gebhart/patrepeval huggingface dataset:
Method for targeting protein destruction by using a ubiquitin-independent, proteasome-mediated degradation pathway (2005)

With the euchromatic portion of several mammalian genomes now sequenced, emphasis has turned to ascertaining the functions of gene products. A method for targeting destruction of selected proteins in mammalian cells is described, based on the ubiquitin-independent mechanism by which ornithine decarboxylase (ODC) is degraded by the 26S proteasome in collaboration with antizyme (AZ). We show that expressing whole proteins, protein domains, or peptide ligands fused to the N terminus of ODC promotes proteasome-dependent degradation of these chimeric fusion proteins and their interacting cellular target proteins. Moreover, the degradation of the interacting (targeted) protein depends on coexpression of AZ in about half of cases, providing an inducible switch for triggering the degradation process. By using 12 pairs of interacting proteins for testing, direct comparisons with several alternative strategies for achieving targeted protein destruction based on the concept of induced ubiquitination revealed advantages of the ODC/AZ system, which does not require posttranslational attachment of ubiquitin to target proteins. As proof of concept, the ODC/AZ system was used to ablate expression of specific endogenous proteins (e.g., TRAF6; Rb), and was shown to create the expected lesions in cellular pathways that require these proteins. Altogether, these findings reveal a strategy for achieving targeted destruction of cellular proteins, thus providing an additional tool for revealing the cellular phenotypes of gene products.
PRODUCTION OF GERMLINE CHIMERIC CHICKENS BY TRANSFER OF CULTURED PRIMORDIAL GERM CELLS (1997)

Primordial germ cells (PGCs) from stage 27 (5.5-day-old) Korean native ogol chicken embryonic germinal ridges were cultured in vitro for 5 days. As in in vivo culture, these cultured PGCs were expected to have already passed beyond the migration stage. Approximately 200 of these PGCs were transferred into 2.5-day-old white leghorn embryonic blood stream, and then the recipient embryos were incubated until hatching. The rate of hatching was 58.8% in the manipulated eggs. Six out of 60 recipients were identified as germline chimeric chickens by their feather colour. The frequency of germline transmission of donor PGCs was 1.3-3.1% regardless of sex. The stage 27 PGCs will be very useful for collecting large numbers of PGCs, handling of exogenous DNA transfection during culture, and for the production of desired transgenic chickens.
Mechanical nonlinear generation with coupled torsional harmonic cantilevers for sensitive and quantitative atomic force microscopy of material characteristics (2005)

Tapping-mode has been the most widely used mode of operation in atomic force microscopy. Recent studies have shown that higher harmonics of the cantilever vibrations carries information about material properties such as stiffness, viscoelasticity or capillary forces. A major problem with higher harmonic imaging is the low signal to noise ratio. Here we present a micromachined cantilever that enhances the signal levels at a particular higher harmonic by 40 dB. We demonstrate that the higher harmonic signal is sensitive to the thickness of an oxide film thermally grown on silicon, and enable mapping of chemical composition variations across a polymer surface.
Serum Ferritin as a Predictor of the Acute Respiratory Distress Syndrome (1997)

We investigated serum ferritin levels as a predictor of the acute respiratory distress syndrome (ARDS) because: (1) proinflammatory cytokines, which are implicated in ARDS, increase ferritin synthesis; and (2) oxidative stress in patients at risk for ARDS might liberate iron from ferritin, accelerating toxic hydroxyl radical (.OH) formation. Serum ferritin levels measured by radioimmunoassay (RIA) were greater in 75 patients at risk for ARDS (women, p < 0.0001; men, p < 0.0001) and 8 patients with ARDS (women, p = 0.001; men, p = 0.0009) than in healthy control subjects. Serum ferritin levels were also greater in female (p = 0.003) and male (p = 0.003) at-risk patients who developed ARDS than in patients who did not develop ARDS. In women, a value exceeding 270 ng/ml predicted ARDS with an 83% sensitivity, 71% specificity, 67% positive, and 86% negative predictive value. In men, a value exceeding 680 ng/ml predicted ARDS with a 60% sensitivity, 90% specificity, 75% positive, and 82% negative predictive value. Serum ferritin levels did not correlate with C-reactive protein levels, were not different in medical or surgical at-risk patients, and were not accounted for by liver disease. Evaluating serum ferritin levels in at-risk patients may help predict the development of ARDS and thereby improve study and treatment of ARDS. Elevated serum ferritin levels may also regulate the participation of iron in the oxidative responses that contribute to ARDS.
Laser scanning endoscope for diagnostic medicine (1990)

