bluuebunny/crossref_metadata_2025 huggingface dataset:
Empirical correlations between black carbon aerosol and carbon monoxide in the lower and middle troposphere
Authors: Spackman J. R. , Schwarz J. P. , Gao R. S. , Watts L. A. , Thomson D. S. , Fahey D. W. , Holloway J. S. , de Gouw J. A. , Trainer M. , Ryerson T. B.
Published: October 2008

Single‐particle measurements of black carbon (BC) aerosol and simultaneous measurements of carbon monoxide (CO) were acquired aboard the NOAA WP‐3D aircraft during the 2006 Texas Air Quality Study (TexAQS). Observed average BC mass loadings, estimated to account for ∼90% of the ambient BC mass, decreased by more than 2 orders of magnitude from the polluted boundary layer to the clean middle troposphere (6 km). A strong positive, but non‐linear, correlation was observed between simultaneous measurements of BC and CO. Based on an analysis of all the data below 1 km, we report a compact relationship between BC and CO with a slope of 5.8 ± 1.0 ng BC (kg dry air)−1 (ppb CO)−1 that is representative of regional urban and industrial emissions from Houston and Dallas. The BC/CO emission ratio for a fresh biomass‐burning plume was estimated at 9 ± 2 ng kg−1 ppb−1.
Neural network analysis of crosshole tomographic images: The seismic signature of gas hydrate bearing sediments in the Mackenzie Delta (NW Canada)
Authors: Bauer K. , Pratt R. G. , Haberland C. , Weber M.
Published: October 2008

Crosshole seismic experiments were conducted to study the in‐situ properties of gas hydrate bearing sediments (GHBS) in the Mackenzie Delta (NW Canada). Seismic tomography provided images of P velocity, anisotropy, and attenuation. Self‐organizing maps (SOM) are powerful neural network techniques to classify and interpret multi‐attribute data sets. The coincident tomographic images are translated to a set of data vectors in order to train a Kohonen layer. The total gradient of the model vectors is determined for the trained SOM and a watershed segmentation algorithm is used to visualize and map the lithological clusters with well‐defined seismic signatures. Application to the Mallik data reveals four major litho‐types: (1) GHBS, (2) sands, (3) shale/coal interlayering, and (4) silt. The signature of seismic P wave characteristics distinguished for the GHBS (high velocities, strong anisotropy and attenuation) is new and can be used for new exploration strategies to map and quantify gas hydrates.
Blocking systems over an aqua planet
Authors: Hu Yongyun , Yang Da , Yang Jun
Published: October 2008

It is well established that forced planetary waves are critically important for blocking formation. To test whether blocking can be generated and maintained in the absence of topographic forcing, we carry out aqua‐planet simulations using NCAR CAM2. Results show that blockings occur frequently under the aqua‐planet conditions which have no forcing such as land‐sea contrast, orography and stationary remote tropical forcing. Features of simulated blockings well resemble that in the real atmosphere, showing typical Ω‐like patterns, persistence, and quasi‐stationary behavior with occasionally westward shifting. It is found that the onset and maintenance of simulated blockings are due to interaction between quasi‐stationary free Rossby waves and baroclinic eddies. For 10‐year simulations, the blocking frequency is slightly higher than that in the Northern Hemisphere (NH) in the real atmosphere. These suggest that blocking is a natural consequence of rotating and baroclinic atmospheres, while locally topographic forcing and remote tropical forcing are not necessary conditions.
Phyllosilicate and sulfate‐hematite deposits within Miyamoto crater in southern Sinus Meridiani, Mars
Authors: Wiseman Sandra M. , Arvidson R. E. , Andrews‐Hanna J. C. , Clark R. N. , Lanza N. L. , Des Marais D. , Marzo G. A. , Morris R. V. , Murchie S. L. , Newsom H. E. , Noe Dobrea E. Z. , Ollila A. M. , Poulet F. , Roush T. L. , Seelos F. P. , Swayze G. A.
Published: October 2008

Orbital topographic, image, and spectral data show that sulfate‐ and hematite‐bearing plains deposits similar to those explored by the MER rover Opportunity unconformably overlie the northeastern portion of the 160 km in diameter Miyamoto crater. Crater floor materials exhumed to the west of the contact exhibit CRISM and OMEGA NIR spectral signatures consistent with the presence of Fe/Mg‐rich smectite phyllosilicates. Based on superposition relationships, the phyllosilicate‐bearing deposits formed either in‐situ or were deposited on the floor of Miyamoto crater prior to the formation of the sulfate‐rich plains unit. These findings support the hypothesis that neutral pH aqueous conditions transitioned to a ground‐water driven acid sulfate system in the Sinus Meridiani region. The presence of both phyllosilicate and sulfate‐ and hematite‐bearing deposits within Miyamoto crater make it an attractive site for exploration by future rover missions.
Functional metagenomics reveals diverse β-lactamases in a remote Alaskan soil
Authors: Allen Heather K , Moe Luke A , Rodbumrer Jitsupang , Gaarder Andra , Handelsman Jo
Published: October 2008

