bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of Satellite Estimates of Land Surface Temperature from GOES over the United States
Authors: Pinker Rachel T. , Sun Donglian , Hung Meng-Pai , Li Chuan , Basara Jeffrey B. 
Published: July 2008

Abstract
A comprehensive evaluation of split-window and triple-window algorithms to estimate land surface temperature (LST) from Geostationary Operational Environmental Satellites (GOES) that were previously described by Sun and Pinker is presented. The evaluation of the split-window algorithm is done against ground observations and against independently developed algorithms. The triple-window algorithm is evaluated only for nighttime against ground observations and against the Sun and Pinker split-window (SP-SW) algorithm. The ground observations used are from the Atmospheric Radiation Measurement Program (ARM) Central Facility, Southern Great Plains site (April 1997–March 1998); from five Surface Radiation Budget Network (SURFRAD) stations (1996–2000); and from the Oklahoma Mesonet. The independent algorithms used for comparison include the National Oceanic and Atmospheric Administration/National Environmental Satellite, Data and Information Service operational method and the following split-window algorithms: that of Price, that of Prata and Platt, two versions of that of Ulivieri, that of Vidal, two versions of that of Sobrino, that of Coll and others, the generalized split-window algorithm as described by Becker and Li and by Wan and Dozier, and the Becker and Li algorithm with water vapor correction. The evaluation against the ARM and SURFRAD observations indicates that the LST retrievals from the SP-SW algorithm are in closer agreement with the ground observations than are the other algorithms tested. When evaluated against observations from the Oklahoma Mesonet, the triple-window algorithm is found to perform better than the split-window algorithm during nighttime.
Ship Observations of the Tropical Pacific Ocean along the Coast of South America
Authors: de Szoeke S. P. , Fairall C. W. , Pezoa Sergio 
Published: July 2008

Abstract
In October 2007 the NOAA ship Ronald H. Brown sailed southward within 300 km of the coast of Ecuador and Peru, sampling surface meteorology, air–sea turbulent and radiative fluxes, cloud properties, and upper-air soundings from the equator to 20°S. Two distinct water masses characterize the coastal region: cold-pool water below 19°C in the Southern Hemisphere, and warm-pool water above 20°C to the north, with a transition between the water masses at 2.5°S. Net turbulent and radiative fluxes warm the cool water south of 2.5°S by 100 W m−2 but do not warm the equatorial water significantly. Winds blow parallel to the shore, about 5 m s−1 over the cold pool and 7 m s−1 over the equator. Stratocumulus clouds are remarkably solid over the coastal cold pool, with only brief periods of partial clearing, mostly in the afternoon. Lower aerosol concentrations and thicker clouds observed farther from the coast on 22–23 October are coincident with a pocket of open cells seen to the west and southwest of the ship. Observations from this cruise and other NOAA Stratus cruises (2001 and 2003–07) are suitable for comparison with model simulations and provide context for future field experiments. These datasets are publicly available.
Magnetic resonance imaging measures of brain and spinal cord atrophy correlate with clinical impairment in secondary progressive multiple sclerosis
Authors: Furby J , Hayton T , Anderson V , Altmann D , Brenner R , Chataway J , Hughes RAC , Smith KJ , Miller DH , Kapoor R 
Published: July 2008

Background Neuroaxonal loss is a pathological substrate of disability in progressive multiple sclerosis (MS) and can be estimated in vivo by measuring tissue atrophy on magnetic resonance imaging (MRI). While there is some evidence that brain atrophy correlates better with disability than T2 lesion load in secondary progressive MS, the clinical relevance of atrophy within specific regions of the central nervous system requires further evaluation. Methods Clinical and MRI examinations were performed in 117 subjects with secondary progressive MS. MRI analysis included measures of normalized brain volume (NBV), normalized grey matter (NGMV) and white matter volume (NWMV), central cerebral volume (CCV), spinal cord cross-sectional area (SCCA), and brain T2 and T1 lesion volume. Clinical assessments included the expanded disability status scale (EDSS) and MS functional composite (MSFC). Results All MRI measures correlated significantly with the MSFC score, with the strongest correlation being for the NBV ( r = 0.47; P < 0.001). NBV and SCCA were the only significant independent predictors of the MSFC score in a stepwise regression model containing all the MRI measures, and SCCA was the only MRI measure to show a significant association with the EDSS. While NGMV had stronger correlations with the clinical variables than NWMV, NBV was more correlated with clinical impairment than either measure. Conclusions This data suggests that measures of atrophy, particularly of the whole brain and spinal cord, are relevant and useful disease markers in secondary progressive MS.
Setting the agenda for multiple sclerosis rehabilitation research
Authors: Kraft GH , Johnson KL , Yorkston K , Amtmann D , Bamer A , Bombardier C , Ehde D , Fraser R , Starks H 
Published: July 2008

