gebhart/patrepeval huggingface dataset:
Roles of StearoylCoA Desaturase-1 in the Regulation of Cancer Cell Growth, Survival and Tumorigenesis (2011)

The development and maintenance of defining features of cancer, such as unremitting cell proliferation, evasion of programmed cell death, and the capacity for colonizing local tissues and distant organs, demand a massive production of structural, signaling and energy-storing lipid biomolecules of appropriate fatty acid composition. Due to constitutive activation of fatty acid biosynthesis, cancer cell lipids are enriched with saturated (SFA) and, in particular, monounsaturated fatty acids (MUFA), which are generated by StearoylCoA desaturase-1, the main enzyme that transforms SFA into MUFA. An increasing number of experimental and epidemiological studies suggest that high levels of SCD1 activity is a major factor in establishing the biochemical and metabolic perturbations that favors the oncogenic process. This review examines evidence that suggests the critical implication of SCD1 in the modulation of multiple biological mechanisms, specifically lipid biosynthesis and proliferation and survival signaling pathways that contribute to the development and progression of cancer.
Technology Update: Haradh III: A Milestone for Smart Fields (2006)

The Haradh III project came on stream in February 2006, adding 300,000 B/D of Arabian light crude production capacity to Ghawar, the world's largest oil field. The project's main significance, however, derives from the fact that it sets a milestone for smart technologies at a scale and complexity unprecedented for Saudi Aramco and, arguably, for the industry. Haradh III might be regarded as the entry point to a new era in upstream projects and specifically into the domain of real-time reservoir management. The project spanned a period of 21 months. It entailed construction of a grassroots surface-facility network, integrated with a complex subsurface development program. Maximum-reservoir-contact (MRC) wells, smart completions, geosteering, and i-field features provided the four main technology components. Their efficient integration was the key to the project's success. Background Haradh constitutes the southernmost portion of the Ghawar complex and covers an area 75 km long and 26 km wide at its widest section (Fig. 1). The field consists of three subsegments of approximately equivalent reserves, with an aggregate oil initially in place of 38 billion STB. Initial production from Haradh I occurred in May 1996, followed up by Haradh II and Haradh III in April 2003 and February 2006, respectively. The field developments, occurring over a span of a decade, offer a unique opportunity in gauging the impact of technologies, the main thrust of this article. Haradh I was developed exclusively with vertical wells, whereas horizontal completions provided the primary configuration for producers/injectors in Haradh II. Haradh III, the main focus here, was developed by relying mainly on smart MRC completions within an i-field framework (Fig. 2). The total Haradh production capacity is 900,000 B/D, with equal contributions from the three respective subsegments I, II, and III. Arab-D, the producing horizon, belongs to the lower member of the Arab formation of the Jurassic period. It is characterized by a complex sequence of anhydrite and limestone events, with varying degrees of "'dolomitization'." Faults, fractures, and fracture swarms were known to be part of the regional geology and attracted considerable attention in the project planning, given their propensity for creating water-encroachment problems. Project Statistics Table 1 presents the key project statistics for Haradh III. It entailed a production target of 300,000 B/D, using 32 multilateral wells. A peripheral water-injection program (with an ultimate capacity of 560,000 BWPD) preceded the crude production by 4 months as part of the planned pressure-maintenance program.
E-broidery: Design and fabrication of textile-based computing (2000)

Highly durable, flexible, and even washable multilayer electronic circuitry can be constructed on textile substrates, using conductive yarns and suitably packaged components. In this paper we describe the development of e-broidery (electronic embroidery, i.e., the patterning of conductive textiles by numerically controlled sewing or weaving processes) as a means of creating computationally active textiles. We compare textiles to existing flexible circuit substrates with regard to durability, conformability, and wearability. We also report on: some unique applications enabled by our work; the construction of sensors and user interface elements in textiles; and a complete process for creating flexible multilayer circuits on fabric substrates. This process maintains close compatibility with existing electronic components and design tools, while optimizing design techniques and component packages for use in textiles.
High power DPDT antenna switch MMIC for digital cellular systems (1996)

