bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of Artificial Neural Networks in Assessing the Equilibrium Depth of Local Scour Around Bridge Piers
Authors: Sarshari Ehsan , Mullhaupt Philippe 
Published: October 2015

Scour can have the effect of subsidence of the piers in bridges, which can ultimately lead to the total collapse of these systems. Effective bridge design needs appropriate information on the equilibrium depth of local scour. The flow field around bridge piers is complex so that deriving a theoretical model for predicting the exact equilibrium depth of local scour seems to be near impossible. On the other hand, the assessment of empirical models highly depends on local conditions, which is usually too conservative.
In the present study, artificial neural networks are used to estimate the equilibrium depth of the local scour around bridge piers. Assuming such equilibrium depth is a function of five variables, and using experimental data, a neural network model is trained to predict this equilibrium depth. Multilayer neural networks with backpropagation algorithm with different learning rules are investigated and implemented. Different methods of data normalization besides the effect of initial weightings and overtraining phenomenon are addressed. The results show well adoption of the neural network predictions against experimental data in comparison with the estimation of empirical models.
“Bigfoot” DVA Semi-Submersible Model Tests and Comparison With Numerical Predictions
Authors: Liapis Stergios , Li Yile , Lu Haining , Peng Tao 
Published: October 2015

The Bigfoot direct vertical access (DVA) semisubmersible is a novel floating drilling and production host that provides an attractive alternative to the spar. This concept utilizes heave plates (big feet) that improve the motion characteristics of a semisubmersible in all mild environments (S.E. Asia, W. Africa and Brazil). Bigfoot offers direct-vertical access (DVA) which is often a project requirement. This floater works in all water depths, in particular ultra-deepwater (5000+ ft) where a tension leg platform (TLP) is not an option, supports top tensioned risers and enables drilling and workover operations. The Bigfoot has several advantages over a spar. These include: 1) Quayside topsides integration. This eliminates offshore topsides integration, a significant issue for all spar projects in terms of cost, safety and schedule. 2) A more open deck layout compared to a spar, 3) No fabrication location restrictions as it can be built by many yards worldwide potentially offering local content to a project.
Model tests were undertaken at the Shanghai Jiao Tong University (SJTU) Offshore Basin to assess the dynamic response of the Bigfoot in waves, swell, wind and current. Five mild (non-Gulf of Mexico) environments were considered. In all cases, the floater motions are an order of magnitude smaller than those of a conventional semisubmersible for similar deck payload thus enabling drilling operations and top-tensioned production risers. In a parallel effort, a COSMOS numerical model of the Bigfoot was developed for coupled motion analysis. The experimental results and the COSMOS numerical predictions are in close agreement. In addition to measuring global motions, two heave plates were instrumented with load cells to measure forces and moments. The force measurements from the model tests are in good agreement with numerical predictions using computational fluid dynamics (CFD).
Cardiovascular and Metabolic Responses to On-Water Upwind Sailing in Optimist Sailors
Authors: Lopez Santiago , Bourgois Jan G. , Tam Enrico , Bruseghini Paolo , Capelli Carlo 
Published: October 2015

