gebhart/patrepeval huggingface dataset:
Molecular changes in human melanoma metastasis. (1998)

The molecular changes associated with the transition of melanoma cells from radial growth phase to vertical growth phase (metastatic phenotype) are not well defined. Our recent studies have demonstrated that the two tumor suppressor genes, p53 and p16/CDKN2, do not play a major role in the acquisition of the metastatic phenotype in human melanoma. Mutations in p53 are infrequent and do not correlate with the metastatic potential of human melanoma cells while p16/CDKN2 abnormalities are frequent, but are not pre-requisite for the acquisition of the metastatic phenotype. On the other hand, the tyrosine-kinase receptor c-KIT and the cell adhesion molecule MCAM/MUC-18 play active roles in the progression of human melanoma. Metastatic melanoma cells overexpress MCAM and do not express the c-KIT receptor. Enforced c-KIT expression in metastatic cells significantly inhibited their growth and metastatic potential in nude mice. Furthermore, exposure of c-KIT-positive melanoma cells in vitro and in vivo to stem cell factor (SCF), the ligand for c-KIT, triggered apoptosis of these cells but not of normal melanocytes. Ectopic expression of MCAM into primary cutaneous melanoma cells enhanced their tumorigenicity and metastatic ability in vivo. We found that both genes, c-KIT and MCAM, are regulated by the transcription factor AP-2 and that metastatic melanoma cells do not express AP-2. We therefore propose that loss of AP-2 might be a crucial event in the progression of human melanoma.
A "humanized" green fluorescent protein cDNA adapted for high-level expression in mammalian cells (1996)

We constructed gfph, a synthetic version of the jellyfish Aequorea victoria green fluorescent protein (gfp) cDNA that is adapted for high-level expression in mammalian cells, especially those of human origin. A total of 92 base substitutions were made in 88 codons in order to change the codon usage within the gfp10 coding sequence so that it was more appropriate for expression in mammalian cells. We also describe a series of versatile recombinant adeno-associated virus and adenovirus vectors for delivery and expression of genes into mammalian cells and, using these vectors, demonstrate the efficient transduction and expression of the gfph gene in the human cell line 293 and also in vivo, within neurosensory cells of guinea pig eye. Cells infected with recombinant adeno-associated virus-GFPH can be readily sorted by fluorescence-activated cell sorting, suggesting that the newly designed gfph gene could be widely used as a reporter in many gene delivery technologies, including human gene therapy.
Intramuscular Deoxygenation during Exercise in Patients Who Have Chronic Anterior Compartment Syndrome of the Leg* (1997)

Currently, the definitive diagnosis of chronic compartment syndrome is based on invasive measurements of intracompartmental pressure. We measured the intramuscular pressure and the relative oxygenation in the anterior compartment of the leg in eighteen patients who were suspected of having chronic compartment syndrome as well as in ten control subjects before, during, and after exercise. Chronic compartment syndrome was considered to be present if the intramuscular pressure was at least fifteen millimeters of mercury (2.00 kilopascals) before exercise, at least thirty millimeters of mercury (4.00 kilopascals) one minute after exercise, or at least twenty millimeters of mercury (2.67 kilopascals) five minutes after exercise. Changes in relative oxygenation were measured with use of the non-invasive method of near-infrared spectroscopy. In all patients and subjects, there was rapid relative deoxygenation after the initiation of exercise, the level of oxygenation remained relatively stable during continued exercise, and there was reoxygenation to a level that exceeded the pre-exercise resting level after the cessation of exercise. During exercise, maximum relative deoxygenation in the patients who had chronic compartment syndrome (mean relative deoxygenation [and standard error], -290 +/- 39 millivolts) was significantly greater than that in the patients who did not have chronic compartment syndrome (-190 +/- 10 millivolts) and that in the control subjects (-179 +/- 14 millivolts) (p < 0.05 for both comparisons). In addition, the interval between the cessation of exercise and the recovery of the pre-exercise resting level of oxygenation was significantly longer for the patients who had chronic compartment syndrome (184 +/- 54 seconds) than for the patients who did not have chronic compartment syndrome (39 +/- 19 seconds) and the control subjects (33 +/- 10 seconds) (p < 0.05 for both comparisons).
Effect of Additional N-Glycosylation Signal in the N-Terminal Region on Intracellular Function of the Human Gonadotropin .ALPHA.-Subunit (2003)

