gebhart/patrepeval huggingface dataset:
α,β-Difluoromethylene Deoxynucleoside 5′-Triphosphates: A Convenient Synthesis of Useful Probes for DNA Polymerase β Structure and Function (2009)

Alpha,beta-difluoromethylene deoxynucleoside 5'-triphosphates (dNTPs, N = A or C) are advantageously obtained via phosphorylation of corresponding dNDP analogues using catalytic ATP, PEP, nucleoside diphosphate kinase, and pyruvate kinase. DNA pol beta K(d) values for the alpha,beta-CF(2) and unmodified dNTPs, alpha,beta-NH dUTP, and the alpha,beta-CH(2) analogues of dATP and dGTP are discussed in relation to the conformations of alpha,beta-CF(2) dTTP versus alpha,beta-NH dUTP bound into the enzyme active site.
HPLC resolution of atropoisomeric compounds on a csp derived from (1R;2R)‐diaminocyclohexane: Thermodynamic data from variable temperature chromatography (1992)

Abstract The preparation and a preliminary chromatographic evaluation of a novel polymeric chiral stationary phase (CSP) derived from (1R;2R)‐diaminocyclohexane (DACH) are presented. A radical copolymerization process has been employed to generate a silica‐based chiral sorbent, showing considerable high chemical and thermal stability and stereoselectivity toward racemic compounds capable of H‐bonding (3‐hydroxy‐benzodiazepin‐2‐ones, chlorthalidone, atropoisomeric sulfur compounds, etc.); in the present paper we present the investigation on the resolution of racemic dihydroxy biarylic atropoisomers; the effects of eluent composition and of temperature on the separation ability of the CSP have been studied in order to elucidate the recognition mechanism operating in these chiral separations. © 1992 Wiley‐Liss, Inc.
Novel thermotropic and lyotropic double headed diol-based mesogens (1990)

The double headed amphiphilic diol docosane-1,2,21,22-tetraol has been prepared, and it exhibits liquid crystalline behaviour with a much higher clearing temperature than the corresponding half unit undecane-1,2-diol.
Human CMV Transcripts: An Overview (2012)

The human CMV (HCMV) genome consists of an approximately 230-kb dsDNA and is predicted to contain over 165 open reading frames. Although the entire sequence of the laboratory-adapted AD169 strain of HCMV was first available in 1991, the precise number and nature of viral genes and gene products are still unclear. Fewer than 100 predicted genes have been convincingly elucidated with respect to their expression patterns, transcript structure and transcription characteristics. The high gene number of HCMV creates a crowded genome with many overlapping transcriptional units. 3´- or 5´-coterminal overlapping polycistronic transcripts could use a common promoter element or a poly-A signal. 3´-coterminal monocistronic transcripts could encode 'nested' open reading frames, which possess different initiation but the same termination sites. As a virus with eukaryotic cells as the host, HCMV has the capacity to splice out introns during transcription. Major alternately spliced mRNA species of HCMV originate primarily, but not exclusively, from the immediate early gene regions. Alternate splicing patterns of the mRNAs could encode a number of gene products with different sizes. In recent years, some antisense and noncoding transcripts of HCMV have been reported. These RNAs probably have functions in genomic replication or the regulation of gene expression.
Abstract LB-237: Vaccination increases the breadth and diversity of melanoma neoantigen-specific T cells in humans (2015)

