gebhart/patrepeval huggingface dataset:
Selenoprotein H Is a Nucleolar Thioredoxin-like Protein with a Unique Expression Pattern (2007)

The human selenoproteome consists of 25 known selenoproteins, but functions of many of these proteins are not known. Selenoprotein H (SelH) is a recently discovered 14-kDa mammalian protein with no sequence homology to functionally characterized proteins. By sensitive sequence and structure analyses, we identified SelH as a thioredoxin fold-like protein in which a conserved CXXU motif (cysteine separated by two other residues from selenocysteine) corresponds to the CXXC motif in thioredoxins. These data suggest a redox function of SelH. Indeed, a recombinant SelH shows significant glutathione peroxidase activity. In addition, SelH has a conserved RKRK motif in the N-terminal sequence. We cloned wild-type and cysteine mutant forms of SelH either upstream or downstream of green fluorescent protein (GFP) and localized this fusion protein to the nucleus in transfected mammalian cells, whereas mutations in the RKRK motif resulted in the cytosolic protein. Interestingly, the full-length SelH-GFP fusion protein localized specifically to nucleoli, whereas the N-terminal sequence of SelH fused to GFP had a diffuse nucleoplasm location. Northern blot analyses revealed low expression levels of SelH mRNA in various mouse tissues, but it was elevated in the early stages of embryonic development. In addition, SelH mRNA was overexpressed in human prostate cancer LNCaP and mouse lung cancer LCC1 cells. Down-regulation of SelH by RNA interference made LCC1 cells more sensitive to hydrogen peroxide but not to other peroxides tested. Overall, these data establish SelH as a novel nucleolar oxidoreductase and suggest that some functions in this compartment are regulated by redox and dependent on the trace element selenium.
D-π-A-A-π-D Prototype 2,2′-Bipyridine Dyads Exhibiting Large Structure and Environment-Sensitive Fluorescence: Synthesis, Photophysics, and Computation (2011)

A series of 4,4'-π-conjugated-2,2'-bipyridine chromophores (MS 1-8) were synthesized, and their photophysical and thermal properties were investigated. The title "push-pull' chromophores", except MS 1, were integrated with both alkoxy and alkylamino donor functionalities that differ in their donation capabilities. The oligophenylenevinylene (OPV) chromophores MS 4-8 are associated with a π-extended backbone in which the position and the number of alkoxy donors were systematically varied. All of the studied systems possess a D-π-A-A-π-D dyad archetype in which the A-A is the central 2,2'-bipyridine acceptor core that is electronically attached with the donor termini through π-linkers. The fluorescence quantum yields of the synthesized chromophores are found to be sensitive to the molecular archetype and the solvent medium. Out of the eight fluorescent compounds reported in this article, the compound MS 5 exhibits fluorescence in the solid state also. The modulating effect of the nature, position, and number of donor functionalities on the optical properties of these classes of compounds has further been comprehended on the basis of DFT and TD-DFT computation in a solvent reaction field.
An assay for peptide binding to HLA‐Cw*0102 (1999)

The assembly assay for peptide binding to class I major histocompatibility complex (MHC) molecules is based on the ability of peptides to stabilize MHC class I molecules synthesized by transporter associated with antigen processing (TAP)-deficient cell. The TAP-deficient cell line T2 has previously been used in the assembly assay to analyze peptide binding to HLA-A*0201 and -B*5101. In this study, we have extended this technique to assay for peptides binding to endogenous HLA-Cw*0102 molecules. We have analyzed the peptide binding of 20 peptides with primary anchor motifs for HLA-Cw*0102. One-third of the peptides analyzed bound with high affinity, half of the peptides examined did not bind, whereas the remaining peptides displayed intermediate binding activity. Interest in HLA-C molecules has increased significantly in recent years, since it has been shown that HLA-C molecules both can present peptides to cytotoxic T lymphocytes (CTL) and in addition are able to inhibit natural killer (NK)-mediated lysis.
Light‐Gated Synthetic Protocells for Plasmon‐Enhanced Chemiosmotic Gradient Generation and ATP Synthesis (2019)

