gebhart/patrepeval huggingface dataset:
Structure-Based Virtual Screening of the Nociceptin Receptor: Hybrid Docking and Shape-Based Approaches for Improved Hit Identification (2014)

The antagonist-bound crystal structure of the nociceptin receptor (NOP), from the opioid receptor family, was recently reported along with those of the other opioid receptors bound to opioid antagonists. We recently reported the first homology model of the 'active-state' of the NOP receptor, which when docked with 'agonist' ligands showed differences in the TM helices and residues, consistent with GPCR activation after agonist binding. In this study, we explored the use of the active-state NOP homology model for structure-based virtual screening to discover NOP ligands containing new chemical scaffolds. Several NOP agonist and antagonist ligands previously reported are based on a common piperidine scaffold. Given the structure-activity relationships for known NOP ligands, we developed a hybrid method that combines a structure-based and ligand-based approach, utilizing the active-state NOP receptor as well as the pharmacophoric features of known NOP ligands, to identify novel NOP binding scaffolds by virtual screening. Multiple conformations of the NOP active site including the flexible second extracellular loop (EL2) loop were generated by simulated annealing and ranked using enrichment factor (EF) analysis and a ligand-decoy dataset containing known NOP agonist ligands. The enrichment factors were further improved by combining shape-based screening of this ligand-decoy dataset and calculation of consensus scores. This combined structure-based and ligand-based EF analysis yielded higher enrichment factors than the individual methods, suggesting the effectiveness of the hybrid approach. Virtual screening of the CNS Permeable subset of the ZINC database was carried out using the above-mentioned hybrid approach in a tiered fashion utilizing a ligand pharmacophore-based filtering step, followed by structure-based virtual screening using the refined NOP active-state models from the enrichment analysis. Determination of the NOP receptor binding affinity of a selected set of top-scoring hits resulted in identification of several compounds with measurable binding affinity at the NOP receptor, one of which had a new chemotype for NOP receptor binding. The hybrid ligand-based and structure-based methodology demonstrates an effective approach for virtual screening that leverages existing SAR and receptor structure information for identifying novel hits for NOP receptor binding. The refined active-state NOP homology models obtained from the enrichment studies can be further used for structure-based optimization of these new chemotypes to obtain potent and selective NOP receptor ligands for therapeutic development.
AC Losses in a High Temperature Superconducting Generator (2005)

As part of the DOE-SPI funded project a commercial HTS utility-size generator is being developed based on GE's iron core superconducting generator technology. The iron core concept has significant advantages over air core designs. The rotor consists of a cold superconducting field coil and coil supports and a warm iron core, which takes the torque and transmits to the shafts. Heat load due to AC losses in the cold mass of the rotor are a key design constraint. Analyses have been performed both at the component and system levels. AC loss tests have been conducted on an HTS generator. This paper presents and discusses the analytical and test results.
Biodegradation of Used Metalworking Fluids in Wastewater Treatment (2005)

A biotechnological method for metalworking fluids (MWF) wastewater treatment was developed. The research, conducted in a lab-scale bioreactor, proved that the process of eliminating pollutants from MWF wastewater proceeds effectively when the following are applied: multiple reinoculating of biomass by adding active microorganisms into the bioreactor, immobilizing microorganisms on the PVC foam carrier, and carrying out the process in the anoxic/aerobic conditions at phase durations of 0.5 and 5.5 hours, respectively. The above parameters allowed us to obtain the following eliminations: 87% of chemical oxygen demand (COD), 97% of biochemical oxygen demand (BOD 5 ), 98% of petroleum ether extractable organic (PEEO) and more than 96% of total content of hydrocarbons determined by infrared (IR) spectrophotometry. The chromatographic analyses showed almost complete reduction of oily hydrocarbons contained in the used MWF.
Nucleic Acid Beacons for Long-Term Real-Time Intracellular Monitoring (2008)

