gebhart/patrepeval huggingface dataset:
Crystal structures of an archaeal oligosaccharyltransferase provide insights into the catalytic cycle of N-linked protein glycosylation (2013)

Oligosaccharyltransferase transfers an oligosaccharide chain to the asparagine residues in proteins. The archaeal and eubacterial oligosaccharyltransferases are single subunit membrane enzymes, referred to as "AglB" (archaeal glycosylation B) and "PglB" (protein glycosylation B), respectively. Only one crystal structure of a full-length PglB has been solved. Here we report the crystal structures of the full-length AglB from a hyperthermophilic archaeon, Archaeoglobus fulgidus. The AglB and PglB proteins share the common overall topology of the 13 transmembrane helices, and a characteristic long plastic loop in the transmembrane region. This is the structural basis for the formation of the catalytic center, consisting of conserved acidic residues coordinating a divalent metal ion. In one crystal form, a sulfate ion was bound next to the metal ion. This structure appears to represent a dolichol-phosphate binding state, and suggests the release mechanism for the glycosylated product. The structure in the other crystal form corresponds to the resting state conformation with the well-ordered plastic loop in the transmembrane region. The overall structural similarity between the distantly related AglB and PglB proteins strongly indicates the conserved catalytic mechanism in the eukaryotic counterpart, the STT3 (stauroporine and temperature sensitivity 3) protein. The detailed structural comparison provided the dynamic view of the N-glycosylation reaction, involving the conversion between the structured and unstructured states of the plastic loop in the transmembrane region and the formation and collapse of the Ser/Thr-binding pocket in the C-terminal globular domain.
The <i>Medicago truncatula</i> Lysine Motif-Receptor-Like Kinase Gene Family Includes <i>NFP</i> and New Nodule-Expressed Genes (2006)

Rhizobial Nod factors are key symbiotic signals responsible for starting the nodulation process in host legume plants. Of the six Medicago truncatula genes controlling a Nod factor signaling pathway, Nod Factor Perception (NFP) was reported as a candidate Nod factor receptor gene. Here, we provide further evidence for this by showing that NFP is a lysin [corrected] motif (LysM)-receptor-like kinase (RLK). NFP was shown both to be expressed in association with infection thread development and to be involved in the infection process. Consistent with deviations from conserved kinase domain sequences, NFP did not show autophosphorylation activity, suggesting that NFP needs to associate with an active kinase or has unusual functional characteristics different from classical kinases. Identification of nine new M. truncatula LysM-RLK genes revealed a larger family than in the nonlegumes Arabidopsis (Arabidopsis thaliana) or rice (Oryza sativa) of at least 17 members that can be divided into three subfamilies. Three LysM domains could be structurally predicted for all M. truncatula LysM-RLK proteins, whereas one subfamily, which includes NFP, was characterized by deviations from conserved kinase sequences. Most of the newly identified genes were found to be expressed in roots and nodules, suggesting this class of receptors may be more extensively involved in nodulation than was previously known.
Multidimensional NMR spectroscopy for the study of histone H4–Ni(<scp>ii</scp>) interaction (2006)

The N-terminal 30-amino acid tail of histone H4, a nuclear protein, was studied as a model for the interaction of this protein with Ni(ii) ions. The behaviour of the ends-blocked Ac-SGRGKGGKGLGKGGA(15)K(16)R(17)H(18)R(19)KVLRDNIQGIT-Am fragment towards Ni(ii) was analyzed with multidimensional NMR (1D, 2D TOCSY, NOESY) and UV-Vis spectroscopy. As expected, the coordination involved the imidazolic nitrogen of the His(18) residue and the three deprotonated amidic nitrogens of the His(18), Arg(17) and Lys(16) residues, respectively. A model for the structure of the complex was calculated from the inter-residual NOEs recorded in 2D NOESY spectra. The structure obtained shows that the interaction with the metal is responsible for deep changes in the conformation of the peptide, blocking the side chain of Arg(17) and Lys(16) residues above the coordination plane. These structural modifications may be physiologically relevant to the mechanism of nickel carcinogenesis.
2-Deoxy-2-[F-18]fluoro-D-glucose Joint Uptake on Positron Emission Tomography Images: Rheumatoid Arthritis Versus Osteoarthritis (2007)

