gebhart/patrepeval huggingface dataset:
Nanocrystal-Based Bioelectronic Coding of Single Nucleotide Polymorphisms (2004)

A bioelectronic method for coding unknown single nucleotide polymorphisms (SNPs) based on the use of different encoding nanocrystals is described. Four such nanocrystals, ZnS, CdS, PbS, and CuS, linked to the adenosine, cytidine, guanosine and thymidine mononucleotides, respectively, are sequentially introduced to the DNA hybrid-coated magnetic-bead solution. Each mutation captures via base pairing different nanocrystal-mononucleotide conjugates, and yields a characteristic multipotential voltammogram, whose peak potentials reflect the identity of the mismatch. The mismatch recognition events are being amplified by the metal accumulation feature of the stripping voltammetric transduction mode. Each of the eight possible one-base mismatches can thus be identified in a single voltammetric run. The use of nanocrystal tracers for detecting two known mutations in a single DNA target is also illustrated in connection to nanocrystals linked to two nucleotides along with a single voltammetric run. The protocol presented should facilitate the rapid, simple, low-cost, and high throughput screening for SNPs.
Do cortical gamma oscillations promote or suppress perception? An under-asked question with an over-assumed answer (2013)

Cortical gamma oscillations occur alongside perceptual processes, and in proportion to perceptual salience. They have a number of properties that make them ideal candidates to explain perception, including incorporating synchronized discharges of neural assemblies, and their emergence over a fast timescale consistent with that of perception. These observations have led to widespread assumptions that gamma oscillations' role is to cause or facilitate conscious perception (i.e., a "positive" role). While the majority of the human literature on gamma oscillations is consistent with this interpretation, many or most of these studies could equally be interpreted as showing a suppressive or inhibitory (i.e., "negative") role. For example, presenting a stimulus and recording a response of increased gamma oscillations would only suggest a role for gamma oscillations in the representation of that stimulus, and would not specify what that role were; if gamma oscillations were inhibitory, then they would become selectively activated in response to the stimulus they acted to inhibit. In this review, we consider two classes of gamma oscillations: "broadband" and "narrowband," which have very different properties (and likely roles). We first discuss studies on gamma oscillations that are non-discriminatory, with respect to the role of gamma oscillations, followed by studies that specifically support specifically a positive or negative role. These include work on perception in healthy individuals, and in the pathological contexts of phantom perception and epilepsy. Reference is based as much as possible on magnetoencephalography (MEG) and electroencephalography (EEG) studies, but we also consider evidence from invasive recordings in humans and other animals. Attempts are made to reconcile findings within a common framework. We conclude with a summary of the pertinent questions that remain unanswered, and suggest how future studies might address these.
Isolation and characterization of endophytic bacteria from endorhizosphere of sugarcane and ryegrass (2009)

The present study was conducted with a view to isolate and characterize endophytic bacterial diversity from endorhizosphere of sugarcane (Saccharum sp.) and rye grass (Lolium perenne). Eight bacterial isolates from sugarcane and seven from rye grass were obtained and identified as Azospirillum, Bacillus, E. coli and Pseudomonas. S1 and R1 (Azospirillum) sugarcane and ryegrass isolate exhibited maximum nitrogenase activity of 1221.0 and 1168.3 nM C 2H 4h -1 mg -1 protein respectively while the maximum IAA production was recorded in S5 (E. coli) and R7 (Bacillus) i.e. 19.3 and 20.0 mg ml -1 respectively. The maximum siderophore production was observed in S6 (E.coli) and R6 (Pseudomonas) i.e. 2.4 and 3.0 mg ml -1 respectively. Only S5 (E.coli) was observed to be solubilize phosphate (21 mg P). The endorhizosphere of sugarcane and rye grass exhibited endophytic bacterial diversity not only in terms of different types of isolates but also in terms of functional diversity.
Use of peak-to-average power reduction technique in HIPERLAN2 and its performance in fading channel (2002)

