gebhart/patrepeval huggingface dataset:
ARTIFICIAL SURFACTANTS BASED ON ANALOGUES OF SP-B AND SP-C (2001)

The hydrophobic proteins SP-B and SP-C are important components of natural surfactant preparations currently used in clinical practice, and physiologically active surfactants can be made from isolated SP-B and/or SP-C reconstituted with synthetic lipids. Efforts have been made to produce these polypeptides, or analogues with similarfunction, by organic synthesis or expression in heterologous systems. It is important to obtain proper folding of the synthetic peptides, as required for optimal interaction with the surfactant lipids. Another issue is to avoid loss of SP-C activity due to alpha-helix to beta-sheet transition. This latter problem can be circumvented by replacing the polyvaline stretch of SP-C with a polyleucine stretch containing a few lysines. Palmitoylation of cysteines or serines at positions 5 and 6 also seems important for the properties of SP-C. SP-B, which is too big a molecule to be easily produced by organic synthesis. apparently can be replaced in an artificial surfactant by a peptide capable of cross-linking phospholipid bilayers. The development of synthetic analogues of the surfacant proteins might make it possible to tailor artificial surfactants for specific therapeutic missions, for instance by enhancing resistance to inactivation by meconium, plasma proteins, or oxygen radicals or maximizing bacteriostatic effects.
Driving Force and Electronic Coupling Effects on Photoinduced Electron Transfer in a Fullerene-based Molecular Triad¶ (2000)

Tuning thermodynamic driving force and electronic coupling through structural modifications of a carotene (C) porphyrin (P) fullerene (C60) molecular triad has permitted control of five electron and energy transfer rate constants and two excited state lifetimes in order to prepare a high-energy charge-separated state by photoinduced electron transfer with a quantum yield of essentially unity (> or = 96%). Excitation of the porphyrin moiety of C-P-C60 is followed by a combination of photoinduced electron transfer to give C-P(.+)-C60.- and singlet-singlet energy transfer to yield C-P-1C60. The fullerene excited state accepts an electron from the porphyrin to also generate C-P(.+)-C60.-. Overall, this initial state is formed with a quantum yield of 0.97. Charge shift from the carotenoid to yield C(.+)-P-C60.- is at least 60 times faster than recombination of C-P(.+)-C60.-, leading to the overall quantum yield near unity for the final state. Formation of a similar charge-separate species from the zinc analog of the triad with a yield of 40% is also observed. Charge recombination of C(.+)-P-C60.- in 2-methyltetrahydrofuran yields the carotenoid triplet state, rather than the ground state. Comparison of the results for this triad with those for related triads with different structural features provides information concerning the effects of driving force and electronic coupling on each of the electron transfer steps.
Treatment of psoriasis vulgaris with a synthetic metalloporphyrin and UVA light. (1989)

Sn-protoporphyrin is a synthetic heme analogue which inhibits the catabolism of natural heme to bilirubin and can suppress a wide variety of experimentally induced or naturally occurring forms of jaundice in animals and man. Ten patients, 9 of whom were substantially or completely unresponsive to other forms of therapy, received 2.0 mumol/kg body weight of Sn-protoporphyrin on day 0 of this study followed by UVA light treatment for 21 days. Severity of psoriatic plaques, clinically scored (erythema 0-3; scaling, 0-3; infiltration, 0-3;) declined from a mean +/- score of 7 +/- 0.3 on day 0 to 3.6 +/- 0.7 on day 21. Psoriatic lesions were improved in all patients and in some the effect was dramatic. No deleterious side effects were registered. As shown in this study, one-day treatment with Sn-protoporphyrin followed by conventional UVA light treatment may be a useful therapeutic modality for psoriasis patients and merits further investigation.
Wave Direction Measurement By a Single Wave Follower Buoy (1978)