A new type of endoscope is being developed which utilizes an optical raster scanning system for imaging through an endoscope. The optical raster scanner utilizes a high speed, multifaceted, rotating polygon mirror system for horizontal deflection, and a slower speed galvanometer driven mirror as the vertical deflection system. When used in combination, the optical raster scanner traces out a raster similar to an electron beam raster used in television systems. This flying spot of light can then be detected by various types of photosensitive detectors to generate a video image of the surface or scene being illuminated by the scanning beam. The optical raster scanner has been coupled to an endoscope. The raster is projected down the endoscope, thereby illuminating the object to be imaged at the distal end of the endoscope. Elemental photodetectors are placed at the distal or proximal end of the endoscope to detect the reflected illumination from the flying spot of light. This time sequenced signal is captured by an image processor for display and processing. This technique offers the possibility for very small diameter endoscopes since illumination channel requirements are eliminated. Using various lasers, very specific spectral selectivity can be achieved to optimum contrast of specific lesions of interest. Using several laser lines, or a white light source, with detectors of specific spectral response, multiple spectrally selected images can be acquired simultaneously. The potential for co-linear therapy delivery while imaging is also possible.
Topology Variation and Loop Structural Homology in Crystal and Simulated Structures of a Bimolecular DNA Quadruplex (2006)

The topology of DNA quadruplexes depends on the nature and number of the nucleotides linking G-quartet motifs. To assess the effects of a three-nucleotide TTT linker, the crystal structure of the DNA sequence d(G(4)T(3)G(4)) has been determined at 1.5 A resolution, together with that of the brominated analogue d(G(4)(Br)UTTG(4)) at 2.4 A resolution. Both sequences form bimolecular intermolecular G-quadruplexes with lateral loops. d(G(4)(Br)UTTG(4)) crystallized in the monoclinic space group P2(1) with three quadruplex molecules in the asymmetric unit, two associating together as a head-to-head stacked dimer, and the third as a single head-to-tail dimer. The head-to-head dimers have two lateral loops on the same G-quadruplex face and form an eight-G-quartet stack, with a linear array of seven K(+) ions between the quartets. d(G(4)T(3)G(4)) crystallized in the orthorhombic space group C222 and has a structure very similar to the head-to-tail dimer in the P2(1) unit cell. The sequence studied here is able to form several different folds; however, all four quadruplexes in the two structures have lateral loops, in contrast to the diagonal loops reported for the analogous quadruplex with T(4) loops. A total of seven independent T(3) loops were observed in the two structures. These can be classified into two discrete conformational classes, suggesting that these represent preferred loop conformations that are independent of crystal-packing forces.
Augmentation of the bactericidal and LPS-neutralizing activities of guinea pig cathelicidin CAP11-derived antimicrobial peptides by amino acid substitutions (2006)

rds antibacterial peptide, Lipopolysaccharide(LPS), cathelicidin, LPS-neutralization, endotoxin Mini Review
Paracrine Regulation of Matrix Metalloproteinase Expression in Endometriosis (2002)

