gebhart/patrepeval huggingface dataset:
Expression of tumor markers hyaluronic acid and hyaluronidase (HYAL1) in head and neck tumors (2003)

Characteristic behaviors of head and neck squamous cell carcinoma (HNSCC) include a propensity to occur as multiple synchronous and metachronous tumors, frequent recurrence and metastasis. Early detection of HNSCC and monitoring its recurrence are necessary to improve prognosis. Hyaluronic acid (HA), a component of extracellular matrix, promotes metastasis. Small fragments of HA stimulate angiogenesis. HA fragments are generated when hyaluronidase (HAase), an endoglycosidase, degrades the HA polymer. Using the HA test (an ELISA-like assay) we found that saliva HA levels are 4.9-fold elevated in 11 HNSCC patients (2841 +/- 887 ng/mg protein) when compared to 6 normal controls (579.3 +/- 122.6 ng/mg protein; p = 0.00238). HNSCC patients included in our study were patients with cancers of the oral cavity (n = 4), pharynx (n = 7) and larynx (n = 1). The HA levels were also elevated in MDA-1483, FaDu and HEp-2 cell lines when compared to the transformed keratinocyte line HEK-001. Saliva HAase levels measured using the HAase test (an ELISA-like assay) were 3.7-fold elevated in HNSCC patients (10.4 +/- 1.4 mU/mg protein) when compared to normal controls (2.8 +/- 0.7 mU/mg protein; p = 0.0028). MDA-1483 and HEp-2 cells secreted 7- to 11-fold higher levels of HAase in their conditioned media (CM) when compared to FaDu cells, and the latter secreted 1.5-fold more HAase than HEK-001 cells. Reverse transcriptase (RT)-PCR analysis detected the expression of full-length HYAL1 type HAase transcript in tumor cells. None of the cells exhibited the expression of PH20 in RT-PCR analysis. Immunoblot analysis confirmed the expression of a approximately 55 kDa HYAL-related protein in tumor cell CM and in patients' saliva. The pH activity profile and optimum (pH 4.4) of the HAase activity present in HNSCC patients' or normal saliva and that secreted in the CM of tumor cells closely resembled that of the partially purified HYAL1 type HAase. The profiles of HA species in HNSCC patients' and normal saliva are different. The high-stage HNSCC patients' saliva contains a high-molecular-mass HA species and HA fragments, in addition to the HA species present in the normal individual's saliva. These results show that HYAL1 is the major tumor-derived HAase expressed in HNSCC. Furthermore, HA and HAase may be sensitive and specific markers for detecting HNSCC and monitoring its recurrence. Further studies are needed to confirm these preliminary studies.
Hydrogen plasma dry etching method for field emission application (2006)

The ability to fabricate large-area, uniform emitters is an important factor in many vacuum microelectronics applications, especially for field emission displays. In this letter, we measured the field emission properties of uniform silicon nanowire emitters prepared by hydrogen plasma etching using in situ high-resolution scanning electron microscopy and a tungsten anode of 1μm diameter. Our results indicate that the field emission properties are improved upon increasing the etching time; this process sharpens the nanowires’ geometry and lowers their work function. These highly uniform (with respect to length, diameter, and distribution) nanowires display great potential for application within many field emission nanoelectronics devices.
Regulation of carbohydrate metabolism by 2,5-anhydro-D-mannitol. (1983)

In hepatocytes isolated from fasted rats, 2,5-anhydromannitol inhibits gluconeogenesis from lactate plus pyruvate and from substrates that enter the gluconeogenic pathway as triose phosphate. This fructose analog has no effect, however, on gluconeogenesis from xylitol, a substrate that enters the pathway primarily as fructose 6-phosphate. The sensitivity of gluconeogenesis to 2,5-anhydromannitol depends on the substrate metabolized; concentrations of 2,5-anhydromannitol required for 50% inhibition increase in the order lactate plus pyruvate less than dihydroxyacetone less than glycerol less than sorbitol less than fructose. The inhibition by 2,5-anhydromannitol of gluconeogenesis from dihydroxyacetone is accompanied by an increase in lactate formation and by two distinct crossovers in gluconeogenic-glycolytic metabolite patterns-i.e., increases in pyruvate concentrations with decreases in phosphoenolpyruvate and increases in fructose-1,6-bisphosphate concentrations with little change in fructose 6-phosphate. In addition, 2,5-anhydromannitol blocks the ability of glucagon to stimulate gluconeogenesis and inhibit lactate production from dihydroxyacetone. 2,5-Anhydromannitol decreases cellular fructose 2,6-bisphosphate content in hepatocytes; therefore the effects of the fructose analog are not mediated by fructose 2,6-bisphosphate, a naturally occurring allosteric regulator. 2,5-Anhydromannitol also inhibits gluconeogenesis in hepatocytes isolated from fasted diabetic rats, but higher concentrations of the analog are required.
A Contribution to the Theory of Economic Growth (1956)

