Simulation of position sensitivity of the anomalous Hall effect on a single magnetic dot

To overcome the superparamagnetic effect caused by scaling bit and grain sizes in magnetic storage media different approaches are investigated. One alternative is bit patterned magnetic media (BPM) where each bit is represented by a single domain magnetic dot. A key problem with BPM is the large difference in magnetic field necessary to switch the magnetization direction of the various dot which is characterized by the switching field distribution

Human Immunodeficiency Virus Type 1 Vif causes dysfunction of Cdk1 and CyclinB1: implications for cell cycle arrest

The two major cytopathic factors in human immunodeficiency virus type 1 (HIV-1), the accessory proteins viral infectivity factor (Vif) and viral protein R (Vpr), inhibit cell-cycle progression at the G2 phase of the cell cycle. Although Vpr-induced blockade and the associated T-cell death have been well studied, the molecular mechanism of G2 arrest by Vif remains undefined. To elucidate how Vif induces arrest, we infected synchronized Jurkat T-cells and examined the effect of Vif on the activation of Cdk1 and CyclinB1, the chief cell-cycle factors for the G2 to M phase transition. We found that the characteristic dephosphorylation of an inhibitory phosphate on Cdk1 did not occur in infected cells expressing Vif. In addition, the nuclear translocation of Cdk1 and CyclinB1 was disregulated. Finally, Vif-induced cell cycle arrest was correlated with proviral expression of Vif. Taken together, our results suggest that Vif impairs mitotic entry by interfering with Cdk1-CyclinB1 activation

10 simple rules to create a serious game, illustrated with examples from structural biology

Serious scientific games are games whose purpose is not only fun. In the field of science, the serious goals include crucial activities for scientists: outreach, teaching and research. The number of serious games is increasing rapidly, in particular citizen science games, games that allow people to produce and/or analyze scientific data. Interestingly, it is possible to build a set of rules providing a guideline to create or improve serious games. We present arguments gathered from our own experience ( Phylo , DocMolecules , HiRE-RNA contest and Pangu) as well as examples from the growing literature on scientific serious games

Interplay between transcription regulators RUNX1 and FUBP1 activates an enhancer of the oncogene c-KIT and amplifies cell proliferation.

Runt-related transcription factor 1 (RUNX1) is a well-known master regulator of hematopoietic lineages but its mechanisms of action are still not fully understood. Here, we found that RUNX1 localizes on active chromatin together with Far Upstream Binding Protein 1 (FUBP1) in human B-cell precursor lymphoblasts, and that both factors interact in the same transcriptional regulatory complex. RUNX1 and FUBP1 chromatin localization identified c-KIT as a common target gene. We characterized two regulatory regions, at +700 bp and +30 kb within the first intron of c-KIT, bound by both RUNX1 and FUBP1, and that present active histone marks. Based on these regions, we proposed a novel FUBP1 FUSE-like DNA-binding sequence on the +30 kb enhancer. We demonstrated that FUBP1 and RUNX1 cooperate for the regulation of the expression of the oncogene c-KIT. Notably, upregulation of c-KIT expression by FUBP1 and RUNX1 promotes cell proliferation and renders cells more resistant to the c-KIT inhibitor imatinib mesylate, a common therapeutic drug. These results reveal a new mechanism of action of RUNX1 that implicates FUBP1, as a facilitator, to trigger transcriptional regulation of c-KIT and to regulate cell proliferation. Deregulation of this regulatory mechanism may explain some oncogenic function of RUNX1 and FUBP1

A GPU-accelerated immersive audio-visual framework for interaction with molecular dynamics using consumer depth sensors

