gebhart/patrepeval huggingface dataset:
A Multiplex Protein Panel Applied to Cerebrospinal Fluid Reveals Three New Biomarker Candidates in ALS but None in Neuropathic Pain Patients (2016)

The objective of this study was to develop and apply a novel multiplex panel of solid-phase proximity ligation assays (SP-PLA) requiring only 20 μL of samples, as a tool for discovering protein biomarkers for neurological disease and treatment thereof in cerebrospinal fluid (CSF). We applied the SP-PLA to samples from two sets of patients with poorly understood nervous system pathologies amyotrophic lateral sclerosis (ALS) and neuropathic pain, where patients were treated with spinal cord stimulation (SCS). Forty-seven inflammatory and neurotrophic proteins were measured in samples from 20 ALS patients and 15 neuropathic pain patients, and compared to normal concentrations in CSF from control individuals. Nineteen of the 47 proteins were detectable in more than 95% of the 72 controls. None of the 21 proteins detectable in CSF from neuropathic pain patients were significantly altered by SCS. The levels of the three proteins, follistatin, interleukin-1 alpha, and kallikrein-5 were all significantly reduced in the ALS group compared to age-matched controls. These results demonstrate the utility of purpose designed multiplex SP-PLA panels in CSF biomarker research for understanding neuropathological and neurotherapeutic mechanisms. The protein changes found in the CSF of ALS patients may be of diagnostic interest.
Display System Image Quality (1988)

High performance aircraft employ several types of display systems including panel-mounted cathode-ray tube (CRT) displays, head-up displays (HUDs) and helmet-mounted displays (HMDs). These may be usd to produce imagery from onboard sensors or to provide information in a symbolic format. There are a number of parameters that are used to characterize these displays such as resolution, contrast ratio, luminance, number of gray shades, line rate, interlace ratio, luminance, number of gray shades, line rate, interlace ratio, bandwidth, and modulation transfer function. In the case of the HUDs and HMDs, there are other parameters that further describe the display such as distortion, transmittance, field of view, exit pupil diameter, vergence, and field curvature. This paper will describe these systems, the measurement of various parameters, and how they affect the quality of the display system. In addition, methods will be presented that combine the display parameters with human visual system characteristics to produce image quality metrics that are related to operator performance.
Deep learning based noise reduction method for automatic 3D segmentation of the anterior of lamina cribrosa in optical coherence tomography volumetric scans (2019)

A deep-learning (DL) based noise reduction algorithm, in combination with a vessel shadow compensation method and a three-dimensional (3D) segmentation technique, has been developed to achieve, to the authors best knowledge, the first automatic segmentation of the anterior surface of the lamina cribrosa (LC) in volumetric ophthalmic optical coherence tomography (OCT) scans. The present DL-based OCT noise reduction algorithm was trained without the need of noise-free ground truth images by utilizing the latest development in deep learning of de-noising from single noisy images, and was demonstrated to be able to cover more locations in the retina and disease cases of different types to achieve high robustness. Compared with the original single OCT images, a 6.6 dB improvement in peak signal-to-noise ratio and a 0.65 improvement in the structural similarity index were achieved. The vessel shadow compensation method analyzes the energy profile in each A-line and automatically compensates the pixel intensity of locations underneath the detected blood vessel. Combining the noise reduction algorithm and the shadow compensation and contrast enhancement technique, medical experts were able to identify the anterior surface of the LC in 98.3% of the OCT images. The 3D segmentation algorithm employs a two-round procedure based on gradients information and information from neighboring images. An accuracy of 90.6% was achieved in a validation study involving 180 individual B-scans from 36 subjects, compared to 64.4% in raw images. This imaging and analysis strategy enables the first automatic complete view of the anterior LC surface, to the authors best knowledge, which may have the potentials in new LC parameters development for glaucoma diagnosis and management.
A high-resolution multi-attribute method for product characterization, process characterization, and quality control of therapeutic proteins (2022)

