gebhart/patrepeval huggingface dataset:
Partial Shotgun Sequencing of the Boechera stricta Genome Reveals Extensive Microsynteny and Promoter Conservation with Arabidopsis (2006)

Comparative genomics provides insight into the evolutionary dynamics that shape discrete sequences as well as whole genomes. To advance comparative genomics within the Brassicaceae, we have end sequenced 23,136 medium-sized insert clones from Boechera stricta, a wild relative of Arabidopsis (Arabidopsis thaliana). A significant proportion of these sequences, 18,797, are nonredundant and display highly significant similarity (BLASTn e-value < or = 10(-30)) to low copy number Arabidopsis genomic regions, including more than 9,000 annotated coding sequences. We have used this dataset to identify orthologous gene pairs in the two species and to perform a global comparison of DNA regions 5' to annotated coding regions. On average, the 500 nucleotides upstream to coding sequences display 71.4% identity between the two species. In a similar analysis, 61.4% identity was observed between 5' noncoding sequences of Brassica oleracea and Arabidopsis, indicating that regulatory regions are not as diverged among these lineages as previously anticipated. By mapping the B. stricta end sequences onto the Arabidopsis genome, we have identified nearly 2,000 conserved blocks of microsynteny (bracketing 26% of the Arabidopsis genome). A comparison of fully sequenced B. stricta inserts to their homologous Arabidopsis genomic regions indicates that indel polymorphisms >5 kb contribute substantially to the genome size difference observed between the two species. Further, we demonstrate that microsynteny inferred from end-sequence data can be applied to the rapid identification and cloning of genomic regions of interest from nonmodel species. These results suggest that among diploid relatives of Arabidopsis, small- to medium-scale shotgun sequencing approaches can provide rapid and cost-effective benefits to evolutionary and/or functional comparative genomic frameworks.
Structure of a Hydroxyproline (Hyp)-Arabinogalactan Polysaccharide from Repetitive Ala-Hyp Expressed in Transgenic Nicotiana tabacum (2004)

A synthetic gene encoding the fusion protein (Ala-Hyp)(51)-enhanced green fluorescent protein expressed in Nicotiana tabacum cells produced a fusion glycoprotein with all proline residues hydroxylated and substituted with an arabinogalactan polysaccharide. Alkaline hydrolysis of the fusion glycoprotein yielded a population of hydroxyproline (Hyp)-arabinogalactan polysaccharides ranging in size from 13 to 26 saccharide residues/Hyp, with a median size of 15-17 residues. We isolated a 15-residue Hyp-arabinogalactan for structure determination by sugar analyses and one- and two-dimensional nuclear magnetic resonance techniques that provided the assignment of proton and carbon signals of a small polysaccharide O-linked to the hydroxyl group of Hyp. The polysaccharide consisted of a 1,3-linked beta-D-Galp backbone with a single 1,6-linked beta-D-Galp "kink." The backbone had two side chains of Galp substituted at position 3 with an arabinose di- or trisaccharide and at position 6 with glucuronic acid or rhamnosyl glucuronic acid. Energy-minimized space-filling molecular models showed hydrogen bonding within polysaccharides attached to repetitive Ala-Hyp and also between polysaccharides and the peptide backbone. Polysaccharides distorted the peptide Ramachandran angles consistent with the circular dichroic spectra of isolated (Ala-Hyp)(51) and its reversion to a polyproline II-like helix after deglycosylation. This first complete structure of a Hyp-arabinogalactan polysaccharide shows that computer-based molecular modeling of Hyp-rich glycoproteins is now feasible and supports the suggestion that small repetitive subunits comprise larger arabinogalactan polysaccharides.
Metabolic Engineering of <i>Corynebacterium glutamicum</i> for Fuel Ethanol Production under Oxygen-Deprivation Conditions (2004)