© the Partner Organisations 2014. With advances in computational power, the rapidly growing role of computational/simulation methodologies in the physical sciences, and the development of new human-computer interaction technologies, the field of interactive molecular dynamics seems destined to expand. In this paper, we describe and benchmark the software algorithms and hardware setup for carrying out interactive molecular dynamics utilizing an array of consumer depth sensors. The system works by interpreting the human form as an energy landscape, and superimposing this landscape on a molecular dynamics simulation to chaperone the motion of the simulated atoms, affecting both graphics and sonified simulation data. GPU acceleration has been key to achieving our target of 60 frames per second (FPS), giving an extremely fluid interactive experience. GPU acceleration has also allowed us to scale the system for use in immersive 360° spaces with an array of up to ten depth sensors, allowing several users to simultaneously chaperone the dynamics. The flexibility of our platform for carrying out molecular dynamics simulations has been considerably enhanced by wrappers that facilitate fast communication with a portable selection of GPU-accelerated molecular force evaluation routines. In this paper, we describe a 360°atmospheric molecular dynamics simulation we have run in a chemistry/physics education context. We also describe initial tests in which users have been able to chaperone the dynamics of 10-alanine peptide embedded in an explicit water solvent. Using this system, both expert and novice users have been able to accelerate peptide rare event dynamics by 3-4 orders of magnitude. This journal i

Combined immunodeficiency and Epstein-Barr virus-induced B cell malignancy in humans with inherited CD70 deficiency

In this study, we describe four patients from two unrelated families of different ethnicities with a primary immunodeficiency, predominantly manifesting as susceptibility to Epstein-Barr virus (EBV)–related diseases. Three patients presented with EBV-associated Hodgkin’s lymphoma and hypogammaglobulinemia; one also had severe varicella infection. The fourth had viral encephalitis during infancy. Homozygous frameshift or in-frame deletions in CD70 in these patients abolished either CD70 surface expression or binding to its cognate receptor CD27. Blood lymphocyte numbers were normal, but the proportions of memory B cells and EBV-specific effector memory CD8+ T cells were reduced. Furthermore, although T cell proliferation was normal, in vitro–generated EBV-specific cytotoxic T cell activity was reduced because of CD70 deficiency. This reflected impaired activation by, rather than effects during killing of, EBV-transformed B cells. Notably, expression of 2B4 and NKG2D, receptors implicated in controlling EBV infection, on memory CD8+ T cells from CD70-deficient individuals was reduced, consistent with their impaired killing of EBV-infected cells. Thus, autosomal recessive CD70 deficiency is a novel cause of combined immunodeficiency and EBV-associated diseases, reminiscent of inherited CD27 deficiency. Overall, human CD70–CD27 interactions therefore play a nonredundant role in T and B cell–mediated immunity, especially for protection against EBV and humoral immunity

Exposed Hydrophobic Residues in Human Immunodeficiency Virus Type 1 Vpr Helix-1 Are Important for Cell Cycle Arrest and Cell Death

The human immunodeficiency virus type 1 (HIV-1) accessory protein viral protein R (Vpr) is a major determinant for virus-induced G2/M cell cycle arrest and cytopathicity. Vpr is thought to perform these functions through the interaction with partner proteins. The NMR structure of Vpr revealed solvent exposed hydrophobic amino acids along helices 1 and 3 of Vpr, which could be putative protein binding domains. We previously showed that the hydrophobic patch along helix-3 was important for G2/M blockade and cytopathicity. Mutations of the exposed hydrophobic residues along helix-1 were found to reduce Vpr-induced cell cycle arrest and cell death as well. The levels of toxicity during virion delivery of Vpr correlated with G2/M arrest. Thus, the exposed hydrophobic amino acids in the amino-terminal helix-1 are important for the cell cycle arrest and cytopathicity functions of Vpr

Natalizumab treatment shows low cumulative probabilities of confirmed disability worsening to EDSS milestones in the long-term setting.