Abstract Melanoma genomes harbor somatic mutations that are caused by exposure to mutagens such as UV light. Tumor missense mutations (MM), translated into amino acid substitutions (AAS), may provide a form of non-self that elicits tumor specific T cell immunity. Indeed, T cell immunity directed against tumor encoded AAS has been reported in humans with cutaneous melanoma, thus implicating MM as a source of patient specific (private) neoantigens. However, a systematic evaluation of these putative neoantigens as validated targets is lacking and it is unknown whether the immune response directed against tumor encoded AAS can be augmented by vaccination. Here we show that vaccination against melanoma AAS-encoding peptides augments naturally occurring T cell immunity and reveals new HLA class I restricted private neoantigens in patients with advanced melanoma. Neoantigen specific T cells recognized naturally processed and presented antigen but failed to recognize wild type (non-mutated) antigen. The presentation of neoantigens by HLA-A*02:01 in human melanoma was confirmed by mass spectrometry. As determined by TCRβ CDR3 DNA sequencing, vaccination promotes a repertoire of neoantigen-specific T cells that is highly diverse in terms of both TCRβ usage and clonal composition. No evidence of autoimmunity was apparent after vaccination. Our results demonstrate that tumor MM can be targeted as neoantigens and vaccination directed at tumor AAS somatic mutations broadens the antigenic breadth and clonal diversity of anti-tumor immunity. These findings provide a new paradigm for private neoantigen identification in neoplasia and may form the basis of personalized cancer immunotherapies targeting somatic mutations. Citation Format: Beatriz M. Carreno, Vincent Magrini, Michelle Becker-Hapak, Saghar Kaabinejadian, Jasreet Hundal, Allegra A. Petti, Amy Ly, Wen-Rong Lie, William H. Hildebrand, Elaine R. Mardis, Gerald P. Linette. Vaccination increases the breadth and diversity of melanoma neoantigen-specific T cells in humans. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-237. doi:10.1158/1538-7445.AM2015-LB-237
Radiation-Induced Increase in Plasma Flt3 Ligand Concentration in Mice: Evidence for the Implication of Several Cell Types (2005)

Circulating T lymphocytes were proposed as the main producer of Flt3 ligand. However, during aplasia, there is a drastic reduction in the number of T lymphocytes, while plasma Flt3 ligand concentration is increased. This contradiction prompted us to compare variations in plasma Flt3 ligand during radiation-induced aplasia in BALB/c mice and in T-lymphocyte-deficient NOD-SCID mice to delineate the role of T lymphocytes in the increase in Flt3 ligand concentration. The results showed that plasma Flt3 ligand concentration was increased similarly in the two strains of mice, and that Flt3 ligand concentration was negatively correlated to the number of residual hematopoietic progenitors. Moreover, the Flt3 ligand mRNA expression and Flt3 ligand protein concentration were similar in the two strains of mice in all organs tested, i.e. thymus, spleen, bone marrow, liver, brain and blood cells. These results confirm that Flt3 ligand concentration in the blood is a reflection of bone marrow function and that T lymphocytes are not the main regulator of Flt3 ligand variations during aplasia.
Meconium stained amniotic fluid: antenatal, intrapartum and neonatal attributes. (1996)

Selective approach can be adopted for babies with MSAF reserving intratracheal suctioning at birth for depressed neonate or evidence of fetal distress in utero. Rest of the neonates only need careful observation after thorough oronasopharyngeal suctioning.
Capacity of Epstein–Barr virus to infect monocytes and inhibit their development into dendritic cells is affected by the cell type supporting virus replication (2004)

Epstein-Barr virus (EBV) is a ubiquitous human herpesvirus that is involved in the pathogenesis of a wide spectrum of malignant and non-malignant diseases. Strong evidence implicates T lymphocytes in the control of EBV replication and tumorigenesis, but cellular components of the innate immune system are poorly characterized in terms of their function in the development of EBV-specific immunity or interaction with the virus. This study demonstrates that EBV virions produced in epithelial cells surpass their B cell-derived counterparts in the capacity to enter monocytes and inhibit their development into dendritic cells (DCs). Different ratios of the gp42 and gH glycoproteins in the envelope of virions that were derived from major histocompatibility complex class II-positive or -negative cells accounted primarily for the differences in EBV tropism. EBV is shown to enter both monocytes and DCs, although the cells are susceptible to virus-induced apoptosis only if infected at early stages of DC differentiation. The purified gH/gL heterodimer binds efficiently to monocytes and DCs, but not to B cells, suggesting that high expression levels of a putative binding partner for gH contribute to virus entry. This entry takes place despite very low or undetectable expression of CD21, the canonical EBV receptor. These results indicate that the site of virus replication, either in B cells or epithelial cells, alters EBV tropism for monocytes and DCs. This results in a change in the virus's immunomodulating capacity and may have important implications for the regulation of virus-host interactions during primary and chronic EBV infection.
Regulated Nuclear-Cytoplasmic Localization of Interferon Regulatory Factor 3, a Subunit of Double-Stranded RNA-Activated Factor 1 (2000)