ABSTRACT This paper describes a system for measuring the direction of ocean wave propagation, as well as wave height and period. The system employs a conventional wave-follower buoy, modified so as to provide compass, pitch, and roll signals in addition to the vertical component of buoy acceleration. The modifications are indicated in the paper, and the buoy was used in rough water conditions in Narragansett Bay for a test. The pitch, roll, compass, and heave acceleration signals were all processed on the computer in the laboratory to provide a variety of results. This test condition was ideal in that the wind and wave conditions were changing steadily throughout the data recording process. The results presented in the paper include the wave height power spectral density, a polar tilt histogram for the buoy motion, and a family of polar plots of the average tilt angle in each 5° sector of azimuth of the buoy pitch/roll. INTRODUCTION This paper is the third in a series of OTC papers on the subject of the continuous development of wave-follower buoys, starting in 1975. The first paper was OTC 2424 in 1975 on the mathematical analysis of wave data making optimum use of fast computer techniques. The next paper was OTC 2597 in 1976 and it was devoted to ways to handle the problem of spectral compensation of acceleration data from a buoy to produce a true wave height power spectral density (PSD). This last paper also was condensed and published in the June 1977 issue of the Journal of Petroleum technology. It is the purpose of the present paper to extend this buoy development history to include not only the PSD of an open-sea wave field, but the direction of propagation of the dominant wave mode (or modes) that are present. In many important ocean operations, either on the open sea or near shore, the direction of propagation is often of more importance than the significant wave height, or the power spectrum. This clearly is the case, for instance, for storm waves striking a beach, a harbor channel, a breakwater, or any sort of offshore structure. Up to the present time, anyone needing wave-incidence direction data has been forced to deploy complex, complicated, and expensive spatially distributed arrays of wave measurement devices. Using wave staffs on a structure requires spatial separation on the order of the wave length of interest in order to obtain reliable results. The buoy used in this study was a Model WF-100 wave Follower Buoy manufactured by Coastal Data Service, Inc. (licensed to Hydro Products, San Diego) on loan to the U. of Rhode Island for purposes of the present development. It was necessary for Coastal Data Service to modify their standard buoy, by the addition of tilt and compass sensors, to make it possible to measure propagation directions. Some internal modifications were required to provide space for the necessary additional sensors.
HeNet: A Deep Learning Approach on Intel$^\circledR$ Processor Trace for Effective Exploit Detection (2018)

This paper presents HeNet, a hierarchical ensemble neural network, applied to classify hardware-generated control flow traces for malware detection. Deep learning-based malware detection has so far focused on analyzing executable files and runtime API calls. Static code analysis approaches face challenges due to obfuscated code and adversarial perturbations. Behavioral data collected during execution is more difficult to obfuscate but recent research has shown successful attacks against API call based malware classifiers. We investigate control flow based characterization of a program execution to build robust deep learning malware classifiers. HeNet consists of a low-level behavior model and a top-level ensemble model. The low-level model is a per-application behavior model, trained via transfer learning on a time-series of images generated from control flow trace of an execution. We use Intel$^\circledR$ Processor Trace enabled processor for low overhead execution tracing and design a lightweight image conversion and segmentation of the control flow trace. The top-level ensemble model aggregates the behavior classification of all the trace segments and detects an attack. The use of hardware trace adds portability to our system and the use of deep learning eliminates the manual effort of feature engineering. We evaluate HeNet against real-world exploitations of PDF readers. HeNet achieves 100\% accuracy and 0\% false positive on test set, and higher classification accuracy compared to classical machine learning algorithms.
Multi-Pass Adaptive Voting for Nuclei Detection in Histopathological Images (2016)

Nuclei detection is often a critical initial step in the development of computer aided diagnosis and prognosis schemes in the context of digital pathology images. While over the last few years, a number of nuclei detection methods have been proposed, most of these approaches make idealistic assumptions about the staining quality of the tissue. In this paper, we present a new Multi-Pass Adaptive Voting (MPAV) for nuclei detection which is specifically geared towards images with poor quality staining and noise on account of tissue preparation artifacts. The MPAV utilizes the symmetric property of nuclear boundary and adaptively selects gradient from edge fragments to perform voting for a potential nucleus location. The MPAV was evaluated in three cohorts with different staining methods: Hematoxylin &Eosin, CD31 &Hematoxylin, and Ki-67 and where most of the nuclei were unevenly and imprecisely stained. Across a total of 47 images and nearly 17,700 manually labeled nuclei serving as the ground truth, MPAV was able to achieve a superior performance, with an area under the precision-recall curve (AUC) of 0.73. Additionally, MPAV also outperformed three state-of-the-art nuclei detection methods, a single pass voting method, a multi-pass voting method, and a deep learning based method.
Development of Industrially Important .ALPHA.-Amylases. (1999)