I. Introduction, 65. — II. A model of long-run growth, 66. — III. Possible growth patterns, 68. — IV. Examples, 73. — V. Behavior of interest and wage rates, 78. — VI. Extensions, 85. — VII. Qualifications, 91.
Interferon RNA of embryonic origin is expressed transiently during early pregnancy in the ewe. (1988)

Ovine trophoblast protein-1 (oTP-1), an interferon of embryonic origin, is produced during the peri-implantation period of early pregnancy. Secretion of oTP-1 is detectable between days 13 and 21, but not beyond. In this study, the levels of oTP-1 mRNA in embryos were analyzed to determine if they reflected the transient nature of oTP-1 production. Total cellular RNA (tcRNA) was isolated from embryos representing day 12 (n = 5), 14 (n = 7), 16 (n = 5), 18 (n = 6), 20 (n = 4), and 22 (n = 5) of pregnancy and spotted on nylon membranes. Complementary RNA was transcribed from a specific oTP-1 cDNA (550 base pairs) template and applied (16-1000 pg) to nylon membranes to develop a standard curve. The fixed RNA samples were then allowed to hybridize with the 32P-labeled oTP-1 cDNA. oTP-1 mRNA was not detectable on day 12, increased to high levels (3.6 +/- 1.6 ng/ug of embryo DNA) on day 14, decreased about 5-fold by day 16, 15-fold by day 18, 170-fold by day 20, and 200-fold by day 22 of pregnancy. At day 14 oTP-1 mRNA comprised 0.060 +/- 0.019% of the tcRNA and was more abundant than actin mRNA. Northern analyses of pooled tcRNA representing each day of pregnancy showed that the oTP-1 probe hybridized to a single class of mRNA (approximately 1.1 kilobases) and confirmed the results obtained with dot blots.
MODEL SYSTEMS FOR THE STUDY OF SEVEN-TRANSMEMBRANE-SEGMENT RECEPTORS (1991)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Apolipoprotein E‐derived antimicrobial peptide analogues with altered membrane affinity and increased potency and breadth of activity (2007)

Host-derived anti-infective proteins represent an important source of sequences for designing antimicrobial peptides (AMPs). However such sequences are often long and comprise diverse amino acids with uncertain contribution to biological effects. Previously, we identified a simple highly cationic peptide derivative of human apolipoprotein E (apoEdp) that inhibited a range of microorganisms. Here, we have dissected the protein chemistry underlying this activity. We report that basic residues and peptide length of around 18 residues were required for activity; however, the Leu residues can be substituted by several other residues without loss of activity and, when substituted with Phe or Trp, resulted in peptides with increased potency. These apoEdp-derived AMPs (apoE-AMPs) showed no cytotoxicity and minimal haemolytic activity, and were active against HIV and Plasmodium via an extracellular target. CXCR4 and CCR5 strains of HIV were inhibited though an early stage in viral infection upstream of fusion, and a lack of inhibition of vesicular stomatitis virus G protein pseudotyped HIV-1 suggested the anti-HIV activity was relatively selective. Inhibition of Plasmodium invasion of hepatocytes was observed without a direct action on Plasmodium integrity or attachment to cells. The Trp-substituted apoE-AMP adhered to mammalian cells irreversibly, explaining its increased potency; NMR experiments confirmed that the aromatic peptides also showed stronger perturbation of membrane lipids (relative to apoEdp). Our data highlight the contribution of specific amino acids to the activity of apoEdp (and also potentially unrelated AMPs) and suggest that apoE-AMPs may be useful as lead agents for preventing the early stages of HIV and Plasmodium cellular entry.
The binding affinity and dissociation rates of peptides for class I major histocompatibility complex molecules (1991)

