gebhart/patrepeval huggingface dataset:
A Polyketide Synthase Component for Oxygen Insertion into Polyketide Backbones (2018)

Abstract Enzymatic core components from trans ‐acyltransferase polyketide synthases (trans‐AT PKSs) catalyze exceptionally diverse biosynthetic transformations to generate structurally complex bioactive compounds. Here we focus on a group of oxygenases identified in various trans‐AT PKS pathways, including those for pederin, oocydins, and toblerols. Using the oocydin pathway homologue (OocK) from Serratia plymuthica 4Rx13 and N ‐acetylcysteamine (SNAC) thioesters as test surrogates for acyl carrier protein (ACP)‐tethered intermediates, we show that the enzyme inserts oxygen into β‐ketoacyl moieties to yield malonyl ester SNAC products. Based on these data and the identification of a non‐hydrolyzed oocydin congener with retained ester moiety, we propose a unified biosynthetic pathway of oocydins, haterumalides, and biselides. By providing access to internal ester, carboxylate pseudostarter, and terminal hydroxyl functions, oxygen insertion into polyketide backbones greatly expands the biosynthetic scope of PKSs.
Oblique laser incidence to select laser-generated acoustic modes (2011)

The purpose of this paper is to study the effect of a non-normal optical penetration due to an obliquely incident laser source. It is shown that the loss of symmetry due to such a penetration influences specific bulk acoustic modes. For a given detection position, increase in shear wave amplitude is obtained by orienting the incident laser source. 1. Introduction Since the first quantitative approaches in the 60's [1], a large number of studies has been conducted to better understand the generation of laser-generated acoustic waves. Models for the acoustic generation in the thermoelastic regime, taking into account the optical penetration of the source [2] or the effect of source width [3], were developed. A more general approach based on Green's function formalism also included thermal diffusion in the medium [4]. These works have dealt with the modeling of a circular spot of laser illumination. However, modeling of the acoustic field generated by a line source is of interest, since the signal-to-noise ratio may be increased in this experimental situation [5]. All the works cited above assume a normal incidence of the laser beam with respect to the illuminated surface of the sample. The purpose of this paper is to analyse the effects of oblique incidence on acoustic waves generated by a line-focused laser source. We present a theoretical model accounting for the effects of optical penetration, finite width of the beam and pulse duration of the laser source. The absorbed energy density is first calculated by solving Maxwell's equations. Then the thermoelastic equations are solved to obtain the displacement field through a semi-analytical calculation based on a double Fourier transform in space and time. It is shown that oblique incidence increases shear wave amplitude. Changes of the longitudinal waveforms are also discussed.
Effective Treatment of Staphylococcal Enterotoxin B Aerosol Intoxication in Rhesus Macaques by Using Two Parenterally Administered High-Affinity Monoclonal Antibodies (2019)

Staphylococcal enterotoxin B (SEB) is a protein exotoxin found on the cell surface of <i>Staphylococcus aureus</i> that is the source for multiple pathologies in humans. When purified and concentrated in aerosol form, SEB can cause an acute and often fatal intoxication and thus is considered a biological threat agent. There are currently no vaccines or treatments approved for human use. Studies with rodent models of SEB intoxication show that antibody therapy may be a promising treatment strategy; however, many have used antibodies only prophylactically or well before any clinical signs of intoxication are apparent. We assessed and compared the protective efficacies of two monoclonal antibodies, Ig121 and c19F1, when administered after aerosol exposure in a uniformly lethal nonhuman primate model of SEB intoxication. Rhesus macaques were challenged using small-particle aerosols of SEB and then were infused intravenously with a single dose of either Ig121 or c19F1 (10 mg/kg of body weight) at either 0.5, 2, or 4 h postexposure. Onset of clinical signs and hematological and cytokine response in untreated controls confirmed the acute onset and potency of the toxin used in the challenge. All animals administered either Ig121 or c19F1 survived SEB challenge, whereas the untreated controls succumbed to SEB intoxication 30 to 48 h postexposure. These results represent the successful therapeutic <i>in vivo</i> protection by two investigational drugs against SEB in a severe nonhuman primate disease model and punctuate the therapeutic value of monoclonal antibodies when faced with treatment options for SEB-induced toxicity in a postexposure setting.
A modelling study of atrial septostomy for pulmonary arterial hypertension, and its effect on the state of tissue oxygenation and systemic blood flow (2010)

