bluuebunny/crossref_metadata_2025_split huggingface dataset:
Relationships between metabolic fluxes and enzyme amino acid composition
Authors: Kampenusa Inara , Zikmanis Peteris 
Published: December 2012

AbstractMetabolic fluxes are a key parameter of metabolic pathways being closely related to the kinetic properties of enzymes and could be conditional on their sequence characteristics. This study examines possible relationships between the metabolic fluxes and the amino acid (AA) composition (AAC) for enzymes from the yeast Saccharomyces cerevisiae glycolysis pathway. Metabolic fluxes were quantified by the COPASI tool using the kinetic models of Hynne and Teusink at 25 mM, 50 mM, and 100 mM of external glucose or employing literature data for cognate kinetic or stoichiometric models. The enzyme sequences were taken from the UniProtKB, and the AAC computed by the ExPASy/ProtParam tool. Multiple linear regressions (89.07% < R2 adjusted < 91.82%; P<0.00001) were found between the values of metabolic fluxes and the selected sets of AA frequencies (5 to 7 for each model). Selected AA differed from the rest by their physicochemical and structural propensities, thus suggesting a distinctive contribution to the properties of enzymes, and hence the metabolic fluxes. The results provide evidence that metabolic fluxes of the yeast glycolysis pathway are closely related to the AAC of relevant enzymes and support the view that catalytic, binding and structural residues are interdependent to ensure the efficiency of biocatalysts.
Characterisation of hydroxyapatite surface modified by poly(ethylene glycol) and poly(hydroxyethyl methacrylate) grafting
Authors: Adamska Katarzyna , Szubert Magdalena , Voelkel Adam , Okulus Zuzanna 
Published: December 2012

AbstractHydroxyapatite (HA) has many applications in medicine as a biocompatible and bioactive biomaterial. Numerous studies have shown that modification of the HA surface can improve its biological and chemical properties. However, little is known about the surface properties of modified materials. In this paper the influence of organic polymers: polyethylene glycol (PEG) and polyhydroxyethyl methacrylate (pHEMA) on the surface properties and surface chemistry of hydroxyapatite (HA) is presented. The surface properties of modified HA were characterised by the FT-IR, XPS, BET, and zeta potential measurements. Specific surface area was determined by BET. Infrared and XPS spectra confirmed the presence of PEG and pHEMA on the surface of HA. The BET N2 adsorption revealed slight changes in the HA surface chemistry after grafting modification. The surface chemical properties of the HA were considered to be based on the zeta potential. The decrease in zeta potential results in the increasing stability of the modified material and also in the reduction of bacterial adhesion. The reaction for surface modification of HA is proposed and described.
Bi-hybrid coatings: polyaniline-montmorillonite filler in organic-inorganic polymer matrix
Authors: Špírková Milena , Bober Patrycja , Kotek Jiří , Stejskal Jaroslav 
Published: December 2012

AbstractA bi-hybrid composite is represented by an organic-inorganic (O-I) filler dispersed in an O-I matrix. Polyaniline-montmorillonite, as a nanocomposite filler, was synthesised by two independent processes: (1) montmorillonite was surface-modified with a conducting polymer, polyaniline, during the in-situ oxidation of aniline or (2) montmorillonite was pre-treated with aniline, then the aniline was polymerised and the polyaniline subsequently produced penetrated the montmorillonite structure. The organic-inorganic polymer matrix was formed in two independent steps: (1) inorganic building units were formed in situ by the sol-gel process, (2) followed by organic polymeric matrix formation by polyaddition reactions of epoxy groups with amines. Polyaniline-montmorillonite filler was added to the reaction system between these two steps, i.e. when the inorganic structures of the O-I matrix have already been formed but prior to formation of the organic polymeric matrix. Two different O-I matrices were prepared from functionalised organosilicon precursors and oligomeric amines. 3-[(Glycidyloxy)propyl]trimethoxysilane reacted with α,ω-oligo(propylene oxide) diamine and diethoxy[3-(glycidyloxy)propyl]-methylsilane reacted with α,ω-oligo(propylene oxide) triamine. The resulting bi-hybrid coatings, the O-I filler dispersed in the O-I matrix, were characterised by atomic-force and optical microscopies, and also by tensile tests. The filler composition affected both the mechanical and surface properties of the coatings.
The relationship between antibiotic therapy in early childhood and the symptoms of allergy in children aged 6–8 years — the questionnaire study results
Authors: Raciborski Filip , Tomaszewska Aneta , Komorowski Jarosław , Samel-Kowalik Piotr , Białoszewski Artur , Artur Walkiewicz , Lusawa Adam , Szymański Jakub , Opoczyńska Dagmara , Drużba Michał , Borowicz Jacek , Lipiec Agnieszka , Kapalczynski Wojciech , Samoliński Bolesław 
Published: December 2012

