bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated Clinical Scale Manufacturing System for Cellular Products Derived by Magnetic Cell Separation, Centrifugation and Cell Culture
Authors: Apel Michael , Brüning Mareke , Granzin Markus , Essl Mike , Stuth Juliane , Blaschke Jessica , Spiegel Iris , Müller Sabine , Kabaha Eiad , Fahrendorff Elmar , Miltenyi Stefan , Schmitz Jürgen , Balshüsemann Dirk , Huppert Volker 
Published: January 2013

AbstractManufacturing of cellular products for therapeutic purposes like stem cell or cancer therapy requires equipment with specific characteristics not always addressed by conventional technologies. A new integrated cell processing device is presented that can handle all current technical requirements for manufacturing cellular products by automation of the complete process in a GMP‐compliant single‐use tubing set. Its capabilities are exemplified in the presented study by successful processing of adult stem cells, natural killer cells, and several cell lines. Multiple cell processing workflows can be automated in a functionally closed environment: from cell separation through cell culture to formulation of the final product.
Fusion of multi‐resolution surface (terrestrial laser scanning) and subsurface geodata (ERT, SRT) for karst landform investigation and geomorphometric quantification
Authors: Siart Christoph , Forbriger Markus , Nowaczinski Erich , Hecht Stefan , Höfle Bernhard 
Published: January 2013

ABSTRACTA multi‐method research design based on terrestrial laser scanning, GIS, geophysical prospecting (electrical resistivity tomography, refraction seismics) and sedimentology is applied for the first time to investigate enclosed karst depressions in an integrated way. Fusing multi‐resolution surface and subsurface geodata provides profound insights into the formation, geometry and geomorphologic processes of dolines. The studied landforms, which are located in the Dikti Mountains of East Crete, are shown to be filled by loose sediments of thicknesses of up to 30 m that mainly consist of fine‐grained material overlying solid bedrock at depths below 35 to 45 m. By combining subsurface observations with geomorphometric calculations, local doline genesis can be traced back to initial collapse of fractured bedrock followed by subsequent infilling with colluvials. In order to define crucial methodological requirements and guidelines for data fusion, both the impact of different elevation models and the influence of data resolution are assessed. Surface volumes of depressions derived by the digital surface model are 7–21% higher than the results obtained from the terrain model due to vegetation. Similarly, estimates of infill volume calculated on the basis of geophysical outcomes and elevation data differ by up to 13%. Calculations of the landforms' current volumes (i.e. total surface and subsurface volume), however, are fairly insensitive to raster resolution. Hence, the distinct geomorphologic properties of landforms (e.g. shape, terrain roughness, slope inclination) substantially determine the geomorphometric analysis of both surface and subsurface data. As shown by the findings, data fusion to integrate digital terrain, geophysical and sedimentological datasets of varied resolutions benefits geomorphologic studies and helps provide a comprehensive image of landforms. Copyright © 2013 John Wiley & Sons, Ltd.
Adjustment of Born‐Oppenheimer electronic wave functions to simplify close coupling calculations
Authors: Buenker Robert J. , Liebermann Heinz‐Peter , Zhang Yu , Wu Yong , Yan Lingling , Liu Chunhua , Qu Yizhi , Wang Jianguo 
Published: January 2013

AbstractTechnical problems connected with use of the Born‐Oppenheimer clamped‐nuclei approximation to generate electronic wave functions, potential energy surfaces (PES), and associated properties are discussed. A computational procedure for adjusting the phases of the wave functions, as well as their order when potential crossings occur, is presented which is based on the calculation of overlaps between sets of molecular orbitals and configuration interaction eigenfunctions obtained at neighboring nuclear conformations. This approach has significant advantages for theoretical treatments describing atomic collisions and photo‐dissociation processes by means of ab initio PES, electronic transition moments, and nonadiabatic radial and rotational coupling matrix elements. It ensures that the electronic wave functions are continuous over the entire range of nuclear conformations considered, thereby greatly simplifying the process of obtaining the above quantities from the results of single‐point Born‐Oppenheimer calculations. The overlap results are also used to define a diabatic transformation of the wave functions obtained for conical intersections that greatly simplifies the computation of off‐diagonal matrix elements by eliminating the need for complex phase factors. © 2013 Wiley Periodicals, Inc.
Enhancement of Streptomyces transglutaminase activity and pro-peptide cleavage efficiency by introducing linker peptide in the C-terminus of the pro-peptide
Authors: Chen Kangkang , Liu Song , Wang Guangsheng , Zhang Dongxu , Du Guocheng , Chen Jian , Shi Zhongping 
Published: January 2013

