bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrating Constrained Random Waves in Endurance Time Analysis of Offshore Structures Subjected to Sea Waves
Authors: Nikoo H. Matin , Zeinoddini M. , Estekanchi H. , Golestani M. 
Published: August 2013

This paper introduces a novel methodology for design and assessment of offshore structures exposed to irregular sea waves. For this, Constrained NewWave (CNW) is integrated with the Endurance Time Analysis (ETA) methodology, which is basically developed for the performance based analysis of onshore structures to earthquake loads. In this approach, the offshore structure is simulated in time-domain under a set of calibrated intensifying wave functions. They are devised to represent a gradually increasing roughness of the sea state by time. A performance index such as base shear, drift or stress in a critical structural members are monitored until they reach to a predefined maximum value. A higher endurance time (corresponding to a higher wave height) is to be interpreted as a better performance of structure.
Ability to consider spectral features of waves, waves’ irregularity, the wave-in-deck impacts, utilizing a relatively simple approach, requiring relatively low computational times and capability to consider any desirable damage indices are the advantages of this novel method. The method can be used in the design stage, collapse analysis and for the assessment of existing offshore platforms.
In this paper the effectiveness of this method has been examined on offshore jacket platforms. The results obviously have highlighted the potentials of this approach for the dynamic, time-domain, non-linear analysis and assessment of offshore platforms.
Motion Response Control of the DWSC Spar Based on State-Space Model
Authors: Yu Xiaochuan , Falzarano Jeffrey 
Published: August 2013

In 2007, the Office of Naval Research (ONR) started a technology development program called STLVAST (Small to Large Vessel At-Sea Transfer), in order to develop ‘enabling capabilities’ in the realm of logistic transfer (i.e. stores, equipment, vehicles) between a large transport vessel and a smaller T-craft ship, using a Deep Water Stable Crane (DWSC) spar between them.
In this paper, the equation of motions of the single DWSC spar is initially expressed as the standard state-space model. Then the ODE solver of Matlab is directly employed to obtain the motion responses at each time step. Two levels of approximation of hydrodynamic coefficients are considered in this study. One is the Constant Coefficient Method (CCM), and the other one is the Impulse Response Function (IRF) method, with fluid memory effects considered. WAMIT software is used to calculate the hydrodynamic coefficients, including the added mass, radiation damping, IRF, the first order and second order waves loads transfer functions, etc. The motion response control is achieved by assuming the thrusters can provide the optimal feedback force derived from Linear Quadratic Regulator (LQR) method.
Genome Sequence of Salmonella enterica Serovar Typhi Oral Vaccine Strain Ty21a
Authors: Xu DeQi , Cisar John O. , Poly Frédéric , Yang Jinghua , Albanese Jason , Dharmasena Madushini , Wai Tint , Guerry Patricia , Kopecko Dennis J. 
Published: August 2013

ABSTRACT

Attenuated
Salmonella enterica
serovar Typhi strain Ty21a is an important vaccine for controlling typhoid fever and serves as an oral vector for delivering heterologous antigens. The key attenuating features of this randomly mutated strain remain in question. Genome sequencing has revealed 679 single nucleotide polymorphisms (SNPs), and will help define alterations contributing to Ty21a safety and immunogenicity.
Complete Genomic Sequences of an H3N8 Equine Influenza Virus Strain Isolated in China
Authors: Zhu Chao , Li Qian , Guo Wei , Lu Gang , Yin Xin , Qi Ting , Xiang Wenhua , Ran Duoliang , Qu Juanjuan 
Published: August 2013

ABSTRACT
We report the complete genomic sequence of A/equine/Heilongjiang/1/2010, a strain of Florida sublineage clade 2 of H3N8 subtype equine influenza virus (EIV) isolated in northern China. This is the first announcement of a complete genomic sequence of EIV of such a clade in China.
Draft Genome Sequence of Lactobacillus pasteurii CRBIP 24.76
T
Authors: Cousin Sylvie , Clermont Dominique , Creno Sophie , Ma Laurence , Loux Valentin , Bizet Chantal , Bouchier Christiane 
Published: August 2013

