bluuebunny/crossref_metadata_2025_split huggingface dataset:
Experiments with a Simple Tropical Cyclone Intensity Consensus
Authors: Sampson Charles R. , Franklin James L. , Knaff John A. , DeMaria Mark 
Published: April 2008

Abstract
Consensus forecasts (forecasts created by combining output from individual forecasts) have become an integral part of operational tropical cyclone track forecasting. Consensus aids, which generally have lower average errors than individual models, benefit from the skill and independence of the consensus members, both of which are present in track forecasting, but are limited in intensity forecasting. This study conducts experiments with intensity forecast aids on 4 yr of data (2003–06). First, the skill of the models is assessed; then simple consensus computations are constructed for the Atlantic, eastern North Pacific, and western North Pacific basins. A simple (i.e., equally weighted) consensus of three top-performing intensity forecast models is found to generally outperform the individual members in both the Atlantic and eastern North Pacific, and a simple consensus of two top-performing intensity forecast models is found to generally outperform the individual members in the western North Pacific.
An experiment using an ensemble of dynamical model track forecasts and a selection of model fields as input in a statistical–dynamical intensity forecast model to produce intensity consensus members is conducted for the western North Pacific only. Consensus member skill at 72 h is low (−0.4% to 14.2%), and there is little independence among the members. This experiment demonstrates that a consensus of these highly dependent members yields an aid that performs as well as the most skillful member. Finally, adding a less skillful, but more independent, dynamical model-based forecast aid to the consensus yields an 11-member consensus with mixed yet promising performance compared with the 10-model consensus.
Based on these findings, the simple three-member consensus model could be used as a standard of comparison for other deterministic ensemble methods for the Atlantic and eastern North Pacific. Both the two- and three-member consensus forecasts may also provide useful guidance for operational forecasters. Likewise, in the western North Pacific, the 10- and 11-member consensus could be used as operational forecast aids and standards of comparison for other ensemble intensity forecast methods.
Errors of Naturally Ventilated Air Temperature Measurements in a Spatial Observation Network
Authors: Mauder Matthias , Desjardins R. L. , Gao Zhiling , van Haarlem Ronald 
Published: April 2008

AbstractA spatial network of 25 air temperature sensors was deployed over an area of 3.5 km × 3.5 km of agricultural land, aiming to calculate the sensible heat flux by spatial averaging instead of temporal averaging. Since temperature sensors in naturally ventilated solar radiation shields were used for these measurements, a correction for radiative heating had to be applied. In this study, the approach of Anderson and Baumgartner was adapted to the cube-shaped HOBO solar radiation shields. This semiempirical correction depends on the shield’s area normal to the sun in addition to solar radiation and wind speed. The required correction coefficients, which can be universally applied for this type of shield, were obtained through comparison with fan-aspirated temperature measurements at one site. The root-mean-square error of the HOBO temperature measurements was reduced from 0.49° to 0.15°C after applying this radiation correction.
Development of an Atlantic Canadian Coastal Water Level Neural Network Model
Authors: Han Guoqi , Shi Yu 
Published: April 2008

Abstract
Coastal water-level information is essential for coastal zone management, navigation, and oceanographic research. However, long-term water-level observations are usually only available at a limited number of locations. This study discusses a complementary and simple neural network (NN) approach, to predict water levels at a specified coastal site from the data gathered at other nearby or remote permanent stations. A simple three-layer, feed-forward, back-propagation network and a neural network ensemble, named Atlantic Canadian Coastal Water Level Neural Network (ACCSLENNT) models, was developed to correlate the nonlinear relationship of sea level data among stations by learning from their historical characteristics. Instantaneous hourly observations of water level from five stations along the coast of Atlantic Canada—Argentia, Belledune, Halifax, North Sydney, and St. John’s—are used to formulate and validate the ACCSLENNT models. Qualitative and quantitative comparisons of the network output with target observations showed that despite significant changes in sea level amplitudes and phases in the study area, appropriately trained NN models could provide accurate and robust long-term predictions of both tidal and nontidal (tide subtracted) water levels when only short-term data are available. The robust results indicate that the NN models in conjunction with limited permanent stations are able to supplement long-term historical water-level data along the Atlantic Canadian coast. Because field data collection is usually expensive, the ACCSLENNT models provide a cost-effective alternative to obtain long-term data along Atlantic Canada.
Neutrophil stress and apoptosis underlie myeloid dysfunction in glycogen storage disease type Ib
Authors: Kim So Youn , Jun Hyun Sik , Mead Paul A. , Mansfield Brian C. , Chou Janice Y. 
Published: April 2008

