gebhart/patrepeval huggingface dataset:
Cloning and Characterization of Purple Acid Phosphatase Phytases from Wheat, Barley, Maize, and Rice  (2011)

Barley (Hordeum vulgare) and wheat (Triticum aestivum) possess significant phytase activity in the mature grains. Maize (Zea mays) and rice (Oryza sativa) possess little or virtually no preformed phytase activity in the mature grain and depend fully on de novo synthesis during germination. Here, it is demonstrated that wheat, barley, maize, and rice all possess purple acid phosphatase (PAP) genes that, expressed in Pichia pastoris, give fully functional phytases (PAPhys) with very similar enzyme kinetics. Preformed wheat PAPhy was localized to the protein crystalloid of the aleurone vacuole. Phylogenetic analyses indicated that PAPhys possess four conserved domains unique to the PAPhys. In barley and wheat, the PAPhy genes can be grouped as PAPhy_a or PAPhy_b isogenes (barley, HvPAPhy_a, HvPAPhy_b1, and HvPAPhy_b2; wheat, TaPAPhy_a1, TaPAPhy_a2, TaPAPhy_b1, and TaPAPhy_b2). In rice and maize, only the b type (OsPAPhy_b and ZmPAPhy_b, respectively) were identified. HvPAPhy_a and HvPAPhy_b1/b2 share 86% and TaPAPhya1/a2 and TaPAPhyb1/b2 share up to 90% (TaPAPhy_a2 and TaPAPhy_b2) identical amino acid sequences. despite of this, PAPhy_a and PAPhy_b isogenes are differentially expressed during grain development and germination. In wheat, it was demonstrated that a and b isogene expression is driven by different promoters (approximately 31% identity). TaPAPhy_a/b promoter reporter gene expression in transgenic grains and peptide mapping of TaPAPhy purified from wheat bran and germinating grains confirmed that the PAPhy_a isogene set present in wheat/barley but not in rice/maize is the origin of high phytase activity in mature grains.
Safety of Fitness Equipment Cables (2013)

There is a family of fitness machines that provides a manual workout task requiring the user to push or pull against a resistance provided by a stack of weight plates. The weight system is usually linked with a single cable to a gripping or user interface device to produce a constant resistance. A fracture of the tensioned cable along its length or at its end connectors causes a sudden acceleration of the grip or other interface device driven by the operator’s push or pull. The sudden loss of resistance often results in an exerciser pulling a heavy bar into his or her face. Because falling weights, accelerating grips and rapidly unloading muscles are all hazardous, manufacturers of exercise machines want to maintain the structural integrity of the cables. To accomplish this, manufacturers usually recommend “scheduled servicing” of their cables. This Preventive Maintenance (PM) strategy is frustrated by nylon sheathing that hides the cable failures. Further, the swedged or silver soldered connectors often fail covertly by internal fatigue fractures. A more effective PM strategy has been adopted by many manufacturers called “Scheduled Replacement”; they advocate annual cable replacement. Here the nemeses are sloth and greed, best expressed by the philosophy, “if it ain’t broke, don’t fix it.” As a first consideration of fault tolerant design, a redundant duplication of the cable system was added to a fitness machine; this is called “active redundancy.” This paper demonstrates the inadequacy of active redundancy for eliminating the catastrophic failure mode. Instead, the adoption of a “dormant/standby” redundancy is shown to provide the requisite safety. The proposed system not only eliminates the “fail-to-danger” mode, it provides the most economical use of the cable in the sense that it never discards a cable until its life is exhausted.
ZnO cone-shaped blue light emitting diodes (2008)

We report on ZnO wafer bonded III-nitride light emitting diodes (LEDs). ZnO wafer was selectively etched to form a hexagonal pyramid shape. For enhancing light extraction and heat conductivity, two types of LED structures were demonstrated: one is having patterned GaN at the wafer bonded interface between GaN and ZnO, the other is the LED having no sapphire. The experimental results of electrical and optical characteristics indicate the high potential of these types of LEDs for solid state lighting sources.
Three-dimensional localization of fluorescent targets in turbid media using time reversal optical tomography (2012)

