bluuebunny/crossref_metadata_2025_split huggingface dataset:
NM+: software implementing parentage‐based models for estimating gene dispersal and mating patterns in plants
Authors: CHYBICKI IGOR J. , BURCZYK JAROSLAW 
Published: March 2010

AbstractNM+ is computer software designed for making inferences on plant gene dispersal and mating patterns by modelling parentage probabilities of offspring based on the spatially explicit neighbourhood model. NM+ requires a sample of mapped and genotyped candidate parents and offspring; however, offspring may optionally be assigned to single maternal parents (forming so‐called half‐sib progeny arrays). Using maximum likelihood, NM+ estimates a number of parameters, including proportions of offspring due to self‐fertilization, pollen immigration from outside of a defined study site, parameters of pollen (and/or seed) dispersal kernels (exponential‐power, Weibull, geometric or 2Dt) and selection gradients relating covariates (phenotypic traits) with male (and/or female) reproductive success. NM+ allows for missing data both in parents and in offspring. It accounts for null alleles and their frequencies can optionally be considered as estimable parameters. Data files are formatted in a table‐like structure so they can be easily prepared in a spreadsheet software. By default NM+ is for studying plant populations, however, it can be used for any organism as long as data requirements and model assumptions are met. NM+ runs under Windows, but it can be launched under Linux using WINE emulator. NM+ can be downloaded free of charge from http://www.genetyka.ukw.edu.pl/index_pliki/software.htm.
Ultrasound biomicroscopic study of the stability of intraocular lens implants after phacoemulsification cataract surgery
Authors: Ang Ghee Soon , Duncan Laura , Atta Hatem R. 
Published: March 2010

Abstract.Purpose:  To assess the postoperative stability of three‐piece intraocular lens (IOL) implants using ultrasound biomicroscopy (UBM).Methods:  This is a prospective observational cohort case series. Best‐corrected visual acuity (BCVA) assessment, slit lamp examination, refraction and UBM evaluation were performed preoperatively and at 1, 6, 12, 18 and 24 months postoperatively. The anterior chamber depth (ACD) and IOL tilt angles at the 12, 6, 3 and 9 o’clock meridians were assessed.Results:  Twenty‐one consecutive adult patients (21 study eyes) were recruited, but two dropped out from the study. The average age during cataract surgery was 71.7 years (60–83, SD 6.0). There were very slight changes in the refraction and IOL stability characteristics at all the postoperative follow‐up time points. These were not found to be statistically significant, apart from the increase in ACD from months one (3.85 ± SD 0.29) to six (3.91 ± SD 0.26) (p = 0.01, paired t‐test).Conclusion:  There was a small but statistically significant increase in ACD between the first and sixth postoperative month, but ACD remained stable thereafter. This was not associated with any significant changes in refraction or BCVA. In contrast, IOL optic tilt remained statistically unchanged throughout the 24‐month study duration.
Combined Antibacterial and Anti-Inflammatory Activity of a Cationic Disubstituted Dexamethasone-Spermine Conjugate
Authors: Bucki Robert , Leszczyńska Katarzyna , Byfield Fitzroy J. , Fein David E. , Won Esther , Cruz Katrina , Namiot Andrzej , Kułakowska Alina , Namiot Zbigniew , Savage Paul B. , Diamond Scott L. , Janmey Paul A. 
Published: March 2010

