gebhart/patrepeval huggingface dataset:
Enkephalin Glycopeptide Analogues Produce Analgesia with Reduced Dependence Liability (2000)

Endogenous peptides (e.g. enkephalins) control many aspects of brain function, cognition, and perception. The use of these neuroactive peptides in diverse studies has led to an increased understanding of brain function. Unfortunately, the use of brain-derived peptides as pharmaceutical agents to alter brain chemistry in vivo has lagged because peptides do not readily penetrate the blood-brain barrier. Attachment of simple sugars to enkephalins increases their penetration of the blood-brain barrier and allows the resulting glycopeptide analogues to function effectively as drugs. The delta-selective glycosylated Leu-enkephalin amide 2, H(2)N-Tyr-D-Thr-Gly-Phe-Leu-Ser(beta-D-Glc)-CONH(2), produces analgesic effects similar to morphine, even when administered peripherally, yet possesses reduced dependence liability as indicated by naloxone-precipitated withdrawal studies. Similar glycopeptide-based pharmaceuticals hold forth the promise of pain relief with improved side-effect profiles over currently available opioid analgesics.
Structural basis of replication origin recognition by the DnaA protein (2003)

Escherichia coli DnaA binds to 9 bp sequences (DnaA boxes) in the replication origin, oriC, to form a complex initiating chromosomal DNA replication. In the present study, we determined the crystal structure of its DNA-binding domain (domain IV) complexed with a DnaA box at 2.1 A resolution. DnaA domain IV contains a helix-turn-helix motif for DNA binding. One helix and a loop of the helix- turn-helix motif are inserted into the major groove and 5 bp (3' two-thirds of the DnaA box sequence) are recognized through base-specific hydrogen bonds and van der Waals contacts with the C5-methyl groups of thymines. In the minor groove, Arg399, located in the loop adjacent to the motif, recognizes three more base pairs (5' one-third of the DnaA box sequence) by base-specific hydrogen bonds. DNA bending by approximately 28 degrees was also observed in the complex. These base-specific interactions explain how DnaA exhibits higher affinity for the strong DnaA boxes (R1, R2 and R4) than the weak DnaA boxes (R3 and M) in the replication origin.
Using Kintsch's computational model to improve instructional text: Effects of repairing inference calls on recall and cognitive structures. (1991)

The goal of this study was to link a computational psychological model to instructional practice. Kintsch's (Kintsch & van Dijk, 1978; Miller & Kintsch, 1980) reading comprehension model was used to identify locations where inferences were called for in a 1000-word expository text. Then each location was repaired to produce a principled revision
Alteration of cell cycle kinase complexes in human papillomavirus E6- and E7-expressing fibroblasts precedes neoplastic transformation (1996)

Expression of viral oncoproteins results in the loss of cell cycle checkpoint control and the accumulation of chromosomal abnormalities. Expression of both human papillomavirus type 16 oncoproteins, E6 and E7, in normal human fibroblasts completely dissociates p21 and proliferating cell nuclear antigen from the quarternary cyclin-cyclin-dependent kinase (CDK) complexes present in normal cells, causes disruption of the cyclin D-CDK4 complex and replacement with a CDK4-p16 complex, and leaves binary complexes of cyclin B1-CDC2 and cyclin A-CDK2 intact. These results are identical to those observed in fully transformed cells. The expression of the individual oncoproteins dramatically affects the association of proliferating cell nuclear antigen into the complexes while leaving the total cellular levels unaltered. Expression of low-risk human papillomavirus has no effect on cyclin complexes. These findings provide evidence for the gross alteration of cyclin-CDK complexes in preneoplastic cells and links this alteration to the loss of genomic stability.
Affine Motion Based CMOS Distortion Analysis and CMOS Digital Image Stabilization (2007)

