bluuebunny/crossref_metadata_2025_split huggingface dataset:
New Zealand Vegetarians: At Odds with Their Nation
Authors: White Mandala , Potts Annie 
Published: November 2008

AbstractThis qualitative study, conducted between August and December 2006, explored the opinions and experiences of New Zealanders who challenge orthodox attitudes to the use and consumption of nonhuman animals. To date, New Zealand (NZ) has under-investigated the perspectives of those who oppose animal farming, the eating of nonhuman animals, and the exploitation of nonhuman animals. Agriculture substantially influences the economy and cultural heritage of the nation. Given that national identity in New Zealand strongly associates with farming and meat production, this paper investigates how vegetarians living in this country experience and challenge prevalent imagery and ideas about New Zealand. In particular, the paper examines the ways in which “kiwi” vegetarians are disputing the dominant image of New Zealand as “clean and green” and a land of "animal lovers" and how they are experiencing mainstream (meat-loving) kiwi culture in their everyday lives. The paper also examines some of the more positive aspects for vegetarians of living in New Zealand.
Derivation of Nighttime Urban Air Temperatures Using a Satellite Thermal Image
Authors: Fung W. Y. , Lam K. S. , Nichol Janet , Wong Man Sing 
Published: November 2008

Abstract
The aim of this study is to characterize the urban heat island (UHI) intensity in Hong Kong. The first objective is to explore the UHI intensity in Hong Kong by using the mobile transverse and remote sensing techniques. The second objective is to produce a satellite-derived air temperature image by integrating satellite remote sensing with a mobile survey, the methodology involved in making simultaneous ground measurements when the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) satellite made an overpass. The average UHI intensity of Hong Kong was about 2°–3.5°C, although a very high value of 12°C UHI was observed on a calm winter night by ASTER. The satellite-derived surface temperature was compared with the in situ measurements. The bias was found to be only about 1.1°C. A good correlation was also found between the in situ surface and air temperature pair of readings at nighttime on 31 January 2007. The linear regression lines of temperatures in urban and suburban areas were then used to convert the satellite-derived surface temperatures into air temperatures. The satellite-derived air temperatures showed a good correlation with temperatures observed by 12 fixed stations. It is possible to derive the nighttime air temperature from the satellite surface temperature on calm and clear winter nights.
Gravity Wave Instability Dynamics at High Reynolds Numbers. Part I: Wave Field Evolution at Large Amplitudes and High Frequencies
Authors: Fritts David C. , Wang Ling , Werne Joe , Lund Tom , Wan Kam 
Published: November 2008

Abstract
Direct numerical simulations are employed to examine gravity wave instability dynamics at a high intrinsic frequency, wave amplitudes both above and below nominal convective instability, and a Reynolds number sufficiently high to allow a fully developed turbulence spectrum. Assumptions include no mean shear, uniform stratification, and a monochromatic gravity wave to isolate fluxes due to gravity wave and turbulence structures from those arising from environmental shears or varying wave amplitudes. The results reveal strong wave breaking for both wave amplitudes, severe primary wave amplitude reductions within ∼1 or 2 wave periods, an extended turbulence inertial range, significant excitation of additional wave motions exhibiting upward and downward propagation, and a net positive vertical potential temperature flux due to the primary wave motion, with secondary waves and turbulence contributing variable and negative potential temperature fluxes, respectively. Turbulence maximizes within ∼1 buoyancy period of the onset of breaking, arises almost entirely owing to shear production, and decays rapidly following primary wave amplitude decay. Secondary waves are excited by wave–wave interactions and the turbulence dynamics accompanying wave breaking; they typically have lower frequencies and smaller momentum fluxes than the primary wave following breaking.
Gravity Wave Instability Dynamics at High Reynolds Numbers. Part II: Turbulence Evolution, Structure, and Anisotropy
Authors: Fritts David C. , Wang Ling , Werne Joe , Lund Tom , Wan Kam 
Published: November 2008

