gebhart/patrepeval huggingface dataset:
Studies on the Mechanism of <i>p-</i>Hydroxyphenylacetate 3-Hydroxylase from <i>Pseudomonas aeruginosa</i>: A System Composed of a Small Flavin Reductase and a Large Flavin-Dependent Oxygenase (2009)

There are two known types of microbial two-component flavin-dependent monooxygenases that catalyze oxygenation of p-hydroxyphenylacetate (HPA), and they are distinguished by having structurally distinct reductases and oxygenases. This paper presents a detailed analysis of the properties of the enzyme from Pseudomonas aeruginosa, an example of one group, and compares its properties to those published for the Acinetobacter baumannii enzyme, an example of the alternative group. The reductase and oxygenase from P. aeruginosa were expressed in Escherichia coli. The reductase was purified as a stable C-terminally His-tagged yellow protein containing weakly bound FAD, and the oxygenase was purified as a stable colorless N-terminally His-tagged protein. The reductase catalyzes the reduction of FAD by NADH and releases the FADH(-) product into solution, but unlike the reductase from A. baumannii, this catalysis is not influenced by HPA. The oxygenase binds the released FADH(-) and catalyzes the oxygenation of HPA to form 3,4-dihydroxyphenylacetate, after which the FAD dissociates to be re-reduced by the reductase, a common overall pattern for two-component flavin-dependent oxygenases. With this system, it appears that interactions between the reductase and the oxygenase can facillitate the transfer of FADH(-) to the oxygenase, although they are not required. We show that the P. aeruginosa oxygenase system in complex with FADH(-) reacts with O(2) to form a quasi-stable, unusually high-extinction flavin hydroperoxide species that binds HPA and reacts to form the product. The resultant flavin hydroxide decomposes to FAD and water while still bound to the oxygenase and then releases product and FAD from the protein. Unlike the enzyme from A. baumannii, during normal catalysis involving both the reductase and oxygenase, the rate-determining step in catalysis is the dissociation of FAD from the oxygenase in a process that is independent of the concentration of HPA. Structures for the reductases and oxygenases from A. baumannii and from Thermus thermophilus (similar to the P. aeruginosa system) form a basis for interpreting the molecular origins of the differences between the two groups of flavin-dependent two-component oxygenases.
Advanced ground truth for snow and glacier sensing (1998)

Snow development characteristic and the liquid water content dynamic on glacier snow packs are very important parameters that may be monitored by radar. Accurate ground reference is required for the radar image calibration. The authors developed a new in-situ snow moisture and density measuring device. Measurements were made with this advanced device in the winter of 1995/96 in Germany and in the winter of 1996/97 on the glacier Plaine de la Morte, Switzerland. The authors report on the correlation between in-situ and remotely sensed data concerning liquid water content and density. Furthermore they compare the gravimetric measured snow densities with their method. This winter one device is installed in Germany and a second one is delivered to the Antarctic Peninsula, where the project crew of DYPAG will operate it. The device consists of a net of radio frequency transmission lines and of high and low frequency impedance analyzers. Preinstalled lines are enclosed by snow fall. The analyzers measure the dielectric coefficients a of the snow mixture along the transmission lines. One sensor line can have a length of approx. 100 m. In a cross laid pattern the covered area can be larger than the pixel size. In this manner a representative area can be measured non-destructive and long-term. Every in-situ snow measuring device has a disturbing air gap to snow. The authors' new device cancels out this basic drawback. The determination of liquid water content needs the knowledge of density, too. In this case, the same device, the net of lines, measures the density inherent. With reconstruction of transmission line parameters it is possible to localize ice lenses and percolation downflows along the line. The sensor is equipped with an hourly data logging.
Conserved expression of intestinal trefoil factor in the human colonic adenoma-carcinoma sequence. (1996)

