gebhart/patrepeval huggingface dataset:
Transcriptional Repression by RING Finger Protein TIF1 That Interacts with the KRAB Repressor Domain of KOX1 (1996)

Many of the vertebrate zinc finger factors of the Kruppel type (C2H2 zinc fingers) contain in their N-terminus a conserved sequence referred to as the KRAB (Kruppel-associated box) domain that, when tethered to DNA, efficiently represses transcription. Using the yeast two-hybrid system, we have isolated an 835 amino acid RING finger (C3HC4 zinc finger) protein, TIF1 beta (also named KAP-1), that specifically interacts with the KRAB domain of the human zinc finger factor KOX1/ZNF10. TIF1 beta, TIF1 alpha, PML and efp belong to a characteristic subgroup of RING finger proteins that contain one or two other Cys/His-rich clusters (B boxes) and a putative coiled-coil in addition to the classical C3HC4 RING finger motif (RBCC configuration). Like TIF1 alpha, TIF1 beta also contains an additional Cys/His cluster (PHD finger) and a bromo-related domain. When tethered to DNA, TIF1 beta can repress transcription in transiently transfected mammalian cells both from promoter-proximal and remote (enhancer) positions, similarly to the KRAB domain itself. We propose that TIF1 beta is a mediator of the transcriptional repression exerted by the KRAB domain.
Attenuation of the Neuropsychiatric Effects of Ketamine With Lamotrigine (2000)

Glutamate release-inhibiting drugs may reduce the hyperglutamatergic consequences of NMDA receptor dysfunction implicated in the pathophysiologic processes of neuropsychiatric illnesses such as schizophrenia. Further study is needed.
Immunostimulatory DNA for Allergic Asthma (2002)

Asthma is a common disease afflicting 17 million Americans, or approx 7% of the United States population (1). Asthma has increased in prevalence and has been associated with increased morbidity and mortality over the past two decades (2). In some developed Western countries, such as Great Britain and Australia, the estimated incidence of asthma is one in four children under the age of 14 (3). Although the reason for the increase in asthma prevalence is not well understood, one of the proposed explanations for the increased incidence of atopy in developed countries is the “hygiene hypothesis.” The hygiene hypothesis is based on the principle that, during a critical period of immune system maturation in infants genetically predisposed to atopy and Th2 responses to antigen, a reduction in previously encountered infectious stimuli (particularly with organisms such as mycobacteria, measles, and hepatitis A, which induce strong cell-mediated Th1 immune responses), has altered the Th1/Th2 lymphocyte balance in favor of Th2 responses (4). A reduced incidence of mycobacterial and viral infections is hypothesized to result in decreased IL-12 production by dendritic cells, and a consequent decrease in interferon-y generating Th1 lymphocytes, which would normally bias the immune response to a Th1 response to newly encountered antigens, and thus, inhibit the release of pro-allergic cytokines, such as IL-4 by Th2 lymphocytes (4).
MS New Dead-Crude Oil Asphaltene Inhibitor Test Method (2014)

