gebhart/patrepeval huggingface dataset:
Pneumococcus: the sugar-coated bacteria. (2006)

The study of Streptococcus pneumoniae (the pneumococcus) had been a central issue in medicine for many decades until the use of antibiotics became generalized. Many fundamental contributions to the history of microbiology should credit this bacterium: the capsular precipitin reaction, the major role this reaction plays in the development of immunology through the identification of polysaccharides as antigens, and, mainly, the demonstration, by genetic transformation, that genes are composed of DNA-the finding from the study of bacteria that has had the greatest impact on biology. Currently, pneumococcus is the most common etiologic agent in acute otitis media, sinusitis, and pneumonia requiring the hospitalization of adults. Moreover, meningitis is the leading cause of death among children in developing countries. Here I discuss the contributions that led to the explosion of knowledge about pneumococcus and also report some of the contributions of our group to the understanding of the molecular basis of three important virulence factors: lytic enzymes, pneumococcal phages, and the genes coding for capsular polysaccharides.
Ammonium tolerance and the regulation of two cytosolic glutamine synthetases in the roots of sorghum (2010)

Tolerance to ammonium nutrition in plants can be related to their ability to detoxify ammonium via nitrogen assimilation in roots. Here, we report that sorghum–sudangrass (Sorghum bicolor L. × S. bicolor var. sudanense) hybrids exhibited enhanced biomass production under high levels of inorganic nitrogen supply as well as increased capacity for nitrogen assimilation in roots. Glutamine synthetase (GS, EC 6.3.1.2) activity and protein accumulated in roots at increasing concentrations of either nitrate or ammonium, with particularly high levels of GS in ammonium-treated plants. Ammonium but not nitrate differentially regulated two distinct cytosolic GS (GS1) isoforms composed by polypeptides of similar size but different charge. The comparative analysis of GS gene sequences and the deduced GS1 polypeptides suggested that the two GS1 isoforms were the expression products of SbGln1.2 and SbGln1.3 genes. SbGln1.3 expression was shown to be upregulated by high levels of inorganic nitrogen supply, with a maximal abundance of SbGln1.3 transcripts in ammonium-grown plants. SbGln1.2 expression was uniform along the root axis meanwhile protein and transcript levels for SbGln1.3 were particularly abundant in the upper part of the axis where lateral roots are prominent. Kinetic analysis revealed that the two GS1 isoenzymes have relatively low-affinity for ammonium ions. The spatial distribution of low-affinity GS1 isoenzymes would provide a sustained glutamine biosynthesis at high levels of ammonium supply and may represent at the same time an efficient system of ammonium detoxification. Such a mechanism may prevent transport of ammonium to leaves alleviating symptoms of toxicity and therefore contributing to sorghum ammonium tolerance.
Water-Mediated Association Provides an Ion Pair Receptor (2003)

In this paper, we report on the formation and properties of a water-stabilized dimer comprising calix[4]arene-guanosine conjugate cG 2. The 1,3-alternate calixarene cG 2 was poorly soluble in dry CDCl(3) and gave an ill-resolved NMR spectrum, consistent with its nonspecific aggregation. The compound was much more soluble in water-saturated CDCl(3). Two sets of well-resolved (1)H NMR signals for the guanosine residues in cG 2, present in a 1:1 ratio, indicated that the compound's D(2) symmetry had been broken and provided the first hint that cG 2 dimerizes in water-saturated CDCl(3). The resulting dimer, (cG 2)(2).(H(2)O)(n)(), has a unique property: it extracts alkali halide salts from water into organic solution. This dimer is a rare example of a self-assembled ion pair receptor. The identity of the (cG 2)(2).NaCl.(H(2)O)(n)() dimer was confirmed by comparing its self-diffusion coefficient in CDCl(3), determined by pulsed-field gradient NMR, with that of control compound cA 3, an adenosine analogue. The dimer's stoichiometry was also confirmed by quantitative measurement of the cation and anion using ion chromatrography. Two-dimensional NMR and ion-induced NMR shifts indicated that the cation binding site is formed by an intermolecular G-quartet and the anion binding site is provided by the 5'-amide NH groups. Once bound, the salt increases the dimer's thermal stability. Both (1)H NMR and ion chromatography measurements indicated that the cG 2 dimer has a modest selectivity for extracting K(+) over Na(+) and Br(-) over Cl(-). The anion's identity also influences the association process: NaCl gives a soluble, discrete dimer whereas addition of NaBPh(4) to (cG 2)(2).(H(2)O)(n)() leads to extensive aggregation and precipitation. This study suggests a new direction for ion pair receptors, namely, the use of molecular self-assembly. The study also highlights water's ability to stabilize a functional noncovalent assembly.
Conformationally constrained single-chain peptide mimics of relaxin B-chain secondary structure (2005)

