bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trends in Human Fecal Carriage of Extended-Spectrum β-Lactamases in the Community: Toward the Globalization of CTX-M
Authors: Woerther Paul-Louis , Burdet Charles , Chachaty Elisabeth , Andremont Antoine 
Published: October 2013

SUMMARY
In the last 10 years, extended-spectrum β-lactamase-producing enterobacteria (ESBL-E) have become one of the main challenges for antibiotic treatment of enterobacterial infections, largely because of the current CTX-M enzyme pandemic. However, most studies have focused on hospitalized patients, though today it appears that the community is strongly affected as well. We therefore decided to devote our investigation to trends in ESBL-E fecal carriage rates and comprehensively reviewed data from studies conducted on healthy populations in various parts of the world. We show that (i) community ESBL-E fecal carriage, which was unknown before the turn of the millennium, has since increased significantly everywhere, with developing countries being the most affected; (ii) intercontinental travel may have emphasized and globalized the issue; and (iii) CTX-M enzymes, especially CTX-M-15, are the dominant type of ESBL. Altogether, these results suggest that CTX-M carriage is evolving toward a global pandemic but is still insufficiently described. Only a better knowledge of its dynamics and biology will lead to further development of appropriate control measures.
A Current Perspective on Daptomycin for the Clinical Microbiologist
Authors: Humphries Romney M. , Pollett Simon , Sakoulas George 
Published: October 2013

SUMMARY

Daptomycin is a lipopeptide antimicrobial with
in vitro
bactericidal activity against Gram-positive bacteria that was first approved for clinical use in 2004 in the United States. Since this time, significant data have emerged regarding the use of daptomycin for the treatment of serious infections, such as bacteremia and endocarditis, caused by Gram-positive pathogens. However, there are also increasing reports of daptomycin nonsusceptibility, in
Staphylococcus aureus
and, in particular,
Enterococcus faecium
and
Enterococcus faecalis
. Such nonsusceptibility is largely in the context of prolonged treatment courses and infections with high bacterial burdens, but it may occur in the absence of prior daptomycin exposure. Nonsusceptibility in both
S. aureus
and
Enterococcus
is mediated by adaptations to cell wall homeostasis and membrane phospholipid metabolism. This review summarizes the data on daptomycin, including daptomycin's unique mode of action and spectrum of activity and mechanisms for nonsusceptibility in key pathogens, including
S. aureus
,
E. faecium
, and
E. faecalis
. The challenges faced by the clinical laboratory in obtaining accurate susceptibility results and reporting daptomycin MICs are also discussed.
Evaluation of Commercially Available Reagents for Diagnosis of Histoplasmosis Infection in Immunocompromised Patients
Authors: Zhang Xiaochun , Gibson Bill , Daly Thomas M. 
Published: October 2013

ABSTRACT

Urinary histoplasma antigen measurement can be useful for diagnosing systemic histoplasmosis and for monitoring treatment response, especially in immunocompromised patients. However, testing has traditionally been limited to specialized reference laboratories, as immunoassay reagents for the antigen were not widely available. Recently, a polyclonal-antibody-based
in vitro
diagnostic (IVD) kit for histoplasma antigen detection was released, as well as monoclonal-antibody reagents against the target. We evaluated the analytical and clinical performance of the two reagents. Both assays were capable of detecting histoplasma antigen in urine samples over a wide dynamic range, although the monoclonal assay showed improved precision and analytical sensitivity relative to the polyclonal IVD. In a test set of clinically characterized patient samples, the monoclonal laboratory-developed test (LDT) demonstrated 90.5% sensitivity and 96.3% specificity versus 61.9% sensitivity and 79.3% specificity for the polyclonal IVD, with areas under the curve (AUCs) of 0.987 and 0.754, respectively. The major differences between the two assays were higher background reactivity in healthy donors with the polyclonal assay and an increased signal response in positive samples for the monoclonal assay. The impact of these differences on monitoring treatment response was evaluated in a series of patients undergoing treatment for histoplasmosis. While all the assays gave similar qualitative estimates of treatment response, responses were more evident using the monoclonal assay. In summary, we conclude that while multiple assays are available for measuring histoplasma antigen in urine, a monoclonal-antibody-based assay appears to provide improved analytical performance for management of immunocompromised histoplasmosis patients.
Absence of CD14 Delays Progression of Prion Diseases Accompanied by Increased Microglial Activation
Authors: Sakai Keiko , Hasebe Rie , Takahashi Yusuke , Song Chang-Hyun , Suzuki Akio , Yamasaki Takeshi , Horiuchi Motohiro 
Published: October 2013

