gebhart/patrepeval huggingface dataset:
Direct Expression and Validation of Phage-selected Peptide Variants in Mammalian Cells (2013)

Phage display is a key technology for the identification and maturation of high affinity peptides, antibodies, and other proteins. However, limitations of bacterial expression restrict the range and sensitivity of assays that can be used to evaluate phage-selected variants. To address this problem, selected genes are typically transferred to mammalian expression vectors, a major rate-limiting step in the iterative improvement of peptides and proteins. Here we describe a system that combines phage display and efficient mammalian expression in a single vector, pDQ1. This system permits immediate expression of phage-selected genes as IgG1-Fc fusions in mammalian cells, facilitating the rapid, sensitive characterization of a large number of library outputs for their biochemical and functional properties. We demonstrate the utility of this system by improving the ability of a CD4-mimetic peptide to bind the HIV-1 envelope glycoprotein and neutralize HIV-1 entry. We further improved the potency of the resulting peptide, CD4mim6, by limiting its ability to induce the CD4-bound conformation of the envelope glycoprotein. Thus, CD4mim6 and its variants can be used to investigate the properties of the HIV-1 envelope glycoprotein, and pDQ1 can accelerate the discovery of new peptides and proteins through phage display.
Intrinsic Tryptophan Fluorescence of Equinatoxin II, a Pore‐Forming Polypeptide from the Sea Anemone <i>Actinia Equina</i> L, Monitors its Interaction with Lipid Membranes (1995)

Equinatoxin II is a cytolytic polypeptide from the sea anemone Actinia equina L. which forms pores in natural and artificial membranes. The intrinsic fluorescence of its five tryptophanyl residues was used to monitor the conformational changes induced by denaturing agents, pH and lipids. In the presence of denaturants, the emitted fluorescence peak, normally occurring at 335 nm, was reduced in height by about 65% and red-shifted to 354 nm indicating unfolding. The toxin fluorescence intensity reversibly decreased by increasing the pH, whereas lipid vesicles, at every pH, caused an increase and a blue shift. The amount of toxin binding to the lipid vesicle was increased by the presence of sphingomyelin. With sphingomyelin-containing vesicles half-saturation occurred at a lipid/toxin molar ratio of about 40, whereas with phosphatidylcholine no saturation appeared up to a ratio of 300. One hydrophilic neutral quencher (acrylamide) and two lipid-confined phosphatidyltype quenchers [bis(9,10-dibromostearoyl)-sn-glycero-3-phosphocholine and 1-palmitoyl-2-(1-pyrenedecanoyl)-sn-glycero-3-phosphocholine] were used to assess the exposure of the emitting centres to the solvent and/or to the lipid. Most of the indolyl residues were found to be solvent-exposed in the water-soluble form of the toxin, as inferred from acrylamide quenching. Upon association with lipid vesicles, the fraction accessible to acrylamide dropped considerably, meanwhile the toxin became sensitive to lipid-soluble quenchers. Taken together these results suggest that insertion of equinatoxin II into sphingomyelin-containing bilayers is facilitated by high pH and results in the transfer of one or more exposed tryptophanyl residues into the liquid phase. Calcein-loaded vesicles, with or without a lipid quencher, were used to monitor simultaneously the formation of pores and the transfer of the tryptophans to the lipid phase. We found that the rate constants for vesicles permeabilization and for changes of intrinsic tryptophanyl fluorescence had a different dependence on the lipid/toxin ratio suggesting they correspond to separate steps in the toxin lipid interaction.
Sensitivity of patients with painful temporomandibular disorders to experimentally evoked pain: evidence for altered temporal summation of pain (1998)

