bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prototype Data Analysis on LH11-1 Semisubmersible Platform in South China Sea
Authors: Du Yu , Wu Wenhua , Wang Yanlin , Yue Qianjin 
Published: September 2014

There are still uncertainties and challenges by using floating platforms as the main oil exploitation mode due to lake of actual drilling experience in South China Sea. In order to ensure the safety of platform operation, large amounts of prototype data are needed for environment and structure analysis. From 2011 till now, a prototype measurement project is carried out on a semisubmersible platform “NanHaiTiaoZhan” FPS. Large amounts of data have been collected including parameters of ocean environmental loading, motions of floater and underwater responses of mooring and risers.
In this paper, statistical analysis of floater responses together with marine environmental conditions are carried out for deep understanding of the characteristics of semisubmersible floating platform. In order to study the motion behaviors of floater under harsh storm, the data recorded in a typical typhoon “Nock-ten” are chosen to perform the deep analysis. The measured data, wind, wave, current and floater motions, are analyzed in time-domain and frequency-domain separately. The comparison study of theoretical prediction and prototype measurement result in typhoon weather has been carried out. The data recorded by standalone sensors are processed by program MoorForce. The result of frequency-domain analysis of measured mooring force proves that the significant wave frequency dynamic behavior of mooring line during typhoon weather should be considered in design.
Parametric Estimation in the Wave Buoy Analogy: An Elaborated Approach Based on Energy Considerations
Authors: Montazeri Najmeh , Nielsen Ulrik Dam 
Published: September 2014

An accurate estimation of the ocean wave directional spectrum at the location of an advancing ship is very useful for the ship master to improve operation and safety in a seaway. Research has been conducted to obtain sea state estimates by the Wave Buoy Analogy. The method deals with processing the ship’s wave-induced responses based on different statistical inferences including parametric and non-parametric approaches.
This paper considers a concept to improve the estimate obtained by the parametric method for sea state estimation. The idea is illustrated by an analysis made on full-scale response measurements carried out on a 9400 TEU container ship. The process of fitting a standard JONSWAP spectrum takes into account an analysis of residuals formed by the difference between measured and estimated amount of energy of the response(s).
A couple of motion responses and also bending moment are considered as the input of the estimation process. A comparison is made between the results and also with some inhand outputs from other estimation sources, e.g., wave radar measurements and sea surface elevation by microwave sensors. The discussed and analyzed procedure could also lead to an automatic selection of response combinations for sea state estimation.
Wave Spectra Partitioning and Identification of Wind Sea and Swell Events
Authors: Kpogo-Nuwoklo Komlan A. , Olagnon Michel , Guédé Zakoua 
Published: September 2014

Wave spectra often exhibit several peaks due to the coexistence of wind sea generated by local wind conditions and swells originating from distant weather systems. For an accurate description of sea states, those spectra can be partitioned and the partitions can be interpreted physically as representing independent wave systems. Furthermore, partitions can be associated in time to track the evolutions of wave systems originating from the same meteorological event (storm, depression, etc).
This paper proposes a new method to identify temporal sequences of wave systems parameters, consistent with respect to the meteorological events that are the sources of the phenomena. This method, as many conventional partitioning ones, is based on the watershed algorithm which is however directly applied in our case to the whole time-history of wave spectra. Using appropriate criteria, the identified events are classified into swell or wind sea events. Field data from West Africa are used to illustrate the method and the results are compared with those of conventional software. Hindcast data from the Iroise Sea are also used to validate the proposed method and the results show a good identification of wave systems events with a good correlation between wind sea events and wind characteristics.
Extracellular DNA Impedes the Transport of Vancomycin in Staphylococcus epidermidis Biofilms Preexposed to Subinhibitory Concentrations of Vancomycin
Authors: Doroshenko Natalya , Tseng Boo Shan , Howlin Robert P. , Deacon Jill , Wharton Julian A. , Thurner Philipp J. , Gilmore Brendan F. , Parsek Matthew R. , Stoodley Paul 
Published: September 2014