Abstract Asphaltene deposition is a serious problem for deepwater subsea production systems. The potential for immense production losses coupled with the difficulties and expense in remediating deposition in subsea systems make it imperative that deepwater fields are evaluated for asphaltene concerns. If concerns exist, effective prevention treatments must be designed and employed. Therefore, having effective asphaltene inhibitors and correspondingly, better methods to evaluate inhibitor performance is extremely valuable for deepwater operators. This paper discusses a new dead-oil asphaltene stability analysis method which has shown to be effective in comparing asphaltene inhibitor performance. The method can also be used in field monitor programs. Although not a live-fluid deposition test, the method offers advantages over some currently used methods, like ASTM D7601-04. The method uses an analytical centrifuge to evaluate the stability of asphaltenes in crude oils which have been simultaneously subjected to a solvent that destabilizes asphaltenes and centrifugal force. In comparison to ASTM D7601-04, use of the new method provides a better measure of asphaltene inhibitor effectiveness in crude oils due to:the application of centrifugal force andthe ability to perform testing with higher crude oil concentrations / less destabilizing solvent. Note, ASTM D7601–04 uses more than 97 % destabilizing solvent. Its maximum recommended crude oil concentration is 2.67 %. The new asphaltene stability analysis method has been run at crude oil concentrations from 5 – 40 volume %. The ability to perform testing with less destabilizing solvent is particularly significant as only a fraction of the total asphaltenes deposit during production. In field conditions, only the more "insoluble" asphaltenes precipitate and deposit. By reducing the destabilized asphaltene fraction to only the more insoluble species, dead-crude oil test method conditions can be moved closer towards field conditions. The amount of asphaltenes destabilized can be altered with the choice of destabilizing solvent and amount of destabilizing solvent used. This is the approach used in the new test method. Also, by using significantly higher crude oil concentrations in the method, more destabilized asphaltenes can be generated during the test despite reducing the fraction of asphaltenes destabilized. By increasing the amount of destabilized asphaltenes, more stringent asphaltene inhibitor conditions are created in the testing since asphaltene agglomeration occurs more easily in higher-concentration environments. Further increasingly stringent conditions are created with the simultaneous application of the centrifugal force. It has been found that these more stringent conditions allow better differentiation in evaluating asphaltene inhibitor performance. This paper shows results from the new Asphaltene-Analytical Centrifuge Stability Analysis (Asphaltene-ACSA) method with different crude oils, destabilizing solvents, and asphaltene inhibitors.
Analyzing and Modifying Chord's Stabilization Algorithm to Handle High Churn Rates (2006)

Peer-to-peer (P2P) networks offer reliable and efficient services in different application scenarios. In particular, structured P2P protocols (like Chord (L. Stoica et al., 2001)) have to handle changes in the overlay topology fast and with as little signaling overhead as possible. This paper analyzes the ability of the Chord protocol to keep the network structure up to date, even in environments with high churn rates, i.e. nodes joining and leaving the network frequently. High churn rates occur, e.g., in mobile environments, where participants have to deal with the limited resources of their mobile devices, such as short battery lifetimes or high communication costs. In this paper, we analyze different design parameters and their influence on the stability of Chord-based network structures. We also present several modifications to the basic Chord stabilization scheme, resulting in a much more stable overlay topology.
Role of Aldehydic Derivatives in the Condensation of Phenolic Compounds with Emphasis on the Sensorial Properties of Fruit-Derived Foods (2002)

The reactions between (epi)catechin, mavidin 3-O-glucoside, and some aldehydes were investigated by LC/DAD and LC/ESI-MS analysis. The obtained results showed that the acetaldehyde-mediated condensation occurred more generally and glyoxylic acid, furfural, and 5-(hydroxymethyl)furfural (HMF) react in the same way in the first stages of the reactions. In terms of reactivity, reactions were faster with acetaldehyde than with glyoxylic acid, furfural, or HMF, where the reactions were slower. In the case of acetaldehyde, the obtained purple derivatives were more predominant and stable than the colorless adducts and no xanthylium salt was detected. Interactions involving glyoxylic acid yield purple adducts, which were obtained in small amount compared to the colorless ones. The latter were shown to proceed to more polymerized and yellowish derivatives. Finally, in the case of furfural and HMF, purple compounds involving flavanol and anthocyanin units were detected, and colorless compounds were shown to be predominant and to yield yellowish xanthylium salts.
How to read radiographs according to the Sharp/van der Heijde method. (1999)

This article is a short overview of the development of the Sharp/van der Heijde method for scoring radiographs of hands and feet in rheumatoid arthritis, in addition to a detailed description on how to use the scoring method.
The epithelial sodium channel. Subunit number and location of the amiloride binding site. (1987)

Sodium dodecyl sulfate gel electrophoresis of the radioiodinated native amiloride-sensitive epithelial sodium channel protein isolated from bovine renal papilla and cultured amphibian A6 cells under denatured and nonreduced conditions revealed an 125I-labeled protein band of Mr approximately 730,000. Upon reduction, this protein was resolved into five major polypeptide bands with apparent average Mr values of 315,000, 149,000, 95,000, 71,000, and 55,000. The amiloride analog [3H]methylbromoamiloride has been used as a photoaffinity label to determine the location of the binding site for amiloride on the epithelial sodium channel protein. [3H]Methylbromoamiloride binds covalently to the sodium channel at high affinity binding sites with a half-maximal binding concentration of 0.2 microM. [3H]Methylbromoamiloride was specifically photoincorporated into the Mr approximately 150,000 polypeptide and this incorporation was blocked by addition of excess amiloride. These data suggest that the epithelial sodium channel protein is composed of at least five nonidentical polypeptide subunits, only one of which specifically binds amiloride.
Plant Succinic Semialdehyde Dehydrogenase. Cloning, Purification, Localization in Mitochondria, and Regulation by Adenine Nucleotides (1999)

