gebhart/patrepeval huggingface dataset:
Mutation of Arginine 98, Which Serves as a Substrate-Recognition Site of D-Amino Acid Aminotransferase, Can Be Partly Compensated for by Mutation of Tyrosine 88 to an Arginyl Residue (1997)

D-Amino acid aminotransferase is the only aminotransferase that catalyzes the transamination of D-amino acids. We studied the role of the binding site for the alpha-carboxyl group of substrates, which is presumably crucial for the unique stereospecificity of the enzyme. The site-directed mutagenesis of Arg98, which is the putative carboxyl-binding site, as judged on the basis of X-ray crystallographic studies [Sugio, S., Petsko, G.A., Manning, J.M., Soda, K., and Ringe, D. (1995) Biochemistry 34, 9661-9669], by replacement with methionine and lysine, resulted in decreases in the kmax values and increases in the Kd values for both amino donors and amino acceptors. The introduction of another mutation, that of Tyr88, which is located near Arg98 in the spacial structure, by replacement with arginine, in addition to the above Arg98 mutation, resulted in increases in the kmax values but little change in the Kd values. These results suggest that Arg98 constitutes the carboxyl-binding site for the substrate, efficient catalysis by the enzyme being facilitated upon binding. The mutant enzymes are also relieved from inhibition by high concentrations of alpha-ketoglutarate, which is an inherent character of the wild-type enzyme. Therefore, Arg98 is also responsible for the inhibition by alpha-ketoglutarate.
Ozone- and Thermally Activated Films of Palladium Monolayer-Protected Clusters for Chemiresistive Hydrogen Sensing (2006)

Here we describe the chemiresistive H2-sensing properties of drop-cast films comprised of 3.0 nm average diameter hexanethiolate-coated Pd monolayer-protected clusters (C6 Pd MPCs) bridging a pair of electrodes separated by a 23 microm gap. The gas-sensing properties were measured for 9.6-0.11% H2 in a H2/N2 mixture. The sensing mechanism is based on changes in the resistance of the film upon reaction of Pd with H2 to form PdH(x), which is known to be larger in volume and more resistive than pure Pd. As-prepared Pd MPC films are highly insensitive to H2, requiring O3 and thermal treatment to enhance changes in film resistance in the presence of H2. Exposure to O3 for 15 min followed by activation in 100% H2 leads to an increase in film conductivity in the presence of H2, with a detection limit of 0.11% H2. When exposed to temperatures of 180-200 degrees C, the conductivity of the film increases and a decrease in conductivity occurs in the presence of H2 with a detection limit of 0.21%. The sensing behavior reverses after further heating to 260 degrees C, exhibiting an increase in conductivity in the presence of H2 as in O3-treated films and a detection limit of 0.11%. The sensitivity of the variously treated films follows the order O3 > high temp > low temp, and the response times at 1.0% H2 range from 10 to 50s, depending on the treatment. FTIR spectroscopy, Raman spectroscopy, and atomic force microscopy provide information about the C6 monolayer, Pd metal, and film morphology, respectively, as a function of O3 and heat treatment to aid in understanding the observed sensing behavior. This work demonstrates a simple chemical approach toward fabricating a fast, reversible sensor capable of detecting low concentrations of H2.
Si resonant interband tunnel diodes grown by low-temperature molecular-beam epitaxy (1999)

Si resonant interband tunnel diodes that demonstrate negative differential resistance at room temperature, with peak-to-valley current ratios greater than 2, are presented. The structures were grown using low-temperature (320 °C) molecular-beam epitaxy followed by a postgrowth anneal. After a 650 °C, 1 min rapid thermal anneal, the average peak-to-valley current ratio was 2.05 for a set of seven adjacent diodes. The atomic distribution profiles of the as-grown and annealed structures were obtained by secondary ion mass spectrometry. Based on these measurements, the band structure was modeled and current–voltage trends were predicted. These diodes are compatible with transistor integration.
Induction of an Antitumoral Immune Response by Wild-Type Adeno-Associated Virus Type 2 in an In Vivo Model of Pancreatic Carcinoma (2007)

