bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of the GDI Spray Dynamics Through Multidimensional Modeling and Flow Visualization in an Optically Accessible SI Engine
Authors: Costa Michela , Sorge Ugo , Sementa Paolo , Montanaro Alessandro 
Published: October 2014

Present work is aimed at studying into detail mixture formation and combustion in a gasoline direct injection (GDI) engine working under stoichiometric mixture conditions. The study is performed both numerically and experimentally. From the experimental side, the engine, optically accessible, is characterized by collecting, for various injection strategies, in-cylinder pressure cycles and digital images. From the numerical side, a 3D engine model is developed, that includes proper sub-models for the spray dynamics and the spray-wall interaction. This last phenomenon is studied into detail by resorting to a preliminary 3D simulation of the spray impingement realized in a proper experiment, where the engine injector is mounted at a certain distance from a cold or hot wall.
An interesting comparison between numerical and experimental images of the in-cylinder spray dynamics is presented, that also allows individuating the difference in the wallfilm deposition under various injection strategies. This opens the way to understand the difference in the combustion development arising as injection is anticipated or retarded in the engine working cycle.
Optimal Operation of Small Geothermal Systems Through Entropy Generation Analysis
Authors: Cosentino Sara , Sciacovelli Adriano , Verda Vittorio 
Published: October 2014

Geothermal systems often experience non homogeneous behavior between the various boreholes, due to possible issues in the installation or to differences in the stratigraphy. In the case of small systems, this may create important inefficiencies or operational problems. In this paper, the use of entropy generation analysis is proposed in order to optimize the global performances, taking fluid dynamic and thermal phenomena into account.
The possible anomalous scenarios that are considered include borehole ovalization and differences in the heat transfer between borehole and ground due to fouling, groundwater level, etc. The analysis is conducted considering a transient model of the entire system, composed by the ground, boreholes and heat pump. Various operating scenarios are also considered. Results show that non negligible improvements in the efficiency can be obtained by proper selection of the operating conditions.
Effect of Turbocharger Cut Out on Two-Stroke Marine Diesel Engine Performance and NOx Emissions at Part Load Operation
Authors: Hountalas Dimitrios T. , Sakellaridis Nikolaos F. , Pariotis Efthimios , Antonopoulos Antonis K. , Zissimatos Leonidas , Papadakis Nikiforos 
Published: October 2014

The diesel engine is widely used for marine vessel propulsion due to its relatively high efficiency compared to existing alternative propulsion systems. The majority of these engines are slow speed two stroke ones. Despite the improvement of their efficiency there now exists a demand for drastic reduction of daily fuel oil consumption as a result of the global financial situation and continuously increasing fuel prices.
Towards this effort, slow steaming is a promising solution for the drastic reduction of daily and specific fuel consumption when expressed in tn/mile. This requires engine operation in the low load (low speed) range where these engines are not designed to operate for long term. The main problem related to slow-steaming, is the lack of air which has a negative impact on the engine and its subsystems. A promising solution to the problem is turbocharger (T/C) cut-out at low load when more than one T/C exists.
In the present work a combined computational and experimental investigation is conducted to evaluate the operation potential of a large two stroke marine diesel engine equipped with two T/Cs using T/C cut-out, for which the specific technology presents various challenges. This is achieved using an in-house engine simulation model and measurements with and without T/C cut-out. From the results it is revealed that using this technique the scavenging air and peak firing pressure increase while the specific fuel consumption decreases. In this way, some major problems related with the long term operation of the engine under low load conditions, i.e. accumulation of carbon deposits on the exhaust gas side and continuous operation of the auxiliary air blowers, are surpassed. Moreover, a theoretical investigation is conducted considering fuel injection retard to minimize the peak firing pressure penalty while taking care to limit the corresponding negative impact on specific fuel consumption. For NOx emissions the effect of T/C cut-out is also considered using tail pipe emission data measured during the official shop tests.
From the analysis conducted it has been revealed that the technique of turbocharger cut–out (one of two) is technically feasible and could offer certain advantages when slow-steaming is implemented. Moreover, comparing the calculated with the measured results, it has been revealed that the simulation model successfully estimates engine operation with and without T/C cut-out, being a valuable tool for the engineers to investigate combustion and pollutant formation mechanisms under various engine configurations.
Global Sensitivity Analysis of Railway Vehicle Dynamics on Curved Tracks
Authors: Bigoni Daniele , Engisg-Karup Allan P. , True Hans 
Published: October 2014

