bluuebunny/crossref_metadata_2025 huggingface dataset:
Genomewide Scan Reveals Amplification of
mdr1
as a Common Denominator of Resistance to Mefloquine, Lumefantrine, and Artemisinin in Plasmodium chabaudi Malaria Parasites
Authors: Borges Sofia , Cravo Pedro , Creasey Alison , Fawcett Richard , Modrzynska Katarzyna , Rodrigues Louise , Martinelli Axel , Hunt Paul
Published: June 2011

Multidrug-resistant
Plasmodium falciparum
malaria parasites pose a threat to effective drug control, even to artemisinin-based combination therapies (ACTs). Here we used linkage group selection and Solexa whole-genome resequencing to investigate the genetic basis of resistance to component drugs of ACTs. Using the rodent malaria parasite
P. chabaudi
, we analyzed the uncloned progeny of a genetic backcross between the mefloquine-, lumefantrine-, and artemisinin-resistant mutant AS-15MF and a genetically distinct sensitive clone, AJ, following drug treatment. Genomewide scans of selection showed that parasites surviving each drug treatment bore a duplication of a segment of chromosome 12 (translocated to chromosome 04) present in AS-15MF. Whole-genome resequencing identified the size of the duplicated segment and its position on chromosome 4. The duplicated fragment extends for ∼393 kbp and contains over 100 genes, including
mdr1
, encoding the multidrug resistance P-glycoprotein homologue 1. We therefore show that resistance to chemically distinct components of ACTs is mediated by the same genetic mutation, highlighting a possible limitation of these therapies.
Borrelia burgdorferi Linear Plasmid 38 Is Dispensable for Completion of the Mouse-Tick Infectious Cycle
Authors: Dulebohn Daniel P. , Bestor Aaron , Rego Ryan O. M. , Stewart Philip E. , Rosa Patricia A.
Published: June 2011

Borrelia burgdorferi
, the causative agent of Lyme disease, exists in a complex enzootic cycle, transiting between its vector,
Ixodes
ticks, and a diverse range of vertebrate hosts.
B. burgdorferi
linear plasmid 38 (lp38) contains several genes that are differentially regulated in response to conditions mimicking the tick or mouse environments, suggesting that these plasmid-borne genes may encode proteins important for the
B. burgdorferi
infectious cycle. Some of these genes encode potential virulence factors, including hypothetical lipoproteins as well as a putative membrane transport system. To characterize the role of lp38 in the
B. burgdorferi
infectious cycle, we constructed a shuttle vector to selectively displace lp38 from the
B. burgdorferi
genome and analyzed the resulting clones to confirm the loss of lp38. We found that,
in vitro
, clones lacking lp38 were similar to isogenic wild-type bacteria, both in growth rate and in antigenic protein production. We analyzed these strains in an experimental mouse-tick infectious cycle, and our results demonstrate that clones lacking lp38 are fully infectious in a mouse, can efficiently colonize the tick vector, and are readily transmitted to a naive host.
The Neisseria meningitidis Macrophage Infectivity Potentiator Protein Induces Cross-Strain Serum Bactericidal Activity and Is a Potential Serogroup B Vaccine Candidate
Authors: Hung Miao-Chiu , Salim Omar , Williams Jeannette N. , Heckels John E. , Christodoulides Myron
Published: June 2011

A gene encoding a 29-kDa protein from
Neisseria meningitidis
serogroup B strain MC58 with homology to the macrophage infectivity potentiator (MIP) protein of
Legionella pneumophila
was cloned and expressed in
Escherichia coli
, and the purified soluble recombinant protein (rMIP) was used for immunization studies. Analysis of the predicted amino acid sequences of MIP from 13 well-characterized meningococcal strains, isolated from carriers or patients and differing in serogroup, serotype, and subtype, showed that the protein was highly conserved (98 to 100%), with only three distinct sequence types (designated I, II, and III) found. Western blotting showed that the MIP protein was expressed at similar levels by all of these strains. Immunization of mice with type I MC58 rMIP in detergent micelles and liposomes containing monophosphoryl lipid A (MPLA) induced high levels of surface-reactive antibodies with serum bactericidal activity (SBA) titers of 1/1,024 against the homologous strain. Bactericidal antibodies were also induced with the protein in saline alone and liposomes alone (titers, 1/128) but not following adsorption to Al(OH)
3
. Significantly, antisera raised against type I rMIP administered in saline or liposomes killed strains of heterologous sequence types II and III with similar SBA titers (1/128 to 1/256). Taken together, these findings suggest that rMIP can provide cross-strain protection against meningococci and should be considered a potential antigen for inclusion in new vaccines against meningococcal infection.
The Sbi Protein Is a Multifunctional Immune Evasion Factor of Staphylococcus aureus
Authors: Smith Emma Jane , Visai Livia , Kerrigan Steven W. , Speziale Pietro , Foster Timothy J.
Published: June 2011

