gebhart/patrepeval huggingface dataset:
Identification of essential nucleotides of the FP1 element responsible for enhancement of low density lipoprotein receptor gene transcription (1997)

Low density lipoprotein (LDL) receptor gene is regulated at the transcriptional level by the intracellular level of sterols in animal cells. We have recently identified a 20 bp long region (-145 to -126), designated Footprint 1 (FP1), participating in maximal expression of the human LDL receptor gene in the absence of sterols in HepG2 cells [Mehta, K. D., Chang, R., Underwood, J., Wise, J. and Kumar, A. (1996) J. Biol. Chem ., 271, 33616-33622]. To determine the minimal FP1 sequence and to define the critical nucleotides required for function, a series of single nucleotide substitutions were introduced in the FP1 region. Twenty-three independent mutations were analyzed by transfection into HepG2 cells. These studies localize the regulatory region to 14 bp and demonstrate the requirement for essential guanine nucleotides at positions -135 and -136 for FP1 function. Furthermore, transfection studies suggest that the FP1-dependent increase in reporter gene expression is possibly mediated through interaction with the sterol-regulatory element. UV cross-linking and Southwestern blot analysis identified FP1-binding factors of approximately 50 and 125 kDa, which we have denoted p50 and p125. Mutations of the critical guanine residues (-135/-136) decreased the formation of the specific protein-DNA complex with the FP1 sequence and abolished its binding to the p125. We conclude that direct interaction of the p125 factor with these nucleotides of the FP1 element potentially contributes to FP1-dependent induction of LDL receptor gene expression.
A Specific Groove Pattern Can Effectively Induce Osteoblast Differentiation (2017)

Abstract Little is known about the principles of surface structure design for orthopedic and dental implants. To find topographical groove patterns that could enhance osteoblast differentiation according to cell type, groove patterns are fabricated with ridges (0.35−7 µm) and grooves (0.65−6 µm) of various widths and explored their mechanisms in improving osteoblast differentiation. This study finds that a groove pattern enhancing osteoblast differentiation is associated with the ability of the cell to extend its length and that it is able to overcome the inhibition of osteoblast differentiation that takes place under inflammatory conditions. The groove pattern suppresses the generation of reactive oxygen species, a reaction that is increased in inflammatory conditions. It also modulates the expression of osteogenic factors according to differentiation time. Importantly, specific groove patterns AZ‐2 and AZ‐4, with ridge width of 2 µm and groove width of 2 or 4 µm, respectively, effectively promote bone regeneration in critical‐sized calvarial defects without additional factors. This knowledge of groove patterns can be applied to the development of orthopedic and dental devices.
Recombinant antigens prepared from the urease subunits of Helicobacter spp.: evidence of protection in a mouse model of gastric infection (1994)

Urease is an important virulence factor for gastric Helicobacter spp. To elucidate the efficacy of individual urease subunits to act as mucosal immunogens, the genes encoding the respective urease subunits (UreA and UreB) of Helicobacter pylori and Helicobacter felis were cloned in an expression vector (pMAL) and expressed in Escherichia coli cells as translational fusion proteins. The recombinant UreA and UreB proteins were purified by affinity and anion-exchange chromatography techniques and had predicted molecular masses of approximately 68 and 103 kDa, respectively. Western blotting (immunoblotting) studies indicated that the urease components of the fusion proteins were strongly immunogenic and were specifically recognized by polyclonal rabbit anti-Helicobacter sp. sera. The fusion proteins (50 micrograms) were used, in combination with a mucosal adjuvant (cholera toxin), to orogastrically immunize mice against H. felis infection. Gastric tissues from H. felis-challenged mice were assessed by the biopsy urease test and by histology. In mice immunized with recombinant H. felis UreB, 60% of animals (n = 7) were histologically negative for H. felis bacteria after challenge at 17 weeks. This compared with 25% (n = 8) for mice immunized with the heterologous H. pylori UreB antigen. Neither the homologous nor the heterologous UreA subunit elicited protective responses against H. felis infection in mice. The study demonstrated that a recombinant subunit antigen could induce an immunoprotective response against gastric Helicobacter infection.
Operating system upgrade in high availability environment (2013)