Relaxin is a member of the insulin superfamily and has many biological actions including angiogenesis and collagen degradation. It is a 6 kDa peptide hormone consisting of two peptide chains (A and B) tethered by two disulphide bonds. Past structure-function relationship studies have shown the key receptor binding site of relaxin to be principally situated within the B-chain alpha-helix. Molecular dynamic simulations were performed to aid the design of conformationally constrained relaxin B-chain analogues that possess alpha-helical structure and relaxin-like activity. Restraints included disulphide bonds, both single and double, and lactam bonds. Each peptide was prepared by solid phase synthesis and, following purification, subjected to detailed conformational analysis by circular dichroism spectroscopy. Of 15 prepared relaxin B-chain mimetics, one was able to mimic the secondary structure of the native ligand as indicated by biomolecular recognition/interaction analysis using surface enhanced laser desorption ionization mass spectroscopy together with a relaxin antibody. However, none of the mimetics possess characteristic relaxin-like biological activity which strongly indicates that the pharmacophore comprises additional structural elements other than the relaxin B-chain alpha-helix. These findings will assist in the design and preparation of novel relaxin agonists and antagonists.
Theoretical Studies of Ziegler-Natta Catalysis: Structural Variations and Tacticity Control (1994)

Models for the likely active catalysts in homogeneous Ziegler-Natta systems have been studied using ab initio quantum chemical methods. We investigated the geometries of the isoelectronic model complexes, X_2M-R where X = Cl or Cp = (η^5-C_5H_5); where M = Sc and Ti^+ (and also Ti); and where R = H, CH_3, or SiH_3. The general trend is that the M = Sc compounds strongly prefer a planar configuration, whereas the M = Ti^+ cases generally prefer pyramidal geometries. This difference in geometry can be related to the differing ground-state electronic configurations for the metals: Sc is (4s)^2(3d)^1, whereas Ti^+ is (4s)^1(3d)^2. The nonplanar geometry for [Cp_2Ti-R]^+ suggests an explanation for the origin of stereospecificity in the syndiotactic polymerization by unsymmetric metallocene catalysts. These results suggest that {(η^5-C_5H_4)CMe_2(η^5-fluorenyl)}Sc-R would not catalyze syndiotactic polymerization under these conditions.
Preparation of Nearly Monodisperse Nanoscale Inorganic Pigments (2006)

Many different important commercial pigments have been synthesized based on the liquid-solid-solution (LSS) phase-transfer and separation process. Transmission electron microscopy (TEM) measurement results show that they are very small in size and have a narrow size distribution. Visible absorption spectra were taken to examine the very pure and brilliant colors of the pigments. They can be well-dispersed in cyclohexane and remain non-agglomerated, even over several months. These nearly monodisperse nanoscale inorganic pigments may have wide applications in many important fields and could bring about new developments in the pigment industry.
Phase I/II trial of Arginine Butyrate and ganciclovir in Epstein-Barr virus-associated lymphoid malignancies (2006)