ABSTRACT

We report the draft genome sequence of the type strain
Lactobacillus pasteurii
CRBIP 24.76, which is closely related to
L. gigeriorum
CRBIP 24.85
T
, isolated from a chicken crop. The total length of the 29 contigs is about 1.9 Mb, with a G+C content of 40% and 1,946 coding sequences.
Draft Genome Sequence of Holospora undulata Strain HU1, a Micronucleus-Specific Symbiont of the Ciliate
Paramecium caudatum
Authors: Dohra Hideo , Suzuki Haruo , Suzuki Tomohiro , Tanaka Kenya , Fujishima Masahiro 
Published: August 2013

ABSTRACT

Holospora undulata
is a micronucleus-specific symbiont of the ciliate
Paramecium caudatum
. We report here the draft genome sequence of
H. undulata
strain HU1. This genome information will contribute to the study of symbiosis between
H. undulata
and the host
P. caudatum
.
Identification, Typing, and Phylogenetic Relationships of the Main Clinical Nocardia Species in Spain According to Their
gyrB
and
rpoB
Genes
Authors: Carrasco Gema , Valdezate Sylvia , Garrido Noelia , Villalón Pilar , Medina-Pascual Maria J. , Sáez-Nieto Juan A. 
Published: August 2013

ABSTRACT

This study compares the identification, typing, and phylogenetic relationships of the most prevalent clinical
Nocardia
species in Spain, as determined via sequence analysis of their housekeeping genes
gyrB
and
rpoB
, with the results returned by the gold standard 16S rRNA method.
gyrB
and
rpoB
analyses identified
Nocardia abscessus
,
N. cyriacigeorgica
,
N. farcinica
, and the
N. nova
complex, species that together account for more than half of the human nocardiosis cases recorded in Spain. The individual discriminatory power of
gyrB
and
rpoB
with respect to intraspecies typing, calculated using the Hunter-Gaston discriminatory index (HGDI), was generally high (HGDI, 0.85 to 1), except for
rpoB
with respect to
N. farcinica
(HGDI, 0.71). Phylogenetically, different degrees of intra- and interspecies microheterogeneity were observed for
gyrB
and
rpoB
in a group of 119 clinical strains. A single 16S haplotype was obtained for each species, except for the
N. nova
complex (8 types), while
gyrB
and
rpoB
were more polymorphic:
N. abscessus
had 14 and 18 haplotypes,
N. cyriacigeorgica
had 17 and 12,
N. farcinica
had 11 and 5, and the
N. nova
complex had 26 and 29 haplotypes, respectively. A diversity gradient was therefore seen, with
N. farcinica
at the bottom followed by
N. abscessus
and
N. cyriacigeorgica
in the middle and
N. nova
complex at the top. The complexity of the
N. nova
complex is highlighted by its six variations in the GyrB
126
AAAPEH motif.
gyrB
sequencing (with or without
rpoB
sequencing) offers a simple means for identifying the most prevalent
Nocardia
species in Spanish medical laboratories and for determining the intraspecific diversity among their strains.
Anal Human Papillomavirus Genotype Distribution in HIV-Infected Men Who Have Sex with Men by Geographical Origin, Age, and Cytological Status in a Spanish Cohort
Authors: Torres Montserrat , González Cristina , del Romero Jorge , Viciana Pompeyo , Ocampo Antonio , Rodríguez-Fortúnez Patricia , Masiá Mar , Blanco José Ramón , Portilla Joaquín , Rodríguez Carmen , Hernández-Novoa Beatriz , del Amo Julia , Ortiz Marta 
Published: August 2013