Abstract
This paper examines the character, intermittency, and anisotropy of turbulence accompanying wave instability, breaking, and turbulence evolution and decay for gravity waves (GW) having a high intrinsic frequency, amplitudes above and below nominal convective instability, and a high Reynolds number. Wave breaking at both amplitudes leads to an extended inertial range of turbulence, with turbulence energies that maximize within ∼1 wave period of the onset of breaking. Turbulence sources include both shear and buoyancy, with shear being the major contributor. Turbulence displays considerable intermittency both within and across the phase of the breaking gravity wave and exhibits clear anisotropy throughout the evolution. Turbulence anisotropy is found at all spatial scales and all times but is most pronounced in the most statically stable phase of the GW and at late times as the turbulent flow restratifies.
Large-Eddy Simulation of Moist Convection during a Cold Air Outbreak over the Gulf Stream
Authors: Skyllingstad Eric D. , Edson James B. 
Published: November 2008

Abstract
Cold air outflow over the Gulf Stream is modeled using a cloud-resolving large-eddy simulation model with three classes of precipitation. Simulations are conducted in a quasi-Lagrangian framework using an idealized sounding and uniform geostrophic winds based on observations taken on 20 February 2007 as part of the World Climate Research Program Climate Variability and Predictability (CLIVAR) Mode Water Dynamics Experiment (CLIMODE) project. Two cases are considered, one with an increasing sea surface temperature (SST) representing the crossing of the Gulf Stream front, and a second case with constant SST.
Cloud systems develop in the model with strong convective plumes that spread into regions of stratus clouds at the top of the boundary layer. Simulated boundary layer growth is forced by a combination of evaporative cooling at the cloud top, upward radiative flux, and mechanical entrainment of the overlying warmer and drier air. Constant growth of the boundary layer acts to maintain a near-constant water vapor level in the boundary layer, promoting high latent and sensible heat fluxes. Frictional surface drag is distributed throughout the boundary layer by convection, causing increased shear at the cloud top, qualitatively agreeing with observed sounding profiles. Overall, the frontal case develops stronger precipitation and turbulence in comparison with the constant SST case. A near-uniform stratocumulus layer and stronger radiative cooling are produced in the constant SST case, whereas the frontal case generates open cumuliform clouds with reduced cloud coverage. Cloud evolution in the frontal case is similar to the transition from stratocumulus to shallow cumulus observed in the subtropics, as cumuliform clouds enhance cloud-top entrainment and evaporation of stratus clouds.
A Method for Identifying the Sensitive Areas in Targeted Observations for Tropical Cyclone Prediction: Conditional Nonlinear Optimal Perturbation
Authors: Mu Mu , Zhou Feifan , Wang Hongli 
Published: November 2008

AbstractConditional nonlinear optimal perturbation (CNOP), which is a natural extension of the linear singular vector into the nonlinear regime, is proposed in this study for the determination of sensitive areas in adaptive observations for tropical cyclone prediction. Three tropical cyclone cases, Mindulle (2004), Meari (2004), and Matsa (2005), are investigated. Using the metrics of kinetic and dry energies, CNOPs and the first singular vectors (FSVs) are obtained over a 24-h optimization interval. Their spatial structures, their energies, and their nonlinear evolutions as well as the induced humidity changes are compared. A series of sensitivity experiments are designed to find out what benefit can be obtained by reductions of CNOP-type errors versus FSV-type errors. It is found that the structures of CNOPs may differ much from those of FSVs depending on the constraint, metric, and the basic state. The CNOP-type errors have larger impact on the forecasts in the verification area as well as the tropical cyclones than the FSV-types errors. The results of sensitivity experiments indicate that reductions of CNOP-type errors in the initial states provide more benefits than reductions of FSV-type errors. These results suggest that it is worthwhile to use CNOP as a method to identify the sensitive areas in adaptive observation for tropical cyclone prediction.
Variability of Updraft and Downdraft Characteristics in a Large Parameter Space Study of Convective Storms
Authors: Kirkpatrick Cody , McCaul Eugene W. , Cohen Charles 
Published: November 2008