Temporomandibular disorders (TMD) represent a group of chronic painful conditions involving the muscles of mastication and the temporomandibular joint. Several studies have reported that TMD is associated with enhanced sensitivity to experimental pain. Twenty-three TMD subjects and 24 pain-free matched control subjects participated in a set of studies which were designed to evaluate whether the temporal integrative aspects of thermal pain perception are altered in TMD patients compared with control subjects. Specifically, we have examined in both TMD patients and in age- and gender-matched control subjects: (1) the time-course and magnitude of perceived pain evoked by the application of sustained 7-s noxious thermal stimuli (45-48 degrees C) to the face and forearm, (2) the central summation of C-fiber-mediated pain produced by applying brief trains of noxious heat pulses to the skin overlying the ventral aspect of the right palm and (3) the ability to discriminate small increments in noxious heat applied to facial and volar forearm skin. Data collected from these studies indicate that TMD patients show enhanced temporal integration of thermal pain compared with control subjects. TMD patients show greater thermal C-fiber-mediated temporal summation than pain-free subjects and they report a greater magnitude of sustained noxious heat pulses applied to either the face or the forearm than control subjects. In contrast to these findings, TMD and pain-free subjects are equally able to discriminate and detect small increments of heat applied to noxious adapting temperatures. These findings suggest that the augmented temporal integration of noxious stimuli may result from alterations in central nervous system processes which contribute to the enhanced pain sensitivity observed in TMD patients.
An image embedding in image by a complexity based region segmentation method (2002)

This paper describes a new technique to embed secret data into a dummy image by using image segmentation based on a local complexity measure. The key idea to this approach is that a binary image can be categorized as "informative" and "noise-like" regions which are segmented by a "complexity measure". If the embedding data is noise-like, we can hide it in the noise-like region of the dummy image. If a part of embedding data is simple, then we apply "image conjugate" operation to it. This operation transform a simple pattern into a complex pattern. In our experiment, we could embed two color images in a 512/spl times/512 (8 bits/pixel) size gray image (which was dummy) without losing any information. The total amount of the two embedded images was 115 KB, which was about 45% of the dummy image.
A role for the CPF 3′-end processing machinery in RNAP II-dependent gene looping (2005)

The prevailing view of the RNA polymerase II (RNAP II) transcription cycle is that RNAP II is recruited to the promoter, transcribes a linear DNA template, then terminates transcription and dissociates from the template. Subsequent rounds of transcription are thought to require de novo recruitment of RNAP II to the promoter. Several recent findings, including physical interaction of 3'-end processing factors with both promoter and terminator regions, challenge this concept. Here we report a physical association of promoter and terminator regions of the yeast BUD3 and SEN1 genes. These interactions are transcription-dependent, require the Ssu72 and Pta1 components of the CPF 3'-end processing complex, and require the phosphatase activity of Ssu72. We propose a model for RNAP II transcription in which promoter and terminator regions are juxtaposed, and that the resulting gene loops facilitate transcription reinitiation by the same molecule of RNAP II in a manner dependent upon Ssu72-mediated CTD dephosphorylation.
20th-century microtonal notation (1990)

Prelude The Notation of Quarter and Three-Quarter Tones The Notation of Eighth and Sixteenth Tones The Notation of Third, Sixth, and Twelfth-Tones The Notation of Fifth-Tones and the 31-Tone Scale The Notation of Extended and Compressed Microtonal Scales Postlude Bibliography Index
A Study on the Characteristics of Fast Distributed Power Control Schemes in Cellular Network under Dynamic Channel (2008)

To address the convergence issue of power control algorithms, a number of algorithms have been developed hat shape the dynamics of up-link power control for cellular network. Power algorithms based on fixed point iterations can be accelerated by the use of various methods, one of the simplest being the use of Newton iterations, however, this method has the disadvantage which not only needs derivatives of the cost function but also may be weak to noisy environment. we showed performance of the power control schemes to solve the fixed point problem under static or stationary channel. They proved goof performance to solve the fixed point problem due to their predictor based optimal control and quadratic convergence rate. Here, we apply the proposed power control schemes to the problem of the dynamic channel or to dynamic time varying link gains. The rigorous simulation results demonstrated the validity of our approach.
Deterministic aperiodic arrays of metal nanoparticles for surface-enhanced Raman scattering (SERS) (2009)