Abstract: A technique that uses clipping has been recently proposed to reduce the peak-toaverage-power ratio (PAPR) in orthogonal frequency divisional multiplexing (OFDM) signals. The technique uses a discrete Fourier transform (DFT) based filter to reduce out-ofband (OOB) power after the interpolated baseband OFDM signal is clipped. In this paper, the technique is applied to HIPERLAN2 to reduce the PAPR of the transmitted signals. Like many other OFDM systems, HIPERLAN2 has a number of unused subcarriers. The DFT based filter is used to null the unused subcarriers at the band edge. The effect of in-band distortion on the system’s bit error rate (BER) is studied. Results show that effect of clipping noise on the system’s BER is minimal in the fading environment. 1.
A High-Confidence Human Plasma Proteome Reference Set with Estimated Concentrations in PeptideAtlas (2011)

Human blood plasma can be obtained relatively noninvasively and contains proteins from most, if not all, tissues of the body. Therefore, an extensive, quantitative catalog of plasma proteins is an important starting point for the discovery of disease biomarkers. In 2005, we showed that different proteomics measurements using different sample preparation and analysis techniques identify significantly different sets of proteins, and that a comprehensive plasma proteome can be compiled only by combining data from many different experiments. Applying advanced computational methods developed for the analysis and integration of very large and diverse data sets generated by tandem MS measurements of tryptic peptides, we have now compiled a high-confidence human plasma proteome reference set with well over twice the identified proteins of previous high-confidence sets. It includes a hierarchy of protein identifications at different levels of redundancy following a clearly defined scheme, which we propose as a standard that can be applied to any proteomics data set to facilitate cross-proteome analyses. Further, to aid in development of blood-based diagnostics using techniques such as selected reaction monitoring, we provide a rough estimate of protein concentrations using spectral counting. We identified 20,433 distinct peptides, from which we inferred a highly nonredundant set of 1929 protein sequences at a false discovery rate of 1%. We have made this resource available via PeptideAtlas, a large, multiorganism, publicly accessible compendium of peptides identified in tandem MS experiments conducted by laboratories around the world.
Partial d -amino acid substitution: Improved enzymatic stability and preserved Ab recognition of a MUC2 epitope peptide (2005)

The stability of an immunogen against enzymatic degradation is considered an important factor for the design of synthetic vaccines. For our studies, we have selected an epitope from the tandem-repeat unit of the high-molecular-weight MUC2 mucin glycoprotein, which can be underglycosylated in case of colon cancer. In this study, we prepared a MUC2 peptide containing the PTGTQ epitope of a MUC2 protein backbone-specific mAb 996 and its derivatives. In these peptides, the N- and C-terminal flanking regions were systematically substituted by up to three d-amino acids. Peptides prepared by solid-phase synthesis were tested for their mAb 996 binding in competitive ELISA experiments, and their stability was studied in serum and lysosomal preparation. Our data show that the epitope function of peptide (15)TPTPTGTQTPT(25) is retained even in the presence of two d-amino acid residues at its N-terminal flanking region and up to three at its C-terminal flanking region (tpTPTGTQtpt). Also, this partly d peptide shows high resistance against proteolytic degradation in diluted human serum and in lysosomal preparation. These findings suggest that, by appropriate combination of structural modifications (namely, d-amino acid substitution) in the flanks of an Ab epitope, it is feasible to construct a synthetic antigen with preserved recognition properties and high stability against enzymatic degradation. Peptides tPTPTGTQTpt and tpTPTGTQTpt derived from this study can be used for immunization experiments and as potential components of synthetic vaccines for tumor therapy.
Enantiomeric Inclusion of α-Hydroxy Esters by (R)-(1-Naphthyl)glycyl-(R)-phenylglycine and the Crystal Structures of the Inclusion Cavities (1999)

A simple dipeptide, (R)-(1-naphthyl)glycyl-(R)-phenylglycine [(R,R)-1], formed inclusion compounds with several α-hydroxy esters (2) with high enantioselectivity. By crystallization of a mixture of the dipeptide [(R,R)-1] and racemic 2a [MeCH(OH)COOMe] from methanol, asymmetric recognition occurred to give an inclusion compound that contains the S form of 2a in 89% ee. X-ray crystallographic study of the inclusion compound elucidated that the dipeptide molecules arrange in a “folded antiparallel” β-sheetlike structure to accommodate the α-hydroxy ester in the pocket-type cavity surrounded by naphthyl and phenyl groups on the sheet. Similarly, 2b [MeCH(OH)COOEt] and 2f [dihydro-3-hydroxy-4,4-dimethyl-2(3H)-furanone] were included with high enantioselectivity of the S form. When bulkier 2l [t-BuCH(OH)COOMe] was used as a guest molecule, the arrangement of dipeptide molecules changed to an “extended antiparallel” mode, where the naphthyl and phenyl groups arranged in a “parallel stacked and displaced” mode and a channel-type cavity was constructed. The guest molecules were accommodated via hydrogen bonding in the channel-type cavity with high enantioselectivity of the S form (82% ee). In the case of 2k [i-PrCH(OH)COOMe], optically pure (S)-2k formed the dipeptide sheet with the “folded antiparallel” structure by cocrystallization with (R,R)-1, while the “extended antiparallel” structure appeared in the inclusion of racemic 2k.
The ubiquitin‐activating enzyme (E1) gene family in Arabidopsis thaliana (1997)

