bluuebunny/crossref_metadata_2025 huggingface dataset:
Towards peptide‐based 2D and 3D scaffolds for tissue engineering in Otolaryngology
Authors: Abelardo E. , Banwell E. , Birchall M. , Woolfson D.
Published: December 2008

Background.  There is no ideal substitute for the extracellular matrix (ECM) in tissue engineering. We aim to develop peptide‐based fibrous and hydrogel materials as potential scaffolds for 2‐/3‐D culture in vitro and in vivo.

Methods.  Unlike other peptide scaffolds, we employed a system using α‐helical units with two complementary peptides, which combine to yield a sticky ended building block for fibre assembly (self‐assembly fibres, SAFs). This allows control over assembly, and brings utility as either peptide can be complemented or replaced by targeted bioactive peptides to alter morphology and/or add function.

Results.  Our first designs, standard SAFs, exclusively rendered thickened, lengthened and stiff fibres (dimensions ≅ 50 nm × 10 μm) that settled out of solution. In recent designs (hSAFs), the solvent‐exposed surfaces of the α‐helices were engineered to promote fibre–fibre interactions and gel formation.

Conclusions.  We have produced a series of responsive materials with properties of interest in the search for an ideal ECM replacement. These designs give hSAFs great promise for future human application, such as laryngeal nerve repair, tissue engineering support or vocal lamina propria replacement.
Diagnosis of laryngotracheal stenosis during routine spirometry using the ‘Expiratory Disproportion Index’
Authors: Nouraei S.A.R. , Murphy K. , Nouraei S.M. , Patel A. , Cummin A.R. , Howard D.J. , Sandhu G.S.
Published: December 2008

Objectives.  Laryngotracheal stenosis (LTS) is an under‐recognized cause of dyspnoea and ‘wheeze’. Early treatment improves outcome while diagnostic failure leads to treatment for presumed ‘resistant’ broncho‐pulmonary pathology which increases morbidity and places the patient at ongoing risk of acute‐on‐chronic airway obstruction. The diagnostic challenge of LTS, which is an uncommon cause of a common clinical presentation lies in identifying index cases without having to subject masses of patients to unnecessary and invasive tests. We evaluated the utility of spirometry, particularly the ‘Expiratory Disproportion Index’ (EDI) in differentiating between LTS and other respiratory conditions.

Methods.  Diagnostic utility of EDI (FEV1/PEFR) was investigated in 9621 patients, including 3118 volunteers, 3461 patients with COPD, 1650 asthmatics, 920 patients with pulmonary fibroses, 332 patients with rare lung diseases, and 140 patients with LTS. The dataset was randomly spliced. One set was used for diagnostic rule extraction and the second for validation.

Results.  Area under the ROC curve for differentiating LTS from other broncho‐pulmonary diagnoses was 0.985 ± 0.011. At a threshold of 9, sensitivity of 93.4% and specificity of 96.8% were achieved. There was a significant correlation between residual tracheal cross‐section and EDI (r = 0.61; P < 0.0001).

Conclusions.  EDI is a sensitive and specific spirometric test for LTS and can reliably rule in or rule out this diagnosis. It is based on PEFR‐FEV1 disproportionation, which almost exclusively occurs in patients with supra‐carinal stenosis. We recommend its use for screening defined at‐risk populations like post‐intensive‐care and Wegener's patients, and suggest more general application in evaluating patients with dyspnoea.
Contamination of postoperative head and neck wounds with urogenital microbes
Authors: Anwar M. , Awad Z. , Ghufoor K.
Published: December 2008

Objectives.  To investigate the impact of mixing surgical subspecialty patients on postoperative wound infections.

Method.  A retrospective analysis of postoperative wound infections in head and neck surgery patients before and after mixing them with urology patients. We selected two periods that are identical in duration and seasonal spread. The first was from March 2005 to November 2005 and the second was from March 2006 to November 2006.

Results.  1381 patients underwent head and neck surgery at our institute in the two periods; 705 in the first and 676 in the second. The number of patients with positive swabs was 19 (2.7%) in the first group and 28 (4.1%) in the second group. Positive swabs (infective episodes) increased from 93 (13.2%) to 135 (20%) and the monthly breakdown of the two periods showed a statistically significant increase (P = 0.047). Urogenital microorganisms were the main factor contributing to the increase in wound infection rates in the second period (P = 0.008). Other organisms like MRSA, remained statistically unchanged (P = 0.464).

Conclusions.  We recommend that head and neck surgery patients are better managed on separate wards. If this is not possible, extra attention should be paid to prevent cross infection. Clinicians must have a low threshold of suspecting relevant microorganisms when other specialty patients are on the same ward.
Clinical Characteristics of an Afrikaner Founder Population Recruited for a Schizophrenia Genetic Study
Authors: Roos Johannes Lodewikus , Pretorius Herman Walter , Karayiorgou Maria
Published: December 2008

