Miracle-dz/UniFAR-FTUs huggingface dataset:
Ultrasound-assisted extraction of biomaterials and the design of sono-reactors

Biomaterial extraction with the ultrasound is one of very ellective technique procedures in the Chinese traditional medicine manufacture. The yield of the extraction was used to examine the effect of sonication. It was determined by the parameters of ultrasonic field and the characteristics of the medium. A design of a large-scale sono-reactor so called multidimensional reactor Is introduced in the paper. The key problems of reactor design are the realizations of high intensity and uniformity of the ultrasonic field in a large-scale. The second upright phase-latch (SUPL), FSK and mix-sound response are utilized in the design of multi-dimensional sono-reactor. An ultrasonic field of high intensity and uniformity is upbuilt in the reactor.
Prediction of disulfide‐bonded cysteines in proteomes with a hidden neural network

A hidden neural network‐based method is used to predict the bonding state of cysteines starting from the residue sequence of the protein chain. The method scores as high as 89% and 86% per cysteine residue and per protein, respectively, and in this overcomes other predictors of the same category. We then explore the efficacy of our predictor in computing the disulfide content of the whole proteome of Escherichia coli (K12 and O157), Aeropirum pernix, Thermotoga maritima, and Homo sapiens. We find that the percentage of extracellular disulfide containing proteins is higher than that of intracellular one, and that the human proteome is by far the one with the highest content of sulfur‐sulfur linkages in proteins.
A graph-based plane segmentation approach for noisy point clouds

Semantic mapping is a long term goal to understand environment for mobile robots. The indoor environments usually consist of a large amount of planar surfaces. Thus, plane segmentation is an essential prerequisite to build a semantic map. In this paper, we develop an algorithm to segment planar surfaces from noisy point clouds of indoor scenes. The proposed segmentation algorithm is based on a graph-based representation of the 3D data to determine the mergence of two adjacent regions, which is able to detect all the planes accurately. We apply the algorithm to plane segmentation and illustrate the results with the synthetic point cloud and two point clouds of real-world indoor scenes, respectively. The experiment results show that our proposed segmentation algorithm is accurate to extract all the planar surfaces and adaptive to cope with the point cloud noise.
Charge sharing measurements of pixilated CdTe using Medipix-II chip

One important consideration of the design and the operation of pixilated detector is the ratio of the pixel size to the thickness of the detector. When the e-h pairs are generated and the charge drifts toward the pixel electrodes under the influence of the bias field, the charge spread is directly related to the drift time, which strongly depends on the carrier mobility and distance travelled by the carriers. This study has general impact on the design of pixilated detector; however its impact on the design and the operation of pixilated detector coupled to photon counting electronics is more profound. The results imply that designing a Cd(Zn)Te detector with very small pixel size, say 25/spl mu/m and a detector 1 mm thick, is unrealistic because in reality such intrinsic fine spatial resolution can not be attained in the corresponding image due to charge sharing.
Standards to support information systems integration in anatomic pathology.

CONTEXT Integrating anatomic pathology information- text and images-into electronic health care records is a key challenge for enhancing clinical information exchange between anatomic pathologists and clinicians. The aim of the Integrating the Healthcare Enterprise (IHE) international initiative is precisely to ensure interoperability of clinical information systems by using existing widespread industry standards such as Digital Imaging and Communication in Medicine (DICOM) and Health Level Seven (HL7). OBJECTIVE To define standard-based informatics transactions to integrate anatomic pathology information to the Healthcare Enterprise. DESIGN We used the methodology of the IHE initiative. Working groups from IHE, HL7, and DICOM, with special interest in anatomic pathology, defined consensual technical solutions to provide end-users with improved access to consistent information across multiple information systems. RESULTS The IHE anatomic pathology technical framework describes a first integration profile, "Anatomic Pathology Workflow," dedicated to the diagnostic process including basic image acquisition and reporting solutions. This integration profile relies on 10 transactions based on HL7 or DICOM standards. A common specimen model was defined to consistently identify and describe specimens in both HL7 and DICOM transactions. CONCLUSION The IHE anatomic pathology working group has defined standard-based informatics transactions to support the basic diagnostic workflow in anatomic pathology laboratories. In further stages, the technical framework will be completed to manage whole-slide images and semantically rich structured reports in the diagnostic workflow and to integrate systems used for patient care and those used for research activities (such as tissue bank databases or tissue microarrayers).
Evaluating Visualizations to Unearth Behavior and Insight

