gebhart/patrepeval huggingface dataset:
Design and implementation of a prototype Human Protein Index. (1982)

Abstract This paper describes information-handling aspects of the TYCHO I analysis system (Clin, Chem. 27: 1807--1820, 1981), which analyzes two-dimensional electrophoresis gels, matches the individual protein spots with those in a reference pattern, and stores various information--including spot measurements, identifications, treatment profiles, set memberships, and comments--in a computerized database. This and additional information such as amino acid composition and cellular localization is then accessible from an interactive program that includes a pictorial user interface and presents much of the data in graphical form. Use of the TYCHO I system is illustrated by examples drawn from analyses of gel patterns from human leukocytes.
Search for pair-produced scalar and vector leptoquarks decaying into third-generation quarks and first- or second-generation leptons in pp collisions with the ATLAS detector (2023)

A bstract A search for pair-produced scalar and vector leptoquarks decaying into quarks and leptons of different generations is presented. It uses the full LHC Run 2 (2015–2018) data set of 139 fb − 1 collected with the ATLAS detector in proton–proton collisions at a centre-of-mass energy of $$ \sqrt{s} $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msqrt> <mml:mi>s</mml:mi> </mml:msqrt> </mml:math> = 13 TeV. Scalar leptoquarks with charge −(1 / 3) e as well as scalar and vector leptoquarks with charge +(2 / 3) e are considered. All possible decays of the pair-produced leptoquarks into quarks of the third generation ( t, b ) and charged or neutral leptons of the first or second generation ( e, μ, ν ) with exactly one electron or muon in the final state are investigated. No significant deviations from the Standard Model expectation are observed. Upper limits on the production cross-section are provided for eight models as a function of the leptoquark mass and the branching ratio of the leptoquark into the charged or neutral lepton. In addition, lower limits on the leptoquark masses are derived for all models across a range of branching ratios. Two of these models have the goal of providing an explanation for the recent B -anomalies. In both models, a vector leptoquark decays into charged and neutral leptons of the second generation with a similar branching fraction. Lower limits of 1980 GeV and 1710 GeV are set on the leptoquark mass for these two models.
Efficient elastic optical path network for transmission beyond 100G (2010)

Optical networks of tomorrow are expected to support the rapid growth of data services such as the broadband access, including broadband mobile access, storage area networks with long connection times and large transfer capacities, as well as data center interconnections, requiring ultra-high capacity links. Those services with differing capacities and patterns will converge in the same optical platform. The standardization bodies have reached an agreement on the format of the optical 100 Gb/s transmission. However, the large variety of services is likely to generate traffics both below 100 Gb/s as well as exceeding that maximum port speed. In order to address this demand efficiently it is necessary to consider more flexible methods of traffic allocation. One solution may be provided by a spectrum-sliced elastic optical path network (SLICE). The aim of SLICE is to efficiently allocate client traffic while performing the necessary networking functionality directly in the optical domain. Technologies and concepts employed in SLICE enable efficient utilization of network resources by providing optical paths with bandwidths ranging from 40 Gb/s to over 400 Gb/s. Basing on the concept of elastic optical path, we discuss the following concepts: path bandwidth flexibly following client traffic with capacity of 40 to 400Gb/s, grooming and aggregation performed optically: seamless aggregation of optical paths exceeding the maximum speed of a single port to form a super-wavelength optical path; sharing of resources through reduction of the overall number of required resources; distance adaptation through reduction of consumed resources by transmission margin optimization.
Amyloid-like Behavior in Abiotic, Amphiphilic Foldamers (2008)

Previously, we reported an abiotic amphiphilic foldamer that, upon heating, undergoes an irreversible conformational change to a highly aggregated state (Nguyen, J.Q.; Iverson, B.L. J. Am. Chem. Soc. 1999, 121, 2639-2640.). Herein, we extend this work through the study of a series of structurally related amphiphilic foldamers and present a more refined model of their conformational switching behavior. Prior to heating, all foldamers of the series exhibited spectral characteristics consistent with folding in the pleated, stacked geometry characteristic of this class of foldamer. Following heating at 80 degrees C, three of the four molecules exhibited irreversible aggregation to produce hydrogels. The hydrogels were characterized by rheology measurements, and circular dichroism spectra revealed that hydrogel formation was dependent on highly ordered intermolecular assembly, conceptually analogous to protein amyloid formation. Hydrogel formation had the effect of amplifying the subtle structural differences between molecules, as the three amphiphilic foldamer constitutional isomers that formed hydrogels upon heating displayed significant differences in hydrogel properties. Taking a global view, our results indicate that amyloid-like behavior is not unique to proteins but may be a relatively general property of amphiphilic folding molecules in aqueous solution.
Automatic induction of rules for text simplification (1997)