ABSTRACTPrion diseases are fatal neurodegenerative disorders characterized by accumulation of PrPSc, vacuolation of neurons and neuropil, astrocytosis, and microglial activation. Upregulation of gene expressions of innate immunity-related factors, including complement factors and CD14, is observed in the brains of mice infected with prions even in the early stage of infections. When CD14 knockout (CD14−/−) mice were infected intracerebrally with the Chandler and Obihiro prion strains, the mice survived longer than wild-type (WT) mice, suggesting that CD14 influences the progression of the prion disease. Immunofluorescence staining that can distinguish normal prion protein from the disease-specific form of prion protein (PrPSc) revealed that deposition of PrPScwas delayed in CD14−/−mice compared with WT mice by the middle stage of the infection. Immunohistochemical staining with Iba1, a marker for activated microglia, showed an increased microglial activation in prion-infected CD14−/−mice compared to WT mice. Interestingly, accompanied by the increased microglial activation, anti-inflammatory cytokines interleukin-10 (IL-10) and transforming growth factor β (TGF-β) appeared to be expressed earlier in prion-infected CD14−/−mice. In contrast, IL-1β expression appeared to be reduced in the CD14−/−mice in the early stage of infection. Double immunofluorescence staining demonstrated that CD11b- and Iba1-positive microglia mainly produced the anti-inflammatory cytokines, suggesting anti-inflammatory status of microglia in the CD14−/−mice in the early stage of infection. These results imply that CD14 plays a role in the disease progression by suppressing anti-inflammatory responses in the brain in the early stage of infection.
Mutations in the Parainfluenza Virus 5 Fusion Protein Reveal Domains Important for Fusion Triggering and Metastability
Authors: Bose Sayantan , Heath Carissa M. , Shah Priya A. , Alayyoubi Maher , Jardetzky Theodore S. , Lamb Robert A. 
Published: October 2013

ABSTRACTParamyxovirus membrane glycoproteins F (fusion protein) and HN, H, or G (attachment protein) are critical for virus entry, which occurs through fusion of viral and cellular envelopes. The F protein folds into a homotrimeric, metastable prefusion form that can be triggered by the attachment protein to undergo a series of structural rearrangements, ultimately folding into a stable postfusion form. In paramyxovirus-infected cells, the F protein is activated in the Golgi apparatus by cleavage adjacent to a hydrophobic fusion peptide that inserts into the target membrane, eventually bringing the membranes together by F refolding. However, it is not clear how the attachment protein, known as HN in parainfluenza virus 5 (PIV5), interacts with F and triggers F to initiate fusion. To understand the roles of various F protein domains in fusion triggering and metastability, single point mutations were introduced into the PIV5 F protein. By extensive study of F protein cleavage activation, surface expression, and energetics of fusion triggering, we found a role for an immunoglobulin-like (Ig-like) domain, where multiple hydrophobic residues on the PIV5 F protein may mediate F-HN interactions. Additionally, destabilizing mutations of PIV5 F that resulted in HN trigger-independent mutant F proteins were identified in a region along the border of F trimer subunits. The positions of the potential HN-interacting region and the region important for F stability in the lower part of the PIV5 F prefusion structure provide clues to the receptor-binding initiated, HN-mediated F trigger.
Dynamic and Double-Diffusive Instabilities in a Weak Pycnocline. Part I: Observations of Heat Flux and Diffusivity in the Vicinity of Maud Rise, Weddell Sea
Authors: Shaw William J. , Stanton Timothy P. 
Published: October 2013

