bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tailormade Microfluidic Devices Through Photochemical Surface Modification
Authors: Samuel J. D. Jeyaprakash S. , Brenner Thilo , Prucker Oswald , Grumann Markus , Ducree Jens , Zengerle Roland , Rühe Jürgen 
Published: January 2010

AbstractA new pathway for the generation of polymer‐based microfluidic devices with tailor‐made surface chemistry is described. A simple photochemical process is used to covalently bind polymer molecules to the surfaces of microchannels fabricated by hot embossing. The substrates for the embossing process have the format of a compact disk (CD). CDs from polymethylmethacrylate and polyethylene‐co‐norbornene were chosen due to their good optical properties. Thin films of polymers containing photoactive benzophenone units were deposited onto the surface of the thus generated devices. These films were subsequently irradiated with UV light leading to the surface‐attachment of ultrathin polymer networks. In contrast to their unmodified peers, the obtained, modified microfluidic channels coated with hydrophilic, photoattached layers can be filled in a straightforward manner with water by capillary forces. Channels coated by thin films of poly(ethyloxazoline) show complete resistance to non‐specific protein binding. Generation of hydrophobic patches inside the modified microfluidic channels using benzophenone‐containing fluoropolymers allows the generation of passive microfluidic valves to direct fluid motion in these CD‐based devices.magnified image
The variability of the Superficial Inferior Epigastric Artery (SIEA) and its angiosome: A clinical anatomical study
Authors: Rozen Warren M. , Chubb Daniel , Grinsell Damien , Ashton Mark W. 
Published: January 2010

AbstractIntroduction: The superficial inferior epigastric artery (SIEA) is a useful pedicle in supply to the lower abdominal integument, with its use sparing damage to rectus abdominis muscle or sheath. However, it is limited in usefulness due to its anatomical variability. While previous anatomical studies have been limited in number and study design, the use of preoperative imaging has enabled the analysis of this vasculature in large numbers and greater anatomical detail. Methods: A clinical anatomical study of 500 hemi‐abdominal walls in 250 consecutive patients undergoing preoperative computed tomographic angiography (CTA) prior to autologous breast reconstruction was undertaken. The presence, size, location, and branching pattern of the SIEA were assessed in each case. Results: The SIEA was identified in 468 cases, an incidence of 94%. Its mean diameter was 0.6 mm, and in 24% of cases was of a diameter >1.5 mm. SIEA location was highly variable, with mean position 2‐cm lateral to the linea semilunaris (range 0–8 cm lateral), and relationship to the superficial inferior epigastric vein (SIEV) was also highly variable, with the distance between them ranging from 0.3 to 8.5 cm apart. SIEA branches directly crossed the abdominal midline in 5% of cases. Larger SIEA diameters correlated with a decrease in diameter of ipsilateral DIEA perforators. Conclusion: The SIEA is present more frequently than previously demonstrated, but is typically too small for use in free tissue transfer. The variable degree of SIEA branching suggests that its territory of supply is also variable, and that preoperative imaging may be useful in planning SIEA flaps. © 2010 Wiley‐Liss, Inc. Microsurgery 30:386–391, 2010.
Amino acid metabolism of bovine blastocysts: a biomarker of sex and viability
Authors: Sturmey R.G. , Bermejo‐Alvarez P. , Gutierrez‐Adan A. , Rizos D. , Leese H.J. , Lonergan P. 
Published: January 2010

