bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Structure and Distribution of the Colibactin Genomic Island among Members of the Family
Enterobacteriaceae
Authors: Putze Johannes , Hennequin Claire , Nougayrède Jean-Philippe , Zhang Wenlan , Homburg Stefan , Karch Helge , Bringer Marie-Agnés , Fayolle Corinne , Carniel Elisabeth , Rabsch Wolfgang , Oelschlaeger Tobias A. , Oswald Eric , Forestier Christiane , Hacker Jörg , Dobrindt Ulrich 
Published: September 2009

ABSTRACT

A genomic island encoding the biosynthesis and secretion pathway of putative hybrid nonribosomal peptide-polyketide colibactin has been recently described in
Escherichia coli
. Colibactin acts as a cyclomodulin and blocks the eukaryotic cell cycle. The origin and prevalence of the colibactin island among enterobacteria are unknown. We therefore screened 1,565 isolates of different genera and species related to the
Enterobacteriaceae
by PCR for the presence of this DNA element. The island was detected not only in
E. coli
but also in
Klebsiella pneumoniae
,
Enterobacter aerogenes
, and
Citrobacter koseri
isolates. It was highly conserved among these species and was always associated with the yersiniabactin determinant. Structural variations between individual strains were only observed in an intergenic region containing variable numbers of tandem repeats. In
E. coli
, the colibactin island was usually restricted to isolates of phylogenetic group B2 and inserted at the
asnW
tRNA locus. Interestingly, in
K. pneumoniae
,
E. aerogenes
,
C. koseri
, and three
E. coli
strains of phylogenetic group B1, the functional colibactin determinant was associated with a genetic element similar to the integrative and conjugative elements ICE
Ec1
and ICE
Kp1
and to several enterobacterial plasmids. Different
asn
tRNA genes served as chromosomal insertion sites of the ICE-associated colibactin determinant:
asnU
in the three
E. coli
strains of ECOR group B1, and different
asn
tRNA loci in
K. pneumoniae
. The detection of the colibactin genes associated with an ICE-like element in several enterobacteria provides new insights into the spread of this gene cluster and its putative mode of transfer. Our results shed light on the mechanisms of genetic exchange between members of the family
Enterobacteriaceae
.
Mycobacteria Exploit p38 Signaling To Affect CD1 Expression and Lipid Antigen Presentation by Human Dendritic Cells
Authors: Gagliardi Maria Cristina , Teloni Raffaela , Giannoni Federico , Mariotti Sabrina , Remoli Maria Elena , Sargentini Valeria , Videtta Melissa , Pardini Manuela , De Libero Gennaro , Coccia Eliana Marina , Nisini Roberto 
Published: September 2009

ABSTRACTGroup I CD1 proteins are specialized antigen-presenting molecules that present both microbial and self lipid antigens to CD1-restricted α/β T lymphocytes. The production of high levels of gamma interferon and lysis of infected macrophages by lipid-specific T lymphocytes are believed to play pivotal roles mainly in the defense against mycobacterial infections. We previously demonstrated thatMycobacterium tuberculosisand bacillus Calmette-Guérin (Mycobacterium bovisBCG) induce human monocytes to differentiate into CD1−dendritic cells (DC), which cannot present lipid antigens to specific T cells. Here, we show that in human monocytes mycobacteria trigger phosphorylation of p38 mitogen-activated protein kinase to inhibit CD1 expression in DC derived from infected monocytes. Pretreatment with a specific p38 inhibitor renders monocytes insensitive to mycobacterial subversion and allows them to differentiate into CD1+DC, which are fully capable of presenting lipid antigens to specific T cells. We also report that one of the pathogen recognition receptors triggered by BCG to activate p38 is complement receptor 3 (CR3), as shown by reduced p38 phosphorylation and partial reestablishment of CD1 membrane expression obtained by CR3 blockade before infection. In conclusion, we propose that p38 signaling is a novel pathway exploited by mycobacteria to affect the expression of CD1 antigen-presenting cells and avoid immune recognition.
The Major Neutralizing Antibody Responses to Recombinant Anthrax Lethal and Edema Factors Are Directed to Non-Cross-Reactive Epitopes
Authors: Nguyen Melissa L. , Terzyan Simon , Ballard Jimmy D. , James Judith A. , Farris A. Darise 
Published: September 2009

