bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spectrally Consistent Scattering, Absorption, and Polarization Properties of Atmospheric Ice Crystals at Wavelengths from 0.2 to 100 μm
Authors: Yang Ping , Bi Lei , Baum Bryan A. , Liou Kuo-Nan , Kattawar George W. , Mishchenko Michael I. , Cole Benjamin 
Published: September 2012

Abstract
A data library is developed containing the scattering, absorption, and polarization properties of ice particles in the spectral range from 0.2 to 100 μm. The properties are computed based on a combination of the Amsterdam discrete dipole approximation (ADDA), the T-matrix method, and the improved geometric optics method (IGOM). The electromagnetic edge effect is incorporated into the extinction and absorption efficiencies computed from the IGOM. A full set of single-scattering properties is provided by considering three-dimensional random orientations for 11 ice crystal habits: droxtals, prolate spheroids, oblate spheroids, solid and hollow columns, compact aggregates composed of eight solid columns, hexagonal plates, small spatial aggregates composed of 5 plates, large spatial aggregates composed of 10 plates, and solid and hollow bullet rosettes. The maximum dimension of each habit ranges from 2 to 10 000 μm in 189 discrete sizes. For each ice crystal habit, three surface roughness conditions (i.e., smooth, moderately roughened, and severely roughened) are considered to account for the surface texture of large particles in the IGOM applicable domain. The data library contains the extinction efficiency, single-scattering albedo, asymmetry parameter, six independent nonzero elements of the phase matrix (P11, P12, P22, P33, P43, and P44), particle projected area, and particle volume to provide the basic single-scattering properties for remote sensing applications and radiative transfer simulations involving ice clouds. Furthermore, a comparison of satellite observations and theoretical simulations for the polarization characteristics of ice clouds demonstrates that ice cloud optical models assuming severely roughened ice crystals significantly outperform their counterparts assuming smooth ice crystals.
Incorporating the Effects of 3D Radiative Transfer in the Presence of Clouds into Two-Stream Multilayer Radiation Schemes
Authors: Hogan Robin J. , Shonk Jonathan K. P. 
Published: September 2012

AbstractThis paper presents a new method for representing the important effects of horizontal radiation transport through cloud sides in two-stream radiation schemes. Ordinarily, the radiative transfer equations are discretized separately for the clear and cloudy regions within each model level, but here terms are introduced that represent the exchange of radiation laterally between regions and the resulting coupled equations are solved for each layer. This approach may be taken with both the direct incoming shortwave radiation, which is governed by Beer’s law, and the diffuse shortwave and longwave radiation, governed by the two-stream equations. The rate of lateral exchange is determined by the area of cloud “edge.” The validity of the method is demonstrated by comparing with rigorous 3D radiative transfer calculations in the literature for two cloud types in which the 3D effect is strong, specifically cumulus and aircraft contrails. The 3D effect on shortwave cloud radiative forcing varies between around −25% and around +100%, depending on solar zenith angle. Even with an otherwise very simplistic representation of the cloud, the new scheme exhibits good agreement with the rigorous calculations in the shortwave, opening the way for efficient yet accurate representation of this important effect in climate models.
The Regional Atmospheric Water Budget over Southwestern Germany under Different Synoptic Conditions
Authors: Sasse Romi , Schädler Gerd , Kottmeier Christoph 
Published: September 2012

