gebhart/patrepeval huggingface dataset:
Crystal structure of a Baeyer–Villiger monooxygenase (2004)

Flavin-containing Baeyer-Villiger monooxygenases employ NADPH and molecular oxygen to catalyze the insertion of an oxygen atom into a carbon-carbon bond of a carbonylic substrate. These enzymes can potentially be exploited in a variety of biocatalytic applications given the wide use of Baeyer-Villiger reactions in synthetic organic chemistry. The catalytic activity of these enzymes involves the formation of two crucial intermediates: a flavin peroxide generated by the reaction of the reduced flavin with molecular oxygen and the "Criegee" intermediate resulting from the attack of the flavin peroxide onto the substrate that is being oxygenated. The crystal structure of phenylacetone monooxygenase, a Baeyer-Villiger monooxygenase from the thermophilic bacterium Thermobifida fusca, exhibits a two-domain architecture resembling that of the disulfide oxidoreductases. The active site is located in a cleft at the domain interface. An arginine residue lays above the flavin ring in a position suited to stabilize the negatively charged flavin-peroxide and Criegee intermediates. This amino acid residue is predicted to exist in two positions; the "IN" position found in the crystal structure and an "OUT" position that allows NADPH to approach the flavin to reduce the cofactor. Domain rotations are proposed to bring about the conformational changes involved in catalysis. The structural studies highlight the functional complexity of this class of flavoenzymes, which coordinate the binding of three substrates (molecular oxygen, NADPH, and phenylacetone) in proximity of the flavin cofactor with formation of two distinct catalytic intermediates.
WDM coding for high-capacity lightwave systems (1994)

An interchannel parallel coding scheme in the wavelength domain/spl minus/the WDM coding system/spl minus/is proposed. The system differs from the usual serial coding systems and provides many advantages. First, data channels are completely unaltered in the coding process, rendering it very suitable for practical lightwave systems with standard bit rate. Second, parallel encoding/decoding systems are simpler than those of serial coding systems, being easier to be implemented in high-speed optical systems. Third, compared with serial coding, WDM coding is able to reduce heavily the number of encoding/decoding pairs. For example, a (15, 11) Hamming coded WDM system reduces the number from 12/spl times/11=132 to 1 at the line rate of STS-12. Fourth, the WDM coding system could offer infinite coding gain in dispersion-limited lightwave systems. Finally, WDM coding systems could correct single-channel burst error. The system performance was evaluated and the system limitation imposed by bit-skew among wavelength channels was analyzed. The results indicated that a 15-channel Hamming coded WDM system can reduce the uncoded BER from 10/sup /spl minus/9/ to 3/spl times/10/sup /spl minus/17/ and the distance limitation imposed by bit-skew is 250 km if a dispersion-shifted fiber is used and a channel span of 30 nm is assumed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Oxidation of Formaldehyde by Chlorite in Basic and Slightly Acidic Media (1998)

The reaction of chlorite and formaldehyde was studied in basic and slightly acidic media. Though the expected product was CO2, the oxidation of HCHO, however, gave nearly quantitative formation of ClO2, the oxidation product of ClO2-. In excess HCHO the stoichiometry of the reaction was deduced as 3ClO2- + HCHO + 2H+ → HCOOH + 2ClO2(aq) + Cl- + 2H2O; but in high excess of ClO2- the stoichiometry was 6ClO2- + HCHO + 4H+ → CO2(g) + 4ClO2(aq) + 3H2O + 2Cl-. The reaction is autocatalytic in HOCl. The first step of the reaction produces HOCl, which catalyzes the formation of ClO2 and further oxidation of HCOOH to CO2. ClO2 was found to be relatively unreactive toward HCHO and HCOOH, and hence it accumulated rapidly.
A mitochondrial DNA clone is associated with increased risk for Alzheimer disease. (1995)