Peptides of various lengths derived from the influenza nucleoprotein (NP) bind to H-2Db class I molecules with affinities at 4 degrees C between approximately 3 x 10(5)- approximately 3 x 10(7) M-1. The peptide with the highest affinity corresponds to the sequence of nine amino acids (NP366-374) recently isolated from cells infected with influenza. This peptide forms stable complexes with half-lives greater than 110 h at 4 degrees C, 39 h at 22 degrees C and 3 h at 37 degrees C. Small increases in length of the peptide greatly reduce the stability of the complex (t1/2 approximately 1-10 h at 4 degrees C). These results may explain the homogeneous length of peptides isolated from class I molecules formed in vivo, and suggest that class I and II may differ in their dependence on the length of peptides for the formation of stable complexes.
Dynamics of the Galactic Bulge using Planetary Nebulae (1996)

Evidence for a bar at the center of the Milky Way triggered a renewed enthusiasm for dynamical modelling of the Galactic bar-bulge. Our goal is to compare the kinematics of a sample of tracers, planetary nebulae, widely distributed over the bulge with the corresponding kinematics for a range of models of the inner Galaxy. Three of these models are N-body barred systems arising from the instabilities of a stellar disk (Sellwood, Fux and Kalnajs), and one is a Schwarzschild system constructed to represent the 3D distribution of the COBE/DIRBE near-IR light and then evolved as an N-body system for a few dynamical times (Zhao). For the comparison of our data with the models, we use a new technique developed by Saha (1998). The procedure finds the parameters of each model, i.e. the solar galactocentric distance R_o in model units, the orientation angle phi, the velocity scale (in km/s per model unit), and the solar tangential velocity which best fit the data.
Production and propagation of single-event transients in high-speed digital logic ICs (2004)

The production and propagation of single-event transients in scaled metal oxide semiconductor (CMOS) digital logic circuits are examined. Scaling trends to the 100-nm technology node are explored using three-dimensional mixed-level simulations, including both bulk CMOS and silicon-on-insulator (SOI) technologies. Significant transients in deep submicron circuits are predicted for particle strikes with linear energy transfer as low as 2 MeV-cm/sup 2//mg, and unattenuated propagation of such transients can occur in bulk CMOS circuits at the 100-nm technology node. Transients approaching 1 ns in duration are predicted in bulk CMOS circuits. Body-tied SOI circuits produce much shorter transients than their bulk counterparts, making them more amenable to transient filtering schemes based on temporal redundancy. Body-tied SOI circuits also maintain a significant advantage in single-event transient immunity with scaling.
Submicron Multiphoton Free-Form Fabrication of Proteins and Polymers:  Studies of Reaction Efficiencies and Applications in Sustained Release (2000)

Nonlinear multiphoton photo-cross-linking and photopolymerization of proteins and polymers in solution have been used to direct the three-dimensional assembly of micron scale objects. Two aspects of fabricated proteinatious matrixes are examined in this paper: the efficiency of protein photopolymerization and the application of fabricated matrixes as sustained release devices. The efficiency of photoactivated cross-linking of the proteins bovine serum albumin and fibrinogen, using rose bengal, have been determined and found to vary with photosensitizer concentration. This concentration dependence suggests that the mechanism for protein cross-linking is a direct hydrogen transfer between an amino acid residue of the protein and the dye molecule itself. A comparison of the surface structure of single and multiple protein oligomers is undertaken and shown to vary significantly depending on fabrication materials. Alkaline phosphatase bioactivity, upon entrapment in a protein structure, is maintained. The properties of fabricated protein matrixes as sustained release devices is also examined. The rates of diffusion of fluorescently labeled dextrans (10 and 40 kDa) from an optically fabricated BSA matrix vary with molecular weight and are linear with cross-link density. The half-life of release of 10 kDa dextran-TMR from a BSA micron scale structure is less than or equal to 6 min while 40 kDa dextran-TMR half-life of release is 25 min. Finally, rhodamine 610, a typical drug size molecule, was entrapped in an acrylamide structure, and its release is found to be diffusion-limited with half-lives of 10−31 min, depending on cross-link density.
Optical Coherence Elastography of Engineered and Developing Tissue (2006)