Real time intracellular monitoring of biological molecules inside living cells is important in many biomedical studies and reveals valuable information unobtainable by conventional molecular biology techniques. A variety of methods and molecular probes have been developed, but long term (from a few hours to days) intracellular monitoring with high sensitivity and selectivity is impossible and has not been accomplished. We have used locked nucleic acids (LNA) to engineer novel molecular beacons (MBs) for long-term intracellular monitoring. The LNA-MBs were made of a mixed LNA and DNA bases to have extremely high biostability. The new beacons were tested with MDA-MB-231 cancer cells and used effectively to monitor mRNA expression levels in real-time for 5-24 h. After 24 h inside living cells, the LNA-MBs were still functional, demonstrating a greatly enhanced stability enabling the measurement of intracellular gene expression over an extended period of time.
Analysis of Time Series Structure: SSA and related techniques (2001)

Over the last 15 years, singular spectrum analysis (SSA) has proven very successful. It has already become a standard tool in climatic and meteorological time series analysis and well known in nonlinear physics and signal processing. However, despite the promise it holds for time series applications in other disciplines, SSA is not widely known among statisticians and econometrists, and although the basic SSA algorithm looks simple, understanding what it does and where its pitfalls lay is by no means simple. Analysis of Time Series Structure: SSA and Related Techniques provides a careful, lucid description of its general theory and methodology. Part I introduces the basic concepts, and sets forth the main findings and results, then presents a detailed treatment of the methodology. After introducing the basic SSA algorithm, the authors explore forecasting and apply SSA ideas to change-point detection algorithms. Part II is devoted to the theory of SSA. Here the authors formulate and prove the statements of Part I. They address the singular value decomposition (SVD) of real matrices, time series of finite rank, and SVD of trajectory matrices. Based on the authors' original work and filled with applications illustrated with real data sets, this book offers an outstanding opportunity to obtain a working knowledge of why, when, and how SSA works. It builds a strong foundation for successfully using the technique in applications ranging from mathematics and nonlinear physics to economics, biology, oceanology, social science, engineering, financial econometrics, and market research.
Nine Cases of Bilateral Femoral Shaft Fractures (1980)

Nine cases of bilateral femoral shaft fractures were seen in a series of 126 patients treated from 1973--1977. Patients were multitrauma cases from automobile accidents. Treatment by traction followed by cast-bracing resulted in a high percentage of unsatisfactory results, lengthy recoveries, and the necessity of secondary surgical procedures to improve the results.
Synthesis and anti-HIV activity of carbovir and related carbocyclic nucleosides. (1991)

(+/-) Carbocyclic 2',3'-didehydro-2',3'-dideoxyguanosine (Carbovir) is an antiretroviral agent which is undergoing preclinical evaluation for the treatment of AIDS. Its hydrolytic stability and its ability to inhibit infectivity and replication of HIV in T-cells at concentrations of approximately 400-fold below toxic concentrations make Carbovir an excellent candidate for development as a potential antiretroviral agent.
Ranking Universities Using Linked Open Data (2013)

Ranking of universities represents a complex endeavor which involves gathering, weighting, and analyzing diverse data. Emerging semantic technologies enable the Web of Data, a giant graph of interconnected information resources, also known as Linked Data. A recent community effort, Linking Open Data project, offers the possibility of accessing a large number of semantically described and linked concepts in various domains. In this paper, we propose a novel approach to take advantage of this structured data in the domain of universities to develop proxy measures of their relative standing for ranking purposes. Derived from information theory, our approach of computing the Information Content for universities and ranking them based on these scores achieved results comparable to the international ranking systems such as Shanghai Jiao Tong University, Times Higher Education, and QS. The metric we developed can also be used for innovative semantic applications in a range of domains for entity ranking, information filtering, and multi-faceted browsing.
Digital transmission scheme for ISDB-T and reception characteristics of digital terrestrial television broadcasting system in Japan (1999)

