gebhart/patrepeval huggingface dataset:
PHOTODYNAMIC THERAPY OF B16 PIGMENTED MELANOMA WITH LIPOSOME‐DELIVERED Si(IV)‐NAPHTHALOCYANINE (1994)

The possibility of extending photodynamic therapy to the treatment of highly pigmented neoplastic lesions was tested by using Si(IV)-naphthalocyanine (SiNc) as a tumor-localizing agent. Si(IV)-naphthalocyanine displays intense absorbance at 776 nm (epsilon = 5 x 10(5) M-1 cm-1), where melanin absorption becomes weaker. As an experimental model we selected B16 pigmented melanoma subcutaneously transplanted to C57BL mice. Upon injection of 0.5 or 1 mg kg-1 of liposome-incorporated SiNc, maximal accumulation of the photosensitizer in the tumor was observed at 24 h with recoveries of 0.35 and 0.57 microgram g-1, respectively. However, the tumor targeting by SiNc shows essentially no selectivity, since the photosensitizer concentrations in the skin (peritumoral tissue) were very similar to those found in the tumor at all postinjection times examined by us. Irradiation of SiNc-loaded melanoma with 776 nm light from a diode laser at 24 h postinjection induces tumor necrosis and delay of tumor growth. The effect appears to be of purely photochemical nature at dose rates up to 260 mW cm-2; at higher dose rates, thermal effects are likely to become important.
Structural, Kinetic, and Pharmacodynamic Mechanisms of <scp>d</scp>-Amino Acid Oxidase Inhibition by Small Molecules (2013)

We characterized the mechanism and pharmacodynamics of five structurally distinct inhibitors of d-amino acid oxidase. All inhibitors bound the oxidized form of human enzyme with affinity slightly higher than that of benzoate (Kd ≈ 2-4 μM). Stopped-flow experiments showed that pyrrole-based inhibitors possessed high affinity (Kd ≈ 100-200 nM) and slow release kinetics (k < 0.01 s(-1)) in the presence of substrate, while inhibitors with pendent aromatic groups altered conformations of the active site lid, as evidenced by X-ray crystallography, and showed slower kinetics of association. Rigid bioisosteres of benzoic acid induced a closed-lid conformation, had slower release in the presence of substrate, and were more potent than benzoate. Steady-state d-serine concentrations were described in a PK/PD model, and competition for d-serine sites on NMDA receptors was demonstrated in vivo. DAAO inhibition increased the spatiotemporal influence of glial-derived d-serine, suggesting localized effects on neuronal circuits where DAAO can exert a neuromodulatory role.
A practical salient region feature based 3D multi-modality registration method for medical images (2006)

We present a novel representation of 3D <i>salient region features</i> and its integration into a hybrid rigid-body registration framework. We adopt scale, translation and rotation invariance properties of those intrinsic 3D features to estimate a transform between underlying mono- or multi-modal 3D medical images. Our method combines advantageous aspects of both feature- and intensity-based approaches and consists of three steps: an automatic extraction of a set of 3D salient region features on each image, a robust estimation of correspondences and their sub-pixel accurate refinement with outliers elimination. We propose a region-growing based approach for the extraction of 3D salient region features, a solution to the problem of feature clustering and a reduction of the correspondence search space complexity. Results of the developed algorithm are presented for both mono- and multi-modal intra-patient 3D image pairs (CT, PET and SPECT) that have been acquired for change detection, tumor localization, and time based intra-person studies. The accuracy of the method is clinically evaluated by a medical expert with an approach that measures the distance between a set of selected corresponding points consisting of both anatomical and functional structures or lesion sites. This demonstrates the robustness of the proposed method to image overlap, missing information and artefacts. We conclude by discussing potential medical applications and possibilities for integration into a non-rigid registration framework.
Enhanced FIB-SEM systems for large-volume 3D imaging (2017)

Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) can automatically generate 3D images with superior z-axis resolution, yielding data that needs minimal image registration and related post-processing. Obstacles blocking wider adoption of FIB-SEM include slow imaging speed and lack of long-term system stability, which caps the maximum possible acquisition volume. Here, we present techniques that accelerate image acquisition while greatly improving FIB-SEM reliability, allowing the system to operate for months and generating continuously imaged volumes > 10<sup>6</sup> µm<sup>3</sup>. These volumes are large enough for connectomics, where the excellent z resolution can help in tracing of small neuronal processes and accelerate the tedious and time-consuming human proofreading effort. Even higher resolution can be achieved on smaller volumes. We present example data sets from mammalian neural tissue, <i>Drosophila</i> brain, and <i>Chlamydomonas reinhardtii</i> to illustrate the power of this novel high-resolution technique to address questions in both connectomics and cell biology.
Fast and Accurate Point Cloud Registration using Trees of Gaussian Mixtures (2018)

Point cloud registration sits at the core of many important and challenging 3D perception problems including autonomous navigation, SLAM, object/scene recognition, and augmented reality. In this paper, we present a new registration algorithm that is able to achieve state-of-the-art speed and accuracy through its use of a hierarchical Gaussian Mixture Model (GMM) representation. Our method constructs a top-down multi-scale representation of point cloud data by recursively running many small-scale data likelihood segmentations in parallel on a GPU. We leverage the resulting representation using a novel PCA-based optimization criterion that adaptively finds the best scale to perform data association between spatial subsets of point cloud data. Compared to previous Iterative Closest Point and GMM-based techniques, our tree-based point association algorithm performs data association in logarithmic-time while dynamically adjusting the level of detail to best match the complexity and spatial distribution characteristics of local scene geometry. In addition, unlike other GMM methods that restrict covariances to be isotropic, our new PCA-based optimization criterion well-approximates the true MLE solution even when fully anisotropic Gaussian covariances are used. Efficient data association, multi-scale adaptability, and a robust MLE approximation produce an algorithm that is up to an order of magnitude both faster and more accurate than current state-of-the-art on a wide variety of 3D datasets captured from LiDAR to structured light.
High Performance, Continuously Tunable Microwave Filters using MEMS Devices with Very Large, Controlled, Out-of-Plane Actuation (2018)

Software defined radios (SDR) in the microwave X and K bands offer the promise of low cost, programmable operation with real-time frequency agility. However, the real world in which such radios operate requires them to be able to detect nanowatt signals in the vicinity of 100 kW transmitters. This imposes the need for selective RF filters on the front end of the receiver to block the large, out of band RF signals so that the finite dynamic range of the SDR is not overwhelmed and the desired nanowatt signals can be detected and digitally processed. This is currently typically done with a number of narrow band filters that are switched in and out under program control. What is needed is a small, fast, wide tuning range, high Q, low loss filter that can continuously tune over large regions of the microwave spectrum. In this paper we show how extreme throw MEMS actuators can be used to build such filters operating up to 15 GHz and beyond. The key enabling attribute of our MEMS actuators is that they have large, controllable, out-of-plane actuation ranges of a millimeter or more. In a capacitance-post loaded cavity filter geometry, this gives sufficient precisely controllable motion to produce widely tunable devices in the 4-15 GHz regime.
Nucleic Acid-Based Aptamers as Promising Therapeutics in Neoplastic Diseases (2006)

Isolated through combinatorial libraries by an iterative in vitro selection process, small single-stranded nucleic acid compounds, named aptamers, have been developed as high-affinity ligands for a variety of targets, ranging from small chemical compounds to large proteins. In the last years, an increasing number of aptamers has been generated that represent potential antagonists of the disease-associated target proteins. These molecules have been shown to discriminate between even closely related targets, thus representing a valid alternative to antibodies or other biomimetic receptors for the development of biosensors and other bioanalytical methods. Moreover, they can be easily stabilized by chemical modifications for in vivo applications and numerous examples have shown that stabilized aptamers against extracellular targets such as growth factors, receptors, hormones, or coagulation factors are very effective inhibitors of the corresponding protein function, thus resulting as useful reagents for target validation in a variety of diseases, including cancer. Indeed, many signaling proteins involved in diverse functions such as cell growth and differentiation can act as oncogenes and cause cellular transformation, thus making these high affinity ligands promising tools for cancer diagnosis or therapy.
Kidney N-Acetylgalactosamine (GalNAc)-1-phosphate Kinase, a New Pathway of GalNAc Activation (1996)