Purpose:To explore the cardiovascular and metabolic responses of 9 Optimist sailors (12.7 ± 0.8 y, 153 ± 9 cm, 41 ± 6 kg, sailing career 6.2 ± 1 y, peak oxygen uptake [V̇O2peak] 50.5 ± 4.5 mL · min−1 · kg−1) during on-water upwind sailing with various wind intensities (W).Methods:In a laboratory session, peak V̇O2, beat-by-beat cardiac output (Q̇), mean arterial blood pressure (MAP), and heart rate (fH) were measured using a progressive cycle ramp protocol. Steady-state V̇O2, Q̇, MAP, and fH at 4 submaximal workloads were also determined. During 2 on-water upwind sailing tests (constant course and with tacks), W, Q̇, MAP, and fH were measured for 15 min. On-water V̇O2 was estimated on the basis of steady-state fH measured on water and of the individual ΔV̇O2/ΔfH relationship obtained in the laboratory.Results:V̇O2, fH, and Q̇ expressed as percentage of the corresponding peak values were linearly related with W; exercise intensity during on-water sailing corresponded to 46–48% of V̇O2peak. MAP and total vascular peripheral resistance (TPR = MAP/Q̇) were larger (P < .005) during on-water tests (+39% and +50%, respectively) than during cycling, and they were correlated with W. These responses were responsible for larger values of the double (DP) and triple (TP) products of the heart during sailing than during cycling (P < .005) (+37% and +32%, respectively).Conclusions:These data indicate that the cardiovascular system was particularly stressed during upwind sailing even though the exercise intensity of this activity was not particularly high.
Effect of Performance Level on the Prediction of Middle-Distance-Running Performances Using a Nomogram
Authors: Tabben Montassar , Bosquet Laurent , Coquart Jeremy B. 
Published: October 2015

Purpose:This study examined the effect of performance level on the validity and accuracy of middle-distance running-performance predictions obtained from the nomogram of Mercier et al in male runners.Methods:Official French track-running rankings for the 3000-, 5000-, and 10,000-m events from 2006 to 2014 were examined. The performance level was determined from the official reference table of the Fédération Française d’Athlétisme, and the runners were divided in 3 groups (ie, low, moderate, and high levels). Only male runners who performed in the 3 distance events within the same year were included (N = 443). Each performance over any distance was predicted using the nomogram from the 2 other performances.Results:No difference was found in low- and moderate-performance-level athletes (0.02 ≤ effect size [ES] ≤ 0.06, 95% limits of agreement [LoA] ≤ 6%). By contrast, a small difference in high-performance-level athletes (P < .01, 0.23 ≤ ES ≤ 0.45, 95% LoA ≤ 11.6%) was found.Conclusion:The study confirms the validity of the nomogram to predict track-running performance with a high level of accuracy, except for male runners with high performance level (ie, national or international). Consequently, the predictions from the nomogram may be used in training programs (eg, to prescribe tempo runs with realistic training velocities) and competitions (eg, to plan realistic split times to reach the best performance).
Neonatal Pasteurella multocida subsp. septica Meningitis Traced to Household Cats: Molecular Linkage Analysis Using Repetitive-Sequence-Based PCR
Authors: Boyanton Bobby L. , Freij Bishara J. , Robinson-Dunn Barbara , Makin Jacob , Runge Jessica K. , Luna Ruth Ann 
Published: October 2015

ABSTRACT

Pasteurella multocida
is a rare cause of neonatal bacterial meningitis. We describe such a case and verify two household cats as the source of infection using repetitive-element PCR (rep-PCR) molecular fingering.
Multicenter Evaluation of Anyplex Plus MTB/NTM MDR-TB Assay for Rapid Detection of Mycobacterium tuberculosis Complex and Multidrug-Resistant Isolates in Pulmonary and Extrapulmonary Specimens
Authors: Sali Michela , De Maio Flavio , Caccuri Francesca , Campilongo Federica , Sanguinetti Maurizio , Fiorentini Simona , Delogu Giovanni , Giagulli Cinzia 
Published: October 2015