Deterministic Aperiodic (DA) arrays of gold (Au) nanoparticles are proposed as a novel approach for the engineering of reproducible surface enhanced Raman scattering (SERS) substrates. A set of DA and periodic arrays of cylindrical and triangular Au nanoparticles with diameters ranging between 50-110 nm and inter-particle separations between 25-100 nm were fabricated by e-beam lithography on quartz substrates. Using a molecular monolayer of pMA (p-mercaptoaniline) as a Raman reporter, we show that higher values of SERS enhancement factors can be achieved in DA structures compared to their periodic counterparts, and discuss the specific scaling rules of DA arrays with different morphologies. Electromagnetic field calculations based on the semi-analytical generalized Mie theory (GMT) fully support our findings and demonstrate the importance of morphology-dependent diffractive coupling (long-range interactions) for the engineering of the SERS response of DA arrays. Finally, we discuss optimization strategies based on the control of particles sizes and shapes, and we demonstrate that spatially-averaged SERS enhancement factors of the order of approximately 10(7) can be reproducibly obtained using DA arrays of Au nano-triangles. The ability to rigorously design lithographically fabricated DA arrays of metal nanoparticles enables the optimization and control of highly localized plasmonic fields for a variety of chip-scale devices, such as more reproducible SERS substrates, label-free bio-sensors and non-linear elements for nano-plasmonics.
Laboratory animals in vaccine production and control: Replacement, reduction and refinement (1988)

9. REFERENCES 90 CHAPTER 9: OPPORTUNITIES FOR REPLACEMENT, REDUCTION AND REFINEMENT: HUMAN VIRAL VACCINES 93 1. INTRODUCTION 93 2. TESTS FOR EXTRANEOUS MICROORGANISMS 94 3. MUMPS VACCINE . . . 94 4. HEPATITIS B VACCINE 95 4. 1. Test for freedom from live hepatitis virus 95 4. 2. Potency test 95 5. INFLUENZA VACCINE 96 5. 1. Potency test 96 5. 2. Abnormal-toxicity test 96 6. MEASLES VACCINE. . . . . 96 6. 1. Tests for extraneous agents 97 6. 1. 1. Test for Mycobacterium tuberculosis 97 6. 1. 2. Test for extraneous viruses 97 6. 2. Abnormal-toxicity test 98 7. POLIOMYELITIS VACCINE. . . 99 7. A. Inactivated poliomyelitis vaccine 99 7. A. l. Production. . . . . . 99 7. A. 2. Test for residual live virus 99 7. A. 3. Tests for extraneous agents 100 7. A. 3. l. Test for Mycobacterium tuberculosis . . . . . 100 7. A. 3. 2. Test for extraneous viruses 100 7. A. 4. Tumourigenicity test. . . . . 100 XII 7 . A. 5. Potency test . . . . . . . 101 7. A. 6. Test for abnormal toxicity 102 7. B. Live, oral poliomyelitis vaccine 103 7. B. l. Test for extraneous agents 103 7. B. 2. Test for neurovirulence 105 7. B. 3. Test for abnormal toxicity 106 8. RABIES VACCINE 106 8. 1. Production 106 8. 2. Test for residual live virus 107 8. 3. Tests for extraneous microorganisms 107 8. 3. 1. Test for Mycobacterium tuberculosis 107 8. 3. 2. Tests for extraneous viruses 108 8. 3. 2. 1. In dogs 108 8. 3. 2. 2.
Production of micron‐size monodisperse polymer particles by seeded polymerization utilizing dynamic swelling method with cooling process (1993)

Abstract Monodisperse polystyrene particles (6.6 μm diameter) were produced by seeded polymerization utilizing the dynamic swelling method with cooling process as follows. Monodisperse polystyrene seed particles (1.8 μm diameter) were dispersed in ethanol/water (3/4 w/w) medium containing styrene monomer, benzoyl peroxide as initiator and poly(vinyl alcohol) as stabilizer at 65d̀C. By lowering the temperature to −5d̀C at a speed of −1d̀C/min the polystyrene seed particles were swollen from 1.8 to 7.7 μm by the absorption of styrene monomer, keeping the high monodispersity. An appropriate amount of water was then added to the dispersion at −5d̀C to depress the redissolution of styrene from the swollen particles into the medium. By elevating the temperature the seeded polymerization was carried out at 70d̀C. The production of submicron‐size polystyrene new particles as a by‐product was depressed by the addition of NaNO 2 to the medium.
Protocols for Neural Cell Culture (2009)

