bluuebunny/crossref_metadata_2025_split huggingface dataset:
The North American Regional Climate Change Assessment Program: Overview of Phase I Results
Authors: Mearns Linda O. , Arritt Ray , Biner Sébastien , Bukovsky Melissa S. , McGinnis Seth , Sain Stephan , Caya Daniel , Correia James , Flory Dave , Gutowski William , Takle Eugene S. , Jones Richard , Leung Ruby , Moufouma-Okia Wilfran , McDaniel Larry , Nunes Ana M. B. , Qian Yun , Roads John , Sloan Lisa , Snyder Mark 
Published: March 2012

The North American Regional Climate Change Assessment Program (NARCCAP) is an international effort designed to investigate the uncertainties in regional-scale projections of future climate and produce highresolution climate change scenarios using multiple regional climate models (RCMs) nested within atmosphere–ocean general circulation models (AOGCMs) forced with the Special Report on Emission Scenarios (SRES) A2 scenario, with a common domain covering the conterminous United States, northern Mexico, and most of Canada. The program also includes an evaluation component (phase I) wherein the participating RCMs, with a grid spacing of 50 km, are nested within 25 years of National Centers for Environmental Prediction–Department of Energy (NCEP–DOE) Reanalysis II.
This paper provides an overview of evaluations of the phase I domain-wide simulations focusing on monthly and seasonal temperature and precipitation, as well as more detailed investigation of four subregions. The overall quality of the simulations is determined, comparing the model performances with each other as well as with other regional model evaluations over North America. The metrics used herein do differentiate among the models but, as found in previous studies, it is not possible to determine a “best” model among them. The ensemble average of the six models does not perform best for all measures, as has been reported in a number of global climate model studies. The subset ensemble of the two models using spectral nudging is more often successful for domain-wide root-mean-square error (RMSE), especially for temperature. This evaluation phase of NARCCAP will inform later program elements concerning differentially weighting the models for use in producing robust regional probabilities of future climate change.
A Conceptual Model for the Identification of Active Red Sea Trough Synoptic Events over the Southeastern Mediterranean
Authors: Krichak Simon O. , Breitgand Joseph S. , Feldstein Steven B. 
Published: March 2012

AbstractA phenomenon characterized by a tongue of low pressure extending northward from the southern Red Sea [Red Sea Trough (RST)] toward the eastern Mediterranean Sea (EM) is analyzed. In general, the RST is associated with hot and dry weather, resulting from east-southeasterly flows in the lower troposphere. In some cases, the RST is found to be accompanied by an upper-tropospheric trough extending from the north over the EM. Such conditions are associated with unstable stratification, favoring the development of mesoscale convective systems. This kind of RST has been defined as an “active” RST (ARST). The ARST phenomenon represents a serious threat to human society in the northeastern Africa–southeastern Mediterranean region, being in some cases associated with devastating floods. In this study, a conceptual model of the ARST phenomenon is discussed, and then an algorithm for the identification of ARST events is presented. The identification algorithm has been applied to a multiyear NCEP–NCAR reanalysis data archive for both RST and ARST events. From the results of a composite analysis of several different atmospheric flow parameters associated with ARST events, the key features associated with ARST events are identified. The results from the analysis of the composite patterns support the suggestion that high amounts of moisture transported from tropical Africa in the form of an atmospheric river to the Red Sea–EM play a key role in determining the intensity of the ARST events.
Projection of Tropical Cyclones on Wavenumber–Frequency-Filtered Equatorial Waves
Authors: Aiyyer Anantha , Mekonnen Ademe , Schreck Carl J. 
Published: March 2012

Abstract
The impact of localized convection associated with tropical cyclones (TCs) on activity ascribed to equatorial waves is estimated. An algorithm is used to remove outgoing longwave radiation (OLR) signal in the vicinity of observed tropical cyclones, and equatorial wave modes are extracted using the standard wavenumber–frequency decomposition method. The results suggest that climatological activity of convection-coupled equatorial waves is overestimated where TC tracks are densest. The greatest impact is found for equatorial Rossby (ER)- and tropical depression (TD)-type waves followed by the Madden–Julian oscillation (MJO). The basins most affected are the eastern and western North Pacific Ocean where, on average, TCs may contribute up to 10%–15% of the climatological wave amplitude variance in these modes. In contrast, Kelvin waves are least impacted by the projection of TCs. The results are likely relevant for studies on the climatology of equatorial waves in observations and global climate model simulations and for those examining individual cases of TC genesis modulated by equatorial wave activity.
An Evaluation of Acoustic Doppler Velocimeters as Sensors to Obtain the Concentration of Suspended Mass in Water
Authors: Russo Clementina R. , Boss Emmanuel S. 
Published: March 2012