Despite the threat posed by antibiotic resistance in infectious bacteria, little is known about the diversity, distribution and origins of resistance genes, particularly among the as yet unculturable environmental bacteria. One potentially rich but largely unstudied environmental reservoir is soil. The complexity of its microbial community coupled with its high density of antibiotic-producing bacteria makes the soil a likely origin for diverse antibiotic resistance determinants. To investigate antibiotic resistance genes among uncultured bacteria in an undisturbed soil environment, we undertook a functional metagenomic analysis of a remote Alaskan soil. We report that this soil is a reservoir for β-lactamases that function in Escherichia coli, including divergent β-lactamases and the first bifunctional β-lactamase. Our findings suggest that even in the absence of selective pressure imposed by anthropogenic activity, the soil microbial community in an unpolluted site harbors unique and ancient β-lactam resistance determinants. Moreover, despite their evolutionary distance from previously known genes, the Alaskan β-lactamases confer resistance on E. coli without manipulating its gene expression machinery, demonstrating the potential for soil resistance genes to compromise human health, if transferred to pathogens.
Transcriptome ofGeobacter uraniireducensgrowing in uranium-contaminated subsurface sediments
Authors: Holmes Dawn E , O'Neil Regina A , Chavan Milind A , N'Guessan Lucie A , Vrionis Helen A , Perpetua Lorrie A , Larrahondo M Juliana , DiDonato Raymond , Liu Anna , Lovley Derek R
Published: October 2008

To learn more about the physiological state of Geobacter species living in subsurface sediments, heat-sterilized sediments from a uranium-contaminated aquifer in Rifle, Colorado, were inoculated with Geobacter uraniireducens, a pure culture representative of the Geobacter species that predominates during in situ uranium bioremediation at this site. Whole-genome microarray analysis comparing sediment-grown G. uraniireducens with cells grown in defined culture medium indicated that there were 1084 genes that had higher transcript levels during growth in sediments. Thirty-four c-type cytochrome genes were upregulated in the sediment-grown cells, including several genes that are homologous to cytochromes that are required for optimal Fe(III) and U(VI) reduction by G. sulfurreducens. Sediment-grown cells also had higher levels of transcripts, indicative of such physiological states as nitrogen limitation, phosphate limitation and heavy metal stress. Quantitative reverse transcription PCR showed that many of the metabolic indicator genes that appeared to be upregulated in sediment-grown G. uraniireducens also showed an increase in expression in the natural community of Geobacter species present during an in situ uranium bioremediation field experiment at the Rifle site. These results demonstrate that it is feasible to monitor gene expression of a microorganism growing in sediments on a genome scale and that analysis of the physiological status of a pure culture growing in subsurface sediments can provide insights into the factors controlling the physiology of natural subsurface communities.
Prokaryotic diversity, distribution, and insights into their role in biogeochemical cycling in marine basalts
Authors: Mason Olivia U , Di Meo-Savoie Carol A , Van Nostrand Joy D , Zhou Jizhong , Fisk Martin R , Giovannoni Stephen J
Published: October 2008

We used molecular techniques to analyze basalts of varying ages that were collected from the East Pacific Rise, 9° N, from the rift axis of the Juan de Fuca Ridge and from neighboring seamounts. Cluster analysis of 16S rDNA terminal restriction fragment polymorphism data revealed that basalt endoliths are distinct from seawater and that communities clustered, to some degree, based on the age of the host rock. This age-based clustering suggests that alteration processes may affect community structure. Cloning and sequencing of bacterial and archaeal 16S rRNA genes revealed 12 different phyla and subphyla associated with basalts. These include the Gemmatimonadetes, Nitrospirae, the candidate phylum SBR1093 in the bacteria, and in the Archaea Marine Benthic Group B, none of which have been previously reported in basalts. We delineated novel ocean crust clades in the γ-Proteobacteria, Planctomycetes and Actinobacteria that are composed entirely of basalt-associated microflora, and may represent basalt ecotypes. Finally, microarray analysis of functional genes in basalt revealed that genes coding for previously unreported processes such as carbon fixation, methane oxidation, methanogenesis and nitrogen fixation are present, suggesting that basalts harbor previously unrecognized metabolic diversity. These novel processes could exert a profound influence on ocean chemistry.
Filter preconditioning enables representative scaled‐down modelling of filter capacity and viral clearance by mitigating the impact of virus spike impurities
Authors: Khan Navid Z. , Parrella Joseph J. , Genest Paul W. , Colman Michael S.
Published: October 2008

Endogenous and adventitious virus removal by size‐exclusion membrane filtration is a critical dedicated step in an overall viral clearance strategy employed by biologics manufacturers as required by industry regulators. However, the addition of impurities from virus spike preparations used in validation studies can significantly reduce filter capacity, resulting in an oversized and suboptimal virus filtration step. The hydraulic filter performance and virus retention observed in conventional scaled‐downed validation models may not necessarily represent performance observed during process development, nor be predictive of manufacturing performance. Using filter flow decay as a relevant processing endpoint, an alternative and more comprehensive approach to virus filter validation has been developed to overcome the limitations imposed by virus spike impurities. With a model feedstream, we have demonstrated comparable virus removal using the conventional virus spiking approach and a complementary preconditioned virus challenge. Similar to a currently accepted method used in the validation of sterilizing‐grade filters, this method entails processing non‐spiked feed to a volumetric throughput target, followed by processing virus‐spiked feed to a final flow decay endpoint to determine viral clearance. This comprehensive approach yields predictive virus retention data under protein‐dominant fouling conditions that better model the hydraulic performance of the manufacturing‐scale virus filtration operation.
Interaction of retinal guanylate cyclase with the α subunit of transducin: potential role in transducin localization
Authors: Rosenzweig Derek H. , Saidas Nair K. , Levay Konstantin , Peshenko Igor V. , Crabb John W. , Dizhoor Alexander M. , Slepak Vladlen Z.
Published: October 2008