Viral double-stranded RNA (dsRNA) generated during the course of infection leads to the activation of a latent transcription factor, dsRNA-activated factor 1 (DRAF1). DRAF1 binds to a DNA target containing the type I interferon-stimulated response element and induces transcription of responsive genes. DRAF1 is a multimeric transcription factor containing the interferon regulatory factor 3 (IRF-3) protein and one of the histone acetyl transferases, CREB binding protein (CBP) or p300 (CBP/p300). In uninfected cells, the IRF-3 component of DRAF1 resides in the cytoplasm. The cytoplasmic localization of IRF-3 is dependent on a nuclear export signal, and we demonstrate IRF-3 recognition by the chromosome region maintenance 1 (CRM1) (also known as exportin 1) shuttling receptor. Following infection and specific phosphorylation, IRF-3 accumulates in the nucleus where it associates with CBP and p300. We identify a nuclear localization signal (NLS) in IRF-3 that is critical for nuclear accumulation. Mutation of the NLS abrogates nuclear localization even following infection. The NLS appears to be active constitutively, but it is recognized by only a subset of importin-alpha shuttling receptors. Evidence is presented to support a model in which IRF-3 normally shuttles between the nucleus and the cytoplasm but cytoplasmic localization is dominant prior to infection. Following infection, phosphorylated IRF-3 can bind to the CBP/p300 proteins resident in the nucleus. We provide the evidence of a role for CBP/p300 binding in the nuclear sequestration of a transcription factor that normally resides in the cytoplasm.
<title>Conical Rotating Aperture Geometries In Digital Radiography</title> (1981)

Applications of conical rotating aperture (RA) geometries to digital radiography are described. Two kinds of conical RA imaging systems are the conical scanning beam and the conical scanning grid assemblies. These assemblies comprise coaxial conical surface(s) the axis of which is collinear with the x-ray focal spot. This geometry allows accurate alignment and continuous focusing of the slits or the grid lines. Image receptors which use solid state photodiode arrays are described for each type of conical RA system: multiple linear arrays for the conical scanning beam assembly and multiple area arrays for the conical scanning grid assembly. The digital rotating-aperture systems combine the wide dynamic range characteristics of solid state detectors with the superior scatter-rejection advantages of scanned beam approaches. The high scanning-beam velocities attainable by the use of rotating apertures should make it possible to obtain digital images for those procedures such as chest radiography which require large fields of view and short exposure times.
Elemental Sulfur Corrosion and Inhibition in the Presence of Sulfur Solvent (2011)

Abstract Elemental sulfur is often produced by sour gas wells and carried by the sour gas during the production and transportation. When temperatures and pressures change, sulfur may first precipitate out from the sour gas and then deposit on the production tubing or pipeline wall. Sulfur deposition can significantly affect the production by blocking the production tubing. In the presence of water, sulfur can also lead to a catastrophic corrosion problem. Applying the combination of sulfur solvent and corrosion inhibitor to the gas production is the most common way to mitigate the blockage and corrosion problems caused by sulfur deposition. The objective of this project is to develop and evaluate the testing protocol for screening the elemental sulfur solvent and sulfur corrosion inhibitor. In this project, two sulfur solvents (SA and SC) and two corrosion inhibitors (CIB1 and CIB2) were investigated. All tests were conducted in autoclaves. Solvent efficiency was studied first, followed with the corrosion study. In the corrosion study, the steel surfaces with or without direct contact with sulfur were both simulated by putting an under-deposit specimen covered with sulfur on the bottom of the autoclave, and an electrochemical electrode not in contact with sulfur, directly above the under-deposit specimen. The experimental results suggest that the test apparatus and newly developed test protocol were proven to be able to screen the elemental sulfur solvent and sulfur corrosion inhibitor.
Bringing the Author Forward: Frankenstein Through Mary Shelley’s Letters (1988)