AbstractOver 200 convective storm simulations are analyzed to examine the variability in storm vertical velocity and updraft area characteristics as a function of basic environmental parameters. While it is known that bulk properties of the troposphere such as convective available potential energy (CAPE) and deep-layer wind shear exert significant influence over updraft intensity and area, additional parameters such as the temperature at the cloud base, the height of the level of free convection (LFC), and the vertical distribution of buoyancy also have an effect. For example, at low CAPE, updraft strength is strongly related to the vertical distribution of buoyancy, and also to the bulk environmental wind shear. More generally, updraft area and its temporal variability both tend to increase in environments where the LFC is raised. Additionally, in environments with persistent storms, downdraft strength is sensitive to the bulk shear, environmental temperature, and LFC height. Using multiple linear regression methods, the best combinations of environmental parameters explain up to 81% of the interexperiment variance in second-hour mean peak updraft velocity, 74% for midlevel updraft area, and 64% for downdraft velocity. Downdraft variability is explained even less well (49%) when only persistent storms are considered. These idealized simulation results show that it is easier to predict storm updraft characteristics than those of the downdraft.
Estimating Maximum Surface Winds from Hurricane Reconnaissance Measurements
Authors: Powell Mark D. , Uhlhorn Eric W. , Kepert Jeffrey D. 
Published: November 2008

Abstract
Radial profiles of surface winds measured by the Stepped Frequency Microwave Radiometer (SFMR) are compared to radial profiles of flight-level winds to determine the slant ratio of the maximum surface wind speed to the maximum flight-level wind speed, for flight altitude ranges of 2–4 km. The radius of maximum surface wind is found on average to be 0.875 of the radius of the maximum flight-level wind, and very few cases have a surface wind maximum at greater radius than the flight-level maximum. The mean slant reduction factor is 0.84 with a standard deviation of 0.09 and varies with storm-relative azimuth from a maximum of 0.89 on the left side of the storm to a minimum of 0.79 on the right side. Larger slant reduction factors are found in small storms with large values of inertial stability and small values of relative angular momentum at the flight-level radius of maximum wind, which is consistent with Kepert’s recent boundary layer theories. The global positioning system (GPS) dropwindsonde-based reduction factors that are assessed using this new dataset have a high bias and substantially larger RMS errors than the new technique. A new regression model for the slant reduction factor based upon SFMR data is presented, and used to make retrospective estimates of maximum surface wind speeds for significant Atlantic basin storms, including Hurricanes Allen (1980), Gilbert (1988), Hugo (1989), Andrew (1992), and Mitch (1998).
Verification of the NOAA Smoke Forecasting System: Model Sensitivity to the Injection Height
Authors: Stein Ariel F. , Rolph Glenn D. , Draxler Roland R. , Stunder Barbara , Ruminski Mark 
Published: November 2008

Abstract
A detailed evaluation of NOAA’s Smoke Forecasting System (SFS) is a fundamental part of its development and further refinement. In this work, particulate matter with a diameter less than or equal to 2.5-μm (PM2.5) concentration levels, simulated by the SFS, have been evaluated against satellite and surface measurements. Four multiday forest fire case studies, one covering the continental United States, two in California, and one near the Georgia–Florida border, have been analyzed. The column-integrated PM2.5 concentrations for these cases compared to the satellite measurements showed a similar or better statistical performance than the mean performance of the SFS for the period covering 1 September 2006–1 November 2007. However, near the surface, the model shows a tendency to overpredict the measured PM2.5 concentrations in the western United States and underpredict concentrations for the Georgia–Florida case. Furthermore, a sensitivity analysis of the model response to changes in the smoke release height shows that the simulated surface and column-integrated PM2.5 concentrations are very sensitive to variations in this parameter. Indeed, the model capability to represent the measured values is highly dependent on the accuracy of the determination of the actual injection height and in particular to whether the smoke injection actually occurred below or above the planetary boundary layer.
Uniparental disomies, homozygous deletions, amplifications, and target genes in mantle cell lymphoma revealed by integrative high-resolution whole-genome profiling
Authors: Beà Sílvia , Salaverria Itziar , Armengol Lluís , Pinyol Magda , Fernández Verónica , Hartmann Elena M. , Jares Pedro , Amador Virginia , Hernández Luís , Navarro Alba , Ott German , Rosenwald Andreas , Estivill Xavier , Campo Elias 
Published: November 2008

