bluuebunny/crossref_metadata_2025_split huggingface dataset:
Otitis media with effusion in Lebanese children: prevalence and pathogen susceptibility
Authors: Nasser S C , Moukarzel N , Nehme A , Haidar H , Kabbara B , Haddad A 
Published: July 2011

AbstractObjective:To determine the prevalence and resistance profile of bacterial pathogens present in the middle ear of children with otitis media with effusion, and to report beta-lactamase-negative, ampicillin-resistant bacteria for the first time in Lebanese children.Method:We included 62 patients younger than 12 year (107 ears), who underwent myringotomy with tympanostomy tube placement for persistent otitis media with effusion. Bacteria were identified by Gram staining and biochemical tests, and antibiotic sensitivities tested by the disc diffusion method and via minimum inhibitory concentration (E-test).Results:The commonest pathogen wasHaemophilus influenzae(62 per cent), followed byStreptococcus pneumoniae(26 per cent). TheH influenzaeresistance profile was highest for amoxicillin (81.0 per cent) and lowest for cefotaxime (19.0 per cent). There was a high risk of developingH influenzaeantibiotic resistance among children with a history of smoking exposure (p = 0.001), recurrent upper respiratory tract infection (p = 0.001) or previous antibiotic treatment (p = 0.005). Fifty-two per cent ofH influenzaecolonies were found to be beta-lactamase-negative and ampicillin-resistant.Conclusion:In these children with persistent otitis media with effusion,H influenzaewas the most prevalent bacteria. It showed a high incidence of resistance to the antibiotics most commonly prescribed to treat acute otitis media.
Measures for the control of Senecio aquaticus in managed grassland
Authors: SUTER M , LÜSCHER A 
Published: July 2011

Suter M & Lüscher A (2011). Measures for the control of Senecio aquaticus in managed grassland. Weed Research51, 601–611.SummarySenecio aquaticus, a plant containing toxic alkaloids, has been increasing in grasslands of Central Europe. This study aimed to identify control measures for established S. aquaticus populations. A multisite field experiment tested six control measures: ploughing followed by re‐sowing, harrowing followed by re‐sowing, application of a selective herbicide, pulling or digging of individuals, reduction of management intensity to a level of one annual mowing and lastly an untreated control. In the short term, herbicides and mowing once a year reduced the number of individuals of S. aquaticus most efficiently by up to 88%. No clear effects were observed for the remaining measures. Three years following application, herbicides and one annual mowing still performed best, but hardly any significant reduction in S. aquaticus was achieved compared with pre‐treatment conditions. Senecio aquaticus formed large seedbanks with more than 1000 germinable seeds m−2; the seedbank contributed to the failure of control measures, because any elimination of S. aquaticus resulted in germination and replacement by new seedlings. We conclude that owing to its seedbank, the control of established populations of S. aquaticus remains a challenge, requiring control measures over several years. Any measures that hinder the formation of populations of S. aquaticus and its seedbank in agricultural grassland will be the most efficient for its control.
Safety‐Enhanced Optimal Control of Turbodynamic Blood Pumps
Authors: Gwak Kwan‐Woong , Antaki James F. , Paden Brad E. , Kang ByoungHun 
Published: July 2011

AbstractA safety‐enhanced optimal (SEO) control algorithm for turbodynamic blood pump is proposed. Analysis of in vivo animal experimental data reveals that two new control indices—the gradient of pulsatility of pump pressure head with respect to pump speed and the gradient of minimum pump flow—have their peak within a proximity to the suction point but not at the exact suction point. They were also verified to satisfy the requirement of cost function for the extremum seeking control (ESC). New cost functions were tested for ESC to find and track the new operating point—SEO operating point—where sufficient cardiac perfusion and safety margin to suction is guaranteed. By computer simulation, it is confirmed that the SEO operating point was successfully found and tracked in both fixed and varying hemodynamic load scenarios using proposed control indices without resorting to a slope seeking control algorithm where the reference slope must be supplied.
The Seasonal Cycle and Interannual Variability in Stratospheric Temperatures and Links to the Brewer–Dobson Circulation: An Analysis of MSU and SSU Data
Authors: Young Paul J. , Thompson David W. J. , Rosenlof Karen H. , Solomon Susan , Lamarque Jean-François 
Published: July 2011

