gebhart/patrepeval huggingface dataset:
A min-max framework of cascaded classifier with multiple instance learning for computer aided diagnosis (2009)

The computer aided diagnosis (CAD) problems of detecting potentially diseased structures from medical images are typically distinguished by the following challenging characteristics: extremely unbalanced data between negative and positive classes; stringent real-time requirement of online execution; multiple positive candidates generated for the same malignant structure that are highly correlated and spatially close to each other. To address all these problems, we propose a novel learning formulation to combine cascade classification and multiple instance learning (MIL) in a unified min-max framework, leading to a joint optimization problem which can be converted to a tractable quadratically constrained quadratic program and efficiently solved by block-coordinate optimization algorithms. We apply the proposed approach to the CAD problems of detecting pulmonary embolism and colon cancer from computed tomography images. Experimental results show that our approach significantly reduces the computational cost while yielding comparable detection accuracy to the current state-of-the-art MIL or cascaded classifiers. Although not specifically designed for balanced MIL problems, the proposed method achieves superior performance on balanced MIL benchmark data such as MUSK and image data sets.
Proprioception of the Ankle: A Comparison Between Female Teenaged Gymnasts and Controls (2002)

Proprioceptive mechanisms appear to play a role in stabilizing the joints and may serve as a means for interplay between static stabilizers and dynamic muscular restraints. The purpose of our study was to investigate whether or not gymnastic training has any effect on the balance and on proprioception in an ankle, as seen in gymnasts and in nongymnasts. We evaluated the proprioceptive ability of the ankle using four different tests (a one-leg-standing test, a single-limb-hopping test, an active angle-reproduction test, and a passive angle-reproduction test). Proprioception of the ankle was measured in 40 subjects who were assigned to two experimental groups. Group 1 (n: 20) were healthy control subjects, and group 2 (n: 20) were teenaged female gymnasts. The sense of position of a joint was actively measured using a Cybex NORMTM isokinetic dynamometer and measured passively with a proprioception-testing device. A Mann-Whitney U test was used to compare mean values of the gymnasts to the controls. Results revealed statistically significant differences (p&lt;0.05) between two groups. We found no statistically significant differences between the dominant and nondominant ankle in volunteers or in gymnasts, in all tests. The results of this study suggest that gymnastic training has a positive influence on sense of position of the ankle joint and on balance, in addition to increasing muscle tone.
Protection against 17D yellow fever encephalitis in mice by passive transfer of monoclonal antibodies to the nonstructural glycoprotein gp48 and by active immunization with gp48. (1985)

The protective capacity of antiviral antibodies has generally been considered to depend on their interactions with structural components of the virion. Here we report protection against lethal 17D yellow fever virus (YF) encephalitis of mice by passive administration of nonneutralizing monoclonal antibodies to a 17D YF-specified nonstructural glycoprotein, gp48, and by active immunization with purified gp48. Among five anti-gp48 monoclonal antibodies tested, two with high titer complement-fixing (CF) activity were protective, whereas three antibodies with little or no CF activity were not. The ability of antibodies to protect correlated with their ability to promote complement-mediated cytolysis (CMC) of 51Cr-labeled 17D YF-infected mouse neuroblastoma (Neuro 2a) cells. Purified gp48, prepared from lysates of 17D YF-infected Vero cells by immunoaffinity chromatography, was shown to bear both YF type-specific and flavivirus group-reactive determinants in a solid phase radioimmunoassay. Immunization of mice with purified gp48 resulted in solid protection in the absence of detectable anti-virion antibody, measured by neutralization and radioimmunoprecipitation assays. The results are consistent with plasma membrane expression of gp48 and susceptibility of 17D YF-infected neural cells to CMC, a possible mechanism of host defense in 17D YF encephalitis. Protection provided by immunization with gp48, which bears a group-reactive determinant and is highly conserved among flaviviruses, may have implications in regard to flavivirus vaccine design.
On optimal, minimal BRDF sampling for reflectance acquisition (2015)

