gebhart/patrepeval huggingface dataset:
A new structural type for <i>Haemophilus influenzae</i> lipopolysaccharide (2001)

Structural elucidation of the sialylated lipopolysaccharide (LPS) of non-typeable Haemophilus influenzae (NTHi) strain 486 has been achieved by the application of high-field NMR techniques and ESI-MS along with composition and linkage analyses on O-deacylated LPS and oligosaccharide samples. It was found that the LPS contains the common element of H. influenzae, L-alpha-D-Hepp-(1-->2)-[PEtn-->6]-L-alpha-D-Hepp-(1-->3)-[beta-D-Glcp-(1-->4)]-L-alpha-D-Hepp-(1-->5)-[PPEtn-->4]-alpha-Kdop-(2-->6)-Lipid A, but instead of glycosyl substitution of the terminal heptose residue (HepIII) at the O2 position observed in other H. influenzae strains, HepIII is chain elongated at the O3 position by either lactose or sialyllactose (i.e. alpha-Neu5Ac-(2-->3)-beta-D-Galp-(1-->4)-beta-D-Glcp). The LPS is substituted by an O-acetyl group linked to the O2 position of HepIII and phosphocholine (PCho) which was located at the O6 position of a terminal alpha-D-Glcp residue attached to the central heptose, a molecular environment different from what has been reported earlier for PCho. In addition, minor substitution by O-linked glycine to the LPS was observed. By investigation of LPS from a lpsA mutant of NTHi strain 486, it was demonstrated that the lpsA gene product also is responsible for chain extension from HepIII in this strain. The involvement of lic1 in expression of PCho was established by investigation of a lic1 mutant of NTHi strain 486.
Join Query Optimization Techniques for Complex Event Processing\n Applications (2018)

Complex event processing (CEP) is a prominent technology used in many modern\napplications for monitoring and tracking events of interest in massive data\nstreams. CEP engines inspect real-time information flows and attempt to detect\ncombinations of occurrences matching predefined patterns. This is done by\ncombining basic data items, also called primitive events, according to a\npattern detection plan, in a manner similar to the execution of multi-join\nqueries in traditional data management systems. Despite this similarity, little\nwork has been done on utilizing existing join optimization methods to improve\nthe performance of CEP-based systems. In this paper, we provide the first\ntheoretical and experimental study of the relationship between these two\nresearch areas. We formally prove that the CEP Plan Generation problem is\nequivalent to the Join Query Plan Generation problem for a restricted class of\npatterns and can be reduced to it for a considerably wider range of classes.\nThis result implies the NP-completeness of the CEP Plan Generation problem. We\nfurther show how join query optimization techniques developed over the last\ndecades can be adapted and utilized to provide practically efficient solutions\nfor complex event detection. Our experiments demonstrate the superiority of\nthese techniques over existing strategies for CEP optimization in terms of\nthroughput, latency, and memory consumption.\n
A Novel Aqueous Dual‐Channel Aluminum‐Hydrogen Peroxide Battery (1994)

A dual‐channel aluminum hydrogen peroxide battery is introduced with an open‐circuit voltage of 1.9 volts, polarization losses of 0.9 mV cm2 mA−1, and power densities of 1 W/cm2. Catholyte and anolyte cell compartments are separated by an Ir/Pd modified porous nickel cathode. Separation of catholyte and anolyte chambers prevents hydrogen peroxide poisoning of the aluminum anode. The battery is expressed by aluminum oxidation and aqueous solution phase hydrogen peroxide reduction for an overall battery discharge consisting of
Characteristics of undoped and europium-doped SrI<inf>2</inf> scintillator detectors (2011)