In this position paper, I describe three case studies of evaluations of visualization systems focused on social interaction. For the Vizster social network visualization, we conducted qualitative observation of a public installation of the visualization. For the sense.us collaborative visualization environment, we conducted both unstructured usage sessions and a live deployment on the IBM corporate intranet, followed by a formal content analysis of user activity. To evaluate the use of visual social navigation cues in social data analysis environments, we used a task-driven experimental design to measure the number of unique discoveries uncovered by subjects. Though quite different in terms of methods, each of these evaluations helped unearth how the visualization contributed to an analysis process (whether formal or informal) and revealed patterns of behavior and insight generation that have served to guide future designs.
A data acquisition and analysis pipeline for scanning angle interference microscopy

We describe open source software and hardware tools for calibrating, acquiring, and analyzing images for scanning angle interference microscopy (SAIM) analysis. These tools make it possible for any user with a TIRF microscope equipped with a motorized illumination unit to generate reconstructed images with nanometer precision in the axial (z) direction and diffraction-limited resolution in the lateral (xy) plane.
Quantitative x-ray microanalysis of spherical inclusions embedded in a matrix using a SEM and Monte Carlo simulations

The current schemes of quantification of x-ray microanalysis in the SEM [ZAF and σ(ρZ) methods] are valid for specimens of homogeneous composition. The determination of the chemical composition of small inclusions using these techniques is impossible because the volume of x-ray emission is not of homogeneous composition. A scheme of quantification to determine the composition of small inclusions embedded in a matrix has been developed using Monte Carlo simulations. This scheme is similar to that developed by Kyser and Murata (1974) for the quantification of thin foils deposited on a substrate using x-ray microanalysis in the SEM.
Dynamic clonal analysis based on chronic in vivo imaging allows multiscale quantification of growth in the Drosophila wing disc

In the course of morphogenesis, tissues change shape and grow. How this is orchestrated is largely unknown, partly owing to the lack of experimental methods to visualize and quantify growth. Here, we describe a novel experimental approach to investigate the growth of tissues in vivo on a time-scale of days, as employed to study the Drosophila larval imaginal wing disc, the precursor of the adult wing. We developed a protocol to image wing discs at regular intervals in living anesthetized larvae so as to follow the growth of the tissue over extended periods of time. This approach can be used to image cells at high resolution in vivo. At intermediate scale, we tracked the increase in cell number within clones as well as the changes in clone area and shape. At scales extending to the tissue level, clones can be used as landmarks for measuring strain, as a proxy for growth. We developed general computational tools to extract strain maps from clonal shapes and landmark displacements in individual tissues, and to combine multiple datasets into a mean strain. In the disc, we use these to compare properties of growth at the scale of clones (a few cells) and at larger regional scales.
Briareus: Accelerating Python Applications with Cloud

Briareus provides convenient tools to make use of computing resources provided by cloud to accelerate Python applications. In this paper, three techniques are presented. First, some of the functions in a Python program can be migrated to cloud and be evaluated using the hardware and software provided by that cloud platform, while the other parts still running locally. Second, Briareus can automatically parallelize specified loops in a program to accelerate it. And third, specified functions can be called asynchronously after being patched, so that two or more functions can be evaluated simultaneously. By combining these three methods, a Python application can make part of itself to run in a remote cloud platform in parallel. To use Briareus, developers do not need to modify the existing source much, but only need to insert some descriptive comments and invoke a patching function at the beginning. Experiments show that Briareus can significantly speed up the running of programs written by Python, especially for those for scientific and engineering computing. The early beta version of Briareus has been developed for testing and all sources are accessible to public via GitHub and installable via PyPI.
On Generalized Gaussian Quadrature Rules for Singular and Nearly Singular Integrals

We construct and analyze generalized Gaussian quadrature rules for integrands with endpoint singularities or near endpoint singularities. The rules have quadrature points inside the interval of integration, and the weights are all strictly positive. Such rules date back to the study of Chebyshev sets, but their use in applications has only recently been appreciated. We provide error estimates, and we show that the convergence rate is unaffected by the singularity of the integrand. We characterize the quadrature rules in terms of two families of functions that share many properties with orthogonal polynomials but that are orthogonal with respect to a discrete scalar product that, in most cases, is not known a priori.
Gene Array Analyzer: alternative usage of gene arrays to study alternative splicing events

Exon arrays are regularly used to analyze differential splicing events. GeneChip Gene 1.0 ST Arrays (gene arrays) manufactured by Affymetrix, Inc. are primarily used to determine expression levels of transcripts, although their basic design is rather similar to GeneChip Exon 1.0 ST Arrays (exon arrays). Here, we show that the newly developed Gene Array Analyzer (GAA), which evolved from our previously published Exon Array Analyzer (EAA), enables economic and user-friendly analysis of alternative splicing events using gene arrays. To demonstrate the applicability of GAA, we profiled alternative splicing events during embryonic heart development. In addition, we found that numerous developmental splicing events are also activated under pathological conditions. We reason that the usage of GAA considerably expands the analysis of gene expression based on gene arrays and supplies an additional level of information without further costs and with only little effort.
Balancing a humanoid robot with a prioritized contact force distribution

