Miracle-dz/UniFAR-FTUs huggingface dataset:
Resolution-improved Fourier ptychographic microscopy using high-numerical-aperture condenser

High-resolution (HR) and wide field-of-view (FOV) microscopic imaging plays a central role in diverse applications such as high-throughput screening and digital pathology. However, for bright-field microscopy system, high-resolution and wide field-of-view (FOV) always could not be achieved simultaneously, limiting its applications which require large space-bandwidth-product (SBP). Various super-resolution techniques have been proposed to break this limitation, such as on-chip sub-pixel scanning methods, structured illumination microscopy, and Fourier ptychographic microscopy (FPM). Among these super-resolution techniques, FPM became increasingly popular recently since it can combine the numerical apertures (NAs) of the objective lens and the illumination light to form a larger synthetic system NA without sacrificing the FOV. Thus, the resolution-FOV tradeoff can be effectively decoupled in FPM. In addition, it is also very convenient to build an FPM system by simply replacing the illumination system of a bright-field microscope with a commercial programmable LED board. Lately, a lot of efforts have been made to improve the accuracy and efficiency of FPM, however, to date, the effective imaging NA achievable with a typical FPM system is still limited to the range of 0.4-0.7. Here, we build an FPM platform using an oil-immersion condenser to boost the resolution of a bright-field microscopy system and significantly increase its SBP. This FPM system involves a 10X 0.4NA objective lens and a 1.2NA oil-immersion condenser to synthesize a system NA of 1.6. We confirmed the accuracy of this technique by achieving a half-pitch resolution of 154 nm at a wavelength of 435 nm with a FOV of 2.34 mm2, corresponding to an SBP of 98.5 megapixels (~ 50 times higher than that of the conventional incoherent microscope with the same resolution). We also demonstrated the effectiveness of this approach by imaging various biological samples, such as human blood smears. Our work indicates that FPM is an attractive method which could broadly benefit wide-field imaging applications that demand large SBP, and it still has a great potential to achieve much larger SBP of bright-field microscopes.
Phenomenological Modeling of Sheet Moulding Compound Composites Under Quasi-Static Three-Point Bending

A phenomenological model is implemented to model the behaviour of a glass fiber reinforced sheet moulding composite material. Previous characterization of SMC composites, which included the tensile, compressive, in-plane shear and three-point flexure test, found that the material exhibits tension-compression asymmetry and in-plane anisotropy. Based on the experimental results, a model, which incorporates an anisotropic and asymmetric yield function, is implemented in LS-DYNA as a user-defined material model. The model is calibrated to the experimental tension, compression and in-plane shear test results and is validated using the experimental three-point flexure test results. The model is able to capture the flexure stress-strain response within 8% of experimental results. Parametric studies are conducted to determine the sensitivity of the flexure test simulation results to various modeling and material parameters.
TinyTate: Identity-Based Encryption for Sensor Networks

In spite of several years of intense research, the area of security and cryptography in Wireless Sensor Networks (WSNs) still has a number of open problems. On the other hand, the advent of Identity-Based Encryption (IBE) has enabled a wide range of new cryptographic solutions. In this work, we argue that IBE is ideal for WSNs and vice versa. We discuss the synergy between the systems, describe how WSNs can take advantage of IBE, and present results for computation of the Tate pairing over resource constrained nodes. keywords: identity-based encryption, bilinear pairings, key management, sensor networks
Lempel-Ziv complexity of cortical activity during sleep and waking in rats