Severe mitochondrial genetic mutations lead to early degeneration of specific human tissues; milder mitochondrial mutations may cause degeneration at a later point in life. A mutation at position 4336 was reported to occur at increased frequency in individuals with Alzheimer disease (AD) and Parkinson disease [Shoffner, J. M., Brown, M. D., Torroni, A., Lott, M. T., Cabell, M. F., Mirra, S. S., Beal, M. F., Yang, C.-C., Gearing, M., Salvo, R., Watts, R. L., Juncos, J. L., Hansen, L. A., Crain, B. J., Fayad, M., Reckord, C. L. & Wallace, D. C. (1993) Genomics 17, 171-184]. We have investigated the notion that this mutation leads to excess risk of AD by using a case-control study design of 72 AD autopsies and 296 race- and age-matched controls. The 4336G mutation occurred at higher frequency in AD autopsies than age-matched controls, a statistically significant difference. Evolutionary analysis of mtDNAs bearing the 4336G mutation indicated they were more closely related to each other than to other mtDNAs, consistent with the model of a single origin for this mutation. The tight evolutionary relatedness and homoplasmy of mtDNAs that confer elevated risk for a late-onset disease contrast strikingly with the distant relatedness and heteroplasmy of mitochondrial genomes that cause early-onset disease. The dichotomy can be explained by a lack of selection against mutations that confer a phenotype at advanced age during most of the evolution of humans. We estimate that approximately 1.5 million Caucasians in the United States bear the 4336G mutation and are at significantly increased risk of developing mitochondrial AD in their lifetime. A mechanism for 4336G-mediated cell death is proposed.
Redox status expressed as GSH:GSSG ratio as a marker for oxidative stress in paediatric tumour patients (2012)

Oxidative stress causes profound alterations of various biological structures, including cellular membranes, lipids, proteins and nucleic acids, and it is involved in numerous malignancies. Reduced glutathione (GSH) is considered to be one of the most important scavengers of reactive oxygen species (ROS), and its ratio with oxidised glutathione (GSSG) may be used as a marker of oxidative stress. The main aim of this study was to determine GSH:GSSG ratio in the blood serum of paediatric cancer patients to use this ratio as a potential marker of oxidative stress. The whole procedure was optimised and the recoveries for both substances were greater than 80% under the optimised conditions. We analysed a group of paediatric patients (n=116) with various types of cancer, including neuroblastoma, anaplastic ependymoma, germ cell tumour, genital tract tumour, lymphadenopathy, rhabdomyosarcoma, nephroblastoma, Ewing's sarcoma, osteosarcoma, Hodgkin's lymphoma, medulloblastoma and retinoblastoma. We simultaneously determined the levels of reduced and oxidised glutathione, and thus, its ratio in the blood serum of the patients. The highest ratio was observed in retinoblastoma patients and the lowest in anaplastic ependymoma. We were able to distinguish between the diagnoses based on the results of the obtained GSH:GSSG ratio.
Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays (2002)

We compared the accuracy of microarray measurements obtained with oligonucleotide arrays (GeneChip, Affymetrix) with a laboratory-developed cDNA array by assaying test RNA samples from an experiment using a paradigm known to regulate many genes measured on both arrays. We selected 47 genes represented on both arrays, including both known regulated and unregulated transcripts, and established reference relative expression measurements for these genes in the test RNA samples using quantitative reverse transcriptase real-time PCR (QRTPCR) assays. The validity of the reproducible (average coefficient of variation = 11.8%) QRTPCR measurements were established through application of a new mathematical model. The performance of both array platforms in identifying regulated and non-regulated genes was identical. With either platform, 16 of 17 definitely regulated genes were correctly identified, and no definitely unregulated transcript was falsely identified as regulated. Accuracy of the fold-change measurements obtained with each platform was assessed by determining measurement bias. Both platforms consistently underestimate the relative changes in mRNA expression between experimental and control samples. The bias observed with cDNA arrays was predictable for fold-changes <250-fold by QRTPCR and could be corrected by the calibration function F(c) = F(a(cDNA))(q), where F(a(cDNA)) is the microarray-determined fold-change comparing experimental with control samples, q is the correction factor and F(c) is the calibrated value. The bias observed with the commercial oligonucleotide arrays was less predictable and calibration was unfeasible. Following calibration, fold-change measurements generated by custom cDNA arrays were more accurate than those obtained by commercial oligonucleotide arrays. Our study demonstrates systematic bias of microarray measurements and identifies a calibration function that improves the accuracy of cDNA array data.
Mesoscale hydrodynamics via stochastic rotation dynamics: Comparison with Lennard-Jones fluid (2010)