Abstract
Previous studies have shown that lower-stratosphere temperatures display a near-perfect cancellation between tropical and extratropical latitudes on both annual and interannual time scales. The out-of-phase relationship between tropical and high-latitude lower-stratospheric temperatures is a consequence of variability in the strength of the Brewer–Dobson circulation (BDC). In this study, the signal of the BDC in stratospheric temperature variability is examined throughout the depth of the stratosphere using data from the Stratospheric Sounding Unit (SSU).
While the BDC has a seemingly modest signal in the annual cycle in zonal-mean temperatures in the mid- and upper stratosphere, it has a pronounced signal in the month-to-month and interannual variability. Tropical and extratropical temperatures are significantly negatively correlated in all SSU channels on interannual time scales, suggesting that variations in wave driving are a major factor controlling global-scale temperature variability not only in the lower stratosphere (as shown in previous studies), but also in the mid- and upper stratosphere. The out-of-phase relationship between tropical and high latitudes peaks at all levels during the cold-season months: December–March in the Northern Hemisphere and July–October in the Southern Hemisphere. In the upper stratosphere, the out-of-phase relationship with high-latitude temperatures extends beyond the tropics and well into the extratropics of the opposite hemisphere.
The seasonal cycle in stratospheric temperatures follows the annual march of insolation at all levels and latitudes except in the mid- to upper tropical stratosphere, where it is dominated by the semiannual oscillation. Mid- to upper-stratospheric temperatures also exhibit a distinct but small semiannual cycle at extratropical latitudes.
Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data
Authors: Lopez David , Casero David , Cokus Shawn J , Merchant Sabeeha S , Pellegrini Matteo 
Published: July 2011

Abstract

Background
Progress in genome sequencing is proceeding at an exponential pace, and several new algal genomes are becoming available every year. One of the challenges facing the community is the association of protein sequences encoded in the genomes with biological function. While most genome assembly projects generate annotations for predicted protein sequences, they are usually limited and integrate functional terms from a limited number of databases. Another challenge is the use of annotations to interpret large lists of 'interesting' genes generated by genome-scale datasets. Previously, these gene lists had to be analyzed across several independent biological databases, often on a gene-by-gene basis. In contrast, several annotation databases, such as DAVID, integrate data from multiple functional databases and reveal underlying biological themes of large gene lists. While several such databases have been constructed for animals, none is currently available for the study of algae. Due to renewed interest in algae as potential sources of biofuels and the emergence of multiple algal genome sequences, a significant need has arisen for such a database to process the growing compendiums of algal genomic data.

Description
The Algal Functional Annotation Tool is a web-based comprehensive analysis suite integrating annotation data from several pathway, ontology, and protein family databases. The current version provides annotation for the model alga Chlamydomonas reinhardtii, and in the future will include additional genomes. The site allows users to interpret large gene lists by identifying associated functional terms, and their enrichment. Additionally, expression data for several experimental conditions were compiled and analyzed to provide an expression-based enrichment search. A tool to search for functionally-related genes based on gene expression across these conditions is also provided. Other features include dynamic visualization of genes on KEGG pathway maps and batch gene identifier conversion.

Conclusions
The Algal Functional Annotation Tool aims to provide an integrated data-mining environment for algal genomics by combining data from multiple annotation databases into a centralized tool. This site is designed to expedite the process of functional annotation and the interpretation of gene lists, such as those derived from high-throughput RNA-seq experiments. The tool is publicly available at http://pathways.mcdb.ucla.edu.
The monoclonal antibody Zt/f2 targeting RON receptor tyrosine kinase as potential therapeutics against tumor growth-mediated by colon cancer cells
Authors: Yao Hang-Ping , Zhou Yong-Qing , Ma Qi , Guin Sunny , Padhye Snehal S , Zhang Rui-Wen , Wang Ming-Hai 
Published: July 2011

Abstract

Background
Overexpression of the RON receptor tyrosine kinase contributes to epithelial cell transformation, malignant progression, and acquired drug resistance. RON also has been considered as a potential target for therapeutic intervention. This study determines biochemical features and inhibitory activity of a mouse monoclonal antibody (mAb) Zt/f2 in experimental cancer therapy.