The high availability requirement for services does not allow for more than five minutes of down time per year including downtime scheduled for maintenance and upgrades. The upgrade of applications providing such services is challenging and has to be planned very carefully. The challenge becomes even bigger when it comes to the upgrade of the underlying supporting lower layers, the middleware and the operating system (OS). In this paper, we explore the challenges of OS upgrade and propose solutions built on an existing standard middleware service for software management.
Fast response time atomic filter at 423 nm (1993)

Atomic resonance filters are optical bandpass filters that employ sharp atomic transitions to perform ultra-narrow-band (0.001 nm) filtering of light.1 Further, the bandwidth is independent of aperture size and field-of-view, These devices are designed to exclude sunlight in laser receivers. Applications include laser radar, lasercom, remote sensing, and underwater communications.
Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize (2007)

Flowering time is a fundamental trait of maize adaptation to different agricultural environments. Although a large body of information is available on the map position of quantitative trait loci for flowering time, little is known about the molecular basis of quantitative trait loci. Through positional cloning and association mapping, we resolved the major flowering-time quantitative trait locus, Vegetative to generative transition 1 (Vgt1), to an approximately 2-kb noncoding region positioned 70 kb upstream of an Ap2-like transcription factor that we have shown to be involved in flowering-time control. Vgt1 functions as a cis-acting regulatory element as indicated by the correlation of the Vgt1 alleles with the transcript expression levels of the downstream gene. Additionally, within Vgt1, we identified evolutionarily conserved noncoding sequences across the maize-sorghum-rice lineages. Our results support the notion that changes in distant cis-acting regulatory regions are a key component of plant genetic adaptation throughout breeding and evolution.
<title>Restoration of compressed images</title> (1994)

Post-processing can alleviate or remove artifacts introduced by compression. However without a priori information, image enhancement schemes may fail. What is noise in one image may be important data in another. Fortunately, in image compression, we have an advantage. Before an image is stored or transmitted, we have access to the original and the distorted versions. The enhanced codec is compared to the original block by block to determine which blocks have been improved by the enhancement. These blocks are then flagged for post- processing in a way that is compliant with the JPEG standard and adds nothing to the compressed images` bandwidth. A single JPEG coefficient is adjusted so that the sum of the coefficients contains the flag for post-processing as the parity of the block. Half of the blocks already have the correct parity. In the other blocks, a coefficient that is close to being half way between two values will be chosen and rounded in the other direction. This distorts the image by a very tiny amount. The end result is a compressed image that can be decompressed on any standard JPEG decompressor, but that can be enhanced by a sophisticated decompressor.
miR-29b is activated during neuronal maturation and targets BH3-only genes to restrict apoptosis (2011)

The execution of apoptosis is critical for proper development of the nervous system. However, it is equally important that neurons strictly inhibit apoptosis after development to ensure their survival throughout the lifetime of the organism. Here we show that a microRNA, miR-29b, is markedly induced with neuronal maturation and functions as a novel inhibitor of neuronal apoptosis. The prosurvival function of miR-29b is mediated by targeting genes in the proapoptotic BH3-only family. Our results identify a unique strategy evolved by maturing neurons that uses a single microRNA to inhibit the multiple, redundant BH3-only proteins that are key initiators of apoptosis.
Pasteurisation of a Factor I (C3b Inactivator) Concentrate from Human Plasma (1989)

A method of pasteurising a concentrate of factor I (C3b inactivator) prepared from human blood plasma is described. As well as obtaining a high yield of factor I by this virus inactivation procedure it is furthermore possible, by adjustment of the stabiliser concentration, to obtain a very pronounced reduction in the concentration of factor B, a component of the complement system which is unwanted in the treatment of factor I deficiency. The product so produced is in two respects superior to plasma infusions for factor I replacement therapy: it has been submitted to virus inactivation and factor B depletion.
Gigahertz frequency flexible carbon nanotube transistors (2007)

We investigate the high frequency performances of flexible field-effect transistors based on carbon nanotubes. A large density of mostly aligned carbon nanotubes deposited on a flexible substrate by dielectrophoresis serves as the channel. The transistors display a constant transconductance up to at least 6GHz and a current gain cutoff frequency (fT) as high as 1GHz at VDS=−700mV. Bending tests show that the devices can withstand a high degree of flexion characterized by a constant transconductance for radius of curvature as small as 3.3mm.
Cheese Base for Processing. A High Yield Product from Whole Milk by Ultrafiltration (1980)