ABSTRACT

The rising number of antibiotic-resistant bacterial strains represents an emerging health problem that has motivated efforts to develop new antibacterial agents. Endogenous cationic antibacterial peptides (CAPs) that are produced in tissues exposed to the external environment are one model for the design of novel antibacterial compounds. Here, we report evidence that disubstituted dexamethasone-spermine (D2S), a cationic corticosteroid derivative initially identified as a by-product of synthesis of dexamethasone-spermine (DS) for the purpose of improving cellular gene delivery, functions as an antibacterial peptide-mimicking molecule. This moiety exhibits bacterial killing activity against clinical isolates of
Staphylococcus aureus
,
Pseudomonas aeruginosa
present in cystic fibrosis (CF) sputa, and
Pseudomonas aeruginosa
biofilm. Although compromised in the presence of plasma, D2S antibacterial activity resists the proteolytic activity of pepsin and is maintained in ascites, cerebrospinal fluid, saliva, and bronchoalveolar lavage (BAL) fluid. D2S also enhances
S. aureus
susceptibility to antibiotics, such as amoxicillin (AMC), tetracycline (T), and amikacin (AN). Inhibition of interleukin-6 (IL-6) and IL-8 release from lipopolysaccharide (LPS)- or lipoteichoic acid (LTA)-treated neutrophils in the presence of D2S suggests that this molecule might also prevent systemic inflammation caused by bacterial wall products. D2S-mediated translocation of green fluorescent protein (GFP)-labeled glucocorticoid receptor (GR) in bovine aorta endothelial cells (BAECs) suggests that some of its anti-inflammatory activities involve engagement of glucocorticoid receptors. The combined antibacterial and anti-inflammatory activities of D2S suggest its potential as an alternative to natural CAPs in the prevention and treatment of some bacterial infections.
Fine-Tuning Synthesis ofYersinia pestisLcrV from Runaway-Like Replication Balanced-Lethal Plasmid in aSalmonella entericaSerovar Typhimurium Vaccine Induces Protection against a LethalY. pestisChallenge in Mice
Authors: Torres-Escobar Ascención , Juárez-Rodríguez María Dolores , Gunn Bronwyn M. , Branger Christine G. , Tinge Steven A. , Curtiss Roy 
Published: March 2010

ABSTRACTA balanced-lethal plasmid expression system that switches from low-copy-number to runaway-like high-copy-number replication (pYA4534) was constructed for the regulated delayedin vivosynthesis of heterologous antigens by vaccine strains. This is an antibiotic resistance-free maintenance system containing theasdAgene (essential for peptidoglycan synthesis) as a selectable marker to complement the lethal chromosomal ΔasdAallele in live recombinant attenuatedSalmonellavaccines (RASVs) such asSalmonella entericaserovar Typhimurium strain χ9447. pYA4534 harbors two origins of replication, pSC101 and pUC (low and high copy numbers, respectively). The pUC replication origin is controlled by a genetic switch formed by the operator/promoter of the P22crogene (O/Pcro) (PR), which is negatively regulated by an arabinose-inducible P22c2gene located on both the plasmid and the chromosome (araCPBADc2). The absence of arabinose, which is unavailablein vivo, triggers replication to a high-copy-number plasmid state. To validate these vector attributes, theYersinia pestisvirulence antigen LcrV was used to develop a vaccine against plague. AnlcrVsequence encoding amino acids 131 to 326 (LcrV196) was optimized for expression inSalmonella, flanked with nucleotide sequences encoding the signal peptide (SS) and the carboxy-terminal domain (CT) of β-lactamase, and cloned into pYA4534 under the control of the Ptrcpromoter to generate plasmid pYA4535. Our results indicate that the liveSalmonellavaccine strain χ9447 harboring pYA4535 efficiently stimulated a mixed Th1/Th2 immune response that protected mice against lethal challenge withY. pestisstrain CO92 introduced through either the intranasal or subcutaneous route.
Association of Pathogen Strain-Specific Gene Transcription and Transmission Efficiency Phenotype ofAnaplasma marginale
Authors: Agnes Joseph T. , Herndon David , Ueti Massaro W. , Ramabu Solomon S. , Evans Marc , Brayton Kelly A. , Palmer Guy H. 
Published: March 2010

ABSTRACTEfficient transmission of pathogens by an arthropod vector is influenced by the ability of the pathogen to replicate and develop infectiousness within the arthropod host. While the basic life cycle of development within and transmission from the arthropod vector are known for many bacterial and protozoan pathogens, the determinants of transmission efficiency are largely unknown and represent a significant gap in our knowledge. The St. Maries strain ofAnaplasma marginaleis a high-transmission-efficiency strain that replicates to a high titer in the tick salivary gland and can be transmitted by <10 ticks. In contrast,A. marginalesubsp.centrale(Israel vaccine strain) has an identical life cycle but replicates to a significantly lower level in the salivary gland, with transmission requiring >30-fold more ticks. We hypothesized that strain-specific genes expressed in the tick salivary gland at the time of transmission are linked to the differences in the transmission efficiency phenotype. Using both annotation-dependent and -independent analyses of the complete genome sequences, we identified 58 strain-specific genes. These genes most likely represent divergence from common ancestral genes in one or both strains based on analysis of synteny and lack of statistical support for acquisition as islands by lateral gene transfer. Twenty of the St. Maries strain-specific genes and 16 of the strain-specific genes in the Israel strain were transcribed in the tick salivary gland at the time of transmission. Although associated with the transmission phenotype, the expression levels of strain-specific genes were equal to or less than the expression levels in infected erythrocytes in the mammalian host, suggesting that function is not limited to salivary gland colonization.
Genome Sequencing of Recent Clinical
Chlamydia trachomatis
Strains Identifies Loci Associated with Tissue Tropism and Regions of Apparent Recombination
Authors: Jeffrey Brendan M. , Suchland Robert J. , Quinn Kelsey L. , Davidson John R. , Stamm Walter E. , Rockey Daniel D. 
Published: March 2010