An optical tomography approach for locating fluorescent targets embedded inside a turbid medium is introduced. It uses multi-source probing and multi-detector signal acquisition to collect diffuse fluorescence signal, and time reversal matrix formalism with subspace based signal processing for image reconstruction. It could provide three-dimensional position co-ordinates of two small fluorescent targets embedded in Intralipid-20% suspension of thickness ∼60 times the transport mean free path with an accuracy of ∼1 mm. Fast reconstruction and high spatial resolution make the approach potentially suited for detecting and locating contrast-enhanced breast tumor at early stages of growth.
CYP46A1 inhibition, brain cholesterol accumulation and neurodegeneration pave the way for Alzheimer’s disease (2015)

Abnormalities in neuronal cholesterol homeostasis have been suspected or observed in several neurodegenerative disorders including Alzheimer's disease, Parkinson's disease and Huntington's disease. However, it has not been demonstrated whether an increased abundance of cholesterol in neurons in vivo contributes to neurodegeneration. To address this issue, we used RNA interference methodology to inhibit the expression of cholesterol 24-hydroxylase, encoded by the Cyp46a1 gene, in the hippocampus of normal mice. Cholesterol 24-hydroxylase controls cholesterol efflux from the brain and thereby plays a major role in regulating brain cholesterol homeostasis. We used an adeno-associated virus vector encoding short hairpin RNA directed against the mouse Cyp46a1 mRNA to decrease the expression of the Cyp46a1 gene in hippocampal neurons of normal mice. This increased the cholesterol concentration in neurons, followed by cognitive deficits and hippocampal atrophy due to apoptotic neuronal death. Prior to neuronal death, the recruitment of the amyloid protein precursor to lipid rafts was enhanced leading to the production of β-C-terminal fragment and amyloid-β peptides. Abnormal phosphorylation of tau and endoplasmic reticulum stress were also observed. In the APP23 mouse model of Alzheimer's disease, the abundance of amyloid-β peptides increased following inhibition of Cyp46a1 expression, and neuronal death was more widespread than in normal mice. Altogether, these results suggest that increased amounts of neuronal cholesterol within the brain may contribute to inducing and/or aggravating Alzheimer's disease.
[Beneficial effect of a retinoic acid responsive gene product, midkine, on constant light-induced retinal damage in albino mice]. (1995)

We studied the protective effects of midkine, a growth factor produced by a retinoic acid responsive gene, on constant light-induced retinal damage in albino BALB/C adult mice. Two days before exposure to constant light, midkine was injected into the vitreous of the left eye and a phosphate buffer saline into the right eye (control eyes). After 7 days of constant light, control eyes exhibited shortening of the photoreceptor outer segments and decreased thickness of the outer nuclear layer, whereas in midkine-treated eyes photoreceptor cells were virtually intact. Although midkine-treated eyes also showed photoreceptor damage after longer light exposure of up to 21 days, the damage was significantly less than in control eyes. Measurement of the thickness of the outer nuclear layer showed the protective effect of intravitreous midkine on the constant light-induced retinal damage. These findings suggest that midkine is a potential agent for the prevention of photoreceptor degeneration.
Bruton's Tyrosine Kinase Inhibitors Prevent Therapeutic Escape in Breast Cancer Cells (2016)

We have reported that a novel isoform of BTK (BTK-C) expressed in breast cancer protects these cells from apoptosis. In this study, we show that recently developed inhibitors of BTK, such as ibrutinib (PCI-32765), AVL-292, and CGI-1746, reduce breast cancer cell survival and prevent drug-resistant clones from arising. Ibrutinib treatment impacts HER2(+) breast cancer cell viability at lower concentrations than the established breast cancer therapeutic lapatinib. In addition to inhibiting BTK, ibrutinib, but not AVL-292 and CGI-1746, efficiently blocks the activation of EGFR, HER2, ErbB3, and ErbB4. Consequently, the activation of AKT and ERK signaling pathways are also blocked leading to a G1-S cell-cycle delay and increased apoptosis. Importantly, inhibition of BTK prevents activation of the AKT signaling pathway by NRG or EGF that has been shown to promote growth factor-driven lapatinib resistance in HER2(+) breast cancer cells. HER2(+) breast cancer cell proliferation is blocked by ibrutinib even in the presence of these factors. AVL-292, which has no effect on EGFR family activation, prevents NRG- and EGF-dependent growth factor-driven resistance to lapatinib in HER2(+) breast cancer cells. In vivo, ibrutinib inhibits HER2(+) xenograft tumor growth. Consistent with this, immunofluorescence analysis of xenograft tumors shows that ibrutinib reduces the phosphorylation of HER2, BTK, Akt, and Erk and histone H3 and increases cleaved caspase-3 signals. As BTK-C and HER2 are often coexpressed in human breast cancers, these observations indicate that BTK-C is a potential therapeutic target and that ibrutinib could be an effective drug especially for HER2(+) breast cancer. Mol Cancer Ther; 15(9); 2198-208. ©2016 AACR.
In vivo induced antigenic determinants of<i>Actinobacillus actinomycetemcomitans</i> (2004)

