gebhart/patrepeval huggingface dataset:
Major extracellular protease of Neurospora crassa (1984)

The inducible extracellular alkaline protease of Neurospora crassa was demonstrated to be a glycoprotein containing D-galactose residues by use of the enzyme-lectin conjugate horseradish peroxidase-Ricinus communis-agglutinin-120. The carbohydrate moiety of the protease appears to be a poor antigen since an antiserum made to the native enzyme recognizes epitopes determined only by the polypeptide portion of the enzyme. Immunochemical techniques were used to quantitatively precipitate protease labeled in vivo for electrophoretic analysis. Protease synthesis could not be detected in control, uninduced cultures, whereas ca. 0.4% of total cellular protein synthesis is devoted to protease formation under inducing conditions.
The C-terminal Domain of 4-Hydroxyphenylacetate 3-Hydroxylase from Acinetobacter baumannii Is an Autoinhibitory Domain (2012)

p-Hydroxyphenylacetate (HPA) 3-hydroxylase from Acinetobacter baumannii consists of a reductase component (C(1)) and an oxygenase component (C(2)). C(1) catalyzes the reduction of FMN by NADH to provide FMNH(-) as a substrate for C(2). The rate of reduction of flavin is enhanced ∼20-fold by binding HPA. The N-terminal domain of C(1) is homologous to other flavin reductases, whereas the C-terminal domain (residues 192-315) is similar to MarR, a repressor protein involved in bacterial antibiotic resistance. In this study, three forms of truncated C(1) variants and single site mutation variants of residues Arg-21, Phe-216, Arg-217, Ile-246, and Arg-247 were constructed to investigate the role of the C-terminal domain in regulating C(1). In the absence of HPA, the C(1) variant in which residues 179-315 were removed (t178C(1)) was reduced by NADH and released FMNH(-) at the same rates as wild-type enzyme carries out these functions in the presence of HPA. In contrast, variants with residues 231-315 removed behaved similarly to the wild-type enzyme. Thus, residues 179-230 are involved in repressing the production of FMNH(-) in the absence of HPA. These results are consistent with the C-terminal domain in the wild-type enzyme being an autoinhibitory domain that upon binding the effector HPA undergoes conformational changes to allow faster flavin reduction and release. Most of the single site variants investigated had catalytic properties similar to those of the wild-type enzyme except for the F216A variant, which had a rate of reduction that was not stimulated by HPA. F216A could be involved with HPA binding or in the required conformational change for stimulation of flavin reduction by HPA.
Nucleotide sequence and genome organization of a Canadian isolate of the common strain of potato virus Y (PVY°) (1996)

(1996). Nucleotide sequence and genome organization of a Canadian isolate of the common strain of potato virus Y (PVY°) Canadian Journal of Plant Pathology: Vol. 18, No. 3, pp. 209-224.
BROADBAND GREEN'S FUNCTION WITH LOW WAVENUMBER EXTRACTION FOR ARBITRARY SHAPED WAVEGUIDE AND APPLICATIONS TO MODELING OF VIAS IN FINITE POWER/GROUND PLANE (2015)

In this paper we developed the method of broadband Green's function with low wavenumber extraction (BBGFL) for arbitrary shaped waveguide. The case of Neumann boundary condition is treated. The BBGFL has the advantage that when using it to solve boundary value problems in a waveguide, the boundary conditions have been satisfied already. The broadband Green's function is expressed in modal expansion of modes that are frequency independent. To accelerate the convergence of the Green's function, a low wavenumber extraction is performed. The singularity of the Green's function is also extracted by such low wavenumber extraction. Numerical results show that BBGLF and direct MoM are in good agreement. We next illustrate the application of BBGFL for broadband simulations of vias in printed circuit boards (PCB) by combining with the method of Foldy-Lax multiple scattering equation. The results show that BBGFL are in good agreement with MoM and HFSS. It is also shown that BBGFL is many times faster than direct MoM and HFSS. The computational efficiency in broadband simulations makes this technique useful for fast computer-aided design (CAD).
VALIDATION OF THE AATSR LST PRODUCT AT THE VALENCIA TEST SITE: 2002 - 2005 CAMPAIGNS (2006)