AbstractGlycogen storage disease type Ib (GSD-Ib) is caused by a deficiency in the glucose-6-phosphate (G6P) transporter (G6PT) that works with a liver/kidney/intestine–restricted glucose-6-phosphatase-α (G6Pase-α) to maintain glucose homeostasis between meals. Clinically, GSD-Ib patients manifest disturbed glucose homeostasis and neutrophil dysfunctions but the cause of the latter is unclear. Neutrophils express the ubiquitously expressed G6PT and G6Pase-β that together transport G6P into the endoplasmic reticulum (ER) lumen and hydrolyze it to glucose. Because we expected G6PT-deficient neutrophils to be unable to produce endogenous glucose, we hypothesized this would lead to ER stress and increased apoptosis. Using GSD-Ib mice, we showed that GSD-Ib neutrophils exhibited increased production of ER chaperones and oxidative stress, consistent with ER stress, increased annexin V binding and caspase-3 activation, consistent with an increased rate of apoptosis. Bax activation, mitochondrial release of proapoptotic effectors, and caspase-9 activation demonstrated the involvement of the intrinsic mitochondrial pathway in these processes. The results demonstrate that G6P translocation and hydrolysis are required for normal neutrophil functions and support the hypothesis that neutrophil dysfunction in GSD-Ib is due, at least in part, to ER stress and increased apoptosis.
Reliable identification of mycobacterial species by PCR-restriction enzyme analysis (PRA)-hsp65 in a reference laboratory and elaboration of a sequence-based extended algorithm of PRA-hsp65patterns
Authors: Chimara Erica , Ferrazoli Lucilaine , Ueky Suely Yoko Misuka , Martins Maria Conceição , Durham Alan Mitchel , Arbeit Robert D , Leão Sylvia Cardoso 
Published: April 2008

Abstract

Background
Identification of nontuberculous mycobacteria (NTM) based on phenotypic tests is time-consuming, labor-intensive, expensive and often provides erroneous or inconclusive results. In the molecular method referred to as PRA-hsp65, a fragment of the hsp65 gene is amplified by PCR and then analyzed by restriction digest; this rapid approach offers the promise of accurate, cost-effective species identification. The aim of this study was to determine whether species identification of NTM using PRA-hsp65 is sufficiently reliable to serve as the routine methodology in a reference laboratory.

Results
A total of 434 NTM isolates were obtained from 5019 cultures submitted to the Institute Adolpho Lutz, Sao Paulo Brazil, between January 2000 and January 2001. Species identification was performed for all isolates using conventional phenotypic methods and PRA-hsp65. For isolates for which these methods gave discordant results, definitive species identification was obtained by sequencing a 441 bp fragment of hsp65. Phenotypic evaluation and PRA-hsp65 were concordant for 321 (74%) isolates. These assignments were presumed to be correct. For the remaining 113 discordant isolates, definitive identification was based on sequencing a 441 bp fragment of hsp65. PRA-hsp65 identified 30 isolates with hsp65 alleles representing 13 previously unreported PRA-hsp65 patterns. Overall, species identification by PRA-hsp65 was significantly more accurate than by phenotype methods (392 (90.3%) vs. 338 (77.9%), respectively; p < .0001, Fisher's test). Among the 333 isolates representing the most common pathogenic species, PRA-hsp65 provided an incorrect result for only 1.2%.