Herein, we present a light-gated protocell model made of plasmonic colloidal capsules (CCs) assembled with bacteriorhodopsin for converting solar energy into electrochemical gradients to drive the synthesis of energy-storage molecules. This synthetic protocell incorporated an important intrinsic property of noble metal colloidal particles, namely, plasmonic resonance. In particular, the near-field coupling between adjacent metal nanoparticles gave rise to strongly localized electric fields and resulted in a broad absorption in the whole visible spectra, which in turn promoted the flux of photons to bacteriorhodopsin and accelerated the proton pumping kinetics. The cell-like potential of this design was further demonstrated by leveraging the outward pumped protons as "chemical signals" for triggering ATP biosynthesis in a coexistent synthetic protocell population. Hereby, we lay the ground work for the engineering of colloidal supraparticle-based synthetic protocells with higher-order functionalities.
Effect of reducing temporal intensity modulations on sentence intelligibility (1997)

Modulations in the temporal intensity envelope of 24 1/4-octave bands were reduced by proportionally raising the troughs and lowering the peaks relative to the mean intensity in each band. The effect on intelligibility of various degrees of modulation reduction was investigated by measuring the speech-reception threshold (SRT) in noise. For conditions of severe modulation reduction, the number of correctly received sentences in quiet was scored. The effect of this deterministic modulation reduction was compared to the effect of stochastic modulation reduction obtained with addition of noise. Results for 12 normal-hearing subjects show that in the case of deterministic modulation reduction, intelligibility is reduced to 50% when the modulation-transfer factor equals 0.10, whereas in the case of modulation reduction by addition of noise, this intelligibility is reached already at a modulation-transfer factor of 0.27. This confirms that the effect of additive noise on intelligibility cannot be understood completely as a result of only modulation reduction. As suggested by Drullman [J. Acoust. Soc. Am. 97, 585-592 (1995)] two other factors associated with the addition of noise have to be taken into account: (1) the introduction of nonrelevant modulations, and (2) the corruption of the fine structure.
Solid-State Anion Exchange Reactions for Color Tuning of CsPbX<sub>3</sub> Perovskite Nanocrystals (2016)

Herein, we report on a room-temperature anion exchange reaction of highly emitting, all-inorganic CsPbBr3 nanocrystals (NCs) taking place entirely in the solid state. A fast exchange from Br to I and Br to mixed Br/Cl without exertion of additional energy is observed within minutes to hours, taking place by immobilization of the perovskite NCs on pure potassium halide salts (KCl, KBr, and KI). Via adjustment of the halide ratios of the embedding salt matrix, the bright fluorescence of the CsPbX3 (X = Cl, Br, or I) NCs can be tuned over a wide spectral range (400–700 nm) while maintaining the initial photoluminescence quantum yields of ∼80% and narrow full widths at half-maximum. We found that combinations of different initial CsPbX3 NCs and KX matrices result in different final halogen contents of the NCs. This is explained with a host-lattice limiting exchange mechanism. The anion exchange rate can be accelerated by pressing the soft, NC-loaded salts under pressure of 2.2 GPa. Because of the "cold flow" behavior of the potassium salts during the pressing, a complete embedding of the NCs into transparent salt pellets is achieved. This strategy allows for an easy adjustment of the NC loading as well as the form and thickness of the resulting composite. An encapsulation of the NC−salt pellets with silicone yields robustness and stability of the embedded NCs under ambient conditions. The ease of handling and the superior stability make the resulting perovskite composite materials attractive for various photonic and optoelectronic applications as demonstrated in a proof-of-concept color-converting layer for a light−emitting diode.
N-Glycosylation Site Analysis of Proteins from <i>Saccharomyces cerevisiae</i> by Using Hydrophilic Interaction Liquid Chromatography-Based Enrichment, Parallel Deglycosylation, and Mass Spectrometry (2014)