In this paper, we propose two new types of dual-pole double-throw (DPDT) switch GaAs JFET monolithic microwave integrated circuits (MMICs) for digital cellular handsets. These ICs have the excellent characteristics of low insertion loss and high power handling capability, even with a low control voltage by stacking three JFETs with shallow V/sub p/ and using a novel bias circuit using p-n junction diodes. One DPDT switch IC has two shunt FET blocks and can achieve high isolation without external parts. An insertion loss less than 0.6 dB and isolation over 25 dB up to 2 GHz were achieved. P/sub 1dB/ was about 35 dBm even with a control voltage of 0/3 V. Another DPDT switch IC utilizes parallel resonance of external inductors and parasitic capacitance between the drain and the source of the OFF-state FETs. By attaching 15 nH inductors, for example, the IC exhibited an insertion loss as low as 0.4 dB, an isolation of better than 40 dB at 1.5 GHz, a bandwidth of about 400 MHz for 20 dB isolation, and P/sub 1dB/ of about 34 dBm with the 0/3 V control.
Mediators of Blood-Brain Barrier Dysfunction and Formation of Vasogenic Brain Edema (1988)

The characteristics and mechanisms enabling the blood-brain barrier (BBB) to maintain the milieu of the brain have been reviewed in detail elsewhere (Banks and Kastin, 1987; Bradbury, 1985; Crone, 1986a, 1987; Cornford, 1985; Davson, 1976; Er­ misch et aI. , 1985; Fenstermacher, 1985; Gjedde, 1983; Goldstein and Betz, 1986; Meisenberg and Simmons, 1983; Oldendorf, 1974; Pardridge, 1983; Rapoport, 1976a; Rapoport and Robinson, 1986). Before discussing the possible role of mediators in BBB opening some pertinent aspects of the BBB will be discussed briefly. The morphological substrate of the BBB in cere­ bral vessels is the continuous layer of endothelial cells with junctions and no or minimal vesic­ ular transport. The functional characteristics of BBB are the same as of tight epithelium such as (a) low diffusional permeability for water-soluble compounds, (b) low hydraulic conductivity, (c) high reflection coefficient, and (d) high electrical resis­ tance. All these parameters are indicative of low diffusional exchange of water-soluble solutes. As well as by the restricted diffusion the penetration of several mediators is also inhibited by an enzymatic degradation at the endothelial border. Although li­ pophilic compounds can easily cross the BBB by simple diffusion, the trans cellular transport of hy­ drophilic solutes is made possible by facilitated dif­ fusion and active transport. All these mechanisms permit a highly selective exchange between blood and brain and provide an optimally controlled ho-
Using events to build distributed applications (2002)

We have extended an Interface Definition Language to handle event registration and notification. Clients register interest in specified classes of events and servers then notify them of any occurrence asynchronously. Event occurrences are identified by parameters which conform to IDL typing constraints and can therefore be used in synchronous method invocations. Methods to handle registration and notification are generic and can be inherited by objects of any class: as a by-product of IDL processing the stubs to handle event creation and decoding are generated automatically. We have implemented a prototype composite event recogniser based on non-deterministic finite state machines. Initial experience with this prototype is encouraging.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Nutrition and nitrosamine formation (1985)

Nutrition and the fmmation of N-nitroso compounds N-nitroso compounds are an important group of chemical carcinogens that could be involved in human cancer (Magee, 1982). Only a few examples have been found in food and beverages (Assembly of Life Sciences, 1981) but suitable precursors are common dietary constituents (Assembly of Life Sciences, 1981), and the mildly acidic conditions of the stomach are favourable for their formation Over 90% of the N-nitroso compounds tested have proven to be carcinogenic, some in as many as thirty species ranging from mice to primates (Magee et al. 1976). Many are organ-specific carcinogens, producing tumours remote from the site of their administration (Magee et al. I 976). Nonetheless, unequivocal evidence that N-nitroso compounds cause human cancer has proven elusive.
Synthese des (±)‐Oncinotins (1974)

Abstract (±)‐Oncinotin ( 19 ) is synthesized through the crucial intermediates 11 and 15 . By comparison of the synthetic product with natural (−)‐oncinotin, it is found that the latter contains an isomeric substance, represented by structure 20 .
Binding of factor VIIa to tissue factor permits rapid antithrombin III/heparin inhibition of factor VIIa (1993)