Atrial septostomy is performed in patients with severe pulmonary arterial hypertension, and has been shown to improve symptoms, quality of life and survival. Despite recognized clinical benefits, the underlying pathophysiologic mechanisms are poorly understood. We aimed to assess the effects of right-to-left shunting on arterial delivery of oxygen, mixed venous content of oxygen, and systemic cardiac output in patients with pulmonary arterial hypertension and a fixed flow of blood to the lungs. We formulated equations defining the mandatory relationship between physiologic variables and delivery of oxygen in patients with right-to-left shunting. Using calculus and computer modelling, we considered the simultaneous effects of right-to-left shunting on physiologies with different pulmonary flows, total metabolic rates, and capacities for carrying oxygen. Our study indicates that, when the flow of blood to the lungs is fixed, increasing right-to-left shunting improves systemic cardiac output, arterial blood pressure, and arterial delivery of oxygen. In contrast, the mixed venous content of oxygen, which mirrors the average state of tissue oxygenation, remains unchanged. Our model suggests that increasing the volume of right-to-left shunting cannot compensate for right ventricular failure. Atrial septostomy in the setting of pulmonary arterial hypertension, therefore, increases the arterial delivery of oxygen, but the mixed systemic saturation of oxygen, arguably the most important index of tissue oxygenation, stays constant. Our data suggest that the clinically observed beneficial effects of atrial septostomy are the result of improved flow of blood rather than augmented tissue oxygenation, provided that right ventricular function is adequate.
Features of the Influenceof a DNA Sequence on ItsAdjacent Sequence (2020)

To explore the features of the influence
of a DNA sequence (here
called sequence A) on its adjacent sequence (here called sequence
B), we linked some DNA repeated sequences to the 5′-end of
the T7 promoter in the plasmid pET-42a (+) or the 5′- and/or
3′-end(s) of the EcoRI site in some DNA fragments using PCR
and other molecular cloning methods. As a result, we found that the
efficiency of the T7 promoter and EcoRI could be impacted by some
flanking sequences, indicating that sequence B could be impacted by
sequence A. The features of such influence include the following:
(i) sequence A can directly impact sequence B without changing/modifying
the base composition of sequence B or destroying the inherent connection
between sequence B and its function-related sequences; (ii) such influence
does not need the participation of trans-acting factors or products
of sequence A (if any); (iii) such an influence might be undetectable
when the activities of trans-acting factors of sequence B are normal
but might become detectable when those are lower than the normal one;
(iv) such an influence might be enhancive, inhibitory, or unobvious;
(v) the influence of sequence A linked to the 5′-end of sequence
B might be the same as or opposite to that of sequence A linked to
the 3′-end; and (vi) the influences of sequence A linked to
different ends of sequence B could enhance or partially offset
each other when sequence A is linked to both 5′- and
3′-ends of sequence B. These findings might give us a further
understanding of the interaction of two adjacent DNA sequences.
Contact Sex Pheromones Identified for Two Species of Longhorned Beetles (Coleoptera: Cerambycidae)Tetropium fuscumandT. cinnamopterumin the Subfamily Spondylidinae (2011)

