gebhart/patrepeval huggingface dataset:
Coherent array imaging using phased subarrays. Part II: simulations and experimental results (2005)

The basic principles and theory of phased subarray (PSA) imaging imaging provides the flexibility of reducing the number of front-end hardware channels between that of classical synthetic aperture (CSA) imaging--which uses only one element per firing event--and full-phased array (FPA) imaging-which uses all elements for each firing. The performance of PSA generally ranges between that obtained by CSA and FPA using the same array, and depends on the amount of hardware complexity reduction. For the work described in this paper, we performed FPA, CSA, and PSA imaging of a resolution phantom using both simulated and experimental data from a 3-MHz, 3.2-cm, 128-element capacitive micromachined ultrasound transducer (CMUT) array. The simulated system point responses in the spatial and frequency domains are presented as a means of studying the effects of signal bandwidth, reconstruction filter size, and subsampling rate on the PSA system performance. The PSA and FPA sector-scanned images were reconstructed using the wideband experimental data with 80% fractional bandwidth, with seven 32-element subarrays used for PSA imaging. The measurements on the experimental sector images indicate that, at the transmit focal zone, the PSA method provides a 10% improvement in the 6-dB lateral resolution, and the axial point resolution of PSA imaging is identical to that of FPA imaging. The signal-to-noise ratio (SNR) of PSA image was 58.3 dB, 4.9 dB below that of the FPA image, and the contrast-to-noise ratio (CNR) is reduced by 10%. The simulated and experimental test results presented in this paper validate theoretical expectations and illustrate the flexibility of PSA imaging as a way to exchange SNR and frame rate for simplified front-end hardware.
Increasing quantitation in spatial single-cell metabolomics by using fluorescence as ground truth (2022)

Imaging mass spectrometry (MS) is becoming increasingly applied for single-cell analyses. Multiple methods for imaging MS-based single-cell metabolomics were proposed, including our recent method SpaceM. An important step in imaging MS-based single-cell metabolomics is the assignment of MS intensities from individual pixels to single cells. In this process, referred to as pixel-cell deconvolution, the MS intensities of regions sampled by the imaging MS laser are assigned to the segmented single cells. The complexity of the contributions from multiple cells and the background, as well as lack of full understanding of how input from molecularly-heterogeneous areas translates into mass spectrometry intensities make the cell-pixel deconvolution a challenging problem. Here, we propose a novel approach to evaluate pixel-cell deconvolution methods by using a molecule detectable both by mass spectrometry and fluorescent microscopy, namely fluorescein diacetate (FDA). FDA is a cell-permeable small molecule that becomes fluorescent after internalisation in the cell and subsequent cleavage of the acetate groups. Intracellular fluorescein can be easily imaged using fluorescence microscopy. Additionally, it is detectable by matrix-assisted laser desorption/ionisation (MALDI) imaging MS. The key idea of our approach is to use the fluorescent levels of fluorescein as the ground truth to evaluate the impact of using various pixel-cell deconvolution methods onto single-cell fluorescein intensities obtained by the SpaceM method. Following this approach, we evaluated multiple pixel-cell deconvolution methods, the 'weighted average' method originally proposed in the SpaceM method as well as the novel 'linear inverse modelling' method. Despite the potential of the latter method in resolving contributions from individual cells, this method was outperformed by the weighted average approach. Using the ground truth approach, we demonstrate the extent of the ion suppression effect which considerably worsens the pixel-cell deconvolution quality. For compensating the ion suppression individually for each analyte, we propose a novel data-driven approach. We show that compensating the ion suppression effect in a single-cell metabolomics dataset of co-cultured HeLa and NIH3T3 cells considerably improved the separation between both cell types. Finally, using the same ground truth, we evaluate the impact of drop-outs in the measurements and discuss the optimal filtering parameters of SpaceM processing steps before pixel-cell deconvolution.
Cloning of NruI and Sbo13I restriction and modification sstems in E. coli and amino acid sequence comparison of M.NruI and M.Sbo13I with other amino-methyltransferases (2010)