Understanding the dynamics of brain activity manifested in the EEG, local field potentials (LFP), and neuronal spiking is essential for explaining their underlying mechanisms and physiological significance. Much has been learned about sleep regulation using conventional EEG power spectrum, coherence, and period-amplitude analyses, which focus primarily on frequency and amplitude characteristics of the signals and on their spatio-temporal synchronicity. However, little is known about the effects of ongoing brain state or preceding sleep-wake history on the nonlinear dynamics of brain activity. Recent advances in developing novel mathematical approaches for investigating temporal structure of brain activity based on such measures, as Lempel-Ziv complexity (LZC) can provide insights that go beyond those obtained with conventional techniques of signal analysis. Here, we used extensive data sets obtained in spontaneously awake and sleeping adult male laboratory rats, as well as during and after sleep deprivation, to perform a detailed analysis of cortical LFP and neuronal activity with LZC approach. We found that activated brain states—waking and rapid eye movement (REM) sleep are characterized by higher LZC compared with non-rapid eye movement (NREM) sleep. Notably, LZC values derived from the LFP were especially low during early NREM sleep after sleep deprivation and toward the middle of individual NREM sleep episodes. We conclude that LZC is an important and yet largely unexplored measure with a high potential for investigating neurophysiological mechanisms of brain activity in health and disease.
Changes due to age in internodal length in the sural nerve in man.

In the peripheral nerve trunks of vertebrates, the distance between the nodes of Ranvier is normally greater on fibres of larger diameter than on those of smaller size (Ranvier, 1875; Key and Retzius, 1876). At the time of myelination during development, internodal length is uniformly short, the nodes being spaced about 150 to 300 ,u apart. Each internode represents the territory of an individual Schwann cell and it is of interest that the basic length of Schwann cells in tissue culture is of this order (Weiss and Wang, 1945). As growth proceeds, the number of nodes normally remains constant and the internodes therefore increase in length (Boycott, 1904). It has been shown that there is a direct proportionality between internodal length and the growth in length of the part in which the nerve lies (Vizoso, 1950; Thomas, 1955). All the fibres in a peripheral nerve trunk do not become myelinated at the same time and those that become myelinated later remain of smaller diameter (Thomas, 1956). As these fibres will be stretched less during growth, their internodal length will be shorter (Vizoso and Young, 1948; Vizoso, 1950; Thomas, 1955). The dependence of internodal length on growth is also shown by the observation that in nerve fibres that have regenerated after Wallerian degeneration in an adult animal when growth has ceased, intemodal length is short on fibres of all diameters (Hiscoe, 1947; Vizoso and Young, 1948; Cragg and Thomas, 1964b). During development, the growth rates of internodal length and fibre diameter differ and the precise relationship between these two variables in a nerve is therefore complex and alters during development (see Thomas, 1955). In adult mammalian nerves, including man, it is approximately linear (Vizoso and Young, 1948; Vizoso, 1950). However, a number of authors have drawn attention to the fact that irregularities of internodal length occur, especially in the nerves of older animals. This was shown for human nerves by Vizoso (1950), who
Multigroup-Decodable STBCs from Clifford Algebras

A space-time block code (STBC) in K symbols (variables) is called g-group decodable STBC if its maximum-likelihood decoding metric can be written as a sum of g terms such that each term is a function of a subset of the K variables and each variable appears in only one term. In this paper we provide a general structure of the weight matrices of multi-group decodable codes using Clifford algebras. Without assuming that the number of variables in each group to be the same, a method of explicitly constructing the weight matrices of full-diversity, delay-optimal g-group decodable codes is presented for arbitrary number of antennas. For the special case of Nt = 2a we construct two subclass of codes: (i) A class of 2a-group decodable codes with rate a/(2(a-1)), which is, equivalently, a class of single-symbol decodable codes, (ii) A class of (2a-2)-group decodable with rate (a-1)/(2(a-2)), i.e., a class of double-symbol decodable codes. Simulation results show that the DSD codes of this paper perform better than previously known quasi-orthogonal designs
Galactic Foreground Constraints from the Python V Cosmic Microwave Background Anisotropy Data

