gebhart/patrepeval huggingface dataset:
Plasmonic AuNP/g-C<sub>3</sub>N<sub>4</sub>Nanohybrid-based Photoelectrochemical Sensing Platform for Ultrasensitive Monitoring of Polynucleotide Kinase Activity Accompanying DNAzyme-Catalyzed Precipitation Amplification (2015)

A convenient and feasible photoelectrochemical (PEC) sensing platform based on gold nanoparticles-decorated g-C3N4 nanosheets (AuNP/g-C3N4) was designed for highly sensitive monitoring of T4 polynucleotide kinase (PNK) activity, using DNAzyme-mediated catalytic precipitation amplification. To realize our design, the AuNP/g-C3N4 nanohybrid was initially synthesized through in situ reduction of Au(III) on the g-C3N4 nanosheets, which was utilized for the immobilization of hairpin DNA1 (HP1) on the sensing interface. Thereafter, a target-induced isothermal amplification was automatically carried out on hairpin DNA2 (HP2) in the solution phase through PNK-catalyzed 5'-phosphorylation accompanying formation of numerous trigger DNA fragments, which could induce generation of hemin/G-quadruplex-based DNAzyme on hairpin DNA1. Subsequently, the DNAzyme could catalyze the 4-chloro-1-naphthol (4-CN) oxidation to produce an insoluble precipitation on the AuNP/g-C3N4 surface, thereby resulting in the local alternation of the photocurrent. Experimental results revealed that introduction of AuNP on the g-C3N4 could cause a ∼100% increase in the photocurrent because of surface plasmon resonance-enhanced light harvesting and separation of photogenerated e-/h+ pairs. Under the optimal conditions, the percentage of photocurrent decrement (ΔI/I0, relative to background signal) increased with the increasing PNK activity in a dynamic working range from 2 to 100 mU mL(-1) with a low detection limit (LOD) of 1.0 mU mL(-1). The inhibition effect of adenosine diphosphate also received a good performance in PNK inhibitor screening research, thereby providing a useful scheme for practical use in quantitative PNK activity assay for life science and biological research.
Synthesis, spectral studies and antimicrobial activity of 7-chloro-2-alkyl/ aryl-4-alkyl/aryl-3- arylidene-3H-1,5- benzodiazepines (2007)

Condensation of various β-dikelones 2 with appropriate araldehydes 1 in the presence of piperidene has afforded 2-arylidene-1,3-diketones 3 which in turn on condensation with 4-chloro-1,2-phenylene diamine in acidic medium give a series of 7-chloro-2-alkyl / aryl-4-alkyl / aryl-3-arylidene-3H-1,5-bcnzodiazc-pines 5a-j. All the newly synthesized compounds arc characterized on the basis of their spectral (IR, 'H NMR, Mass) and analytical data. Representative compounds have been screened for their antibacterial and antifungal activities. Some of the compounds have been found to exhibit promising antibacterial and antifungal activities.
Soluble CD4-PE40 Is Cytotoxic for a Transfected Mammalian Cell Line Stably Expressing the Envelope Protein of Human Immunodeficiency Virus (HIV-1), and Cytotoxicity Is Variably Inhibited by the Sera of HIV-1-Infected Patients (1991)

Sera were obtained from 50 individuals infected with human immunodeficiency virus type 1 or from HIV-1-uninfected individuals before or after vaccination with recombinant gp160. These sera were evaluated for activity antagonistic to the cell-killing activity of the chimeric Pseudomonas exotoxin hybrid protein, sCD4-PE40. For these studies, Chinese hamster ovary (CHO) cells were transfected with a chimeric plasmid encoding the tat, rev, and envelope genes of HIV-1 and a cell line was selected for stable expression of the envelope glycoproteins at the cell surface (CHO-env). Cytotoxicity of sCD4-PE40 for CHO-env in the presence or absence of added human serum was quantitated spectrophometrically following enzymatic reduction of a tetrazolium bromide within the mitochondria of viable cells (MTT assay). Several HIV+ sera inhibited the cytotoxic activity of sCD4-PE40; the antagonist had properties consistent with those of immunoglobulins in that it was heat stable, absorbed by protein A, and reversible by increasing the concentration of sCD4-PE40. Of 15 HIV+ sera which strongly reacted with gp120, 11 (73%) also potently inhibited sCD4-PE40 cytotoxicity, and cytotoxicity was inhibited by sera from some HIV- individuals after, but not before, immunization with gp160. These data suggested a role for antibody to gp120 in the antagonistic activity. However, not all sera with antibody to gp120 antagonized sCD4-PE40 cytotoxicity and high levels of antagonist activity were frequently (40%) found in HIV+ sera lacking immunoblot-detectable antibody to gp120, or antibody to either CD4 or PE40. Grouping of the HIV+ sera according to the patients' absolute number of CD4+ cells revealed that the degree of inhibition of sCD4-PE40 cytotoxicity approached a Gaussian distribution, suggesting that persons with CD4+ cell counts between 200 and 700/mm3 may be more likely to possess significant levels of serum antagonist. This data have implications for the clinical development of sCD4-PE40 or other sCD4-based therapeutics in the management of HIV-1 infection.
Performance Analysis of Protocol Stack for Inter-Processor Ethernet Communication in Automotive Industry (2018)

