gebhart/patrepeval huggingface dataset:
Direct observation of “dynamic” chirality by Coulomb explosion imaging (2001)

Instantaneous chirality induced by zero-point vibrations was observed directly by using the Coulomb explosion imaging (CEI) technique. The present results suggest the CEI would be generally applicable to diagnosis of the chirality of the isolated molecules in gas phase.
Fuzzy intrusion detection (2002)

The Fuzzy Intrusion Recognition Engine (FIRE) is a network intrusion detection system that uses fuzzy systems to assess malicious activity against computer networks. The system uses an agent-based approach to separate monitoring tasks. Individual agents perform their own fuzzification of input data sources. All agents communicate with a fuzzy evaluation engine that combines the results of individual agents using fuzzy rules to produce alerts that are true to a degree. Several intrusion scenarios are presented along with the fuzzy systems for detecting the intrusions. The fuzzy systems are tested using data obtained from networks under simulated attacks. The results show that fuzzy systems can easily identify port scanning and denial of service attacks. The system can be effective at detecting some types of backdoor and Trojan horse attacks.
Enhancement of power margin and scalability inWDMlinks adopting dispersion-shifted fibresusing periodic-unequally-spaced-channel allocation (1999)

The authors transmitted 16 × 10 Gbit/s wavelength division multiplexed signals over 240 km of dispersion-shifted fibre using periodic-unequally-spaced-channel allocation. A similar power margin to that obtained using unequally-spaced-channel allocation (USCA) was obtained, with far greater channel number scalability than USCA.
Regulation and dysregulation of axon infrastructure by myelinating glia (2017)

Axon loss and neurodegeneration constitute clinically debilitating sequelae in demyelinating diseases such as multiple sclerosis, but the underlying mechanisms of secondary degeneration are not well understood. Myelinating glia play a fundamental role in promoting the maturation of the axon cytoskeleton, regulating axon trafficking parameters, and imposing architectural rearrangements such as the nodes of Ranvier and their associated molecular domains. In the setting of demyelination, these changes may be reversed or persist as maladaptive features, leading to axon degeneration. In this review, we consider recent insights into axon-glial interactions during development and disease to propose that disruption of the cytoskeleton, nodal architecture, and other components of axon infrastructure is a potential mediator of pathophysiological damage after demyelination.
Expression of both B7‐1 and CD28 contributes to the IL‐2 responsiveness of CTLL‐2 cells (1996)

The CTLL-2 bioassay is used frequently to determine interleukin-2 (IL-2) concentrations in experimental samples, including samples that contain reagents which affect the CD28-B7 interaction. We therefore evaluated whether the CD28-B7 pathway plays a role in the growth of CTLL-2 cells. Flow cytometry demonstrated that CTLL-2 cells express both CD28 and B7-1. CTLA4-immunoglobulin (CTLA4-Ig) inhibited the growth of CTLL-2 cells over a range of IL-2 concentrations, suggesting that the CD28-B7 interaction plays an important role in the growth of CTLL-2 cells. Anti-B7-1 antibody also inhibited CTLL-2 proliferation at all concentrations of IL-2. These results indicate that the CTLL-2 bioassay may not be a reliable means of determining IL-2 levels in experimental samples containing reagents that affect the CD28-B7 interaction. They also suggest that co-expression of CD28 and B7 may contribute to the growth of malignant T cells.
Vehicle-to-grid automatic load sharing with driver preference in micro-grids (2014)

Integration of Electrical Vehicles (EVs) with power grid not only brings new challenges for load management, but also opportunities for distributed storage and generation. This paper comprehensively models and analyzes distributed Vehicle-to-Grid (V2G) for automatic load sharing with driver preference. In a micro-grid with limited communications, V2G EVs need to decide load sharing based on their own power and voltage profile. A droop based controller taking into account driver preference is proposed in this paper to address the distributed control of EVs. Simulations are designed for three fundamental V2G automatic load sharing scenarios that include all system dynamics of such applications. Simulation results demonstrate that active power sharing is achieved proportionally among V2G EVs with consideration of driver preference. In additional, the results also verify the system stability and reactive power sharing analysis in system modelling, which sheds light on large scale V2G automatic load sharing in more complicated cases.
Initiation of assembly of tau(273-284) and its ΔK280 mutant: an experimental and computational study (2013)

