gebhart/patrepeval huggingface dataset:
A receptor-like protein mediates plant immune responses to herbivore-associated molecular patterns (2020)

Herbivory is fundamental to the regulation of both global food webs and the extent of agricultural crop losses. Induced plant responses to herbivores promote resistance and often involve the perception of specific herbivore-associated molecular patterns (HAMPs); however, precisely defined receptors and elicitors associated with herbivore recognition remain elusive. Here, we show that a receptor confers signaling and defense outputs in response to a defined HAMP common in caterpillar oral secretions (OS). Staple food crops, including cowpea (<i>Vigna unguiculata</i>) and common bean (<i>Phaseolus vulgaris</i>), specifically respond to OS via recognition of proteolytic fragments of chloroplastic ATP synthase, termed inceptins. Using forward-genetic mapping of inceptin-induced plant responses, we identified a corresponding leucine-rich repeat receptor, termed INR, specific to select legume species and sufficient to confer inceptin-induced responses and enhanced defense against armyworms (<i>Spodoptera exigua</i>) in tobacco. Our results support the role of plant immune receptors in the perception of chewing herbivores and defense.
Mechanism of Chalcone Synthase (2000)

Polyketide synthases (PKS) assemble structurally diverse natural products using a common mechanistic strategy that relies on a cysteine residue to anchor the polyketide during a series of decarboxylative condensation reactions that build the final reaction product. Crystallographic and functional studies of chalcone synthase (CHS), a plant-specific PKS, indicate that a cysteine-histidine pair (Cys(164)-His(303)) forms part of the catalytic machinery. Thiol-specific inactivation and the pH dependence of the malonyl-CoA decarboxylation reaction were used to evaluate the potential interaction between these two residues. Inactivation of CHS by iodoacetamide and iodoacetic acid targets Cys(164) in a pH-dependent manner (pK(a) = 5.50). The acidic pK(a) of Cys(164) suggests that an ionic interaction with His(303) stabilizes the thiolate anion. Consistent with this assertion, substitution of a glutamine for His(303) maintains catalytic activity but shifts the pK(a) of the thiol to 6.61. Although the H303A mutant was catalytically inactive, the pH-dependent incorporation of [(14)C]iodoacetamide into this mutant exhibits a pK(a) = 7.62. Subsequent analysis of the pH dependence of the malonyl-CoA decarboxylation reaction catalyzed by wild-type CHS and the H303Q and C164A mutants also supports the presence of an ion pair at the CHS active site. Structural and sequence conservation of a cysteine-histidine pair in the active sites of other PKS implies that a thiolate-imidazolium ion pair plays a central role in polyketide biosynthesis.
In Vitro and In Vivo Activities of Syn2190, a Novel β-Lactamase Inhibitor (1999)

Syn2190, a monobactam derivative containing 1,5-dihydroxy-4-pyridone as the C-3 side chain, is a potent inhibitor of group 1 beta-lactamase. The concentrations of inhibitor needed to reduce the initial rate of hydrolysis of substrate by 50% for Syn2190 against these enzymes were in the range of 0.002 to 0.01 microM. These values were 220- to 850-fold lower than those of tazobactam. Syn2190 showed in vitro synergy with ceftazidime and cefpirome. This synergy was dependent on the concentration of the inhibitor against group 1 beta-lactamase-producing strains, such as Pseudomonas aeruginosa, Enterobacter cloacae, Citrobacter freundii, and Morganella morganii. However, against beta-lactamase-derepressed mutants of P. aeruginosa, the MICs of ceftazidime plus Syn2190 were not affected by the amount of beta-lactamase, and the values were the same for the parent strains. The MICs at which 50% of isolates are inhibited (MIC(50)s) of ceftazidime plus Syn2190 were 2- to 16-fold lower than those of ceftazidime alone for ceftazidime-resistant, clinically isolated gram-negative bacteria. Similarly, the MIC(50)s of cefpirome plus Syn2190 were two- to eightfold lower for cefpirome-resistant clinical isolates. The synergies of Syn2190 plus ceftazidime or cefpirome observed in vitro were also reflected in vivo. Syn2190 improved the efficacies of both cephalosporins in both a murine systemic infection model with cephalosporin-resistant rods and urinary tract infection models with cephalosporin-resistant P. aeruginosa.
Dissecting the Behavior of a Promiscuous Solvate Former Supported in part by the National Institutes of Health Grant R01 AI47450. We thank GMP[verbar]Immunotherapeutics for samples of Bz-423 and Bz-430 and Jeff W. Kampf for the crystal structure determination. (2006)

