gebhart/patrepeval huggingface dataset:
The Brugia malayi genome project: expressed sequence tags and gene discovery (2002)

To advance and facilitate molecular studies of Brugia malayi, one of the causative agents of human lymphatic filariasis, an expressed sequence tag (EST)-based gene discovery programme has been carried out. Over 22,000 ESTs have been produced and deposited in the public databases by a consortium of laboratories from endemic and non-endemic countries. The ESTs have been analysed using custom informatic tools to reveal patterns of individual gene expression that may point to potential targets for future research on anti-filarial drugs and vaccines. Many genes first discovered as ESTs are now being analysed by researchers for immunodiagnostic, vaccine and drug target potential. Building on the success of the B. malayi EST programme, significant EST datasets are being generated for a number of other major parasites of humans and domesticated animals, and model parasitic species.
Short-Term Dose–Response Characteristics of 2-Iminobiotin Immediately Postinsult in the Neonatal Piglet After Hypoxia-Ischemia (2013)

Based on survival with a normal aEEG, 0.2 mg/kg 2-IB is likely to be the most appropriate dose for use in future clinical trials in neonates with perinatal hypoxia-ischemia.
Purification and Characteristics of a Novel Transglutaminase Derived from Microorganisms (1989)

A microorganism producing transglutaminase was screened as an indication of hydroxamate- forming activity. The microbial transglutaminase was purified from the culture filtrate of the strain, S- 8112, which was supposed to belong to the genus Streptoverticillium. The molecular weight of the purified enzyme was found to be about 40,000 on SDS-polyacrylamide gel electrophoresis, the isoelectric point 8.9 and the optimal pH of the reaction 6~7. The present enzyme requires no calcium ions for its activity. Thus, it clearly differs from known transglutaminases derived from mammalian organs, which have been defined as calcium-dependent enzymes.
Characterization of cDNA clones encoding guinea pig neutrophil cationic peptides (1991)

cDNA clones encoding antimicrobial guinea pig neutrophil cationic peptides GNCP-1 and GNCP-2 were isolated from a bone marrow cell cDNA library. Analysis of these clones indicated that both GNCPs were produced as precursor proteins comprising 93 amino acid residues, which were composed of signal sequences (N-terminal 19 residues), pro-peptide sequences (43 residues) and mature GNCP sequences (31 residues). The deduced amino acid sequences showed that there were only two amino acid differences between GNCP-1 and GNCP-2, one in the pro-peptide region and one in the mature peptide region. Interestingly, Northern blot analysis and transcription run-off assay revealed that the expression of GNCP mRNA and the transcription of GNCP gene was observed in bone marrow cells but not in mature neutrophils. These observations suggest that mature neutrophils, despite their abundant content of GNCPs, lose the capacity to synthesize GNCPs.
Deep Adaptive Sampling for Low Sample Count Rendering (2018)

Abstract Recently, deep learning approaches have proven successful at removing noise from Monte Carlo (MC) rendered images at extremely low sampling rates, e.g., 1–4 samples per pixel (spp). While these methods provide dramatic speedups, they operate on uniformly sampled MC rendered images. However, the full promise of low sample counts requires both adaptive sampling and reconstruction/denoising. Unfortunately, the traditional adaptive sampling techniques fail to handle the cases with low sampling rates, since there is insufficient information to reliably calculate their required features, such as variance and contrast. In this paper, we address this issue by proposing a deep learning approach for joint adaptive sampling and reconstruction of MC rendered images with extremely low sample counts. Our system consists of two convolutional neural networks (CNN), responsible for estimating the sampling map and denoising, separated by a renderer. Specifically, we first render a scene with one spp and then use the first CNN to estimate a sampling map, which is used to distribute three additional samples per pixel on average adaptively. We then filter the resulting render with the second CNN to produce the final denoised image. We train both networks by minimizing the error between the denoised and ground truth images on a set of training scenes. To use backpropagation for training both networks, we propose an approach to effectively compute the gradient of the renderer. We demonstrate that our approach produces better results compared to other sampling techniques. On average, our 4 spp renders are comparable to 6 spp from uniform sampling with deep learning‐based denoising. Therefore, 50% more uniformly distributed samples are required to achieve equal quality without adaptive sampling.
Genetic analysis of homomeric interactions of human immunodeficiency virus type 1 integrase using the yeast two-hybrid system. (1993)