High energy resolution gamma-ray detectors that can be formed into relatively large sizes while operating at room temperature offer many advantages for national security applications. We are working toward that goal through the development of SrI <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> (Eu) scintillator detectors, which routinely provide <;3.0% energy resolution at 662 keV with volumes >;10 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> . In this study, we have tested pure, undoped SrI <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> to gain a better understanding of the scintillation properties and spectroscopic performance achievable without activation. An undoped crystal grown from 99.999% pure SrI <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> pellets was tested for its spectroscopic performance, its light yield, and uniformity of scintillation light collection as a function of gamma-ray interaction position relative to the crystal growth direction. Undoped SrI <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> was found to provide energy resolution of 5.3% at 662 keV, and the light collection nonuniformity varied by only 0.72% over the length of the crystal. Measurements of both a 3% Eu-doped and the undoped SrI <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> crystal were carried out in the SLYNCI facility and indicate differences in their light yield non-proportionality. The surprisingly good scintillation properties of the pure SrI <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> crystal suggests that with high-purity feedstock, further reduction of the Eu concentration can be made to grow larger crystals while not adversely impacting the spectroscopic performance.
Hypergraph based reorderings of outer join queries with complex predicates (1995)

Complex queries containing outer joins are, for the most part, executed by commercial DBMS products in an "as written" manner. Only a very few reorderings of the operations are considered and the benefits of considering comprehensive reordering schemes are not exploited. This is largely due to the fact there are no readily usable results for reordering such operations for relations with duplicates and/or outer join predicates that are other than "simple." Most previous approaches have ignored duplicates and complex predicates; the very few that have considered these aspects have suggested approaches that lead to a possibly exponential number of, and redundant intermediate joins. Since traditional query graph models are inadequate for modeling outer join queries with complex predicates, we present the needed hypergraph abstraction and algorithms for reordering such queries with joins and outer joins. As a result, the query optimizer can explore a significantly larger space of execution plans, and choose one with a low cost. Further, these algorithms are easily incorporated into well known and widely used enumeration methods such as dynamic programming.
Improving Food Safety by Using One- and Two-Photon- Induced Fluorescence Spectroscopy for the Detection of Mycotoxins (2016)

The presence of mycotoxins in food products is a major worldwide problem. Nowadays, mycotoxins can only be detected by the use of sample-based chemical analyses. Therefore, we demonstrate the use of one- and two-photon-induced fluorescence spectroscopy for the non-destructive detection of mycotoxins in unprocessed food products. We first explain our optical set-up, which is able to measure the localized one- and two-photon-induced fluorescence spectra. Following, as a case study, the detection of aflatoxin in maize kernels is discussed. We present our research methodology, from the characterization of the fluorescence of pure aflatoxin, to the study of the one- and two- photon-induced fluorescence spectra of maize kernels and the development of an optical detection criterion. During both one- and two-photon-induced fluorescence processes, the fluorescence of the aflatoxin influences the intrinsic fluorescence of the maize. Based on the fluorescence spectrum between 400 and 550 nm, a detection criterion to sense the contaminated kernels is defined. Furthermore, we successfully monitored the localized contamination level on the kernel’s surface, showing both contaminated kernels with a high contamination in a limited surface area (a few square millimetres) and kernels with a low contamination spread over a large surface area (up to 20 mm2). Finally, the extensibility of our research methodology to other fluorescent mycotoxins is discussed.
Kronecker product matrices for compressive sensing (2010)

Compressive sensing (CS) is an emerging approach for acquisition of signals having a sparse or compressible representation in some basis. While CS literature has mostly focused on problems involving 1-D and 2-D signals, many important applications involve signals that are multidimensional. We propose the use of Kronecker product matrices in CS for two purposes. First, we can use such matrices as sparsifying bases that jointly model the different types of structure present in the signal. Second, the measurement matrices used in distributed measurement settings can be easily expressed as Kronecker products. This new formulation enables the derivation of analytical bounds for sparse approximation and CS recovery of multidimensional signals.
Cooperative effects of genes controlling the G<sub>2</sub>/M checkpoint (2000)

