Fast DNA sequence alignment using optical computing

Alignment of DNA sequences is a necessary step prior to comparison of sequence data. High-speed alignment is needed due to the large size of DNA databases. Correlation, a standard pattern recognition technique, can be used to perform alignment. Correlation can be performed rapidly using optical techniques. Thus, optical correlation offers the potential for high-speed processing of DNA sequence data. This report describes research efforts to apply one-dimensional acousto-optical correlation methods to the problem of DNA sequence alignment. Experimental results are presented

Low-power multi-chip module and board-level links for data transfer

Advanced device technologies such as Vertical Cavity Surface-Emitting Lasers (VCSELs) and diffractive micro lenses can be obtained with novel packaging techniques to allow low-power interconnection of parallel optical signals. These interconnections can be realized directly on circuit boards, in a multi-chip module format, or in packages that emulate electrical connectors. For applications such as stacking of Multi-Chip Module (MCM) layers, the links may be realized in bi-directional form using integrated diffractive microlenses. In the stacked MCM design, consumed electrical power is minimized by use of a relatively high laser output from high efficiency VCSELs, and a receiver design that is optimized for low power, at the expense of dynamic range. Within certain constraints, the design may be extended to other forms such as board-level interconnects

New insights into the genetic etiology of Alzheimer's disease and related dementias

Characterization of the genetic landscape of Alzheimer's disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage genome-wide association study totaling 111,326 clinically diagnosed/'proxy' AD cases and 677,663 controls. We found 75 risk loci, of which 42 were new at the time of analysis. Pathway enrichment analyses confirmed the involvement of amyloid/tau pathways and highlighted microglia implication. Gene prioritization in the new loci identified 31 genes that were suggestive of new genetically associated processes, including the tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. We also built a new genetic risk score associated with the risk of future AD/dementia or progression from mild cognitive impairment to AD/dementia. The improvement in prediction led to a 1.6- to 1.9-fold increase in AD risk from the lowest to the highest decile, in addition to effects of age and the APOE ε4 allele

The Energetic Particle Detector (EPD) Investigation and the Energetic Ion Spectrometer (EIS) for the Magnetospheric Multiscale (MMS) Mission

Abstract The Energetic Particle Detector (EPD) Investigation is one of 5 fields-and-particles investigations on the Magnetospheric Multiscale (MMS) mission. MMS comprises 4 spacecraft flying in close formation in highly elliptical, near-Earth-equatorial orbits targeting understanding of the fundamental physics of the important physical process called magnetic reconnection using Earth’s magnetosphere as a plasma laboratory. EPD comprises two sensor types, the Energetic Ion Spectrometer (EIS) with one instrument on each of the 4 spacecraft, and the Fly’s Eye Energetic Particle Spectrometer (FEEPS) with 2 instruments on each of the 4 spacecraft. EIS measures energetic ion energy, angle and elemental compositional distributions from a required low energy limit of 20 keV for protons and 45 keV for oxygen ions, up to \u3e0.5 MeV (with capabilities to measure up to \u3e1 MeV). FEEPS measures instantaneous all sky images of energetic electrons from 25 keV to \u3e0.5 MeV, and also measures total ion energy distributions from 45 keV to \u3e0.5 MeV to be used in conjunction with EIS to measure all sky ion distributions. In this report we describe the EPD investigation and the details of the EIS sensor. Specifically we describe EPD-level science objectives, the science and measurement requirements, and the challenges that the EPD team had in meeting these requirements. Here we also describe the design and operation of the EIS instruments, their calibrated performances, and the EIS in-flight and ground operations. Blake et al. (The Flys Eye Energetic Particle Spectrometer (FEEPS) contribution to the Energetic Particle Detector (EPD) investigation of the Magnetospheric Magnetoscale (MMS) Mission, this issue) describe the design and operation of the FEEPS instruments, their calibrated performances, and the FEEPS in-flight and ground operations. The MMS spacecraft will launch in early 2015, and over its 2-year mission will provide comprehensive measurements of magnetic reconnection at Earth’s magnetopause during the 18 months that comprise orbital phase 1, and magnetic reconnection within Earth’s magnetotail during the about 6 months that comprise orbital phase 2

Ultra-low-power, long-wavelength photoreceivers for massively-parllel optical data links

