Using Ontology Fingerprints to evaluate genome-wide association study results

We describe an approach to characterize genes or phenotypes via ontology fingerprints which are composed of Gene Ontology (GO) terms overrepresented among those PubMed abstracts linked to the genes or phenotypes. We then quantify the biological relevance between genes and phenotypes by comparing their ontology fingerprints to calculate a similarity score. We validated this approach by correctly identifying genes belong to their biological pathways with high accuracy, and applied this approach to evaluate GWA study by ranking genes associated with the lipid concentrations in plasma as well as to prioritize genes within linkage disequilibrium (LD) block. We found that the genes with highest scores were: ABCA1, LPL, and CETP for HDL; LDLR, APOE and APOB for LDL; and LPL, APOA1 and APOB for triglyceride. In addition, we identified some top ranked genes linking to lipid metabolism from the literature even in cases where such knowledge was not reflected in current annotation of these genes. These results demonstrate that ontology fingerprints can be used effectively to prioritize genes from GWA studies for experimental validation

Interaction Of Electrons With Spin Waves In The Bulk And In Multilayers

The exchange interaction between electrons and magnetic spins is considerably enhanced near interfaces, in magnetic multilayers. As a result, a dc current can be used to generate spin oscillations. We review theory and experimental evidence. The s-d exchange interaction causes a rapid precession of itinerant conduction-electron spins s around the localized spins S of magnetic electrons. Because of the precession, the time-averaged interaction torque between s and S vanishes. An interface between a magnetic layer and a spacer causes a local coherence between the precession phases of differnt electrons, within 10 nm from the interface, and restores the torque. Also, a second magnetic layer with pinned S is used to prepare s in a specific direction. the current-induced drive torque of s on S in the active layer may be calculated from the spin current (Slonczewski) or from the spin imbalance Delta-mu (Berger). Spin current and Delta-mu are proportional to each other, and can arise from Fermi-surface translation, as well as from expansion/contraction.Comment: Invited paper at Seattle MMM01 Conference, Nov. 2001 (to appear in J. Appl. Phys.

Investigation of Magnetic Interactions in Large Arrays of Magnetic Nanowires

The magnetic interactions in large arrays of ordered magnetic nanowires with 12-48 nm diameter and 55-95 nm spacing were investigated using modified Henkel plots. The measurements for nanowire arrays ac demagnetized with the field applied parallel to the nanowire axis (the easy magnetization axis) indicate that the dominant interaction during the switching process is the magnetostatic coupling between the nanowires. Nevertheless, while the strength of the magnetostatic interactions increases with the magnetic moment associated with the nanowires, the increase is not linear with respect to the volume of the nanowires. Moreover, the dependence of the remanence curves on the field history suggests that even for magnetic nanowire systems with high geometric anisotropy, the magnetic pole structure of the nanowires can be complex. This conclusion is also supported by the field dependence of the initial magnetization curves. (c) 2008 American Institute of Physics

An unexpected journey of a suction catheter in a preterm neonate

Foreign bodies are extremely rare in preterm neonates. The majority are iatrogenic. We describe a neonate of 27 weeks gestation who was found to have an 18 mm long suction catheter at the right main bronchi after resuscitation in another hospital. It was first detected by chest X-ray after endotracheal intubation. Repeat X-ray revealed the catheter moved to the stomach and migrated to the lower gastrointestinal tract in a few hours. The patient was treated conservatively and the catheter was passed out on day 14. Newborn resuscitation may result in iatrogenic foreign body in neonates. Serious complications such as respiratory compromise, perforations or abscess may occur. Early referral to a specialized tertiary center with pediatric surgical service is recommended. We hope our experience demonstrated the importance of preventing iatrogenic foreign body in clinical setting. Access to endoscopic instrumentation for foreign body removal in preterm neonates should be available at all times.published_or_final_versio