We analyzed the immunologic impact of adeno-associated virus type 2 (AAV-2), a small single-stranded parvovirus with tumorsuppressive properties, on DSL6A pancreatic carcinoma in syngeneic rats. Established tumors of animals treated with AAV-2 or mock infected were resected (Ro), and DSL6A cells were rechallenged on the different site. Eleven (92%) of 12 mock-infected animals but only 3 (25%) of 12 AAV-2-treated animals redeveloped tumors. Adeno-associated virus type 2 infection provoked systemic raises in monocytes and neutrophils numbers and in levels of the proinflammatory monocyte chemoattractant protein 1 and interleukin 10. Adeno-associated virus type 2-treated tumors were infiltrated with monocytes, macrophages, natural killer cells, CD4+ T cells, and especially CD8+ T cells. In cytotoxicity assays, AAV-2-infected DSL6A tumor cells were recognized by lymphocytes from AAV-2-treated animals and from controls. Yet, uninfected DSL6A cells were exclusively killed by lymphocytes from AAV-2-treated animals. Additionally, those lymphocytes displayed high natural killer cell activity but failed to attack unrelated tumor targets. Taken together, these results suggest that the antiviral response toward AAV-2 cross-activates the immune system toward simultaneously present tumor disease. This and the known potential to significantly reduce toxic side effects of chemotherapy make nonpathogenic viruses such as AAV-2 as "1-agent combination therapy" to an interesting treatment option of residual tumor disease.
Alteration of the Substrate and Inhibitor Specificities of Blood Coagulation Factor VIIa: Importance of Amino Acid Residue K192 (1995)

Initiation of blood coagulation occurs when the plasma serine protease factor VIIa (fVIIa) binds to its cell-surface receptor/cofactor, tissue factor (TF). This binding interaction mediates a large enhancement in both the proteolytic activity and the amidolytic activity (hydrolysis of small peptidylamide substrates) of fVIIa. This necessitates local changes in the catalytic center of fVIIa of which little is understood. Studies with thrombin and activated protein C have demonstrated that residue E192 (chymotrypsinogen numbering system) near the active site of these proteases is an important determinant for substrate and inhibitor specificity. By homology, residue 192 in fVIIa is K, bringing into question the potential role of this residue in fVIIa. We have prepared two mutants of fVIIa in which K192 has been replaced by either Q (as in factors IX and X) or E (as in thrombin). Both mutants were found to be defective in clotting: fVIIK 192Q was 44% active, while fVIIK192E was completely ineffective. This defect was attributable to proportional decreases in specificity constants for activation of factor X. Although both mutant enzymes were catalytically competent with respect to amidolytic activity, the selectivity of fVIIaK192E was greatly altered. Inhibition of both mutants by the TF pathway inhibitor (TFPI) and bovine pancreatic trypsin inhibitor (BPTI) was also drastically altered. Neither mutant was inhibited by TFPI, while fVIIaK192Q was inhibited by BPTI better than wild-type fVIIa. In contrast, fVIIaK192E was poorly inhibited by BPTI and made more refractory to inhibition when bound to TF. These results suggest a potential role for K192 in governing the substrate and inhibitor specificities of fVIIa.
A history of medical and biological imaging with polyvinylidene fluoride (PVDF) transducers (2000)

Polyvinylidene fluoride (PVDF) is a ferroelectric polymer with unique properties suitable for use in a wide range of medical and biological imaging applications. Most notable among these is its low acoustic impedance, which matches that of the body reasonably well, and its flexible mechanical properties. This paper traces the exploitation of PVDF as a transducer material from its early beginnings for thyroid and breast imaging to its current well-established applications in ultrasound biomicroscopy. Although PVDF's electromechanical properties fall short of composite ceramic materials in the traditional diagnostic frequency range, it has significant advantages in the 25-to 100-MHz range. Design criteria for high frequency transducers are reviewed, and examples of relevant medical and biological images are used to illustrate the excellent image quality obtained with this remarkable material.
Adaptive modulation for MIMO systems with V-BLAST detection (2004)