Conjugation of multiple ubiquitins serves as a committed step in the degradation of a variety of intracellular eukaryotic proteins by the 26S proteasome. Conjugates are formed via a three-enzyme cascade; the initial step requires ubiquitin-activating enzyme (E1), which couples ubiquitin activation to ATP hydrolysis. Previously, we showed that many higher plants contain multiple E1 proteins and described several E1 genes from wheat. To facilitate understanding of the roles of the different plant E1s, we characterized the E1 gene and protein family from Arabidopsis thaliana. Arabidopsis E1s are encoded by two genes (AtUBA1 and AtUBA2) that synthesize approximately 123-kDa proteins with 81% amino acid sequence identity to each other and 44-75% sequence identity with confirmed E1s from other organisms. Like other E1 proteins, AtUBA1 and 2 contain a cysteine residue in the putative active site for forming the ubiquitin thiol-ester intermediate. Enzymatic analysis of the corresponding proteins expressed in Escherichia coli demonstrated that both proteins activate ubiquitin in an ATP-dependent reaction and transfer the activated ubiquitin to a variety of Arabidopsis E2s with near equal specificity. Expression studies by quantitative RT-PCR and histochemistry with transgenic plants containing AtUBA promoter-beta-glucuronidase-coding region fusions showed that the AtUBA1 and 2 genes are co-expressed in most, if not all, Arabidopsis tissues and cells. Collectively, the data indicate that E1 proteins, and presumably the rest of the ubiquitin pathway, are present throughout Arabidopsis. They also show that the AtUBA1 and 2 genes are not differentially expressed nor do they encode E1s with dramatically distinct enzymatic properties.
Properties and sequence of the coenzyme B12-dependent glycerol dehydratase of Clostridium pasteurianum (1998)

The genes encoding coenzyme B12-dependent glycerol dehydratase of Clostridium pasteurianum were subcloned and expressed in Escherichia coli. The native molecular mass of the enzyme is 190 000 Da. The enzyme converts glycerol, 1,2-propanediol and 1,2-ethanediol to 3-hydroxypropionaldehyde, propionaldehyde and acetaldehyde, respectively, but glycerol is the preferred substrate. The nucleotide sequences of the dhaBCE genes encoding the three subunits of glycerol dehydratase and of orfZ whose function is unknown were determined. The deduced products of the dhaBCE genes with calculated molecular masses of 60 813, 19 549 and 16 722 Da, respectively, revealed high similarity to amino acid sequences of subunits of coenzyme B12-dependent glycerol and diol dehydratases from other organisms.
Large-Scale Structure –Function Analysis of the Arabidopsis RPM1 Disease Resistance Protein (2002)

The Arabidopsis RPM1 gene confers resistance against Pseudomonas syringae expressing either the AvrRpm1 or the AvrB type III effector protein. We present an exhaustive genetic screen for mutants that no longer recognize avrRpm1. Using an inducible avrRpm1 expression system, we identified 110 independent mutations. These mutations represent six complementation groups. None discriminates between avrRpm1 and avrB recognition. We identified 95 rpm1 alleles and present a detailed structure--function analysis of the RPM1 protein. Several rpm1 mutants retain partial function, and we deduce that their residual activity is dependent on the level of avrRpm1 signal. In these mutants, the hypersensitive response remains activated if the signal goes above a certain threshold. Missense mutations in rpm1 are highly enriched in the nucleotide binding domain, suggesting that this region plays a key role either in the hypersensitive response associated with RPM1 activation or in RPM1 stability. Cluster analysis of rpm1 alleles defines functionally important residues that are highly conserved between nucleotide binding site leucine-rich repeat R proteins and those that are unique to RPM1. Regions of RPM1 to which no loss-of-function alleles map may represent domains in which variation is tolerated and may contribute to the evolution of new R gene specificities.
Diverse and tissue-enriched small RNAs in the plant pathogenic fungus, Magnaporthe oryzae (2011)