ABSTRACT

The rapid diagnosis of tuberculosis (TB) and the detection of drug-resistant
Mycobacterium tuberculosis
strains are critical for successful public health interventions. Therefore, TB diagnosis requires the availability of diagnostic tools that allow the rapid detection of
M. tuberculosis
and drug resistance in clinical samples. Here, we performed a multicenter study to evaluate the performance of the Seegene Anyplex MTB/NTM MDR-TB assay, a new molecular method based on a multiplex real-time PCR system, for detection of
Mycobacterium tuberculosis
complex (MTBC), nontuberculous mycobacteria (NTM), and genetic determinants of drug resistance. In total, the results for 755 samples (534 pulmonary and 221 extrapulmonary samples) were compared with the results of smears and cultures. For pulmonary specimens, the sensitivities of the Anyplex assay and acid-fast bacillus smear testing were 86.4% and 75.0%, respectively, and the specificities were 99% and 99.4%. For extrapulmonary specimens, the sensitivities of the Anyplex assay and acid-fast bacillus smear testing were 83.3% and 50.0%, respectively, and the specificities of both were 100%. The negative and positive predictive values of the Anyplex assay for pulmonary specimens were 97% and 100%, respectively, and those for extrapulmonary specimens were 84.6% and 100%. The sensitivities of the Anyplex assay for detecting isoniazid resistance in MTBC strains from pulmonary and extrapulmonary specimens were 83.3% and 50%, respectively, while the specificities were 100% for both specimen types. These results demonstrate that the Anyplex MTB/NTM MDR-TB assay is an efficient and rapid method for the diagnosis of pulmonary and extrapulmonary TB and the detection of isoniazid resistance.
Clinical and Laboratory Testing for Trichomonas vaginalis Infection
Authors: Van Der Pol Barbara 
Published: October 2015

ABSTRACT

Trichomonas vaginalis
infection is highly prevalent in the United States and worldwide. Traditional clinical diagnostic methods fail to identify more than half of these infections that, if left untreated, can result in adverse pregnancy outcomes and an exacerbated risk of both acquisition and transmission of HIV. Women bear a disproportionate amount of the burden of these infections, and testing among populations at risk for this disease should be provided. Molecular technologies have expanded our capacity for laboratory-based detection of infection and can be used on samples already being collected for chlamydia/gonorrhea screening.
Development of a TaqMan Array Card for Acute-Febrile-Illness Outbreak Investigation and Surveillance of Emerging Pathogens, Including Ebola Virus
Authors: Liu Jie , Ochieng Caroline , Wiersma Steve , Ströher Ute , Towner Jonathan S. , Whitmer Shannon , Nichol Stuart T. , Moore Christopher C. , Kersh Gilbert J. , Kato Cecilia , Sexton Christopher , Petersen Jeannine , Massung Robert , Hercik Christine , Crump John A. , Kibiki Gibson , Maro Athanasia , Mujaga Buliga , Gratz Jean , Jacob Shevin T. , Banura Patrick , Scheld W. Michael , Juma Bonventure , Onyango Clayton O. , Montgomery Joel M. , Houpt Eric , Fields Barry 
Published: October 2015

ABSTRACT

Acute febrile illness (AFI) is associated with substantial morbidity and mortality worldwide, yet an etiologic agent is often not identified. Convalescent-phase serology is impractical, blood culture is slow, and many pathogens are fastidious or impossible to cultivate. We developed a real-time PCR-based TaqMan array card (TAC) that can test six to eight samples within 2.5 h from sample to results and can simultaneously detect 26 AFI-associated organisms, including 15 viruses (chikungunya, Crimean-Congo hemorrhagic fever [CCHF] virus, dengue, Ebola virus, Bundibugyo virus, Sudan virus, hantaviruses [Hantaan and Seoul], hepatitis E, Marburg, Nipah virus, o'nyong-nyong virus, Rift Valley fever virus, West Nile virus, and yellow fever virus), 8 bacteria (
Bartonella
spp.,
Brucella
spp.,
Coxiella burnetii
,
Leptospira
spp.,
Rickettsia
spp.,
Salmonella enterica
and
Salmonella enterica
serovar Typhi, and
Yersinia pestis
), and 3 protozoa (
Leishmania
spp.,
Plasmodium
spp., and
Trypanosoma brucei
). Two extrinsic controls (phocine herpesvirus 1 and bacteriophage MS2) were included to ensure extraction and amplification efficiency. Analytical validation was performed on spiked specimens for linearity, intra-assay precision, interassay precision, limit of detection, and specificity. The performance of the card on clinical specimens was evaluated with 1,050 blood samples by comparison to the individual real-time PCR assays, and the TAC exhibited an overall 88% (278/315; 95% confidence interval [CI], 84% to 92%) sensitivity and a 99% (5,261/5,326, 98% to 99%) specificity. This TaqMan array card can be used in field settings as a rapid screen for outbreak investigation or for the surveillance of pathogens, including Ebola virus.
Cytomegalovirus-Specific CD4 T Cells Are Cytolytic and Mediate Vaccine Protection
Authors: Verma Shilpi , Weiskopf Daniela , Gupta Ankan , McDonald Bryan , Peters Bjoern , Sette Alessandro , Benedict Chris A. 
Published: October 2015