Abstract
Tracking the motion of recognizable sea-ice objects from coastal radar image sequences
Authors: Karvonen Juha 
Published: December 2012

AbstractThe Finnish Meteorological Institute has installed image-capturing devices on some Baltic Sea coastal radars for operational sea-ice monitoring and ice product validation. These devices produce radar images, which are saved operationally at about every 2 min. These data can efficiently be utilized in automated tracking of ice motion over sequences of radar images. Reliable estimates of point-wise ice drift can be used as virtual drifter buoys to validate fine-scale ice models. For this purpose we have developed an algorithm, which first locates objects that can reliably be recognized from one radar image to another, and then tracks the motion of these objects until they are lost by the algorithm. The recognizable objects in the first image of an image sequence are located by requiring an object to include a textural content, i.e. the object does not solely consist of a uniform area, and detected edge corner points. The corner points are required to exclude straight linear edges. After locating a suitable number of traceable objects, the tracking is performed between each pair of successive images using a two-resolution phase-correlation algorithm. We have tested the tracking algorithm using image sequences of two coastal radars collected during the 2010/11 and 2011/12 winters.
Raised Vaginal Fluid Fibronectin Level Indicates Premature Rupture of Membrane
Authors: Rahman Shamima , Jahan Samsad , Habib Samira Humaira , Sultana Nasrin , Sultana Mst Nigar , Paul Debashish , Bhowmik Amrita , Begum Khodeja 
Published: December 2012

Background: Premature rupture of membrane (PROM) is one of the common complications of pregnancy that has major impact on fetal and neonatal outcome. It is the commonest clinical event where a normal pregnancy becomes suddenly a high-risk one for mother and fetus or neonate. Objective: The study was undertaken to investigate whether raised fibronectin level in vaginal fluid may indicate premature rupture of membrane. Materials and Methods: This cross sectional study was conducted in the department of Obstetrics and Gynecology in Sir Salimullah Medical College & Mitford Hospital, Dhaka during the period of January 2006 to December 2007. A total of 114 pregnant women with gestational age 28th week up to 40th week were included. Sixty were PROM (Group I) and 54 were non-PROM (Group II) subjects. Fibronectin in vaginal fluid was measured by an immunochemical reaction by nephelometer. Statistical analysis was done by SPSS version 10.0. Results: The PROM patients had significantly higher concentration of fibronectin (225.77 ± 115.18 ng/mL) compared to that in non-PROM subjects (8.04 ± 16.17 ng/mL) (p < 0.001). Conclusion: It can be concluded that in cases of unequivocal rupture or intactness of the membranes, the result of the fibronectin test corresponds well with the clinical situation. So fibronectin is a sensitive test for detection of amniotic fluid in the vagina. DOI: http://dx.doi.org/10.3329/jemc.v2i2.12841 J Enam Med Col 2012; 2(2): 74-79
Isolation and characterization of microsatellite loci in a polyploid alpine herb, Callianthemum miyabeanum (Ranunculaceae)
Authors: Abe Harue , Nishikawa Yoko , Shimamura Takashi , Sato Ken , Suyama Yoshihisa 
Published: December 2012