Abstract Background Though the Expanded Disability Status Scale (EDSS) is commonly used to assess disability level in relapsing-remitting multiple sclerosis (RRMS), the criteria defining disability progression are used for patients with a wide range of baseline levels of disability in relatively short-term trials. As a result, not all EDSS changes carry the same weight in terms of future disability, and treatment benefits such as decreased risk of reaching particular disability milestones may not be reliably captured. The objectives of this analysis are to assess the probability of confirmed disability worsening to specific EDSS milestones (i.e., EDSS scores ≥3.0, ≥4.0, or ≥6.0) at 288 weeks in the Tysabri Observational Program (TOP) and to examine the impact of relapses occurring during natalizumab therapy in TOP patients who had received natalizumab for ≥24 months. Methods TOP is an ongoing, open-label, observational, prospective study of patients with RRMS in clinical practice. Enrolled patients were naive to natalizumab at treatment initiation or had received ≤3 doses at the time of enrollment. Intravenous natalizumab (300 mg) infusions were given every 4 weeks, and the EDSS was assessed at baseline and every 24 weeks during treatment. Results Of the 4161 patients enrolled in TOP with follow-up of at least 24 months, 3253 patients with available baseline EDSS scores had continued natalizumab treatment and 908 had discontinued (5.4% due to a reported lack of efficacy and 16.4% for other reasons) at the 24-month time point. Those who discontinued due to lack of efficacy had higher baseline EDSS scores (median 4.5 vs. 3.5), higher on-treatment relapse rates (0.82 vs. 0.23), and higher cumulative probabilities of EDSS worsening (16% vs. 9%) at 24 months than those completing therapy. Among 24-month completers, after approximately 5.5 years of natalizumab treatment, the cumulative probabilities of confirmed EDSS worsening by 1.0 and 2.0 points were 18.5% and 7.9%, respectively (24-week confirmation), and 13.5% and 5.3%, respectively (48-week confirmation). The risks of 24- and 48-week confirmed EDSS worsening were significantly higher in patients with on-treatment relapses than in those without relapses. An analysis of time to specific EDSS milestones showed that the probabilities of 48-week confirmed transition from EDSS scores of 0.0–2.0 to ≥3.0, 2.0–3.0 to ≥4.0, and 4.0–5.0 to ≥6.0 at week 288 in TOP were 11.1%, 11.8%, and 9.5%, respectively, with lower probabilities observed among patients without on-treatment relapses (8.1%, 8.4%, and 5.7%, respectively). Conclusions In TOP patients with a median (range) baseline EDSS score of 3.5 (0.0–9.5) who completed 24 months of natalizumab treatment, the rate of 48-week confirmed disability worsening events was below 15%; after approximately 5.5 years of natalizumab treatment, 86.5% and 94.7% of patients did not have EDSS score increases of ≥1.0 or ≥2.0 points, respectively. The presence of relapses was associated with higher rates of overall disability worsening. These results were confirmed by assessing transition to EDSS milestones. Lower rates of overall 48-week confirmed EDSS worsening and of transitioning from EDSS score 4.0–5.0 to ≥6.0 in the absence of relapses suggest that relapses remain a significant driver of disability worsening and that on-treatment relapses in natalizumab-treated patients are of prognostic importance

Synthèse chimique, structure et propriétés magnétiques de nanoparticules d'alliage FePt

FePt nanoparticles are of significant importance because of their potential application in magnetic storage devices beyond Tbit/in2. This work deals with the study of the structural and magnetic properties of chemically synthesised FePt particles. We show that structural and magnetic properties of the as-grown particles indicate a core-shell structure for nanoparticles prepared with various methods : an iron-depleted core (Fe30Pt70) surrounded by a iron-rich shell. Combining structural, magnetic and chemical data, we suggest this structure originates from the difference in the kinetics of incorporation of Pt and Fe, which are mainly controlled by the two ligands (oleic amine and acide). We then investigated a novel combinations of ligands (replacing the amine by pentadecanenitrile), and indeed obtained nanoparticles with a more homogeneous composition. As-synthesised FePt nanoparticles are in the chemically disordered structure and thermal annealing at 650°C is required to obtain the L10 phase. We proved that iron atoms of the shell are available to form of the ordered phase in core-shell nanoparticles. However, thermal annealing of assemblies of nanoparticles results in large sintering. We then started to explore an alternative process relying on irradiation by light ions at moderate temperatures. First results are encouraging as irradiation at 300°C leads to both a more homogeneous composition and a higher magnetisation of the nanoparticles.Les nanoparticules d'alliage FePt, obtenues dans la phase chimiquement ordonnée L10, présentent un fort intérêt pour la réalisation de média magnétiques à très haute densité de stockage (>1 Tb/in2). Cette thèse concerne l'étude des propriétés structurales et magnétiques de telles nanoparticules synthétisées par voie chimique. L'étude détaillée, structurale et magnétique, de particules de FePt (3-4 nm) met en évidence une structure hétérogène en composition : un coeur riche en Pt (Fe30Pt70) et une surface riche en Fe. Cette structure, obtenue pour plusieurs protocoles de synthèse étudiés, est liée à l'influence des ligands (amine et acide oléiques) sur les vitesses d'incorporation du Fe et du Pt. À partir de cette observation, nous avons mis en oeuvre un nouveau ligand en remplacement de l'amine, le pentadécanenitrile. Nous avons ainsi obtenu des particules de composition plus homogène, et également aptes à l'auto-organisation sur des substrats. Les méthodes de synthèse chimique donnent des particules dans la phase chimiquement désordonnée et des recuits à haute température sont nécessaires pour obtenir la phase L10. Malgré, la présence d'une structure coeur-coquille, la phase L10 est obtenue après un recuit sous vide à 650°C, indiquant que le fer de surface est disponible. Ces recuits s'accompagnent systématiquement d'une forte coalescence des particules. Nous avons donc étudié une voie alternative pour obtenir la phase L10 à des températures modérées : l'irradiation par des ions He+. Les premiers résultats, encourageants, indiquent une homogénéisation de la composition après irradiation des particules à température modérée, ainsi qu'un accroissement de leur aimantation