The second immunoglobulin-binding protein (Sbi) of
Staphylococcus aureus
has two N-terminal domains that bind the Fc region of IgG in a fashion similar to that of protein A and two domains that can bind to the complement protein C3 and promote its futile consumption in the fluid phase. It has been proposed that Sbi helps bacteria to avoid innate immune defenses. By comparing a mutant defective in Sbi with mutants defective in protein A, clumping factor A, iron-regulated surface determinant H, and capsular polysaccharide, it was shown that Sbi is indeed an immune evasion factor that promotes bacterial survival in whole human blood and the avoidance of neutrophil-mediated opsonophagocytosis. Sbi is present in the culture supernatant and is also associated with the cell envelope.
S. aureus
strains that expressed truncates of Sbi lacking N-terminal domains D1 and D2 (D1D2) or D3 and D4 (D3D4) or a C-terminal truncate that was no longer retained in the cell envelope were analyzed. Both the secreted and envelope-associated forms of Sbi contributed to immune evasion. The IgG-binding domains contributed only when Sbi was attached to the cell, while only the secreted C3-binding domains were biologically active.
CD23b Isoform Expression in Human Schistosomiasis Identifies a Novel Subset of Activated B Cells
Authors: Onguru Daniel , Liang YanMei , Elliot Jennifer , Mwinzi Pauline , Ganley-Leal Lisa
Published: June 2011

Resistance to schistosomiasis is associated with increased levels of serum parasite-specific IgE. IgE exerts its functions through its cellular receptors, FcεRI and FcεRII/CD23; however, its functional significance in humans requires further characterization. We previously reported that increased levels of CD23+B cells correlate with resistance to schistosomiasis in hyperexposed populations and sought to define their potential function and relationship with IgE. We found that CD23+B cells are a heterogeneous cell population with functional and phenotypic differences. Circulating CD23+B cells are uniquely activated in schistosomiasis and express the CD23b isoform and CXCR5, the homing receptor for lymphoid follicles. High CXCR5 expression by CD23+B cells was associated with the capacity to home to the cognate ligand CXCL13. CD23-bound IgE cross-linking increased surface expression of CXCR5, suggesting that CD23+B cells home directly into the lymphoid follicles upon antigen capture. As human schistosomiasis is an intravascular parasitic infection associated with a high antigenic burden in the blood, circulating CD23+B cells may play a role in the capture and shuttling of antigens directly to splenic follicles, highlighting a new role for circulating B cells. This function likely plays an important role in the development of protective immunity to infection with schistosomes.
Differential Response of the Human Renal Proximal Tubular Epithelial Cell Line HK-2 to Shiga Toxin Types 1 and 2
Authors: Lentz Erin K. , Leyva-Illades Dinorah , Lee Moo-Seung , Cherla Rama P. , Tesh Vernon L.
Published: June 2011

Shiga toxins (Stxs) are expressed by the enteric pathogens
Shigella dysenteriae
serotype 1 and certain serotypes of
Escherichia coli
. Stx-producing bacteria cause bloody diarrhea with the potential to progress to acute renal failure. Stxs are potent protein synthesis inhibitors and are the primary virulence factors responsible for renal damage that may follow diarrheal disease. We explored the use of the immortalized human proximal tubule epithelial cell line HK-2 as an
in vitro
model of Stx-induced renal damage. We showed that these cells express abundant membrane Gb
3
and are differentially susceptible to the cytotoxic action of Stxs, being more sensitive to Shiga toxin type 1 (Stx1) than to Stx2. At early time points (24 h), HK-2 cells were significantly more sensitive to Stxs than Vero cells; however, by 72 h, Vero cell monolayers were completely destroyed while some HK-2 cells survived toxin challenge, suggesting that a subpopulation of HK-2 cells are relatively toxin resistant. Fluorescently labeled Stx1 B subunits localized to both lysosomal and endoplasmic reticulum (ER) compartments in HK-2 cells, suggesting that differences in intracellular trafficking may play a role in susceptibility to Stx-mediated cytotoxicity. Although proinflammatory cytokines were not upregulated by toxin challenge, Stx2 selectively induced the expression of two chemokines, macrophage inflammatory protein-1α (MIP-1α) and MIP-1β. Stx1 and Stx2 differentially activated components of the ER stress response in HK-2 cells. Finally, we demonstrated significant poly(ADP-ribose) polymerase (PARP) cleavage after exposure to Stx1 or Stx2. However, procaspase 3 cleavage was undetectable, suggesting that HK-2 cells may undergo apoptosis in response to Stxs in a caspase 3-independent manner.
Analysis of the Networks Controlling the Antimicrobial-Peptide-Dependent Induction of Klebsiella pneumoniae Virulence Factors
Authors: Llobet Enrique , Campos Miguel A. , Giménez Paloma , Moranta David , Bengoechea José A.
Published: June 2011

Antimicrobial peptides (APs) impose a threat to the survival of pathogens, and it is reasonable to postulate that bacteria have developed strategies to counteract them. Polymyxins are becoming the last resort to treat infections caused by multidrug-resistant Gram-negative bacteria and, similar to APs, they interact with the anionic lipopolysaccharide. Given that polymyxins and APs share the initial target, it is possible that bacterial defense mechanisms against polymyxins will be also effective against host APs. We sought to determine whether exposure to polymyxin will increase
Klebsiella pneumoniae
resistance to host APs. Indeed, exposure of
K. pneumoniae
to polymyxin induces cross-resistance not only to polymyxin itself but also to APs present in the airways. Polymyxin treatment upregulates the expression of the capsule polysaccharide operon and the loci required to modify the lipid A with aminoarabinose and palmitate with a concomitant increase in capsule and lipid A species containing such modifications. Moreover, these surface changes contribute to APs resistance and also to polymyxin-induced cross-resistance to APs. Bacterial loads of lipid A mutants in trachea and lungs of intranasally infected mice were lower than those of wild-type strain. PhoPQ, PmrAB, and the Rcs system govern polymyxin-induced transcriptional changes, and there is a cross talk between PhoPQ and the Rcs system. Our findings support the notion that
Klebsiella
activates a defense program against APs that is controlled by three signaling systems. Therapeutic strategies directed to prevent the activation of this program could be a new approach worth exploring to facilitate the clearance of the pathogen from the airways.
Long Polar Fimbriae of Enterohemorrhagic Escherichia coli O157:H7 Bind to Extracellular Matrix Proteins
Authors: Farfan Mauricio J. , Cantero Lidia , Vidal Roberto , Botkin Douglas J. , Torres Alfredo G.
Published: June 2011