The bidirectional reflectance distribution function (BRDF) is critical for rendering, and accurate material representation requires data-driven reflectance models. However, isotropic BRDFs are 3D functions, and measuring the reflectance of a flat sample can require a million incident and outgoing direction pairs, making the use of measured BRDFs impractical. In this paper, we address the problem of reconstructing a measured BRDF from a limited number of samples. We present a novel mapping of the BRDF space, allowing for extraction of descriptive principal components from measured databases, such as the MERL BRDF database. We optimize for the best sampling directions, and explicitly provide the optimal set of incident and outgoing directions in the Rusinkiewicz parameterization for n = {1, 2, 5, 10, 20} samples. Based on the principal components, we describe a method for accurately reconstructing BRDF data from these limited sets of samples. We validate our results on the MERL BRDF database, including favorable comparisons to previous sets of industry-standard sampling directions, as well as with BRDF measurements of new flat material samples acquired with a gantry system. As an extension, we also demonstrate how this method can be used to find optimal sampling directions when imaging a sphere of a homogeneous material; in this case, only two images are often adequate for high accuracy.
Compensating for visco‐acoustic effects in reverse‐time migration (2010)

Anelastic properties of the earth cause frequency dependent energy attenuation and phase distortion in seismic wave propagation. These unwanted effects are preferred to be corrected in a prestack depth migration. Based on the dispersion relation under a linear attenuation assumption, we derive a visco‐acoustic wave equation in the time domain and apply it in a prestack reverse time migration to compensate for the anelastic effects in the seismic data. The equation is defined by a pseudo‐differential operator, and the energy increases with frequencies when back propagating the seismic data in migration. Using a regularization process, we show that our method provides stable and amplitude balanced reverse time migration images.
An optimal filter for short photoplethysmogram signals (2018)

A photoplethysmogram (PPG) contains a wealth of cardiovascular system information, and with the development of wearable technology, it has become the basic technique for evaluating cardiovascular health and detecting diseases. However, due to the varying environments in which wearable devices are used and, consequently, their varying susceptibility to noise interference, effective processing of PPG signals is challenging. Thus, the aim of this study was to determine the optimal filter and filter order to be used for PPG signal processing to make the systolic and diastolic waves more salient in the filtered PPG signal using the skewness quality index. Nine types of filters with 10 different orders were used to filter 219 (2.1s) short PPG signals. The signals were divided into three categories by PPG experts according to their noise levels: excellent, acceptable, or unfit. Results show that the Chebyshev II filter can improve the PPG signal quality more effectively than other types of filters and that the optimal order for the Chebyshev II filter is the 4<sup>th</sup> order.
Rac-1 Regulates Nuclear Factor of Activated T Cells (NFAT) C1 Nuclear Translocation in Response to Fcε Receptor Type 1 Stimulation of Mast Cells (1998)

Transcription factors of the nuclear factor of activated T cells (NFAT) family play a key role in antigen receptor-mediated responses in lymphocytes by controlling induction of a wide variety of cytokine genes. The GTPases Ras and Rac-1 have essential functions in regulation of NFAT transcriptional activity in the mast cell system, where Fcepsilon receptor type 1 (FcepsilonR1) ligation results in induction of multiple NFAT target genes. This report examines the precise biochemical basis for the Rac-1 dependency of FcepsilonR1 activation of NFAT in mast cells. We are able to place Rac-1 in two positions in the signaling network that regulates the assembly and activation of NFAT transcriptional complexes in lymphocytes. First, we show that activity of Rac-1 is required for FcepsilonR1-mediated NFATC1 dephosphorylation and nuclear import. Regulation of NFAT localization by the FcepsilonR1 is a Rac-dependent but Ras-independent process. This novel signaling role for Rac-1 is distinct from its established regulation of the actin cytoskeleton. Our data also reveal a second GTPase signaling pathway regulating NFAT transcriptional activity, in which Rac-1 mediates a Ras signal. These data illustrate that the GTPase Rac-1 should now be considered as a component of the therapeutically important pathways controlling NFATC1 subcellular localization. They also reveal that GTPases may serve multiple functions in cellular responses to antigen receptor ligation.
Arthroscopic Second-Generation Autologous Chondrocyte Implantation Compared with Microfracture for Chondral Lesions of the Knee (2008)