FDG-uptake was observed in the majority of clinically inflamed RA joints and in a few OA joints with no significant difference in uptake level. The latter may be due to secondary synovitis.
Catalytic reaction on both sides of a metalloporphyrin plane. Alternating copolymerization of phthalic anhydride and epoxypropane with an aluminum porphyrin-quaternary salt system (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCatalytic reaction on both sides of a metalloporphyrin plane. Alternating copolymerization of phthalic anhydride and epoxypropane with an aluminum porphyrin-quaternary salt systemTakuzo Aida and Shohei InoueCite this: J. Am. Chem. Soc. 1985, 107, 5, 1358–1364Publication Date (Print):March 1, 1985Publication History Published online1 May 2002Published inissue 1 March 1985https://doi.org/10.1021/ja00291a041RIGHTS & PERMISSIONSArticle Views1276Altmetric-Citations125LEARN 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 InReddit PDF (722 KB) Get e-Alertsclose Get e-Alerts
Toleration of Intravenous Azithromycin (1997)

Single doses of azithromycin 1 g at infusate concentrations up to 2 mg/mL were well tolerated when administered over 1 hour to healthy men.
Characterization of a New Rat Model of Penetrating Ballistic Brain Injury (2005)

Penetrating brain injury (PBI) is a leading cause of mortality and morbidity in modern warfare and accounts for a significant number of traumatic brain injuries worldwide. Here we characterize the pathophysiology of a new rat model of PBI that simulates the large temporary cavity caused by energy dissipation from a penetrating bullet round. Male Sprague-Dawley rats (250-300 g) were subjected to a simulated ballistic wound to the right frontal hemisphere implemented by an inflatable penetrating probe. Three levels of injury severity were compared to control animals. Neurological and physiological outcome was assessed over a 3-day recovery period and brain tissue collected at 72 h for histopathological evaluation. Brain-injured regions included the ipsilateral frontal cortex and striatum with volumetric increases in intracranial hemorrhage (5-18 mm3) and lesion size (9-86 mm3) related to severity. Similarly, hemispheric swelling increased (3-14%) following PBI, associated with a significant rise in intracranial pressure. Astrogliosis was present in regions adjacent to the core-injury along with microglial and leukocyte infiltration. Injury remote to the lesion was observed in the cerebral peduncle that may have accounted, in part, for observed neurological deficits. Neurological and balance beam testing revealed sensorimotor deficits that persisted through 72 h. Severe electroencephalographic disturbances included the occurrence of cortical spreading depression, slow-waves, and brain seizure activity. In conclusion, this rat PBI model replicates diverse, salient features of clinical PBI pathology, generates reproducible and quantifiable measures of outcome, and is scalable by injury severity, rendering it an attractive vehicle for experimental brain trauma research.
Remarkable Improvement of Catalytic Performance for a New Cobalt‐Decorated Cu/HMS Catalyst in the Hydrogenation of Dimethyloxalate (2012)

Evaporate to invigorate: The catalytic activity of the Cu/HMS catalyst is greatly enhanced by decorating with only 1 wt. % of cobalt. The co-ammonia-evaporation method leads to stronger interactions between the copper and cobalt species and more metallic cobalt may facilitate the activation of hydrogen. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Analysis of Samples Stored as Individual Plugs in a Capillary by Electrospray Ionization Mass Spectrometry (2009)

