gebhart/patrepeval huggingface dataset:
Gastrointestinal motility responses to the S and R enantiomers of zacopride, a 5‐HT4 agonist and 5‐HT3 antagonist (1992)

Abstract Zacopride is an antiemetic agent whose (S) and (R) stereoisomers demonstrate differential pharmacology at 5‐HT3 receptors, emphasizing the importance of pharmacologic profiling of each enantiomer of a racemic drug mixture. Characterization of the gastrointestinal motility‐enhancing activities of the enantiomers relative to their 5‐HT3 antagonist properties was done both in vivo and in vitro. In dogs at a dose of 0.3 mg/kg, IV, the (S) antipode was more active in stimulating gastric antral contractions and gastric emptying of a solid meal than (R) zacopride. The (S) enantiomer was also at least 10 times more potent in enhancing gastric emptying in rats. The potency of (S) zacopride at the putative prokinetic receptor (5‐HT4) was 3.3 times greater than that of (R) zacopride in rat esophageal tunica muscularis mucosae strips. The greater potency of (S) zacopride over the (R) antipode for motility stimulation was also observed for its 5‐HT3 antagonism in dogs. (S) zacopride almost completely blocked cisplatin emesis at 0.01 mg/kg, IV, while (R) zacopride was inactive. However, both enantiomers were more active as antiemetics than as prokinetics in the dog. More potent activity at the 5‐HT3 than the 5‐HT4 receptor was also demonstrated for both enantiomers in vitro. Additionally, in antagonizing 2‐methyl‐5‐HT contractions in guinea pig ileum, the (S) antipode was again more potent than the (R). In summary, (S) zacopride is more potent than the (R) enantiomer for both 5‐HT3 antagonism and prokinetic activity, with 5‐HT3 antagonism, rather than motility enhancement (5‐HT4 agonism), being the primary activity of both zacopride stereoisomers. © 1992 Wiley‐Liss, Inc.
Deep Learning Based Speech Beamforming (2018)

Multi-channel speech enhancement with ad-hoc sensors has been a challenging task. Speech model guided beamforming algorithms are able to recover natural sounding speech, but the speech models tend to be oversimplified or the inference would otherwise be too complicated. On the other hand, deep learning based enhancement approaches are able to learn complicated speech distributions and perform efficient inference, but they are unable to deal with variable number of input channels. Also, deep learning approaches introduce a lot of errors, particularly in the presence of unseen noise types and settings. We have therefore proposed an enhancement framework called DEEPBEAM, which combines the two complementary classes of algorithms. DEEPBEAM introduces a beamforming filter to produce natural sounding speech, but the filter coefficients are determined with the help of a monaural speech enhancement neural network. Experiments on synthetic and real-world data show that DEEPBEAM is able to produce clean, dry and natural sounding speech, and is robust against unseen noise.
Oxygen Free Radical Induced Damage in Kidneys Subjected to Warm Ischemia and Reperfusion (1985)

Superoxide anion free radical (O2-.) has been implicated in the pathogenesis of tissue injury consequent to ischemia/reperfusion in several different organs, including heart and bowel. Superoxide dismutase (SOD), an enzyme free radical scavenger specific for O2-., has been used successfully to protect these organs from structural damage during reoxygenation of ischemic tissue. It has been suggested that the catalytic action of xanthine oxidase in injured tissue is an important source of O2-. during reoxygenation. In order to evaluate the potential of SOD to protect against kidney damage resulting from transient ischemia followed by reperfusion with oxygenated blood, a model of warm renal ischemia was studied. LBNF1 rats underwent right nephrectomy and occlusion of the left renal artery for 45 minutes. Survival in the group of ischemic untreated rats (N = 30) was 56% at 7 days and serum creatinine was greatly elevated (p less than 0.01) in rats remaining alive over the full 7-day period. In strong contrast to these results, all of the animals treated with SOD before reperfusion (N = 18) were alive after 7 days similar to sham operated control rats (N = 8). Serum creatinine in the SOD treated rats was significantly elevated only to postoperative day 3 and thereafter returned to normal. Rats treated with inactive SOD (N = 4) or SOD before ischemia (N = 4) had decreased survival rates compared to ischemic untreated animals and prolonged elevation of serum creatinine. When the ischemia time was extended to 60 minutes, only 19% of the untreated animals (N = 16) survived at 7 days whereas nearly 60% of the SOD-treated animals survived (N = 19). Serum creatinine was greatly elevated during the full 7-day observation period in all surviving rats in the untreated ischemic group, whereas serum creatinine returned to normal (p less than 0.05) after 4 days in the surviving rats treated with SOD. To test whether the action of xanthine oxidase contributed to the kidney damage after reoxygenation, 45 min. ischemic rat kidneys were treated with allopurinol. All of the animals treated with allopurinol (N = 12) were alive at 7 days. Serum creatinine values returned to normal after the episode of ischemia and reperfusion but more slowly than after SOD treatment. Histologic evaluation of kidney tissue taken from animals after ischemia alone showed extensive renal tubular damage, which was essentially absent in kidneys from SOD-treated animals.(ABSTRACT TRUNCATED AT 400 WORDS)
The Adeno-Associated Virus Genome Packaging Puzzle (2015)