Both methods have shown satisfactory clinical outcome at medium-term follow-up. Better clinical results and sport activity resumption were noted in the group treated with second-generation autologous chondrocyte transplantation.
Single crystalline ZnO films grown on lattice-matched ScAlMgO4(0001) substrates (1999)

Lattice-matched (Δa/a=0.09%) ScAlMgO4(0001) substrates were employed to grow single crystalline quality ZnO films by laser molecular-beam epitaxy. Extremely smooth surface represented by atomically flat terraces and half unit cell (0.26 nm) high steps and extremely small orientation fluctuations both in-plane (&amp;lt;0.02°) and out-of-plane (&amp;lt;0.01°) are achieved. The films have high mobility (∼100 cm2/V s) together with low residual carrier concentration (∼1015 cm−3). Excellent optical properties, including a clear doublet of A and B exciton peaks in absorption spectra, were also observed. These features could not be simultaneously achieved for ZnO films grown on sapphire(0001) having a large lattice mismatch (Δa/a=18%).
Laminins: Structure and genetic regulation (2000)

The laminins form a large family of modular proteins found in basement membranes, but also elsewhere. They function as structural components and are essential for morphogenesis, but in addition interact with cell surface receptors such as integrins and alpha-dystroglycan. By virtue of their receptor interactions, they initiate intracellular signalling events that regulate cellular organization and differentiation. The many interactions of laminins are mediated by binding sites, often contributed by single domains, which may differ between different forms of laminin. In the present article, we describe how the diversity of laminins and the genetic regulation of the expression of different laminin forms lead to the formation of extracellular matrices with variable laminin composition and thereby different biological properties.
Quantification of the Adenylate Cyclase Toxin of Bordetella pertussisIn Vitroand during Respiratory Infection (2013)

Whooping cough results from infection of the respiratory tract with Bordetella pertussis, and the secreted adenylate cyclase toxin (ACT) is essential for the bacterium to establish infection. Despite extensive study of the mechanism of ACT cytotoxicity and its effects over a range of concentrations in vitro, ACT has not been observed or quantified in vivo, and thus the concentration of ACT at the site of infection is unknown. The recently developed baboon model of infection mimics the prolonged cough and transmissibility of pertussis, and we hypothesized that measurement of ACT in nasopharyngeal washes (NPW) from baboons, combined with human and in vitro data, would provide an estimate of the ACT concentration in the airway during infection. NPW contained up to ≈ 10(8) CFU/ml B. pertussis and 1 to 5 ng/ml ACT at the peak of infection. Nasal aspirate specimens from two human infants with pertussis contained bacterial concentrations similar to those in the baboons, with 12 to 20 ng/ml ACT. When ≈ 10(8) CFU/ml of a laboratory strain of B. pertussis was cultured in vitro, ACT production was detected in 60 min and reached a plateau of ≈ 60 ng/ml in 6 h. Furthermore, when bacteria were brought into close proximity to target cells by centrifugation, intoxication was increased 4-fold. Collectively, these data suggest that at the bacterium-target cell interface during infection of the respiratory tract, the concentration of ACT can exceed 100 ng/ml, providing a reference point for future studies of ACT and pertussis pathogenesis.
Development of phosphonate derivatives of gadolinium chelates for NMR imaging of calcified soft tissues (1989)

We have synthesized several classes of gadolinium (Gd) complexes for use as NMR contrast agents in the detection of soft-tissue calcification. Class I was made up of strongly chelated GdDTPA complexes with one carboxylate arm coupled to a phosphonate-containing molecule through an amide link. Class II complexes were formed by Gd with several aminophosphonates and phosphono carboxylic acids. Class III were Gd complexes of weak chelates containing no phosphonate. The calcium-seeking ability of each complex was assessed by in vivo bone uptake. Tissue distribution in normal rats showed that only the complexes of GdDTPA modified with a diphosphonate group and GdEDTMP (EDTMP is ethylenediaminetetrakis(methylenephosponate] showed adequate bone localization at the concentrations required for NMR contrast enhancement (approximately 20% of a 100 mumol/kg dose).
Rotor Axial Vibration Caused by Gear Coupling (1985)