In modern cars, Electronic Control Units (ECUs) can have more than one CPU which can exchange data over built-in communication network. Since majority of these ECUs can be categorized as real-time system, special attention should be given to the communication performance between processors. In this paper, analysis of TCP/IP protocol stack for 100 Base-TX Ethernet used for Inter-Processor communication for a specific system on a chip is given. The analysis is performed regarding throughput, goodput and latency from application layer using a test application. On the transport layer UDP was used. The obtained results revealed the impact of the Linux scheduler on the performance of data sending. Apart from that, an optimal packet size was determined by taking into account obtained latency and throughput.
The Function of Olfactory Input in Pigeon Orientation: Does it Provide Navigational Information or Play Another Role? (1996)

In 1972, Papi and his colleagues reported that anosmic pigeons were severely impaired in orientation and homing performance. This observation was followed up in a series of experiments involving numerous elaborate experimental manipulations. On the basis of their results, the hypothesis of olfactory navigation was proposed. Attempts to replicate these findings at other lofts produced widely differing effects, which suggested a highly variable role of olfaction. However, meteorological data, as well as certain other aspects of the findings, throw doubt on the role of odours as navigational cues. (1) Odours of the required characteristics and distribution do not seem to exist. (2) Some effects of 'olfactory' manipulations do not seem to depend on the availability of odours. (3) Olfactory treatments proved mostly effective, but often the effect was not as predicted. In view of these findings, explanations other than olfactory orientation cannot be excluded; accepting olfactory input as navigational information seems premature. Some of the findings are in agreement with the assumption that olfactory manipulations impair the birds' general processing and integration of information in some unknown way.
Induction of Apoptosis by Protein Inhibitor of Activated Stat1 through c-Jun NH2-terminal Kinase Activation (2001)

Members of the protein inhibitor of activated signal transducer and activator of transcription (STAT) family (PIAS family) of proteins act as negative regulators of STATs in cytokine signaling. We report here that PIAS proteins have proapoptotic activity. PIAS1 induced apoptosis in both human 293T cells and human osteosarcoma U2OS cells. PIAS1 is localized in the nucleus as distinct nuclear dots. Ectopic expression of PIAS1 in U2OS cells activated JNK1 (c-Jun NH(2)-terminal kinase). A dominant-negative JNK1, capable of inhibiting PIAS1-induced JNK1 activation, blocked PIAS1-mediated apoptosis. Furthermore, a mutant PIAS1, lacking the first 9 amino acid residues, failed to repress Stat1-mediated gene activation although it retained its ability to activate JNK and to trigger apoptosis. Our results identify a novel function of PIAS1 in the induction of JNK-dependent apoptosis, independent of the previously known inhibitory activity of PIAS1 in STAT-mediated gene activation.
The Influence of Luting Systems on the Microtensile Bond Strength of Dentin to Indirect Resin-based Composite and Ceramic Restorations (2009)