ABSTRACTAnthrax lethal and edema toxins (LeTx and EdTx, respectively) form by binding of lethal factor (LF) or edema factor (EF) to the pore-forming moiety protective antigen (PA). Immunity to LF and EF protects animals from anthrax spore challenge and neutralizes anthrax toxins. The goal of the present study is to identify linear B-cell epitopes of EF and to determine the relative contributions of cross-reactive antibodies of EF and LF to LeTx and EdTx neutralization. A/J mice were immunized with recombinant LF (rLF) or rEF. Pools of LF or EF immune sera were tested for reactivity to rLF or rEF by enzyme-linked immunosorbent assays, in vitro neutralization of LeTx and EdTx, and binding to solid-phase LF and EF decapeptides. Cross-reactive antibodies were isolated by column absorption of EF-binding antibodies from LF immune sera and by column absorption of LF-binding antibodies from EF immune sera. The resulting fractions were subjected to the same assays. Major cross-reactive epitopes were identified as EF amino acids (aa) 257 to 268 and LF aa 265 to 274. Whole LF and EF immune sera neutralized LeTx and EdTx, respectively. However, LF sera did not neutralize EdTx, nor did EF sera neutralize LeTx. Purified cross-reactive immunoglobulin G also failed to cross-neutralize. Cross-reactive B-cell epitopes in the PA-binding domains of whole rLF and rEF occur and have been identified; however, the major anthrax toxin-neutralizing humoral responses to these antigens are constituted by non-cross-reactive epitopes. This work increases understanding of the immunogenicity of EF and LF and offers perspective for the development of new strategies for vaccination against anthrax.
Yersinia pseudotuberculosisVirulence Determinants Invasin, YopE, and YopT Modulate RhoG Activity and Localization
Authors: Mohammadi Sina , Isberg Ralph R. 
Published: September 2009

ABSTRACTTheYersinia pseudotuberculosissurface protein invasin binds to multiple β1 integrins with high affinity, leading to misregulation of Rac1 activity. Upon host cell binding, alteration of Rho GTPase activity results from the action of severalYersiniaouter proteins (Yops) that are translocated into the cytoplasm. We report here that three virulence determinants encoded byY. pseudotuberculosismanipulate the Rho GTPase RhoG.Y. pseudotuberculosisbinding to cells caused robust recruitment of RhoG to the site of attachment, which required high-affinity invasin-β1 integrin association. Furthermore, inactivation of RhoG significantly reduced the efficiency of invasin-mediated bacterial internalization. To investigate the activation state of RhoG, a fluorescence resonance energy transfer-based activation biosensor was developed and used to show distinct spatial activation of RhoG at the site of bacterial attachment. The biosensor was also used to show efficient RhoG inactivation byY. pseudotuberculosisYopE, a potent Rho GTPase activating protein. Additionally, RhoG mislocalization by the prenylcysteine endoprotease YopT was demonstrated by two independent assays. Functional bacterial uptake experiments demonstrated that RhoG activation can bypass a deficit in Rac1 activity. Interestingly, increasing the size of the particle gave results more consistent with a linear pathway, in which RhoG acts as an upstream activator of Rac1, indicating that increased surface area introduces constraints on the signaling pathways required for efficient internalization. Taken together, these data demonstrate the misregulation of RhoG by multipleY. pseudotuberculosisvirulence determinants. Since RhoG is imperative for proper neutrophil function, this misregulation may represent a unique mechanism by whichYersiniaspecies dampen the immune response.
Babesia divergens
Apical Membrane Antigen 1 and Its Interaction with the Human Red Blood Cell
Authors: Montero Estrella , Rodriguez Marilis , Oksov Yelena , Lobo Cheryl A. 
Published: September 2009