We constrain Galactic foreground contamination of the Python V cosmic microwave background anisotropy data by cross-correlating it with foreground contaminant emission templates. To model foreground emission, we use 100 and 12 μm dust templates and two point-source templates based on the Parkes-MIT-NRAO survey. The analysis takes account of intermodulation correlations in eight modulations of the data that are sensitive to a large range of angular scales and also densely sample a large area of sky. As a consequence, the analysis here is highly constraining. We find little evidence for foreground contamination in an analysis of the whole data set. However, there is indication that foregrounds are present in the data from the larger angular scale modulations of those Python V fields that overlap the region scanned earlier by the University of California at Santa Barbara South Pole 1994 experiment. This is an independent consistency cross-check of findings from the South Pole 1994 data.
POPULATION STRUCTURE OF A HERBIVOROUS INSECT AND ITS HOST PLANT ON A MICROGEOGRAPHIC SCALE

Parasites typically live in a patchy environment. This environment is often heterogeneous, in the sense that parasites may encounter hosts with different degrees of suitability for the parasite's development and reproduction. Therefore, knowledge of the gene flow ofboth the parasite and the host would be valuable to infer the heterogeneity of the environment of the parasite (i.e., the heterogeneity of the host populations) and the potential for parasites to become locally adapted. The study of the genetic structure in host-parasite interactions has been used, so far, to attest the existence of host races, and therefore, only the genetic structure of the parasite is well studied. One well-known example is the existence of sympatric host races in the apple maggot fly Rhagoletis pomonella, which has been demonstrated by allozyme electrophoresis (Feder et al. 1988; McPheron et al. 1988). The only study, to our knowledge, in which the genetic structure of populations of both the
Product Line Concepts

As autonomous, self-contained software building blocks, components provide a solid foundation for software reuse. However, simply developing software in terms of components is not, on its own, likely to lead to significant increases in reuse levels. Experience indicates that reusing a component usually involves more than simply plugging it into a new context, and unless components are carefully written to maximize their reusability they tend to be difficult to reuse beyond the application for which they were written. Despite this fact, most methods that aim to support components, such as Catalysis [DW98], RUP [Kru00] and UML Components [CD00], assume that simply decomposing software in terms of components is sufficient to promote reuse. In other words, they fail to make the distinction between "developing for use" (i.e. developing a component for a specific application) and "developing for reuse" (developing a component for numerous applications) [FHA00]. However, recognizing and separating these two concepts is essential if the reuse potential of components is to be fully exploited [Lim98]. Promoting the latter is also the underlying motivation for product lines as explained in the following subsections. The distinction between "developing for use" and "developing for reuse" applies to all software assets, not just components. Figure 14-2 illustrates the traditional "reuse" life cycle based on software artifacts (e.g. components) initially developed for use with one application in mind. Basically, the artifacts created in one application engineering project are stored in an asset base so that they can be reused in other applications. Future application engineering projects then attempt to develop parts of the application by reusing assets existing in the asset base. However, as many organizations have experienced, this approach usually fails to achieve the expected improvements in reuse because it does not solve the following problems: • Documentation: Each asset placed in the asset base must be documented to facilitate its reuse. However determining what information, to what level of detail, is needed by potential reusers is a non-trivial problem. • Classification: All assets and associated documentation must be structured according to a common classification scheme. This classification scheme is the key for accessing the asset base, and must, therefore, be defined in a way that optimally supports the reuse process. • Identification: As Tracz [Trac95] pointed out, reusable software must exist before you can reuse it. Consequently, during the application engineering process an engineer must be aware of assets that are potentially reusable …
Implications of the CKD-EPI GFR estimation equation in clinical practice.