The order of the conserved amino acid motifs (blocks) in M.NruI/M.Sbo13I is similar to the gamma. group amino-methyltranferases, but with two distinct features: In motif IV, the sequence is DPPY instead of NPPY; there are two additional conserved motifs, IVa and Xa as extension of motifs IV and X, in this family of enzymes. We propose that M.NruI and M.Sbo13I form a subgroup in the gamma group of amino-methyltransferases.
A selective N-type calcium channel antagonist protects against neuronal loss after global cerebral ischemia. (1993)

Calcium influx is believed to play a critical role in the cascade of biochemical events leading to neuronal cell death in a variety of pathological settings, including cerebral ischemia. The synthetic omega-conotoxin peptide SNX-111, which selectively blocks depolarization-induced calcium fluxes through neuronal N-type voltage-sensitive calcium channels, protected the pyramidal neurons in the CA1 subfield of the hippocampus from damage caused by transient forebrain ischemia in the rat model of four-vessel occlusion. SNX-111 provided neuroprotection when a single bolus injection was administered intravenously up to 24 hr after the ischemic insult. These results suggest that the window of opportunity for therapeutic intervention after cerebral ischemia may be much longer than previously thought and point to the potential use of omega-conopeptides and their derivatives in the prevention or reduction of neuronal damage resulting from ischemic episodes due to cardiac arrest, head trauma, or stroke. Microdialysis studies showed that SNX-111 was 3 orders of magnitude less potent in blocking potassium-induced glutamate release in the hippocampus than the conopeptide SNX-230, which, in contrast to SNX-111, failed to show any efficacy in the four-vessel occlusion model of ischemia. These results imply that the ability of a conopeptide to block excitatory amino acid release does not correlate with its neuroprotective efficacy.
Cephalosporin formation by cell-free extracts from Streptomyces clavuligerus. (1982)

Cell-free extracts of Streptomyces clavuligerus convert delta-L-(alpha-aminoadipyl)-L-cysteinyl-D-valine (ACV) into an antibiotic product which is 30 approximately 50% penicillinase-insensitive. Thin-layer chromatography resolves this antibiotic product into one major penicillinase-sensitive component and one major and one minor penicillinase-resistant component. The major and minor penicillinase-resistant antibiotics co-chromatograph with deacetoxycephalosporin C and deacetylcephalosporin C, respectively. Ring expansion of a penicillin intermediate, as evidenced by the production of penicillinase-resistant antibiotic, shows an absolute requirement for alpha-ketoglutarate, while ATP, K+ and Mg2+ have lesser effects. Ring expansion activity is not sedimented by high speed centrifugation and is unaffected by membrane-disrupting treatments. Penicillin N and ACV (presumably via penicillin N) are the only substrates so far accepted by the ring expanding enzyme. New syntheses of penicillin N and isopenicillin N are described.
A New Strategy of Transforming Pharmaceutical Crystal Forms (2011)

The robust nature of network materials allows them to (for example) respond to external stimuli such as pressure, temperature, light, or gas/solvent adsorption and desorption. There is difficulty in retaining long-range order in purely molecular organic solids, due to weak intermolecular interactions such as van der Waals forces. Here, we show gas-induced transformations of the well-known pharmaceuticals clarithromycin and lansoprazole. For clarithromycin, the stimulus is capable of converting the kinetic solvate and guest-free crystal forms to the commercial thermodynamically stable polymorph with a huge saving in energy cost relative to industrially employed methods. The synthesis of the marketing form of lansoprazole involves a solvate that readily decomposes and that is stirred in water, filtered, and dried intensively. Our method readily circumvents such synthetic problems and transforms the sensitive solvate to the marketed drug substance with ease. Such expedient transformations hold great implications for the pharmaceutical industry in general when considering the ease of transformation and mild conditions employed.
Stable and high‐level production of recombinant Factor IX in human hepatic cell line (2011)

