bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete Nucleotide Sequence of KPC-3-Encoding Plasmid pKpQIL in the Epidemic
Klebsiella pneumoniae
Sequence Type 258
Authors: Leavitt Azita , Chmelnitsky Inna , Carmeli Yehuda , Navon-Venezia Shiri 
Published: August 2010

ABSTRACT

We have determined the entire DNA sequence of plasmid pKpQIL, the
bla
KPC-3
-carrying plasmid harbored by the carbapenem-resistant
Klebsiella pneumoniae
clone sequence type 258 (ST 258) in Israel. pKpQIL is a 113,637-bp, self-transmissible plasmid that belongs to the incompatibility group IncFII. It consists of a large backbone of a pKPN4-like plasmid and carries the
bla
KPC-3
-containing Tn
4401
a transposon of a pNYC-like plasmid.
Efficacy of the Combination of Tobramycin and a Macrolide in an
I
n
V
itro
Pseudomonas aeruginosa
Mature Biofilm Model
Authors: Tré-Hardy Marie , Nagant Carole , El Manssouri Naïma , Vanderbist Francis , Traore Hamidou , Vaneechoutte Mario , Dehaye Jean-Paul 
Published: August 2010

ABSTRACT

Respiratory disease is the main cause of morbidity and mortality in patients with cystic fibrosis (CF). In particular, patients suffer from chronic infection due to biofilm formation by opportunistic
Pseudomonas aeruginosa
(32). Therefore, there is an urgent need to develop alternative ways to treat biofilm-associated clinical infections. The aim of this study was to compare the antimicrobial effects
in vitro
of the combinations tobramycin-clarithromycin and tobramycin-azithromycin against five
P. aeruginosa
biofilms and to establish the most effective combination. We performed a kinetic study over a period of 28 days of a twice-daily coadministration of the combinations tobramycin-clarithromycin and tobramycin-azithromycin on 12-day-old, mature
P. aeruginosa
biofilms formed on microplate pegs for 4 clinical isolates and one laboratory strain (PAO1) to simulate the treatment of CF patients with tobramycin inhalation solution (TOBI) through aerosolization. A synergy between tobramycin and clarithromycin was recorded for 3/5 biofilms, with a bacterial decrease of more than 5 log. Conversely, we found an antagonistic activity when 4 μg/ml tobramycin was administered with azithromycin at 2 μg/ml for
P. aeruginosa
PAO1 and with azithromycin at 2, 20, 50, 100, and 200 μg/ml for
P. aeruginosa
PYO1. Treatment with tobramycin at 4 μg/ml combined with clarithromycin at 200 μg/ml eradicated all five biofilms, while tobramycin-azithromycin at the same concentrations eradicated only three biofilms. Results of this study suggest that local administration of tobramycin and clarithromycin into the respiratory tract represents a better strategy than the combination tobramycin-azithromycin for the treatment of
P. aeruginosa
-associated pulmonary infections.
Affinity of Ceftobiprole for Penicillin-Binding Protein 2b in
Streptococcus pneumoniae
Strains with Various Susceptibilities to Penicillin
Authors: Davies Todd A. , He Wenping , Bush Karen , Flamm Robert K. 
Published: August 2010

ABSTRACT

Wild-type penicillin-binding protein (PBP) 2b from penicillin-susceptible
Streptococcus pneumoniae
had high affinity for ceftobiprole and penicillin (50% inhibitory concentrations [IC
50
s] of ≤0.15 μg/ml) but not ceftriaxone (IC
50
of >8 μg/ml). In clinical isolates, ceftobiprole and PBP 2b affinities were reduced 15- to 30-fold with a Thr-446-Ala substitution and further still with an additional Ala-619-Gly PBP 2b substitution. Ceftobiprole remained active (MICs of ≤1 μg/ml) against all strains tested and behaved more like penicillin than ceftriaxone with respect to PBP 2b binding.
Allele Specificity of Gamma Interferon Responses to the Carboxyl-Terminal Region ofPlasmodium falciparumMerozoite Surface Protein 1 by Kenyan Adults with Naturally Acquired Immunity to Malaria
Authors: Spring Michele D. , Chelimo Kiprotich , Tisch Daniel J. , Sumba Peter Odada , Rochford Rosemary , Long Carole A. , Kazura James W. , Moormann Ann M. 
Published: August 2010