N-Glycosylation site analysis of baker's yeast Saccharomyces cerevisiae is of fundamental significance to elucidate the molecular mechanism of human congenital disorders of glycosylation (CDG). Here we present a mass spectrometry (MS)-based workflow for the profiling of N-glycosylated sites in S. cerevisiae proteins. In this workflow, proteolytic glycopeptides were enriched by using a hydrophilic material named Click TE-Cys to improve the glycopeptide selectivity and coverage. To enhance the reliability of the identified results, the enriched glycopeptides were subjected to parallel deglycosylation by using two endoglycosidases (i.e., PNGase F and Endo Hf), respectively, prior to LC-MS/MS analysis. On the basis of the workflow, a total of 135 N-glycosylated sites including 6 known, 93 potential, and 36 novel sites were identified and mapped to 79 proteins. Among the novel-type sites, nine sites from eight proteins, which were simultaneously identified via PNGase F and Endo Hf deglycosylation, are believed to possess high confidence. The established workflow, together with the profile of N-glycosylated sites, will contribute to the improvement of S. cerevisiae model for revealing the pathogenesis of CDG.
A program behavior matching architecture for probabilistic file system forensics (2008)

Even the most secure computing system can be successfully attacked by a sufficiently motivated entity. To investigate the means of entry, the victim machine will come under the scrutiny of forensic analysis tools. In this era where system compromises occur on a regular basis, the design and implementation of operating systems should consider the necessity of computer forensics. Additionally, forensics techniques should take advantage of existing system capabilities such as the journaling feature of the Ext3 file system. With our forensics enabling architecture, we provide a means of using the metadata inherent in the Ext3 file system to reconstruct probable sequences of events that occurred during the journaling process. The reconstruction procedure is achieved by generating program behavior signatures. These signatures allow forensic investigators to perform probabilistic analysis by using information theory models to extract a more significant set of data.
Potential Efficacy of Chlorhexidine against Mutans Streptococci and Human Dental Caries (1994)

Chemotherapeutic agents have been considered as having potential for the prevention of dental caries. Several substances have been evaluated as possible candidates, but no antimicrobial agent, with the exception of fluoride, has received as much experimental attention as the bisbiguanide chlorhexidine. This substance represents, so far, the most effective and best-documented agent. To be effective against caries, therapeutic dosages of the antimicrobial agent have to be given for a sufficient but finite time period to sites with established cariogenic plaque. In studies where this principle has been used, the aim has been to eliminate or strongly suppress the population of mutans streptococci. Of various antimicrobial agents and methods tested, the most persistent reduction of mutants streptococci has been achieved by chlorhexidine varnishes, followed by gels and mouthwashes. The best clinical effect resulting in a considerable caries reduction has been obtained when persons highly colonized with mutans streptococci have been treated with gels and when the results of the antimicrobial measures have been verified by microbiological examination.
“Salt Templating”: A Simple and Sustainable Pathway toward Highly Porous Functional Carbons from Ionic Liquids (2012)

A facile method to fabricate high-surface area functional carbons via convenient "salt templating" is presented. Exemplarily, nitrogen- as well as nitrogen-/boron-co-doped carbons were synthesized using ionic liquids as precursors and eutectics as porogen. The porogen is easily removable with water and the porosities can be adjusted from micro- to mesoporous depending on the salt nature and amount.
Query transformation for exact cardinality computing (2011)

In general, query optimizers rely on a cost model to choose an appropriate query execution plan for the given queries. An important key parameter of the cost estimation is the cardinality of sub-expressions of the queries. Traditionally, the optimizers may use the estimation cardinality techniques, which can lead to the estimation errors, and hence the poor execution plans. The exact cardinality approach can be applied to resolve such problem, though its computational expense can be costly. A possible way to improve the efficiency is the query transformation since it can provide the alternation to the optimizers. In this paper, we focus on investigation at the effects of the query transformation to the exact cardinality computing processes. The query transformation techniques to be considered in our work are the traditional but widely applied techniques, i.e. subquery unnesting, group-by view merging, join factorization, and join predicate pushdown. The experiment results on the real-life datasets have been presented to validate such proposed work.
Neural fuzzy agents that learn a user's preference map (2002)