Background Recognizing the need for more evidence-based multiple sclerosis (MS) rehabilitation, in the mid-2000s several initiatives were undertaken to explore why there had been a paucity of such research and to determine strategies to reverse this pattern. Expert-Opinion-Paper In 2004 the National Multiple Sclerosis Society (NMSS) convened an expert opinion panel, reviewed evidence-based MS rehabilitation research, and published the paper on the web. It was concluded that much of the MS rehabilitation carried out was based on experience, with little research backing it up. Increasing the Quality and Quantity of MS Rehabilitation Research Largely as a result of the conclusions of the Expert-Opinion-Paper, the NMSS convened a conference of a large number of MS and rehabilitation experts in New York in May, 2005. This conference made many recommendations of ways to increase the quantity and quality of MS research. State of the Science Conference In September, 2006, a follow-up conference was held in Washington, D.C... This conference, primarily sponsored by the University of Washington Multiple Sclerosis Rehabilitation Research and Training Center (MS RRTC), focused on some of the under-studied “hidden” disabilities present in persons with MS. This paper discusses the details and recommendations of these latter two conferences.
Distribution of germanium between phenocrysts and melt in peralkaline
rhyolites from the Kenya Rift Valley
Authors: Macdonald R. , Rogers N. W. , Tindle A. G. 
Published: July 2008

Abstract
Germanium abundances, determined by laser ablation-inductively coupled
plasma-mass spectrometry, are presented for phenocrysts and glass matrices from a
metaluminous trachyte and four peralkaline rhyolites from the Greater Olkaria
Volcanic Complex, Kenya Rift Valley, Africa. Abundances (in ppm) are: sanidine
0.45–0.61; fayalite 4.8–11.7; hedenbergite 5.1–9.0; titanomagnetite 2.7; ilmenite
0.48; amphibole 8.3–8.9; biotite 7.0; chevkinite-(Ce) 309; trachyte glass 3.0;
rhyolitic glasses 2.3–3.9. These values are generally greater than those recorded
for silicic rocks in the literature, whilst the chevkinite-(Ce) value is the
largest yet found in a magmatic mineral. Apparent partition coefficients range
from 0.15–0.26 in sanidine to 124 in chevkinite-(Ce). Those for fayalite and
hedenbergite increase with whole-rock peralkalinity and Fe content. The
possibility of a role for accessory phases in influencing Ge distribution in
rock-forming minerals is also raised.
Long-term progression-free survival of mantle cell lymphoma after intensive front-line immunochemotherapy with in vivo–purged stem cell rescue: a nonrandomized phase 2 multicenter study by the Nordic Lymphoma Group
Authors: Geisler Christian H. , Kolstad Arne , Laurell Anna , Andersen Niels S. , Pedersen Lone B. , Jerkeman Mats , Eriksson Mikael , Nordström Marie , Kimby Eva , Boesen Anne Marie , Kuittinen Outi , Lauritzsen Grete F. , Nilsson-Ehle Herman , Ralfkiær Elisabeth , Åkerman Måns , Ehinger Mats , Sundström Christer , Langholm Ruth , Delabie Jan , Karjalainen-Lindsberg Marja-Liisa , Brown Peter , Elonen Erkki ,   for the Nordic Lymphoma Group
Published: July 2008