Actinobacillus actinomycetemcomitans is a Gram-negative capnophilic rod and the etiological agent of localized aggressive periodontitis. The genome-wide survey of A. actinomycetemcomitans using in vivo induced antigen technology (IVIAT) has previously resulted in the discovery of antigenic determinants expressed specifically in diseased patients. The present study evaluated the potential of these antigens as putative disease markers, and investigating their contribution to the pathogenesis of the microorganism. Sera from patients had a significantly greater antibody titer than sera from healthy controls against six antigens, which supports the in vivo expression of these antigens, and suggests their usefulness as disease markers. A. actinomycetemcomitans invasion of epithelium-derived HeLa cells resulted in the induction of all three genes tested, as evidenced by real-time PCR. Isogenic mutants of these three genes were constructed and the adhesion and intracellular survival of the mutants was assayed in a competition assay with the wild-type strain. A significant defect in the intracellular survival of two of these mutant strains (orf1402 and orf859) was found. This defect could not be attributed to an adhesion defect. In contrast, a mutation in vapA, a homologue of a novel putative transcriptional regulator, out-competed the wild-type strain in the same assay. The virulent phenotype was restored for a mutant strain in orf859 upon complementation. This data provided new insight into the pathogenic personality of A. actinomycetemcomitans in vivo and supported the use of HeLa cells as a valid in vitro host–pathogen interactions model for that microorganism. IVIAT is applicable to most pathogens and will undoubtedly lead to the discovery of novel therapies, antibiotics and diagnostic tools.
ChemInform Abstract: Bicyclic Pyrazolidinones, a New Class of Antibacterial Agent Based on the β‐Lactam Model. Bicyclic Pyrazolidinones, Steric and Electronic Effects on Antibacterial Activity. (1987)

Abstract The pyrazolidinium ylides (I), (VII), and (XI) undergo 1,3‐dipolar cycloaddition reaction with the acetylenedicarboxylates (II) or (XIII) to produce bicyclic pyrazole derivatives such as (XII).
Noninvasive bone replacement with a new injectable calcium phosphate biomaterial (2003)

The use of injectable calcium phosphate (CaP) biomaterials in noninvasive surgery should provide efficient bone colonization and implantation. Two different kinds of injectable biomaterials are presently under development: ionic hydraulic bone cements that harden in vivo after injection, and an association of biphasic calcium phosphate (BCP) ceramic granules and a water-soluble polymer vehicle (a technique particularly investigated by our group), providing an injectable CaP bone substitute (IBS). In our study, we compared these two approaches, using physicochemical characterizations and in vivo evaluations in light microscopy, scanning electron microscopy, and three-dimensional microtomography with synchrotron technology. Three weeks after implantation in rabbit bone, both biomaterials showed perfect biocompatibility and bioactivity, but new bone formation and degradation of the biomaterial were significantly greater for BCP granules than for ionic cement. Newly formed bone developed, binding the BCP granules together, whereas new bone grew only on the surface of the cement, which remained dense, with no obvious degradation 3 weeks after implantation. This study confirms that BCP granules carried by a cellulosic polymer conserve bioactivity and are conducive to earlier and more extensive bone substitution than a carbonated-hydroxyapatite bone cement. The presence of intergranular spaces in the BCP preparation, as shown on microtomography imaging, seems particularly favorable, allowing body fluids to reach each BCP granule immediately after implantation. Thus, the IBS functions as a completely interconnected ceramic with total open macroporosity. This new bone replacement approach should facilitate microinvasive bone surgery and local delivery of bone therapy agents.
Trading Relative Performance with Alpha Indexes (2011)