Abstract
During the last two decades, acoustic Doppler velocimeters (ADVs) and other acoustic sensors have been used by researchers in the ocean science community to acquire information on current velocity and turbulence. More recently, acoustic backscatter systems (ABS) and acoustic Doppler current profilers (ADCPs) have been investigated for their use in determining sediment concentrations and particle sizes. Acoustic systems tend to be less prone to biofouling than optical turbidity sensors, and the high-frequency velocity measurements allow for a direct estimation of turbulence by the flux of particulate materials.
This work investigates the responses of two commercially available ADVs to changes in mass concentrations of particles. A careful laboratory characterization of each sensor’s response to concentrations of three different size classes of polymer beads is evaluated and compared with the predicted response from acoustic scattering theory. Within uncertainties, experimental results are shown to agree with theory and these results demonstrate that, if the basic acoustic properties of the scatterers are known or if a local, vicarious calibration is performed, then ADV-type sensors can provide a robust estimate of particle concentrations from the measured acoustic return.
Orographic Effects and Evaporative Cooling along a Subtropical Cold Front: The Case of the Spectacular Saharan Dust Outbreak of March 2004
Authors: Gläser Gregor , Knippertz Peter , Heinold Bernd 
Published: March 2012

Abstract
On 2 March 2004 a marked upper-level trough and an associated surface cold front penetrated into the Sahara. High winds along and behind this frontal system led to an extraordinary, large-scale, and long-lived dust outbreak, accompanied by significant precipitation over parts of Algeria, Tunisia, and Libya.
This paper uses sensitivity simulations with the limited-area model developed by the Consortium for Small-Scale Modeling (COSMO) together with analysis data and surface observations to test several hypotheses on the dynamics of this case proposed in previous work. It is demonstrated that air over central Algeria is cooled by evaporation of frontal precipitation, substantially enhancing winds at the leading edge of the cold front. This process is supported by very dry low-level air in the lee of the Atlas Mountains associated with a foehn situation. Flattening the mountain chain in a sensitivity experiment, however, has complex effects on the wind. While reduced evaporative cooling weakens the front, the elimination of the orographic blocking accelerates its penetration into the Sahara. The simulations also indicate high winds associated with a hydraulic jump at the southern slopes of the Tell Atlas.
Feeding the simulated winds into a dust emission parameterization reveals reduced emissions on the order of 20%–30% for suppressed latent heating and even more when effects of the increased precipitation on soil moisture are considered. In the experiment with the Atlas removed, effects of the overall increase in high winds are compensated by an increase in precipitation. The results suggest that a realistic representation of frontal precipitation is an important requisite to accurately model dust emission in such situations.
Polo-like kinase 1 (PLK1) inhibition suppresses cell growth and enhances radiation sensitivity in medulloblastoma cells
Authors: Harris Peter S , Venkataraman Sujatha , Alimova Irina , Birks Diane K , Donson Andrew M , Knipstein Jeffrey , Dubuc Adrian , Taylor Michael D , Handler Michael H , Foreman Nicholas K , Vibhakar Rajeev 
Published: March 2012

Abstract

Background
Medulloblastoma is the most common malignant brain tumor in children and remains a therapeutic challenge due to its significant therapy-related morbidity. Polo-like kinase 1 (PLK1) is highly expressed in many cancers and regulates critical steps in mitotic progression. Recent studies suggest that targeting PLK1 with small molecule inhibitors is a promising approach to tumor therapy.

Methods
We examined the expression of PLK1 mRNA in medulloblastoma tumor samples using microarray analysis. The impact of PLK1 on cell proliferation was evaluated by depleting expression with RNA interference (RNAi) or by inhibiting function with the small molecule inhibitor BI 2536. Colony formation studies were performed to examine the impact of BI 2536 on medulloblastoma cell radiosensitivity. In addition, the impact of depleting PLK1 mRNA on tumor-initiating cells was evaluated using tumor sphere assays.