The CMOS image distortion is due to the rolling shutter in CMOS image sensors (CISs) and it can be more exaggerated when a CIS camera moves rapidly. Several methods have been proposed to remove CMOS distortions made by the translational motion. But, in this paper, we propose the affine motion based CMOS distortion correction method combined with digital image stabilization. To remove CMOS distortions due to the affine global image motion, CMOS distortion model is proposed to explain the effect of the affine global image motion on the CMOS distortion in CISs. To improve CMOS video's visuals, we propose CMOS digital image stabilization to remove the jittering motions in the new image sequence obtained by our correction method. In addition, to reduce the computational time and the outlier effect, a reliable feature selection method is proposed to be used in the affine global image motion estimation. In the experiment results, we show that the proposed CMOS distortion correction method is more general than previous ones. Also, we show that our stabilization method can improve CMOS video's visuals running in real-time.
Phase-resolved functional optical coherence tomography: simultaneous imaging of in situ tissue structure, blood flow velocity, standard deviation, birefringence, and Stokes vectors in human skin (2002)

We describe a phase-resolved functional optical coherence tomography system that can simultaneously yieldin situ images of tissue structure, blood flow velocity, standard deviation, birefringence, and the Stokes vectors in human skin. Multifunctional images were obtained by processing of analytical interference fringe signals derived from two perpendicular polarization-detection channels. The blood flow velocity and standard deviation images were obtained by comparison of the phases from pairs of analytical signals in neighboring A-lines in the same polarization state. The analytical signals from two polarization-diversity detection channels were used to determine the four Stokes vectors for four reference polarization states. From the four Stokes vectors, the birefringence image, which is not sensitive to the orientation of the optical axis in the sample, was obtained. Multifunctional in situ images of a port wine stain birthmark in human skin are presented.
Staphylococcus aureus (1991)

Abstract The analytical methods for the detection of the staphylococcal enterotoxins can be divided into 2 categories: (1) methods for detection of enterotoxin-producing staphylococcal strains; (2) methods for detection of enterotoxin in foods. Gel diffusion methods (Ouchterlony, microslide), in which the enterotoxin produced by any given strain is compared to one of the identified enterotoxins, are used most frequently for strain testing. The sensitivity of these methods is from 0.1 to 0.5 μg enterotoxin/mL, which is normally adequate to determine the enterotoxigenicity of strains. The methods for the detection of enterotoxin in foods need to be much more sensitive to detect less than 1 ng of enterotoxin/g of food that may be present. The radioimmunoassay (RIA), the enzymelinked immunosorbent assay (ELISA), and the reversed passive latex agglutination (RPLA) method have the necessary sensitivity to detect 1 ng/g of enterotoxin in foods without the use of complicated extraction-concentration procedures. Kits based on the ELISA and RPLA methods are now available commercially for the detection of enterotoxins in foods. Tests have shown that the ELISA methods are somewhat more sensitive than the RPLA method.
Proximity-Based Authentication for Mobile Devices (2005)

On the basis of preclinical data suggesting the possibility of maximising the efficacy of 5-fluorouracil and cisplatin by interferon, a pilot clinical trial was initiated in recurrent and/or metastatic head and neck cancer. Thirty-four patients were treated with cisplatin at 100 mg m-2, followed by 5-fluorouracil at 1,000 mg m-2 by continuous infusion for 5 days. Interferon alpha 2b was administered at the dose of 3 million U i.m. daily for 7 days, beginning the day before chemotherapy. Courses were repeated every 3 weeks. Two patients achieved a complete remission, six a partial response, 14 had stable disease and 12 progressed on therapy, for an overall response rate of 23% (95% confidence interval 10-36%). Median survival time was 5 months. Toxicity was severe. Stomatitis, diarrhoea and myelosuppression were the most common side-effects. Because of the poor response rate and the presence of severe toxicity, in our opinion further clinical trials in head and neck cancer should be attempted only after a better definition in preclinical studies of interactions among 5-fluorouracil, cisplatin and interferon.
Corrosion Inhibitor Testing in Dense Phase Hydrocarbon Systems (2012)