Whole milk of normal pH or acidified to pH 5.7 was concentrated by ultrafiltration to 40% original milk weight, diafiltered at constant volume until a desired ratio of lactose to buffer capacity was established, and concentrated by ultrafiltration to 20% milk weight. The retentates were inoculated with cheese starter and incubated to ferment completely the residual lactose. Precise control of final pH was achieved readily.
Successful Laboratory Testing of Practical Methods of Hydraulic-Control-System Failure Diagnosis Using Valve Signatures (2011)

Summary The two hydraulic-diagnostic methods detailed in this paper can monitor the "health" of a subsea hydraulic-control system, diagnose or predict a system problem (particularly leaking or clogging problems), and locate its source by using readily available valve-signature data. The methods were tested in a laboratory environment using a hydraulic system with simulated clogging and leaking mechanisms. Leak detection was performed using both signature-matching and mass-balance methods. The results showed a mean accuracy of 93% for mass-balance method and 82% for the signature-matching method. Clog detection by signature matching showed high accuracy in the controlled laboratory condition. The difference between the simulated and actual clogging is within 1%. The methods provide a monitoring tool for detecting and locating potential leaks, blockages, and other system changes or anomalies, which could be used to estimate the potential high cost of intervention, possible downtime, and lost revenue.
Mechanical properties of molybdenum-sealing glass-ceramics (1975)

Elastic constants, thermal expansion, strength, and fracture toughness were determined for a molybdenum-sealing glass-ceramic containing approximately 31 volume percent Zn{sub 2}SiO{sub 4} crystals In a glass matrix. The microstructure was studied for two different crystallization treatments and moderate changes in composition. Mechanical properties of the composite were compared to the properties of the constituent phases through application of mixture theory and by fractographic observations. The reinforcing effects of the crystal phase at room temperature are evident in comparison to the properties of the residual glass but not necessarily in comparison to the parent glass. Fracture toughness of the composite depends primarily on additive properties of the separate phases instead of by interactive effects such as microcracks.
Human-robot interaction through real-time auditory and visual multiple-talker tracking (2002)

Nakadai et al. (2001) have developed a real-time auditory and visual multiple-talker tracking technique. In this paper, this technique is applied to human-robot interaction including a receptionist robot and a companion robot at a party. The system includes face identification, speech recognition, focus-of-attention control, and sensorimotor task in tracking multiple talkers. The system is implemented on a upper-torso humanoid and the talker tracking is attained by distributed processing on three nodes connected by 100Base-TX network. The delay of tracking is 200 msec. Focus-of-attention is controlled by associating auditory and visual streams by using the sound source direction and talker position as a clue. Once an association is established, the humanoid keeps its face to the direction of the associated talker.
Jenseniin G, a heat-stable bacteriocin produced by Propionibacterium jensenii P126 (1992)

The genus Propionibacterium includes cutaneous species typically found on human skin and the dairy or classical species (Propionibacterium freudenreichii, P. jensenii, P. thoenii, and P. acidipropionici) used industrially for the production of Swiss cheese and propionic acid. Grinstead (1989, M.S. thesis, Iowa State University, Ames) has previously observed that some dairy propionibacteria inhibit other species in the classical grouping. We further investigated the inhibitor(s) produced by P. jensenii P126 (ATCC 4872). An antagonist(s) from anaerobic agar cultures of P126 strongly inhibited two closely related strains of propionibacteria, P. acidipropionici P5 and P. jensenii P54, and Lactobacillus bulgaricus NCDO 1489, Lactobacillus delbrueckii subsp. lactis ATCC 4797, Lactococcus cremoris NCDO 799, and Lactococcus lactis subsp. lactis C2. The inhibitor, designated jenseniin G, was active at pH 7.0; inactivated by treatment with pronase E, proteinase K, and type 14 protease; insensitive to catalase; and stable to freezing, cold storage (4 degrees C, 3 days), and heat (100 degrees C, 15 min). Classification of the inhibitor as a bacteriocin is supported by its proteinaceous nature and its bactericidal activity against L. delbrueckii subsp. lactis ATCC 4797. The lack of detectable plasmids suggests a chromosomal location for the determinant(s) of jenseniin G.
ChemInform Abstract: A Silicogermanate with a Si:Ge Ratio ≥ 2. ‐ A Novel MFI‐Zeolite. (1989)