ABSTRACT

The human pathogen
Chlamydia trachomatis
exists as multiple serovariants that have distinct organotropisms for different tissue sites. Culture and epidemiologic data have demonstrated that serovar G is more prevalent, while serovar E is less prevalent, for rectal isolates from men having sex with men (MSM). The relative prevalence of these serovars is the opposite for isolates from female cervical infections. In contrast, the prevalence of serovar J isolates is approximately the same at the different tissue sites, and these isolates are the only C-class strains that are routinely cultured from MSM populations. These correlations led us to hypothesize that polymorphisms in open reading frame (ORF) sequences correlate with the different tissue tropisms of these serovars. To explore this possibility, we sequenced and compared the genomes of clinical anorectal and cervical isolates belonging to serovars E, G, and J and compared these genomes with each other, as well as with a set of previously sequenced genomes. We then used PCR- and restriction digestion-based genotyping assays performed with a large collection of recent clinical isolates to show that polymorphisms in ORFs CT144, CT154, and CT326 were highly associated with rectal tropism in serovar G isolates and that polymorphisms in CT869 and CT870 were associated with tissue tropism across all serovars tested. The genome sequences collected were also used to identify regions of likely recombination in recent clinical strains. This work demonstrated that whole-genome sequencing along with comparative genomics is an effective approach for discovering variable loci in
Chlamydia
spp. that are associated with clinical presentation.
Distinct Physiologic and Inflammatory Responses Elicited in Baboons after Challenge with Shiga Toxin Type 1 or 2 from Enterohemorrhagic
Escherichia coli
Authors: Stearns-Kurosawa D. J. , Collins Valta , Freeman Scott , Tesh Vernon L. , Kurosawa Shinichiro 
Published: March 2010

ABSTRACT

Shiga toxin-producing
Escherichia coli
is a principal source of regional outbreaks of bloody diarrhea and hemolytic-uremic syndrome in the United States and worldwide. Primary bacterial virulence factors are Shiga toxin types 1 and 2 (Stx1 and Stx2), and we performed parallel analyses of the pathophysiologies elicited by the toxins in nonhuman primate models to identify shared and unique consequences of the toxemias. After a single intravenous challenge with purified Stx1 or Stx2, baboons (
Papio
) developed thrombocytopenia, anemia, and acute renal failure with loss of glomerular function, in a dose-dependent manner. Differences in the timing and magnitude of physiologic responses were observed between the toxins. The animals were more sensitive to Stx2, with mortality at lower doses, but Stx2-induced renal injury and mortality were delayed 2 to 3 days compared to those after Stx1 challenge. Multiplex analyses of plasma inflammatory cytokines revealed similarities (macrophage chemoattractant protein 1 [MCP-1] and tumor necrosis factor alpha [TNF-α]) and differences (interleukin-6 [IL-6] and granulocyte colony-stimulating factor [G-CSF]) elicited by the toxins with respect to the mediator induced and timing of the responses. Neither toxin induced detectable levels of plasma TNF-α. To our knowledge, this is the first time that the
in vivo
consequences of the toxins have been compared in a parallel and reproducible manner in nonhuman primates, and the data show similarities to patient observations. The availability of experimental nonhuman primate models for Stx toxemias provides a reproducible platform for testing antitoxin compounds and immunotherapeutics with outcome criteria that have clinical meaning.
THE NUMBERS OF PERIODIC ORBITS HIDDEN AT FIXED POINTS OF THREE-DIMENSIONAL HOLOMORPHIC MAPPINGS
Authors: ZHANG GUANG YUAN 
Published: March 2010

