide, suggesting efflux pump inhibition as the mechanism of MDR reversal.
Activity of Glycopeptides against
Staphylococcus aureus
Infection in a Rabbit Endocarditis Model: MICs Do Not Predict In Vivo Efficacy
Authors: Asseray Nathalie , Jacqueline Cedric , Le Mabecque Virginie , Batard Eric , Bugnon Denis , Potel Gilles , Caillon Jocelyne 
Published: January 2005

ABSTRACT

The in vivo efficacy of vancomycin and teicoplanin against five
Staphylococcus aureus
strains with different susceptibilities to them and methicillin was studied. Rabbits were allocated at random to groups for endocarditis induction with one of these five strains and then treated for 2 days with vancomycin or teicoplanin. Each treated group was compared with a control group infected with the same strain. Vancomycin and teicoplanin showed similar activities. Low MICs did not predict better in vivo results.
Coupling and cohesion metrics for knowledge-based systems using frames and rules
Authors: Kramer Stefan , Kaindl Hermann 
Published: January 2005

Software systems and in particular also knowledge-based systems (KBS) become increasingly large and complex. In response to this challenge, software engineering has a long tradition of advocating modularity. This has also heavily influenced object-oriented development. For measuring certain important aspects of modularity, coupling and cohesion metrics have been developed. Metrics have also attracted considerable attention for object-oriented development. For KBS development, however, no such metrics are available yet.
This article presents the core of the first metrics suite for KBS development, its coupling and cohesion metrics. These metrics measure modularity in terms of the relations induced between slots of frames through their common references in rules. We show the soundness of these metrics according to theory and report on their usefulness in practice. As a consequence, we propose using our metrics in order to improve KBS development, and developing other important metrics and assessing their theoretical soundness along these lines.
Market-based recommendation
Authors: Bohte Sander M. , Gerding Enrico , Poutré Han La 
Published: January 2005

The amount of attention space available for recommending suppliers to consumers on e-commerce sites is typically limited. We present a competitive distributed recommendation mechanism based on adaptive software agents for efficiently allocating the "consumer attention space," or banners. In the example of an electronic shopping mall, the task is delegated to the individual shops, each of which evaluates the information that is available about the consumer and his or her interests (e.g. keywords, product queries, and available parts of a profile). Shops make a monetary bid in an auction where a limited amount of "consumer attention space" for the arriving consumer is sold. Each shop is represented by a software agent that bids for each consumer. This allows shops to rapidly adapt their bidding strategy to focus on consumers interested in their offerings.
For various basic and simple models for on-line consumers, shops, and profiles, we demonstrate the feasibility of our system by evolutionary simulations as in the field of agent-based computational economics (ACE). We also develop adaptive software agents that learn bidding-strategies, based on neural networks and strategy exploration heuristics. Furthermore, we address the commercial and technological advantages of this distributed market-based approach. The mechanism we describe is not limited to the example of the electronic shopping mall, but can easily be extended to other domains.
On the scaling of congestion in the internet graph
Authors: Akella Aditya , Chawla Shuchi , Kannan Arvind , Seshan Srinivasan 
Published: January 2005

As the Internet grows in size, it becomes crucial to understand how the speeds of links in the network must improve in order to sustain the pressure of new end-nodes being added each day. Although the speeds of links in the core and at the edges improve roughly according to Moore's law, this improvement alone might not be enough. Indeed, the structure of the Internet graph and routing in the network might necessitate much faster improvements in the speeds of key links in the network.
In this paper, using a combination of analysis and extensive simulations, we show that the worst congestion in the Internet AS-level graph in fact scales poorly with the network size (<i>n</i><sup>1+ω(1)</sup>, where <i>n</i> is the number of nodes), when shortest-path routing is used to route traffic between ASes. We also show, somewhat surprisingly, that policy-based routing <i>does not</i> exacerbate the maximum congestion when compared to shortest-path routing.
Our results show that it is crucial to identify ways to alleviate this congestion to avoid some links from being perpetually congested. To this end, we show that the congestion scaling properties of Internet-like graphs can be improved dramatically by introducing moderate amounts of redundancy in the graph in terms of parallel edges between pairs of adjacent nodes.
Capacity bounds for ad hoc and hybrid wireless networks
Authors: Agarwal Ashish , Kumar P. R. 
Published: January 2005

We study the capacity of static wireless networks, both ad hoc and hybrid, under the Protocol and Physical Models of communication, proposed in [1]. For ad hoc networks with <i>n</i> nodes, we show that under the Physical Model, where signal power is assumed to attenuate as 1/r<sup>α</sup>, α > 2, the transport capacity scales as Θ(√<i>n</i>) bit-meters/sec. The same bound holds even when the nodes are allowed to approach arbitrarily close to each other and even under a more generalized notion of the Physical Model wherein the data rate is Shannon's logarithmic function of the SINR at the receiver. This result is sharp since it closes the gap that existed between the previous best known upper bound of O(<i>n</i><sup>α-1/α</sup>) and lower bound of Ω(√n).
We also show that any spatio-temporal scheduling of transmissions and their ranges that is feasible under the Protocol Model can also be realized under the Physical Model by an appropriate choice of power levels for appropriate thresholds. This allows the generalization of various lower bound constructions from the Protocol Model to the Physical Model. In particular, this provides a better lower bound on the best case transport capacity than in [1].
For hybrid networks, we consider an overlay of μ<i>n</i> randomly placed wired base stations. It has previously been shown in [6] that if all nodes adopt a common power level, then each node can be provided a throughput of at most Θ(1/log <i>n</i>) to randomly chosen destinations. Here we show that by allowing nodes to perform power control and properly choosing ν(1/log <i>n</i>), it is further possible to provide a throughput of Θ(1) to any fraction <i>f</i>, 0 < <i>f</i> < 1, of nodes. This result holds under both the Protocol and Physical models of communication. On the one hand, it shows that that the aggregate throughput capacity, measured as the sum of individual throughputs, can scale linearly in the number of nodes. On the other hand, the result underscores the importance of choosing minimum power levels for communication and suggests that simply communicating with the closest node or base station could yield good capacity even for multihop hybrid wireless networks.
Achieving speed and flexibility by separating management from protection
Authors: Leschke Tim 
Published: January 2005

