bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mature Microsatellites: Mechanisms Underlying Dinucleotide Microsatellite Mutational Biases in Human Cells
Authors: Baptiste Beverly A , Ananda Guruprasad , Strubczewski Noelle , Lutzkanin Andrew , Khoo Su Jen , Srikanth Abhinaya , Kim Nari , Makova Kateryna D , Krasilnikova Maria M , Eckert Kristin A 
Published: March 2013

AbstractDinucleotide microsatellites are dynamic DNA sequences that affect genome stability. Here, we focused on mature microsatellites, defined as pure repeats of lengths above the threshold and unlikely to mutate below it in a single mutational event. We investigated the prevalence and mutational behavior of these sequences by using human genome sequence data, human cells in culture, and purified DNA polymerases. Mature dinucleotides (≥10 units) are present within exonic sequences of &gt;350 genes, resulting in vulnerability to cellular genetic integrity. Mature dinucleotide mutagenesis was examined experimentally using ex vivo and in vitro approaches. We observe an expansion bias for dinucleotide microsatellites up to 20 units in length in somatic human cells, in agreement with previous computational analyses of germ-line biases. Using purified DNA polymerases and human cell lines deficient for mismatch repair (MMR), we show that the expansion bias is caused by functional MMR and is not due to DNA polymerase error biases. Specifically, we observe that the MutSα and MutLα complexes protect against expansion mutations. Our data support a model wherein different MMR complexes shift the balance of mutations toward deletion or expansion. Finally, we show that replication fork progression is stalled within long dinucleotides, suggesting that mutational mechanisms within long repeats may be distinct from shorter lengths, depending on the biochemistry of fork resolution. Our work combines computational and experimental approaches to explain the complex mutational behavior of dinucleotide microsatellites in humans.
PolyCat: A Resource for Genome Categorization of Sequencing Reads From Allopolyploid Organisms
Authors: Page Justin T , Gingle Alan R , Udall Joshua A 
Published: March 2013

Abstract
Read mapping is a fundamental part of next-generation genomic research but is complicated by genome duplication in many plants. Categorizing DNA sequence reads into their respective genomes enables current methods to analyze polyploid genomes as if they were diploid. We present PolyCat—a pipeline for mapping and categorizing all types of next-generation sequence data produced from allopolyploid organisms. PolyCat uses GSNAP’s single-nucleotide polymorphism (SNP)-tolerant mapping to minimize the mapping efficiency bias caused by SNPs between genomes. PolyCat then uses SNPs between genomes to categorize reads according to their respective genomes. Bisulfite-treated reads have a significant reduction in nucleotide complexity because nucleotide conversion events are confounded with transition substitutions. PolyCat includes special provisions to properly handle bisulfite-treated data. We demonstrate the functionality of PolyCat on allotetraploid cotton, Gossypium hirsutum, and create a functional SNP index for efficiently mapping sequence reads to the D-genome sequence of G. raimondii. PolyCat is appropriate for all allopolyploids and all types of next-generation genome analysis, including differential expression (RNA sequencing), differential methylation (bisulfite sequencing), differential DNA-protein binding (chromatin immunoprecipitation sequencing), and population diversity.
Imputation of Unordered Markers and the Impact on Genomic Selection Accuracy
Authors: Rutkoski Jessica E , Poland Jesse , Jannink Jean-Luc , Sorrells Mark E 
Published: March 2013

AbstractGenomic selection, a breeding method that promises to accelerate rates of genetic gain, requires dense, genome-wide marker data. Genotyping-by-sequencing can generate a large number of de novo markers. However, without a reference genome, these markers are unordered and typically have a large proportion of missing data. Because marker imputation algorithms were developed for species with a reference genome, algorithms suited for unordered markers have not been rigorously evaluated. Using four empirical datasets, we evaluate and characterize four such imputation methods, referred to as k-nearest neighbors, singular value decomposition, random forest regression, and expectation maximization imputation, in terms of their imputation accuracies and the factors affecting accuracy. The effect of imputation method on the genomic selection accuracy is assessed in comparison with mean imputation. The effect of excluding markers with a large proportion of missing data on the genomic selection accuracy is also examined. Our results show that imputation of unordered markers can be accurate, especially when linkage disequilibrium between markers is high and genotyped individuals are related. Of the methods evaluated, random forest regression imputation produced superior accuracy. In comparison with mean imputation, all four imputation methods we evaluated led to greater genomic selection accuracies when the level of missing data was high. Including rather than excluding markers with a large proportion of missing data nearly always led to greater GS accuracies. We conclude that high levels of missing data in dense marker sets is not a major obstacle for genomic selection, even when marker order is not known.
Fine-Mapping and Identification of a Candidate Gene Underlying thed2Dwarfing Phenotype in Pearl Millet,Cenchrus americanus(L.) Morrone
Authors: Parvathaneni Rajiv K , Jakkula Vinod , Padi Francis K , Faure Sebastien , Nagarajappa Nethra , Pontaroli Ana C , Wu Xiaomei , Bennetzen Jeffrey L , Devos Katrien M 
Published: March 2013