You know me—or you do not, in which case I will tell you what I am—a silly goose—who far from wishing to stand forward to assert myself in any way, now than [sic] I am alone in the world, have but the desire to wrap night and the obscurity of insignificance around me. This is weakness—but I cannot help it—to be in print—the subject of men's observa tions—of the bitter hard world's commentaries, to be at tacked or defended!—this ill becomes one who knows how little she possesses worthy to attract attention—and whose chief merit—if it be one—is a love of that privacy which no woman can emerge from without regret—Shelley's life must be written—I hope one day to do it myself, but it must not be published now—1
Improved Few-Shot Visual Classification (2020)

Few-shot learning is a fundamental task in computer vision that carries the promise of alleviating the need for exhaustively labeled data. Most few-shot learning approaches to date have focused on progressively more complex neural feature extractors and classifier adaptation strategies, and the refinement of the task definition itself. In this paper, we explore the hypothesis that a simple class-covariance-based distance metric, namely the Mahalanobis distance, adopted into a state of the art few-shot learning approach (CNAPS) can, in and of itself, lead to a significant performance improvement. We also discover that it is possible to learn adaptive feature extractors that allow useful estimation of the high dimensional feature covariances required by this metric from surprisingly few samples. The result of our work is a new ``Simple CNAPS'' architecture which has up to 9.2% fewer trainable parameters than CNAPS and performs up to 6.1% better than state of the art on the standard few-shot image classification benchmark dataset.
Cone-shaped Metal-Insulator-Semiconductor cathode for vacuum microelectronics (2002)

The structure and operating characteristics of a cone-shaped MIS cathode without the outside electrodes were reported. It was confirmed that the emission efficiency reached 8% in spite of the emission instability. Fabrication of a cone-shaped MIS cathode with outside electrode is now proceeding allowing for further improvement of the cathode.
Modeling and dynamic regulation of a wind farm (2002)

Electrical systems endowed with variable generating units will dominate the electrical landscape in the near future. These types of generating units will bring new opportunities to utilities, companies and customers, but they will also bring new problems to electrical companies. As wind power generation is one of the most important sources, because its production is environmentally clean, it is important to achieve proper locations for new wind farms. So, to evaluate their impact on the electrical network it is necessary to develop an accurate wind farm model for the network analysis program. This paper presents the modeling and control of a wind farm exclusively made up of doubly fed induction machines.
Where is My Parking Spot? (2015)

Parking occupancy information is central to the management of parking and traffic demand. This study proposed efficient unsupervised learning algorithms to predict parking occupancy rates. Two types of predictions were studied: (a) an offline prediction, in which next-day occupancy was predicted by using historical data along with various features (day of week, weather, seasonality), and (b) an online prediction, in which occupancy of future hours of the current day was predicted with both historical and real-time data. The two models can be applied to both off-street and on-street parking. Two data sources were used: parking payment kiosks for a visitors' parking garage and newly deployed real-time spot-by-spot parking sensors for a commuter garage. It was found that, with a proper set of features, the offline method could successfully distinguish different flow patterns, congested or underused, with intensive or mild arrival and departure rates. The offline procedure significantly outperformed both the historical and the previous day's average. The online method provided generally more accurate predictions than the offline method because it learned from the real-time occupancy data. As time progressed, the mean and maximum error rates of the online prediction decreased to a level well below both the historical average and the offline prediction error. A sharp decline of the prediction error could be obtained when sufficient real-time occupancy data were collected and the type of flow pattern was identified (around 9:00 a.m. in a case study).
Optimization by reduction to maximum clique (2002)

MAX-CLIQUE is the optimization problem of finding a largest clique in a given graph. By reduction to MAX-CLIQUE, the following three NP-hard optimization problems in a binary weights Hopfield net special case are solved: minimum vertex and set cover, constraint satisfaction problems (N-queens), and Boolean satisfiability (using a recent reduction). The approximation performance is experimentally determined on uniformly-at-random generated instances. The author's optimizing dynamics are discrete and converge, independently of the problem, in O(number of units) unit-switches. Several problems are optimized in a single binary weights (0/-1) network, which, for all problems, admits no invalid solutions. All reductions, except one, are goodness-preserving in a formal sense. This is contrasted with the variety of handcrafted energy functions for the same individual problems in the literature, several of which admit invalid solutions.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
High-field dark currents in thin CVD silicon nitride with graded interfacial composition (1979)