The microtubule associated protein tau is essential for the development and maintenance of the nervous system. Tau dysfunction is associated with a class of diseases called tauopathies, in which tau is found in an aggregated form. This paper focuses on a small aggregating fragment of tau, (273)GKVQIINKKLDL(284), encompassing the (PHF6*) region that plays a central role in tau aggregation. Using a combination of simulations and experiments, we probe the self-assembly of this peptide, with an emphasis on characterizing the early steps of aggregation. Ion-mobility mass spectrometry experiments provide a size distribution of early oligomers, TEM studies provide a time course of aggregation, and enhanced sampling molecular dynamics simulations provide atomistically detailed structural information about this intrinsically disordered peptide. Our studies indicate that a point mutation, as well the addition of heparin, lead to a shift in the conformations populated by the earliest oligomers, affecting the kinetics of subsequent fibril formation as well as the morphology of the resulting aggregates. In particular, a mutant associated with a K280 deletion (a mutation that causes a heritable form of neurodegeneration/dementia in the context of full length tau) is seen to aggregate more readily than its wild-type counterpart. Simulations and experiment reveal that the ΔK280 mutant peptide adopts extended conformations to a greater extent than the wild-type peptide, facilitating aggregation through the pre-structuring of the peptide into a fibril-competent structure.
Association of Conventional Cardiovascular Risk Factors With Cardiovascular Disease After Hypertensive Disorders of Pregnancy (2019)

In this study, the risk of excess CVD in women with history of HDP was associated with conventional cardiovascular risk factors, indicating that these risk factors are important targets for cardiovascular prevention in these women.
Exploration of Karhunen-Loeve transform for multichannel audio coding (2000)

A new quality-scalable multichannel audio compression algorithm based on MPEG-2 Advanced Audio Coding (AAC) is developed in this work. The Karhunen-Loeve Transform (KLT) is applied to multichannel audio signals in the preprocessing stage to remove the inter-channel redundancy. Then, signals in de-correlated channels are compressed by using a modified AAC main profile encoder. Finally, a channel transmission control mechanism is used to re-organize the bit stream so that the multichannel audio bit stream has a quality scalable property when it is transmitted over a heterogeneous network. Experimental results show that, compared with AAC, the proposed algorithm achieves a better performance with the objective Mask-to-Noise-Ratio (MNR) measurement while maintaining a similar computational complexity at the regular bit rate of 64 kbit/sec/ch. When the bit stream is transmitted to narrowband end users at a lower bit rate, packets of some channels can be dropped and audio of full channel can still be reconstructed in a reasonable fashion.
Induction and Measurement of Cytotoxic T Lymphocyte Activity (2018)

Abstract Cytotoxic T cells (CTLs) are important immune effector cells in the adaptive immune response. It has been well documented that CTLs are important in host immune responses to viral and bacterial intracellular pathogens, tumors, and transplanted tissues. The properties of CTLs have been studied extensively in murine models, and their roles validated in the human setting. Frequently, the presence of these cells correlates well with protective immunity, so the ability to readily measure the activity of these cells is an important immunological measurement. In this unit, several assays are described that are commonly utilized to induce CTLs and to measure CTL activity both in vitro and in vivo . These assays are adaptable to many experimental and/or disease models, and in the case of the in vitro assays can be applied to measure CTL activity in human samples. © 2018 by John Wiley & Sons, Inc.
Controlling laser-induced jet formation for bioprinting mesenchymal stem cells with high viability and high resolution (2014)

