bluuebunny/crossref_metadata_2025_split huggingface dataset:
Host Immunity to Clostridium difficile PCR Ribotype 017 Strains
Authors: Jafari Nazila V. , Songane Mario , Stabler Richard A. , Elawad Mamoun , Wren Brendan W. , Allan Elaine , Bajaj-Elliott Mona 
Published: September 2014

ABSTRACT

Clostridium difficile
is an important nosocomial pathogen and the leading cause of antibiotic-associated diarrhea. Multilocus sequence typing indicates that
C. difficile
strains belong to five distinct genetic clades encompassing several PCR ribotypes (RT). Since their emergence in 2003, hypervirulent RT027 strains have been a major focus of research; in contrast, our current understanding of RT017-mediated disease pathogenesis lags far behind. In this study, we aimed to characterize host immunity to CF5 and M68, two genetically well-defined RT017 strains. Both strains engaged with host Toll-like receptor 2/6 (TLR2/6), TLR2-CD14, and TLR5 to similar extents in a model cell line. Despite this, CF5 mediated significantly greater dendritic cell (DC) interleukin-12 (IL-12), IL-27, and IL-10 immunity than M68. Both strains elicited similar IL-1β mRNA levels, and yet only M68 caused a marked increase in secretory IL-1β. A CF5 cocultured-DC cytokine milieu drove an equipotent Th1 and Th17 response, while M68 promoted greater Th17 immunity. Human gastrointestinal
ex vivo
cytokine responses to both strains were characterized. Taken together, our data suggest that
C. difficile
strains mediate overlapping and yet distinct mucosal and DC/T cell immunity. Finally, toxin-driven IL-1β release supports the hypothesis that this cytokine axis is a likely target for therapeutic intervention for
C. difficile
infection.
Involvement of PG2212 Zinc Finger Protein in the Regulation of Oxidative Stress Resistance in Porphyromonas gingivalis W83
Authors: Dou Yuetan , Aruni Wilson , Luo Tianlong , Roy Francis , Wang Charles , Fletcher Hansel M. 
Published: September 2014

ABSTRACT

The adaptation of
Porphyromonas gingivalis
to H
2
O
2
-induced stress while inducible is modulated by an unknown OxyR-independent mechanism. Previously, we reported that the PG_2212 gene was highly upregulated in
P. gingivalis
under conditions of prolonged oxidative stress. Because this gene may have regulatory properties, its function in response to H
2
O
2
was further characterized. PG2212, annotated as a hypothetical protein of unknown function, is a 10.3-kDa protein with a cysteine 2-histidine 2 (Cys
2
His
2
) zinc finger domain. The isogenic mutant
P. gingivalis
FLL366 (ΔPG_2212) showed increased sensitivity to H
2
O
2
and decreased gingipain activity compared to the parent strain. Transcriptome analysis of
P. gingivalis
FLL366 revealed that approximately 11% of the genome displayed altered expression (130 downregulated genes and 120 upregulated genes) in response to prolonged H
2
O
2
-induced stress. The majority of the modulated genes were hypothetical or of unknown function, although some are known to participate in oxidative stress resistance. The promoter region of several of the most highly modulated genes contained conserved motifs. In electrophoretic mobility shift assays, the purified rPG2212 protein did not bind its own promoter region but bound a similar region in several of the genes modulated in the PG_2212-deficient mutant. A metabolome analysis revealed that PG2212 can regulate a number of genes coding for proteins involved in metabolic pathways critical for its survival under the conditions of oxidative stress. Collectively, our data suggest that PG2212 is a transcriptional regulator that plays an important role in oxidative stress resistance and virulence regulation in
P. gingivalis
.
The PqsR and RhlR Transcriptional Regulators Determine the Level of Pseudomonas Quinolone Signal Synthesis in Pseudomonas aeruginosa by Producing Two Different
pqsABCDE
mRNA Isoforms
Authors: Brouwer Stephan , Pustelny Christian , Ritter Christiane , Klinkert Birgit , Narberhaus Franz , Häussler Susanne 
Published: September 2014