Adaptive modulation for multiple-input multiple-output (MIMO) systems with zero forcing (ZF) V-BLAST is considered. Motivated by the observation that the detection ordering of the original V-BLAST algorithm, called the forward ordering, is not suitable for adaptive modulation, a new detection ordering for V-BLAST-based adaptive modulation is proposed. This ordering, called the reverse ordering, selects the symbol corresponding to the minimum gain at each iteration, in contrast to the forward ordering which always gives priority to the maximum gain. The advantage of the reverse ordering over the forward ordering is demonstrated through analysis and simulation. It is shown that the reverse ordering can provide about 2 dB gain as compared with the forward ordering and almost comparable to the optimal ordering which is found through an exhaustive search. The V-BLAST based adaptive modulation with reverse ordering performs somewhat worse than the singular value decomposition (SVD) based method [G.G Raleigh et al., March 1998], but the former is shown to be considerably simpler to implement than the latter.
Biochemistry and molecular biology of lignification (1995)

Lignins, which result from the dehydrogenative polymerization of cinnamyl alcohols, are complex heteropolymers deposited in the walls of specific cells of higher plants. Lignins have probably been associated to land colonization by plants but several aspects concerning their biosynthesis, structure and function are still only partially understood. This review focuses on the modern physicochemical methods of structural analysis of lignins, and on the new approaches of molecular biology and genetic engineering applied to lignification. The principles, advantages and limitations of three important analytical tools for studying lignin structure are presented. They include carbon 13 nuclear magnetic resonance, analytical pyrolysis and thioacidolysis. The use of these methods is illustrated by several examples concerning the characterization of grass lignins,'lignin-like'materials in protection barriers of plants and lignins produced by cell suspension cultures. Our present limited knowledge of the spatio temporal deposition of lignins during cell wall differentiation including the nature of the wall components associated to lignin deposition and of the cross-links between the different wall polymers is briefly reviewed. Emphasis is placed on the phenylpropanoid pathway enzymes and their corresponding genes which are described in relation to their potential roles in the quantitative and qualitative control of lignification. Recent findings concerning the promoter sequence elements responsible for the vascular expression of some of these genes are presented. A section is devoted to the enzymes specifically involved in the synthesis of monolignols: cinnamoyl CoA reductase and cinnamyl alcohol dehydrogenase. The recent characterization of the corresponding cDNAs/genes offers new possibilities for a better understanding of the regulation of lignification. Finally, at the level of the synthesis, the potential involvement of peroxidases and laccases in the polymerization of monolignols is critically discussed. In addition to previously characterized naturally occurring lignin mutants, induced lignin mutants have been obtained during the last years through genetic engineering. Some examples include plants transformed by O-methyltransferase and cinnamyl alcohol dehydrogenase antisense constructs which exhibit modified lignins. Such strategies offer promising perspectives in gaining a better understanding of lignin metabolism and functions and represent a realistic way to improve plant biomass. Contents Summary 203 I. Introduction 204 II. Main structural features of lignins 205 III. Lignification and cell wall differentiation: spatio-temporal deposition of lignins and inter-relations with other wall components 213 IV. Enzymes and genes involved in the biosynthesis and polymerization of monolignols 216 V. Lignin mutants as a way to improve plant biomass and to explore lignin biochemistry and metabolism 226 VI. Concluding remarks 229 Acknowledgements 230 References 230.
Development of a commercially successful wearable data collection system (2002)

Symbol Technologies has completed a unique accomplishment; it has created a commercially successful Wearable Computer. The success of this product is directly due to a structured development effort. This effort took into account the varied requirements of a device worn on the human body in a heavy industrial environment. It is designed to decode bar codes and transmit the decoded information in real time to a host device via a wireless local area network. This document contains anthropometric data tables.
Synthetic peptide vaccines yield monoclonal antibodies to cellular and pathological prion proteins of ruminants. (1998)