A new calcium independent α-amylase has been developed for starch liquefaction. This amylase Termamyl LCTM gives the same performance in the absence of free calcium compared to TermamylTM, in the presence of 40 ppm free calcium. The improvement is a result of 5 single amino acid substitutions and one N-terminal alteration. Several new alkaline α-amylases were identified in Nature. We have isolated two amylases that display the desired activity profile but lack the overall stability necessary for a detergent a-amylase. A two amino acid deletion in the region from position 180-184 increased the overall stability both with respect to temperature and calcium sensitivity, to a satisfactory level comparable to that of TermamylTM.
Abstract 5400: Photoimmunotherapy (PIT) combined with a nanosized cancer agent successfully treated heterogenous antigen-expressing tumors based on super-enhanced permeability and retention (SUPR) effect (2014)

Abstract A major barrier to cancer treatment is the inability to deliver sufficient concentrations of drug to the interior of tumors without incurring systemic toxicities. Nanomaterials are appealing because they can carry a large drug payload, however, tumor delivery is limited by modest leakage and retention in most tumors. Photoimmunotherapy (PIT) is a newly developed therapy involving the injection of a conjugate composed of an armed monoclonal antibody (mAb) and a near infrared phthalocyanine dye, IR700 [Mitsunaga M. Nature Med 2011;17:1685]. When exposed to NIR light, the conjugate induces a highly-selective necrotic cell death only in mAb-IR700 bound cancer cells. This target-specific necrotic cell death occurs within 10 minutes of exposure to NIR light and results in rapid morphologic changes including cellular swelling, bleb formation, and rupture of vesicles and cell death. Meanwhile, immediately adjacent receptor-negative cells are unharmed. Because PIT initially damages antigen bearing tumor cells immediately adjacent to the vasculature, it causes marked increases in vascular permeability leading to 20-fold enhanced nano-particle delivery into cancer tissue compared with untreated tumor bed. This effect has been termed “super-enhanced permeability and retention (SUPR)” to differentiate it from enhanced permeability and retention (EPR) which is common in tumors. In this study, we used a mixed tumor model containing 99% (EGFR)-positive A431 cells mixed with 1% EGFR-negative Balb3T3/DsRed cells in order to simulate tumor heterogeneity. Mixed tumors were treated with PIT alone or PIT combined with liposomes containing daunorubicin (Daunoxome), utilizing the SUPR effect. PIT completely treated EGFR+ cells, however, EGFR- cells quickly became the dominant cell type leading to death in mice. However, co-injection of Daunoxome could cure tumors following PIT. Therefore, although PIT alone does not eliminate all cancer cells due to heterogeneity of tumor, SUPR allows the delivery of extremely high concentrations of nano-sized anti-cancer reagents (e.g. Daunoxome), resulting in synergistic therapeutic effects of PIT and nano-sized agents. In conclusion, target-selective PIT can induce a SUPR effect leading to the accumulation of dramatically higher concentrations of nano-sized reagents within tumors thus improving the effectiveness of PIT in heterogeneous tumors. Citation Format: Hisataka Kobayashi, Kohei Sano, Takahito Nakajima, Kazuhide Sato, Peter L. Choyke. Photoimmunotherapy (PIT) combined with a nanosized cancer agent successfully treated heterogenous antigen-expressing tumors based on super-enhanced permeability and retention (SUPR) effect. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5400. doi:10.1158/1538-7445.AM2014-5400
Highly Enantioselective Hydrogenation of α-Arylmethylene Cycloalkanones Catalyzed by Iridium Complexes of Chiral Spiro Aminophosphine Ligands (2010)

The highly efficient asymmetric hydrogenation of alpha-arylmethylene cycloalkanones catalyzed by Ir-complexes of chiral spiro aminophosphine ligands was developed, providing chiral exo-cyclic allylic alcohols at high yields with excellent enantioselectivities (up to 97% ee) and high turnover numbers (S/C up to 10,000). This new reaction provided an efficient method for the synthesis of the key intermediate of the active form of the anti-inflammatory loxoprofen.
Continuous-Time Digital Signal Processing Based Controller for High-Frequency DC-DC Converters (2007)

