gebhart/patrepeval huggingface dataset:
Identification of Cytokines Regulated by Phosphatidylinositol-3 Kinase in Ovarian Cancer. (2005)

Activation of phosphatidylinositol-3 kinase (PI3K) is a frequent event in ovarian cancer, leading to increased cell proliferation and inhibition of apoptosis. Although a number of proteins are reported to be involved in PI3K signalling, many targets of this pathway remain unknown. We have previously used proteomic tools to identify several cytokines, including chemokines IL-8 and CXCL1, regulated by PI3K in ovarian cancer. This study aims to identify further novel cytokine targets of PI3K signalling which may point to candidate markers for this pathway and lead to novel therapeutic targets for ovarian cancer. We measured the expression of 120 cytokines in conditioned media and cell lysates from OV167 ovarian adenocarcinoma cells using RayBiocytokine antibody arrays (RayBiotech, Norcross, GA, USA). Cells were subjected to the following treatments for 48h: (1) untreated control; (2) 50 mg/ml EGF; (3) 10 M PI3Kinhibitor LY294002; (4) EGF + LY294002. Conditioned media or cell lysates were incubated with the blocked arrays at 4C overnight and arrays were processed according to the manufacturer's instructions. The chemiluminescent signal was detected usingthe Fuji LAS3000 chemiluminescence reader and quantified by Image Gauge software. Proteins induced at least 2-fold by EGF and inhibited by LY294002 were considered regulated by PI3K signalling. To validate this approach, the concentration of CXCL1was also measured by in-house RIA and compared to the chemiluminescent signal intensity detected on the cytokine arrays. The array signal intensity for CXCL1 showed good correlation to RIA concentrations (R2 = 0.94), confirming the quantitative nature of the arrays. Several cytokines up-regulated by EGF and inhibited by LY294002were identified. These cytokines included IL-6, IL-8 and CXCL1, previously associated with ovarian cancer, as well as a number of other cytokines, not previously reported to beinvolved in PI3K signalling in ovarian cancer. Validation of these results is being performed by immunoassays. This study illustrates the use of antibody arrays in the identification of potential pathway-specific therapeutic targets using a cell model of ovarian cancer. This study was supported by an Australian Postgraduate Award and the Cancer Institute NSW.
Direct spectrophotometry of total bile acids in serum. (1981)

In this simple and direct method for determining total bile acids in serum, the serum was mixed with sodium pyruvate, a lactate dehydrogenase blocker, and bile acids were then measured spectrophotometrically after the following enzyme reaction. Bile acids are converted to 3-oxo bile acids with 3 alpha-hydroxysteroid dehydrogenase (EC 1.1.1.50) with concomitant reduction of NAD+ to NADH. The hydrogen in the NADH generated is transferred by diaphorase (EC 1.6.4.3) to nitrotetrazolium blue to yield diformazan 540 nm). Analytical recovery of the various bile acids in serum averaged 96.2%. The CV for the day-to-day variation was 4.3%. Normal values are less than 7 mumol/L. Total serum bile acids were estimated by this method in 118 fasting patients with various liver diseases. This determination is clearly shown to be useful as a liver-function test.
<title>System specification and requirements for fiber-in-the-loop systems</title> (1993)

In Europe, massive deployment of Fiber in the Loop (FITL) in the 1990's will require that systems meet different national standards as well as international (CCITT and ETSI) recommendations. In addition, the US based Bellcore recommendations are used as a reference by some European operating companies. A number of technical issues are under study, and data from field trials is being collected by various operating companies to aid in definition of system specifications and requirements. However, specification differences between countries will continue to exist, and arriving at general and global specifications will require detailed study of a number of issues. In this paper we examine such issues encompassing: 1-fiber and 2-fiber transmission techniques for FITL telephony systems, including Time Division Multiplexing/Time Division Multiple Access (TDM/TDMA) and Time Compression Multiplexing (TCM), optical plant requirements including backreflection and directivity requirements on passive optical network components, and the effect of FITL round trip delay (RTD) on network performance. The goal of this work is to provide an analysis of these issues in order to clarify some of the discrepancies between standardization organizations and provide operating companies a global solution for FITL.
Dissecting the human BDNF locus: Bidirectional transcription, complex splicing, and multiple promoters (2007)

