gebhart/patrepeval huggingface dataset:
Neutralizing Epitopes of Influenza Virus Hemagglutinin: Target for the Development of a Universal Vaccine against H5N1 Lineages (2010)

The nature of influenza virus to randomly mutate and evolve into new types with diverse antigenic determinants is an important challenge in the control of influenza infection. Particularly, variations within the amino acid sequences of major neutralizing epitopes of influenza virus hemagglutinin (HA) hindered the development of universal vaccines against H5N1 lineages. Based on distribution analyses of the identified major neutralizing epitopes of hemagglutinin, we selected three vaccine strains that cover the entire variants in the neutralizing epitopes among the H5N1 lineages. HA proteins of selected vaccine strains were expressed on the baculovirus surface (BacHA), and the preclinical efficacy of the vaccine formulations was evaluated in a mouse model. The combination of three selected vaccine strains could effectively neutralize viruses from clades 1, 2.1, 2.2, 4, 7, and 8 of influenza H5N1 viruses. In contrast, a vaccine formulation containing only adjuvanted monovalent BacHA (mono-BacHA) or a single strain of inactivated whole viral vaccine was able to neutralize only clade 1 (homologous), clade 2.1, and clade 8.0 viruses. Also, the trivalent BacHA vaccine was able to protect 100% of the mice against challenge with three different clades (clade 1.0, clade 2.1, and clade 7.0) of H5N1 strains compared to mono-BacHA or inactivated whole viral vaccine. The present findings provide a rationale for the development of a universal vaccine against H5N1 lineages. Furthermore, baculoviruses displaying HA will serve as an ideal choice for a vaccine in prepandemic or pandemic situations and expedite vaccine technology without the requirement of high-level-biocontainment facilities or tedious protein purification processes.
Subject-adaptive real-time sleep stage classification based on conditional random field. (2007)

Sleep staging is the pattern recognition task of classifying sleep recordings into sleep stages. This task is one of the most important steps in sleep analysis. It is crucial for the diagnosis and treatment of various sleep disorders, and also relates closely to brain-machine interfaces. We report an automatic, online sleep stager using electroencephalogram (EEG) signal based on a recently-developed statistical pattern recognition method, conditional random field, and novel potential functions that have explicit physical meanings. Using sleep recordings from human subjects, we show that the average classification accuracy of our sleep stager almost approaches the theoretical limit and is about 8% higher than that of existing systems. Moreover, for a new subject S(new) with limited training data D(new), we perform subject adaptation to improve classification accuracy. Our idea is to use the knowledge learned from old subjects to obtain from D(new) a regulated estimate of CRF's parameters. Using sleep recordings from human subjects, we show that even without any D(new), our sleep stager can achieve an average classification accuracy of 70% on S(new). This accuracy increases with the size of D(new) and eventually becomes close to the theoretical limit.
Surface modification of magnetic recording heads by plasma immersion ion implantation and deposition (1994)

Plasma immersion ion implantation and deposition is a novel process for surface modification. By combining plasma deposition and ion implantation and using filtered vacuum arc plasmas, thin film formation, direct and recoil ion implantation, and ion-beam-assisted intermixing of the film and substrate can be accomplished simultaneously. The implications of this technique in tribology of magnetic recording media have been investigated experimentally. Surfaces of Al2O3-TiC heads were modified with silver, carbon, and titanium ions at doses of 3×1016 ions/cm2 and mean implantation energies between 2.0 and 4.2 keV. Simulation results indicated that the modified regions exhibited high concentrations of implanted species in the top 2–3 nm, atomically mixed interfaces, and thicknesses between 10 and 25 nm. Surface imaging with an atomic force microscope and nanoindentation testing revealed that the modified heads possessed smoother topographies and increased hardnesses. Contact start-stop and continuous sliding experiments with modified heads and carbon-coated magnetic rigid disks and microscopy observations demonstrated that significant enhancement of the friction and wear characteristics can be achieved with the present surface modification technique. The possible reasons for the improved tribological behavior and the predominant mechanisms during contact start-stop and continuous sliding are interpreted in light of the obtained experimental results.
Microwave‐Assisted Synthesis of Stable and Highly Active Ir Oxohydroxides for Electrochemical Oxidation of Water (2017)