ABSTRACT

Multiple parasite ligand-erythrocyte receptor interactions must occur for successful
Babesia
and
Plasmodium
invasion of the human red cell. One such parasite ligand is the apical membrane antigen 1 (AMA1) which is a conserved apicomplexan protein present in the micronemes and then secreted onto the surface of the merozoite. Much evidence exists for a vital role for AMA1 in host cell invasion; however, its interaction with the host erythrocyte has remained controversial. In this paper, we present a detailed characterization of a
Babesia divergens
homolog of AMA1 (BdAMA1), and taking advantage of the relatively high amounts of native BdAMA1 available from the parasite culture system, show that proteolytic products of native BdAMA1 bind to a trypsin- and chymotrypsin-sensitive receptor on the red blood cell. Moreover, immuno-electron microscopic images of the
B. divergens
merozoite captured during invasion offer additional evidence of the presence of BdAMA1 on the red cell membrane. Given the importance of AMA1 in invasion and the central role invasion plays in pathogenesis, these studies have implications both for novel drug design and for the development of new vaccine approaches aimed at interfering with AMA1 function.
Restriction of
L
egionella pneumophila
Replication in Macrophages Requires Concerted Action of the Transcriptional Regulators Irf1 and Irf8 and Nod-Like Receptors Naip5 and Nlrc4
Authors: Fortier Anne , Doiron Karine , Saleh Maya , Grinstein Sergio , Gros Philippe 
Published: September 2009

ABSTRACT

The unique permissiveness of A/J mouse macrophages for replication of
Legionella pneumophila
is caused by a deficiency in the Nod-like receptor (NLR) protein and intracellular sensor for
L. pneumophila
flagellin (
Naip5
). The signaling pathways and proteins activated by Naip5 sensing in macrophages were investigated. Transcript profiling of macrophages from susceptible A/J mice and from resistant A/J mice harboring a transgenic wild-type copy of
Naip5
at 4 h following
L. pneumophila
infection suggested that two members of the Irf transcriptional regulator family, Irf1 and Irf8, are regulated in response to Naip5 sensing of
L. pneumophila
. We show that macrophages having defective alleles of either
Irf1
(
Irf1
−
/
−
) or its heterodimerization partner gene
Irf8
(

Irf8
R294C

) become permissive for
L. pneumophila
replication, indicating that both the Irf1 and Irf8 proteins are essential for macrophage defense against
L. pneumophila
. Moreover, macrophages doubly heterozygous (

Naip5
AJ/WT
Irf8
R294C/WT

or
Nlrc4
−/+

Irf8
R294C/WT

) for combined loss-of-function mutations in
Irf8
and in either
Naip5
or
Nlrc4
are highly susceptible to
L. pneumophila
, indicating that there is a strong genetic interaction between
Irf8
and the NLR protein family in the macrophage response to
L. pneumophila. Legionella
-containing phagosomes (LCPs) formed in permissive
Irf1
−
/
−
or

Irf8
R294C

macrophages behave like LCPs formed in
Naip5
-insufficient and
Nlrc4
-deficient macrophages which fail to acidify. These results suggest that, in addition to
Naip5
and
Nlrc4
,
Irf1
and
Irf8
play a critical role in the early response of macrophages to infection with
L. pneumophila
, including antagonizing the ability of
L. pneumophila
to block phagosome acidification. They also suggest that flagellin sensing by the NLR proteins Naip5 and Nlrc4 may be coupled to Irf1-Irf8-mediated transcriptional activation of key effector genes essential for macrophage resistance to
L. pneumophila
infection.
PERTURBATIONS OF DARK MATTER GRAVITY
Authors: MAIA M. D. , CAPISTRANO A. J. S. , MULLER D. 
Published: September 2009