Adherence to intestinal cells is a key process in infection caused by enterohemorrhagic
Escherichia coli
(EHEC). Several adhesion factors that mediate the binding of EHEC to intestinal cells have been described, but the receptors involved in their recognition are not fully characterized. Extracellular matrix (ECM) proteins might act as receptors involved in the recognition of enteric pathogens, including EHEC. In this study, we sought to characterize the binding of EHEC O157:H7 to ECM proteins commonly present in the intestine. We found that EHEC prototype strains as well as other clinical isolates adhered more abundantly to surfaces coated with fibronectin, laminin, and collagen IV. Further characterization of this phenotype, by using antiserum raised against the LpfA1 putative major fimbrial subunit and by addition of mannose, showed that a reduced binding of EHEC to ECM proteins was observed in a long polar fimbria (
lpf
) mutant. We also found that the two regulators, H-NS and Ler, had an effect in EHEC Lpf-mediated binding to ECM, supporting the roles of these tightly regulated fimbriae as adherence factors. Purified Lpf major subunit bound to all of the ECM proteins tested. Finally, increased bacterial adherence was observed when T84 cells, preincubated with ECM proteins, were infected with EHEC. Taken together, these findings suggest that the interaction of Lpf and ECM proteins contributes to the EHEC colonization of the gastrointestinal tract.
Protective Efficacy and Safety of Brucella melitensis 16MΔmucRagainst Intraperitoneal and Aerosol Challenge in BALB/c Mice
Authors: Arenas-Gamboa A. M. , Rice-Ficht A. C. , Kahl-McDonagh M. M. , Ficht T. A.
Published: June 2011

Brucellosis is a zoonosis of nearly worldwide distribution. Vaccination against this pathogen is an important control strategy to prevent the disease. Currently licensed vaccine strains used in animals are unacceptable for human use due to undesirable side effects and modest protection. Substantial progress has been made during the past 10 years toward the development of improved vaccines for brucellosis. In part, this has been achieved by the identification and characterization of live attenuated mutants that are safer in the host but still can stimulate an adequate immune response. In the present study, the identification and characterization of themucRmutant (BMEI 1364) as a vaccine candidate for brucellosis was conducted. BALB/c mice were vaccinated intraperitoneally at a dose of 105CFU with the mutant to evaluate safety and protective efficacy against intraperitoneal and aerosol challenge. All animals vaccinated with the vaccine candidate demonstrated a statistically significant degree of protection against both intraperitoneal and aerosol challenge. Safety was revealed by the absence ofBrucellaassociated pathological changes, including splenomegaly, hepatomegaly, or granulomatous disease. These results suggest that the 16MΔmucRvaccine is safe, elicits a strong protective immunity, and should be considered as a promising vaccine candidate for human use.
Context-Dependent Activation Kinetics Elicited by Soluble versus Outer Membrane Vesicle-Associated Heat-Labile Enterotoxin
Authors: Chutkan Halima , Kuehn Meta J.
Published: June 2011

EnterotoxigenicEscherichia coli(ETEC) is the leading cause of traveler's diarrhea and children's diarrhea worldwide. Among its virulence factors, ETEC produces heat-labile enterotoxin (LT). Most secreted LT is associated with outer membrane vesicles that are rich in lipopolysaccharide. The majority of prior studies have focused on soluble LT purified from ETEC periplasm. We investigated the hypothesis that the extracellular vesicle context of toxin presentation might be important in eliciting immune responses. We compared the polarized epithelial cell responses to apically applied soluble LT and LT-containing vesicles (LT+vesicles) as well as controls using a catalytically inactive mutant of LT and vesicles lacking LT. Although vesicle treatments with no or catalytically inactive LT induced a modest amount of interleukin-6 (IL-6), samples containing catalytically active LT elicited higher levels. A combination of soluble LT and LT-deficient vesicles induced significantly higher IL-6 levels than either LT or LT+vesicles alone. The responses to LT+vesicles were found to be independent of the canonical LT pathway, because the inhibition of cyclic AMP response element (CRE)-binding protein (CREB) phosphorylation did not lead to a decrease in cytokine gene expression levels. Furthermore, soluble LT caused earlier phosphorylation of CREB and activation of CRE compared with LT+vesicles. Soluble LT also led to the activation of activator protein 1, whereas LT+vesicle IL-6 responses appeared to be mediated by NF-κB. In summary, the results demonstrate that soluble LT and vesicle-bound LT elicit ultimately similar cytokine responses through distinct different activation pathways.
Elbow flexor and extensor muscle weakness in lateral epicondylalgia
Authors: Coombes Brooke K , Bisset Leanne , Vicenzino Bill
Published: June 2011

Objective

To evaluate whether deficits of elbow flexor and extensor muscle strength exist in lateral epicondylalgia (LE) in comparison with a healthy control population.