was validated with ground measurements in a test site close to Valencia, Spain. The test site is located in a large, flat and thermally homogeneous area of rice crops. Experimental campaigns were carried out during the summers of 2002-2005, when the area showed full vegetation cover. Ground LSTs were measured radiometrically along transects covering an area of 1 km 2, concurrently to morning, cloud-free overpasses of the Envisat satellite. A total number of 23 concurrences of ground measurements and AATSR data were obtained. The AATSR LST product is based on the split-window technique (11 and 12 μm channels at nadir), with the algorithm coefficients depending on the land cover type (i) and the vegetation cover fraction (f). Currently, values of i and f are assigned to each pixel according to global maps at spatial resolution of 0.5¥0.5 , which appears too coarse to account for the large heterogeneity of land surfaces. For the Valencia test site, the LST product overestimated the ground LSTs by 3.5 C in average, with a standard deviation of 0.7 C. However, it was shown that the AATSR split-window algorithm worked satisfactorily when the characteristics of the area were adequately prescribed through i and f. In this case, the AATSR derived LSTs agreed with the ground LSTs within ±1.0 C for all 23 concurrences, with nearly zero average error and standard deviation of 0.5 C. Similar results were obtained for other emissivity dependent split-window algorithm also checked with the ground database. Therefore, it is recommended to improve the resolution of i and f to 1 km in the AATSR LST product. 1
[Coral substituted for bone grafting in posterior vertebral arthrodesis in children. Initial results]. (1989)

The authors used natural coral as a substitutive element to bone supply in children in need of posterior vertebral graft. The use of natural coral was part of a protocol aiming at diminishing peroperative bleeding, and as far as possible, at doing away with resorting to homotransfusion. After reviewing the biological, experimental and clinical bases, the authors studied 49 cases of posterior vertebral fusion instrumented with the Cotrel-Dubousset device and with natural coral grafts. Results were appraised with X-ray in all cases, 5 times with scintigraphies and 7 times with biopsies and were encouraging: coral behaves quite similarly to the usual bone graft. From their experience the authors describe how coral is to be used and consider that the use of this substitutive element should spread in the future under various forms.
An Analysis of Bubble Formation Using Microporous Hollow Fiber Membranes (1999)

A study was conducted to characterize bubble formation behavior of pressurized microporous hollow fiber membranes with water flow normal to the fiber axis. The influence of operating conditions such as water velocity (0.07 to 0.6 m/s), gas pressure (275 to 380 kPa), and gas fluxes (0.001 to 0.02 m/s) on bubble formation behavior was examined. Within these operating conditions, bubbles with a diameter smaller than a 100 μm were formed at the membrane surface. Coalescence occurred close to the membrane, which resulted in bubble diameters of 100 to 500 μm above the fiber. Bubble diameters increased with increasing gas flow rate and decreasing water velocity. These effects are expected as they both lead to increased local bubble density and rates of coalescence. Bubble formation behavior of the membrane was predicted well by an empirical equation determined for a single orifice by Ito and Hirata, (1980).
Fluoro‐Substituted n‐Type Conjugated Polymers for Additive‐Free All‐Polymer Bulk Heterojunction Solar Cells with High Power Conversion Efficiency of 6.71% (2015)

Fluorinated n-type conjugated polymers are used as efficient electron acceptor to demonstrate high-performance all-polymer solar cells. The exciton generation, dissociation, and charge-transporting properties of blend films are improved by using these fluorinated n-type polymers to result in enhanced photocurrent and suppressed charge recombination.
A novel dimmable electronic ballast for street lighting with HPS lamps (2002)

A new high frequency dimmable ballast for high-pressure sodium lamps has been developed. This paper describes the novel ELGADI (electronic ballast for gas discharge) topology, which comprises a dedicated interface for dimming and lamp diagnostics. Lamp power can be controlled using a power line modem or an intelligent timer module. A new improved starting technique is also evaluated by monitoring electrode material sputtering. Lamp efficiency is measured over the service life of a lamp with the ELGADI ballast at full power (100%) and in dimming mode (50%). These tests show that dimming has a beneficial effect on costs over the service life of a lamp. The ELGADI ballast has a better lumen efficiency maintenance during lamp service life. The differences between this lamp power control method and ferromagnetic ballasts are explained.
Multiple Transcriptional Domains, With Distinct Left and Right Components, in the Atrial Chambers of the Developing Heart (2000)