This paper models an intelligent agent that helps a user search or filter images in the database. Database search depends on the user's profile of likes and dislikes and how the user ranks similar images. A neural fuzzy system can help learn an agent profile of a user. The fuzzy system uses if-then rules that store and compress the agent's knowledge of the user's likes and dislikes. A neural system uses training data to form and tune the rules. The profile is a preference map or a bumpy utility surface over the space of search objects. Rules define fuzzy patches that cover the bumps as learning unfolds and as the fuzzy agent system gives a finer approximation of the profile. The agent system searches for preferred objects with the learned profile and a new fuzzy measure of similarity. We derive a new supervised learning law that tunes this matching measure with new sample data. Then we test the fuzzy agent profile system on object spaces of flowers and sunsets and test the fuzzy agent matching system on an object space of sunset images.
Dynamic range Vs spectral clarity trade-off in all-digital frequency synthesis via single-bit sinewave quantization (2013)

Single-bit Nyquist-rate quantization of sinewaves with amplitude dithering using a sequence of independent and uniformly distributed random variables has been proposed for all-digital RF frequency synthesis generation. This work demonstrates how we can improve the Dynamic Range using non-uniformly distributed dithering by selectively allowing some of the harmonics to be present in the spectrum (vs. the spurs-free output of the uniform distribution.). MATLAB simulation examples illustrate the results of the proposed approach.
Traffic Analysis of a Ring Switched Data Transmission System (1971)

This paper is concerned with a study of traffic and message delay in a ring switched data transmission system. The system, by asynchronous multiplexing and data storage, shares transmission facilities among many users. It is the random component of message delay due to buffering that is the focal point of our study. The basic configuration of the system is a ring connecting stations where traffic enters or leaves the system. A mathematical model of the ring is developed which accommodates an arbitrary number of stations and any given pattern of traffic between stations. Studied in detail is the uniform traffic pattern in which each user is identical and communicates equally to all others. Intrinsic to the model is a recognition of the bursty nature of data sources. Other factors that are taken into account are line and source rates as well as the blocking of data into fixed size packets. Formulas are derived from which average message delay induced by traffic in the ring can be calculated. The results of the study are presented in a set of curves where normalized delay due to traffic within specific system configurations is plotted as a function of the number of stations and source activity. The delay here is normalized to average message lengths. An important parameter of these curves is the ratio of source rate to line rate. The results show that, in certain quite reasonable circumstances, the delay is less than two average message lengths. Rings of 10, 50, and 100 users have been simulated on a digital computer. Data obtained from these investigations are presented and compared to the theoretical estimates for line busy and idle periods and message delay. The results of simulated average message delay show that, for inter-station link utilizations of about 60 percent, the difference between the theoretical estimates and experimental observations is small.
A proposed polarity standard for multicomponent seismic data (2002)

Abstract This paper proposes a multicomponent acquisition and preprocessing polarity standard that will apply generally to the three Cartesian geophone components and the hydrophone or microphone components of a 2-D or 3-D multicomponent survey on land, at the sea bottom, acquired as a vertical seismic profile, vertical-cable, or marine streamer survey. We use a four-component ocean-bottom data set for purposes of illustration and example. A primary objective is a consistent system of polarity specifications to facilitate consistent horizon correlation among multicomponent data sets and enable determination of correct reflectivity polarity. The basis of this standard is the current SEG polarity standard, first enunciated as a field-recording standard for vertical geophone data and hydrophone streamer data. It is founded on a right-handed coordinate system: z positive downward; x positive in the forward line direction in a 2-D survey, or a specified direction in a 3-D survey, usually that of the receiver-cable lines; and y positive in the direction 90° clockwise from x. The polarities of these axes determine the polarity of ground motion in any component direction (e.g., downward ground motion recording as positive values on the vertical-geophone trace). According also to this SEG standard, a pressure decrease is to be recorded as positive output on the hydrophone trace. We also recommend a cyclic indexing convention, [W, X, Y, Z] or [0, 1, 2, 3], to denote hydrophone or microphone (pressure), inline (radial) geophone, crossline (transverse) geophone, and vertical geophone, respectively. We distinguish among three kinds of polarity standard: acquisition, preprocessing, and final-display standards. The acquisition standard (summarized in the preceding paragraph) relates instrument output solely to sense of ground motion (geophones) and of pressure change (hydrophones). Polarity considerations beyond this [involving, e.g., source type, wave type (P or S), direction of arrival, anisotropy, tap-test adjustments, etc.] fall under preprocessing polarity standards. We largely defer any consideration of a display standard.
The severe acute respiratory syndrome coronavirus in tears (2004)