Since the conception of this acclaimed series of volumes examining neural tissue culture, the expansion of neuroscience has continued to produce vital discoveries that utilize tissue culture methodologies. The expert contributors to the fourth edition of Protocols for Neural Cell Culture refine existing protocols and present the emerging new techniques and culture media formulations linked with the many advances in neuroscience. While highlighting updated experimental procedures for many of the classical neural tissue culture preps, the volume addresses topics such as regenerative medicine and the methods to grow and expand embryonic and adult neural stem cells. Essential techniques for the isolation, expansion, and cryopreservation of neural tissue from mouse, rat, and human sources are covered, as well as methods to assess aspects of cell function (calcium imaging) and cell death. With its detailed, step-by-step laboratory protocols, this volume provides the kind of detailed description and implementation advice that is crucial for getting optimal results. Authoritative and cutting-edge, Protocols for Neural Cell Culture, Fourth Edition continues the previous editions’ tradition of exceptional quality and thorough coverage in tissue culture protocols for today’s neuroscience in order to inspire researchers in the field to further explore this imperative area of study
The Sixth Transmembrane Domains of the Human B1 and B2 Bradykinin Receptors Are Structurally Compatible and Involved in Discriminating between Subtype-selective Agonists (1997)

In order to investigate the molecular basis for the ability of the human B1 and B2 bradykinin (BK) receptor subtypes to discriminate between subtype-selective ligands, we constructed chimeric proteins in which the sixth transmembrane domains (TM-VI) of these receptors were exchanged. The pharmacological profiles of the constructs were analyzed by radioligand binding in particulate preparations of transiently transfected HEK293 cells using the agonist [3H]des-Arg10-kallidin and the antagonist [3H]NPC17731. The ability of these constructs to transmit an intracellular signal was measured in transiently transfected A10 cells, a vascular smooth muscle cell line, by single cell Ca2+ imaging. Substitution of B1 TM-VI into the B2 receptor (B2(B1VI)) dramatically reduced the affinity of the B2-selective agonist BK, whereas the affinity of the B2-selective antagonist NPC17731 was unaltered. High affinity BK binding was fully regained when two residues, Tyr259 and Ala263, near the extracellular surface of TM-VI in B2(B1VI), were replaced with the corresponding residues in the wild-type B2 receptor, which are Phe259 and Thr263. The construct B1(B2VI), produced by substitution of B2 TM-VI into the B1 receptor, did not support high affinity binding of the B1-selective agonist des-Arg10-kallidin. In contrast to BK and des-Arg10-kallidin, the binding of the less subtype-selective agonist kallidin showed little sensitivity to TM-VI exchange. These results show that TM-VI in the human B1 and B2 BK receptor subtypes, although only 36% identical, are structurally compatible. Furthermore, this domain contributes significantly to the ability of these receptors to discriminate between the subtype-selective agonists BK and des-Arg10-kallidin.
Growth of Clinical Isolates of Astro Virus in a Cell Line and the Preparation of Viral RNA (1991)

Astroviruses from three sources, (1) of human origin, adapted to cell culture growth by passage in primary tissue and (2) direct from faeces; (3) of lamb origin, from gut epithelium scrapings were processed to extract the RNA. The first two of these were also compared in their growth on LLCMK2 and Caco-2 cell lines. Virus was successfully isolated direct from faeces in the latter line, though it failed to grow in LLCMK2. Previously adapted virus continued to grow well in both lines. RNA was extracted from the ovine virus in a condition which permitted the production of cDNA grior to cloning, but the RNA from the human astroviruses was more refractory to extraction owing to its aggregation with cell debris.
NEAR &#x2014; Network extractor of anomaly records or traffic split-counting for anomaly detection (2013)

The availability of network communications may be affected or even disrupted by malicious actions or by unexpected usage conditions. The good health of systems connected to the network (or lack thereof) may also reflect on network usage patterns. In order to maintain proper functionality for a significantly large network domain, automated or semi-automated methods of anomaly detection are required and several systems have been developed so far. This paper presents NEAR, the feature collection part of such a system, aiming to detect abnormal conditions by collecting relevant traffic features in key points of the network before analyzing them using signal processing methods.
Electrical Breakdown Strength of Alumina at High Temperatures (1981)

The dc electrical strength of sapphire and poly crystalline alumina was studied up to 1400°C. The electrical strength was essentially identical for both materials. It was > 10 6 V/cm at room temperature and decreased gradually with temperature up to 900°C (2.6×10 5 V/ cm), then dropped rapidly to 2×10 4 V/cm at 1400°C for a sample thickness of ∼ 100 μm. The electrical strength decreased with the sample thickness. It was inversely proportional to the thickness for samples thicker than ∼ 600 μm at 1200°C. The breakdown behavior was explained on the basis of a thermal breakdown model.
EEG-based assessment of video and in-game learning (2013)