Droplets or plugs within multiphase microfluidic systems have rapidly gained interest as a way to manipulate samples and chemical reactions on the femtoliter to microliter scale. Chemical analysis of the plugs remains a challenge. We have discovered that nanoliter plugs of sample separated by air or oil can be analyzed by electrospray ionization mass spectrometry when pumped directly into a fused silica nanospray emitter tip. Using leucine-enkephalin in methanol and 1% acetic acid in water (50:50 v:v) as a model sample, we found carry-over between plugs was <0.1% and relative standard deviation of signal for a series of plugs was 3%. Detection limits were 1 nM. Sample analysis rates of 0.8 Hz were achieved by pumping 13 nL samples separated by 3 mm long air gaps in a 75 microm inner diameter tube. Analysis rates were limited by the scan time of the ion trap mass spectrometer. The system provides a robust, rapid, and information-rich method for chemical analysis of sample in segmented flow systems.
Significance of Diastolic Dysfunction of the Heart (1991)

Diastolic dysfunction is an important cause of the clinical syndrome of congestive heart failure. Traditionally, the syndrome of pulmonary congestion due to the elevation of left heart filling pressure has been attributed to the depressed ability of the heart to eject blood during systole, with a secondary increase in left ventricular volume. However, heart failure can also occur when the left ventricle fails to receive blood during diastole at low filling pressures. With a mild degree of resistance of the left ventricle to diastolic filling, the initial hemodynamic manifestation may just be the elevation of left ventricular diastolic pressure and pulmonary venous pressure. More severe resistance to left ventricular filling may cause an inadequate extent of diastolic filling and insufficient myofiber stretch, which results in the depression of stroke volume. In this review, the factors contributing to diastolic dysfunction are discussed, with a particular focus on the role of diastolic heart failure in patients with ischemic heart disease or hypertrophy.
Transistor test structures for leakage current analysis of partial SOI (2004)

A new test structure to directly measure the junction leakage current between the channel and source/drain region is developed with partially-insulated structure. Si/SiGe epitaxial growth and selective SiGe etch process are used to form PiOX (Partially-Insulating OXide) under source and drain. With this structure, the junction leakage current between source/drain and substrate is diminished and the leakage current component from channel region and source/drain is easily measured.
Estimating neural sources from each time-frequency component of magnetoencephalographic data (2002)

We have developed a method that incorporates the time-frequency characteristics of neural sources into magnetoencephalographic (MEG) source estimation. This method calculates a time-frequency matrix in which diagonal and off-diagonal terms are the auto- and cross-time-frequency distributions of multi-channel MEG recordings, respectively. The method averages this matrix over the time-frequency region of interest. The locations of neural sources are then estimated by checking the orthogonality between the noise subspace of this averaged matrix and the sensor lead field. The method therefore allows neural sources to be estimated from any time-frequency component of measured data. We applied the method to estimating sources for gamma-band (frequency range between 30 and 100 Hz) auditory activity, and the results demonstrating the method's effectiveness were obtained.
Resource Allocation for Performance Enhancement in Mobile Ad Hoc Networks (2019)

The low-cost and easy-deployable mobile ad hoc networks (MANETs) have great potential to serve as the underlay network architecture for implementing lots of critical applications. In order to support different demands in such applications, understanding the fundamental performance of the MANETs and exploring their performance enhancement are of great importance. To this end, this paper, for the first time, investigates the performance enhancement of the MANETs by appropriately allocating the network resource. Specifically, we consider both the transmission resource and storage resource of a network node and use a two-tuple to depict a general resource allocation configuration. First, for a MANET with any given resource allocation configuration, we establish an analytical framework to model the network dynamics as queuing processes. With the help of the network modeling, we then derive the expressions of fundamental performance metrics, including per node throughput, expected an end-to-end delay, and throughput capacity. Based on these results, we further develop optimal resource allocation algorithms to determine the optimal setting of resource allocation, for enhancing network performance. Finally, we provide extensive simulation and numerical results to verify the efficiency of our theoretical modeling and illustrate the effects of resource allocation on network performance.
Use of High-Resolution Accurate Mass Spectrometry to Detect Reported and Previously Unreported Cannabinomimetics in "Herbal High" Products (2010)