Let M be a positive integer and let f be a holomorphic mapping from a ball Δn = {x ∈ ℂn;|x| < δ} into ℂn such that the origin 0 is an isolated fixed point of both f and the M-th iteration fM of f. Then one can define the number [Formula: see text], which can be interpreted to be the number of periodic orbits of f with period M hidden at the fixed point 0. For a 3 × 3 matrix A, of which the eigenvalues are all distinct primitive M-th roots of unity, we will give a sufficient and necessary condition for A such that for any holomorphic mapping f: Δ 3 → ℂ3 with f(0) = 0 and Df(0) = A, if 0 is an isolated fixed point of the M-th iteration fM, then [Formula: see text].
TOWARDS SPECIAL DAEMON-SENSITIVE ELECTRON MULTIPLIER: POSITIVE OUTCOME OF MARCH 2009 EXPERIMENT
Authors: DROBYSHEVSKI E. M. , DROBYSHEVSKI M. E. 
Published: March 2010

Results of the experiments on daemon detection performed in St-Petersburg in March 2009 are presented. Adding the data obtained with the daemon-sensitive FEU-167-1 PM tubes to the data amassed in our previous measurements (starting from 2000) raises the confidence level of existence of the spring maximum in NEACHO (near-Earth almost circular heliocentric orbit) daemon flux to ~ 5σ. The first test experiments conducted with the "dark" electron multiplier tubes, TEU-167 with a thick (~ 0.5 μm) Al coating over all of the inner surface of the near-cathode multiplier section, including also its front screen, look encouraging. They provide supportive evidence for the existence of diurnal modulation of the daemon flux and offer ~ 3.4 × 10-7 cm-2s-1 for its lower limit in March, in good agreement with our earlier estimates and measurements.
USING ACCURACY-BASED LEARNING CLASSIFIER SYSTEMS FOR ADAPTABLE STRATEGY GENERATION IN GAMES AND INTERACTIVE VIRTUAL SIMULATIONS
Authors: JUAN ALEJANDRO , PAZZI RICHARD W. , BOUKERCHE AZZEDINE 
Published: March 2010

Historically, the artificial intelligence (AI) of interactive virtual simulations or games is usually driven by pre-defined static scripts. One of the disadvantages of such scripted opponents is that they can be deciphered and countered by an intelligent user. Thus, the user has the opportunity to find weaknesses and an easy solution against the virtual simulation, which diminishes the efficiency aspect of a training session or entertaining value drastically. While randomization can be used to mask the static behaviour of a scripted AI, it is possible to develop much richer solutions by applying Learning Classifier System (LCS) techniques to create agents with intelligent-like behaviors. Learning Classifier Systems are rule-based machine learning techniques that rely on a Genetic Algorithm to discover a knowledge map used to classify an input space into a set of actions.In this paper, we propose the use of an unsupervised machine learning technique called Accuracy-based Learning Classifier Systems (XCS) for adaptable strategy generation that can be used in virtual simulations or games. XCS use a Genetic Algorithm to evolve a knowledge base in the form of rules. The performance and adaptability of the strategies and tactics developed with the XCS is analyzed by facing these against scripted opponents on a real time strategy game. According to our experiments, the rulesets are able to adapt to a wide array of behaviors from its opponents, as opposed to a linear game script, which is limited in its ability to adapt to its environment.
Improvement of Surface Longwave Flux Algorithms Used in CERES Processing
Authors: Gupta Shashi K. , Kratz David P. , Stackhouse Paul W. , Wilber Anne C. , Zhang Taiping , Sothcott Victor E. 
Published: March 2010

Abstract
An improvement was developed and tested for surface longwave flux algorithms used in the Clouds and the Earth’s Radiant Energy System processing based on lessons learned during the validation of global results of those algorithms. The algorithms involved showed significant overestimation of downward longwave flux for certain regions, especially dry–arid regions during hot times of the day. The primary cause of this overestimation was identified and the algorithms were modified to (i) detect meteorological conditions that would produce an overestimation, and (ii) apply a correction when the overestimation occurred. The application of this correction largely eliminated the positive bias that was observed in earlier validation studies. Comparisons of validation results before and after the application of correction are presented.
Role of Polar Amplification in Long-Term Surface Air Temperature Variations and Modern Arctic Warming
Authors: Bekryaev Roman V. , Polyakov Igor V. , Alexeev Vladimir A. 
Published: March 2010