This paper deals with an axial vibration of a horizontal rotor which is driven through a single craw type gear coupling under no load operating conditions. The effects of coupling misalignment on the vibration are experimentally investigated. Under good alignment conditions, remarkable axial vibrations with large amplitude and long period (in some cases 3mm in amplitude and 3sec. in period) were observed in certain narrow speed ranges. The period, which almost coincides with that of beat of the torsional vibration of a rotor, becomes larger with an increase in amplitude. When a large angular misalignment exists, the rotor axial vibration is not likely to occur. In order to illustrate the mechanisms of the axial vibration, three models are proposed on the basis of experimental results.
Long codes for generalized FH-OFDMA through unknown multipath channels (2001)

A generalized frequency-hopping (GFH) orthogonal frequency-division multiple-access (OFDMA) system is developed in this paper as a structured long code direct-sequence code-division multiple-access (DS-CDMA) system in order to bridge frequency-hopped multicarrier transmissions with long code DS-CDMA. Through judicious code design, multiuser interference is eliminated deterministically in the presence of unknown frequency-selective multipath channels. Thanks to frequency-hopping, no single user suffers from consistent fading effects and constellation-irrespective channel identifiability is guaranteed regardless of channel nulls. A host of blind channel estimation algorithms are developed trading off complexity with performance. Two important variants, corresponding to slow- and fast-hopping, are also addressed with the latter offering symbol recovery guarantees. Performance analysis and simulation results illustrate the merits of GFH-OFDMA relative to conventional OFDMA and long code DS-CDMA with pseudorandom noise codes and RAKE reception.
Self-quenching Mechanism: the Influence of Quencher and Spacer on Quencher-fluorescein Probes (2007)

Fluorescent chemosensors provide an extremely sensitive optical method for the real-time monitoring of molecular recognition events. An understanding of the fluorescent on/ off mechanism is essential for the rational design of fluorescent chemosensors. The majority of fluorescent chemosensors working in aqueous media operate by one of three mechanisms: (1) the suppression of photoinduced electron transfer (PET); (2) alteration of the microenvironment of a solvatochromic fluorophore; and (3) modulation of the fluorescence resonance energy transfer (FRET) between two fluorophores. The first two mechanisms are suitable for small molecule sensing (e.g., cations, small organic compounds, etc.), but FRET is very useful in the biopolymer state, for its distance information can be obtained in the 10 to 100 A region. In spite of the excellent applications of FRET for biomolecule sensing (c-AMP, insulin, etc.), the operations depend on a complicated biological pathway. Peptides with an FRET pair have been used as monitoring probes for a given enzyme activity. However, in various fluorophore pairs that have been examined, FRET peptide probes did not operate properly i.e., they were self-quenched. This self-quenching can be explained in terms of an intramolecular ground-state dimer complex between the FRET fluorophore pair in an aqueous solution. The strength of the aggregation between the two dye molecules depends on the molecular structure, solvent, temperature, and the presence or absence of electrolytes. Our aim is to systematically study the self-quenching mechanism for covalently linked fluorophore pairs. For simplicity, the factors influencing the efficiency of selfquenching are disassembled into four components (Figure 1). A FRET pair was replaced by a quencher-fluorophore pair as the reporting group. This overcomes the restriction for the FRET donor-acceptor resonance condition. From a practical viewpoint, water and fluorescein were chosen as the solvent and fluorophore, respectively; water is a crucial solvent for physiological systems; furthermore, fluorescein has a high fluorescence quantum yield in aqueous solution and its synthetic handling has been well established. As the quencher part, carbazole, methyl red and 1,8naphthalimide were selected. The effect of the spacer can be controlled by varying the alkyl chain length (-(CH2)n-, n = 5, 11, 15) and a flexible tetraethylene glycol unit (Figure 2). At pH 7.5 (50 mM HEPES buffer, I = 0.1 (NaNO3)), the fluorescence emission of C-n (n = 5, 11, 15) and C-TE ([probes] = 1 μM) was measured (Figure 3). It has been reported that there are two opposing factors determining the stability of aggregates of the derivatives containing two Rose Bengal moieties: the longer the chain, the easier it is to
Large-scale silicon nitride nanophotonic phased arrays at infrared and visible wavelengths (2016)