The modern operating system is currently caught in a tug-of-war between two forces. At one end, there is a force that is demanding that the operating system become more flexible to handle the needs of evolving hardware and evolving user applications. At the other end, there is a force that is demanding that the operating system become more efficient to meet the needs of faster hardware. If the modern operating system does not keep pace with these two forces, it could cause the progress in computer design to become stagnant.
One possible solution to this problem is the Exokernel Operating System - an extensible (or easily modifiable) operating system developed at the Massachusetts Institute of Technology. Extensibility allows the operating system to be flexible to change and also open to optimization.
Extensibility within an operating system has resulted in several new issues. For example, extensibility seems to make customer-support harder to provide. Furthermore, some multithreaded applications perform worse in an extensible environment. Lastly, some have argued that it is optimization, not extensibility, that should be credited for the enhanced operating system speeds.
In this paper, we discuss the Exokernel Operating System with some detail. We explore some of the issues that have kept the Exokernel design from being the main-stream approach. We propose solutions to these issues and we conclude by trying to motivate the reader to embrace the Exokernel approach.
A maximum-entropy chinese parser augmented by transformation-based learning
Authors: Fung Pascale , Ngai Grace , Yang Yongsheng , Chen Benfeng 
Published: January 2005

Parsing, the task of identifying syntactic components, e.g., noun and verb phrases, in a sentence, is one of the fundamental tasks in natural language processing. Many natural language applications such as spoken-language understanding, machine translation, and information extraction, would benefit from, or even require, high accuracy parsing as a preprocessing step.
Even though most state-of-the-art statistical parsers were initially constructed for parsing in English, most of them are not language-specific, in that they do not rely on properties of the language that are specific to English. Therefore, construction of a parser in a given language becomes a matter of retraining the statistical parameters with a Treebank in the corresponding language.
The development of the Chinese treebank [Xia et al. 2000] spurred the construction of parsers for Chinese. However, Chinese as a language poses some unique problems for the development of a statistical parser, the most apparent being word segmentation. Since words in written Chinese are not delimited in the same way as in Western languages, the first problem that needs to be solved before an existing statistical method can be applied to Chinese is to identify the word boundaries. This is a step that is neglected by most pre-existing Chinese parsers, which assume that the input data has already been pre-segmented.
This article describes a character-based statistical parser, which gives the best performance to-date on the Chinese treebank data. We augment an existing maximum entropy parser with transformation-based learning, creating a parser that can operate at the character level. We present experiments that show that our parser achieves results that are close to those achievable under perfect word segmentation conditions.
Information systems outsourcing
Authors: Dibbern Jens , Goles Tim , Hirschheim Rudy , Jayatilaka Bandula 
Published: January 2005

In the last fifteen years, academic research on information systems (IS) outsourcing has evolved rapidly. Indeed the field of outsourcing research has grown so fast that there has been scant opportunity for the research community to take a collective breath, and complete a global assessment of research activities to date. This paper seeks to address this need by exploring and synthesizing the academic literature on IS outsourcing. It offers a roadmap of the IS outsourcing literature, highlighting what has been done so far, how the work fits together under a common umbrella, and what the future directions might be.
In order to adequately address the immense diversity of research on IS outsourcing and outsourcing in general, we develop a conceptual framework that helps us to categorize the literature. In particular, we look at the research objectives, methods used and theoretical foundations of the papers. In identifying the major research objectives, we view outsourcing as an organizational decision process and adapt Simon's stage model of decision making. This allows us to identify five major sourcing issues, from which at least one is covered by each academic article. These are the questions of <i>why</i> to outsource, <i>what</i> to outsource, <i>which</i> decision process to take, <i>how</i> to implement the sourcing decision, and what is the outcome of the sourcing decision. In analyzing the literature, we identify and structure the main explanatory factors and theoretical relationships within each of these sourcing stages. Based on our discussion of the research objectives, theoretical foundations and research approaches taken in the literature, we show how the various research streams hang together and we come up with a number of implications for research. Moreover, we identify a number of emerging sourcing issues. We believe that research on these "new" phenomena such as offshore outsourcing, application service providing and business process outsourcing would benefit from 'standing on the shoulders' of what has already been accomplished in the field of IS outsourcing.
Firmato
Authors: Bartal Yair , Mayer Alain , Nissim Kobbi , Wool Avishai 
Published: January 2005

In recent years packet-filtering firewalls have seen some impressive technological advances (e.g., stateful inspection, transparency, performance, etc.) and wide-spread deployment. In contrast, firewall and security <i>management</i> technology is lacking. In this paper we present <i>Firmato</i>, a firewall management toolkit, with the following distinguishing properties and components: (1) an entity-relationship model containing, in a unified form, global knowledge of the security policy and of the network topology; (2) a model definition language, which we use as an interface to define an instance of the entity-relationship model; (3) a model compiler, translating the global knowledge of the model into firewall-specific configuration files; and (4) a graphical firewall rule illustrator.
We implemented a prototype of our toolkit to work with several commercially available firewall products. This prototype was used to control an operational firewall for several months. We believe that our approach is an important step toward streamlining the process of configuring and managing firewalls, especially in complex, multi-firewall installations.