Hemophilia B is a genetic disease of the coagulation system that affects one in 30,000 males worldwide. Recombinant human Factor IX (rhFIX) has been used for hemophilia B treatment, but the amount of active protein generated by these systems is inefficient, resulting in a high-cost production of rhFIX. In this study, we developed an alternative for rhFIX production. We used a retrovirus system to obtain two recombinant cell lines. We first tested rhFIX production in the human embryonic kidney 293 cells (293). Next, we tested a hepatic cell line (HepG2) because FIX is primarily expressed in the liver. Our results reveal that intracellular rhFIX expression was more efficient in HepG2/rhFIX (46%) than in 293/rhFIX (21%). The activated partial thromboplastin time test showed that HepG2/rhFIX expressed biologically active rhFIX 1.5 times higher than 293/rhFIX (P = 0.016). Recovery of rhFIX from the HepG2 by reversed-phase chromatography was straightforward. We found that rhFIX has a pharmacokinetic profile similar to that of FIX purified from human plasma when tested in hemophilic B model. HepG2/rhFIX cell line produced the highest levels of rhFIX, representing an efficient in vitro expression system. This work opens up the possibility of significantly reducing the costs of rhFIX production, with implications for expanding hemophilia B treatment in developing countries.
Reduced Delay Uncertainty in High Performance Clock Distribution Networks (2003)

The design of clock distribution networks in synchronous digital systems presents enormous challenges. Controlling the clock signal delay in the presence of various noise sources, process parameter variations, and environmental effects represents a fundamental problem in the design of high speed synchronous circuits. A polynomial time algorithm that improves the tolerance of a clock distribution network to process and environmental variations is presented in this paper. The algorithm generates a clock tree topology that minimizes the uncertainty of the clock signal delay to the most critical data paths. Strategies for enhancing the physical layout of the clock tree to decrease delay uncertainty are also presented. Application of the methodology on benchmark circuits demonstrates clock tree topologies with decreased delay uncertainties of up to 90%. Techniques to enhance a clock tree layout have been applied on a set of benchmark circuits, yielding a reduction in delay uncertainty of up to 48%.
Abstract 15508: Development of a Small Peptide-Based Molecular Imaging Probe Targeting LOX-1 for Noninvasive Identification of Atherosclerotic Plaque (2010)

Objective: The oxidized low density lipoprotein (ox-LDL) receptor, LOX-1, mediates the initiation, progression, and destabilization of atherosclerotic plaques, and may be an ideal target for molecu...
Controlling Arc Length in Plasma Welding (1986)

Circuit maintains arc length on irregularly shaped workpieces. Length of plasma arc continuously adjusted by control circuit to maintain commanded value. After pilot arc is established, contactor closed and transfers arc to workpiece. Control circuit then half-wave rectifies ac arc voltage to produce dc control signal proportional to arc length. Circuit added to plasma arc welding machines with few wiring changes. Welds made with circuit cleaner and require less rework than welds made without it. Beads smooth and free of inclusions.
Macroporous Calcium Phosphate Cement (MCPC<sup>®</sup>) for Bone Reconstruction in Cranioplasty: Animal Study Performance (2008)

We have developed a novel macroporous calcium phosphate cement MCPC® that sets to poorly crystalline apatite after mixing the powder component with an aqueous solution and has interconnective macroporosity We performed cranioplasty on rat model by injecting the new macroporous calcium phosphate cement MCPC®. The mechanical property of the cement is about 12MPa after 24 hours (compression test). The cement matrix is totally transformed into poorly crystalline apatite in 48 hours. This study demonstrates that MCPC® cement was suitable and efficient for parietal bone reconstruction. Its injectability and moldability allows to be used in bone reconstruction surgery and its mechanical properties are compatible to support calvarial reconstruction. In addition, a bone ingrowth onto the BCP granules occurred on time.
Large-scale damage detection using satellite imagery (2015)