hCG, LH, FSH, and TSH are a family of heterodimeric glycoprotein hormones that contain a common alpha-subunit, but differ in their hormone-specific beta-subunits. The alpha-subunit has two N-glycosylation sites at Asn52 and Asn78. To obtain more information on the relationship between the structure and function of the alpha-subunit, we introduced a novel N-glycosylation site in the N-terminal region by mutating Asp3 and Gln5 into Asn and Thr, respectively. Glycosylation mutants were expressed alone or with hCGbeta-subunit in Chinese hamster ovary cells. New N-linked oligosaccharides were efficiently added to the wild-type and mutant alpha-subunits lacking N-glycan at Asn52 (alpha deltaAsn1), Asn78 (alpha deltaAsn2), and both (alpha deltaAsn(1 + 2)). The new sugar chain did not affect secretion and assembly except that 1) it increased the intracellular degradation of alpha deltaAsn(1 + 2), and 2) it augmented the assembly of alpha deltaAsn1 with hCGbeta-subunit. Amino acid changes generated the attachment of O-glycosylation in free alpha-subunit but not in assembled form. These data indicate that the newly introduced N-glycosylation consensus sequence is functional, and that the N-terminal region of the alpha-subunit is flexible and can be modified without affecting the intracellular function. Furthermore, amino acid sequences in the N-terminus are involved in the O-glycosylation in free alpha-subunit.
Activation of insulin-secreting cells by pyruvate and halogenated derivatives (1990)

Addition of pyruvate to rat islets perifused in the presence of 5 mM-glucose elicited an immediate pronounced biphasic stimulation of insulin secretion. At lower concentrations of glucose (2.5 mM), only the initial, transient, phase of secretion was observed. Pyruvate inhibited 45Ca2+ efflux from islets at 2.5 mM-glucose and stimulated efflux at 5 mM-glucose. Pyruvate also decreased the rate of efflux of 86Rb+ from perifused islets. A marked stimulation of insulin secretion and 45Ca2+ efflux rate was observed in response to 3-fluoropyruvate and 3-bromopyruvate, compounds which inhibited oxidative metabolism of [14C]glucose and [14C]pyruvate in islets. The stimulatory effects of 3-fluoro- and 3-bromo-pyruvate were associated with enhanced 86Rb+ efflux. Withdrawal of pyruvate or halogenated analogues from the perfusate resulted in a secondary stimulation of insulin release, 45Ca2+ efflux and, to some extent, 86Rb+ efflux rates. Pyruvate, 3-fluoropyruvate and 3-bromopyruvate were all effective in promoting intracellular acidification and a rise in cytosolic Ca2+ concentration, as judged from fluorescence measurements in HIT-T15 cells loaded with 2',7'-biscarboxyethyl-5'(6')-carboxyfluorescein and Quin 2 respectively. It is proposed that oxidative metabolism of pyruvate is not a prerequisite for its stimulatory actions on pancreatic beta-cells. An alternative mechanism of activation by pyruvate and its halogenated derivatives is proposed, based on the possible electrogenic flux of these anions across the cell membrane.
Exploring Förster electronic energy transfer in a decoupled anthracenyl-based borondipyrromethene (bodipy) dyad (2012)

An anthracenyl-Bodipy dyad containing a triazole bridge, that acts to decouple the two units in the ground state, has been synthesised and structurally characterised. Efficient electronic energy transfer occurs from the anthracenyl-based unit to the Bodipy system in toluene in around 12 ps, and becomes faster in solvents of lower refractive index. The rate of electronic energy transfer is discussed in terms of Förster theory.
APPLICATION OF TEXTURE PROFILE ANALYSIS TO INSTRUMENTAL FOOD TEXTURE EVALUATION* (1975)