People often learn game-related information in video games by taking turns playing and watching each other play. This type of in-game learning involves both observation and imitation of actions. However, games are also made to be learnt individually during gameplay. Our study seeks to assess which is more effective for learning: just playing a game yourself or watching somebody play it first. We compare two gameplay situations: playing a digital game before watching a game-play video and playing a digital game after watching a gameplay video. Using a between-participants design, to measure learning effectiveness we recorded Mu rhythms, which are indirectly linked to mirror neuron activation during imitation learning. We also analyze hemispheric frontal alpha asymmetry. Our results indicate that presentation order of the video game matters and players are more aroused when watching a gameplay video before playing.
The Impact of Cost Stickiness on Audit Pricing (2019)

This study investigates the impact of the cost stickiness on audit pricing. The author finds that the company’s asymmetric cost behavior, cost stickiness, is one of the important determinants of the audit pricing. The test results exhibit that firm’s cost stickiness driven by empire building incentives is positively associated with the audit fees, and it has an incremental effect on the audit fees compared to “Future Expectation” group. It implicates that auditors recognize cost stickiness as audit risk, but they price cost stickiness discriminately according to the motives.
Efficient Data Replication Scheme based on Hadoop Distributed File System (2015)

Hadoop distributed file system (HDFS) is designed to store huge data set reliably, has been widely used for processing massive-scale data in parallel. In HDFS, the data locality problem is one of critical problem that causes the performance decrement of a file system. To solve the data locality problem, we propose an efficient data replication scheme based on access count prediction in a Hadoop framework. By the previous data access count, the existing data replication scheme predicts the next access count of data files using Lagrange’s interpolation. Then, the proposed data replication scheme determines the replication factor with the predicted data access count, whether it generates a new replica or it uses the loaded data as cache selectively. Finally, the proposed scheme provides improvement of data locality. By performance evaluation, proposed efficient data replication scheme is compared with default data replication setting of Hadoop that shows proposed scheme reduces averagely 8.9% of the task completion time in the map phase. Regarding the data locality, proposed scheme provides the increase of node locality by 6.6% and the decrease of rack and rack-off locality by 38.9% and 56.5%.
Synthesis, Structure, and Density Functional Theory Analysis of a Scandium Dinitrogen Complex, [(C<sub>5</sub>Me<sub>4</sub>H)<sub>2</sub>Sc]<sub>2</sub>(μ-η<sup>2</sup>:η<sup>2</sup>-N<sub>2</sub>) (2010)

Investigation of the bis(tetramethylcyclopentadienyl) metallocene chemistry of scandium has revealed that the method involving reduction of trivalent salts with alkali metals used with lanthanides can also be applied to scandium to make a dinitrogen complex of the first member of the transition metal series. ScCl(3) reacts with 2 equiv of KC(5)Me(4)H to form (C(5)Me(4)H)(2)ScCl(THF), 1, which reacts with allylmagnesium chloride to make (C(5)Me(4)H)(2)Sc(eta(3)-C(3)H(5)), 2. Complex 2 reacts with [HNEt(3)][BPh(4)] to yield [(C(5)Me(4)H)(2)Sc][(mu-Ph)BPh(3)], 3, which has just one primary Sc-C(phenyl) contact connecting the tetraphenylborate anion and the metallocene cation. Treatment of 3 with KC(8) in THF under N(2) generates [(C(5)Me(4)H)(2)Sc](2)(mu-eta(2):eta(2)-N(2)), which has a coplanar arrangement of scandium and nitrogen atoms within a square planar array of tetramethylcyclopentadienyl rings. Density functional calculations explain the bonding that results in the 1.239(3) A N-N bond distance in the (N=N)(2-) moiety.
<i>In Vivo</i> Visualization of Senile‐Plaque‐Like Pathology in Alzheimer's Disease Patients by MR Microscopy on a 7T System (2007)

Although the precise mechanisms leading to the higher susceptibility rendering SP-like pathology observable within the cortical mantle are not totally understood, the study unambiguously demonstrated that MR microscopy is capable of directly visualizing cortical pathology in AD patients in vivo.