Brain-derived neurotrophic factor (BDNF), a member of the nerve growth factor family of neurotrophins, has central roles in the development, physiology, and pathology of the nervous system. We have elucidated the structure of the human BDNF gene, identified alternative transcripts, and studied their expression in adult human tissues and brain regions. In addition, the transcription initiation sites for human BDNF transcripts were determined and the activities of BDNF promoters were analyzed in transient overexpression assays. Our results show that the human BDNF gene has 11 exons and nine functional promoters that are used tissue and brain-region specifically. Furthermore, noncoding natural antisense RNAs that display complex splicing and expression patterns are transcribed in the BDNF gene locus from the antiBDNF gene (approved gene symbol BDNFOS). We show that BDNF and antiBDNF transcripts form dsRNA duplexes in the brain in vivo, suggesting an important role for antiBDNF in regulating BDNF expression in human.
Black Box Features for the WMT 2012 Quality Estimation Shared Task (2012)

In this paper we introduce a number of new features for quality estimation in machine translation that were developed for the WMT 2012 quality estimation shared task. We find that very simple features such as indicators of certain characters are able to outperform complex features that aim to model the connection between two languages. 1
Subtractive hybridization system using single-stranded phagemids with directional inserts (1990)

We describe a subtractive hybridization protocol which is designed to permit subtractions between cDNA libraries. The method uses single-stranded phagemids with directional inserts as both the driver and the target. We modified the M13 phagemid vector pBluescript for the directional cDNA cloning and subtractive hybridization. Two simplified methods for efficient construction of directional cDNA libraries are also described. Using a model system, we found that one round of subtractive hybridization results in a 5,000-fold specific subtraction of abundant molecules. We used two methods to quantify the efficiency and verify the specificity of the subtraction. In order to obtain these subtraction efficiencies, it was necessary to develop a method to purify the single-stranded DNA to homogeneity. The single-stranded purification involved using potassium iodide (KI) density centrifugation, restriction endonuclease digestion and phenol extraction in the presence of magnesium. We describe the several advantages of using directional inserts for the subtraction procedure.
Properties of Nicotinamide Adenine Dinucleotide Phosphate-Dependent Formate Dehydrogenase from Clostridium thermoaceticum (1966)

Li, Lan-Fun (Western Reserve University School of Medicine, Cleveland, Ohio), Lars Ljungdahl, and Harland G. Wood. Properties of nicotinamide adenine dinucleotide phosphate-dependent formate dehydrogenase from Clostridium thermoaceticum. J. Bacteriol. 92: 405-412. 1966.-A nicotinamide adenine dinucleotide phosphate (NADP)-dependent formate dehydrogenase has been isolated from C. thermoaceticum. The enzyme is very sensitive to oxygen and requires sulfhydryl compounds for activity. The apparent K(m) at 50 C and pH 7.0 for NADP is 5.9 x 10(-5)m and for formate, 2.2 x 10(-4)m. The enzyme is most active at about 60 C and at pH values between 7.0 and 9.0. The enzyme catalyzes an exchange between C(14)O(2) and formate, which requires NADP, but net synthesis of formate from CO(2) and reduced nicotinamide adenine dinucleotide phosphate could not be demonstrated. The reaction does not involve ferredoxin.
Condensed heteroaromatic ring systems. VIII Synthesis of 3-substituted isocoumarins from o-halobenzoic acid derivatives. (1986)

The hydration of o-ethynylbenzoic acid derivatives, such as ethyl o-ethynylbenzoate, o-ethynylbenzonitrile, and o-ethynylbenzamide, in sulfuric acid in the presence of marcuric sulfate, afforded 3-substituted isocoumarins. The palladium-catalyzed reaction of o-halobenzoic acid derivatives with terminal acetylenes to obstain the starting materials for the cyclization is also described.
Dissolution studies on tablets of ibuprofen using chitosan. (1999)