The clinical characteristics of an Afrikaner founder population sample recruited for a schizophrenia genetic study are described. Comparisons on several clinical characteristics between this sample and a U.S. sample of schizophrenia patients show that generalization of findings in a founder population to the population at large is applicable. The assessment of the frequency of the 22q11 deletion in Afrikaner schizophrenia patients is approximately 2%, similar to findings in a U.S. sample. Results of analysis of early non‐psychotic deviant behavior in subjects under the age of 10 years in the Afrikaner population broadly replicated findings in a U.S. sample. Approximately half of male schizophrenia patients and a quarter of female patients in the Afrikaner schizophrenia database used or abused cannabis. Male users of cannabis with severe early deviant behavior had the lowest mean age of criteria onset, namely 18.4 years. These findings confirm previous findings, indicating that early deviance is linked to later outcome of disease. The clinical characteristics and premorbid variables in 12 childhood‐onset Afrikaner schizophrenia patients thus far recruited in this study compare favorably with what is known about childhood‐onset schizophrenia in a U.S. sample. The prevalence of co‐morbid OCD/OCS in this Afrikaner schizophrenia founder sample was 13.2% which is in keeping with that of co‐morbid OCD in schizophrenia, estimated at 12.2% by the U.S. National Institute of Mental Health. These findings confirm that the clinical characteristics of a schizophrenia sample drawn from the Afrikaner founder population can be generalized to the schizophrenia population at large when compared to findings reported in the literature.
The Year in Human and Medical Genetics
Authors: Smith Moyra
Published: December 2008

The breadth and scope of new information makes difficult a selection of topics to be included in a limited review of highlights of the year. Admittedly, the choices are idiosyncratic. The eight topics presented here are (1) structural and copy number variants in the human genome; (2) progress in defining genetic factors in the etiology of schizophrenia; (3) microRNAs in central nervous system development and function; (4) progress in elucidation of risk factors for complex common disorders through large scale association studies; (5) epigenetics and the epigenomic era; (6) reprogramming of somatic cell nuclei to generate pluripotent stem cells; (7) new concepts regarding factors involved in sexual differentiation; and (8) Duffy blood group antigens: new concepts, and new discoveries on the role of these antigens in malaria and HIV–AIDS.
Developing an Effective Romani Integration Strategy: Experiences of Ethnoculturally Neutral and Specific Policies in the Czech Republic1
Authors: Cashman Laura
Published: December 2008

While the question of how to integrate Romani communities has increased in political significance since the 1990s, a consensus has yet to be reached on how best to design integration policies for such a heterogeneous group of people. This article examines debates on whether ethnoculturally specific or neutral policies are more appropriate. Using the Czech Romani integration policy as a case study, it identifies as a significant problem the conflation of the Romani ethnic identity with the low socio‐economic status of many (but not all) Roma. This has led to a policy focus on programmes to tackle social deprivation rather than addressing the discrimination which affects all Roma regardless of class. As a consequence of the decentralisation of power in the Czech Republic and the ingrained nature of anti‐Romani prejudice, policies, whether ethnoculturally neutral or specific, will be implemented or rejected at the local level on the basis of local priorities.
Civic and Ethnic Conceptions of Nationhood on the Peruvian–Chilean Frontier, 1880–1930*
Authors: Skuban William E.
Published: December 2008

Using Hans Kohn's classic distinction between the Western, political, or civic model of nationalism, and the Eastern, genealogical, or ethnic model, this article analyses the process of nationalism during perhaps the most contentious border dispute in South American history: the Peruvian–Chilean frontier after the War of the Pacific (1879–1883). This article argues that while Kohn's modular dichotomy remains analytically useful in isolating the principles arbitrarily used by Chilean and Peruvian political elites in their official national projects, it underestimates the ways in which various sectors of local society responded to, rejected, or renegotiated these projects.
Transnationalism and the Development of the Deterritorialised Tongan Nation‐State
Authors: Wallis Joanne
Published: December 2008

The Kingdom of Tonga is commonly referred to as a ‘small island developing state’, and is consequently said to experience challenges that hinder its development. Yet significant levels of Tongan migration – and subsequent remittances – have led commentators to challenge this pessimistic view. In particular, Tonga has been characterised as a ‘deterritorialised nation‐state’, whereby the ‘state’ remains the geographically bounded territory of Tonga; while the ‘nation‐state’ consists of all Tongans, including those overseas. This article seeks to build on previous literature to provide a detailed consideration of how the deterritorialised Tongan nation‐state works in relation to the different dimensions of Tongan life.
The Importance of Culture in Civic Nations: Culture and the Republic in France
Authors: Martigny Vincent
Published: December 2008

This article discusses Hans Kohn's argument that civic nations pay little attention to cultural claims in their definition and practice of citizenship, by looking at the political system in France and its relation to culture. Contrary to Kohn's analysis, culture has played – and still plays – a fundamental role in the definition and modus vivendi of the civic republic in France, through a form of cultural nationalism implemented by the state. It is also argued that the opposition between civic and ethno‐cultural nations can be misguided. Indeed the French civic nation can be conceived of as ‘cultural’ while rejecting ethnicity in its definition of citizenship. This calls for the redefinition of Kohn's dichotomy and mismatch between culture and ethnicity.
Ethno‐Religious Identity and Sectarian Civil Society: A Case from India
Authors: Sahoo Sarbeswar
Published: December 2008

This paper analyses the role of Rajasthan Vanvasi Kalyan Parishad (RVKP), an ethnic Hindu(tva) organisation, among the tribal populations in south Rajasthan. It argues that the RVKP has been able to enhance its legitimacy and expand its socio‐political support base among the tribals through a well‐articulated and planned process of ‘ethnification’. This process has been carried out in four basic ways: (1) utilising development projects as means to spread the ideology of Hindutva, (2) bringing religious awakening and organising mass re‐conversion programmes, (3) redefining indigenous identity and characterising certain communities as ‘the other’, and (4) with the support of the various state institutions. The paper concludes that by ethnicising indigenous identity, the RVKP has not just created a ‘culture of fear and violence’ in the tribal regions but also threatened the secular democratic ethos of Indian society.
Four new species of Goniothalamus (Annonaceae) from Borneo
Authors: Turner IanM. , Saunders Richard M. K.
Published: December 2008