Results
Analysis of gene expression in two independent cohorts revealed that PLK1 mRNA is overexpressed in some, but not all, medulloblastoma patient samples when compared to normal cerebellum. Inhibition of PLK1 by RNAi significantly decreased medulloblastoma cell proliferation and clonogenic potential and increased cell apoptosis. Similarly, a low nanomolar concentration of BI 2536, a small molecule inhibitor of PLK1, potently inhibited cell growth, strongly suppressed the colony-forming ability, and increased cellular apoptosis of medulloblastoma cells. Furthermore, BI 2536 pretreatment sensitized medulloblastoma cells to ionizing radiation. Inhibition of PLK1 impaired tumor sphere formation of medulloblastoma cells and decreased the expression of SRY (sex determining region Y)-box 2 (SOX2) mRNA in tumor spheres indicating a possible role in targeting tumor inititiating cells.

Conclusions
Our data suggest that targeting PLK1 with small molecule inhibitors, in combination with radiation therapy, is a novel strategy in the treatment of medulloblastoma that warrants further investigation.
Hyperglycemic conditions inhibit C3-mediated immunologic control of Staphylococcus aureus
Authors: Hair Pamela S , Echague Charlene G , Rohn Reuben D , Krishna Neel K , Nyalwidhe Julius O , Cunnion Kenji M 
Published: March 2012

AbstractBackgroundDiabetic patients are at increased risk for bacterial infections; these studies provide new insight into the role of the host defense complement system in controlling bacterial pathogens in hyperglycemic environments.MethodsThe interactions of complement C3 with bacteria in elevated glucose were assayed for complement activation to opsonic forms, phagocytosis and bacterial killing. C3 was analyzed in euglycemic and hyperglycemic conditions by mass spectrometry to measure glycation and structural differences.ResultsElevated glucose inhibitedS. aureusactivation of C3 and deposition of C3b and iC3b on the bacterial surface.S. aureus-generated C5a and serum-mediated phagocytosis by neutrophils were both decreased in elevated glucose conditions. Interestingly, elevated glucose increased the binding of unactivated C3 toS. aureus, which was reversible on return to normal glucose concentrations. In a model of polymicrobial infection,S. aureusin elevated glucose conditions depleted C3 from serum resulting in decreased complement-mediated killing ofE. coli. To investigate the effect of differing glucose concentration on C3 structure and glycation, purified C3 incubated with varying glucose concentrations was analyzed by mass spectrometry. Glycation was limited to the same three lysine residues in both euglycemic and hyperglycemic conditions over one hour, thus glycation could not account for observed changes between glucose conditions. However, surface labeling of C3 with sulfo-NHS-biotin showed significant changes in the surface availability of seven lysine residues in response to increasing glucose concentrations. These results suggest that the tertiary structure of C3 changes in response to hyperglycemic conditions leading to an altered interaction of C3 with bacterial pathogens.ConclusionsThese results demonstrate that hyperglycemic conditions inhibit C3-mediated complement effectors important in the immunological control ofS. aureus. Mass spectrometric analysis reveals that the glycation state of C3 is the same regardless of glucose concentration over a one-hour time period. However, in conditions of elevated glucose C3 appears to undergo structural changes.
MGMT promoter methylation in gliomas-assessment by pyrosequencing and quantitative methylation-specific PCR
Authors: Håvik Annette Bentsen , Brandal Petter , Honne Hilde , Dahlback Hanne-Sofie Spenning , Scheie David , Hektoen Merete , Meling Torstein Ragnar , Helseth Eirik , Heim Sverre , Lothe Ragnhild A , Lind Guro Elisabeth 
Published: March 2012

Abstract

Background
Methylation of the O6-methylguanine-DNA methyltransferase (MGMT) gene promoter is a favorable prognostic factor in glioblastoma patients. However, reported methylation frequencies vary significantly partly due to lack of consensus in the choice of analytical method.

Method
We examined 35 low- and 99 high-grade gliomas using quantitative methylation specific PCR (qMSP) and pyrosequencing. Gene expression level of MGMT was analyzed by RT-PCR.