We introduce a transmission scheme for ISDB-T, and proposes a soft-decision decoding technique for ISDB-T receivers to improve the reception performance under multipath distortion and interference from analog television signals. We propose two techniques that apply estimated the channel frequency response for each carrier to the derivation of soft-decision metrics in 64QAM-OFDM. We present Viterbi soft-decision decoding characteristics by these proposed techniques for AWGN transmission paths, multipath conditions. We also propose a soft-decision technique that erases the data of carriers exhibiting large disturbance.
Heavy Metal Pollution and Decomposition of Spruce Needle Litter (1973)

Comparisons were made on the decomposition rates of different fractions of spruce needle litter from numerous sites around two metal processing industries in central and southeastern Sweden, emitting Cu, Zn, Cd and Ni, and Pb, Ni and Cd, respectively. All measurements were performed under controlled laboratory conditions. At water capacity and 15?C a C02 evolution rate in partly disintegrated litter of ca 0.23 mg C/g dry matter, 24 hr was measured in samples with > 10 prmol Zn + Cu + Cd + Ni per g, compared with ca 0.50 mg C in samples with < 5 jimol/g. Highly significant negative correlations were obtained in all materials between heavy metal concentration and C02 evolution rate or dehydrogenase activity. It is concluded that, in acid forest sites, the general decomposition rate will be depressed even by moderate concentrations of heavy metal ions, at least during those parts of the year when the water supply is adequate.
3-D Correlation-Based Speckle Tracking (2005)

Widely-used 1-D/2-D speckle tracking techniques in elasticity imaging often experience significant speckle decorrelation in applications involving large elevational motion (i.e., out of plane motion). The problem is more pronounced for cardiac strain rate imaging (SRI) since it is very difficult to confine cardiac motion to a single image plane. Here, we present a 3-D correlation-based speckle tracking algorithm. Conceptually, 3-D speckle tracking is just an extension of 2-D phase-sensitive correlation-based speckle tracking. However, due to its high computational cost, optimization schemes, such as dynamic programming, decimation and two-path processing, are introduced to reduce the computational burden. To evaluate the proposed approach, a 3-D bar phantom under uniaxial compression was simulated for benchmark tests. A more sophisticated 3-D simulation of the left ventricle of the heart was also made to test the applicability of 3-D speckle tracking in cardiac SRI. Results from both simulations clearly demonstrated the feasibility of 3-D correlation-based speckle tracking. With the ability to follow 3-D speckle in 3-D space, 3-D speckle tracking outperforms lower-dimensional speckle tracking by minimizing decorrelation caused by pure elevational translation. In other words, 3-D tracking can push toward solely deformation-limited, decorrelation-optimized speckle tracking. Hardware implementation of the proposed 3-D speckle tracking algorithm using field programmable gate arrays (FPGA) is also discussed.
Analysis of effects of rebounds and aerodynamics for trajectory of table tennis ball (2010)

In this paper, we firstly analyze the effects of the rebounds and aerodynamics for trajectory of a table tennis ball. We firstly analyze the effect of the aerodynamics with a criterion of evaluation, where the half area of the table is considered as 9 divided areas. Furthermore, the drag and lift coefficients are identified by assuming that the rotational velocity is invalid during the ball flying. With the identified coefficients, the modeling errors of the table and racket are secondly verified by the criterion mentioned previously. Some conclusions are finally shown.
Design of haptic force feedback for catheter insertion mechanism (2006)

Thesis (M.S.)--Wichita State University, College of Engineering, Dept. of Mechanical Engineering
Application of Least Squares Lattice Algorithms to Adaptive Equalization (1981)

In many applications of adaptive data equalization, rapid initial convergence of the adaptive equalizer is of paramount importance. Apparently, the fastest known equalizer adaptation algorithm is based on a recursive least squares estimation algorithm. In this paper we show how the least squares lattice algorithms, recently introduced by Morf and Lee, can be adapted to the equalizer adjustment algorithm. The resulting algorithm, although computationally more complex than certain other equalizer algorithms (including the fast Kalman algorithm), has a number of desirable features which should prove useful in many applications.
Solnatide Demonstrates Profound Therapeutic Activity in a Rat Model of Pulmonary Edema Induced by Acute Hypobaric Hypoxia and Exercise (2016)