This work addresses the problem of the reliability of simulations for realistic nonlinear systems, by using efficient techniques for the analysis of the propagation of the uncertainties of the model parameters through the dynamics of the system. We present the sensitivity analysis of the critical speed of a railway vehicle with respect to its suspension design. The variance that stems from parameter tolerances of the suspension is taken into account and its propagation through the dynamics of a full car with a couple of two-axle Cooperrider bogies running on curved track is studied.
Modern Uncertainty Quantification methods, such as Stochastic Collocation and Latin Hypercube, are employed in order to assess the global uncertainty in the computation of the critical speed. The sensitivity analysis of the critical speed to each parameter and combination of parameters is then carried out in order to quantify the importance of different suspension components. This is achieved using combined approaches of sampling methods, ANOVA expansions, Total Sensitivity Indices and Low-dimensional Cubature Rules.
Habitual and Maximal Dual-Task Gait Speeds Among Sedentary, Recreationally Active, and Masters Athlete Late Middle-Aged Adults
Authors: Glenn Jordan M. , Vincenzo Jennifer , Canella Collin K. , Binns Ashley , Gray Michelle 
Published: October 2014

Gait speed predicts survival in older adults; however, gait has not been evaluated in late middle-aged (LMA) populations.Purpose:Evaluate single- and dual-task gait speeds among sedentary (SED), recreationally active (RA), and masters athlete (MA) LMA adults.Methods:Participants were SED (n = 20, age = 61.0 ± 5.8), RA (n = 57, age = 63.5 ± 8.4), and MA (n = 25, age = 57.5 ± 7.9). Two trials of each task (10 m) were completed: habitual speed (HS), maximal speed (MS), dual-task (counting backward from a number by 3) habitual speed (DT-HS), and dual-task maximal speed (DT-MS).Results:MA (2.08 ± 0.63 m/s) had significantly (p < .05) greater MS compared with SED (1.94 ± 0.30 m/s) and RA (1.99 ± 0.53 m/s). Similar differences existed for DT-MS (SED = 1.77 ± 0.32 m/s, RA = 1.80 ± 0.51 m/s, MA = 1.89 ± 0.63 m/s). MA had smaller MS and DT-MS changes (difference between MS and DT-MS speeds) compared with RA (12%) and SED (13%).Conclusion:Maintaining a competitively active lifestyle increases MS in LMA adults and may support healthy aging.
Comparison of Test Specificities of Commercial Antigen-Based Assays and In-House PCR Methods for Detection of Rotavirus in Stool Specimens
Authors: Ye S. , Lambert S. B. , Grimwood K. , Roczo-Farkas S. , Nimmo G. R. , Sloots T. P. , Kirkwood C. D. , Whiley D. M. 
Published: October 2014

ABSTRACT
Seven commercial rotavirus antigen assays were compared with in-house PCR methods for detecting rotavirus in stool specimens. The assay sensitivities were 80% to 100%, while the specificities were 54.3% for one commercial immunochromatographic (ICT) method and 99.4% to 100% for other assays. Thus, except for one commercial ICT, all the assays were generally reliable for rotavirus detection.
Identification and Characterization of HIV-1 Latent Viral Reservoirs In Peripheral Blood
Authors: Chargin Amanda , Yin Fangfang , Song Min , Subramaniam Srividyabhuvaneswari , Knutson Grace , Patterson Bruce K. 
Published: October 2014