A range of "Herbal High" products were tested for synthetic cannabinoids (cannabinomimetics) to qualitatively determine and compare their individual and relative content. Liquid chromatography-high resolution accurate mass spectrometry was used to rapidly screen samples for a range of cannabinomimetics using mono-isotopic masses derived from the elemental composition of target analytes. A screening database of over 140 compounds was rapidly created. This approach, combined with further tandem mass spectrometric experiments, also facilitated the detection and identification of compounds for which reference materials were not available. Previously reported cannabinomimetics, including JWH-018 and CP47,497 and its homologues, were detected in varying relative proportions along with several tentatively identified unreported cannabinomimetics. In some countries, the decision has been made to include these substances within their drug control legislation, and other countries are considering similar action. The currently applied drug screening techniques are unlikely to be effective in providing scientific evidence to support their identification in seized products. The application of high-resolution accurate mass spectrometry offers a solution. In addition, the technology provides a relatively simple and quick method for screening products, building substance databases, and even identifying novel substances using a combination of accurate mass derived elemental composition and fragment ions combined with fragmentation prediction software.
Synthesis of new polymers containing α‐(trifluoromethyl)‐acrylate units (1995)

Abstract Free radical polymerization of both α‐(trifluoromethyl)acrylic acid (TFMAA) and its methyl ester MTFMA is shown to be possible in the presence of bis(4‐ tert ‐butylcyclohexyl) peroxycarbonate (Percadox) as initiator and dioxane or THF as solvent. Also it is shown that copolymers of TFMAA with α‐olefins (1‐decene, 2‐methyl‐1‐hexene) and of methyl α‐(trifluoromethyl)acrylate (MTFMA) with vinyl ethers (butyl, 2‐ethylhexyl, and menthyl vinyl ether) can be simply obtained with AIBN as initiator; these copolymers have a predominantly alternating structure.
Characterization and growth factor requirements of SJL lymphomas. I. Development of a B cell growth factor-dependent in vitro cell line, cRCS-X. (1988)

Reticulum cell sarcomas (RCS) of SJL mice are completely dependent on host cells for their growth and therefore fail to grow in vitro. RCS cells induce marked proliferation in SJL Ly-1+2- T cells accompanied by lymphokine production. In an attempt to fully understand the host-tumor cell interaction, an RCS cell line, cRCS-X, was established in vitro from a transplantable tumor by the addition, every 3 wk, of gamma-irradiated syngeneic lymph node (LN) cells to the culture. cRCS-X maintains all of the characteristics of the parent tumor, RCS-X, including cell surface phenotype (Ks and I-As positive, Ds negative and B cell marker 14.8 positive), ability to stimulate host T cells, and ability to grow in nonirradiated but not in gamma-irradiated SJL mice. The growth factor requirements of cRCS-X were examined. It was found that human BCGF can replace gamma-irradiated LN cells in the maintenance of long term in vitro growth of cRCS-X. cRCS-X cells respond to human B cell growth factor (BCGF) or to recombinant murine interleukin (IL)-5 in a short term proliferation assay [( 3H]thymidine incorporation) in a dose-dependent manner in the presence and absence of fetal calf serum. BCGF also promotes colony formation in soft agar by cRCS-X cells. Although both IL-1 and interferon-gamma can synergize with BCGF in the induction of cRCS-X proliferation, these lymphokines, as well as IL-2, IL-3, granulocyte-macrophage colony-stimulating factor, and IL-4 have no effect on cRCS-X growth when added alone. In addition, it was shown that SJL LN cells produce both IL-4 and BCGF II activities as assayed on murine B cells, after stimulation with gamma-irradiated cRCS-X cells. In light of these results it is postulated that IL-5, [corrected] produced by syngeneic T cells [corrected] after stimulation with RCS, is essential for RCS growth, both in vitro and in vivo.
Synthesis and Antiviral Activity of 9-alkoxypurines: New 9-(hydroxyalkoxy) Derivatives of Guanine and 8-methylguanine (1994)