• Premise of the study: Nuclear microsatellite primers were developed to analyze the clonal diversity and population genetic structure of the endemic polyploid herb Callianthemum miyabeanum.• Methods and Results: Using a protocol for constructing microsatellite‐enriched libraries, 15 primer sets were developed for use in C. miyabeanum. The number of alleles found ranged from five to 22. The estimated range of expected heterozygosities was 0.574 to 0.907, and the Shannon–Weiner diversity index ranged from 1.061 to 2.733. Cross‐amplification of all loci was also successful in the closely related endemic species C. kirigishiense and C. hondoense.• Conclusions: The development of these microsatellite loci will facilitate a deeper understanding of the genetic diversity, mode of reproduction, and population structure of not only C. miyabeanum, but also the other Callianthemum species endemic to Japan.
Diversification of the newly recognized lichen‐forming fungal lineage Montanelia (Parmeliaceae, Ascomycota) and its relation to key geological and climatic events
Authors: Divakar Pradeep K. , Del‐Prado Ruth , Lumbsch H. Thorsten , Wedin Mats , Esslinger Theodore L. , Leavitt Steven D. , Crespo Ana 
Published: December 2012

• Premise of the study: In spite of the recent advances in generic and species circumscriptions and in recognizing species diversity in lichen‐forming fungi, the timing of speciation and the factors that promote diversification in lichens remain largely unexplored. We used brown parmelioids as a model to assess the timing of divergence and explore the impact of geological and climatic events on lineage divergence and diversification in lichenized fungi. Additionally, to clarify the phylogenetic position of the species currently placed in Melanelia disjuncta group, we evaluated the taxonomic status and phylogenetic relationships within Parmeliaceae.• Methods: Phylogenetic relationships and divergence time estimates were inferred from a four‐loci data set. Alternative hypotheses were tested using Shimodaira‐Hasegawa and expected likelihood weights tests.• Key results: The M. disjuncta group forms a strongly supported, monophyletic lineage independent from Melanelia s.s. The M. disjuncta clade arose ca. 23.1 million years ago (Ma). Our results suggest that most of the lineages within the clade diversified during the Miocene (17.6 to 11.2 Ma). The split of other brown parmelioids, such as Emodomelanelia‐Melanelixia occurred ca. 41.70 Ma, and the radiation of Melanelixia began during the Eocene–Oligocene transition (ca. 33.75 Ma).• Conclusions: Montanelia is described here as a new genus to accommodate species of the Melanelia disjuncta group. Further, the study indicates that the current species delimitation within the newly described genus requires revision. We provide evidence of lineage divergence of Montanelia at the Oligocene–Miocene boundary. Our results indicate that the diversification during Miocene would have happened during major mountain uplifts.
Episodic recruitment of the seedling banks in balsam fir and white spruce
Authors: Rossi Sergio , Morin Hubert , Gionest François , Laprise Danielle 
Published: December 2012

• Premise of the study: In ecosystems where seed production is low and masting years are sporadic, or with species that have short‐lived seeds, regeneration is assured by seedling banks rather than seed banks. Seedling establishment and survival play a critical role in determining the composition of these plant communities by supplying new individuals for their maintenance. Seedling emergence and mortality were investigated to test the hypothesis that recruitment into the seedling bank is periodic.• Materials and methods: Seed production and seedling emergence and survival was monitored during 1994‐2007 in balsam fir (Abies balsamea) and white spruce (Picea glauca) in four pristine stands of the boreal forest of Quebec, Canada. Measurements were collected twice per month by sampling one permanent plot of 20 × 20 m per stand.• Key results: Seed‐rain abundance reached 9 × 103 seeds m−2 year−1, and was characterized by synchronous sequences of low and high seed production. New seedlings appeared only during the year following a seed production of at least 1 × 103 and 1.5 × 102 seeds m−2 year−1 for balsam fir and white spruce, respectively. Seedlings emerged in July and survived 34‐52 d on average, with balsam fir showing a longer lifespan and lower mortality, although 85–99% of seedlings died before completing one year of life.• Conclusions: The emergence of young seedlings was coupled with massive seed rains, which allowed synchronous replenishment of the seedling banks among stands and species, and generated different cohorts, yielding a discontinuous age structure.
Interrelationships of petiolar air canal architecture, water depth, and convective air flow in Nymphaea odorata (Nymphaeaceae)
Authors: Richards Jennifer H. , Kuhn David N. , Bishop Kristin 
Published: December 2012