Abstract Dense phase conditions are expected in several gas export pipelines in deep water fields where high pressure and low temperature can give hydrocarbon gas as a dense phase. Problems with dewatering may introduce a free water phase in the pipeline, so corrosion inhibitors must be used to mitigate CO2 corrosion. Since dense hydrocarbon fluids are good solvents, partitioning of corrosion inhibitors to the dense phase could be a potential problem. A corrosion loop where a dense hydrocarbon phase at 180 bar pressure can be used together with a water phase was used to study the partitioning process. The experiments showed that partitioning to the dense hydrocarbon phase may reduce the inhibitor efficiency somewhat, but no dramatic effects were seen compared to the more familiar situation with oil or condensate.
Safety and Tolerability Study of Aptiganel Hydrochloride in Patients With an Acute Ischemic Stroke (1999)

A 4.5-mg intravenous bolus of aptiganel HCl followed by infusion of 0.75 mg/h for 12 hours is a tolerable dose that can produce plasma drug concentrations shown to be neuroprotective in animal models. However, increases in systolic blood pressure and an excess of CNS effects were both observed at this dose.
Privacy via pseudorandom sketches (2006)

Imagine a collection of individuals who each possess private data that they do not wish to share with a third party. This paper considers how individuals may represent and publish their own data so as to simultaneously preserve their privacy and to ensure that it is possible to extract large-scale statistical behavior from the original unperturbed data. Existing techniques for perturbing data are limited by the number of users required to obtain approximate answers to queries, the richness of preserved statistical behavior, the privacy guarantees given and/or the amount of data that each individual must publish.This paper introduces a new technique to describe parts of an individual's data that is based on pseudorandom sketches. The sketches guarantee that each individual's privacy is provably maintained assuming one of the strongest definitions of privacy that we are aware of: given unlimited computational power and arbitrary partial knowledge, the attacker can not learn any additional private information from the published sketches. However, sketches from multiple users that describe a subset of attributes can be used to estimate the fraction of users that satisfy any conjunction over the full set of negated or unnegated attributes provided that there are enough users. We show that the error of approximation is independent of the number of attributes involved and only depends on the number of users available. An additional benefit is that the size of the sketch is minuscule: [log log O(M)] bits, where M is the number of users. Finally, we show how sketches can be combined to answer more complex queries. An interesting property of our approach is that despite using cryptographic primitives, our privacy guarantees do not rely on any unproven cryptographic conjectures.
Novel Roles for the Polyphenol Oxidase Enzyme in Secondary Metabolism and the Regulation of Cell Death in Walnut (2014)

The enzyme polyphenol oxidase (PPO) catalyzes the oxidation of phenolic compounds into highly reactive quinones. Polymerization of PPO-derived quinones causes the postharvest browning of cut or bruised fruit, but the native physiological functions of PPOs in undamaged, intact plant cells are not well understood. Walnut (Juglans regia) produces a rich array of phenolic compounds and possesses a single PPO enzyme, rendering it an ideal model to study PPO. We generated a series of PPO-silenced transgenic walnut lines that display less than 5% of wild-type PPO activity. Strikingly, the PPO-silenced plants developed spontaneous necrotic lesions on their leaves in the absence of pathogen challenge (i.e. a lesion mimic phenotype). To gain a clearer perspective on the potential functions of PPO and its possible connection to cell death, we compared the leaf transcriptomes and metabolomes of wild-type and PPO-silenced plants. Silencing of PPO caused major alterations in the metabolism of phenolic compounds and their derivatives (e.g. coumaric acid and catechin) and in the expression of phenylpropanoid pathway genes. Several observed metabolic changes point to a direct role for PPO in the metabolism of tyrosine and in the biosynthesis of the hydroxycoumarin esculetin in vivo. In addition, PPO-silenced plants displayed massive (9-fold) increases in the tyrosine-derived metabolite tyramine, whose exogenous application elicits cell death in walnut and several other plant species. Overall, these results suggest that PPO plays a novel and fundamental role in secondary metabolism and acts as an indirect regulator of cell death in walnut.
Experimental performance comparison for various continuous-wave supercontinuum schemes: ring cavity and single pass structures (2005)