Conclusion
PRA-hsp65 is a rapid and highly reliable method and deserves consideration by any clinical microbiology laboratory charged with performing species identification of NTM.
The influence of in vitro fitness defects on pneumococcal ability to colonize and to cause invasive disease
Authors: Fernebro Jenny , Blomberg Christel , Morfeldt Eva , Wolf-Watz Hans , Normark Staffan , Normark Birgitta Henriques 
Published: April 2008

AbstractBackgroundStreptococcus pneumoniaeis a genetically diverse major human pathogen, yet a common colonizer of the nasopharynx. Here we analyzed the influence of defects affectingin vitrogrowth rate, on the ability ofS. pneumoniaeto colonize and to cause invasive diseasein vivo.ResultsOf eleven different clinical isolates one serotype 14 carrier isolate showed a significantly longer generation time as compared to other isolates, and was severely attenuated in mice. To directly investigate the impact of growth rate on virulence, a panel of mutants in five non-essential housekeeping genes was constructed in the virulent TIGR4 background by insertion-deletion mutagenesis. Three of these mutants (ychF,hemKandyebC) were, to different degrees, growth defective, and showed a reduced invasiveness in an intranasal murine challenge model that correlated to theirin vitrogrowth rate, but remained capable of colonizing the upper airways. The growth defect, as well as virulence defect of thehemKinsertion-deletion mutant, was mediated by polarity effects on the downstreamyrdCgene, encoding a probable chaperone in ribosome assembly.ConclusionWe conclude that large fitness defects are needed to completely prevent pneumococci from causing invasive disease after intranasal challenge. However, even severe growth defects still allow pneumococci to persistently colonize the upper airways.
The IBR5 phosphatase promotes Arabidopsis auxin responses through a novel mechanism distinct from TIR1-mediated repressor degradation
Authors: Strader Lucia C , Monroe-Augustus Melanie , Bartel Bonnie 
Published: April 2008

Abstract

Background
In Arabidopsis, INDOLE-3-BUTYRIC ACID RESPONSE5 (IBR5), a putative dual-specificity protein phosphatase, is a positive regulator of auxin response. Mutations in IBR5 result in decreased plant height, defective vascular development, increased leaf serration, fewer lateral roots, and resistance to the phytohormones auxin and abscisic acid. However, the pathways through which IBR5 influences auxin responses are not fully understood.

Results
We analyzed double mutants of ibr5 with other mutants that dampen auxin responses and found that combining ibr5 with an auxin receptor mutant, tir1, enhanced auxin resistance relative to either parent. Like other auxin-response mutants, auxin-responsive reporter accumulation was reduced in ibr5. Unlike other auxin-resistant mutants, the Aux/IAA repressor reporter protein AXR3NT-GUS was not stabilized in ibr5. Similarly, the Aux/IAA repressor IAA28 was less abundant in ibr5 than in wild type. ibr5 defects were not fully rescued by overexpression of a mutant form of IBR5 lacking the catalytic cysteine residue.

Conclusion
Our genetic and molecular evidence suggests that IBR5 is a phosphatase that promotes auxin responses, including auxin-inducible transcription, differently than the TIR1 auxin receptor and without destabilizing Aux/IAA repressor proteins. Our data are consistent with the possibility that auxin-responsive transcription can be modulated downstream of TIR1-mediated repressor degradation.
Overexpression of mtDNA-associated AtWhy2 compromises mitochondrial function
Authors: Maréchal Alexandre , Parent Jean-Sébastien , Sabar Mohammed , Véronneau-Lafortune Félix , Abou-Rached Charbel , Brisson Normand 
Published: April 2008

Abstract

Background
StWhy1, a member of the plant-specific Whirly single-stranded DNA-binding protein family, was first characterized as a transcription factor involved in the activation of the nuclear PR-10a gene following defense-related stress in potato. In Arabidopsis thaliana, Whirlies have recently been shown to be primarily localized in organelles. Two representatives of the family, AtWhy1 and AtWhy3 are imported into plastids while AtWhy2 localizes to mitochondria. Their function in organelles is currently unknown.

Results
To understand the role of mitochondrial Whirlies in higher plants, we produced A. thaliana lines with altered expression of the atwhy2 gene. Organellar DNA immunoprecipitation experiments demonstrated that AtWhy2 binds to mitochondrial DNA. Overexpression of atwhy2 in plants perturbs mitochondrial function by causing a diminution in transcript levels and mtDNA content which translates into a low activity level of respiratory chain complexes containing mtDNA-encoded subunits. This lowered activity of mitochondria yielded plants that were reduced in size and had distorted leaves that exhibited accelerated senescence. Overexpression of atwhy2 also led to early accumulation of senescence marker transcripts in mature leaves. Inactivation of the atwhy2 gene did not affect plant development and had no detectable effect on mitochondrial morphology, activity of respiratory chain complexes, transcription or the amount of mtDNA present. This lack of phenotype upon abrogation of atwhy2 expression suggests the presence of functional homologues of the Whirlies or the activation of compensating mechanisms in mitochondria.