ABSTRACTCross-sectional seroepidemiological studies of populations naturally exposed toPlasmodium falciparumsuggest an association between protection from malaria and circulating antibodies to the carboxyl terminus of merozoite surface protein 1 (MSP1). Questions remain regarding the significance of cell-mediated immunity to MSP1 in conferring protection and inducing immunologic memory. Vaccine constructs have been based on the 42-kDa recombinant MSP1 protein (MSP142), which includes the 19-kDa (MSP119) and 33-kDa (MSP133) fragments containing the major B- and T-cell epitopes, respectively. To evaluate T-cell responses to the MSP133fragment, two libraries of overlapping 18-mer peptides from the 3D7 and FVO MSP133regions were used to screen a cohort of asymptomatic Kenyan adults. Gamma interferon (IFN-γ) measured by enzyme-linked immunospot assay (ELISPOT) at multiple time points assessed the magnitude and stability of these responses. The percentage of individuals with IFN-γ responses to single MSP133peptides ranged from nil to 24%, were clustered among a subset of peptides, and were not consistently recalled over time. In comparison to peptide responses, IFN-γ ELISPOT responses to recombinant MSP142were more prevalent, more frequently elicited by the 3D7 as opposed to the FVO allele, and more stable over time. The prevailing MSP133genotype infection was 3D7, with few mixed infections and no sole FVO infections. This study demonstrates that immunity against MSP133after cumulative natural infections consists of low-magnitude and difficult-to-detect IFN-γ responses. Although immunity against MSP1 alone will not confer protection against malaria, demonstrating a relative and sustained increase in T-cell immunity to MSP1 after vaccination would be a reasonable measurement of vaccine responsiveness.
Pic, an Autotransporter Protein Secreted by Different Pathogens in theEnterobacteriaceaeFamily, Is a Potent Mucus Secretagogue
Authors: Navarro-Garcia Fernando , Gutierrez-Jimenez Javier , Garcia-Tovar Carlos , Castro Luis A. , Salazar-Gonzalez Hector , Cordova Vanessa 
Published: August 2010

ABSTRACTA hallmark of enteroaggregativeEscherichia coli(EAEC) infection is a formation of biofilm, which comprises a mucus layer with immersed bacteria in the intestines of patients. While studying the mucinolytic activity of Pic in anin vivosystem, rat ileal loops, we surprisingly found that EAEC induced hypersecretion of mucus, which was accompanied by an increase in the number of mucus-containing goblet cells. Interestingly, an isogenicpicmutant (EAEC Δpic) was unable to cause this mucus hypersecretion. Furthermore, purified Pic was also able to induce intestinal mucus hypersecretion, and this effect was abolished when Pic was heat denatured. Site-directed mutagenesis of the serine protease catalytic residue of Pic showed that, unlike the mucinolytic activity, secretagogue activity did not depend on this catalytic serine protease motif. Other pathogens harboring thepicgene, such asShigella flexneriand uropathogenicE. coli(UPEC), also showed results similar to those for EAEC, and construction of isogenicpicmutants ofS. flexneriand UPEC confirmed this secretagogue activity. Thus, Pic mucinase is responsible for one of the pathophysiologic features of the diarrhea mediated by EAEC and the mucoid diarrhea induced byS. flexneri.
Sublingual Immunization Protects against
Helicobacter pylori
Infection and Induces T and B Cell Responses in the Stomach
Authors: Raghavan Sukanya , Östberg Anna Karin , Flach Carl-Fredrik , Ekman Annelie , Blomquist Margareta , Czerkinsky Cecil , Holmgren Jan 
Published: August 2010

