bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validation of a set of reference genes to study response to herbicide stress in grasses
Authors: Petit Cécile , Pernin Fanny , Heydel Jean-Marie , Délye Christophe 
Published: January 2012

Abstract

Background
Non-target-site based resistance to herbicides is a major threat to the chemical control of agronomically noxious weeds. This adaptive trait is endowed by differences in the expression of a number of genes in plants that are resistant or sensitive to herbicides. Quantification of the expression of such genes requires normalising qPCR data using reference genes with stable expression in the system studied as internal standards. The aim of this study was to validate reference genes in Alopecurus myosuroides, a grass (Poaceae) weed of economic and agronomic importance with no genomic resources.

Results
The stability of 11 candidate reference genes was assessed in plants resistant or sensitive to herbicides subjected or not to herbicide stress using the complementary statistical methods implemented by NormFinder, BestKeeper and geNorm. Ubiquitin, beta-tubulin and glyceraldehyde-3-phosphate dehydrogenase were identified as the best reference genes. The reference gene set accuracy was confirmed by analysing the expression of the gene encoding acetyl-coenzyme A carboxylase, a major herbicide target enzyme, and of an herbicide-induced gene encoding a glutathione-S-transferase.

Conclusions
This is the first study describing a set of reference genes (ubiquitin, beta-tubulin and glyceraldehyde-3-phosphate dehydrogenase) with a stable expression under herbicide stress in grasses. These genes are also candidate reference genes of choice for studies seeking to identify stress-responsive genes in grasses.
Inhibition of microRNA function by antimiR oligonucleotides
Authors: Stenvang Jan , Petri Andreas , Lindow Morten , Obad Susanna , Kauppinen Sakari 
Published: January 2012

Abstract
MicroRNAs (miRNAs) have emerged as important post-transcriptional regulators of gene expression in many developmental and cellular processes. Moreover, there is now ample evidence that perturbations in the levels of individual or entire families of miRNAs are strongly associated with the pathogenesis of a wide range of human diseases. Indeed, disease-associated miRNAs represent a new class of targets for the development of miRNA-based therapeutic modalities, which may yield patient benefits unobtainable by other therapeutic approaches. The recent explosion in miRNA research has accelerated the development of several computational and experimental approaches for probing miRNA functions in cell culture and in vivo. In this review, we focus on the use of antisense oligonucleotides (antimiRs) in miRNA inhibition for loss-of-function studies. We provide an overview of the currently employed antisense chemistries and their utility in designing antimiR oligonucleotides. Furthermore, we describe the most commonly used in vivo delivery strategies and discuss different approaches for assessment of miRNA inhibition and potential off-target effects. Finally, we summarize recent progress in antimiR mediated pharmacological inhibition of disease-associated miRNAs, which shows great promise in the development of novel miRNA-based therapeutics.
Complete Remission With Tyrosine Kinase Inhibitors in Renal Cell Carcinoma
Authors: Albiges Laurence , Oudard Stéphane , Negrier Sylvie , Caty Armelle , Gravis Gwenaëlle , Joly Florence , Duclos Brigitte , Geoffrois Lionel , Rolland Frédéric , Guillot Aline , Laguerre Brigitte , Legouffe Eric , Kohser Frédéric , Dietrich Pierre-Yves , Theodore Christine A. , Escudier Bernard 
Published: January 2012

Purpose Complete remission (CR) is uncommon during treatment for metastatic renal cell carcinoma (mRCC) with tyrosine kinase inhibitors (TKIs), but it may occur in some patients. It remains a matter of debate whether therapy should be continued after CR. Methods A multicenter, retrospective analysis of a series of patients with mRCC who obtained CR during treatment with TKIs (sunitinib or sorafenib), either alone or with local treatment (surgery, radiotherapy, or radiofrequency ablation), was performed. Results CR was identified in 64 patients; 36 patients had received TKI treatment alone and 28 had also received local treatment. Most patients had clear cell histology (60 of 64 patients), and all had undergone previous nephrectomy. The majority of patients were favorable or intermediate risk; however, three patients were poor risk. Most patients developed CR during sunitinib treatment (59 of 64 patients). Among the 36 patients who achieved CR with TKI alone, eight continued TKI treatment after CR, whereas 28 stopped treatment. Seventeen patients who stopped treatment (61%) are still in CR, with a median follow-up of 255 days. Among the 28 patients in CR after TKI plus local treatment, 25 patients stopped treatment, and 12 of these patients (48%) are still in CR, with a median follow-up of 322 days. Conclusion CR can occur after TKI treatment alone or when combined with local treatment. CR was observed at every metastatic site and in every prognostic group.
Online Tool to Guide Decisions forBRCA1/2Mutation Carriers
Authors: Kurian Allison W. , Munoz Diego F. , Rust Peter , Schackmann Elizabeth A. , Smith Michael , Clarke Lauren , Mills Meredith A. , Plevritis Sylvia K. 
Published: January 2012