Abstract
Streptomyces transglutaminase (TGase) has been widely used in food, pharmaceutical and textile industries. Streptomyces TGase is naturally synthesized as zymogen (pro-TGase), which is then processed to produce active enzyme by removing its N-terminal pro-peptide. Although the pro-peptide is essential for TGase folding and secretion, few studies have been reported on improving the properties of TGase by pro-peptide engineering. In this study, we developed a new approach to improve the properties of TGase based on pro-peptide engineering. When the α-helix37G−42S in pro-peptide was substituted with three glycines and three alanines respectively, the mutants exhibited higher specific activity and the efficiency of pro-peptide cleavage was enhanced. To further improve the properties of TGase, relevant mutations were constructed by introducing linker peptides in the C-terminus of the pro-peptide. Mutants with GS (GGGGS) and PT (PTPPTTPT) linker peptide exhibited 1.28 fold and 1.5 fold higher specific activity than the wild-type enzyme, respectively. This new method could be used to improve the properties of TGase by pro-peptide modification, which is a promising technology for creating unique TGase with various beneficial properties.
Prediction of scaled feed intake in weaner pigs using physico-chemical properties of fibrous feeds
Authors: Ndou S. P. , Gous R. M. , Chimonyo M. 
Published: January 2013

The objective of the present study was to predict scaled feed intake (SFI) using the physico-chemical measurements of feed bulk, such that gut capacity can be estimated in weaner pigs. A basal feed with 13·7 MJ digestible energy and 180 g crude protein per kg DM was diluted to six inclusion levels (0, 80, 160, 240, 320 and 400 g/kg DM) using lucerne hay, maize cob, maize stover, sawdust, sunflower husks or grass hay (veld grass). A total of 124 pigs weighing 18·1 (sd1·37) kg body weight were used. Water-holding capacity (WHC; g water/g DM), bulk density (g DM/ml), neutral-detergent fibre (NDF) and acid-detergent fibre (ADF) influenced the SFI. The quadratic relationship between SFI and WHC was SFI = 19·1 (sem3·49)+10·04 (sem1·61) WHC–1·11 (sem0·17) WHC2(P< 0·01). SFI was also related (P< 0·01) to NDF and ADF by quadratic functions SFI = 24·3 (sem3·55)+0·12 (sem0·229) NDF − 0·00 012 (sem0·000036) NDF2and SFI = 30·2 (sem1·95)+0·112 (sem0·0232) ADF–0·000343 (sem0·0000612) ADF2, respectively. Using broken-stick analyses, the gut capacity was attained when WHC = 4·53 (sem1·25) g water/g DM, NDF = 367 (sem29) g/kg DM and ADF = 138 (sem77) g/kg DM. In conclusion, although threshold values for each were different, WHC, NDF and ADF contents of bulk feeds provide relationships with SFI that can be used to predict gut capacity in weaner pigs.
Wheat bulb fly (Delia coarctata, Fallén, Diptera: Anthomyiidae) larval response to hydroxamic acid constituents of host-plant root exudates
Authors: Rogers C.D. , Evans K.A. 
Published: January 2013

AbstractWheat bulb fly (WBF, Delia coarctata, Fallén, Diptera: Anthomyiidae) is a pest of commercial importance in wheat, barley and rye, with attacked crops failing to produce full potential yields. Females do not oviposit in association with a host-plant; therefore, prompt location of a suitable host is critical to the survival of the newly hatched larvae. The objective of this study was to conduct choice test bioassays to assess the attraction of WBF larvae to specific chemical constituents of WBF host-plant root exudates, the hydroxamic acids DIMBOA (2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one) and MBOA (6-methoxy-benzoxazolin-2-one). The larval response to four concentrations of each test compound was assessed in arena bioassays. Analysis using a Rayleigh test of uniformity of the final resting positions of larvae in response to these chemicals indicated attraction. These results go some way to explaining the mechanisms by which WBF larvae locate host plants, giving the potential to develop semiochemical based control strategies.
The epidemiology and molecular characterization of methicillin-resistant staphylococci sampled from a healthy Jordanian population
Authors: AL-BAKRI A. G. , AL-HADITHI H. , KASABRI V. , OTHMAN G. , KRIEGESKORTE A. , BECKER K. 
Published: January 2013