Long and complicated sentences pose various problems to many state-of-the-art natural language technologies. We have been exploring methods to automatically transform such sentences in order to make them simpler. These methods involve the use of a rule-based system, driven by the syntax of the text in the domain of interest. Hand-crafting rules for every domain is time-consuming and impractical. The paper describes an algorithm and an implementation by which generalized rules for simplification are automatically induced from annotated training material using a novel partial parsing technique which combines constituent structure and dependency information. The algorithm described in the paper employs example-based generalizations on linguistically motivated structures.
Characterization of cytokine interactions by flow cytometry and factorial analysis (2000)

Factorial analysis provides a powerful methodology to study the integration of multiple signals at the cellular and molecular level.
A novel method for quantifying peripheral tissue amyloid load by using the radiolabeled amyloidophilic peptide, p5 (2013)

Quantitation of peripheral amyloid deposits by non-invasive molecular imaging can be useful for diagnosis, prognostication and monitoring response to therapy. In order to obtain reliable quantitative data, it is necessary to show a linear positive correlation between the uptake of the molecular probe and the tissue amyloid load. The transgenic H-2/IL-6 mouse model of AA amyloidosis was used to generate animals with varied stages of visceral amyloid disease. The mice were injected with 125I-labeled peptide p5 and tissues analyzed 2 h post-injection using Congo red (CR) staining, radioisotope biodistribution and micro-autoradiography (ARG). Micro-ARG confirmed that 125I-p5 was deposited at all amyloid deposits and sites of Congophilia but not at amyloid-free sites within the tissues evaluated. Furthermore, biodistribution studies revealed that the amount of 125I deposited in liver and spleen correlated with the amount of CR birefringence (expressed as 0-4+ or as tissue area [µm2]) in these tissues with correlation coefficients of r > 0.7 (p < 10(-6)). Deposition of 125I-p5 is a quantitative measure of the amount of AA amyloid in liver and spleen in this mouse model. The p5 peptide has potential as a quantitative amyloid imaging agent in human disease.
POST MORTEM ACTIVATION OF HUMAN BLOOD FIBRINOLYTIC ENZYME IN SUDDEN AND NATURAL DEATHS. (1963)

With the purpose to elucidate the cause and difference of blood fluidity in sudden death and natural one, we have observed the fibrinolysis of the blood in medico-legal and pathological autopsies by means of Fibrin Plate Method, a routine method devised in our laboratory. As the result it has been found that in the blood serum of sudden death and in some of natural deaths from tumors, leukemias, etc., the decrease in fibrinolytic activity is equivalent to the amount of proactivator that combined with the SK-like substance liberated into blood. On the other hand, in the blood of most of natural deaths, and in that bled from vessels and stored in body cavities, no natural fibrinolysis is observable and the same fibrinolytic activity with SK as normal one is demonstrated. Thus it is concluded that the cause of blood fluidity in sudden death is due to the fibrinolysis.
Towards Dynamically-Favourable Quad-Rotor Aerial Robots (2004)

This paper outlines progress towards realising practical quad-rotor robot helicopters and, in particular, the Australian National University’s ‘X-4 Flyer’ platform. Two challenges facing the X-4 are generating sufficient thrust and managing unstable dynamic behaviour. We address these issues with a rotor design technique for maximising thrust and the application of a novel rotor mast configuration. An aero-elastic blade design is described and its performance results are presented. A sprung teetering rotor hub that allows adjustment of the blade flapping characteristics and a quad-rotor dynamic model with blade flapping are introduced. The use of inverted rotors is shown to produce favorable stability properties for the Mark II X-4 Flyer.
Fiber Optic Sensors Based upon the Fabry–Perot Interferometer (2017)