AbstractThe ratio of male/female embryos may be modified by environmental factors such as maternal diet in vivo and the composition of embryo culture media in vitro. We have used amino acid profiling, a noninvasive marker of developmental potential to compare the effect of sex on the metabolism of bovine blastocysts conceived in vivo and in vitro. Blastocysts were incubated individually for 24 hr in a close‐to‐physiological mixture of amino acids and the depletion or appearance of 18 amino acids measured using HPLC. Blastocysts were then sexed by PCR. Amino acid depletion by in vitro‐produced blastocysts and expanded blastocysts was higher than in embryos conceived in vivo (P = 0.02). When cultured in vitro, female embryos exhibited increased depletion of arginine, glutamate, and methionine and appearance of glycine, while male embryos displayed increased depletion of phenylalanine, tyrosine, and valine. Overall, in vitro‐produced blastocysts exhibited sex‐specific differences in metabolic profiles of 7 out of 18 amino acids; in vivo‐produced, in 2 out of 18. These differences had disappeared by the expanded blastocyst stages. We have also shown that amino acid metabolism can predict the ability of bovine zygotes to develop to the blastocyst stage, providing “proof of principle” for the use of this technology in clinical IVF to select single embryos for transfer and thereby avoid the problem of multiple births. Mol. Reprod. Dev. 77: 285–296, 2010. © 2010 Wiley‐Liss, Inc.
An axiomatic characterization of a value for games in partition function form
Authors: Hu Cheng-Cheng , Yang Yi-You 
Published: January 2010

Abstract
An extension of the Shapley value for games in partition function form is proposed in the paper. We introduce a version of the marginal contributions for environments with externalities. The dummy property related to it is defined. We adapt the system of axioms provided by Shapley (A value for n-Person games. In: Kuhn H, Tucker A (eds) Contributions to the theory of games II. Princeton University Press, Princeton, pp 307–317, 1953) to characterize our value. In addition, we discuss a relationship between the α-Shapley values proposed by Fujinaka (On the marginality principle in partition function form games. Mimeo, Graduate School of Economics, Kobe University, Japan, 2004) and the values constructed through the average approach provided by Macho-Stadler et al. (J Econ Theory 135:339–356, 2007).
Uterotonic use at home births in low‐income countries: A literature review
Authors: Flandermeyer Dawn , Stanton Cynthia , Armbruster Deborah 
Published: January 2010

AbstractObjectivesThis literature review compiles data on rates of use, indications, types of provider, mode of administration, and dose of uterotonics used for home births in low‐income countries, and identifies gaps meriting further research.MethodsPublished and unpublished English language articles from 1995 through 2008 pertaining to home use of uterotonics were identified via electronic searches of medical and social science databases. In addition, bibliographies of articles were examined for eligible studies. Data were abstracted and analyzed by the objectives outlined for this review.ResultsTwenty‐three articles met the inclusion/exclusion criteria. Use rates of uterotonics at home births ranged widely from 1% to 69%, with the large majority of observations from South Asia. Descriptive studies suggest that home use of uterotonics before delivery of the baby are predominantly administered by nonprofessionals to accelerate labor, and are not perceived as unsafe.ConclusionsTo achieve maximum benefit and minimal harm, programs that increase access to uterotonics for postpartum hemorrhage prevention must take into account existing practices among pregnant women. Further research regarding access to uterotonics and intervention studies for provider behavior change regarding uterotonic use is warranted.
Middle Jurassic rhyolite volcanism of eastern Graham Land, Antarctic Peninsula: age correlations and stratigraphic relationships
Authors: RILEY TEAL R. , FLOWERDEW MICHAEL J. , HUNTER MORAG A. , WHITEHOUSE MARTIN J. 
Published: January 2010

AbstractSilicic volcanism atc.168 Ma has been identified previously on the Antarctic Peninsula, and the Mapple Formation, which includes those volcanic rocks, has been defined and documented from one area of the east coast of Graham Land. Based on age and geochemical criteria, correlations have been made to the extensive Chon Aike Province of South America, which has been demonstrated to be one of the largest silicic volcanic provinces in the world. Rhyolitic and intermediate composition volcanic successions from six separate localities on the east coast of the Antarctic Peninsula are described here and are confirmed as correlatives of the Mapple Formation, based on newly acquired geochronology and field observations. They are dominantly rhyolitic crystal tuffs and/or ignimbrites with ages in the interval 162–168 Ma, overlapping with the age of the Mapple Formation (167–171 Ma) at the type locality. Andesitic agglomerates are also described, which are included in the same event and demonstrate the occurrence of rare intermediate volcanism, which is also seen in the Chon Aike Province. A new group, the Graham Land Volcanic Group, is defined here, and criteria are established which allow the separation of some volcanic successions out of the previously defined Antarctic Peninsula Volcanic Group, which takes no account of tectonic setting, eruption age or geochemistry.
Distinct flavobacterial communities in contrasting water masses of the North Atlantic Ocean
Authors: Gómez-Pereira Paola R , Fuchs Bernhard M , Alonso Cecilia , Oliver Matthew J , van Beusekom Justus E E , Amann Rudolf 
Published: January 2010

