Piecewise Affine Registration of Biological Images for Volume Reconstruction

This manuscript tackles the reconstruction of 3D volumes via mono-modal registration of series of 2D biological images (histological sections, autoradiographs, cryosections, etc.). The process of acquiring these images typically induces composite transformations that we model as a number of rigid or affine local transformations embedded in an elastic one. We propose a registration approach closely derived from this model. Given a pair of input images, we first compute a dense similarity field between them with a block matching algorithm. We use as a similarity measure an extension of the classical correlation coefficient that improves the consistency of the field. A hierarchical clustering algorithm then automatically partitions the field into a number of classes from which we extract independent pairs of sub-images. Our clustering algorithm relies on the Earth mover’s distribution metric and is additionally guided by robust least-square estimation of the transformations associated with each cluster. Finally, the pairs of sub-images are, independently, affinely registered and a hybrid affine/non-linear interpolation scheme is used to compose the output registered image. We investigate the behavior of our approach on several batches of histological data and discuss its sensitivity to parameters and noise

LDA+DMFT Approach to Magnetocrystalline Anisotropy of Strong Magnets

The new challenges posed by the need of finding strong rare-earth free magnets demand methods that can predict magnetization and magnetocrystalline anisotropy energy (MAE). We argue that correlated electron effects, which are normally underestimated in band structure calculations, play a crucial role in the development of the orbital component of the magnetic moments. Because magnetic anisotropy arises from this orbital component, the ability to include correlation effects has profound consequences on our predictive power of the MAE of strong magnets. Here we show that incorporating the local effects of electronic correlations with dynamical mean-field theory provides reliable estimates of the orbital moment, the mass enhancement and the MAE of YCo5.Comment: 7 pages, 4 figures, published versio

Ground-Based Reduced-Gravity Facilities

For the past 30 years, NASA Lewis Research Center's ground-based reduced-gravity facilities have supported numerous investigations for several research disciplines. Lewis' two drop towers and its DC-9 aircraft have provided a low-gravity environment (gravitational levels that range from 1 percent of Earth's gravitational acceleration to onemillionth of that measured at the Earth's surface) for brief periods of time. "Zero gravity," the weightless condition also known as microgravity, can be produced in these facilities by creating a free-fall or semi-free-fall condition where the force of gravity on an experiment is offset by its linear acceleration during a "fall" (a drop in a tower or a parabolic maneuver by an aircraft). The low-gravity environment obtained "on the ground" in NASA facilities is the same as that of a spacecraft in orbit around the Earth

Reorganization of sea urchin gene regulatory networks at least 268 million years ago as revealed by oldest fossil cidaroid echinoid

Echinoids, or sea urchins, are rare in the Palaeozoic fossil record, and thus the details regarding the early diversification of crown group echinoids are unclear. Here we report on the earliest probable crown group echinoid from the fossil record, recovered from Permian (Roadian-Capitanian) rocks of west Texas, which has important implications for the timing of the divergence of crown group echinoids. The presence of apophyses and rigidly sutured interambulacral areas with two columns of plates indicates this species is a cidaroid echinoid. The species, Eotiaris guadalupensis, n. sp. is therefore the earliest stem group cidaroid. The occurrence of this species in Roadian strata pushes back the divergence of cidaroids and euechinoids, the clades that comprise all living echinoids, to at least 268.8 Ma, ten million years older than the previously oldest known cidaroid. Furthermore, the genomic regulation of development in echinoids is amongst the best known, and this new species informs the timing of large-scale reorganization in echinoid gene regulatory networks that occurred at the cidaroid-euechinoid divergence, indicating that these changes took place by the Roadian stage of the Permian

Chandra Monitoring of the Candidate Anomalous X-ray Pulsar AX J1845.0-0258

The population of clearly identified anomalous X-ray pulsars has recently grown to seven, however, one candidate anomalous X-ray pulsar (AXP) still eludes re-confirmation. Here, we present a set of seven Chandra ACIS-S observations of the transient pulsar AX J1845.0-0258, obtained during 2003. Our observations reveal a faint X-ray point source within the ASCA error circle of AX J1845.0-0258's discovery, which we designate CXOU J184454.6-025653 and tentatively identify as the quiescent AXP. Its spectrum is well described by an absorbed single-component blackbody (kT~2.0 keV) or power law (Gamma~1.0) that is steady in flux on timescales of at least months, but fainter than AX J1845.0-0258 was during its 1993 period of X-ray enhancement by at least a factor of 13. Compared to the outburst spectrum of AX J1845.0-0258, CXOU J184454.6-025653 is considerably harder: if truly the counterpart, then its spectral behaviour is contrary to that seen in the established transient AXP XTE J1810-197, which softened from kT~0.67 keV to ~0.18 keV in quiescence. This unexpected result prompts us to examine the possibility that we have observed an unrelated source, and we discuss the implications for AXPs, and magnetars in general.Comment: 4 pages, 3 figures. To be published in the proceedings of the conference "Isolated Neutron Stars: from the Interior to the Surface" (April 24-28, 2006, London, UK), eds. D. Page, R. Turolla, & S. Zan

Assessing a Longitudinal Reflection Curriculum: A Case Study Of Student Self-Awareness Expressed Through Rotation Goal Achievement

