gebhart/patrepeval huggingface dataset:
Isotope‐Coded Affinity Tags with Tunable Reactivities for Protein Footprinting (2008)

Another foot forward: Isotope-coded affinity tag (ICAT) reagents are versatile probes for footprinting dynamic protein structure. To render ICAT footprinting effective, a series of ICAT reagents with alkylation rates that span five orders of magnitude was designed. With this toolkit, an unprecedented range of Cys residues can be footprinted, including those deeply buried in the protein core and those involved in protein–protein interactions of modest affinity.
Surface Modification Studies of Edge-Oriented Molybdenum Sulfide Nanosheets (2004)

We have synthesized edge-oriented MoS2 nanosheets by the evaporation of a single source precursor based on Mo(IV)-tetrakis(diethylaminodithiocarbomato). The surface chemistry of the MoS2 nanosheets has been studied in order to evaluate the chemical reactivities of the basal planes and edges. By irradiating the MoS2 nanosheet with a scanning infrared laser, micron-scale lithographical structures can be created due to laser-induced oxidation of MoS2 to form nanocrystalline MoO3. Preferential reactivities of the MoS2 basal edges in an electrochemical environment and during vapor phase deposition have been demonstrated. Functionalization of the basal plane with 1-pyrene acetic acid allows the immobilization of DNA and immunoglobins on the MoS2 basal plane.
Conformation changes of a polyelectrolyte chain in a poor solvent (1991)

We study theoretically the behaviour of an isolated polyelectrolyte chain in a poor solvent in the presence of salt. The conformation properties of the chain result from the competition between the repulsive Coulomb interactions and the attractive short-range excluded volume interactions. We show in particular that if the solvent is sufficiently poor, the shape of the chain may change abruptly between cylindrical and spherical configurations at a certain critical salt concentration, rather than following a smooth crossover between scaling regimes. The predicted conformational change is not an effect of counterion condensation, and comes only from the competing interactions between the monomers.
Kinetics and mechanism of the Pudovik reaction in the azomethine series: III. Acid-catalyzed hydrophosphorylation of imines (2006)

A complex spectral (UV, IR, and 31P NMR), preparative, and kinetic investigation of the mechanism of the noncatalytic variant of the Pudovik reaction in the series of imines was carried out. The reaction proceeds through a four-center cyclic transition state. The transition state is highly labile, which determines its high sensitivity to the structure of the reagents, the nature of the solvent and catalyst, and some other factors. The necessary condition for the hydrophosphorylation of imines to occur is the participation of proton-donor reagents and acidic admixtures, specifically hydrolysis products of dialkyl hydrogen phosphites, such as monoalkyl dihydrogen phosphates and phosphorous acid, which act as acid catalysts. When the starting reagents are thoroughly purified and no such catalysts are present, the Pudovik reaction fails to occur in the imine series.
Simultaneous oscillation of wavelength-tunable, singlemode lasers using an Er-doped fibre amplifier (1992)

A compound fibre-ring cavity with just one Er-doped fibre amplifier yields wavelength-multiplexed laser lights, each of which is wavelength-tunable and singlemoded with a spectral linewidth <1MHz. The allowable cavity-loss fluctuation for maintaining simultaneous lasing is ∼1dB.
Photometric stereo under a light source with arbitrary motion (1994)

A new photometric-stereo method for estimating the surface normal and the surface reflectance of objects without a priori knowledge of the light-source direction or the light-source intensity is proposed. First, I construct a p × f image data matrix I from p pixel image intensity data through f frames by moving a light source arbitrarily. Under the Lambertian assumption the image data matrix I can be written as the product of two matrices S and L, with S representing the surface normal and the surface reflectance and L representing the light-source direction and the light-source intensity. Using this formulation, I show that the image data matrix I is of rank 3. On the basis of this observation, I use a singular-value decomposition technique and useful constraints to factorize the image data matrix. This method can also be used to treat cast shadows and self-shadows without assumptions. The effectiveness of this method is demonstrated through performance analysis, laboratory experiment, and out-of-laboratory experiment.
Obesity Predicts Differential Response to Cancer Prevention Interventions Among African Americans (2010)