Our findings suggest M. oryzae small RNAs differentially accumulate in vegetative and specialized-infection tissues and may play an active role in genome integrity and regulating growth and development.
Serotype-specific inhibition of colonization of the tonsils and nasopharynx of calves after Pasteurella haemolytica serotype A1 after vaccination with the organism. (1994)

Vaccination of cattle with a tissue culture-derived Pasteurella haemolytica serotype 1 vaccine elicited a serotype-specific inhibition of nasal and tonsillar colonization by the homologous serotype under field conditions. Calves (n = 101) originated from a single farm, where half the calves were vaccinated. The calves were delivered to an order-buyer barn 105 days later, and given a second dose of vaccine. At the order-buyer barn, calves were mixed with 27 calves, some of which had clinical signs consistent with respiratory tract disease. Also 12 of the original calves were infected with P haemolytica serotype 1 by tonsillar instillation. After 6 days at the order-buyer barn, calves were shipped 1,600 km by truck to a feedyard, and arrived the next day. Tonsillar wash and nasal secretion aspiration specimens were collected for culture of P haemolytica on days 1, 8, and 29 at the feedyard. Inhibition of colonization was evidenced by lower frequency of isolations from the vaccinates than from the nonvaccinates after transport to the feedyard. Selectively lowering the frequency of colonization by P haemolytica serotype 1 could reduce losses attributable to pneumonic pasteurellosis.
The effects of estrone (Ogen) on spinal bone density of postmenopausal women (1991)

The effects of cyclical treatment with estrone sulfate (0.3, 0.625, or 1.25 mg), plus calcium carbonate, on spinal trabecular bone density were compared with placebo in 120 postmenopausal women in this 2-year, multicenter, doubleblind study. While the placebo and 0.3-mg treatment groups lost bone density (-3.6% and -5.1%), the 0.625- and 1.25-mg treatment groups experienced no significant change from baseline at 24 months (-0.8% and +0.7%). The 1.25-mg treatment group was significantly different from the placebo group at 12,18, and 24 months. Although the 0.625-mg treatment group was significantly different from the placebo group only at 18 months, the data suggest that 0.625 and 1.25 mg of estrone sulfate had different effects than placebo and 0.3 mg of estrone sulfate and, given with supplemental calcium, are effective doses for the prevention of spinal bone loss. (<i>Arch Intern Med</i>. 1991;151:1980-1984)
Preparation of Sterically Protected 3,4-Bis[(2,4,6-tri-tert-butylphenyl)phosphinidene]cyclobutene Derivatives Having Ring-Fused Structures (2002)

[reaction: see text] Sterically protected 3,4-diphosphinidenecyclobutenes, having ring-fused structures, were prepared. Structures of 8,9-bis[(2,4,6-tri-tert-butylphenyl)phosphinidene]bicyclo[5.2.0]non-1(7)-ene and its dichloropalladium(II) complex were analyzed by X-ray crystallography. A geometrical change induced by the complex formation was exhibited by X-ray crystallographic analysis. The geometrical change in solution was also suggested by (1)H NMR spectroscopy in CDCl(3).
Profiling of cell cycle genes of breast cells exposed to etodolac (2010)

Breast cancer represents the second leading cause of cancer-related deaths in the world. There is increasing evidence that perturbation of cell cycle regulation is an important contributing factor to various cancer progression stages. There are key checkpoints in the cell cycle involving various regulatory proteins. The relationship between these cell cycle regulatory proteins and cell cycle arrest by cyclo-oxygenase (COX) inhibitors during neoplastic progression remains largely unknown. Preclinical studies and epidemiological investigations have consistently shown that non-steroidal anti-inflammatory drugs have some anti-proliferative and anti-oxidative stress response on various tumors. In this study, the effect of etodolac, a 1,8-diethyl-1,3,4,9-tetrahydro-pyrano (3,4-beta) indole-1-acetic acid on signaling pathways was investigated by examining the differential expression of various cell cycle regulatory protein genes. A human cell cycle gene array was used to profile the expression of 96 genes involved in the cell cycle regulation. Differentially expressed genes were highly altered by etodolac treatment. Twenty-six genes were up- and 20 down-regulated with 0.5 and 2 mM etodolac treatment, respectively. Seven genes (ATM, BAX, CCNA2, CDC27, RAD50 and p21) were prominently altered, and six (ATM, CCND2, CCNF, CDC20, CDK1A and RAD50) were commonly altered with both concentrations. This finding indicated that etodolac could play a critical role on cancer cells by inducing cell death.
IGES and PDES, the current status of product data exchange standard (2003)