AbstractMantle cell lymphoma (MCL) is genetically characterized by the t(11;14)(q13;q32) translocation and a high number of secondary chromosomal alterations. However, only a limited number of target genes have been identified. We have studied 10 MCL cell lines and 28 primary tumors with a combination of a high-density single-nucleotide polymorphism array and gene expression profiling. We detected highly altered genomes in the majority of the samples with a high number of partial uniparental disomies (UPDs). The UPD at 17p was one of the most common, and it was associated with TP53 gene inactivation. Homozygous deletions targeted 4 known tumor suppressor genes (CDKN2C, BCL2L11, CDKN2A, and RB1) and 6 new genes (FAF1, MAP2, SP100, MOBKL2B, ZNF280A, and PRAME). Gene amplification coupled with overexpression was identified in 35 different regions. The most recurrent amplified regions were 11q13.3-q13.5, 13q31.3, and 18q21.33, which targeted CCND1, C13orf25, and BCL2, respectively. Interestingly, the breakpoints flanking all the genomic alterations, including UPDs, were significantly associated with genomic regions enriched in copy number variants and segmental duplications, suggesting that the recombination at these regions may play a role in the genomic instability of MCL. This integrative genomic analysis has revealed target genes that may be potentially relevant in MCL pathogenesis.
Psiscan: a computational approach to identify H/ACA-like and AGA-like non-coding RNA in trypanosomatid genomes
Authors: Myslyuk Inna , Doniger Tirza , Horesh Yair , Hury Avraham , Hoffer Ran , Ziporen Yaara , Michaeli Shulamit , Unger Ron 
Published: November 2008

Abstract

Background
Detection of non coding RNA (ncRNA) molecules is a major bioinformatics challenge. This challenge is particularly difficult when attempting to detect H/ACA molecules which are involved in converting uridine to pseudouridine on rRNA in trypanosomes, because these organisms have unique H/ACA molecules (termed H/ACA-like) that lack several of the features that characterize H/ACA molecules in most other organisms.

Results
We present here a computational tool called Psiscan, which was designed to detect H/ACA-like molecules in trypanosomes. We started by analyzing known H/ACA-like molecules and characterized their crucial elements both computationally and experimentally.
Next, we set up constraints based on this analysis and additional phylogenic and functional data to rapidly scan three trypanosome genomes (T. brucei, T. cruzi and L. major) for sequences that observe these constraints and are conserved among the species. In the next step, we used minimal energy calculation to select the molecules that are predicted to fold into a lowest energy structure that is consistent with the constraints. In the final computational step, we used a Support Vector Machine that was trained on known H/ACA-like molecules as positive examples and on negative examples of molecules that were identified by the computational analyses but were shown experimentally not to be H/ACA-like molecules. The leading candidate molecules predicted by the SVM model were then subjected to experimental validation.

Conclusion
The experimental validation showed 11 molecules to be expressed (4 out of 25 in the intermediate stage and 7 out of 19 in the final validation after the machine learning stage). Five of these 11 molecules were further shown to be bona fide H/ACA-like molecules. As snoRNA in trypanosomes are organized in clusters, the new H/ACA-like molecules could be used as starting points to manually search for additional molecules in their neighbourhood. All together this study increased our repertoire by fourteen H/ACA-like and six C/D snoRNAs molecules from T. brucei and L. Major. In addition the experimental analysis revealed that six ncRNA molecules that are expressed are not downregulated in CBF5 silenced cells, suggesting that they have structural features of H/ACA-like molecules but do not have their standard function. We termed this novel class of molecules AGA-like, and we are exploring their function.
This study demonstrates the power of tight collaboration between computational and experimental approaches in a combined effort to reveal the repertoire of ncRNA molecles.
Thyroid hormone components are expressed in three sequential waves during development of the chick retina
Authors: Trimarchi Jeffrey M , Harpavat Sanjiv , Billings Nathan A , Cepko Constance L 
Published: November 2008

