bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biogeographical affinities of Jurassic and Cretaceous continental vertebrate assemblages from SE Asia
Authors: Fernandez Vincent , Claude Julien , Escarguel Gilles , Buffetaut Eric , Suteethorn Varavudh 
Published: May 2009

Abstract
Over the last 25 years, rich vertebrate assemblages have been discovered in three distinct formations of the Late Jurassic and Early Cretaceous of Thailand. This work aims to compare the taxonomic assemblages of SE Asia within their palaeogeographical context in Asia. Occurrences of 477 taxa in 94 Regional Faunal Assemblages (RFA) have provided the raw material for producing a dissimilarity matrix based on the Raup & Crick index. These distances have been investigated statistically to infer relationships between the diverse faunal assemblages in space and time. Our results show that the Thai formations are more similar to each other than to any other formations, suggesting a strong provincialism. The relationship of SE Asian RFAs with other Asian RFAs is more influenced by the presence of freshwater or near-shore taxa than by strictly terrestrial ones. Our analysis shows that the faunal interchange between RFAs was rather low from the Late Jurassic to the end of the Early Cretaceous. However, faunal dispersals dramatically decreased during the mid-Early Cretaceous in Asia. The faunas show an overall stronger provincialism during the mid-Early Cretaceous, indicating the role of possible geographical barriers. This event is characterized by the absence of ornithischian dinosaurs in the Sao Khua Formation although they are present in the under- and overlying formations. Taxonomic diversity and exchanges between faunal assemblages recovered rapidly as early as the Aptian in Asia, but the fauna of SE Asia still retained a strong biogeographical signature.
Late Permian dicynodont fauna from Laos
Authors: Battail Bernard 
Published: May 2009

Abstract

In Laos, dicynodonts have long been known only from one specimen, now lost, a partial skull discovered by Counillon in the purple beds of the area of Luang Prabang, and initially described by Repelin as
Dicynodon incisivum
. Subsequent researchers attributed the specimen either to the Late Permian genus
Dicynodon
or to the Early Triassic genus
Lystrosaurus.
Recent Franco-Laotian expeditions have gathered, from the same purple beds, a collection of tetrapods composed mainly of dicynodonts. They can all be ascribed to
Dicynodon
, and the available evidence suggests that the purple beds are Late Permian in age. The genus
Lystrosaurus
remains unknown in Laos.
Mesozoic red bed sequences from SE Asia and the significance of the Khorat Group of NE Thailand
Authors: Racey Andrew 
Published: May 2009

Abstract
New geological data are presented and previously published information is reviewed to demonstrate that much of the Khorat Group (Phu Kradung to Khok Kruat Formations) of NE Thailand is Early Cretaceous in age. It is suggested that the Mesozoic red bed sequences of neighbouring Indochina are likely to be of similar age rather than spanning the entire Late Triassic to Early Cretaceous as previously assumed. Moreover, the Lower Nam Phong Formation dated as Late Triassic and previously included as the basal formation of the Khorat Group is now removed from this group, thus creating a hiatus within the Jurassic. There is therefore no clear relationship between the Indosinian Orogeny and the Triassic collision of the Sibumasu (also referred to as Shan-Thai) and Indochina Blocks and the subsequent deposition of the Khorat Group in a Late Triassic–Early Cretaceous thermal sag basin. It is now proposed that much of the sequence was deposited during the Late Jurassic–Early Cretaceous. Jurassic sediments may be absent across much of the Khorat Plateau whereas marine Jurassic sediments to the west and east show no sediments younger than Bajocian. Because sea levels were generally rising in the Middle and Late Jurassic it is likely that the Khorat region was uplifted at this time. It is suggested that the Khorat Group was originally deposited in a foreland basin setting rather than a thermal sag basin following Late Triassic rifting. Moreover, the original site of deposition was to the north in southern China, with the present-day location being the result of movement along the Red River Fault coupled with a clockwise rotation of the Indochina Block (on which the Khorat Group sits) with respect to the South China Block.
Silhouette and palaeoecology of Mesozoic trees in Thailand
Authors: Philippe Marc , Daviero-Gomez Véronique , Suteethorn Varavudh 
Published: May 2009