A number of 9-(hydroxyalkoxy) derivatives of guanine (27a-h and 27l-n) and of 8-methylguanine (27i-k) have been synthesized and evaluated as antiviral agents against herpes viruses (HSV-1, HSV-2, VZV) and visna virus, a lentivirus. The synthesis Involved reaction of hydroxyl-protected derivatives of hydroxyalkoxy-amines (6a-m) with 4,6-dichloro-2,5-diformamidopy-rimidine (24) followed by cyclization of the resultant 6-alkoxyaminopyrimidines (25a-m) to either guanine derivatives (27a-h and 27l-n) or 8-methylguanine derivatives (27i-k). Modest antiviral activity was seen with 27b, 27c, 27f, 27i and 271 against the herpesvirus and with 27e and 27m against visna virus. Only 27e showed any cytotoxicity in MRC-5 cells at concentrations ≤400μM.
OPERATION GREENHOUSE. Scientific Director's Report of Atomic Weapon Tests at Eniwetok, 1951. Annex 6.7. Contamination-Decontamination Studies (1951)

Abstract : This 1951 NTPR report describes experiments conducted in Operation Greenhouse at Eniwetok on certain processes and materials associated with contamination and decontamination phenomena. For this type of contaminating event, in which surfaces are contaminated by being carried by aircraft through an atomic cloud, information was obtained which will assist in development of effective protective measures and recovery measures from contaminating atomic detonations. The contaminant which was deposited on surfaces mounted on drone planes was shown to be nonuniform under various contaminating conditions, both as to distribution and composition. Data have been obtained on the relative importance of such surface characteristics as roughness, porosity, retentivity, and contact angle. The relative behavior of various chemical agents as decontaminants was determined and use of industrial cleaning methods employing chemical additives to effect decontamination was investigated.
Effects of near-infrared low-level laser irradiation on microcirculation (2000)

The circulatory changes observed seemed to be mediated largely by LLLI-induced reduction of [Ca2+]i in VSMCs, in addition to the involvement of NO in the initial phase.
Amiloride selectively inhibits the urokinase‐type plasminogen activator (1987)

The diuretic drug amiloride, an inhibitor of Na+ uptake, competitively inhibits the catalytic activity of the urokinase-type plasminogen activator (u-PA), with a Ki of 7 X 10(-6) M. Generation of plasmin, cleavage of peptide substrates, and interaction of u-PA with a specific macromolecular proteinase inhibitor are all prevented in the presence of the drug. In contrast, amiloride does not affect the activity of either tissue-type plasminogen activator, plasmin, plasma kallikrein or thrombin. The inhibition of u-PA by amiloride may be related to the previously reported inhibition of u-PA-type enzymes by Na+. Amiloride or related compounds could prove useful in selectively controlling u-PA-catalyzed extracellular proteolysis.
Molecular determinants of polyreactive antibody binding: HCDR3 and cyclic peptides (2000)

Human monoclonal antibody 63 (mAb63) is an IgM/lambda polyreactive antibody that binds to multiple self and non-self antigens. The molecular basis of polyreactivity is still unclear. The present study was initiated to prepare a recombinant Fab of mAb63 and use it to study the determinants involved in polyreactivity. The baculovirus system was employed to express large amounts of mAb63 Fab in Sf9 cells. Our experiments showed that infected Sf9 cells secreted a soluble 50-kD Fab heterodimer that bound to multiple self and non-self antigens. The antigen-binding activity of mAb63 Fab was inhibited by both homologous and heterologous antigens. To study in more detail the molecular determinants involved in polyreactivity, the heavy chain complementarity-determining region 3 (HCDR3), which is known to play a key role in the binding of monoreactive antibodies to antigens, was subjected to site-directed mutagenesis. A single substitution, alanine for arginine, at position 100A resulted in complete loss of antigen-binding activity. The 19 amino acids comprising the HCDR3 of mAb63 were then synthesized and a cyclic peptide prepared. The cyclic peptide showed the same antigen-binding pattern as the parental mAb63 and the recombinant mAb63 Fab. A five amino acid motif (RFLEW), present in the HCDR3 of mAb63, was found by searching the GenBank in three of 50 other human polyreactive antibodies, but in none of nearly 2500 human antibodies thought to be monoreactive. It is concluded that HCDR3 plays a major role in polyreactivity and that in some cases cyclic peptides comprising the HCDR3, by themselves, may be polyreactive.