Abstract Substitution of Ge for Si in pure SiO 2 ‐zeolites yields microporous materials containing Si and Ge in a tetrahedral framework of the MFI‐type.
Flapping Wing Micro-Air-Vehicle Control Employing Triangular Wave Strokes and Cycle-Averaging (2010)

The recent development of the world’s rst robotic insect capable of vertical takeo at the Harvard Microrobotics Lab has sparked research e orts into devising similar vehicles capable of untethered ight. The vehicle design has been extended in simulation to use one actuator per wing to produce sinusoidal apping motion in a plane. This work proposes employing a generic triangular wave to generate the apping wing stroke angle. The resulting expressions for the wing beat cycle-averaged aerodynamic forces and moment are signi cantly simpler than those computed using sinusoidal waveforms, thus easing algebraic manipulation and analytical analysis. Wing beat parameters are employed as control inputs, a ecting the cycle-averaged aerodynamic forces and moments. The resulting control authority is assessed analytically. A ve degree-of-freedom control design is devised and used to control a six degree-of-freedom simulation of the vehicle. The simulation model is driven by the instantaneous aerodynamic forces and moments; and the cycle-averaged expressions are only used for control design. Three sets of wing beat parameters are used as control inputs to illustrate the freedom in control design and implementation. One mimics the sinusoidal waveform studies cases. The others illustrate how amplitude modulation can replace frequency modulation to achieve comparable performance results.
A Novel Buffering Design and Performance Evaluation of Optical Flow Switch with Smart Scheduling Algorithms (2018)

In this paper, a novel buffering design and performance evaluation of optical flow switch with smart scheduling algorithms are proposed. The input buffer scheduling methods are used for a hybrid switching module or all-optical switching module on the data center. Using the smart input buffer scheduling methods can make the overall exchange throughput further effectively increased. In the hybrid switching module, we propose the offload scheme. The overall switching efficiency will be improved significantly. In the future all-optical switching module, four schemes which include discard scheme, padding scheme, free-riding scheme, and aggregate scheme are proposed and simulated. The results of performance evaluation also show that aggregate scheme has a better switching efficiency.
The Synthesis and Stereochemistry of (±)-(4a,13b-<i>trans</i>)-2,3,4,4a,8,9,13b,14-Octahydro-1<i>H</i>-benzo[6,7]cyclohepta[1,2,3-<i>de</i>]pyrido[2,1-<i>a</i>]-isoquinoline Hydrochloride (Taclamine Hydrochloride), a Novel Psychotropic Agent (1974)

Two synthetic routes to (±)-(4a,13b-trans)-2,3,4,4a,8,9,13b,14-octahydro-1H-benzo[6,7]cyclohepta[1,2,3-de]pyrido[2,1-a]isoquinoline hydrochloride (1) (taclamine hydrochloride) are described. Configurational assignments have been made on the basis of n.m.r. spectral interpretations and mechanistic considerations.
High-Speed Defect Detection in Rails by Noncontact Guided Ultrasonic Testing (2005)

Recent train accidents have reaffirmed the need to develop rail defect detection systems that are more effective than those used today. This paper proposes new inspection systems for detecting transverse-type cracks in the rail head, notoriously the most dangerous flaws in rails. In principle these systems can be applied to both continuous welded rail and jointed tracks because bidirectional inspection can be implemented. However, the systems may fail to detect defects located close to a joint. The proposed technology uses ultrasonic guided waves that are detected by remote sensors positioned as far away as 76 mm (3 in.) from the top of the rail head. An impulse hammer is used to generate waves below 50 kHz that can successfully detect cracks larger than 15% of the head cross-sectional area. For smaller cracks-those as shallow as 1 mm-a pulsed laser is used for generating waves above 100 kHz. The inspection ranges are at least 10 m (32 ft) for cracks larger than 15% of the head area and at least 500 mm (20 in.) for surface head cracks as shallow as 1 mm. The defect detection reliability is improved by using both reflection and transmission measurements.
Metallothionein: A Novel Therapeutic Target for Treatment of Inflammatory Bowel Disease (2018)