Wellness for African Americans Through Churches was a randomized trial that tested the effectiveness of tailored print and video (TPV) and/or lay health advisors (LHA) at increasing recreational physical activity (RPA), fruit and vegetable (F&V) consumption, and colorectal cancer (CRC) screening in African American churches. Baseline data revealed lower screening and RPA rates among obese individuals but no weight-related differences in F&V consumption. This analysis examined if intervention effectiveness was also moderated by participant weight group. Regression analyses tested for interactions between intervention and weight group for screening and RPA. Weight group was found to be a moderator of intervention effectiveness (p = .02); normal and overweight individuals receiving the LHA intervention increased RPA more, whereas obese individuals responded better to TPV. For CRC screening, the interaction term was not significant; weight alone was related to screening at follow-up (p = .049), with obese individuals reporting less screening. These results suggest that weight tailoring may improve the effectiveness of behavior change interventions.
The 14 kDa <i>β</i>-galactoside binding lectin in myoblast and myotube cultures: localization by confocal microscopy (1992)

The endogenous 14 kDa beta-galactoside-specific lectin has been localised in myoblasts and myotubes by indirect immunofluorescence using confocal microscopy. The antibodies used in these experiments suggest that in myoblast cultures the lectin is abundant on the cell surface and concentrated at ruffled edges of migrating cells. The quantity and distribution of cell surface lectin is independent of the nature of the substratum and undiminished by brief trypsinisation or lactose-washing of the cell suspension. The lectin is also abundant intracellularly, apparently relatively free in the cytoplasm until the cells approach confluency, when the lectin is concentrated into particular areas of cytoplasm resulting in a 'patchy' appearance of stained cells. After fusion to form multinucleate myotubes, intracellular lectin is less abundant and concentrated at the periphery of myotubes, from where lectin appears to be released in vesicles packed with lectin which 'bud off' from the myotube surface. In recolonising cultures, lectin is apparently more abundant and lectin-packed vesicles can also be seen 'budding off' from myoblasts. In differentiated cultures, extracellular lectin is detected both on the myotube surface and in fibrillar arrays of extracellular material.
Home monitoring in Hawaii: the first 1,000 patients. (1989)

By February 1988, 1,000 Hawaii infants had been prescribed cardiorespiratory monitors for use at home. By 1986, 12.3/1000 live births were being monitored, principally for apnea related to prematurity but also following Apparent Life Threatening Episodes, (ALTE) as subsequent siblings of Sudden Infant Death Syndrome (SIDS) victims, and for an increasing variety of other conditions. Less than 3% of families used the monitor less than 1 week; 30% discontinued sooner than the program recommended. Twenty-seven percent of the monitored infants were judged to have experienced real apnea or bradycardia while on their monitors. Seventeen of the patients are known to be dead, with 2 of these deaths occurring while the symptomatic patient was not monitored. Parents responding to a quality assurance questionnaire were highly enthusiastic about monitoring and felt it was a source of reassurance rather than a stressor. Major problems encountered by monitoring families were related to equipment performance.
Tunneling magnetoresistance sensors with different coupled free layers (2017)

Large differences of magnetic coercivity (HC), exchange coupling field (HE), and tunneling magnetoresistance ratio (TMR) in magnetic tunnel junctions with different coupled free layers are discussed. We demonstrate that the magnetization behavior of the free layer is not only dominated by the interfacial barrier layer but also affected largely by the magnetic or non-magnetic coupled free layers. All these parameters are sensitively controlled by the magnetic nanostructure, which can be tuned also by the magnetic annealing process. The optimized sensors exhibit a large field sensitivity of up to 261%/mT in the region of the reversal synthetic ferrimagnet at the pinned layers.
Sympathetic and Parasympathetic Interactions upon the Left Ventricle of the Dog (1966)