PurposeWomen with BRCA1 or BRCA2 (BRCA1/2) mutations must choose between prophylactic surgeries and screening to manage their high risks of breast and ovarian cancer, comparing options in terms of cancer incidence, survival, and quality of life. A clinical decision tool could guide these complex choices.MethodsWe built a Monte Carlo model for BRCA1/2 mutation carriers, simulating breast screening with annual mammography plus magnetic resonance imaging (MRI) from ages 25 to 69 years and prophylactic mastectomy (PM) and/or prophylactic oophorectomy (PO) at various ages. Modeled outcomes were cancer incidence, tumor features that shape treatment recommendations, overall survival, and cause-specific mortality. We adapted the model into an online tool to support shared decision making.ResultsWe compared strategies on cancer incidence and survival to age 70 years; for example, PO plus PM at age 25 years optimizes both outcomes (incidence, 4% to 11%; survival, 80% to 83%), whereas PO at age 40 years plus MRI screening offers less effective prevention, yet similar survival (incidence, 36% to 57%; survival, 74% to 80%). To characterize patients' treatment and survivorship experiences, we reported the tumor features and treatments associated with risk-reducing interventions; for example, in most BRCA2 mutation carriers (81%), MRI screening diagnoses stage I, hormone receptor-positive breast cancers, which may not require chemotherapy.ConclusionCancer risk-reducing options for BRCA1/2 mutation carriers vary in their impact on cancer incidence, recommended treatments, quality of life, and survival. To guide decisions informed by multiple health outcomes, we provide an online tool for joint use by patients with their physicians ( http://brcatool.stanford.edu ).
Crystal structure and infrared spectrum of new magnesium tetra-ammonium cyclotriphosphate tetrahydrate Mg(NH4)4(P3O9)2 · 4 H2O
Authors: Ezzaafrani M. , Ennaciri Abdelaziz , Harcharras Mohamed , Khaoulaf Redouane , Capitelli Francesco 
Published: January 2012

Abstract
The new cyclotriphosphate Mg(NH4)4(P3O9)2 · 4 H2O was synthesized by the metathesis reaction of Boullé and characterized by single crystal X-ray diffraction and infrared spectroscopy. The compound crystallizes in the monoclinic system, space group P21/c, with the following unit cell parameters: a = 8.6120(5), b = 14.6390(10), and c = 8.8610(17) Å; β = 95.330(8)°; V = 1112.3(2) Å3. The crystal structure was refined up to a final R value of 0.0277 using 2543 independent reflections. Magnesium cation is coordinated by two P3O9
3– ring anions and four water molecules, displaying quite regular octahedral geometry. Ammonium polyhedra NH41O6 and NH42O6 are, respectively, connected to the MgO6 octahedron by O10—O4 edge and the O11 water molecule. The three-dimensional framework is built up from [Mg(P3O9)2(H2O)4]4– complex anions linked together via hydrogen bonds interactions made up by (NH4)+ cations. Last, the infrared spectrum of title compound was recorded and interpreted.
Genetic Diversity and Genomic Plasticity ofCryptococcus neoformansAD Hybrid Strains
Authors: Li Wenjun , Averette Anna Floyd , Desnos-Ollivier Marie , Ni Min , Dromer Françoise , Heitman Joseph 
Published: January 2012