The Center for the Advancement of Pharmacy Education 2013 Affective Domain mandates students develop self-awareness of personal attributes affecting professional growth. Students should self-identify needs, create and implement goals, and evaluate success. This case study describes the qualitative and quantitative findings of an intentional reflection assignment prompting students to engage in a cycle of goal writing – monitoring – reflection – new goal writing, during an immersive clinical practice experience. A blinded review of 144 student assignments is presented in the context of a curricular review of the Reflective Practitioner Program (RPP), a longitudinal reflective thread spanning four years of professional pharmacy training. Evidence gathered in the assignment review indicates that students are sufficiently capable of establishing meaningful goals and describing why the goal is important to their professional development. In contrast, students struggle with articulating strategies for goal achievement and emotions experienced during goal monitoring. In consideration of these findings, RPP faculty identified three major themes when discussing key aspects of the RPP curricular design: 1) students need to articulate strategies for goal achievement in addition to stated aims, 2) students hesitate to identify emotions when reflecting, and 3) reflection needs to be both retrospective and prospective in nature.  This case study has resulted in meaningful changes to RPP curricular design and illustrates how programs may approach assessment of the Affective Domain via common curricular elements. Conflict of Interst: None   Type: Case Stud

Influence of vegetation structure on the small mammal community in a shortgrass prairie ecosystem

Abstract The structure of vegetation, and how this structure varies across a landscape, is crucial to understanding the distribution of wildlife species. Between 2002 and 2004, we sampled small mammal communities and measured vegetation structure at 185 locations across a range of disturbance regimes in a shortgrass prairie ecosystem in southeastern Colorado, USA. At each sampling location, the local disturbance regime was some combination of varying intensity of livestock grazing, military training activity, and fire. Vegetation structural characteristics measured included percent bare ground, basal cover, litter, shrub density, and mean grass and shrub height. Rodent communities were described by richness, diversity, total and per capita biomass, and species abundances. Northern grasshopper mice (Onychomys leucogaster), Ord's kangaroo rats (Dipodomys ordii), silky pocket mice (Perognathus flavus), western harvest mice (Reithrodontomys megalotis), white-footed mice (Peromyscus leucopus), southern plains wood rats (Neotoma micropus), thirteen-lined ground squirrels (Spermophilus tridecemlineatus), deer mice (Peromyscus maniculatus), and spotted ground squirrels (Spermophilus spilosoma) accounted for >99 % of all captures. Canonical correlation analysis was used to assess the relationship between small mammals and vegetation structure. The first two canonical variates explained over 50 % of the variation in vegetation structure and were related to the ratio of bare ground to basal coverage and litter accumulation. Rodent community indices were most strongly related to litter accumulation and shrub density, though the models had low explanatory power. Our results agreed with published findings regarding microhabitat associations and indicated small mammal communities benefited from a system of interacting disturbances and the resulting landscape mosaic

Live-cell Microscopy and Fluorescence-based Measurement of Luminal pH in Intracellular Organelles

Luminal pH is an important functional feature of intracellular organelles. Acidification of the lumen of organelles such as endosomes, lysosomes, and the Golgi apparatus plays a critical role in fundamental cellular processes. As such, measurement of the luminal pH of these organelles has relevance to both basic research and translational research. At the same time, accurate measurement of intraorganellar pH in living cells can be challenging and may be a limiting hurdle for research in some areas. Here, we describe three powerful methods to measure rigorously the luminal pH of different intracellular organelles, focusing on endosomes, lysosomes, and the Golgi apparatus. The described methods are based on live imaging of pH-sensitive fluorescent probes and include: (1) A protocol based on quantitative, ratiometric measurement of endocytosis of pH-sensitive and pH-insensitive fluorescent conjugates of transferrin; (2) A protocol for the use of proteins tagged with a ratiometric variant of the pH-sensitive intrinsically fluorescent protein pHluorin; and (3) A protocol using the fluorescent dye LysoSensor™. We describe necessary reagents, key procedures, and methods and equipment for data acquisition and analysis. Examples of implementation of the protocols are provided for cultured cells derived from a cancer cell line and for primary cultures of mouse hippocampal neurons. In addition, we present strengths and weaknesses of the different described intraorganellar pH measurement methods. These protocols are likely to be of benefit to many researchers, from basic scientists to those conducting translational research with a focus on diseases in patient-derived cells

The Vulnerabilities of Orphaned Children Participating in Research: A Critical Review and Factors for Consideration for Participation in Biomedical and Behavioral Research

Orphans are a subpopulation with a unique set of additional vulnerabilities. Increasing focus on children’s rights, pediatric global health, and pediatric research makes it imperative to recognize and address unique vulnerabilities of orphaned children. This paper describes the unique vulnerabilities of the orphaned pediatric population and offers a structured set of factors that require consideration when including orphans in biomedical research. Pediatric orphans are particularly vulnerable due to decreased economic resources, psychosocial instability, increased risk of abuse, and delayed/decreased access to healthcare. These vulnerabilities are significant. By carefully considering each issue in a population in a culturally specific and study-specific manner, researchers can make valuable contributions to the overall health and well-being of this uniquely vulnerable population