Conclusion
AtWhy2 is associated with mtDNA and its overexpression results in the production of dysfunctional mitochondria. This report constitutes the first evidence of a function for the Whirlies in organelles. We propose that they could play a role in the regulation of the gene expression machinery of organelles.
Implication of Xenobiotic Metabolizing Enzyme gene (CYP2E1, CYP2C19, CYP2D6, mEH and NAT2) Polymorphisms in Breast Carcinoma
Authors: Khedhaier Achraf , Hassen Elham , Bouaouina Noureddine , Gabbouj Sallouha , Ahmed Slim Ben , Chouchane Lotfi 
Published: April 2008

Abstract

Background
Xenobiotic Metabolizing Enzymes (XMEs) contribute to the detoxification of numerous cancer therapy-induced products. This study investigated the susceptibility and prognostic implications of the CYP2E1, CYP2C19, CYP2D6, mEH and NAT2 gene polymorphisms in breast carcinoma patients.

Methods
The authors used polymerase chain reaction and restriction enzyme digestion to characterize the variation of the CYP2E1, CYP2C19, CYP2D6, mEH and NAT2 gene in a total of 560 unrelated subjects (246 controls and 314 patients).

Results
The mEH (C/C) mutant and the NAT2 slow acetylator genotypes were significantly associated with breast carcinoma risk (p = 0.02; p = 0.01, respectively). For NAT2 the association was more pronounced among postmenopausal patients (p = 0.006). A significant association was found between CYP2D6 (G/G) wild type and breast carcinoma risk only in postmenopausal patients (p = 0.04). Association studies of genetic markers with the rates of breast carcinoma specific overall survival (OVS) and the disease-free survival (DFS) revealed among all breast carcinoma patients no association to DFS but significant differences in OVS only with the mEH gene polymorphisms (p = 0.02). In addition, the mEH wild genotype showed a significant association with decreased OVS in patients with axillary lymph node-negative patients (p = 0.03) and with decreasesd DFS in patients with axillary lymph node-positive patients (p = 0.001). However, the NAT2 intermediate acetylator genotype was associated with decreased DFS in axillary lymph node-negative patients.

Conclusion
The present study may prove that polymorphisms of some XME genes may predict the onset of breast carcinoma as well as survival after treatment.
Survival time in severe hemorrhagic shock after perioperative hemodilution is longer with PEG-conjugated human serum albumin than with HES 130/0.4: a microvascular perspective
Authors: Martini Judith , Cabrales Pedro , K Ananda , Acharya Seetharama A , Intaglietta Marcos , Tsai Amy G 
Published: April 2008

Abstract
Introduction
Preoperative hemodilution is an established practice that is applied to reduce surgical blood loss. It has been proposed that polyethylene glycol (PEG) surface decorated proteins such as PEG-conjugated human serum albumin may be used as non-oxygen-carrying plasma expanders. The purpose of this study was to determine whether there is any difference in survival time after severe hemorrhagic shock following extreme hemodilution using a conventional hydroxyethyl starch (HES)-based plasma expander or PEG-albumin.

Methods
Experiments were performed using the hamster skinfold window preparation. Human serum albumin that was surface decorated with PEG was compared with Voluven 6% (Fresenius Kabi, Austria; a starch solution that is of low molecular weight and has a low degree of substitution; HES). These plasma expanders were used for a 50% (blood volume) exchange transfusion to simulate preoperative hemodilution. Exchange transfusion was followed by a 60% (blood volume) hemorrhage to reproduce a severe surgical bleed over a 1 hour period. Observation of the animal was continued for another hour during the shock phase.