Male Tetropium fuscum (F.) and T. cinnamopterum Kirby mated with live and dead (freeze-killed) conspecific females upon antennal contact, but did not respond to dead females after cuticular waxes were removed by hexane rinsing. Significantly fewer males of each species attempted to copulate with live or dead heterospecific females than with conspecifics, indicating that mate recognition was mediated by species-specific contact sex pheromones in the female's cuticular hydrocarbons. GC/MS analysis of T. fuscum elytra identified n-alkanes and mono-methyl branched alkanes of which 11-methylheptacosane and 3- and 5-methyltricosanes were dominant in females. Full male responses, including copulatory behavior, were restored with application of enantiomerically pure synthetic (S)-11-methyl-heptacosane at 40 μg/female (one female equivalent) but not with racemic or (R)-11-methyl-heptacosane. The cuticular hydrocarbons on T. cinnamopterum elytra included 11-methyl-heptacosane as well as n-alkanes, methyl-branched alkanes, mono-alkenes, and (Z, Z)-6, 9-alkadienes. (Z)-9-pentacosene, (Z)-9-heptacosene, and 11-methyl-heptacosane were female dominant, but only (Z)-9-pentacosene elicited precopulatory behaviors in conspecific males at levels similar to those behaviors elicited by unrinsed females, but elicited copulation in fewer than half of males. At female equivalent dosages (10 μg), neither (Z)-9-heptacosene nor (S)-11-methyl- heptacosane elicited responses in males that were significantly different from those responses to a rinsed female but when applied together, the proportion of males responding was significantly increased. 11-methyl-heptacosene is thus a contact pheromone component common to both species, which may explain the heterospecific mating attempts by some males.
Electrochemically Controllable Conjugation of Proteins on Surfaces (2007)

The rational design of surfaces for immobilization of proteins is essential to a variety of biological and medical applications ranging from molecular diagnostics to advanced platforms for fundamental studies of molecular and cell biology. We have developed an advanced electrochemically based approach for site-selective and reaction-controlled immobilization of proteins on surfaces. When a molecular monolayer of 4-nitrothiophenol on gold electrode surfaces is reduced electrochemically in a selective fashion at its nitro groups, to afford amino groups by potentiometric scans, the amine can be employed to orchestrate the immobilization of proteins to the surface. This protein immobilization strategy could allow one to fabricate intricate protein structures on surfaces for addressing fundamental and applied problems in biology and medicine.
Effect of thin twine on gill net size-selectivity analyzed with the direct estimation method (2001)

To analyze the effect of thin twine on gill net size selectivity, a series of fishing experiments using gill nets of two twine thicknesses (no. 0.8 of 0.16 mm diameter and no. 3 of 0.28 mm diameter) and three nominal mesh sizes (41 mm, 46 mm and 51 mm) was conducted in outdoor water tanks containing a rainbow trout (Oncorhynchus mykiss) population of known size frequency. For nets of the same nominal mesh size, mesh openings of the no. 0.8 twine nets were approximately 2 mm larger than those of the no. 3 twine nets. The effects of both mesh opening and twine thickness are combined in the conventional analysis with the selectivity curve against fish length. Selectivity against the ratio of fish girth to mesh perimeter was calculated to avoid the direct effect of changes in mesh openings due to twine diameter at the same nominal mesh size. Results demonstrated that the thinner twine gill net was more likely to capture rainbow trout of smaller girth than the mesh perimeter. Fish with girths smaller than the mesh perimeter were often retained by the net with its body tangled by the thinner twine, possibly due to the increased flexibility of the thinner twine.
Thermal response of rat fibroblasts stably transfected with the human 70-kDa heat shock protein-encoding gene. (1991)

The major heat shock protein hsp70 is synthesized by cells of a wide variety of organisms in response to heat shock or other environmental stresses and is assumed to play an important role in protecting cells from thermal stress. We have tested this hypothesis directly by transfecting a constitutively expressed recombinant human hsp70-encoding gene into rat fibroblasts and examining the relationship between the levels of human hsp70 expressed and thermal resistance of the stably transfected rat cells. Successful transfection and expression of the gene for human hsp70 were characterized by RNA hybridization analysis, two-dimensional gel electrophoresis, and immunoblot analysis. When individual cloned cell lines were exposed to 45 degrees C and their thermal survivals were determined by colony-formation assay, we found that the expression of human hsp70 conferred heat resistance to the rat cells. These results reinforce the hypothesis that hsp70 has a protective function against thermal stress.
Major sites of metal binding in Bacillus licheniformis walls (1982)