Design

Cross-sectional study.

Participants

150 participants with unilateral LE were compared with 54 healthy control participants.

Main outcome measures

Maximal isometric elbow flexion and extension strength were measured bilaterally using a purpose-built standing frame such that gripping was avoided.

Results

The authors found significant side differences in elbow extensor (−6.54 N, 95% CI −11.43 to −1.65, p=0.008, standardised mean difference (SMD) −0.45) and flexor muscle strength (−11.26 N, 95% CI −19.59 to −2.94, p=0.009, SMD −0.46) between LE and control groups. Within the LE group, only elbow extensor muscle strength deficits between sides was significant (affected–unaffected: −2.94 N, 95% CI −5.44 to −0.44).

Conclusion

Small significant deficits of elbow extensor and flexor muscle strength exist in the affected arm of unilateral LE in comparison with healthy controls. Notably, comparing elbow strength between the affected and unaffected sides in unilateral epicondylalgia is likely to underestimate these deficits.

Trial Registration

Australian New Zealand Clinical Trials Register ACTRN12609000051246.
Do guidelines on euthanasia and physician-assisted suicide in Dutch hospitals and nursing homes reflect the law? A content analysis
Authors: Hesselink B A M , Onwuteaka-Philipsen B D , Janssen A J G M , Buiting H M , Kollau M , Rietjens J A C , Pasman H R W
Published: June 2011

To describe the content of practice guidelines on euthanasia and assisted suicide (EAS) and to compare differences between settings and guidelines developed before or after enactment of the euthanasia law in 2002 by means of a content analysis. Most guidelines stated that the attending physician is responsible for the decision to grant or refuse an EAS request. Due care criteria were described in the majority of guidelines, but aspects relevant for assessing these criteria were not always described. Half of the guidelines described the role of the nurse in the performance of euthanasia. Compared with hospital guidelines, nursing home guidelines were more often stricter than the law in excluding patients with dementia (30% vs 4%) and incompetent patients (25% vs 4%). As from 2002, the guidelines were less strict in categorically excluding patients groups (32% vs 64%) and in particular incompetent patients (10% vs 29%). Healthcare institutions should accurately state the boundaries of the law, also when they prefer to set stricter boundaries for their own institution. Only then can guidelines provide adequate support for physicians and nurses in the difficult EAS decision-making process.
A clear case for conscience in healthcare practice
Authors: Birchley Giles
Published: June 2011

The value of conscience in healthcare ethics is widely debated. While some sources present it as an unquestionably positive attribute, others question both the veracity of its decisions and the effect of conscientious objection on patient access to health care. This paper argues that the right to object conscientiously should be broadened, subject to certain previsos, as there are many benefits to healthcare practice in the development of the consciences of practitioners. While effects such as the preservation of moral integrity are widely considered to benefit practitioners, this paper draws on the work of Hannah Arendt to offer several original arguments in defence of conscience that may more directly benefit patients, namely that a pang of conscience may be useful in rapidly unfolding situations in which there is no time to reflect satisfactorily upon activities and that, given the hierarchical nature of healthcare institutions, a right to defy authority on the basis of conscience may benefit junior staff who lack the institutional power to challenge the orders of superiors.
Social and cultural influences on tobacco-related health disparities among South Asians in the USA
Authors: Mukherjea Arnab , Morgan Patricia A , Snowden Lonnie R , Ling Pamela M , Ivey Susan L
Published: June 2011

Objective

To explore and understand key cultural contexts of tobacco use among South Asian communities in the USA.

Design

Focus groups, with homogeneous compositions of gender, generational status and length of time in the USA, were conducted in two distinct South Asian ethnic enclaves. Focus group findings were triangulated with observational data regarding the availability of culturally specific tobacco from commercial ethnic outlets and cultural events.

Subjects

Respondents included 88 men and women of South Asian descent, aged 18–65 years, immigrant and native born, representing diversity of religion, socioeconomic status and region of origin, with the use of at least one culturally specific tobacco product in previous 24 months.

Results

A large number of culturally specific products were commonly used by community members. Knowledge of product-specific health risks was lacking or inaccurate. Many culturally specific tobacco products were considered to have beneficial properties. South Asian tobacco items were used to preserve cultural traditions and express ethnic identity in a new dominant culture. The social and cultural values ascribed to use helped distinguish community members from mainstream society and from other minority populations.