Abstract Although the Texturometer was used in establishing the GF objective Texture Profile Analysis (TPA) of foods, it has been largely supplanted by the Instron. The Instron GF TPA parameters have been determined for the most part by the original Texturometer procedures. Some workers have chosen to measure only one or several of the GF TPA parameters; others have added new ones. Changes proposed to make parameter names more descriptive have not been universally adopted. Testing conditions (crosshead and chart speed, % deformation, etc.) have varied considerably and have often been poorly described. Multiple point non‐GF TPA has been performed on foods using homemade as well as commercial instruments, e.g., Instron, Ottawa Texture Measuring System. Major shortcomings of studies involving TPA include poor experimental design, absence or improper use of statistical analysis and incomplete description of experimental materials and testing conditions. Despite certain shortcomings, TPA (GF or non‐GF) via interpretation of stress‐strain curves is, and will continue to be, extremely useful in evaluating the textural quality of foods, particularly when parameters can be correlated with sensory assessments.
Pedestrian detection at 100 frames per second (2012)

We present a new pedestrian detector that improves both in speed and quality over state-of-the-art. By efficiently handling different scales and transferring computation from test time to training time, detection speed is improved. When processing monocular images, our system provides high quality detections at 50 fps. We also propose a new method for exploiting geometric context extracted from stereo images. On a single CPU+GPU desktop machine, we reach 135 fps, when processing street scenes, from rectified input to detections output.
Inhomogeneous Noise Correction Combined with Uniform Filter and Sensitivity Map (INCUS) for Multi-coil Imaging Including Parallel Imaging (2013)

The INCUS technique provides a straightforward, higher degree of freedom, and computationally feasible implementation of a general purpose de-noising filter for surface coil-based imaging including parallel imaging in commercial MR imaging.
Production of a complement inhibitor possessing sialyl Lewis X moieties by in vitro glycosylation technology (2004)

Recombinant soluble human complement receptor type 1 (sCR1) is a highly glycosylated glycoprotein intended for use as a drug to treat ischemia-reperfusion injury and other complement-mediated diseases and injuries. sCR1-sLe(x) produced in the FT-VI-expressing mutant CHO cell line LEC11 exists as a heterogeneous mixture of glycoforms, a fraction of which include structures with one or more antennae terminated by the sialyl Lewis X (sLe(x)) [Neu5Acalpha2-3Galbeta1-4(Fucalpha1-3)GlcNAc]) epitope. Such multivalent presentation of sLe(x) was shown previously to effectively target sCR1 to activated endothelial cells expressing E-selectin. Here, we describe the use of the soluble, recombinant alpha2-3 sialyltransferase ST3Gal-III and the alpha1-3 fucosyltransferase FT-VI in vitro to introduce sLe(x) moieties onto the N-glycan chains of sCR1 overexpressed in standard CHO cell lines. The product (sCR1-S/F) of these in vitro enzymatic glycan remodeling reactions performed at the 10-g scale has approximately 14 N-glycan chains per sCR1 molecule, comprised of biantennary (90%), triantennary (8.5%), and tetraantennary (1.5%) structures, nearly all of whose antennae terminate with sLe(x) moieties. sCR1-S/F retained complement inhibitory activity and, in comparison with sCR1-sLe(x) produced in the LEC11 cell line, contained twice the number of sLe(x) moieties per mole glycoprotein, exhibited a twofold increase in area under the intravenous clearance curve in a rat pharmacokinetic model, and exhibited a 10-fold increase in affinity for E-selectin in an in vitro binding assay. These results demonstrate that in vitro glycosylation of the sCR1 drug product reduces heterogeneity of the glycan profile, improves pharmacokinetics, and enhances carbohydrate-mediated binding to E-selectin.
Automated detection of lung nodules in CT scans: Preliminary results (2001)

We have developed a fully automated computerized method for the detection of lung nodules in helical computed tomography (CT) scans of the thorax. This method is based on two-dimensional and three-dimensional analyses of the image data acquired during diagnostic CT scans. Lung segmentation proceeds on a section-by-section basis to construct a segmented lung volume within which further analysis is performed. Multiple gray-level thresholds are applied to the segmented lung volume to create a series of thresholded lung volumes. An 18-point connectivity scheme is used to identify contiguous three-dimensional structures within each thresholded lung volume, and those structures that satisfy a volume criterion are selected as initial lung nodule candidates. Morphological and gray-level features are computed for each nodule candidate. After a rule-based approach is applied to greatly reduce the number of nodule candidates that corresponds to nonnodules, the features of remaining candidates are merged through linear discriminant analysis. The automated method was applied to a database of 43 diagnostic thoracic CT scans. Receiver operating characteristic (ROC) analysis was used to evaluate the ability of the classifier to differentiate nodule candidates that correspond to actual nodules from false-positive candidates. The area under the ROC curve for this categorization task attained a value of 0.90 during leave-one-out-by-case evaluation. The automated method yielded an overall nodule detection sensitivity of 70% with an average of 1.5 false-positive detections per section when applied to the complete 43-case database. A corresponding nodule detection sensitivity of 89% with an average of 1.3 false-positive detections per section was achieved with a subset of 20 cases that contained only one or two nodules per case.
Fibrotic Idiopathic Interstitial Pneumonia (2003)