Results
Zt/f2 is a mouse IgG2a mAb that is highly specific and sensitive to human RON and its oncogenic variants such as RON160 (ED50 = 2.3 nmol/L). Receptor binding studies revealed that Zt/f2 interacts with an epitope(s) located in a 49 amino acid sequence coded by exon 11 in the RON β-chain extracellular sequences. This sequence is critical in regulating RON maturation and phosphorylation. Zt/f2 did not compete with ligand macrophage-stimulating protein for binding to RON; however, its engagement effectively induced RON internalization, which diminishes RON expression and impairs downstream signaling activation. These biochemical features provide the cellular basis for the use of Zt/f2 to inhibit tumor growth in animal model. Repeated administration of Zt/f2 as a single agent into Balb/c mice results in partial inhibition of tumor growth caused by transformed NIH-3T3 cells expressing oncogenic RON160. Colon cancer HT-29 cell-mediated tumor growth in athymic nude mice also was attenuated following Zt/f2 treatment. In both cases, ~50% inhibition of tumor growth as measured by tumor volume was achieved. Moreover, Zt/f2 in combination with 5-fluorouracil showed an enhanced inhibition effect of ~80% on HT-29 cell-mediated tumor growth in vivo.

Conclusions
Zt/f2 is a potential therapeutic mAb capable of inhibiting RON-mediated oncogenesis by colon cancer cells in animal models. The inhibitory effect of Zt/f2 in vivo in combination with chemoagent 5-fluorouracil could represent a novel strategy for future colon cancer therapy.
Deep-sea echinoderm oxygen consumption rates and an interclass comparison of metabolic rates in Asteroidea, Crinoidea, Echinoidea, Holothuroidea and Ophiuroidea
Authors: Hughes Sarah Jane Murty , Ruhl Henry A. , Hawkins Lawrence E. , Hauton Chris , Boorman Ben , Billett David S. M. 
Published: July 2011

SUMMARY
Echinoderms are important components of deep-sea communities because of their abundance and the fact that their activities contribute to carbon cycling. Estimating the echinoderm contribution to food webs and carbon cycling is important to our understanding of the functioning of the deep-sea environment and how this may alter in the future as climatic changes take place. Metabolic rate data from deep-sea echinoderm species are, however, scarce. To obtain such data from abyssal echinoderms, a novel in situ respirometer system, the benthic incubation chamber system (BICS), was deployed by remotely operated vehicle (ROV) at depths ranging from 2200 to 3600 m. Oxygen consumption rates were obtained in situ from four species of abyssal echinoderm (Ophiuroidea and Holothuroidea). The design and operation of two versions of BICS are presented here, together with the in situ respirometry measurements. These results were then incorporated into a larger echinoderm metabolic rate data set, which included the metabolic rates of 84 echinoderm species from all five classes (Asteroidea, Crinoidea, Echinoidea, Holothuroidea and Ophiuroidea). The allometric scaling relationships between metabolic rate and body mass derived in this study for each echinoderm class were found to vary. Analysis of the data set indicated no change in echinoderm metabolic rate with depth (by class or phylum). The allometric scaling relationships presented here provide updated information for mass-dependent deep-sea echinoderm metabolic rate for use in ecosystem models, which will contribute to the study of both shallow water and deep-sea ecosystem functioning and biogeochemistry.
The Genetic Basis of Rapidly Evolving Male Genital Morphology inDrosophila
Authors: Masly John P , Dalton Justin E , Srivastava Sudeep , Chen Liang , Arbeitman Michelle N 
Published: July 2011