Abstract
This study addresses the question of how complex topography in a low-mountain region affects the partitioning and the variability of the atmospheric water budget components (WBCs) as a function of synoptic-scale flow conditions. The WBCs are calculated for regions of different size and location in southwestern Germany and the summer months from 2005 to 2009 using the high-resolution regional climate model COSMO-CLM driven by Global Model (GME) analyses. Comparisons with observations from the Convective and Orographically-induced Precipitation Study (COPS) performed in summer 2007 show that the model is capable of simulating the atmospheric water budget reasonably (absolute mean error between 0.1 and 0.7 kg m−2 day−1). To investigate the influence of synoptic weather conditions, the daily WBCs are classified based on the inflow direction of the air masses and the cyclonality at 500 hPa. Using statistical tests, four groups out of the six synoptic conditions have significantly different distributions of the WBCs. This can be explained by differences in the air mass features and the influence of high/low pressure systems. The sensitivity of the modeled WBCs to topography and land cover is investigated by comparing a region in the flat upper Rhine Valley with one in the mountainous Black Forest/Swabian Jura. Compared to the Rhine Valley, increases of evapotranspiration (+5% to +16%), precipitation (+26% to +57%), and moisture convergence (+24% to +93%) are noticeable in the low-mountain region. Local modifications of the synoptic-scale flow, thermally induced winds, and land use cause this intensification of the atmospheric water budget, especially on the windward slopes of the mountains.
Dissipation of Turbulent Kinetic Energy Inferred from Seagliders: An Application to the Eastern Nordic Seas Overflows
Authors: Beaird Nicholas , Fer Ilker , Rhines Peter , Eriksen Charles 
Published: September 2012

Abstract
Turbulent mixing is an important process controlling the descent rate, water mass modification, and volume transport augmentation due to entrainment in the dense overflows across the Greenland–Scotland Ridge. These overflows, along with entrained Atlantic waters, form a major portion of the North Atlantic Deep Water, which pervades the abyssal ocean. Three years of Seaglider observations of the overflows across the eastern Greenland–Scotland Ridge are leveraged to map the distribution of dissipation of turbulent kinetic energy on the Iceland–Faroe Ridge. A method has been applied using the finescale vertical velocity and density measurements from the glider to infer dissipation. The method, termed the large-eddy method (LEM), is compared with a microstructure survey of the Faroe Bank Channel (FBC). The LEM reproduces the patterns of dissipation observed in the microstructure survey, which vary over several orders of magnitude. Agreement between the inferred LEM and more direct microstructure measurements is within a factor of 2. Application to the 9432 dives that encountered overflow waters on the Iceland–Faroe Ridge reveals three regions of enhanced dissipation: one downstream of the primary FBC sill, another downstream of the secondary FBC sill, and a final region in a narrow jet of overflow along the Iceland shelf break.
Massive Flap Donor Sites and the Role of Negative Pressure Wound Therapy
Authors: Schmedes Gregg W. , Banks Caroline A. , Malin Barry T. , Srinivas Pamela B. , Skoner Judith M. 
Published: September 2012

ObjectiveReport our experience with negative pressure wound therapy (NPWT) applied to massive scapular and latissimus free flap donor sites, in the setting of microvascular reconstruction for extensive head and neck defects.Study DesignRetrospective case series with chart review.SettingTertiary academic referral center.Subjects and MethodsRetrospective review was conducted of all patients who underwent scapular or latissimus free tissue transfer by the senior author for head and neck reconstruction, over a 5‐year period (2006‐2011). In addition to NPWT details, comprehensive patient data were abstracted and compiled, including demographics, operative details, hospital stay, postoperative follow‐up, and donor site complications.ResultsNinety‐four patients underwent reconstruction of extensive postablative head and neck defects using either a scapular or latissimus free flap. Mean harvested flap skin paddle size was 140 cm2. All donor sites were closed primarily. Fifty‐two patients (55%) had NPWT applied over closed donor site incisions postoperatively. The other 42 patients (45%) received only conventional incision care. Major donor site complications occurred in 12% (n = 5) of the patients who did not undergo NPWT, as compared with a 6% (n = 3) complication rate among patients in the NPWT‐treated group.ConclusionThis is the first study to examine NPWT in the postoperative treatment of closed high‐tension wounds following scapular or latissimus dorsi harvest for reconstruction of extensive head and neck defects. Our results suggest that NPWT is a safe technique in the management of massive scapular and latissimus free flap harvest sites that may decrease associated major donor wound complications.
Simultaneous SNP identification and assessment of allele-specific bias from ChIP-seq data
Authors: Ni Yunyun , Weber Hall Amelia , Battenhouse Anna , Iyer Vishwanath R 
Published: September 2012

Abstract

Background
Single nucleotide polymorphisms (SNPs) have been associated with many aspects of human development and disease, and many non-coding SNPs associated with disease risk are presumed to affect gene regulation. We have previously shown that SNPs within transcription factor binding sites can affect transcription factor binding in an allele-specific and heritable manner. However, such analysis has relied on prior whole-genome genotypes provided by large external projects such as HapMap and the 1000 Genomes Project. This requirement limits the study of allele-specific effects of SNPs in primary patient samples from diseases of interest, where complete genotypes are not readily available.

