gebhart/patrepeval huggingface dataset:
Extracellular DNA: A Major Proinflammatory Component of Pseudomonas aeruginosa Biofilms (2010)

We previously demonstrated that extracellular bacterial DNA activates neutrophils through a CpG- and TLR9-independent mechanism. Biofilms are microbial communities enclosed in a polymeric matrix that play a critical role in the pathogenesis of many infectious diseases. Because extracellular DNA is a key component of biofilms of different bacterial species, the aim of this study was to determine whether it plays a role in the ability of biofilms to induce human neutrophil activation. We found that degradation of matrix extracellular DNA with DNase I markedly reduced the capacity of Pseudomonas aeruginosa biofilms to induce the release of the neutrophil proinflammatory cytokines IL-8 and IL-1beta (>75%); reduced the upregulation of neutrophil activation markers CD18, CD11b, and CD66b (p < 0.001); reduced the number of bacteria phagocytosed per neutrophil contacting the biofilm; and reduced the production of neutrophil extracellular traps. Consistent with these findings, we found that biofilms formed by the lasI rhlI P. aeruginosa mutant strain, exhibiting a very low content of matrix extracellular DNA, displayed a lower capacity to stimulate the release of proinflammatory cytokines by neutrophils, which was not decreased further by DNase I treatment. Together, our findings support that matrix extracellular DNA is a major proinflammatory component of P. aeruginosa biofilms.
Novel Synthesis of 4,5-Bis(arylthio)-2,3,4,5-tetrahydro-1-benzothiepins: Noteworthy Cyclization by the Reaction of 2-Butynediol with Arenethiols in the Presence of Zinc Iodide (1987)

New cyclization products, 4,5-bis(arylthio)-2,3,4, 5-tetrahydro-1-benzothiepins were obtained in good yield by the reaction of 2-butynediol with arenethiols in the presence of zinc iodide. The reaction is assumed to proceed through intramolecular cyclization of a cationic intermediate generated in situ.
The 14.6 kd rubber elongation factor (Hev b 1) and 24 kd (Hev b 3) rubber particle proteins are recognized by IgE from patients with spina bifida and latex allergy (1996)

Two major water-insoluble proteins are located on the surface of rubber particles in Hevea brasiliensis latex. A 14.6 kd protein (Hev b 1), found mainly on large rubber particles (> 350 mm in diameter), and a 24 kd protein (Hev b 3), found mainly on small rubber particles (average diameter, 70 nm), are recognized by IgE from patients with spina bifida and latex allergy. Although Hev b 1 (also called the rubber elongation factor [REF]) has previously been reported as a major latex allergen, this conclusion has been disputed on the basis of results from other studies. The allergenicity of Hev b 1 is verified in this study by testing the recombinant protein generated from its gene. Because allergenicity is confined to patients with spina bifida and not observed in adults sensitive to latex, it is not a major latex allergen. The identification of Hev b 3 as another allergen originating from rubber particles is confirmed by immunogold labeling and electron microscopy. Observations with the monoclonal antibody USM/RC2 developed against Hev b 3 show that the protein has a tendency to fragment into several polypeptides of lower molecular weight (from 24 kd to about 5 kd) when stored at -20 degrees C. There is also indication of protein aggregation from the appearance of proteins with molecular weights greater than 24 kd. Fragmentation of Hev b 3 is induced immediately on he addition of latex B-serum, which is normally compartmentalized in the lutoids in fresh latex. In the preparation of ammoniated latex (used for the manufacture of latex products), the lutoids are ruptured, and the released B-serum reacts with Hev b 3 on the rubber particles to give rise to an array of low molecular weight polypeptides that are allergenic to patients with spina bifida.
Cloning and characterization of oriL2, a large palindromic DNA replication origin of herpes simplex virus type 2 (1986)