Microtensile bond strength (microTBS) evaluation and fractographic analysis were used to compare four luting systems in the cementation of resin-based composite (RBC) and ceramic disks to dentin. Forty freshly-extracted molars were transversally sectioned to expose flat, deep dentin surfaces. Forty cylindrical specimens (5-mm diameter and 10-mm height), consisting of 20 RBC disks and 20 leucite-based glass ceramic disks, were produced. The RBC disks were sandblasted with 50-microm Al2O3. The ceramic disks were conditioned with 9.5% hydrofluoric acid gel and silane application. All the disks were then bonded to dentin surfaces according to the luting cements to be used: two etch-and-rinse luting agents (XP bond/CoreXFlow; Dentsply [XP]) (Enabond/EnaCem HF; Micerium [ENA]), a self-etch luting system (ED Primer II A+B/Panavia F2.0; Kuraray-Dental [PAN]) and a self-adhesive luting agent (RelyX Unicem; 3M ESPE [UNI]). The adhesive/luting cement systems were applied according to the manufacturers' instructions. The specimens were sectioned perpendicular to the adhesive interface to produce multiple beams, approximately 1 mm2 in area. All the specimen preparations were performed by the same operator. The beams were tested under tension at a crosshead speed of 0.5 mm/minute until failure. The microTBS data were analyzed by two different one-way-ANOVA and multiple comparison Tukey tests (alpha = 0.05). All the fractured beams were observed using a Scanning Electron Microscope (SEM) at 200x magnification for fracture mode determination. The mean bond strength in MPa (SD) for the RBC (Co) and ceramic (Ce) groups were: XP-Co = 31.39 (13.51), ENA-Co = 30.93 (10.17), PAN-Co = 18.29 (10.02), UNI-Co = 19.33 (7.91); XP-Ce = 4.83 (1.86), ENA-Ce = 5.15 (1.66), PAN-Ce = 4.36 (1.80), UNI-Ce = 7.16 (2.52). Statistical analysis showed that the bond strengths were significantly affected by the luting agent employed for both the RBC and ceramic groups (p<0.001). In particular, the XP-Co group and the ENA-Co group did not differ from each other (p > 0.05) and showed significantly higher bond strengths than the PAN-Co and UNI-Co groups (p < 0.05). On the contrary, the UNI-Ce group showed the highest bond strengths compared to the other ceramic experimental groups (p < 0.05). Regarding failure mode, differences were found between the RBC groups: for the etch-and-rinse luting systems (XP-Co and ENA-Co groups), most failures occurred cohesively in the luting agent, while the self-etch luting system (PAN-Co group) and self-adhesive luting system (UNI-Co group) failed predominantly adhesively at the luting agent-dentin interface. Little differences were found between the ceramic groups, where failure type was primarily adhesive between cement and ceramic.
Inclusion of Thermal Motion in Crystallographic Structures by Restrained Molecular Dynamics (1990)

A protein crystal structure is usually described by one single structure, which largely omits the dynamical behavior of the molecule. A molecular dynamics method with a time-averaged crystallographic restraint was used to overcome this limitation. This method yields an ensemble of structures in which all possible thermal motions are allowed, that is, in additional to isotropic distributions, anisotropic and anharmonic positional distributions occur as well. In the case of bovine pancreatic phospholipase A2, this description markedly improves agreement with the observed x-ray diffraction data compared to the results of the classical one-model structure description. Time-averaged crystallographically restrained molecular dynamics reveals large mobilities in the loops involved in lipid bilayer association.
An Energy-efficiency and Collision-free MAC Protocol for Wireless Sensor Networks (2005)

This paper presents a TDMA-based medium-access control (MAC) protocol designed for wireless sensor networks, which aims at the primary goal of energy-efficient. In this protocol, through broadcasting control messages in their own scheduled slots, sensor nodes optimize the allocation of control-slots and adapt the size of control sub-frame in a distributed way, and reserve data-slots for data-packets to their one-hop neighbors. In addition, sleeping mechanism and power control technique are used to reduce energy-consumption.
Phase Separation of Polyfluorene‐Based Blend Films and Its Influence on Device Operations (2006)

Vertical phase separations have been found in blend films (TFB:F8BT) of polymer light-emitting diodes, giving rise to better device performances. A TFB wetting layer is present over most of the bottom interface with the substrate, as evidenced by the fluorescent microscopy images after top layers are etched away by oxygen plasma (see figure).
Nature of ligand affinity and dimerization of corticotrophin-releasing factor-binding protein may be detected by circular dichroism (1996)

