Miracle-dz/UniFAR-FTUs huggingface dataset:
Treponema pallidum Surface Immunofluorescence Assay for Serologic Diagnosis of Syphilis

ABSTRACT A surface immunofluorescence assay (SIFA) using live spirochetes was analyzed and compared with Western blot (WB), fluorescent treponemal antibody absorption (FTA-ABS), microhemagglutination (MHA-TP), and Treponema pallidum immobilization (TPI) assays for detecting serum antibodies to T. pallidum in patients with syphilis, in disease controls, and in healthy subjects. SIFA and WB were 99% sensitive (99 of 100 positive specimens) and specific (140 of 140 negative specimens); FTA-ABS showed a sensitivity and a specificity of 90 and 89% (90 of 100 positive and 125 of 140 negative specimens), respectively. MHA-TP showed a sensitivity of 84% (84 of 100 positive specimens) and a specificity of 98.5% (138 of 140 negative specimens). Finally, TPI had a sensitivity of 52% (52 of 100 positive specimens) and a specificity of 100% (140 of 140 negative specimens). The T. pallidum SIFA was therefore highly specific, showing no equivocal reactivities with control sera, and sensitive. The results suggest the possible use of SIFA as a confirmatory test in the serologic diagnosis of syphilis.
Low-Frequency Noise in SONOS-TFT With a Trigate Nanowire Structure Under Program/Erase Operation

This letter investigates low-frequency noise (LFN) in polycrystalline silicon thin-film transistor (TFT) nonvolatile memory (NVM) under Fowler-Nordheim tunneling program/erase (P/E) operation. The NVM utilizes a silicon-oxide-nitride-oxide-silicon (SONOS)-type structure with a trigate multiple nanowire (NW) channels. The difference in the flicker noise (1/f) level between a multiple-channel NW device and a standard single-channel device became smaller after P/E cycling. The observation can be explained by the quantity of grain-boundary traps introduced by higher electric field at the NW corner during the P/E cycle, subsequently increasing the LFN level in the multiple NW SONOS-TFT.
On Regular Resource Grid for Filtered OFDM

Filtered orthogonal frequency division multiplexing (F-OFDM) can accommodate diverse service requirements by introducing additional filtering to OFDM and flexibly adapting the filter according to the service requirement. However, when block filtering is flexibly adapted per-subband, the regular resource grid could be violated. In this letter, we propose a solution to maintain the regular resource grid for F-OFDM. The proposed solution is twofold: 1) it allocates guard bands inside the filter bandwidth, which is kept independent of guard band and 2) it introduces timing advance according to the filter used. It is shown in practically relevant scenarios that the proposed solution, despite its simplicity, performs better than another more complex approach.
Research Statement

I have a very diverse background in computational and applied mathematics. Areas of my research include variational methods, computational fluid dynamics, level set methods, multigrid methods, and information theory. I applied knowledge of these areas to solve problems in computer vision, image processing, and biomedical image analysis. In particular, my dissertation work links all aforementioned areas of computational and applied mathematics to solve image registration and segmentation problems in computer vision and medical imaging. I have been fortunate to work under the guidance of my advisor Prof. Stanley Osher and collaborate with one of the world’s best known brain imaging groups in the Lab of Neuro Imaging at UCLA. For my doctoral dissertation, I proposed the Unbiased Large-Deformation Nonlinear Image Registration model, which is described in Section 1. My thesis work also includes a novel technique for segmentation of homogeneous deformation described in Section 3. Besides my dissertation work, my research included the areas of multiphase image segmentation, surface denoising, surface reconstruction, and Eulerian vortex motion.
Characterization of the Phosphatidylserine-binding Region of Rat MARCKS (Myristoylated, Alanine-rich Protein Kinase C Substrate)