The Fabry–Perot interferometer (FPI), sometimes called the Fabry–Perot etalon, consists of two mirrors of reflectance R 1 and R 2 separated by a cavity 36of length L, as in Figure 2.1. Since its invention in the late 19th century [1], the bulk-optics version of the FPI has been widely used for high-resolution spectroscopy. In the early 1980s, the first results on fiber optic versions of the FPI were reported. In the late 1980s, fiber Fabry–Perot interferometers began to be applied to the sensing of temperature, strain, and ultrasonic pressure in composite materials. This early work laid the foundation for extensive research and development as well as commercialization, which followed during the 1990s.
Search for the exotic decay of the Higgs boson into two light pseudoscalars with four photons in the final state in proton-proton collisions at $$ \sqrt{s} $$ = 13 TeV (2023)

A bstract A search for the exotic decay of the Higgs boson to a pair of light pseudoscalars, each of which subsequently decays into a pair of photons, is presented. The search uses data from proton-proton collisions at $$ \sqrt{s} $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msqrt> <mml:mi>s</mml:mi> </mml:msqrt> </mml:math> = 13 TeV recorded with the CMS detector at the LHC that corresponds to an integrated luminosity of 132 fb − 1 . The analysis probes pseudoscalar bosons with masses in the range 15–62 GeV, coming from the Higgs boson decay, which leads to four well-isolated photons in the final state. No significant deviation from the background-only hypothesis is observed. Upper limits are set on the product of the Higgs boson production cross section and branching fraction into four photons. The observed (expected) limits range from 0.80 (1.00) fb for a pseudoscalar boson mass of 15 GeV to 0.26 (0.24) fb for a mass of 62 GeV at 95% confidence level.
Factors Associated with Negative Patient Experiences with Essure Sterilization (2020)

Our study provides new follow-up data with respect to hysteroscopic sterilization. This research is the first to examine any cause for negative patient experiences with Essure. Understanding factors associated with negative patient experiences could improve patient counseling regarding the extent to which symptoms could be attributed to Essure as well as counseling women who want to undergo removal of the device. These factors could in turn prove to be predictors for successful resolution of symptoms after removal of Essure. Results of this study could also be used for developing future hysteroscopic sterilization techniques.
EFFECT OF SEED SIZE ON GERMINATION, SEEDLING VIGOR, ELECTROLYTE LEAKAGE, AND ESTABLISHMENT OF BIRD’S-FOOT TREFOIL (Lotus corniculatus L.) (1981)

Seed viability, seedling vigor, and field establishment were measured on five seed sizes from five commercial, Certified seed lots of bird’s-foot trefoil (Lotus corniculatus L. ’Leo’). Viability as determined by percent germination at 20 °C varied among seed lots and among seed sizes, but a consistent relationship between viability and seed size was not observed. Similarly, speed of germination did not vary in response to seed size but did vary among lots. Within a seed lot, seedling length after 7 days growth varied in response to seed size; the larger seeds produced longer seedlings. However, this relationship was not observed among seed lots because seed lots with the highest average seed weight did not produce the longest seedlings. The seedling vigor ranking on the basis of electrolyte leakage differed if leakage was expressed relative to seed weight or the seed number. Leakage per 100 seeds was significantly and negatively correlated with percent germination, but not with seedling length or field establishment. On the other hand, leakage per gram of seed was significantly and negatively correlated with percent germination, seedling length, and field establishment. The larger seed sizes within a lot tended to have improved field establishment, so field establishment was highly correlated with seedling length (r = 0.76). Electrolyte leakage per gram of seed, and percentage germination were also significantly correlated with establishment (r = − 0.59 and 0.45, respectively). Germination potential and ability of the seedling to elongate rapidly are related to the field establishment of bird’s-foot trefoil. Germination potential was primarily influenced by the seed lot, whereas the ability to elongate was influenced by seed size (within a seed lot).
Renal function is the same 6 months after robot‐assisted partial nephrectomy regardless of clamp technique: analysis of outcomes for off‐clamp, selective arterial clamp and main artery clamp techniques, with a minimum follow‐up of 1 year (2014)