Chen Ling1,2, Yuan Wang1-3, Yuan Lu4, Lina Wang1-3, Giridhara R Jayandharan5, George V Aslanidi1,2, Baozheng Li1,2, Binbin Cheng1,3, Wenqin Ma1,2, Thomas Lentz6, Changquan Ling3, Xiao Xiao6,7, R Jude Samulski6, Nicholas Muzyczka2,8,9 and Arun Srivastava1,2,8-10* 1Division of Cellular and Molecular Therapy, Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL, USA 2Powell Gene Therapy Center, University of Florida College of Medicine, Gainesville, FL, USA 3Department of Traditional Chinese Medicine, Changhai Hospital, Second Military Medical University, Shanghai, China 4Department of Orthopedics & Rehabilitative Medicine, University of Florida College of Medicine, Gainesville, FL, USA 5Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India 6Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA 7Division of Molecular Pharmaceutics, University of North Carolina School of Pharmacy, Chapel Hill, NC, USA 8Department of Molecular Genetics & Microbiology, University of Florida College of Medicine, Gainesville, FL, USA 9Genetics Institute, University of Florida College of Medicine, Gainesville, FL, USA 10Shands Cancer Center, University of Florida College of Medicine, Gainesville, FL, USA *Corresponding author: Arun Srivastava, Division of Cellular & Molecular Therapy, Cancer and Genetics Research Complex, 2033 Mowry Road, Room 492-A, Gainesville, FL 32611-3633, USA, Tel: (352) 273-8259; Fax: (352) 273-8342; E-mail: aruns@peds.ufl.edu
Role of Selected Indian Plants in Management of Type 2 Diabetes: A Review (2004)

Type 2 diabetes has become a global epidemic. Modern medicines, despite offering a variety of effective treatment options, can have several adverse effects. Ayurveda, a science that uses herbal medicines extensively, originated in India. Of considerable interest is the adoption of Ayurveda by the mainstream medical system in some European countries (e.g., Hungary), emphasizing this modality is increasing worldwide recognition. From ancient times, some of these herbal preparations have been used in the treatment of diabetes. This paper reviews the accumulated literature for 10 Indian herbs that have antidiabetic activity and that have been scientifically tested. Few of these herbs, such as Momordica charantia, Pterocarpus marsupium, and Trigonella foenum greacum, have been reported to be beneficial for treating type 2 diabetes. Mechanisms such as the stimulating or regenerating effect on beta cells or extrapancreatic effects are proposed for the hypoglycemic action of these herbs.
Adiabatically widened silicon microrings for improved variation tolerance (2014)

We show that silicon microrings with adiabatically widened bends are more tolerant to dimensional variations than conventional microring designs with uniform waveguide widths. Through wafer-scale measurements of test structures fabricated in the IMEC Standard Passives process (193 nm DUV lithography, 200 mm SOI wafer), improvements in the intra-die and wafer-scale variation of the resonance wavelength are demonstrated. A 2.1× reduction in the standard deviation of the resonance wavelength across the wafer was observed.
Transfer of experimental allergic orchitis with immune RNA studies in vivo. (1978)

Ribonucleic acid extracts (RNA) obtained from the lymph nodes and spleens of guinea pigs, which were immunized with testicular antigen emulsified in Freund's complete adjuvant (FCA), were injected intraperitoneally into normal guinea pigs. The transferred guinea pigs developed a delayed hypersensitivity to sperm antigens and testicular lesions which resembled the lesions obtained in the donor RNA guinea pigs. When the transfer was performed with RNA extracted from guinea pigs immunized with FCA alone or with 'immune' RNA treated with Ribonuclease, neither cellular immunity nor testicular lesions were observed.
N-centered radicals (1998)