This is the first case series reported with the detection of the SARS coronavirus from tears, and has important implications for the practice of ophthalmology and medicine. The ability to detect and isolate the virus in the early phase of the disease may be an important diagnostic tool for future patients and tear sampling is both simple and easily repeatable. Many healthcare workers are in close proximity to the eyes of patients and this may be a source of spread among healthcare workers and inoculating patients. Ophthalmic practices may need to change as more stringent barrier methods, appropriate quarantine, and isolation measures are vital when managing patients with SARS.
Do two Libor reforms reduce the effect of incentives on submitted rates (2017)

Thesis (Ph.D.)--University of Washington, 2016-12
A solution to a special case of the synchronization problem (1988)

A synchronizer that exhibits an arbitrarily low failure rate and a short propagation delay for the special case of synchronizing a signal that is synchronous with some periodic signal is described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Design and Development of Peptides and Peptide Mimetics as Antagonists for Therapeutic Intervention (2010)

The concept of peptides as therapeutic agents has been historically disregarded by the pharmaceutical industry on account of their susceptibility to degradation, their size and consequent limitations in methods of delivery. Recently, however, there has been a surge of interest in peptides and their mimetics as potential antagonists for therapeutic intervention. This is in part due to the increased half-life and oral availability that has been achieved for a number of peptide-based systems, the introduction and acceptance of alternative delivery methods, and the prevalence of proteomics to identify countless protein-protein interaction targets. The use of peptides and molecules that mimic their function therefore has great potential to effectively target a range of proteins that are pathogenically implicated in numerous diseases.
Microstructure of ultrananocrystalline diamond films grown by microwave Ar–CH4 plasma chemical vapor deposition with or without added H2 (2001)

Ultrananocrystalline diamond (UNCD) films, grown using microwave plasma-enhanced chemical vapor deposition with gas mixtures of Ar–1%CH4 or Ar–1%CH4–5%H2, have been examined with transmission electron microscopy (TEM). The films consist of equiaxed nanograins (2–10 nm in diameter) and elongated twinned dendritic grains. The area occupied by dendritic grains increases with the addition of H2. High resolution electron microscopy shows no evidence of an amorphous phase at grain boundaries, which are typically one or two atomic layer thick (0.2–0.4 nm). Cross-section TEM reveals a noncolumnar structure of the films. The initial nucleation of diamond occurs directly on the Si substrate when H2 is present in the plasma. For the case of UNCD growth from a plasma without addition of H2, the initial nucleation occurs on an amorphous carbon layer about 10–15 nm thick directly grown on the Si substrate. This result indicates that hydrogen plays a critical role in determining the nucleation interface between the UNCD films and the Si substrate. The relation between diamond nuclei and Si is primarily random and occasionally epitaxial.
Thermal Induction of an Alternatively Folded State in Human IgG-Fc (2011)

We report the formation of a non-native, folded state of human IgG4-Fc induced by a high temperature at neutral pH and at a physiological salt concentration. This structure is similar to the molten globule state in that it displays a high degree of secondary structure content and surface-exposed hydrophobic residues. However, it is highly resistant to chemical denaturation. The thermally induced state of human IgG4-Fc is thus associated with typical properties of the so-called alternatively folded state previously described for murine IgG, IgG-Fab, and individual antibody domains (V(L), V(H), C(H)1, and C(H)3) under acidic conditions in the presence of anions. Like some of these molecules, human IgG4-Fc in its alternative fold exists as a mixture of different oligomeric structures, dominated by an equilibrium between monomeric and heptameric species. Heating further induces the formation of fibrous structures in the micrometer range.