Because free factor VIIa is inactivated only very slowly by a plasma concentration of antithrombin III (AT III) even in the presence of heparin, it has been assumed that AT III plays no significant role in regulating the initiation of tissue factor-dependent blood coagulation. However, in the present study, we present evidence that factor VIIa bound to tissue factor, unlike free factor VIIa, is readily inactivated by AT III in the presence of heparin. In a reaction mixture containing calcium ions and approximately equimolar concentrations of relipidated tissue factor (8.9 nmol/L) and factor VIIa (10 nmol/L), AT III (100 micrograms/mL) plus heparin (1 U/mL) inhibited 50% of the factor VIIa coagulant activity of the reaction mixture within 5 minutes. AT III/heparin was also shown to inhibit the catalytic activity towards factor X of factor VIIa/tissue factor complexes formed on monolayers of an ovarian carcinoma cell line (OC-2008) that constitutively expresses surface membrane tissue factor. AT III, even in the absence of exogenously added heparin, substantially inhibited the functional activity of factor VIIa/cell surface tissue factor complexes on intact monolayers. AT III alone and AT III/heparin, to a greater extent, also inhibited factor VIIa on “nonfunctional” factor VIIa/tissue factor complexes on intact monolayers, with resultant inhibition of their expression of factor VIIa/tissue factor catalytic activity toward factor X after cell lysis. The potential physiologic significance of these findings is discussed.
The cytokine microenvironment of human colon carcinoma: Lymphocyte expression of tumor necrosis factor-α and interleukin-4 predicts improved survival (1996)

There are differences between the immune microenvironment of primary tumors and metastases. Although IL-10 is expressed by colon carcinoma cells and TIL, it is unlikely that it plays an important immunosuppressive role. TNF-alpha and IL-4 are commonly expressed by colon carcinoma TIL and both are associated with improved survival.
Inter-vehicle communications for merging control (2003)

This paper proposes a data transmission algorithm over inter-vehicle communications and a merging control algorithm, and describes the simulation studies and experiments using autonomous mobile robots with wireless LAN for the evaluation of the feasibility of the data transmission and merging control algorithms. The merging control algorithm uses a virtual vehicle which is generated by mapping a vehicle on a main lane or a ramp in order to achieve longitudinal control between a vehicle at a ramp and one on a main lane. The results of the simulations show the efficiency of the data transmission and the feasibility of the merging control using this algorithm. This algorithm was implemented in autonomous mobile robots with a control system and an on-board communications system using wireless LAN for the evaluation.
A Human Single-Domain Antibody Elicits Potent Antitumor Activity by Targeting an Epitope in Mesothelin Close to the Cancer Cell Surface (2013)

Monoclonal antibodies against mesothelin are being evaluated for the treatment of mesothelioma and multiple forms of cancers, and show great promise for clinical development for solid cancers. Antibodies against mesothelin have been shown to act via immunotoxin-based inhibition of tumor growth and induction of antibody-dependent cell-mediated cytotoxicity (ADCC). However, complement-dependent cytotoxicity (CDC), considered an important additional mechanism of therapeutic antibodies against tumors, is inactive for such antibodies. Here, we used phage display antibody engineering technology and synthetic peptide screening to identify SD1, a human single-domain antibody to mesothelin. SD1 recognizes a conformational epitope at the C-terminal end (residues 539-588) of mesothelin close to the cell surface. To investigate SD1 as a potential therapeutic agent, we generated a recombinant human Fc (SD1-hFc) fusion protein. Interestingly, the SD1-hFc protein exhibits strong CDC activity, in addition to ADCC, against mesothelin-expressing tumor cells. Furthermore, it causes growth inhibition of human tumor xenografts in nude mice as a single agent. SD1 is the first human single-domain antibody targeting mesothelin-expressing tumors, shows potential as a cancer therapeutic candidate, and may improve current antibody therapy targeting mesothelin-expressing tumors.
Isolation of an efficient actin promoter for use in rice transformation. (1990)