Laser-assisted bioprinting is a versatile, non-contact, nozzle-free printing technique which has demonstrated high potential for cell printing with high resolution. Improving cell viability requires determining printing conditions which minimize shear stress for cells within the jet and cell impact at droplet landing. In this context, this study deals with laser-induced jet dynamics to determine conditions from which jets arise with minimum kinetic energies. The transition from a sub-threshold regime to jetting regime has been associated with a geometrical parameter (vertex angle) which can be harnessed to print mesenchymal stem cells with high viability using slow jet conditions. Finally, hydrodynamic jet stability is also studied for higher laser pulse energies which give rise to supersonic but turbulent jets.
Device analysis of two‐dimensional electron gas (2DEG)FET (1988)

Abstract A one‐dimensional analytical model of 2DEG‐FETs has been developed in which the effect of the source‐gate resistance R sq and velocity saturation are included. When the electron mobility μ, the electron drift peak velocity V e , the source‐gate resistance R sg and the AlGaAs film thickness d are varied, the corresponding transconductance g m and the conductance coefficient K are numerically studied in detail. With the present model, the device characteristics of the “MIS”‐like 2DEG‐FET with a thick n + ‐GaAs cap layer and an undoped AlGaAs gate have been analyzed. From the point of application of 2DEG‐FETs to a high speed LSI, the design guideline of the device has been studied. For the device parameters of the gate length L g = 0.2 μm, the transistor width W = 10 μm, R sg = 15 Ω, d = 22 mm, μ = 8000 cm 2 /Vs and V e = 2 × 10 7 cm/s, the expected device characteristics are K = 10.0 mA/V 2 , the sourcegate capacitance C gs = 10.0 fF, g m = 700 mS/mm and f T = 110 GHz.
A Convenient Synthesis of Protected α-Hydroxyacetaldehydes (1988)

Abstract Starting from 2, 3-O-isopropylideneglycerol (1), a general procedure for the preparation of protected α-hydroxyacetaldehydes has been developed.
Amino Acids and Keto Acids in the Treatment of Chronic Renal Failure (1988)

Clinical trials using very low protein supply supplemented with amino acid or keto acid preparations have shown the possibility of slowing the rate of decline of renal function in patients with advanced chronic renal failure together with preservation of nutritional status. The possible mechanisms by which this effect is obtained are reviewed. The potential advantages of keto acids upon amino acids, the optimal composition of the preparations used, and the best time to start treatment in chronic uremics are discussed. Projection of recent data indicate that a prolongation of renal autonomy of about 4 years instead of a spontaneous duration of 15 months until dialysis can be expected using keto acid treatment if started when plasma creatinine reaches 500 mumol/l.
Vaccine Development against COVID-19: Study from Pre-Clinical Phases to Clinical Trials and Global Use (2021)

As per the World Health Organization (WHO), more than 288 vaccines against COVID-19 are being developed, with an estimated 184 being presently investigated in the pre-clinical phases, while 104 of these vaccine candidates are at various stages of clinical trials. Twelve of these are in the advanced stages of clinical investigation, and promising results in the phase 3 trials have already paved the way for their regulatory approval and subsequent dissemination for global use. Preliminary and interim results of some of these candidate vaccines are being analyzed for public dissemination. Some of these vaccines have already been rolled out to immunize not only the highest risk individuals but also the general population in several countries. Once their safety and efficacy are established, the next limiting step would be their mass manufacturing by the pharmaceutical companies to fulfill the global demand. The challenge of manufacturing billions of doses of high-quality vaccines is under-appreciated at the moment. A massive vaccination drive would be needed to protect people of all ages. The timely and coordinated execution of the vaccination effort would require unprecedented coordination at the national and international levels for generating funds to purchase the required doses of vaccines, fair distribution of doses and managing the mechanics of delivering vaccines throughout the world.
THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data (2013)