As the association of corticotrophin-releasing factor (CRF) with its binding protein (BP) to form a dimer complex (CRF2/BP2) appears to be dependent on the nature of the ligand we have compared the circular dichroism difference spectra after association of the BP with ovine (o) CRF, human (h) CRF and the alpha-helical CRF (9-41) antagonist. All three ligands caused a negative change in molar ellipticity above 210 nm, with oCRF having the least and hCRF the greatest effect. Below 210 nm there was a marked divergence of difference spectra, with the reaction with the natural peptides, hCRF and oCRF, resulting in a positive change in ellipticity, whilst that with the antagonist produced a negative change. In view of the BP spectrum indicating predominantly beta-sheet and the peptides showing mainly alpha-helix these results were interpreted as the changes above 210 nm being due to dimerization and below 210 nm to a change in the conformation of ligand on binding. The opposite change in alpha-helicity of the antagonist observed on binding compared with the two natural CRF peptides could have fundamental pharmacological implications.
Concept of modes in optics and photonics (2000)

The concept of modes, or eigenfunctions, is fundamental for all wave phenomena in physics like optics, acoustics and quantum mechanics. In optics and photonics, the concept of modes is well suited to describe emission and absorption, coherence and interference, propagation and dispersion. The concept of modes consists of two aspects: first, the modes are solutions for the propagation of the light; second, the number of photons int he different modes describes the transport of energy or information. The energy density of the black body radiation, given by Planck's law, is the production of the density of modes in free space and the average number of photons per mode, given by the Bose- Einstein distribution. The transverse shape of the modes is determined by diffraction and boundary conditions. The longitudinal extension is given by the coherence length.
Motion-corrected 3D whole-heart water-fat high-resolution late gadolinium enhancement cardiovascular magnetic resonance imaging (2020)

A novel framework for motion-corrected whole-heart 3D water/fat LGE imaging has been introduced. The method was validated in patients with known or suspected cardiovascular disease, showing good agreement with conventional breath-held 2D LGE imaging, but offering higher spatial resolution, improved volumetric coverage and good image quality from a free-breathing acquisition with 100% scan efficiency and predictable scan time.
Development of ability to penetrate the cumulus oophorus by hamster spermatozoa capacitated in vitro, in relation to the timing of the acrosome reaction (1986)

Abstract Hamster spermatozoa were tested for their ability to penetrate the intact cumulus matrix at low sperm:egg ratios (approximately 3:1). Uncapacitated spermatozoa attached to the surface of the cumulus and could not penetrate. Spermatozoa capacitated in vitro began to be able to penetrate after about 2 hr of preincubation, coincidentally with the first appearance of hyperactivation and spontaneous acrosome reactions. In all, 628 in vitro incubated spermatozoa were evaluated on and in cumuli: 270 could penetrate, but only ten of these were judged to have intact, “unmodified” acrosomes. Almost all spermatozoa capable of penetrating showed optically “modified” and swelling acrosomal caps, and this confirms previous observations on cumulus penetration in vivo. Penetration appeared limited to a phase in capacitation prior to completion of the acrosome reaction, as spermatozoa that had lost the acrosomal cap penetrated poorly and showed reduced viability. Penetration of the cumulus was inhibited by the hyaluronidase inhibitor sodium aurothiomalate. Cumulus penetrating ability could result either from a change in surface properties of the sperm at capacitation, which renders them less “sticky” to the matrix, or from release or activation of a “cumulus lysin.” We conclude that the ability to enter the cumulus matrix coincides with physiological changes in spermatozoa that occur during a terminal phase of capacitation preceding complete loss of the acrosomal cap, and that initiation of this process in vivo must precede sperm‐zona contact.
James E. Brookshire (2017)

James E. Brookshire currently serves as the Executive Director of the Federal Circuit Bar Association.
Chemical modification of Torpedo acetylcholinesterase by disulfides: appearance of a "molten globule" state (1992)

Modification of Torpedo californica acetylcholinesterase (AChE) both by bis(1-oxy-2,2,5,5-tetramethyl-3-imidazolin-4-yl)disulfide (biradical) and by 4,4'-dithiopyridine, via a thiol-disulfide exchange reaction, was monitored by EPR and optical spectroscopy, respectively. Incubation with these reagents caused complete loss of enzymic activity. Treatment with glutathione of AChE modified by either of the two disulfides led to rapid release of the bound reagent with simultaneous regeneration of the single free thiol group of the enzyme. However, no concomitant recovery of catalytic activity was observed. SDS-PAGE showed that both the modified and demodified enzymes retained their structure as a disulfide-linked dimer. Circular dichroism revealed that modification of AChE by the disulfide agents with or without demodification by glutathione led to a complete disappearance of the ellipticity in the near-UV and to a much smaller decrease in ellipticity in the far-UV. The CD spectra observed are typical of the "molten globule" state of proteins. 1-Anilino-8-naphthalenesulfonate binding measurements and an enhanced susceptibility to trypsinolysis supported the supposition that chemical modification had transformed native AChE to a "molten globule".
Multi-Pass and Frame Parallel Algorithms of Motion Estimation in H.264/AVC for Generic GPU (2007)

