bluuebunny/crossref_metadata_2025_split huggingface dataset:
Serine Lipids of Porphyromonas gingivalis Are Human and Mouse Toll-Like Receptor 2 Ligands
Authors: Clark Robert B. , Cervantes Jorge L. , Maciejewski Mark W. , Farrokhi Vahid , Nemati Reza , Yao Xudong , Anstadt Emily , Fujiwara Mai , Wright Kyle T. , Riddle Caroline , La Vake Carson J. , Salazar Juan C. , Finegold Sydney , Nichols Frank C. 
Published: July 2013

ABSTRACT

The total cellular lipids of
Porphyromas gingivalis
, a known periodontal pathogen, were previously shown to promote dendritic cell activation and inhibition of osteoblasts through engagement of Toll-like receptor 2 (TLR2). The purpose of the present investigation was to fractionate all lipids of
P. gingivalis
and define which lipid classes account for the TLR2 engagement, based on both
in vitro
human cell assays and
in vivo
studies in mice. Specific serine-containing lipids of
P. gingivalis
, called lipid 654 and lipid 430, were identified in specific high-performance liquid chromatography fractions as the TLR2-activating lipids. The structures of these lipids were defined using tandem mass spectrometry and nuclear magnetic resonance methods.
In vitro
, both lipid 654 and lipid 430 activated TLR2-expressing HEK cells, and this activation was inhibited by anti-TLR2 antibody. In contrast, TLR4-expressing HEK cells failed to be activated by either lipid 654 or lipid 430. Wild-type (WT) or TLR2-deficient (TLR2
−/−
) mice were injected with either lipid 654 or lipid 430, and the effects on serum levels of the chemokine CCL2 were measured 4 h later. Administration of either lipid 654 or lipid 430 to WT mice resulted in a significant increase in serum CCL2 levels; in contrast, the administration of lipid 654 or lipid 430 to TLR2
−/−
mice resulted in no increase in serum CCL2. These results thus identify a new class of TLR2 ligands that are produced by
P. gingivalis
that likely play a significant role in mediating inflammatory responses both at periodontal sites and, potentially, in other tissues where these lipids might accumulate.
Shrinking the FadE Proteome of Mycobacterium tuberculosis: Insights into Cholesterol Metabolism through Identification of an α
2
β
2
Heterotetrameric Acyl Coenzyme A Dehydrogenase Family
Authors: Wipperman Matthew F. , Yang Meng , Thomas Suzanne T. , Sampson Nicole S. 
Published: July 2013

ABSTRACT

The ability of the pathogen
Mycobacterium tuberculosis
to metabolize steroids like cholesterol and the roles that these compounds play in the virulence and pathogenesis of this organism are increasingly evident. Here, we demonstrate through experiments and bioinformatic analysis the existence of an architecturally distinct subfamily of acyl coenzyme A (acyl-CoA) dehydrogenase (ACAD) enzymes that are α
2
β
2
heterotetramers with two active sites. These enzymes are encoded by two adjacent ACAD (
fadE
) genes that are regulated by cholesterol. FadE26-FadE27 catalyzes the dehydrogenation of 3β-hydroxy-chol-5-en-24-oyl-CoA, an analog of the 5-carbon side chain cholesterol degradation intermediate. Genes encoding the α
2
β
2
heterotetrameric ACAD structures are present in multiple regions of the
M. tuberculosis
genome, and subsets of these genes are regulated by four different transcriptional repressors or activators: KstR1 (also known as KstR), KstR2, Mce3R, and SigE. Homologous ACAD gene pairs are found in other
Actinobacteria
, as well as
Proteobacteria
. Their structures and genomic locations suggest that the α
2
β
2
heterotetrameric structural motif has evolved to enable catalysis of dehydrogenation of steroid- or polycyclic-CoA substrates and that they function in four subpathways of cholesterol metabolism.
Multiyear assessment of the sedimentological impacts of the removal of the Munroe Falls Dam on the middle Cuyahoga River, Ohio
Authors: Peck John A. , Kasper Nicholas R. 
Published: July 2013