ABSTRACT

Staphylococcus epidermidis
biofilm formation is responsible for the persistence of orthopedic implant infections. Previous studies have shown that exposure of
S. epidermidis
biofilms to sub-MICs of antibiotics induced an increased level of biofilm persistence. BODIPY FL-vancomycin (a fluorescent vancomycin conjugate) and confocal microscopy were used to show that the penetration of vancomycin through sub-MIC-vancomycin-treated
S. epidermidis
biofilms was impeded compared to that of control, untreated biofilms. Further experiments showed an increase in the extracellular DNA (eDNA) concentration in biofilms preexposed to sub-MIC vancomycin, suggesting a potential role for eDNA in the hindrance of vancomycin activity. Exogenously added,
S. epidermidis
DNA increased the planktonic vancomycin MIC and protected biofilm cells from lethal vancomycin concentrations. Finally, isothermal titration calorimetry (ITC) revealed that the binding constant of DNA and vancomycin was 100-fold higher than the previously reported binding constant of vancomycin and its intended cellular
d
-Ala-
d
-Ala peptide target. This study provides an explanation of the eDNA-based mechanism of antibiotic tolerance in sub-MIC-vancomycin-treated
S. epidermidis
biofilms, which might be an important factor for the persistence of biofilm infections.
New Colistin Population Pharmacokinetic Data in Critically Ill Patients Suggesting an Alternative Loading Dose Rationale
Authors: Grégoire N. , Mimoz O. , Mégarbane B. , Comets E. , Chatelier D. , Lasocki S. , Gauzit R. , Balayn D. , Gobin P. , Marchand S. , Couet W. 
Published: September 2014

ABSTRACT

Colistin is an old antibiotic that has recently gained a considerable renewal of interest as the last-line defense therapy against multidrug-resistant Gram-negative bacteria. It is administered as colistin methanesulfonate (CMS), an inactive prodrug, and it was shown that due to slow CMS conversion, colistin plasma concentrations increase very slowly after treatment initiation, which constitutes the rationale for a loading dose in critically ill patients. However, faster CMS conversion was observed in healthy volunteers but using a different CMS brand, which may also have a major impact on colistin pharmacokinetics. Seventy-three critically ill patients not undergoing dialysis received multiple doses of CMS. The CMS concentrations were measured by liquid chromatography-tandem mass spectrometry (LC-MS/MS), and a pharmacokinetic analysis was conducted using a population approach. We confirmed that CMS renal clearance and colistin concentrations at steady state are mostly governed by creatinine clearance, but we predict a typical maximum concentration of drug in serum (
C
max
) of colistin close to 2 mg/liter, occurring 3 h after an initial dose of 2 million international units (MIU) of CMS. Accordingly, the estimated colistin half-life (
t
1/2
) was relatively short (3.1 h), with rapid attainment of steady state. Our results are only partially consistent with other recently published results. We confirm that the CMS maintenance dose should be adjusted according to renal function in critically ill patients. However, much higher than expected colistin concentrations were observed after the initial CMS dose, with rapid steady-state achievement. These discrepancies challenge the pharmacokinetic rationale for a loading dose, which may still be appropriate for rapid bacterial eradication and an improved clinical cure rate.
A Novel Target and Approach for Identifying Antivirals against Molluscum Contagiosum Virus
Authors: Guan Hancheng , Nuth Manunya , Zhukovskaya Natalia , Saw Yih Ling , Bell Edward , Isaacs Stuart N. , Ricciardi Robert P. 
Published: September 2014

ABSTRACT

The dermatological disease molluscum contagiosum (MC) presents as lesions restricted solely to the skin. The poxvirus molluscum contagiosum virus (MCV) is responsible for this skin disease that is easily transmitted through casual contact among all populations, with greater frequency in children and immunosuppressed individuals. In addition, sexual transmission of MCV in adolescents and adults is a health concern. Although the skin lesions ultimately resolve in immunocompetent individuals, they can persist for extended periods, be painful, and result in scarring. Treatment is problematic, and there is no drug that specifically targets MCV. The inability of MCV to propagate in cell culture has impeded drug development. To overcome these barriers, we integrated three new developments. First, we identified a new MCV drug target (mD4) that is essential for processive DNA synthesis
in vitro
. Second, we discovered a small chemical compound that binds to mD4 and prevents DNA synthesis
in vitro
. Third, and most significant, we engineered a hybrid vaccinia virus (mD4-VV) in which the natural vaccinia D4 (vD4) gene is replaced by the mD4 target gene. This hybrid virus is dependent on mD4 for viral growth in culture and is inhibited by the small compound. This target system provides, for the first time, a platform and approach for the discovery and evaluation of new therapeutics that can be used to treat MC.
Differential Roles of RND Efflux Pumps in Antimicrobial Drug Resistance of Sessile and Planktonic Burkholderia cenocepacia Cells
Authors: Buroni Silvia , Matthijs Nele , Spadaro Francesca , Van Acker Heleen , Scoffone Viola C. , Pasca Maria Rosalia , Riccardi Giovanna , Coenye Tom 
Published: September 2014