An ultra-low-power, long-wavelength photoreceiver based on InGaAs/InP heterojunction bipolar transistors is reported. The photoreceivers were designed for massively parallel applications where low-power density is necessary for both electrical and thermal reasons. We demonstrate two-dimensional, four-by-four arrays of photoreceivers for free-space optical data links that interface directly with 3.3 V CMOS ASICs and dissipate less than 12 mW/channel; lower power is possible. Propagation delays of {approx}1 nsec were measured and large signal operation of 800 Mbits/sec is demonstrated. The array is on a 500 {mu}m pitch and can be easily scaled to much higher density. The photoreceivers can be utilized in both free-space and guided-wave applications

Low-power modular parallel photonic data links

Many of the potential applications for parallel photonic data links could benefit from a bi-directional Optoelectronic Multi-Chip Module (OEMCM), where the optical transmitter, receiver, and first-level interface electronics are combined into a single package. It would be desirable for such a module to exhibit low power consumption, have a simple electronic interface that can operate at a variety of speeds, and possess a capability to use interchangeable optics for a variety of external connections. Here, we describe initial results for a parallel photonic link technology that exhibits those properties. This link uses high-efficiency, back-emitting, two-dimensional Vertical Cavity Surface-Emitting Laser (VCSEL) arrays operating at 980 nm. The lasers are matched, via integrated microlenses, to corresponding monolithically-integrated photoreceiver arrays that are constructed in a InGaAs/InP Heterojunction Bipolar Transistor (HBT) technology. In initial breadboard-level tests, the photonic data channels built with these devices have been demonstrated with direct (3.3 V) CMOS drive of the VCSELs and a corresponding CMOS interface at the photoreceiver outputs. These links have shown electrical power consumption as low as 42 mW per channel for a 50% average duty cycle while operating at 100 Mb/s

Species-specific spatiotemporal patterns of leopard, lion and tiger attacks on humans

1. Large carnivores of the genus Panthera can pose serious threats to public safety. Although the annual number of attacks on humans is rare compared to livestock depredation, such incidents undermine popular support for wildlife conservation and require immediate responses to protect human life. 2. We used a space–time scan method to perform a novel spatiotemporal analysis of 908 attacks on humans by lions, leopards, and tigers to estimate the risks of further attacks in the same locales. 3. We found that a substantial proportion of attacks were clustered in time and space, but the dimension of these outbreaks varied between species. Lion outbreaks included more human fatalities, persisted for longer periods of time, and extended over larger areas than tiger or leopard outbreaks. 4. Synthesis and applications. Our analysis reveals the typical spatiotemporal patterns of past lion, leopard, and tiger attacks on humans. In future, this technique could be used by relevant agencies to warn local people of risks from further attacks within a certain time and distance following an initial incident by each species. Furthermore, the approach can help identify areas requiring management interventions to address such threats. anthropogenic landscape, attacks on humans, big cats, human–wildlife conflict, Panthera,space–time scan, spatiotemporal clusteringSpecies-specific spatiotemporal patterns of leopard, lion and tiger attacks on humansacceptedVersio

Meta-Analysis of Efficacy of Interventions for Elevated Depressive Symptoms in Adults Diagnosed With Cancer

BACKGROUND: Cancer patients are at increased risk for depression compared with individuals with no cancer diagnosis, yet few interventions target depressed cancer patients. METHODS: Efficacy of psychotherapeutic and pharmacologic interventions for depression in cancer patients who met an entry threshold for depressive symptoms was examined by meta-analysis. Five electronic databases were systematically reviewed to identify randomized controlled trials meeting the selection criteria. Effect sizes were calculated using Hedges’ g and were pooled to compare pre- and postrandomization depressive symptoms with a random effects model. Subgroup analyses tested moderators of effect sizes, such as comparison of different intervention modalities, with a mixed effects model. All statistical tests were two-sided. RESULTS: Ten randomized controlled trials (six psychotherapeutic and four pharmacologic studies) met the selection criteria; 1362 participants with mixed cancer types and stages had been randomly assigned to treatment groups. One outlier trial was removed from analyses. The random effects model showed interventions to be superior to control conditions on reducing depressive symptoms postintervention (Hedges’ g = 0.43, 95% confidence interval = 0.30 to 0.56, P < .001). In the four psychotherapeutic trials with follow-up assessment, interventions were more effective than control conditions up to 12–18 months after patients were randomly assigned to treatment groups (P < .001). Although each approach was more effective than the control conditions in improving depressive symptoms (P < .001), subgroup analyses showed that cognitive behavioral therapy appeared more effective than problem-solving therapy (P = .01), but not more effective than pharmacologic intervention (P = .07). CONCLUSIONS: Our findings suggest that psychological and pharmacologic approaches can be targeted productively toward cancer patients with elevated depressive symptoms. Research is needed to maximize effectiveness, accessibility, and integration into clinical care of interventions for depressed cancer patients