Abstract
Members of the class Flavobacteria in the phylum Bacteroidetes are among the most abundant picoplankton in coastal and polar oceans. Their diversity is high in marine waters. However, quantitative information about distribution patterns of flavobacterial clades is scarce. We analyzed the diversity and clade-specific abundances of individual Flavobacteria in different oceanic provinces in the North Atlantic Ocean. Samples were taken along the 30°W meridian between the East Greenland current and the North Atlantic subtropical gyre. Comparative sequence analysis of 16S ribosomal RNA (rRNA) gene libraries revealed high diversity and significant spatial variability within the class Flavobacteria. Published and newly designed oligonucleotide probes were used to enumerate eleven flavobacterial clades by catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH). We found that different provinces harbor distinct flavobacterial communities. Clade DE2 accounted for a substantial fraction of total Flavobacteria only in the Polar Biome (BPLR), whereas the VISION clades VIS1 and VIS4 significantly increased in the Arctic (ARCT) province. Members of the genus Polaribacter were the most abundant clade in all the water masses analyzed, with highest absolute numbers in BPLR and ARCT. We improved the CARD-FISH protocol to quantify the rare clades VIS2, VIS3, VIS5 and VIS6, which were present in abundances below 0.5%. They all showed pronounced regional distribution patterns. Microscopic analysis proved a specific enrichment of Flavobacteria in the phycosphere of nanophytoplankton of BPLR and ARCT. Our results suggest that different marine flavobacterial clades have distinct niches and different life strategies.
Characterization of non-cytosolic hexokinase activity in white skeletal muscle from goldfish (Carassius auratus L.) and the effect of cold acclimation
Authors: dos Santos Reinaldo Sousa , Diniz Luan Pereira , Galina Antonio , da-Silva Wagner Seixas 
Published: January 2010

HK (hexokinase) is an enzyme involved in the first step in the glucose metabolism pathway, converting glucose into G6P (glucose 6-phosphate). Owing to the importance of skeletal muscle for fish swimming and acclimation processes, we used goldfish (Carassius auratus L.) white muscle in order to investigate subcellular distribution and kinetics of HK. In this study, we report that HK activity is predominantly localized in the mitochondrial fraction [NC-HK (non-cytosolic HK)] in goldfish white muscle. Studies of the kinetic parameters revealed that the Km (Michaelis–Menten constant) for glucose was 0.41±0.03 mM and that for mannose was 3-fold lower, whereas the affinity for fructose was too low to be measured. The Km for ATP was 0.88±0.05 mM, whereas no activity was observed when either GTP or ITP was used as a phosphate donor. A moderate inhibition (20–40%) was found for ADP and AMP. Similar to mammalian HK, G6P and glucose analogues were able to promote an inhibition of between 85 and 100% of activity. Here, we found that acclimation of goldfish at 5°C promoted a 2.5-fold increase in NC-HK compared with its counterpart acclimated at 25°C. However, cytosolic HK activity was not altered after thermal acclimation. In summary, our results suggest that the goldfish has a constitutive NC-HK that shows some similarities to mammalian HK-II and, curiously, may play a role in the broad metabolic changes required during the cold acclimation process.
Structure of intact
Thermus thermophilus
V-ATPase by cryo-EM reveals organization of the membrane-bound V
O
motor
Authors: Lau Wilson C. Y. , Rubinstein John L. 
Published: January 2010