AbstractPearl millet is one of the most important subsistence crops grown in India and sub-Saharan Africa. In many cereal crops, reduced height is a key trait for enhancing yield, and dwarf mutants have been extensively used in breeding to reduce yield loss due to lodging under intense management. In pearl millet, the recessive d2 dwarfing gene has been deployed widely in commercial germplasm grown in India, the United States, and Australia. Despite its importance, very little research has gone into determining the identity of the d2 gene. We used comparative information, genetic mapping in two F2 populations representing a total of some 1500 progeny, and haplotype analysis of three tall and three dwarf inbred lines to delineate the d2 region by two genetic markers that, in sorghum, define a region of 410 kb with 40 annotated genes. One of the sorghum genes annotated within this region is ABCB1, which encodes a P-glycoprotein involved in auxin transport. This gene had previously been shown to underlie the economically important dw3 dwarf mutation in sorghum. The cosegregation of ABCB1 with the d2 phenotype, its differential expression in the tall inbred ICMP 451 and the dwarf inbred Tift 23DB, and the similar phenotype of stacked lower internodes in the sorghum dw3 and pearl millet d2 mutants suggest that ABCB1 is a likely candidate for d2.
Cats in the forest: predicting habitat adaptations from humerus morphometry in extant and fossil Felidae (Carnivora)
Authors: Meloro Carlo , Elton Sarah , Louys Julien , Bishop Laura C. , Ditchfield Peter 
Published: March 2013

Mammalian carnivores are rarely incorporated in paleoenvironmental reconstructions, largely because of their rarity within the fossil record. However, multivariate statistical modeling can be successfully used to quantify specific anatomical features as environmental predictors. Here we explore morphological variability of the humerus in a closely related group of predators (Felidae) to investigate the relationship between morphometric descriptors and habitat categories. We analyze linear measurements of the humerus in three different morphometric combinations (log-transformed, size-free, and ratio), and explore four distinct ways of categorizing habitat adaptations. Open, Mixed, and Closed categories are defined according to criteria based on traditional descriptions of species, distributions, and biome occupancy. Extensive exploratory work is presented using linear discriminant analyses and several fossils are included to provide paleoecological reconstructions.We found no significant differences in the predictive power of distinct morphometric descriptors or habitat criteria, although sample splitting into small and large cat guilds greatly improves the stability of the models. Significant insights emerge for three long-canine cats:Smilodon populator,Paramachairodus orientalis, andDinofelissp. from Olduvai Gorge (East Africa).S. populatorandP. orientalisare both predicted to have been closed-habitat adapted taxa. The false “sabertooth”Dinofelissp. from Olduvai Gorge is predicted to be adapted to mixed habitat. The application of felid humerus ecomorphology to the carnivoran record of Olduvai Gorge shows that the older stratigraphic levels (Bed I, 1.99–1.79 Ma) included a broader range of environments than Beds II or V, where there is an abundance of cats adapted to open environments.
Thrombin generation assay and transmission electron microscopy: a useful combination to study tissue factor‐bearing microvesicles
Authors: Gheldof Damien , Hardij Julie , Cecchet Francesca , Chatelain Bernard , Dogné Jean‐Michel , Mullier François 
Published: March 2013