During heart development, 2 fast-conducting regions of working myocardium balloon out from the slow-conducting primary myocardium of the tubular heart. Three regions of primary myocardium persist: the outflow tract, atrioventricular canal, and inflow tract, which are contiguous throughout the inner curvature of the heart. The contribution of the inflow tract to the definitive atrial chambers has remained enigmatic largely because of the lack of molecular markers that permit unambiguous identification of this myocardial domain. We now report that the genes encoding atrial natriuretic factor, myosin light chain (MLC) 3F, MLC2V, and Pitx-2, and transgenic mouse lines expressing nlacZ under the control of regulatory sequences of the mouse MLC1F/3F gene, display regionalized patterns of expression in the atrial component of the developing mouse heart. These data distinguish 4 broad transcriptional domains in the atrial myocardium: (1) the atrioventricular canal that will form the smooth-walled lower atrial rim proximal to the ventricles; (2) the atrial appendages; (3) the caval vein myocardium (systemic inlet); and (4) the mediastinal myocardium (pulmonary inlet), including the atrial septa. The pattern of expression of Pitx-2 reveals that each of these transcriptional domains has a distinct left and right component. This study reveals for the first time differential gene expression in the systemic and pulmonary inlets, which is not shared by the contiguous atrial appendages and provides evidence for multiple molecular compartments within the atrial chambers. Furthermore, this work will allow the contribution of each of these myocardial components to be studied in congenitally malformed hearts, such as those with abnormal venous return.
How to Apply a Blocking Gel System for Bullhead Selective Water Shutoff: from Laboratory to Field (2006)

Abstract This paper describes a new method for water control by the use of bullhead injection. A water based gelant is emulsified in oil and injected into the formation. The emulsion is designed to separate into a water phase and an oil phase at static conditions in the formation. Upon reaction in the formation the water phase gels up while the oil phase remains mobile. It has been found that the controlling parameter for disproportionate permeability reduction (DPR) is to control the fraction of gel occupying the porous media. The water fraction in the emulsion controls the reduction in relative oil and water permeabilities. A program was undertaken to verify this DPR method in a field test, using a commercial blocking gel system. The first treatment was performed in well 30/3-A-16 T2 at the Statoil operated Veslefrikk field offshore Norway. Results show that water production was reduced by 30% after the pilot test, while maintaining the oil rate. As expected, total well productivity was reduced by more than 80%. The treatment consisted of 124 m3 emulsion, bullheaded from surface. Step rate testing and ion water analysis were combined to study the relative change in flow contribution between the 6 perforated intervals.
Probiotics and prebiotics in inflammatory bowel disease: microflora ‘on the scope’ (2008)

The intestinal microflora is a large bacterial community that colonizes the gut, with a metabolic activity equal to an organ and various functions that affect the physiology and pathology of the host's mucosal immune system. Intestinal bacteria are useful in promotion of human health, but certain components of microflora, in genetically susceptible individuals, contribute to various pathological disorders, including inflammatory bowel disease. Clinical and experimental observations indicate an imbalance in protective and harmful microflora components in these disorders. Manipulation of gut flora to enhance its protective and beneficial role represents a promising field of new therapeutic strategies of inflammatory bowel disease. In this review, we discuss the implication of gut flora in the intestinal inflammation that justifies the role of probiotics and prebiotics in the prevention and treatment of inflammatory bowel disease and we address the evidence for therapeutic benefits from their use in experimental models of colitis and clinical trials.
Essentiality of fatty acids (1999)