The eubacterium
Thermus thermophilus
uses a macromolecular assembly closely related to eukaryotic V-ATPase to produce its supply of ATP. This simplified V-ATPase offers several advantages over eukaryotic V-ATPases for structural analysis and investigation of the mechanism of the enzyme. Here we report the structure of the complex at ∼16
Å
resolution as determined by single particle electron cryomicroscopy (cryo-EM). The resolution of the map and our use of cryo-EM, rather than negative stain EM, reveals detailed information about the internal organization of the assembly. We could separate the map into segments corresponding to subunits A and B, the threefold pseudosymmetric C-subunit, a central rotor consisting of subunits D and F, the L-ring, the stator subcomplex consisting of subunits I, E, and G, and a micelle of bound detergent. The architecture of the V
O
region shows a remarkably small area of contact between the I-subunit and the ring of L-subunits and is consistent with a two half-channel model for proton translocation. The arrangement of structural elements in V
O
gives insight into the mechanism of torque generation from proton translocation.
dbTEU: a protein database of trace element utilization
Authors: Zhang Yan , Gladyshev Vadim N. 
Published: January 2010

Abstract
Summary: Biological trace elements are required for numerous biological processes and by all organisms. We describe a database, dbTEU (DataBase of Trace Element Utilization), that features known transporters and user proteins for five trace elements (copper, molybdenum, nickel, cobalt and selenium) and represents sequenced organisms from the three domains of life. The manually curated dbTEU currently includes ∼16 500 proteins from &gt;700 organisms, and offers interactive trace element, protein, organism and sequence search and browse tools.
Availability and Implementation: dbTEU is freely available at http://gladyshevlab.bwh.harvard.edu/trace_element/
Contact: vgladyshev@rics.bwh.harvard.edu
GWAS Analyzer: integrating genotype, phenotype and public annotation data for genome-wide association study analysis
Authors: Fong Christine , Ko Dennis C. , Wasnick Michael , Radey Matthew , Miller Samuel I. , Brittnacher Mitchell 
Published: January 2010

Abstract
Motivation: Genome-wide association studies are beginning to elucidate how our genetic differences contribute to susceptibility and severity of disease. While computational tools have previously been developed to support various aspects of genome-wide association studies, there is currently a need for informatics solutions that facilitate the integration of data from multiple sources.
Results: Here we present GWAS Analyzer, a database driven web-based tool that integrates genotype and phenotype data, association analysis results and genomic annotations from multiple public resources. GWAS Analyzer contains features for browsing these interrelated data, exploring phenotypic values by family or genotype, and filtering association results based on multiple criteria. The utility of the tool has been demonstrated by a genome-wide association study of human in vitro susceptibility to bacterial infection. GWAS Analyzer facilitated management of large sets of phenotype and genotype data, analysis of phenotypic variation and heritability, and most importantly, generation of a refined set of candidate single nucleotide polymorphisms (SNPs). The tool revealed a SNP that was experimentally validated to be associated with increased cell death among Salmonella infected HapMap cell lines.
Availability: http://www.nwrce.org/gwas-analyzer
Contact: mbrittna@u.washington.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
Xper2: introducing e-taxonomy
Authors: Ung Visotheary , Dubus Guillaume , Zaragüeta-Bagils René , Vignes-Lebbe Régine 
Published: January 2010

Abstract
Motivation: Computer Aided Identification systems provide users with the resources to relate morpho-anatomic observations with taxa names and to subsequently access other knowledge about the organisms. They have the ability to manage descriptive data and make identifications through interactive keys. They are essential for both authors and users of biodiversity information. Xper2 version 2.0 is one of the most user-friendly tools in its category and provides a complete environment dedicated to taxonomic management.
Availability: Xper2 software can be freely downloaded at http://lis-upmc.snv.jussieu.fr/lis/?q=en/resources/softwares/xper2
Contact: visotheary.riviere-ung@snv.jussieu.fr
A linked separable–ADAPT VPA assessment model for western horse mackerel (Trachurus trachurus), accounting for realized fecundity as a function of fish weight
Authors: De Oliveira José A. A. , Darby Chris D. , Roel Beatriz A. 
Published: January 2010