Human intestinal trefoil factor (ITF), a mucosa-associated trefoil peptide, has been implicated in maintenance of mucosal integrity and may denote commitment to goblet cell differentiation. We have quantitated and localized ITF expression in normal and neoplastic colons, determined the molecular forms present, and examined the relationships among ITF expression and mucin production and increasing dysplasia. Normal and neoplastic human colonic mucosa (n = 30) were extracted for quantitation by ITF radioimmunoassay and size determination by gel filtration and immunoblotting. Paraffin sections of normal bowel, hyperplastic polyps, adenomatous polyps, and adenocarcinoma were examined for ITF immunohistochemistry and mucin histochemistry. The predominant molecular species in both normal and neoplastic colon was a 7-kd monomer. Staining was localized to goblet and Paneth cells and the luminal surface in normal colon and in most adenomatous polyps but not hyperplastic polyps; this colocalized with periodic acid-Schiff histochemistry. ITF staining of undifferentiated cells was seen with increasing dysplasia, and Golgi region immunoreactivity was highly conserved in adenocarcinoma, independent of the presence of periodic acid-Schiff-positive mucin. ITF concentration in colonic extracts was 10 to 200 pmol/g. Levels in normal (88.1 +/- 15.1 pmol/g) and malignant (90.1 +/- 12.7 pmol/g) tissue were comparable. In carcinomas, there were significant associations among ITF expression and degree of differentiation and mucin presence. Loss of expression was associated with tumor necrosis and advanced Duke's stage. ITF is uniformly processed in normal and neoplastic colons. Goblet cell-derived ITF is associated with stainable mucin production. ITF synthesis by non-goblet colonocytes, however, is highly conserved in neoplastic differentiation.
Gaseous combustion at high pressures. Part VI.— The explosion of argon- and helium-diluted knall-gases (1926)

Abstract In this paper are recorded the results of experiments made during the past year upon the explosion of argon- or helium-diluted hydrogen- and CO-knall-gases at various initial pressures between 10 and 150 atmospheres. Nearly all of these were made in our nickel-chrome-steel bomb No. 3 (spherical explosion chamber of 239 c. c. capacity), particulars of which were given in the previous paper of this series (q. v.), the only exception being four experiments, all at initial pressures below about 50 atmospheres,which were made in our nickel-steel bomb No. 2 (spherical explosion chamber of 242 c. c. capacity). Although in the course of these researches up to the end of 1924 we had carried out several experiments with argon-diluted CO-knall-gas at various initial pressures, chiefly for comparison with the corresponding nitrogen- diluted knall-gas, we had never been able to make any systematic comparisons between argon and helium-diluted knall-gases, through lack of sufficient helium for experiments at high initial pressures. Some time ago, through the kindness of Sir William Pope, we got a small supply of it, which enabled us to make a few preliminary experiments at initial pressures up to 50 atmospheres; but it was not until early in 1925, when we were presented by the U. S. Bureau of Mines in Washington, through the kindness of Dr. S. C. Lind, their chief chemist, with a cylinder containing 60 cubic feet of helium at a pressure of 45 atmospheres for the purpose of our experiments, that we were able to carry out the main part of our programme.
Detection of Parkinson Disease Rest Tremor (2014)

Parkinson Disease (PD) is a debilitating and progressive movement disorder that is estimated to affect over six million worldwide. One of the most characteristic symptoms of PD is resting tremor, which involves unintentional and rhythmic muscle oscillations of an afflicted extremity while the muscles of said extremity are relaxed. This study involved measuring the rest tremor of 10 PD subjects, 10 Essential Tremor subjects, and 10 healthy control subjects using two devices. One device was an FDA approved accelerometry system to measure human tremor known as the TremorometerTM and the other was a consumer three-dimensional camera known as the Leap MotionTM Controller. The study compares tremor characteristics calculated from both devices to compare the Leap Motion Controller to the Tremorometer System. The tremor characteristics obtained from the Leap Motion Controller were also used in an attempt to classify the subjects used in the study as either PD or non-PD subjects.
Metal fluoride-based transparent nanocomposites with low refractive indices (2013)

The utilisation of magnesium and aluminium fluoride nanoparticles in the preparation of transparent composites leading to materials with superior properties was investigated. Nanoscopic magnesium and aluminium fluoride has been prepared by the fluorolytic sol-gel route from the alkoxides and was surface modified by the reaction with trifluoroacetic acid or perfluorobutyric acid. IR spectroscopic experiments of the xerogels and crystal structure analysis of a trinuclear [Mg3(μ3F)(μ-TFA)6(OCH3)2(py)](3-) cluster unit indicate that the carboxylate group is bound to the particle surface in a monodentate or bidentate bridging fashion. These particles were successfully incorporated into acrylate polymers with up to 40 wt% content to give fully transparent material. Ellipsometry and m-line measurements of thin films show the reduction of the refractive index of composite films with increasing metal fluoride filler content.
pABC11 (Also Known as MOAT-C and MRP5), a Member of the ABC Family of Proteins, Has Anion Transporter Activity but Does Not Confer Multidrug Resistance When Overexpressed in Human Embryonic Kidney 293 Cells (1999)