We reported previously that recombinant myristoylated, alanine-rich protein kinase C substrate (MARCKS) expressed in Escherichia coli as well as MARCKS purified from rat brain specifically bound to phosphatidylserine (PS) in a calcium-independent manner and that the binding was regulated through phosphorylation of MARCKS (Nakaoka, T., Kojima, N., Hamamoto, T., Kurosawa, N., Lee, Y. C., Kawasaki, H., Suzuki, K., and Tsuji, S. (1993) J. Biochem. (Tokyo) 114, 449-452). In this study, to identify the minimum PS-binding region of MARCKS and the regulatory phosphorylation site, the binding of MARCKS to PS was examined in deletion mutants producing glutathione S-transferase (GST) fusion proteins. The mutant proteins GST-6-180 and GST-127-160 had almost the same ability to bind to immobilized PS as MARCKS purified from rat brain, whereas GST-127-152 did not bind to it. In addition, the binding of GST-6-156 to immobilized PS was 62% of that of GST-6-180, but that of GST-6-152 was only 8% and that of GST-6-135 was not detected. The effect of phosphorylation by protein kinase C was examined in several mutants of GST-6-180 whose serine residues were substituted with alanine. After phosphorylation, the mutants GST-6-180[S156A and S163A], GST-6-180[S156A], and GST-6-180[S163A] did not bind to immobilized PS like native MARCKS and GST-6-180. However, even after phosphorylation, GST-6-180[S152A] and GST-6-180[S152A and S156A] could bind to immobilized PS. These results strongly suggest that MARCKS binds to PS molecules in the inner leaflet of the plasma membrane through residues 127-156, with residues 153-156 (FKKS) being particularly important in the binding of MARCKS to PS, and that the binding is regulated through the protein kinase C-catalyzed phosphorylation of the serine at residue 152.
Additive effects of social and non-social attention during infancy relate to later autism spectrum disorder

Emerging findings from studies with infants at familial high risk for autism spectrum disorder (ASD), owing to an older sibling with a diagnosis, suggest that those who go on to develop ASD show early impairments in the processing of stimuli with both social and non-social content. Although ASD is defined by social-communication impairments and restricted and repetitive behaviours, the majority of cognitive theories of ASD posit a single underlying factor, which over development has secondary effects across domains. This is the first high-risk study to statistically differentiate theoretical models of the development of ASD in high-risk siblings using multiple risk factors. We examined the prediction of ASD outcome by attention to social and non-social stimuli: gaze following and attentional disengagement assessed at 13 months in low-risk controls and high-risk ASD infants (who were subsequently diagnosed with ASD at 3 years). When included in the same regression model, these 13-month measures independently predicted ASD outcome at 3 years of age. The data were best described by an additive model, suggesting that non-social attention, disengagement, and social attention as evidenced by gaze following, have a cumulative impact on ASD risk. These data argue against cognitive theories of ASD which propose that a single underlying factor has cascading effects across early development leading to an ASD outcome, and support multiple impairment models of ASD that are more consistent with recent genetic and neurobiological evidence.
seeMotif: exploring and visualizing sequence motifs in 3D structures

Sequence motifs are important in the study of molecular biology. Motif discovery tools efficiently deliver many function related signatures of proteins and largely facilitate sequence annotation. As increasing numbers of motifs are detected experimentally or predicted computationally, characterizing the functional roles of motifs and identifying the potential synergetic relationships between them are important next steps. A good way to investigate novel motifs is to utilize the abundant 3D structures that have also been accumulated at an astounding rate in recent years. This article reports the development of the web service seeMotif, which provides users with an interactive interface for visualizing sequence motifs on protein structures from the Protein Data Bank (PDB). Researchers can quickly see the locations and conformation of multiple motifs among a number of related structures simultaneously. Considering the fact that PDB sequences are usually shorter than those in sequence databases and/or may have missing residues, seeMotif has two complementary approaches for selecting structures and mapping motifs to protein chains in structures. As more and more structures belonging to previously uncharacterized protein families become available, combining sequence and structure information gives good opportunities to facilitate understanding of protein functions in large-scale genome projects. Available at: http://seemotif.csie. ntu.edu. tw,http://seemotif.ee. ncku.edu. tw or http://seemotif.csbb. ntu.edu. tw.
Cluster analysis of entrepreneurial developing level of Chinese cities