Vertebrate phototransduction is mediated by cGMP, which is generated by retGC (retinal guanylate cyclase) and degraded by cGMP phosphodiesterase. Light stimulates cGMP hydrolysis via the G-protein transducin, which directly binds to and activates phosphodiesterase. Bright light also causes relocalization of transducin from the OS (outer segments) of the rod cells to the inner compartments. In the present study, we show experimental evidence for a previously unknown interaction between Gαt (the transducin α subunit) and retGC. Gαt co-immunoprecipitates with retGC from the retina or from co-transfected COS-7 cells. The retGC–Gαt complex is also present in cones. The interaction also occurs in mice lacking RGS9 (regulator of G-protein signalling 9), a protein previously shown to associate with both Gαt and retGC. The Gαt–retGC interaction is mediated primarily by the kinase homology domain of retGC, which binds GDP-bound Gαt stronger than the GTP[S] (GTPγS; guanosine 5′-[γ-thio]triphosphate) form. Neither Gαt nor Gβγ affect retGC-mediated cGMP synthesis, regardless of the presence of GCAP (guanylate cyclase activating protein) and Ca2+. The rate of light-dependent transducin redistribution from the OS to the inner segments is markedly accelerated in the retGC-1-knockout mice, while the migration of transducin to the OS after the onset of darkness is delayed. Supplementation of permeabilized photoreceptors with cGMP does not affect transducin translocation. Taken together, these results suggest that the protein–protein interaction between Gαt and retGC represents a novel mechanism regulating light-dependent translocation of transducin in rod photoreceptors.
Increased hepatic lipogenesis in insulin resistance and Type 2 diabetes is associated with AMPK signalling pathway up-regulation in Psammomys obesus
Authors: Ben Djoudi Ouadda Ali , Levy Emile , Ziv Ehud , Lalonde Geneviève , Sané Alain T. , Delvin Edgar , Elchebly Mounib
Published: October 2008

AMPK (AMP-activated protein kinase) has been suggested to be a central player regulating FA (fatty acid) metabolism through its ability to regulate ACC (acetyl-CoA carboxylase) activity. Nevertheless, its involvement in insulin resistance- and TD2 (Type 2 diabetes)-associated dyslipidaemia remains enigmatic. In the present study, we employed the Psammomys obesus gerbil, a well-established model of insulin resistance and TD2, in order to appreciate the contribution of the AMPK/ACC pathway to the abnormal hepatic lipid synthesis and increased lipid accumulation in the liver. Our investigation provided evidence that the development of insulin resistance/diabetic state in P. obesus is accompanied by (i) body weight gain and hyperlipidaemia; (ii) elevations of hepatic ACC-Ser79 phosphorylation and ACC protein levels; (iii) a rise in the gene expression of cytosolic ACC1 concomitant with invariable mitochondrial ACC2; (iv) an increase in hepatic AMPKα-Thr172 phosphorylation and protein expression without any modification in the calculated ratio of phospho-AMPKα to total AMPKα; (v) a stimulation in ACC activity despite increased AMPKα phosphorylation and protein expression; and (vi) a trend of increase in mRNA levels of key lipogenic enzymes [SCD-1 (stearoyl-CoA desaturase-1), mGPAT (mitochondrial isoform of glycerol-3-phosphate acyltransferase) and FAS (FA synthase)] and transcription factors [SREBP-1 (sterol-regulatory-element-binding protein-1) and ChREBP (carbohydrate responsive element-binding protein)]. Altogether, our findings suggest that up-regulation of the AMPK pathway seems to be a natural response in order to reduce lipid metabolism abnormalities, thus supporting the role of AMPK as a promising target for the treatment of TD2-associated dyslipidaemia.
Assessing English Language Learners: A Perplexing Puzzle
Authors: Gottlieb Margo , Sanchez-Lopez Cristina
Published: October 2008

The intersection of language education and special education is not clearly marked for linguistically and culturally diverse students; some qualify as English language learners; others as English language learners with disabilities or specific language impairment; still others with only disabilities or specific language impairment. It is often perplexing to try to decipher which category is most appropriate and, consequently, how best to serve these students. Assessment data, if reliable and valid, coupled with historical information, can help define the pathway to educational success for the fastest growing segment of our school population. This article shares the challenges facing educators of English language learners and attempts to show how proper assessment can guide educational decision making. We pose that for English language learners, assessment must entail the gathering of information from multiple sources on their language proficiency and academic achievement in both English and their native language. In that way, we obtain a comprehensive portrait of the students' full complement of knowledge and skills. Ultimately, English as a Second Language or bilingual teachers working along with speech-language pathologists need to collaborate in the collection, analysis, and interpretation of data to afford English language learners optimal opportunities for success in school.
Feasibility of Computer-Administered Language Assessment
Authors: Brandone Amanda C. , Golinkoff Roberta Michnick , Hirsh-Pasek Kathy
Published: October 2008