Survival is linked to the histopathologic distinction between usual interstitial pneumonia (UIP) and nonspecific interstitial pneumonia (NSIP), the most commonly encountered fibrotic idiopathic interstitial pneumonia. We retrospectively compared the prognostic significance of histopathologic diagnoses, baseline pulmonary function indices, and serial trends in pulmonary function indices (diffusing capacity, FVC, FEV1, the recently defined composite physiologic index) at 6 and 12 months in 104 patients (UIP, n = 63; fibrotic NSIP, n = 41). Survival was lower in UIP than in fibrotic NSIP (p = 0.001) but not in patients with severe functional impairment; mortality during the first 2 years was linked solely to the severity of functional impairment at presentation. The composite physiologic index was the strongest determinant of outcome (p < 0.001). At 6 months, serial diffusing capacity levels (p = 0.003) and histopathologic diagnosis (p = 0.002) were prognostically equivalent. At 12 months, serial pulmonary function trends were the only major prognostic determinant (p < 0.0005 for all variables), with no independent significance associated with the distinction between UIP and fibrotic NSIP. We conclude that at 12 months, serial pulmonary function trends have considerable prognostic value in UIP and NSIP. Their histologic distinction provides no additional prognostic information when pulmonary function trends are clear cut or when functional impairment is severe.
Facile Discrimination of Aldose Enantiomers by Reversed-Phase HPLC (2007)

One-pot reactions of aldoses with L-cysteine methyl ester and o-tolyl isothiocyanate yielded methyl 2-(polyhydroxyalkyl)-3-(o-tolylthiocarbamoyl)-thiazolidine-4(R)-carboxylates. Direct HPLC analysis of the reaction mixture and UV detection at 250 nm discriminated D- and L-enantiomers of aldoses. The reaction was applied to the determination of absolute configuration the sugar residues of an aroma precursor.
Control of Domain Wall Polarity by Current Pulses (2008)

Direct observation of current-induced propagation of purely transverse magnetic domain walls with spin-polarized scanning electron microscopy is reported in Fe30Ni70 nanowires. After propagation, the domain walls keep their transverse nature but switch polarity in some cases. For uniform Ni70Fe30 wires, the effect is random and illustrates domain-wall propagation above the Walker threshold. In the case of Ni{70}Fe_{30}/Fe wires, the transverse magnetization component in the wall is entirely determined by the polarity of the current pulse, an effect that is not reconciled by present theories even when taking into account the nonuniform Oersted field generated by the current.
On the synthesis of fractal radiation patterns (1995)

The fundamental relationship between self‐similar, that is, fractal, arrays and their ability to generate radiation patterns which possess fractal features is examined in this paper. The theoretical foundation and design procedures are developed for using fractal arrays to synthesize fractal radiation patterns having certain desired characteristics. A family of functions, known as generalized Weierstrass functions, are shown to play a pivotal role in the theory of fractal radiation pattern synthesis. These functions are everywhere continuous but nowhere differentiable and exhibit fractal behavior at all scales. It will be demonstrated that the array factor for a nonuniformly but symmetrically spaced linear array can be expressed in terms of a Weierstrass partial sum (band‐limited Weierstrass function) for an appropriate choice of array element spacings and excitations. The resulting fractal radiation patterns from these arrays possess structure over a finite range of scales. This range of scales can be controlled by the number of elements in the array. For a fixed array geometry, the fractal dimension of the radiation pattern may be varied by changing the array current distribution. A general and highly flexible synthesis technique is introduced which is based on the theory of Fourier‐Weierstrass expansions. One of the appealing attributes of this synthesis technique is that it provides the freedom to select an appropriate generating function, in addition to the dimension, for a desired fractal radiation pattern. It is shown that this synthesis procedure results in fractal arrays which are composed of a sequence of self‐similar uniformly spaced linear subarrays. Finally, a synthesis technique for application to continuous line sources is presented which also makes use of Fourier‐Weierstrass expansions.
Direct Synthesis of Narrowly Dispersed Silver Nanoparticles Using a Single-Source Precursor (2003)

