bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of molecular markers to wheat breeding in Canada
Authors: Randhawa Harpinder S. , Asif Muhammad , Pozniak Curtis , Clarke John M. , Graf Robert J. , Fox Stephen L. , Humphreys D. Gavin , Knox Ron E. , DePauw Ron M. , Singh Asheesh K. , Cuthbert Richard D. , Hucl Pierre , Spaner Dean 
Published: May 2013

AbstractMarker‐assisted breeding provides an opportunity for wheat breeders to introgress/pyramid genes of interest into breeding lines and to identify genes and/or quantitative trait loci in germplasm to be used as parents. Molecular markers were deployed to assist selection for disease resistance, agronomic and quality traits in several wheat cultivars released for commercial cultivation in Canada. Marker‐assisted breeding is routinely used in most wheat breeding programmes for rust resistance (leaf, stem and stripe rust), orange wheat blossom midge resistance, high grain protein concentration, Fusarium head blight and common bunt resistance. Markers are being used selectively within breeding programmes to target traits that relate to market class or regional adaptation. For example, marker‐assisted breeding for low lipoxygenase activity and low grain cadmium is being performed in durum breeding programmes and for enhancing stem solidness in programmes targeting resistance to the wheat stem sawfly. Markers are also being utilized for ergot resistance in durum wheat. Increased gluten strength is being selected with a marker for the overexpression of the Bx7 high‐molecular‐weight glutenin subunit. Marker‐assisted breeding is also being used to pyramid resistance genes against a group of stem rust races related to TTKS (Ug99), a disease that poses a serious threat to global wheat production. Development of tightly linked diagnostic markers and high‐throughput genotyping with SNP markers will result in more effective molecular wheat breeding in the near future and will open the door to genomic selection.
Hybridization between Camelina sativa (L.) Crantz (false flax) and North American Camelina species
Authors: Séguin‐Swartz Ginette , Nettleton Jacqueline A. , Sauder Connie , Warwick Suzanne I. , Gugel Richard K. 
Published: May 2013

AbstractThe potential for gene flow between Camelina sativa, a promising edible and industrial oil crop in Canada, and its wild North American relatives C. alyssum, C. microcarpa and C. rumelica subsp. rumelica, was investigated. Sequence analysis of the nuclear ribosomal internal transcribed spacer region (ITS) was used to differentiate Camelina species and/or accession‐specific nucleotide markers and identify interspecific F1 hybrids. ITS analysis identified hybrids in progeny of C. alyssum × C. sativa, C. microcarpa accession 36010 × C. sativa and C. sativa × C. rumelica subsp. rumelica. Seed set on C. alyssum × C. sativa F1 and F2 progeny was similar to the parents; few seeds were produced on hybrid progeny of C. microcarpa accession 36010 × C. sativa and C. sativa × C. rumelica subsp. rumelica. The study provided evidence that should the species have sympatric distributions and overlapping flowering periods, gene flow between C. sativa and its wild North American relatives is possible and that it would most likely occur with C. alyssum given the high fertility of the F1 hybrids recovered.
Dissection of a major QTL for seed colour and fibre content in Brassica napus reveals colocalization with candidate genes for phenylpropanoid biosynthesis and flavonoid deposition
Authors: Stein Anna , Wittkop Benjamin , Liu Liezhao , Obermeier Christian , Friedt Wolfgang , Snowdon Rod J. 
Published: May 2013

AbstractA major quantitative trait locus (QTL) influencing seed fibre and colour in Brassica napus was dissected by marker saturation in a doubled haploid (DH) population from the black‐seeded oilseed rape line ‘Express 617’ crossed with a yellow‐seeded B. napus line, ‘1012–98’. The marker at the peak of a sub‐QTL with a strong effect on both seed colour and acid detergent lignin content lay only 4 kb away from a Brassica (H+)‐ATPase gene orthologous to the transparent testa gene AHA10. Near the peak of a second sub‐QTL, we mapped a copy of the key phenylpropanoid biosynthesis gene cinnamyl alcohol dehydrogenase, while another key phenylpropanoid biosynthesis gene, cinnamoyl co‐a reductase 1, was found nearby. In a cross between ‘Express 617’ and another dark‐seeded parent, ‘V8’, Bna.CCR1 was localized in silico near the peak of a corresponding seed fibre QTL, whereas in this case Bna.CAD2/CAD3 lay nearby. Re‐sequencing of the two phenylpropanoid genes via next‐generation amplicon sequencing revealed intragenic rearrangements and functionally relevant allelic variation in the three parents.
Novel molecular marker associated with Tm2a gene conferring resistance to tomato mosaic virus in tomato
Authors: Panthee Dilip R. , Brown Allan F. , Yousef Gad G. , Ibrahem Ragy , Anderson Candice 
Published: May 2013