Conclusions

Many cultural factors govern tobacco use among diverse global populations. Especially for migrants with a common regional origin, the role of ethnic identity may strongly influence culturally specific tobacco patterns. Qualitative inquiry helps elucidate such culturally framed behaviour in culturally diverse populations. These cultural contexts should be integrated into research and practice. Understanding multidimensional factors influencing non-traditional tobacco use is essential to ensure that comprehensive tobacco control strategies address tobacco-related disparities.
Selected haematological and plasma chemistry parameters in juvenile and adult degus (Octodon degus)
Authors: Jekl V. , Hauptman K. , Jeklova E. , Knotek Z.
Published: June 2011

Thirty‐five juvenile (mean age 6.3 weeks) and 35 adult (mean age 2.0 years) healthy degus (Octodon degus) were studied to investigate selected haematological and plasma biochemistry parameters. Animals were anaesthetised with isoflurane, and blood was withdrawn from the cranial vena cava. Erythrocyte, haematocrit and neutrophil counts (including the percentage of neutrophils) were significantly higher in the adult degus than in the juveniles. In contrast, the reticulocyte count, mean corpuscular volume, mean corpuscular haemoglobin, number of platelets and percentage of lymphocytes were significantly lower in the adult animals. Total protein and globulin levels were significantly higher in the adult degus. The albumin:globulin ratio and plasma levels of urea nitrogen, cholesterol, alanine aminotransferase, aspartate aminotransferase, alkaline phosphatase, potassium, total calcium and inorganic phosphorus were significantly lower in adults than in juveniles.
DETECTING COMMUTING PATTERNS BY CLUSTERING SUBTRAJECTORIES
Authors: BUCHIN KEVIN , BUCHIN MAIKE , GUDMUNDSSON JOACHIM , LÖFFLER MAARTEN , LUO JUN
Published: June 2011

In this paper we consider the problem of detecting commuting patterns in a trajectory. For this we search for similar subtrajectories. To measure spatial similarity we choose the Fréchet distance and the discrete Fréchet distance between subtrajectories, which are invariant under differences in speed. We give several approximation algorithms, and also show that the problem of finding the 'longest' subtrajectory cluster is as hard as MaxClique to compute and approximate.
STATISTICAL INFERENCE ABOUT AVAILABILITY OF SYSTEM WITH GAMMA LIFETIME AND REPAIR TIME
Authors: LU MENGYING , MI JIE
Published: June 2011

Availability is an important measure of performance of repairable system. The steady state system availability has special importance since it demonstrates the performance of a system after it has been operated for long. The statistical inference about the steady state availability are particularly useful for practitioners. Much work has been done in this regard. Most of these researches proposed certain pivotal quantities for constructing confidence intervals of the steady state availability. Assuming both the lifetime and repair time follow gamma distribution with known shape parameters and unknown scale parameters, we propose a pivotal quantity for making inferences, and further derive the likelihood ratio tests. Tables of critical values are given for the convenience of applying the two-sided likelihood ratio test. Confidence intervals are also obtained by converting the acceptance regions.
A HIERARCHICAL MARKOV RELIABILITY MODEL FOR DATA STORAGE SYSTEMS WITH MEDIA SELF-RECOVERY
Authors: JIN TONGDAN , XING LIUDONG , YU YING
Published: June 2011

A Redundant Array of Independent Disks (RAID) system with n disks or hard drives can be modeled as a k-out-of-n repairable system for which at least k operational disks are required. This paper proposes a hierarchical Markov model to estimate the reliability of RAID systems. The method encompasses Markov models for evaluating the reliability of individual disks at the lower level and the redundant model for evaluating the reliability of entire RAID at the system level. Both hardware and media failures are considered, and the media failures can be potentially recovered via the disk self-restoration mechanism. The system mean-time-to-data-loss is also derived and results are compared to those estimated from system-based Markov models. The major contribution of this work is that the reliability for RAID systems is approached by combining the redundant modeling technique with the single disk-based Markov model, thus simplifying the computational efforts. The proposed method is applied on RAID-5 and RAID-6 systems to demonstrate the applicability and performance of the new model.
REDUNDANCY ISSUES IN SOFTWARE AND HARDWARE SYSTEMS: AN OVERVIEW
Authors: JAIN MADHU , GUPTA RITU
Published: June 2011

The redundancy is a widely spread technology of building computing systems that continue to operate satisfactorily in the presence of faults occurring in hardware and software components. The principle objective of applying redundancy is achieve reliability goals subject to techno-economic constraints. Due to a plenty of applications arising virtually in both industrial and military organizations especially in embedded fault tolerance systems including telecommunication, distributed computer systems, automated manufacturing systems, etc., the reliability and its dependability measures of redundant computer-based systems have become attractive features for the systems designers and production engineers. However, even with the best design of redundant computer-based systems, software and hardware failures may still occur due to many failure mechanisms leading to serious consequences such as huge economic losses, risk to human life, etc. The objective of present survey article is to discuss various key aspects, failure consequences, methodologies of redundant systems along with software and hardware redundancy techniques which have been developed at the reliability engineering level. The methodological aspects which depict the required steps to build a block diagram composed of components in different configurations as well as Markov and non-Markov state transition diagram representing the structural system has been elaborated. Furthermore, we describe the reliability of a specific redundant system and its comparison with a non redundant system to demonstrate the tractability of proposed models and its performance analysis.
ON THE FROBENIUS–PERRON EIGENVALUES OF CARTAN MATRICES FOR SOME FINITE GROUPS
Authors: YOSHII YUTAKA
Published: June 2011

We study integrality of the Frobenius–Perron eigenvalues of the Cartan matrices for the principal blocks of some finite groups of Lie type with noncyclic abelian Sylow p-subgroups.
VIRUS AND WARNING SPREAD IN DYNAMICAL NETWORKS
Authors: LUCATERO CARLOS RODRIGUEZ , JAQUEZ ROBERTO BERNAL
Published: June 2011