ABSTRACT

CD4 T cells provide protection against cytomegalovirus (CMV) and other persistent viruses, and the ability to quantify and characterize epitope-specific responses is essential to gain a more precise understanding of their effector roles in this regard. Here, we report the first two I-A
d
-restricted CD4 T cell responses specific for mouse CMV (MCMV) epitopes and use a major histocompatibility complex class II (MHC-II) tetramer to characterize their phenotypes and functions. We demonstrate that MCMV-specific CD4 T cells can express high levels of granzyme B and kill target cells in an epitope- and organ-specific manner. In addition, CD4 T cell epitope vaccination of immunocompetent mice reduced MCMV replication in the same organs where CD4 cytotoxic T lymphocyte (CTL) activity was observed. Together, our studies show that MCMV epitope-specific CD4 T cells have the potential to mediate antiviral defense by multiple effector mechanisms
in vivo
.

IMPORTANCE
CD4 T cells mediate immune protection by using their T cell receptors to recognize specific portions of viral proteins, called epitopes, that are presented by major histocompatibility complex class II (MHC-II) molecules on the surfaces of professional antigen-presenting cells (APCs). In this study, we discovered the first two epitopes derived from mouse cytomegalovirus (MCMV) that are recognized by CD4 T cells in BALB/c mice, a mouse strain commonly used to study the pathogenesis of this virus infection. Here, we report the sequences of these epitopes, characterize the CD4 T cells that recognize them to fight off MCMV infection, and show that we can use the epitopes to vaccinate mice and protect against MCMV.
Interferon Kappa Inhibits Human Papillomavirus 31 Transcription by Inducing Sp100 Proteins
Authors: Habiger Christina , Jäger Günter , Walter Michael , Iftner Thomas , Stubenrauch Frank 
Published: October 2015

ABSTRACTHigh-risk human papillomaviruses (hr-HPV) establish persistent infections in keratinocytes, which can lead to cancer of the anogenital tract. Interferons (IFNs) are a family of secreted cytokines that induce IFN-stimulated genes (ISGs), many of which display antiviral activities. Transcriptome studies have indicated that established hr-HPV-positive cell lines display a reduced expression of ISGs, which correlates with decreased levels of interferon kappa (IFN-κ), a type I IFN constitutively expressed in keratinocytes. Prior studies have also suggested that IFN-β has anti-hr-HPV activity but the underlying mechanisms are not well understood. The downregulation of IFN-κ by hr-HPV raises the possibility that IFN-κ has anti-HPV activity. Using doxycycline-inducible IFN-κ expression in CIN612-9E cells, which maintain extrachromosomally replicating HPV31 genomes, we demonstrated that IFN-κ inhibits the growth of these cells and reduces viral transcription and replication. Interestingly, the initiation of viral early transcription was already inhibited at 4 to 6 h after IFN-κ expression. This was also observed with recombinant IFN-β, suggesting a common mechanism of IFNs. Transcriptome sequencing (RNA-seq) analysis identified 1,367 IFN-κ-regulated genes, of which 221 were modulated >2-fold. The majority of those (71%) matched known ISGs, confirming that IFN-κ acts as abona fidetype I IFN in hr-HPV-positive keratinocytes. RNA interference (RNAi) and cotransfection experiments indicated that the inhibition of viral transcription is mainly due to the induction of Sp100 proteins by IFN-κ. Consistent with published data showing that Sp100 acts as a restriction factor for HPV18 infection, our results suggest that hr-HPV target IFN-κ to prevent Sp100 expression and identify Sp100 as an ISG with anti-HPV activity.IMPORTANCEHigh-risk HPV can establish persistent infections which may progress to anogenital cancers. hr-HPV interfere with the expression of interferon (IFN)-stimulated genes (ISGs), which is due to reduced levels of IFN-κ, an IFN that is constitutively expressed in human keratinocytes. This study reveals that IFN-κ rapidly inhibits HPV transcription and that this is due to the induction of Sp100 proteins. Thus, Sp100 represents an ISG for hr-HPV.
Targeting Swine Leukocyte Antigen Class I Molecules for Proteasomal Degradation by the nsp1α Replicase Protein of the Chinese Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus Strain JXwn06
Authors: Du Jige , Ge Xinna , Liu Ying , Jiang Ping , Wang Zhe , Zhang Ruimin , Zhou Lei , Guo Xin , Han Jun , Yang Hanchun 
Published: October 2015