Isolated and purified walls of Bacillus licheniformis NCTC 6346 his contained peptidoglycan, teichoic acid, and teichuronic acid (0.36 mumol of diaminopimelic acid, 0.85 mumol of organic phosphorus, and 0.43 mumol of glucuronic acid per mg [dry weight] of walls, respectively). The walls also contained a total of 0.208 mumol of metal per mg. When these walls were subjected to metal-binding conditions (T. J. Beveridge and R. G. E. Murray, J. Bacteriol. 127:1502-1518, 1976) for nine metals, the amount of bound metal above background ranged from 0.910 mumol of Na to 0.031 mumol of Au per mg of walls. Most were in the 0.500-mumol mg-1 range. Electron-scattering profiles from unstained thin sections indicated that the metal was dispersed throughout the wall fabric. Mild alkali treatment extracted teichoic acid from the walls (97% based on phosphorus) but left the peptidoglycan and teichuronic acid intact. This treatment reduced their capacity for all metals but Au. Thin sections revealed that the wall thickness had been reduced by one-third, but metal was still dispersed throughout the wall fabric. Trichloroacetic acid treatment of the teichoic acid-less walls removed 95% of the teichuronic acid (based on glucuronic acid) but left the peptidoglycan intact (based on sedimentable diaminopimelic acid). The thickness of these walls was not further reduced, but little binding capacity remained (usually less than 10% of the original binding). The staining of these walls with Au produced a 14.4-nm repeat frequency within the peptidoglycan fabric. Sedimentation velocity experiments with the extracted teichuronic acid in the presence of metal confirmed it to be a potent metal-complexing polymer. These results indicated that teichoic and teichuronic acids are the prime sites of metal binding in B. licheniformis walls.
Complete parameterization of piecewise-polynomial interpolation kernels (2003)

Every now and then, a new design of an interpolation kernel appears in the literature. While interesting results have emerged, the traditional design methodology proves laborious and is riddled with very large systems of linear equations that must be solved analytically. We propose to ease this burden by providing an explicit formula that can generate every possible piecewise-polynomial kernel given its degree, its support, its regularity, and its order of approximation. This formula contains a set of coefficients that can be chosen freely and do not interfere with the four main design parameters; it is thus easy to tune the design to achieve any additional constraints that the designer may care for.
Lead(II)/platinum(II) complexes with and without Pb-Pt interactions (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLead(II)/platinum(II) complexes with and without Pb-Pt interactionsAlan L. Balch, Ella Y. Fung, Jeffrey K. Nagle, Marilyn M. Olmstead, and Stephen P. RowleyCite this: Inorg. Chem. 1993, 32, 15, 3295–3299Publication Date (Print):July 1, 1993Publication History Published online1 May 2002Published inissue 1 July 1993https://pubs.acs.org/doi/10.1021/ic00067a017https://doi.org/10.1021/ic00067a017research-articleACS PublicationsRequest reuse permissionsArticle Views172Altmetric-Citations32LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
A validated miRNA expression profile for response to neoadjuvant therapy in esophageal cancer. (2013)

4078 Background: For patients with esophageal adenocarcinoma (EAC) preoperative chemoradiation (trimodality therapy) is the preferred approach. We examined several patient cohorts to create and validate a miRNA signature predictive for response to this therapy in esophageal carcinoma. Methods: Pre-treatment tumor specimens from 10 patients with EAC treated with trimodality therapy were examined using a TaqMan Human MicroRNA Card Set (v3.0) for expression of 754 miRNAs, of which 306 were overexpressed. miRNA expression between patients with a pathologic complete response (pCR) and those with a non-pCR was then analyzed. 44 miRNAs differentially expressed between pCR and non-pCR patients were then examined in an additional 42 EAC patientsÕ tumors (model set) using the Fluodigm 48.48 Dynamic Array and were used to generate a miRNA expression profile (MEP) predicting for response in three groups: low, intermediate and high-risk. The MEP was then validated in an additional 72 EAC patients using the Illumina miRNA Expression Array. ROC curves were generated for clinical stage, MEP and a combination of both. Results: For the model set, pCR rates in low risk patients based on the MEP were 75%, 42.9% in intermediate risk and 12.5% in high-risk patients (p trend =0.008). In the validation set the pCR rates were 66.7%, 36.5% and 15.7% for low, intermediate and high-risk patients respectively (p trend =0.025). The AUC for the ROC using the MEP was 0.72 (p=7.8x10-12) in the model set, 0.69 (p=1x10-4) in the validation set and 0.7 for the two cohorts combined (p=1.4x10-18). When clinical stage was added to the predictive model, the ROC for each group was 0.79 (p=2.6x10-19), 0.75 (p=8.7x10-27) and 0.77 (p=2x10-41) respectively. Conclusions: The MEP represents the first validated miRNA signature for therapeutic response in esophageal carcinoma and improves significantly on clinical staging. Its use could select patients at high-risk for therapeutic resistance for trial-based therapy, as well as low-risk patients for whom resection may possibly be safely omitted.
Synthesis and study of the luminescent properties of terbium-activated gadolinium tantalum-niobate (2022)