Solnatide reduced pulmonary edema, increased occludin expression, and improved gas-blood barrier function during acute hypobaric hypoxia and exercise in rats. These results provide a rationale for the clinical application of solnatide to patients with pulmonary edema and exposure to a high-altitude hypoxic environment.
Morphine and oxycodone hydrochloride in the management of cancer pain (1990)

In a double-blind crossover study, morphine and oxycodone hydrochloride were administered to 20 patients who were experiencing severe cancer pain. The peroral doses were determined on the basis of patient-controlled intravenous titration. The assumed oral bioavailability ratios were 44% (group 1, first 10 patients) and 33% (group 2, last 10 patients) for morphine and 66% (group 1) and 50% (group 2) for oxycodone hydrochloride, respectively. However, the patients were able to readjust their oral dosings. Equal analgesia was achieved with both drugs, but the intravenous dose of oxycodone hydrochloride needed was 30% higher than that of morphine. The median calculated oral/intravenous ratios giving comparable analgesia were 0.31 for morphine and 0.70 for oxycodone hydrochloride. Morphine caused more nausea than oxycodone hydrochloride and hallucinations occurred only during morphine treatment. Otherwise, there were no major differences in the side effects between these two opioids.
The detection of small quantities of war gases (Dijkstra's method) (1940)

Abstract Translator's Note.‐The following paper was published as a report from the Chemical Laboratory of the Dutch Artillery School at Delft, where the practical details were elaborated. In a preface to the report the author expresses his indebtedness to Dr. D. W. Dijkstra, who suggested this method of air flow analysis (Chem. Weekblad 34, 351, 1937); to his collaborators, Dr. 6. Verkaaik and Dr. W. G. Perdok, and to the publication of Dr. A. Tasrnan (Chern. Weekblad.36, 534, 1939). I should also like to add my acknowledgments to Dr. Hoogeveen for his kind permission to publish the translation.
Co-contraction in the hemiparetic forearm: quantitative EMG evaluation. (1988)

Co-contraction of antagonist muscles is a recognized clinical phenomenon in patients surviving a cerebrovascular accident. Yet, discrepancies persist in the literature as to whether or not antagonist electromyographic activity is increased in hemiparesis. We have developed a technique to obtain simultaneous counts of motor unit activity in a wrist flexor and extensor muscle using monopolar needle electromyography. Stable stroke patients and age/sex matched control subjects were tested during maximal voluntary isometric wrist flexion and extension. Fewer agonist events (p less than 0.05) and more antagonist events (p less than 0.10) were counted in paretic than in control muscles. A co-contraction ratio of antagonist activity to total (agonist and antagonist) activity was much greater for patients than controls (p less than 0.01). We conclude that both agonist recruitment and antagonist inhibition are impaired in the hemiparetic arm.
Facile, general and productive syntheses of the fluorescent wye (4,9-dihydro-4,6-dimethyl-9-oxo-1H-imidazo[1,2-a]purine) in phenylalanine tRNA, its 2-substituted derivatives and 7-aza analogues (1995)

Novel syntheses of 4,9-dihydro-4,6-dimethyl-9-oxo-1H-imidazo[1,2-a]purine (Y base skeleton), its 2-substituted derivatives and 7-aza analogues and their fluorescence characteristics in relation to their structures are described.
Inducing Effect of Diamines on Transcription of the Cephamycin C Genes from the <i>lat</i> and <i>pcbAB</i> Promoters in <i>Nocardia lactamdurans</i> (1999)

