Changepoint detection in base-resolution methylome data reveals a robust signature of methylated domain landscape

ABSTRACTLotta Dalenius Hahlin (2010) Mentorskap utifrån ett lösningsinriktat fokus. (Mentorship based on a solution-oriented focus. Skolutveckling och ledarskap, Lärarutbildningen halvfart/distans, Malmö HögskolaMånga elever hoppar av sin gymnasieutbildning pga. av olika orsaker. En av orsakerna kan vara att eleven inte har tillräckligt stöd i sin mentor på skolan. En mentor skall ju inte bara ta hand om elevens studiemässiga resultat utan får även ta hand om de många sociala frågor som ofta uppstår runt eleven. Kan det vara så att mentorn behöver en ram och metod att arbeta utifrån för att kunna stödja eleverna på bästa sätt?Syftet med arbetet är att beskriva den metodik som ligger bakom ett lösningsinriktat mentorskap,och att skapa ett kompendium av användbara verktyg utifrån lösningsinriktad pedagogik. Detta kompendium kan mentorn använda som mall/ram i sin arbetsuppgift som mentor.Forskningen tyder på att lyckade och bra samtal bygger på bra förberedelse, på öppna frågor och på ömsesidig respekt för varandra och att man använder sig av ett visst förhållningssätt gentemot varandra. Vidare pekar litteraturstudien på att mentorssamtalet bör ha tydliga mål och en gemensam uppfattning om vad man vill komma fram till för att eleven skall nå ökat ansvar, större självinsikt och önskat läge.Arbetet tar upp de olika verktyg som man främst använder inom lösningsinriktade metoder, och är utifrån litteraturen kommenterat för att ge en grundläggande kunskap och förförståelse för läsaren.Genom att som resultat skapa ett kompendium som mentorer kan använda i sitt arbete med det dagliga samtalet med eleverna, vill uppsatsen beskriva och ge grundläggande kunskap om de verktyg som finns i den lösningsinriktade verktygslådan. Syftet nås även med en enkätundersökning där mentorer som fått pröva på metoden plockat ut fördelar och nackdelar med metoden.Uppsatsen visar att regelbunden användning och övning krävs för att kunna tillgodogöra sig metoden, och även att mentorn genomgår en grundläggande utbildning. Den kommer också att visa att vinsterna och fördelarna med metoden överstiger de eventuella nackdelar som kan uppstå när man som mentor börjar arbeta med metoden

N-body simulation for self-gravitating collisional systems with a new SIMD instruction set extension to the x86 architecture, Advanced Vector eXtensions

We present a high-performance N-body code for self-gravitating collisional systems accelerated with the aid of a new SIMD instruction set extension of the x86 architecture: Advanced Vector eXtensions (AVX), an enhanced version of the Streaming SIMD Extensions (SSE). With one processor core of Intel Core i7-2600 processor (8 MB cache and 3.40 GHz) based on Sandy Bridge micro-architecture, we implemented a fourth-order Hermite scheme with individual timestep scheme (Makino and Aarseth, 1992), and achieved the performance of 20 giga floating point number operations per second (GFLOPS) for double-precision accuracy, which is two times and five times higher than that of the previously developed code implemented with the SSE instructions (Nitadori et al., 2006b), and that of a code implemented without any explicit use of SIMD instructions with the same processor core, respectively. We have parallelized the code by using so-called NINJA scheme (Nitadori et al., 2006a), and achieved 90 GFLOPS for a system containing more than N = 8192 particles with 8 MPI processes on four cores. We expect to achieve about 10 tera FLOPS (TFLOPS) for a self-gravitating collisional system with N 105 on massively parallel systems with at most 800 cores with Sandy Bridge micro-architecture. This performance will be comparable to that of Graphic Processing Unit (GPU) cluster systems, such as the one with about 200 Tesla C1070 GPUs (Spurzem et al., 2010). This paper offers an alternative to collisional N-body simulations with GRAPEs and GPUs.Comment: 14 pages, 9 figures, 3 tables, accepted for publication in New Astronomy. The code is publicly available at http://code.google.com/p/phantom-grape