The retroviral integrase protein (IN) is responsible for catalyzing a concerted integration reaction in which the two termini of linear viral DNA are joined to host DNA. To probe the potential for IN to form protein multimers, we used the yeast two-hybrid system. The coexpression of a GAL4 DNA binding domain-IN fusion and a GAL4 activation domain-IN fusion together resulted in the successful activation of a GAL4-responsive LacZ reporter gene. The system was used to examine a variety of IN deletion mutants. The results suggest that the central region of the protein is necessary for multimerization and that the N-terminal zinc finger region is not important.
Gene expression of the dibasic-pair cleaving enzyme NRD convertase (N-arginine dibasic convertase) is differentially regulated in the GH3 pituitary and Mat-Lu prostate cell lines (2000)

NRD convertase (N-arginine dibasic convertase, NRD-C) is a dibasic selective metalloprotease which cleaves on the N-terminal side of an arginine residue in a dibasic pair. Abundant in endocrine tissues, the highest levels are found in testis. The mechanism whereby NRD-C expression is regulated at the transcriptional level has been examined by reporter-gene assay and electrophoretic-mobility-shift assays. Analysis of the rat and human promoters show that they are highly conserved, containing a number of motifs which may correspond to transcription-factor binding sites. The rat promoter has been cloned into a luciferase reporter vector and analysed in a number of cell lines. Full functionality of the promoter is observed with 5' deletions to 411 bp upstream of the transcriptional start site in spermatid, prostate and pituitary cell lines. Further deletion to 101 bp causes a complete loss of activity in spermatid and prostate lines. By contrast, GH3 pituitary cells display no reduction in promoter activity with deletion to 101 bp of upstream sequence. A number of transcription-factor binding sites have been identified by electrophoretic-mobility-shift assays in the region 411-101; however, no differences in binding between the cell lines were observed.
A technique towards automatic audio classification and retrieval (2002)

Audio classification is very important in many audio applications so that different audio signals can be processed appropriately. We propose an audio classification scheme which will categorise audio signals based on a number of audio features. These features include silence ratio, spectral centroid, harmonicity and pitch.
Discovery and Development of Fatty Acid Amide Hydrolase (FAAH) Inhibitors (2008)

ADVERTISEMENT RETURN TO ISSUEPerspectiveNEXTDiscovery and Development of Fatty Acid Amide Hydrolase (FAAH) InhibitorsMark Seierstad and J. Guy Breitenbucher*View Author Information Johnson & Johnson Pharmaceutical Research and Development, L.L.C., 3210 Merryfield Row, San Diego, California 92121* To whom correspondence should be addressed. Phone: 858-784-3036. Fax: 858-784-3116. E-mail: [email protected]Cite this: J. Med. Chem. 2008, 51, 23, 7327–7343Publication Date (Web):November 5, 2008Publication History Received19 March 2008Published online5 November 2008Published inissue 11 December 2008https://pubs.acs.org/doi/10.1021/jm800311khttps://doi.org/10.1021/jm800311kreview-articleACS PublicationsCopyright © 2008 American Chemical SocietyRequest reuse permissionsArticle Views4972Altmetric-Citations150LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Inhibition,Inhibitors,Ketones,Peptides and proteins,Rodent models Get e-Alerts
Improvement of Phase-Shifter Edge Line Mask Method (1991)

Two kinds of improved phase-shifter edge line (PEL) masks have been developed for critical dimension control. One new mask consists of a chrome line and partially overlapped shifter film. In this mask, exposed pattern sizes are controlled by adjusting the chrome linewidth. It has been found that a set of repeated fine-chrome lines (“blind”) acts as a uniform light attenuator. The other new mask (“blind PEL mask”) has been devised by combining the “blind” and shifter pattern. These new masks make it possible to delineate different-sized fine patterns (≥0.2 µm) at the same exposure dose. With the “blind PEL-mask”, unnecessary shifter edge patterns can be eliminated by only one-time exposure.
Evaluation of membrane physiology following fluorescence activated or magnetic cell separation (1999)

Both separation procedures modify cell membrane with neither technique being physiologically preferable for subsequent analysis or recultivation of the sorted cells.
New method for high-range resolution measurements of light scattering in optically dense inhomogeneous media (1977)