Four new species of Goniothalamus (Annonaceae) are described from Borneo. Goniothalamus bygravei sp. nov., from Sarawak and Brunei, is similar to G. borneensis but is easily distinguished as it has longer petioles and more secondary veins per leaf. The name Goniothalamus kamarudinii sp. nov. is published for collections from Mt Kinabalu in Sabah, which were previously assigned to G. montanus; the latter species is confirmed as endemic to Peninsular Malaysia. Goniothalamus megalocalyx sp. nov., from Brunei, Kalimantan Timur and Sarawak, is remarkable for its large calyx which distinguishes it from all other congeneric species in the region. Goniothalamus phaeotrichus sp. nov. from Sabah, Sarawak and Kalimantan, has a densely hairy young twigs, similar to G. rufus, G. tomentosus and G. velutinus.
Shear on the Flow Surface of Metallic Crystals
Authors: Darrieulat Michel G. , Aoufi Asdin
Published: December 2008

The present article addresses the following question: How is it that shears are so common in the plastic deformation of metallic alloys? An answer is sought in a geometric description of the shear flow when the deformation is produced by slip systems gliding according to the Schmid law. Such flows are represented schematically by what is called “simple shear” and a kinematic study is done of the way these shears can be produced by the joint activity of various slip systems. This implies specific conditions on the glide rates, which can be known analytically thanks to adequate parametrizations. All the possible shears have been calculated in the case of cubic metals deforming with identical critical resolved shear stresses (Bishop and Hill polyhedron). Three dimensional representations are given in the space of the Bunge angles associated with the principal directions of the shears. A special attention has been given to the number of slip systems involved. Most of the shears are not far from some combination of two or three systems. This is quantified by defining the misorientation ω between a shear taken at random and the set of shears produced by the glide on two or three octahedral slip systems. It is found that in most cases, ω<15 deg. The maximum value of ω (30.5 deg) is found for the orientations called Cube and U in rolled metals.
Obtaining a Relationship Between Process Parameters and Fracture Characteristics for Hybrid CO2 Laser∕Waterjet Machining of Ceramics
Authors: Kalyanasundaram Dinesh , Shrotriya Pranav , Molian Pal
Published: December 2008

A combined experimental and analytical approach is undertaken to identify the relationship between process parameters and fracture behavior in the cutting of a 1mm thick alumina samples by a hybrid CO2 laser∕waterjet (LWJ) manufacturing process. In LWJ machining, a 200W power laser was used for local heating followed by waterjet quenching of the sample surface leading to thermal shock fracture in the heated zone. Experimental results indicate three characteristic fracture responses: scribing, controlled separation, and uncontrolled fracture. A Green’s function based approach is used to develop an analytical solution for temperatures and stress fields generated in the workpiece during laser heating and subsequent waterjet quenching along the machining path. Temperature distribution was experimentally measured using thermocouples and compared with analytical predictions in order to validate the model assumptions. Computed thermal stress fields are utilized to determine the stress intensity factor and energy release rate for different configurations of cracks that caused scribing or separation of the workpiece. Calculated crack driving forces are compared with fracture toughness and critical energy release rates to predict the equilibrium crack length for scribed samples and the process parameters associated with transition from scribing to separation. Both of these predictions are in good agreement with experimental observations. An empirical parameter is developed to identify the transition from controlled separation to uncontrolled cracking because the equilibrium crack length based analysis is unable to predict this transition. Finally, the analytical model and empirical parameter are utilized to create a map that relates the process parameters to the fracture behavior of alumina samples.
Determination of Critical Strains in Isotactic Polypropylene by Cyclic Loading-Unloading
Authors: Spieckermann Florian C. , Wilhem Harald R. , Schafler Erhard , Alfantis Elias C. , Zehetbauer Michael J.
Published: December 2008

By analyzing the deformation of α—isotactic polypropylene through cyclic uniaxial compression at different temperatures—conclusions are drawn on the contribution of the crystalline phase and the amorphous phase to the hardening curve. The deformation of the crystalline phase, which deforms mainly by simple shear of the crystallites, strongly depends on the properties of the amorphous phase. A separation of strain in a relaxing and a quasipermanent part, as introduced by the work of Hiss et al. (1999, “Network Stretching, Slip Processes and Fragmentation of Crystallites During Uniaxial Drawing of Polyethylene and Related Copolymers,” Macromolecules, 32, pp. 4390–4403), is undertaken. By this experimental procedure it is possible to characterize the deformation dependence of several physical quantities such as Young’s modulus or the stored energy associated to each loading-unloading cycle. Furthermore specific transition strains, A, B, C, and D, can be determined where the recovery properties change. It is demonstrated that beyond point C the strain hardening can be described by the simple rubber hardening model of Haward (1987, “The Application of a Simplified Model for the Stress-Strain Curve of Polymers,” Polymer, 28, pp. 1485–1488).
Texture and Mechanical Behavior of Magnesium During Free-End Torsion
Authors: Beausir Benoît , Tóth László S. , Qods Fathallah , Neale Kenneth W.
Published: December 2008