AbstractMantle cell lymphoma (MCL) is considered incurable. Intensive immunochemotherapy with stem cell support has not been tested in large, prospective series. In the 2nd Nordic MCL trial, we treated 160 consecutive, untreated patients younger than 66 years in a phase 2 protocol with dose-intensified induction immunochemotherapy with rituximab (R) + cyclophosphamide, vincristine, doxorubicin, prednisone (maxi-CHOP), alternating with R + high-dose cytarabine. Responders received high-dose chemotherapy with BEAM or BEAC (carmustine, etoposide, cytarabine, and melphalan/cyclophosphamide) with R-in vivo purged autologous stem cell support. Overall and complete response was achieved in 96% and 54%, respectively. The 6-year overall, event-free, and progression-free survival were 70%, 56%, and 66%, respectively, with no relapses occurring after 5 years. Multivariate analysis showed Ki-67 to be the sole independent predictor of event-free survival. The nonrelapse mortality was 5%. The majority of stem cell products and patients assessed with polymerase chain reaction (PCR) after transplantation were negative. Compared with our historical control, the Nordic MCL-1 trial, the event-free, overall, and progression-free survival, the duration of molecular remission, and the proportion of PCR-negative stem cell products were significantly increased (P < .001). Intensive immunochemotherapy with in vivo purged stem cell support can lead to long-term progression-free survival of MCL and perhaps cure. Registered at www.isrctn.org as #ISRCTN 87866680.
Low nucleosome occupancy is encoded around functional human transcription factor binding sites
Authors: Daenen Floris , van Roy Frans , De Bleser Pieter J 
Published: July 2008

Abstract

Background
Transcriptional regulation of genes in eukaryotes is achieved by the interactions of multiple transcription factors with arrays of transcription factor binding sites (TFBSs) on DNA and with each other. Identification of these TFBSs is an essential step in our understanding of gene regulatory networks, but computational prediction of TFBSs with either consensus or commonly used stochastic models such as Position-Specific Scoring Matrices (PSSMs) results in an unacceptably high number of hits consisting of a few true functional binding sites and numerous false non-functional binding sites. This is due to the inability of the models to incorporate higher order properties of sequences including sequences surrounding TFBSs and influencing the positioning of nucleosomes and/or the interactions that might occur between transcription factors.

Results
Significant improvement can be expected through the development of a new framework for the modeling and prediction of TFBSs that considers explicitly these higher order sequence properties. It would be particularly interesting to include in the new modeling framework the information present in the nucleosome positioning sequences (NPSs) surrounding TFBSs, as it can be hypothesized that genomes use this information to encode the formation of stable nucleosomes over non-functional sites, while functional sites have a more open chromatin configuration.
In this report we evaluate the usefulness of the latter feature by comparing the nucleosome occupancy probabilities around experimentally verified human TFBSs with the nucleosome occupancy probabilities around false positive TFBSs and in random sequences.

Conclusion
We present evidence that nucleosome occupancy is remarkably lower around true functional human TFBSs as compared to non-functional human TFBSs, which supports the use of this feature to improve current TFBS prediction approaches in higher eukaryotes.
Specific genetic markers for detecting subtypes of dengue virus serotype-2 in isolates from the states of Oaxaca and Veracruz, Mexico
Authors: Gardella-Garcia Catalina E , Perez-Ramirez Gerardo , Navarrete-Espinosa Joel , Cisneros Alejandro , Jimenez-Rojas Fabiola , Ramírez-Palacios Luis R , Rosado-Leon Rocio , Camacho-Nuez Minerva , Munoz Maria de L 
Published: July 2008

Abstract

Background
Dengue (DEN) is an infectious disease caused by the DEN virus (DENV), which belongs to the Flavivirus genus in the family Flaviviridae. It has a (+) sense RNA genome and is mainly transmitted to humans by the vector mosquito Aedes aegypti. Dengue fever (DF) and dengue hemorrhagic fever (DHF) are caused by one of four closely related virus serotypes (DENV-1, DENV-2, DENV-3 and DENV-4). Epidemiological and evolutionary studies have indicated that host and viral factors are involved in determining disease outcome and have proved the importance of viral genotype in causing severe epidemics. Host immune status and mosquito vectorial capacity are also important influences on the severity of infection. Therefore, an understanding of the relationship between virus variants with altered amino acids and high pathogenicity will provide more information on the molecular epidemiology of DEN. Accordingly, knowledge of the DENV serotypes and genotypes circulating in the latest DEN outbreaks around the world, including Mexico, will contribute to understanding DEN infections.