Tumor samples are typically heterogeneous, containing admixture by normal, non-cancerous cells and one or more subpopulations of cancerous cells. Whole-genome sequencing of a tumor sample yields reads from this mixture, but does not directly reveal the cell of origin for each read. We introduce THetA (Tumor Heterogeneity Analysis), an algorithm that infers the most likely collection of genomes and their proportions in a sample, for the case where copy number aberrations distinguish subpopulations. THetA successfully estimates normal admixture and recovers clonal and subclonal copy number aberrations in real and simulated sequencing data. THetA is available at http://compbio.cs.brown.edu/software/.
Fluorescent Labeling of RAFT-Generated Poly(<i>N</i>-isopropylacrylamide) via a Facile Maleimide−Thiol Coupling Reaction (2006)

We report a facile labeling technique in which the telechelic thiocarbonylthio functionality of well-defined poly(N-isopropylacrylamide) (PNIPAM) prepared by room temperature RAFT polymerization is first converted to the thiol and subsequently reacted with a maleimido-functional fluorescent dye, N-(1-pyrene)maleimide (PM). Nearly monodisperse PNIPAM (M(n) = 39 500 g/mol, M(w)/M(n) = 1.07) was synthesized using a trithiocarbonate-based CTA, 2-dodecylsulfanylthiocarbonylsulfanyl-2-methyl propionic acid (DMP), and a conventional azo-initiator, namely, 2,2'-azobis(4-methoxy-2,4-dimethylvaleronitrile) (V-70), as the primary source of radicals. The key to successful conjugation of PM to PNIPAM is the implementation of a two-step reduction process involving (1) the cleavage of the trithiocarbonate with a strong reducing agent, in this case, NaBH4, to form a mixture of polymeric thiols and disulfides and (2) the conjugation of PM to the pure polymeric thiol in the presence of tris(2-carboxyethyl)phosphine.HCl (TCEP). We show that TCEP efficiently eliminates the formation of polymeric disulfides and thus allows for the desired addition of the free polymeric thiol across the maleimide double bond. This concept is demonstrated using SEC-MALLS and UV-vis spectroscopy measurements.
Word Frequency and Word Difficulty: A Comparison of Counts in Four Corpora (1996)

This article compares word counts made using four different collections of text, including one based on collections of electronic text For each of the collections, standard word frequency indices were computed and compared with a carefully developed list of words ranked in order of difficulty as determined by vocabulary tests Correlations between the word frequency indices and word difficulty ranks show that word frequencies for all four corpora are highly correlated with word difficulty Despite these high correlations, the results show also that the difficulty of some words is not estimated accurately by word frequency The reasons for disparities between word frequency and word difficulty are not clear The high correlations obtained for the corpus based on electronic text suggest that this method of text sampling has potential but that caution is advisable in conducting such collections
Truth or consequences in the diagnosis of substance use disorders (2014)

Negative psychosocial and health consequences of substance use should play a fundamentally reduced role in modern diagnostic systems for, and definitions of, addictive disorders.
Blue Laser Annealed Sub-Micron Channel P-Type Low Temperature Poly-Si TFT Without Kink Effect for High-Resolution Display (2020)

We report sub-micron channel length (0.5 μm), low-temperature polysilicon(LTPS) thin-film transistor (TFT) using blue laser annealing (BLA) for ultra-high-resolution displays. The TFTs exhibited negligible kink effect in output characteristics with excellent negative bias temperature stability. Protrusion-free BLA LTPS is evident from the transmission electron microscopy (TEM) image. Technology computer-aided design (TCAD) simulation reveals that the protruded LTPS with grain boundaries has ~1.4 times higher electric field than protrusion-free LTPS. This causes high impact generation rate of 3.76 x 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">14</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> s <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> (~8 times) compared to 4.64 x 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">13</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> s <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> for protrusion-free LTPS TFTs. It is demonstrated that protrusion-free LTPS can achieve kink-free, sub-micron short channel devices.
Linking C5 Deficiency to an Exonic Splicing Enhancer Mutation (2005)