During the manufacturing of therapeutic proteins, Critical Quality Attributes (CQAs) have been monitored by conventional methods, such as cation exchange chromatography (CEX), reduced capillary electrophoresis-sodium dodecyl sulfate (rCE-SDS), and 1,2-diamino-4,5-methylenedioxybenzene (DMB) labelling method. The conventional methods often generate individual peaks that contain multiple components, which may obscure the detection and the quantification of individual critical quality attributes (CQAs). Alternatively, Multi-Attribute Method (MAM) enables detection and quantification of specific CQAs. A high resolution MAM has been developed and qualified to replace several conventional methods in monitoring product quality attributes, such as oxidation, deamidation, clipping, and glycosylation. The qualified MAM was implemented in process characterization, as well as release and stability assays in quality control (QC). In combination with a design-of-experiments (DoE), the MAM method identified multivariate process parameter ranges that yield acceptable CQA level, which provides operational flexibility for manufacturing.
AEROSOL SIZE CHARACTERISTICS OVER THE ARABIAN SEA AND INDIAN OCEAN : EXTENSIVE SUB-MICRON AEROSOL LOADING IN THE NORTHERN HEMISPHERE (1999)

Aerosol optical depth (AOD) measurements in the
spectral range 0.3–1.6 mm have been carried out using
a multi-channel solar radiometer onboard ORV Sagar
Kanya to understand the interaction between continental
and marine aerosols. Experiments have been
carried out under clear sky conditions for 22 days
during 20 January–12 March 1999 covering the latitude
belt between 17°N and 20°S, and longitude belt
between 71°E and 59°E, over Indian Ocean and Arabian
Sea as part of INDOEX IFP-99. Results show
larger particle abundance, close to the Indian coast
during forward leg compared to that of return leg of
the cruise. AODs, in general, exhibit larger values
north of ITCZ compared to that of south of ITCZ.
The spatial distribution of AOD at 0.502 mm shows
greater values north of ITCZ with significant latitudinal
gradient compared to that of south of ITCZ.
Aerosol size spectrum, derived from spectral AODs,
shows monomodal distribution for both pristine
oceanic environment (south of ITCZ) and for polluted
environment (north of ITCZ).
Structural Basis for the Recognition of Isoleucyl-Adenylate and an Antibiotic, Mupirocin, by Isoleucyl-tRNA Synthetase (2001)

An analogue of isoleucyl-adenylate (Ile-AMS) potently inhibits the isoleucyl-tRNA synthetases (IleRSs) from the three primary kingdoms, whereas the antibiotic mupirocin inhibits only the eubacterial and archaeal IleRSs, but not the eukaryotic enzymes, and therefore is clinically used against methicillin-resistant Staphylococcus aureus. We determined the crystal structures of the IleRS from the thermophilic eubacterium, Thermus thermophilus, in complexes with Ile-AMS and mupirocin at 3.0- and 2.5-A resolutions, respectively. A structural comparison of the IleRS.Ile-AMS complex with the adenylate complexes of other aminoacyl-tRNA synthetases revealed the common recognition mode of aminoacyl-adenylate by the class I aminoacyl-tRNA synthetases. The Ile-AMS and mupirocin, which have significantly different chemical structures, are recognized by many of the same amino acid residues of the IleRS, suggesting that the antibiotic inhibits the enzymatic activity by blocking the binding site of the high energy intermediate, Ile-AMP. In contrast, the two amino acid residues that concomitantly recognize Ile-AMS and mupirocin are different between the eubacterial/archaeal IleRSs and the eukaryotic IleRSs. Mutagenic analyses revealed that the replacement of the two residues significantly changed the sensitivity to mupirocin.
The Magnitude of Androgen Receptor Positivity in Breast Cancer Is Critical for Reliable Prediction of Disease Outcome (2018)