Recent work on information survival in sensor and human P2P networks try to study the datum preservation or the virus spreading in a network under the dynamical system approach. Some interesting solutions propose to use non-linear dynamical systems and fixed point stability theorems, providing closed form formulas that depend on the largest eigenvalue of the dynamic system matrix. Given that in the Web there can be messages from one place to another, and that these messages can be, with some probability, new unclassified virus warning messages as well as worms or other kind of viruses, the sites can be infected very fast. The question to answer is how and when a network infection can become global and how it can be controlled or at least how to stabilize the spreading in such a way that it becomes confined below a fixed portion of the network. In this paper, we try to be a step ahead in this direction and apply classic results of the dynamical systems theory to model the behavior of a network where warning messages and viruses spread.
FINDING ATTRACTORS IN ASYNCHRONOUS BOOLEAN DYNAMICS
Authors: SKODAWESSELY THOMAS , KLEMM KONSTANTIN
Published: June 2011

We present a computational method for finding attractors (ergodic sets of states) of Boolean networks under asynchronous update. The approach is based on a systematic removal of state transitions to render the state transition graph acyclic. In this reduced state transition graph, all attractors are fixed points that can be enumerated with little effort in most instances. This attractor set is then extended to the attractor set of the original dynamics. Our numerical tests on standard Kauffman networks indicate that the method is efficient in the sense that the total number of state vectors visited grows moderately with the number of states contained in attractors.
A GRAPH-BASED SEMANTIC SIMILARITY MEASURE FOR THE GENE ONTOLOGY
Authors: ALVAREZ MARCO A. , YAN CHANGHUI
Published: June 2011

Existing methods for calculating semantic similarities between pairs of Gene Ontology (GO) terms and gene products often rely on external databases like Gene Ontology Annotation (GOA) that annotate gene products using the GO terms. This dependency leads to some limitations in real applications. Here, we present a semantic similarity algorithm (SSA), that relies exclusively on the GO. When calculating the semantic similarity between a pair of input GO terms, SSA takes into account the shortest path between them, the depth of their nearest common ancestor, and a novel similarity score calculated between the definitions of the involved GO terms. In our work, we use SSA to calculate semantic similarities between pairs of proteins by combining pairwise semantic similarities between the GO terms that annotate the involved proteins. The reliability of SSA was evaluated by comparing the resulting semantic similarities between proteins with the functional similarities between proteins derived from expert annotations or sequence similarity. Comparisons with existing state-of-the-art methods showed that SSA is highly competitive with the other methods. SSA provides a reliable measure for semantics similarity independent of external databases of functional-annotation observations.
Structural and stratigraphic evolution of the Savu Basin, Indonesia
Authors: Rigg James W. D. , Hall Robert
Published: June 2011

The Savu Basin is located in the Sunda–Banda fore-arc at the position of change from oceanic subduction to continent–arc collision. It narrows eastward and is bounded to the west by the island of Sumba that obliquely crosses the fore-arc. New seismic data and published geological observations are used to interpret Australia–Sundaland convergence history. We suggest the basin is underlain by continental crust and was close to sea level in the Early Miocene. Normal faulting in the Middle Miocene and rapid subsidence to several kilometres was driven by subduction rollback. Arc-derived volcaniclastic turbidites were transported ESE, parallel to the Sumba Ridge, and then NE. The ridge was elevated as the Australian continental margin arrived at the Banda Trench, causing debris flows and turbidites to flow northwards into the basin which is little deformed except for tilting and slumping. South of the ridge fore-arc sediments and Australian sedimentary cover were incorporated in a large accretionary complex formed as continental crust was thrust beneath the fore-arc. This is bounded to the north by the Savu and Roti Thrusts and to the south by a trough connecting the Java Trench and Timor Trough which formed by south-directed thrusting and loading.
Tectonic post-collision processes in Timor
Authors: Audley-Charles M. G.
Published: June 2011

Indian Ocean crust subducted northwards at the Banda Trench from about 12 to 4 Ma. The Australian continental margin collided with the Asian fore-arc at about 4 Ma. Gradually the Banda Trench was transformed into the fold and thrust mountains of Timor Island. Tectonic collision processes developed when all ocean crust had been subducted and Australian continental crust was refused entry to the subduction path below the Asian fore-arc. The Banda Trench was then gradually converted into a Tectonic Collision Zone (TCZ) progressively filled by two highly deformed Australian continental upper crust mega-sequences. Slowing subduction of Australian sub-crustal lithosphere after
c
. 2.5 Ma led to uplift of the TCZ that raised Timor 3 km above sea level. Asian Banda fore-arc deformation is linked to
c
. 30 km southeastwards rollback of the subducting Australian mantle lithosphere. Two Asian fore-arc nappes were thrust southwards from the Banda fore-arc onto the older of two highly deformed Australian continental margin upper crust mega-sequences. The Wetar Suture was created as a thrust at the base of Australian partially detached continental lower crust propagated into the Asian fore-arc. Re-interpretation of BIRPS seismic and gravity data for the Timor region supports this collision model.
Physical oceanography of the present day Indonesian Throughflow
Authors: Tillinger Debra
Published: June 2011