7542 Background: Malignancies associated with latent Epstein-Barr virus (EBV) are resistant to nucleoside-type anti-viral agents because the viral enzyme target of these drugs, thymidine kinase (TK), is not expressed. Short-chain fatty acids, such as butyrate, induce EBV-TK expression in latently-infected B cells. In preclinical studies, we have shown that butyrate sensitizes EBV(+) lymphoblastoid cells, tumor lines and primary lymphoma cultures to apoptosis induced by ganciclovir. Methods: We conducted a Phase I/II trial of Arginine Butyrate in combination with ganciclovir in patients with refractory EBV(+) lymphoid malignancies to evaluate toxicity, pharmacokinetic parameters, and clinical responses. Fifteen patients with heavily-pretreated, refractory EBV(+) lymphoid malignancies, consisting of monoclonal refractory lymphoproliferative disease (PTLD), B cell non-Hodgkin’s lymphomas (NHL) (including one HIV-associated anaplastic B cell lymphoma), T cell NHL (including one cutaneous lymphoma), T/NK cell lymphomas, and Hodgkin disease were studied. Ganciclovir was administered twice daily and Arginine Butyrate was administered in an intra-patient dose-escalation. Arginine Butyrate was instituted at 500 mg/kg/day by continuous infusion, and escalated to 2000 mg/kg/day, as tolerated. Results: The MTD for Arginine Butyrate was established as 1000 mg/kg/day. Overall the combination was well-tolerated, with the most common toxicities being nausea and headache. Complications from rapid tumor lysis occurred in three patients, including acute hepatic necrosis in one patient. Reversible grade 3–4 somnolence or stupor occurred in three patients at Arginine Butyrate doses of greater than 1000 mg/kg/day. Ten of fifteen patients showed significant anti-tumor responses, with 5 CR and 5 PR. In certain patients who demonstrated a clinical CR, subsequent pathological analysis showed elimination of all tumor cells. Conclusions: The combination of Arginine Butyrate and ganciclovir was reasonably well-tolerated and appears to have significant biological activity in vitro and in vivo against refractory EBV(+) lymphoid malignancies. No significant financial relationships to disclose.
Resource assessment based on 4D seismic and inversion at Ringhorne Field, Norwegian North Sea (2012)

Time-lapse (4D) seismic data from Ringhorne Field in the North Sea are used to monitor water movement in both Paleocene- and Jurassic-age reservoir sands, improve existing geologic and simulation models, and enable more cost-effective field operations. The structural complexity of the reservoirs, their proximity to the high-impedance Cretaceous chalk, and a relatively small 4D response has required a significant effort in seismic acquisition and processing which resulted in highly repeatable surveys (Johnston et al., 2010). In addition to the 4D interpretation, VP/VS derived from simultaneous elastic inversion is diagnostic of sand and provides additional constraints on Ringhorne subsurface models. Connected volumes based on VP/VS correlate to areas of water sweep seen in the 4D data and reduce uncertainty in 4D interpretation. Relative P-wave impedance changes calculated from inversion are consistent with presurvey 4D predictions. The 4D seismic data and inversion help explain water breakthrough timing, improve our understanding of field production history, and have resulted in the identification of additional infill well opportunities.
Conserved C-terminal residues within the lectin-like domain of LOX-1 are essential for oxidized low-density-lipoprotein binding (2001)

Lectin-like oxidized low-density-lipoprotein (oxLDL) receptor-1 (LOX-1) is a cell-surface endocytosis receptor for atherogenic oxLDL, which is highly expressed in endothelial cells. Recent studies suggest that it may play significant roles in atherogenesis. LOX-1 is a type-II membrane protein that structurally belongs to the C-type lectin family molecules. This study was designed to characterize the specific domain on LOX-1 that recognizes oxLDL. Truncation of the lectin domain of LOX-1 abrogated oxLDL-binding activity. Deletion of the utmost C-terminal ten amino acid residues (261-270) was enough to disrupt the oxLDL-binding activity. Substitutions of Lys-262 and/or Lys-263 with Ala additively attenuated the activity. Serial-deletion analysis showed that residues up to 265 are required for the expression of minimal binding activity, although deletion of the C-terminal three residues (268-270) still retained full binding activity. Consistently, these alterations in LOX-1 impaired the recognition by a functionally blocking monoclonal antibody for LOX-1. These data demonstrated the distinct role of the lectin domain as the functional domain recognizing LOX-1 ligand. The conserved C-terminal residues of lectin-like domain are essential for binding oxLDL. Particularly, the basic amino acid pair is important for the binding.
DNAJC13 mutations in Parkinson disease (2013)