Stochastic rotation dynamics (SRD) is a relatively recent technique, closely related to lattice Boltzmann, for capturing hydrodynamic fluid flow at the mesoscale. The SRD method is based on simple constituent fluid particle interactions and dynamics. Here we parametrize the SRD fluid to provide a one to one match in the shear viscosity of a Lennard-Jones fluid and present viscosity measurements for a range of such parameters. We demonstrate how to apply the Müller-Plathe reverse perturbation method for determining the shear viscosity of the SRD fluid and discuss how finite system size and momentum exchange rates effect the measured viscosity. The implementation and performance of SRD in a parallel molecular dynamics code is also described.
The Stability of Cysteine and Cystine during Acid Hydrolysis of Proteins and Peptides (1970)

Abstract When solutions of cystine and cysteine are treated with dithiothreitol and then with sodium tetrathionate, quantitative yields of S-sulfocysteine can be obtained. This reaction has been applied to protein hydrolysates and the resulting S-sulfocysteine has been determined by ion exchange chromatography on an amino acid analyzer. With ribonuclease and reduced glutathione this procedure has given accurate values for the cystine or cysteine content of the protein or peptide. When tryptophan is also present, the addition of a small amount of sodium tetrathionate to the 6 n HCl used for the hydrolysis has usually proved to be desirable; the function of the tetrathionate appears to be to react with the indole nucleus. With this modification, the procedure has given precise results for the cysteine plus cystine contents of streptococcal proteinase, lysozyme, and wool. The results indicate that, in terms of their primary structures, cysteine and cystine are not destroyed during acid hydrolysis under these conditions; treatment with dithiothreitol and tetrathionate serves to convert any altered forms of the amino acids in the hydrolysates to S-sulfocysteine and to permit quantitative recovery in the form of this derivative. This method for determining the half-cystine content of proteins provides an alternative to the determinations of the amino acids as cysteic acid or S-carboxymethylcysteine. The treatment does not affect the recoveries of other amino acids in the hydrolysate, with the possible exception of tyrosine.
Intraoperative Electrophysiological Monitoring in Spine Surgery (2010)

As spine surgery, and patient comorbidity, becomes increasingly complex, IOM permits more aggressive deformity correction and tumor resection. Combination of SSEP and MEP monitoring provides assessment of entire spinal cord functionality in real time. Spontaneous and triggered electromyography add assessment of nerve roots. The wake-up test can continue to serve as a supplement when needed. MIOM may prove useful in preservation of neurologic function where an alteration of approach is possible. IOM is a valuable tool for optimization of outcome in complex spinal surgery.
Lateral motion of beta receptors in membranes of cultured liver cells. (1982)

We have studied the lateral mobility and distribution of beta receptors on Chang human liver cells by fluorescence photobleaching recovery and video intensification microscopy. The beta receptors were labeled with the fluorescent antagonist 7-(2-allylphenoxy)-2,2-dimethyl-6-hydroxy-1-(4-nitrobenzo-2-oxa-1,3-diazolyl)-1 ,4-diazaheptane (Alp-NBD). Sixty to 75% of the staining was specific (displaceable by unlabeled antagonists). Most of the antagonist-occupied beta receptors were immobile, because only 15-25% of their fluorescence recovered on the experimental time scale at 23 degrees C. This immobility correlates with the clustered distribution of Alp-NBD--beta-receptor complexes at 4 degrees C and 37 degrees C. The beta receptors appear to be aggregated prior to antagonist binding, because visible patches were observed immediately after labeling for 30 sec at 4 degrees C. Preincubation at 37 degrees C with (--)-isoproterenol, a beta agonist, prior to Alp-NBD labeling induced a time-dependent release of the beta receptors to a more homogeneous distribution and increased the mobile fraction to 70-80% (lateral diffusion coefficient = 1.4 X 10(-9) cm2/sec at 23 degrees C). This is not due to an effect on membrane fluidity, because the diffusion coefficient of a lipid probe was not altered. The time course of agonist-induced beta-receptor mobilization correlates with receptor loss and adenylate cyclase desensitization but is much slower than adenylate cyclase activation. This indicates that adenylate cyclase activation by beta receptors does not require macroscopic lateral mobility of the majority of the beta receptors.
Rapid shape acquisition using color structured light and multi-pass dynamic programming (2003)