In canine, isovolumetric, left ventricle preparations, stimulation of the cardiac end of a cut cervical vagus nerve evokes a biphasic change of left ventricular systolic pressure (LVSP). Characteristically, there is a definite reduction of LVSP during the stimulus, followed by a slight increase of LVSP after cessation of stimulation. The magnitude of the reduction of LVSP during vagal stimulation is considerably augmented when sympathetic activity is increased either directly (by electrical stimulation of the left stellate ganglion) or reflexly (by lowering carotid sinus pressure). These results indicate that the effect of vagal stimulation is mediated, at least in part, by antagonizing the positive inotropic influence of the prevailing sympathetic nervous activity. The mechanism of the poststimulation rebound is unknown. It may be due to cardiac sympathetic fibers in the canine vagosympathetic nerve trunks and to the release of catecholamine-like substances in the myocardium.
Saving money on drawings (1993)

Some isolates of Chlamydia pecorum from sheep feces failed to produce inclusions on passage in cycloheximide-treated monolayers, but chlamydiae could be recovered several weeks later. Chlamydia psittaci from sheep abortions did not show this phenomenon.
Changes in cartilage metabolism in arthritis are reflected by altered serum and synovial fluid levels of the cartilage proteoglycan aggrecan. Implications for pathogenesis. (1994)

The metabolism of the cartilage proteoglycan aggrecan was studied in patients with osteoarthritis (OA, n = 83), rheumatoid arthritis (RA, n = 127), and in controls (n = 117) using monoclonal antibody-based radioimmunoassays for glycosaminoglycans in the serum and synovial fluid (SF) to detect epitope 846 on chondroitin sulfate (probably only on recently synthesized molecules) and a keratan sulfate (KS) epitope AN9PI, present on intact and degraded molecules. Epitope 846 levels were always elevated in SF over serum (mean 38-fold in OA and 8.6-fold in RA) being highest in OA patients with the longest disease duration and greatest loss of cartilage, and lowest in RA joints with high leucocyte counts. Serum levels were more often elevated in RA (56%) than in OA (19%) and probably reflect increased aggrecan synthesis in diseased joints. KS levels were higher in SF than in serum in 69% of patients (up to 2.3-fold); levels were inversely (OA) and directly (RA) related to SF leucocyte counts. Serum KS was reduced in both diseases and in RA was inversely related to both systemic and joint inflammation markers. SF 846 levels were inversely related to SF KS in both diseases. These epitopes may provide a measure of the balance between cartilage synthesis and degradation in these diseases.
Time domain operation of the TRAPATT diode for picosecond-kilovolt pulse generation (1994)

Operation of the trapped plasma avalanche transit time (TRAPATT) diode in the time domain is presented. When operated in the time domain, pulses with amplitudes greater than 1,000 V and risetimes well under 300 ps can be achieved. Selection of a diode for use as a TRAPATT diode is discussed. Experimental results demonstrate pulse generation with an amplitude of 2000 V into 50 Ω and a risetime of 200 ps using a single diode and a power MOSFET driving circuit.
Shear stress increases hydraulic conductivity of cultured endothelial monolayers (1995)

To examine the effect of shear stress on hydraulic conductivity (Lp) of bovine aortic endothelial cell monolayers grown on polycarbonate filters, we developed a rotating disk system, which imposed a defined shear stress while Lp was measured. A 10-cmH2O pressure differential was applied to monolayers, and baseline Lp was established between 1.65 +/- 0.85 and 4.94 +/- 1.05 x 10(-7) cm.s-1.cmH2O-1. One-hour exposure to 10 dyn/cm2 shear stress caused a significant (P < 0.05) increase in Lp by 2.16-fold (+/- 0.42), and Lp remained elevated when shear stress was removed. Three-hour exposure to shear stresses between 0.1 and 20.0 dyn/cm2 revealed a threshold for shear-induced increase in Lp of 0.5 dyn/cm2. At 20 dyn/cm2, Lp initially decreased by 30% (+/- 13.4%, P < 0.05) and then increased to a level 3.76-fold (+/- 0.83, P < 0.05) greater than baseline Lp at 3 h. The shear-induced increase in Lp was reversed with dibutyryl adenosine 3',5'-cyclic monophosphate (DBcAMP, 1 mM) and could be significantly (P < 0.05) inhibited when monolayers were preincubated with 0.3 mM DBcAMP, a concentration that did not significantly affect baseline Lp. Furthermore, preincubation with a general phosphodiesterase inhibitor, 3-isobutyl-1-methylxanthine (1 mM), completely blocked the shear-induced increase in Lp. On the basis of these results, we conclude that shear stress alters endothelial Lp through a cellular mechanism involving signal transduction, not by a purely physical mechanism.
Optical properties of GeO_2 glass and optical fibers (1997)