Abstract

Trees are an obvious component of most landscapes. Artists' views of Mesozoic landscapes regularly feature modern trees such as firs (
Abies
and
Picea
) and monkey-puzzle trees (
Araucaria araucana
). However, these reconstructions are highly hypothetical and, in reality, very little is known about the silhouettes of Mesozoic trees. In Mesozoic (Middle Jurassic to Early Cretaceous) strata of Thailand, large conifer logs with different types of architecture are evident, a rare opportunity for architectural studies. Various methods to estimate the original diameter and height of the trees are assessed. Among our material some trees have the classical Christmas-tree shape, whereas others are more oak-like in silhouette. All these trees lived in forest environments. Tree shape is strongly related to environment, and is still under-used as a palaeoecological tool. Reconstructing trees and vegetation has wide implications, from evaluating dinosaur herbivory to calculating elements of the carbon cycle.
A new elasmobranch fauna from the Middle Jurassic of southern Thailand
Authors: Cuny Gilles , Srisuk Paladej , Khamha Suchada , Suteethorn Varavudh , Tong Haiyan 
Published: May 2009

Abstract

We describe a new elasmobranch fauna from the lower part of the Khlong Min Formation in Thailand. The fauna includes
Hybodus
sp.,
Asteracanthus
sp.,
Lonchidion reesunderwoodi
sp. nov.,
Belemnobatis aominensis
sp. nov., and possibly a second species of
Belemnobatis.
This fauna supports a Bathonian–Callovian age for the Khlong Min Formation, and suggests a close taxonomic relationship between the Middle Jurassic elasmobranch faunas of Europe and Thailand. The presence of a monolayered enameloid in
Belemnobatis aominensis
sp. nov. and other primitive batoids is interpreted as the retention of a primitive character for neoselachians, which would suggest a divergence time between the batoids and the rest of the neoselachian sharks as early as the Carboniferous–Permian boundary.
Morphometric and taphonomic study of a ray-finned fish assemblage (Lepidotes buddhabutrensis, Semionotidae) from the Late Jurassic-earliest Cretaceous of NE Thailand
Authors: Deesri Uthumporn , Cavin Lionel , Claude Julien , Suteethorn Varavudh , Yuangdetkla Phisit 
Published: May 2009

AbstractMost Mesozoic vertebrate species are represented by scarce and incomplete specimens, preventing statistical studies of morphometric features. Moreover, rich vertebrate assemblages are rarely excavated in conditions that allow taphonomical studies.Lepidotes buddhabutrensisis a common species found in the Late Jurassic–Early Cretaceous locality of Phu Nam Jun, Phu Kradung Formation, in NE Thailand. Individuals, collected during systematic excavation since 2002, show great variations in preservation states and body postures. In this paper we study the mode of variation of morphometric features of the fish population, the growth mode, and the relationship between morphology and size. We assess the range of variation in preservation and taphonomy, based on arbitrarily defined scales, to test if vertical variations occur in the sample of individuals within the site. We test possible favoured orientation of specimens within the assemblage. In contrast to preliminary field observations, statistical analyses show that all individuals belong to a single Gaussian population and that gross morphological shape variations are related only to size during fish growth.L. buddhabutrensisshows a positive allometric growth for the pectoral to dorsal, and pectoral to anal fin distances, and a negative allometric growth for the unpaired fins (dorsal and anal fins lengths). We detected no relationships between the vertical location of the fishes within the fossiliferous deposit and the body shape of the specimens, nor between the state of preservation and the taphonomy, but there are significant differences in the state of preservation according to the position of the fishes in the fossiliferous deposit. The occurrence of a single Gaussian population and the absence of morphological and preservational variations through the depositional column are evidence that the fish assemblage is probably the result of a single mass mortality event. The apparent diversity in morphology is probably due to variations in the mode of preservation. The fish appear to have been oriented by a current at the time of deposition at the top of the fossiliferous deposit only.
A Controlled Trial of Objective Measures of Sunscreen and Moisturizing Lotion
Authors: Elliott Tom , Nehl Eric J. , Glanz Karen 
Published: May 2009