Abstract Succinic semialdehyde dehydrogenase (SSADH) is one of three enzymes constituting the γ-aminobutyric acid shunt. We have cloned the cDNA for SSADH from Arabidopsis, which we designated SSADH1. SSADH1 cDNA encodes a protein of 528 amino acids (56 kD) with high similarity to SSADH fromEscherichia coli and human (&amp;gt;59% identity). A sequence similar to a mitochondrial protease cleavage site is present 33 amino acids from the N terminus, indicating that the mature mitochondrial protein may contain 495 amino acids (53 kD). The native recombinant enzyme and the plant mitochondrial protein have a tetrameric molecular mass of 197 kD. Fractionation of plant mitochondria revealed its localization in the matrix. The purified recombinant enzyme showed maximal activity at pH 9.0 to 9.5, was specific for succinic semialdehyde (K 0.5 = 15 μm), and exclusively used NAD+ as a cofactor (K m = 130 ± 77 μm). NADH was a competitive inhibitor with respect to NAD+(K i = 122 ± 86 μm). AMP, ADP, and ATP inhibited the activity of SSADH (K i = 2.5–8 mm). The mechanism of inhibition was competitive for AMP, noncompetitive for ATP, and mixed competitive for ADP with respect to NAD+. Plant SSADH may be responsive to mitochondrial energy charge and reducing potential in controlling metabolism of γ-aminobutyric acid.
Impaired eye movements in post-concussion syndrome indicate suboptimal brain function beyond the influence of depression, malingering or intellectual ability (2009)

Post-concussion syndrome (PCS) can affect up to 20%-30% of patients with mild closed head injury (mCHI), comprising incomplete recovery and debilitating persistence of post-concussional symptoms. Eye movements relate closely to the functional integrity of the injured brain and eye movement function is impaired post-acutely in mCHI. Here, we examined whether PCS patients continue to show disparities in eye movement function at 3-5 months following mCHI compared with patients with good recovery. We hypothesized that eye movements might provide sensitive and objective functional markers of ongoing cerebral impairment in PCS. We compared 36 PCS participants (adapted World Health Organization guidelines) and 36 individually matched controls (i.e. mCHI patients of similar injury severity but good recovery) on reflexive, anti- and self-paced saccades, memory-guided sequences and smooth pursuit. All completed neuropsychological testing and health status questionnaires. Mean time post-injury was 140 days in the PCS group and 163 days in the control group. The PCS group performed worse on anti-saccades, self-paced saccades, memory-guided sequences and smooth pursuit, suggesting problems in response inhibition, short-term spatial memory, motor-sequence programming, visuospatial processing and visual attention. This poorer oculomotor performance included several measures beyond conscious control, indicating that subcortical functionality in the PCS group was poorer than expected after mCHI. The PCS group had poorer neuropsychological function (memory, complex attention and executive function). Analysis of covariance showed oculomotor differences to be practically unaffected by group disparities in depression and estimated intellectual ability. Compared with neuropsychological tests, eye movements were more likely to be markedly impaired in PCS cases with high symptom load. Poorer eye movement function, and particularly poorer subcortical oculomotor function, correlated more with post-concussive symptom load and problems on activities of daily living whilst poorer neuropsychological function exhibited slightly better correlations with measures of mental health. Our findings that eye movement function in PCS does not follow the normal recovery path of eye movements after mCHI are indicative of ongoing cerebral impairment. Whilst oculomotor and neuropsychological tests partially overlapped in identifying impairment, eye movements showed additional dysfunction in motor/visuospatial areas, response inhibition, visual attention and subcortical function. Poorer subconscious oculomotor function in the PCS group supports the notion that PCS is not merely a psychological entity, but also has a biological substrate. Measurement of oculomotor function may be of value in PCS cases with a high symptom load but an otherwise unremarkable assessment profile. Routine oculomotor testing should be feasible in centres with existing access to this technology.
In Vitro Gene Transfer with a Novel Galactosylated Spermine Bolaamphiphile (2001)