<b>Purpose:</b> Consensus is lacking regarding the androgen receptor (AR) as a prognostic marker in breast cancer. The objectives of this study were to comprehensively review the literature on AR prognostication and determine optimal criteria for AR as an independent predictor of breast cancer survival.<b>Experimental Design:</b> AR positivity was assessed by immunostaining in two clinically validated primary breast cancer cohorts [training cohort, <i>n</i> = 219; validation cohort, <i>n</i> = 418; 77% and 79% estrogen receptor alpha (ERα) positive, respectively]. The optimal AR cut-point was determined by ROC analysis in the training cohort and applied to both cohorts.<b>Results:</b> AR was an independent prognostic marker of breast cancer outcome in 22 of 46 (48%) previous studies that performed multivariate analyses. Most studies used cut-points of 1% or 10% nuclear positivity. Herein, neither 1% nor 10% cut-points were robustly prognostic. ROC analysis revealed that a higher AR cut-point (78% positivity) provided optimal sensitivity and specificity to predict breast cancer survival in the training (HR, 0.41; <i>P</i> = 0.015) and validation (HR, 0.50; <i>P</i> = 0.014) cohorts. Tenfold cross-validation confirmed the robustness of this AR cut-point. Patients with ERα-positive tumors and AR positivity ≥78% had the best survival in both cohorts (<i>P</i> < 0.0001). Among the combined ERα-positive cases, those with comparable or higher levels of AR (AR:ERα-positivity ratio >0.87) had the best outcomes (<i>P</i> < 0.0001).<b>Conclusions:</b> This study defines an optimal AR cut-point to reliably predict breast cancer survival. Testing this cut-point in prospective cohorts is warranted for implementation of AR as a prognostic factor in the clinical management of breast cancer. <i>Clin Cancer Res; 24(10); 2328-41. ©2018 AACR</i>.
Ionic charge-transfer complexes. 1. Cationic complexes with delocalized and partially localized .pi. systems (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIonic charge-transfer complexes. 1. Cationic complexes with delocalized and partially localized .pi. systemsM. Michael. Meot-Ner and M. Samy. El-ShallCite this: J. Am. Chem. Soc. 1986, 108, 15, 4386–4390Publication Date (Print):July 1, 1986Publication History Published online1 May 2002Published inissue 1 July 1986https://pubs.acs.org/doi/10.1021/ja00275a026https://doi.org/10.1021/ja00275a026research-articleACS PublicationsRequest reuse permissionsArticle Views223Altmetric-Citations20LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Improving Dwell-Based Gaze Typing with Dynamic, Cascading Dwell Times (2017)

We present cascading dwell gaze typing, a novel approach to dwell-based eye typing that dynamically adjusts the dwell time of keys in an on-screen keyboard based on the likelihood that a key will be selected next, and the location of the key on the keyboard. Our approach makes unlikely keys more difficult to select and likely keys easier to select by increasing and decreasing their required dwell times, respectively. To maintain a smooth typing rhythm for the user, we cascade the dwell time of likely keys, slowly decreasing the minimum allowable dwell time as a user enters text. Cascading the dwell time affords users the benefits of faster dwell times while causing little disruption to users' typing cadence. Results from a longitudinal study with 17 non-disabled participants show that our dynamic cascading dwell technique was significantly faster than a static dwell approach. Participants were able to achieve typing speeds of 12.39 WPM on average with our cascading technique, whereas participants were able to achieve typing speeds of 10.62 WPM on average with a static dwell time approach. In a small evaluation conducted with five people with ALS, participants achieved average typing speeds of 9.51 WPM with our cascading dwell approach. These results show that our dynamic cascading dwell technique has the potential to improve gaze typing for users with and without disabilities.
The Effect of Tert-butylammonium Addition in Methylammonium Lead Iodide Perovskite Solar Cells (2019)

Although methylammonium lead iodide (MAPI) perovskite solar cells have reached efficiencies above 20%, the material is environmentally unstable. Mixing MAPI with lower dimensional (LD) perovskites has been suggested to improve its stability in recent studies. However, the LD-mixed perovskites have lower device performance, likely as a result of limited charge-carrier mobility due to their decreased structural dimensionality. To understand this effect, we mixed large-A-site cation LD perovskites, tert-butylammonium lead iodide, with MAPI, and performed a device performance diagnostics. The results suggested although the charge-carrier lifetime was improved, the mobility decreased by a factor of 20. This contributed to a reduction in device efficiency by 2 orders of magnitude, indicating that mobility plays an important role in 3D/LD perovskite mixtures.
Lattice-plane orientation mapping of homo-epitaxial GaN(0001) thin films via grazing-incidence X-ray diffraction topography in 2-in. wafer (2018)