Off-clamp and selective artery clamp techniques result in superior short-term renal functional outcomes compared with the main artery clamp approach; however, after the 6th postoperative month, there were no significant differences regarding the functional outcome among the above surgical techniques, as long as the warm ischaemia time was 20-30 min.
Electrochemical Stability of Garnet-Type Li7La2.75Ca0.25Zr1.75Nb0.25O12 with and without Atomic Layer Deposited-Al2O3 under CO2 and Humidity (2019)

Interest toward developing all-solid-state batteries incorporating lithium-stuffed garnet electrolytes (LSGEs) has been on the constant rise. However, LSGEs are known to react with humidity, and subsequently, CO<SUB>2</SUB> during preparation or storage, leading to Li<SUB>2</SUB>CO<SUB>3</SUB> formation. In this study, we report the long-term exposure effects of CO<SUB>2</SUB> and humidity on the lithium-ion conductivity of typical garnet-type Li<SUB>7</SUB>La<SUB>2.75</SUB>Ca<SUB>0.25</SUB>Zr<SUB>1.75</SUB>Nb<SUB>0.25</SUB>O<SUB>12</SUB> with and without Al<SUB>2</SUB>O<SUB>3</SUB> deposited by atomic layer deposition (ALD). The ionic conductivity of the samples was investigated by electrochemical impedance spectroscopy as a function of time for up to 1000 h. The impedance spectra of ALD-coated garnet-type Li<SUB>7</SUB>La<SUB>2.75</SUB>Ca<SUB>0.25</SUB>Zr<SUB>1.75</SUB>Nb<SUB>0.25</SUB>O<SUB>12</SUB> sample was unaffected by long-term exposure to 400 ppm up to pure CO<SUB>2</SUB> while the uncoated garnet-type sample show at least 8% increase in total resistance. Both samples show increased resistance in the presence of humidity, but the resistance recovers upon removal of the humidity.
Evaluation of coronal shift as an indicator of neuroaxial abnormalities in adolescent idiopathic scoliosis: a prospective study (2014)

A total spine MRI is recommended at presentation in patients with younger age, abnormal neurologic findings and severe coronal shift.
Efficient Inference of Flexible Interaction in Spiking-neuron Networks (2020)

Hawkes process provides an effective statistical framework for analyzing the time-dependent interaction of neuronal spiking activities. Although utilized in many real applications, the classic Hawkes process is incapable of modelling inhibitory interactions among neurons. Instead, the nonlinear Hawkes process allows for a more flexible influence pattern with excitatory or inhibitory interactions. In this paper, three sets of auxiliary latent variables (Pólya-Gamma variables, latent marked Poisson processes and sparsity variables) are augmented to make functional connection weights in a Gaussian form, which allows for a simple iterative algorithm with analytical updates. As a result, an efficient expectation-maximization (EM) algorithm is derived to obtain the maximum a posteriori (MAP) estimate. We demonstrate the accuracy and efficiency performance of our algorithm on synthetic and real data. For real neural recordings, we show our algorithm can estimate the temporal dynamics of interaction and reveal the interpretable functional connectivity underlying neural spike trains.
Friedreich Ataxia Clinical Outcome Measures (2012)

Friedreich ataxia is an autosomal recessive neurodegenerative disorder characterized by ataxia, dysarthria, and areflexia. The authors report the progress of a large international noninterventional cohort (n = 410), tracking the natural history of disease progression using the neurologic examination-based Friedreich Ataxia Rating Scale. The authors analyzed the rate of progression with cross-sectional analysis and longitudinal analysis over a 2-year period. The Friedreich Ataxia Rating Scale captured disease progression when used at 1 and 2 years following initial evaluation, with a lower ratio of standard deviation of change to mean change over 2 years of evaluation. However, modeling of disease progression identified substantial ceiling effects in the Friedreich Ataxia Rating Scale, suggesting this measure is most useful in subjects before maximal deficit is approached.
A Peptoid with Extended Shape in Water (2019)

