Detecting simultaneous variant intervals in aligned sequences

Given a set of aligned sequences of independent noisy observations, we are concerned with detecting intervals where the mean values of the observations change simultaneously in a subset of the sequences. The intervals of changed means are typically short relative to the length of the sequences, the subset where the change occurs, the "carriers," can be relatively small, and the sizes of the changes can vary from one sequence to another. This problem is motivated by the scientific problem of detecting inherited copy number variants in aligned DNA samples. We suggest a statistic based on the assumption that for any given interval of changed means there is a given fraction of samples that carry the change. We derive an analytic approximation for the false positive error probability of a scan, which is shown by simulations to be reasonably accurate. We show that the new method usually improves on methods that analyze a single sample at a time and on our earlier multi-sample method, which is most efficient when the carriers form a large fraction of the set of sequences. The proposed procedure is also shown to be robust with respect to the assumed fraction of carriers of the changes.Comment: Published in at http://dx.doi.org/10.1214/10-AOAS400 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Report of the ultraviolet and visible sensors panel

In order to meet the science objectives of the Astrotech 21 mission set the Ultraviolet (UV) and Visible Sensors Panel made a number of recommendations. In the UV wavelength range of 0.01 to 0.3 micro-m the focus is on the need for large format high quantum efficiency, radiation hard 'solar-blind' detectors. Options recommended for support include Si and non-Si charge coupled devices (CCDs) as well as photocathodes with improved microchannel plate readouts. For the 0.3 to 0.9 micro-m range, it was felt that Si CCDs offer the best option for high quantum efficiencies at these wavelengths. In the 0.9 to 2.5 micro-m the panel recommended support for the investigation of monolithic arrays. Finally, the panel noted that the implementation of very large arrays will require new data transmission, data recording, and data handling technologies

Fiber-diffraction Interferometer using Coherent Fiber Optic Taper

We present a fiber-diffraction interferometer using a coherent fiber optic taper for optical testing in an uncontrolled environment. We use a coherent fiber optic taper and a single-mode fiber having thermally-expanded core. Part of the measurement wave coming from a test target is condensed through a fiber optic taper and spatially filtered from a single-mode fiber to be reference wave. Vibration of the cavity between the target and the interferometer probe is common to both reference and measurement waves, thus the interference fringe is stabilized in an optical way. Generation of the reference wave is stable even with the target movement. Focus shift of the input measurement wave is desensitized by a coherent fiber optic taper

Can Deterministic Mechanical Size Effects Contribute to Fracture and Microdamage Accumulation in Trabecular Bone?

Failure of bone under monotonic and cyclic loading is related to the bone mineral density, the quality of the bone matrix, and the evolution of microcracks. The theory of linear elastic fracture mechanics has commonly been applied to describe fracture in bone. Evidence is presented that bone failure can be described through a non-linear theory of fracture. Thereby, deterministic size effects are introduced. Concepts of a non-linear theory are applied to discern how the interaction among bone matrix constituents (collagen and mineral), microcrack characteristics, and trabecular architecture can create distinctively differences in the fracture resistance at the bone tissue level. The non-linear model is applied to interpret pre-clinical data concerning the effects of anti-osteoporotic agents on bone properties. The results show that bisphosphonate (BP) treatments that suppress bone remodeling will change trabecular bone in ways such that the size of the failure process zone relative to the trabecular thickness is reduced. Selective estrogen receptor modulators (SERMs) that suppress bone remodeling will change trabecular bone in ways such that the size of the failure process zone relative to the trabecular thickness is increased. The consequences of these changes are reflected in bone mechanical response and predictions are consistent with experimental observations in the animal model which show that BP treatment is associated with more brittle fracture and microcracks without altering the average length of the cracks, whereas SERM treatments lead to a more ductile fracture and mainly increase crack length with a smaller increase in microcrack density. The model suggests that BPs may be more effective in cases in which bone mass is very low, whereas SERMS may be more effective when milder osteoporotic symptoms are present

The ARGUS Vertex Trigger

A fast second level trigger has been developed for the ARGUS experiment which recognizes tracks originating from the interaction region. The processor compares the hits in the ARGUS Micro Vertex Drift Chamber to 245760 masks stored in random access memories. The masks which are fully defined in three dimensions are able to reject tracks originating in the wall of the narrow beampipe of 10.5\,mm radius.Comment: gzipped Postscript, 27 page