Synthèse chimique, structure et propriétés magnétiques de nanoparticules d'alliage FePt

FePt nanoparticles are of significant importance because of their potential application in magnetic storage devices beyond Tbit/in2. This work deals with the study of the structural and magnetic properties of chemically synthesised FePt particles. We show that structural and magnetic properties of the as-grown particles indicate a core-shell structure for nanoparticles prepared with various methods : an iron-depleted core (Fe30Pt70) surrounded by a iron-rich shell. Combining structural, magnetic and chemical data, we suggest this structure originates from the difference in the kinetics of incorporation of Pt and Fe, which are mainly controlled by the two ligands (oleic amine and acide). We then investigated a novel combinations of ligands (replacing the amine by pentadecanenitrile), and indeed obtained nanoparticles with a more homogeneous composition. As-synthesised FePt nanoparticles are in the chemically disordered structure and thermal annealing at 650°C is required to obtain the L10 phase. We proved that iron atoms of the shell are available to form of the ordered phase in core-shell nanoparticles. However, thermal annealing of assemblies of nanoparticles results in large sintering. We then started to explore an alternative process relying on irradiation by light ions at moderate temperatures. First results are encouraging as irradiation at 300°C leads to both a more homogeneous composition and a higher magnetisation of the nanoparticles.Les nanoparticules d'alliage FePt, obtenues dans la phase chimiquement ordonnée L10, présentent un fort intérêt pour la réalisation de média magnétiques à très haute densité de stockage (>1 Tb/in2). Cette thèse concerne l'étude des propriétés structurales et magnétiques de telles nanoparticules synthétisées par voie chimique. L'étude détaillée, structurale et magnétique, de particules de FePt (3-4 nm) met en évidence une structure hétérogène en composition : un coeur riche en Pt (Fe30Pt70) et une surface riche en Fe. Cette structure, obtenue pour plusieurs protocoles de synthèse étudiés, est liée à l'influence des ligands (amine et acide oléiques) sur les vitesses d'incorporation du Fe et du Pt. À partir de cette observation, nous avons mis en oeuvre un nouveau ligand en remplacement de l'amine, le pentadécanenitrile. Nous avons ainsi obtenu des particules de composition plus homogène, et également aptes à l'auto-organisation sur des substrats. Les méthodes de synthèse chimique donnent des particules dans la phase chimiquement désordonnée et des recuits à haute température sont nécessaires pour obtenir la phase L10. Malgré, la présence d'une structure coeur-coquille, la phase L10 est obtenue après un recuit sous vide à 650°C, indiquant que le fer de surface est disponible. Ces recuits s'accompagnent systématiquement d'une forte coalescence des particules. Nous avons donc étudié une voie alternative pour obtenir la phase L10 à des températures modérées : l'irradiation par des ions He+. Les premiers résultats, encourageants, indiquent une homogénéisation de la composition après irradiation des particules à température modérée, ainsi qu'un accroissement de leur aimantation