In this paper, multi-pass and frame parallel algorithms are proposed to accelerate various motion estimation (ME) tools in H.264 with the graphics processing unit (GPU). By the multi-pass method to unroll and rearrange the multiple nested loops, the integer-pel ME can be implemented with two-pass process on GPU. Moreover, fractional ME needs six passes for frame interpolation with six-tap filter and motion vector refinement. Motion estimation with multiple reference frames can be implemented with two-pass process with frame-level parallel scheme by use of SIMD vector operations of GPU. Experimental results show that, compared to implementations with only CPU, about 6 times to 56 times speed-up can be achieved for different ME algorithms.
Failure of Topical Prostaglandin Inhibitors to Improve Wound Healing following Deep Partial-thickness Burns (1983)

The present study was designed to determine the efficacy of topical inhibitors of prostaglandins on wound healing. Two uniform deep partial-thickness burns were inflicted on mirror-image areas of guinea pig backs by an aluminum template heated to 75 degrees C and applied for 10 seconds. Indomethacin was tested extensively in a wide range of concentrations in groups of six or more animals each. The healing rates measured at 21 days postburn showed that topical indomethacin at each concentration tested was not effective for improving wound healing. In fact, the treated sites were consistently worse than the control sites. Moreover, the drug adversely affected the healing process proportional to the concentration and was associated with death, which was related to perforations of the GI tract. Also, the India ink filling in the dermal microcirculation was no better in the experimental wounds than in the controls. The evaluations for hair growth were definitely in favor of the controls. The other tested inhibitors, ibuprofen, flurbiprofen, tolmetin, zomepirac, piroxicam, and dipyridamole, also failed to show any benefit.
Accuracy in the measurement of magnetic fields using nitrogen-vacancy centers in nanodiamonds (2016)

We have measured 10 and 20 mT magnetic fields using NV centers in nanodiamonds and have demonstrated that the accuracy of these measurements is about 20 μT. This value is an order of magnitude larger than the precision defined by random fluctuations in the measurements. The presented analysis indicates that the 20 μT systematic errors at such fields are intrinsic to the nanodiamonds. The possible reason for this error is coupling of NV centers with paramagnetic entities in the nanodiamonds such as other NV centers, C13, and N14 nuclei.
Expression of N-acetylglucosaminyltransferase III in hepatic nodules generated by different models of rat liver carcinogenesis (1989)

Our earlier studies revealed that N-acetylglucosaminyltransferase III (GnTase III), which catalyzes the insertion of a bisecting N-acetylglucosamine (bi-Gn) in the complex-type N-linked glycans of cellular glycoproteins, is present in hepatic nodules promoted by the orotic acid model. Neither the bi-Gn residues nor the activity of GnTase III is detectable in normal livers and in the surrounding non-nodular liver of the rat. The present study was designed to find out whether an expression of activity of GnTase III is a phenotypic property characteristic of hepatic nodules or simply unique to nodules produced by the orotic acid model. Fischer male 344 rats were initiated with two different carcinogens namely 1,2-dimethyl-hydrazine or diethylnitrosamine and promoted by other models such as the resistant hepatocyte model and the choline deficient diet model, in addition to the orotic acid model. The hepatic nodules generated by these three different models and hepatocellular carcinomas exhibited significant levels of activity of GnTase III while non-nodular surrounding liver, regenerating liver after 2/3 partial hepatectomy or livers of age and sex matched control rats, had no detectable activity. The detection of the activity of GnTase III in nodules and in cancer is in agreement with the presence of bi-Gn residues reported in gamma-glutamyltranspeptidase of cancer tissues of rats. These results are consistent with the conclusion that the expression of GnTase III is activated during hepatocarcinogenesis and is not related to any particular initiator or promoter.