An attempt has been made to study the release retardant behaviour of chitosan in ibuprofen tablets. Three different ibuprofen tablets were prepared by using 1,3 and 5% chitosan paste. In vitro evaluations were carried out by using dissolution testing apparatus U.S.P (XXI). The dissolution pattern indicated the role of chitosan in sustained release. Bioavailability studies in male beagle dogs clearly showed the sustained nature of release from chitosan based ibuprofen tablet as compared to conventional ibuprofen marketed formulation. Potential use of chitosan as a new matrix forming material for sustained release preparation has been examined. Chitosan, a natural polysaccharide, has structural characteristics similar to glycosamino glycons. Chitosan has been shown to be non-toxic and biodegradable. It is inexpensive and has been explored in the present investigation as a release retarding agent in ibuprofen tablets.
Fines in Fluidized Bed Silane Pyrolysis (1984)

Silicon deposition on silicon seed particles by silane pyrolysis in a fluidized bed reactor is being investigated as a low cost, high throughput method to produce high purity polysilicon for solar cell applications. Studies of fines, particles 0.1–10μ diam, initiated from homogeneous decomposition in the reactor were conducted using 2 and 6 in. diam fluidized beds. The studies show functional dependences of fines elutriation on operating parameters such as silane feed concentration, temperature, gas velocity, and bubble size. The observation that the fines elutriation is generally below 10% of the silicon‐in‐silane feed is explained using a concept of scavenging by large particles in an environment of less free space for homogeneous nucleation. Preliminary results suggest that, with proper conditions and distributor design, high silane concentration ( in ) feed may be used for silicon production in fluidized bed reactors.
SDP: Session Description Protocol (2006)

This memo defines the Session Description Protocol (SDP). SDP is intended for describing multimedia sessions for the purposes of session announcement, session invitation, and other forms of multimedia session initiation. This document obsoletes RFC 4566.
Surface Analysis of Polymers Treated by Remote Atmospheric Pressure Plasma (2009)

The surfaces of high-density polyethylene (HDPE), poly(methyl methacrylate) (PMMA), and polyethersulfone (PES) were treated with a low-temperature, atmospheric pressure oxygen and helium plasma. The polymers were exposed to the downstream afterglow of the plasma, which contained primarily oxygen atoms and metastable oxygen molecules ((1)Delta(g) O(2)), and no ions or electrons. X-ray photoelectron spectroscopy (XPS) of HDPE revealed that 20% of the carbon atoms were converted into oxidized functional groups, with about half of these being carboxylic acids. Attenuated total reflection infrared spectroscopy of all three polymers was obtained in order to determine the types of functional groups formed by atmospheric plasma exposure. It was found that the polymers were rapidly oxidized with addition of alcohols, ketones, and carboxylic acids to the carbon backbone. Chain scission occurred on HDPE and PMMA, while on PES the aromatic groups underwent ring-opening and insertion of carboxylic acid.
Quantitative Analysis of Nuclear Localization Signal (NLS)-Importin α Interaction through Fluorescence Depolarization (2000)

We have developed a quantitative in vitro steady-state fluorescence depolarization assay to measure the interaction of a nuclear localization signal (NLS) substrate with its receptors. This assay relies on the change in fluorescence depolarization of an NLS fused to the green fluorescent protein upon binding to receptor. No binding is observed in the absence of a functional NLS, and binding affinities measured correlate with previous in vivo studies of NLS function. We have used this assay to test an auto-inhibitory model for the interaction of an NLS with the NLS receptor complex. This model suggests that NLS binding to importin alpha is modulated by an auto-inhibitory sequence within the N terminus of importin alpha, which is displaced by importin beta binding. Consistent with this model, NLS substrates bind tightly to an N-terminally truncated importin alpha lacking the auto-inhibitory domain (K(d) approximately 10 nm), but measurable binding to full-length importin alpha is only observed upon addition of importin beta. Our quantitative results support the auto-inhibitory model and suggest a mechanism for a switch between a cytoplasmic, high affinity and a nuclear, low affinity NLS receptor. This predicted mode of interaction would facilitate binding of substrate in the cytoplasm and its subsequent release into the nucleus.
The lyophilization of pharmaceuticals: a literature review. (1984)