The central metabolic pathway of Corynebacterium glutamicum was engineered to produce ethanol. A recombinant strain which expressed the Zymomonas mobilis genes coding for pyruvate decarboxylase (pdc) and alcohol dehydrogenase (adhB) was constructed. Both genes placed under the control of the C. glutamicum ldhA promoter were expressed at high levels in C. glutamicum, resulting, under oxygen-deprivation conditions, in a significant yield ofethanol from glucose in a process characterized by the absence of cellular growth. Addition of pyruvate in trace amounts to the reaction mixture induced a 2-fold increase in the ethanol production rate. A similar effect was observed when acetaldehyde was added. Disruption of the lactate dehydrogenase (ldhA) gene led to a 3-fold higher ethanol yield than wild type, with no lactate production. Moreover, inactivation of the phosphoenolpyruvate carboxylase (ppc) and ldhA genes revealed a significant amount of ethanol production and a dramatic decrease in succinate without any lactate production, when pyruvate was added. Since the reaction occurred in the absence of cell growth, the ethanol volumetric productivity increased in proportion to cell density of ethanologenic C. glutamicum in a process under oxygen-deprivation conditions. These observations corroborate the view that intracellular NADH concentrations in C. glutamicum are correlated to oxygen-deprived metabolic flows.
Is paraoxon hydrolytic activity in serum predictive of myocardial infarction? (1987)

Journal Article Is paraoxon hydrolytic activity in serum predictive of myocardial infarction? Get access F Szabó, F Szabó Search for other works by this author on: Oxford Academic Google Scholar K Róna, K Róna Search for other works by this author on: Oxford Academic Google Scholar A Czinner, A Czinner Search for other works by this author on: Oxford Academic Google Scholar B Gachályi, B Gachályi Search for other works by this author on: Oxford Academic Google Scholar A Káldor A Káldor Search for other works by this author on: Oxford Academic Google Scholar Clinical Chemistry, Volume 33, Issue 5, 1 May 1987, Pages 742–743, https://doi.org/10.1093/clinchem/33.5.742 Published: 01 May 1987
ChemInform Abstract: SYNTHESIS AND BIOLOGICAL ACTIVITY OF DIGITOXIGENIN AMINO ESTERS (1982)

A series of 3 beta-esters of digitoxigenin (3 beta-hydroxy-14 beta-hydroxy-5 beta-card-20(22)-enolide) with alpha-aminoacids, were synthesized and tested for inotropic activity on the guinea-pig isolated heart and by slow infusion in the cat in comparison with digitoxigenin, Lanatoside C and Strophantin K. Esterification of the 3 beta-hydroxy group of digitoxigenin with various amino acids led to compounds still retaining inotropic activity with low in vivo potency and short duration of action. The compounds are inactive when administered orally.
Auditory Thalamus Neurons During Sleep: Changes in Frequency Selectivity, Threshold, and Receptive Field Size (2000)

The present study describes how the frequency receptive fields (RF) of auditory thalamus neurons are modified when the state of vigilance of an unanesthetized animal naturally fluctuates among wakefulness (W), slow-wave sleep (SWS), and paradoxical sleep (PS). Systematic quantification of several RF parameters-including strength of the evoked responses, response latency, acoustic threshold, shape of rate-level function, frequency selectivity, and RF size-was performed while undrugged, restrained guinea pigs presented spontaneous alternances of W, SWS, and PS. Data are from 102 cells recorded during W and SWS and from 53 cells recorded during W, SWS, and PS. During SWS, thalamic cells behaved as an homogeneous population: as compared with W, most of them (97/102 cells) exhibited decreased evoked spike rates. The frequency selectivity was enhanced and the RF size was reduced. In contrast during PS, two populations of cells were identified: one (32/53 cells) showed the same pattern of changes as during SWS, whereas the other (21/53 cells) expressed values of evoked spike rates and RF properties that did not significantly differ from those in W. These two populations were equally distributed in the different anatomical divisions of the auditory thalamus. Last, during both SWS and PS, the responses latency was longer and the acoustic threshold was higher than in W but the proportion of monotonic versus nonmonotonic rate-level functions was unchanged. During both SWS and PS, no relationship was found between the changes in burst percentage and the changes of the RF properties. These results point out the dual aspect of sensory processing during sleep. On the one hand, they show that the auditory messages sent by thalamic cells to cortical neurons are reduced both in terms of firing rate at a given frequency and in terms of frequency range. On the other hand, the fact that the frequency selectivity and the rate-level function are preserved suggests that the messages sent to cortical cells are not deprived of informative content, and that the analysis of complex acoustic sounds should remain possible. This can explain why, although attenuated, reactivity to biologically relevant stimuli is possible during sleep.
Sugar pucker and phosphodiester conformations in viral genomes of filamentous bacteriophages: fd, If1, IKe, Pf1, Xf, and Pf3 (1988)