Spin-spiral structures in free-standing Fe(110) monolayers

科研費報告書収録論文(課題番号:16310081/研究代表者:白井正文/ナノ磁性材料におけるスピン構造とそのダイナミクスに関する理論研究

Half-Metallic Exchange Bias Ferromagnetic/Antiferromagnetic Interfaces in Transition-Metal Chalcogenides

科研費報告書収録論文(課題番号:16310081/研究代表者:白井正文/ナノ磁性材料におけるスピン構造とそのダイナミクスに関する理論研究

Rice Annotation Database (RAD): a contig-oriented database for map-based rice genomics

A contig-oriented database for annotation of the rice genome has been constructed to facilitate map-based rice genomics. The Rice Annotation Database has the following functional features: (i) extensive effort of manual annotations of P1-derived artificial chromosome/bacterial artificial chromosome clones can be merged at chromosome and contig-level; (ii) concise visualization of the annotation information such as the predicted genes, results of various prediction programs (RiceHMM, Genscan, Genscan+, Fgenesh, GeneMark, etc.), homology to expressed sequence tag, full-length cDNA and protein; (iii) user-friendly clone / gene query system; (iv) download functions for nucleotide, amino acid and coding sequences; (v) analysis of various features of the genome (GC-content, average value, etc.); and (vi) genome-wide homology search (BLAST) of contig- and chromosome-level genome sequence to allow comparative analysis with the genome sequence of other organisms. As of October 2004, the database contains a total of 215 Mb sequence with relevant annotation results including 30 000 manually curated genes. The database can provide the latest information on manual annotation as well as a comprehensive structural analysis of various features of the rice genome. The database can be accessed at http://rad.dna.affrc.go.jp/

Predictive Value of the Cardio-Ankle Vascular Index for Cardiovascular Events in Patients at Cardiovascular Risk

BACKGROUND: Arterial stiffness is an important predictor of cardiovascular events; however, indexes for measuring arterial stiffness have not been widely incorporated into routine clinical practice. This study aimed to determine whether the cardio-ankle vascular index (CAVI), based on the blood pressure-independent stiffness parameter beta and reflecting arterial stiffness from the origin of the ascending aorta, is a good predictor of cardiovascular events in patients with cardiovascular disease risk factors in a large prospective cohort. METHODS AND RESULTS: This multicenter prospective cohort study, commencing in May 2013, with a 5-year follow-up period, included patients (aged 40-74 years) with cardiovascular disease risks. The primary outcome was the composite of cardiovascular death, nonfatal stroke, or nonfatal myocardial infarction. Among 2932 included patients, 2001 (68.3%) were men; the mean (SD) age at diagnosis was 63 (8) years. During the median follow-up of 4.9 years, 82 participants experienced primary outcomes. The CAVI predicted the primary outcome (hazard ratio, 1.38; 95% CI, 1.16-1.65; P CONCLUSIONS: This large cohort study demonstrated that the CAVI predicted cardiovascular events

Rapid Nucleotide Exchange Renders Asp-11 Mutant Actins Resistant to Depolymerizing Activity of Cofilin, Leading to Dominant Toxicity in Vivo

Conserved Asp-11 of actin is a part of the nucleotide binding pocket, and its mutation to Gln is dominant lethal in yeast, whereas the mutation to Asn in human alpha-actin dominantly causes congenital myopathy. To elucidate the molecular mechanism of those dominant negative effects, we prepared Dictyostelium versions of D11N and D11Q mutant actins and characterized them in vitro. D11N and D11Q actins underwent salt-dependent reversible polymerization, although the resultant polymerization products contained small anomalous structures in addition to filaments of normal appearance. Both monomeric and polymeric D11Q actin released bound nucleotides more rapidly than the wild type, and intriguingly, both monomeric and polymeric D11Q actins hardly bound cofilin. The deficiency in cofilin binding can be explained by rapid exchange of bound nucleotide with ATP in solution, because cofilin does not bind ATP-bound actin. Copolymers of D11Q and wild type actins bound cofilin, but cofilin-induced depolymerization of the copolymers was slower than that of wild type filaments, which may presumably be the primary reason why this mutant actin is dominantly toxic in vivo. Purified D11N actin was unstable, which made its quantitative biochemical characterization difficult. However, monomeric D11N actin released nucleotides even faster than D11Q, and we speculate that D11N actin also exerts its toxic effects in vivo through a defective interaction with cofilin. We have recently found that two other dominant negative actin mutants are also defective in cofilin binding, and we propose that the defective cofilin binder is a major class of dominant negative actin mutants