It is believed that multiple effectors independently control the checkpoints permitting transitions between cell cycle phases. However, this has not been rigorously demonstrated in mammalian cells. The p53-induced genes p21 and 14-3-3sigma are each required for the G(2) arrest and allow a specific test of this fundamental tenet. We generated human cells deficient in both p21 and 14-3-3sigma and determined whether the double knockout was more sensitive to DNA damage than either single knockout. p21(-/-) 14-3-3sigma(-/-) cells were significantly more sensitive to DNA damage or to the exogenous expression of p53 than cells lacking only p21 or only 14-3-3sigma. Thus, p21 and 14-3-3sigma play distinct but complementary roles in the G(2)/M checkpoint, and help explain why genes at the nodal points of growth arrest pathways, like p53, are the targets of mutation in cancer cells.
Molecular weight dependence of the physical properties of protonated polyaniline films and fibers (2001)

Polyaniline, (PANI) in the form of emeraldine base, was synthesized by polymerizing aniline in acid solutions at different sub-zero temperatures to give a range of molecular weights between 100,000 and 300,000 gmol<SUP>-1</SUP>. Molecular weights were measured using gel permeation chromatography (GPC). The polymers were formed into solvent-cast films using an acid processing technique, involving 2-acrylamido-2-methyl-1-propanesulfonic acid (AMPSA) as the solvating/protonating acid group and dichloroacetic acid (DCA) plus formic acid (FA) as the solvent. The dried, free-standing films were stretched by drawing over a hot pin to align the polymer chains. Fibers were prepared by spinning more concentrated solutions into a butanone coagulation bath. Conductivity measurements were then made on the drawn films and fibers, and tensile test measurements performed to determine the peak stress and modulus of the drawn films and fibers. The reaction conditions under which the different polyanilines were synthesized, and their molecular weight, were found to have a definite effect upon both the electrical and mechanical properties of the drawn films and fibers. The drawn films and fibers can be used as mechanical actuators.
ABCG transporters and disease (2011)

ATP-binding cassette (ABC) transporters form a large family of transmembrane proteins that facilitate the transport of specific substrates across membranes in an ATP-dependent manner. Transported substrates include lipids, lipopolysaccharides, amino acids, peptides, proteins, inorganic ions, sugars and xenobiotics. Despite this broad array of substrates, the physiological substrate of many ABC transporters has remained elusive. ABC transporters are divided into seven subfamilies, A-G, based on sequence similarity and domain organization. Here we review the role of members of the ABCG subfamily in human disease and how the identification of disease genes helped to determine physiological substrates for specific ABC transporters. We focus on the recent discovery of mutations in ABCG2 causing hyperuricemia and gout, which has led to the identification of urate as a physiological substrate for ABCG2.
Abstract 4459: Characterization of a novel magnetic nanoparticles formulation for cancer therapeutic applications (2014)

Abstract We have successfully engineered a magnetic nanoparticles (MAG-NPs) formulation using a multi-layer approach which can be used for drug/gene/biomolecule delivery, hyperthermia, and magnetic resonance imaging (MRI) applications in cancer therapeutics. Overcoming nanoparticles clearance by the immune system remains a major challenge. This formulation is designed to provide an additional surface layer as molecular “authentication” that the body does not recognize as foreign material. The interaction between the surface of nanoparticles and plasma proteins leads to nanoparticle-protein complex which determines the rational design of clinically useful formulations for cancer therapeutics. This formulation was very effective for inhibiting tumorigenic features in in vitro and in vivo cancer models. Therefore, we further studied our MAG-NPs formulation for biologically and clinically relevant characteristic features for its clinical translation. For this, we have examined the change in particle size, zeta potential, human serum protein adsorption, hemotoxicity, uptake, targeting cancer cells, and magnetic resonance imaging of the MAG-NPs formulation. No significant change was observed in particle size and zeta potential of nanoformulation with the incubation of 0.5 to 50 wt/wt% human serum. With increase of serum concentration and particle concentration there was a clear indication that apart from serum albumin and transferrin; apolipoprotein E (Apo-E, a surrogate marker for improved circulation of nanoparticles and enhanced crossing of the blood-brain barrier) also adsorbed on the surface of nanoparticles (determined by Western blot analysis). No significant primary or secondary structural alterations were observed in serum proteins through circular dichroism study. Hemolysis assay demonstrated almost no hemolysis at the tested concentrations (up to 1 mg/mL) for nanoparticles compared to the positive control (sodium dodecyl sulphate). Particle internalization and targeting cancer cells were observed in dose dependent manner and were not influenced by protein architecture on surface of nanoparticles. Additionally, this formulation has exhibited identical T1 relaxation times (∼1.1-1.6 s) and T2 relaxation times (∼ 13-14 ms) which suggests that our nanoparticles retained MRI properties even after serum proteins adsorption and drug/biomolecular encapsulation. Based on all these superior clinical characteristics, this MAG-NPs formulation can effectively be used for the delivery of drug/siRNA/miRNAs for cancer therapy, diagnosis, and imaging. Citation Format: Murali M. Yallapu, Neeraj Chauhan, Shadi F. Othman, Vahid Khalilzad-Sharghi, Meena Jaggi, Subhash C. Chauhan. Characterization of a novel magnetic nanoparticles formulation for cancer therapeutic applications. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4459. doi:10.1158/1538-7445.AM2014-4459
Transduction of CD34+ enriched cord blood and Gaucher bone marrow cells by a retroviral vector carrying the glucocerebrosidase gene. (1994)