Biomechanical elastic properties are among the many variables used to characterize in vivo and in vitro tissues. Since these properties depend largely on the micro- and macroscopic structural organization tissue, it is crucial to understand the mechanical properties and the alterations that occur tissues respond to external forces or to disease processes. Using a novel technique called coherence elastography (OCE), we mapped the spatially distributed mechanical displacements strains in a representative model of a developing, engineered tissue as cells began to proliferate attach within a three-dimensional collagen matrix. OCE was also performed in the complex tissue of the Xenopus laevis (African frog) tadpole. Displacements were quantified a cross-correlation algorithm on pre- and postcompression images, which were acquired using coherence tomography (OCT). The images of the engineered tissue were acquired over a 10-development period to observe the relative strain differences in various regions. OCE was able differentiate changes in strain over time, which corresponded with cell proliferation and matrix as confirmed with histological observations. By anatomically mapping the regional variation stiffness with micron resolution, it may be possible to provide new insight into the complex by which engineered and natural tissues develop complex structures.
Conoscopic holography I Basic principles and physical basis (1992)

Conoscopic holography is an incoherent holographic technique based on the properties of crystal optics. More precisely, for each point of the object, the interference pattern between the ordinary and the extraordinary rays is presented. The pattern is a Gabor-zone-lens pattern, with a scale parameter that is a function of the distance of the point. The superposition of the Gabor zone lens from each point of the object is the hologram, which contains information on the shape of the object through the scale-parameter dependence of each point is presented. I present a simplified version of the theory of conoscopic holography. The point-spread function and the transfer function of the conoscopic system are presented by using simple arguments, and the conoscopic hologram is defined. The basic schemes for reconstruction, i.e., retrieving, optically or numerically, this three-dimensional information about the object from the recorded hologram, are presented. Finally, the resolution of the system is quantified.
Influence of glycosylation on allelic and cell-specific Mr variation, receptor processing, and ligand binding of the human complement C3b/C4b receptor. (1986)

The human complement C3b/C4b receptor (CR1), a single chain membrane glycoprotein of Mr approximately 200,000, has several cell-specific Mr variations as well as an allelic variation involving four phenotypes whose Mr values span a range of 90,000. We investigated the role of glycosylation in these structural variations and in receptor metabolism. In the human HL-60 promyelocytic leukemic cell line differentiated toward granulocytes or monocytes and in Epstein-Barr virus-transformed B lymphoblastoid cell lines of the common phenotype, CR1 is synthesized as a precursor of Mr = 222,000 that is converted into mature CR1s with differing Mr values. Endoglycosidase F treatment of mature CR1 from all these cell types produced the same lower Mr band. Additionally, the previously noted 5,000 higher Mr of CR1 from human peripheral granulocytes versus erythrocytes was abrogated by endoglycosidase F. Hence these cell-specific variations are due to differences in N-glycosylation. Lectin affinity chromatography shows that these N-linked oligosaccharides are mostly tri- and tetraantennary complex-type species with specific differences in fractionation patterns that correlate with their differing Mrs. In lymphoblastoid cell lines, the four allelic variants each have a precursor 6,000 lower in Mr than the respective mature CR1. In the presence of tunicamycin, each of the CR1 allelic products is 25,000 lower in Mr than the glycosylated receptor. The failure to radiolabel CR1 with [3H]glucosamine in the presence of tunicamycin indicates the lack of O-linked oligosaccharide on CR1. These data, taken together, strongly suggest that the CR1 polymorphism resides at the polypeptide level. Nonglycosylated CR1 synthesized in the presence of tunicamycin had twice the turnover rate of glycosylated CR1. The efficiency of surface membrane insertion and of ligand binding to hemolytically inactive C3 were markedly reduced for nonglycosylated CR1, suggesting that glycosylation is important for the proper expression of CR1 function.
Using reading behavior to predict grammatical functions (2015)

This paper investigates to what extent grammatical functions of a word can be predicted from gaze features obtained using eye-tracking. A recent study showed that reading behavior can be used to predict coarse-grained part of speech, but we go beyond this, and show that gaze features can also be used to make more finegrained distinctions between grammatical functions, e.g., subjects and objects. In addition, we show that gaze features can be used to improve a discriminative transition-based dependency parser.
Development of Intracoronary Local Adhesive Delivery Technique (1997)