The assessment of language in early childhood is essential for the early identification of children with special needs. However, administering traditional language assessments to large preschool populations can be prohibitively time-consuming and complicated. Thus, there is clear value in developing a standardized, norm-referenced, computer-administered language assessment battery that is both time-efficient and fun for children, that yields a meaningful profile of children's specific language competencies, and that can be administered by testers in a consistent manner without extensive training. Here we discuss research undertaken as part of an evaluation of the feasibility of developing such a language assessment tool for use with preschool children. Preschoolers (M = 3.60 years) were tested using a traditional, standardized language assessment (PLS-4) and a computer-administered task assessing (via the use of a touch-screen computer) verb vocabulary and comprehension of plural morphology, negation, and noun-verb agreement. All participants completed the entire test without difficulty. Moreover, analyses revealed significant correlations between performance on the computer-based language assessment, age, and performance on the PLS-4. These data support the notion that a computer-administered language assessment is methodologically feasible and can provide a practical and valid means by which to assess early language abilities.
Assessing Language and Literacy Skills of School-Aged Children
Authors: Garrett Jennifer Walz
Published: October 2008

School-based speech-language pathologists assess students to establish eligibility, collect baselines for treatment goals, determine progress during intervention and verify generalization of skills. Selecting appropriate assessment tools and methods can be challenging due to time constraints, agency regulations, and availability of tests. This article will describe legal considerations, types of assessments, and the factors involved with the selection and use of various assessment procedures and tools. In addition, speech-language pathologists will learn to calculate words correct per minute (WCPM) and perform miscue analysis, which can provide additional language and literacy information about a child's educational needs.
Ethical Implications of Using Outdated Standardized Tests
Authors: Jakubowitz Melissa , Schill Mary Jo
Published: October 2008

The Code of Ethics of the American Speech-Language-Hearing Association (ASHA) defines the expected ethical conduct of members and provides guidance to professionals in making appropriate decisions, including those related to ethical clinical practices. This article addresses issues and questions centered on using older versions of standardized tests after newer editions of the test or assessment protocol have been published. If the most recent edition is not available, clinicians need to decide if it is ever appropriate to use the older version, including the factors that must be considered when making such a decision. In addition, the clinician must consider how to interpret and report results and what information must be retained related to the test results. Applicable areas of the ASHA Code of Ethics are identified and discussed, and some suggestions are provided for clinicians to consider when making decision in this area of practice.
Visual Prosthesis
Authors: Schiller Peter H , Tehovnik Edward J
Published: October 2008

There are more than forty million blind individuals in the world whose plight would be greatly ameliorated by creating a visual prosthesis. We begin by outlining the basic operational characteristics of the visual system, as this knowledge is essential for producing a prosthetic device based on electrical stimulation through arrays of implanted electrodes. We then list a series of tenets that we believe need to be followed in this effort. Central among these is our belief that the initial research in this area, which is in its infancy, should first be carried out on animals. We suggest that implantation of area V1 holds high promise as the area is of a large volume and can therefore accommodate extensive electrode arrays. We then proceed to consider coding operations that can effectively convert visual images viewed by a camera to stimulate electrode arrays to yield visual impressions that can provide shape, motion, and depth information. We advocate experimental work that mimics electrical stimulation effects non-invasively in sighted human subjects with a camera from which visual images are converted into displays on a monitor akin to those created by electrical stimulation.
A cyclophilin links redox and light signals to cysteine biosynthesis and stress responses in chloroplasts
Authors: Dominguez-Solis Jose R. , He Zengyong , Lima Amparo , Ting Julie , Buchanan Bob B. , Luan Sheng
Published: October 2008

Cyclophilins belong to a large family of enzymes called “peptidyl prolyl isomerases” that assist protein folding and assembly. The cyclophilin CYP20–3 (also known as “ROC4”) is the only member of this group located in the stroma (soluble phase) of chloroplasts. In the present study we isolated mutant
Arabidopsis
plants defective in the
CYP20–3
gene and found them to be hypersensitive to oxidative stress conditions created by high light levels, rose bengal, high salt levels, and osmotic shock. Chloroplast serine acetyltransferase (SAT1), a rate-limiting enzyme in cysteine biosynthesis, was identified as an interacting partner for CYP20–3 by protein interaction analyses. In the present experiments, SAT1 activity increased significantly under conditions of light and oxidative stress in concert with total thiols in wild-type plants. By contrast, these parameters changed only marginally in experiments with the
cyp20–3
mutant, suggesting that CYP20–3 links light and stress to SAT1 activity and cysteine biosynthesis. In further support of this conclusion, our analyses showed that the salt-hypersensitive phenotype of the mutant developed under illumination and not in the dark. Together with the earlier report that CYP20–3 foldase activity is enhanced by thioredoxin-mediated reduction, our findings suggest that CYP20–3 links photosynthetic electron transport and redox regulation to the folding of SAT1, thereby enabling the cysteine-based thiol biosynthesis pathway to adjust to light and stress conditions.
Efficacy of percutaneous needle aspiration and open biopsy for sperm retrieval in men with non‐obstructive azoospermia
Authors: HOUWEN JUUL , LUNDIN KERSTI , SÖDERLUND BRITA , BERGH CHRISTINA , KREMER JAN A.M. , EKERHOVD ERLING
Published: October 2008