A Saskatchewan multi-incident family was clinically characterized with Parkinson disease (PD) and Lewy body pathology. PD segregates as an autosomal-dominant trait, which could not be ascribed to any known mutation. DNA from three affected members was subjected to exome sequencing. Genome alignment, variant annotation and comparative analyses were used to identify shared coding mutations. Sanger sequencing was performed within the extended family and ethnically matched controls. Subsequent genotyping was performed in a multi-ethnic case-control series consisting of 2928 patients and 2676 control subjects from Canada, Norway, Taiwan, Tunisia, and the USA. A novel mutation in receptor-mediated endocytosis 8/RME-8 (DNAJC13 p.Asn855Ser) was found to segregate with disease. Screening of cases and controls identified four additional patients with the mutation, of which two had familial parkinsonism. All carriers shared an ancestral DNAJC13 p.Asn855Ser haplotype and claimed Dutch-German-Russian Mennonite heritage. DNAJC13 regulates the dynamics of clathrin coats on early endosomes. Cellular analysis shows that the mutation confers a toxic gain-of-function and impairs endosomal transport. DNAJC13 immunoreactivity was also noted within Lewy body inclusions. In late-onset disease which is most reminiscent of idiopathic PD subtle deficits in endosomal receptor-sorting/recycling are highlighted by the discovery of pathogenic mutations VPS35, LRRK2 and now DNAJC13. With this latest discovery, and from a neuronal perspective, a temporal and functional ecology is emerging that connects synaptic exo- and endocytosis, vesicular trafficking, endosomal recycling and the endo-lysosomal degradative pathway. Molecular deficits in these processes are genetically linked to the phenotypic spectrum of parkinsonism associated with Lewy body pathology.
Flow injection analysis. New tool for old assays. New approach to analytical measurements (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFlow injection analysis. New tool for old assays. New approach to analytical measurementsKent K. StewartCite this: Anal. Chem. 1983, 55, 9, 931A–940APublication Date (Print):August 1, 1983Publication History Published online22 September 2008Published inissue 1 August 1983https://pubs.acs.org/doi/10.1021/ac00260a001https://doi.org/10.1021/ac00260a001research-articleACS PublicationsRequest reuse permissionsArticle Views130Altmetric-Citations22LEARN 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-Alertsclose Get e-Alerts
Feasibility of seismic characterization of multiple fracture sets (2003)

Abstract Estimation of parameters of multiple fracture sets is often required for successful exploration and development of naturally fractured reservoirs. The goal of this paper is to determine the maximum number of fracture sets of a certain rheological type which, in principle, can be resolved from seismic data. The main underlying assumption is that an estimate of the complete effective stiffness tensor has been obtained, for example, from multiazimuth, multicomponent surface seismic and vertical seismic profiling (VSP) data. Although typically only a subset of the stiffness elements (or some of their combinations) may be available, this study helps to establish the limits of seismic fracture-detection algorithms. The number of uniquely resolvable fracture systems depends on the anisotropy of the host rock and the rheology and orientation of the fractures. Somewhat surprisingly, it is possible to characterize fewer vertical fracture sets than dipping ones, even though in the latter case the fracture dip has to be found from the data. For the simplest, rotationally invariant fractures embedded in either isotropic or transversely isotropic with a vertical symmetry axis (VTI) host rock, the stiffness tensor can be inverted for up to two vertical or four dipping fracture sets. In contrast, only one fracture set of the most general (microcorrugated) type, regardless of its orientation, is constrained by the effective stiffnesses. These results can be used to guide the development of seismic fracture-characterization algorithms that should address important practical issues of data acquisition, processing, and inversion for particular fracture models.
Red blood cell microparticles show altered inflammatory chemokine binding and release ligand upon interaction with platelets (2010)

Microparticle burden in transfusates, as determined by functional chemokine binding, is considerable. Altered membrane properties of RBC microparticles enhance PLT interactions to increase inflammatory chemokine bioavailability in vitro.
Bioinspired spring origami (2018)