Currently, IGES (Initial Graphic Exchange Specification) is the international standard for exchange product definition data between CAD (computer-aided design) systems. However, due to its efficiencies, a new standard is in the process of development and will gradually replace IGES. It is believed that PDES will be less error-prone than IGES. Its improvements include free-form format representation of objects, a three-level database architecture, and reduced memory and time requirements. Future IGES developments will be suspended when PDES is introduced to general use. But though PDES will contain all functions of IGES, IGES will remain in use for some time.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Nanoscale Organization of Collagen and Mixed Collagen−Pluronic Adsorbed Layers (2003)

Adsorption of collagen (300 nm length, 1.5 nm diameter) on poly(ethylene terephthalate) and the influence of Pluronic PE6800, a triblock poly(ethylene oxide)−poly(propylene oxide)−poly(ethylene oxide) copolymer, were investigated by the combination of three techniques. The adsorbed amounts of the two adsorbates were determined by radiolabeling. X-ray photoelectron spectroscopy was used to get quantitative information on the adsorbed layer. Selected samples were observed by atomic force microscopy (AFM) under water and in air; data on morphology, mechanical resistance, and molecular interactions were obtained. In the absence of Pluronic, two collagen layer morphologies were observed. Under water, at an adsorbed amount equal to half the maximum, collagen formed a dense granular layer; at the maximum adsorbed amount (equivalent to six layers of lying molecules), the adsorbed layer was soft, appeared as a pattern of elongated structures, and showed adhesion of the AFM probe with rupture lengths as long as several hundred nanometers. This was attributed to collagen molecules or bundles protruding into the solution. After fast drying, the collagen layer was smooth with a low surface fraction occupied by holes at the lower protein adsorbed amount, while it showed spindle-shape relief features at the maximum adsorbed amount. In the presence of Pluronic, the amount of adsorbed collagen was reduced considerably, due to rapid adsorption of the surfactant. In these conditions, the collagen layer obtained from high protein concentration solutions was also constituted by granules and was very sensitive to the alteration by the AFM probe.
Enhanced Immunoglobulin Formation of Immortalized B Cells From Hypertensive Patients (1995)

Increased immunoglobulin levels and leukocyte counts have frequently been reported in essential hypertension. The underlying mechanisms, however, have remained obscure. Enhanced Na(+)-H+ exchanger activity is another frequently observed abnormality in essential hypertension that persists in immortalized B lymphoblasts and coincides with enhanced proliferation. We investigated the capacity of B lymphoblasts from essential hypertensive patients to synthesize and secrete immunoglobulins. Six B cell lines from essential hypertensive patients with enhanced Na(+)-H+ exchanger phenotype and six cell lines from normotensive subjects were studied. Lymphocyte markers were visualized by immunostaining. Immunoglobulin secretion was analyzed by enzyme-linked immunosorbent assay. These cell lines did not differ with respect to B cell markers. In response to 100 nmol/L platelet-activating factor, cells from hypertensive patients proliferated distinctly more quickly and their cell number increased by 3.9 +/- 0.4-fold (mean +/- SD) within 4 days, whereas the number of cells from normotensive subjects increased by only 2.6 +/- 0.1-fold. Furthermore, platelet-activating factor induced average increases in IgM and IgG formation of 13.3- and 5.4-fold, respectively, in lymphoblasts from hypertensive patients, which was significantly higher than increases in cells from normotensive subjects (1.4- and 1.2-fold, respectively). Thus, lymphoblasts from hypertensive patients proliferate more quickly and secrete more immunoglobulins in response to a physiological stimulus in vitro. This may contribute to the raised immunoglobulin levels and leukocyte counts reported in vivo.