AbstractTomato mosaic virus (ToMV) is an important Tobamovirus that causes significant crop losses. Resistance to the ToMV is conferred by the genes Tm1, Tm2 and Tm2a. Among these three genes, Tm2a confers resistance to most strains of the ToMV. Screening of genetic lines under field conditions based on phenotype is time‐consuming and challenging due to concerns associated with stability of the virus and its potential transmission to other plants. Tightly linked molecular markers associated with resistance genes can improve selection efficiency and avoid these problems. This study developed a PCR‐based marker based on restriction site differences from Tm2a locus‐specific sequences, which was found to be useful in identifying the resistant and susceptible genotypes and was consistent with phenotypic data. The marker is a codominant cleaved amplified polymorphic sequence (CAPS) marker producing 270‐ and 600‐bp DNA fragments from resistant genotypes and an 870‐bp fragment from susceptible genotypes when digested with HaeIII restriction enzyme. This novel marker can be useful for tomato breeders to screen progeny from segregating populations for ToMV resistance.
Implicit conditioning of faces via the social regulation of emotion: ERP evidence of early attentional biases for security conditioned faces
Authors: Beckes Lane , Coan James A. , Morris James P. 
Published: May 2013

AbstractNot much is known about the neural and psychological processes that promote the initial conditions necessary for positive social bonding. This study explores one method of conditioned bonding utilizing dynamics related to the social regulation of emotion and attachment theory. This form of conditioning involves repeated presentations of negative stimuli followed by images of warm, smiling faces. L. Beckes, J. Simpson, and A. Erickson (2010) found that this conditioning procedure results in positive associations with the faces measured via a lexical decision task, suggesting they are perceived as comforting. This study found that the P1 ERP was similarly modified by this conditioning procedure and the P1 amplitude predicted lexical decision times to insecure words primed by the faces. The findings have implications for understanding how the brain detects supportive people, the flexibility and modifiability of early ERP components, and social bonding more broadly.
Effects of long‐term azithromycin therapy on airway oxidative stress markers in non‐cystic fibrosis bronchiectasis
Authors: Diego Afredo De , Milara Javier , Martinez‐Moragón Eva , Palop Marta , León Montse , Cortijo Julio 
Published: May 2013

AbstractBackground and objectiveTo explore the effect of long‐term therapy with azithromycin in regards to airway oxidative stress markers in exhaled breath condensate (EBC) of adult patients with stable non‐cystic fibrosis (CF) bronchiectasis.MethodsOpen‐label prospective study of 30 patients randomized to azithromycin 250 mg three times per week during 3 months (16 patients) or control (14 patients). Primary outcome were changes in nitric oxide, 8‐isoprostane, pH, nitrites and nitrates in EBC. Secondary outcomes were changes in exacerbation rates, dyspnoea (Borg scale), sputum volume (cc), sputum colour (15‐point scale), bacterial infection, health‐related quality of life (St George's Respiratory Questionnaire), lung function and radiological extension.ResultsAzithromycin produced a significant decrease in sputum volume (8.9 (1.8) mL vs 2.1 (3.4) mL) and number of exacerbations (0.1 (0.6) vs 1.2 (0.9)). Dyspnoea (0.4 (0.1) vs 0.1 (0.2)) and health‐related quality of life also improved after therapy. However, oxidative stress markers in EBC, systemic inflammatory markers as well as functional respiratory tests did not differ from the control group after therapy. A post‐hoc analysis comparing patients infected or not with Pseudomonas aeruginosa revealed that these effects were more pronounced in infected patients. In this subgroup, treatment was followed by a significant reduction in sputum volume, number of exacerbations, dyspnoea and St George's Respiratory Questionnaire total score. Of all airway oxidative stress markers, only nitrates in EBC were reduced after therapy.ConclusionsLong‐term azythromicin treatment has some clinical benefits in patients with non‐CF stable bronchiectasis, but it does not affect airway oxidative stress markers.
Infliximab Inhibits Activation and Effector Functions of Peripheral Blood T Cells in vitro from Patients with Clinically Active Ulcerative Colitis
Authors: Dahlén R. , Strid H. , Lundgren A. , Isaksson S. , Raghavan S. , Magnusson M. K. , Simrén M. , Sjövall H. , Öhman L. 
Published: May 2013