The optical properties of GeO(2) glass were investigated to clarify its potentiality as an optical fiber material. Glass samples were prepared by the flame hydrolysis and the melting techniques, and their Rayleigh scattering and infrared absorption properties were examined. Optical fibers composed of a pure GeO(2) core and an F-doped GeO(2) cladding were drawn to clarify the scattering loss characteristics. The Rayleigh-scattering intensity obtained from spectral loss measurements on the fibers agreed with that measured in bulk samples, and the intensity relative to that of SiO(2) glass was found to be approximately 3. These results suggest that a minimum loss of 0.15 dB/km is expected at a wavelength of 2 microm.
A load awareness medium access control protocol for wireless ad hoc network (2004)

A contention-based wireless ad hoc medium access control (MAC) protocol, such as carrier sense multiple access with collision avoidance (CSMA/CA), has the excellence of simple and efficient when the system is light-loaded. The main drawback of such protocols is their inefficiency and unbounded delay when system load is heavy. On the other hand, a contention-free MAC protocol, such as token passing, has better and fair throughput when the system is heavy-loaded. The main drawback of such protocols is their inefficiency when only a small amount of users want to transmit. In this paper, we propose a new load awareness wireless ad hoc MAC protocol (which is called the LA protocol) that exploits the benefits of both contention-based and contention-free protocols. A contention-based MAC protocol is used when system is light-loaded and a contention-free one is used otherwise. Our LA protocol, which operates distributed and is fully compatible with IEEE 802.11 wireless local area network (WLAN) standard, can switch smoothly between the contention-based protocol and the contention-free one. Simulation results show that our protocol indeed extracts the better part of two kinds of protocols and performs well in all systems loads.
Digital image processing (1974)

The field of digital image processing is growing exponentially, and as more researchers enter the arena, application areas continue to open with surprising rapidity. This special issue presents both a survey of the field as well as specific examples of projects currently in progress. Two main subjects are treated: image coding and image restoration-enhancement. The former area has particular application to the important task of sending images over digital communication networks, examples of which might include nationwide computer and timesharing networks for conferences, image sharing, and medical consultation. Other areas of image coding applications might include multispectral satellite imaging, spacecraft probes, remote piloted vehicles, facsimile transmission of images ranging from fingerprints to text, and even image transmission over existing telephone networks.
Integration of measurements of interaural cross-correlation coefficient and interaural time difference within a single model of perceived source width (2004)

A measurement model based on the interaural cross-correlation coefficient (IACC) that attempts to predict the perceived source width of a range of auditory stimuli is currently under development. It is necessary to combine the predictions of this model with measurements of interaural time difference (ITD) to allow the model to provide its output on a meaningful scale and to allow integration of results across frequency. A detailed subjective experiment was undertaken using narrow-band stimuli with a number of centre frequencies, IACCs and ITDs. Subjects were asked to indicate the perceived position of the left and right boundaries of a number of these stimuli by altering the ITD of a pair of white noise comparison stimuli. It is shown that an existing IACC-based model provides a poor prediction of the subjective results but that modifications to the model significantly increase its accuracy.
The Consequences of Short-Range Stiffness and Fluctuating Muscle Activity for Proprioception of Postural Joint Rotations: The Relevance to Human Standing (2009)