ABSTRACT

Sublingual (SL) immunization has been described as an effective novel way to induce mucosal immune responses in the respiratory and genital tracts. We examined the potential of SL immunization against
Helicobacter pylori
to stimulate immune responses in the gastrointestinal mucosa and protect against
H. pylori
infection. Mice received two SL immunizations with
H. pylori
lysate antigens and cholera toxin as an adjuvant, and after challenge with live
H. pylori
bacteria, their immune responses and protection were evaluated, as were immune responses prior to challenge. SL immunization induced enhanced proliferative responses to
H. pylori
antigens in cervicomandibular lymph nodes and provided at least the same level of immune responses and protection as corresponding intragastric immunization. Protection in SL-immunized mice was associated with strong
H. pylori
-specific serum IgG and IgA antibody responses in the stomach and intestine, with strong proliferation and gamma interferon (IFN-γ) and interleukin-17 (IL-17) production by spleen and mesenteric lymph node T cells stimulated with
H. pylori
antigens
in vitro
, and with increased IFN-γ and IL-17 gene expression in the stomach compared to levels in infected unimmunized mice. Immunohistochemical studies showed enhanced infiltration of CD4
+
T cells and CD19
+
B cells into the
H. pylori
-infected stomach mucosa of SL-immunized but not unimmunized
H. pylori
-infected mice, which coincided with increased expression of the mucosal addressin cell adhesion molecule (MAdCAM-1) and T and B cell-attracting chemokines CXCL10 and CCL28. We conclude that, in mice, SL immunization can effectively induce protection against
H. pylori
infection in association with strong T and B cell infiltration into the stomach.
Wheat dependent exercise induced anaphylaxis: is this an appropriate terminology?
Authors: Wong G K Y , Huissoon A P , Goddard S , Collins D M , Krishna M T 
Published: August 2010

BackgroundThe presentation of wheat dependent exercise induced anaphylaxis (WDEIA) can be variable. A high index of clinical suspicion is required to initiate the investigation pathway. Double blind placebo controlled food-exercise challenge is the gold standard investigation but the practicality of this test limits its application.AimTo critically analyse the symptoms of WDEIA and their correlation with serum specific IgE (sIgE) to rω-5-gliadin.Methods17 patients were tested for serum sIgE to rω-5-gliadin. The clinical response to a diet/exercise intervention protocol was used to assess specificity of a positive sIgE to rω-5-gliadin. Length of time to diagnosis, clinical likelihood scores, exercise intensity involved and the severity of allergic reactions were examined retrospectively.Result8/10 patients with positive sIgE to rω-5-gliadin had a confirmed diagnosis of WDEIA. Half of the WDEIA patients had a prolonged time lag to diagnosis (32–62 months) and were initially diagnosed with idiopathic anaphylaxis or chronic idiopathic urticaria and angioedema. Only three patients had experienced life threatening symptoms (Mueller grading 4). A close association was observed between requirements of lower exercise intensity to provoke a reaction and diagnostic delay.ConclusionSpecific IgE to rω-5-gliadin can provide supportive evidence for WDEIA without the need of a food-exercise challenge. The wheat-exercise association is not obvious in many patients, highlighting the need to consider WDEIA in the differential diagnosis of all patients presenting with idiopathic systemic reactions. The term anaphylaxis may be inappropriate and it is therefore worth considering an alternative terminology such as ‘activity dependent wheat allergy’ to describe this condition.
The Sanders Barotropic Tropical Cyclone Track Prediction Model (SANBAR)
Authors: Burpee Robert W. 
Published: August 2010

Abstract
Sanders designed a barotropic tropical cyclone (TC) track prediction model for the North Atlantic TC basin that became known as the Sanders barotropic (SANBAR) model. It predicted the streamfunction of the deeplayer mean winds (tropical circulation vertically averaged from 1000 to 100 hPa) that represents the vertically averaged tropical circulations. Originally, the wind input for the operational objective analysis (OA) consisted of winds measured by radiosondes and 44 bogus winds provided by analysis at the National Hurricane Center (NHC), which corresponded to the vertically averaged flow over sparsely observed tropical, subtropical, and midlatitude oceanic regions. The model covered a fixed regional area and had a grid size of ~ 154 km. It estimated the initial storm motion solely on the basis of the large-scale flow from the OA, not taking into account the observed storm motion.
During 1970, the SANBAR model became the first dynamical TC track model to be run operationally at NHC. Track forecasts of SANBAR were verified from the 1971 TC season when track model verifications began at NHC until its retirement after the 1989 Atlantic TC season. The average annual SANBAR forecast track errors were verified relative to Climatology and Persistence (CLIPER), the standard no-skill track forecast. Comparison with CLIPER determines the skill of track forecast methods. Verifications are presented for two different versions of the SANBAR model system used operationally during 1973–84 and 1985–89. In homogeneous comparisons (i.e., includes only forecasts for the same initial times) for the former period, SANBAR's track forecasts were slightly better than CLIPER at 24–48-h forecast intervals; however, from 1985 to 1989 the average SANBAR track forecast errors from 24–72 h were ~10% more skillful than homogeneous CLIPER track forecasts.
Fred Sanders' Roles in the Transformation of Synoptic Meteorology, the Study of Rapid Cyclogenesis, the Prediction of Marine Cyclones, and the Forecast of New York City's “Big Snow” of December 1947
Authors: Uccellini Louis W. , Kocin Paul J. , Sienkiewicz Joseph , Kistler Robert , Baker Michael 
Published: August 2010