AbstractMany patients with inflammatory bowel disease (IBD) are undergoing therapy with infliximab, an antibody specific for TNF. However, the exact mechanisms of action of infliximab are not completely understood. The aim of this study was to determine the in vitro effects of infliximab on blood T cells derived from anti‐TNF therapy–naïve ulcerative colitis (UC) patients with clinically active disease. Peripheral blood mononuclear cells were stimulated polyclonally or by antigen in the presence or absence of infliximab. The T cell phenotype was investigated by flow cytometry, cytokine secretion was determined by ELISA, and cell proliferation was determined by thymidine assay or CFSE dye. Presence of infliximab resulted in reduced expression of CD25 in CD4+ and CD8+ T cell populations and inhibited secretion of IFN‐γ, IL‐13, IL‐17A, TNF as well as granzyme A. Infliximab also suppressed CD4+ and CD8+ T cell proliferation. These effects of infliximab were recorded both in T cells activated by polyclonal and antigen‐specific stimulation. The effects of infliximab on T cell apoptosis and induction of FOXP3+CD4+ T regulatory cells were ambiguous and depended on the originating cellular source and/or the stimulation mode and strength. In conclusion, infliximab is able to reduce T cell activation as measured by CD25, proliferation and cytokine secretion in vitro from UC patients with clinically active disease. These data suggest that suppression of T cell activity may be important for infliximab‐mediated disease remission in patients with UC.
Assessing the Effect of Data Imports on the Completeness of OpenStreetMap – A United States Case Study
Authors: Zielstra Dennis , Hochmair Hartwig H. , Neis Pascal 
Published: May 2013

AbstractThe assessment of OpenStreetMap (OSM) data quality has become an interdisciplinary research area over the recent years. The question of whether the OSM road network should be updated through periodic data imports from public domain data, or whether the currency of OSM data should rather rely on more traditional data collection efforts by active contributors, has led to perpetual debates within the OSM community. A US Census TIGER/Line 2005 import into OSM was accomplished in early 2008, which generated a road network foundation for the active community members in the US. In this study we perform a longitudinal analysis of road data for the US by comparing the development of OSM and TIGER/Line data since the initial TIGER/Line import. The analysis is performed for the 50 US states and the District of Columbia, and 70 Urbanized Areas. In almost all tested states and Urbanized Areas, OSM misses roads for motorized traffic when compared with TIGER/Line street data, while significant contributions could be observed in pedestrian related network data in OSM compared with corresponding TIGER/Line data. We conclude that the quality of OSM road data could be improved through new OSM editor tools allowing contributors to trace current TIGER/Line data.
Toward an Immersive 3D Virtual BoK Exploratorium: A Proof of Concept
Authors: DeMers Michael , Klimaszewski‐Patterson Anna , Richman Rebecca , Ahearn Sean , Plewe Brandon , Skupin André 
Published: May 2013

AbstractThe UCGIS GIS&T Body of Knowledge document provided an opportunity for the GIS educational community to link course content and curricular sequencing to a catalog of subject matter. Focusing on learning objectives, a selection of relevant citations, and basic background for each topic, it has been used to a limited degree for both course topic selection and curriculum development. However, the static format of the document, lack of an index, and dated nature of the material limit its utility for education. Based on the success of our research team in developing a virtual platform for a new, more interactive, and collaborative environment to catalogue and interactively add to the body knowledge (Ahearn et al. 2013), this article describes efforts to develop a multi‐user virtual user environment that will add social presence to the experience. It describes the successes and failures of using Second Life as the initial platform for this work, illustrates the available interactions and limitations, and depicts ongoing efforts to move beyond Second Life for this development. Finally it discusses a possible methodology to leverage the power of virtual crowd sourcing within competitive gaming environments such as Unity to allow for the creation of on‐demand virtual 3‐D visualizations of GIS&T concepts in a digital Exploratorium.
Modeling and Communicating the Conceptual Intent of Geo‐Analytical Tasks for Human‐GISInteraction
Authors: Cai Guoray , Yu Bo , Chen Dong 
Published: May 2013