ABSTRACT
Knowledge of human papillomavirus (HPV) type distribution in populations at risk for anal cancer is needed. Here, we describe the anal HPV genotype distribution in a large Spanish cohort (Cohort of the Spanish HIV Research Network HPV [CoRIS-HPV]) of HIV-positive men who have sex with men (MSM) according to geographical origin, age, and cytological status. A cross-sectional analysis of baseline data from 1,439 HIV-infected MSM (2007 to 2012) was performed. Anal HPV genotyping was performed using the Linear Array HPV genotyping test. Descriptive analyses of subject characteristics, prevalences, and 95% confidence intervals (CI) were performed. The global prevalences of HPV, high-risk HPV (HR-HPV), and low-risk HPV (LR-HPV) types were 95.8%, 83.0%, and 72.7%, respectively. Among the HR-HPV types, HPV16 was the most common, followed by HPV59, -39, -51, -18, and -52. The prevalence of multiple HR-HPV infections was 58.5%. There were no differences in the crude analyses between Spanish and Latin-American MSM for most HPV types, and a peak in prevalence for most HPV types was seen in patients in their late thirties. Globally and by specific HPV groups, men with abnormal anal cytologies had a higher prevalence of infection than those with normal cytologies. This study has the largest number of HIV-positive MSM with HPV genotype data analyzed according to cytological status as far as we know. The information gained from this study can help with the design of anal cancer prevention strategies in HIV-positive patients.
Correlation between Clostridium difficile Bacterial Load, Commercial Real-Time PCR Cycle Thresholds, and Results of Diagnostic Tests Based on Enzyme Immunoassay and Cell Culture Cytotoxicity Assay
Authors: Dionne Léa-Laurence , Raymond Frédéric , Corbeil Jacques , Longtin Jean , Gervais Philippe , Longtin Yves 
Published: August 2013

ABSTRACT

The impact of
Clostridium difficile
fecal loads on diagnostic test results is poorly understood, but it may have clinical importance. In this study, we investigated the relationship between
C. difficile
fecal load and the results of four assays: a glutamate dehydrogenase (GDH) enzyme immunoassay (EIA), a toxin A/B antigen EIA (ToxAB), a cell culture cytotoxicity assay (CCA), and PCR targeting the
tcdB
gene. We also compared the PCR cycle threshold (

C
T

) with the results of quantitative culture using Spearman's rank correlation coefficient. Finally, we sequenced the genomes of 24 strains with different detection profiles. A total of 203 clinical samples harboring toxigenic
C. difficile
were analyzed and sorted into one of four groups: 17 PCR
+
(group 1), 37 PCR
+
GDH
+
(group 2), 24 PCR
+
GDH
+
CCA
+
(group 3), and 125 PCR
+
GDH
+
ToxAB
+
(group 4). The overall median fecal load in log
10
CFU/g was 6.67 (interquartile range [IQR], 5.57 to 7.54). The median fecal bacterial load of groups 1, 2, 3, and 4 were 4.15 (IQR, 3.00 to 4.98), 5.74 (IQR, 4.75 to 6.16), 6.20 (IQR, 5.23 to 6.80), and 7.08 (IQR, 6.35 to 7.83), respectively. Group 1 samples had lower fecal loads than those from each of the other groups (
P
< 0.001). Group 2 samples had lower fecal loads than those from groups 3 and 4 (
P
< 0.001). There was a significant correlation between PCR

C
T

and fecal loads (ρ = −0.697;
P
< 0.001). NAP1 strains were associated with the detection of toxins by EIA or CCA (
P
= 0.041). This study demonstrates an association between
C. difficile
fecal load and the results of routinely used diagnostic tests.
Serotype 5 Pneumococci Causing Invasive Pneumococcal Disease Outbreaks in Barcelona, Spain (1997 to 2011)
Authors: Rolo Dora , Fenoll Asunción , Fontanals Dionísia , Larrosa Nieves , Giménez Montserrat , Grau Immaculada , Pallarés Román , Liñares Josefina , Ardanuy Carmen ,   the Serotype 5 Study Group
Published: August 2013