The diamines putrescine, cadaverine, and diaminopropane stimulate cephamycin biosynthesis in Nocardia lactamdurans, in shake flasks and fermentors, without altering cell growth. Intracellular levels of the P7 protein (a component of the methoxylation system involved in cephamycin biosynthesis) were increased by diaminopropane, as shown by immunoblotting studies. Lysine-6-aminotransferase and piperideine-6-carboxylate dehydrogenase activities involved in biosynthesis of the alpha-aminoadipic acid precursor were also greatly stimulated. The diamine stimulatory effect is exerted at the transcriptional level, as shown by low-resolution S1 protection studies. The transcript corresponding to the pcbAB gene and to a lesser extent also the lat transcript were significantly increased in diaminopropane-supplemented cultures, whereas transcription from the cefD promoter was not affected. Coupling of the lat and pcbAB promoters to the reporter xylE gene showed that expression from the lat and pcbAB promoters was increased by addition of diaminopropane in Streptomyces lividans. Intracellular accumulation of diamines in Nocardia may be a signal to trigger antibiotic production.
Optimizing acoustic parameters for phonetic features (1996)

In developing acoustic parameters based on phonetic features for speaker-independent speech recognition, it is important that the parameters (1) be based on relative measures as opposed to absolute ones to minimize speaker-dependent effects and (2) be selected from a pool of candidates according to some ‘‘goodness’’ criteria. In this study, place-of-articulation phonetic features are targeted to help classify obstruent sounds. It will be shown how acoustic phonetic knowledge and statistical analysis were combined to go from qualitative definitions of the acoustic correlates for phonetic features to computational algorithms for extraction of the relevant acoustic properties using discriminant analysis and classification trees. Further, it will be shown how using relative measures reduces speaker-dependent effects, specifically gender, on the acoustic parameters while honing on the phonetic information contained in the speech signal. [Work supported by NSF Research Grant No. IRI-9310518.]
Fault-Tolerant Multiprocessor Link and Bus Network Architectures (1985)

This paper presents a general class of regular networks which provide optimal (near-optimal) fault tolerance.
TGFF: task graphs for free (1998)

We present a user-controllable, general-purpose, pseudorandom task graph generator called Task Graphs For Free (TGFF). TGFF creates problem instances for use in allocation and scheduling research. It has the ability to generate independent tasks as well as task sets which are composed of partially ordered task graphs. A complete description of a scheduling problem instance is created, including attributes for processors, communication resources, tasks, and inter-task communication. The user may parametrically control the correlations between attributes. Sharing TGFF's parameter settings allows researchers to easily reproduce the examples used by others, regardless of the platform on which TGFF is run.
Blend Uniformity and Unit Dose Sampling (1995)

Process validation for solid dosage forms must include a component that demonstrates content uniformity of the final blend. As a result of a recent court ruling this aspect of validation has received increased attention from both industry and government. In particular, the court ruled that the appropriate sample size for content uniformity testing of the final blend in validation batches is three times the run weight of the finished product. Furthermore, recent FDA communications suggest that the uniformity of the final blend should be held to a higher standard than that of the tablet in order to provide reasonable assurance that the finished product will exhibit acceptable uniformity. The purpose of this article is to communicate some problems that our firm encountered during the validation of a lower strength of a currently marketed tablet. The validated process for the marketed product has a long history of providing tablets that exhibit acceptable content uniformity at the higher strength. Extensive data from three validation batches manufactured at each of two production sites demonstrate consistently and significantly lower drug content in the lubricated granulation than in the finished product. The variability of the granulation data as characterized by the standard deviation is, for the most part, acceptable and comparable to that of the tablets. Unfortunately, these batches fail validation when subjected to the acceptance criteria suggested in recent FDA communications. We attribute the lower assay values of the granulation to sampling bias that occurs when small volumes of powder are extracted from a large V-blender with a sampling thief. In order to circumvent this problem and avoid rejecting acceptable processes we recommend an alternative acceptance criteria in which the mean assay of the powder samples is not relevant, This criteria relies solely on the standard deviation of the blend.