Objective. To assess the efficacy of the two most common sperm retrieval procedures, testicular sperm aspiration (TESA) and testicular sperm extraction (TESE) as part of the diagnostic work‐up in men with non‐obstructive azoospermia. Design. Retrospective cohort study. Setting. Center for Reproductive Medicine, Sahlgrenska University Hospital, Gothenburg, Sweden. Sample. Three hundred fifty men who underwent diagnostic surgical sperm recovery between January 1997 and December 2006. Methods. A diagnostic TESA was initially performed in 281 men with testes of >12 mm3. If no spermatozoa or an insufficient number of spermatozoa was found, most of the men underwent a diagnostic TESE. Diagnostic TESE was performed as the only surgical procedure in 69 men who had at least one testis ≤12 mm3. Main outcome measures. Success rates of diagnostic TESA and diagnostic TESE. Results. Spermatozoa were found in 129 (45.9%) of the 281 men who underwent TESA. However, in 29 of these men too few spermatozoa were identified for the men to be accepted for IVF/ICSI. The subsequent TESE resulted in 26 additional men being accepted for IVF/ICSI. In men with testes ≤12 mm3 a sufficient number of spermatozoa were found in 27 out of 69 men following TESE. Conclusions. The study shows that in 52% of the men with non‐obstructive azoospermia spermatozoa useful for ICSI can be identified. For at least one‐third of the men with testes >12 mm3 TESA is a sufficient procedure. Sperm retrieval rate is further increased following a subsequent TESE.
Why are some ectopic pregnancies characterized as pregnancies of unknown location at the initial transvaginal ultrasound examination?
Authors: KIRK EMMA , DAEMEN ANNELEEN , PAPAGEORGHIOU ARIS T. , BOTTOMLEY CECILIA , CONDOUS GEORGE , DE MOOR BART , TIMMERMAN DIRK , BOURNE TOM
Published: October 2008

Objective. To compare the appearance and behavior of ectopic pregnancies (EPs) initially classified as pregnancies of unknown location (PULs) to those visualized on the initial transvaginal ultrasound scan (TVS). Methods. An observational study over a four‐year period on women undergoing a TVS prior to diagnosis of a tubal EP. Demographic details, presenting symptoms, TVS findings, serum hCG and progesterone levels were recorded at the time of the initial TVS and at the time of diagnosis of the EP in those initially classified as a PUL. Results. 411 women with a tubal EP underwent a TVS prior to treatment. In 85.9% (353/411) the EP was visualized on the initial TVS while 14.1%(58/411) were initially classified as PULs. Those initially classified as PULs had significantly lower mean gestational age and mean initial human chorionic gonadotrophin (hCG) levels, and significantly higher mean progesterone level at presentation than those where the EP was visualized on the initial TVS. Of those with a PUL, 60.3% (35/58) had the EP subsequently visualized on TVS. At the time of diagnosis these EPs were significantly smaller (p<0.0001); the appearance of the EPs, serum hCG and progesterone levels at the time of visualization on TVS were not significantly different from those visualized on the initial TVS. Conclusion. In women with EPs who are initially classified as PULs, failure of visualization of the EP on the initial TVS is likely to be due to the fact that they are too small and probably too early in the disease process.
Reduced adaptation of the pancreatic B cells during pregnancy is the major causal factor for gestational diabetes: Current knowledge and metabolic effects on the offspring
Authors: DEVLIEGER ROLAND , CASTEELS KRISTINA , VAN ASSCHE FRANS A.
Published: October 2008

This commentary summarizes current knowledge on the pathophysiology of gestational diabetes, focusing on the role of the endocrine pancreas and the β‐cells, their adaptation in normal pregnancy, and recent insights in the molecular basis for deficient adaptation in diabetes occurring during pregnancy. Additionally, the effects of disturbed maternal glucose metabolism during pregnancy on the glucose metabolism of the offspring are discussed.
Treatment of deep venous thrombosis in pregnant women
Authors: LYKKE JACOB A. , GRØNLYKKE THOR , LANGHOFF‐ROOS JENS
Published: October 2008

The recommended dosage of tinzaparin in the treatment of thromboembolism during pregnancy is 175 IU/kg/day, as for non‐pregnant subjects. In clinical practice, we have experienced a need for a higher dosage, especially in the initial phase of the treatment of deep vein thrombosis, based on four‐hour post‐dose measurements of anti‐Xa activity.