Humanoid robots propel themselves and perform tasks by interacting with their environment through contact forces. Typically, nonuniqueness of these forces is dealt with by distributing them evenly between the contacts. In the present paper, we introduce strict prioritization in contact force distribution, to reflect situations when an application of certain contact forces should be avoided as much as possible, for example, due to a fragility of the support. We illustrate this by designing a whole body motion controller for a setting with multiple noncoplanar contacts, where application of an optional contact force is allowed only if it is necessary to maintain balance and execute a task. Balance preservation is addressed by imposing a capturability constraint based on anticipation with a linear model adapted to multiple noncoplanar contacts. The controller is evaluated in simulations.
Gene Expression Profiles for Genotoxic Effects of Silica-Free and Silica-Coated Cobalt Ferrite Nanoparticles

Nanomaterials have been widely evaluated for potential use as efficient delivery carriers for cancer diagnosis and therapy. To translate these nanomaterials to the clinic, their safety needs to be verified, particularly in terms of genotoxicity and cytotoxicity. We investigated changes in gene expression profiles influenced by silica-coated cobalt ferrite magnetic-fluorescence nanoparticles and silica-free cobalt ferrite magnetic-core nanoparticles in vivo and in vitro. Methods: 68Ga-labeled cobalt ferrite nanoparticles produced by synthesis of 2-(p-isothio-cyanatobenzyl)-1,4,7-triazacyclonane-1,4,7-triacetic acid chelator were established after labeling efficiency had been validated through a thin-layer chromatography method. The expression of genes associated with the stress and toxicity pathways was verified by a commercially available polymerase chain reaction array kit. Results: In comparison with magnetic-fluorescence nanoparticles, magnetic-core nanoparticles revealed severe cytotoxic effects at various doses and treatment times as determined by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay. Whole-body small-animal PET and biodistribution studies, including transmission electron microscope analysis, showed that tail-vein injection of magnetic-core or magnetic-fluorescence nanoparticles exhibited substantial liver accumulation. Real-time polymerase chain reaction array using 52 genes related to cellular toxicity demonstrated that 17 genes from the magnetic-core–treated liver samples were significantly affected, mostly in relation to DNA damage or repair and to oxidative or metabolic stress. The magnetic-fluorescence–treated liver samples showed gene expression approximately 90% similar to that of untreated liver samples. Conclusion: We compared a variety of gene expression profiles in mice injected with magnetic-fluorescence or magnetic-core nanoparticles. This study of gene expression profiles affected by nanotoxicity provides critical information for the clinical use of silica-coated cobalt ferrite.
Tris(tetramethylammonium) tetra-μ2-sulfido-tetrasulfidocopper(I)dimolybdenum(VI) N,N-dimethylformamide solvate

The title compound, (C4H12N)3[CuMo2S8]·C3H7NO, was obtained from the self-assembly of tetrathiomolybdate, tetramethylammonium nitrate and cuprous sulfide in dimethylformamide (DMF). The asymmetric unit contains three (NMe4)+ cations, one [Mo2S8Cu]3− anion and one DMF solvent molecule, and no obvious interactions are observed between these species. The trinuclear anion can be viewed as fused [MoS4Cu]− units sharing a copper center. The geometric parameters of the trivalent anion are comparable to those reported for other related salts including isomorphous anions, namely (NEt4)2(PPh4)[Mo2S8Cu] (a) and (Ph3P=N=PPh3)2(NEt4)[W2S8Cu]·2CH3CN (b). However, the Mo—Cu—Mo angle is found to be 160.24 (3)° for the title salt, while this angle is 162.97 (2)° in (a) and the W—Cu—W angle is 170.3 (2)° in (b), indicating that the largest deviation from linearity is in the title compound.
Super-hydrophobic surfaces of layer-by-layer structured film-coated electrospun nanofibrous membranes

We have recently fabricated super-hydrophobic membrane surfaces based on the inspiration of self-cleaning silver ragwort leaves. This biomimetic super-hydrophobic surface was composed of fluoroalkylsilane (FAS)-modified layer-by-layer (LBL) structured film-coated electrospun nanofibrous membranes. The rough fibre surface caused by the electrostatic LBL coating of TiO2 nanoparticles and poly(acrylic acid) (PAA) was used to imitate the rough surface of nanosized grooves along the silver ragwort leaf fibre axis. The results showed that the FAS modification was the key process for increasing the surface hydrophobicity of the fibrous membranes. Additionally, the dependence of the hydrophobicity of the membrane surfaces upon the number of LBL coating bilayers was affected by the membrane surface roughness. Moreover, x-ray photoelectron spectroscopy (XPS) results further indicated that the surface of LBL film-coated fibres absorbed more fluoro groups than the fibre surface without the LBL coating. A (TiO2/PAA)10 film-coated cellulose acetate nanofibrous membrane with FAS surface modification showed the highest water contact angle of 162° and lowest water-roll angle of 2°.
Effects of going electronic in the publishing value system