A method is presented for high-range resolution measurement of the backscatter from a scattering medium located in one arm of an interferometer. The technique is interferometric in nature and relies on the availability of a cw laser with a significant linewidth. The measurement is based on observing coherent interference (equivalent to white-light fringes) between the return from the two arms of the interferometer for the portion of the backscatter that makes the path lengths equal. Experimental results are presented for backscatter from a turbid medium and from a stack of glass plates.
Modification of stevioside using transglucosylation activity of Bacillus amyloliquefaciens α-amylase to reduce its bitter aftertaste (2012)

Stevioside is a natural high-intensity sweetener with low calorie. However, the intrinsic bitter aftertaste limits its application in food products. Transglucosylation of stevioside by α-amylase from Bacillus amyloliquefaciens in the starch solution to produce transglucosylated steviosides with reduced bitter aftertaste was investigated. Under the optimal conditions, the conversion yield of stevioside attained 38.3%. Two major transglucosylated steviosides, which accounted for 96 g/100 g of the total transglucosylated steviosides, were identified to be 13-{[2-O-(β-d-glucopyranosyl)-β-d-glucopyranosyl]oxy} ent-kaur-16-en-19-oic acid 2-O-(α-d-glucopyranosyl)-β-d-glucopyranosyl ester, and 13-{[2-O-(β-d-glucopyranosyl)-β-d-glucopyranosyl]oxy} ent-kaur-16-en-19-oic acid 2-O-[(4- O-α-d-glucopyranosyl)-α-d-glucopyranosyl]-β-d-glucopyranosyl ester by liquid chromatography-tandem mass spectrometry and nuclear magnetic resonance spectroscopy. Sensory evaluation demonstrated that, by enzymatic modification, the sweetness of two major transglucosylated steviosides was significantly improved and the bitter aftertaste was significantly reduced.
Molecular and industrial aspects of glucose isomerase (1996)

Glucose isomerase (GI) (D-xylose ketol-isomerase; EC. 5.3.1.5) catalyzes the reversible isomerization of D-glucose and D-xylose to D-fructose and D-xylulose, respectively. The enzyme has the largest market in the food industry because of its application in the production of high-fructose corn syrup (HFCS). HFCS, an equilibrium mixture of glucose and fructose, is 1.3 times sweeter than sucrose and serves as a sweetener for use by diabetics. Interconversion of xylose to xylulose by GI serves a nutritional requirement in saprophytic bacteria and has a potential application in the bioconversion of hemicellulose to ethanol. The enzyme is widely distributed in prokaryotes. Intensive research efforts are directed toward improving its suitability for industrial application. Development of microbial strains capable of utilizing xylan-containing raw materials for growth or screening for constitutive mutants of GI is expected to lead to discontinuation of the use of xylose as an inducer for the production of the enzyme. Elimination of Co2+ from the fermentation medium is desirable for avoiding health problems arising from human consumption of HFCS. Immobilization of GI provides an efficient means for its easy recovery and reuse and lowers the cost of its use. X-ray crystallographic and genetic engineering studies support a hydride shift mechanism for the action of GI. Cloning of GI in homologous as well as heterologous hosts has been carried out, with the prime aim of overproducing the enzyme and deciphering the genetic organization of individual genes (xylA, xylB, and xylR) in the xyl operon of different microorganisms. The organization of xylA and xylB seems to be highly conserved in all bacteria. The two genes are transcribed from the same strand in Escherichia coli and Bacillus and Lactobacillus species, whereas they are transcribed divergently on different strands in Streptomyces species. A comparison of the xylA sequences from several bacterial sources revealed the presence of two signature sequences, VXW(GP)GREG(YSTAE)E and (LIVM)EPKPX(EQ)P. The use of an inexpensive inducer in the fermentation medium devoid of Co2+ and redesigning of a tailor-made GI with increased thermostability, higher affinity for glucose, and lower pH optimum will contribute significantly to the development of an economically feasible commercial process for enzymatic isomerization of glucose to fructose. Manipulation of the GI gene by site-directed mutagenesis holds promise that a GI suitable for biotechnological applications will be produced in the foreseeable future.
Performance test and analysis of silicon-based microchannel heat sink (1999)