An origin of replication within the long unique sequence of herpes simplex virus type 2 designated oriL2 has been identified in a position homologous to its type 1 counterpart, oriL1, between map coordinates 0.398 and 0.413. The difficulties encountered in previous attempts to clone both oriL2 and oriL1 in an undeleted form were surmounted by minimizing the growth of the host Escherichia coli, using a recBC sbcB E. coli host, and purifying the full-length plasmid from delected forms by using a novel method which exploits the ability of a palindrome-containing plasmid to adopt a cruciform conformation, thereby decreasing its supercoiling. In a previously developed assay for functional origin activity, oriL2 was localized to a 241-base-pair ApaI-SstII fragment. DNA sequence analysis revealed a 136-base pair, almost perfect palindrome. Comparison with oriL1 showed a very high degree of conservation: the two origins differ in only 16 of the 144-base-pair oriL1 palindromic region. Most significantly, the differences between oriL1 and oriL2 mainly occur in pairs so as to generally preserve the potential for intrastrand base pairing. The central region of oriL2 is homologous with the shorter palindromic structures detected in origins located within the repetitive sequences of the short component of herpes simplex virus type 1 or 2.
Thin-Film Light-Emitting Devices Based on Sequentially Adsorbed Multilayers of Water-Soluble Poly(p-phenylene)s (1998)

In thin-film electroluminescent devices, conjugated polymers are used as efficient emitters. Here the authors demonstrate that thin films of combined anionic (see Figure for the chemical structure) and cationic water-soluble poly(p-phenylene) polyelectrolytes can be readily processed into multilayer light-emitting devices. Fabrication with solely one type of conjugated backbone—as here—may greatly improve device efficiency.
Intracellular Fragmentation of Bone Resorption Products by Reactive Oxygen Species Generated by Osteoclastic Tartrate-resistant Acid Phosphatase (1999)

Tartrate-resistant acid phosphatase (TRAP) is highly expressed in bone-resorbing osteoclasts and activated macrophages. It has been suggested that a redox-active iron in the binuclear iron center of TRAP could have the capacity to react with hydrogen peroxide to produce highly destructive reactive oxygen species (ROS). Here we show that TRAP can generate ROS in vitro and that cells over-expressing TRAP produce higher amounts of intracellular ROS than their parent cells. We further demonstrate that these ROS can be targeted to destroy collagen and other proteins. In resorbing osteoclasts, TRAP was found in transcytotic vesicles transporting matrix degradation products through the cell, suggesting that TRAP-facilitated fragmentation of endocytosed material takes place in a specific cellular compartment. These results suggest that bone matrix degradation occurs not only extracellularly in the resorption lacunae but also intracellularly in the transcytotic vesicles. We propose that proteins containing redox-active iron could represent a novel mechanism of physiological fragmentation of organic molecules. This mechanism could be important in tissue remodeling and as a defense mechanism of phagocytosing cells.
Study on fail-safe strategy of electric power steering system (2009)

Based on the six-freedom-degree model of fourwheel-drive electric vehicles, the fail-safe problem of (Electric Power Steering system) EPS is analyzed, and an EPS fail-safe strategy based on state observer is proposed in this paper. When EPS failed, by detecting the cornering angle of the steer wheel or the torsion of the steer wheel, the yaw rate command can be estimated. The vehicle's body is forced to turn around to the desired direction by the distribution of the proper brake torque to the four wheels. In order to speed up system's response, a yaw feed forward compensator is employed in the controller. The simulation results show that when EPS failed, by distributing brake torques, the vehicle turns to the expected direction without steering angle. Consequently, the effectiveness of EPS fail-safe control strategy is validated.
A Gradient Reversed Phase HPLC Procedure for Smokeless Powder Comparison (2002)

Abstract Smokeless powder comparisons are commonly carried out by extracting additives and stabilizer degradation products from the powder using methylene chloride, and analyzing the results by gas chromatography/mass spectrometry. Some of these components are thermally unstable, making comparison of similar powders or of powders originating from different manufacturing lots difficult when GC is used. Isocratic HPLC analysis using C-18 stationary columns can be unsatisfactory due to a wide range of polarities of the additives and stabilizer degradation products and the presence of geometrical isomers. In this paper, a gradient procedure using a C-8 column is described for the analysis of smokeless powders. The procedure provides separation of a wide range of components present in smokeless powders. In this work, analytical figures of merit are provided, UV spectra of each of the components are presented, and the procedure is evaluated by comparing four different lots of smokeless powder from the same manufacturer.
Domain characteristics of the carboxyl‐terminal fragment 206–316 of thermolysin (1983)