Several members of the ABC family of proteins have been implicated in multidrug resistance associated with cancer therapies. A novel member of this gene family, designated pABC11, has been identified using degenerate polymerase chain reaction. The full-length cDNA spans 5881 base pairs and encodes an open reading frame of 1437 amino acids predicted to contain two sets of transmembrane domains and two nucleotide binding domains characteristic of ABC proteins. The nucleotide sequence described herein extends that of three recently reported sequences, MRP5 (Kool, M., de Haas, M., Scheffer, G., Scheper, R., van Eijk, M., Juijn, J., Baas, F., and Borst, P. (1997) Cancer Res. 57, 3537-3547), SMRP (Suzuki, T., Nishio, K., Sasaki, H., Kurokawa, H., Saito-Ohara, F., Ikeuchi, T., Tanabe, S., Terada, M., and Saijo, N. (1997) Biochem. Biophys. Res. Commun. 238, 790-794), and MOAT-C (Belinsky, M., Bain, L., Balsara, B., Testa, J., and Kruh, G. (1998) J. Natl. Cancer Inst. 90, 1735-1741), in the 5' direction. Northern blot analysis detected five transcripts that were differentially expressed in several tissue types, and the gene encoding pABC11 was mapped to chromosome 3. Confocal imaging of HEK293 cells expressing a green fluorescent protein-pABC11 construct confirmed plasma membrane localization of the fusion protein. Overexpression of pABC11 resulted in reduced labeling with the fluorochromes 5-chloromethylfluorescein diacetate, fluorescein diacetate, and 2',7'-bis-(2-carboxyethyl)-5 (and-6)-carboxyfluorescein acetoxymethyl ester but not with calcein or rhodamine derivatives, consistent with pABC11 being an anion transporter. Fluorochrome export was ATP-dependent but glutathione-independent. We also show that this export pump does not confer resistance to various classes of cytotoxic drugs but does provide small but significant resistance to CdCl(2) and potassium antimonyl tartrate.
Analysis of Deflection Enhancement Using Epsilon Assembly Microcantilevers Based Sensors (2011)

The present work analyzes theoretically and verifies the advantage of utilizing ɛ-microcantilever assemblies in microsensing applications. The deflection profile of these innovative ɛ-assembly microcantilevers is compared with that of the rectangular microcantilever and modified triangular microcantlever. Various force-loading conditions are considered. The theorem of linear elasticity for thin beams is used to obtain the deflections. The obtained defections are validated against an accurate numerical solution utilizing finite element method with maximum deviation less than 10 percent. It is found that the ɛ-assembly produces larger deflections than the rectangular microcantilever under the same base surface stress and same extension length. In addition, the ɛ-microcantilever assembly is found to produce larger deflection than the modified triangular microcantilever. This deflection enhancement is found to increase as the ɛ-assembly's free length decreases for various types of force loading conditions. Consequently, the ɛ-microcantilever is shown to be superior in microsensing applications as it provides favorable high detection capability with a reduced susceptibility to external noises. Finally, this work paves a way for experimentally testing the ɛ-assembly to show whether detective potential of microsensors can be increased.
Evolution of a Mesoporous Bioactive Glass Scaffold Implanted in Rat Femur Evaluated by <sup>45</sup>Ca Labeling, Tracing, and Histological Analysis (2014)