Following retrograde menstruation, shed endometrial tissue fragments attach to and invade the peritoneal surface to form established endometriotic lesions. With disease progression, the biochemically active lesions undergo remodeling and become fibrotic. Matrix metalloproteinase enzymes (MMPs) and the tissue inhibitors of metalloproteinases (TIMPs) play a significant role in normal endometrial remodeling during menses. Anomalous expression of MMPs and TIMPs has been identified in endometriotic lesions as compared to their highly regulated expression in eutopic endometrium. The paracrine mechanisms regulating misexpression of MMPs and TIMPs by endometriotic lesions are, however, not well defined. Misexpression of the MMPs and TIMPs may be due to innate anomalies in the eutopic endometrium from women with endometriosis, in the resident immune cells and peritoneal cells that juxtapose the ectopic endometrium, and/or numerous substances present in peritoneal fluid of women with endometriosis. The majority of MMPs are under strict transcriptional regulation. Steroid hormones and cytokines appear to act on the MMP promoter, either independently or in consort, to provide both positive and negative regulation of these genes. Misregulated expression of MMPs and TIMPs is associated with a more aggressive phenotype and a cascade of events facilitating peritoneal extracellular matrix degradation and establishment or remodeling of endometriotic lesions. The mechanisms by which MMP and TIMP expression are misregulated warrant further investigation as such information may provide insight into novel therapeutic modalities for endometriosis.
Space time block coded transmit antenna diversity scheme for WCDMA (2003)

In this paper we present a new space time block code as an antenna diversity scheme for transmit antenna diversity. The space-time-transmit-diversity (STTD) method is an open loop transmit diversity scheme, i.e. it does not require any knowledge of the channel at the transmitter. Simulations have shown that the STTD scheme significantly outperforms the case where no antenna diversity is used. In fact, it even outperforms the non-diversity (ND) case even when soft handoff is used. STTD exploits the extra path diversity afforded by the second antennas and therefore outperforms two other open loop transmit antenna diversity techniques, viz. the orthogonal transmit diversity (OTD) and the time switched time diversity (TSTD). These techniques use multiple transmit antennas to provide some interleaver time diversity against fading, particularly at low Doppler rates and when the mobile receiver does not have enough paths at the RAKE receiver. STTD has the added advantages of being a power amplifier (PA) balanced technique, is easily backward compatible with ND systems and does not need careful interleaver design.
Effects of thermomechanical processing on strength and toughness of iron - 12-percent-nickel - reactive metal alloys at -196 C (1978)

Thermomechanical processing (TMP) was evaluated as a method of strengthening normally tough iron-12-nickel-reactive metal alloys at cryogenic temperatures. Five iron-12 nickel alloys with reactive metal additions of aluminum, niobium, titanium, vanadium, and aluminum plus niobium were investigated. Primary evaluation was based on the yield strength and fracture toughness of the thermomechanically processed alloys at -196 C.
Aqueous synthesis and transmission electron microscopy observation of seed-grown spherical ferrite nanoparticles (2012)

Uniform-sized spherical iron ferrite nanoparticles grew on seed crystals in an aqueous solution containing sucrose. Using the seed crystals which were highly dispersed in acidic or alkaline seed-crystal suspension without relation to pH of the suspension, we widely controlled the particle diameter in the range 20–200 nm by changing the additive amount of the seed crystals. By transmission electron microscopy observation and X-ray diffraction analysis, it indicated that the particles were highly crystalline but not amorphous. Selected area diffraction patterns of the particles by using transmission electron microscope revealed that the particles were composed of one to several crystals. Thus we provided the evidence that the particles grew on clusters composed of one to several seed crystals to which those of several dozen seed crystals were disintegrated.
Tracking users' capture intention (2005)

In this paper, we present a novel view to home video content analysis, which aims at tracking the capture intention of camcorder users. Based on the study of intention mechanism in psychology, a set of domain-specific capture intention concepts are defined. A comprehensive and extensible scheme consisting of video structuring, intention oriented feature analysis, as well as intention unit segmentation and classification is proposed to mine the users' capture intention. Experiments were carried on home video sequences of 90 hours in total, taken by 16 persons in recent 20 years. Both the user study and objective evaluations indicate that our proposed intention-based approach is an effective complement to existing home video content analysis schemes.
Micro fuel cell (1998)

An ambient temperature, liquid feed, direct methanol fuel cell device is under development. A metal barrier layer was used to block methanol crossover from the anode to the cathode side while still allowing for the transport of protons from the anode to the cathode. A direct methanol fuel cell (DMFC) is an electrochemical engine that converts chemical energy into clean electrical power by the direct oxidation of methanol at the fuel cell anode. This direct use of a liquid fuel eliminates the need for a reformer to convert the fuel to hydrogen before it is fed into the fuel cell.
Specificity of Interactions among the DNA-packaging Machine Components of T4-related Bacteriophages (2010)