All fatty acids have important functions, but the term "essential" is applied only to those polyunsaturated fatty acids (PUFA) that are necessary for good health and cannot be completely synthesized in the body. The need for arachidonic acid, which is utilized for eicosanoid synthesis and is a constituent of membrane phospholipids involved in signal transduction, is the main reason why the n-6 class of PUFA are essential. Physiological data indicate that n-3 PUFA also are essential. Although eicosapentaenoic acid also is a substrate for eicosanoid synthesis, docosahexaenoic acid (DHA) is more likely to be the essential n-3 constituent because it is necessary for optimal visual acuity and neural development. DHA is present in large amounts in the ethanolamine and serine phospholipids, suggesting that its function involves membrane structure. Because the metabolism of n-6 PUFA is geared primarily to produce arachidonic acid, only small amounts of 22-carbon n-6 PUFA are ordinarily formed. Thus, the essentiality of n-3 PUFA may be due to their ability to supply enough 22-carbon PUFA for optimal membrane function rather than to a unique biochemical property of DHA.
Inhibition of nuclear factor kappa B and induction of apoptosis in T‐lymphocytes by sulfasalazine (1999)

1. Chronic inflammatory diseases have been shown to be associated with NF-kappaB activation and impaired apoptosis of immune cells. The aim of the present study was to investigate if sulfasalazine and its colonic metabolites 5-aminosalicylic acid (5ASA) and sulfapyridine affect NF-kappaB/Rel activation and viability of T-lymphocytes. 2. Sulfasalazine inhibits NF-kappaB/Rel activation in the murine T-lymphocyte cell line RBL5 using electrophoretic mobility shift assays. In transfection assays sulfasalazine treatment for 4 h inhibits kappaB-dependent transcription with an IC50 value of approximately 0.625 mM. 3. Higher doses or prolonged treatment result in cell death of T-lymphocytes in a dose- and time-dependent manner. Cell death is caused by apoptosis as judged by DNA fragmentation, annexin V and Apo 2.7 staining. Induction of apoptosis is a fast event with 50% apoptotic cells after a 4 h incubation with 2.5 mM sulfasalazine. The ED50 value for apoptosis induction after 24 h treatment was approximately 0.625 mM. 4. In contrast, 5ASA and sulfapyridine neither inhibit NF-kappaB/Rel activation nor induce apoptosis in T-lymphocytes at doses up to 5.0 mM. 5. These results demonstrate that sulfasalazine, but not 5ASA or sulfapyridine, strongly inhibits NF-kappaB activation and potently induces apoptosis in T-lymphocytes. Inhibition of NF-kappaB/Rel activation and subsequent clearance of activated T-lymphocytes by apoptosis might thus explain the beneficial effects of sulfasalazine in the treatment of chronic inflammatory disorders.
Fast Training of Triplet-based Deep Binary Embedding Networks (2016)

In this paper, we aim to learn a mapping (or embedding) from images to a compact binary space in which Hamming distances correspond to a ranking measure for the image retrieval task. We make use of a triplet loss because this has been shown to be most effective for ranking problems. However, training in previous works can be prohibitively expensive due to the fact that optimization is directly performed on the triplet space, where the number of possible triplets for training is cubic in the number of training examples. To address this issue, we propose to formulate high-order binary codes learning as a multi-label classification problem by explicitly separating learning into two interleaved stages. To solve the first stage, we design a large-scale high-order binary codes inference algorithm to reduce the high-order objective to a standard binary quadratic problem such that graph cuts can be used to efficiently infer the binary code which serve as the label of each training datum. In the second stage we propose to map the original image to compact binary codes via carefully designed deep convolutional neural networks (CNNs) and the hashing function fitting can be solved by training binary CNN classifiers. An incremental/interleaved optimization strategy is proffered to ensure that these two steps are interactive with each other during training for better accuracy. We conduct experiments on several benchmark datasets, which demonstrate both improved training time (by as much as two orders of magnitude) as well as producing state-of-the-art hashing for various retrieval tasks.
Basal Activation of Transcription Factor Signal Transducer and Activator of Transcription (Stat5) in Nonpregnant Mouse and Human Breast Epithelium (2002)