ABSTRACT

Burkholderia cenocepacia
is notorious for causing respiratory tract infections in people with cystic fibrosis. Infections with this organism are particularly difficult to treat due to its high level of intrinsic resistance to most antibiotics. Multidrug resistance in
B. cenocepacia
can be ascribed to different mechanisms, including the activity of efflux pumps and biofilm formation. In the present study, the effects of deletion of the 16 operons encoding resistance-nodulation-cell division (RND)-type efflux pumps in
B. cenocepacia
strain J2315 were investigated by determining the MICs of various antibiotics and by investigating the antibiofilm effect of these antibiotics. Finally, the expression levels of selected RND genes in treated and untreated cultures were investigated using reverse transcriptase quantitative PCR (RT-qPCR). Our data indicate that the RND-3 and RND-4 efflux pumps are important for resistance to various antimicrobial drugs (including tobramycin and ciprofloxacin) in planktonic
B. cenocepacia
J2315 populations, while the RND-3, RND-8, and RND-9 efflux systems protect biofilm-grown cells against tobramycin. The RND-8 and RND-9 efflux pumps are not involved in ciprofloxacin resistance. Results from the RT-qPCR experiments on the wild-type strain
B. cenocepacia
J2315 suggest that there is little regulation at the level of mRNA expression for these efflux pumps under the conditions tested.
Small-Molecule Inhibitors of the Pseudaminic Acid Biosynthetic Pathway: Targeting Motility as a Key Bacterial Virulence Factor
Authors: Ménard Robert , Schoenhofen Ian C. , Tao Limei , Aubry Annie , Bouchard Patrice , Reid Christopher W. , Lachance Paule , Twine Susan M. , Fulton Kelly M. , Cui Qizhi , Hogues Hervé , Purisima Enrico O. , Sulea Traian , Logan Susan M. 
Published: September 2014

ABSTRACT

Helicobacter pylori
is motile by means of polar flagella, and this motility has been shown to play a critical role in pathogenicity. The major structural flagellin proteins have been shown to be glycosylated with the nonulosonate sugar, pseudaminic acid (Pse). This glycan is unique to microorganisms, and the process of flagellin glycosylation is required for
H. pylori
flagellar assembly and consequent motility. As such, the Pse biosynthetic pathway offers considerable potential as an antivirulence drug target, especially since motility is required for
H. pylori
colonization and persistence in the host. This report describes screening the five Pse biosynthetic enzymes for small-molecule inhibitors using both high-throughput screening (HTS) and
in silico
(virtual screening [VS]) approaches. Using a 100,000-compound library, 1,773 hits that exhibited a 40% threshold inhibition at a 10 μM concentration were identified by HTS. In addition, VS efforts using a 1.6-million compound library directed at two pathway enzymes identified 80 hits, 4 of which exhibited reasonable inhibition at a 10 μM concentration
in vitro
. Further secondary screening which identified 320 unique molecular structures or validated hits was performed. Following kinetic studies and structure-activity relationship (SAR) analysis of selected inhibitors from our refined list of 320 compounds, we demonstrated that three inhibitors with 50% inhibitory concentrations (IC
50
s) of approximately 14 μM, which belonged to a distinct chemical cluster, were able to penetrate the Gram-negative cell membrane and prevent formation of flagella.
Molecular Characteristics of Salmonella Genomic Island 1 in Proteus mirabilis Isolates from Poultry Farms in China
Authors: Lei Chang-Wei , Zhang An-Yun , Liu Bi-Hui , Wang Hong-Ning , Guan Zhong-Bin , Xu Chang-Wen , Xia Qing-Qing , Cheng Han , Zhang Dong-Dong 
Published: September 2014