One promising strategy for gene therapy of Gaucher disease involves ex vivo retroviral transduction of autologous hematopoietic stem cells. Studies in small animals have demonstrated that this approach provides a life-long supply of the glucocerebrosidase (GC) enzyme. Human application has developed to the stage of a clinical trial. In this study, we describe development of a high titer amphotropic producer line for the vector, MFG-GC, and explore transduction of CD34+ cells from various human sources. Higher than three times the normal levels of glucocerebrosidase activity in non-transduced cells were achieved following transduction of CD34+ cells obtained from bone marrow or cord blood from normal donors. The improvement in enzyme activity in Gaucher marrow was about 40-fold above deficient levels. We examined the timing and stepwise effect of multiple rounds of infection and evaluated post-infection expansion of cells in two different cytokine mixtures. Transduction efficiency was determined using immunocytochemistry and Southern blot hybridization.
Are we reaching the limits or our ability to detect skin effects with our current testing and measuring methods for consumer products? (2005)

Testing for potential adverse skin effects is a key part of both the overall safety assessment for many consumer products and the evaluation of potential product improvements in mildness. Whilst modern tissue and paper products (i.e. facial tissues, catamenial products, baby wipes and baby and adult diapers) are inherently very mild to skin, current test methodology may not be robust enough to evaluate future improvements in such products. This article provides a commentary on several technologies we have been exploring to improve the sensitivity of test methods for tissue and paper products. The focus has been on three approaches: (i) further exaggerating exposure conditions using novel approaches to sample application, (ii) increasing the sensitivity of the manner in which we score for irritant effects, either visually or via instrumentation and (iii) quantitatively measuring additional endpoints, i.e. subjective sensory effects.
Compressively strained multiple quantum well InAsSb lasers emitting at 3.6 μm grown by metal-organic chemical vapor deposition (1997)

A compressively strained InAsSb/InAs multiple quantum-well (MQW) structure was grown by low-pressure metal-organic chemical vapor deposition. Maximum output power (from two facets) up to 1 W with differential efficiency about 70% was obtained from a MQW laser with stripe width of 100 μm and cavity length of 700 μm for emitting wavelength of 3.65 μm at 90 K in pulse mode operation. About 2 times lower threshold current density was obtained from the MQW lasers for a temperature range of 90 to 140 K compared to the double heterostructure lasers grown on the same growth conditions.
Comparison of Feeding and Olfactory Behaviors Between Laboratory-Reared and Overwintered Native Boll Weevils (Coleoptera: Curculionidae) (1992)