Relative performance is central to investment management, and yet relative performance securities do not trade directly. Complex trading strategies must be devised to capture relative gains. The authors introduce a suite of relative performance indexes and index derivatives that offer new and attractive payoff structures. They demonstrate a variety of ways in which these products can provide a more efficient and cost-effective means of realizing investment objectives than can traditional futures and option markets.
Highly efficient nonlinear filter for femtosecond pulse contrast enhancement and pulse shortening (2008)

We propose a highly efficient scheme for temporal filters devoted to femtosecond pulse contrast enhancement. The filter is based on cross-polarized wave generation with a spatially suger-Gaussian-shaped beam. In a single nonlinear crystal scheme the energy conversion to the cross-polarized pulse can reach 28%. We demonstrate that the process enables a significant spectral broadening. For an efficiency of 23% the pulse shortening is estimated to 2.2, leading to an intensity transmission of the nonlinear filter of 50%.
Dispersionless metasurfaces using dispersive meta-atoms (2016)

We introduce a technique for engineering the chromatic dispersion of metasurfaces using dispersive meta-atoms. Using this technique, we experimentally demonstrate dispersionless dielectric metasurface focusing mirrors with negligible chromatic dispersion over a 10% fractional bandwidth.
HSPC117 Is the Essential Subunit of a Human tRNA Splicing Ligase Complex (2011)

Splicing of mammalian precursor transfer RNA (tRNA) molecules involves two enzymatic steps. First, intron removal by the tRNA splicing endonuclease generates separate 5' and 3' exons. In animals, the second step predominantly entails direct exon ligation by an elusive RNA ligase. Using activity-guided purification of tRNA ligase from HeLa cell extracts, we identified HSPC117, a member of the UPF0027 (RtcB) family, as the essential subunit of a tRNA ligase complex. RNA interference-mediated depletion of HSPC117 inhibited maturation of intron-containing pre-tRNA both in vitro and in living cells. The high sequence conservation of HSPC117/RtcB proteins is suggestive of RNA ligase roles of this protein family in various organisms.
An Additive Manufacturing Technique for the Facile and Rapid Fabrication of Hydrogel-based Micromachines with Magnetically Responsive Components (2018)

Polyethylene glycol (PEG)-based hydrogels are biocompatible hydrogels that have been approved for use in humans by the FDA. Typical PEG-based hydrogels have simple monolithic architectures and often function as scaffolding materials for tissue engineering applications. More sophisticated structures typically take a long time to fabricate and do not contain moving components. This protocol describes a photolithography method that allows for facile and rapid microfabrication of PEG structures and devices. This strategy involves an in-house developed fabrication stage that allows for the rapid fabrication of 3D structures by building upwards in a layer-by-layer fashion. Independent moving components can also be aligned and assembled onto support structures to form integrated devices. These independent components are doped with superparamagnetic iron oxide nanoparticles that are sensitive to magnetic actuation. In this manner, the fabricated devices can be actuated using external magnets to yield movement of the components within. Hence, this technique allows for the fabrication of sophisticated MEMS-like devices (micromachines) that are composed entirely out of a biocompatible hydrogel, able to function without an onboard power source, and respond to a contact-less method of actuation. This manuscript describes the fabrication of both the fabrication set-up as well as the step-by-step method for the microfabrication of these hydrogels-based MEMS-like devices.
How We Found The Missing Memristor (2008)

It's time to stop shrinking. Moore's Law, the semiconductor industry's obsession with the shrinking of transistors and their commensurate steady doubling on a chip about every two years, has been the source of a 50-year technical and economic revolution. Whether this scaling paradigm lasts for five more years or 15, it will eventually come to an end. The emphasis in electronics design will have to shift to devices that are not just increasingly infinitesimal but increasingly capable.
A Modular Subsea Direct-Current Electrical-Power System (2014)