We describe the synthesis of a alpha-galacto-omega-spermine bolaamphiphile (GalSper) and report on the gene transfer mediated with lipoplexes it forms either when used alone or in conjunction with DOPE or with DOGS (Transfectam). Lipofection with GalSper was investigated with human HepG2 or murine BNL-CL2 hepatocytes expressing the asialo-glycoprotein (ASGP) receptor, which displays a high affinity for galactosyl residues, or with A549 cells which do not express ASGP. Although lower luciferase expression levels in BNL-CL2 and in HepG2 cells were obtained with GalSper/DOPE N/P 2.5 lipoplexes as compared with control DOGS/DOPE N/P 2.5 particles or with the more positively charged N/P 5 particles (yet through a different mechanism), specific receptor-mediated endocytosis of DNA can be achieved with this targeted cationic GalSper bolaamphiphile presenting a single galactose residue. The present work suggests that GalSper-based DNA formulations appear as promising synthetic vectors for specific gene delivery to ASGP(+) cells.
Site-specific mutagenesis of the calcium-binding photoprotein aequorin (1986)

The luminescent protein aequorin from the jellyfish Aequoria victoria emits light by an intramolecular reaction in the presence of a trace amount of Ca(2+). In order to understand the mechanism of the reaction, a study of structure-function relationships was undertaken with respect to modifying certain of its amino acid residues. This was done by carrying out oligonucleotide-directed site-specific mutagenesis of apoaequorin cDNA and expressing the mutagenized cDNA in Escherichia coli. Amino acid substitutions were made at the three Ca(2+)-binding sites, the three cysteines, and a histidine in one of the hydrophobic regions. Subsequent assay of the modified aequorin showed that the Ca(2+)-binding sites, the cysteines, and probably the histidine all play a role in the bioluminescence reaction of aequorin.
Emergence of Phase- and Shift-Invariant Features by Decomposition of Natural Images into Independent Feature Subspaces (2000)

Olshausen and Field (1996) applied the principle of independence maximization by sparse coding to extract features from natural images. This leads to the emergence of oriented linear filters that have simultaneous localization in space and in frequency, thus resembling Gabor functions and simple cell receptive fields. In this article, we show that the same principle of independence maximization can explain the emergence of phase- and shift-invariant features, similar to those found in complex cells. This new kind of emergence is obtained by maximizing the independence between norms of projections on linear subspaces (instead of the independence of simple linear filter outputs). The norms of the projections on such "independent feature subspaces" then indicate the values of invariant features.
A Single Cycle of Rituximab for the Treatment of Severe Pemphigus (2007)

A single cycle of rituximab is an effective treatment for pemphigus. Because of its potentially severe side effects, its use should be limited to the most severe types of the disease. (ClinicalTrials.gov number, NCT00213512 [ClinicalTrials.gov].).
Structural (n,m) Determination of Isolated Single-Wall Carbon Nanotubes by Resonant Raman Scattering (2001)

We show that the Raman scattering technique can give complete structural information for one-dimensional systems, such as carbon nanotubes. Resonant confocal micro-Raman spectroscopy of an (n,m) individual single-wall nanotube makes it possible to assign its chirality uniquely by measuring one radial breathing mode frequency omega(RBM) and using the theory of resonant transitions. A unique chirality assignment can be made for both metallic and semiconducting nanotubes of diameter d(t), using the parameters gamma(0) = 2.9 eV and omega(RBM) = 248/d(t). For example, the strong RBM intensity observed at 156 cm(-1) for 785 nm laser excitation is assigned to the (13,10) metallic chiral nanotube on a Si/SiO2 surface.
Role of carbohydrate recognition domains of pertussis toxin in adherence of Bordetella pertussis to human macrophages (1992)