Twenty‐two pregnant patients with a confirmed deep venous thrombosis were treated with tinzaparin either in a once‐ or twice‐daily regimen. Four‐hour post‐dosage plasma anti‐Xa activity was measured in 357 sequential blood samples during treatment. An higher dosage than recommended, was required to maintain anti‐Xa activity in the target range. We suggest that the starting dosage should be 250 IU/kg/day in a twice‐daily regimen, and that the dose in the initial phase be adjusted by daily monitoring of anti‐Xa.
Measurement of lower-leg volume change by quantitative computed tomography
Authors: Angelhed J.-E. , Strid L. , Bergelin E. , Fagerberg B.
Published: October 2008

Background: Lower-leg edema is a common symptom in many diseases. A precise method with low variability for measurement of edema is warranted in order to obtain optimal conditions for investigation of treatment effects.

Purpose: To evaluate computed tomography for precise measurement of lower-leg muscle and adipose tissue volumes using a very low level of effective radiation dose.

Material and Methods: Eleven volunteers were examined three times during 1 day, either as two consecutive examinations in the morning and one single examination in the afternoon, or as one examination in the morning and two in the afternoon. Eleven scans with computed tomography were made at each examination, and lower-leg volumes were calculated from automatically measured scan areas and interscan distances. Volumes for muscle, adipose tissue, and bone were calculated separately. Minimal radiation dose was used.

Results: Mean difference between the repeated examinations was −0.1 ml for total volume, −1.4 ml for muscle, and 1.6 ml for adipose tissue volume. The corresponding 95% confidence intervals were −6.5 to 6.0 ml, −3.5 to 6.5 ml, and −7.0 to 4.0 ml, respectively. The resulting effective dose was 0.5 µSv to one leg.

Conclusion: Computed tomography can be used as a precise quantitative method to measure small volume changes of the lower leg as a whole, and separately for muscle and adipose tissue. The results were obtained with a negligible effective dose, lower than that delivered by modern fan-beam dual-energy X-ray absorptiometry whole-body examinations and equal to a few hours of background radiation.
A MODEL FOR THE CHROMOSPHERE/WIND OF 31 CYGNI AND ITS IMPLICATIONS FOR SINGLE STARS
Authors: Eaton Joel A.
Published: October 2008

I develop a detailed empirical model for the chromosphere and wind of 31 Cyg based on a previously published analysis of International Ultraviolet Explorer spectra from the 1993 eclipse and on the thermodynamics of how the wind must be driven. I then use this model to interpret observations of single supergiant stars and to assess the evidence that their winds are fundamentally different from those of supergiants in binary systems. This model naturally predicts a certain level of clumping of the gas to balance the pressure that drives the wind. It also predicts that anisotropic turbulence, such as would result from transverse displacements of Alfven waves directed along radial magnetic flux lines, would not give the roughly Gaussian profiles of emission lines seen in cool giant stars. Furthermore, it implies that C ii] may not tell us much at all about general conditions in chromospheres. Finally, I speculate that chaotic magnetic fields, in dynamical equilibrium with the gas of the wind, are the actual driving mechanism.
Fast unfolding of communities in large networks
Authors: Blondel Vincent D , Guillaume Jean-Loup , Lambiotte Renaud , Lefebvre Etienne
Published: October 2008

We propose a simple method to extract the community structure of large networks. Our
method is a heuristic method that is based on modularity optimization. It is shown to
outperform all other known community detection methods in terms of computation time.
Moreover, the quality of the communities detected is very good, as measured by the
so-called modularity. This is shown first by identifying language communities in a Belgian
mobile phone network of 2 million customers and by analysing a web graph of 118 million
nodes and more than one billion links. The accuracy of our algorithm is also verified on ad
hoc modular networks.
A bioinformatics analysis of the cell line nomenclature
Authors: Sarntivijai Sirarat , Ade Alexander S. , Athey Brian D. , States David J.
Published: October 2008

Motivation: Cell lines are used extensively in biomedical research, but the nomenclature describing cell lines has not been standardized. The problems are both linguistic and experimental. Many ambiguous cell line names appear in the published literature. Users of the same cell line may refer to it in different ways, and cell lines may mutate or become contaminated without the knowledge of the user. As a first step towards rationalizing this nomenclature, we created a cell line knowledgebase (CLKB) with a well-structured collection of names and descriptive data for cell lines cultured in vitro. The objectives of this work are: (i) to assist users in extracting useful information from biomedical text and (ii) to highlight the importance of standardizing cell line names in biomedical research. This CLKB contains a broad collection of cell line names compiled from ATCC, Hyper CLDB and MeSH. In addition to names, the knowledgebase specifies relationships between cell lines. We analyze the use of cell line names in biomedical text. Issues include ambiguous names, polymorphisms in the use of names and the fact that some cell line names are also common English words. Linguistic patterns associated with the occurrence of cell line names are analyzed. Applying these patterns to find additional cell line names in the literature identifies only a small number of additional names. Annotation of microarray gene expression studies is used as a test case. The CLKB facilitates data exploration and comparison of different cell lines in support of clinical and experimental research.

Availability: The web ontology file for this cell line collection can be downloaded at http://www.stateslab.org/data/celllineOntology/cellline.zip.

Contact:  dstates@umich.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Profile Comparer: a program for scoring and aligning profile hidden Markov models
Authors: Madera Martin
Published: October 2008

Summary: Profile Comparer (PRC) is a stand-alone program for scoring and aligning profile hidden Markov models (HMMs) of protein families. PRC can read models produced by SAM and HMMER, two popular profile HMM packages, as well as PSI-BLAST checkpoint files. This application note provides a brief description of the profile–profile algorithm used by PRC.