First, a micro cross flow heat sink made of (110)-orientated silicon is fabricated by bulk micromachining, and wafers with hundreds of high aspect ratio channels are bonded together by diffusion bonding with aluminum as medium layers. The core of the micro heat sink is about 0.918 cm<SUP>-3</SUP>, and the density of the heat transfer area if 15,294 m<SUP>2</SUP>/m<SUP>3</SUP>. Using pure water as the working fluid, as the maximum pressure drop reaches 2.47 bar, the flow rate is greater than 4.5 l/min, and that makes the overall heat transfer coefficient up to 24.7 kW/m<SUP>2</SUP>K, corresponds to a volumetric heat transfer coefficient of 188.5 MW/m<SUP>3</SUP>K. Second, we fabricate a series of 40 micrometers wide and 30 mm long micro channels with different aspect ratio is 12 cm<SUP>2</SUP> (110) silicon wafer area. The silicon is anodic bonded with #7740 Pyrex glass to form the micro channel structure. Using pure water as the working fluid, hydraulic resistance and thermal performance of the micro channel structure are evaluated experimentally. As the maximum pressure drop reaches 3.3 bar, the flow rate is 0.3 l/min, and that make the heat transfer coefficient up to 32,598 W/m<SUP>2</SUP>K.
Histone demethylase JMJD2A drives prostate tumorigenesis through transcription factor ETV1 (2016)

Histone demethylase upregulation has been observed in human cancers, yet it is unknown whether this is a bystander event or a driver of tumorigenesis. We found that overexpression of lysine-specific demethylase 4A (KDM4A, also known as JMJD2A) was positively correlated with Gleason score and metastasis in human prostate tumors. Overexpression of JMJD2A resulted in the development of prostatic intraepithelial neoplasia in mice, demonstrating that JMJD2A can initiate prostate cancer development. Moreover, combined overexpression of JMJD2A and the ETS transcription factor ETV1, a JMJD2A-binding protein, resulted in prostate carcinoma formation in mice haplodeficient for the phosphatase and tensin homolog (Pten) tumor-suppressor gene. Additionally, JMJD2A cooperated with ETV1 to increase expression of yes associated protein 1 (YAP1), a Hippo pathway component that itself was associated with prostate tumor aggressiveness. ETV1 facilitated the recruitment of JMJD2A to the YAP1 promoter, leading to changes in histone lysine methylation in a human prostate cancer cell line. Further, YAP1 expression largely rescued the growth inhibitory effects of JMJD2A depletion in prostate cancer cells, indicating that YAP1 is a downstream effector of JMJD2A. Taken together, these data reveal a JMJD2A/ETV1/YAP1 axis that promotes prostate cancer initiation and that may be a suitable target for therapeutic inhibition.
A pharmacologic study of ortho-methoxy-beta-phenyl-Isopropyl methylamine hydrochloride, and 13 related methoxy analogues. (1948)

In the study of a large series of phenyl propylamines several members of the group were found to possess greater bronchodilator activity than ephedrine with little or no pressor action. According to stability and activity the methoxyphenylisopropylamines seemed most interesting. The intravenous toxicities, pressor actions, and bronchodilator properties of 14 of these amines are reported. Ortho-methoxy-β-phenylisopropyl methylamine hydrochloride (‘Orthoxine’), because of its relatively high activity and low toxicity, was investigated further with the following results:

1. In perfusion experiments with isolated lungs using pilocarpine, histamine, or acetyicholine as the constrictor agents, ‘Orthoxine’ was found to be on the average a much more effective agent than ephedrine for relieving bronchoconstriction. Against pilocarpine and histamine it is more than twice as effective as ephedrine and about 1/5 to 1/20 as effective as epinephrine.

2. When tested for activity in relieving intestinal smooth-muscle spasms, using isolated strips of jejunum or ileum, ‘Orthoxine’ was found to be 4 to 8 times as effective as ephedrine against the spasmogenic agents, histamine, acetylcholine and barium chloride. Compared to epinephrine, ‘Orthoxine’ is about 1/10 as effective a barium chloride antagonist. In quieting the normal contractions of the unstimulated intestinal muscle, ‘Orthoxine’ is 5 times as effective as ephedrine. On the non-pregnant uterus, ‘Orthoxine’ is only 1/2 as active as ephedrine in stimulating the muscle to contraction.

3. ‘Orthoxine’ produces little or no pressor response, possessing at most in this regard 1/2000 the activity of epinephrine and 1/8 that of ephedrine. Four times as much ‘Orthoxine’ as ephedrine must be administered to normal dogs to produce the bradycardia characteristic of the latter.