Satellite imagery is a valuable source of information for assessing damages in distressed areas undergoing a calamity, such as an earthquake or an armed conflict. However, the sheer amount of data required to be inspected for this assessment makes it impractical to do it manually. To address this problem, we present a semi-supervised learning framework for large-scale damage detection in satellite imagery. We present a comparative evaluation of our framework using over 88 million images collected from 4, 665 KM <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> from 12 different locations around the world. To enable accurate and efficient damage detection, we introduce a novel use of hierarchical shape features in the bags-of-visual words setting. We analyze how practical factors such as sun, sensor-resolution, satellite-angle, and registration differences impact the effectiveness our proposed representation, and compare it to five alternative features in multiple learning settings. Finally, we demonstrate through a user-study that our semi-supervised framework results in a ten-fold reduction in human annotation time at a minimal loss in detection accuracy compared to manual inspection.
Naltrexone at low doses upregulates a unique gene expression not seen with normal doses: Implications for its use in cancer therapy (2016)

It has been reported that lower doses of the opioid antagonist naltrexone are able to reduce tumour growth by interfering with cell signalling as well as by modifying the immune system. We have evaluated the gene expression profile of a cancer cell line after treatment with low-dose naltrexone (LDN), and assessed the effect that adapting treatment schedules with LDN may have on enhancing efficacy. LDN had a selective impact on genes involved with cell cycle regulation and immune modulation. Similarly, the pro-apoptotic genes BAD and BIK1 were increased only after LDN. Continuous treatment with LDN had little effect on growth in different cell lines; however, altering the treatment schedule to include a phase of culture in the absence of drug following an initial round of LDN treatment, resulted in enhanced cell killing. Furthermore, cells pre-treated with LDN were more sensitive to the cytotoxic effects of a number of common chemotherapy agents. For example, priming HCT116 with LDN before treatment with oxaliplatin significantly increased cell killing to 49±7.0 vs. 14±2.4% in cultures where priming was not used. Interestingly, priming with NTX before oxaliplatin resulted in just 32±1.8% cell killing. Our data support further the idea that LDN possesses anticancer activity, which can be improved by modifying the treatment schedule.
A texture descriptor for image retrieval and browsing (2003)

Image texture is an important visual primitive in image search and retrieval applications. To characterize texture information of images, a texture descriptor is proposed to capture both the perceptual information and the statistics of textures. The descriptor consists of two parts: a Perceptual Browsing Component (PBC) and a Similarity Retrieval Component (SRC). The emphasis of the paper is to introduce the extraction method for the PBC which is based on multidimensional decomposition of images using Gabor filters. By analyzing the one dimensional projections resulting from filtered images, PBC gives a quantitative measure about the structuredness of textures and also identifies the directionality and coarseness (scale). Our experimental results demonstrate that PBC can capture these texture properties quite well.
Gaussian beam migration (1990)

Abstract Just as synthetic seismic data can be created by expressing the wave field radiating from a seismic source as a set of Gaussian beams, recorded data can be downward continued by expressing the recorded wave field as a set of Gaussian beams emerging at the earth's surface. In both cases, the Gaussian beam description of the seismic-wave propagation can be advantageous when there are lateral variations in the seismic velocities. Gaussian-beam downward continuation enables wave-equation calculation of seismic propagation, while it retains the interpretive raypath description of this propagation. This paper describes a zero-offset depth migration method that employs Gaussian beam downward continuation of the recorded wave field.The Gaussian-beam migration method has advantages for imaging complex structures. Like finite-difference migration, it is especially compatible with lateral variations in velocity, but Gaussian beam migration can image steeply dipping reflectors and will not produce unwanted reflections from structure in the velocity model. Unlike other raypath methods, Gaussian beam migration has guaranteed regular behavior at caustics and shadows. In addition, the method determines the beam spacing that ensures efficient, accurate calculations. The images produced by Gaussian beam migration are usually stable with respect to changes in beam parameters.
Examination of Morphological Changes of Active Materials for Solution-Based Rechargeable Fluoride Shuttle Batteries Using <i>In Situ</i> Electrochemical Atomic Force Microscopy Measurements (2022)