AbstractIntroductionPatients with cancer have a 7‐ to 10‐fold increased risk of developing venous thromboembolism. Circulating microvesicles could be a useful predictive biomarker for venous thromboembolism in cancer. Validated and standardised techniques that could be used to determine the complete microvesicle phenotype are required.ObjectivesThese were two‐fold: a) to characterise tissue factor (TF)‐bearing microvesicles released by cultured breast cancer cells MDA‐MB‐231 by flow cytometry (FCM), transmission electron microscopy (TEM) and thrombin generation assay (TGA); and b) to validate the sensitivity and variability intra/inter‐assay of TGA as a useful method to study the procoagulant activity (PCA) of microvesicles.MethodsCultured breast cancer cells MDA‐MB‐231 were incubated for 45 minutes at 37°C. Samples were then centrifuged or not at 4,500 g for 15 minutes, and cells and MVs or MV‐containing supernatants were used for TEM, FCM and TGA. In activity assays, microvesicles (i.e. cell‐depleted supernatants) were incubated with anti‐TF antibodies or with annexin V to assess the contribution of TF and phospholipids to the PCA. Alternatively, supernatants were filtered through 0.1, 0.22, 0.45 or 0.65 µm membranes and subjected to TGA.ResultsThe majority of the PCA was associated with microvesicles smaller than 0.1 µm, and the mean microvesicle size estimated by TEM after 10,000 g centrifugation was 121±54 nm with a majority of vesicles between 100 and 200 nm. Microvesicles derived from 5,000 MDA‐MB‐231cells/ml were sufficient to significantly increase the thrombin generation of normal pooled plasma.ConclusionsTEM, FCM and filtration coupled to TGA represent a useful combination to study the PCA of TF‐bearing microvesicles, whatever their size. And it will be interesting to implement these techniques in patients.
Radioaktivität mit dem Smartphone messen
Authors: Freudenberg R. , Andreeff M. , Kotzerke J. , Hartmann H. 
Published: March 2013

SummaryThe interest in the detection of radioactive materials has strongly increased after the accident in the nuclear power plant Fukushima and has led to a bottleneck of suitable measuring instruments. Smartphones equipped with a commercially available software tool could be used for dose rate measurements following a calibration according to the specific camera module. Aim: We examined whether such measurements provide reliable data for typical activities and radionuclides in nuclear medicine. Methods: For the nuclides 99mTc (10 – 1000 MBq), 131I (3.7 – 1800 MBq, therapy capsule) and 68Ga (50 – 600 MBq) radioactivity with defined geo metry in different distances was measured. The smartphones Milestone Droid 1 (Motorola) and HTC Desire (HTC Corporation) were compared with the standard instruments AD6 (automess) and DoseGUARD (AEA Technology). Results: Measurements with the smartphones and the other devices show a good agreement: linear signal increase with rising activity and dose rate. The long time measurement (131I, 729 MBq, 0.5 m, 60 min) demonstrates a considerably higher variation (by 20%) of the measured smartphone data values compared with the AD6. For low dose rates (< 1 μGy/h), the sensitivity decreases so that measurements of e. g. the natural radiation exposure do not lead to valid results. The calibration of the camera responsivity for the smartphone has a big influence on the results caused by the small detector surface of the camera semiconductor. Conclusions: With commercial software the camera module of a smartphone can be used for the measurement of radioactivity. Dose rates resulting from typical nuclear medicine procedures can be measured reliably (e. g., dismissal dose after radioiodine therapy). The signal shows a high correlation to measured values of conventional dose measurement devices.
La France périphérique et marginalisée : les raisons du ressentiment
Authors: Davezies Laurent , Guilluy Christophe , Donzelot Jacques , Béja Alice 
Published: March 2013

Les dernières élections présidentielles ont fait émerger l’importance du vote FN dans les espaces « périurbains ». L’angle territorial permet-il à lui seul de comprendre ce vote, et ne faut-il pas l’associer aux questions économiques et sociales, voire sortir du « périurbain » pour parler, plus globalement, d’« espaces périphériques » (non métropolitains), dont les habitants ont de plus en plus l’impression de ne pas être « là où il faut » ?
Sous les cartes, les habitants
Authors: Rivière Jean 
Published: March 2013