The Indonesian Throughflow (ITF) transfers
c
. 15 Sv (1 Sv=10
6
m
3
s
−1
) of relatively cool, fresh water from the tropical Pacific Ocean to the tropical Indian Ocean. Additionally, the ITF is a key interocean component of the global ocean warm water route, which returns water from the Pacific Ocean to the Atlantic Ocean to close the loop of the thermohaline overturning circulation associated with North Atlantic Deep Water. That flow consequently freshens the Indian Ocean and transports heat between basins. The ITF can also be described by the island rule, which relates the winds over the entire South Pacific Ocean to the magnitude of the ITF. El Niño-Southern Oscillation (ENSO) dominates the regional variability in the Pacific Ocean and exerts a strong control over the variability of ITF transport. The Indian Ocean responds to the ENSO signal as well, but is also influenced by the Indian Ocean Dipole, a climate phenomenon that may act independently of ENSO to affect the ITF.
The impact of ocean gateways on ENSO variability in the Miocene
Authors: Von Der Heydt Anna S. , Dijkstra Henk A.
Published: June 2011

The existence of El Niño/Southern Oscillation (ENSO) variability in past climates is still debated. Based on evidence from geological records indicating a different long-term mean climate in the tropical Pacific, a permanent El Niño state has been hyothesized to exist prior to the Plio-Pleistocene transition. However, model studies of past climate and geological records suggest that ENSO variability has existed on Earth as far back as in the Eocene and the Miocene. In the early-to-middle Miocene, climate was not only warmer than today, but oceanic gateways such as the Indonesian Passage and the Central American Seaway established deep connections between the main ocean basins. Here, we analyse the effect of increased levels of atmospheric greenhouse gases and open tropical gateways on the amplitude, period and pattern of ENSO variability using results of fully coupled climate model simulations. While our model shows only small changes in ENSO variability under increased greenhouse gas levels, it suggests a significantly stronger and less frequent ENSO due to altered oceanic gateways. In particular, a deeper and more open Indonesian Passage does not prevent a Western Pacific warm pool from developing, but it allows the warm pool to shift into the Indian Ocean.
Subsidence and uplift by slab-related mantle dynamics: a driving mechanism for the Late Cretaceous and Cenozoic evolution of continental SE Asia?
Authors: Clements Benjamin , Burgess Peter M. , Hall Robert , Cottam Michael A.
Published: June 2011

Continental SE Asia is the site of an extensive Cretaceous–Paleocene regional unconformity that extends from Indochina to Java, covering an area of
c
. 5 600 000 km
2
. The unconformity has previously been related to microcontinental collision at the Java margin that halted subduction of Tethyan oceanic lithosphere in the Late Cretaceous. However, given the disparity in size between the accreted continental fragments and area of the unconformity, together with lack of evidence for requisite crustal shortening and thickening, the unconformity is unlikely to have resulted from collisional tectonics alone. Instead, mapping of the spatial extent of the mid–Late Cretaceous subduction zone and the Cretaceous–Paleocene unconformity suggests that the unconformity could be a consequence of subduction-driven mantle processes. Cessation of subduction, descent of a northward dipping slab into the mantle, and consequent uplift and denudation of a sediment-filled Late Jurassic and Early Cretaceous dynamic topographic low help explain the extent and timing of the unconformity. Sediments started to accumulate above the unconformity from the Middle Eocene when subduction recommenced beneath Sundaland.
Basement character and basin formation in Gorontalo Bay, Sulawesi, Indonesia: new observations from the Togian Islands
Authors: Cottam M. A. , Hall R. , Forster M. A. , Boudagher-Fadel M. K.
Published: June 2011

We present a new stratigraphy for the Togian Islands, Sulawesi, and interpret the age, character and evolution of Gorontalo Bay. At its western end the bay is underlain by continental crust. The central part is underlain by Eocene to Miocene oceanic and arc rocks, although the area south of the Togian Islands could have continental crust of the Banggai-Sula microcontinent thrust beneath this and the East Arm ophiolite. Gorontalo Bay was not a significant deep bathymetric feature before the Miocene. Field relationships indicate a latest Miocene to Pliocene age for inception of the basin. Medium-K to shoshonitic volcanism in the Togian Islands is not due to subduction but reflects crustal thinning and extension in the Pliocene and Pleistocene, causing the underlying mantle to rise, decompress and melt. Extension is continuing today and is probably the cause of volcanism at Una-Una. Volcanic activity migrated west with time and volcanic products have been offset by dextral strike-slip displacement along the Balantak Fault. Extension and subsidence was driven by rollback of the subduction hinge at the North Sulawesi Trench with a possible contribution due to flow of the lower crust.
Brave, new social world
Authors: McCafferty Dennis
Published: June 2011

How three different individuals in three different countries---Brazil, Egypt, and Japan---use Facebook, Twitter, and other social-media tools.
Algorithmic composition
Authors: Edwards Michael
Published: June 2011

The composer still composes but also gets to take a programming-enabled journey of musical discovery.
Searching for Jim Gray
Authors: Hellerstein Joseph M. , Tennenhouse David L.
Published: June 2011

The volunteer search for Jim Gray, lost at sea in 2007, highlights the challenges of computer-aided emergency response.
Debugging in the (very) large
Authors: Kinshumann Kinshuman , Glerum Kirk , Greenberg Steve , Aul Gabriel , Orgovan Vince , Nichols Greg , Grant David , Loihle Gretchen , Hunt Galen
Published: June 2011