ABSTRACT
Plasma viral load and CD4 counts are effective for clinical monitoring, but they do not give a full representation of HIV-1 quasispecies in cellular reservoirs, the major repository of replication-competent HIV-1 in infected individuals. We sought to develop a diagnostic system that might stimulate the replication-competent HIV-1 reservoirs for enhanced clinical monitoring, including selection of antiretroviral regimens. Whole-blood samples from 45 HIV-infected individuals were collected into 1 ViraStim HIV-1 activation tube and 1 EDTA tube. Samples were tested for viral load and cell type-specific HIV-1 replication. Further, 7 matched activated/nonactivated samples were sequenced using the Trugene HIV-1 genotyping kit. The percentage of patients with replication-competent virus in peripheral blood mononuclear cells (PBMCs) varied, depending on the baseline plasma viral load in the EDTA tubes. Six out of 24 patients with a starting plasma viral load of <20 copies/ml (cp/ml), 6 out of 8 patients with starting viral loads of >20 and <1,000 cp/ml, and 8 out of 13 patients with starting viral loads of >1,000 all showed increases in viral replication of >5-fold. These increases came from cellular reservoirs in blood as determined by simultaneous ultrasensitive subpopulation staining/hybridization in situ (SUSHI). When resistance genotypes in plasma from activation tubes were compared to those from EDTA tubes for 7 patients, all patients showed additional mutations in the activation tube, while 3 patients demonstrated additional genotypic resistance determinants. We show that HIV-1 viral replication can be stimulated directly from infected whole blood. The sequencing results showed that 3 of 7 cases demonstrated additional drug resistance following stimulation.
Whole-Genome Sequencing of Burkholderia pseudomallei Isolates from an Unusual Melioidosis Case Identifies a Polyclonal Infection with the Same Multilocus Sequence Type
Authors: Price Erin P. , Sarovich Derek S. , Viberg Linda , Mayo Mark , Kaestli Mirjam , Tuanyok Apichai , Foster Jeffrey T. , Keim Paul , Pearson Talima , Currie Bart J. 
Published: October 2014

ABSTRACT

Twelve
Burkholderia pseudomallei
isolates collected over a 32-month period from a patient with chronic melioidosis demonstrated identical multilocus sequence types (STs). However, whole-genome sequencing suggests a polyclonal infection. This study is the first to report a mixed infection with the same ST.
Identification of Capsid Mutations That Alter the Rate of HIV-1 Uncoating in Infected Cells
Authors: Hulme Amy E. , Kelley Z , Okocha Eneniziaogochukwu A. , Hope Thomas J. 
Published: October 2014

ABSTRACT

After viral fusion with the cell membrane, the conical capsid of HIV-1 disassembles by a process called uncoating. We recently utilized the cyclosporine (CsA) washout assay, in which TRIM-CypA-mediated restriction of viral replication is used to detect the state of the viral capsid, to study the kinetics of uncoating in HIV-1-infected cells. Here we have extended this analysis to examine the effects of p24 capsid protein (p24
CA
) mutations and cellular environment on the kinetics of uncoating in infected cells. We found that p24
CA
mutations can significantly increase (A92E), delay (E45A and N74D), or have no effect (G94D) on the rate of uncoating and that these alterations are not due to changes in reverse transcription. Inhibition of reverse transcription delayed uncoating kinetics to an extent similar to that of the wild-type virus with all the p24
CA
mutant viruses tested. In addition, we observed differences in uncoating in two cell lines, which suggests that the cellular environment can differentially impact the disassembly of wild-type and mutant capsids. Collectively, these experiments suggest that viral and cellular factors are important for the process of uncoating. Finally, these data support the model whereby early steps in reverse transcription facilitate HIV-1 uncoating.

IMPORTANCE
The HIV-1 capsid is a cone-shaped structure, composed of the HIV-1-encoded protein p24
CA
, which contains the viral RNA and other proteins needed for infection. After the virus enters a target cell, this capsid must disassemble by a process called uncoating. Uncoating is required for HIV-1 infection to progress, but the details of how this process occurs is not known. In this study, we used an
in vivo
assay to examine the uncoating process in HIV-1-infected cells. We determined that p24
CA
mutations could increase or decrease the rate of uncoating and that this rate varied in different cell lines. We also found that reverse transcription of the viral RNA altered the process of uncoating before the p24
CA
mutations. Collectively, these experiments provide a better understanding of how viral and cellular factors are involved with a poorly understood step in HIV-1 infection.
Antibody Informatics: IMGT, the International ImMunoGeneTics Information System
Authors: Lefranc Marie-Paule 
Published: October 2014