The laser Raman spectra of filamentous viruses contain discrete bands which are assignable to molecular vibrations of the encapsidated, single-stranded DNA genomes and which are informative of their molecular conformations. Discrimination between Raman bands of the DNA and those of the coat proteins is facilitated by analysis of viruses containing deuterium-labeled amino acids. Specific DNA vibrational assignments are based upon previous studies of A-, B-, and Z-DNA oligonucleotide crystals of known structure [Thomas, G.J., Jr., & Wang, A.H.-J. (1988) in Nucleic Acids and Molecular Biology (Eckstein, F., & Lilley, D.M.J., Eds.) Vol. 2, Springer-Verlag, Berlin]. The present results show that canonical DNA structures are absent from six filamentous viruses: fd, If1, IKe, Pfl, Xf, and Pf3. The DNAs in three viruses of symmetry class I (fd, If1, IKe) contain very similar nucleoside sugar puckers and glycosyl torsions, deduced to be C3'-endo/anti. However, nucleoside conformations are not the same among the three class II viruses examined: Pf1 and Xf DNAs contain similar conformers, deduced to be C2'-endo/anti, whereas Pf3 DNA exhibits bands usually associated with C3'-endo/anti conformers. Conformation-sensitive Raman bands of the DNA 3'-C-O-P-O-C-5' groups show that in all class I viruses and in Pf1 the ssDNA backbones do not contain regularly ordered phosphodiester group geometries, like those found in ordered single- and double-stranded nucleic acids.(ABSTRACT TRUNCATED AT 250 WORDS)
Functional consequences of engagement of the T cell receptor by low affinity ligands (1993)

The mechanisms involved in TCR antagonism by Ag analog/MHC have been analyzed. A detailed structure-activity relationship study indicated that modification of any of the major T cell contact residues of the peptide molecule can yield a powerful antagonist. It was also shown that as the analog structure increased in similarity to the Ag, the capacity to antagonize Ag-TCR interaction increased up to the point that the analogs themselves became antigenic. These data strongly suggest an affinity-related mechanism whereby a certain affinity is required for signaling through the TCR, and that below this level there can be sufficient affinity to engage the receptor such that triggering does not occur and antagonism can be detected. Taking advantage of this information, antagonist peptides active down to the 10 nM range were engineered. Thus, this approach demonstrates for the first time a rational approach to designing effective, selective low m.w. compounds with high potential in treatment of allergies and autoimmune diseases.
Prostaglandin concentrations in uterine fluid of cows with pyometra. (1985)

Uterine fluid was obtained from eight clinical cases of pyometra with retained corpus luteum and nine additional samples of fluid were collected from animals slaughtered at an abattoir. These samples, along with uterine flushes from normal cows in their luteal phase were analyzed for prostaglandin of the F (PGF) and E (PGE) groups. Blood samples were also obtained from the clinical cases for analysis of 13,14-dihydro-15-keto PGF (PGFM) the major metabolite of PGF. Pyometrial exudate from clinical cases of abattoir samples had high concentrations of PGF (17.9 ng/mL) and PGE (33.2 ng/mL) and the total amount of PGF and PGE in the uterus was calculated to be several hundred times as great as in normal cows. Furthermore, clinical cases had elevated PGFM in their blood compared to that of controls, which suggests that at least some of the PGF was being absorbed from the uterus. These results are discussed in light of our current understanding of the maternal recognition of pregnancy in cattle.
Synthesis and properties of 5-styryl-2-furancarboxylic acids (1981)