Water splitting for hydrogen production in acidic media has been limited by the poor stability of the anodic electrocatalyst devoted to the oxygen evolution reaction (OER). To help circumvent this problem we have synthesized a class of novel Ir oxohydroxides by rapid microwave-asisted hydrothermal synthesis, which bridges the gap between electrodeposited amorphous IrO<sub>x</sub> films and crystalline IrO<sub>2</sub> electrocatalysts prepared by calcination routes. For electrode loadings two orders of magnitude below current standards, the synthesized compounds present an unrivalled combination of high activity and stability under commercially relevant OER conditions in comparison to reported benchmarks, without need for pretreatment. The best compound achieved a lifetime 33 times longer than the best commercial Ir benchmark. Thus, the reported efficient synthesis of an Ir oxohydroxide phase with superior intrinsic OER performance constitutes a major step towards the targeted design of cost-efficient Ir based OER electrocatalysts for acidic media.
A General Palladium‐Catalyzed Sonogashira Coupling of Aryl and Heteroaryl Tosylates (2010)

Coupled up: A new general palladium-catalyzed procedure for the cross-coupling of aryl and heteroaryl tosylates is described. This highly versatile and efficient process can be used for the synthesis of a wide variety of functionalized alkynes (see scheme).
Evaluation of New Biomarker Genes for Differentiating Haemophilus influenzae from Haemophilus haemolyticus (2012)

ABSTRACT PCR detecting the protein D ( hpd ) and fuculose kinase ( fucK ) genes showed high sensitivity and specificity for identifying Haemophilus influenzae and differentiating it from H. haemolyticus . Phylogenetic analysis using the 16S rRNA gene demonstrated two distinct groups for H. influenzae and H. haemolyticus .
Radiologists' Performance for Differentiating Benign from Malignant Lung Nodules on High-Resolution CT Using Computer-Estimated Likelihood of Malignancy (2004)

CAD has the potential to improve radiologists' diagnostic accuracy in distinguishing small benign nodules from malignant ones on HRCT.
Preparation and Properties of 2,4,8,10-Tetranitro-5<i>H</i>-Pyrido[3′,2′:4,5][1,2,3] Triazolo[1,2–a]Benzotriazol-6-ium Inner Salt as a Thermally Stable High Explosive (2004)

The synthesis and explosive properties of 2,4,8,10-tetranitro-5H-pyrido[3′, 2′:4, 5] [1,2,3] triazolo [1,2-a] benzotriazol-6-ium inner salt (7) are given. This material is a very thermally stable high explosive that has a differential scanning calorimetry (DSC) onset of 365°C with fast decomposition occurring at 375°C. The material is readily prepared in three steps from inexpensive starting materials. The final compound is insensitive to initiation by spark and friction and has a drop height of 59 cm (Type 12, 2.5 kg weight, HMX = 23 cm). In addition, it has a failure diameter of less than 3 mm. A detonation velocity of 7.43 km/s and detonation pressure of 294 kbar were determined on 0.5 inch pellets at a density of 1.78 g/cm3.
Methods of Machine Learning for Space Object Pattern Classification (2019)

Space superiority requires space protection and space situational awareness (SSA), which rely on rapid and accurate space object behavioral and operational intent discovery. The analytics required for space object detection, tracking, and pattern classification include machine learning. The development of deep learning (DL) methods shows promise in many areas. In this paper, a convolutional neural network (CNN) classifies the behaviors of space objects for evasive satellite behaviors detection. Additionally, within the Adaptive Markov Inference Game Optimization (AMIGO) engine, a game theoretic approach describes the situation versus a control problem. Using data-level fusion, stochastic modeling/propagation, and DL pattern classification. Numerical simulations demonstrate the advantage of DL methods for space object pattern classification improving from 34% to 98% with training.
Speaker selection training for large vocabulary continuous speech recognition (2002)