Abstract
The 2005 removal of the 3.6-m-high Munroe Falls Dam from the middle Cuyahoga River, Ohio, provided an opportunity to assess dam removal channel-evolution models and to anticipate impacts from additional dam removals on the Cuyahoga River. Preremoval geomorphic and sedimentologic conditions were characterized. Monitoring of the river response to dam removal has continued for 5 yr. The dam removal lowered base level and increased flow velocity upstream of the former dam site. Postremoval, the initial channel response was rapid incision to the predam substrate, followed by rapid lateral erosion of the exposed impoundment fill. Four to nine months after removal, dewatering and vegetation of the exposed impoundment fill greatly reduced the rate of lateral erosion. For 2.5 yr post -removal, sandy bar forms were present upstream of the former dam, and sand was transported under all flow conditions of the year. Subsequently, the bed has become armored with gravel. Downstream of the former dam site, the channel aggraded with sand, causing flow to occupy meander bend chutes that had formerly only been active during high flow. A sandy deltaic feature has accumulated 3.3 km downstream in the impoundment created by the Le Fever Dam. The impacts of the Munroe Falls Dam removal are generally well described by published channel-evolution models with minor exceptions due to local geology and hydrology. The similarities between the Munroe Falls and Le Fever Dam impoundments suggest that this study can aid in understanding the impacts of the possible future removal of the Le Fever Dam.
Engineering Seismology
Authors: Neumann Frank 
Published: July 2013

Abstract
Engineering seismology consists of those branches of seismology that have application to the aseismic design of structures. The expression "earthquake engineering" applies primarily to the design problem itself, but the two terms are sometimes used interchangeably.
Engineering semismology experienced its most rapid development in Japan, and present practices in aseismic design are based largely on Japanese research. In recent years the Coast and Geodetic Survey filled a serious void in all such programs by establishing a network of strong-motion seismograph stations in the Pacific Coast area to register damaging ground and building vibrations. This yielded new information on the nature and magnitude of such motions and inaugurated new approaches to the aseismic-design problem.
Former efforts to associate various grades of earthquake intensity with acceleration alone are giving way to more logical relationships involving the frequencies and energies of seismic waves. The wide ranges of intensity and ground motion measured on different types of geological formations (under otherwise similar conditions) are more than substantiating earlier findings pointing to the importance of the foundation factor in earthquake-engineering problems. New interpretations are being made of intensity-distribution maps, and isoseismal lines may be replaced by efforts to evaluate basement rock and surface intensities quantitatively using both instrumental and noninstrumental data. Other phases of the seismic-risk problem are also discussed.
Steady progress is being made in determining the maximum lateral forces that specific earthquake motions impress on structures and in overcoming the mathematical bottlenecks associated with the problem. The so-called "earthquake spectrum" appears to be the engineer's answer to the former problem, but effort is still required to derive the maximum benefit from this analytical tool. A spectrum shows the maximum theoretical responses of multi-period oscillators to a recorded earthquake motion. Some examples are cited of the use of seismological techniques in solving other types of vibration problems including blast vibrations.
Geology And Pedology in Highway Soil Engineering
Authors: Thornburn Thomas H. 
Published: July 2013