Pertussis toxin (PT) and filamentous hemagglutinin can each mediate the association of Bordetella pertussis with human macrophages. Adherence via filamentous hemagglutinin leads to integrin-mediated entry and survival of the bacteria within the human cell. We determined the contribution of PT to bacterial adherence to human macrophages. Plating macrophages on wells coated with recombinant PT subunit 2 (S2) or S3 decreased PT-dependent bacterial binding by greater than 60%; S1, S4, and S5 were ineffective. S3-dependent adherence was reduced 63% +/- 8% by sialic acid, while S2-dependent adherence was reduced 53% +/- 11% by galactose. Loss of the carbohydrate recognition properties of S2 by deletion of residues 40 to 54 or site-specific mutations at Asn-93, His-47, or Arg-50 eliminated the ability of the subunit protein to competitively inhibit bacterial binding. Peptides corresponding to residues 28 to 45 of S2 and S3 competitively inhibited adherence. Treatment of macrophages with antibodies to Le(a) or Le(x) but not CD14, CD15, CD18, or HLA interfered with PT-mediated binding. Exposure of the macrophages to the B oligomer, S2, or S3 increased binding to the CD11b/CD18 integrin. These results indicate that the carbohydrate recognition domains of both S2 and S3 participate in adherence of B. pertussis to human macrophages. The PT receptor(s), as yet unidentified, appears to carry the Le(a) or Le(x) determinants and is functionally capable of modulating integrin-mediated binding to the macrophage.
Cluster analysis for hypertext systems (1993)

Identifying nodes of information that are highly related has many applications in any information systems, and in particular in hypertext systems. In this paper we present a technique to identify “natural” clusters in a hypertext. A natural cluster is a cluster that is not arbitrary, but depends only on intrinsic properties of the hypertext. In our case, the property we will use to identify the clusters is the number of independent paths between nodes. Using the graph theoretic definition of k-edge-components we present an aggregation technique to cluster the nodes. We then use this techniques to cluster three medium sized hypertexts that were developed by different authors for different users, using different methodologies. We also show how to use clustering to improve data display, browsing and retrieval.
Dynein- and Microtubule-Mediated Translocation of Adenovirus Serotype 5 Occurs after Endosomal Lysis (2000)

Modified viruses are used as gene transfer vectors because of their ability to transfer genetic material efficiently to the nucleus of a target cell. To better understand intracellular translocation of adenovirus serotype 5 (Ad), fluorophores were covalently conjugated to Ad capsids, and movement of fluorescent Ad within the cytoplasm was observed during the first hour of infection of a human lung epithelial carcinoma cell line (A549). Ad translocation was characterized with respect to its ability to achieve nuclear envelope localization as well as directed movement in the cytoplasm. Whereas Ad achieved efficient nuclear localization 60 min after infection of A549 cells under control conditions, depolymerization of the microtubule cytoskeleton by addition of 25 microM nocodazole reversibly inhibited development of nuclear localization. In contrast, depolymerization of microfilaments by addition of 1 microM cytochalasin D had no effect on nuclear localization. Direct video observation of Ad motility showed that nocodazole, but not cytochalasin D, caused a reversible decrease in rapid linear translocations of Ad in the cytoplasm of A549 cells. Microinjection of function-blocking antibodies against the microtubule-dependent motor protein, cytoplasmic dynein, but not kinesin, blocked nuclear localization of Ad, consistent with net minus end-directed motility indicated by accumulation of Ad at mitotic spindles. Fluorescence ratio imaging revealed a neutral pH in the environment of translocating Ad, leading to a model in which the interaction of Ad with an intact microtubule cytoskeleton and functional cytoplasmic dynein occurs after escape from endosomes and is a necessary prerequisite to nuclear localization of adenovirus serotype 5.
The Cytoplasmic and Periplasmic Expression Levels and Folding of Organophosphorus Hydrolase Enzyme in Escherichia coli (2015)

The activities studied by the production of PNP were determined by following the increase at 410 nm. The maximum PNP was produced at 30°C with an optical density of 10.62 in the presence of cytoplasmic expression of OPH (pET21a-opd). Consequently, our results suggest cytoplasmic expression system as an appropriate candidate with a high amount of OPH in spite of inclusion body formation, which needs an additional refolding step.