Results
In this study, we show that we are able to identify SNPs de novo and accurately from ChIP-seq data generated in the ENCODE Project. Our de novo identified SNPs from ChIP-seq data are highly concordant with published genotypes. Independent experimental verification of more than 100 sites estimates our false discovery rate at less than 5%. Analysis of transcription factor binding at de novo identified SNPs revealed widespread heritable allele-specific binding, confirming previous observations. SNPs identified from ChIP-seq datasets were significantly enriched for disease-associated variants, and we identified dozens of allele-specific binding events in non-coding regions that could distinguish between disease and normal haplotypes.

Conclusions
Our approach combines SNP discovery, genotyping and allele-specific analysis, but is selectively focused on functional regulatory elements occupied by transcription factors or epigenetic marks, and will therefore be valuable for identifying the functional regulatory consequences of non-coding SNPs in primary disease samples.
An expanded myeloid derived suppressor cell population does not play a role in gammaherpesvirus-exacerbated breast cancer metastases
Authors: Nelson Daniel A , Chauhan Vinita S , Tolbert Melanie D , Bost Kenneth L 
Published: September 2012

AbstractBackgroundMice latently infected with murine gammaherpesvirus 68 (HV-68) and transplanted with 4 T1 breast cancer cells developed exacerbated metastatic lesions when compared to controls. The mechanisms responsible for this viral-exacerbated disease were not clear. The ability of HV-68 infection to induce S100A8 and S100A9 production and to expand a population of CD11b+Gr-1+ cells suggested that increased numbers, or activity, of viral-expanded myeloid derived suppressor cells (MDSCs) might contribute to HV-68-associated metastatic breast cancer in this model. We questioned whether mock or HV-68 infected mice with significant breast cancer might have differences in the number and/or activity of MDSCs.MethodsMyeloid-derived macrophages and dendritic cells were isolated from normal mice and cultured in vitro with HV-68 to assess S100A8 and S100A9 mRNA and protein expression. In vivo studies were performed using groups of mice that were mock treated or infected with HV-68. After viral latency was established, 4 T1 breast cancer cells were transplanted in mice. When primary breast tumors were present mice were euthanized and cells isolated for phenotyping of myeloid cell populations using FACS, and for ex vivo analysis of suppressor activity. Serum from these animals was also collected to quantify S100A8 and S100A9 levels.ResultsIn vitro studies demonstrated that direct exposure of myeloid cells to HV-68 did not induce increased expression of S100A8 or S100A9 mRNAs or secreted protein. HV-68 infected mice with metastatic breast cancer disease had no increases in S100A8/A9 levels and no significant increases in the numbers or activation of CD11b+Gr-1+MDSCs when compared to mock treated mice with breast cancer.ConclusionsTogether these studies are consistent with the notion that expanded myeloid derived suppressor cells do not play a role in gammaherpesvirus-exacerbated breast cancer metastases. The mechanisms responsible for HV-68 induced exacerbation of metastatic breast cancer remain unclear.
Population genetic structure of the malaria vector Anopheles funestus, in a recently re-colonized area of the Senegal River basin and human-induced environmental changes
Authors: Samb Badara , Dia Ibrahima , Konate Lassana , Ayala Diego , Fontenille Didier , Cohuet Anna 
Published: September 2012

Abstract

Background

Anopheles funestus is one of the major malaria vectors in tropical Africa. Because of several cycles of drought events that occurred during the 1970s, this species had disappeared from many parts of sahelian Africa, including the Senegal River basin. However, this zone has been re-colonized during the last decade by An. funestus, following the implementation of two dams on the Senegal River. Previous studies in that area revealed heterogeneity at the biological and chromosomal level among these recent populations.

Methods
Here, we studied the genetic structure of the newly established mosquito populations using eleven microsatellite markers in four villages of the Senegal River basin and compared it to another An. funestus population located in the sudanian domain.