Tailed bacteriophages use powerful molecular motors to package the viral genome into a preformed capsid. Packaging at a rate of up to ∼2000 bp/s and generating a power density twice that of an automobile engine, the phage T4 motor is the fastest and most powerful reported to date. Central to DNA packaging are dynamic interactions among the packaging components, capsid (gp23), portal (gp20), motor (gp17, large "terminase"), and regulator (gp16, small terminase), leading to precise orchestration of the packaging process, but the mechanisms are poorly understood. Here we analyzed the interactions between small and large terminases of T4-related phages. Our results show that the gp17 packaging ATPase is maximally stimulated by homologous, but not heterologous, gp16. Multiple interaction sites are identified in both gp16 and gp17. The specificity determinants in gp16 are clustered in the diverged N- and C-terminal domains (regions I-III). Swapping of diverged region(s), such as replacing C-terminal RB49 region III with that of T4, switched ATPase stimulation specificity. Two specificity regions, amino acids 37-52 and 290-315, are identified in or near the gp17-ATPase "transmission" subdomain II. gp16 binding at these sites might cause a conformational change positioning the ATPase-coupling residues into the catalytic pocket, triggering ATP hydrolysis. These results lead to a model in which multiple weak interactions between motor and regulator allow dynamic assembly and disassembly of various packaging complexes, depending on the functional state of the packaging machine. This might be a general mechanism for regulation of the phage packaging machine and other complex molecular machines.
Design of a Portable Orthogonal Surface Acoustic Wave Sensor System for Simultaneous Sensing and Removal of Nonspecifically Bound Proteins (2019)

One challenge for current surface acoustic wave (SAW) biosensors is reducing nonspecific adsorption. A device propagating Rayleigh and shear horizontal surface acoustic waves in orthogonal directions fabricated in ST quartz has the capability of achieving simultaneous detection and nonspecific binding (NSB) protein removal. Current measurement methods for a SAW sensor system based on this device require large-size and expensive equipment such as a vector network analyzer (VNA), signal generator, and frequency counter, which are not suitable for portable, especially point-of-care, applications. In this work, a portable platform based on a direct digital synthesizer (DDS) is investigated for the orthogonal SAW sensor, integrating signal synthesis, gain control, phase/amplitude measurement, and data processing in a small, portable electronic system. This prototype was verified for both stability and repeatability, and the results matched very well with VNA measurements. Finally, system performance in real-time sensing and NSB removal was evaluated.
Doping Profile Recognition Applied to Silicon Photovoltaic Cells Using Terahertz Time-Domain Spectroscopy (2014)

Here we demonstrate for the first time that terahertz time-domain spectroscopy (THz-TDS) can be used to monitor doping profiles in standard industry silicon wafers and commercial multi-crystalline silicon (mc-Si) solar cells. The proof-of-concept results presented here demonstrate the suitability of the technique for in-line, or close to real-time, process and quality control applications in the photovoltaic (PV) industry. The experimental results show that THz pulses can detect changes in implant dosage in both the time and frequency domains. It is also shown that the spectral content of THz pulses can be used to distinguish between doping profiles with identical implant dosages but different profile shapes (resulting from different diffusion times). The reliability and repeatability of these measurements is demonstrated. It is found that the average change in THz spectrum (12.3%) corresponding to the smallest doping profile difference detected is an order of magnitude bigger than the average day-to-day measurement error (1.1%). The THz measurement approach is shown to be fully compatible with the surface morphology (texturing) of commercial mc-Si solar cells.
Organizing Documented Processes (2009)

A frequent hurdle in applying Business Process Management(BPM) to large enterprises is that, since business processes are not only numerous but also documented in an engagement in multiple representations,it is difficult to work with the documented 'as-is' or 'to-be' state of the business, leave aside make accurate transformation decisions. In this paper, we consider the problem of how to reconcile and organize documented information about processes into groups that convey inter-process similarity. The discovered knowledge can be used for many applications like search, e.g., find all requirements across all available processes that are similar to those of the "Account Receivable" process. The method has been tested on a dataset consisting of hundreds of processes documented in Word and Visio, wherefrom it could find process clusters that significantly boosted search performance.
Millimeter-wave-band amplitude-shift-keyed radio-on-fiber signal generation with a reciprocating optical modulator (2004)