ABSTRACT

Regulation of gene expression plays a key role in bacterial adaptability to changes in the environment. An integral part of this gene regulatory network is achieved via quorum sensing (QS) systems that coordinate bacterial responses under high cellular densities. In the nosocomial pathogen
Pseudomonas aeruginosa
, the 2-alkyl-4-quinolone (
pqs
) signaling pathway is crucial for bacterial survival under stressful conditions. Biosynthesis of the
Pseudomonas
quinolone signal (PQS) is dependent on the
pqsABCDE
operon, which is positively regulated by the LysR family regulator PqsR and repressed by the transcriptional regulator protein RhlR. However, the molecular mechanisms underlying this inhibition have remained elusive. Here, we demonstrate that not only PqsR but also RhlR activates transcription of
pqsA
. The latter uses an alternative transcriptional start site and induces expression of a longer transcript that forms a secondary structure in the 5′ untranslated leader region. As a consequence, access of the ribosome to the Shine-Dalgarno sequence is restricted and translation efficiency reduced. We propose a model of a novel posttranscriptional regulation mechanism that fine-tunes PQS biosynthesis, thus highlighting the complexity of quorum sensing in
P. aeruginosa
.
Two Fis Regulators Directly Repress the Expression of Numerous Effector-Encoding Genes in Legionella pneumophila
Authors: Zusman Tal , Speiser Yariv , Segal Gil 
Published: September 2014

ABSTRACT

Legionella pneumophila
is an intracellular human pathogen that utilizes the Icm/Dot type IVB secretion system to translocate a large repertoire of effectors into host cells. For most of these effectors, there is no information regarding their regulation. Therefore, the aim of this study was to examine the involvement of the three
L. pneumophila
Fis homologs in the regulation of effector-encoding genes. Deletion mutants constructed in the genes encoding the three Fis regulators revealed that Fis1 (lpg0542 gene) and Fis3 (lpg1743) but not Fis2 (lpg1370) are partially required for intracellular growth of
L. pneumophila
in
Acanthamoeba castellanii
. To identify pathogenesis-related genes directly regulated by Fis, we established a novel
in vivo
system which resulted in the discovery of numerous effector-encoding genes directly regulated by Fis. Further examination of these genes revealed that Fis1 and Fis3 repress the level of expression of effector-encoding genes during exponential phase. Three groups of effector-encoding genes were identified: (i) effectors regulated mainly by Fis1, (ii) effectors regulated mainly by Fis3, and (iii) effectors regulated by both Fis1 and Fis3. Examination of the upstream regulatory region of all of these effector-encoding genes revealed multiple putative Fis regulatory elements, and site-directed mutagenesis confirmed that a few of these sites constitute part of a repressor binding element. Furthermore, gel mobility shift assays demonstrated the direct relation between the Fis1 and Fis3 regulators and these regulatory elements. Collectively, our results demonstrate for the first time that two of the three
L. pneumophila
Fis regulators directly repress the expression of Icm/Dot effector-encoding genes.
Conservative treatment of adhesive small bowel obstruction in children: a systematic review
Authors: Lin Lung-Huang , Lee Chee-Yew , Hung Min-Hsuan , Chen Der-Fang 
Published: September 2014

ObjectiveTo assess the effectiveness of conservative treatment for adhesive small bowel obstruction (ASBO) in children.DesignSystematic review of studies involved children with ASBO who received initial conservative/non-operative treatment.SettingThe search was performed in April 2013 using PubMed (see online supplementary file 1), current contents, and the Cochrane database.ParticipantsChildren with ASBO.InterventionsConservative treatment included nasogastric decompression, parenteral fluids and correction of electrolyte and fluid imbalance.Primary outcomeTreatment success.Secondary outcomesLength of hospital stay and the time to first feeding after hospital admission.Results7 studies (six retrospective, one prospective), involving 8–109 patients (age: 1 month to 16 years) treated conservatively, were included in the review. The nature of conservative treatment was generally consistent between studies (nasogastric decompression, parenteral fluids and correction of electrolyte and fluid imbalance), although patients in one study also received Gastrografin. The rate of conservative treatment success ranged from 16% to 75% among the five studies, but one trial showed 0% successful rate. The hospital length of stay ranged from 3 to 6.5 days for conservative treatment (vs 10.2–13 days for operative treatment). The time to first feeding ranged from 31 to 84 h for conservative treatment.ConclusionsIn conclusion, in the majority of cases, conservative treatment is an effective means of managing ASBO in children.
Calcific extension towards the mitral valve causes non-rheumatic mitral stenosis in degenerative aortic stenosis: real-time 3D transoesophageal echocardiography study
Authors: Iwataki Mai , Takeuchi Masaaki , Otani Kyoko , Kuwaki Hiroshi , Yoshitani Hidetoshi , Abe Haruhiko , Lang Roberto M , Levine Robert A , Otsuji Yutaka 
Published: September 2014