Abstract
Taking an alcohol swab of a person's forearm and analyzing it using a spectrophotometer has been shown to be a reliable method for detecting the presence of sunscreen. The aims of this study were to determine if moisturizing lotions or other non-sunscreen products influence the absorbance readings from skin swabs in a controlled setting, and to establish the cutoff point in determining the presence or absence of sunscreen using a crystal cuvette instead of a plastic one. In a controlled trial of 30 volunteer office workers, absorbance readings from two popular brands of sunscreen with sun-protection factors (SPF) of 30 and 45 were compared with absorbance readings from two different moisturizing lotions, one with an SPF of 15 and another with no stated SPF. Moisturizers with SPF 15 tested positive for sunscreen, with absorbance readings (mean, 3.77; min, 3.30) comparable to sunblock with SPF 30 or 45 (mean, 3.51; min, 2.02). Moisturizers with no stated SPF factor tested negative for the presence of sunscreen, with extremely low absorbance readings (mean, 0.06; max, 0.19) similar to control readings. The skin swabbing technique remains a valid and useful method for detecting the presence of sunscreen and does not result in false positives when moisturizers with no stated SPF are present. Using a conservative cutoff point of 0.30 with a crystal cuvette reduces any chance of false-positive readings and remains robust when sunscreen of SPF 15 or higher is present. (Cancer Epidemiol Biomarkers Prev 2009;18(5):1399–402)
Computational Cost and Accuracy in Calculating Three-Dimensional Radiative Transfer: Results for New Implementations of Monte Carlo and SHDOM
Authors: Pincus Robert , Evans K. Franklin 
Published: May 2009

Abstract
This paper examines the tradeoffs between computational cost and accuracy for two new state-of-the-art codes for computing three-dimensional radiative transfer: a community Monte Carlo model and a parallel implementation of the Spherical Harmonics Discrete Ordinate Method (SHDOM). Both codes are described and algorithmic choices are elaborated. Two prototype problems are considered: a domain filled with stratocumulus clouds and another containing scattered shallow cumulus, absorbing aerosols, and molecular scatterers. Calculations are performed for a range of resolutions and the relationships between accuracy and computational cost, measured by memory use and time to solution, are compared.
Monte Carlo accuracy depends primarily on the number of trajectories used in the integration. Monte Carlo estimates of intensity are computationally expensive and may be subject to large sampling noise from highly peaked phase functions. This noise can be decreased using a range of variance reduction techniques, but these techniques can compromise the excellent agreement between the true error and estimates obtained from unbiased calculations. SHDOM accuracy is controlled by both spatial and angular resolution; different output fields are sensitive to different aspects of this resolution, so the optimum accuracy parameters depend on which quantities are desired as well as on the characteristics of the problem being solved. The accuracy of SHDOM must be assessed through convergence tests and all results from unconverged solutions may be biased.
SHDOM is more efficient (i.e., has lower error for a given computational cost) than Monte Carlo when computing pixel-by-pixel upwelling fluxes in the cumulus scene, whereas Monte Carlo is more efficient in computing flux divergence and downwelling flux in the stratocumulus scene, especially at higher accuracies. The two models are comparable for downwelling flux and flux divergence in cumulus and upwelling flux in stratocumulus. SHDOM is substantially more efficient when computing pixel-by-pixel intensity in multiple directions; the models are comparable when computing domain-average intensities. In some cases memory use, rather than computation time, may limit the resolution of SHDOM calculations.
In-Flight Spectral Characterization and Calibration Stability Estimates for the Clouds and the Earth’s Radiant Energy System (CERES)
Authors: Matthews Grant 
Published: May 2009