ABSTRACT

In this study, we analyzed the clinical and molecular epidemiology of invasive serotype 5 (Ser5) pneumococcal isolates in four teaching hospitals in the Barcelona, Spain, area (from 1997 to 2011). Among 5,093 invasive pneumococcal isolates collected, 134 (2.6%) Ser5 isolates were detected. Although the overall incidence of Ser5-related invasive pneumococcal disease (IPD) was low (0.25 cases/100,000 inhabitants), three incidence peaks were detected: 0.63/100,000 in 1999, 1.15/100,000 in 2005, and 0.37/100,000 in 2009. The rates of Ser5 IPD were higher among young adults (18 to 64 years old) and older adults (>64 years old) in the first two peaks, whereas they were higher among children in 2009. The majority (88.8%) of the patients presented with pneumonia. Comorbid conditions were present in young adults (47.6%) and older adults (78.7%), the most common comorbid conditions being chronic obstructive pulmonary disease (20.6% and 38.3%, respectively) and cardiovascular diseases (11.1% and 38.3%, respectively). The mortality rates were higher among older adults (8.5%). All Ser5 pneumococci tested were fully susceptible to penicillin, cefotaxime, erythromycin, and ciprofloxacin. The resistance rates were 48.5% for co-trimoxazole, 6.7% for chloramphenicol, and 6% for tetracycline. Two major related sequence types (STs), ST1223 (
n
= 65) and ST289 (
n
= 61), were detected. The Colombia
5
-ST289 clone was responsible for all the cases in the Ser5 outbreak in 1999, whereas the ST1223 clone accounted for 73.8% and 61.5% of the isolates in 2005 and 2009, respectively. Ser5 pneumococci are a frequent cause of IPD outbreaks in the community and involve children and adults with or without comorbidities. The implementation of the new pneumococcal conjugated vaccines (PCV10 and PCV13) might prevent such outbreaks.
Novel Approach for Improving Sensitivity of Microscopic Detection of Acid-Fast Bacilli (AFB) by Use of the ReaSLR Method
Authors: Verma Sheetal , Dhole Tapan N. , Kumar Manoj , Kashyap Saurabh 
Published: August 2013

ABSTRACT

The ReaSLR methodology developed for sputum processing is a novel, low-cost, and simple technique that has improved the sensitivity of smear microscopy for the diagnosis of tuberculosis (TB). Sample processing consists of rapid liquefaction of the sputum specimen with the ReaSLR reagent, followed by syringe filtration, concentration by centrifugation, and use of the sediment for smear microscopy. The performance of the ReaSLR kit was evaluated on 150 sputum samples and was compared with that of the modified Petroff method for sputum decontamination and concentration. Ziehl-Neelsen staining was performed for smear microscopy after processing by these two techniques; simultaneously, culture on Lowenstein-Jensen (LJ) medium was done to evaluate the two methods. The efficiency of smear microscopy was 18/150 (12%) with the modified Petroff method compared to 47/150 (31.33%) with the ReaSLR method, and this difference was statistically significant (
P
< 0.001). The ReaSLR method for smear microscopy demonstrated a sensitivity and specificity of 90.47% and 91.6%, respectively, whereas the modified Petroff method showed a sensitivity and specificity of 40.47% and 99.07%, respectively, compared to those of culture, which was used as the gold standard. With the newer ReaSLR method, the kappa coefficient (κ) was 0.8, which implies an excellent positive agreement. The ReaSLR method was found to be more sensitive than the conventional method for sputum smear microscopy. The newer ReaSLR method holds promise for adoption in TB control programs across the globe, as it was found suitable for the laboratory diagnosis of pulmonary TB. Further large-scale studies are needed to evaluate other aspects of this method.
Comparison of Matrix-Assisted Laser Desorption Ionization–Time of Flight (MALDI-TOF) Mass Spectrometry Platforms for the Identification of Gram-Negative Rods from Patients with Cystic Fibrosis
Authors: Alby Kevin , Gilligan Peter H. , Miller Melissa B. 
Published: August 2013