ObjectiveMitral annular/leaflet calcification (MALC) is frequently observed in patients with degenerative aortic stenosis (AS). However, the impact of MALC on mitral valve function has not been established. We aimed to investigate whether MALC reduces mitral annular area and restricts leaflet opening, resulting in non-rheumatic mitral stenosis.MethodsReal-time three-dimensional transoesophageal images of the mitral valve were acquired in 101 patients with degenerative AS and 26 control participants. The outer and inner borders of the mitral annular area (MAA) and the maximal leaflet opening angle were measured at early diastole. The mitral valve area (MVA) was calculated as the left ventricular stroke volume divided by the velocity time integral of the transmitral flow velocity.ResultsAlthough the outer MAA was significantly larger in patients with AS compared to control participants (8.2±1.3 vs 7.3±0.9 cm2, p<0.001), the inner MAA was significantly smaller (4.5±1.1 vs 5.9±0.9 cm2, p<0.001), resulting in an average decrease of 45% in the effective MAA. The maximal anterior and posterior leaflet opening angle was also significantly smaller in patients with AS (64±10 vs 72±8°, p<0.001, 71±12 vs 87±7°, p<0.001). Thus, MVA was significantly smaller in patients with AS (2.5±1.0 vs 3.8±0.8 cm2, p<0.001). Twenty-four (24%) patients with AS showed MVA <1.5 cm2. Multivariate regression analysis including parameters for mitral valve geometry revealed that a decrease in effective MAA and a reduced posterior leaflet opening angle were independent predictors for MVA.ConclusionsCalcific extension to the mitral valve in patients with AS reduced effective MAA and the leaflet opening, resulting in a significant non-rheumatic mitral stenosis in one-fourth of the patients.
Beyond Standard Noise Models: Evaluating Denoising Algorithms with Respect to Realistic Camera Noise
Authors: Seybold Tamara , Knopp Marion , Keimel Christian , Stechele Walter 
Published: September 2014

The development and tuning of denoising algorithms is usually based on readily processed test images that are artificially degraded with additive white Gaussian noise (AWGN). While AWGN allows us to easily generate test data in a repeatable manner, it does not reflect the noise characteristics in a real digital camera. Realistic camera noise is signal-dependent and spatially correlated due to the demosaicking step required to obtain full-color images. Hence, the noise characteristic is fundamentally different from AWGN. Using such unrealistic data to test, optimize and compare denoising algorithms may lead to incorrect parameter tuning or suboptimal choices in research on denoising algorithms. In this paper, we therefore propose an approach to evaluate denoising algorithms with respect to realistic camera noise: we describe a new camera noise model that includes the full processing chain of a single sensor camera. We determine the visual quality of noisy and denoised test sequences using a subjective test with 18 participants. We show that the noise characteristics have a significant effect on visual quality. Quality metrics, which are required to compare denoising results, are applied, and we first evaluate the performance of 12 full-reference metrics. As no-reference metrics are especially useful for parameter tuning, we additionally evaluate five no-reference metrics with our realistic test data. We conclude that a more realistic noise model should be used in future research to improve the quality estimation of digital images and videos and to improve the research on denoising algorithms.
Eastern Pacific Intraseasonal Variability: A Predictability Perspective
Authors: Neena J. M. , Jiang Xianan , Waliser Duane , Lee June-Yi , Wang Bin 
Published: September 2014