No Abstract
Genome-wide association study implicates immune dysfunction in the development of Hodgkin lymphoma (2018)

To further our understanding of inherited susceptibility to Hodgkin lymphoma (HL), we performed a meta-analysis of 7 genome-wide association studies totaling 5325 HL cases and 22 423 control patients. We identify 5 new HL risk loci at 6p21.31 (rs649775; <i>P</i> = 2.11 × 10<sup>-10</sup>), 6q23.3 (rs1002658; <i>P</i> = 2.97 × 10<sup>-8</sup>), 11q23.1 (rs7111520; <i>P</i> = 1.44 × 10<sup>-11</sup>), 16p11.2 (rs6565176; <i>P</i> = 4.00 × 10<sup>-8</sup>), and 20q13.12 (rs2425752; <i>P</i> = 2.01 × 10<sup>-8</sup>). Integration of gene expression, histone modification, and in situ promoter capture Hi-C data at the 5 new and 13 known risk loci implicates dysfunction of the germinal center reaction, disrupted T-cell differentiation and function, and constitutive NF-κB activation as mechanisms of predisposition. These data provide further insights into the genetic susceptibility and biology of HL.
Expression of the chemokine receptor CCR2 on immature B cells negatively regulates their cytoskeletal rearrangement and migration (2004)

Immature B cells are targeted to specific areas in the spleen, where a fraction of these cells receive signals that induce them to mature and participate in the immune response. In this study, we show that the C-C chemokine receptor 2 (CCR2) is transcribed in immature B cells, while its message is dramatically down-regulated at the mature stage. CCR2-deficient cells exhibit up-regulation of chemokine-induced actin polymerization, migration, and homing to the lymph nodes of immature B cells. In addition, we demonstrate that control of homing by CCR2 is mediated by its ligand, CCL2/JE, which is secreted by B cells and down-regulates the stromal derived factor-1 (SDF-1) signaling cascade. Thus, this study describes an additional, previously uncharacterized, role for CCR2 and its ligand as negative regulators of the homing of immature B cells.
BioMOFs: Metal–Organic Frameworks for Biological and Medical Applications (2010)

The class of highly porous materials called metal-organic frameworks offer many opportunities for applications across biology and medicine. Their wide range of chemical composition makes toxicologically acceptable formulation possible, and their high level of functionality enables possible applications as imaging agents and as delivery vehicles for therapeutic agents. The challenges in the area encompass not only the development of new solids but also improvements in the formulation and processing of the materials, including tailoring the morphology and surface chemistry of the frameworks to fit the proposed applications.
Interim Report on SNP analysis and forensic microarray probe design for South American hemorrhagic fever viruses, tick-borne encephalitis virus, henipaviruses, Old World Arenaviruses, filoviruses, Crimean-Congo hemorrhagic fever viruses, Rift Valley fever (2012)

The goal of this project is to develop forensic genotyping assays for select agent viruses, enhancing the current capabilities for the viral bioforensics and law enforcement community. We used a multipronged approach combining bioinformatics analysis, PCR-enriched samples, microarrays and TaqMan assays to develop high resolution and cost effective genotyping methods for strain level forensic discrimination of viruses. We have leveraged substantial experience and efficiency gained through year 1 on software development, SNP discovery, TaqMan signature design and phylogenetic signature mapping to scale up the development of forensics signatures in year 2. In this report, we have summarized the whole genome wide SNP analysis and microarray probe design for forensics characterization of South American hemorrhagic fever viruses, tick-borne encephalitis viruses and henipaviruses, Old World Arenaviruses, filoviruses, Crimean-Congo hemorrhagic fever virus, Rift Valley fever virus and Japanese encephalitis virus.
Effects of gases on the field emission performance of silicon gated field emitter array (2023)

