gebhart/patrepeval huggingface dataset:
The Structure of the Extracellular Domain of Triggering Receptor Expressed on Myeloid Cells Like Transcript-1 and Evidence for a Naturally Occurring Soluble Fragment (2006)

Triggering receptor expressed on myeloid cells like transcript-1 (TLT-1) is an abundant platelet-specific, type I transmembrane receptor. The extracellular fragment of TLT-1 consists of a single, immunoglobulin-like domain connected to the platelet cell membrane by a linker region called the stalk. Here we present evidence that a soluble fragment of the TLT-1 extracellular domain is found in serum of humans and mice and that an isoform of similar mass is released from platelets following activation with thrombin. We also report the crystal structure of the immunoglobulin domain of TLT-1 determined at the resolution of 1.19 A. The structure of TLT-1 is similar to other immunoglobulin-like variable domains, particularly those of triggering receptor expressed on myeloid cells-1 (TREM-1), the natural killer cell-activating receptor NKp44, and the polymeric immunoglobulin receptor. Particularly interesting is a 17-amino acid segment of TLT-1, homologous to a fragment of murine TREM-1, which, in turn, showed activity in blocking the TREM-1-mediated inflammatory responses in mice. Structural similarity to TREM-1 and polymeric immunoglobulin receptor, and evidence for a naturally occurring soluble fragment of the TLT-1 extracellular domain, suggest that this immunoglobulin-like domain autonomously plays an as yet unidentified, functional role.
Proteome-wide Profiling of Isoniazid Targets in Mycobacterium tuberculosis (2006)

Isoniazid (INH) is an essential drug used to treat tuberculosis. The mycobactericidal agents are INH adducts [INH-NAD(P)] of the pyridine nucleotide coenzymes, which are generated in vivo after INH activation and which bind to, and inhibit, essential enzymes. The NADH-dependent enoyl-ACP reductase (InhA) and the NADPH-dependent dihydrofolate reductase (DfrA) have both been shown to be inhibited by INH-NAD(P) adducts with nanomolar affinity. In this paper, we profiled the Mycobacterium tuberculosis proteome using both the INH-NAD and INH-NADP adducts coupled to solid supports and identified, in addition to InhA and DfrA, 16 other proteins that bind these adducts with high affinity. The majority of these are predicted to be pyridine nucleotide-dependent dehydrogenases/reductases. They are involved in many cellular processes, including S-adenosylmethionine-dependent methyl transfer reactions, pyrimidine and valine catabolism, the arginine degradative pathway, proton and potassium transport, stress response, lipid metabolism, and riboflavin biosynthesis. The targeting of multiple enzymes could, thus, account for the pleiotropic effects of, and powerful mycobactericidal properties of, INH.
Lesions of the dorsal hippocampal formation interfere with background but not foreground contextual fear conditioning. (1994)

The effects of hippocampal lesions on the conditioning of fear responses (freezing responses) to contextual stimuli (static, continuously present stimuli) were examined in three conditioning paradigms: forward pairing of a phasic tone conditioned stimulus (CS) with a footshock unconditioned stimulus (US), unpaired presentations of the CS and US, or presentations of the US alone. All three procedures resulted in the acquisition of conditioned freezing to contextual stimuli. Lesions of the dorsal hippocampus prevented the acquisition of contextual conditioning in the Paired procedure, as reported previously, but not in the Unpaired or US Alone procedures. In the Paired procedure, static contextual cues occur in the background, with the phasic tone CS being the primary stimulus that enters into the association with the US. However, in the other two procedures, where there is no phasic CS, the primary associations with the US involve static contextual stimuli, which are therefore in the foreground. We refer to these types of contextual conditioning as background and foreground contextual conditioning, respectively, and argue that the hippocampus is only involved in background contextual conditioning. These results have implications for understanding both fear conditioning and hippocampal function.
Thyroid-stimulating autoantibodies in Graves disease preferentially recognize the free A subunit, not the thyrotropin holoreceptor (2002)

Graves disease is directly caused by thyroid-stimulating autoantibodies (TSAb’s) that activate the thyrotropin receptor (TSHR). We observed upon flow cytometry using intact cells that a mouse mAb (3BD10) recognized the TSHR ectodomain with a glycosidylphosphatidylinositol (ECD-GPI) anchor approximately tenfold better than the same ectodomain on the wild-type TSHR, despite the far higher level of expression of the latter. The 3BD10 epitope contains the N-terminal cysteine cluster critical for TSAb action. Consequently, we hypothesized and confirmed that TSAb (but not thyrotropin-blocking autoantibodies [TBAb’s]) also poorly recognize the wild-type TSHR relative to the ECD-GPI. Despite poor recognition by TSAb of the holoreceptor, soluble TSHR A subunits (known to be shed from surface TSHR) fully neutralized autoantibody-binding activity. These data indicate that the epitope(s) for TSAb’s, but not for TBAb’s, are partially sterically hindered on the holoreceptor by the plasma membrane, the serpentine region of the TSHR, or by TSHR dimerization. However, the TSAb epitope on the soluble A subunit is freely accessible. This observation, as well as other evidence, supports the concept that A subunit shedding either initiates or amplifies the autoimmune response to the TSHR, thereby causing Graves disease in genetically susceptible individuals.
A post-compensation scheme for peak-detect channel (1990)

A postcompensation procedure for peak detection in disk-drive systems has been tested using a software channel on
Decrease in Nucleoside Diphosphate Kinase (NDPK/nm23) Expression during Hematopoietic Maturation (1998)