Results
Our results presume Hardy Weinberg equilibrium in each An. funestus population, suggesting a situation of panmixia. Moreover, no signal from bottleneck or population expansion was detected across populations. The tests of genetic differentiation between sites revealed a slight but significant division into three distinct genetic entities. Genetic distance between populations from the Senegal River basin and sudanian domain was correlated to geographical distance. In contrast, sub-division into the Senegal River basin was not correlated to geographic distance, rather to local adaptation.

Conclusions
The high genetic diversity among populations from Senegal River basin coupled with no evidence of bottleneck and with a gene flow with southern population suggests that the re-colonization was likely carried out by a massive and repeated stepping-stone dispersion starting from the neighboring areas where An. funestus endured.
Growth Hormone Secretagogues Preserve the Electrophysiological Properties of Mouse Cardiomyocytes Isolated from in Vitro Ischemia/Reperfusion Heart
Authors: Ma Yi , Zhang Lin , Launikonis Bradley S. , Chen Chen 
Published: September 2012

Abstract
Ischemic heart diseases often induce cardiac arrhythmia with irregular cardiac action potential (AP). This study aims to demonstrate that GH secretagogues (GHS) ghrelin and its synthetic analog hexarelin can preserve the electrophysiological properties of cardiomyocytes experiencing ischemia/reperfusion (I/R). Isolated hearts from adult male mice underwent 20 min global ischemia followed by 30 min reperfusion using a Langendorff apparatus. Ghrelin (10 nm) or hexarelin (1 nm) was administered in the perfusion solution either 10 min before or after ischemia, termed pre- or posttreatments. Cardiomyocytes isolated from these hearts were used for whole-cell patch clamping to measure AP, voltage-gated L-type calcium current (ICaL), transient outward potassium current (Ito), and sodium current (INa). AP amplitude and duration were significantly decreased by I/R, but GHS treatments maintained their normality. GHS treatments prevented the decrease in ICaL and INa after I/R, thereby maintaining AP amplitude. Although the significant increase in Ito after I/R partially explained the shortened AP duration, the normalization of it by GHS treatments might contribute to the preservation of AP duration. Phosphorylated p38 and c-Jun NH2-terminal kinase and the downstream active caspase-9 in the cellular apoptosis pathway were significantly increased after I/R but not when GHS treatments were included, whereas phosphorylation of ERK1/2 associated with cell survival showed increase after I/R and a further increase after GHS treatments by binding to its receptor GHS receptor type 1a. These results suggest GHS can not only preserve the electrophysiological properties of cardiomyocytes after I/R but also inhibit cardiomyocyte apoptosis and promote cell survival by modification of MAPK pathways through activating GHS receptor type 1a.
Thyroid Hormone Reduces Cholesterol via a Non-LDL Receptor-Mediated Pathway
Authors: Goldberg Ira J. , Huang Li-Shin , Huggins Lesley A. , Yu Shuiqing , Nagareddy Prabhakara R. , Scanlan Thomas S. , Ehrenkranz Joel R. 
Published: September 2012

AbstractAlthough studies in vitro and in hypothyroid animals show that thyroid hormone can, under some circumstances, modulate the actions of low-density lipoprotein (LDL) receptors, the mechanisms responsible for thyroid hormone's lipid-lowering effects are not completely understood. We tested whether LDL receptor (LDLR) expression was required for cholesterol reduction by treating control and LDLR-knockout mice with two forms of thyroid hormone T3 and 3,5-diiodo-l-thyronine. High doses of both 3,5-diiodo-l-thyronine and T3 dramatically reduced circulating total and very low-density lipoprotein/LDL cholesterol (∼70%) and were associated with reduced plasma T4 level. The cholesterol reduction was especially evident in the LDLR-knockout mice. Circulating levels of both apolipoprotein B (apo)B48 and apoB100 were decreased. Surprisingly, this reduction was not associated with increased protein or mRNA expression of the hepatic lipoprotein receptors LDLR-related protein 1 or scavenger receptor-B1. Liver production of apoB was markedly reduced, whereas triglyceride production was increased. Thus, thyroid hormones reduce apoB lipoproteins via a non-LDLR pathway that leads to decreased liver apoB production. This suggests that drugs that operate in a similar manner could be a new therapy for patients with genetic defects in the LDLR.
Market Crashes, Correlated Illiquidity, and Portfolio Choice
Authors: Liu Hong , Loewenstein Mark 
Published: September 2012