SUMMARYThe prevalence of natural carriage and molecular epidemiology of methicillin-resistantStaphylococcus aureus(MRSA) and methicillin-resistant coagulase-negative staphylococci (MR-CoNS) isolates in a Jordanian community were investigated. The MRSA nasal carriage rate in 227 healthy volunteers was 7·5% and the majority (81%) of MRSA harboured the resistance element SCCmectype IVe and were of a novelspatype t9519 (76%); other significantspagene types were t223 (14·7%) and t044 (5·9%). All MRSA isolates were susceptible to other classes of antibiotics, and tested positive for at least three virulence factor encoding genes, but only two harboured thepvlgene. MR-CoNS carriage was 54·2% and these isolates were characterized by single, double and untypable SCCmecelements, withStaphylococcus epidermidisSCCmectype IVa predominating. Of eight subjects with nasal co-colonization of MR-CoNS + MRSA, three shared SCCmectype IV in both groups of organisms. This is the first report of methicillin-resistant staphylococci carriage in a Jordanian community and its findings are important for epidemiological study and infection control measures of these organisms.
Pre‐fire fuel reduction treatments influence plant communities and exotic species 9 years after a large wildfire
Authors: Shive Kristen L. , Kuenzi Amanda M. , Sieg Carolyn H. , Fulé Peter Z. 
Published: January 2013

AbstractQuestionsHow did post‐wildfire understorey plant community response, including exotic species response, differ between pre‐fire treated areas that were less severely burned, and pre‐fire untreated areas that were more severely burned? Were these differences consistent through time?LocationEast‐centralArizona, southwesternUS.MethodsWe used a multi‐year data set from the 2002Rodeo–ChediskiFire to detect post‐fire trends in plant community response in burned ponderosa pine forests. Within the burn perimeter, we examined the effects of pre‐fire fuels treatments on post‐fire vegetation by comparing paired treated and untreated sites on theApache‐SitgreavesNationalForest. We sampled these paired sites in 2004, 2005 and 2011.ResultsThere were significant differences in pre‐fire treated and untreated plant communities by species composition and abundance in 2004 and 2005, but these communities were beginning to converge in 2011. Total understorey plant cover was significantly higher in untreated areas for all 3 yr. Plant cover generally increased between 2004 and 2005 and markedly decreased in 2011, with the exception of shrub cover, which steadily increased through time. The sharp decrease in forb and graminoid cover in 2011 is likely related to drought conditions since the fire. Annual/biennial forb and graminoid cover decreased relative to perennial cover through time, consistent with the initial floristics hypothesis. Exotic plant response was highly variable and not limited to the immediate post‐fire, annual/biennial community. Despite low overall exotic forb and graminoid cover for all years (<2.5%), several exotic species increased in frequency, and the relative proportion of exotic to native cover increased through time.ConclusionsPre‐treatment fuel reduction treatments helped maintain foundation overstorey species and associated native plant communities following this large wildfire. The overall low cover of exotic species on these sites supports other findings that the disturbance associated with high‐severity fire does not always result in exotic species invasions. The increase in relative cover and frequency though time indicates that some species are proliferating, and continued monitoring is recommended. Patterns of exotic species invasions after severe burning are not easily predicted, and are likely more dependent on site‐specific factors such as propagules, weather patterns and management.
Caries management by risk assessment
Authors: Young Douglas A. , Featherstone John D. B. 
Published: January 2013

AbstractCaries disease is multifactorial. Whether caries disease will be expressed and damage dental hard tissue is dependent on the patient's own unique make‐up of pathogenic risk factors and protective factors.ObjectivesThis manuscript will review the science of managing caries disease based on assessing caries risk.MethodsThe caries balance/imbalance model and a practical caries risk assessment procedure for patients aged 6 years through adult will illustrate how treatment options can be based on caries risk.ResultsNeither the forms nor the clinical protocols are meant to imply there is currently only one correct way this can be achieved, rather are used in this manuscript as examples only.ConclusionsIt is important to have the forms and protocols simple and easy to understand when implementing caries management by risk assessment into clinical practice. The science of CAMBRA based on the caries balance/imbalance model was reviewed and an example protocol was presented.
The ecological tale of Gonyleptidae (Arachnida, Opiliones) evolution: phylogeny of a Neotropical lineage of armoured harvestmen using ecological, behavioural and chemical characters
Authors: Caetano Daniel S. , Machado Glauco 
Published: January 2013