We report on the effects of going electronic in the publishing value system that starts with the author and ends with the reader. In between we find several contribuants to the final product, the publication. The organization and economics of publishing are analysed and described as it transforms from a hardcopy business-via CD-I and CD-ROM as an in-between stage-into full fledged online electronic publishing of text-oriented publications (i.e. newspapers, journals and books). This report focuses on the situation in the Netherlands, where a number of big publishers have their head office.
Alternative fuzzy c-lines and comparison with noise clustering in cluster validation

Alternative c-means is a robustified version of k-means-type clustering that uses a robust distance measure instead of the conventional Euclidean distance based on an Mestimation concept. This paper proposes a linear clustering model for estimating intrinsic linear sub-structures in a robust way based on a similar manner to alternative c-means. In order to replace the least square measure with alternative c-means-type robust measure, the clustering criteria of distances between data samples and linear prototypes are calculated by the lower rank approximation concept. In numerical experiments, the model is compared with the conventional noise clustering model, where noise samples are dumped into the additional noise cluster while they are still assigned to normal clusters in the alternative c-means-type model. Several experimental results demonstrate the robust feature of the proposed model from both view points of noise sensitivity and cluster validation.
Asymptotic properties of the algebraic constant modulus algorithm

The algebraic constant modulus algorithm (ACMA) is a noniterative blind source separation algorithm. It computes jointly beamforming vectors for all constant modulus sources as the solution of a joint diagonalization problem. We analyze its asymptotic properties and show that (unlike CMA) it converges to the Wiener beamformer when the number of samples or the signal-to-noise ratio (SNR) goes to infinity. We also sketch its connection to the related JADE algorithm and derive a version of ACMA that converges to a zero-forcing beamformer. This gives improved performance in applications that use the estimated mixing matrix, such as in direction finding.
Average Torque Separation in Permanent Magnet Synchronous Machines Using Frozen Permeability

This paper investigates the average torque separation in permanent magnet (PM) synchronous machines. In order to accurately separate the PM and armature fields, and, hence, the torque components accounting for the magnetic saturation and crosscoupling, the frozen permeability (FP) method is often employed, while the torque can be calculated by different methods, such as Maxwell stress tensor and virtual work principle. Although these two methods result in identical torques in normal finite element (FE) analyses when appropriate FE meshes are used, the average torques calculated by these two methods are found to be different when the FP method is employed due to the influence of equivalent rotational magnetic saliency in the stator, which causes a part of PM torque being improperly attributed to the reluctance torque when Maxwell stress tensor method is employed. However, by using the virtual work principle, this is eliminated, and, hence, the average torque components can still be appropriately separated and analyzed.
Dietary Protein and Blood Pressure: A Systematic Review

Background Elevated blood pressure (BP), which is a major risk factor for cardiovascular disease, is highly prevalent worldwide. Recently, interest has grown in the role of dietary protein in human BP. We performed a systematic review of all published scientific literature on dietary protein, including protein from various sources, in relation to human BP. Methodology/Principal Findings We performed a MEDLINE search and a manual search to identify English language studies on the association between protein and blood pressure, published before June 2010. A total of 46 papers met the inclusion criteria. Most observational studies showed no association or an inverse association between total dietary protein and BP or incident hypertension. Results of biomarker studies and randomized controlled trials indicated a beneficial effect of protein on BP. This beneficial effect may be mainly driven by plant protein, according to results in observational studies. Data on protein from specific sources (e.g. from fish, dairy, grain, soy, and nut) were scarce. There was some evidence that BP in people with elevated BP and/or older age could be more sensitive to dietary protein. Conclusions/Significance In conclusion, evidence suggests a small beneficial effect of protein on BP, especially for plant protein. A blood pressure lowering effect of protein may have important public health implications. However, this warrants further investigation in randomized controlled trials. Furthermore, more data are needed on protein from specific sources in relation to BP, and on the protein-BP relation in population subgroups.
Novel GCC-PHAT model in diffuse sound field for microphone array pairwise distance based calibration

We propose a novel formulation of the generalized cross correlation with phase transform (GCC-PHAT) for a pair of microphones in diffuse sound field. This formulation elucidates the links between the microphone distances and the GCC-PHAT output. Hence, it leads to a new model that enables estimation of the pairwise distances by optimizing over the distances best matching the GCC-PHAT observations. Furthermore, the relation of this model to the coherence function is elaborated along with the dependency on the signal bandwidth. The experiments conducted on real data recordings demonstrate the theories and support the effectiveness of the proposed method.