Until recently the study of the gravitational field of dark matter was primarily concerned with its local effects on the motion of stars in galaxies and galaxy clusters. On the other hand, the WMAP experiment has shown that the gravitational field produced by dark matter amplifies the higher acoustic modes of the CMBR power spectrum, more intensely than the gravitational field of baryons. Such a wide range of experimental evidences from cosmology to local gravity suggests the necessity of a comprehensive analysis of the dark matter gravitational field per se, regardless of any other attributes that dark matter may eventually possess. In this paper we introduce and apply Nash's theory of perturbative geometry to the study of the dark matter gravitational field alone, in a higher-dimensional framework. It is shown that the dark matter gravitational perturbations in the early universe can be explained by the extrinsic curvature of the standard cosmology. Together with the estimated presence of massive neutrinos, such geometric perturbation is compatible not only with the observed power spectrum in the WMAP experiment but also with the most recent data on the accelerated expansion of the universe. It is possible that the same structure formation exists locally, such as in the cases of young galaxies or in cluster collisions. In most other cases it seems to have ceased when the extrinsic curvature becomes negligible, leading to Einstein's equations in four dimensions. The slow motion of stars in galaxies and the motion of plasma substructures in nearly colliding clusters are calculated with the geodesic equation for a slowly moving object in a gravitational field of arbitrary strength.
Small synopses for group-by query verification on outsourced data streams
Authors: Yi Ke , Li Feifei , Cormode Graham , Hadjieleftheriou Marios , Kollios George , Srivastava Divesh 
Published: September 2009

Due to the overwhelming flow of information in many data stream applications, data outsourcing is a natural and effective paradigm for individual businesses to address the issue of scale. In the standard data outsourcing model, the data owner outsources streaming data to one or more third-party servers, which answer queries posed by a potentially large number of clients on the data owner's behalf. Data outsourcing intrinsically raises issues of trust, making outsourced query assurance on data streams a problem with important practical implications. Existing solutions proposed in this model all build upon cryptographic primitives such as signatures and collision-resistant hash functions, which only work for certain types of queries, for example, simple selection/aggregation queries.
In this article, we consider another common type of queries, namely, “GROUP BY, SUM” queries, which previous techniques fail to support. Our new solutions are not based on cryptographic primitives, but instead use algebraic and probabilistic techniques to compute a small synopsis on the true query result, which is then communicated to the client so as to verify the correctness of the query result returned by the server. The synopsis uses a constant amount of space irrespective of the result size, has an extremely small probability of failure, and can be maintained using no extra space when the query result changes as elements stream by. We then generalize our synopsis to allow some tolerance on the number of erroneous groups, in order to support semantic load shedding on the server. When the number of erroneous groups is indeed tolerable, the synopsis can be strengthened so that we can locate and even correct these errors. Finally, we implement our techniques and perform an empirical evaluation using live network traffic.
Student use of the PeerWise system
Authors: Denny Paul , Luxton-Reilly Andrew , Hamer John 
Published: September 2009

PeerWise is a web-based system that supports the creation of student-generated test banks of multiple choice questions. Students contribute question stems and answers, provide explanations, answer questions contributed by other students, rate questions for difficulty and quality, and participate in on-line discussions of all these activities.
In 2007, the system was used in four computing classes that varied in level, instructors, and student reward. We present results that show common patterns of response from students, and outline some initial investigations into the impact of the system on student performance. Our main findings are: external motivators are needed only for question generation; exam performance is correlated with participation in on-line discussions; and, despite student enthusiasm, drill-and-practice use does not contribute to exam success.
VDE
Authors: Goldweber Michael , Davoli Renzo 
Published: September 2009

Emulators have long been a valuable tool in teaching. Particularly in the OS course, emulators have allowed students to experiment meaningfully with different machine architectures. Furthermore, many such tools run in user-mode, allowing students to operate as system administrators without the concomitant security risks. Virtual Distributed Ethernet (VDE) is a system which emulates, in user-mode, all aspects of an internet, including switches, routers, communication lines, etc, in a completely realistic manner, consistent with the operation of such artifacts in the real world.
VDE's can be implemented on a single computer, spread over several machines on the same LAN or scattered across the Internet. A VDE can interoperate with both real systems (via standard virtual interface/connectivity tools) and several virtual machine environments, support encryption, and actually run fast enough to support real applications. Furthermore, a VDE can interface/interoperate with real networks. VDN's have proven highly effective in supporting both undergraduate and graduate networking courses, and a wide range of student experiments and projects.
Spamulator
Authors: Aycock John , Crawford Heather , deGraaf Rennie 
Published: September 2009