Proprioception comes from muscles and tendons. Tendon compliance, muscle stiffness, and fluctuating activity complicate transduction of joint rotation to a proprioceptive signal. These problems are acute in postural regulation because of tiny joint rotations and substantial short-range muscle stiffness. When studying locomotion or perturbed balance these problems are less applicable. We recently measured short-range stiffness in standing and considered the implications for load stability. Here, using an appropriately simplified model we analyze the conversion of joint rotation to spindle input and tendon tension while considering the effect of short-range stiffness, tendon compliance, fluctuating muscle activity, and fusimotor activity. Basic principles determine that when muscle stiffness and tendon compliance are high, fluctuating muscle activity is the greatest factor confounding registration of postural movements, such as ankle rotations during standing. Passive and isoactive muscle, uncomplicated by active length fluctuations, enable much better registration of joint rotation and require fewer spindles. Short-range muscle stiffness is a degrading factor for spindle input and enhancing factor for Golgi input. Constant fusimotor activity does not enhance spindle registration of postural joint rotations in actively modulated muscle: spindle input remains more strongly associated with muscle activity than joint rotation. A hypothesized rigid alpha-gamma linkage could remove this association with activity but would require large numbers of spindles in active postural muscles. Using microneurography, the existence of a rigid alpha-gamma linkage could be identified from the correlation between spindle output and muscle activity. Basic principles predict a proprioceptive "dead zone" in the active agonist muscle that is related to the short-range muscle stiffness.
Assessing EUV mask defectivity (2010)

This paper assesses the readiness of EUV masks for pilot line production. The printability of well characterized reticle defects, with particular emphasis on those reticle defects that cause electrical errors on wafer test chips, is investigated. The reticles are equipped with test marks that are inspected in a die-to-die mode (using DUV inspection tool) and reviewed (using a SEM tool), and which also comprise electrically testable patterns. The reticles have three modules comprising features with 32 nm ground rules in 104 nm pitch, 22 nm ground rules with 80 nm pitch, and 16 nm ground rules with 56 nm pitch (on the wafer scale). In order to determine whether specific defects originate from the substrate, the multilayer film, the absorber stack, or from the patterning process, the reticles were inspected after each fabrication step. Following fabrication, the reticles were used to print wafers on a 0.25 NA full-field ASML EUV exposure tool. The printed wafers were inspected with state of the art bright-field and Deep UV inspection tools. It is observed that the printability of EUV mask defects down to a pitch of 56 nm shows a trend of increased printability as the pitch of the printed pattern gets smaller - a well established trend at larger pitches of 80 nm and 104 nm, respectively. The sensitivity of state-of-the-art reticle inspection tools is greatly improved over that of the previous generation of tools. There appears to be no apparent decline in the sensitivity of these state-of-the-art reticle inspection tools for higher density (smaller) patterns on the mask, even down to 56nm pitch (1x). Preliminary results indicate that a blank defect density of the order of 0.25 defects/cm<sup>2</sup> can support very early learning on EUV pilot line production at the 16nm node.
A Propellor-Type Vertical Anemometer (1964)

A vertical anemometer of the propeller type is described. The instrument is sensitive and economical and output is acceptable to most zero-center millivolt recorders. The voltage output reverses in polarity when the direction of rotation reverses (updrafts or downdrafts).
Probe selection for high-density oligonucleotide arrays (2003)

High-density oligonucleotide microarrays enable simultaneous monitoring of expression levels of tens of thousands of transcripts. For accurate detection and quantitation of transcripts in the presence of cellular mRNA, it is essential to design microarrays whose oligonucleotide probes produce hybridization intensities that accurately reflect the concentration of original mRNA. We present a model-based approach that predicts optimal probes by using sequence and empirical information. We constructed a thermodynamic model for hybridization behavior and determined the influence of empirical factors on the effective fitting parameters. We designed Affymetrix GeneChip probe arrays that contained all 25-mer probes for hundreds of human and yeast transcripts and collected data over a 4,000-fold concentration range. Multiple linear regression models were built to predict hybridization intensities of each probe at given target concentrations, and each intensity profile is summarized by a probe response metric. We selected probe sets to represent each transcript that were optimized with respect to responsiveness, independence (degree to which probe sequences are nonoverlapping), and uniqueness (lack of similarity to sequences in the expressed genomic background). We show that this approach is capable of selecting probes with high sensitivity and specificity for high-density oligonucleotide arrays.
Efficacy of Probiotic Prophylaxis After The First Febrile Urinary Tract Infection in Children With Normal Urinary Tracts (2019)

The probiotics were more effective than placebo at reducing the risk of recurrent UTI in children with a normal urinary tract after their first episode of febrile UTI.