Acoustic variability across speakers is one of the challenges of speaker independent (SI) speech recognition systems. As a powerful solution, dominant speaker adaptation technologies such as MLLR and MAP may become inefficient because of the lack of enough enrollment data. In this paper, we propose an adaptation method based on speaker selection training, which makes full use of statistics of training corpus. Relative error rate reduction of 5.31 % is achieved when only one utterance is available. We compare different speaker selection strategies, namely. PCA, HMM and GMM based methods. In addition, impacts of number of selected cohort speakers and number of utterances from target speaker are investigated. Furthermore, comparison and integration with MLLR adaptation are also shown. Finally, some ongoing work such as dynamicalJy varying number of selected speakers, measuring the relative contribution among the selected speakers and speeding up the computationally expensive procedure of re-estimation with model synthesis are also discussed.
Reversible Uptake of COS, CS<sub>2</sub>, and SO<sub>2</sub>: Ionic Liquids with <i>O</i>‐Alkylxanthate, <i>O</i>‐Alkylthiocarbonyl, and <i>O</i>‐Alkylsulfite Anions (2009)

CO(2)-binding organic liquids (CO(2)BOLs) are mixtures of a base (typically an amidine or guanidine) and an alcohol, and have been shown to reversibly capture and release CO(2) with low reaction energies and high gravimetric CO(2) capacity. We now report the ability of such liquid blends to chemically bind and release other acid gases such as CS(2), COS, and SO(2) analogously to CO(2). These systems bind with sulfur-containing acid gases to form colored ionic liquids with new O-alkylxanthate, O-alkylthiocarbonyl, and O-alkylsulfite anions. The capture and thermal stripping of each acid gas from these systems and their applicability towards flue gas desulfurization is discussed.
The Future of Biological Mass Spectrometry (2011)

Biological applications of mass spectrometry have grown exponentially since the discovery of MALDI and electrospray ionization techniques. This growth has been further fueled by the massive volume of DNA sequence information that is now available. An ambitious goal of some of this research is to monitor the level and modification of all proteins and metabolites in a biological sample such as plasma. A major research effort in mass spectrometry and related disciplines has been expended over the past several years toward reaching this and other less ambitious goals, and considerable progress has been made; but the presently available tools are clearly not sufficient for these very difficult tasks. In this "critical insight" discussion we suggest that recent advances in time-of-flight (TOF) technology with MALDI ionization may provide some important new tools for achieving the goals of biological research.
Achillea fragrantissima extract exerts its anticancer effect via induction of differentiation, cell cycle arrest and apoptosis in chronic myeloid leukemia (CML) cell line K562 (2013)

The advantages of herbs in cancer therapy/prevention are attributed to their broad inhibitory activity against multiple aberrant cancer specific pathways and non-toxic nature. Achillea fragrantissima (Af) is a traditional herb used to treat viral fever and chronic diseases such as arthritis and diabetes. However, the anticancer potential of Af has not been studied yet. Anticancer properties of extract from Af leaves were studied using human chronic myeloid leukemia (CML) (K562), T cell lymphoma (Jurkat) and hepatocellular carcinoma (HepG2) cell lines. Af extract induced morphological changes were studied using inverted light microscope and its effect on viability of cells was measured by trypan blue assay. Af extract altered the morphology of K562 and Jurkat cells from spherical to spindle shape. This shape change was considered indicative of initiation of differentiation and occurred at a low concentration of the extract (0.5 mg/ml) in K562 cells and at this concentration viability of K562 cells was not significantly affected. At higher (≥1 mg/ml) concentrations, Af extract induced elongation of K562 cells, which was considered indicative of cell cycle arrest.  Increasing concentration of Af extract also caused plasma membrane rupture in a higher proportion of K562 cells resulting in reduced viability. Af extract reduced the viability of K562 cells in a time and dose dependent manner. Results from our study indicated Af extract as a potent inducer of differentiation, cell cycle arrest and apoptosis in K562 and Jurkat cells. Af extract activated these anticancer mechanisms in a concentration dependent manner. Anticancer activity of Af extract on K562 and Jurkat cells, mediated by multiple independent mechanisms, suggests its potential use in the treatment of drug resistant leukemia and other cancers.