5-(4-X-Styryl)-2-furancarboxylic acids (X = H, Br, NO 2 , COOCH 3 , (CH 3 ) 2 N) were prepared by oxidation of the appropriate 5-(4-X-styryl)-2-furaldehydes, or alternatively by alkaline hydrolysis of the corresponding methyl esters. The latter were obtained by reacting the 4-substituted benzaldehydes with 5-methoxycarbonylfuryltriphenylphosphonium chloride. The UV and IR spectra of products are commented. The apparent p K values of the synthesized acids were employed for calculation of the transmission coefficient π' through the benzene-furan system bridged by a -CH=CH- group.
A domain-specific software architecture for adaptive intelligent systems (1995)

A good software architecture facilitates application system development, promotes achievement of functional requirements, and supports system reconfiguration. We present a domain-specific software architecture (DSSA) that we have developed for a large application domain of adaptive intelligent systems (AISs). The DSSA provides: (a) an AIS reference architecture designed to meet the functional requirements shared by applications in this domain, (b) principles for decomposing expertise into highly reusable components, and (c) an application configuration method for selecting relevant components from a library and automatically configuring instances of those components in an instance of the architecture. The AIS reference architecture incorporates features of layered, pipe and filter, and blackboard style architectures. We describe three studies demonstrating the utility of our architecture in the subdomain of mobile office robots and identify software engineering principles embodied in the architecture.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A Study of Anisotropic Chemical Etching on Crystalline Silicon (2014)

It is known that chemical reaction rates can be different on different crystal planes. KOH is a common etchant for Si and the reaction rate on {100} planes is much faster than the {111} planes. Therefore a square etch window on a (100) Si surface can become an inverse pyramid at some point after KOH etch. However, it is not clear how a 3-­‐dimensional cubic crystal will evolve by KOH etching. In this study we use a dicing saw to create arrays of rectangular crystal pillars of different dimensions in two different orientations followed by 6M KOH etch at 50º C. We use scanning electron microscopy to record the evolution of the pillar morphology with and without an oxide cap layer. We find that the complex geometry is a result of the competition between different crystal planes.
Vaccination for Malignant Melanoma: Recent Developments (2000)

The identification of tumor-associated antigens recognized by cellular or humoral effectors of the immune system has opened new perspectives for cancer immunotherapy. Different categories of cancer-associated antigens have been described as targets for CD8+ T cells in vitro and in vivo: (1) 'cancer-testis' (CT) antigens expressed in different tumors and normal testis; (2) melanocyte differentiation antigens; (3) point mutations of normal genes; (4) antigens that are overexpressed in malignant tissues, and (5) viral antigens. Clinical trials with antigenic peptides have been initiated to induce specific immunological responses in vivo. Immunological and clinical parameters for the assessment of peptide-specific reactions have been defined: DTH, CD8+ T cell, autoimmune and tumor regression responses. Preliminary results show that tumor-associated peptides alone elicit specific DTH and CD8+ T cell responses associated with tumor regression after intradermal vaccination. Granulocyte macrophage colony-stimulating factor has been shown to enhance peptide-specific immune reactions by amplification of dermal antigen-presenting dendritic cells. Complete tumor regressions have been observed after the induction of CD8+ T cell responses by peptide immunization. Based on these results, active immunotherapy with tumor-associated antigens may be a promising approach for patients in adjuvant treatment situations, who are at high risk for tumor recurrence. Recently, a strategy utilizing spontaneous antibody responses to tumor-associated antigens (SEREX) has led to the identification of a new CT antigen, NY-ESO-1. NY-ESO-1-specific spontaneous humoral and cellular immune responses were found in approximately 50% of patients with NY-ESO-1-positive tumors. Clinical studies have been initiated to evaluate the immunological effects of immunization with NY-ESO-1 peptides in cancer patients with detectable or absent immunity against NY-ESO-1.
Selective synthesis of double helices of carbon nanotube bundles grown on treated metallic substrates (2012)