ABSTRACT
There has been a close historical connection between developments in geology and civil engineering. Highway engineers, in particular, not only design and build heavy structures covering relatively small areas of earth material, but they also construct lightly loaded pavement structures covering large areas. In both cases, information is needed about the soil conditions. Detailed soil mechanics investigations can usually be justified for the design of heavy bridge and overpass structures; however, the engineer concerned with roadway design can seldom afford the time and money that are necessary for a detailed survey of a right-of-way, which is often 300 feet wide and several miles long. Proper roadway design, therefore, requires the use of every available aid in order to relate a small amount of test and pavement performance data to the largest possible mass of earth. The principal sources of such assistance are geologic and agricultural (pedologic) soil reports, which provide information on the distribution and character of surficial deposits, and vertical aerial photographs. Significant progress has been made in the correlation of geologic, pedologic, and air photo map units with engineering characteristics of soils. In the beginning, such correlations were based primarily on qualitative field observations; later, representative test data were included; and finally, through the use of statistical methods, some measure of the variability of natural soils was obtained. The statistical correlation of quantitative engineering data with map units is still in its infancy, but it gives promise of providing a rational basis for the design of highway pavements. This review is primarily a discussion of the development of procedures of engineering soil survey and classification which rely upon geology, pedology, and air photo interpretation for exploration, presentation of data, extrapolation of data, and formulation of design criteria. Particular emphasis is given to pedologic classification and its engineering applications.
Clay as a Canal Sealant
Authors: Dirmeyer R. D. 
Published: July 2013

ABSTRACT
Conveyance losses in irrigation canals commonly range from 20 to 40 per cent: however, the high costs of construction of conventional canal linings, such as those of concrete, asphalt, and plastic, often prevent large-scale efforts to control seepage. Thus, the idea of lowering costs by utilizing flowing canal water for placement of sealing clays in the leaky zones of canals is an attractive one. This paper traces the development of water-borne clay sealants for canals, from natural silting to the recently developed methods of sediment-sealing with bentonite.
In general, the water-borne clays are best for sealing coarsely rocky to gravelly canal bed materials. Less favorable results are obtained when clays are used for sealing fine-grained silty to sandy canal materials. Lack of penetration and short life are the main problems with clays used for sealing fine-grained soils.
The cost of clay-sealing ranges from less than $.01/square yard of canal area to an extreme value of about $2.00/square yard. Concrete linings, which are usually considered the best answer to most seepage loss problems, seldom cost less than $2.00 per square yard.
Consent processes in cluster-randomised trials in residential facilities for older adults: a systematic review of reporting practices and proposed guidelines
Authors: DiazOrdaz Karla , Slowther Anne-Marie , Potter Rachel , Eldridge Sandra 
Published: July 2013

ObjectiveTo assess the quality of reported consent processes of cluster-randomised trials conducted in residential facilities for older people and to explore whether the focus on improving the general conduct and reporting of cluster-randomised trials influenced the quality of conduct and reporting of ethical processes in these trials.DesignSystematic review of cluster-randomised trials reports, published up to the end of 2010.Data sourcesNational Library of Medicine (Medline) via PubMed, hand-searches ofBMJ,Journal of the American Medical Association,BMC Health Services Research,Age and Ageing and Journal of the American Geriatrics Society, reference search in Web of Knowledge and consultation with experts.Eligibility for selecting studiesPublished cluster-randomised trials where the unit of randomisation is a part or the whole of a residential facility for older people, without language or year of publication restrictions.ResultsWe included 73 trials. Authors reported ethical approval in 59, obtaining individual consent in 51, and using proxies for this consent in 37, but the process to assess residents’ capacity to consent was clearly reported in only eight. We rated only six trials high for the quality of consent processes. We considered that individual informed consent could have been waived legitimately in 14 of 22 trials not reporting obtaining consent. The proportions reporting ethical approval and quality of consent processes were higher in recent trials.ConclusionsRecently published international recommendations regarding ethical conduct in cluster-randomised trials are much needed. In relation to consent processes when cognitively impaired individuals are included in these trials, we provide a six-point checklist and recommend the minimum information to be reported. Those who lack capacity in trials with complex designs should be afforded the same care in relation to consent as competent adults in trials with simpler designs.
An Analysis of Language-Level Support for Self-Adaptive Software
Authors: Salvaneschi Guido , Ghezzi Carlo , Pradella Matteo 
Published: July 2013