Reactions of NO in the Gaseous Phase (G. Dorthe). Gas Phase Reactions of Nitrogen Dioxide (B. Weiner & K. Barnhard). Nitrogen Dioxide Reactivity Toward Organic Donors in the Liquid Phase (E. Bosch & J. Kochi). Reactions of NO2 in Argon Matrices (M. Nakata). Nitrogen Dioxide in Biology: Correlating Chemical Kinetics with Biological Effects (P. Wardman). Toxicity of Nitrogen Oxides (N. Elsayed). Experimental Study of the Nitrate Radical (R. Wayne). Reactions of NO3 Radicals in the Gas Phase (G. LeBras). Reactions of NO3-Radicals in Aqueous Solution (H. Hermann & R. Zellner). Reactions of NO3 Radicals in Organic Solvents (O. Ito). NOx in the Atmosphere (C. Cantrell). NO2 and NO3 Radicals in the Radiolysis of Nitric Acid Solutions (Y. Katsumura). NH Radical Reactions (W. Hack). Reactions of NH2 in the Gas Phase (A. Mebel, et al.). The NH2 Radical in Aqueous Solutions (Z. Alfassi, et al.). Reactions of NCO and NCS Radicals (J. Hershberger). SCN and OCN Radicals in Aqueous Solutions (Z. Alfassi). Imidyl Radicals (J. Lind & G. Merenyi). Indolyl Radicals (L. Candeias). Anilinyl Radicals (G. Merenyi & J. Lind). Chemistry of Nitroarene and Aromatic N-oxide Radicals (P. Wardman). Homolytic Addition Reactions of Dialkylaminyl Radicals (B. Maxwell & J. Tsanaktsidis). Thermochemistry of N-Centered Radicals (D. Armstrong). Index.
Human IgG1 and IgG3 recognition of Schistosoma mansoni 14kDa fatty acid-binding recombinant protein. (2000)

The Schistosoma mansoni gene coding for a 14-kDa fatty acid-binding protein was amplified by PCR and subcloned into the prokaryotic expression vector pMAL-c2. Escherichia coli DH5alpha was transformed with the pMAL-Sm14 construct, and gene expression was induced hr isopropyl-beta-D-thiogalactopyranoside. The resulting recombinant (r) fusion protein was purified by affinity chromatography and confirmed by immunoblot analysis using antimaltose-binding protein or anti-Sm14 antibodies. Additionally, an antibody isotype profile was determined in sera of schistosomiasis patients to rSm14 or soluble adult worm antigen preparation. IgG1 and IgG3 subclass antibodies to rSm14 were predominant in sera of all patients studied whereas low levels of IgM, IgA or IgE were measured. Expression of a S. mansoni gene encoding a vaccine candidate is an important step to better study human immune responses to defined antigens.
Content-addressable memories for storing and processing recursively subdivided images and trees (1987)

Content-addressable memories may be arranged to store three-state information in a reliable and efficient manner. They can be applied to the representation of tree structures used in some graphic display applications, such as quadtrees and octrees, avoiding the need for pointers, and speeding up many operations. Examples are given for picture updating and scan conversion.
Next major application systems and key techniques in speech recognition technology (2002)

We discuss several major speech recognition applications which will contribute to some human activities in a decade. At first, Japanese speech-related national projects directed toward future intelligent systems are reviewed. Then we discuss three systems as the next major speech applications: substantially robust systems, multimodal interaction systems and multilingual dialogue systems. The evaluation of the performance of these systems is separately discussed in view of both total systems and specific technologies. We suggest that the degree of the difficulty of some kinds of specific tasks can be even more precisely measured, while the total system performance evaluation will become more difficult in future complex systems. Last, we take up phrase spotting, distance calculation for phonetic symbol sequences, adaptation/learning, and software modularization/multi-agents as the key techniques in constructing the above applications.
Cofactor Regeneration by a Soluble Pyridine Nucleotide Transhydrogenase for Biological Production of Hydromorphone (2000)

