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In the context of microbiology, recent studies show the importance of ribonucleo-protein aggregates (RNPs) for the understanding of mechanisms involved in cell responses to specific environmental conditions. The assembly and disassembly of aggregates is a dynamic process, the characterization of the stage of their evolution can be performed by the evaluation of their number. The aim of this study is to propose a method to automatically determine the count of RNPs. We show that the determination of a precise count is an issue by itself and hence, we propose three textural approaches: a classical point of view using Haralick features, a frequency point of view with generalized Fourier descriptors, and a structural point of view with Zernike moment descriptors (ZMD). These parameters are then used as inputs for a supervised classification in order to determine the most relevant. An experiment using a specific Saccharomyces cerevisiae strain presenting a fusion between a protein found in RNPs (PAB1) and the green fluorescent protein was performed to benchmark this approach. The fluorescence was observed with two-photon fluorescence microscopy. Results show that the textural approach, by mixing ZMD with Haralick features, allows for the characterization of the number of RNPs.
Kristina Daugirdas's important new article prompts two kinds of responses. By providing a sophisticated analysis of the role of reputation in influencing the behavior of international actors, it invites further thoughts about what we might think reputation is and does. By taking a moral position—the UN should do more to reduce sexual abuse by UN-sponsored peacekeepers in conflict zones—she provokes us to consider how to optimize institutional design in light of particular goals. In this essay, I don't quarrel with anything she says. Rather, I will respond to her prompting. I will discuss methodological issues first, then normative ones.
Cognitive models of obsessive–compulsive disorder (OCD) posit dysfunctional appraisal of disorder-relevant stimuli in patients, suggesting disturbances in the processes relying on amygdala–prefrontal connectivity. Recent neuroanatomical models add to the traditional view of dysfunction in corticostriatal circuits by proposing alterations in an affective circuit including amygdala–prefrontal connections. However, abnormalities in amygdala–prefrontal coupling during symptom provocation, and particularly during conditions that require stimulus appraisal, remain to be demonstrated directly.
Amygdala–prefrontal connectivity was examined in unmedicated OCD patients during appraisal (v. distraction) of symptom-provoking stimuli compared with an emotional control condition. Subsequent analyses tested whether hypothesized connectivity alterations could be also identified during passive viewing and the resting state in two independent samples.
During symptom provocation, reductions in positive coupling between amygdala and orbitofrontal cortex were observed in OCD patients relative to healthy control participants during appraisal and passive viewing of OCD-relevant stimuli, whereas abnormally high amygdala–ventromedial prefrontal cortex coupling was found when appraisal was distracted by a secondary task. In contrast, there were no group differences in amygdala connectivity at rest.
Our finding of abnormal amygdala–prefrontal connectivity during appraisal of symptom-related (relative to generally aversive) stimuli is consistent with the involvement of affective circuits in the functional neuroanatomy of OCD. Aberrant connectivity can be assumed to impact stimulus appraisal and emotion regulation, but might also relate to fear extinction deficits, which have recently been described in OCD. Taken together, we propose to integrate abnormalities in amygdala–prefrontal coupling in affective models of OCD.
A multidecadal-scale lake-level reconstruction for Lago Wiñaymarca, the southern basin of Lake Titicaca, has been generated from diatom species abundance data. These data suggest that ~6500 cal yr BP Lago Wiñaymarca was dry, as indicated by a sediment unconformity. At ~4400 cal yr BP, the basin began to fill, as indicated by the dominance of shallow epiphytic species. It remained somewhat saline with extensive wetlands and abundant aquatic plants until ~3800 cal yr BP, when epiphytic species were replaced by planktic saline-indifferent species, suggesting a saline shallow lake. Wiñaymarca remained a relatively shallow lake that fluctuated on a multidecadal scale until ~1250 cal yr BP, when freshwater planktic species increased, suggesting a rise in lake level with a concomitant decrease in salinity. The lake became gradually fresher, dominated by deep, freshwater species from ~850 cal yr BP. By ~80 cal yr BP, saline-tolerant species were rare, and the lake was dominated by freshwater planktic diatoms, resembling the fresh and deep lake of today. These results reveal a more dynamic and chronologically specific record of lake-level fluctuations and associated ecological conditions that provide important new data for paleoclimatologists and archaeologists, to better understand human-environmental dynamics during the mid- to late Holocene.