AbstractThe large Neotropical family Gonyleptidae comprises nearly 820 species divided into 16 subfamilies. The majority of publications on harvestman ecology, behaviour and scent gland secretion chemistry have focused on this family. We used the information available in the literature and combined it with an intensive search for ecological, behavioural and chemical data to infer the phylogeny of the Gonyleptidae. We included 28 species belonging to 14 of the 16 gonyleptid subfamilies in the ingroup and four species belonging to the families Cosmetidae, Stygnidae and Manaosbiidae in the outgroup. We performed the analyses using equally weighted characters and coded 63 characters comprising 153 states, which makes this the largest non‐morphological, non‐molecular phylogenetic data matrix published to date. We obtained five most parsimonious trees, and the strict consensus resulted in six collapsed nodes. The results show that the monophyly of Gonyleptidae is equivocal because Metasarcinae is placed at a basal polytomy with the outgroups Cosmetidae and Stygnidae. Gonyleptinae, Pachylinae and Progonyleptoidellinae are polyphyletic groups, but the remaining subfamilies are monophyletic and have several synapomorphies. Based on the resulting topology, we discuss the performance of ecological, behavioural and chemical characters, and map a selected set of characters to discuss their evolutionary patterns in the family.
Biological interplay between proteoglycans and their innate immune receptors in inflammation
Authors: Frey Helena , Schroeder Nina , Manon‐Jensen Tina , Iozzo Renato V. , Schaefer Liliana 
Published: January 2013

An emerging body of evidence indicates that secreted proteoglycans act as signaling molecules, in addition to their canonical function in maintaining and regulating the architecture of various extracellular matrices. Proteoglycans interact with a number of receptors that regulate growth, motility and immune response. In part, as a consequence of their complex structure, proteoglycans can induce crosstalk among various families of receptors and can also interact with natural receptor ligands, often blocking and sequestering their bioactivity. In their soluble form, originating from either partial proteolytic processing or through de novo synthesis by activated cells, some proteoglycans can become potent danger signals, denoting tissue stress and injury. Recently, it has been shown that proteoglycans, especially those belonging to the small leucine‐rich and hyaluronan‐binding gene families as well as the glycosaminoglycan hyaluronan, act as endogenous ligands of the toll‐like receptors, a group of central receptors regulating innate immunity. Furthermore, proteoglycans can activate intracellular inflammasomes and trigger sterile inflammation. In this review, we critically assess the signaling events induced by the proteoglycans biglycan, decorin, lumican and versican as well as hyaluronan during inflammation. We discuss the intriguing emerging notion that, in spite of structural diversity of biglycan, decorin, versican and hyaluronan, all of them signal through the same toll‐like receptors, albeit triggering differential responses and biological outcomes. Finally, we review the modes of action of these endogenous ligands of toll‐like receptors and their ability to specifically modify the final signaling events and the inflammatory response.
Evaluation of shear bond strength of silorane resin to conventional, resin‐modified glass ionomers and nano‐ionomer cements
Authors: Babannavar Roopa , Shenoy Arvind 
Published: January 2013

AbstractAimTo evaluate the shear bond strength of silorane composite resin to conventional and resin‐modified glass ionomer cements.Materials and methodsShear bond strengths of Vitrebond (Group I), Ketac N100 (Group II) and Ketac Bond (Group III) glass ionomer cements to the composite Filtek P90 were evaluated. The bond strength was tested using a universal testing machine at a cross‐head speed of 0.5 mm/min. Comparison between the groups was carried out using an analysis of variance test and pairwise comparison using Tukey's post‐hoc test with a significance level of P ≤ 0.05.ResultsThe measured bond strengths were 17.14 ± 3.39 MPA for Group I (Vitrebond), 15.34 ± 3.39 MPa for Group II (Ketac N100) and 14.12 ± 2.79 MPa for Group III (Ketac Bond). Group I achieved higher bond strength than Groups II and III.ConclusionsResin‐modified glass ionomer cement (i.e. Vitrebond) appears to be preferable to nano‐ionomer glass ionomer cement (i.e. Ketac N100) and conventional glass ionomer cement (i.e. Ketac Bond) as a base under low‐shrink posterior composite (i.e. Filtek P90).
Phylogenetic group‐associated differences in regulation of the common colonization factor Mat fimbria in Escherichia coli
Authors: Lehti Timo A. , Bauchart Philippe , Kukkonen Maini , Dobrindt Ulrich , Korhonen Timo K. , Westerlund‐Wikström Benita 
Published: January 2013