Abstract The existence, location, and characteristics of protein domains have been investigated by studying the structural properties of the carboxyl‐terminal cyanogen bromide fragment 206–316 of thermolysin. As judged by far‐uv CD measurements in aqueous solution under neutral conditions, the fragment attains a substantial degree of α‐helical structure comparable to that exhibited by the corresponding region in native thermolysin. By radioimmunoassay techniques, a considerable degree of nativeness of fragment conformation has been deduced from comparison of the relative affinities of thermolysin and fragment 206–316 for antibodies specific for the 206–316 region in the intact protein. The fragment shows noteworthy stability to protein denaturants. The overall spectroscopic and immunochemical data suggest that fragment 206–316 is able to refold into a stable, nativelike structure independently from the rest of the molecule, thus providing support for the view that this fragment may contain a substantial part, if not all, of a protein domain structure.
Animal models of transfusion-related acute lung injury (2006)

Experimental animal models support both the antibody and lipid theories of TRALI. The essential role of neutrophils to producing lung injury is common to all existing models of TRALI. There is a lack of clinically relevant animal models that explain why transfusion of donor antibodies to cognate antigens in the recipient does not always lead to TRALI.
Modulation of oligonucleotide duplex and triplex stability via hydrophobic interactions (1993)

Synthetic oligonucleotides have been proposed as a new rationally designed class of pharmaceuticals with a mechanism of action based upon a Watson-Crick and/or Hoogsteen type of base pairing with RNA or DNA regions of interest. Two series of 3'-cholesterol and/or 5'-cholesterol conjugated oligonucleotides have been synthesized. The primary structure of these compounds was conceived in a way that should allow a hydrophobic interaction to take place upon bringing the cholesteryl moieties into proximity via a hybridization event. In the first group of compounds the cholesteryl group was tethered to the opposite ends of two oligonucleotides, tandemly addressed to the same complementary strand. An increase in the Tm of duplexes up to 13.3 degrees C was observed in comparison to unmodified oligomers. We observed a higher level of mismatch discrimination for the two contiguous oligonucleotide cholesterol conjugates compared to one continuous oligomer of the same length. A second group of compounds was synthesized as 5',3'-bis-cholesterol containing oligomers, capable of forming 'clamp-shaped' triple-stranded complexes, where cholesterol groups were attached to the termini of duplex and triplex forming domains. Stabilization of triplexes by up to 30 degrees C due to inter-cholesteryl interaction was observed. We detected no triplex formation with a mismatched target. These data suggest that significant stabilization of complexes of nucleic acids could be achieved through inter-cholesteryl hydrophobic interaction.
Learning Community Embedding with Community Detection and Node Embedding on Graphs (2017)

In this paper, we study an important yet largely under-explored setting of graph embedding, i.e., embedding communities instead of each individual nodes. We find that community embedding is not only useful for community-level applications such as graph visualization, but also beneficial to both community detection and node classification. To learn such embedding, our insight hinges upon a closed loop among community embedding, community detection and node embedding. On the one hand, node embedding can help improve community detection, which outputs good communities for fitting better community embedding. On the other hand, community embedding can be used to optimize the node embedding by introducing a community-aware high-order proximity. Guided by this insight, we propose a novel community embedding framework that jointly solves the three tasks together. We evaluate such a framework on multiple real-world datasets, and show that it improves graph visualization and outperforms state-of-the-art baselines in various application tasks, e.g., community detection and node classification.
Myeloid progenitors protect against invasive aspergillosis andPseudomonas aeruginosa infection following hematopoietic stem cell transplantation (2002)