4. Inhibition of histamine bronchoconstriction, vasodepression, and smooth-muscle spasm shows that ‘Orthoxine’ possesses antihistaminic properties. The intestinal smooth-muscle tests indicate that the order of activity is 1/20 that of ‘Benadryl’ but is much greater than that of ephedrine.

5. Except for a higher intravenous toxicity, acute and chronic toxicity tests in rats, rabbits and guinea pigs show that the toxicity of ‘Orthoxine’ is of the same order as that of ephedrine. No pathological changes were found after the continuous daily administration of either 20 or 100 mgm. per kgm. doses for 21 days.

6. The pharmacological properties of ‘Orthoxine’ suggest that it may be of value in the treatment of asthma, for which it is presently being clinically evaluated.
Dynamics of Oxidation of Aluminum Nanoclusters using Variable Charge Molecular-Dynamics Simulations on Parallel Computers (1999)

Oxidation of aluminum nanoclusters is investigated with a parallel molecular-dynamics approach based on dynamic charge transfer among atoms. Structural and dynamic correlations reveal that significant charge transfer gives rise to large negative pressure in the oxide which dominates the positive pressure due to steric forces. As a result, aluminum moves outward and oxygen moves towards the interior of the cluster with the aluminum diffusivity $60%$ higher than that of oxygen. A stable 40 \AA{} thick amorphous oxide is formed; this is in excellent agreement with experiments.
Suppression of juvenile chronic myelogenous leukemia colony growth by interleukin-1 receptor antagonist [see comments] (1994)

Abstract Bone marrow (BM) and peripheral blood (PB) cells from patients with juvenile chronic myelogenous leukemia (JCML) exhibit spontaneous in vitro proliferation. Several cytokines including granulocyte-macrophage colony-stimulating factor (GM-CSF), interleukin-1 beta (IL-1 beta), and tumor necrosis factor alpha (TNF alpha) have been implicated in supporting the growth of leukemic monocyte-macrophage colonies either by autocrine or paracrine pathways. In seven untreated JCML patients, we investigated the role of IL-1 in the spontaneous growth of these cells by specifically blocking IL-1 receptors. The IL-1 receptor antagonist (IL-1 Ra) was added to the clonogenic assays, and in each case significant (mean = 63%, range = 35% to 82%) inhibition of spontaneous proliferation was observed. Uncultured circulating cells from PB or BM of four out of five patients expressed IL-1 beta-specific mRNA and secreted the protein into the culture supernatants. Moreover, by means of reverse transcriptase-polymerase chain reaction (RT-PCR), we demonstrated that most of the spontaneously growing leukemic colony- forming unit cells (CFU-C) obtained from BM cells of two patients were positive for the presence of the IL-1 beta-specific mRNA. Despite the presence of a measurable amount of GM-CSF in JCML cell culture supernatants, GM-CSF-specific mRNA in CFU-C cells of four cases was not detected by RT-PCR. These data further support a central role for IL-1 beta in the pathogenesis of JCML and suggest that the use of IL-1 Ra could represent a novel therapeutic strategy against this disorder.
Aminoacyl-tRNA Synthesis by a Resin-Immobilized Ribozyme (2002)

We report herein a new method for the aminoacylation of tRNA, using a resin-immobilized ribozyme and the cyanomethyl ester (CME) of an amino acid substrate. The oxidized form of the ribozyme was immobilized on a hydrazine resin via covalent linkage. We performed aminoacylation of tRNAs using this ribozyme-resin to isolate aminoacyl-tRNAs. The column was recycled up to 5 times without significant activity loss. Thus, our ribozyme-based aminoacylation system has significant potential to be a powerful and practical technique for supplying various nonnatural aminoacyl-tRNAs for a highly efficient in vitro translation system.
The Anti-Allergic Effects of Lactic Acid Bacteria Are Strain Dependent and Mediated by Effects on both Th1/Th2 Cytokine Expression and Balance (2004)

Improving the consequences of the Th1/Th2 imbalance by administration of LAB was dependent upon the LAB strain rather than the LAB species. Oral KW3110 administration in the mouse allergy model directed the Th1/Th2 balance toward Th1 through the maturation of APCs and inhibition of serum IgE elevation.