Transmissible spongiform encephalopathies are closely linked to the accumulation of a pathological isoform of a host-encoded prion protein (PrP(C)), designated PrP(Sc). In an attempt to generate mono- and polyclonal antibodies to ruminant PrP, 32 mice were vaccinated with peptide vaccines which were synthesized according to the amino acid sequence of ovine PrP. By this approach five PrP-reactive polyclonal antisera directed against four different domains of the protein were stimulated. Splenocytes of mice which had developed PrP-reactive antibodies were used for the generation of monoclonal antibodies (MAbs). Obtained PrP-specific MAbs were directed to three different domains of ruminant PrP which differed from the three previously described major MAb binding sites in rodent PrP. MAbs exhibited reactivity with non-denatured ruminant PrP(C) in ELISA and immunoprecipitation and with denatured ovine and bovine PrP(Sc) in immunoblot. Cross-reactivity was observed with PrP(C) of nine other mammalian species and with pathological PrP preferably of ruminants and weakly with that of hamster and mouse. The generated MAbs will be useful tools for the development of diagnostic tests for BSE and scrapie as well as for pathogenesis studies of these diseases.
Starch Synthesis in Maize Endosperms (1995)

Research over the past three decades has greatly increased our understanding of starch biosynthesis in storage tissues, but our knowledge is still incomplete. Advances and areas of uncertainty are discussed with a focus on the maize mutants that have been useful in elucidating the process. This emphasis on mutant genes promises additional insights when we discover the role of several mutants known to affect starch synthesis and when we isolate mutations in genes encoding enzymes that have important roles in the process. The goal is a complete understanding of starch synthesis. This understanding will also facilitate the design of transgenic plants that might produce unique starches with promise as raw materials for industrial processes.
An Automatic Method for Colorimetric Analysis (1957)

An Automatic Method for Colorimetric Analysis Get access Leonard T. Skeggs, Jr., Ph.D. Leonard T. Skeggs, Jr., Ph.D. Department of Pathology, Western Reserve University School of Medicine, Cleveland, Ohio Dr. Skeggs is Assistant Professor of Biochemistry. Search for other works by this author on: Oxford Academic Google Scholar American Journal of Clinical Pathology, Volume 28, Issue 3_ts, September 1957, Pages 311–322, https://doi.org/10.1093/ajcp/28.3_ts.311 Published: 01 September 1957 Article history Received: 25 February 1957 Accepted: 01 May 1957 Published: 01 September 1957
High frequency of plant regeneration from anther culture in flax, Linum usitatissimum L. (1998)

Abstract The effects of induction medium compositions on flax anther culture were investigated in order to improve the efficiency of callus induction and plant regeneration. Anthers were inoculated onto the modified MS medium supplemented with five different combinations of plant growth regulators. The medium containing the combination of 2mg/l 2,4‐ dichlorophenoxy‐acetic acid (2,4‐D) and 1 mg/1 6‐benzylaminopurine (BAP) produced a significantly higher number of calli forming shoots/100 responded anthers and a significant increase in overall efficiency of regeneration than the same basal medium containing 1 mg/1 a‐naphthalene‐acetic acid (NAA) and 2 mg/1 BAP (CK). Among the five levels of thiamin hydrochloride tested, the modified MS medium containing 10 mg/1 thiamin hydrochloride significantly increased the number of calli forming shoots/100 responded anthers and the overall efficiency of regeneration compared with the same basal medium containing 0.1 mg/1 thiamin hydrochloride. Maltose concentration had a significant effect on the percentage of anthers producing call, the number of calli forming shoots/100 responded anthers and the overall efficiency of regeneration. The medium containing 6% or 9% maltose produced the highest overall efficiency of regeneration among the five levels of maltose evaluated. Sucrose concentration significantly affected the number of calli forming shoots/100 responded anthers and the overall efficiency of regeneration, and dramatically affected the frequency of microspore‐derived plants and the frequency of spontaneous chromosome doubling in microspore‐derived plants. The efficiency of doubled haploid line production obtained in this study appears adequate for applied breeding programmes.
Nanoscale Fe 2 O 3 -Based Catalysts for Selective Hydrogenation of Nitroarenes to Anilines (2013)