&lt;div&gt; &lt;div&gt; &lt;div&gt; &lt;p&gt;“Peptoids” was proposed, over decades ago, as a term describing analogs of peptides that exhibit better physicochemical and pharmacokinetic properties than peptides. Oligo-(N-substituted glycines) (oligo-NSG) was previously proposed as a peptoid due to its high proteolytic resistance and membrane permeability. However, oligo-NSG is conformationally flexible and is difficult to achieve a defined shape in water. This conformational flexibility is severely limiting biological application of oligo-NSG. Here, we propose oligo-(N-substituted alanines) (oligo-NSA) as a new peptoid that forms a defined shape in water. A synthetic method established in this study enabled the first isolation and conformational study of optically pure oligo-NSA. Computational simulations, crystallographic studies and spectroscopic analysis demonstrated the well-defined extended shape of oligo-NSA realized by backbone steric effects. The new class of peptoid achieves the constrained conformation without any assistance of N-substituents and serves as an ideal scaffold for displaying functional groups in well-defined three-dimensional space, which leads to effective biomolecular recognition. &lt;/p&gt; &lt;/div&gt; &lt;/div&gt; &lt;/div&gt;
Nanoscale Interfacial Engineering for Flexible Barrier Films (2015)

Alternating layers of organic and oxide thin films used as diffusion barriers in emerging flexible device technologies are vulnerable to degradation under the influence of mechanical stresses, temperature cycling, photodegradation, and chemically active environmental species. Delamination of the internal organic to oxide interfaces often limits the operational lifetime of the barrier system. We demonstrate a method for increasing the adhesion of organic and oxide thin films by generating nanostructures at the interface. We show that the adhesion of an acrylate to silicon oxide model system can be increased by up to an order of magnitude (from ∼2 J/m(2) to 24 J/m(2)). By altering the diameter and depth of the patterns in the model systems, the adhesion energy can be changed, and the delamination pathway can be controlled. In addition, we show that a patterned interface maintains a higher adhesion than its planar counterpart for all durations of UV-A and UV-B exposure.
Nitric Oxide-Dependent Protein Post-Translational Modifications Impair Mitochondrial Function and Metabolism to Contribute to Neurodegenerative Diseases (2019)

<b><i>Significance:</i></b> Most brains affected by neurodegenerative diseases manifest mitochondrial dysfunction as well as elevated production of reactive oxygen species and reactive nitrogen species (RNS), contributing to synapse loss and neuronal injury. <b><i>Recent Advances:</i></b> Excessive production of RNS triggers nitric oxide (NO)-mediated post-translational modifications of proteins, such as S-nitrosylation of cysteine residues and nitration of tyrosine residues. Proteins thus affected impair mitochondrial metabolism, mitochondrial dynamics, and mitophagy in the nervous system. <b><i>Critical Issues:</i></b> Identification and better characterization of underlying molecular mechanisms for NO-mediated mitochondrial dysfunction will provide important insights into the pathogenesis of neurodegenerative disorders. In this review, we highlight recent discoveries concerning S-nitrosylation of the tricarboxylic acid cycle enzymes, mitochondrial fission GTPase dynamin-related protein 1, and mitophagy-related proteins Parkin and phosphatase and tensin homolog-induced putative kinase protein 1. We delineate signaling cascades affected by pathologically S-nitrosylated proteins that diminish mitochondrial function in neurodegenerative diseases. <b><i>Future Directions:</i></b> Further elucidation of the pathological events resulting from aberrant <i>S</i>-nitrosothiol or nitrotyrosine formation may lead to new therapeutic approaches to ameliorate neurodegenerative disorders.
Synthesis and analysis of novel polymers with potential for providing both high permselectivity and permeability in gas separation applications: Summary technical report, April 1986--December 1988 (1988)

We have gained significant insights into the basic principles governing sorption and transport in glassy materials. The following three important areas can be identified in which advances in the basic science controlling gas separation membrane operations were made. Extremely attractive new membrane materials have been identified. These materials will be compared to conventional materials to illustrate the value of the systematic structure- property approach. Two basic rules were formulated that provide improved guidance in selecting candidate materials for gas separation membranes. The permeability and permselectivity parameters mentioned below determine the productivity and the product purity, respectively, that can be achieved using a membrane material. Important preliminary insights into the process of plasticization of a series of structurally-related glassy polymers were achieved. Extensive experimental work involving three classes of polymers, the polycarbonates, the polyimides and the polysulfones have proven that the more restricted glassy environment provides a greater ability than that in rubbery materials to regulate the relative permeation rates of passage of gaseous penetrants that have only subtly different molecular sizes or shapes. 22 refs., 5 figs., 4 tabs.