Abstract
This study uses an extensive dataset of monthly surface air temperature (SAT) records (including previously unutilized) from high-latitude (&gt;60°N) meteorological land stations. Most records have been updated by very recent observations (up to December 2008). Using these data, a high-latitude warming rate of 1.36°C century−1 is documented for 1875–2008—the trend is almost 2 times stronger than the Northern Hemisphere trend (0.79°C century−1), with an accelerated warming rate in the most recent decade (1.35°C decade−1). Stronger warming in high-latitude regions is a manifestation of polar amplification (PA). Changes in SAT suggest two spatial scales of PA—hemispheric and local. A new stable statistical measure of PA linking high-latitude and hemispheric temperature anomalies via a regression relationship is proposed. For 1875–2008, this measure yields PA of ∼1.62. Local PA related to the ice–albedo feedback mechanisms is autumnal and coastal, extending several hundred kilometers inland. Heat budget estimates suggest that a recent reduction of arctic ice and anomalously high SATs cannot be explained by ice–albedo feedback mechanisms alone, and the role of large-scale mechanisms of PA of global warming should not be overlooked.
The Upstream Spreading of Bottom-Trapped Plumes
Authors: Matano Ricardo P. , Palma Elbio D. 
Published: March 2010

Abstract
It is well known that numerical simulations of freshwater discharges produce plumes that spread in the direction opposite to that of the propagation of coastally trapped waves (the upstream direction). The lack of a theory explaining these motions in unforced environments deemed the numerical results suspect. Thus, it became a common practice in numerical studies to add a downstream mean flow to arrest the development of the upstream perturbation. This approach is generally unjustified, and it remains a matter of interest to determine if the upstream displacement produced by models is a geophysical phenomenon or a consequence of erroneous assumptions in the model setup. In this article, the results of highly idealized numerical experiments are used to investigate these matters. It is shown that this phenomenon is associated with the geostrophic adjustment of the discharge and that upstream motion is endemic to the baroclinic structure of bottom-trapped plumes. It is also shown that downstream displacements are generated by the cross-shelf barotropic pressure gradient generated by the propagation of coastally trapped waves. Sensitivity experiments indicate that the speed of upstream propagation and the density structure of the plume are affected by bottom friction, the slope of the bottom, and the magnitude of the density anomaly. Bottom friction in particular slows down the progression of the plume and changes its density structure, producing a more homogeneous downstream region and a more stratified upstream region.
Dependence of Wind-Driven Current on Wind Stress Direction in a Small Semienclosed, Homogeneous Rotating Basin
Authors: Hinata Hirofumi , Kanatsu Nobuyoshi , Fujii Satoshi 
Published: March 2010

Abstract
The dependence of wind-driven current (WDC) on wind stress direction in a small semienclosed, homogeneous rotating basin is investigated using a linear steady-state analytical model based on Ekman solutions. The model is applicable to the middle of the basin (midbasin), and the current is driven by a constant wind stress of an arbitrary direction. The WDC is made up of wind stress–driven current (WSDC) and pressure-driven current (PDC) components. The laterally varying water depth of the basin confines the total volume transport in the longitudinal direction while the wind stress–driven volume transport changes direction according to the wind stress direction. Therefore, the pressure-driven volume transport or, equivalent, the pressure gradient depends on the wind stress direction: the relationship between the pressure gradient and the wind stress is anisotropic. As a result, the midbasin WDC is also dependent on the wind stress direction. The dependence varies according to the lateral position and Ekman number E. For large E (small rotation), the longitudinal volume transport is generally proportional to the longitudinal wind stress component. Hence, the ratio of the volume transport driven by the wind stress of direction θ (θ &gt; 0) to that driven by the longitudinal wind stress (θ = 0) becomes cosθ. For small E (large rotation), the ratio becomes larger than cosθ. The extent to which each component of wind stress contributes to the generation of the pressure gradient to satisfy no-net-longitudinal and no-lateral transports is determined by a wind stress–pressure gradient transformation matrix, whose components depend on the lateral position and E.