Results
1. We obtained 88 isolates of DENV, 27 from Oaxaca and 61 from Veracruz. 2. Of these 88 isolates, 16 were serotype 1; 62 serotype 2; 7 serotype 3; and 2 serotype 4. One isolate had 2 serotypes (DENV-2 and -1). 3. Partial nucleotide sequences of the genes encoding C- prM (14 sequences), the NS3 helicase domain (7 sequences), the NS5 S-adenosyl methionine transferase domain (7 sequences) and the RNA-dependent RNA polymerase (RdRp) domain (18 sequences) were obtained. Phylogenetic analysis showed that DENV-2 isolates belonged to the Asian/American genotype. In addition, the Asian/American genotype was divided into two clusters, one containing the isolates from 2001 and the other the isolates from 2005–2006 with high bootstrap support of 94%.

Conclusion
DENV-2 was the predominant serotype in the DF and DHF outbreak from 2005 to 2006 in Oaxaca State as well as in the 2006 outbreak in Veracruz State, with the Asian/American genotype prevalent in both states. Interestingly, DENV-1 and DENV-2 were the only serotypes related to DHF cases. In contrast, DENV-3 and DENV-4 were poorly represented according to epidemiological data reported in Mexico. We found that isoleucine was replaced by valine at residue 106 of protein C in the isolates from these 2005–2006 outbreaks and in those from the 1997, 1998 and 2001 outbreaks in the Caribbean islands. We suggested that this amino acid change may be used as a signature for isolates arising in the Caribbean islands and pertaining to the Asian/American genotype. Other amino acid changes are specific for the Asian/American, Asian and American strains.
A dengue receptor as possible genetic marker of vector competence in Aedes aegypti
Authors: Mercado-Curiel Ricardo F , Black William C , Muñoz Maria de L 
Published: July 2008

AbstractBackgroundVector competence refers to the intrinsic permissiveness of an arthropod vector for infection, replication and transmission of a virus. Notwithstanding studies of Quantitative Trait Loci (QTL) that influence the ability ofAedes aegyptimidgut (MG) to become infected with dengue virus (DENV), no study to date has been undertaken to identify genetic markers of vector competence. Furthermore, it is known that mosquito populations differ greatly in their susceptibility to flaviviruses. Differences in vector competence may, at least in part, be due to the presence of specific midgut epithelial receptors and their identification would be a significant step forward in understanding the interaction of the virus with the mosquito. The first interaction of DENV with the insect is through proteins in the apical membrane of the midgut epithelium resulting in binding and receptor-mediated endocytosis of the virus, and this determines cell permissiveness to infection. The susceptibility of mosquitoes to infection may therefore depend on their specific virus receptors. To study this interaction inAe. aegyptistrains that differ in their vector competence for DENV, we investigated theDS3strain (susceptible to DENV), theIBO-11strain (refractory to infection) and the membrane escape barrier strain,DMEB, which is infected exclusively in the midgut epithelial cells.Results(1) We determined the MG proteins that bind DENV by an overlay protein binding assay (VOPBA) inAe. aegyptimosquitoes of theDS3,DMEBandIBO-11strains. The main protein identified had an apparent molecular weight of 67 kDa, although the protein identified in theIBO-11strain showed a lower mass (64 kDa). (2) The midgut proteins recognized by DENV were also determined by VOPBA after two-dimensional gel electrophoresis. (3) To determine whether the same proteins were identified in all three strains, we obtained polyclonal antibodies against R67 and R64 and tested them against the three strains by immunoblotting; both antibodies recognized the 67 and 64 kDa proteins, corroborating the VOPBA results. (4) Specific antibodies against both proteins were used for immunofluorescent location by confocal microscopy; the antibodies recognized the basal lamina all along the MG, and cell membranes and intercellular spaces from the middle to the end of the posterior midgut (pPMG) in the neighborhood of the hindgut. (5) Quantitative analysis showed more intense fluorescence inDS3andDMEBthan inIBO-11. (6) The viral envelope antigen was not homogeneously distributed during MG infection but correlated with MG density and the distribution of R67/R64.ConclusionIn this paper we provide evidence that the 67 kDa protein (R67/R64), described previously as a DENV receptor, is related to vector competence inAe. aegypti. Consequently, our results strongly suggest that this protein may be a marker of vector competence for DENV inAe. aegyptimosquitoes.
Xenohormone transactivities are inversely associated to serum POPs in Inuit
Authors: Krüger Tanja , Ghisari Mandana , Hjelmborg Philip S , Deutch Bente , Bonefeld-Jorgensen Eva C 
Published: July 2008