Mesoporous bioactive glass (MBG) as a biodegradable scaffold with a nanostructure has attracted significant attention. However, the in vivo evolution of MBG, which includes in situ degradation, the local effect induced by degradation, and the disposition of degradation products, remains unclear. In this study, we performed in situ labeling and synthesis of an MBG scaffold for the first time using (45)CaCl2. The obtained (45)Ca-MBG scaffolds possessed a mesoporous-macroporous cross-linked structure. These (45)Ca-MBG scaffolds were implanted in critical-sized rat femur defects (3 × 3 mm) for 1 day and for 1, 4, 8, and 12 weeks and analyzed by isotopic quantitative tracing. The results illustrated that the MBG scaffolds gradually degraded over time and persisted at a local level of approximately 9.63% at week 12. This finding suggests that only a very small amount of MBG-released calcium ions may have been transformed into calcium components of the new bone matrix. The research also confirmed that the active ingredients derived from the degradation of MBG scaffolds could actively regulate the mRNA expression levels of osteoblast-related genes in rat bone marrow-derived mesenchymal stem cells (rBMSCs) and promote bone regeneration in vivo. Moreover, through isotopic tracing of the entire body, (45)Ca, which disappeared in situ after implantation, could be detected in the heart, lungs, spleen, kidneys, intestines, and brain via the blood and was mainly accumulated in distal bone tissue, including the radius and cranium. However, (45)Ca radioactivity in the body tissues significantly decreased or disappeared after 12 weeks. Systemic toxicological studies on MBG scaffolds demonstrated the degradation products that spread to major organs did not cause abnormal histopathological changes. The above discoveries comprehensively address crucial issues regarding the application of MBG in vivo, and these findings provide a scientific basis for introducing a material with mesoporous structure into clinical applications.
Cascaded frequency upconversion for high-speed single-photon detection at 1550 nm (2012)

We present a device for two-stage frequency upconversion of single-photon-level signals in the 1.55 μm telecom band to the green spectral region with low excess noise, suitable for detection by low-timing-jitter silicon single-photon avalanche photodiodes (APDs). We achieve a net conversion efficiency of 87% and a system timing jitter below 70 ps FWHM, dominated by the jitter of the APD. Modifications of our device are suitable for downconversion of single photons from visible-wavelength quantum emitters into the telecom band.
Effect of Magnesium Ions and Ethylenediamine Tetra‐acetic Acid on the Activity of Vancomycin against <i>Escherichia coli</i> and <i>Staphylococcus aureus</i> (1967)

SUMMARY When added to logarithmically dividing Encherichia coli , vancomycin caused lysis only when the nutrient medium was deficient in magnesium ions. They did not prevent vancomycin from exerting an inhibitory effect on Staphylococcus aureus growing in the log phase. Ethylenediamine tetra‐acetic acid (EDTA) was less inhibitory to E. coli than to Staph. aureus , but in sub‐bacteriostatic concentrations it potentiated the activity of sub‐inhibitory doses of vancomycin against E. coli. EDTA probably removes some cations in the cell wall, thus facilitating the entry of vancomycin; it does not potentiate the activity of sub‐bacteriostatic doses of vancomycin against Staph. aureus.
Antioxidant potentials and degrees of polymerization of six wild fruits (2006)

Aqueous methanolic extracts of six wild fruits, Ximenia caffra (sour plum), Sclerocarya birrea (marula), Parinari curatellifolia (mobola plum), Vitex payos (chocolate berry),Bridelia molis (velvet sweet-berry) and Berchemia zeyheri (red ivory) were assayed for radical scavenging effect on DPPH radical, reducing power, superoxide anion radical scavenging effect and the inhibition of phospholipids peroxidation using colorimetric method. The peels and pulps of sour plum exhibited high activity compared to the peels and pulps of the other fruits. Sour plum showed high reducing capacities both in the peel and pulp compared to all the other fruits. At high concentrations of extract over 75% superoxide anion scavenging effect was observed for velvet sweet-berry whilst at concentrations of 40 and 60 mg sample equivalent/μl red ivory fruits showed a high anion scavenging capacity. Velvet sweet-berry, sour plum peel and pulp and chocolate berry peel showed high capacities to inhibit lipid peroxidation at high concentrations. The degrees of polymerization varied between 7 to 16 monomer units of catechin per polymer of phenolic compounds in the different portions of the six fruits.