We have characterized the 5' region of the rice actin 1 gene (Act1) and show that it is an efficient promoter for regulating the constitutive expression of a foreign gene in transgenic rice. By constructing plasmids with 5' regions from the rice Act1 gene fused to the coding sequence of a gene encoding bacterial beta-glucuronidase, we demonstrate that a region 1.3 kilobases upstream of the Act1 translation initiation codon contains all of the 5'-regulatory elements necessary for high-level beta-glucuronidase (GUS) expression in transient assays of transformed rice protoplasts. The rice Act1 primary transcript has a noncoding exon separated by a 5' intron from the first coding exon. Fusions that lack this Act1 intron showed no detectable GUS activity in transient assays of transformed rice protoplasts. Deletion analysis of the Act1 5' intron suggests that the intron-mediated stimulation of GUS expression is associated, in part, with an in vivo requirement for efficient intron splicing.
Performance Modeling and Scalability Optimization of Distributed Deep Learning Systems (2015)

Big deep neural network (DNN) models trained on large amounts of data have recently achieved the best accuracy on hard tasks, such as image and speech recognition. Training these DNNs using a cluster of commodity machines is a promising approach since training is time consuming and compute-intensive. To enable training of extremely large DNNs, models are partitioned across machines. To expedite training on very large data sets, multiple model replicas are trained in parallel on different subsets of the training examples with a global parameter server maintaining shared weights across these replicas. The correct choice for model and data partitioning and overall system provisioning is highly dependent on the DNN and distributed system hardware characteristics. These decisions currently require significant domain expertise and time consuming empirical state space exploration.
Loading of Arabidopsis Centromeric Histone CENH3 Occurs Mainly during G2 and Requires the Presence of the Histone Fold Domain (2006)

The centromeric histone H3 (CENH3) substitutes histone H3 within the nucleosomes of active centromeres in all eukaryotes. CENH3 deposition at centromeres is needed to assemble the kinetochore, a complex of conserved proteins responsible for correct chromosome segregation during nuclear division. Histones of regular nucleosomes are loaded during replication in S phase, while CENH3 deposition deviates from this pattern in yeast, human, and Drosophila melanogaster cells. Little is known about when and how CENH3 targets centromeric loci. Therefore, we determined the location and quantity of recombinant enhanced yellow fluorescent protein (EYFP)-CENH3 in mitotic root and endopolyploid leaf nuclei of transgenic Arabidopsis thaliana cells. Our data indicate significant loading of A. thaliana CENH3 during G2 (before splitting into sister kinetochores) rather than during the S or M phase of the cell cycle. The histone fold domain of the C-terminal part of CENH3 is sufficient to target A. thaliana centromeres. A. thaliana EYFP-CENH3 can recognize and target three different centromeric repeats of Arabidopsis lyrata but not field bean (Vicia faba) centromeres.
Hit and go CAS9 delivered through a lentiviral based self-limiting circuit (2017)

In vivo application of the CRISPR-Cas9 technology is still limited by unwanted Cas9 genomic cleavages. Long-term expression of Cas9 increases the number of genomic loci non-specifically cleaved by the nuclease. Here we develop a Self-Limiting Cas9 circuit for Enhanced Safety and specificity (SLiCES) which consists of an expression unit for Streptococcus pyogenes Cas9 (SpCas9), a self-targeting sgRNA and a second sgRNA targeting a chosen genomic locus. The self-limiting circuit results in increased genome editing specificity by controlling Cas9 levels. For its in vivo utilization, we next integrate SLiCES into a lentiviral delivery system (lentiSLiCES) via circuit inhibition to achieve viral particle production. Upon delivery into target cells, the lentiSLiCES circuit switches on to edit the intended genomic locus while simultaneously stepping up its own neutralization through SpCas9 inactivation. By preserving target cells from residual nuclease activity, our hit and go system increases safety margins for genome editing.
The Dendritic Cell Lineage: Ontogeny and Function of Dendritic Cells and Their Subsets in the Steady State and the Inflamed Setting (2013)