Tillage is a foundational management practice in many cropping systems. Although effective at reducing weed populations and preparing a crop seedbed, tillage and cultivation can also dramatically alter weed community composition. We examined the impact of soil tillage timing on weed community structure at four sites across the northeastern United States. Soil was tilled every 2 wk throughout the growing season (late April to late September 2013), and weed seedling density was quantified by species 6 wk after each tillage event. We used a randomized complete block design with four replicates for each tillage-timing treatment; a total of 196 plots were sampled. The timing of tillage was an important factor in shaping weed community composition and structure at all sites. We identified three main periods of tillage timing that resulted in similar communities. Across all sites, total weed density tended to be greatest and weed evenness tended to be lowest when soils were tilled early in the growing season. From the earliest to latest group of timings, total abundance decreased on average from 428±393 to 159±189 plants m−2, and evenness increased from 0.53±0.25 to 0.72±0.20. The effect of tillage timing on weed species richness varied by site. Our results show that tillage timing affects weed community structure, suggesting that farmers can manage weed communities and the potential for weed interference by adjusting the timing of their tillage and cropping practices.
The local electrode atom probe (LEAP) has become the primary instrument used for atom probe tomography measurements. Recent advances in detector and laser design, together with updated hit detection algorithms, have been incorporated into the latest LEAP 5000 instrument, but the implications of these changes on measurements, particularly the size and chemistry of small clusters and elemental segregations, have not been explored. In this study, we compare data sets from a variety of materials with small-scale chemical heterogeneity using both a LEAP 3000 instrument with 37% detector efficiency and a 532-nm green laser and a new LEAP 5000 instrument with a manufacturer estimated increase to 52% detector efficiency, and a 355-nm ultraviolet laser. In general, it was found that the number of atoms within small clusters or surface segregation increased in the LEAP 5000, as would be expected by the reported increase in detector efficiency from the LEAP 3000 architecture, but subtle differences in chemistry were observed which are attributed to changes in the way multiple hit detection is calculated using the LEAP 5000.
An automated procedure has been developed for the reconstruction of field ion microscopy (FIM) data that maintains its atomistic nature. FIM characterizes individual atoms on the specimen’s surface, evolving subject to field evaporation, in a series of two-dimensional (2D) images. Its unique spatial resolution enables direct imaging of crystal defects as small as single vacancies. To fully exploit FIM’s potential, automated analysis tools are required. The reconstruction algorithm developed here relies on minimal assumptions and is sensitive to atomic coordinates of all imaged atoms. It tracks the atoms across a sequence of images, allocating each to its respective crystallographic plane. The result is a highly accurate 3D lattice-resolved reconstruction. The procedure is applied to over 2000 tungsten atoms, including ion-implanted planes. The approach is further adapted to analyze carbides in a steel matrix, demonstrating its applicability to a range of materials. A vast amount of information is collected during the experiment that can underpin advanced analyses such as automated detection of “out of sequence” events, subangstrom surface displacements and defects effects on neighboring atoms. These analyses have the potential to reveal new insights into the field evaporation process and contribute to improving accuracy and scope of 3D FIM and atom probe characterization.
We present a computational method for pseudo-circular object detection and quantitative characterization in digital images, using the gradient accumulation matrix as a basic tool. This Gradient Accumulation Transform (GAT) was first introduced in 1992 by Kierkegaard and recently used by Kaytanli & Valentine. In the present article, we modify the approach by using the phase coding studied by Cicconet, and by adding a “local contributor list” (LCL) as well as a “used contributor matrix” (UCM), which allow for accurate peak detection and exploitation. These changes help make the GAT algorithm a robust and precise method to automatically detect pseudo-circular objects in a microscopic image. We then present an application of the method to cell counting in microbiological images.
The functional properties of the high-temperature superconductor Y1Ba2Cu3O7−δ (Y-123) are closely correlated to the exact stoichiometry and oxygen content. Exceeding the critical value of 1 oxygen vacancy for every five unit cells (δ>0.2, which translates to a 1.5 at% deviation from the nominal oxygen stoichiometry of Y7.7Ba15.3Cu23O54−δ) is sufficient to alter the superconducting properties. Stoichiometry at the nanometer scale, particularly of oxygen and other lighter elements, is extremely difficult to quantify in complex functional ceramics by most currently available analytical techniques. The present study is an analysis and optimization of the experimental conditions required to quantify the local nanoscale stoichiometry of single crystal yttrium barium copper oxide (YBCO) samples in three dimensions by atom probe tomography (APT). APT analysis required systematic exploration of a wide range of data acquisition and processing conditions to calibrate the measurements. Laser pulse energy, ion identification, and the choice of range widths were all found to influence composition measurements. The final composition obtained from melt-grown crystals with optimized superconducting properties was Y7.9Ba10.4Cu24.4O57.2.