ABSTRACT

Antibody informatics, a part of immunoinformatics, refers to the concepts, databases, and tools developed and used to explore and to analyze the particular properties of the immunoglobulins (IG) or antibodies, compared with conventional genes and proteins. Antibody informatics is based on a unique ontology, IMGT-ONTOLOGY, created in 1989 by IMGT, the international ImMunoGeneTics information system (
http://www.imgt.org
). IMGT-ONTOLOGY defined, for the first time, the concept of ‘genes’ for the IG and the T cell receptors (TR), which led to their gene and allele nomenclature and allowed their entry in databases and tools. A second IMGT-ONTOLOGY revolutionizing and definitive concept was the IMGT unique numbering that bridged the gap between sequences and structures for the variable (V) and constant (C) domains of the IG and TR, and for the groove (G) domains of the major histocompatibility (MH). These breakthroughs contributed to the development of IMGT databases and tools for antibody informatics and its diverse applications, such as repertoire analysis in infectious diseases, antibody engineering and humanization, and study of antibody/antigen interactions. Nucleotide sequences of antibody V domains from deep sequencing (Next Generation Sequencing or High Throughput Sequencing) are analyzed with IMGT/HighV-QUEST, the high-throughput version of IMGT/V-QUEST and IMGT/JunctionAnalysis. Amino acid sequences of V and C domains are represented with the IMGT/Collier-de-Perles tool and analyzed with IMGT/DomainGapAlign. Three-dimensional (3D) structures (including contact analysis and paratope/epitope) are described in IMGT/3Dstructure-DB. Based on a friendly interface, IMGT/mAb-DB contains therapeutic monoclonal antibodies (INN suffix–mab) that can be queried on their specificity, for example, in infectious diseases, on bacterial or viral targets.
Vector-Mediated
In Vivo
Antibody Expression
Authors: Schnepp Bruce C. , Johnson Philip R. 
Published: October 2014

ABSTRACT

This article focuses on a novel vaccine strategy known as vector-mediated antibody gene transfer, with a particular focus on human immunodeficiency virus (HIV). This strategy provides a solution to the problem of current vaccines that fail to generate neutralizing antibodies to prevent HIV-1 infection and AIDS. Antibody gene transfer allows for predetermination of antibody affinity and specificity prior to “immunization” and avoids the need for an active humoral immune response against the HIV envelope protein. This approach uses recombinant adeno-associated viral (rAAV) vectors, which have been shown to transduce muscle with high efficiency and direct the long-term expression of a variety of transgenes, to deliver the
gene
encoding a broadly neutralizing antibody into the muscle. Following rAAV vector gene delivery, the broadly neutralizing antibodies are endogenously synthesized in myofibers and passively distributed to the circulatory system. This is an improvement over classical passive immunization strategies that administer antibody
proteins
to the host to provide protection from infection. Vector-mediated gene transfer studies in mice and monkeys with anti-HIV and simian immunodeficiency virus (SIV)-neutralizing antibodies demonstrated long-lasting neutralizing activity in serum with complete protection against intravenous challenge with virulent HIV and SIV. These results indicate that existing potent anti-HIV antibodies can be rapidly moved into the clinic. However, this methodology need not be confined to HIV. The general strategy of vector-mediated antibody gene transfer can be applied to other difficult vaccine targets such as hepatitis C virus, malaria, respiratory syncytial virus, and tuberculosis.
“Preharvest” Food Safety for
Escherichia coli
O157 and Other Pathogenic Shiga Toxin-Producing Strains
Authors: Besser Thomas E. , Schmidt Carrie E. , Shah Devendra H. , Shringi Smriti 
Published: October 2014