AbstractThe external genitalia are some of the most rapidly evolving morphological structures in insects. The posterior lobe of the male genital arch shows striking differences in both size and shape among closely related species of the Drosophila melanogaster species subgroup. Here, we dissect the genetic basis of posterior lobe morphology between D. mauritiana and D. sechellia, two island endemic species that last shared a common ancestor ∼300,000 years ago. We test a large collection of genome-wide homozygous D. mauritiana genetic introgressions, which collectively cover ∼50% of the genome, for their morphological effects when placed in a D. sechellia genetic background. We find several introgressions that have large effects on posterior lobe morphology and that posterior lobe size and posterior lobe shape can be separated genetically for some of the loci that specify morphology. Using next generation sequencing technology, we perform whole transcriptome gene expression analyses of the larval genital imaginal disc of D. mauritiana, D. sechellia, and two D. mauritiana–D. sechellia hybrid introgression genotypes that each have large effects on either posterior lobe size or posterior lobe shape. Many of the genes we identify as differentially expressed are expressed at levels similar to D. mauritiana in one introgression hybrid, but are expressed at levels similar to D. sechellia in the other introgression hybrid. However, we also find that both introgression hybrids express some of the same genes at levels similar to D. mauritiana, and notably, that both introgression hybrids possess genes in the insulin receptor signaling pathway, which are expressed at D. mauritiana expression levels. These results suggest the possibility that the insulin signaling pathway might integrate size and shape genetic inputs to establish differences in overall posterior lobe morphology between D. mauritiana and D. sechellia.
Sudden onset blindness treated with pulse steroid therapy in a patient with microscopic polyangiitis
Authors: Horai Yoshiro , Miyamura Tomoya , Shimada Karin , Takahama Soichiro , Minami Rumi , Yamamoto Masahiro , Suematsu Eiichi 
Published: July 2011

Abstract
We report a 71-year-old male with microscopic polyangiitis (MPA) who developed sudden-onset, progressive, bilateral visual loss associated with a relapse of MPA symptoms. The patient was referred to our hospital, and treated with intravenous pulse steroid therapy and high-dose oral prednisolone. Although the right eye remained vision deficient, visual acuity in the left eye recovered. Ocular manifestations of MPA are quite uncommon. This case emphasizes the necessity of early detection and initiation of prompt therapy where ocular manifestations of MPA occur.
Femtosecond Laser–assisted Corneal Pocket Creation Using a Mask for Inlay Implantation
Authors: Bouzoukis Dimitrios I. , Kymionis George D. , Limnopoulou Aliki N. , Kounis George A. , Pallikaris Ioannis G. 
Published: July 2011

Purpose:
To describe the technique of femtosecond laser–assisted intracorneal pocket creation, using a mask for the implantation of a corneal inlay in the non-dominant eye of a 56-year-old, emmetropic, presbyopic woman for the correction of presbyopia.

Methods:
Using the iFlap treatment-type software of the femtosecond laser (IntraLase 150, Abbott Medical Optics), a full lamellar cut was created at 280-μm depth. A keyhole-shaped mask was placed at the internal part of the glass of the applanation cone. A separator was used to separate the stroma, and an inserter was used to implant the inlay at the center of the line of sight. To determine the line of sight, the microscope and centration system of the excimer laser (Allegretto Wave 400 Hz, WaveLight Laser Technologie AG) were used. The Flexivue Microlens inlay (Presbia) was implanted.

Results:
No intra- or postoperative complications occurred during follow-up. Uncorrected near visual acuity improved from 20/50 to 20/20 at the first postoperative week.

Conclusions:
Femtosecond-assisted intracorneal pocket creation using a mask is a simple, safe, and efficient approach for the implantation of corneal inlays.
Are bycatch rates sufficient as the principal fishery performance measure and method of assessment for seabirds?
Authors: Tuck Geoffrey Neil 
Published: July 2011