Abstract
Fred Sanders' career extended over 55 yr, touching upon many of the revolutionary transformations in the field of meteorology during that period. In this paper, his contributions to the transformation of synoptic meteorology, his research into the nature of explosive cyclogenesis, and related advances in the ability to predict these storms are reviewed. In addition to this review, the current status of forecasting oceanic cyclones 4.5 days in advance is presented, illustrating the progress that has been made and the challenges that persist, especially for forecasting those extreme extratropical cyclones that are marked by surface wind speeds exceeding hurricane force. Last, Fred Sanders' participation in a forecast for the historic 1947 snowstorm (that produced snowfall amounts in the New York City area that set records at that time) is reviewed along with an attempt to use today's operational global model to simulate this storm using data that were available at the time. The study reveals the predictive limitations involved with this case based on the scarcity of upper-air data in 1947, while confirming Fred Sanders' forecasting skills when dealing with these types of major storm events, even as a young aviation forecaster at New York's LaGuardia Airport.
Closed Anticyclones of the Subtropics and Midlatitudes: A 54-Yr Climatology (1950–2003) and Three Case Studies
Authors: Galarneau Thomas J. , Bosart Lance F. , Aiyyer Anantha R. 
Published: August 2010

Abstract
The pioneering large-scale studies of cyclone frequency, location, and intensity conducted by Fred Sanders prompt similar questions about lesser-studied anticyclone development. The results of a climatology of closed anticyclones (CAs) at 200, 500, and 850 hPa, with an emphasis on the subtropics and midlatitudes, is presented to assess the seasonally varying distribution and hemispheric differences of these features. To construct the CA climatology, a counting program was applied to twice-daily 2.5° NCEP–NCAR reanalysis 200-, 500-, and 850-hPa geopotential height fields for the period 1950–2003. Stationary CAs, defined as those CAs that were located at a particular location for consecutive time periods, were counted only once.
The climatology results show that 200-hPa CAs occur preferentially during summer over subtropical continental regions, while 500-hPa CAs occur preferentially over subtropical oceans in all seasons and over subtropical continents in summer. Conversely, 850-hPa CAs occur preferentially over oceanic regions beneath upper-level midocean troughs, and are most prominent in the Northern Hemisphere, and over midlatitude continents in winter.
Three case studies of objectively identified CAs that produced heal waves over the United States, Europe, and Australia in 1995, 2003, and 2004, respectively, are presented to supplement the climatological results. The case studies, examining the subset of CAs than can produce heat waves, illustrate how climatologically hot continental tropical air masses produced over arid and semiarid regions of the subtropics and lower midlatitudes can become abnormally hot in conjunction with dynamically driven upper-level ridge amplification. Subsequently, these abnormally hot air masses are advected downstream away from their source regions in conjunction with transient disturbances embedded in anomalously strong westerly jets.
Surface Boundaries of the Southern Plains: Their Role in the Initiation of Convective Storms
Authors: Bluestein Howard B. 
Published: August 2010