Production of anilines--key intermediates for the fine chemical, agrochemical, and pharmaceutical industries--relies on precious metal catalysts that selectively hydrogenate aryl nitro groups in the presence of other easily reducible functionalities. Herein, we report convenient and stable iron oxide (Fe2O3)-based catalysts as a more earth-abundant alternative for this transformation. Pyrolysis of iron-phenanthroline complexes on carbon furnishes a unique structure in which the active Fe2O3 particles are surrounded by a nitrogen-doped carbon layer. Highly selective hydrogenation of numerous structurally diverse nitroarenes (more than 80 examples) proceeded in good to excellent yield under industrially viable conditions.
Tolerability, Gut Effects, and Pharmacokinetics of Methylnaltrexone Following Repeated Intravenous Administration in Humans (2005)

Previous studies have shown that a single dose of methylnaltrexone, a unique peripheral opioid antagonist, reverses opioid-induced gut hypomotility in humans. Because repeated drug doses are likely to be needed to treat patients with opioid-induced or postsurgical bowel dysfunction, the authors have now examined the safety, pharmacological activity, and pharmacokinetics of a multiple-dose regimen of methylnaltrexone, administered as 12 consecutive intravenous doses (0.3 mg/kg every 6 hours) in 12 healthy subjects. Steady state was achieved rapidly, and after repeated dosing for 3 days, methylnaltrexone decreased oral-cecal transit time from a pretreatment baseline value of 101.3 +/- 29.4 min (mean +/- SD) to 82.5 +/- 20.7 min. Maximum observed plasma concentrations, measured 5 minutes postdose, were 538 +/- 237 and 675 +/- 180 ng/mL after doses 1 and 2, respectively. Based on 6-hour sampling periods, the plasma half-life, 2.5 +/- 0.5 and 2.9 +/- 0.9 hours following the 1st and 12th doses, respectively, was unchanged at steady state. There was essentially no accumulation of methylnaltrexone, based on the ratio of AUC values after doses 12 and 1. This study showed that repeated administration of intravenous methylnaltrexone is well tolerated in humans, with no significant adverse events or changes in opioid subjective ratings and no clinically noteworthy alterations in pharmacokinetics. The observation of a significant reduction in the gut transit time after repeated administration of methylnaltrexone to these opioid-naive volunteers suggests that endogenous opioids modulate human gut motility.
The Nature of Androgen Action on Male Sexuality: A Combined Laboratory-Self-Report Study on Hypogonadal Men* (1983)

Sexual function and the effects thereon of testosterone enanthate were studied in six hypogonadal men with the objective of delineating the specific components of male sexuality affected by androgen. To obtain a detailed picture of these components, prospective self-report data (from daily logs) of sexual activity and feelings, recordings of all night penile tumescence, and laboratory psychophysiological data were assessed. Double blind placebo experiments with cross-over design were used to compare the effects of placebo and 200- and 400-mg doses of testosterone enanthate. Erectile responses to erotic film and fantasy were not lower in the hypogonadal patients than in normal men and, in fact, were higher on some parameters, especially prolongation of detumescence time after exposure to film or fantasy. Three subjects who kept consistent daily logs had increased frequencies of sexual acts and feelings, orgasms, and spontaneous erections after testosterone administration. Nocturnal penile tumescence and spontaneous daytime erections were reduced in untreated hypogonadal men and were significantly increased after testosterone treatment, but the laboratory-tested erectile responses to film and fantasy were not affected by testosterone. These data and previous findings lead to the conclusion that the major androgen action on male sexuality involves libido factors (i.e. sexual motivation/interest). Though stimulus-bound erections elicited in the laboratory were not reduced in hypogonadal men, spontaneous (sleep or waking) erections were clearly testosterone dependent.
Elevated soluble c-erbB-2 antigen levels in the serum and effusions of a proportion of breast cancer patients. (1992)

Serum c-erbB-2 levels are elevated in approximately one fourth of patients with locally advanced or metastatic breast cancer.
A Gnotobiotic Mouse Model Demonstrates That Dietary Fiber Protects against Colorectal Tumorigenesis in a Microbiota- and Butyrate-Dependent Manner (2014)

These results, which link diet and microbiota to a tumor-suppressive metabolite, provide insight into conflicting epidemiologic findings and suggest that probiotic/prebiotic strategies can modulate an endogenous HDAC inhibitor for anticancer chemoprevention without the adverse effects associated with synthetic HDAC inhibitors used in chemotherapy.