We experimentally perform a comparative study on performance of three different schemes for generation of continuous-wave (CW) supercontinuum by use of nonlinear optical fiber, i.e. our proposed erbium-doped fiber (EDF)-based ring laser scheme incorporating a highly-nonlinear dispersion-shifted fiber (HNL-DSF), the Raman gain-based ring laser scheme incorporating an HNL-DSF, and the conventional scheme based on pump beam single propagation through an HNL-DSF. The three schemes show different physical mechanisms of supercontinuum evolution from a CW pump beam. In particular, our proposed EDF-based ring laser configuration is found to have a better relative intensity noise performance than the other two schemes.
Cytokinetic analysis of the impaired proliferative response of peripheral lymphocytes from aged humans to phytohemagglutinin. (1979)

The effect of donor age on the rate of cell entry into the proliferating pool and subsequent cell cycle duration for peripheral lymphocytes stimulated by phytohemagglutinin (PHA) were examined by using the bromodeoxyuridine incorporation-differential staining technique. Distribution curves for the appearance of metaphase cells in successive generations as a function of culture time were obtained and analyzed both graphically and by a computer simulation model. Peripheral lymphocytes from aged individuals (approximately 75 yr) were stimulated by PHA at approximately one-half of the rate of peripheral lymphocytes from young individuals (approximately 21 yr). Subsequent cell-cycle durations were estimated to range from 10.0 to 25.0 h for aged individual lymphocyte cultures and 10.6-15.6 h for young individual lymphocyte cultures. The possible significance of these findings to aging in general is discussed.
A fast new algorithm for training feedforward neural networks (1992)

A fast algorithm is presented for training multilayer perceptrons as an alternative to the backpropagation algorithm. The number of iterations required by the new algorithm to converge is less than 20% of what is required by the backpropagation algorithm. Also, it is less affected by the choice of initial weights and setup parameters. The algorithm uses a modified form of the backpropagation algorithm to minimize the mean-squared error between the desired and actual outputs with respect to the inputs to the nonlinearities. This is in contrast to the standard algorithm which minimizes the mean-squared error with respect to the weights. Error signals, generated by the modified backpropagation algorithm, are used to estimate the inputs to the nonlinearities, which along with the input vectors to the respective nodes, are used to produce an updated set of weights through a system of linear equations at each node. These systems of linear equations are solved using a Kalman filter at each layer.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A framework for the experimental comparison of solar and skydome illumination (2014)

The illumination and appearance of the solar/skydome is critical for many applications in computer graphics, computer vision, and daylighting studies. Unfortunately, physically accurate measurements of this rapidly changing illumination source are difficult to achieve, but necessary for the development of accurate physically-based sky illumination models and comparison studies of existing simulation models. To obtain baseline data of this time-dependent anisotropic light source, we design a novel acquisition setup to simultaneously measure the comprehensive illumination properties. Our hardware design simultaneously acquires its spectral, spatial, and temporal information of the skydome. To achieve this goal, we use a custom built spectral radiance measurement scanner to measure the directional spectral radiance, a pyranometer to measure the irradiance of the entire hemisphere, and a camera to capture high-dynamic range imagery of the sky. The combination of these computer-controlled measurement devices provides a fast way to acquire accurate physical measurements of the solar/skydome. We use the results of our measurements to evaluate many of the strengths and weaknesses of several sun-sky simulation models. We also provide a measurement dataset of sky illumination data for various clear sky conditions and an interactive visualization tool for model comparison analysis available at http://www.graphics.cornell.edu/resources/clearsky/.
A method of service quality estimation with a network measurement tool (1999)

Recently, many kinds of real-time applications have become available over IP networks. It is important to measure network performance for such applications before making use of real applications. The authors developed a general purpose traffic measurement tool for IP networks. This system can generate any kind of traffic flexibly and calculate network performance such as throughput, delay and loss rate according to the packers to be observed. In this paper, the concept and implementation of this tool are described in detail. As an example of network measurements, we also conducted subjective assessment tests for Internet telephony and demonstrated the validity of this tool.
Continuous mobile authentication using touchscreen gestures (2012)