Gene Organization in Rice Revealed by Full-Length cDNA Mapping and Gene Expression Analysis through Microarray

Rice (Oryza sativa L.) is a model organism for the functional genomics of monocotyledonous plants since the genome size is considerably smaller than those of other monocotyledonous plants. Although highly accurate genome sequences of indica and japonica rice are available, additional resources such as full-length complementary DNA (FL-cDNA) sequences are also indispensable for comprehensive analyses of gene structure and function. We cross-referenced 28.5K individual loci in the rice genome defined by mapping of 578K FL-cDNA clones with the 56K loci predicted in the TIGR genome assembly. Based on the annotation status and the presence of corresponding cDNA clones, genes were classified into 23K annotated expressed (AE) genes, 33K annotated non-expressed (ANE) genes, and 5.5K non-annotated expressed (NAE) genes. We developed a 60mer oligo-array for analysis of gene expression from each locus. Analysis of gene structures and expression levels revealed that the general features of gene structure and expression of NAE and ANE genes were considerably different from those of AE genes. The results also suggested that the cloning efficiency of rice FL-cDNA is associated with the transcription activity of the corresponding genetic locus, although other factors may also have an effect. Comparison of the coverage of FL-cDNA among gene families suggested that FL-cDNA from genes encoding rice- or eukaryote-specific domains, and those involved in regulatory functions were difficult to produce in bacterial cells. Collectively, these results indicate that rice genes can be divided into distinct groups based on transcription activity and gene structure, and that the coverage bias of FL-cDNA clones exists due to the incompatibility of certain eukaryotic genes in bacteria

Age-Related Neuronal Degeneration: Complementary Roles of Nucleotide Excision Repair and Transcription-Coupled Repair in Preventing Neuropathology

Neuronal degeneration is a hallmark of many DNA repair syndromes. Yet, how DNA damage causes neuronal degeneration and whether defects in different repair systems affect the brain differently is largely unknown. Here, we performed a systematic detailed analysis of neurodegenerative changes in mouse models deficient in nucleotide excision repair (NER) and transcription-coupled repair (TCR), two partially overlapping DNA repair systems that remove helix-distorting and transcription-blocking lesions, respectively, and that are associated with the UV-sensitive syndromes xeroderma pigmentosum (XP) and Cockayne syndrome (CS). TCR–deficient Csa−/− and Csb−/− CS mice showed activated microglia cells surrounding oligodendrocytes in regions with myelinated axons throughout the nervous system. This white matter microglia activation was not observed in NER–deficient Xpa−/− and Xpc−/− XP mice, but also occurred in XpdXPCS mice carrying a point mutation (G602D) in the Xpd gene that is associated with a combined XPCS disorder and causes a partial NER and TCR defect. The white matter abnormalities in TCR–deficient mice are compatible with focal dysmyelination in CS patients. Both TCR–deficient and NER–deficient mice showed no evidence for neuronal degeneration apart from p53 activation in sporadic (Csa−/−, Csb−/−) or highly sporadic (Xpa−/−, Xpc−/−) neurons and astrocytes. To examine to what extent overlap occurs between both repair systems, we generated TCR–deficient mice with selective inactivation of NER in postnatal neurons. These mice develop dramatic age-related cumulative neuronal loss indicating DNA damage substrate overlap and synergism between TCR and NER pathways in neurons, and they uncover the occurrence of spontaneous DNA injury that may trigger neuronal degeneration. We propose that, while Csa−/− and Csb−/− TCR–deficient mice represent powerful animal models to study the mechanisms underlying myelin abnormalities in CS, neuron-specific inactivation of NER in TCR–deficient mice represents a valuable model for the role of NER in neuronal maintenance and survival