Journal Article Comparison of Feeding and Olfactory Behaviors Between Laboratory-Reared and Overwintered Native Boll Weevils (Coleoptera: Curculionidae) Get access M. J. Grodowitz, M. J. Grodowitz 1 Boll Weevil Research Laboratory, USDA–ARS, Mississippi State, MS 39762–5367 1Current address: USDA-ARS, c/o U.S. Army Engineers, Waterways Experiment Station (CEWES-ER-A), 3909 Halls Ferry Road, Vicksburg, MS 39180-6199. Search for other works by this author on: Oxford Academic PubMed Google Scholar E. P. Lloyd, E. P. Lloyd Boll Weevil Research Laboratory, USDA–ARS, Mississippi State, MS 39762–5367 Search for other works by this author on: Oxford Academic PubMed Google Scholar G. H. McKibben G. H. McKibben 3 Boll Weevil Research Laboratory, USDA–ARS, Mississippi State, MS 39762–5367 3Current address: Crop Science Research Laboratory, USDA–ARS, P.O. Box 5367, Mississippi State, MS 39762–5367. Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Economic Entomology, Volume 85, Issue 6, 1 December 1992, Pages 2201–2210, https://doi.org/10.1093/jee/85.6.2201 Published: 01 December 1992 Article history Received: 18 September 1990 Accepted: 15 June 1992 Published: 01 December 1992
An epitope-resurfaced virus-like particle can induce broad neutralizing antibody against four serotypes of dengue virus (2018)

Abstract Dengue fever is caused by four different serotypes of dengue virus (DENV) which is the leading cause of worldwide arboviral diseases in humans. Virus-like particles (VLPs) containing flavivirus prM/E proteins have been demonstrated to be a potential vaccine candidate; however, the structure of dengue VLP is poorly understood. Herein we show for the first time that mD2VLP particles possess a T=1 icosahedral symmetry with a groove located within the E-protein dimers near the 2-fold vertices that exposed highly overlapping, cryptic neutralizing epitopes through cryo-electron microscopy reconstruction. Mice vaccinated with highly matured virus-like particles derived from DENV serotype 2 (mD2VLP) can generate higher cross reactive (CR) neutralization antibodies (NtAbs) and were protected against all 4 serotypes of DENV through clonal expansion supported by hybridoma and B-cell repertoire analysis. Our results revealed that a “epitope-resurfaced” mature-form dengue VLP has the potential to induce quaternary structure-recognizing broad CR NtAbs.
Automatic Design Optimization of Plasmon Antenna for Thermally Assisted Magnetic Recording (2009)

We developed auxiliary differential equation finite-difference time-domain (ADE-FDTD) method for dispersive Drude medium, and simulated the optical part of the plasmon antenna (PA) and waveguide (WG) system for thermally assisted magnetic recording (TAMR) heads. To achieve higher efficiency without sacrificing the small spot size, our newly developed automatic computational shape optimization program was carried out for the PA designs with a variety of configurations: no recording media, with-media, with magnetic write pole, and only-PA models. The optimized designs for these cases show an enhancement of the electrical field at the PA tip compared to the initial configuration. In addition, both the PA body as well as the tip affects the performance of the guiding and focusing of the plasmon. However, the optimized detail shape and the sensitivity of the dimension are dependent upon the configuration.
Soluble 3-O-sulfated heparan sulfate can trigger herpes simplex virus type 1 entry into resistant Chinese hamster ovary (CHO-K1) cells (2007)

Herpes simplex virus type 1 (HSV-1) interaction with glycoprotein D (gD) receptors facilitates virus entry into cells. Chinese hamster ovary (CHO-K1) cells lacking cellular receptors allow virus to attach, but not to enter, implying a role for receptors during the post-attachment (entry) phase of HSV-1 infection. Here, it is shown that the presence of soluble heparan sulfate (HS) modified by 3-O-sulfotransferase-3 (3-OST-3), but not by 3-OST-1, triggered HSV-1 entry into resistant CHO-K1 cells. It was further demonstrated that a CHO-K1 mutant deficient in glycosaminoglycan synthesis became susceptible to entry when spinoculated in the presence of 3-OST-3-modified soluble HS, indicating that the role of the gD receptor is to trigger entry rather than cell attachment. In separate experiments, 3-OST-3-modified soluble HS also triggered fusion of HSV-1 glycoprotein-expressing cells with CHO-K1 cells. Taken together, these results show that association of gD with cell surface-bound receptor is not essential for HSV-1 entry and spread.