• Premise of the study: Nymphaea odorata grows in water up to 2 m deep, producing fewer larger leaves in deeper water. This species has a convective flow system that moves gases from younger leaves through submerged parts to older leaves, aerating submerged parts. Petiolar air canals are the convective flow pathways. This study describes the structure of these canals, how this structure varies with water depth, and models how convective flow varies with depth.• Methods: Nymphaea odorata plants were grown at water depths from 30 to 90 cm. Lamina area, petiolar cross‐sectional area, and number and area of air canals were measured. Field‐collected leaves and leaves from juvenile plants were analyzed similarly. Using these data and data from the literature, we modeled how convective flow changes with water depth.• Key results: Petioles of N. odorata produce two central pairs of air canals; additional pairs are added peripherally, and succeeding pairs are smaller. The first three pairs account for 96% of air canal area. Air canals form 24% of petiolar cross‐sectional area. Petiolar and air canal cross‐sectional areas increase with water depth. Petiolar area scales with lamina area, but the slope of this relationship is lower in 90 cm water than at shallower depths. In our model, the rate of convective flow varied with depth and with the balance of influx to efflux leaves.• Conclusions: Air canals in N. odorata petioles increase in size and number in deeper water but at a decreasing amount in relation to lamina area. Convective flow also depends on the number of influx to efflux laminae.
Within‐ and trans‐generational plasticity affects the opportunity for selection in barbed goatgrass (Aegilops triuncialis)
Authors: Espeland Erin K. , Rice Kevin J. 
Published: December 2012

•Premise of the study:Environments are composed of selective agents, and environments may also modify the efficacy of these agents. Environments affect the rate of maximum evolutionary change by influencing variation in relative fitness (i.e., the opportunity for selection, orI). Within‐ and transgenerational plastic environmental responses may affectI, speeding or slowing processes of local adaptation.•Methods:We determined whether environmental factors affected the opportunity for selection (I) inAegilops triuncialis(barbed goatgrass) by measuringIas a within‐ and transgenerational plastic response to two maternal glasshouse environments (serpentine/dry and loam/moist). We also determined whether this species’ two most common genetic lineages (determined by DNA microsatellite length polymorphism) varied in response to glasshouse treatments.•Key Results:Opportunity for selection was less for plants grown in the dry serpentine environment than for plants grown in the moist loam environment. This response varied between genetic lineages. The east lineage exhibited a within‐generation response to the dry serpentine environment. For both seed mass and average seed weight in this lineage, the opportunity for selection was lower in dry serpentine than in moist loam. The west lineage had a transgenerational response to the dry serpentine such that the opportunity for selection for seed number and seed mass was lower for plants produced by mothers grown in dry serpentine than for plants produced by mothers in moist loam.•Conclusions:Phenotypic variation in relative fitness is constrained by the dry serpentine environment, which leads to lower evolvability in this environment. Within‐ and transgenerational effects of the environment may slow local adaptation to serpentine soils.
Deep sequencing of amplicons reveals widespread intraspecific hybridization and multiple origins of polyploidy in big sagebrush (Artemisia tridentata; Asteraceae)
Authors: Richardson Bryce A. , Page Justin T. , Bajgain Prabin , Sanderson Stewart C. , Udall Joshua A. 
Published: December 2012

• Premise of the study: Hybridization has played an important role in the evolution and ecological adaptation of diploid and polyploid plants. Artemisia tridentata (Asteraceae) tetraploids are extremely widespread and of great ecological importance. These tetraploids are often taxonomically identified as A. tridentata subsp. wyomingensis or as autotetraploids of diploid subspecies tridentata and vaseyana. Few details are available as to how these tetraploids are formed or how they are related to diploid subspecies.• Methods: We used amplicon sequencing to assess phylogenetic relationships among three recognized subspecies: tridentata, vaseyana, and wyomingensis. DNA sequence data from putative genes were pyrosequenced and assembled from 329 samples. Nucleotide diversity and putative haplotypes were estimated from the high‐read coverage. Phylogenies were constructed from Bayesian coalescence and neighbor‐net network analyses.• Key results: Analyses support distinct diploid subspecies of tridentata and vaseyana in spite of known hybridization in ecotones. Nucleotide diversity estimates of populations compared to the total diversity indicate the relationships are predominately driven by a small proportion of the amplicons. Tetraploids, including subspecies wyomingensis, are polyphyletic occurring within and between diploid subspecies groups.• Conclusions: Artemisia tridentata is a species comprising phylogenetically distinct diploid progenitors and a tetraploid complex with varying degrees of phylogenetic and morphological affinities to the diploid subspecies. These analyses suggest tetraploids are formed locally or regionally from diploid tridentata and vaseyana populations via autotetraploidy, followed by introgression between tetraploid groups. Understanding the phylogenetic vs. ecological relationships of A. tridentata subspecies will have bearing on how to restore these desert ecosystems.
Mycobacterial Interferon-γ Release Variations During Longterm Treatment with Tumor Necrosis Factor Blockers: Lack of Correlation with Clinical Outcome
Authors: SCRIVO ROSSANA , SAUZULLO ILARIA , MENGONI FABIO , PRIORI ROBERTA , COPPOLA MARIATERESA , IAIANI GIANCARLO , DI FRANCO MANUELA , VULLO VINCENZO , MASTROIANNI CLAUDIO MARIA , VALESINI GUIDO 
Published: December 2012