As an important component of the innate immune system, complement provides the initial response to prevent infections by pathogenic microorganisms. Patients with dysfunction of C5 display a propensity for severe recurrent infections. In this study, we present a patient with C5 deficiency demonstrated by immunochemical and functional analyses. Direct sequencing of all C5 exons displayed no mutation of obvious functional significance, except for an A to G transition in exon 10 predicting an exchange from lysine to arginine. This sequence alteration was present in only one allele of family members with a reduced serum C5 concentration and in both alleles of the patient with almost complete C5 deficiency, suggesting that this alteration may be producing the phenotype. Recent findings indicate that distinct nucleotide sequences, termed exonic splicing enhancers (ESEs), influence the splicing process. cDNA from all family members harboring the mutated allele showed skipping of exon 10, which resulted in a premature STOP codon, explaining the lack of C5 in the propositus. Sequence analysis of the mutated region revealed the substitution to be located within an ESE, as predicted by the RESCUE-ESE program. The altered ESE sequence is located close to the 5' splicing site and also lowers the predicted strength of the splice site itself. This apparently inconsequential sequence alteration represents a noncanonical splicing mutation altering an ESE. Our finding sheds a new light on the role of putative silent/conservative mutations in disease-associated genes.
Factors limiting motor recovery after facial nerve transection in the rat: combined structural and functional analyses (2005)

It is believed that a major reason for the poor functional recovery after peripheral nerve lesion is collateral branching and regrowth of axons to incorrect muscles. Using a facial nerve injury protocol in rats, we previously identified a novel and clinically feasible approach to combat axonal misguidance--the application of neutralizing antibodies against neurotrophic factors to the injured nerve. Here, we investigated whether reduced collateral branching at the lesion site leads to better functional recovery. Treatment of rats with antibodies against nerve growth factor, brain-derived neurotrophic factor, fibroblast growth factor, insulin-like neurotrophic factor I, ciliary neurotrophic factor or glial cell line-derived neurotrophic factor increased the precision of reinnervation, as evaluated by multiple retrograde labelling of motoneurons, more than two-fold as compared with control animals. However, biometric analysis of vibrissae movements did not show positive effects on functional recovery, suggesting that polyneuronal reinnervation--rather than collateral branching --may be the critical limiting factor. In support of this hypothesis, we found that motor end-plates with morphological signs of multiple innervation were much more frequent in reinnervated muscles of rats that did not recover after injury (51% of all end-plates) than in animals with good functional performance (10%). Because polyneuronal innervation of muscle fibres is activity-dependent and can be manipulated, the present findings raise hopes that clinically feasible and effective therapies could be soon designed and tested.
Mechanically Enhanced Catalytic Reduction of Carbon Dioxide over Defect Hexagonal Boron Nitride (2021)

The hydrogenation of waste gas carbon dioxide into value added molecules could reduce greenhouse gas emissions and our dependence on nonrenewable energy sources. Catalytic paths toward this goal typically involve high pressures and low abundance transition metal catalysts. Here, we have found that vacancies induced in defect-laden hexagonal boron nitride (dh-BN) can effectively activate the CO2 molecule for hydrogenation. Subsequent hydrogenation to formic acid (HCOOH) and methanol (CH3OH) occur through vacancy facilitated coadsorption of hydrogen and CO2. More importantly, we find that dh-BN catalyzes formic acid formation observable at reaction temperatures above 160 °C and pressures of 583 kPa, while methanol formation is observed at lower temperatures (as low as 20 °C). Methanol formation occurs with a TOF of 1.52 × 10–2 s–1 and TON of 289 at 20 °C. Carbon dioxide (CO2) is a major greenhouse gas and the main component of all combustion products produced in power generation and transportation. In addition, boron and nitrogen are abundant elements and thus, catalysts prepared from h-BN would allow catalytic recovery of value-added molecules facilitating efforts to reduce the emissions of this gas.
An intelligent directory system with a genre inference function (1996)

We developed an intelligent directory system which consists of a X.500 directory and an intelligent agent with a genre inference function, in order to create an intelligent yellow page service where a user can get information by only entering natural language text representing his/her desire. This paper describes the system structure of the intelligent directory system and its technology. An evaluation of the implementation based on our study indicates the inference precision of 88.6% and an inference throughput of less than 0.1 second per inquiry.