La lecture « spatiale » du vote en faveur du Front national a eu tendance à assimiler périurbain et populisme, et a fait le bonheur des médias. Or, une telle approche tend à stigmatiser des populations en raison de leur mode de vie, au risque de faire équivaloir choix résidentiels et choix électoraux, en disqualifiant ainsi un outil – la carte – qui peut pourtant apporter beaucoup – mais pas tout – à l’analyse politique.
Pour en finir avec le périurbain
Authors: Roux Jean-Michel 
Published: March 2013

La ville est sortie de ses murs, et, plutôt que de stigmatiser tel ou tel comportement ou d’essayer de définir un espace « périurbain » toujours débordant, il vaudrait bien mieux comprendre comment l’urbain réinvente les campagnes elles-mêmes, reconnaître qu’il n’y aura pas de retour à la ville, et qu’il faut donc réapprendre l’aménagement du territoire.
De la ville industrielle à la ville des flux
Authors: Donzelot Jacques 
Published: March 2013

La construction des grands ensembles, les « cités » de banlieue, est liée à une certaine conception, fonctionnelle, de l’urbanisme. Mais, à l’heure où les flux prennent le pas sur les lieux, ces grands ensembles apparaissent totalement caducs. La rénovation urbaine peut-elle suffire à reconnecter les populations aux villes centres, et à leurs opportunités ?
Se porter à la périphérie, là où la ville rejoint la campagne
Authors: Corajoud Michel , Charbonneau Jean-Pierre , Mongin Olivier 
Published: March 2013

La reconnaissance de la profession de paysagiste va de pair avec une nouvelle approche du paysage ; on ne cherche plus à le transformer, mais à l’intensifier. Le paysagiste, alors, doit se garder du formalisme, pour penser la relation au milieu vivant, ce qui n’empêche pas de faire bouger les lignes, de sortir des délimitations pour avoir toujours l’œil sur l’horizon.
Terrence Malick : de la nature à la grâce
Authors: Amiel Vincent 
Published: March 2013

La nature, dans les films de Terrence Malick, est souvent présentée en parallèle à la parole humaine, qui ne parvient jamais vraiment à la saisir. Cette insaisissabilité ne l’enferme pas dans le spectre de la nostalgie, mais montre qu’il est possible d’excéder le langage. Il ne s’agit pas pour l’homme de maîtriser ce qui l’entoure, mais peut-être de s’en sentir responsable, de changer de regard ; c’est la grâce, alors, qui vient donner cette nouvelle perspective dans les derniers films, The Tree of Life et À la merveille .
Quelques pas vers l'accueil des familles. L'entretien avec les parents à la crèche
Authors: Catarsi Enzo , Sharmahd Nima 
Published: March 2013

L’article prend en compte le panorama italien des services pour la petite enfance, en relation avec les familles. Après une introduction initiale au système contemporain, composé d’une multitude de typologies familiales, de plus en plus isolées du point de vue affectif, l’article met en évidence le rôle de la crèche comme contexte d’éducation/accompagnement familial, en tenant compte de la valeur de la « coéducation ». Dans ce contexte, l’entretien individuel entre l’éducatrice et le couple parental a modifié le sens de la relation qui, auparavant allait des éducatrices vers les parents. En s’inspirant de ces réflexions, une recherche-action a été réalisée en Toscane, durant l’année 2009-2010. Douze entretiens individuels de préadaptation ont été filmés, dans l’objectif de mettre en évidence les points forts et les points difficiles liés aux modalités à travers desquelles les éducatrices ont mené les interactions. Les enregistements vidéos ont été analysés avec les éducatrices, en combinant la recherche avec la formation, afin de réfléchir de manière participative sur les méthodes de communication utilisées avec les familles.
« Rapprocher une école primaire et ses parents d'élèves ». Un outil québécois adapté à une école primaire en France
Authors: Claudel Mélanie , Schneide Benoît , Seiwert Denis 
Published: March 2013

Cet article présente une recherche-action réalisée dans une école primaire de Lorraine (France) ayant pour objectif de rapprocher l’équipe éducative et les parents d’élèves pour une meilleure adaptation des enfants à l’école. Afin de relancer le processus de réflexion de l’équipe et mettre en place des actions en faveur d’un partenariat école-familles, la recherche s’appuie sur l’outil québécois « Rapprocher les familles et l’école primaire » (Gouvernement du Québec, Ministère de l’Éducation, 2004) pour mettre en lien les réponses de l’équipe éducative, recueillies lors de séances de travail portant sur l’inventaire de ses pratiques de collaboration avec les parents, leur analyse et la planification des nouvelles actions, et celles relatives à la passation d’un questionnaire adressé aux parents concernant leurs points de vue, attentes et besoins vis-à-vis de l’école. L’article présente les résultats principaux et les préconisations qu’ils ont permis.
The Shaping of EU-Mercosur Relations: From Altruism to Pragmatism and Liberalism to Illiberalism
Authors: Dudek Carolyn Marie 
Published: March 2013