Effects of gases on field emission performance were measured using silicon-gated field emitter arrays. Gas was injected into a vacuum chamber with a 1000 × 1000 tip array, which was driven by a DC gate and collector voltages. The collector voltage was fixed at 200 V while the gate voltage was swept to 40 V. For the gas exposure study, N2, He, and Ar were used. The sets of partial pressures, 5 × 10−6, 5 × 10−5, and 5 × 10−4 Torr, were used for the experiment. It was observed that N2 had the least effect and Ar had the worst effect on emission current performance. The degradation of collector current at 5 × 10−4 Torr pressure for Ar was ≈65% where for the N2, at the same level of pressure, the degradation was ≈41%. However, further experiments with high purity Ar gas showed that it was the water vapor present in the gas itself that was the primary cause of reduction in emission current and not the gas itself. The results expressed in reduction in emission current versus Langmuir exposure versus the current clearly showed the effect of water vapor. After the vacuum was recovered, the work function again restored partially to its original value. After ultraviolet light cleaning, the emission current was restored completely to the original state.
A Comparison of Neuropathy Quality of Life Tools: Norfolk QOL-DN, PN-QOL-97, and NeuroQOL-28 (2021)

Aims To explore the effectiveness of the Norfolk QOL-DN (QOL-DN), PN-QOL-97, and NeuroQOL-28 as tools for early detection of diabetic peripheral neuropathy in overweight, obese, and inactive (OOI), prediabetes (PD), and type 2 diabetes (T2D) individuals. Methods Thirty-four adults were divided by A1C [(10 OOI, 13 PD, and 11 T2D] and the sural nerves were tested bilaterally via NC-Stat DPN Check, conducting a sural nerve conduction study (NCS). Participants were individually timed, filling out questionnaires (QOL-DN, NeuroQOL-28, and PN-QOL-97) at a self-selected pace. Data were analyzed and compared to NCS findings to determine the best instrument for early neuropathy detection, usability in screening settings, and application for individuals with OOI, PD, and T2D. Results Abnormal NCS results were obtained from 27 individuals, of which 25 were bilateral and symmetrical. Confirmed DSPN criteria were met for 24, and 1 case met criteria for subclinical neuropathy. Normal NCS findings, reported symptoms, and reduced bilateral sensation were found in 7 cases. The QOL-DN and NeuroQOL-28 significantly predict neuropathy criteria in OOI, PD, and T2D subjects. Analyses revealed the QOL-DN as the quickest for completion (M=5.17; SD=1.83), followed by the NeuroQOL-28 (M=5.58; SD=3.56), and the PN-QOL-97 (M=13.23; SD=3.606). Conclusions The QOL-DN and NeuroQOL-28 are valid early screening measures for DPN detection. Time completion studies revealed that the QOL-DN and NeuroQOL-28 may be used as excellent short screening measures, completed in approximately 6 minutes or less, with reasonable scoring for both. The NeuroQOL-28 is a better fit for immediate feedback, time constraints, or limited staff. Future investigations should evaluate these tools for detection in DPN-prone individuals and in subclinical populations screenings.
Long-lived dilute photocarriers in individually-suspended single-walled carbon nanotubes (2004)

Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text Y. Hashimoto, A. Srivastava, J. Shaver, G. Ostojic, S. Zaric, V. Moore, R. Hauge, R. Smalley, and J. Kono, "Long-lived dilute photocarriers in individually-suspended single-walled carbon nanotubes," in Conference on Lasers and Electro-Optics/International Quantum Electronics Conference and Photonic Applications Systems Technologies, Technical Digest (CD) (Optica Publishing Group, 2004), paper IPDB4. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Lithium‐Ion Batteries: 3D‐Printed Cathodes of LiMn1−xFexPO4 Nanocrystals Achieve Both Ultrahigh Rate and High Capacity for Advanced Lithium‐Ion Battery (Adv. Energy Mater. 18/2016) (2016)

Rechargeable lithium-ion batteries (LIBs) play a key role in energy storage devices. In article number 1600856, Feng Pan and co-workers report the development of a 3D-printing technology and the printing of 3D LIBs based on LiMn0.21Fe0.79PO4@C (LMFP) nanocrystals. The 3D-printed electrode battery delivers 108.45 mA h g−1 at 100 C, ranking it as the highest rate capability among LMFP LIBs. The cover picture shows the 3D printing equipment, the 3D-printed electrodes (green flaps) and 3D-printed LIBs.
Neuronal nicotinic acetylcholine receptor ligands as potential analgesics (2003)