ABSTRACT
We evaluated the performance of the Bruker Biotyper and the bioMérieux Vitek MS with both the SARAMIS v4.09 and Knowledge Base v2.0 databases for the identification of 203 non-glucose-fermenting Gram-negative rods that had previously been identified by 16S rRNA gene sequencing. Including those that underwent repeat testing, 96.6%, 90.1%, and 93.6% of isolates, respectively, had identifications that agreed with the previous identification.
Validation of an
rpoB
Gene PCR Assay for Detection of Tropheryma whipplei: 10 Years' Experience in a National Reference Laboratory
Authors: Moter Annette , Schmiedel Dinah , Petrich Annett , Wiessner Alexandra , Kikhney Judith , Schneider Thomas , Moos Verena , Göbel Ulf B. , Reischl Udo 
Published: August 2013

ABSTRACT

The performance of a real-time PCR assay targeting the
Tropheryma whipplei
rpoB
gene was evaluated using test strains and 1,236 clinical specimens in a national reference laboratory. The novel
rpoB
-PCR assay proved to be specific, revealed improved analytical sensitivity, and substantially accelerated detection of
T. whipplei
DNA in clinical specimens.
Rapid and Direct Real-Time Detection of
bla
KPC
and
bla
NDM
from Surveillance Samples
Authors: Vasoo Shawn , Cunningham Scott A. , Kohner Peggy C. , Mandrekar Jayawant N. , Lolans Karen , Hayden Mary K. , Patel Robin 
Published: August 2013

ABSTRACT

We assessed the performance of a duplex real-time PCR assay for
bla
KPC
and
bla
NDM
performed directly (D-PCR) on perianal and perirectal swabs and stool. Spiked specimens and 126 clinical surveillance swabs (comprising a sensitivity panel of 46 perirectal double swabs previously determined to be culture positive for
bla
KPC
-PCR-positive
Enterobacteriaceae
and a specificity panel of 80 perianal swabs from patients at risk of carbapenemase-producing
Enterobacteriaceae
[CPE] colonization) were studied. For the surveillance swabs, D-PCR was compared to PCR after broth enrichment (BE-PCR) and two culture-based methods: the HardyCHROM ESBL agar (HC-A) and the CDC screening (CDC-A) methods. PCR was performed on morphologically distinct colonies that were isolated by culture. All of the initial PCR testing was done without extraction using a simple lysis procedure. The analytical sensitivities of D-PCR for
bla
KPC
were 9 CFU/μl (for swabs) and 90 CFU/μl (for stool), and for
bla
NDM
, it was 1.9 CFU/μl (for both swabs and stool). In the clinical sensitivity panel, D-PCR and BE-PCR were initially positive for
bla
KPC
in 41/46 (89.1%) and 43/46 (93.5%) swabs, respectively. The swabs that were initially negative by D-PCR (
n
= 5) and BE-PCR (
n
= 3) were visibly stool soiled; all swabs were
bla
KPC
positive upon repeat testing after lysate extraction. The CDC-A and HC-A yielded
bla
KPC
-positive
Enterobacteriaceae
from 36/46 (78.3%) and 35/46 (76.1%) swabs, respectively (sensitivities of D-PCR/BE-PCR postextraction of soiled specimens versus HC-A,
P
= 0.0009, and versus CDC-A,
P
= 0.0016). All swabs in the specificity panel were negative for CPE by all four methods. D-PCR allows for the timely detection of
bla
KPC
and
bla
NDM
carriage with excellent sensitivity when specimens visibly soiled with stool undergo preparatory extraction.
Evaluation of an Enzyme Immunoassay for Detection of Histoplasma capsulatum Antigen from Urine Specimens
Authors: Theel Elitza S. , Jespersen Deborah J. , Harring Julie , Mandrekar Jay , Binnicker Matthew J. 
Published: August 2013