We propose a method for evaluating the lattice-plane orientation of homo-epitaxial GaN thin films using X-ray diffraction topography. The GaN diffraction peak and its rocking curve at every point in the wafer were recorded using an area detector. In addition, we describe the reconstruction method for the [0001] vector with qx, qy, and qz components of the physical surface of the sample using a matrix obtained from two equivalent diffraction topographic images. We obtained the qx, qy, and qz components of every point of the 2-in. wafer from images recorded at azimuthal angles of 0 and 120°.
I n s i t u characterization of diamond nucleation and growth (1989)

Filament-assisted chemical vapor deposition (CVD) diamond film growth on Si(100) was studied using x-ray photoelectron spectroscopy (XPS) to examine the sample at selected intervals during the nucleation and growth processes. The sample was transferred under vacuum from the growth chamber to the attached XPS analysis chamber without exposure to air. Before growth XPS showed that the Si sample is covered by a layer of SiO2 and carbonaceous residue; however, after 15 min of growth both of these substances are removed and replaced by a distinct SiC layer [Si(2p)=100.3 eV and C(1s)=282.7 eV].
Uplink scheduling in OFDMA systems using opportunistic beamforming (2009)

Opportunistic beamforming is investigated in OFDMA uplink. A low complexity scheduling algorithm for utility maximization with opportunistic beamforming is presented. Scheduling with greedy and proportional fair utilities is studied. A beam is formed in a pseudorandom fashion thus leading to artificial fading variations. This allows users to opportunistically benefit from the antenna gain. Results show improved throughput and fairness in the case of opportunistic beamforming even when only a single beam is used.
The Knee Society System of Standardized Abbreviations for Surgery of the Arthritic Knee (2005)

A new standardized system of abbreviations has been adopted by the Knee Society to bring clarity and brevity to scientific reports involving the arthritic knee. This system works by using a set of core abbreviations that are modified with prefixes, suffixes, and superscript notations to indicate succinctly the surgical approach, the procedure used, and the type of prosthesis implanted.
C–N bond hydrogenolysis of aniline and cyclohexylamine over TaOx–Al2O3 (2016)

Aniline denitrogenation over TaO<sub>x</sub>–Al<sub>2</sub>O<sub>3</sub> leads to chemically inert Ta-imido species.
Functions of blood group antigens (2019)

This chapter reviews knowledge about erythrocyte membrane proteins that bear blood group antigens and whose functional importance has been characterized. It focuses on two of the most interesting of these proteins: the anion exchanger protein, which bears antigens of the Diego blood group system, and the Rh proteins. The chapter briefly summarizes functional information about other proteins. Glycophorins C and D (GPC/GPD) are 32 and 23 kDa membrane glycoproteins arising from the same four-exon gene via alternative in-frame mRNA translation initiation sites, giving rise to the Gerbich erythrocyte antigens. A number of erythrocyte membrane proteins have been identified as adhesion molecules. CD44 was the first erythrocyte membrane protein to be characterized as an adhesion molecule and bears homology to the cartilage link and proteoglycan core proteins, which are known to interact with hyaluronan.
Coherent, directional supercontinuum generation (2017)

We demonstrate a novel approach to producing coherent, directional supercontinuum and cascaded dispersive waves using dispersion engineering in waveguides. By pumping in the normal group-velocity dispersion (GVD) regime, with two zero-GVD points to one side of the pump, pulse compression of the first dispersive wave generated in the anomalous GVD region results in the generation of a second dispersive wave beyond the second zero-GVD point in the normal GVD regime. As a result, we achieve an octave-spanning supercontinuum generated primarily to one side of the pump spectrum. We theoretically investigate the dynamics and show that the generated spectrum is highly coherent. We experimentally confirm this dynamical behavior and the coherence properties in silicon nitride waveguides by performing direct detection of the carrier-envelope-offset frequency of our femtosecond pump source using an f-2f interferometer. Our technique offers a path towards a stabilized, high-power, integrated supercontinuum source with low noise and high coherence, with applications including direct comb spectroscopy.
Frequency-Domain Analysis of <inline-formula> <tex-math notation="LaTeX">$N$</tex-math></inline-formula>-Path Filters Using Conversion Matrices (2015)