The recent financial crisis highlights the importance of market crashes and the subsequent market illiquidity for optimal portfolio selection. We propose a tractable and flexible portfolio choice model where market crashes can trigger switching into another regime with a different investment opportunity set. We characterize the optimal trading strategy in terms of coupled integro-differential equations and develop a quite general iterative numerical solution procedure. We conduct an extensive analysis of the optimal trading strategy. In contrast to standard portfolio choice models, changes in the investment opportunity set in one regime can affect the optimal trading strategy in another regime even in the absence of transaction costs. In addition, an increase in the expected jump size can increase stock investment even when the expected return remains the same and the volatility increases. Moreover, we show that misestimating the correlation between market crashes and market illiquidity can be costly to investors. This paper was accepted by Wei Xiong, finance.
Mineral Preferred Orientation and Microstructure in the Posidonia Shale in Relation to Different Degrees of Thermal Maturity
Authors: Kanitpanyacharoen Waruntorn , Kets Frans B. , Wenk Hans-Rudolf , Wirth Richard 
Published: September 2012

AbstractThe thermal maturity of samples of the Posidonia Shale collected from the Hils Syncline, northern Germany, varies significantly as a function of location indicating variations in local history. Synchrotron X-ray diffraction was used to document the composition and the preferred orientation of four samples of the Posidonia Shale with different degrees of maturity (0.68–1.45%, Ro) to determine possible effects on diagenesis and preferred orientation. Overall, the degree of preferred orientation of all clay minerals (illite-smectite, illite-mica, and kaolinite) and in all samples is similar, with (001) pole figure maxima ranging from 3.7 to 6.3 multiples of a random distribution (m.r.d.). Calcite displays weak preferred orientation, with c axes perpendicular to the bedding plane (1.1–1.3 m.r.d.). Other constituent phases such as quartz, feldspars, and pyrite have a random orientation distribution. The difference in thermal history, which causes significant changes in the maturity of organic matter, influenced the preferred orientation of clay minerals only marginally as most of the alignment seems to have evolved early in their history. Synchrotron X-ray microtomography was used to characterize the three-dimensional microstructure of a high-maturity sample. Low-density features, including porosity, fractures, and kerogen, were observed to be elongated and aligned roughly parallel to the bedding plane. The volume of low-density features was estimated to be ~7 vol.%, consistent with previous petrophysical measurements of porosity of 8–10 vol.%. Transmission electron microscopy analysis of samples with different degrees of maturity (0.74%Ro and 1.45%Ro) was used to document microstructures at the nanoscale as well as the presence of kerogen. In the high-maturity sample, pores were less abundant while minerals were more deformed as shown by fractured calcite and by kinked and folded illite. Some of the porosity was aligned with clay platelets.
ITRS lithography roadmap: status and challenges
Authors: Neisser Mark , Wurm Stefan 
Published: September 2012

Abstract
Recent ITRS lithography roadmaps show a big technology decision approaching the semiconductor industry about how to do leading edge lithography. The need is rapidly approaching for the industry to select an option for the 22-nm half pitch, but no decision has been made yet. The main options for the 22-nm half pitch are extreme ultraviolet (EUV), ArF immersion lithography with multiple patterning, and maskless lithography. For the 16-nm half pitch, directed self-assembly (DSA) is also an option. The EUV has the most industry investment and is the closest to current lithography in the way it works but still faces challenges in tool productivity and defect-free masks. The nanoimprint needs to overcome the defect, contamination, and overlay challenges before it can be applied to the semiconductor production. Maskless lithography may be used first for prototyping and small volume products where mask costs per chip produced would be very high. Double patterning could be extended to multiple pattering, but would give tremendous process complexity and exponentially rising mask costs due to the many exposures needed per level. The DSA, which only recently has emerged from the research stage, has the potential for very high resolution but represents a huge change in how critical dimensions are formed and controlled.