ABSTRACT

Detection of
Histoplasma capsulatum
urinary antigen (UAg) is important for the initial diagnosis of infection and for monitoring of patient responses to antifungal therapy. This study evaluated an analyte-specific reagent (ASR) enzyme immunoassay (EIA) for the detection of
H. capsulatum
UAg from Immuno Mycologics, Inc. (IMMY) (Norman, OK) in comparison with routine testing with the MiraVista (MVista)
H. capsulatum
quantitative EIA (MiraVista Diagnostics, Indianapolis, IN). Using prospectively collected urine specimens (
n
= 1,003), we observed an overall percent agreement between the two assays of 97.6% (979/1,003 samples). Compared with the MVista EIA, the sensitivity and specificity of the IMMY ASR EIA were 64.5% (40/62 samples) and 99.8% (939/941 samples), respectively, using a cutoff value of 0.5 ng/ml. Based on available clinical histories for 23/24 discordant samples, 5 IMMY assay-negative/MVista assay-positive samples were considered falsely positive. Furthermore, 10/23 discordant samples were positive by the MVista EIA but were below the limit of quantitation (<0.4 ng/ml). The clinical significance of these low positive results in the MVista EIA is unclear. In addition to the prospective study, we tested 11 urine specimens collected from patients with culture-confirmed
Histoplasma
infections, and 100% (11/11 samples) were positive by the IMMY ASR EIA. In conclusion, the IMMY ASR EIA may offer an alternative approach for the detection of
Histoplasma
UAg. Additional prospective studies are needed to better characterize the performance of the IMMY ASR EIA in conjunction with clinical and laboratory findings.
Inhibition of Megakaryocyte Development in the Bone Marrow Underlies Dengue Virus-Induced Thrombocytopenia in Humanized Mice
Authors: Sridharan Aishwarya , Chen Qingfeng , Tang Kin Fai , Ooi Eng Eong , Hibberd Martin L. , Chen Jianzhu 
Published: August 2013

ABSTRACTA characteristic clinical feature of dengue virus infection is thrombocytopenia, though its underlying mechanism is not definitively determined. By adoptive transfer of human CD34+fetal liver cells into immunodeficient mice, we have constructed humanized mice with significant levels of human platelets, monocytes/macrophages, and hepatocytes. Infection of these mice with both lab-adapted and clinical strains of dengue virus induces characteristic human hematological changes, including transient leukopenia and thrombocytopenia. We show that the specific depletion of human platelets is not mediated by antibodies in the periphery or reduced production of human thrombopoietin in the liver but reduction of human megakaryocytes and megakaryocyte progenitors in the bone marrow of the infected mice. These findings identify inhibition of platelet production in the bone marrow as a key mechanism underlying dengue-induced thrombocytopenia and suggest the utility of the improved humanized mouse model in studying dengue virus infection and pathogenesis in a human cell context.
Phosphorylation of Measles Virus Nucleoprotein Affects Viral Growth by Changing Gene Expression and Genomic RNA Stability
Authors: Sugai Akihiro , Sato Hiroki , Yoneda Misako , Kai Chieko 
Published: August 2013

ABSTRACTThe measles virus (MV) nucleoprotein associates with the viral RNA genome to form the N-RNA complex, providing a template for viral RNA synthesis. In our previous study, major phosphorylation sites of the nucleoprotein were identified as S479 and S510. However, the functions of these phosphorylation sites have not been clarified. In this study, we rescued recombinant MVs (rMVs) whose phosphorylation sites in the nucleoprotein were substituted (rMV-S479A, rMV-S510A, and rMV-S479A/S510A) by reverse genetics and used them in subsequent analyses. In a one-step growth experiment, rMVs showed rapid growth kinetics compared with wild-type MV, although the peak titer of the wild-type MV was the same as or slightly higher than those of the rMVs. Time course analysis of nucleoprotein accumulation also revealed that viral gene expression of rMV was enhanced during the early phase of infection. These findings suggest that nucleoprotein phosphorylation has an important role in controlling viral growth rate through the regulation of viral gene expression. Conversely, multistep growth curves revealed that nucleoprotein-phosphorylation intensity inversely correlated with viral titer at the plateau phase. Additionally, the phosphorylation intensity of the wild-type nucleoprotein in infected cells was significantly reduced through nucleoprotein-phosphoprotein binding. Excessive nucleoprotein-phosphorylation resulted in lower stability against RNase and faster turnover of viral genomic RNA. These results suggest that nucleoprotein-phosphorylation is also involved in viral genomic RNA stability.