Availability: The C source code licensed under the GNU General Public Licence and Linux and Mac OS X binaries can be downloaded from http://supfam.org/PRC.

Contact:  martin.madera@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database
Authors: Carver Tim , Berriman Matthew , Tivey Adrian , Patel Chinmay , Böhme Ulrike , Barrell Barclay G. , Parkhill Julian , Rajandream Marie-Adèle
Published: October 2008

Motivation: Artemis and Artemis Comparison Tool (ACT) have become mainstream tools for viewing and annotating sequence data, particularly for microbial genomes. Since its first release, Artemis has been continuously developed and supported with additional functionality for editing and analysing sequences based on feedback from an active user community of laboratory biologists and professional annotators. Nevertheless, its utility has been somewhat restricted by its limitation to reading and writing from flat files. Therefore, a new version of Artemis has been developed, which reads from and writes to a relational database schema, and allows users to annotate more complex, often large and fragmented, genome sequences.

Results: Artemis and ACT have now been extended to read and write directly to the Generic Model Organism Database (GMOD, http://www.gmod.org) Chado relational database schema. In addition, a Gene Builder tool has been developed to provide structured forms and tables to edit coordinates of gene models and edit functional annotation, based on standard ontologies, controlled vocabularies and free text.

Availability: Artemis and ACT are freely available (under a GPL licence) for download (for MacOSX, UNIX and Windows) at the Wellcome Trust Sanger Institute web sites: http://www.sanger.ac.uk/Software/Artemis/http://www.sanger.ac.uk/Software/ACT/

Contact:  artemis@sanger.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Impact of dimeric organization of enzyme on its function: the case of photosynthetic water splitting
Authors: Jablonsky Jiri , Susila Petr , Lazar Dusan
Published: October 2008

Motivation: It is a question of whether the supramolecular organization of the protein complex has an impact on its function, or not. In the case of the photosystem II (PSII), water splitting might be influenced by cooperation of the PSIIs. Since PSII is the source of the atmospheric oxygen and because better understanding of the water splitting may contribute to the effective use of water as an alternative energy source, possible cooperation should be analyzed and discussed.

Results: We suggest that the dimeric organization of the PSII induces cooperation in the water splitting. We show that the model of monomeric PSII is unable to produce the oxygen after the second short flash (associated with the double turnover of the PSII), in contrast to the experimental data and model of dimeric PSII with considered cooperation. On the basis of this fact and partially from the support from other studies, we concluded that the double turnover of the PSII induced by short flashes might be caused by the cooperation in the water splitting. We further discuss a possibility that the known pathway of the electron transport through the PSII might be incomplete and besides D1-Y161, other cofactor which is able to oxidize the special chlorophyll pair (P680) must be considered in the monomeric PSII to explain the oxygen production after the second short flash.

Availability: Commented SBML codes (.XML files) of the monomeric and dimeric PSII models will be available (at the time of publication) in the BioModels database (www.ebi.ac.uk/biomodels).

Contact:  lazard@seznam.cz

Supplementary information:  Supplementary data are available at Bioinformatics online.
Addendum. Cytoprophet: aCytoscapeplug-in for protein and domain interaction networks inference
Authors: Morcos Faruck , Lamanna Charles , Sikora Marcin , Izaguirre Jesús
Published: October 2008

An additional reference is needed in the article Cytoprophet: a Cytoscape plug-in for protein and domain interaction networks inference. We include this reference as a matter of addendum.

Contact:  cytoprophet@cse.nd.edu
Aqueous Extract of Black Maca (Lepidium meyenii) on Memory Impairment Induced by Ovariectomy in Mice
Authors: Rubio Julio , Qiong Wang , Liu Xinmin , Jiang Zhen , Dang Haixia , Chen Shi-Lin , Gonzales Gustavo F.
Published: October 2008

The present study aims to test two different doses of aqueous extract of black maca on learning and memory in ovariectomized (OVX) mice and their relation with malonalehyde (MDA), acetylcholinesterase (Ache) and monoamine oxidase (MAO) brain levels. Female mice were divided into five groups: (i) naive (control), (ii) sham, (iii) OVX mice and OVX mice treated with (iv) 0.50 g kg−1and (v) 2.00 g kg−1black maca. Mice were orally treated with distilled water or black maca during 35 days starting 7 days after surgery. Memory and learning were assessed using the water Morris maze (from day 23–27) and the step‐down avoidance test (days 34 and 35). At the end of each treatment, mice were sacrificed by decapitation and brains were dissected out for MDA, Ache and MAO determinations. Black maca (0.5 and 2.0 g/kg) increased step‐down latency when compared to OVX control mice. Black maca decreased MDA and Ache levels in OVX mice; whereas, no differences were observed in MAO levels. Finally, black maca improved experimental memory impairment induced by ovariectomy, due in part, by its antioxidant and Ache inhibitory activities.
Factors Affecting Quality of Life of Children and Adolescents With Anorectal Malformations or Hirschsprung Disease
Authors: Hartman Esther E , Oort Frans J , Sprangers Mirjam AG , Hanneman Marianne JG , van Heurn LW Ernest , de Langen Zacharias J , Madern Gerard C , Rieu Paul NMA , van der Zee David C , Looyaard Nic , van Silfhout‐Bezemer Marina , Aronson Daniel C
Published: October 2008

Objectives:

First, to compare the quality of life (QL) and perceived self‐competence of children and adolescents with anorectal malformations or Hirschsprung disease with that of reference groups. Second, to identify predictors of QL.