The article selects the 24 cities from the 2007–2008 GEM survey as the research objects. By using “the number of private enterprise or self-employed household per ten thousands persons”, “the proportion of private economy in GDP”, “the entrepreneurial support service conditions”, “the entrepreneurial fundamental support service conditions” and “ the entrepreneurial atmosphere support conditions” as five cluster variables, the article assesses the entrepreneurial developing level of these 24 cities by applying the cluster analysis methodology. The article also analyzes four types of entrepreneurial city features and suggests the ways for the entrepreneurial environment improvement and enhancement.
A High Order Accurate Nodal Discontinuous Galerkin Method (DGM) for Numerical Solution of Hyperbolic Equation

—This paper deals with a high-order accurate Nodal Discontinuous Galerkin (DG) method for the numerical solution of the inviscid Burgers equation, which is a simplest case of nonlinear, hyperbolic partial differential equation. This method combines mainly two key ideas which are based on the finite volume and finite element methods. The physics of wave propagation being accounted for by means of Riemann problems and accuracy is obtained by means of high-order polynomial approximations within elements. In Nodal DG method a finite element space discretization is obtained by element wise discontinuous approximations. Whereas low-storage, high order accurate, explicit Runge-Kutta (LSERK) method is used for temporal discretization. The resulting RKDG methods are stable, high-order accurate and highly parallelizable schemes that can easily handle complicated geometries and boundary conditions. Exponential filter is used to remove spurious oscillations near the shock waves. The and errorsin the solution show that the scheme is accurate and effective. Hence, the method is well suited to achieve high order accurate solution for the hyperbolic partial differential equations.
Design and application of optical nanosensors for pH imaging in cell compartments

VI within a timeframe of up to 24 h in response to any of the investigated PEIs. In relation to these findings we do not reject the “proton sponge” hypothesis, but suggest that the effect is not associated with changes in lysosomal pH. Finally, we investigated the pH profiles of a positively charged nanosensor in six different cell lines as well as the profile of a hyaluronic acid conjugated nanosensor tested in one cell line. After 24 h of incubations all sensors resided in compartments with low pH, recognized as lysosomes in HeLa cells, and responded with an increase in pH to the treatment with Bafilomycin A1. This indicates that all internalized material eventually ends up in the lysosomes, even though the hyaluronic acid conjugated nanosensor showed uptake directed by the CD44 receptor. The initial uptake pathway employed by this nanosensor could potentially be different from the one employed by the positively charged nanosensor. In conclusion, we have developed a triple-labelled pH nanosensor which was shown to be superior to conventional dual-labelled nanosensors with respect to the pH sensitive range. With proper calibration and image analysis we performed pH measurements of lysosomes in different mammalian cells in response to the transfection agent PEI and in relation to different functionalizations.
Searching for a best LAD-solution of an overdetermined system of linear equations motivated by searching for a best LAD-hyperplane on the basis of given data

We consider the problem of searching for a best LAD-solution of an overdetermined system of linear equations Xa = z, X ∈ Rm×n, m ≥ n, a ∈ R, z ∈ R. This problem is equivalent to the problem of determining a best LAD-hyperplane x → a x, x ∈ R on the basis of given data (xi, zi), xi = (x (i) 1 , . , x (i) n ) ∈ R, zi ∈ R, i = 1, . ,m, whereby the minimizing functional is of the form F (a) = ‖z− Xa‖1 = m ∑
Impulse Radio UWB Signal Detection Based on Compressed Sensing

The extremely high sampling rate is a challenge for ultra-wideband (UWB) communication. In this paper, we study the compressed sensing (CS) based impulse radio UWB (IR-UWB) signal detection and propose an IR-UWB signal detection algorithm based on compressive sampling matching pursuit (CoSaMP). The proposed algorithm relies on the fact that UWB received signal is sparse in the time domain. The new algorithm can significantly reduce the sampling rate required by the detection and provides a better performance in case of the low signal-to-noise ratio when comparing with the existing matching pursuit (MP) based detection algorithm. Simulation results demonstrate the effectiveness of the proposed algorithm.
The relationship between the number of synaptic vesicles and the amount of transmitter released