Ellipsometric measurements of thin CVD Si3N4 films deposited on Si reveal a graded composition of silicon oxynitride with increasing oxygen content as the Si-Si3N4 interface is approached. Measurements of steady-state dark currents, injected into Si3N4 from negatively biased Al contacts at constant average field, Eav=Vτ−1=6 MV/cm, have been fitted to an empirical relation, J=J0 exp(τ0/τ), where τ is the film thickness and τ0=1039 Å. Increased film conductivity with decreasing thickness τ is attributed to diminished electron trapping as τ approaches the centroid of trapped charge, δ∼100 Å.
Surface topology of the Escherichia coli K-12 ferric enterobactin receptor (1990)

Monoclonal antibodies (MAb) were raised to the Escherichia coli K-12 ferric enterobactin receptor, FepA, and used to identify regions of the polypeptide that are involved in interaction with its ligands ferric enterobactin and colicins B and D. A total of 11 distinct FepA epitopes were identified. The locations of these epitopes within the primary sequence of FepA were mapped by screening MAb against a library of FepA::PhoA fusion proteins, a FepA deletion mutant, and proteolytically modified FepA. These experiments localized the 11 epitopes to seven different regions within the FepA polypeptide, including residues 2 to 24, 27 to 37, 100 to 178, 204 to 227, 258 to 290, 290 to 339, and 382 to 400 of the mature protein. Cell surface-exposed epitopes of FepA were identified and discriminated by cytofluorimetry and by the ability of MAb that recognize them to block the interaction of FepA with its ligands. Seven surface epitopes were defined, including one each in regions 27 to 37, 204 to 227, and 258 to 290 and two each in regions 290 to 339 and 382 to 400. One of these, within region 290 to 339, was recognized by MAb in bacteria containing intact (rfa+) lipopolysaccharide (LPS); all other surface epitopes were susceptible to MAb binding only in a strain containing a truncated (rfaD) LPS core, suggesting that they are physically shielded by E. coli K-12 LPS core sugars. Antibody binding to FepA surface epitopes within region 290 to 339 or 382 to 400 inhibited killing by colicin B or D and the uptake of ferric enterobactin. In addition to the FepA-specific MAb, antibodies that recognized other outer membrane components, including Cir, OmpA, TonA, and LPS, were identified. Immunochemical and biochemical characterization of the surface structures of FepA and analysis of its hydrophobicity and amphilicity were used to generate a model of the ferric enterobactin receptor's transmembrane strands, surface peptides, and ligand-binding domains.
Inside Servlets: Server-Side Programming for the Java Platform with Other (1999)

From the Publisher:
With superior performance, cross-platform portability, and crash resistance, Java servlets offer the technical advantages that Internet developers need and high-traffic Web sites demand. Inside Servlets teaches everything you need to know to exploit the power and portability of Java servlets for your Internet applications.
Modification of chitosan films with environmentally benign reagents for increased water resistance (2011)

Abstract Chitosan is a non-toxic, renewable, abundant natural material with excellent film-forming properties. It is shown here that water absorption by chitosan films can be decreased by chemical modification with the bio-based reagents citric acid and glycerol. Infrared spectroscopy showed that citric acid reacted with chitosan amine groups to form an acyclic amide structure. Glycerol imparted flexibility and water repellency to the films. When soaked in water for six hours, a chitosan–citric acid–glycerol (1:1:9) film absorbed 44% water by weight after initial exposure and remained unchanged for the duration of the experiment. In comparison, a pure chitosan membrane initially absorbed 70% water and gradually increased to 96%. After soaking, the modified film swelled by only 11% compared to 42% for pure chitosan. Similar results were observed for water contact angle with the film surfaces. For the modified film, change in contact angle over time could be attributed solely to evaporation, whereas the pure chitosan film absorbed the droplets. These results show that the properties of chitosan can be improved using environmentally benign reagents in accordance with green chemistry principles.