Patients and Methods:

A total of 491 patients with anorectal malformations or Hirschsprung disease were sent a questionnaire, which assessed QL (mental, physical), disease‐specific functioning (defecation‐related), perceived self‐competence (self‐esteem, athletic competencies, school attitude), and demographic characteristics (sex, age). The clinical characteristics (disease severity, presence of congenital anomalies) were extracted from medical records.

Results:

More than 50% (316, 64%) of patients with anorectal malformations or Hirschsprung disease completed the questionnaire. On average, children and adolescents in both patient groups reported no differences in QL domains compared with the reference groups. However, standard deviations revealed considerable individual variation, indicating the presence of patients with high levels of QL as well as patients with low levels of QL. Children and adolescents in both patient groups reported psychosocial problems in all domains, compared with the reference groups. Females, older patients, and those with a severe form of the disease reported lower levels of perceived self‐competence and global disease‐specific functioning, which in turn predicted QL.

Conclusions:

Our results should alert clinicians to patients who are at risk for QL problems and may therefore be in need of extra care. Our findings illustrate the importance of both global disease‐specific functioning and perceived psychosocial competencies for enhancing the QL of these patients.
Long‐term Outcome of Colon Interposition After Esophagectomy in Children
Authors: Coopman S , Michaud L , Halna‐Tamine M , Bonnevalle M , Bourgois B , Turck D , Gottrand F
Published: October 2008

Background and Objectives:

Tissues derived from the colon, stomach, and jejunum have been used to replace the esophagus in childhood to cure esophageal atresia or stricture secondary to gastroesophageal reflux or the ingestion of corrosive agents. The outcome in adulthood of colon interposition performed at an early age has yet to be satisfactorily assessed. The aim of this single‐center retrospective study was to evaluate the long‐term nutritional, digestive, and respiratory outcome of all patients (n = 32) who underwent colon interposition during childhood in our hospital (1970–2001).

Patients and Methods:

Medical records of these subjects were reviewed and their nutritional (weight, height, 24‐hour food diary), digestive (questionnaire), and pulmonary function status evaluated.

Results:

Of the patients, 17 had esophageal atresia (7 males, median age at surgery 11 months, range 0.5–61) and 15 had ingested corrosive substances (10 males, median age at surgery 50 months, range 22–113). Complications occurred less than 1 year postoperatively in 53% and long‐term complications (occurring >1 year after surgery) in 84%. Long‐term complications were common: digestive symptoms were found in 85% (most frequently observed during the first 5 years of follow‐up), abnormal lung function in 7 (58%) of those tested (n = 12), feeding difficulties in 50%, scoliosis in 35%, and nutritional complications in 25%.

Conclusions:

Our study showed a high rate of sequelae following esophageal replacement. This highlights the need for multidisciplinary long‐term follow‐up into adulthood, and research into alternatives to colon interposition as treatment for esophageal strictures.
Lymphocytic Gastritis and Celiac Disease in Indian Children: Evidence of a Positive Relation
Authors: Prasad Kaushal K , Thapa Babu R , Lal Sadhna , Sharma Arun K , Nain Chander K , Singh Kartar
Published: October 2008

Objectives:

Lymphocytic gastritis (LG) is characterized by the presence of ≥25 lymphocytes/100 epithelial cells in the gastric surface and pit epithelium. An association of LG with Helicobacter pylori infection or celiac disease (CD) has been suggested. The aim of this study was to verify the relation of LG with CD, with and without H pylori infection, in children.

Patients and Methods:

A total of 164 children with CD diagnosed between June 2003 and October 2005, in whom gastric and duodenal biopsies were performed simultaneously, were enrolled prospectively. The control group was composed of 164 children without CD, matched for sex and age, who were undergoing upper digestive endoscopy. H pylori was searched for in gastric biopsy specimens sectioned and stained with hematoxylin and eosin, and a modified Giemsa stain for H pylori was performed for confirmation. The Student t test was used to compare quantitative measurements between groups.

Results:

LG was found in 69 (42.1%) patients with CD. Positive cases had a mean of 43.9 ± 1.5 intraepithelial lymphocytes per 100 surface epithelial cells, compared with a mean of 13.4 ± 0.4 in negative cases and 7.8 ± 0.5 in non‐CD control children (P < 0.0001). Patients not showing LG did, however, show significantly increased gastric intraepithelial lymphocytes compared with the control children. Nine of 164 CD patients, and 4 of 69 patients with LG, had positive results for H pylori.

Conclusions:

This study supports a pathogenetic relation between CD and LG. CD without LG also showed increased gastric intraepithelial lymphocytes. H pylori infection may be another cause of LG in children.