Abstract
An expedition to study the stability of the weakly stratified water column in the eastern Weddell Sea was undertaken in the austral winter of 2005. A regional CTD survey around Maud Rise delineated water mass boundaries associated with flow around the seamount and identified areas most susceptible to overturning. A downstream region of the seamount Taylor column was found least stable, with a potential density difference across the pycnocline less than 0.018 kg m−3. Intensive water column measurements, including 1300 profiles of temperature, conductivity, and fast-response microconductivity, were made during a series of 13 drift stations to investigate vertical turbulent transports and the evolution of water column stability. The dependence of pycnocline turbulent diffusivity kT on Froude number Fr (turbulence generated by internal wave shear) and density ratio Rρ (turbulence generated by diffusive layering and possibly diapycnal cabbeling) is investigated. The Fr alone cannot explain completely the observed kT variability. Instead, there is also a strong dependence on Rρ. Turbulent diffusivity is an order of magnitude larger in the weakly stratified Taylor cap over Maud Rise (where Rρ approaches one) than in the surrounding water column that is unaffected by flow around Maud Rise. In terms of water column stability, diffusive heat flux across the pycnocline inhibits winter ice growth and densification of the surface layer. The observed Rρ dependence of kT thus provides a strong negative feedback on the winter evolution of the Maud Rise area water column toward overturning instability.
Coastal Trapped Waves, Alongshore Pressure Gradients, and the California Undercurrent*
Authors: Connolly Thomas P. , Hickey Barbara M. , Shulman Igor , Thomson Richard E. 
Published: October 2013

Abstract
The California Undercurrent (CUC), a poleward-flowing feature over the continental slope, is a key transport pathway along the west coast of North America and an important component of regional upwelling dynamics. This study examines the poleward undercurrent and alongshore pressure gradients in the northern California Current System (CCS), where local wind stress forcing is relatively weak. The dynamics of the undercurrent are compared in the primitive equation Navy Coastal Ocean Model and a linear coastal trapped wave model. Both models are validated using hydrographic data and current-meter observations in the core of the undercurrent in the northern CCS. In the linear model, variability in the predominantly equatorward wind stress along the U.S. West Coast produces episodic reversals to poleward flow over the northern CCS slope during summer. However, reproducing the persistence of the undercurrent during late summer requires additional incoming energy from sea level variability applied south of the region of the strongest wind forcing. The relative importance of the barotropic and baroclinic components of the modeled alongshore pressure gradient changes with latitude. In contrast to the southern and central portions of the CCS, the baroclinic component of the alongshore pressure gradient provides the primary poleward force at CUC depths over the northern CCS slope. At time scales from weeks to months, the alongshore pressure gradient force is primarily balanced by the Coriolis force associated with onshore flow.
RNA-Seq analysis of Citrus reticulata in the early stages of Xylella fastidiosa infection reveals auxin-related genes as a defense response
Authors: Rodrigues Carolina M , de Souza Alessandra A , Takita Marco A , Kishi Luciano T , Machado Marcos A 
Published: October 2013

Abstract

Background
Citrus variegated chlorosis (CVC), caused by Xylella fastidiosa, is one the most important citrus diseases, and affects all varieties of sweet orange (Citrus sinensis L. Osb). On the other hand, among the Citrus genus there are different sources of resistance against X. fastidiosa. For these species identifying these defense genes could be an important step towards obtaining sweet orange resistant varieties through breeding or genetic engineering. To assess these genes we made use of mandarin (C. reticulata Blanco) that is known to be resistant to CVC and shares agronomical characteristics with sweet orange. Thus, we investigated the gene expression in Ponkan mandarin at one day after infection with X. fastidiosa, using RNA-seq. A set of genes considered key elements in the resistance was used to confirm its regulation in mandarin compared with the susceptible sweet orange.

Results
Gene expression analysis of mock inoculated and infected tissues of Ponkan mandarin identified 667 transcripts repressed and 724 significantly induced in the later. Among the induced transcripts, we identified genes encoding proteins similar to Pattern Recognition Receptors. Furthermore, many genes involved in secondary metabolism, biosynthesis and cell wall modification were upregulated as well as in synthesis of abscisic acid, jasmonic acid and auxin.