This paper presents a color structured light technique for recovering object shape from one or more images. The technique works by projecting a pattern of stripes of alternating colors and matching the projected color transitions with observed edges in the image. The correspondence problem is solved using a novel, multi-pass dynamic programming algorithm that eliminates global smoothness assumptions and strict ordering constraints present in previous formulations. The resulting approach is suitable for generating both high-speed scans of moving objects when projecting a single stripe pattern and high-resolution scans of static scenes using a short sequence of time-shifted stripe patterns. In the latter case, space-time analysis is used at each sensor pixel to obtain inter-frame depth localization. Results are demonstrated for a variety of complex scenes.
Norbornenyl-Based RAFT Agents for the Preparation of Functional Polymers via Thiol–Ene Chemistry (2011)

A synthetic platform for the preparation of various norbornenyl (Nb) containing reversible addition–fragmentation chain transfer (RAFT) agents has been developed. The design of the chain transfer agents (CTAs) is based on the desymmetrization of α,α′-dibromo-p-xylene by monosubstitution with an alkoxide anion and subsequent replacement of the residual bromine atom in the benzylic bromide to create several series of RAFT CTA including trithiocarbonate, xanthate and dithiobenzoate CTAs, allowing for the possibility to introduce other functional groups besides Nb, such as an allyl group. While a norbornene functionality was chosen as most reactive functional group toward thiols in radical-mediated thiol–ene chemistry, an allyl group was introduced for the sake of direct comparison of the double bond reactivity in the thiol–ene reaction. Control of the radical polymerization of acrylates, styrene and vinyl acetate has been achieved by using this novel family of CTAs. The results indicate that the Nb group remained intact at low monomer conversions (e.g., below 50% for styrene and vinyl acetate, below 30% for acrylates) and at optimal reaction temperatures (e.g., 70 °C for styrene and vinyl acetate, 62 and 65 °C for 1-ethoxyethyl acrylate and methyl acrylate, respectively), while the monomer-to-CTA ratio was kept high. Polymers with high end-group fidelity were modified with a series of thiol-containing compounds, leading to α-semitelechelics with different chain-end structures. While allyl-containing polymers exhibited a significantly lower reactivity, modification of the Nb-containing semitelechelics was rapid and fully accomplished under the same reaction conditions. However, for the given conditions, dodecanethiol and benzyl mercaptan showed a lower reactivity toward Nb-containing polymers, as evidenced by the obtained modification efficiency of 70% and 45%, respectively.
Hypotheses for the richness of gall insects: a review considering the intraespecific, interespecific and community levels (2007)

In the literature there are several hypotheses that try to explain the patterns of global, regional and local richness of insects associated to plants. These hypotheses can be recognized in different ecological levels, explaining variations in the number of insects associated to individuals or populations of same host species, to different host species, and to different communities. However, the patterns of richness found in each of these levels are result of distinct ecological processes, thus each hypothesis has particularities related to its application depending on the processes considered and on the characteristics of the insect taxa. The objective of this review is to expose the hypotheses that have been used to explain the richness patterns of insects associated to plants, identifying the validity and the use status of each hypothesis in the intraespecific, interespecific, and community levels to gall insect – plant systems. In this review are explicitly enunciated 13 hypotheses considering the levels of ecological organization. This way of view represents a progress because it makes possible an objective analysis of what has been made in the field and a clear visualization of the gaps in the literature. Few hypotheses were enough tested in all levels, mostly in the intraespecific and interespecific levels. Thus it is evident that it is early to reach a general synthesis that explains the patterns of gall insects’ richness in all levels. This review expects, when enunciating the hypotheses in the different levels, to collaborate to the development of the field pointing directions to future studies. Key words: gall insect, richness patters, hypothesis.
Colicin Import intoEscherichia coliCells (1998)