ABSTRACT
Porcine reproductive and respiratory syndrome virus (PRRSV) is a critical pathogen of swine, and infections by this virus often result in delayed, low-level induction of cytotoxic T lymphocyte (CTL) responses in pigs. Here, we report that a Chinese highly pathogenic PRRSV strain possessed the ability to downregulate swine leukocyte antigen class I (SLA-I) molecules on the cell surface of porcine alveolar macrophages and target them for degradation in a manner that was dependent on the ubiquitin-proteasome system. Moreover, we found that the nsp1α replicase protein contributed to this property of PRRSV. Further mutagenesis analyses revealed that this function of nsp1α required the intact molecule, including the zinc finger domain, but not the cysteine protease activity. More importantly, we found that nsp1α was able to interact with both chains of SLA-I, a requirement that is commonly needed for many viral proteins to target their cellular substrates for proteasomal degradation. Together, our findings provide critical insights into the mechanisms of how PRRSV might evade cellular immunity and also add a new role for nsp1α in PRRSV infection.

IMPORTANCE
PRRSV infections often result in delayed, low-level induction of CTL responses in pigs. Deregulation of this immunity is thought to prevent the virus from clearance in an efficient and timely manner, contributing to persistent infections in swineherds. Our studies in this report provide critical insight into the mechanism of how PRRSV might evade CTL responses. In addition, our findings add a new role for nsp1α, a critical viral factor involved in antagonizing host innate immunity.
Env-Specific IgA from Viremic HIV-Infected Subjects Compromises Antibody-Dependent Cellular Cytotoxicity
Authors: Ruiz María Julia , Ghiglione Yanina , Falivene Juliana , Laufer Natalia , Holgado María Pía , Socías María Eugenia , Cahn Pedro , Sued Omar , Giavedoni Luis , Salomón Horacio , Gherardi María Magdalena , Rodríguez Ana María , Turk Gabriela 
Published: October 2015