Abstract
It is essential to maintain global measurements of the earth radiation budget (ERB) from space, the scattered solar and emitted thermal radiative fluxes leaving the planet. These are required for the purpose of validating current climate model predictions of the planet’s future response to anthropogenic greenhouse gas forcing. The measurement accuracy and calibration stability required to resolve the magnitude of model-suggested cloud–climate feedbacks on the ERB have recently been estimated. The suggestion is for ERB data to strive for a calibration stability of ±0.3% decade−1 for scattered solar, ±0.5% decade−1 for emitted thermal, and an overall absolute accuracy of 1 W m−2. The Clouds and the Earth’s Radiant Energy System (CERES) is currently the only satellite program to make global ERB measurements, beginning in January 1998. However, the new climate calibration standards are beyond those originally specified by the NASA CERES program for its edition 2 data release. Furthermore, the CERES instrument optics have been discovered to undergo substantial in-flight degradation because of contaminant issues. This is not directly detectable by using established calibration methods. Hence, user-applied revisions for edition 2 shortwave (SW) data were derived to compensate for this effect, which is described as “spectral darkening.” Also, an entirely new in-flight calibration protocol has been developed for CERES that uses deep convective cloud albedo as a primary solar wavelength stability metric. This is then combined with a sophisticated contamination mobilization/polymerization model. The intention is to assign spectral coloration to any optical degradation occurring to the different CERES Earth observing telescopes. This paper quantifies the stability of revised edition 2 data. It also calculates stability, which the new protocols could give CERES measurements if used. The conclusion is that the edition 2 revisions restore the originally specified stability of CERES SW data. It is also determined that the climate calibration stability goals are reachable by using the new in-flight methodologies presented in this paper. However, this will require datasets of longer than approximately 10 yr. It will also require obtaining regular raster scans of the Moon by all operational CERES instruments.
Estimating parameters for generalized mass action models with connectivity information
Authors: Ko Chih-Lung , Voit Eberhard O , Wang Feng-Sheng 
Published: May 2009

Abstract

Background
Determining the parameters of a mathematical model from quantitative measurements is the main bottleneck of modelling biological systems. Parameter values can be estimated from steady-state data or from dynamic data. The nature of suitable data for these two types of estimation is rather different. For instance, estimations of parameter values in pathway models, such as kinetic orders, rate constants, flux control coefficients or elasticities, from steady-state data are generally based on experiments that measure how a biochemical system responds to small perturbations around the steady state. In contrast, parameter estimation from dynamic data requires time series measurements for all dependent variables. Almost no literature has so far discussed the combined use of both steady-state and transient data for estimating parameter values of biochemical systems.

Results
In this study we introduce a constrained optimization method for estimating parameter values of biochemical pathway models using steady-state information and transient measurements. The constraints are derived from the flux connectivity relationships of the system at the steady state. Two case studies demonstrate the estimation results with and without flux connectivity constraints. The unconstrained optimal estimates from dynamic data may fit the experiments well, but they do not necessarily maintain the connectivity relationships. As a consequence, individual fluxes may be misrepresented, which may cause problems in later extrapolations. By contrast, the constrained estimation accounting for flux connectivity information reduces this misrepresentation and thereby yields improved model parameters.

Conclusion
The method combines transient metabolic profiles and steady-state information and leads to the formulation of an inverse parameter estimation task as a constrained optimization problem. Parameter estimation and model selection are simultaneously carried out on the constrained optimization problem and yield realistic model parameters that are more likely to hold up in extrapolations with the model.
A network-based integrative approach to prioritize reliable hits from multiple genome-wide RNAi screens in Drosophila
Authors: Wang Li , Tu Zhidong , Sun Fengzhu 
Published: May 2009

Abstract

Background
The recently developed RNA interference (RNAi) technology has created an unprecedented opportunity which allows the function of individual genes in whole organisms or cell lines to be interrogated at genome-wide scale. However, multiple issues, such as off-target effects or low efficacies in knocking down certain genes, have produced RNAi screening results that are often noisy and that potentially yield both high rates of false positives and false negatives. Therefore, integrating RNAi screening results with other information, such as protein-protein interaction (PPI), may help to address these issues.