Neuronal nicotinic acetylcholine receptors (nAChRs) are ligand-gated cation channels that mediate fast responses of neurons to the neurotransmitter acetylcholine (ACh). Although related to muscle nAChRs, neuronal nAChRs display a different pharmacology. Neuronal nAChR-mediated analgesia is observed in rodent pain models but activation of nAChRs can also produce undesirable effects, many related to autonomic function. However, nAChR subtype diversity provides the opportunity to develop selective agents with improved safety margins, with the α4β2 nAChR subtype important in attenuating acute thermal pain and the α3β4 subtype critical for autonomic function. Recent evidence that α7 nAChRs are involved in pain and inflammation is exciting but requires validation. Recent patent literature reveals increased interest in nAChR ligands for pain, as well as other therapeutic indications. New structure types are being developed, with new α7 ligands being particularly noteworthy but the minimal disclosure of biological data in many recent patents makes evaluation of their utility difficult.
Activation of phosphatidylinositol 3-kinase/Akt pathway by androgen through interaction of p85α, androgen receptor, and Src. (2016)

This article has been withdrawn by the authors. The same data were used to represent different experimental conditions. Specifically, lanes 1–3 of the H2B panel of Fig. 4B were reused in lanes 1–3 of the H2B panel from Fig. 6B. Lanes 1 and 6 of the phospho-Akt panel from Fig. 4C were duplicated. Lanes 3 and 4 of the lower FLAG panel in Fig. 4C were reused in lanes 7 and 8 of the lower FLAG panel in Fig. 5A. The PI(3,4)P2 spots from lanes 1 and 2 from Fig. 7 were reused in lanes 7 and 8 of the same panel.
Simulation insights on the structure of nanoscopically confined poly(ethylene oxide) (2003)

Abstract We employ atomistic computer modeling to investigate the structure and morphology of poly(ethylene oxide) (PEO) chains confined in 1‐nm slit pores defined by montmorillonite silicate layers. Molecular dynamics computer simulations reveal the Li + cations to be located in the immediate vicinity of the silicate surfaces and PEO to adopt highly amorphous conformations in a liquidlike bilayer across the slit pores. Despite the orienting influence of the parallel stacked silicate walls, PEO shows no indication of crystallinity or periodic ordering; in fact, for all temperatures simulated, it is less ordered than the most disordered bulk PEO system. These amorphous PEO film configurations are attributed to the combination of severe spatial confinement and the strong coordination of ether oxygens with the alkali cations present in the interlayer gallery. These conclusions challenge the picture traditionally proposed for intercalated PEO, but they agree with a plethora of experimental observations. Indicatively, the simulation predictions are confirmed by wide‐angle neutron scattering and differential scanning calorimetry experiments on PEO/montmorillonite intercalates. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 3285–3298, 2003
The Role of an Enolase‐Related Molecule in Plasminogen Binding to Cells (1995)

The alpha isoform of enolase is a candidate plasminogen receptor on U937 monocytoid cells [Miles, L. A., Dahlberg, C. L., Plescia, J., Felez, J., Kato, K. & Plow, E. F. (1991) Biochemistry 30, 1682-1691]. In the present study, an enolase-related molecule was detected on the surfaces of peripheral blood monocytes and neutrophils by fluorescence-activated cell sorting. A mRNA transcript encoding a unique membrane form of an enolase-related molecule was not detected by Northern-blotting and primer-extension analyses, consistent with the cell-surface protein being authentic alpha-enolase. Both the alpha and beta isoforms of purified enolase, bound plasminogen with an affinity similar to that of the cell surface. Moreover, immunopurified alpha-enolase enhanced plasminogen activation by tissue plasminogen activator and blocked the binding of plasminogen to alpha 2-antiplasmin, mimicking functions arising from the association of plasminogen with cells. The interaction of the enolase isoforms with plasminogen was dependent upon recognition of the C-terminal lysyl residue of the enolases by the lysine-binding sites of plasminogen, as the interaction was blocked by (a) peptides with C-terminal lysine residues and (b) an antibody to the C-terminal aspect of enolase. A monoclonal antibody was developed, characterized and utilized to quantify the enolase molecules present on the surface of U937 cells. A substantial number of molecules, 1.8 x 10(6)/cell, was present, accounting for approximately 10% of the plasminogen-binding capacity of these cells. These studies clearly establish the role of enolase as a cell-surface plasminogen-binding site with profibrinolytic functions.
An expedient synthesis of an isofervenulin analogue (2004)