We demonstrated binary amplitude-shift-keyed modulated millimeter-wave signal generation using a reciprocating optical modulator. Due to interference effect of reciprocating lightwaves, ASK of 52.8-GHz signal was achieved by low-voltage (2.0 V) base-band signal, where V/sub /spl pi// was 6.4 V.
Planar radiator with refined slot pattern for electrically small antennas (2006)

The authors present a novel radiator as a basic element of electrically small planar antennas for various short-range wireless applications. The proposed radiator takes advantage of its unique topology in order to improve a bandwidth of otherwise narrow-band conventional antennas. The radiator comprises a thin metal layer preferably formed on a surface of the dielectric substrate, and a slot pattern within that layer configured with four convoluted slot arms terminating a main slot at each end. One pair of terminating slot arms is convoluted clockwise while another pair is convoluted counterclockwise. The combination of clockwise and counterclockwise convoluted slot arms provides the termination with unique electromagnetic features. The slot arms are further formed as mirror-symmetrical couples with respect to the main slot line. The rigorous theoretical analysis is validated by precise prototyping and accurate experiments with UHF microstrip fed antennas. The bandwidth of the antenna with the proposed radiator becomes at least 30% wider without any affect on radiation pattern, gain, and polarisation purity. It is shown that improvement in the bandwidth has been achieved exclusively owing to the refined slot pattern.
Instructions for producing a mouse model of glucocorticoid-induced osteoporosis (2014)

Glucocorticoids are effective drugs used for the treatment of inflammatory diseases such as rheumatoid arthritis or asthma. Furthermore, they regulate various physiological processes, including bone remodeling. However, long-term high- and even low-dose glucocorticoid use is associated with a compromised bone quality and an increased fracture risk. At the cellular level, glucocorticoids suppress bone formation and stimulate bone resorption, which leads to loss of bone mass. To investigate the underlying mechanisms and new therapeutic strategies, the in vivo model for glucocorticoid-induced bone loss is widely used. This protocol outlines the common procedure that is currently used for the induction of bone loss in mice using glucocorticoids. It further provides useful hints and highlights possible pitfalls to take into account before starting an experiment.
Improvement of Western Blot Test Specificity for Detecting Equine Serum Antibodies to <i>Sarcocystis Neurona</i> (2000)

Equine protozoal myeloencephalitis (EPM) is a neurological disease of horses and ponies caused by the apicomplexan protozoan parasite Sarcocystis neurona. The purposes of this study were to develop the most stringent criteria possible for a positive test result, to estimate the sensitivity and specificity of the EPM Western blot antibody test, and to assess the ability of bovine antibodies to Sarcocystis cruzi to act as a blocking agent to minimize false-positive results in the western blot test for S. neurona. Sarcocystis neurona merozoites harvested from equine dermal cell culture were heat denatured, and the proteins were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis in a 12-20% linear gradient gel. Separated proteins were electrophoretically transferred to polyvinylidene fluoride membranes and blocked in 1% bovine serum albumin and 0.5% Tween-Tris-buffered saline. Serum samples from 6 horses with S. neurona infections (confirmed by culture from neural tissue) and 57 horses without infections (horses from the Eastern Hemisphere, where S. neurona does not exist) were tested by Western blot. Horses from both groups had reactivity to the 62-, 30-, 16-, 13-, 11-, 10.5-, and 10-kD bands. Testing was repeated with another step. Blots were treated with bovine S. cruzi antibodies prior to loading the equine samples. After this modification of the Western blot test, positive infection status was significantly associated with reactivity to the 30- and 16-kD bands (P<0.001, Fisher's exact test). The S. cruzi antibody-blocked Western blot had a sample sensitivity of 100% and sample specificity of 98%. It is concluded that the specificity of the Western blot test is improved by blocking proteins not specific to S. neurona and using reactivity to the 30- and 16-kD bands as the criterion for a positive test.