ABSTRACT

Preharvest food safety refers to the concept of reducing the rates of contamination of unprocessed foods with food-borne disease pathogens in order to reduce human exposure and disease. This article addresses the search for effective preharvest food safety practices for application to live cattle to reduce both contamination of foods of bovine origin and environmental contamination resulting from cattle. Although this research has resulted in several practices that significantly decrease contamination by
Escherichia coli
O157, the effects are limited in magnitude and unlikely to affect the incidence of human disease without much wider application and considerably higher efficacy than is presently apparent. Infection of cattle with
E. coli
O157 is transient and seasonally variable, likely resulting from a complex web of exposures. It is likely that better identification of the true maintenance reservoir of this agent and related Shiga toxin-producing
E. coli
is required to develop more effective control measures for these important food- and waterborne disease agents.
Genetics of Mycobacterial Trehalose Metabolism
Authors: Kalscheuer Rainer , Koliwer-Brandl Hendrik 
Published: October 2014

ABSTRACT

Trehalose [alpha-
d
-glucopyranosyl-(1→1)-alpha-
d
-glucopyranoside] is a highly abundant disaccharide in mycobacteria that fulfills many biological roles and has a plethora of possible metabolic fates. Trehalose is synthesized in mycobacteria
de novo
either from glycolytic intermediates or from alpha-glucans via two alternative routes, the OtsA-OtsB and the TreY-TreZ pathways, respectively. Intracellular trehalose can serve as an endogenous remobilizable carbon storage compound and as a biocompatible stress protectant. Furthermore, trehalose functions as the sugar core of many glycolipids with important structural or immunomodulatory functions such as the cord factor trehalose dimycolate, sulfolipids, and polyacyltrehalose. Moreover, trehalose plays a central role in the formation of the mycolic acid cell wall layer because it serves as a carrier molecule that shuttles mycolic acids in the form of the glycolipid trehalose monomycolate between the cytoplasm and the periplasm. In this process, a specific importer recycles the free trehalose that is extracellularly released as a by-product during mycolate processing via the antigen 85 complex, which might represent a specific adaptation to the intracellular lifestyle of
Mycobacterium tuberculosis
with limited carbohydrate availability. Finally, trehalose is converted to glycogen-like branched alpha-glucans by a four-step metabolic pathway involving the essential maltosyltransferase GlgE, which may be further processed to derivatives with intracellular or extracellular destinations such as polymethylated lipopolysaccharides or capsular alpha-glucans, respectively. In this article we summarize the current knowledge of the genetic basis of trehalose biosynthesis and metabolism in mycobacteria, the biological functions of trehalose-based molecules, and their roles in virulence of the human pathogen
M. tuberculosis
.
Mycobacterium tuberculosis
Serine/Threonine Protein Kinases
Authors: Prisic Sladjana , Husson Robert N. 
Published: October 2014

ABSTRACT

The
Mycobacterium tuberculosis
genome encodes 11 serine/threonine protein kinases (STPKs). A similar number of two-component systems are also present, indicating that these two signal transduction mechanisms are both important in the adaptation of this bacterial pathogen to its environment. The
M. tuberculosis
phosphoproteome includes hundreds of Ser- and Thr-phosphorylated proteins that participate in all aspects of
M. tuberculosis
biology, supporting a critical role for the STPKs in regulating
M. tuberculosis
physiology. Nine of the STPKs are receptor type kinases, with an extracytoplasmic sensor domain and an intracellular kinase domain, indicating that these kinases transduce external signals. Two other STPKs are cytoplasmic and have regulatory domains that sense changes within the cell. Structural analysis of some of the STPKs has led to advances in our understanding of the mechanisms by which these STPKs are activated and regulated. Functional analysis has provided insights into the effects of phosphorylation on the activity of several proteins, but for most phosphoproteins the role of phosphorylation in regulating function is unknown. Major future challenges include characterizing the functional effects of phosphorylation for this large number of phosphoproteins, identifying the cognate STPKs for these phosphoproteins, and determining the signals that the STPKs sense. Ultimately, combining these STPK-regulated processes into larger, integrated regulatory networks will provide deeper insight into
M. tuberculosis
adaptive mechanisms that contribute to tuberculosis pathogenesis. Finally, the STPKs offer attractive targets for inhibitor development that may lead to new therapies for drug-susceptible and drug-resistant tuberculosis.