The relationship between the number of synaptic vesicles and the amount of transmitter released from identified synapses was investigated in the dorsal longitudinal flight muscle (DLM) of the temperature- sensitive endocytosis mutant of Drosophila melanogaster, shibirets- 1(shi). In the shi fly at 29 degrees C, vesicle recyling is blocked, but transmitter release proceeds normally. Thus, by inducing transmitter release at 29 degrees C, shi synapses gradually become depleted of synaptic vesicles. In this way it was possible to regulate the number of vesicles in a synapse. Intracellular recordings were made from individual fibers of the DLM in shi flies after various periods at 29 degrees C while stimulating at 0.5 Hz. The amplitude of the evoked excitatory junction potential (ejp), gradually decreased with longer exposure and was brought to various levels. The fiber was then rapidly fixed for electron microscopy. The number of vesicles per synapse was compared with the amplitude of the ejp at the time of fixation. It was observed that the smaller the ejp amplitudes became, the fewer vesicles were in the synapses. Also, as the ejp amplitude decreased, an increased number of synapses contained no vesicles. It is concluded that synaptic vesicles are directly involved in the release process.
Pool and Accuracy Based Stream Classification: A New Ensemble Algorithm on Data Stream Classification Using Recurring Concepts Detection

One of the main challenges of data streams is the occurrence of concept drift. Concept drift is the change of target (or feature) distribution, and can occur in different types: sudden, gradual, incremental or recurring. Because of the forgetting mechanism existing in the data stream learning process, recurring concepts has received much attention recently, and became a challenging problem. This paper tries to exploit the existence of recurring concepts in the learning process and improve the classification of data streams. It uses a pool of concepts to detect the reoccurrence of a concept using two methods: a Bayesian, and a heuristic method. Two approaches are used in the classification process: active classifier and weighted classifier. Experimental results show the effectiveness of the proposed method with respect to the Conceptual Clustering and Prediction (CCP) framework.
Reengineering towards components using "Reconn-exion"

Continuing to develop software from scratch will not be feasible indefinitely. Reusing existing software would seem to be a viable solution to this problem. The paradigm of component-based development (CBD) explicitly accounts for reuse in its process. Unfortunately the majority of existing software systems are not implemented using CBD, thus reusing portions of this software using CBD becomes difficult. Reengineering and maintenance research contains a plethora of software analysis and restructuring techniques that could be used to help us exploit legacy applications for reuse. This thesis focuses on two such techniques and combines variations of them for the purpose of component recovery: A feature location technique called Software Reconnaissance and a design recovery technique called Software Reflexion Modelling. Their combination is called "Component Reconn-exion. " We describe the technique, highlight results and evaluation to date and finally discuss further work necessary to complete our contribution as a PhD. thesis.
Decomposing polygon meshes for interactive applications

This paper discusses an efficient and effective framework to decompose polygon meshes into components. This is useful in various interactive graphics applications, such as, mesh editing, establishing correspondence between objects for morphing, computation of bounding volume hierarchy for collision detection and ray tracing. In this paper, we formalize the notion of a component as a sub-volume of an object with homogeneous geometric and topological features. Next, we describe the proposed framework, which adapts the idea of edge contraction and space sweeping to decompose an object automatically. Finally, we demonstrate an application of this framework to improve bounding volume hierarchies constructed by state-of-theart collision detection systems such as RAPID and QuickCD.
Design and characterization of two-frame all-terrain robot for navigation in unstructured and treacherous environments

Robots designed for navigation use one or more of the three basic locomotion configurations viz rotational devices such as wheels or crawler tracks, legs and articulated bodies. In this paper we present the design and characterization of a hybrid locomotion mechanism for mobile robots navigating in unstructured and possibly treacherous environments. We fuse the advantages offered by the three classes of locomotion to provide for navigation through uneven surfaces. The robot is a single segment, dual chassis, single wheel platform where forward and backward movement is achieved through actuation of links for the chassis. Turning in any direction is achieved by the actuation of a single corrugated disc. The robot can carry nominal payloads for vision based reconnaissance and search and rescue operations. We provide the results and analysis of experiments conducted to validate the maneuverability of this hybrid robot on uneven surfaces. This robot has been tested on smooth, uneven and unstructured terrains as well as underwater.
The Deformed State and Nucleation of Recrystallization