Results
The PEG-albumin group exhibited significantly greater survival rate than did the HES group, in which none of the animals survived the hemorrhage phase of the experiment. Among the treatment groups there were no changes in mean arterial pressure and heart rate from baseline after hemodilution. Both groups experienced gradual increases in arterial oxygen tension and disturbance in acid-base balance, but this response was more pronounced in the HES group during the shock period. Mean arterial pressure remained elevated after the initial hemorrhage period in the PEG-albumin group but not in the HES group. Maintenance of a greater mean arterial pressure during the initial stages of hemorrhage is proposed to be in part due to the improved volume expansion with PEG-albumin, as indicated by the significant decrease in systemic hematocrit compared with the HES group. PEG-albumin treatment yielded higher functional capillary density during the initial stages of hemorrhage as compared with HES treatment.

Conclusion
The ability of PEG-albumin to prolong maintenance of microvascular function better than HES is a finding that would be significant in a clinical setting involving preoperative blood management and extreme blood loss.
The influence of ontogeny and light environment on the expression of visual pigment opsins in the retina of the black bream,Acanthopagrus butcheri
Authors: Shand Julia , Davies Wayne L. , Thomas Nicole , Balmer Lois , Cowing Jill A. , Pointer Marie , Carvalho Livia S. , Trezise Ann E. O. , Collin Shaun P. , Beazley Lyn D. , Hunt David M. 
Published: April 2008

SUMMARYThe correlation between ontogenetic changes in the spectral absorption characteristics of retinal photoreceptors and expression of visual pigment opsins was investigated in the black bream, Acanthopagrus butcheri. To establish whether the spectral qualities of environmental light affected the complement of visual pigments during ontogeny, comparisons were made between fishes reared in: (1) broad spectrum aquarium conditions; (2) short wavelength-reduced conditions similar to the natural environment; or (3) the natural environment (wild-caught). Microspectrophotometry was used to determine the wavelengths of spectral sensitivity of the photoreceptors at four developmental stages: larval, post-settlement, juvenile and adult. The molecular sequences of the rod (Rh1) and six cone (SWS1, SWS2A and B, Rh2Aα and β, and LWS) opsins were obtained and their expression levels in larval and adult stages examined using quantitative RT-PCR. The changes in spectral sensitivity of the cones were related to the differing levels of opsin expression during ontogeny. During the larval stage the predominantly expressed opsin classes were SWS1, SWS2B and Rh2Aα, contrasting with SWS2A, Rh2Aβ and LWS in the adult. An increased proportion of long wavelength-sensitive double cones was found in fishes reared in the short wavelength-reduced conditions and in wild-caught animals, indicating that the expression of cone opsin genes is also regulated by environmental light.
Sugars are complementary resources to ethanol in foods consumed by Egyptian fruit bats
Authors: Sánchez Francisco , Kotler Burt P. , Korine Carmi , Pinshow Berry 
Published: April 2008

SUMMARYFood resources are complementary for a forager if their contribution to fitness is higher when consumed together than when consumed independently,e.g. ingesting one may reduce the toxic effects of another. The concentration of potentially toxic ethanol, [EtOH], in fleshy fruit increases during ripening and affects food choices by Egyptian fruit bats, becoming deterrent at high concentrations (⩾1%). However, ethanol toxicity is apparently reduced when ingested along with some sugars; more with fructose than with sucrose or glucose. We predicted (1) that ingested ethanol is eliminated faster by bats eating fructose than by bats eating sucrose or glucose, (2)that the marginal value of fructose-containing food (food+fructose) increases with increasing [EtOH] more than the marginal value of sucrose- or glucose-containing food (food+sucrose, food+glucose), and (3) that by increasing [EtOH] the marginal value of food+sucose is incremented more than that of food+glucose. Ethanol in bat breath declined faster after they ate fructose than after eating sucrose or glucose. When food [EtOH] increased, the marginal value of food+fructose increased relative to food+glucose. However,the marginal value of food+sucrose increased with increasing [EtOH] more than food+fructose or food+glucose. Although fructose enhanced the rate at which ethanol declined in Egyptian fruit bat breath more than the other sugars, the bats treated both fructose and sucrose as complementary to ethanol. This suggests that in the wild, the amount of ethanol-containing fruit consumed or rejected by Egyptian fruit bats may be related to the fruit's own sugar content and composition, and/or the near-by availability of other sucrose- and fructose-containing fruits.