Securing the sensitive data stored and accessed from mobile devices makes user authentication a problem of paramount importance. The tension between security and usability renders however the task of user authentication on mobile devices a challenging task. This paper introduces FAST (Fingergestures Authentication System using Touchscreen), a novel touchscreen based authentication approach on mobile devices. Besides extracting touch data from touchscreen equipped smartphones, FAST complements and validates this data using a digital sensor glove that we have built using off-the-shelf components. FAST leverages state-of-the-art classification algorithms to provide transparent and continuous mobile system protection. A notable feature is FAST 's continuous, user transparent post-login authentication. We use touch data collected from 40 users to show that FAST achieves a False Accept Rate (FAR) of 4.66% and False Reject Rate of 0.13% for the continuous post-login user authentication. The low FAR and FRR values indicate that FAST provides excellent post-login access security, without disturbing the honest mobile users.
Scaling Factors for the Extrapolation of In Vivo Metabolic Drug Clearance From In Vitro Data: Reaching a Consensus on Values of Human Micro-somal Protein and Hepatocellularity Per Gram of Liver (2006)

Reported predictions of human in vivo hepatic clearance from in vitro data have used a variety of values for the scaling factors human microsomal protein (MPPGL) and hepatocellularity (HPGL) per gram of liver, generally with no consideration of the extent of their inter-individual variability. We have collated and analysed data from a number of sources, to provide weighted meangeo values of human MPPGL and HPGL of 32 mg g-1 (95% Confidence Interval (CI); 29-34 mg.g-1) and 99x10(6) cells.g-1 (95% CI; 74-131 mg.g-1), respectively. Although inter-individual variability in values of MPPGL and HPGL was statistically significant, gender, smoking or alcohol consumption could not be detected as significant covariates by multiple linear regression. However, there was a weak but statistically significant inverse relationship between age and both MPPGL and HPGL. These findings indicate the importance of considering differences between study populations when forecasting in vivo pharmacokinetic behaviour. Typical clinical pharmacology studies, particularly in early drug development, use young, fit, healthy male subjects of around 30 years of age. In contrast, the average age of patients for many diseases is about 60 years of age. The relationship between age and MPPGL observed in this study estimates values of 40 mg.g-1 for a 30 year old individual and 31 mg.g-1 for a 60 year old individual. Investigators may wish to consider the reported covariates in the selection of scaling factors appropriate for the population in which estimates of clearance are being predicted. Further studies are required to clarify the influence of age (especially in paediatric subjects), donor source and ethnicity on values of MPPGL and HPGL. In the meantime, we recommend that the estimates (and their variances) from the current meta-analysis be used when predicting in vivo kinetic parameters from in vitro data.
Arginine-rich cell-penetrating peptide dramatically enhances AMO-mediated ATM aberrant splicing correction and enables delivery to brain and cerebellum (2011)

Antisense morpholino oligonucleotides (AMOs) can reprogram pre-mRNA splicing by complementary binding to a target site and regulating splice site selection, thereby offering a potential therapeutic tool for genetic disorders. However, the application of this technology into a clinical scenario has been limited by the low correction efficiency in vivo and inability of AMOs to efficiently cross the blood brain barrier and target brain cells when applied to neurogenetic disorders such as ataxia-telangiecatasia (A-T). We previously used AMOs to correct subtypes of ATM splicing mutations in A-T cells; AMOs restored up to 20% of the ATM protein and corrected the A-T cellular phenotype. In this study, we demonstrate that an arginine-rich cell-penetrating peptide, (RXRRBR)(2)XB, dramatically improved ATM splicing correction efficiency when conjugated with AMOs, and almost fully corrected aberrant splicing. The restored ATM protein was close to normal levels in cells with homozygous splicing mutations, and a gene dose effect was observed in cells with heterozygous mutations. A significant amount of the ATM protein was still detected 21 days after a single 5 µm treatment. Systemic administration of an fluorescein isothiocyanate-labeled (RXRRBR)(2)XB-AMO in mice showed efficient uptake in the brain. Fluorescence was evident in Purkinje cells after a single intravenous injection of 60 mg/kg. Furthermore, multiple injections significantly increased uptake in all areas of the brain, notably in cerebellum and Purkinje cells, and showed no apparent signs of toxicity. Taken together, these results highlight the therapeutic potential of (RXRRBR)(2)XB-AMOs in A-T and other neurogenetic disorders.