Abstract

Background
The persistent organic pollutants (POPs) are highly lipophilic and resistant to biodegradation and found in e.g. seafood and marine mammals. Greenlandic Inuit have high intake of marine food and thus high POP burden that varies according to local conditions and dietary preference. We do for the very first time report the serum POP related non-steroidal xenohormone activity of Inuit across Greenland.

The aims were 1) to determine the integrated xenohormone bioactivities as an exposure biomarker of the actual lipophilic serum POP mixture measuring the effect on estrogen (ER) and androgen receptor (AR) transactivity in citizens from different Greenlandic districts and 2) to evaluate associations to serum POP markers (14 PCBs and 10 pesticides) and lifestyle characteristics.

Methods
Serum samples from 121 men and 119 women from Nuuk, Sisimiut and Qaanaaq were extracted using SPE-HPLC fractionation to obtain the serum POP fraction free of endogenous hormones. The serum POP fraction was used for determination of xenohormone transactivity using ER and AR reporter gene assays.

Results
In overall, the xenohormone transactivities differed between districts as well as between the genders. Associations between the transactivities and age, n-3/n-6 and smoker years were observed. The xenoestrogenic and xenoandrogenic transactivities correlated negatively to the POPs for the combined female and male data, respectively.

Conclusion
The non-steroidal xenohormone transactivities can be used as an integrated biomarker of POP exposure and lifestyle characteristics. The actual serum POP mixtures antagonized the age adjusted sex hormone receptor functions. Comparison of different study populations requires in addition to age inclusion of diet and lifestyle factors.
(Errors in statistical tests)3
Authors: Phillips Carl V , MacLehose Richard F , Kaufman Jay S 
Published: July 2008

AbstractIn 2004, Garcia-Berthou and Alcaraz published "Incongruence between test statistics and P values in medical papers," a critique of statistical errors that received a tremendous amount of attention. One of their observations was that the final reported digit of p-values in articles published in the journal Nature departed substantially from the uniform distribution that they suggested should be expected. In 2006, Jeng critiqued that critique, observing that the statistical analysis of those terminal digits had been based on comparing the actual distribution to a uniform continuous distribution, when digits obviously are discretely distributed. Jeng corrected the calculation and reported statistics that did not so clearly support the claim of a digit preference. However delightful it may be to read a critique of statistical errors in a critique of statistical errors, we nevertheless found several aspects of the whole exchange to be quite troubling, prompting our own meta-critique of the analysis.The previous discussion emphasized statistical significance testing. But there are various reasons to expect departure from the uniform distribution in terminal digits of p-values, so that simply rejecting the null hypothesis is not terribly informative. Much more importantly, Jeng found that the original p-value of 0.043 should have been 0.086, and suggested this represented an important difference because it was on the other side of 0.05. Among the most widely reiterated (though often ignored) tenets of modern quantitative research methods is that we should not treat statistical significance as a bright line test of whether we have observed a phenomenon. Moreover, it sends the wrong message about the role of statistics to suggest that a result should be dismissed because of limited statistical precision when it is so easy to gather more data.In response to these limitations, we gathered more data to improve the statistical precision, and analyzed the actual pattern of the departure from uniformity, not just its test statistics. We found variation in digit frequencies in the additional data and describe the distinctive pattern of these results. Furthermore, we found that the combined data diverge unambiguously from a uniform distribution. The explanation for this divergence seems unlikely to be that suggested by the previous authors: errors in calculations and transcription.