Torsion experiments were carried out on pure magnesium (99.9%) and the magnesium alloy AZ71 under free-end conditions of testing. The alloy had an axisymmetric initial texture, while the pure Mg samples were prepared from a rolled plate with a nonaxisymmetric initial texture. The torque as a function of the twist angle was measured at different temperatures (room temperature, 150°C, and 250°C). During twisting, systematic shortening of the samples was observed (Swift effect). The evolution of the crystallographic texture was analyzed by electron backscattering diffraction measurements. The occurrence of dynamic recrystallization (DRX) was detected in pure Mg at 250°C. The Swift effect in the axisymmetric samples was simulated with the “equilibrium equation” approach using polycrystal modeling. In the nonaxisymmetric samples, the texture was simulated at different angular positions with the help of the viscoplastic self-consistent model. The changes in the textures due to DRX were explained in terms of the Taylor factor. Finally, the texture evolution was interpreted with the help of the behavior of ideal orientations and persistence characteristics of hexagonal crystals in simple shear.
A Novel Insertion Mutation in
Streptomyces coelicolor
Ribosomal S12 Protein Results in Paromomycin Resistance and Antibiotic Overproduction
Authors: Wang Guojun , Inaoka Takashi , Okamoto Susumu , Ochi Kozo
Published: December 2008

We identified a novel paromomycin resistance-associated mutation in
rpsL
, caused by the insertion of a glycine residue at position 92, in
Streptomyces coelicolor
ribosomal protein S12. This insertion mutation (GI92) resulted in a 20-fold increase in the paromomycin resistance level. In combination with another S12 mutation, K88E, the GI92 mutation markedly enhanced the production of the blue-colored polyketide antibiotic actinorhodin and the red-colored antibiotic undecylprodigiosin. The gene replacement experiments demonstrated that the K88E-GI92 double mutation in the
rpsL
gene was responsible for the marked enhancement of antibiotic production observed. Ribosomes with the K88E-GI92 double mutation were characterized by error restrictiveness (i.e., hyperaccuracy). Using a cell-free translation system, we found that mutant ribosomes harboring the K88E-GI92 double mutation but not ribosomes harboring the GI92 mutation alone displayed sixfold greater translation activity relative to that of the wild-type ribosomes at late growth phase. This resulted in the overproduction of actinorhodin, caused by the transcriptional activation of the pathway-specific regulatory gene
actII-orf4
, possibly due to the increased translation of transcripts encoding activators of
actII-orf4
. The mutant with the K88E-GI92 double mutation accumulated a high level of ribosome recycling factor at late stationary phase, underlying the high level of protein synthesis activity observed.
Oritavancin Kills Stationary-Phase and BiofilmStaphylococcus aureusCells In Vitro
Authors: Belley Adam , Neesham-Grenon Eve , McKay Geoffrey , Arhin Francis F. , Harris Robert , Beveridge Terry , Parr Thomas R. , Moeck Gregory
Published: December 2008

Slow-growing bacteria and biofilms are notoriously tolerant to antibiotics. Oritavancin is a lipoglycopeptide with multiple mechanisms of action that contribute to its bactericidal action against exponentially growing gram-positive pathogens, including the inhibition of cell wall synthesis and perturbation of membrane barrier function. We sought to determine whether oritavancin could eradicate cells known to be tolerant to many antimicrobial agents, that is, stationary-phase and biofilm cultures ofStaphylococcus aureusin vitro. Oritavancin exhibited concentration-dependent bactericidal activity against stationary-phase inocula of methicillin-susceptibleS. aureus(MSSA) ATCC 29213, methicillin-resistantS. aureus(MRSA) ATCC 33591, and vancomycin-resistantS. aureus(VRSA) VRS5 inoculated into nutrient-depleted cation-adjusted Mueller-Hinton broth. As has been described for exponential-phase cells, oritavancin induced membrane depolarization, increased membrane permeability, and caused ultrastructural defects including a loss of nascent septal cross walls in stationary-phase MSSA. Furthermore, oritavancin sterilized biofilms of MSSA, MRSA, and VRSA at minimal biofilm eradication concentrations (MBECs) of between 0.5 and 8 μg/ml. Importantly, MBECs for oritavancin were within 1 doubling dilution of their respective planktonic broth MICs, highlighting the potency of oritavancin against biofilms. These results demonstrate a significant activity of oritavancin againstS. aureusin phases of growth that exhibit tolerance to other antimicrobial agents.
Antibiotic Resistance in Urinary Isolates of
Escherichia coli
from College Women with Urinary Tract Infections
Authors: Olson Ronald P. , Harrell Lizzie J. , Kaye Keith S.
Published: December 2008

Of 176 urine isolates from female students positive for
Escherichia coli
, 29.6% were trimethoprim-sulfamethoxazole resistant and none were nitrofurantoin resistant. Among students with a history of urinary tract infection (UTI) (
n
= 119), resistance to ciprofloxacin was 11.8%, compared to 1.8% among those without prior UTI. Nitrofurantoin should be considered for empirical therapy of lower tract UTI.
Praziquantel Affects the Regulatory Myosin Light Chain of
Schistosoma mansoni
Authors: Gnanasekar Munirathinam , Salunkhe Ashok M. , Mallia A. Krishna , He Yi Xun , Kalyanasundaram Ramaswamy
Published: December 2008