This paper introduces a digital dual-mode controller for low-power high-frequency dc-dc switch-mode power supplies (SMPS) suitable for on-chip implementation. In steady state the controller behaves as a conventional digital PWM controller, and during transients it utilizes continuous-time digital signal processing to achieve very fast transient response. The continuous time DSP is triggered by a sudden change of output voltage. Then it performs a charge-balance based algorithm to achieve voltage recovery through a single on-off action of the power switch. The effectiveness of the method is demonstrated on an experimental 5 V-to- 2V, 400 kHz, 2.5 W buck converter that recovers voltage in the time equivalent to 3 PWM switching cycles, approaching converter physical limitations.
A Denoising algorithm for remote sensing images with impulse noise (2016)

Noise detection and suppression is one of the important issues in digital image processing. In this study, we develop a new algorithm for detection and suppression of the impulse noise in remote sensing images. The algorithm, called Moran's I Spatial Autocorrelation filter (MSAF), is based on the Standard Median Filter and Moran's I which is used to measure the spatial autocorrelation. Our experimental results show that the MSAF has improved outcomes in terms of Peak Signal-to- Noise Ratio (PSNR) and Mean Square Error (MSE) compared to other filtering algorithms including the Standard Median Filter (SMF), Center Weighted Median Filter (CWMF), Adaptive Center Weighted Median Filter (ACWMF), Decision Based Filter (DBF), Signal-Dependent Rank Ordered Mean Filter (SDROMF) and Modified Decision Based Unsymmetric Trimmed Median Filter (MDBUTMF).
Phosphonocarboxylic acids as specific inhibitors of Na+-dependent transport of phosphate across renal brush border membrane. (1986)

We investigated interactions of phosphonoformic acid (PFA), phosphonoacetic acid (PAA), and other phosphonyl derivatives with the Na+ gradient [Na+ extravesicular greater than Na+ intravesicular; Nao+ greater than Na+i]-dependent transport system for phosphate (Pi) in renal cortical brush border membrane vesicles (BBMV). PFA and PAA inhibited in a dose-dependent manner the Na+ gradient [Na+o greater than Na+i]-dependent uptake of Pi by rat kidney BBMV. PFA was a more potent inhibitor than PAA while phosphonopropionic acid, hydroxymethylphosphonic acid, and phenylphosphonic acid had no effect on Pi transport. The inhibitory effect of PFA was competitive (Ki approximately equal to 4.6 X 10(-4) M) and reversible upon dilution. The uptake of Pi by BBMV in the absence of Na+ gradient [Nao+ = Na+i] was also inhibited by PFA. The PFA had no effect on uptake of L-[3H]proline, D-[3H]glucose, or 22Na+ by BBMV nor did it alter intravesicular volume of BBMV. The relative (%) extent of inhibition by PFA was not altered by changes in the extravesicular pH or changes in the steepness of the Na+ gradient [Nao+ greater than Na+i]. The inhibition of PFA was analogous in renal BBMV from rats, mice, rabbits, or dogs. Unlike other known inhibitors of brush border membrane (BBM) transport of Pi, e.g. arsenate, NAD, and ethane-1-hydroxy-1,1-diphosphonate, PFA and PAA had no inhibitory effect on BBM-bound or solubilized alkaline phosphatase. Also, PFA did not interfere with the activity of renal cortical (Na-K)ATPase. Administration of PFA (0.5 g/kg/day, intraperitoneally) to thyroparathyroidectomized rats fed a low Pi diet elicited an increase in urinary excretion of Pi, but did not change the excretion of Na+, K, and Ca2+. The results show that the PFA, and to a lesser degree PAA, are specific competitive inhibitors of the Na+-Pi cotransport in renal cortical BBM and are suitable probes for studies of this transport system.
Rapid and Quantitative Method of Allele-Specific DNA Methylation Analysis (2006)