We have applied the soluble pyridine nucleotide transhydrogenase of Pseudomonas fluorescens to a cell-free system for the regeneration of the nicotinamide cofactors NAD and NADP in the biological production of the important semisynthetic opiate drug hydromorphone. The original recombinant whole-cell system suffered from cofactor depletion resulting from the action of an NADP(+)-dependent morphine dehydrogenase and an NADH-dependent morphinone reductase. By applying a soluble pyridine nucleotide transhydrogenase, which can transfer reducing equivalents between NAD and NADP, we demonstrate with a cell-free system that efficient cofactor cycling in the presence of catalytic amounts of cofactors occurs, resulting in high yields of hydromorphone. The ratio of morphine dehydrogenase, morphinone reductase, and soluble pyridine nucleotide transhydrogenase is critical for diminishing the production of the unwanted by-product dihydromorphine and for optimum hydromorphone yields. Application of the soluble pyridine nucleotide transhydrogenase to the whole-cell system resulted in an improved biocatalyst with an extended lifetime. These results demonstrate the usefulness of the soluble pyridine nucleotide transhydrogenase and its wider application as a tool in metabolic engineering and biocatalysis.
Gene Expression of the Two Heavy Chains and One Light Chain Forming the Inter-Alpha-Trypsin-Inhibitor in Human Tissues. (1998)

Human inter-alpha-trypsin-inhibitor (ITI) is a serine proteinase inhibitor with a molecular weight of 220 kDa which consists of 3 different polypeptides. The constitutive components are 2 heavy chains (H1 and H2 chains) and 1 light chain (L chain), and its inhibitory activity is considered to be derived from this L chain. It has also been reported that this L chain is almost identical to the trypsin inhibitor (UTI) occurring in human urine. We examined the gene expression of the ITI constitutive peptides in human tissues using the reverse transcription (RT) -PCR technique. As a result, the genes of the H1 chain were found to be expressed in various tissues, particularly strongly in the liver. On the other hand, the genes of the H2 chain were found to be strongly expressed in the adrenal glands, brain, kidneys, and lungs, as well as the liver. Further, the PCR amplification product of the L chain was strongly detected not only in the liver but also in the pancreas, kidneys, lungs, stomach and testes. These results suggest the possibility that the major tissue which produces ITI is the liver, and the H chains and L chain (UTI) are produced as a component of ITI- related proteins in other tissues as well as in the liver.
Ultrastructural localization of plasma membrane-associated urokinase-type plasminogen activator at focal contacts. (1988)

We have recently shown that urokinase-type plasminogen activator (u-PA) and plasminogen activator inhibitor type 1 are both found extracellularly beneath cultured human skin fibroblasts and HT-1080 sarcoma cells, but in distinct localizations. Here, the ultrastructural distribution of u-PA was studied using immunoferritin electron microscopy. In HT-1080 cells, u-PA on the extracellular aspect of the plasma membrane was detected at sites of direct contact of the cell with the growth substratum beneath all parts of the ventral cell surface. The ferritin-labeled adhesion plaques, which were enriched in submembraneous microfilaments, were frequently seen at the leading lamellae of the cells as well as in lamellipodia and microspikes. Besides the cell-substratum adhesion plaques, ferritin label was detected at cell-cell contact sites. Double-label immunofluorescence showed a striking colocalization of u-PA and vinculin in both HT-1080 cells and WI-38 lung fibroblasts, which is consistent with u-PA being a focal contact component. The u-PA-containing focal contacts of WI-38 cells had no direct codistribution with fibronectin fibrils. In WI-38 cells made stationary by cultivation in a medium containing 0.5% FCS, vinculin plaques became highly elongated and more centrally located, whereas u-PA immunolabel disappeared from such focal adhesions. These findings show that plasma membrane-associated u-PA is an intrinsic component of focal contacts, where, we propose, it enables directional proteolysis for cell migration and invasion.
Testability prediction for sequential circuits using neural networks (2002)

Test generation algorithms are being developed with the continuous creation of incredibly sophisticated computer systems. Although dozens of algorithms have been proposed to cope with these issues, there still remains much to be desired in solving such problems as to determine: which of the existing test generation algorithms could be the most efficient for some particular sequential circuits because different algorithms will be better in different circuits; which testability parameters will have the most or the least influences on test generations so that the designers of circuits can have a global understanding during the designing stage. Testability predicting methodology for sequential circuits using a neural network model has been presented, which a user usually needs for analyzing his/her own circuits and selecting the most suitable test generation algorithm from all the possible algorithms they have, and which a designer for VLSI circuits always needs for making his/her circuits being designed more testable.
Femtosecond Dynamics of Electron Localization at Interfaces (1998)