A new enzyme that phosphorylates GalNAc at position 1 to form GalNAc-alpha-1P was purified approximately 1275-fold from the cytosolic fraction of pig kidney, and the properties of the enzyme were determined. The kinase is quite specific for GalNAc as the phosphate acceptor and is inactive with GlcNAc, ManNAc, glucose, galactose, mannose, GalN, and GlcN. This enzyme is clearly separated from galactokinase by chromatography on phenyl-Sepharose. The GalNAc kinase has a pH optimum between 8.5 and 9.0 and requires a divalent cation in the order Mg2+ > Mn2+ > Co2+, with optimum Mg2+ concentration at approximately 5 mM. The enzyme was most active with ATP as the phosphate donor, but slight activity was observed with ITP, acetyl-P, and phosphoenolpyruvate. Enzyme activity was highest in porcine and human kidney and porcine liver, but was low in most other tissues. Cultured HT-29 cells also had high activity for this kinase. The purified enzyme fraction was incubated with azido-[32P]ATP, exposed to UV light, and run on SDS gels. A 50-kDa protein was labeled, and this labeling showed saturation kinetics with increasing amounts of the probe and was inhibited by unlabeled ATP. Although the most purified GalNAc kinase preparation still had two bands that labeled with ATP, maximum labeling of the 50-kDa protein, but not the 66-kDa band, was coincident with maximum GalNAc kinase activity on a column of DEAE-Cibacron blue. On Sephacryl S-300, the native enzyme has a molecular mass of 48-51 kDa, indicating that the active kinase is a monomer. The product of the reaction was characterized as GalNAc-alpha-1-P by various chemical procedures.
Design of a bridge to randomly access high speed image sensor pixels in embedded systems (2010)

Most commercially available image sensors send image data at high speed and pixel values can only be accessed sequentially. Random access of pixels is not possible because pixel values are sent row-after-row. On the other hand, commercial microcontrollers run at slower speed compared to the high data-rate of the image sensors and many embedded system applications need random access of pixel values. Also, commercial microcontrollers do not have sufficient internal memory to store a complete image. In this paper, the design of a novel bridge is proposed to interface high speed image sensors in low power and low speed embedded systems. By using the proposed bridge, the image processor or microcontroller can capture and store an image in the bridge's internal memory. Then the pixel values can be accessed in random fashion through a parallel memory access interface at any required speed. The bridge can be used in different embedded system applications such as pattern recognition, robotic vision, bio-medical imaging etc. The proposed bridge was modelled in Very-high-speed integrated circuit Hardware Description Language (VHDL) and implemented in Field Programmable Gate Array (FPGA) to verify its correctness. The model was also synthesized in different FPGA devices and result shows that the bridge can support data-rate of image sensors up to 252.1 MHz in Xilinx Vertex 5 FPGA.
Porous clay heterostructures (PCH) as acid catalysts (1997)

Porous clay heterostructures formed by surfactant assembly of open framework silica in the galleries of a smectite clay represent a new family of solid acid catalysts, as evidenced by the selective dehydration of 2-methylbut-3-yn-2-ol to 2-methylbut-3-yn-1-ene.
Chemical Characterization of Aerosol Particles Using On-chip Photonic\n Cavity Enhanced Spectroscopy (2018)

We demonstrate the chemical characterization of aerosol particles with\non-chip spectroscopy using a photonic cavity enhanced silicon nitride (Si3N4)\nracetrack resonator-based sensor. The sensor operates over a broad and\ncontinuous wavelength range, showing cavity enhanced sensitivity at specific\nresonant wavelengths. Analysis of the relative change in the quality factor of\nthe cavity resonances successfully yields the absorption spectrum of the\naerosol particles deposited on the resonators. Detection of N-methyl\naniline-based aerosol detection in the Near InfraRed (NIR) range of 1500 nm to\n1600 nm is demonstrated. Our aerosol sensor spectral data compares favorably\nwith that from a commercial spectrometer, indicating good accuracy. The small\nsize of the device is advantageous in remote, environmental, medical and\nbody-wearable sensing applications.\n
Quantitative Hepatitis B Core Antibody Level Is a New Predictor for Treatment Response In HBeAg-positive Chronic Hepatitis B Patients Receiving Peginterferon (2014)