The freeze-drying of pharmaceutical products is discussed in successive stages involving the freezing of the product, the sublimation of ice (primary drying) and the desorption of water (secondary drying) from the product. The factors influencing the physical characteristics of the end product and the drying rate, e.g., freezing pattern and chamber pressure, are discussed in detail. Methods for studying the freezing characteristics of drug solutions, namely thermal analysis, resistance measurements, D2 analysis and microscopy, are described. The primary drying stage is influenced by external factors such as chamber pressure and shelf temperature, and by internal factors such as concentration and the degree of crystallization of the water in the sample. Methods for determining the end point of secondary drying and some problems often encountered (including those concerned with the equipment) in freeze-drying are discussed.
Regulatory T Cells in Immunologic Self-Tolerance and Autoimmune Disease (2005)

Naturally arising CD25+ CD4+ regulatory T cells play key roles in the maintenance of immunologic self-tolerance and negative control of various immune responses. The majority, if not all, of them are produced by the normal thymus as a functionally distinct T-cell subpopulation, and their generation is in part developmentally controlled. Genetic abnormality in the development and function of this population can indeed be a cause of autoimmune disease, immunopathology, and allergy in humans. This regulatory population can be exploited to prevent and treat autoimmune disease by strengthening and reestablishing immunologic self-tolerance.
Quantifying carbon-nanotube species with resonance Raman scattering (2005)

The method for quantifying the amount of each carbon nanotube specie, as defined by its diameter and chiral angle, as well as the semiconducting-to-metallic ratio in any type of carbon nanotube sample is discussed. Single-wall carbon nanotubes grown by the cobalt-molybdenum catalyst based (CoMoCAT) process are characterized. The semiconducting-to-metallic ratio is found to be 11:1. A single semiconducting specie, named the (6,5) nanotube represents $2∕5$ of the sample, while the most abundant metallic nanotube is the (7,4), which exhibits a diameter similar to the (6,5).
A HISTORY OF BORON NEUTRON CAPTURE THERAPY OF BRAIN TUMOURS (1991)

Boron neutron capture therapy (BNCT) is a form of radiation therapy mediated by the short-range (less than 10 microns) energetic alpha (4He) and lithium-7 (7Li) ionizing particles that result from the prompt disintegration by slow neutrons of the stable (nonradioactive) nucleus boron-10 (10B). Recent advances in radiobiological and toxicological evaluation of tumour-affinitive boron-containing drugs and in optimization of the energies of neutrons in the incident beam have spurred interest in BNCT. This article presents a history of BNCT that emphasizes studies in the USA. A new dosimetric analysis of the 1959-1961 clinical trials of BNCT at Brookhaven National Laboratory is also presented. This analysis yields an acute radiation dose tolerance limit estimate of approximately 10 Gy-Eq to the capillary endothelium of human basal ganglia from BNCT. (Gy-Eq: Gray-equivalent, or relative biological effectiveness of a radiation component multiplied by the physical dose of the component (Gy), summed over the component kinds of radiation.)
Another application for trellis shaping: PAR reduction for DMT (OFDM) (2000)

A bound for the possible reduction of the peak-to-average ratio (PAR) dependent on the rate as well as possible practical procedures are presented. The idea of trellis shaping, originally used to minimize average transmit power in single-carrier systems, is applied to the problem of PAR reduction in multicarrier transmission. Its impact, as a function of code rate, as well as design practicability is considered using metrics in both the time and frequency domains.
Neuromorphic photonic networks using silicon photonic weight banks (2017)

Photonic systems for high-performance information processing have attracted renewed interest. Neuromorphic silicon photonics has the potential to integrate processing functions that vastly exceed the capabilities of electronics. We report first observations of a recurrent silicon photonic neural network, in which connections are configured by microring weight banks. A mathematical isomorphism between the silicon photonic circuit and a continuous neural network model is demonstrated through dynamical bifurcation analysis. Exploiting this isomorphism, a simulated 24-node silicon photonic neural network is programmed using "neural compiler" to solve a differential system emulation task. A 294-fold acceleration against a conventional benchmark is predicted. We also propose and derive power consumption analysis for modulator-class neurons that, as opposed to laser-class neurons, are compatible with silicon photonic platforms. At increased scale, Neuromorphic silicon photonics could access new regimes of ultrafast information processing for radio, control, and scientific computing.
Enzyme- Linked Immunosorbent Assay (ELISA) (1998)