SummaryHeterogeneity of cell population is a key component behind the evolutionary success of Escherichia coli. The heterogeneity supports species adaptation and mainly results from lateral gene transfer. Adaptation may also involve genomic alterations that affect regulation of conserved genes. Here we analysed regulation of the mat (or ecp) genes that encode a conserved fimbrial adhesin of E. coli. We found that the differential and temperature‐sensitive expression control of the mat operon is dependent on mat promoter polymorphism and closely linked to phylogenetic grouping of E. coli. In the mat promoter lineage favouring fimbriae expression, the mat operon‐encoded regulator MatA forms a positive feedback loop that overcomes the repression by H‐NS and stabilizes the fimbrillin mRNA under low growth temperature, acidic pH or elevated levels of acetate. The study exemplifies phylogenetic group‐associated expression of a highly common surface organelle in E. coli.
Draft Genome Sequences of Pseudomonas fluorescens BS2 and Pusillimonas noertemannii BS8, Soil Bacteria That Cooperate To Degrade the Poly-γ-
d
-Glutamic Acid Anthrax Capsule
Authors: Stabler Richard A. , Negus David , Pain Arnab , Taylor Peter W. 
Published: January 2013

ABSTRACT

A mixed culture of
Pseudomonas fluorescens
BS2 and
Pusillimonas noertemannii
BS8 degraded poly-γ-
d
-glutamic acid; when the 2 strains were cultured separately, no hydrolytic activity was apparent. Here we report the draft genome sequences of both soil isolates.
Whole Genome Sequencing of Thermus oshimai JL-2 and Thermus thermophilus JL-18, Incomplete Denitrifiers from the United States Great Basin
Authors: Murugapiran Senthil K. , Huntemann Marcel , Wei Chia-Lin , Han James , Detter John C. , Han Cliff S. , Erkkila Tracy H. , Teshima Hazuki , Chen Amy , Kyrpides Nikos , Mavrommatis Konstantinos , Markowitz Victor , Szeto Ernest , Ivanova Natalia , Pagani Ioanna , Lam Jenny , McDonald Austin I. , Dodsworth Jeremy A. , Pati Amrita , Goodwin Lynne , Peters Lin , Pitluck Sam , Woyke Tanja , Hedlund Brian P. 
Published: January 2013

ABSTRACT

The strains
Thermus oshimai
JL-2 and
Thermus thermophilus
JL-18 each have a circular chromosome, 2.07 Mb and 1.9 Mb in size, respectively, and each has two plasmids ranging from 0.27 Mb to 57.2 kb. The megaplasmid of each strain contains a gene cluster for the reduction of nitrate to nitrous oxide, consistent with their incomplete denitrification phenotypes.
Princely Burial of the Hellenistic Period in the Mezmay Burial-Ground (North-Western Caucasus)
Authors: Mordvintseva Valentina I. , Shevchenko Nikolai F. , Zaïtsev Yuri P. 
Published: January 2013

Abstract
In 2004 a previously unknown burial-ground consisting of flat graves was discovered by grave-robbers on the northern slopes of the Central Caucasus range at a height of 800 metres above sea-level near the settlement of Mezmay in the Apsheronsk District of the Krasnodar region. In 2005 the first rescue excavations were undertaken.
Among the assemblages so far investigated, the most interesting has been Grave No. 3, in which a warrior of aristocratic descent and high social rank had been laid to rest. Apart from the deceased warrior, there were also horse burials in this funerary complex and a large range of grave goods, the number and quality of which make the complex unique, not only for the Northern Caucasus but also for the whole North Pontic region. Two bronze helmets were found in it for example, iron chain-mail, swords, spear-heads, short spears and arrows, a battle-axe, bronze, glass and pottery vessels, gold jewellery, a bronze mirror, an iron tripod bearing zoomorphic depictions and many other artefacts. The preliminary date which has been assigned to the burial ranges from the late 3rd to the early 2nd century BC, while the necropolis itself is considered as belonging to the Late Hellenistic and Early Roman eras. It is not possible to identify unequivocally the culture with which the Mezmay necropolis is linked, but it can for the time being be classified as linked to the range of Maeotian antiquities of the North-western Caucasus.
Apart from Burial No. 3, bronze and iron helmets from the spoil heaps of the grave-robbers’ excavations are also published in this article.