Abstract An efficient approach has been developed for the synthesis of an isofervenulin analogue 1 employing a one‐pot condensation‐substitution reaction of a chlorocarboethoxytriazine (electrophile) with a urea (nucleophile). The resulting cyclization reaction resulted in the synthesis of a pyrimido‐heterocycle in good yield in either acidic or basic media. The former was assisted by utilizing trimethylsilyl chloride.
Airway hyperresponsiveness is associated with airway remodeling but not inflammation in aging Cav1 -/- mice (2013)

A lack of Cav1 contributed to the thickness of the subepithelial layer in mice as they aged resulting in an increase in AHR independent of inflammation, demonstrating the important contribution of airway structural changes to AHR. In addition, age in the Cav1-/- mice is a contributing factor to airway remodeling in the response to allergen challenge.
SeeThrough: Finding Objects in Heavily Occluded Indoor Scene Images (2018)

Discovering 3D arrangements of objects from single indoor images is important given its many applications such as interior design and content creation for virtual environments. Although heavily researched in the recent years, existing approaches break down under medium to heavy occlusion as the core image-space region detection module fails in absence of directly visible cues. Instead, we take into account holistic contextual 3D information, exploiting the fact that objects in indoor scenes co-occur mostly in typical configurations. First, we use a neural network trained on real indoor annotated images to extract 2D keypoints, and feed them to a 3D candidate object generation stage. Then, we solve a global selection problem among these candidates using pairwise co-occurrence statistics discovered from a large 3D scene database. We iterate the process allowing for candidates with low keypoint response to be incrementally detected based on the location of the already discovered nearby objects. We demonstrate significant performance improvement over combinations of state-of-the-art methods, especially for scenes with moderately to severely occluded objects.
Plasmonic nanostructures for absorption enhancements close to the GaAs band edge (2011)

In this paper we present the optical characterisation of periodic arrays of Au nanoparticles fabricated on both GaAs substrates and a triple junction solar cell structure. The nanoparticle arrays were designed to employ the localised surface plasmon resonances of the nanoparticles and diffraction effects arising from the periodicity of the arrays, at wavelengths close to the GaAs band edge. In principle effects such as these may be used to improve the absorption of light in solar cell structures and hence increase their efficiency. In particular, we aim to build upon the success of high efficiency GaAs based photovoltaic cells by targeting the spectral region close to the band edge, where the absorption strength in conventional GaAs solar cells is poor. We demonstrate from numerical simulations and experimental observation that by careful adjustment of the nanoparticle dimensions we can tune the localised surface plasmon resonance to the desired wavelength. Furthermore, we show evidence of the diffraction of incident light into lateral modes within the absorbing material, increasing the optical path length. This effect is associated with the periodic nature of the arrays, and can therefore also be spectrally tuned by controlling the spacing between the nanoparticles. Such periodic nanoparticle arrays therefore provide two methods of absorption enhancement that may be employed in the same structure.
What Good is Temporal Logic (1983)

This was an invited paper. It describes the state of my views on specification and verification at the time. It is notable for introducing the idea of invariance under stuttering and explaining why it’s a vital attribute of a specification logic. It is also one of my better-written papers.
Querying XML data sources in DB2: the XML wrapper (2005)

The XML Wrapper exploits the federated database capabilities of DB2 to enable SQL applications to query XML data from a variety of sources, including files and web services. The XML Wrapper models hierarchical XML documents as families of virtual relational tables in a federated schema, which can then be queried to extract information from the XML and combine it with data from other sources. To keep the wrapper simple and efficient, we take advantage of the existing capabilitiesof DB2 to the greatest extent possible. Our approach uses the DB2 optimizer’s ability to explore the space of join orders and join methods to find good execution plans for queries that include XML documents. We also leverage DB2’s view and rewrite mechanisms to allow a simple wrapper to support the full range of SQL queries an application might submit.
TA-3037A, a new inhibitor of glutathione S-transferase, produced by actinomycetes. II. Structure determination. (1992)

TA-3037A, a new inhibitor of glutathione S-transferase, has been isolated from the culture broth of Streptomyces sp. TA-3037. The structure of TA-3037A was defined as (Z)-3-benzylidene-3,4-dihydro-2-oxo-2H-1,4-benzoxazine-5-carboxylic acid by an analysis of spectral properties and chemical studies of TA-3037A and its derivatives.