AbstractOne of the fundamental issues of geographical information science is to designGISinterfaces and functionalities in a way that is easy to understand, teach, and use. Unfortunately, current geographical information systems (includingArcGIS) remains very difficult to use as spatial analysis tools, because they organize and expose functionalities according toGISdata structures and processing algorithms. As a result,GISinterfaces are conceptually confusing, cognitively complex, and semantically disconnected from the way human reason about spatial analytical activities. In this article, we propose an approach that structuresGISanalytical functions based on the notion of “analytical intent”. We describe an experiment that replacesArcGISdesktop interface with a conversational interface, to enable mixed‐initiative user‐system interactions at the level of analytical intentions. We initially focus on the subset ofGISfunctions that are relevant to “finding what's inside” as described byMitchell, but the general principles apply to other types of spatial analysis. This work demonstrates the feasibility of delegating some spatial thinking tasks to computational agents, and also raises future research questions that are key to building a better theory of spatial thinking withGIS.
Defining the Jr(a–) phenotype in the Japanese population
Authors: Tanaka Mitsunobu , Kamada Ikuko , Takahashi Junko , Kimura Keiko , Matsukura Harumichi , Tani Yoshihiko 
Published: May 2013

BackgroundThe Jr(a–) phenotype is rare in European and North American populations but is not so rare in Japanese and other Asian populations. Recently, two groups have established the connection between the Jr(a–) phenotype and the ATP‐binding cassette, member G2 (ABCG2) gene and concluded that ABCG2‐null alleles encode the Jr(a–) phenotype. In Japanese Red Cross Blood Centers, the Jr(a–) phenotype is found with a prevalence of 0.05% among blood donors, and we applied DNA‐based genotyping to investigate the molecular basis of the Jr(a–) phenotype in Japan, in addition to serologic typing.Study Design and MethodsPurified genomic DNA extracts of Japanese donor samples [500 Jr(a+) and 85 Jr(a–) phenotypes] were amplified using specific amplification primers for the c.376C>T mutation, which is the most common mutation in the Asian JRnull allele. Polymerase chain reaction products were examined by high‐resolution melt techniques and DNA sequence analyses.ResultsSeventy‐nine of 85 Jr(a–) samples were homozygous for the single‐nucleotide polymorphism c.376C>T (Gln126Stop) change. In other samples, two novel null alleles were detected: c.2T>C and c.421C>A: c.1515delC.ConclusionIn this study, more than 90% of the Japanese Jr(a–) phenotypes had c.376C>T (Gln126Stop) nucleotide change. In the other Jr(a–), a new mutation (c.2T>C) in the start codon encoding Thr instead of Met, c.1515delC encoding Ala505AlafsStop and heterozygous for c.337C/T and c.736C/T were detected. DNA‐based genotyping is accurate and useful for Jr(a–) donor typing.
Evolution of cave Axiokebuita and Speleobregma (Scalibregmatidae, Annelida)
Authors: Martínez Alejandro , Di Domenico Maikon , Worsaae Katrine 
Published: May 2013

The evolutionary history of Axiokebuita and Speleobregma, two poorly known lineages of annelids exclusive from deep‐sea or marine caves but always from crevicular habitats, is explored here. Speleobregma lanzaroteum Bertelsen, 1986, and Axiokebuita cavernicola sp. n. are described from anchialine and marine caves of the Canary Islands using light and electron microscopy. Speleobregma lanzaroteum is previously known only from a single specimen from the water column of an anchialine cave in Lanzarote. Emended diagnosis, details on the ciliary patterns and behavioural observations are provided based on newly collected material and in situ observations. Axiokebuita cavernicola sp. n. is found in Pleistocene gravel deposits in a shallow water marine cave in Tenerife (Canary Islands). The new species is characterized by the presence of dorsal ciliary bands and short knob‐like neuropodial cirri from segment two. The porosity and permeability of the gravelly environment of A. cavernicola sp. n. are shown to be equivalent to the water column or crevices of Speleobregma and other Axiokebuita spp. Phylogenetic analyses of five gene fragments and 44 terminals using maximum‐likelihood and Bayesian methods support a derived position of A. cavernicola sp. n. within Axiokebuita and confirm a sister‐group relationship of Axiokebuita with Speleobregma with high nodal support. The Axiokebuita–Speleobregma clade is morphologically characterized by a globular pygidium with adhesive glands and ventral ungrooved ciliated palps. Our results support two independent cave colonization events, favoured by the preadaptation of the members of Axiokebuita–Speleobregma lineage to crevicular habitats.
Boosting Salt Resistance of Short Antimicrobial Peptides
Authors: Chu Hung-Lun , Yu Hui-Yuan , Yip Bak-Sau , Chih Ya-Han , Liang Chong-Wen , Cheng Hsi-Tsung , Cheng Jya-Wei 
Published: May 2013