Adaptive Mechanical Properties of Topologically Interlocking Material Systems

Topologically interlocked material systems are two-dimensional granular crystals created as ordered and adhesion-less assemblies of unit elements of the shape of platonic solids. The assembly resists transverse forces due to the interlocking geometric arrangement of the unit elements. Topologically interlocked material systems yet require an external constraint to provide resistance under the action of external load. Past work considered fixed and passive constraints only. The objective of the present study is to consider active and adaptive external constraints with the goal to achieve variable stiffness and energy absorption characteristics of the topologically interlocked material system through an active control of the in-plane constraint conditions. Experiments and corresponding model analysis are used to demonstrate control of system stiffness over a wide range, including negative stiffness, and energy absorption characteristics. The adaptive characteristics of the topologically interlocked material system are shown to solve conflicting requirements of simultaneously providing energy absorption while keeping loads controlled. Potential applications can be envisioned in smart structure enhanced response characteristics as desired in shock absorption, protective packaging and catching mechanisms

Incorporating tissue anisotropy and heterogeneity in finite element models of trabecular bone altered predicted local stress distributions

Trabecular bone is composed of organized mineralized collagen fibrils, which results in heterogeneous and anisotropic mechanical properties at the tissue level. Recently, biomechanical models computing stresses and strains in trabecular bone have indicated a significant effect of tissue heterogeneity on predicted stresses and strains. However, the effect of the tissue-level mechanical anisotropy on the trabecular bone biomechanical response is unknown. Here, a computational method was established to automatically impose physiologically relevant orientation inherent in trabecular bone tissue on a trabecular bone microscale finite element model. Spatially varying tissue-level anisotropic elastic properties were then applied according to the bone mineral density and the local tissue orientation. The model was used to test the hypothesis that anisotropy in both homogeneous and heterogeneous models alters the predicted distribution of stress invariants. Linear elastic finite element computations were performed on a 3 mm cube model isolated from a microcomputed tomography scan of human trabecular bone from the distal femur. Hydrostatic stress and von Mises equivalent stress were recorded at every element, and the distributions of these values were analyzed. Anisotropy reduced the range of hydrostatic stress in both tension and compression more strongly than the associated increase in von Mises equivalent stress. The effect of anisotropy was independent of the spatial redistribution high compressive stresses due to tissue elastic heterogeneity. Tissue anisotropy and heterogeneity are likely important mechanisms to protect bone from failure and should be included for stress analyses in trabecular bone

Scanning a Poisson Random Field for Local Signals

The detection of local genomic signals using high-throughput DNA sequencing data can be cast as a problem of scanning a Poisson random field for local changes in the rate of the process. We propose a likelihood-based framework for such scans, and derive formulas for false positive rate control and power calculations. The framework can also accommodate modified processes that involve overdispersion. As a specific, detailed example, we consider the detection of insertions and deletions by paired-end DNA-sequencing. We propose several statistics for this problem, compare their power under current experimental designs, and illustrate their application on an Illumina Platinum Genomes data set

Balance task and head orientation dependency of vestibular reflexes in neck muscles

Human upright posture of both the head and body is facilitated by the CNS’s ability to integrate multiple sensory feedback signals, as well as its discernibility of the motor commands that maintain this stabilization. The vestibular organ in particular detects motion of the head-in-space, which is transformed according to on-going head and body orientation into appropriate motor responses. However, when motor commands do not contribute to the control of standing posture, and are incongruent with their expected sensory consequences, vestibulomuscular responses in the lower limb undergo unconscious suppression. In this study, we investigated whether vestibular response suppression occurs in neck muscles under conditions where the muscles are active but not engaged in a task to balance the head. In addition, we examined the effects of head orientation to identify spatial transformation of vestibular reflex responses. Eight subjects were exposed to stochastic vestibular stimulation (0-75 Hz) in a seated condition while their head was either free or fixed, and rotated at either 0 or 60°. In head-free conditions, subjects were asked to rotate their head 60° to the left in order to activate agonist neck muscle pairs (sternocleidomastoid - SCM and splenius capitis - SPL). In head-fixed conditions, subjects performed isometric neck muscle contractions in yaw at orientations of 0° and 60°, as well as flexion, extension and co-contraction at an orientation of 0°. Intramuscular EMG was collected bilaterally in SCM and SPL muscles. Muscle responses correlated to the input stimuli were significant (P < 0.05) for all conditions provided the muscle was used in contraction. Neither muscle underwent the expected vestibulomuscular suppression when not engaged in the balance task (i.e. head-fixed). Nevertheless, the magnitude of the SPL responses decreased by 22% when the head was fixed whereas SCM responses were unaffected. The effect of head fixation only in SPL suggests differences in neural pathways across muscles, possibly via alternative pathways known to exist in the SPL from the well-established monosynaptic vestibulospinal inputs in SCM and SPL. For both muscles, the effect of orientation and force direction had no effect on muscles responses. Since the stimulation is fixed relative to the head, the same muscles are activated to respond to the input stimulus at both orientations and all force directions. These results indicate that the vestibular pathways connecting neck muscles are less susceptible to suppression than lower limb muscles, most likely because the monosynaptic inputs innervating them are subject to less central control