Deeply-embedded norms of liberalism and protectionism alongside EU policies focusing on promoting development and regional integration have shaped EU-Mercosur relations. These stand in stark contrast to the policies of the US, the historic hegemon in the region. This paper utilizes historical institutionalism to understand how the liberal tenets of EU competition policy and the protectionism of Common Agricultural Policy (CAP) have affected EU-Mercosur relations. Particular foci include Spain’s role in spearheading efforts to promote EU-Latin American relations and the way EU competition policies directed against monopolies in Europe spurred increased investment in Latin America, especially the Southern Cone. The latter prompted the EU to forge closer ties with Mercosur, encouraged cooperation and development programs and spurred regional integration and liberal trade regimes in Latin America.
Real-Time PCR as a New in vitro Biocompatibility Method to Measure Leukocyte Response to Surface Contact in Dialysis Filter Devices
Authors: Brodbeck Katrin , Neubauer Markus , Schnitzer Susanne , Dietrich Ruth , Hulko Michael , Krause Bernd 
Published: March 2013

Introduction The mortality risk of dialysis patients is still elevated. Even though there is continuous improvement in the biocompatibility of dialysis devices and treatments, there is clinical evidence of a negative inflammatory impact. One dialysis-related risk factor to be considered in this regard may be the repeated blood exposure to foreign filter surfaces. Standard test methods do not allow differences to be shown between most of the common dialysis devices. Methods A new highly sensitive in vitro test system was developed by analyzing the response of leukocytes to surface contact in dialysis filter devices by means of quantitative real time PCR and flow cytometry. Membrane surface studies provided additional physical data. Results An increase in the transcription level of specific pro-inflammatory genes, particularly IL-1β, TNF alpha, and IL-8, was observed after blood contact to the filter devices. In two sets of pairwise filter comparisons, radiation-sterilized filters showed stronger cell activation, more hydrophilic membranes, and rougher surfaces. Conclusions Quantitative real time RT-PCR was shown to be a new in vitro test method with increased sensitivity for detecting differences in activation levels of leukocytes upon membrane contact. Correlating leukocyte activation levels with surface properties opens new opportunities for understanding leukocyte activation upon membrane contact and thus guides further improvements in the biocompatibility of dialysis filter devices.
Reduced Sevoflurane Loss during Cardiopulmonary Bypass when using a Polymethylpentane versus a Polypropylene Oxygenator
Authors: Hinz Jose , Molder Jan Martin , Hanekop Gerd-Gunnar , Weyland Andreas , Popov Aron-Frederik , Bauer Martin , Kazmaier Stephan 
Published: March 2013

Purpose The goal of this investigation was to examine the influence of two oxygenators with different membranes, made of either polypropylene (PPL) or polymethylpentane (PMP), on the plasma concentration of sevoflurane during cardiopulmonary bypass. Methods The concentrations of sevoflurane during cardiopulmonary bypass were examined in patient plasma, endotracheal tubes, cardiotomy reservoirs and the outlets of the heart-lung oxygenators in twenty patients who underwent elective heart surgery. Results The sevoflurane losses are smaller in cardiopulmonary bypass when using a polymethylpentane versus a polypropylene oxygenator. Ten minutes after beginning cardiopulmonary bypass, the sevoflurane plasma concentration in the PPL oxygenator group compared to the PMP oxygenator group fell significantly (PPL 0.48-1.79 (0.93) vs. PMP 0.80-2.15 (1.56) μL x 100 mL−1, p = 0.02). This difference persisted until ten minutes after the termination of cardiopulmonary bypass. Conclusion The results of this study show that using a polymethylpentane membrane oxygenator rather than a polypropylene oxygenator significantly reduces the losses of sevoflurane, resulting in higher plasma concentrations and greater depth of anesthesia.