Abstract
De Oliveira, J. A. A., Darby, C. D., and Roel, B. A. 2010. A linked separable–ADAPT VPA assessment model for western horse mackerel (Trachurus trachurus), accounting for realized fecundity as a function of fish weight. – ICES Journal of Marine Science, 67: 916–930. The western horse mackerel stock covers a large area of the Northeast Atlantic and is characterized by the sporadic occurrence of strong year classes. The only fishery-independent data available for its assessments are the estimates of total annual egg production from triennial egg surveys. Horse mackerel are indeterminate spawners, so a direct conversion of total annual egg production to spawning-stock biomass using prespawning-season estimates of fecundity is not viable. There is also evidence that potential fecundity per kg spawning female increases with fish weight. A linked separable–ADAPT VPA (SAD) model was developed that combines data on total catch, catch-at-age, and total annual egg production with data on potential and realized fecundity to provide population estimates for western horse mackerel. The model accounts for potential fecundity as a function of fish weight and for the development of a targeted fishery on the strong 1982 year class. Simulations confirm that the SAD model is able to reproduce population estimates without bias under a range of scenarios, except where there is a trend in realized fecundity. This underscores the need for improved information on realized fecundity, or alternatively the need to develop management plans that are robust to this source of uncertainty.
Fluorescence Resonance Energy Transfer-Sensitized Emission of Yellow Cameleon 3.60 Reveals Root Zone-Specific Calcium Signatures in Arabidopsis in Response to Aluminum and Other Trivalent Cations
Authors: Rincón-Zachary Magaly , Teaster Neal D. , Sparks J. Alan , Valster Aline H. , Motes Christy M. , Blancaflor Elison B. 
Published: January 2010

Abstract
Fluorescence resonance energy transfer-sensitized emission of the yellow cameleon 3.60 was used to study the dynamics of cytoplasmic calcium ([Ca2+]cyt) in different zones of living Arabidopsis (Arabidopsis thaliana) roots. Transient elevations of [Ca2+]cyt were observed in response to glutamic acid (Glu), ATP, and aluminum (Al3+). Each chemical induced a [Ca2+]cyt signature that differed among the three treatments in regard to the onset, duration, and shape of the response. Glu and ATP triggered patterns of [Ca2+]cyt increases that were similar among the different root zones, whereas Al3+ evoked [Ca2+]cyt transients that had monophasic and biphasic shapes, most notably in the root transition zone. The Al3+-induced [Ca2+]cyt increases generally started in the maturation zone and propagated toward the cap, while the earliest [Ca2+]cyt response after Glu or ATP treatment occurred in an area that encompassed the meristem and elongation zone. The biphasic [Ca2+]cyt signature resulting from Al3+ treatment originated mostly from cortical cells located at 300 to 500 μ m from the root tip, which could be triggered in part through ligand-gated Glu receptors. Lanthanum and gadolinium, cations commonly used as Ca2+ channel blockers, elicited [Ca2+]cyt responses similar to those induced by Al3+. The trivalent ion-induced [Ca2+]cyt signatures in roots of an Al3+-resistant and an Al3+-sensitive mutant were similar to those of wild-type plants, indicating that the early [Ca2+]cyt changes we report here may not be tightly linked to Al3+ toxicity but rather to a general response to trivalent cations.
Prolonged responses in patients with MDS and CMML treated with azacitidine and etanercept
Authors: Scott Bart L. , Ramakrishnan Aravind , Storer Barry , Becker Pamela S. , Petersdorf Steve , Estey Elihu H. , Deeg H.Joachim 
Published: January 2010

SummaryCombination therapy with azacitidine and etanercept was hypothesized to lead to improved responses in myelodysplastic syndrome (MDS) patients. Thirty‐two patients with MDS/chronic myelomonocytic leukaemia were treated with azacitidine + etanercept; 30 completed at least three therapy cycles. At 3 months, nine patients had achieved complete response (CR), two had partial response, 10 had marrow CRs, seven had stable disease, two patients had haematological improvement without marrow response and two patients had disease progression. The overall response rate was 72%; median duration of response was not reached at 2 years. Marrow response rates and duration were improved with azacitidine + etanercept compared to azacitidine alone.