ABSTRACT

Six out of the 64 studied
Proteus mirabilis
isolates from 11 poultry farms in China contained
Salmonella
genomic island 1 (SGI1). PCR mapping showed that the complete nucleotide sequences of SGI1s ranged from 33.2 to 42.5 kb. Three novel variants, SGI1-W, SGI1-X, and SGI1-Y, have been characterized. Resistance genes
lnuF
,
dfrA25
, and
qnrB2
were identified in SGI1 for the first time.
Enhanced Transmission of Antibiotic Resistance in Campylobacter jejuni Biofilms by Natural Transformation
Authors: Bae Junghee , Oh Euna , Jeon Byeonghwa 
Published: September 2014

ABSTRACT

Campylobacter jejuni
is a leading food-borne pathogen, and its antibiotic resistance is of serious concern to public health worldwide.
C. jejuni
is naturally competent for DNA transformation and freely takes up foreign DNA harboring genetic information responsible for antibiotic resistance. In this study, we demonstrate that
C. jejuni
transfers antibiotic resistance genes more frequently in biofilms than in planktonic cells by natural transformation.
The
rpoS
Gene Is Predominantly Inactivated during Laboratory Storage and Undergoes Source-Sink Evolution in Escherichia coli Species
Authors: Bleibtreu Alexandre , Clermont Olivier , Darlu Pierre , Glodt Jérémy , Branger Catherine , Picard Bertrand , Denamur Erick 
Published: September 2014

ABSTRACT

The
rpoS
gene codes for an alternative RNA polymerase sigma factor, which acts as a general regulator of the stress response. Inactivating alleles of
rpoS
in collections of natural
Escherichia coli
isolates have been observed at very variable frequencies, from less than 1% to more than 70% of strains.
rpoS
is easily inactivated in nutrient-deprived environments such as stab storage, which makes it difficult to determine the true frequency of
rpoS
inactivation in nature. We studied the evolutionary history of
rpoS
and compared it to the phylogenetic history of bacteria in two collections of 82 human commensal and extraintestinal
E. coli
strains. These strains were representative of the phylogenetic diversity of the species and differed only by their storage conditions. In both collections, the phylogenetic histories of
rpoS
and of the strains were congruent, indicating that horizontal gene transfer had not occurred at the
rpoS
locus, and
rpoS
was under strong purifying selection, with a ratio of the nonsynonymous mutation rate (Ka) to the synonymous substitution rate (Ks) substantially smaller than 1. Stab storage was associated with a high frequency of inactivating alleles, whereas almost no amino acid sequence variation was observed in RpoS in the collection studied directly after isolation of the strains from the host. Furthermore, the accumulation of variations in
rpoS
was typical of source-sink dynamics. In conclusion,
rpoS
is rarely inactivated in natural
E. coli
isolates within their mammalian hosts, probably because such strains rapidly become evolutionary dead ends. Our data should encourage bacteriologists to freeze isolates immediately and to avoid the use of stab storage.
Development, Antibiotic Production, and Ribosome Assembly in Streptomyces venezuelae Are Impacted by RNase J and RNase III Deletion
Authors: Jones Stephanie E. , Leong Vivian , Ortega Joaquin , Elliot Marie A. 
Published: September 2014

ABSTRACT

RNA metabolism is a critical but frequently overlooked control element affecting virtually every cellular process in bacteria. RNA processing and degradation is mediated by a suite of ribonucleases having distinct cleavage and substrate specificity. Here, we probe the role of two ribonucleases (RNase III and RNase J) in the emerging model system
Streptomyces venezuelae
. We show that each enzyme makes a unique contribution to the growth and development of
S. venezuelae
and further affects the secondary metabolism and antibiotic production of this bacterium. We demonstrate a connection between the action of these ribonucleases and translation, with both enzymes being required for the formation of functional ribosomes. RNase III mutants in particular fail to properly process 23S rRNA, form fewer 70S ribosomes, and show reduced translational processivity. The loss of either RNase III or RNase J additionally led to the appearance of a new ribosomal species (the 100S ribosome dimer) during exponential growth and dramatically sensitized these mutants to a range of antibiotics.
Cytosolic Selection Systems To Study Protein Stability
Authors: Malik Ajamaluddin , Mueller-Schickert Antje , Bardwell James C. A. 
Published: September 2014