Self-adaptive software has become increasingly important to address the new challenges of complex computing systems. To achieve adaptation, software must be designed and implemented by following suitable criteria, methods, and strategies. Past research has been mostly addressing adaptation by developing solutions at the software architecture level. This work, instead, focuses on finer-grain programming language-level solutions. We analyze three main linguistic approaches: metaprogramming, aspect-oriented programming, and context-oriented programming. The first two are general-purpose linguistic mechanisms, whereas the third is a specific and focused approach developed to support context-aware applications. This paradigm provides specialized language-level abstractions to implement dynamic adaptation and modularize behavioral variations in adaptive systems.
The article shows how the three approaches can support the implementation of adaptive systems and compares the pros and cons offered by each solution.
A Diabatic Lagrangian Technique for the Analysis of Convective Storms. Part I: Description and Validation via an Observing System Simulation Experiment
Authors: Ziegler Conrad L. 
Published: July 2013

Abstract
A diabatic Lagrangian analysis (DLA) technique for deriving potential temperature, water vapor and cloud water mixing ratios, and virtual buoyancy from three-dimensional time-dependent Doppler radar wind and reflectivity fields in storms is presented. The DLA method proceeds from heat and water substance conservation along discrete air trajectories via microphysical diabatic heating/cooling and simple damping and surface flux parameterizations in a parcel-following ground-relative reference frame to thermodynamic fields on a regular grid of trajectory endpoints at a common analysis time. Rain and graupel precipitation size distributions are parameterized from observed reflectivity at discrete Lagrangian points to simplify the cloud model–based microphysically driven heating and cooling rate calculations. The DLA approximates the precipitation size distributions from reflectivity assuming conventional inverse exponential size distributions and prescribed input intercept parameter values based on the output of a mature simulated storm. The DLA is demonstrated via an observing system simulation experiment (OSSE), and its analysis compares favorably with the known output buoyancy and water substance fields in the simulated storm case. The DLA-analyzed thermal–solenoidal horizontal vorticity tendency is of comparable magnitude to the corresponding modeled solenoidal vorticity tendency. A test application of the DLA to a radar-observed storm is presented in a companion paper (Part II).
Cost-Effective Methods for Accurate Determination of Sea Level Rise Vulnerability: A Solomon Islands Example
Authors: Albert Simon , Abernethy Kirsten , Gibbes Badin , Grinham Alistair , Tooler Nixon , Aswani Shankar 
Published: July 2013

Abstract
For millions of people living along the coastal fringe, sea level rise is perhaps the greatest threat to livelihoods over the coming century. With the refinement and downscaling of global climate models and increasing availability of airborne-lidar-based inundation models, it is possible to predict and quantify these threats with reasonable accuracy where such information is available. For less developed countries, especially small island states, access to high-resolution digital elevation models (DEMs) derived from lidar is limited. The only freely available DEMs that could be used for inundation modeling by these nations are those based on data from the Shuttle Radar Topography Mission (SRTM). These data, with a horizontal resolution of ≈90 m and a vertical accuracy of ±5–10 m, are generally unsuitable for local-scale planning and adaption projects. To address this disparity, low-cost ground-based techniques were tested and applied to accurately determine coastal topography in the Solomon Islands. This method had a significantly improved vertical accuracy (±2 cm) and was readily learned by local community members, who were able to independently map and determine the vulnerability of their costal community to inundation from sea level rise. For areas where lidar is not economically viable, this method is intended to provide an important balance of cost, simplicity, accuracy, and local participation that can assist remote coastal communities with coastal planning decisions. The method can enhance local capacity and arguably promotes more meaningful local engagement in sea level rise planning and adaptation activities.
The Effects of Visual and Cognitive Distractions on Operational and Tactical Driving Behaviors
Authors: Zhang Yu , Kaber David B. , Rogers Meghan , Liang Yulan , Gangakhedkar Shruti 
Published: July 2013