A recent study revealed that quantitative hepatitis B core antibody (qAnti-HBc) level could serve as a novel marker for predicting treatment response. In the present study, we further investigated the predictive value of qAnti-HBc level in HBeAg-positive patients undergoing PEG-IFN therapy. A total of 140 HBeAg-positive patients who underwent PEG-IFN therapy for 48 weeks and follow-up for 24 weeks were enrolled in this study. Serum samples were taken every 12 weeks post-treatment. The predictive value of the baseline qAnti-HBc level for treatment response was evaluated. Patients were further divided into 2 groups according to the baseline qAnti-HBc level, and the response rate was compared. Additionally, the kinetics of the virological and biochemical parameters were analyzed. Patients who achieved response had a significantly higher baseline qAnti-HBc level (serological response [SR], 4.52±0.36 vs. 4.19±0.58, p=0.001; virological response [VR], 4.53±0.35 vs. 4.22±0.57, p=0.005; combined response [CR], 4.50±0.36 vs. 4.22±0.58, p=0.009)). Baseline qAnti-HBc was the only parameter that was independently correlated with SR (p=0.008), VR (p=0.010) and CR(p=0.019). Patients with baseline qAnti-HBc levels ≥30,000 IU/mL had significantly higher response rates, more HBV DNA suppression, and better hepatitis control in PEG-IFN treatment. In conclusion, qAnti-HBc level may be a novel biomarker for predicting treatment response in HBeAg-positive patients receiving PEG-IFN therapy.
Evaluating the Ligand Specificity of Zebrafish Parathyroid Hormone (PTH) Receptors: Comparison of PTH, PTH-Related Protein, and Tuberoinfundibular Peptide of 39 Residues (2000)

Homologs of mammalian PTH1 and PTH2 receptors, and a novel PTH3 receptor have been identified in zebrafish (zPTH1, zPTH2, and zPTH3). zPTH1 receptor ligand specificity is similar to that of mammalian PTH1 receptors. The zPTH2 receptor is selective for PTH over PTH-related protein (PTHrP); however, PTH produces only modest cAMP accumulation. A PTH2 receptor-selective peptide, tuberoinfundibular peptide of 39 residues (TIP39), has recently been purified from bovine hypothalamus. The effect of TIP39 has not previously been examined on zebrafish receptors. The zPTH3 receptor was initially described as PTHrP selective based on comparison with the effects of human PTH. We have now examined the ligand specificity of the zebrafish PTH-recognizing receptors expressed in COS-7 cells using a wide range of ligands. TIP39 is a potent agonist for stimulation of cAMP accumulation at two putative splice variants of the zPTH2 receptor (EC50, 2.6 and 5.2 nM); in comparison, PTH is a partial agonist [maximal effect (Emax) of PTH peptides ranges from 28-49% of the TIP39 Emax]. As TIP39 is much more efficacious than any known PTH-like peptide, a homolog of TIP39 may be the zPTH2 receptor's endogenous ligand. At the zPTH3 receptor, rat PTH-(1-34) and rat PTH-(1-84) (EC50, 0.22 and 0.45 nM) are more potent than PTHrP (EC50, 1.5 nM), and rPTH-(1-34) binds with high affinity (3.2 nM). PTH has not been isolated from fish. PTHrP-like peptides, which have been identified in fish, may be the natural ligands for zPTH1 and zPTH3 receptors.
Lithium- ( F 2 + ) <sub>A</sub> centers in additively colored Kl crystals (1986)

We report the first successful production of ( F 2 + ) A centers in additively colored K:Li crystals. This material now offers the possibility of obtaining a stable laser medium which can be tuned from 2.4 to 4.0 μm. Unlike the electron-beam colored material used in the previously reported KI:Li laser,1 this material will enhance the utility of the laser since it can be easily colored using an enclosed-bomb technique and can be stored indefinitely near room temperature.
Nonlinear Interferometric Vibrational Imaging (2007)