Conclusions
This work demonstrated that the defense response to the perception of bacteria involves cell wall modification and activation of hormone pathways, which probably lead to the induction of other defense-related genes. We also hypothesized the induction of auxin-related genes indicates that resistant plants initially recognize X. fastidiosa as a necrotrophic pathogen.
Isolation, characterization and comparative genomics of bacteriophage SfIV: a novel serotype converting phage from Shigella flexneri
Authors: Jakhetia Richa , Talukder Kaisar A , Verma Naresh K 
Published: October 2013

Abstract

Background

Shigella flexneri is the major cause of shigellosis in the developing countries. The O-antigen component of the lipopolysaccharide is one of the key virulence determinants required for the pathogenesis of S. flexneri. The glucosyltransferase and/or acetyltransferase genes responsible for the modification of the O-antigen are encoded by temperate serotype converting bacteriophage present in the S. flexneri genome. Several serotype converting phages have previously been isolated and characterized, however, attempts to isolate a serotype converting phage which encodes the modification genes of serotypes 4a strain have not been successful.

Results
In this study, a novel temperate serotype converting bacteriophage SfIV was isolated. Lysogenisation of phage SfIV converted serotype Y strain to serotype 4a. Electron microscopy indicated that SfIV belongs to Myoviridae family. The 39,758 bp genome of phage SfIV encompasses 54 open reading frames (orfs). Protein level comparison of SfIV with other serotype converting phages of S. flexneri revealed that SfIV is similar to phage SfII and SfV. The comparative analysis also revealed that SfIV phage contained five proteins which were not found in any other phages of S. flexneri. These proteins were: a tail fiber assembly protein, two hypothetical proteins with no clear function, and two other unknown proteins which were encoded by orfs present on a moron, that presumably got introduced in SfIV genome from another species via a transposon. These unique proteins of SfIV may play a role in the pathogenesis of the host.

Conclusions
This study reports the isolation and complete genome sequence analysis of bacteriophage SfIV. The SfIV phage has a host range significantly different from the other phages of Shigella. Comparative genome analysis identified several proteins unique to SfIV, which may potentially be involved in the survival and pathogenesis of its host. These findings will further our understanding on the evolution of these phages, and will also facilitate studies on development of new phage vectors and therapeutic agents to control infections caused by S. flexneri.
The effects of levosimendan and dobutamine in experimental bupivacaine-induced cardiotoxicity
Authors: Kandemir Ulku , Maltepe Fikret , Ugurlu Baran , Gokmen Necati , Celik Asli 
Published: October 2013

Abstract

Background
Accidental intravenous exposure to bupivacaine is highly cardiotoxic and may lead to death. Positive inotropic agents are usually utilized in resuscitative efforts. We have compared the efficacy of levosimendan, a novel inotropic agent, with dobutamine and their combination in a rat model of bupivacaine intoxication.

Methods
Twenty-eight male Wistar albino rats weighing between 250-300 g were divided into these four groups: control (C), levosimendan (L), dobutamine (D) and dobutamine+levosimendan (D+L). Bupivacaine was administered at a dose of 3 mg/kg/min until cardiac arrest occurred or for 120 min. ECG, heart rate, blood pressure, arterial blood gases, and end tidal CO2 levels were monitored. Levosimendan was administered as a bolus of 12 μg/kg for 10 min and continued as an infusion at 0.3 μg/kg/min. Dobutamine was infused at a dose of 3 μg/kg/min. The time required for a 50% and 75% decrease in heart rate and blood pressure with a total time to cardiac arrest and bupivacaine dose for obtaining cardiac arrest were analyzed.

Results
Time periods for heart rate reductions of 50% and 75% were significantly longer in groups L (903, 1198 s), D (984, 1542 s) and L+D (1705, 3152 s) compared with the control group (345, 538 s p < 0.001). Median times to mean blood pressure reductions of 50% and 75% were 399 - 504 s in the control group, 1005 -1204 s in group L, 685 - 1009 s in group D and 1544- 2982 s in group L+D, and the difference was significant compared with the control group. Median time duration to asystole was 703 s in the control group compared with 1385 s in group L, 1789 s in group D and 3557 s in group L+D. Time to cardiac arrest was significantly higher in all 3 study groups. It was also significantly higher in the L+D group compared with both groups L and D separately.