ABSTRACT
The efficacies of many antimicrobial peptides are greatly reduced under high salt concentrations, therefore limiting their use as pharmaceutical agents. Here, we describe a strategy to boost salt resistance and serum stability of short antimicrobial peptides by adding the nonnatural bulky amino acid β-naphthylalanine to their termini. The activities of the short salt-sensitive tryptophan-rich peptide S1 were diminished at high salt concentrations, whereas the activities of its β-naphthylalanine end-tagged variants were less affected.
Structure-Antifungal Activity Relationships of Polyene Antibiotics of the Amphotericin B Group
Authors: Tevyashova Anna N. , Olsufyeva Evgenia N. , Solovieva Svetlana E. , Printsevskaya Svetlana S. , Reznikova Marina I. , Trenin Aleksei S. , Galatenko Olga A. , Treshalin Ivan D. , Pereverzeva Eleonora R. , Mirchink Elena P. , Isakova Elena B. , Zotchev Sergey B. , Preobrazhenskaya Maria N. 
Published: May 2013

ABSTRACT

A comprehensive comparative analysis of the structure-antifungal activity relationships for the series of biosynthetically engineered nystatin analogues and their novel semisynthetic derivatives, as well as amphotericin B (AMB) and its semisynthetic derivatives, was performed. The data obtained revealed the significant influence of the structure of the C-7 to C-10 polyol region on the antifungal activity of these polyene antibiotics. Comparison of positions of hydroxyl groups in the antibiotics and
in vitro
antifungal activity data showed that the most active are the compounds in which hydroxyl groups are in positions C-8 and C-9 or positions C-7 and C-10. Antibiotics with OH groups at both C-7 and C-9 had the lowest activity. The replacement of the C-16 carboxyl with methyl group did not significantly affect the
in vitro
antifungal activity of antibiotics without modifications at the amino group of mycosamine. In contrast, the activity of the N-modified derivatives was modulated both by the presence of CH
3
or COOH group in the position C-16 and by the structure of the modifying substituent. The most active compounds were tested
in vivo
to determine the maximum tolerated doses and antifungal activity on the model of candidosis sepsis in leukopenic mice (cyclophosphamide-induced). Study of our library of semisynthetic polyene antibiotics led to the discovery of compounds, namely,
N
-(
l
-lysyl)-BSG005 (compound 3n) and, especially,
l
-glutamate of 2-(
N
,
N
-dimethylamino)ethyl amide of S44HP (compound 2j), with high antifungal activity that were comparable in
in vitro
and
in vivo
tests to AMB and that have better toxicological properties.
Lopinavir Plasma Concentrations and Virological Outcome with Lopinavir-Ritonavir Monotherapy in HIV-1-Infected Patients
Authors: Lopez-Cortes Luis F. , Ruiz-Valderas Rosa , Sánchez-Rivas Elena , Lluch Amparo , Gutierrez-Valencia Alicia , Torres-Cornejo Almudena , BenMarzouk-Hidalgo Omar J. , Viciana Pompeyo 
Published: May 2013

ABSTRACTThere is significant intra- and intersubject variability in lopinavir (LPV) plasma concentrations after standard dosing; thus, this prospective study was conducted to determine whether low plasma LPV concentrations could be associated with virological outcome throughout lopinavir-ritonavir maintenance monotherapy (mtLPVr) in the clinical practice setting. If this hypothesis would be confirmed, LPV drug monitoring could improve the efficacy of mtLPVr regimens. Patients with previous virological failure (VF) on protease inhibitor-based regimens were also included if the genotypic resistance tests showed no major resistance mutation associated with reduced susceptibility to lopinavir-ritonavir. VF was defined as 2 consecutive determinations of HIV RNA levels of >200 copies/ml. Efficacy was analyzed by per-protocol analysis. Plasma LPV trough concentrations were measured by high-performance liquid chromatography using a UV detector. A total of 127 patients were included (22% with previous failure on protease inhibitors). After 96 weeks, the efficacy rate was 82.3% (95% confidence interval [CI95], 75.3 to 89.3%). Virological efficacy was independent of LPV plasma concentrations even when LPVr was given once daily. An adherence of <90% (HR, 4.4 [CI95, 1.78 to 10.8;P= 0.001]) and the presence of blips in the preceding 12 months (HR, 3.06 [CI95, 1.17 to 8.01;P= 0.022]) were the only variables independently associated with time to VF. These findings suggest that the LPV concentrations achieved with the standard doses of LPVr are sufficient to maintain virological control during monotherapy and that measurement of LPV concentrations is not useful for predicting virological outcome. Tight control of viral replication in the previous months and strict adherence throughout the mtLPVr regimen could improve the virological efficacy of this maintenance regimen.