When utilizing broadband, short pulses to stimulate Coherent Anti-Stokes Raman Scattering (CARS), frequently the peak power is sufficient to excite other nonlinear, nonresonant processes in the material. These processes produce a fourwave-mixing component in the same frequency band as the CARS signal, so that the two signal types cannot be distinguished on the basis of frequency band alone. Typically in biological materials, the nonresonant component produced by the bulk medium can overwhelm the CARS signals produced by the usually much lower concentration target molecular species. Resonant processes can be distinguished from nonresonant processes in that molecular vibrations and rotations typically last longer than a picosecond, while nonresonant processes are not persistent and last shorter than 10 fs. Interferometry allows the arrival time of the signal to be determined to extremely high accuracy, limited by the bandwidth of the reference pulse. Because resonances are persistent, they can produce anti-Stokes radiation that persists after the nonresonant excitation is produced. Interferometry can distinguish the later arrival of the anti-Stokes radiation and therefore distinguish the resonant and nonresonant signals. More complicated pulse-shaping and interferometry schemes can allow additional flexibility to allow simultaneous sampling of the Raman spectrum while rejecting the nonresonant component. This technique enables an entire region of the Raman spectrum of a sample to be measured with a single brief broadband pulse.
Phase Shading for Light Load Efficiency Improve in Three-Phase Resonant Converter with Integrated PCB Winding Magnetics (2019)

Three-phase resonant converter has attracted a lot of attention due to its ability to reduce current stress on the device, achieve automatic current balancing among each phase and realize good interleaving. However, its light load efficiency is not good due to the excessive switching loss, driving loss and core loss. In this paper, based on an integrated PCB winding magnetic structure, phase shading operation for three-phase resonant converter is analyzed. By shutting down one phase, the three-phase half-bridge structure changes to single-phase full-bridge structure, which helps improve the light load efficiency. In addition, the resonant tank becomes simple and simplified optimal trajectory control can be implemented for burst mode operation to further increase the efficiency. A 12.5 kW bidirectional three-phase CLLC resonant converter with 500 kHz operation frequency is developed to verify the above analysis and the result shows more than 1% efficiency improvement under light load condition.
5-Benzylidene-4-oxazolidinones potently inhibit biofilm formation in Methicillin-resistant Staphylococcus aureus (2017)

Investigation into the biological function of 5-benzylidene-4-oxazolidinones revealed dose-dependent inhibition of biofilm formation in Methicillin-resistant S. aureus (MRSA). This structurally unusual class of small molecules inhibit up to 89% of biofilm formation with IC<sub>50</sub> values as low as 0.78 μM, and disperse pre-formed biofilms with IC<sub>50</sub> values as low as 4.7 μM. Together, these results suggest that 4-oxazolidinones represent new chemotypes to enable the study of bacterial biofilms with small molecule chemical probes.
Cardiac AAV9-S100A1 Gene Therapy Rescues Post-Ischemic Heart Failure in a Preclinical Large Animal Model (2011)

As a prerequisite for clinical application, we determined the long-term therapeutic effectiveness and safety of adeno-associated virus (AAV)-S100A1 gene therapy in a preclinical large animal model of heart failure. S100A1, a positive inotropic regulator of myocardial contractility, becomes depleted in failing cardiomyocytes in humans and animals, and myocardial-targeted S100A1 gene transfer rescues cardiac contractile function by restoring sarcoplasmic reticulum calcium (Ca(2+)) handling in acutely and chronically failing hearts in small animal models. We induced heart failure in domestic pigs by balloon occlusion of the left circumflex coronary artery, resulting in myocardial infarction. After 2 weeks, when the pigs displayed significant left ventricular contractile dysfunction, we administered, by retrograde coronary venous delivery, AAV serotype 9 (AAV9)-S100A1 to the left ventricular, non-infarcted myocardium. AAV9-luciferase and saline treatment served as control. At 14 weeks, both control groups showed significantly decreased myocardial S100A1 protein expression along with progressive deterioration of cardiac performance and left ventricular remodeling. AAV9-S100A1 treatment prevented and reversed these functional and structural changes by restoring cardiac S100A1 protein levels. S100A1 treatment normalized cardiomyocyte Ca(2+) cycling, sarcoplasmic reticulum calcium handling, and energy homeostasis. Transgene expression was restricted to cardiac tissue, and extracardiac organ function was uncompromised. This translational study shows the preclinical feasibility of long-term therapeutic effectiveness of and a favorable safety profile for cardiac AAV9-S100A1 gene therapy in a preclinical model of heart failure. Our results present a strong rationale for a clinical trial of S100A1 gene therapy for human heart failure that could potentially complement current strategies to treat end-stage heart failure.