Myelotoxic treatments for oncologic diseases are often complicated by neutropenia, which renders patients susceptible to potentially lethal infections. In these studies of murine hematopoietic stem cell transplantation (HSCT), cotransplantation of lineage-restricted progenitors known as common myeloid progenitors (CMP) and granulocyte-monocyte progenitors (GMP) protects against death following otherwise lethal challenge with either of 2 pathogens associated with neutropenia: Aspergillus fumigatus and Pseudomonas aeruginosa. Cotransplantation of CMP/GMP resulted in a significant and rapid increase in the absolute number of myeloid cells in the spleen, most of which were derived from the donor CMP/GMP. Despite persistent peripheral neutropenia, improved survival correlated with the measurable appearance of progenitor-derived myeloid cells in the spleen. A marked reduction or elimination of tissue pathogen load was confirmed by culture and correlated with survival. Localization of infection by P aeruginosa and extent of disease was also assessed by in vivo bioluminescent imaging using a strain of P aeruginosa engineered to constitutively express a bacterial luciferase. Imaging confirmed that transplantation with a graft containing hematopoietic stem cells and CMP/GMP reduced the bacterial load as early as 18 hours after infection. These results demonstrate that enhanced reconstitution of a tissue myeloid pool offers protection against lethal challenge with serious fungal and bacterial pathogens.
[Chemical constituents of Oxytropis falcate]. (2008)

All the compounds were isolated from O. falcate for the first time.
Negative Regulation of the SHATTERPROOF Genes by FRUITFULL During Arabidopsis Fruit Development (2000)

The terminal step of fruit development in Arabidopsis involves valve separation from the replum, allowing seed dispersal. This process requires the activities of the SHATTERPROOF MADS-box genes, which promote dehiscence zone differentiation at the valve/replum boundary. Here we show that the FRUITFULL MADS-box gene, which is necessary for fruit valve differentiation, is a negative regulator of SHATTERPROOF expression and that constitutive expression of FRUITFULL is sufficient to prevent formation of the dehiscence zone. Our studies suggest that ectopic expression of FRUITFULL may directly allow the control of pod shatter in oilseed crops such as canola.
Highly Maneuverable Low-Cost Underwater Glider: Design and Development (2016)

This letter presents the design and potential impact of the developed Research Oriented Underwater Glider for Hands-on Investigative Engineering (ROUGHIE). The ROUGHIE is an open-source, highly maneuverable, and low-cost vehicle that enables rapid development and testing of new hardware and software. ROUGHIE is an internally actuated glider capable of performing steady sawtooth glides in shallow water down to 3 m, tight turns with a minimum radius of 3 m, and a minimum endurance of 60 h. The novelty of this study is twofold: 1) a rail-based design to facilitate modularity and ease of assembly and 2) an effective internal rotary mass mechanism to increase maneuverability and perform tight turns. The ROUGHIE design strategically uses 3D printed plastic parts in low stress situations, which allows extreme design flexibility and enables tightly packed modules that can be easily customized.
The Chemical Synthesis of DNA/RNA: Our Gift to Science (2012)

It is a great privilege to contribute to the Reflections essays. In my particular case, this essay has allowed me to weave some of my major scientific contributions into a tapestry held together by what I have learned from three colleagues (Robert Letsinger, Gobind Khorana, and George Rathmann) who molded my career at every important junction. To these individuals, I remain eternally grateful, as they always led by example and showed many of us how to break new ground in both science and biotechnology. Relative to my scientific career, I have focused primarily on two related areas. The first is methodologies we developed for chemically synthesizing DNA and RNA. Synthetic DNA and RNA continue to be an essential research tool for biologists, biochemists, and molecular biologists. The second is developing new approaches for solving important biological problems using synthetic DNA, RNA, and their analogs.
Sterical recognition by T4polynucleotide kinase of non-nucleosidic moieties 5′-attached to oligonucleotides (1994)