	 

	Key words: Phenolic acids, antioxidant, wild fruits, peroxidation and polymerisation.
Phase transition between liquid-like and crystal-like structures of deionized colloidal suspensions (1990)

Transmitted-light spectra exhibiting the characteristic profiles of crystal-like and liquid-like distributions have been observed for suspensions of monodisperse polystyrene spheres (85–173 nm in diameter). The intersphere distance (D) in the liquid-like structures decreases continuously as the sphere concentration increases, and D jumps up by several percent at the critical concentration, at which the liquid-like structure transforms to the crystal-like distribution. A spinodal decomposition type transition is observed in the plots of D against sphere concentration. The critical concentrations of the transition are 0.005, 0.002, 0.005 and 0.025 (in volume fraction) for the spheres of 85, 91, 109 and 173 nm in diameter. The crystal-like distribution transforms to the liquid-like structure at a certain concentration of NaCl accompanied with the dropping down of the D values. A phase diagram containing the regions of (1) liquid-like, (2) face-centred cubic (f.c.c.), (3) body-centred cubic (b.c.c.) distributions and (4) the coexistence of f.c.c. and b.c.c. type crystal-like structures is obtained. These results are consistent with the significant role played by the electrical double layers under the influence of purely electrostatic intersphere repulsion in the effective hard-sphere model.
A novel USP30 inhibitor recapitulates genetic loss of USP30 and sets the trigger for PINK1-PARKIN amplification of mitochondrial ubiquitylation (2020)

Abstract The mitochondrial deubiquitylase USP30 negatively regulates the selective autophagy of damaged mitochondria. It has been proposed as an actionable target to alleviate the loss of function of the mitophagy pathway governed by the Parkinson’s Disease associated genes PINK1 and PRKN. We present the characterisation of a N-cyano pyrrolidine derived compound, FT3967385, with high selectivity for USP30. The compound is well tolerated with no loss of total mitochondrial mass. We demonstrate that ubiquitylation of TOM20, a component of the outer mitochondrial membrane import machinery that directly interacts with USP30, represents a robust biomarker for both USP30 loss and inhibition. We have conducted proteomics analyses on a SHSY5Y neuroblastoma cell line model to directly compare the effects of genetic loss of USP30 with selective inhibition in an unbiased fashion. We have thereby identified a subset of ubiquitylation events consequent to mitochondrial depolarisation that are USP30 sensitive. Within responsive elements of the ubiquitylome, several components of the outer mitochondrial membrane transport (TOM) complex are most prominent. Thus, our data support a model whereby USP30 can regulate the availability of ubiquitin at the specific site of mitochondrial PINK1 accumulation following membrane depolarisation. In this model, USP30 deubiquitylation of TOM complex components dampens the trigger for the Parkin-dependent amplification of mitochondrial ubiquitylation leading to mitophagy. Accordingly, PINK1 generation of phospho-Ser65 Ubiquitin proceeds more rapidly and to a greater extent in cells either lacking USP30 or subject to USP30 inhibition.
Reverse propagation of femtosecond pulses in optical fibers (2003)

We present a numerical technique for reversing femtosecond pulse propagation in an optical fiber, such that given any output pulse it is possible to obtain the input pulse shape by numerically undoing all dispersion and nonlinear effects. The technique is tested against experimental results, and it is shown that it can be used for fiber output pulse optimization in both the anomalous and normal dispersion regimes.
A Low-latency Sparse-Winograd Accelerator for Convolutional Neural Networks (2019)

Low-latency and low-power implementations of Convolutional Neural Network (CNN) are highly desired for budget-restricted scenarios. Pruning and Winograd algorithm are two representative approaches to reduce the computation complexity of CNNs. Coupling them is very attractive, but the Winograd transformation removes data sparsity brought by pruning. In this paper, we present a low-latency sparse-Winograd CNN accelerator (LSW-CNN) for pruned Wino-grad CNN models. The ReLU-modified algorithm is employed to solve the zero refilling issue. Our design fully leverages the sparsity in both weights and activations, and thus eliminates all unnecessary computation and cycles. Moreover, a novel fast mask indexing algorithm for sparse data compression is developed. Accumulation buffers are scaled to reduce the latency brought by irregular serial channel merging. On VGG-16, experimental results demonstrate that the latency of LSW-CNN is reduced by 5.1 and 1.7 times, respectively, compared with state-of-the-art dense-Winograd and sparse-Winograd accelerators. Besides, the consumed hardware resource is also significantly reduced.
BASIC PATHOLOGY (1987)

A study of glaucoma prevalence in Nigeria was undertaken using data from the eye clinic records of 622 females aged between 4 and 80 years and 1055 males aged between 5 and 95 years who attended the Evangelical Churches of West Africa Eye Hospital, Kano, northern Nigeria, in January, 1985. Glaucoma occurred in 8.6% of the patients. Comparative analysis of glaucoma prevalence studies from different parts of the world and using different sampling techniques showed a marked variation.