For the first time, terbium-activated gadolinium tantalo-niobates were synthesized ((Gd 1-x Tb x )Nb y Ta 1-y O 4 ). The synthesis was carried out by the liquid-phase method. All studied materials had the main crystalline modification M GdNbO 4 . The content of impurity phases did not exceed 2-5%. The photo- and cathodoluminescence spectra were studied. Concentration quenching of the terbium ion luminescence for a series of solid solutions containing tantalum ((Gd 1-x Tb x )Nb 0.9 Ta 0.1 O 4 ) occurs earlier than for pure gadolinium niobates ((Gd 1-x Tb x )NbO 4 ). The obtained materials are promising for use as scintillators. Keywords: gadolinium tantalum-niobates, liquid-phase synthesis, Tb 3+ , luminescence, cathodoluminescence.
Blocking Self-avoiding Walks Stops Cyber-epidemics: A Scalable GPU-based\n Approach (2017)

Cyber-epidemics, the widespread of fake news or propaganda through social\nmedia, can cause devastating economic and political consequences. A common\ncountermeasure against cyber-epidemics is to disable a small subset of\nsuspected social connections or accounts to effectively contain the epidemics.\nAn example is the recent shutdown of 125,000 ISIS-related Twitter accounts.\nDespite many proposed methods to identify such subset, none are scalable enough\nto provide high-quality solutions in nowadays billion-size networks.\n To this end, we investigate the Spread Interdiction problems that seek most\neffective links (or nodes) for removal under the well-known Linear Threshold\nmodel. We propose novel CPU-GPU methods that scale to networks with billions of\nedges, yet, possess rigorous theoretical guarantee on the solution quality. At\nthe core of our methods is an $O(1)$-space out-of-core algorithm to generate a\nnew type of random walks, called Hitting Self-avoiding Walks (HSAWs). Such a\nlow memory requirement enables handling of big networks and, more importantly,\nhiding latency via scheduling of millions of threads on GPUs. Comprehensive\nexperiments on real-world networks show that our algorithms provides much\nhigher quality solutions and are several order of magnitude faster than the\nstate-of-the art. Comparing to the (single-core) CPU counterpart, our GPU\nimplementations achieve significant speedup factors up to 177x on a single GPU\nand 338x on a GPU pair.\n
Nociceptive transmission and modulation via P2X receptors in central pain syndrome (2016)

Painful sensations are some of the most frequent complaints of patients who are admitted to local medical clinics. Persistent pain varies according to its causes, often resulting from local tissue damage or inflammation. Central somatosensory pathway lesions that are not adequately relieved can consequently cause central pain syndrome or central neuropathic pain. Research on the molecular mechanisms that underlie this pathogenesis is important for treating such pain. To date, evidence suggests the involvement of ion channels, including adenosine triphosphate (ATP)-gated cation channel P2X receptors, in central nervous system pain transmission and persistent modulation upon and following the occurrence of neuropathic pain. Several P2X receptor subtypes, including P2X2, P2X3, P2X4, and P2X7, have been shown to play diverse roles in the pathogenesis of central pain including the mediation of fast transmission in the peripheral nervous system and modulation of neuronal activity in the central nervous system. This review article highlights the role of the P2X family of ATP receptors in the pathogenesis of central neuropathic pain and pain transmission. We discuss basic research that may be translated to clinical application, suggesting that P2X receptors may be treatment targets for central pain syndrome.