Abstract

Background
Thyroid hormone (TH) is an important developmental regulator in many tissues, including the retina. TH is activated locally via deiodinase 2 (Dio2), and it is destroyed by deiodinase 3 (Dio3). The TH receptors, TRa and TRb, mediate TH activity through hormone and DNA binding, and interactions with transcription regulators.

Results
In the current work, the expression of these TH components was examined in the chick retina over time. Three waves of expression were characterized and found to be correlated with critical developmental events. The first wave occurred as progenitor cells began to make photoreceptors, the second as some cell types adopted a more mature location and differentiation state, and the third as Müller glia were generated. The cell types expressing the components, as well as the kinetics of expression within the cell cycle, were defined. TRb expression initiated during G2 in progenitor cells, concomitant with NeuroD and Otx2, which are expressed in early photoreceptor cells. TRb was expressed in photoreceptor cells for several days and then was reduced in expression level, as the expression of Crx, a later photoreceptor gene, became more evident. Dio3 was expressed throughout the cell cycle in progenitor cells. TRa was in most, if not all, retinal cells. Dio2 appeared transiently in a ventral (high) to dorsal gradient, likely in a subset of photoreceptor cells.

Conclusion
Multiple TH components were expressed in dynamic patterns in cycling progenitor cells and photoreceptors cells across the developing chick retina. These dynamic patterns suggest that TH is playing several roles in retinal development, both within the cycling progenitor cells and possibly with respect to the timing of differentiation of photoreceptor cells.
Overuse of artemisinin-combination therapy in Mto wa Mbu (river of mosquitoes), an area misinterpreted as high endemic for malaria
Authors: Mwanziva Charles , Shekalaghe Seif , Ndaro Arnold , Mengerink Bianca , Megiroo Simon , Mosha Frank , Sauerwein Robert , Drakeley Chris , Gosling Roly , Bousema Teun 
Published: November 2008

Abstract

Background
Adequate malaria diagnosis and treatment remain major difficulties in rural sub-Saharan Africa. These issues deserve renewed attention in the light of first-line treatment with expensive artemisinin-combination therapy (ACT) and changing patterns of transmission intensity. This study describes diagnostic and treatment practices in Mto wa Mbu, an area that used to be hyperendemic for malaria, but where no recent assessments of transmission intensity have been conducted.

Methods
Retrospective and prospective data were collected from the two major village health clinics. The diagnosis in prospectively collected data was confirmed by microscopy. The level of transmission intensity was determined by entomological assessment and by estimating sero-conversion rates using anti-malarial antibody responses.

Results
Malaria transmission intensity by serological assessment was equivalent to < 1 infectious bites per person per year. Despite low transmission intensity, > 40% of outpatients attending the clinics in 2006–2007 were diagnosed with malaria. Prospective data demonstrated a very high overdiagnosis of malaria. Microscopy was unreliable with < 1% of slides regarded as malaria parasite-positive by clinic microscopists being confirmed by trained research microscopists. In addition, many 'slide negatives' received anti-malarial treatment. As a result, 99.6% (248/249) of the individuals who were treated with ACT were in fact free of malaria parasites.

Conclusion
Transmission intensity has dropped considerably in the area of Mto wa Mbu. Despite this, most fevers are still regarded and treated as malaria, thereby ignoring true causes of febrile illness and over-prescribing ACT. The discrepancy between the perceived and actual level of transmission intensity may be present in many areas in sub-Saharan Africa and calls for greater efforts in defining levels of transmission on a local scale to help rational drug-prescribing behaviour.