Dendritic cells (DCs) form a remarkable cellular network that shapes adaptive immune responses according to peripheral cues. After four decades of research, we now know that DCs arise from a hematopoietic lineage distinct from other leukocytes, establishing the DC system as a unique hematopoietic branch. Recent work has also established that tissue DCs consist of developmentally and functionally distinct subsets that differentially regulate T lymphocyte function. This review discusses major advances in our understanding of the regulation of DC lineage commitment, differentiation, diversification, and function in situ.
The Strength of Weak Interactions: Aromatic Fluorine in Drug Design (2006)

Selective aromatic fluorine substitution can increase the affinity of a molecule for a macromolecular recognition site through non-covalent interactions. These effects are evaluated most accurately by direct comparison of binding affinities of selectively fluorinated compounds with their corresponding hydrocarbons. In cases where structural data confirm similar binding geometries for the fluorocarbon and hydrocarbon analogues, reliable estimates for the impact of fluorination upon arene-pi...X and C-F...X interaction energies are possible. Existing studies show that fluorination's impact on any individual molecular interaction is quite modest. Upon binding to a protein receptor, cumulative fluorinated aromatic quadrupolar and C-F...X dipolar interaction energies rarely differ from those the corresponding hydrocarbons by more than 1.3 kcal/mol, and most individual interactions appear to be in the 0.1-0.4 kcal/mol range. Similarly, non-ideal selective fluorination is rarely associated with a dramatic decrease in affinity, because the impact of weak repulsive interactions in the bound state is counterbalanced by increased lipophilicity.
Sterilization of therapeutic immunoadsorbents by ionizing radiation. (1986)

The application of ionizing radiation (gamma-rays from 60Co) to sterilize therapeutic immunoadsorbents (IA)s was investigated. The IAs were porous bead carriers immobilizing anti-IgE antibodies and were irradiated in both the freeze-dried and precipitated (wet) states. The IgE removal (%), the IgE adsorption capacity of IA, was acceptable in terms of practical use even after an irradiation dose of 2.5 Mrad in the precipitated state; the anti-IgE antibody itself lost much of its activity, possibly because of intermolecular crosslinking of antibody molecules, after being irradiated with a dose at least of 0.5 Mrad. In the freeze-dried state only IA consisting of CPG-1400 could tolerate a dose of 2.5 Mrad. Dose-survival curves were obtained using Bacillus pumilus spores in both the freeze-dried and precipitated IAs and the D-values were calculated to be respectively 0.27 and 0.31 Mrad. Thus, ionizing radiation may be applicable for sterilizing IAs in the precipitated state and in the freeze-dried state for an IA consisting of CPG-1400 although the initial bioburden on IA should be low.
Camera Calibration Using Circle and Right Angles (2006)

In this paper, a new method is proposed for camera calibration using planar pattern which includes a circle and right angles. It is shown that a dual conic constraint on the vanishing line of a plane can be derived from a right angle and a circle on the same plane. Given an image of a model plane containing a circle and three right angles, the vanishing line and the images of the circular points can be uniquely determined. As a result, camera calibration can be achieved by taking several images of the model plane from different view angles. There are three advantages of the proposed method. First, no correspondences between images need to be established. Secondly, conies and lines forming the right angles in an image can be extracted and fitted very accurately. Thirdly, it is practical as circular patterns and right angles are widely available. Experiments with real images demonstrate the performance of the presented method
Amino acid sequences of two proline-rich bactenecins. Antimicrobial peptides of bovine neutrophils. (1990)

Bactenecins are highly cationic polypeptides of the large granules of bovine neutrophils, exerting in vitro a potent antimicrobial activity. Two bactenecins, with an approximate molecular weight of 7000 and 5000, called Bac7 and Bac5, are characterized by a high content of proline (greater than 45%) and arginine (greater than 23%) residues. Their complete amino acid sequences were determined by automated Edman degradation combined, in the case of Bac5, with plasma desorption mass spectrometry. Bac7 comprises 59 residues and includes three tandem repeats of a tetradecamer characterized by several Pro-Arg-Pro triplets spaced by single hydrophobic amino acids. Resolution of the primary structure of Bac5 required fragmentation with N-bromosuccinimide as well as digestion of the obtained C-terminal fragment with carboxypeptidases P and Y directly in the mass spectrometer. Bac5 comprises 42 amino acid residues with a repeated motif of Arg-Pro-Pro triplets also alternating with single apolar residues.