Results
When examined by qMSP, 26% of low-grade and 37% of high-grade gliomas were found to be methylated, whereas 97% of low-grade and 55% of high-grade gliomas were found methylated by pyrosequencing. The average MGMT gene expression level was significantly lower in the group of patients with a methylated promoter independent of method used for methylation detection. Primary glioblastoma patients with a methylated MGMT promoter (as evaluated by both methylation detection methods) had approximately 5 months longer median survival compared to patients with an unmethylated promoter (log-rank test; pyrosequencing P = .02, qMSP P = .06). One third of the analyzed samples had conflicting methylation results when comparing the data from the qMSP and pyrosequencing. The overall survival analysis shows that these patients have an intermediate prognosis between the groups with concordant MGMT promoter methylation results when comparing the two methods.

Conclusion
In our opinion, MGMT promoter methylation analysis gives sufficient prognostic information to merit its inclusion in the standard management of patients with high-grade gliomas, and in this study pyrosequencing came across as the better analytical method.
Epitaxial deposition of silver ultra-fine nano-clusters on defect-free surfaces of HOPG-derived few-layer graphene in a UHV multi-chamber by in situ STM, ex situ XPS, and ab initio calculations
Authors: Ndlovu Gebhu F , Roos Wiets D , Wang Zhiming M , Asante Joseph KO , Mashapa Matete G , Jafta Charl J , Mwakikunga Bonex W , Hillie Kenneth T 
Published: March 2012

Abstract
The growth of three-dimensional ultra-fine spherical nano-particles of silver on few layers of graphene derived from highly oriented pyrolytic graphite in ultra-high vacuum were characterized using in situ scanning tunneling microscopy (STM) in conjunction with X-ray photoelectron spectroscopy. The energetics of the Ag clusters was determined by DFT simulations. The Ag clusters appeared spherical with size distribution averaging approximately 2 nm in diameter. STM revealed the preferred site for the position of the Ag atom in the C-benzene ring of graphene. Of the three sites, the C-C bridge, the C-hexagon hollow, and the direct top of the C atom, Ag prefers to stay on top of the C atom, contrary to expectation of the hexagon-close packing. Ab initio calculations confirm the lowest potential energy between Ag and the graphene structure to be at the exact site determined from STM imaging.
Isolation of dimorphic chloroplasts from the single-cell C4 species Bienertia sinuspersici
Authors: Lung Shiu-Cheung , Yanagisawa Makoto , Chuong Simon DX 
Published: March 2012

Abstract
Three terrestrial plants are known to perform C4 photosynthesis without the dual-cell system by partitioning two distinct types of chloroplasts in separate cytoplasmic compartments. We report herein a protocol for isolating the dimorphic chloroplasts from Bienertia sinuspersici. Hypo-osmotically lysed protoplasts under our defined conditions released intact compartments containing the central chloroplasts and intact vacuoles with adhering peripheral chloroplasts. Following Percoll step gradient purification both chloroplast preparations demonstrated high homogeneities as evaluated from the relative abundance of respective protein markers. This protocol will open novel research directions toward understanding the mechanism of single-cell C4 photosynthesis.
Rat tail static compression model mimics extracellular matrix metabolic imbalances of matrix metalloproteinases, aggrecanases, and tissue inhibitors of metalloproteinases in intervertebral disc degeneration
Authors: Yurube Takashi , Takada Toru , Suzuki Teppei , Kakutani Kenichiro , Maeno Koichiro , Doita Minoru , Kurosaka Masahiro , Nishida Kotaro 
Published: March 2012

Abstract

Introduction

The longitudinal degradation mechanism of extracellular matrix (ECM) in the interbertebral disc remains unclear. Our objective was to elucidate catabolic and anabolic gene expression profiles and their balances in intervertebral disc degeneration using a static compression model.