ABSTRACT

Here we describe biosensors that provide readouts for protein stability in the cytosolic compartment of prokaryotes. These biosensors consist of tripartite sandwich fusions that link the
in vitro
stability or aggregation susceptibility of guest proteins to the
in vivo
resistance of host cells to the antibiotics kanamycin, spectinomycin, and nourseothricin. These selectable markers confer antibiotic resistance in a wide range of hosts and are easily quantifiable. We show that mutations within guest proteins that affect their stability alter the antibiotic resistances of the cells expressing the biosensors in a manner that is related to the
in vitro
stabilities of the mutant guest proteins. In addition, we find that polyglutamine tracts of increasing length are associated with an increased tendency to form amyloids
in vivo
and, in our sandwich fusion system, with decreased resistance to aminoglycoside antibiotics. We demonstrate that our approach allows the
in vivo
analysis of protein stability in the cytosolic compartment without the need for prior structural and functional knowledge.
Characterization of
p
-Hydroxycinnamate Catabolism in a Soil Actinobacterium
Authors: Otani Hiroshi , Lee Young-Eun , Casabon Israël , Eltis Lindsay D. 
Published: September 2014

ABSTRACT

p
-Hydroxycinnamates, such as ferulate and
p
-coumarate, are components of plant cell walls and have a number of commercial applications.
Rhodococcus jostii
RHA1 (RHA1) catabolizes ferulate via vanillate and the β-ketoadipate pathway. Here, we used transcriptomics to identify genes in RHA1 that are upregulated during growth on ferulate versus benzoate. The upregulated genes included three transcriptional units predicted to encode the uptake and β-oxidative deacetylation of
p
-hydroxycinnamates:
couHTL
,
couNOM
, and
couR
. Neither Δ
couL
mutants nor Δ
couO
mutants grew on
p
-hydroxycinnamates, but they did grow on vanillate. Among several
p
-hydroxycinnamates, CouL catalyzed the thioesterification of
p
-coumarate and caffeate most efficiently (
k
cat
/

K
m

= ∼400 mM
−1
s
−1
).
p
-Coumarate was also RHA1's preferred growth substrate, suggesting that CouL is a determinant of the pathway's specificity. CouL did not catalyze the activation of sinapate, in similarity to two
p
-coumaric acid:coenzyme A (CoA) ligases from plants, and contains the same bulged loop that helps determine substrate specificity in the plant homologues. The
couO
mutant accumulated 4-hydroxy-3-methoxyphenyl-β-ketopropionate in the culture supernatant when incubated with ferulate, supporting β-oxidative deacetylation. This phenotype was not complemented with a D257N variant of CouO, consistent with the predicted role of Asp257 as a metal ligand in this amidohydrolase superfamily member. These data suggest that CouO functionally replaces the β-ketothiolase and acyl-CoA thioesterase that occur in canonical β-oxidative pathways. Finally, the transcriptomics data suggest the involvement of two distinct formaldehyde detoxification pathways in vanillate catabolism and identify a eugenol catabolic pathway. The results of this study augment our understanding of the bacterial catabolism of aromatics from renewable feedstocks.
An Aerobic Exercise: Defining the Roles of Pseudomonas aeruginosa Terminal Oxidases
Authors: Jo Jeanyoung , Price-Whelan Alexa , Dietrich Lars E. P. 
Published: September 2014

ABSTRACT

The opportunistic pathogen
Pseudomonas aeruginosa
encodes a large and diverse complement of aerobic terminal oxidases, which is thought to contribute to its ability to thrive in settings with low oxygen availability. In this issue,
Arai et al.
(J. Bacteriol. 196:4206–4215, 2014, doi:
http://dx.doi.org/10.1128/JB.02176-14
) present a thorough characterization of these five complexes, enabling a more detailed understanding of aerobic respiration in this organism.