Windows Error Reporting (WER) is a distributed system that automates the processing of error reports coming from an installed base of a billion machines. WER has collected billions of error reports in 10 years of operation. It collects error data automatically and classifies errors into buckets, which are used to prioritize developer effort and report fixes to users. WER uses a progressive approach to data collection, which minimizes overhead for most reports yet allows developers to collect detailed information when needed. WER takes advantage of its scale to use error statistics as a tool in debugging; this allows developers to isolate bugs that cannot be found at smaller scale. WER has been designed for efficient operation at large scale: one pair of database servers records all the errors that occur on all Windows computers worldwide.
Articulation-Disordered Speech Recognition Using Speaker-Adaptive Acoustic Models and Personalized Articulation Patterns
Authors: Wu Chung-Hsien , Su Hung-Yu , Shen Han-Ping
Published: June 2011

This article presents a novel approach to speaker-adaptive recognition of speech from articulation-disordered speakers without a large amount of adaptation data. An unsupervised, incremental adaptation method is adopted for personalized model adaptation based on the recognized syllables with high recognition confidence from an automatic speech recognition (ASR) system. For articulation pattern discovery, the manually transcribed syllables and the corresponding recognized syllables are associated with each other using articulatory features. The Apriori algorithm is applied to discover the articulation patterns in the corpus, which are then used to construct a personalized pronunciation dictionary to improve the recognition accuracy of the ASR. The experimental results indicate that the proposed adaptation method achieves a syllable error rate reduction of 6.1%, outperforming the conventional adaptation methods that have a syllable error rate reduction of 3.8%. In addition, an average syllable error rate reduction of 5.04% is obtained for the ASR using the expanded pronunciation dictionary.
Weighted Vote-Based Classifier Ensemble for Named Entity Recognition
Authors: Ekbal Asif , Saha Sriparna
Published: June 2011

In this article, we report the search capability of Genetic Algorithm (GA) to construct a weighted vote-based classifier ensemble for Named Entity Recognition (NER). Our underlying assumption is that the reliability of predictions of each classifier differs among the various named entity (NE) classes. Thus, it is necessary to quantify the amount of voting of a particular classifier for a particular output class. Here, an attempt is made to determine the appropriate weights of voting for each class in each classifier using GA. The proposed technique is evaluated for four leading Indian languages, namely Bengali, Hindi, Telugu, and Oriya, which are all resource-poor in nature. Evaluation results yield the recall, precision and F-measure values of 92.08%, 92.22%, and 92.15%, respectively for Bengali; 96.07%, 88.63%, and 92.20%, respectively for Hindi; 78.82%, 91.26%, and 84.59%, respectively for Telugu; and 88.56%, 89.98%, and 89.26%, respectively for Oriya. Finally, we evaluate our proposed approach with the benchmark dataset of CoNLL-2003 shared task that yields the overall recall, precision, and
F
-measure values of 88.72%, 88.64%, and 88.68%, respectively. Results also show that the vote based classifier ensemble identified by the GA-based approach outperforms all the individual classifiers, three conventional baseline ensembles, and some other existing ensemble techniques. In a part of the article, we formulate the problem of feature selection in any classifier under the single objective optimization framework and show that our proposed classifier ensemble attains superior performance to it.
Improving performance, perceived usability, and aesthetics with culturally adaptive user interfaces
Authors: Reinecke Katharina , Bernstein Abraham
Published: June 2011

When we investigate the usability and aesthetics of user interfaces, we rarely take into account that what users perceive as beautiful and usable strongly depends on their cultural background. In this paper, we argue that it is not feasible to design one interface that appeals to all users of an increasingly global audience. Instead, we propose to design culturally adaptive systems, which automatically generate personalized interfaces that correspond to cultural preferences. In an evaluation of one such system, we demonstrate that a majority of international participants preferred their personalized versions over a nonadapted interface of the same Website. Results show that users were 22% faster using the culturally adapted interface, needed fewer clicks, and made fewer errors, in line with subjective results demonstrating that they found the adapted version significantly easier to use. Our findings show that interfaces that adapt to cultural preferences can immensely increase the user experience.
Walking improves your cognitive map in environments that are large-scale and large in extent
Authors: Ruddle Roy A. , Volkova Ekaterina , Bülthoff Heinrich H.
Published: June 2011

This study investigated the effect of body-based information (proprioception, etc.) when participants navigated large-scale virtual marketplaces that were either small (Experiment 1) or large in extent (Experiment 2). Extent refers to the size of an environment, whereas scale refers to whether people have to travel through an environment to see the detail necessary for navigation. Each participant was provided with full body-based information (walking through the virtual marketplaces in a large tracking hall or on an omnidirectional treadmill), just the translational component of body-based information (walking on a linear treadmill, but turning with a joystick), just the rotational component (physically turning but using a joystick to translate) or no body-based information (joysticks to translate and rotate). In large and small environments translational body-based information significantly improved the accuracy of participants' cognitive maps, measured using estimates of direction and relative straight line distance but, on its own, rotational body-based information had no effect. In environments of small extent, full body-based information also improved participants' navigational performance. The experiments show that locomotion devices such as linear treadmills would bring substantial benefits to virtual environment applications where large spaces are navigated, and theories of human navigation need to reconsider the contribution made by body-based information, and distinguish between environmental scale and extent.