AbstractNatural hybridization between two strains, varieties, or species is a common phenomenon in both plants and animals. Although hybridization may skew established gene pools, it generates population diversity efficiently and sometimes results in the emergence of newly adapted genotypes. Cryptococcus neoformans, which causes the most frequent opportunistic fungal infection in immunocompromised hosts, has three serotypes: A, D, and AD. Serotype-specific multilocus sequence typing and serotype-specific comparative genome hybridization were applied to investigate the genetic variability and genomic organization of C. neoformans serotype AD isolates. We confirm that C. neoformans serotype AD isolates are hybrids of serotype A and D strains. Compared with haploid strains, most AD hybrid isolates exhibit unique multilocus sequence typing genotypes, suggesting that multiple independent hybridization events punctuated the origin and evolutionary trajectory of AD hybrids. The MATa alleles from both haploid and AD hybrid isolates group closely to form a cluster or subcluster in both the serotype A and D populations. The rare and unique distribution of MATa alleles may restrict sexual reproduction between isolates of opposite mating types. The genetic diversity of the serotype D population, including haploid strains and serotype D genomes of the AD hybrid, is significantly greater than that of serotype A, and there are signatures of recombination within the serotype D population. Given that MATa isolates are relatively rare, both opposite-sex and same-sex mating may contribute to genetic recombination of serotype D in nature. Extensive chromosome loss was observed in AD hybrid isolates, which results in loss of heterozygosity in the otherwise-heterozygous AD hybrid genome. Most AD hybrid isolates exhibit hybrid vigor and are resistant to the antifungal drug FK506. In addition, the C. neoformans AD hybrid genome is highly dynamic, with continuous chromosome loss, which may be a facile route for pathogen evolution through which genotypic and phenotypic variation is generated.
Genetic Analysis of Fibroblast Growth Factor Signaling in theDrosophilaEye
Authors: Mukherjee T , Choi I , Banerjee Utpal 
Published: January 2012

AbstractThe development of eyes in Drosophila involves intricate epithelial reorganization events for accurate positioning of cells and proper formation and organization of ommatidial clusters. We demonstrate that Branchless (Bnl), the fibroblast growth factor ligand, regulates restructuring events in the eye disc primordium from as early as the emergence of clusters from a morphogenetic front to the cellular movements during pupal eye development. Breathless (Btl) functions as the fibroblast growth factor receptor to mediate Bnl signal, and together they regulate expression of DE-cadherin, Crumbs, and Actin. In addition, in the eye Bnl regulates the temporal onset and extent of retinal basal glial cell migration by activating Btl in the glia. We hypothesized that the Bnl functions in the eye are Hedgehog dependent and represent novel aspects of Bnl signaling not explored previously.
Improving the Quality of Immunization Delivery to an At-Risk Population: A Comprehensive Approach
Authors: Fu Linda Y. , Weissman Mark , McLaren Rosie , Thomas Cherie , Campbell Jacquelyn , Mbafor Jacob , Doshi Urvi , Cora-Bramble Denice 
Published: January 2012

OBJECTIVE:
Immunization quality improvement (QI) interventions are rarely tested as multicomponent interventions within the context of a theoretical framework proven to improve outcomes. Our goal was to study a comprehensive QI program to increase immunization rates for underserved children that relied on recommendations from the Centers for Disease Control and Prevention’s Task Force on Community Preventive Services and the framework of the Chronic Care Model.

METHODS:
QI activities occurred from September 2007 to May 2008 at 6 health centers serving a low-income, minority population in Washington, DC. Interventions included family reminders, education, expanding immunization access, reminders and feedback for providers, and coordination of activities with community stakeholders. We determined project effectiveness in improving the 4:3:1:3:3:1:3 vaccination series (4 diphtheria-tetanus-pertussis vaccines, 3 poliovirus vaccines, 1 measles-mumps-rubella vaccine, 3 Haemophilus influenzae type b vaccines, 3 hepatitis B vaccines, 1 varicella vaccine, and three 7-valent pneumococcal conjugate vaccines) compliance.

RESULTS:
We found a 16% increase in immunization rates overall and a 14% increase in on-time immunization by 24 months of age. Improvement was achieved at all 6 health centers and maintained beyond 18 months.

CONCLUSION:
We were able to implement a comprehensive immunization QI program that was sustainable over time.
The Risk of Immune Thrombocytopenic Purpura After Vaccination in Children and Adolescents
Authors: O'Leary Sean T. , Glanz Jason M. , McClure David L. , Akhtar Aysha , Daley Matthew F. , Nakasato Cynthia , Baxter Roger , Davis Robert L. , Izurieta Hector S. , Lieu Tracy A. , Ball Robert 
Published: January 2012

BACKGROUND:
The risk of immune thrombocytopenic purpura (ITP) after childhood vaccines other than measles-mumps-rubella vaccine (MMR) is unknown.

METHODS:
Using data from 5 managed care organizations for 2000 to 2009, we identified a cohort of 1.8 million children ages 6 weeks to 17 years. Potential ITP cases were identified by using diagnostic codes and platelet counts. All cases were verified by chart review. Incidence rate ratios were calculated comparing the risk of ITP in risk (1 to 42 days after vaccination) and control periods.