Abstract The phenomenon of nucleation of new grains during annealing of deformed metals is discussed with respect to various aspects of the deformed state, including the stored energy of cold work and various microstructural features. Attention is drawn to those regions of the deformed metal where there is a rapid change of orientation, such as pre-existing grain boundaries and deformation (transition) bands. The currently accepted theory of nucleation, the growth of favoured sub grains, is discussed in the light of the known low mobility of low-angle sub-boundaries. It is suggested that the high boundary mobility associated with misorentations > 10–18° is the origin of pre-existing grain boundaries and transition bands acting as principal sites for nucleation. Recent evidence concerning the initial growth of subgrain ‘nuclei’ is described and it is suggested that subgrain coalescence may often play a crucial role in this process. Subgrain coalscence appears to occur preferentially in those regions of lat.
Effects of sulfasalazine on biopsy mucosal pathologies and histological grading of patients with active ulcerative colitis.

AIM To investigate the mechanisms of sulfasalazine (SASP) in the treatment of ulcerative colitis (UC). METHODS Changes of pathological signs and histological grading of 106 patients with active UC were observed before and after the treatment with SASP, 1 g, thrice daily for 6 wk. RESULTS The effect of SASP on the vasculitis in lamina propria was 48.2% and 17.4% in the mild active UC (P<0.001) and 68% and 26.7% in the moderate active UC (P<0.001) before and after treatment. Fibroid necrosis of vessel wall was found in one case of mild UC and two cases of moderate UC before treatment and was not found after treatment. No thrombosis was found in mild UC before and after treatment, while thrombosis was found in one case of moderate UC before treatment. The effect on mucosal glandular abnormality was 30.4% and 13.0% in mild UC (P<0.05), and 42% and 40% in moderate UC (P>0.05) before and after treatment. The rate of eosinophil infiltration was 98.2% and 80.4% in mild UC (P<0.01), and 100% and 91.1% in moderate UC (P<0.05) before and after treatment. The effect on crypt abscess was 21.4% and 4.4% in mild UC (P<0.05), and 48% and 13.3% in moderate UC (P<0.001) before and after treatment. The effect on mucosal pathohistological grading was 2.00+/-0.84 and 0.91+/-0.46 in mild UC (P<0.001), and 2.49+/-0.84 and 1.31+/-0.75 in moderate UC (P<0.001) before and after treatment. CONCLUSION SASP can improve small vessel lesions and crypt abscesses and reduce neutrophilic and eosinophilic leukocyte infiltration in inflammatory mucosa of UC.
Genetic Screening of Mutations Associated with Fabry Disease in a Nationwide Cohort of Juvenile Idiopathic Arthritis Patients

Fabry’s disease (FD) is a lysosomal storage disorder associated with an alpha-galactosidase A deficiency. The prevalence of FD among juvenile idiopathic arthritis (JIA) patients with established diagnosis is unknown, but as musculoskeletal pain may be an important complaint at presentation, misdiagnosed cases are anticipated. With this study, we aim to calculate the frequency of FD-associated mutations in a cohort of JIA patients. Children with JIA from a national cohort were selected. Clinical and laboratorial information was recorded in the Portuguese rheumatic diseases register (http://Reuma.pt). Molecular genetic testing to detect GLA gene mutations was performed. After the multiplex polymerase chain reactions technique for DNA amplification, direct sequencing of the complete sequence of GLA gene was completed. From a cohort of 292 patients with JIA (188 females, 104 males), mutations were identified in 5 patients (all female). Four patients had the mutation D313Y, a rare GLA variant, which is associated with low enzymatic levels in plasma, but normal lysosomal levels. One patient presented the missense mutation R118C, which was previously described in Mediterranean patients with FD. This is the first screening of FD mutations in a cohort of JIA patients. No “classic” pathogenic FD mutations were reported. The late-onset FD-associated mutation, R118C, was found in a frequency of 0.34% (1/292).