Abstract
The nature of the different types of surface boundaries that appear in the southern plains of the United States during the convectively active season is reviewed. The following boundaries are discussed: fronts, the dryline, troughs, and outflow boundaries, The boundaries are related to their environment and to local topography. The role these boundaries might play in the initiation of convective storms is emphasized. The various types of boundary-related vertical circulations and their dynamics are discussed. In particular, quasigeostrophic and semigeostrophic dynamics, and the dynamics of solenoidal circulations, density currents, boundary layers, and gravity waves are considered.
Miscellaneous topics pertinent to convective storms and their relationship to surface boundaries such as along-the-boundary variability, boundary collisions, and the role of vertical shear are also discussed. Although some cases of storm initiation along surface boundaries have been well documented using research datasets collected during comprehensive field experiments, much of what we know is based only on empirical forecasting and nowcasting experience. It is suggested that many problems relating to convective-storm formation need to be explored in detail using real datasets with new observing systems and techniques, in conjunction with numerical simulation studies, and through climatological studies.
FACT: Functional annotation transfer between proteins with similar feature architectures
Authors: Koestler Tina , von Haeseler Arndt , Ebersberger Ingo 
Published: August 2010

Abstract

Background
The increasing number of sequenced genomes provides the basis for exploring the genetic and functional diversity within the tree of life. Only a tiny fraction of the encoded proteins undergoes a thorough experimental characterization. For the remainder, bioinformatics annotation tools are the only means to infer their function. Exploiting significant sequence similarities to already characterized proteins, commonly taken as evidence for homology, is the prevalent method to deduce functional equivalence. Such methods fail when homologs are too diverged, or when they have assumed a different function. Finally, due to convergent evolution, functional equivalence is not necessarily linked to common ancestry. Therefore complementary approaches are required to identify functional equivalents.

Results
We present the F eature A rchitecture C omparison T ool http://www.cibiv.at/FACT to search for functionally equivalent proteins. FACT uses the similarity between feature architectures of two proteins, i.e., the arrangements of functional domains, secondary structure elements and compositional properties, as a proxy for their functional equivalence. A scoring function measures feature architecture similarities, which enables searching for functional equivalents in entire proteomes. Our evaluation of 9,570 EC classified enzymes revealed that FACT, using the full feature, set outperformed the existing architecture-based approaches by identifying significantly more functional equivalents as highest scoring proteins. We show that FACT can identify functional equivalents that share no significant sequence similarity. However, when the highest scoring protein of FACT is also the protein with the highest local sequence similarity, it is in 99% of the cases functionally equivalent to the query. We demonstrate the versatility of FACT by identifying a missing link in the yeast glutathione metabolism and also by searching for the human GolgA5 equivalent in Trypanosoma brucei.

Conclusions
FACT facilitates a quick and sensitive search for functionally equivalent proteins in entire proteomes. FACT is complementary to approaches using sequence similarity to identify proteins with the same function. Thus, FACT is particularly useful when functional equivalents need to be identified in evolutionarily distant species, or when functional equivalents are not homologous. The most reliable annotation transfers, however, are achieved when feature architecture similarity and sequence similarity are jointly taken into account.
Peptide aptamers as new tools to modulate clathrin-mediated internalisation — inhibition of MT1-MMP internalisation
Authors: Wickramasinghe Rochana D , Ferrigno Paul Ko , Roghi Christian 
Published: August 2010

AbstractBackgroundPeptide aptamers are combinatorial protein reagents that bind to targets with a high specificity and a strong affinity thus providing a molecular tool kit for modulating the function of their targetsin vivo.ResultsHere we report the isolation of a peptide aptamer named swiggle that interacts with the very short (21 amino acid long) intracellular domain of membrane type 1-metalloproteinase (MT1-MMP), a key cell surface protease involved in numerous and crucial physiological and pathological cellular events. Expression of swiggle in mammalian cells was found to increase the cell surface expression of MT1-MMP by impairing its internalisation. Swiggle interacts with the LLY573internalisation motif of MT1-MMP intracellular domain, thus disrupting the interaction with the μ2 subunit of the AP-2 internalisation complex required for endocytosis of the protease. Interestingly, swiggle-mediated inhibition of MT1-MMP clathrin-mediated internalisation was also found to promote MT1-MMP-mediated cell migration.ConclusionsTaken together, our results provide further evidence that peptide aptamers can be used to dissect molecular events mediated by individual protein domains, in contrast to the pleiotropic effects of RNA interference techniques.