Abstract
The eastern Pacific (EPAC) warm pool is a region of strong intraseasonal variability (ISV) during boreal summer. While the EPAC ISV is known to have large-scale impacts that shape the weather and climate in the region (e.g., tropical cyclones and local monsoon), simulating the EPAC ISV is still a great challenge for present-day global weather and climate models. In the present study, the predictive skill and predictability of the EPAC ISV are explored in eight coupled model hindcasts from the Intraseasonal Variability Hindcast Experiment (ISVHE). Relative to the prediction skill for the boreal winter Madden–Julian oscillation (MJO) in the ISVHE (~15–25 days), the skill for the EPAC ISV is considerably lower in most models, with an average skill around 10 days. On the other hand, while the MJO exhibits a predictability of 35–45 days, the predictability estimate for the EPAC ISV is 20–30 days. The prediction skill was found to be higher when the hindcasts were initialized from the convective phase of the EPAC ISV as opposed to the subsidence phase. Higher prediction skill was also found to be associated with active MJO initial conditions over the western Pacific (evident in four out of eight models), signaling the importance of exploring the dynamic link between the MJO and the EPAC ISV. The results illustrate the possibility and need for improving dynamical prediction systems to facilitate more accurate and longer-lead predictions of the EPAC ISV and associated weather and short-term climate variability.
Representing Forecast Error in a Convection-Permitting Ensemble System
Authors: Romine Glen S. , Schwartz Craig S. , Berner Judith , Fossell Kathryn R. , Snyder Chris , Anderson Jeff L. , Weisman Morris L. 
Published: September 2014

Abstract
Ensembles provide an opportunity to greatly improve short-term prediction of local weather hazards, yet generating reliable predictions remain a significant challenge. In particular, convection-permitting ensemble forecast systems (CPEFSs) have persistent problems with underdispersion. Representing initial and or lateral boundary condition uncertainty along with forecast model error provides a foundation for building a more dependable CPEFS, but the best practice for ensemble system design is not well established.
Several configurations of CPEFSs are examined where ensemble forecasts are nested within a larger domain, drawing initial conditions from a downscaled, continuously cycled, ensemble data assimilation system that provides state-dependent initial condition uncertainty. The control ensemble forecast, with initial condition uncertainty only, is skillful but underdispersive. To improve the reliability of the ensemble forecasts, the control ensemble is supplemented with 1) perturbed lateral boundary conditions; or, model error representation using either 2) stochastic kinetic energy backscatter or 3) stochastically perturbed parameterization tendencies. Forecasts are evaluated against stage IV accumulated precipitation analyses and radiosonde observations. Perturbed ensemble forecasts are also compared to the control forecast to assess the relative impact from adding forecast perturbations. For precipitation forecasts, all perturbation approaches improve ensemble reliability relative to the control CPEFS. Deterministic ensemble member forecast skill, verified against radiosonde observations, decreases when forecast perturbations are added, while ensemble mean forecasts remain similarly skillful to the control.
Assisted reproductive technology in SLE and APS
Authors: Levine AB , Lockshin MD 
Published: September 2014

Assisted reproductive technology (ART) procedures, which include in vitro fertilization (IVF), are performed frequently and may be considered for patients with systemic lupus erythematosus and antiphospholipid syndrome. These procedures do not appear to increase the risk of disease flare or thrombosis in these patients. In addition, the presence of antiphospholipid antibodies (aPL) does not independently predict the outcome of IVF pregnancies. As with pregnancies that are achieved naturally, candidates for ART should have quiescent disease for at least 6 months prior to attempting pregnancy for the best possible outcome for mother and child.
Toll-like receptor 4 and β2 glycoprotein I interaction on endothelial cells
Authors: Borghi MO , Raschi E , Grossi C , Chighizola CB , Meroni PL 
Published: September 2014