The dynamics of two-dimensional small-polaron formation at ultrathin alkane layers on a silver(111) surface have been studied with femtosecond time- and angle-resolved two-photon photoemission spectroscopy. Optical excitation creates interfacial electrons in quasi-free states for motion parallel to the interface. These initially delocalized electrons self-trap as small polarons in a localized state within a few hundred femtoseconds. The localized electrons then decay back to the metal within picoseconds by tunneling through the adlayer potential barrier. The energy dependence of the self-trapping rate has been measured and modeled with a theory analogous to electron transfer theory. This analysis determines the inter- and intramolecular vibrational modes of the overlayer responsible for self-trapping as well as the relaxation energy of the overlayer molecular lattice. These results for a model interface contribute to the fundamental picture of electron behavior in weakly bonded solids and can lead to better understanding of carrier dynamics in many different systems, including organic light-emitting diodes.
Preparation of Genomic DNA from Mammalian Tissue (1993)

There are a number of different procedures for the preparation of genomic DNA. They all start with some form of cell lysis, followed by deproteinization and recovery of DNA. The main differences between various approaches lie in the extent of deproteinization and in molecular weight of the DNA produced. The isolation procedure described here is relatively brief and relies on the powerful proteolytic activity of proteinase K combined with the denaturing ability of the ionic detergent SDS.
A novel lactonohydrolase responsible for the detoxification of zearalenone: enzyme purification and gene cloning (2002)

Zearalenone (ZEN) is converted into a far less oestrogenic product by incubation with Clonostachys rosea IFO 7063. An alkaline hydrolase responsible for the detoxification was purified to homogeneity from the fungus by a combination of salt precipitation and column chromatography methods. The purified enzyme was homodimeric with a subunit molecular mass of 30 kDa and contained an intra-subunit disulphide bridge. On the basis of the internal peptide sequences of the purified protein, we cloned the entire coding region of the gene (designated as zhd101) by PCR techniques. The ZEN degradation activity was detected in heterologous hosts (Schizosaccharomyces pombe and Escherichia coli) carrying the cloned gene. Zhd101 could be a promising genetic resource for in planta detoxification of the mycotoxin in important crops.
Expanding the Scope of C−H Amination through Catalyst Design (2004)

Analysis of the mechanism for Rh-mediated C-H amination has led to the development of a remarkably effective dinuclear Rh catalyst derived from 1,3-benzenedipropionic acid. This unique complex, Rh2(esp)2, is capable of promoting both intra- and intermolecular C-H oxidation reactions, and in all cases is superior to Rh2(O2CtBu)4. For the first time, C-H insertion is described with urea and sulfamide substrates to give 1,2- and 1,3-diamine derivatives, respectively. In addition, intermolecular amination of benzylic and secondary C-H bonds is shown to proceed efficiently even under conditions in which the starting alkane is employed as the limiting reagent.
EWS/FLI1 Regulates EYA3 in Ewing Sarcoma via Modulation of miRNA-708, Resulting in Increased Cell Survival and Chemoresistance (2012)

Ewing sarcoma is an aggressive pediatric cancer of the bone and soft tissue, in which patients whose tumors have a poor histologic response to initial chemotherapy have a poor overall prognosis. Therefore, it is important to identify molecules involved in resistance to chemotherapy. Herein, we show that the DNA repair protein and transcriptional cofactor, EYA3, is highly expressed in Ewing sarcoma tumor samples and cell lines compared with mesenchymal stem cells, the presumed cell-of-origin of Ewing sarcoma, and that it is regulated by the EWS/FLI1 fusion protein transcription factor. We further show that EWS/FLI1 mediates upregulation of EYA3 via repression of miR-708, a miRNA that targets the EYA3 3'-untranslated region, rather than by binding the EYA3 promoter directly. Importantly, we show that high levels of EYA3 significantly correlate with low levels of miR-708 in Ewing sarcoma samples, suggesting that this miR-mediated mechanism of EYA3 regulation holds true in human cancers. Because EYA proteins are important for cell survival during development, we examine, and show, that loss of EYA3 decreases survival of Ewing sarcoma cells. Most importantly, knockdown of EYA3 in Ewing sarcoma cells leads to sensitization to DNA-damaging chemotherapeutics used in the treatment of Ewing sarcoma, and as expected, after chemotherapeutic treatment, EYA3 knockdown cells repair DNA damage less effectively than their control counterparts. These studies identify EYA3 as a novel mediator of chemoresistance in Ewing sarcoma and define the molecular mechanisms of both EYA3 overexpression and of EYA3-mediated chemoresistance.