RESULTS:
There were 197 chart-confirmed ITP cases out of 1.8 million children in the cohort. There was no elevated risk of ITP after any vaccine in early childhood other than MMR in the 12- to 19-month age group. There was a significantly elevated risk of ITP after hepatitis A vaccine at 7 to 17 years of age, and for varicella vaccine and tetanus-diphtheria-acellular pertussis vaccine at 11 to 17 years of age. For hepatitis A, varicella, and tetanus-diphtheria-acellular pertussis vaccines, elevated risks were based on one to two vaccine-exposed cases. Most cases were acute and mild with no long-term sequelae.

CONCLUSIONS:
ITP is unlikely after early childhood vaccines other than MMR. Because of the small number of exposed cases and potential confounding, the possible association of ITP with hepatitis A, varicella, and tetanus-diphtheria-acellular pertussis vaccines in older children requires further investigation.
InN on GaN Heterostructure Growth by Migration Enhanced Epitaxial Afterglow (MEAglow)
Authors: Binsted Peter W. , Butcher Kenneth Scott A. , Alexandrov Dimiter , Terziyska Penka , Georgieva Dimka , Gergova Rositsa , Georgiev Vasil 
Published: January 2012

ABSTRACTIn this paper we discuss the formation of InN on GaN heterostructures. Film growth was accomplished using a new method coined Migration Enhanced Epitaxial Afterglow (MEAglow), an improved form of pulsed delivery Plasma Enhanced Chemical Vapour Deposition (PECVD) [1]. Initial x-ray diffraction (XRD) analysis results indicated that an InGaN alloy layer formed under the InN during growth. No GaN was seen from the original buffer layer. It was postulated that indium metal deposited prior to complete nitridation diffused into the relatively thin GaN layer producing InGaN. To verify the integrity of the insulating GaN layer, a third party GaN substrate was substituted. Results were unchanged. Parameters were then modified to reduce the amount of indium used for the initial metal deposition. XRD results indicated a sharper interface between the semi-insulating GaN and conductive InN layer. Hall Effect measurements are included. We’ve shown that the growth of a device suitable heterostructure is possible using the MEAglow technique.
Role of Voltage Scan Rate on Degradation of Graphite Electrodes Electrochemically Cycled vs. Li/Li+
Authors: Bhattacharya Sandeep , Riahi A. Reza , Alpas Ahmet T. 
Published: January 2012

ABSTRACTGraphite electrode surface degradation mechanisms and formation of solid electrolyte layers (SEI) at the interface with the electrolyte were studied as a function of the applied voltage and voltage scan rates using in situ optical microscopy. Voltammetry tests were initiated from a peak voltage of 3.00 V during which the voltage was decreased to a constant base potential (0.02 V) using different scan rates of 0.05-5.00 mV/s. Cross-sectional FIB microscopy indicated that graphite surface and subsurface damage -- in the form of loss of material from graphite -- was reduced when dense and continuous deposits of SEI formed at low scan rates (e.g. 0.05 mV/s).Whereas, non-uniform and discontinuous SEI formed at high scan rates (∼ 5.00 mV/s) was unable to alleviate graphite surface damage.
When Is Diabetes Distress Clinically Meaningful?
Authors: Fisher Lawrence , Hessler Danielle M. , Polonsky William H. , Mullan Joseph 
Published: January 2012

OBJECTIVETo identify the pattern of relationships between the 17-item Diabetes Distress Scale (DDS17) and diabetes variables to establish scale cut points for high distress among patients with type 2 diabetes.RESEARCH DESIGN AND METHODSRecruited were 506 study 1 and 392 study 2 adults with type 2 diabetes from community medical groups. Multiple regression equations associated the DDS17, a 17-item scale that yields a mean-item score, with HbA1c, diabetes self-efficacy, diet, and physical activity. Associations also were undertaken for the two-item DDS (DDS2) screener. Analyses included control variables, linear, and quadratic (curvilinear) DDS terms.RESULTSSignificant quadratic effects occurred between the DDS17 and each diabetes variable, with increases in distress associated with poorer outcomes: study 1 HbA1c (P &lt; 0.02), self-efficacy (P &lt; 0.001), diet (P &lt; 0.001), physical activity (P &lt; 0.04); study 2 HbA1c (P &lt; 0.03), self-efficacy (P &lt; 0.004), diet (P &lt; 0.04), physical activity (P = NS). Substantive curvilinear associations with all four variables in both studies began at unexpectedly low levels of DDS17: the slope increased linearly between scores 1 and 2, was more muted between 2 and 3, and reached a maximum between 3 and 4. This suggested three patient subgroups: little or no distress, &lt;2.0; moderate distress, 2.0–2.9; high distress, ≥3.0. Parallel findings occurred for the DDS2.CONCLUSIONSIn two samples of type 2 diabetic patients we found a consistent pattern of curvilinear relationships between the DDS and HbA1c, diabetes self-efficacy, diet, and physical activity. The shape of these relationships suggests cut points for three patient groups: little or no, moderate, and high distress.
Oochoristica koubeki n. sp. (Cestoda, Anoplocephalidae) from African Chamaeleo senegalensis (Chamaeleonidae) and emendation of the genus Oochoristica Lühe, 1898
Authors: Mašová Š. , Tenora F. , Baruš V. 
Published: January 2012