Praziquantel (PZQ) is the drug of choice for schistosomiasis and probably is the only highly effective drug currently available for treating schistosomiasis-infected individuals. The mode of action of PZQ involves increasing the calcium uptake of the parasite, resulting in tegumental damage and death of the parasite. Despite its remarkable function, the target of PZQ has not been identified yet. To begin to understand where PZQ acts, in this study we expressed the cDNA library of
Schistosoma mansoni
on the surface of T7 bacteriophages and screened this library with labeled PZQ. This procedure identified a clone that strongly bound to PZQ. Subsequent DNA analysis of inserts showed that the clone coded for regulatory myosin light chain protein. The gene was then cloned, and recombinant
S. mansoni
myosin light chain (SmMLC) was expressed. Immunoblot analysis using antibodies raised to recombinant SmMLC (rSmMLC) showed that SmMLC is abundantly expressed in schistosomula and adult stages compared to the amount in cercarial stages. In vitro analyses also confirmed that PZQ strongly binds to rSmMLC. Further, peptide mapping studies showed that PZQ binds to amino acids 46 to 76 of SmMLC. Immunoprecipitation analysis confirmed that SmMLC is phosphorylated in vivo upon exposure to PZQ. Interestingly, significant levels of anti-SmMLC antibodies were present in vaccinated mice compared to the amount in infected mice, suggesting that SmMLC may be a potential target for protective immunity in schistosomiasis. These findings suggest that PZQ affects SmMLC function, and this may have a role in PZQ action.
Toll-Like Receptor 2 and NALP2 Mediate Induction of Human Beta-Defensins byFusobacterium nucleatumin Gingival Epithelial Cells
Authors: Ji Suk , Shin Ji Eun , Kim Young Sook , Oh Ju-Eun , Min Byung-Moo , Choi Youngnim
Published: December 2008

We previously reported that infection byFusobacterium nucleatumstrongly induced the expression of both human beta-defensin 2 (HBD-2) and HBD-3 by gingival epithelial cells. The aim of this study was to characterize the pattern recognition receptors (PRRs) and regulatory mechanisms involved in the induction of HBD-2 and -3 expression byF. nucleatumin gingival epithelial cells. Immortalized human gingival epithelial HOK-16B cells were infected with live or heat-killedF. nucleatum, and the expression of HBDs and interleukin-8 (IL-8) was examined by real-time reverse transcription-PCR and enzyme-linked immunosorbent assay, respectively. Live, but not heat-killed,F. nucleatuminvaded HOK-16B cells, as seen by confocal microscopy and flow cytometry. LiveF. nucleatuminduced both HBD-2 and -3 efficiently, whereas heat-killed bacteria induced only HBD-3 at a reduced level. Knockdown of NACHT-LRR- and pyrin domain-containing protein 2 (NALP2), the most abundant intracellular PRR in HOK-16B cells, by RNA interference (RNAi) significantly reduced the induction of HBD-3 but not HBD-2 and IL-8. In addition, knockdown of Toll-like receptor 2 (TLR2) by RNAi reduced the upregulation of HBD-2 and -3 but not IL-8. Heat-killedF. nucleatumwas hindered in its ability to activate TLR2 and JNK signaling pathways. Theses data show that TLR2 and NALP2 mediate the induction of HBDs byF. nucleatumin gingival epithelial cells, but thresholds for the two HBD genes are different.
An Engineered Human Antibody Fab Fragment Specific for
Pseudomonas aeruginosa
PcrV Antigen Has Potent Antibacterial Activity
Authors: Baer Mark , Sawa Teiji , Flynn Peter , Luehrsen Kenneth , Martinez David , Wiener-Kronish Jeanine P. , Yarranton Geoffrey , Bebbington Christopher
Published: December 2008

Pseudomonas aeruginosa
is an opportunistic pathogen that can cause acute lung injury and mortality through the delivery of exotoxins by the type III secretion system (TTSS). PcrV is an important structural protein of the TTSS. An engineered human antibody Fab fragment that binds to the
P. aeruginosa
PcrV protein with high affinity has been identified and has potent in vitro neutralization activity against the TTSS. The instillation of a single dose of Fab into the lungs of mice provided protection against lethal pulmonary challenge of
P. aeruginosa
and led to a substantial reduction of viable bacterial counts in the lungs. These results demonstrate that blocking of the TTSS by a Fab lacking antibody Fc-mediated effector functions can be sufficient for the effective clearance of pulmonary
P. aeruginosa
infection.
Role of NADPH Phagocyte Oxidase in Host Defense against Acute Respiratory
Acinetobacter baumannii
Infection in Mice
Authors: Qiu Hongyu , KuoLee Rhonda , Harris Greg , Chen Wangxue
Published: December 2008

Acinetobacter baumannii
is an emerging bacterial pathogen that rapidly develops multiple-drug resistance and is responsible for many nosocomial pulmonary infections. This study investigated the role of the NADPH phagocyte oxidase (phox) and inducible nitric oxide synthase (NOS2) in the host defense against respiratory infection with
A. baumannii
in mouse models of intranasal
A. baumannii
infection. gp91
phox−/−
mice showed higher susceptibility to
A. baumannii
infection than wild-type (WT) C57BL/6 mice, with significantly greater bacterial counts in their lungs (1,000-fold) (
P
< 0.005) and spleens (10-fold) (
P
< 0.05). Moreover, all of the gp91
phox−/−
mice succumbed to infection within 48 h. In contrast, only a moderate increase in bacterial burdens was detected in the lungs of NOS2
−/−
mice, and all NOS2
−/−
mice survived infection. Compared to WT mice, the pulmonary influx of inflammatory cells and serum and local inflammatory cytokine/chemokine responses were not obviously impaired at 4 h and were significantly higher at 24 h (
P
< 0.05) in gp91
phox−/−
mice, but NADPH-deficient neutrophils were unable to control bacterial replication and extrapulmonary dissemination. Thus, NADPH phagocyte oxidase appears to play a crucial role in the neutrophil-mediated host defense against
A. baumannii
.
Role of the
dosR
-
dosS
Two-Component Regulatory System in
Mycobacterium tuberculosis
Virulence in Three Animal Models
Authors: Converse Paul J. , Karakousis Petros C. , Klinkenberg Lee G. , Kesavan Anup K. , Ly Lan H. , Allen Shannon Sedberry , Grosset Jacques H. , Jain Sanjay K. , Lamichhane Gyanu , Manabe Yukari C. , McMurray David N. , Nuermberger Eric L. , Bishai William R.
Published: December 2008