Origami enables folding of objects into a variety of shapes in arts, engineering, and biological systems. In contrast to well-known paper-folded objects, the wing of the earwig has an exquisite natural folding system that cannot be sufficiently described by current origami models. Such an unusual biological system displays incompatible folding patterns, remains open by a bistable locking mechanism during flight, and self-folds rapidly without muscular actuation. We show that these notable functionalities arise from the protein-rich joints of the earwig wing, which work as extensional and rotational springs between facets. Inspired by this biological wing, we establish a spring origami model that broadens the folding design space of traditional origami and allows for the fabrication of precisely tunable, four-dimensional-printed objects with programmable bioinspired morphing functionalities.
Implementation of Synchronization Measurement in Warship Power Monitoring and Control System Based on IEEE 1588 (2010)

Data Synchronization is important in advanced application of Integrated Power System Power Management System. This issue compared the mostly time Synchronization protocols and proposed a data Synchronization collection method based IEEE1588. The theory of IEEE1588 protocol is introduced and the basic methods to control synchronization precision is analyzed. Then a synchronization measurement network was given. And a data collect node was designed. At last the synchronization ability was tested. The result shows it can afford real-time, high precision and strict synchronization measurement to satisfy the measurement demand of warship Integrated Power System Monitoring and Control Network without much more cost.
New Device and Method for Flux-Proportional Sampling of Mobile Solutes in Soil and Groundwater (2004)

The importance of monitoring the transport of organic contaminants in soil and groundwater, and the pros and cons of existing sampling methods, are outlined. A new, alternative sampling method is proposed, using a passive sampler that functions as a water-permeable, semi-infinite sink for passing solutes of interest. Tracers integrated in the device store information on the volume of water passing through the sampler during the installation period. The conceptual basis of the sampling method is described. This device enables flux-proportional monitoring of the concentrations of mobile contaminants in the soil and groundwater. 14C-labeled phenanthrene (PHEN) and glyphosate (GLY) are used as case study compounds in laboratory experiments. The sorption capacities and uptake kinetics of 13 adsorbents are screened and compared, as well as the dissolution kinetics of three tracer salts: calcium citrate, calcium fluoride (CaF2), and calcium hydrogen phosphate (CaHPO4). The application of the passive sampler is then demonstrated in long-term laboratory experiments, using large soil columns under steady-state hydraulic conditions. The accumulated flux of PHEN was sampled with an accuracy of 3.6%-17.8%, using graphitized carbon, hexagonal mesoporous silica, and cross-linked polymers as adsorbents. The accumulated flux of GLY was sampled with an accuracy of 12.4%, using gamma-alumina as an adsorbent. The advantages and limitations of this new environmental monitoring method are discussed.
Load balancing of parallel volume rendering with scattered decomposition (2002)

A scheme for the visualization of large data volumes using volume rendering on a distributed memory MIMD system is described. The data to be rendered is decomposed into subvolumes to reside in the local memories of the system's nodes. A partial image of the local data is generated at each node by ray tracing, and is then composited with partial images on other nodes in the correct order to generate the complete Image. Subvolumes whose voxels are classified as being mapped to zero opacity are not rendered, giving rise to an imbalance of work amongst nodes. Scattered decomposition is used for load balancing, which on one hand: creates additional overheads in compositing and communication, but on the other, provides an improvement in throughput that is dependent on the characteristics of the data. Experimental results for a typical data set rendered on a 1024-node Fujitsu AP1000 are reported.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Synthesis of Tricyclic Spiranoid Lactones via I<sub>2</sub>/Sm(II)- and I<sub>2</sub>/Pd(0)-Mediated Cyclizations of a Common Cycloalkylmethylene Precursor (2015)

A general synthesis of phylogenetically and structurally different tricyclic angularly fused spiranoid lactones, frequently observed as scaffold segments of various biochemical compounds and drugs of natural origin, is demonstrated via controlled cyclization of simple and easily accessible cycloalkylmethylene key precursors. The rapid composition of the key architecture yields an assembly of stable bicyclic iodolactones, which are converted to form a wide range of angularly fused tricyclic scaffolds.