Irradiation of reactor pressure vessel (RPV) steels causes the formation of nanoscale microstructural features (termed radiation damage), which affect the mechanical properties of the vessel. A key tool for characterizing these nanoscale features is atom probe tomography (APT), due to its high spatial resolution and the ability to identify different chemical species in three dimensions. Microstructural observations using APT can underpin development of a mechanistic understanding of defect formation. However, with atom probe analyses there are currently multiple methods for analyzing the data. This can result in inconsistencies between results obtained from different researchers and unnecessary scatter when combining data from multiple sources. This makes interpretation of results more complex and calibration of radiation damage models challenging. In this work simulations of a range of different microstructures are used to directly compare different cluster analysis algorithms and identify their strengths and weaknesses.
In this work, we report on the atom probe tomography analysis of two metallic hydrides formed by pressurized charging using an ex situ hydrogen charging cell, in the pressure range of 200–500 kPa (2–5 bar). Specifically we report on the deuterium charging of Pd/Rh and V systems. Using this ex situ system, we demonstrate the successful loading and subsequent atom probe analysis of deuterium within a Pd/Rh alloy, and demonstrate that deuterium is likely present within the oxide–metal interface of a native oxide formed on vanadium. Through these experiments, we demonstrate the feasibility of ex situ hydrogen analysis for hydrides via atom probe tomography, and thus a practical route to three-dimensional imaging of hydrogen in hydrides at the atomic scale.
In RJR Nabisco v. European Community, the Court added an exclamation point to a long term trend in its jurisprudence. It believes, this trend indicates, that private civil suits pose specific foreign relations issues, at least when the targets are foreign transactions and actors, to which the Court will respond by erecting barriers. To this general point the case adds an unsurprising, but still important codicil: These problems don’t go away when foreign states take advantage of the U.S. civil litigation system by acting as plaintiffs.
A series of recent instrumental advances have facilitated the application of atom probe tomography (APT) to the characterization of an increasingly wide range of materials and devices. Whereas APT was previously mostly limited to the analysis of alloys, advances in areas such as laser pulsing and detectors have enabled characterization of semiconductors and brittle materials. Most recently, ultraviolet laser pulsing has facilitated the analysis of materials previously considered not viable for the atom probe, such as minerals and large bandgap insulator materials. The development of in situ gas reaction cells fully integrated in atom probe instruments has enabled the characterization of surface reactions of materials exposed to highly controlled environments. Finally, current work toward an integrated cryo-transfer system is anticipated to create new directions for APT research.
Solubilizing alkyl chains play a crucial role in the design of semiconducting polymers because they define the materials solubility and processability as well as both the crystallinity and solid-state microstructure. In this paper, we present a scarcely explored design approach by attaching the alkyl side chains on one side (cis-) or on both sides (trans-) of the conjugated backbone. We further investigate the effects of this structural modification on the solid-state properties of the polymers and on the charge-carrier mobilities in organic thin-film transistors.
At first blush, “comparative international law” might sound like an oxymoron. In principle, international law—at least when it arises from multilateral treaties or general custom—applies equally to all parties or states. As a result, international lawyers often resist emphasizing local, national, or regional approaches due to the field’s aspirations to universality and uniformity. Comparativists, meanwhile, frequently overlook the potential to apply comparative law insights to international law on the basis that “rules which are avowedly universal in character do not lend themselves to comparison.”
In biology, hemocytometers such as Malassez slides are widely used and are effective tools for counting cells manually. In a previous work, a robust algorithm was developed for grid extraction in Malassez slide images. This algorithm was evaluated on a set of 135 images and grids were accurately detected in most cases, but there remained failures for the most difficult images. In this work, we present an optimization of this algorithm that allows for 100% grid detection and a 25% improvement in grid positioning accuracy. These improvements make the algorithm fully reliable for grid detection. This optimization also allows complete erasing of the grid without altering the cells, which eases their segmentation.