We demonstrate passive large-scale nanophotonic phased arrays in a CMOS-compatible silicon photonic platform. Silicon nitride waveguides are used to allow for higher input power and lower phase variation compared to a silicon-based distribution network. A phased array at an infrared wavelength of 1550 nm is demonstrated with an ultra-large aperture size of 4 mm×4 mm, achieving a record small and near diffraction-limited spot size of 0.021°×0.021° with a side lobe suppression of 10 dB. A main beam power of 400 mW is observed. Using the same silicon nitride platform and phased array architecture, we also demonstrate, to the best of our knowledge, the first large-aperture visible nanophotonic phased array at 635 nm with an aperture size of 0.5 mm×0.5 mm and a spot size of 0.064°×0.074°.
FMR Measurements of Magnetic Nanostructures (2013)

Ferromagnetic nanowires showed solitary and tunable magnetization properties due to their inherent shape anisotropy. The fabrication of such nanowires in polycarbonate track-etched and anodic alumina membranes have been widely studied during the last 15 years [1-2]. Their potential applications might be explored in spintronic devices and more specifically in magnetic random access memory (MRAM) and magnetic logic devices [3-5]. Furthermore, microwave devices, such as circulators or filters for wireless communication and automotive systems can be fabricated on ferromagnetic nanowires embedded in AAO substrates [6-9].
Insect Cells Encode a Class II α-Mannosidase with Unique Properties (2001)

Previously, we cloned and characterized an insect (Sf9) cell cDNA encoding a class II alpha-mannosidase with amino acid sequence and biochemical similarities to mammalian Golgi alpha-mannosidase II. Since then, it has been demonstrated that other mammalian class II alpha-mannosidases can participate in N-glycan processing. Thus, the present study was performed to evaluate the catalytic properties of the Sf9 class II alpha-mannosidase and to more clearly determine its relationship to mammalian Golgi alpha-mannosidase II. The results showed that the Sf9 enzyme is cobalt-dependent and can hydrolyze Man(5)GlcNAc(2) to Man(3)GlcNAc(2), but it cannot hydrolyze GlcNAcMan(5)GlcNAc(2). These data establish that the Sf9 enzyme is distinct from Golgi alpha-mannosidase II. This enzyme is not a lysosomal alpha-mannosidase because it is not active at acidic pH and it is localized in the Golgi apparatus. In fact, its sensitivity to swainsonine distinguishes the Sf9 enzyme from all other known mammalian class II alpha-mannosidases that can hydrolyze Man(5)GlcNAc(2). Based on these properties, we designated this enzyme Sf9 alpha-mannosidase III and concluded that it probably provides an alternate N-glycan processing pathway in Sf9 cells.
The Chemical Synthesis of Relaxin and Related Peptides (2009)

Successful methods for the chemical assembly of insulin-like peptides allow the detailed study of their structure and function relationships. However, the two-chain, three-disulfide bond structure of this family of peptides, which includes relaxin, has long represented a significant challenge with respect to their chemical synthesis. Early efforts involved the random combination of the two synthetic S-reduced chains under oxidizing conditions to spontaneously form the three disulfide bonds. Such an approach, while generally effective for native sequences, is critically dependent upon the presence of intact secondary structures within the individual chains which guide the subsequent folding and oxidation pathway. This limitation prevents the use of this approach for the preparation of analogs in which these secondary elements are either absent or modified. Nowadays, the use of highly efficient solid-phase peptide synthesis methodologies together with selective S-thiol-protecting groups allows the acquisition of individual chains that can be combined by effective sequential chemically directed formation of each of the three disulfide bonds. These approaches have allowed the high-yield assembly of an array of insulin-like peptides which, in turn, has provided considerable and valuable structural and biological information.