Inflammatory bowel disease (IBD) is a group of disorders characterized by chronic inflammation within the gastrointestinal tract. It is a multifactorial disease associated with immune-cell mediated oxidative damage to the intestinal mucosa. There is no cure for IBD, but anti-cytokine therapy can limit target inflammation and disease progression. Unfortunately, many patients are nonresponsive or develop resistance to anti-cytokine therapy over time creating a need for new therapeutic agents. Metallothionein (MT) is a small, highly conserved stress response protein that has been shown to modulate the immune response as a pro-inflammatory agent, regulates divalent heavy metal homeostasis, and acts as a reactive metabolite scavenger. Our research, as well as other groups studying MT, has described MT induction and release during IBD inflammatory stress response. The release of MT results in activation of inflammatory responses leading to progressive inflammation and subsequent expansion of MT synthesis. A monoclonal antibody specific for MT has been used in murine models of IBD and should only target the extracellular pool of MT, thus representing a novel therapeutic approach to this disease.
Resistance to Tomato Yellow Leaf Curl Virus in Tomato Germplasm (2018)

Tomato yellow leaf curl virus (TYLCV) is a virus species causing epidemics in tomato (<i>Solanum lycopersicum</i>) worldwide. Many efforts have been focused on identification of resistance sources by screening wild tomato species. In many cases, the accession numbers were either not provided in publications or not provided in a consistent manner, which led to redundant screenings. In the current study, we summarized efforts on the screenings of wild tomato species for TYLCV resistance from various publications. In addition, we screened 708 accessions from 13 wild tomato species using different inoculation assays (i.e., whitefly natural infection and Agrobacterium-mediated inoculation) from which 138 accessions exhibited no tomato yellow leaf curl disease (TYLCD) symptoms. These symptomless accessions include 14 accessions from <i>S. arcanum</i>, 43 from <i>S. chilense</i>, 1 from <i>S. chmielewskii</i>, 28 from <i>S. corneliomulleri</i>, 5 from <i>S. habrochaites</i>, 4 from <i>S. huaylasense</i>, 2 from <i>S. neorickii</i>, 1 from <i>S. pennellii</i>, 39 from <i>S. peruvianum</i>, and 1 from <i>S. pimpinellifolium</i>. Most of the screened <i>S. chilense</i> accessions remained symptomless. Many symptomless accessions were also identified in <i>S. arcanum</i>, <i>S. corneliomulleri</i>, and <i>S. peruvianum</i>. A large number of <i>S. pimpinellifolium</i> accessions were screened. However, almost all of the tested accessions showed TYLCD symptoms. Further, we studied allelic variation of the <i>Ty-1</i>/<i>Ty-3</i> gene in few <i>S. chilense</i> accessions by applying virus-induced gene silencing and allele mining, leading to identification of a number of allele-specific polymorphisms. Taken together, we present a comprehensive overview on TYLCV resistance and susceptibility in wild tomato germplasm, and demonstrate how to study allelic variants of the cloned <i>Ty</i>-genes in TYLCV-resistant accessions.
An improved tripod amphiphile for membrane protein solubilization (2000)

Intrinsic membrane proteins represent a large fraction of the proteins produced by living organisms and perform many crucial functions. Structural and functional characterization of membrane proteins generally requires that they be extracted from the native lipid bilayer and solubilized with a small synthetic amphiphile, for example, a detergent. We describe the development of a small molecule with a distinctive amphiphilic architecture, a "tripod amphiphile," that solubilizes both bacteriorhodopsin (BR) and bovine rhodopsin (Rho). The polar portion of this amphiphile contains an amide and an amine-oxide; small variations in this polar segment are found to have profound effects on protein solubilization properties. The optimal tripod amphiphile extracts both BR and Rho from the native membrane environments and maintains each protein in a monomeric native-like form for several weeks after delipidation. Tripod amphiphiles are designed to display greater conformational rigidity than conventional detergents, with the long-range goal of promoting membrane protein crystallization. The results reported here represent an important step toward that ultimate goal.