We have developed an Internet simulator - the "Spamulator" - for a course on spam and spyware, a simulator that allows us to simulate the network services provided by a million domains. The Spamulator is lightweight in its resource usage, running on a single computer, and we currently have implementations for two different platforms.
Students interact with the Spamulator using unmodified client software, like web browsers. Alternatively, students can write their own software to use the simulated Internet using any programming language, without contrived constraints or special libraries. Furthermore, the Spamulator is extensible, making it useful as a research tool. It could easily be used for assignments on networking, peer-to-peer networks, distributed systems, and its lightweight nature allows large-scale experiments to be conducted even by underequipped institutions.
We discuss the motivation, design, and implementation of the Spamulator, and our experience with it in the spam and spyware class.
What is masters level education in informatics?
Authors: Caspersen Michael , Cassell Lillian , Davies Gordon , Pears Arnold , Seidman Stephen , Topi Heikki 
Published: September 2009

Adoption of the Bologna Accord in the European Higher Education Area (EHEA) represents a concerted move towards harmonisation of educational outcomes in higher education at the Bachelor, Masters and PhD levels.
At a time when European systems are undergoing significant examination and modification, this project addresses the need for greater understanding of the nature of Masters level education in the Informatics disciplines across Europe and the United States. The poster presents the current findings of the project, and is intended to prompt discussion about the content and expected outcomes of such programmes world-wide.
Evaluating the extent to which sociability and social presence affects learning performance
Authors: Charlton Terence , Marshall Lindsay , Devlin Marie 
Published: September 2009

Active Learning in Computing (ALiC) is the first Centre for Excellence in Teaching and Learning (CETL) project for Computing Science in England. Funded by HEFCE, the initiative seeks to prepare students for the realities of working in their chosen field by aligning their learning experiences and transferable skill sets with those sought by today's software engineering industry. One way ALiC achieves this is by introducing cross-site, collaborative group-programming tasks into the curriculum. Running over an academic year, this approach encourages active interaction and dialogue between student teams at Newcastle and Durham universities, and develops strong, real-world problem solving skills in participants.
The ALiC project has thus far generated a great deal of positive feedback from undergraduates, and we feel our approach to inter-institutional teamwork offers students a realistic and relevant "real world" experience [2]. However, we are also becoming increasingly aware that time and resource pressures can make it difficult for students to maintain adequate levels of communication for any length of time [4], and once a team disperses it becomes difficult for its members to preserve the channels needed to interact and collaborate effectively.

Consequently, an emerging area of research at Newcastle University concerns how learning can be enhanced through the use of computer-mediated social networking environments - online communities such as
Facebook, Friendster
and
Bebo
- through which registered users connect with friends and colleagues to explore similar interests and activities. In a collaborative educational context, these online social networking services offer an attractive means to foster student interaction and community building by providing a means to explore the common ground that exists between participants. [1]

To that end, we intend to embed the communication and "social awareness" affordances - profile creation, synchronous and asynchronous chat, status updates, etc. - of popular social networking sites into our undergraduate, cross-site software engineering projects [3]. Social network analysis will be used to identify, map and analyse the flow of information and resources between distributed team members.

The pedagogic motivation behind this work is to foster greater group-oriented interaction by filling the communication void that often arises between face-to-face meetings [5]. By reducing the geographic and temporal barriers to interaction and community formation (especially where 'peripheral', passive team members are concerned), team members will become increasingly aware of each others' skills, personalities, work rhythms and needs - both online
and
off - within a pre-existing, persistent, convenient infrastructure.