	 

	Key words: Chronic myeloid leukemia, chronic myeloid leukemia (CML), differentiation therapy, K562, Achillea fragrantissima, Jurkat, hepatocellular carcinoma (HepG2), cell cycle arrest, apoptosis.
A confocal video‐rate laser‐beam scanning reflected‐light microscope with no moving parts (1990)

A no-moving-parts, 30 frames/s, laser-beam scanning confocal reflected-light microscope has been developed. In principle, the technique can be extended to fluorescence and transmission light microscopy. Acousto-optic beam deflectors controlled by digital electronics move a laser beam in a 512-line interlaced 8.5 x 8.5-mm raster. The light passes through a beam splitter, enters an inverted microscope through the side camera port, and is imaged at the object by the microscope objective. Reflected light returns through the objective, exits the camera port, is reflected off the beam splitter, and is imaged on to the photocathode of an image dissector tube (IDT). Confocality is provided by raster scanning the IDT aperture coincident with the congruent image of the laser beam incident on the object. Real-time jitter-free reflected light images of a variety of biological objects have been produced. Computer-controlled alignment of the laser scan and IDT is performed in several seconds.
Adhesive Properties of Cured Phenylethynyl Containing Imides (1997)

Considerable attention has been directed towards acetylene terminated oligomers over the last 20 years and recent work has focused on phenylethynyl terminated imide (PETI) oligomers. These reactive oligomers possess several features which make them attractive candidates for use as composite matrices and adhesives. The phenylethynyl group can be readily incorporated into many different functionalized oligomers. The reactive oligomers possess relatively low melt viscosities and thermally cure without the evolution of volatile by-products. Once cured, they typically display high glass transition temperatures (T\sub{g}s), excellent solvent resistance and high mechanical properties. As an ongoing effort to develop high performance resins for aerospace applications, several new modified phenylethynyl-terminated imide (LaRC MPEI) oligomers were synthesized at various molecular weights utilizing a small amount of trifunctional amine. As long as the amount of triamine is relatively small, this approach produces a mixture of linear, star-shaped and branched polymer chains that has lower melt and solution viscosity than an equivalent molecular weight linear phenylethynyl terminated imide oligomers. The work reported herein involves the synthesis and characterization of a copolymer using this approach and the preparation of blends utilizing a phenylethynyl containing reactive plasticizer of lower molecular weight called LaRC LV-121. The chemistry and properties of this new MPEI as well as some blends of MPEI with LV-121, are presented and compared to the linear version, LARC(R)-PETI-5.
Diode-pumped eye-safe laser source exceeding 1% efficiency (1991)

We describe an all-solid-state, diode-pumped, eye-safe laser source at 1.61 microm, based on a Nd:YAG laser and a noncritically phase-matched KTP optical parametric oscillator. Total energy conversion efficiencies of the 1.064-microm pump to 1.61-microm signal and 3.1-microm idler approach 50%, with 35% conversion to 1.61 microm alone. This device produces 1.6 mJ at 1.61 microm with a wallplug efficiency of 1.1% and is readily scalable to higher energies. Tunability over 1.6 to 1.54 microm is obtained by rotation of the KTP crystal about its z axis, with 1.54-microm output obtained for propagation along the y axis under noncritical phase matching.
Pro PSA: a more cancer specific form of prostate specific antigen for the early detection of prostate cancer. (2003)

BPSA and proPSA are distinct molecular forms of free PSA in serum. BPSA is a form of free PSA that is associated with BPH. The inactive precursor of PSA, proPSA, is associated with prostate tumors. ProPSA is comprised of native proPSA as well as truncated proPSA forms, [-2]pPSA and [-4]pPSA, which have been shown to be more cancer-associated than native proPSA. We have developed highly specific and sensitive research immunoassays for BPSA, and the different forms of proPSA. Free PSA in prostate cancer serum contains a median of 28% BPSA and 32% proPSA, though each form of PSA can range from 0 to more than 50% in individual samples. Early studies revealed that proPSA significantly increases the specificity for prostate cancer, especially in the 2-4 ng/ml PSA range. It is estimated that 20-30% of men with PSA values from 2-4 ng/ml have prostate cancer. In the 2.5-4 ng/ml PSA range proPSA gave a receiver operating characteristic-area under the curve (ROC-AUC) of 0.636 compared with free PSA (0.506) and complex PSA (0.509). At 90% sensitivity the specificity for proPSA was 25% compared to 10% for %FPSA and cPSA (P = < 0.001). ProPSA was superior to %FPSA and complexed PSA in the 4-10 ng/ml PSA range (AUC = 0.689, 0.637 and 0.538, respectively). ProPSA represents a more cancer-specific form of PSA that better discriminates prostate cancer from BPH.
Termination with reverse-connected common-mode choke (T-RECC) for a differential transmission line (2006)