Objective.To assess the performance of serial QuantiFeron-TB Gold In-Tube (QFT-GIT) tests in patients with rheumatic diseases during longterm systemic treatment with biologic therapy, evaluating conversions and reversions in relation to the clinical outcome.Methods.We conducted a prospective study on patients awaiting biologic agents. At baseline, they had chest radiographs, QFT-GIT tests, and tuberculin skin tests (TST); QFT-GIT was repeated at 3, 6, 12, and 18 months after onset of biologic therapy. In patients with no evidence of latent tuberculosis infection (LTBI) at baseline, TST was repeated at 12 months of biologic treatment.Results.Among patients (n = 102; women 65.7%; median age 47 yrs, range 20–82), 14 (13.7%) were considered as having LTBI because of a minimum of 1 abnormal screening test. The agreement between QFT-GIT and TST was 88% (κ = 0.14). During biologic treatment, both patients with (n = 14) and those without (n = 88) evidence of LTBI at baseline showed conversions and reversions in QFT-GIT results at different timepoints. These fluctuations were not paralleled by significant clinical changes. The TST repeated at 12 months in patients with no evidence of LTBI at baseline continued to be negative. The median baseline interferon-γ (IFN-γ) concentration was not significantly different from that observed at each subsequent timepoint.Conclusion.Dynamic changes occur with serial IFN-γ release assay testing in patients treated with biologic therapy that do not correlate with clinical outcome. A careful and integrated evaluation of the patient, including clinical information, should guide the treatment decision. This study was underpowered for definite conclusions and further studies are needed to determine the significance of these findings.
Factors Associated with Achievement of Inactive Disease in Children with Juvenile Idiopathic Arthritis Treated with Etanercept
Authors: SOLARI NICOLETTA , PALMISANI ELENA , CONSOLARO ALESSANDRO , PISTORIO ANGELA , VIOLA STEFANIA , BUONCOMPAGNI ANTONELLA , GATTORNO MARCO , PICCO PAOLO , RUPERTO NICOLINO , MALATTIA CLARA , MARTINI ALBERTO , RAVELLI ANGELO 
Published: December 2012

Objective.To evaluate the rate of inactive disease in children with juvenile idiopathic arthritis (JIA) treated with etanercept, and to identify clinical characteristics associated with attainment of inactive disease.Methods.Clinical charts of patients who were given etanercept between January 2002 and January 2011 were evaluated retrospectively. For each patient, all visits from initiation of etanercept to the last followup evaluation in which the patient was still receiving etanercept were examined to establish whether the patient had reached the state of inactive disease and to identify the first visit in which inactive disease was documented. Clinical characteristics associated with achievement of inactive disease were determined through univariate analyses and Cox regression procedures.Results.A total of 173 patients who received etanercept for a median of 2.2 years (range 0.5–10.5 yrs) were studied. Eighty-seven patients (50.3%) achieved inactive disease after a median of 0.6 years (range 0.1–2.5 yrs) of therapy. At last followup evaluation, 85 patients (49.1%) still had inactive disease and 70 (40.5%) were in clinical remission on medication. The probability of achievement of inactive disease after 6, 12, and 24 months of therapy was 24%, 46% and 57%, respectively. On Cox regression analysis, the attainment of inactive disease was associated with lack of wrist involvement and an age at disease onset < 3.6 years.Conclusion.Around half of our patients with JIA treated with etanercept achieved a state of inactive disease. Children who lacked wrist involvement and were younger at disease onset had a greater likelihood of achieving inactive disease.