Several biological phenomena depend on differential methylation of chromosomal strands. While understanding the role of these processes requires information on allele-specific methylation, the available methodologies are not quantitative or labor-intensive. We describe a novel, rapid method to quantitate allele-specific DNA methylation based on the combination of bisulfite PCR and Pyrosequencing. In this method, DNA is first treated with sodium bisulfite, which converts cytosine but not 5-methylcytosine to uracil. Genes of interest are subsequently amplified using PCR. Allele-specific methylation can then be determined by pyrosequencing each allele individually using sequencing primers that incorporate single nucleotide polymorphisms (SNPs) that allow differentiation between the two parental alleles. This allele-specific methylation methodology can potentially afford quantitative analyses relevant to the regulation of X chromosome inactivation, allele-specific expression of genes in the immune system, repetitive elements, and genomic imprinting. As an illustration of our new method, we quantitated allele-specific methylation of the differentially methylated region of the H19 gene, which is imprinted. Although we could reliably determine allele-specific methylation with our technique, additional studies will be required to confirm the ability of our assay to measure loss of imprinting.
Observer Designs for Simultaneous Temperature and Loss Estimation for Electric Motors: A Comparative Study (2019)

Online temperature monitoring of electric motors is essential to the safety of the system under dynamic operation. The number of temperature sensors and their locations are often limited due to physical constraints and cost of the hardware, and the temperatures for most parts of a motor cannot be directly measured. To estimate the instantaneous temperature distribution of a motor, we design an observer for the real-time temperature monitoring using a thermal circuit model and limited measurements. Challenges imposed to the observer design include unknown heat sources and measurement noises. The observer needs to be able to simultaneously estimate all the hidden states and unknown inputs, while dealing with measurement noises. In this paper, different observers, including Kalman filter, Luenberger observer, adaptive observer, and modified proportional-derivative (PD) observer are designed to address the problem. We first give some background information of the problem, and introduce the thermal circuit model; then describe the observer designs with a focus on PD observer, which is more recently developed. The proposed observers are then implemented with simulations, and their performances are evaluated and compared.
A Survey on Malicious Domains Detection through DNS Data Analysis (2018)

Malicious domains are one of the major resources required for adversaries to run attacks over the Internet. Due to the important role of the Domain Name System (DNS), extensive research has been conducted to identify malicious domains based on their unique behavior reflected in different phases of the life cycle of DNS queries and responses. Existing approaches differ significantly in terms of intuitions, data analysis methods as well as evaluation methodologies. This warrants a thorough systematization of the approaches and a careful review of the advantages and limitations of every group. In this article, we perform such an analysis. To achieve this goal, we present the necessary background knowledge on DNS and malicious activities leveraging DNS. We describe a general framework of malicious domain detection techniques using DNS data. Applying this framework, we categorize existing approaches using several orthogonal viewpoints, namely (1) sources of DNS data and their enrichment, (2) data analysis methods, and (3) evaluation strategies and metrics. In each aspect, we discuss the important challenges that the research community should address in order to fully realize the power of DNS data analysis to fight against attacks leveraging malicious domains.
Arginine-42 and Threonine-45 Are Required for FAD Incorporation and Catalytic Activity in Human Monoamine Oxidase B (1998)

Monoamine oxidase B (MAO B) is an integral protein of the outer mitochondrial membrane that is involved in the deamination of vasoactive and neuroactive amines. The oxidation of these amine substrates requires the cofactor FAD, which is covalently bound to Cys-397 of human MAO B. Previously, Glu-34 and Tyr-44 of MAO B have been identified as residues which engage in noncovalent interactions with FAD that are required for subsequent covalent FAD binding and generation of catalytic activity. In this study, we have identified two additional residues, Arg-42 and Thr-45, which form noncovalent contacts with FAD that are prerequisite steps to the covalent attachment of FAD. Arg-42 and Thr-45, along with Tyr-44, comprise part of a highly conserved flavin binding sequence, RXY(T,S), that is found in other flavoproteins, several of which have well-defined X-ray crystal structures. We tested the roles of Arg-42 and Thr-45 in MAO B by constructing mutant MAO B cDNAs which encode amino acid substitutions at these residues and expressed the variant proteins in COS-7 cells. Substitution of Arg-42 or Thr-45 with alanine resulted in complete loss of MAO B activity and FAD incorporation. However, conservative substitutions of Arg-42 with lysine or Thr-45 with serine resulted in MAO B variants that retain both partial activity and partial FAD incorporation. These results indicate that Arg-42 and Thr-45 form critical noncovalent interactions with FAD that are required for the subsequent activation of MAO B by covalent coupling of FAD.