BACKGROUND AND OBJECTIVES Chronic kidney disease (CKD) is a significant public health problem whose diagnosis and staging relies upon GFR-estimating equations, including the new CKD-EPI equation. CKD-EPI demonstrated superior performance compared with the existing MDRD equation but has not been applied to a healthcare system. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS We identified 53,759 patients with stages 3 to 5 CKD on the basis of either MDRD or CKD-EPI equations using two eGFR values <60 ml/min per 1.73 m² > 90 days apart from an outpatient setting. We compared patient characteristics, presence of related diagnosis codes, and time CKD classification between equations. RESULTS The number of patients identified with CKD decreased 10% applying CKD-EPI versus MDRD. Changes varied substantially by patient characteristics including a 35% decrease among patients < 60 years and a 10% increase among patients > 90 years. Women, non-African Americans, nondiabetics, and obese patients were less likely to be classified on the basis of CKD-EPI. Time to CKD classification was significantly longer with CKD-EPI among younger patients. 14% of patients identified with CKD on the basis of either estimating equation also had a related ICD-9 diagnosis, ranging from 19% among patients < 60 years to 7% among patients > 90 years. CONCLUSIONS Consistent with findings in the general population, CKD-EPI resulted in substantial declines in equation-based CKD diagnoses in a large healthcare system. Further research is needed to determine whether widespread use of CKD-EPI with current guidelines could lead to delayed needed care among younger patients or excessive referrals among older patients.
Towards a Lightweight RDMA Para-Virtualization for HPC

Virtualization has gained increasing attention in the recent High Performance Computing (HPC) development. While HPC provides scalability and computing performance, HPC in the cloud benefits in addition from the agility and flexibility that virtualization brings. One of the major challenges of HPC in virtualized environments is RDMA virtualization. Existing implementations of RDMA virtualization focused on supporting VMs running Linux. However, HPC workloads rarely need a full-blown Linux OS. Compared to traditional Linux OS, emerging Library OSes, such as OSv, are becoming popular choices as they provide efficient, portable and lightweight cloud images. To enable virtualized RDMA for lightweight library OSes, drivers and interfaces must be re-designed to accommodate the underlying virtual devices. In this paper we present a novel design, the virtio-rdma driver for OSv, which aims to provide RDMA para-virtualization for lightweight library OS. We compare this new design with existing implementations for Linux, and analyze the advantages of virtio-rdma's architecture, its ease of migration to different operating systems, and the potential for performance improvement. We also propose a solution for integrating this para-virtualized driver into HPC platforms, enabling HPC application users to deploy their use cases smoothly in a virtualized HPC environment.
CHIMAERA: a high-performance architecture with a tightly-coupled reconfigurable functional unit

Reconfigurable hardware has the potential for significant performance improvements by providing support for application-specific operations. We report our experience with Chimaera, a prototype system that integrates a small and fast reconfigurable functional unit (RFU) into the pipeline of an aggressive, dynamically-scheduled superscalar processor. Chimaera is capable of performing 9-input/1-output operations on integer data. We discuss the Chimaera C compiler that automatically maps computations for execution in the RFU. Chimaera is capable of: (1) collapsing a set of instructions into RFU operations, (2) converting control-flow into RFU operations, and (3) supporting a more powerful fine-grain data-parallel model than that supported by current multimedia extension instruction sets (for integer operations), Using a set of multimedia and communication applications bye show that even with simple optimizations. The Chimaera C compiler is able to map 22% of all instructions to the RFU on the average. A variety of computations are mapped into RFU operations ranging from as simple as add/sub-shift pairs to operations of more than 10 instructions including several branches. Timing experiments demonstrate that for a 4-way out-of-order superscalar processor Chimaera results in average performance improvements of 21%, assuming a very aggressive core processor design (most pessimistic RFU latency model) and communication overheads from and to the RFU.
First principle study of structural, elastic and electronic properties of APt3 (A=Mg, Sc, Y and Zr)

Abstract We report results obtained from first principle calculations on APt3 compounds with A=Mg, Sc, Y and Zr. Our results of the lattice parameter a are in good agreement with experimental data, with deviations less than 0.8%. Single crystal elastic constants are calculated, then polycrystalline elastic moduli (bulk, shear and Young moduli, Poisson ration, anisotropy factor) are presented. Based on Debye model, Debye temperature ϴD is calculated from the sound velocities Vl, Vt and Vm. Band structure results show that the studied compounds are electrical conductors, the conduction mechanism is assured by Pt-d electrons. Different hybridisation states are observed between Pt-d and A-d orbitals. The study of the charge density distribution and the population analysis shows the coexistence of ionic, covalent and metallic bonds.
Geo-temporal Twitter demographics