Antiphospholipid syndrome (APS) is a systemic autoimmune disease characterized by thrombotic events and/or pregnancy morbidity in the persistent presence of antiphospholipid antibodies (aPL). aPL targeting β2 glycoprotein I (anti-β2GPI Abs) provide the main pathogenic autoantibody subset. In monocytes, platelets and endothelial cells (ECs), the interaction of circulating aPL with membrane-bound β2GPI results in cell activation, and EC perturbation provides an important player in clotting. Several receptors have been suggested to mediate β2GPI/EC binding. AnnexinA2 provides a high-affinity binding site for β2GPI but, since it does not span the cell membrane, an adaptor protein is required to trigger signal. Consistent evidence supports the role of Toll-like receptor (TLR) 4 as co-receptor for β2GPI on ECs. β2GPI was recently reported to behave as lipopolysaccharide (LPS) scavenger. In monocytes, TLR4 activation was shown to be apparent, due to LPS/β2GPI complexes. Conversely, our findings in ECs demonstrate that β2GPI interacts directly with TLR4, and that such interaction may contribute to β2GPI-dependent aPL-mediated EC activation. LPS enhanced anti-β2GPI Ab binding to EC only at cell-activating concentrations, able to up-regulate TLR4. This in vitro model may explain why LPS behaves as a second hit increasing the expression of β2GPI in vascular tissues and triggering aPL-mediated thrombosis in vivo.
Antibodies to phosphatidylserine/prothrombin complex and the antiphospholipid syndrome
Authors: Sciascia S , Bertolaccini ML 
Published: September 2014

Antibodies to prothrombin can be detected by ELISA using prothrombin coated onto irradiated plates (aPT) or the phosphatidylserine/prothrombin complex as antigen (aPS/PT) and they have been both related with the clinical manifestation of APS. Current evidence supports the concept that they belong to distinct populations of autoantibodies. Nevertheless, they can both be detected simultaneously in one patient. This mini-review will focus on data available on aPS/PT antibodies and their clinical utility in the diagnosis of APS.
Domain I: the hidden face of antiphospholipid syndrome
Authors: Pericleous C , Rahman A 
Published: September 2014

IgG antiphospholipid antibodies (aPL) against β2-glycoprotein I (β2GPI) can target any of its five domains; however, aPL against the N-terminal domain (anti-DI, aDI) are considered the most clinically relevant in the antiphospholipid syndrome (APS). Circulating levels of aDI are elevated in patients with APS compared with disease and healthy controls, and crucially aDI are prothrombotic in in vivo and in vitro models. In addition, human recombinant DI has been shown to abrogate aPL-induced thrombosis in vivo. Therefore, although the potential of utilizing DI for management of APS is not yet fully defined, there is promise that DI could prove valuable both as a diagnostic and therapeutic tool.
Best proximity point theorems for α-ψ-proximal contractions in intuitionistic fuzzy metric spaces
Authors: Latif Abdul , Hezarjaribi Masoomeh , Salimi Peyman , Hussain Nawab 
Published: September 2014

AbstractThe aim of this paper is to introduce and study certain new concepts ofα-ψ-proximal contractions in an intuitionistic fuzzy metric space. Then we establish certain best proximity point theorems for such proximal contractions in intuitionistic fuzzy metric spaces. As an application, we deduce best proximity and fixed point results in partially ordered intuitionistic fuzzy metric spaces. Several interesting consequences of our obtained results are presented in the form of new fixed point theorems which contain some recent fixed point theorems as special cases. Moreover, we discuss some illustrative examples to highlight the realized improvements.MSC:47H10, 54H25.
Tunable synthesis of SiO2-encapsulated zero-valent iron nanoparticles for degradation of organic dyes
Authors: Mao Zhou , Wu Qingzhi , Wang Min , Yang Yushi , Long Jia , Chen Xiaohui 
Published: September 2014

Abstract
A series of nanocomposites consisting of zero-valent iron nanoparticles (ZVI NPs) encapsulated in SiO2 microspheres were successfully synthesized through a successive two-step method, i.e., the wet chemical reduction by borohydride followed by a modified Stöber method. The as-synthesized nanocomposites were characterized using X-ray diffraction, field emission scanning electron microscopy, vibrating sample magnetometer, and inductively coupled plasma-atomic emission spectrometer. The catalytic performance of SiO2-encapsulated ZVI nanocomposites for the degradation of organic dyes was investigated using methylene blue (MB) as the model dye in the presence of H2O2. The results showed that the degradation efficiency and apparent rate constant of the degradation reaction were significantly enhanced with increased ZVI NPs encapsulated in SiO2 microspheres, whereas the dosage of H2O2 remarkably promoted degradation rate without affecting degradation efficiency. The content-dependent magnetic property ensured the excellent magnetic separation of degradation products under an external magnet. This strategy for the synthesis of SiO2-encapsulated ZVI NPs nanocomposites was low cost and easy to scale-up for industrial production, thereby enabling promising applications in environmental remediation.