Abstract Double‐helix microstructures consisting of two parallel strands of hundreds of multi‐walled carbon nanotubes (MWCNTs) have been synthesized by chemical vapour deposition of ferrocene/toluene vapours on metal substrates. Growth of coiled carbon nanostructures with site selectivity is achieved by varying the duration of thermochemical pretreatment to deposit a layer of SiO x on the metallic substrate. Production of multibranched structures of MWCNTs converging in SiO x microstructure is also reported. magnified image In the abstract figure, panel (a) shows a coloured micrograph of a typical double‐helix coiled microstructure of MWCNTs grown on SiO x covered steel substrate. Green and blue show each of the two individual strands of MWCNTs. Panel (b) is an amplification of a SiO x microparticle (white) on the tip of the double‐stranded coil (green and blue). The microparticle guides the collective growth of hundreds of MWCNTs to form the coiled structure.
MassTag Polymerase‐Chain‐Reaction Detection of Respiratory Pathogens, Including a New Rhinovirus Genotype, That Caused Influenza‐Like Illness in New York State during 2004–2005 (2006)

In New York State during winter 2004, there was a high incidence of influenza-like illness that tested negative both for influenza virus, by molecular methods, and for other respiratory viruses, by virus culture. Concern that a novel pathogen might be implicated led us to implement a new multiplex diagnostic tool. MassTag polymerase chain reaction resolved 26 of 79 previously negative samples, revealing the presence of rhinoviruses in a large proportion of samples, half of which belonged to a previously uncharacterized genetic clade. In some instances, knowledge of the detected viral and/or bacterial (co)infection could have altered clinical management.
Monoclonal Antibody to Human Platelet Glycoprotein I II. EFFECTS ON HUMAN PLATELET FUNCTION (1981)

The effect on platelet function of a monoclonal platelet antibody to platelet membrane glycoprotein I was tested. This antibody, AN51, inhibited ristocetin or bovine factor VIII-induced aggregation but did not modify ADP, collagen type I or type III, thrombin or arachidonic acid induced aggregations. Furthermore, the adhesion-aggregation of platelets induced by microfibrils was also inhibited by the antibody. Platelet adhesion to rabbit aorta subendothelium was impaired by the antibody. The persistent adhesion of platelets to collagenase-treated subendothelium was also inhibited. These findings strongly suggested that platelet membrane glycoprotein I could interact with a non-collagenic microfibrillar component of subendothelium. The binding of factor VIII/von Willebrand factor to platelet membrane in the presence of ristocetin was decreased in the binding site for factor VIII/von Willebrand factor to allow platelet adhesion to subendothelium.
Pathology of experimental inhalation anthrax in the rhesus monkey. (1995)

In our study, compared with previous reports, meningitis and mesenteric lymph node hemorrhages were more common, whereas mediastinal and tracheobronchial lymph node hemorrhages were less common. Immunostaining highlighted intracellular bacilli that would have been otherwise missed by light microscopic examination.
Models for Static and Dynamic Texture Synthesis in Image and Video Compression (2011)

In this paper, we investigate the use of linear, parametric models of static and dynamic texture in the context of conventional transform coding of images and video. We propose a hybrid approach incorporating both conventional transform coding and texture-specific methods for improvement of coding efficiency. Regarding static (i.e., purely spatial) texture, we show that Gaussian Markov random fields (GMRFs) can be used for analysis/synthesis of a certain class of texture. The properties of this model allow us to derive optimal methods for classification, analysis, quantization and synthesis. For video containing dynamic textures, a linear dynamic model can be derived from frames encoded in a conventional fashion. We show that after removing effects from camera motion, this model can be used to synthesize further frames. Beyond that, we show that using synthesized frames in an appropriate fashion for prediction leads to significant bitrate savings while preserving the same peak signal-to-noise ratio (PSNR) for sequences containing dynamic textures.
Darstellung 2‐methoxysubstituierter Pyrrole durch intramolekulare Aza‐Wittig‐Reaktionen (1990)

Preparation of 2‐Methoxy‐Substituted Pyrroles by Aza‐Wittig Reactions α‐Halo ketones and dimethyl malonate can be transformed by Knoevenagel condensation and nucleophilic displacement of halogen with sodium azide into the azide esters 10 . These azides undergo ring closure to 2‐methoxy‐substituted pyrroles 11 by intramolecular Aza‐Wittig reaction.