Transcription factor Stat5 (signal transducer and activator of transcription) is essential for PRL-induced terminal differentiation of mouse mammary epithelial cells during pregnancy and lactation and has been implicated in mammary tumorigenesis. A new and sensitive immunological method to detect active, tyrosine phosphorylated Stat5 in situ revealed that Stat5 is continuously activated in luminal epithelial cells of mouse and human breast, not only during pregnancy and lactation, but also outside of pregnancy. Examination of virgin Stat5a or Stat5b null mice suggested that Stat5a was the primary isoform activated in mammary epithelial cells. Basal activation of Stat5 in mammary epithelium of virgin wild-type mice was continuous throughout estrous cycle and was also detected in 17 of 17 normal human breast tissue specimens analyzed. PRL was identified as the principal factor maintaining basal activation of Stat5 in mammary epithelium of nonpregnant mice based on several lines of evidence. First, administration of PRL, but not GH or epidermal growth factor, uniformly enhanced basal activation of Stat5 in luminal mammary epithelial cells. Second, hypophysectomy disrupted basal activation of Stat5, an effect that was completely reversed by administration of PRL, but only partially by GH. Third, knock-out of the PRL receptor gene markedly reduced basal activation of Stat5, an effect that was maintained in a normalized endocrine environment after transplanting PRL receptor null mammary epithelium into wild-type mice. Continuous activation of Stat5 indicates a role of this transcription factor in normal, nonpregnant breast epithelial cells, and may shed new light on Stat5 involvement in breast tumor promotion.
Implicit time integration for the material point method: Quantitative and algorithmic comparisons with the finite element method (2003)

Abstract An implicit integration strategy was developed and implemented for use with the material point method (MPM). An incremental‐iterative solution strategy was developed around Newton's method to solve the equations of motion with Newmark integration to update the kinematic variables. Test problems directly compared the implicit MPM solutions with those obtained using an explicit MPM code and implicit finite element (FE) code. Results demonstrated very good agreement with FE predictions and also illustrated several advantages in comparison to calculations using the explicit MPM code. In particular, the accuracy of the implicit solution was superior to the explicit MPM when compared to validated FE solutions, and by definition the implicit time integration is unconditionally stable. Similarities between the assembly of the implicit MPM equations and those of the FE method were identified and should allow further algorithmic improvement. Copyright © 2003 John Wiley & Sons, Ltd.
On the effect of Wiener phase noise in OFDM systems (1998)

Multicarrier modulation exhibits a significant sensitivity to the phase noise of the oscillator used for frequency down-conversion at the portable receiver. For this reason, it is important to evaluate the impact of the phase noise on the system performance. We present an accurate method to determine the error probability of an orthogonal frequency-division multiplexing (OFDM) system in the presence of phase noise. In particular, four modulation schemes are analyzed and their performances are compared.
Cecropin P1 and novel nematode cecropins: a bacteria-inducible antimicrobial peptide family in the nematode <i>Ascaris suum</i> (2005)

Cecropin P1 was first identified as a mammalian antimicrobial peptide isolated from the pig intestine. Much research aimed at characterizing this peptide has been reported. Recently, the workers who discovered the peptide corrected their original conclusion, and confirmed that this peptide originates in fact from the pig intestinal parasitic nematode, Ascaris suum. In the present study, we carried out a semi-exhaustive search for bacteria-inducible transcripts in A. suum by the cDNA subtraction method. The transcripts encoding cecropin P1 and novel Ascaris cecropins, designated cecropins P2, P3 and P4, were found to be positively induced factors. Chemically synthesized Ascaris cecropins were bactericidal against a wide range of microbes, i.e. Gram-positive (Staphylococcus aureus, Bacillus subtilis and Micrococcus luteus) and Gram-negative (Pseudomonas aeruginosa, Salmonella typhimurium, Serratia marcescens and Esherichia coli) bacteria, and were weakly but detectably active against yeasts (Saccharomyces cerevisiae and Candida albicans). Cecropin P1-like sequences were also detected at least in two other species (Ascaris lumbricoides and Toxocara canis) of the Ascarididae. All Ascaris cecropin precursors contain an acidic pro-region connected by a tetra-basic cleavage site at the C-terminus. Such an acidic pro-region is also reported to be present in the tunicate cecropin-type antimicrobial peptide styelin. On the basis of the evolutionary position of nematodes and tunicates, the ancestral cecropin may have contained the acidic pro-region at the C-terminus.