The
Mycobacterium tuberculosis dosR
gene (Rv3133c) is part of an operon, Rv3134c-Rv3132c, and encodes a response regulator that has been shown to be upregulated by hypoxia and other in vitro stress conditions and may be important for bacterial survival within granulomatous lesions found in tuberculosis. DosR is activated in response to hypoxia and nitric oxide by DosS (Rv3132c) or DosT (Rv2027c). We compared the virulence levels of an
M. tuberculosis dosR
-
dosS
deletion mutant (Δ
dosR
-
dosS
[Δ
dosR-S
]), a
dosR
-complemented strain, and wild-type H37Rv in rabbits, guinea pigs, and mice infected by the aerosol route and in a mouse hollow-fiber model that may mimic in vivo granulomatous conditions. In the mouse and the guinea pig models, the Δ
dosR
-
S
mutant exhibited a growth defect. In the rabbit, the Δ
dosR
-
S
mutant did not replicate more than the wild type. In the hollow-fiber model, the mutant phenotype was not different from that of the wild-type strain. Our analyses reveal that the
dosR
and
dosS
genes are required for full virulence and that there may be differences in the patterns of attenuation of this mutant between the animal models studied.
Characterization of a γ-Aminobutyric Acid Transport System of
Rhizobium leguminosarum
bv. viciae 3841
Authors: White J. P. , Prell J. , Ramachandran V. K. , Poole P. S.
Published: December 2008

Spontaneous mutants of
Rhizobium leguminosarum
bv. viciae 3841 were isolated that grow faster than the wild type on γ-aminobutyric acid (GABA) as the sole carbon and nitrogen source. These strains (RU1736 and RU1816) have frameshift mutations (
gtsR101
and
gtsR102
, respectively) in a GntR-type regulator (GtsR) that result in a high rate of constitutive GABA transport. Tn
5
mutagenesis and quantitative reverse transcription-PCR showed that GstR regulates expression of a large operon (pRL100242 to pRL100252) on the Sym plasmid that is required for GABA uptake. An ABC transport system, GtsABCD (for GABA transport system) (pRL100248-51), of the spermidine/putrescine family is part of this operon. GtsA is a periplasmic binding protein, GtsB and GtsC are integral membrane proteins, and GtsD is an ATP-binding subunit. Expression of
gtsABCD
from a
lacZ
promoter confirmed that it alone is responsible for high rates of GABA transport, enabling rapid growth of strain 3841 on GABA. Gts transports open-chain compounds with four or five carbon atoms with carboxyl and amino groups at, or close to, opposite termini. However, aromatic compounds with similar spacing between carboxyl and amino groups are excellent inhibitors of GABA uptake so they may also be transported. In addition to the ABC transporter, the operon contains two putative mono-oxygenases, a putative hydrolase, a putative aldehyde dehydrogenase, and a succinate semialdehyde dehydrogenase. This suggests the operon may be involved in the transport and breakdown of a more complex precursor to GABA. Gts is not expressed in pea bacteroids, and
gtsB
mutants are unaltered in their symbiotic phenotype, suggesting that Bra is the only GABA transport system available for amino acid cycling.
Characterization of the Autocleavage Process of the
Escherichia coli
HtrA Protein: Implications for its Physiological Role
Authors: Jomaa Ahmad , Iwanczyk Jack , Tran Julie , Ortega Joaquin
Published: December 2008

The
Escherichia coli
HtrA protein is a periplasmic protease/chaperone that is upregulated under stress conditions. The protease and chaperone activities of HtrA eliminate or refold damaged and unfolded proteins in the bacterial periplasm that are generated upon stress conditions. In the absence of substrates, HtrA oligomerizes into a hexameric cage, but binding of misfolded proteins transforms the hexamers into bigger 12-mer and 24-mer cages that encapsulate the substrates for degradation or refolding. HtrA also undergoes partial degradation as a consequence of self-cleavage of the mature protein, producing short-HtrA protein (s-HtrA). The aim of this study was to examine the physiological role of this self-cleavage process. We found that the only requirement for self-cleavage of HtrA into s-HtrA in vitro was the hydrolysis of protein substrates. In fact, peptides resulting from the hydrolysis of the protein substrates were sufficient to induce autocleavage. However, the continuous presence of full-length substrate delayed the process. In addition, we observed that the hexameric cage structure is required for autocleavage and that s-HtrA accumulates only late in the degradation reaction. These results suggest that self-cleavage occurs when HtrA reassembles back into the resting hexameric structure and peptides resulting from substrate hydrolysis are allosterically stimulating the HtrA proteolytic activity. Our data support a model in which the physiological role of the self-cleavage process is to eliminate the excess of HtrA once the stress conditions cease.
An Intramolecular Upstream Helix Ensures the Stability of a Toxin-Encoding RNA inEnterococcus faecalis
Authors: Shokeen Sonia , Greenfield Tony J. , Ehli Erik A. , Rasmussen Jessica , Perrault Brian E. , Weaver Keith E.
Published: December 2008