Most gram-negative bacteria in search of nutrients and space in which to multiply release toxins that selectively kill competing microorganisms while causing no harm to the producing cell. The highly specific protection function is conferred on producing cells by immunity proteins produced from the
Initiation of mRNA decay in Bacillus subtilis (1993)

Ribosome stalling in the leader region of ermC mRNA results in a 10-15-fold increase in ermC mRNA half-life in Bacillus subtilis. Fusion of the ermC 5' regulatory region to several B. subtilis coding sequences resulted in induced stability of the fusion RNAs, showing that the ermC 5' region acts as a general '5' stabilizer'. RNA products of an ermC-lacZ transcriptional fusion were inducibly stable in the complete absence of translation and included a small RNA that is likely to be a decay product arising by blockage of a 3'-to-5' exoribonuclease activity. Insertion of sequences that encode endonucleolytic cleavage sites into the ermC coding sequence resulted in cleavage products whose stability depended on the nature of their 5' and 3' ends. It can be concluded from this study that initiation of mRNA decay in B. subtilis generally occurs at or near the 5' terminus.
Isovolumetric sphering of erythrocytes for more accurate and precise cell volume measurement by flow cytometry (1983)

Abstract Typical mammalian erythrocytes are biconcave disks. Flow cytometric light‐scattering measurements of red cell volume show large, orientation‐dependent variations in signal size. To eliminate errors caused by shape factors, we sphere erythrocytes isovolumetrically on an Auto‐Analyzer manifold (Technicon Instruments Corp., Tarrytown, N. Y.) using a carefully controlled ratio of concentrations of a salt of long chain sulfated fatty alcohol ( e.g. ), sodium dodecyl sulfate (SDS) to albumin in neutrally buffered isotonic saline, producing a suspension with at least 2 1/2 hours of stability with respect to cell volume, cell count and retention of hemoglobin. A two‐step manifold modification of this procedure is preferred. It uses the endogeneous serum protein and a first SDS‐saline reagent without added albumin at a low dilution, and further dilution with a second SDS‐saline containing a very low concentration of glutaraldehyde. This bypasses a serious shelf life problem with the albumin‐SDS reagent. Microhematocrit and Coulter electronic impedance measurements were correlated with light‐scattering measurements on our own flow cytometer system of unsphered, sphered, and sphered and fixed samples. These reveal marked superiority over unsphered samples ( e.g. , reduced coefficients of variation of cell volume and improved correlation with microhematocrit) of the sphered and of the sphered and lightly fixed cells. The resulting tighter unimodal cell volume distributions also provide the following advantages: (1) The separation of signals of large platelets from that of the smallest red cells is substantially increased permitting better resolution of microcytic red cells in some abnormal bloods, and (2) bimodality of red cell volume distribution in abnormal bloods is more easily resolved.
Key Triggers of Osteoclast-Related Diseases and Available Strategies for Targeted Therapies: A Review (2017)

Osteoclasts, the only cells with bone resorption functions <i>in vivo</i>, maintain the balance of bone metabolism by cooperating with osteoblasts, which are responsible for bone formation. Excessive activity of osteoclasts causes many diseases such as osteoporosis, periprosthetic osteolysis, bone tumors, and Paget's disease. In contrast, osteopetrosis results from osteoclast deficiency. Available strategies for combating over-activated osteoclasts and the subsequently induced diseases can be categorized into three approaches: facilitating osteoclast apoptosis, inhibiting osteoclastogenesis, and impairing bone resorption. Bisphosphonates are representative molecules that function by triggering osteoclast apoptosis. New drugs, such as tumor necrosis factor and receptor activator of nuclear factor kappa-B ligand (RANKL) inhibitors (e.g., denosumab) have been developed for targeting the receptor activator of nuclear factor kappa-B /RANKL/osteoprotegerin system or CSF-1/CSF-1R axis, which play critical roles in osteoclast formation. Furthermore, vacuolar (H<sup>+</sup>)-ATPase inhibitors, cathepsin K inhibitors, and glucagon-like peptide 2 impair different stages of the bone resorption process. Recently, significant achievements have been made in this field. The aim of this review is to provide an updated summary of the current progress in research involving osteoclast-related diseases and of the development of targeted inhibitors of osteoclast formation.