Investigation of Magnetic Interactions in Large Arrays of Magnetic Nanowires

The magnetic interactions in large arrays of ordered magnetic nanowires with 12-48 nm diameter and 55-95 nm spacing were investigated using modified Henkel plots. The measurements for nanowire arrays ac demagnetized with the field applied parallel to the nanowire axis (the easy magnetization axis) indicate that the dominant interaction during the switching process is the magnetostatic coupling between the nanowires. Nevertheless, while the strength of the magnetostatic interactions increases with the magnetic moment associated with the nanowires, the increase is not linear with respect to the volume of the nanowires. Moreover, the dependence of the remanence curves on the field history suggests that even for magnetic nanowire systems with high geometric anisotropy, the magnetic pole structure of the nanowires can be complex. This conclusion is also supported by the field dependence of the initial magnetization curves. (c) 2008 American Institute of Physics

Spin separation in cyclotron motion

Charged carriers with different spin states are spatially separated in a two-dimensional hole gas. Due to strong spin-orbit interaction holes at the Fermi energy have different momenta for two possible spin states travelling in the same direction and, correspondingly, different cyclotron orbits in a weak magnetic field. Two point contacts, acting as a monochromatic source of ballistic holes and a narrow detector in the magnetic focusing geometry are demonstrated to work as a tunable spin filter.Comment: 4 pages, 2 figure

Current induced switching of magnetic domains to a perpendicular configuration

In a ferromagnet--normal-metal--ferromagnet trilayer, a current flowing perpendicularly to the layers creates a torque on the magnetic moments of the ferromagnets. When one of the contacts is superconducting, the torque not only favors parallel or antiparallel alignment of the magnetic moments, as is the case for two normal contacts, but can also favor a configuration where the two moments are perpendicular. In addition, whereas the conductance for parallel and antiparallel magnetic moments is the same, signalling the absence of giant magnetoresistance in the usual sense, the conductance is greater in the perpendicular configuration. Thus, a negative magnetoconductance is predicted, in contrast with the usual giant magnetoresistance.Comment: 4 pages, 3 figures, major rewriting of the technical par

Current-Driven Magnetization Dynamics in Magnetic Multilayers

We develop a quantum analog of the classical spin-torque model for current-driven magnetic dynamics. The current-driven magnetic excitation at finite field becomes significantly incoherent. This excitation is described by an effective magnetic temperature rather than a coherent precession as in the spin-torque model. However, both the spin-torque and effective temperature approximations give qualitatively similar switching diagrams in the current-field coordinates, showing the need for detailed experiments to establish the proper physical model for current-driven dynamics.Comment: 5 pages, 2 figure

Engaging Science Students with Handheld Technology and Applications by Revisiting the Thayer Method of Teaching and Learning

Organic chemistry instructors integrate handheld technology and applications into course lecture and lab to engage students with tools and techniques students use in the modern world. This technology and applications enable instructors to re-visit the Thayer Method of teaching and learning to create an updated method that works with 21st century students. The Thayer Method is based on the premise that students are willing and capable of making substantial preparation before coming to class and lab in order to maximize efficiency of student-instructor contact time. During this student preparation phase, we engage students with handheld technology and content applications including smart phone viewable course administrative materials; “flashcards” containing basic organic chemistry nomenclature, molecular structures, and chemical reactions; mini-lectures prepared using the Smart Board Airliner Interactive Tablet for upcoming class periods and laboratory technique videos demonstrating tasks they will perform as part of laboratory experimentation. Coupled with a student friendly course text, these handheld applications enable substantial student preparation before class and lab. The method, in conjunction with handheld technology and applications, has been used with positive results in our organic chemistry courses

Theory of Current-Induced Magnetization Precession

We solve appropriate drift-diffusion and Landau-Lifshitz-Gilbert equations to demonstrate that unpolarized current flow from a non-magnet into a ferromagnet can produce a precession-type instability of the magnetization. The fundamental origin of the instability is the difference in conductivity between majority spins and minority spins in the ferromagnet. This leads to spin accumulation and spin currents that carry angular momentum across the interface. The component of this angular momentum perpendicular to the magnetization drives precessional motion that is opposed by Gilbert damping. Neglecting magnetic anisotropy and magnetostatics, our approximate analytic and exact numerical solutions using realistic values for the material parameters show (for both semi-infinite and thin film geometries) that a linear instability occurs when both the current density and the excitation wave vector parallel to the interface are neither too small nor too large. For many aspects of the problem, the variation of the magnetization in the direction of the current flows makes an important contribution.Comment: Submitted to Physical Review