Batteries using fluoride anions as the carrier might possess high capacity and energy density. Especially, the fluoride shuttle battery (FSB), which uses a fluoride-ion-conductive liquid electrolyte and operates at room temperature, has been reported previously and is deemed a solution to the global energy and environmental crises. Although several electrolyte solutions have been synthesized, and the fluorination/defluorination reactions of various active materials have been evaluated, no subsequent FSBs using those electrolyte solutions have been reported. In this study, two metal species, Bi and Pb, which have different fluorination/defluorination mechanisms in the electrolyte solution composed of alkylammonium fluoride and an ionic liquid, were used as the positive and negative active materials for the FSB. The fluorination/defluorination mechanisms at each electrode during the reactions were explained by in situ electrochemical atomic force microscopy (EC-AFM) measurements. Differences in the morphological changes by two existing mechanisms, direct fluorination and dissolution–deposition, were clarified with evidence. Furthermore, the charge/discharge process of the FSB, with the electrolyte solution combining the active materials, was demonstrated, and the cycling performance and capacity fading mechanism were discussed based on the characteristic morphological change of the active materials at their interface with the electrolyte solution obtained by in situ EC-AFM measurements.
Selective production of alpha olefins from synthesis gas over ZnO supported Pd-Fe bimetallics (1986)

Olefins are basic raw materials for a wide variety of commercial processes within the chemical industry. A synthesis-gas-based route to low molecular weight ..cap alpha..-olefins would provide the chemical industry with an alternative route to raw materials in the advent of future petroleum shortages or price increases. The catalytic production of ..cap alpha..-olefins from synthesis gas has been the subject of many investigations over the past 50 years. It has been established that, in some systems, olefin selectivity can be enhanced through the addition of various promoters such as K, Mn, Ti, or Zn. Olefin selectivity can also be dependent on process parameters such as temperature, pressure, conversion levels, or feed compositions. Recent reports in the literature indicate that supported Fe-containing bimetallics may also be selective for the production of olefins from synthesis gas. This study reports the use of Pd-FE bimetallics supported on ZnO for the selective production of olefins from synthesis gas.
Peptidyl Carbamates as Novel Elastase Inhibitors: Structure-Activity Relationship Studies (1993)

Twenty-six novel peptidyl carbamates and thiocarbamates were synthesized and evaluated as elastase inhibitors. Eighteen compounds inhibited porcine pancreatic elastase, whereas only eleven of the newly synthesized compounds inhibited human leukocyte elastase. Neither of the other serine dependent proteases, trypsin or chymotrypsin, were affected by any of the active inhibitors. Structure-activity relationship studies indicated that inhibition was dependent on P1 and P'1 substitution as well as on the presence of the carbamate functionality. Placement of an isostere of valine at P1 and a 1-(phenyl mercaptotetrazole at P'1 resulted in the most active human leukocyte elastase inhibitor within this series of compounds (Ki - 3.0 x 10(-7) M).
A Novel Methodology for Assessing the Bounded-Input Bounded-Output Instability in QT Interval Dynamics: Application to Clinical ECG With Ventricular Tachycardia (2011)

The goal of this paper is to present a new methodology for assessing the bounded-input bounded-output (BIBO) stability in QT interval (QTI) dynamics from clinical ECG. The ECG recordings were collected from 15 patients who experienced ventricular tachycardia (VT). Ten-minute-long ECG recordings extracted immediately before the onset of a chosen VT, one per patient, were assembled into a VT group, while the control group comprised 10-min-long ECGs extracted 1 h before VT onset and at least 1 h after any prior arrhythmic event. Each 10-min recording was subdivided into 1-min ECG recordings (minECGs). The QTI dynamics of each minECG was defined as a function of several prior QTIs and RR intervals; the BIBO stability of this function was then assessed in the z -domain. The number of minECGs with unstable QTI dynamics (N (us)) and the frequency of premature activations (PA), f (PA) , were counted for each ECG recording and were compared between the VT and control groups. The results show that the present methodology successfully captured the instability in QTI dynamics leading to VT onset in the studied population. Significantly larger N (us) was found in the VT group compared against the control and a positive correlation between N (us) and f (PA) was identified in both groups.