Theparstability determinant is required for the stable inheritance of the plasmid pAD1 in its native host,Enterococcus faecalis.It is the only antisense RNA-regulated addiction module identified to date in gram-positive bacteria. It encodes two small, convergently transcribed RNAs, RNA I and RNA II. RNA I encodes the Fst toxin and RNA II acts as the antitoxin by interacting with RNA I posttranscriptionally. As the toxin-encoding component of the system, it is important that RNA I is more stable than RNA II. This study reveals that a helix sequestering the 5′ end of RNA I plays a crucial role in maintaining the stability of the RNA I. An adjacent structure previously determined to regulate Fst translation was not required to enhance stability. Results indicated that endoribonuclease J2 contributes significantly to the degradation of a mutant disrupting the upstream helix (UH) of RNA I inBacillus subtilis.Finally, it was shown that interaction with RNA II stabilized the UH mutant of RNA I.
CONVECTIVE FLOW-INDUCED SHORT TIMESCALE SEGREGATION IN A DILUTE BIDISPERSE PARTICLE SUSPENSION
Authors: VALENZUELA J. F. , MONTEROLA C.
Published: December 2008

We examine the segregation and mixing dynamics of a dilute bidisperse suspension of particles in a fluid subjected to a temperature gradient. Configurations corresponding to varying uniform bottom wall temperatures, as well as various bottom wall temperature profiles, are examined. Measures of spatial segregation and aggregation are discussed and used to analyze the suspension's dynamics. The results show that the difference in mass lead to transient segregation at short time scales, together with long-term intermixing and aggregation. Comparison of the segregation and aggregation among different configurations reveal that the strength of the temperature gradient is the primary influence on both segregation and aggregation. The particles are driven the fastest into the long – term steady state in the uniform and Gaussian bottom temperature profiles. In addition, the qualitative features of transient segregation do not change if the difference in mass is varied. The results suggest that a fluid undergoing thermal convection can be used to segregate particles, but only at short times, as fluid reaches its steady state. Keeping a fluid indefinitely in a transient state may improve the duration of segregation.
THE STRONG CONSENSUS OPINION DYNAMICS ON ADAPTIVE NETWORKS
Authors: WANG RU , CAI XU
Published: December 2008

Many real-world networks are characterized by adaptive changes in their topology depending on the state of their nodes. Here we explore the continuous Sznajd opinion model on an adaptive network, where the link between agents with far apart opinion will get rewired. Our investigations reveal that the adaptation of the network topology fosters cluster formation by enhancing communication between agents, though the Sznajd rule is most effective to achieve a full synchronization of the agents. The interplay between dynamics and topology can have important consequences for the spreading of the opinions.
PERSISTENCE IN THE ZERO-TEMPERATURE DYNAMICS OF THE Q-STATES POTTS MODEL ON UNDIRECTED-DIRECTED BARABÁSI–ALBERT NETWORKS AND ERDÖS–RÉNYI RANDOM GRAPHS
Authors: FERNANDES F. P. , LIMA F. W. S.
Published: December 2008

The zero-temperature Glauber dynamics is used to investigate the persistence probability P(t) in the Potts model with Q = 3, 4, 5, 7, 9, 12, 24, 64, 128, 256, 512, 1024, 4096, 16 384, …, 230 states on directed and undirected Barabási–Albert networks and Erdös–Rényi (ER) random graphs. In this model, it is found that P(t) decays exponentially to zero in short times for directed and undirected ER random graphs. For directed and undirected BA networks, in contrast it decays exponentially to a constant value for long times, i.e., P(∞) is different from zero for all Q values (here studied) from Q = 3, 4, 5, …, 230; this shows "blocking" for all these Q values. Except that for Q = 230 in the undirected case P(t) tends exponentially to zero; this could be just a finite-size effect since in the other "blocking" cases you may have only a few unchanged spins.
NUMERICAL TREATMENT OF HARTLE'S PERTURBATION METHOD FOR DIFFERENTIALLY ROTATING NEUTRON STARS SIMULATED BY GENERAL-RELATIVISTIC POLYTROPIC MODELS
Authors: GEROYANNIS V. S. , KATELOUZOS A. G.
Published: December 2008

We compute general-relativistic polytropic models of differentially rotating neutron stars. A brief description of our numerical treatment is given as follows. First, the relativistic Oppenheimer–Volkoff equations of hydrostatic equilibrium are solved for nonrotating models obeying the well-known polytropic equation of state. Then, uniform rotation assumed for such models is treated in the framework of Hartle's perturbation method; thus, corrections to mass and radius, owing to spherical and quadrupole deformations, are calculated. Next, a perturbative approach to the stellar structure up to terms of third order in the angular velocity is carried out; angular momentum, J, moment of inertia, I, rotational kinetic energy, T, and gravitational potential energy, W, are quantities drastically corrected by the third-order approach. Finally, assuming that our polytropic models satisfy a particular differential rotation law, we compute the increase in mass and in some other significant physical characteristics owing to the differential rotation.
ARTIFICIAL NEURAL NETWORK AND GENETIC ALGORITHM HYBRID TECHNIQUE FOR NUCLEUS–NUCLEUS COLLISIONS
Authors: El-DAHSHAN E. , RADI A. , El-BAKRY M. Y.
Published: December 2008