In this paper, a new termination circuit that consists of two common-mode chokes for a differential transmission line is proposed. It dramatically reduces common-mode noise while maintaining the transmission performance of a differential-mode signal. The noise-reduction effect of the circuit is explained here theoretically; it was also verified experimentally using an evaluation board.
5-HT3 receptor antagonists. 1. New quinoline derivatives (1992)

A series of esters and amides of 1-alkyl-2-oxo-1,2-dihydroquinoline-4- carboxylic acid or 2-alkoxy-quinoline-4-carboxylic acid containing a basic azabicycloalkyl moiety has been synthesized and evaluated for affinity for the [3H]quipazine-labeled 5-HT3 receptors. Most of the esters exhibited 10-fold more potent activity than that of ondansetron (1; Ki = 7.6 nM). Lipophilic substituents at the 1- or 2-position of the quinoline ring enhanced affinity for the receptors. Compounds 21 and 37 showed the highest affinity (Ki = 0.32 and 0.31 nM, respectively) among them. On the other hand, most of the amides showed 100-fold lower affinity than that of the esters. Molecular modeling studies indicated that the carbonyl moiety in 19 (ester) or 31 (amide) was not coplanar to the plane of an aromatic ring (over 20 degrees deviation). Although some of the selected compounds exhibited potent activity in the Bezold-Jarisch (B-J) reflex test, good correlation was not observed between the affinity for the 5-HT3 receptors and the activity in the B-J reflex test (in vivo). From these data, it was suggested that our quinoline derivatives might interact with the 5-HT3 receptors in a different way from that of the reported 5-HT3 receptor antagonists presumably due to the presence of the heterogeneity of the 5-HT3 receptors between brain and heart.
Third-Order Distortion Elimination in Phase-Encoded Analog-Photonic Links using a Four-Wave Mixing Comb Source (2014)

We present all-optical distortion cancellation in phase-modulated analog-photonic links by combining the phase-encoded signal with lines from an optical comb generated from signal. Experimentally, we fully cancel third-order distortion increasing the link SFDR by >8.3dB.
A Collaborative Agent-Based Traffic Signal System For Highly Dynamic Traffic Conditions (2018)

In this paper we present DALI, a distributed, collaborative multi-agent Traffic Signal Timing system (TST) for highly dynamic traffic conditions. In DALI, intersection controllers are augmented with software agents which collaboratively adapt signal timings by considering the feedback of all controller agents that may be affected by a change. The model is based on a real-world TST and is intended to be deployed with minimal changes to the infrastructure. DALI has been validated on a simulated model of the City of Richardson, Texas, comprising 128 signalized intersections. The experimental results show that it outperforms the conventional traffic operation modes as well as an RL-based TST in highly dynamic scenarios.
Dynamic management of control plane performance in software-defined networks (2016)

The controller or the “control plane” is at the heart of software defined networks (SDN). As SDN migrates to wide area networks (WAN), scalability and performance are two important factors that differentiate one controller from another, and they are critical for success of SDN for end-to-end service management. We distinguish control flows from data flows, and introduce a novel dynamic control plane architecture to distribute different control flows among multiple controller instances depending on specific controller load and controller processor utilization or on the data flow service type. We propose “control flow tables” — a concept introduced in this paper — that are embedded in OpenFlow flow tables to distribute the control flows among various controller instances. Experimental results demonstrate the improvements in the data plane service performance as a result of the proposed control flow management procedures when the bottleneck is the controller CPU or throughput of links between the controller and switches.
Effect of free bandwidth on VoIP performance in 802.11b WLAN networks (2006)

In this paper we experimentally study the relationship between bandwidth utilization in the wireless LAN and the quality of VoIP calls transmitted over the wireless medium. Specifically we evaluate how the amount of free bandwidth decreases as the number of calls increases and how this influences transmission impairments (i.e. delay, loss, and jitter) and thus degrades call quality. We show that the amount of free bandwidth is a good indicator for predicting VoIP call quality.