Conclusion
A combination of dobutamine with levosimendan significantly increased survival times in this bupivacaine-induced toxicity rat model compared with the control, levosimendan, and dobutamine groups.
Efficacy and safety of thrice weekly DOTS in tuberculosis patients with and without HIV co-infection: an observational study
Authors: Vashishtha Richa , Mohan Krishna , Singh Bhagteshwar , Devarapu Satish K , Sreenivas Vishnubhatla , Ranjan Sanjay , Gupta Deepak , Sinha Sanjeev , Sharma Surendra K 
Published: October 2013

Abstract

Background
Despite the latest World Health Organization guidelines advocating daily therapy in HIV-TB co-infected individuals, there are few recent studies comparing outcomes of thrice-weekly anti-tuberculosis treatment in HIV-positive and HIV-negative patients with TB. The present study sets out to compare TB treatment outcomes in these two groups in the Indian national programme, which currently involves thrice-weekly therapy for all, regardless of HIV status.

Methods
HIV-positive and HIV-negative were consecutively screened for enrolment into this prospective observational study, carried out at the All India Institute of Medical Sciences hospital, New Delhi, India, between 2006 and 2010. Patients were given short-course thrice-weekly rifampicin-based therapy, with all HIV-positive patients being started on highly active antiretroviral therapy at least 14 days after commencing TB treatment. Patients were regularly followed-up for 24 months after completion of treatment.

Results
150 HIV-positive, 155 HIV-negative patients were enrolled consecutively for the study. Significantly higher treatment success (93.5% vs. 76.7% at end of treatment, p < 0.001) and lower mortality (2.8% vs. 21.6% on follow up, p < 0.001) were observed in HIV-negative patients. No significant difference was found in treatment failure (p = 0.16), sputum smear (p = 0.58) and culture conversion (p = 0.55), and non-serious adverse event incidence (p = 0.851) between the two groups. Low baseline CD4 cell count (<100 cells/ mm3) was the only predictor of mortality in HIV-TB patients (odds ratio 8 · 43, p = 0 · 013).

Conclusions
Thrice-weekly anti-tuberculosis therapy is more effective in HIV-negative than in HIV-positive patients. However, outcomes in this HIV co-infected cohort were found to be similar to those reported previously with daily therapy, with no safety concerns. This should prompt further study into whether intermittent or daily therapy should be used universally in resource-poor settings, using large well executed randomised controlled trials.

Trial registration

NCT%20No.%2000698334
Antibacterial activity of Nymphaea nouchali (Burm. f) flower
Authors: Dash Biplab Kumar , Sen Monokesh Kumer , Alam Khasrul , Hossain Kamal , Islam Rezuanul , Banu Nilufa Akhter , Rahman Shahedur , Jamal AbuHena Mostofa 
Published: October 2013

Abstract

Background
The present work aimed to find out the antibacterial activity of Nymphaea nouchali flower on human and plant pathogenic bacteria.

Methods
Antibacterial potency of methanol, acetone, ethyl acetate and petroleum spirit extracts of Nymphaea nouchali flower has been tested against four human pathogenic bacteria Bacillus subtilis (FO 3026) Escherichia coli (IFO 3007), Klebsiella pneumonia (ATTC 10031) and Sarcina lutea (IFO 3232) and one plant pathogenic bacterium Xanthomonas campestris (IAM 1671) by disc diffusion assay. Zone of inhibition produced by different extracts against the test bacteria was measured and compared with standard antibiotic disc.

Results
Methanol extract possessed better antibacterial activity against two pathogenic bacteria, B. subtilis (FO 3026) and S. lutea (IFO 3232) than commercial antibiotic nalidixic acid. Acetone extract showed moderate sensitivity whereas B. subtilis (FO 3026), S. lutea (IFO 3232) and X. campestris (IAM 1671) showed resistance to ethyl acetate and petroleum spirit extracts. The minimum inhibitory concentrations of various extracts were ranged between 128–2048 μgml-1.

Conclusions

Nymphaea nouchali flower could be a potential candidate for future development of novel broad spectrum antibacterial herbal formulation.