ABSTRACT This paper seeks and uses highly disaggregate social media sources to characterize Greater London in terms of flows of people with modelled individual characteristics, as well as conventional measures of land use morphology and night-time residence. We conduct three analyses. First, we use the Shannon Entropy measure to characterize the geography of information creation across the city. Second, we create a geo-temporal demographic classification of Twitter users in London. Third, we begin to use Twitter data to characterize the links between different locations across the city. We see all three elements as data rich, highly disaggregate geo-temporal analysis of urban form and function, albeit one that pertains to no clearly defined population. Our conclusions reflect upon this severe shortcoming in analysis using social media data, and its implications for progressing our understanding of socio-spatial distributions within cities.
An out-of-core sparse symmetric-indefinite factorization method

We present a new out-of-core sparse symmetric-indefinite factorization algorithm. The most significant innovation of the new algorithm is a dynamic partitioning method for the sparse factor. This partitioning method results in very low I/O traffic and allows the algorithm to run at high computational rates, even though the factor is stored on a slow disk. Our implementation of the new code compares well with both high-performance in-core sparse symmetric-indefinite codes and a high-performance out-of-core sparse Cholesky code.
Elastin- and Collagen-Rich Human Carotid Plaques Have Increased Levels of the Cysteine Protease Inhibitor Cystatin C

Background: Cystatin C is a major inhibitor of the elastin- and collagen-degrading cysteine proteases and may therefore have an important role in preserving atherosclerotic plaque stability. In this study we analyzed the associations between human carotid plaque cystatin C expression and the plaque content of collagen and elastin. Methods: Thirty-one plaques were removed by endarterectomy and homogenized. Cystatin C levels were analyzed by densitometry of Western blots and elastin and collagen levels were determined colorimetrically. Results: The plaque content of cystatin C correlated with total elastin (r = 0.58, p = 0.001) and collagen (r = 0.50, p = 0.004), as well as with cross-linked forms of elastin (r = 0.42, p = 0.022) and collagen (r = 0.52, p = 0.003). Immunohistochemical analysis demonstrated that cystatin C colocalized with elastin and collagen. No correlation was seen between cystatin C and the amount of degraded elastin or collagen in plaques. Conclusion: The positive correlation between cystatin C levels and collagen and elastin levels in plaques supports the notion that cystatin C plays an important role in maintaining atherosclerotic plaque stability.
High-Performance Computer-Aided Optimization of Viscous Dampers for Improving the Seismic Performance of a Tall Steel Building

Using fluid viscous dampers (FVDs) has been demonstrated to be an effective method to improve seismic performance of new and existing buildings. In engineering applications, designs of these dampers mainly rely on trial and error, which could be repetitive and labor intensive. To improve this tedious manual process, it is beneficial to explore more formal and automated approaches that rely on recent advances in software applications for nonlinear dynamic analysis, performance-based evaluation, and workflow management and the computational power of high-performance, parallel processing computers. The optimization design procedure follows the framework of Performance Based Earthquake Engineering (PBEE) and uses an automatic tool that incorporates an optimization engine and structural analysis software: Open System for Earthquake Engineering Simulation (OpenSEES). An existing 35-story steel moment frame is selected as a case-study building for verification of this procedure. The goal of the retrofit design of FVDs is to improve the building’s seismic behavior that focuses on avoiding collapse under a basic-safety, level-2 earthquake (BSE-2E). The objective of the optimization procedure is to reduce the building’s total loss under a BSE-2E event and optimal damper patterns will be proposed. The efficiency of the optimization procedure will be demonstrated and compared with a manual refinement procedure.