Objective: This study tested the effects of two fundamental forms of distraction, including visual-manual and cognitive-audio distraction, with comparison under both operational and tactical driving. Strategic control remains for future study. Background: Driving is a complex control task involving operational, tactical, and strategic control. Although operational control, such as lead-car following, has been studied, the influence of in-vehicle distractions on higher levels of control, including tactical and strategic, remains unclear. Method: Two secondary tasks were designed to independently represent visual-manual and cognitive-audio distractions, based on multiple resource theory. Drivers performed operational vehicle control maneuvers (lead-car following) or tactical control maneuvers (passing) along with the distraction tasks in a driving simulator. Response measures included driving performance and visual behavior. Results: Results revealed drivers’ ability to accommodate either visual or cognitive distractions in following tasks but not in passing. The simultaneous distraction condition led to the greatest decrement in performance. Conclusion: Findings support the need to assess the impacts of in-vehicle distraction on different levels of driving control. Future study should investigate driver distraction under strategic control.
Inflammation and schizophrenia
Authors: Al-Asmari AK , Khan Md. W 
Published: July 2013

Objective: Although several theories have been proposed including developmental/neurodegenerative processes, neurotransmitter abnormalities, viral infection, and immune dysfunction, the exact causative factor of schizophrenia is unclear. A relationship between inflammation and schizophrenia has been supported by abnormal cytokine production and altered antioxidant status. This study was aimed to examine the alterations in serum oxidative–antioxidative status and cytokine levels of schizophrenic patients. Methods: A total of 91 schizophrenic patients from Saudi Arabia and 50 age- and sex-matched healthy controls were enrolled in the present study. Fresh blood samples were collected to measure the levels of cytokines and markers of oxidative stress by spectrophotometric assays simultaneously. Results: We observed that there was a significant increase in the levels of tumor necrosis factor-α, interleukin (IL)-1β, and IL-6 and a decrease in the levels of interferon-γ. Lipid peroxides are elevated in serum, while total-sulfhydryl levels were decreased. Also, the activities of superoxide dismutase and glutathione peroxidase were decreased, while the activities of catalase, glutathione reductase, and myeloperoxidase were found to be elevated in serum. Conclusion: We conclude that inflammation resulting from dysregulation of cytokines and altered antioxidant systems may play a critical role in the etiology of schizophrenia.
Gradient echo magnetic resonance imaging correlates with clinical measures and allows visualization of veins within multiple sclerosis lesions
Authors: Luo Jie , Yablonskiy Dmitriy A , Hildebolt Charles F , Lancia Samantha , Cross Anne H 
Published: July 2013

Background: Conventional magnetic resonance imaging (MRI) methods do not quantify the severity of multiple sclerosis (MS) white matter lesions or measure pathology within normal-appearing white matter (NAWM). Objective: Gradient Echo Plural Contrast Imaging (GEPCI), a fast MRI technique producing inherently co-registered images for qualitative and quantitative assessment of MS, was used to 1) correlate with disability; 2) distinguish clinical MS subtypes; 3) determine prevalence of veins co-localized within lesions in WM. Methods: Thirty subjects representing relapsing–remitting MS (RRMS), secondary progressive MS (SPMS) and primary progressive MS (PPMS) subtypes were scanned with clinical and GEPCI protocols. Standard measures of physical disability and cognition were correlated with magnetic resonance metrics. Lesions with central veins were counted for RRMS subjects. Results: Tissue damage load (TDL-GEPCI) and lesion load (LL-GEPCI) derived with GEPCI correlated better with MS functional composite (MSFC) measures and most other neurologic measures than lesion load derived with FLAIR (LL-FLAIR). GEPCI correctly classified clinical subtypes in 70% subjects. A central vein could be identified in 76% of WM lesions in RRMS subjects on GEPCI T2*-SWI images. Conclusion: GEPCI lesion metrics correlated better with neurologic disability than lesion load derived using FLAIR imaging, and showed promise in classifying clinical subtypes of MS. These improvements are likely attributable to the ability of GEPCI to quantify tissue damage.