Enzyme-Linked Immunosorbent Assays (ELISAs) have had many thousands of applications over the past 25 yr The technique has been used in all fields of pure and applied aspects of biology, in particular it forms the backbone of diagnostic tech- niques The systems used to perform ELISAs make use of antibodies These are pro- teins produced in animals in response to antigenic stimuli Antibodies are specific chemicals that bind to the antigens used for their production thus they can be used to detect the particular antigens if binding can be demonstrated Conversely, specific antibodies can be measured by the use of defined antigens, and this forms the basis of many assays in diagnostic biology
Block shuffling on top of error concealment for wireless image transmissions (2002)

Nowadays the image and video compression standards employ variable length coding (VLC). One disadvantage of using VLC is that whenever an error occurs, it propagates until the next resynchronization can be achieved. Error propagation under fading conditions makes severe destruction in a bundle of blocks within an image. In such situations, error concealment may not perform well due to the missing information in consecutive blocks. In this paper, block shuffling is proposed for the purpose of randomizing the blocks' location so as to minimize the chance of getting groups of error blocks. Image transmissions under AWGN and fading channels are simulated and the enhancement of the error concealment performance is investigated.
Hydrogen-bonding patterns in 3-alkyl-3-hydroxyindolin-2-ones (2010)

The molecules of racemic 3-benzoylmethyl-3-hydroxyindolin-2-one, C(16)H(13)NO(3), (I), are linked by a combination of N-H...O and O-H...O hydrogen bonds into a chain of centrosymmetric edge-fused R(2)(2)(10) and R(4)(4)(12) rings. Five monosubstituted analogues of (I), namely racemic 3-hydroxy-3-[(4-methylbenzoyl)methyl]indolin-2-one, C(17)H(15)NO(3), (II), racemic 3-[(4-fluorobenzoyl)methyl]-3-hydroxyindolin-2-one, C(16)H(12)FNO(3), (III), racemic 3-[(4-chlorobenzoyl)methyl]-3-hydroxyindolin-2-one, C(16)H(12)ClNO(3), (IV), racemic 3-[(4-bromobenzoyl)methyl]-3-hydroxyindolin-2-one, C(16)H(12)BrNO(3), (V), and racemic 3-hydroxy-3-[(4-nitrobenzoyl)methyl]indolin-2-one, C(16)H(12)N(2)O(5), (VI), are isomorphous in space group P-1. In each of compounds (II)-(VI), a combination of N-H...O and O-H...O hydrogen bonds generates a chain of centrosymmetric edge-fused R(2)(2)(8) and R(2)(2)(10) rings, and these chains are linked into sheets by an aromatic pi-pi stacking interaction. No two of the structures of (II)-(VI) exhibit the same combination of weak hydrogen bonds of C-H...O and C-H...pi(arene) types. The molecules of racemic 3-hydroxy-3-(2-thienylcarbonylmethyl)indolin-2-one, C(14)H(11)NO(3)S, (VII), form hydrogen-bonded chains very similar to those in (II)-(VI), but here the sheet formation depends upon a weak pi-pi stacking interaction between thienyl rings. Comparisons are drawn between the crystal structures of compounds (I)-(VII) and those of some recently reported analogues having no aromatic group in the side chain.
Retrovirus mutation rates and their role in genetic variation. (1998)

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.
Deposition of Tin Oxide into Porous Silicon by Atomic Layer Epitaxy (1996)

The deposition of conformal coatings into porous silicon layers was successfully demonstrated. Tin oxide films were formed from and precursors by atomic layer epitaxy. The influence of the porous substrate structure on the deposition parameters was analyzed from the viewpoint of formation mechanism, growth rate, and layer composition. The covered porous substrates were characterized by means of Rutherford backscattering, secondary ion mass spectrometry, cross‐sectional transmission electron microscopy, and ellipsometry. The mesoporous structure of the Si substrate uniquely determines the gas‐phase diffusion and physisorption of the precursors. The processing parameters favoring chemisorption are more critical for porous silicon than those for a flat surface. Even a small decrease in the deposition temperature results in a considerable increase in the growth rate through gas‐phase reactions, and the process becomes chemical vapor deposition‐like. Conformal step coverage was obtained on extremely high (140:1) aspect ratio pores if the deposition conditions were chosen such that chemisorption was the growth rate determining step in the process.