The ability of T4 polynucleotide kinase (PNK) to phosphorylate non-nucleosidic moieties 5'-attached to oligodeoxynucleotides (ODNs) has been investigated. Non-nucleosidic phosphoramidite units were prepared from ethane-1,2-diol and propane-1,3-diol backbones. Some of them corresponded to pure enantiomers. They were used to obtain the corresponding 5'-end modified oligothymidylates X(pdT)10. The free primary hydroxyl of the non-nucleosidic moieties (X) of these oligomers was phosphorylated by PNK. We report the stereoselective phosphorylation of the L form of the 5'-end attached non-nucleosidic chiral fragments; the non-chiral moieties were completely phosphorylated. Dimers of glycerol analogue and thymidine 3'-phosphate were not recognized by PNK and the shortest modified ODN able to be phosphorylated was a trinucleotide X(pdT)3. A modified X(pdT)10, bearing a cyclic abasic site (X) at its 5'-end, was prepared by chemical synthesis from 1,2-dideoxyribose phosphoramidite and was phosphorylated with a 90% yield.
A New Class of Guided C2 Subdivision Surfaces Combining Good Shape with Nested Refinement (2017)

Abstract Converting quadrilateral meshes to smooth manifolds, guided subdivision offers a way to combine the good highlight line distribution of recent G‐spline constructions with the refinability of subdivision surfaces. This avoids the complex refinement of G‐spline constructions and the poor shape of standard subdivision. Guided subdivision can then be used both to generate the surface and hierarchically compute functions on the surface. Specifically, we present a C 2 subdivision algorithm of polynomial degree bi‐6 and a curvature bounded algorithm of degree bi‐5. We prove that the common eigenstructure of this class of subdivision algorithms is determined by their guide and demonstrate that their eigenspectrum (speed of contraction) can be adjusted without harming the shape. For practical implementation, a finite number of subdivision steps can be completed by a high‐quality cap. Near irregular points this allows leveraging standard polynomial tools both for rendering of the surface and for approximately integrating functions on the surface.
YAP3 (1996)

In spite of years of effort, plagiarism in student assignment submissions still causes considerable difficulties for course designers; if students' work is not their own, how can anyone be certain they have learnt anything? YAP is a system for detecting suspected plagiarism in computer programs and other texts submitted by students. The paper reviews YAP3, the third version of YAP, focusing on its novel underlying algorithm - Running-Karp-Rabin Greedy-String-Tiling (or RKS-GST ), whose development arose from the observation with YAP and other systems that students shuffle independent code segments. YAP3 is able to detect transposed subsequences, and is less perturbed by spurious additional statements. The paper concludes with a discussion of recent extension of YAP to English texts, further illustrating the flexibility of the YAP approach.
Oxygen regulation of nitrate transport by diversion of electron flow in Escherichia coli. (1990)

Anaerobic nitrate respiration is regulated by oxygen at the level of nitrate transport; however, the mechanism of O2 inhibition is unknown. Potentially, oxygen could inhibit directly by causing conformational changes in the porter system or indirectly through diversion of electron flow from the nitrate reductase complex to oxygen reduction. Inhibition due to electron diversion implies that nitrate reduction is required for nitrate transport. In this regard, nitrate uptake and its regulation by oxygen were studied in mutants of Escherichia coli (strain AN386) deficient in cytochrome d (RG98), cytochrome o (RG101), and a mutant deficient in both cytochrome d and cytochrome o (RG99). Respiratory nitrate uptake in RG99 was highly resistant to the effects of oxygen supporting the indirect mechanism of electron diversion in oxygen regulation. Nitrate transport in RG98 and RG101 is highly sensitive to oxygen; these mutants exhibited 81 and 85% inhibition, respectively, which is similar to inhibition in the wild type. These results indicate that during nitrate respiration, O2 inhibits transport by limiting the supply of electrons to the nitrate reductase complex.
Chirped-pulse amplification of 85-fs pulses at 250 kHz with third-order dispersion compensation by use of holographic transmission gratings (1994)

We demonstrate pulse stretching and compression in a high-repetition-rate chirped-pulse Ti:sapphire regenerative amplifier, using high-efficiency holographic transmission gratings. A quantitative dispersion measurement technique is developed to characterize dispersion of the system to the third order. After recompression with third-order dispersion compensation, 3.1-microJ 85-fs, nearly transform-limited pulses are obtained.