Methods

Forty-eight 12-week-old male Sprague-Dawley rat tails were instrumented with an Ilizarov-type device with springs and loaded statically at 1.3 MPa for up to 56 days. Experimental loaded and distal-unloaded control discs were harvested and analyzed by real-time reverse transcription-polymerase chain reaction (PCR) messenger RNA quantification for catabolic genes [matrix metalloproteinase (MMP)-1a, MMP-2, MMP-3, MMP-7, MMP-9, MMP-13, a disintegrin and metalloproteinase with thrombospondin motifs (ADAMTS)-4, and ADAMTS-5], anti-catabolic genes [tissue inhibitor of metalloproteinases (TIMP)-1, TIMP-2, and TIMP-3], ECM genes [aggrecan-1, collagen type 1-α1, and collagen type 2-α1], and pro-inflammatory cytokine genes [tumor necrosis factor (TNF)-α, interleukin (IL)-1α, IL-1β, and IL-6]. Immunohistochemistry for MMP-3, ADAMTS-4, ADAMTS-5, TIMP-1, TIMP-2, and TIMP-3 was performed to assess their protein expression level and distribution. The presence of MMP- and aggrecanase-cleaved aggrecan neoepitopes was similarly investigated to evaluate aggrecanolytic activity.

Results

Quantitative PCR demonstrated up-regulation of all MMPs and ADAMTS-4 but not ADAMTS-5. TIMP-1 and TIMP-2 were almost unchanged while TIMP-3 was down-regulated. Down-regulation of aggrecan-1 and collagen type 2-α1 and up-regulation of collagen type 1-α1 were observed. Despite TNF-α elevation, ILs developed little to no up-regulation. Immunohistochemistry showed, in the nucleus pulposus, the percentage of immunopositive cells of MMP-cleaved aggrecan neoepitope increased from 7 through 56 days with increased MMP-3 and decreased TIMP-1 and TIMP-2 immunopositivity. The percentage of immunopositive cells of aggrecanase-cleaved aggrecan neoepitope increased at 7 and 28 days only with decreased TIMP-3 immunopositivity. In the annulus fibrosus, MMP-cleaved aggrecan neoepitope presented much the same expression pattern. Aggrecanase-cleaved aggrecan neoepitope increased at 7 and 28 days only with increased ADAMTS-4 and ADAMTS-5 immunopositivity.

Conclusions

This rat tail sustained static compression model mimics ECM metabolic imbalances of MMPs, aggrecanases, and TIMPs in human degenerative discs. A dominant imbalance of MMP-3/TIMP-1 and TIMP-2 relative to ADAMTS-4 and ADAMTS-5/TIMP-3 signifies an advanced stage of intervertebral disc degeneration.
Effects of a pre-visit educational website on information recall and needs fulfilment in breast cancer genetic counselling, a randomized controlled trial
Authors: Albada Akke , van Dulmen Sandra , Bensing Jozien M , Ausems Margreet GEM 
Published: March 2012

Abstract
Introduction
Pre-visit education which helps counselees to prepare for their first visit for breast cancer genetic counseling might enhance information recall and needs fulfilment. This study assessed the effects of a pre-visit website with tailored information and question prompt sheet (QPS), named E-info geneca.

Methods
A total of 197 counselees were randomized to receive usual care (UC) or UC plus E-info geneca. All counselees completed a pre- and post-visit questionnaire and visits were videotaped. We studied effects on counselees' information recall, knowledge about breast cancer and heredity, fulfillment of needs, risk perception alignment, anxiety and perceived personal control, using multilevel regression analyses.

Results
Intent-to-treat analysis showed that counselees in the intervention group (n = 103) had higher levels of recall of information from the consultation (β = .32; confidence interval (CI): .04 to .60; P = .02; d = .17) and post-visit knowledge of breast cancer and heredity (β = .30; CI: .03 to .57; P = .03) than counselees in the UC group (n = 94). Also, intervention group counselees reported better fulfilment of information needs (β = .31; CI: .03 to .60; P = .03). The effects of the intervention were strongest for those counselees who did not receive an indication for DNA testing. Their recall scores showed a larger increase (β = .95; CI: .32 to 1.59; P = .003; d = .30) and their anxiety levels dropped more in the intervention compared to the UC group (β = -.60; CI: -1.12 to -.09; P = .02). No intervention effects were found after the first visit on risk perception alignment or perceived personal control.

Conclusions
This study shows that pre-counseling education, using tailored information technology, leads to more effective first visits for breast cancer genetic counseling, in particular for counselees who received no indication for DNA testing and, therefore, had no indication for a second visit. Future study should focus on the effects of a pre-visit website on the outcomes after a complete series of visits.

Trial registration
Dutch Trial Register ISRCTN82643064.