Acute coronary occlusion may occur in weak coronary atherosclerotic lesions, including dissection, ulceration or thrombus. In some cases of occlusion "bail-out" is performed by using recently developed New Devices. However, these have not yet completely solved the problem to this end, we designed a new method of coronary revascularization, the Intracoronary Local Adhesive Delivery Technique, utilizing antithrombotic and absorbable adhesive injected locally into the fragile and morbid arterial wall using a drug delivery PTCA catheter more flexible than the existing New Devices. This adhesive strengthened and hardened the lesions. In this study, we examined the efficacy of making an adhesive cylinder in arteries of similar size to the coronary, through acute animal experiments using the existing clinical adhesives and drug delivery PTCA catheters and 12 femoral arteries of adult goats. We were successful in forming firm tunnels along the inside of six arteries, infused with approximately 0.04 ml Cyanoacrylate. These tunnels were observed with intravascular ultrasound (IVUS) imaging and evaluated microscopically. These results suggest the feasibility of this method as a new approach for making synthetic resinous stents.
Expression of Amyotrophic Lateral Sclerosis-linked SOD1 Mutant Increases the Neurotoxic Potential of Microglia via TLR2 (2008)

Amyotrophic lateral sclerosis (ALS) is a progressive motor neuron disease, in which activated microglia overexpressing ALS-linked SOD1 mutants (mSOD1) are known to contribute to neuronal death. However, it is unclear how mSOD1 expression affects micoglial activation and subsequently damages neurons. In this study, we created mSOD1-overexpressing BV-2 microglial cell lines. Following TLR2, but not TLR4 stimulation, we observed that overexpression of human SOD1 G93A, L8Q, or G10V mutant, as compared with the wild-type SOD1 or a mock control, significantly enhanced microglial secretion of a neurotoxic cytokine, tumor necrosis factor-alpha (TNF-alpha), which was dependent on the NADPH-oxidase-mediated increased generation of reactive oxygen species (ROS). In further experiments, we demonstrated that mSOD1 expression regulated TNF-alpha secretion at a post-transcriptional level and involved ROS-sensitive TNF-alpha-converting enzymes, e.g. ADAM10 and -17, which shed TNF-alpha from its membrane-anchored precursor. Together with a recent report that the function of SOD1, as a self-regulating redox sensor in NADPH oxidase-dependent ROS production, is lost due to its genetic mutations, we conclude that mSOD1 expression in ALS facilitates microglial neurotoxic inflammatory responses via TLR2, which is mediated by an uncontrolled ROS generation. The link, between mSOD1, innate immunity and NADPH oxidase, offers new opportunities in ALS therapies.
Animal Models for Human Hematopoiesis (1992)

Despite seminal contributions provided by in vitro studies to the field of hematopoiesis, our present knowledge of mammalian lymphohemopoiesis and the mechanisms governing differentiation and self-renewal of hematopoietic stem cells has been derived in most part from elegant in vivo studies. The inability to apply such an approach to the examination of the human hematopoietic system is the primary reason why several aspects of human hematopoiesis including human stem cell biology are still poorly understood. To overcome the inability to probe human hematopoiesis in vivo, researchers have "humanized" animals via the transplantation of human hematopoietic progenitor cells and other tissues in an attempt to create human-animal chimera suitable for investigating human lymphohematopoiesis in vivo. To date, several of these "humanized" animal models have been developed. During their relatively short existence, human-animal models have contributed substantially to the field of experimental hematology. The development, peculiarities, shortcomings, and applications of these animal models as well as their potential use in exploring the field of human lymphohematopoiesis are the focus of this review.
Occurrence of a Quadruplex Motif in a Unique Insert within Exon C of the Bovine Estrogen Receptor α Gene (ESR1) (2010)

The 5' end of exon C of the bovine estrogen receptor alpha gene (bov-ESR1) includes a unique G-rich insert, not found in other closely related mammalian genes, which lies close to both a double E-box transcription factor binding site and the site of a single nucleotide (G/A) polymorphism. Biophysical studies, using CD and UV absorbance measurements, show that this 22 base insert leads to the formation of a family of stable G-quadruplex structures which are unaffected by the G/A polymorphism. Multiplex PCR shows that the region including the G-quadruplex is transcribed into RNA, and studies with a synthetic RNA transcript sequence demonstrated formation of a highly stable parallel-folded quadruplex structure. Luciferase reporter constructs demonstrate that the G-rich sequence reduces rates of translation when present in the 5'-UTR of mRNA transcripts. Mutations (GGG to AAA) that destabilize the quadruplex lead to a 15-fold enhancement of translational efficiency, suggesting that a possible biological role of the insert in exon C of the bov-ESR1 is to regulate translation of this exon.