We describe a direct synthetic method for preparing narrowly dispersed silver nanoparticles without using size-selection processes by thermal reduction of silver trifluoroacetate in isoamyl ether in the presence of oleic acid. This direct synthesis is versatile, easy to control synthetically, and able to make Ag nanoparticles with diameters in the range of 7−11 nm with narrow size distribution. The diameter of these nanoparticles can be tuned by varying the oleic acid to silver trifluoroacetate molar ratio. Ostwald ripening can also be used to make Ag nanoparticles with different sizes. The particles were characterized by transmission electron microscopy, selected area electron diffraction, ultraviolet−visible spectroscopy, and powder X-ray diffraction.
Dependence of Surface Microroughness of CZ, FZ, and EPI Wafers on Wet Chemical Processing (1992)

The effect of the wet chemical cleaning process on the surface microroughness of Si wafers was studied, using CZ, FZ, and EPI wafers. It has been shown that the surface microroughness affects the dielectric breakdown characteristics of the oxide: the dielectric breakdown of the oxide degrades as the microroughness of the Si substrate increases. The microroughness on the Si substrate surface and the oxide surface was evaluated with a scanning tunneling microscope (STM) and an atomic force microscope (AFM). The surface microroughness was found to increase in wet chemical processing, in particular in cleaning (APM cleaning). It has been shown that the microroughness does not increase at all if the mixing ratio in solution is suppressed at a low level: (conventional mixing ratio is 1:1:5), and the room temperature ultrapure water rinsing is introduced right after the APM cleaning. At the same time, the APM cleaning with its mixing ratio suppressed at the low level has been found very effective to remove particles and metallic impurities from the Si surface. The increase of microroughness due to the APM cleaning varies among the wafer types; little increase is observed on EPI wafer but significant increase is observed on CZ and FZ wafers. It has been found, however, that the CZ and FZ wafers which go through the wet oxidation at 1000°C for over 4 h, can suppress the increase of microroughness in the APM cleaning at almost the same level as the EPI wafer. This because the interstitial Si atoms generated in the wet oxidation fill the Si vacancy. In the case of the n‐type CZ wafer, the surface microroughness is also observed to increase in the DHF cleaning. It has been revealed the addition of of over 0.5% to the DHF solution can completely suppress this microroughness increase.
Energy Utilization by Mature, Nonpregnant, Nonlactating Cows of Different Types (1984)

Four types of crossbred cows were used in each of two studies designed to estimate the metabolizable energy (ME) required to maintain weight or energy equilibrium of mature (9-yr-old), nonpregnant, nonlactating cows. The four cow types were chosen to represent cow types having moderate mature size-moderate milk production potential (Angus × Hereford, Hereford × Angus; AHX), large mature size-moderate milk production potential (Charolais × Angus or Hereford; CX), small mature size-high milk production potential (Jersey × Angus or Hereford; JX) and large mature size-high milk production potential (Simmental × Angus or Hereford; SX). In each of two consecutive years, four cows of each type were assigned randomly and fed individually either a low (113 kcal ME·kg−.75·d−1), medium (178 kcal ME·kg−.75·d−1) or a high (ad libitum) level of a corn silage-based diet for 140 d. Body composition of each cow was estimated by deuterium oxide dilution techniques at d 0 and 140 of each study and gains were calculated. The ME required to maintain weight or energy equilibrium was estimated for each type of cow. Estimates of ME required to maintain energy equilibrium (from the regression of log heat production, kcal·kg−.75·d−1 on ME intake kcal·kg−.75·d−1) were 130, 129, 145 and 160 kcal·kg−.75·d−1 for AHX, CX, JX, and SX cows, respectively. Similar trends were observed when other models were used. Cow types with higher milk production potential had higher maintenance (kcal·kg−.75·d−1) than cows with lower milk production potential. Cows of larger size had maintenance requirements (kcal·kg−.75·d−1) similar to those of smaller size. Possible reasons for these differences as well as their potential impact on cow efficiency are discussed.