Subsea processing has been increasingly accepted by the offshore oil and gas industry as a solution to boost production and reduce cost. Accordingly, the subsea power demand is growing to support various processing loads, including pumps and compressors. Depending on the application, the power rating of a field ranges from tens of kilowatts to tens of megawatts, and the step-out distance ranges from a few kilometers to hundreds of kilometers. Considering the hostile and remote environment, a reliable subsea electrical-power system that is suitable for subsea deployment is clearly desired. This paper presents a modular direct-current electrical-power system that is designed for use in a subsea field with medium or long step-out distance. The proposed system consists of multiple modular converters in the subsea station to achieve the required power-conversion functions. It features high reliability, high flexibility, and reduced installation weight. The system operation and protection are presented, and the performance is verified by a laboratory-scale demonstration.
Experimental Demonstration of an Omni-Resonant Optical Micro-cavity (2017)

By simultaneously phase-matching an angularly multiplexed 60-nm-wide spectrum, we render a Fabry-Perot microcavity having 0.7-nm-wide resonances ‘omni-resonant’, such that it continuously resonates across multiple bare-cavity FSRs.
Inhibition of atopic dermatitis‐like skin lesions by topical application of a novel ceramide derivative, K6PC‐9p, in NC/Nga mice (2008)

Atopic dermatitis (AD) is a chronic inflammatory skin disease that commonly begins in childhood. K6PC-9p (N-(Ethyl dihydrogenphosphate)-2-hexyl-3-oxo-decanamide) is a synthetic ceramide derivative of PC-9S (N-Ethanol-2-mirystyl-3-oxo-staramide), which was known to be effective in atopic patients. In this study, we examined the effect of topical application of K6PC-9p on skin inflammation and AD-like skin lesions in mouse models. K6PC-9p dose-dependently inhibited phorbol ester-induced increase in ear thickness in BALB/c mice. Moreover, topical application of K6PC-9p suppressed dust mite extract-induced AD-like skin lesions in NC/Nga mice. Histopathological analysis revealed that both ear swelling and leucocyte infiltration were suppressed by K6PC-9p treatment. K6PC-9p also suppressed IL-4 and TNF-alpha expression in the ears and mast cell infiltration into the ears in NC/Nga mice. Further study demonstrated that K6PC-9p inhibited ConA-induced IL-4 secretion and LPS-induced macrophage activation. Taken together, our results showed that topical application of K6PC-9p exerts beneficial effects in animal model of skin inflammation and AD, suggesting that K6PC-9p might be a promising topical agent for the treatment of inflammatory skin diseases.
An on-chip ESD protection circuit with complementary SCR structures for submicron CMOS ICs (2002)

A new on-chip ESD protection circuit with complementary SCR structures is proposed. This circuit can provide ESD protection above /spl plusmn/6500 V and /spl plusmn/400 V in human-body-mode and machine-mode ESD stresses, respectively, with the total layout area of 108 /spl mu/m/spl times/242 /spl mu/m including the latchup guard-ring of 10-/spl mu/m width and a 90 /spl mu/m/spl times/90 /spl mu/m metal pad for wire bonding.
Recombinant allergens for immunobtot diagnosis of tree-pollen atlergy (1991)

recombinant allergens without additional fused polypeptides, both cDNAs were inserted into the plasmid pKK223-3. E. coli cells expressing Bet v I and birch proj’ilin (Bet v II) were used for the preparation of recombinant proteins. These proteins were tested for their IgE-binding properties on immunoblots with sera from 100 difSerent birch pollen-allergic patients. All patients’ sera, which reacted with the natural allergens, Bet v I and Bet v II, demonstrated an identical IgE-binding pattern to recombinant birch-pollen allergens. Recombinant allergens may therefore be useful for the setup of diagnostic tests that allow the discrimination of difSerent IgE-binding patterns as well as for patient-tailored immunotherapy. (J ALLERGY CLIN IMMIJNOL 1991;88:889-94.)
A real-time auto white balance algorithm for mobile phone cameras (2012)

Auto white balance (AWB), a critical component of the image pipeline in digital cameras, is responsible for producing accurate color by automatically removing the undersired color cast introduced by the illumination. AWB estimates the scene illumination by processing the digital values of the pixels in the captured image; therefore, objects colors in the scene are often confused with the color of the light source, leading to wrong color cast in white balanced images. In this paper, we propose a color histogram based AWB algorithm that is capable of producing accurate color in the presence of dominant object colors. Our approach is based on a statistical estimation of the probabilities of colors in natural scenes under different illuminations. These statistics can be easily collected during the AWB calibration phase using standard equipment. The proposed AWB algorithm is computationally efficient and runs real-time in a mobile phone camera.