Selecting the optimal topology of a neural network for a particular application is a difficult task. Genetic Algorithm (GA) has been used to find the optimal neural network (NN) solution (i.e., hybrid technique) to calculate the pseudo-rapidity distribution of the shower particles for C 12, O 16, Si 28, and S 32 on nuclear emulsion. An efficient NN has been designed by GA to predict the distributions that are not present in the training set and matched them effectively. The proposed method shows a better fitting with experimental data. The hybrid technique GA–ANN simulation results prove a strong presence modeling in heavy ion collisions.
OUTSOURCING AND FRAGMENTATION IN SINGAPORE'S MANUFACTURING INDUSTRY
Authors: THANGAVELU SHANDRE M. , TOH MUN HENG , NG KWAN KEE
Published: December 2008

This paper studies the impact of outsourcing on productive performance of manufacturing industries in Singapore. The paper develops an outsourcing measure based on the narrow definition of intermediate imports given by Feenstra and Hanson (1996, 1999). Based on the input-output tables, the study uses 5-digit industrial-level classifications to measure the impact of outsourcing on productivity of the manufacturing industries in Singapore from 1995–2004. The outsourcing measure is further decomposed by import of services, import of IT services and import of business services. This decomposition allows us to study the impact of outsourcing of services in addition to the cross-border fragmentation of products and components. The results suggest strong positive impact of cross-border sourcing on the productivity of the manufacturing sector. The decomposition of outsourcing measure indicates that the manufacturing industries are more involved in cross-border sourcing of services, particularly in business services.
GEOMETRIC PHASE AND CHIRAL ANOMALY: THEIR BASIC DIFFERENCES
Authors: FUJIKAWA KAZUO
Published: December 2008

All the geometric phases are shown to be topologically trivial by using the second quantized formulation. The exact hidden local symmetry in the Schrödinger equation, which was hitherto unrecognized, controls the holonomy associated with both of the adiabatic and nonadiabatic geometric phases. The second quantized formulation is located in between the first quantized formulation and the field theory, and thus it is convenient to compare the geometric phase with the chiral anomaly in field theory. It is shown that these two notions are completely different.
A REVIEW OF THE MAGNITUDES OF THE CKM MATRIX ELEMENTS
Authors: DI LODOVICO FRANCESCA
Published: December 2008

Flavour mixing is described within the Standard Model by the Cabibbo–Kobayashi–Maskawa (CKM) matrix elements. With the increasingly higher statistics collected by many experiments, the matrix elements are measured with improved precision, allowing for more stringent tests of the Standard Model. In this paper, a review of the current status of the absolute values of the CKM matrix elements is presented, with particular attention to the latest measurements.
PHASE TRANSITION PROPERTIES OF FERROELECTRIC THIN FILM WITH ONE DISTINCT INSERTING-LAYER
Authors: WANG CHUNDONG , TENG BAOHUA , ZHANG XIANJUN , LU XIAOHUA , CHENG DENGMU , LU ZHAOXIN
Published: December 2008

The mean-field expressions derived from the transverse Ising model are used to investigate the second-order ferroelectric phase transition. With this theory, the properties of ferroelectric thin films formed by inserting a monolayer of material B into material A in the middle was studied. Firstly, a recursive equation for the phase transition properties of the ferroelectric thin film with one distinct inserting-layer in the middle was obtained. Next, the effect of the exchange interaction and transverse field parameters of materials A and B on the phase diagrams was investigated. The results show that with the modification of the parameter values of the inserting-layer B, the properties of the phase transition, the crossover value of the transverse field, the polarizations of different layers, and the critical temperature, change sensitively.
VOLUME DEPENDENCE OF GRUNEISEN PARAMETER FOR SOLIDS
Authors: SHARMA S. K.
Published: December 2008

The present paper proposes a new empirical relationship to predict the values of volume dependence of the Gruneisen parameter. ε- Fe , NaCl , Li , Na and K in different pressure ranges have been employed to test the reliability of the model. The obtained results indicate that the model is reliable due to a good agreement between calculated results and the experimental data. Based on this modified model, the temperature dependence of thermal pressure for NaCl is also examined.
COMPUTATIONAL ASPECTS OF THE DISCONTINUOUS GALERKIN METHOD FOR THE WAVE EQUATION
Authors: LÄHIVAARA TIMO , MALINEN MATTI , KAIPIO JARI P. , HUTTUNEN TOMI
Published: December 2008

The Discontinuous Galerkin (DG) method is a powerful tool for numerically simulating wave propagation problems. In this paper, the time-dependent wave equation is solved using the DG method for spatial discretization; and the Crank–Nicolson and fourth-order explicit, singly diagonally implicit Runge–Kutta methods, and, for reference, the explicit Runge–Kutta method, were used for time integration. These simulation methods were studied using two-dimensional numerical experiments. The aim of the experiments was to study the effect of the polynomial degree of the basis functions, grid density, and the Courant–Friedrichs–Lewy number on the accuracy of the approximation. The sensitivity of the methods to distorted finite elements was also examined. Results from the DG method were compared with those computed using a conventional finite element method. Three different model problems were considered. In the first experiment, wave propagation in a homogeneous medium was studied. In the second experiment, the scattering and propagation of waves in an inhomogeneous medium were investigated. The third experiment evaluated wave propagation in a more complicated domain involving multiple scattering waves. The results indicated that the DG method provides more accurate solutions than the conventional finite element method with a reduced computation time and a lower number of degrees of freedom.