ABSTRACT

Seabird bycatch in oceanic and coastal fisheries is believed to be the principal cause of the population declines that have been observed for many seabird populations. Pelagic and demersal longline and trawl operations have been implicated in these declines.
Many government and national fishery bodies have environmental and fishery legislation that requires fisheries to be managed in a manner that is not harmful to non‐target species, including seabirds. A common tool for measuring the impact of a fishery on incidentally caught seabirds is an estimate of the bycatch rate. Unfortunately, the estimation and interpretation of bycatch rates is not trivial and is complicated by poor observer coverage, under‐reporting of bycatch and data lacking species specificity.
In this paper, a stochastic simulation model of two seabird populations affected by a single fishing fleet is presented. The model is used to explore the consequences of applying a bycatch rate management control rule to assess and manage the fishery's incidental mortality of seabirds. Comparisons are also made with values derived from Potential Biological Removal (PBR) theory.
Results conclude that using bycatch rates as a measure to assess performance of the fishery and to reduce bycatch is, under many circumstances, not sufficient to achieve conservation goals. Bycatch rates can be within the limit recommended by management, giving the impression that the fishery has reduced bycatch to sustainable levels, when in fact the low rates are due to the populations having collapsed.
The interpretation of bycatch rates, and any subsequent bycatch rate management rules, needs to be considered with respect to changes in fishing effort, to population‐specific impacts, to levels of compliance, and to the robustness of the bycatch rate estimate. Simply applying a bycatch rate control rule without caution can lead to catastrophic results for incidentally caught populations of seabirds. Copyright © 2011 John Wiley & Sons, Ltd.
A label‐free methodology for selective protein quantification by means of absorption measurements
Authors: Hansen Sigrid K. , Skibsted Erik , Staby Arne , Hubbuch Jürgen 
Published: July 2011

AbstractThe application of high throughput experimentation (HTE) in protein purification process development has created an analytical bottleneck. Using a new label‐free and non‐invasive methodology for analyzing multicomponent protein mixtures by means of spectral measurements, we show that the analytical throughput for selective protein quantification can be increased significantly. An analytical assay based on this new methodology was shown to generate very precise results. Further, the assay was successfully applied as analytics for a resin screening performed in HTE mode. The increase in analytical throughput was obtained without decreasing the level of information when compared to analytical chromatography. This proves its potential as a valuable analytical tool in conjugation with high throughput process development (HTPD). Further, fast selective protein quantification can enhance process control in a commercial production environment and, hence, minimize the need for off‐line release analysis. Biotechnol. Bioeng. 2011;108: 2661–2669. © 2011 Wiley Periodicals, Inc.
A study of QoS guarantee and fairness based on cross‐layer channel state in Worldwide Interoperability for Microwave Access
Authors: Yang Feng‐Ming , Chen Wei‐Mei , Cheng Tzu‐Kai , Wu Jean‐Lien C. 
Published: July 2011

SUMMARYBecause the bandwidth usage of wireless transmission is limited, one of the major research topics in this field is to improve system throughput by supporting multiple users with limited bandwidth resources. Although there are several studies on cross‐layer designs for improving system throughput, previous research on quality‐of‐service guarantee and fairness are relatively rare. This study proposes a cross‐layer subcarrier permutation (CLSP) mechanism that uses cross‐layer strategies to select suboptimal subcarriers. Service flows simulations in the IEEE 802.16e system indicate that CLSP achieved a lower delay time and a long‐term fairness among multiple users. Experimental results further show that the throughput of CLSP is 28 percent higher than that of the partial usage of subchannels model using the orthogonal frequency division multiple access technique. Copyright © 2011 John Wiley & Sons, Ltd.
One‐Pot Synthesis of Diazine‐Bridged Bisindoles and Concise Synthesis of the Marine Alkaloid Hyrtinadine A
Authors: Tasch Boris O. A. , Merkul Eugen , Müller Thomas J. J. 
Published: July 2011

AbstractDiazine‐bridged bisindoles are readily obtained from N‐Boc‐protected 3‐iodoindoles and 3‐iodo‐7‐azaindole in a pseudo three‐component reaction involving a one‐pot Masuda borylation–Suzuki arylation sequence. Some of the title compounds display promising cytotoxic properties. The versatility of this methodology is illustrated by a very concise total synthesis of the marine alkaloid hyrtinadine A.