Results
By analyzing 24 genome-wide RNAi screens interrogating various biological processes in Drosophila, we found that RNAi positive hits were significantly more connected to each other when analyzed within a protein-protein interaction network, as opposed to random cases, for nearly all screens. Based on this finding, we developed a network-based approach to identify false positives (FPs) and false negatives (FNs) in these screening results. This approach relied on a scoring function, which we termed NePhe, to integrate information obtained from both PPI network and RNAi screening results. Using a novel rank-based test, we compared the performance of different NePhe scoring functions and found that diffusion kernel-based methods generally outperformed others, such as direct neighbor-based methods. Using two genome-wide RNAi screens as examples, we validated our approach extensively from multiple aspects. We prioritized hits in the original screens that were more likely to be reproduced by the validation screen and recovered potential FNs whose involvements in the biological process were suggested by previous knowledge and mutant phenotypes. Finally, we demonstrated that the NePhe scoring system helped to biologically interpret RNAi results at the module level.

Conclusion
By comprehensively analyzing multiple genome-wide RNAi screens, we conclude that network information can be effectively integrated with RNAi results to produce suggestive FPs and FNs, and to bring biological insight to the screening results.
Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays
Authors: Bloom Joshua S , Khan Zia , Kruglyak Leonid , Singh Mona , Caudy Amy A 
Published: May 2009

Abstract

Background
High-throughput cDNA synthesis and sequencing of poly(A)-enriched RNA is rapidly emerging as a technology competing to replace microarrays as a quantitative platform for measuring gene expression.

Results
Consequently, we compared full length cDNA sequencing to 2-channel gene expression microarrays in the context of measuring differential gene expression. Because of its comparable cost to a gene expression microarray, our study focused on the data obtainable from a single lane of an Illumina 1 G sequencer. We compared sequencing data to a highly replicated microarray experiment profiling two divergent strains of S. cerevisiae.

Conclusion
Using a large number of quantitative PCR (qPCR) assays, more than previous studies, we found that neither technology is decisively better at measuring differential gene expression. Further, we report sequencing results from a diploid hybrid of two strains of S. cerevisiae that indicate full length cDNA sequencing can discover heterozygosity and measure quantitative allele-specific expression simultaneously.
Paracoccidioides brasiliensis pancreatic destruction in Calomys callosusexperimentally infected
Authors: Fortes Rogério M , Kipnis André , Junqueira-Kipnis Ana Paula 
Published: May 2009

Abstract

Background
The wild rodent Calomys callosus is notably resistant to Trypanosoma cruzi infection. In order to better characterize this animal model for experimental infections, we inoculated C. callosus intraperitoneally with Paracoccidioides brasiliensis, a thermally dimorphic fungus that causes a chronic disease with severe granuloma formation in the mouse and humans. The dissemination of P. brasiliensis cells through the lungs, liver, pancreas, and spleen was assessed by histological analysis.

Results
The animals were susceptible to infection and showed a granulomatous reaction. C. callosus presented peritonitis characterized by the presence of exudates containing a large number of yeast cells. Extensive accumulation of yeast cells with intense destruction of the parenchyma was observed in the pancreas, which reduced the glucose levels of infected animals. These lesions were regressive in the liver, spleen, and lungs until complete recovery. The role of estrogen during C. callosus infection with P. brasiliensis was addressed by infecting ovariectomized animals. It was observed a reduced inflammatory response as well as reduced extension of tissue damage. Removal of ovaries reestablished the normal glucose levels during infection.

Conclusion
Taken together, the results presented here reveal the pancreas as being an important organ for the persistence of P. brasiliensis during infection of C. callosus and that estrogen plays an important role in the susceptibility of the animals to this pathogen.