ABSTRACTElucidating the factors that modulate HIV-specific antibody-dependent cellular cytotoxicity (ADCC) will help in understanding its role in HIV immunity. The aim of this study was to determine whether IgA could modify the magnitude of ADCC in HIV infection, abrogating its protective role. Plasma samples from 20 HIV-positive (HIV+) subjects enrolled during primary HIV infection (PHI), 10 chronically infected subjects (chronic), and 7 elite controllers (EC) were used. ADCC was determined by using a fluorometric ADCC assay, before and after removal of plasma IgA. Data were analyzed by using nonparametric statistics. ADCC was documented in 80% of PHI enrollment samples and in 100% of PHI 12-month, chronic, and EC samples; it peaked after acute infection, reached a plateau in chronic infection, and decreased after initiation of antiretroviral treatment (ART). Significant associations between ADCC and disease progression were found only after removal of plasma IgA from 12-month PHI samples: the magnitude of ADCC not only increased after IgA removal but also correlated with CD4+T-cell preservation. This work provides evidence that gp120-specific IgA was capable of modifying ADCC responses during natural HIV infection for the first time and adds to similar evidence provided in other settings. Furthermore, it underscores the complexity of the ADCC phenomenon and will help in an understanding of its underlying mechanisms.IMPORTANCEAlthough the induction of ADCC-mediating antibodies in HIV-infected subjects has been extensively documented, the association of these antibodies with protection from disease progression is poorly understood. Here, we demonstrate that plasma IgA is a factor capable of modifying the magnitude of IgG-mediated ADCC in HIV infection, mitigating its beneficial effect. These results help in understanding why previous studies failed to demonstrate correlations between ADCC and disease progression, and they also contribute to the notion that an HIV vaccine should stimulate the production of ADCC-mediating IgG antibodies but not IgA.
Characterization of a Herpes Simplex Virus 1 (HSV-1) Chimera in Which the Us3 Protein Kinase Gene Is Replaced with the HSV-2 Us3 Gene
Authors: Shindo Keiko , Kato Akihisa , Koyanagi Naoto , Sagara Hiroshi , Arii Jun , Kawaguchi Yasushi 
Published: October 2015

ABSTRACT

Us3 protein kinases encoded by herpes simplex virus 1 (HSV-1) and 2 (HSV-2) play important roles in viral replication and pathogenicity. To investigate type-specific differences between HSV-1 Us3 and HSV-2 Us3 in cells infected by viruses with all the same viral gene products except for their Us3 kinases, we constructed and characterized a recombinant HSV-1 in which its Us3 gene was replaced with the HSV-2 Us3 gene. Replacement of HSV-1 Us3 with HSV-2 Us3 had no apparent effect on viral growth in cell cultures or on the range of proteins phosphorylated by Us3. HSV-2 Us3 efficiently compensated for HSV-1 Us3 functions, including blocking apoptosis, controlling infected cell morphology, and downregulating cell surface expression of viral envelope glycoprotein B. In contrast, replacement of HSV-1 Us3 by HSV-2 Us3 changed the phosphorylation status of UL31 and UL34, which are critical viral regulators of nuclear egress. It also caused aberrant localization of these viral proteins and aberrant accumulation of primary enveloped virions in membranous vesicle structures adjacent to the nuclear membrane, and it reduced viral cell-cell spread in cell cultures and pathogenesis in mice. These results clearly demonstrated biological differences between HSV-1 Us3 and HSV-2 Us3, especially in regulation of viral nuclear egress and phosphorylation of viral regulators critical for this process. Our study also suggested that the regulatory role(s) of HSV-1 Us3, which was not carried out by HSV-2 Us3, was important for HSV-1 cell-cell spread and pathogenesis
in vivo
.

IMPORTANCE
A previous study comparing the phenotypes of HSV-1 and HSV-2 suggested that the HSV-2 Us3 kinase lacked some of the functions of HSV-1 Us3 kinase. The difference between HSV-1 and HSV-2 Us3 kinases appeared to be due to the fact that some Us3 phosphorylation sites in HSV-1 proteins are not conserved in the corresponding HSV-2 proteins. Therefore, we generated recombinant HSV-1 strains YK781 (Us3-chimera) with HSV-2 Us3 and its repaired virus YK783 (Us3-repair) with HSV-1 Us3, to compare the activities of HSV-1 Us3 and HSV-2 Us3 in cells infected by viruses with the same HSV-1 gene products except for their Us3 kinases. We report here that some processes in viral nuclear egress and pathogenesis
in vivo
that have been attributed to HSV-1 Us3 could not be carried out by HSV-2 Us3. Therefore, our study clarified the biological differences between HSV-1 Us3 and HSV-2 Us3, which may be relevant to viral pathogenesis
in vivo
.