N-path filters are finding increased prominence in recent architectures for tunable transceivers. The clock-programmable center frequency together with programmable baseband bandwidth makes it a natural fit for wide programmability required in software-defined radios and cognitive radios. However, the analysis of such filters remains difficult due to their linear periodically time-varying (LPTV) nature. This brief presents an analysis of N-path filters using conversion matrices. Conversion matrices allow for the analysis of an LPTV circuit with equivalent frequency-domain circuits that can, in turn, be analyzed similar to a linear time-invariant circuit. On applying this method to N-path filters, results already established in prior art are accurately reproduced. Furthermore, the effects of a few important nonidealities, such as clock overlaps, nonideal clock duty cycles, and parasitic elements, are also calculated and verified.
A Desalination Battery (2012)

Water desalination is an important approach to provide fresh water around the world, although its high energy consumption, and thus high cost, call for new, efficient technology. Here, we demonstrate the novel concept of a "desalination battery", which operates by performing cycles in reverse on our previously reported mixing entropy battery. Rather than generating electricity from salinity differences, as in mixing entropy batteries, desalination batteries use an electrical energy input to extract sodium and chloride ions from seawater and to generate fresh water. The desalination battery is comprised by a Na(2-x)Mn(5)O(10) nanorod positive electrode and Ag/AgCl negative electrode. Here, we demonstrate an energy consumption of 0.29 Wh l(-1) for the removal of 25% salt using this novel desalination battery, which is promising when compared to reverse osmosis (~ 0.2 Wh l(-1)), the most efficient technique presently available.
Prediction of Paroxysmal Atrial Fibrillation by Analysis of Atrial Premature Complexes (2004)

Currently, no reliable method exists to predict the onset of paroxysmal atrial fibrillation (PAF). We propose a predictor that includes an analysis of the R-R time series. The predictor uses three criteria: the number of premature atrial complexes (PAC) not followed by a regular R-R interval, runs of atrial bigeminy and trigeminy, and the length of any short run of paroxysmal atrial tachycardia. An increase in activity detected by any of these three criteria is an indication of an imminent episode of PAF. Using the Physionet database of the Computers in Cardiology 2001 Challenge, the predictor achieved a sensitivity of 89% and a specificity of 91%.
Incorporation of ‘click’ chemistry glycomimetics dramatically alters triple-helix stability in an adiponectin model peptide (2017)

Adiponectin (Adpn) has been shown to be a possible therapeutic for Type II diabetes, however the production of a therapeutic version of Adpn has proved to be challenging. Biological studies have highlighted the importance of the glycosylated lysine residues for the formation of bioactive high molecular weight oligomers of Adpn. Through the use of 'click' glycopeptide mimetics, we investigated the role of glycosylated lysine and serine residues for the formation of triple helical structures of the collagenous domain of Adpn, in the context of a collagen model peptide scaffold. The physical properties of the unglycosylated lysine and serine peptides are compared with their glycosylated analogues. Our results highlight the crucial role of lysine residues for formation of the triple helical structure of Adpn, possibly due to the extension of both intra- and interstrand hydrogen bonding networks. Strikingly, we observed a significant decrease in thermal stability upon incorporation of triazole-linked analogues of glycosylated lysine residues into the adiponectin collageneous domain, indicating possible uses of 'click' glycomimetics for bioengineering applications.
1002 (2014)

1Stanford University Medical Center, Palo Alto, CA 2Stanford University, Palo Alto, CA 3Cincinnati Children’s Hospital Medical Center, Cincinnati, OH