Abstract
During a survey of species diversity and ecology of selected West African vertebrates in the Niokolo Koba National Park, Senegal, two Chamaeleo senegalensis Daudin, 1802 (Chamaeleonidae) were collected and examined for parasites. A new species, Oochoristica koubeki n. sp., anoplocephalidian cestode of the genus Oochoristica Lühe, 1898 is described from the intestine of this host. The new species is related to O. theileri Fuhrmann, 1924; O. theileri Fuhrmann, 1924 f. major Baer, 1933; O. celebensis Yamaguti, 1954 and O. rostellata Zschokke, 1905 var. agamicolla Dollfus, 1957. All the forenamed species share characteristic strobila with proglottids wider than long. Oochoristica koubeki n. sp. differs from these species in different proportions of scolex, cirrus sac, ovarium and vitellarium, further differences are in number of testes and presence of reinforced genital atrium. Only O. theileri shares two last mentioned features, however it differs in shape of testes (rounded) and in distribution of testes (two clusters). The new species differs from all other species in extremely high number of egg’s capsules, different host species and zoogeographic distribution. Emendation of genus diagnosis sensu Beveridge (1994) is provided.
Aphelenchus avenae (Nematoda: Aphelenchidae) under the rhizosphere of Brassica napus
Authors: Kumari S. 
Published: January 2012

Abstract
Soil samples under the rhizosphere of Brasicca napus were collected from three localities (Bílé Podolí, Prague, Kylešovice). All three localities were positive for the presence of Aphelenchus avenae. Morphological and molecular features of A. avenae are presented in this research note.
Microstructure of a eutectic NiAl—Mo alloy directionally solidified using an industrial scale and a laboratory scale Bridgman furnace
Authors: Bogner Samuel , Hu Lei , Hollad Simon , Hu Weiping , Gottstein Günter , Bührig-Polaczek Andreas 
Published: January 2012

Abstract
The eutectic NiAl-9Mo (at.%) alloy was directionally solidified using an industrial scale Bridgman furnace and using a liquid metal cooling Bridgman furnace to produce in-situ composites of aligned Mo fibers in an NiAl matrix. In the first part of the experiment, an investment casting shell mold system, produced for NiAl alloys, was used and investigated for the NiAl-9Mo alloy in the industrial scale furnace. Due to the lower temperature gradient of ∼2.8 K mm−1, the microstructure of the samples was dendritic. In the second part of the experiment, samples with well aligned Mo fibers were produced in the laboratory Bridgman furnace using a temperature gradient of ∼11 K mm−1 and growth rates of 0.33–0.66 mm min−1.
Failure behaviour of the superalloy MAR-M247 LC under LCF, HCF and combined LCF/HCF loading
Authors: Gelmedin Domnin , Lang Karl-Heinz 
Published: January 2012

Abstract
Materials for turbine blades experience in service a combined loading of low and high cycle fatigue at high temperatures. In order to understand the failure behaviour under these loading conditions, systematic investigations were carried out. Low cycle fatigue, high cycle fatigue and combined low and high cycle fatigue tests were realised on MAR-M247 LC at 650 °C in an air environment under total strain control. Surface damage and fracture surfaces were analysed. Under combined low and high cycle fatigue, the lifetime is reduced if the low cycle fatigue leads to a degradation of the high cycle fatigue strength caused by crack initiation and crack growth. By analysing the fracture surface, the crack growth rate under combined cycle fatigue loading could be determined and it was significantly higher than under pure low cycle fatigue loading. The accelerated crack growth mainly causes the lifetime reduction.