The nucleoside diphosphate kinase (NDPK/nm23) isoforms H1 and H2 were localized in hematopoietic tissues. Flow cytometric analysis and enzymatic assays were used to quantify the intracellular and extracellular concentrations of NDPK. Bone marrow CD34(+) progenitors contained the highest intracellular levels of both nm23-H1 and nm23-H2. Lower levels were measured in more mature bone marrow cells, whereas peripheral blood leukocytes had the lowest expression of nm23. These data suggest a function of NDPK in early hematopoiesis and a down-regulation of NDPK upon differentiation. In addition, an up-regulation of nm23 expression was observed in lymphocytes after induction of proliferation with phytohemagglutinin. Multiparameter flow cytometry demonstrated that this up-regulation occurred during the G0/G1-transition. Flow cytometric analysis also revealed a weak surface expression of nm23 on a number of hematopoietic cell lines, which was not detected on normal hematopoietic cells. Our data also demonstrated the presence of NDPK in human plasma, probably due to a limited in vivo lysis of red blood cells.
Measurement of milk intake: tracer-to-infant deuterium dilution method (1991)

The tracer-to-infant deuterium dilution method for the measurement of milk intake was evaluated in twenty breast-fed and twenty formula-fed infants. The isotope method was compared with conventional direct-weighing techniques. Human milk intake was assessed by 5 d test-weighing. Intakes of formula, supplemental foods, and water were determined by pre- and post-weighing of feeding bottles. An oral dose of 200 mg 2H2O/kg body-weight was given to each infant, and urine was sampled daily for 14 d. 2H enrichment of the urine was measured by gas-isotope-ratio mass spectrometry. Milk intakes estimated from the deuterium dilution method were consistently higher than those from direct-weighing; the mean difference between methods was 106 (SD 47) g/d or 14% for the breast-fed group and 70 (SD 155) g/d or 8% for the formula-fed group. Estimates of intake for some infants varied substantially between the two methods of measurement. When the estimated values of human milk intake were corrected for environmental water influx and insensible water loss during breast-feeding, the relative bias decreased to 5%. Correction of the estimated values of formula intake for environmental water influx decreased the relative bias to 1-2%. The acceptability of the deuterium dilution method to determine milk intake depends on the goals and the tolerance for error in group and individual intake estimates of a given study.
Regioselective Cross-Coupling Reactions as an Entry into Biologically Relevant Bithiazoles: First Total Synthesis of Cystothiazole E (2001)

No problems have been encountered while using bithiazoles in Pd-catalyzed cross-coupling reactions. It was thus possible to achieve the first synthesis of cystothiazole E (1) with a Suzuki coupling of the building blocks 2 and 3 as the pivotal C-C bond-formation step (94 % yield, TBDMS=tBuMe<sub>2</sub> Si). The bithiazole 3 could be prepared very conveniently from 2,4-dibromothiazole by regioselective cross-coupling reactions.
Creation of the USSR Association of Student Cooperatives (1993)

"Today's seminar is a celebration that we could not even have dreamed of just a year ago"—this is how Viktoria Butenko, head of the "Ottsy i deti" [Fathers and Sons] cooperative in the city of Balashikhi, Moscow Region, began her speech at the seminar-conference of chairpersons of student cooperatives. The seminar was organized at the initiative of the Komsomol Central Committee and was held in Moscow on March 2-4 of this year. It was anticipated that about seventy people would take part in the conference, but twice as many convened in the conference hall of Iunost' Hotel. Along with the heads of school cooperatives, lively interest in the problems of student cooperatives was shown by school and vocational-school principals from Moscow and Moscow Region, workers and organs of public education, and scientists.
Conditionally replicating mycobacteriophages: A system for transposon delivery to Mycobacterium tuberculosis (1997)

Transposon mutagenesis provides a direct selection for mutants and is an extremely powerful technique to analyze genetic functions in a variety of prokaryotes. Transposon mutagenesis of Mycobacterium tuberculosis has been limited in part because of the inefficiency of the delivery systems. This report describes the development of conditionally replicating shuttle phasmids from the mycobacteriophages D29 and TM4 that enable efficient delivery of transposons into both fast- and slow-growing mycobacteria. These shuttle phasmids consist of an Escherichia coli cosmid vector containing either a mini-Tn10(kan) or Tn5367 inserted into a nonessential region of the phage genome. Thermosensitive mutations were created in the mycobacteriophage genome that allow replication at 30 degrees C but not at 37 degrees C (TM4) or 38.5 degrees C (D29). Infection of mycobacteria at the nonpermissive temperature results in highly efficient transposon delivery to the entire population of mycobacterial cells. Transposition of mini-Tn10(kan) occurred in a site-specific fashion in M. smegmatis whereas Tn5367 transposed apparently randomly in M. phlei, Bacille Calmette-Guérin (BCG), and M. tuberculosis. Sequence analysis of the M. tuberculosis and BCG chromosomal regions adjacent to Tn5367 insertions, in combination with M. tuberculosis genomic sequence and physical map data, indicates that the transpositions have occurred randomly in diverse genes in every quadrant of the genome. Using this system, it has been readily possible to generate libraries containing thousands of independent mutants of M. phlei, BCG, and M. tuberculosis.
Light-emitting diode treatment reverses the effect of TTX on cytochrome oxidase in neurons (2001)

Light close to and in the near-infrared range has documented benefits for promoting wound healing in human and animals. However, mechanisms of its action on cells are poorly understood. We hypothesized that light treatment with a light-emitting diode array at 670 nm (LED) is therapeutic in stimulating cellular events involving increases in cytochrome oxidase activity. LED was administered to cultured primary neurons whose voltage-dependent sodium channels were blocked by tetrodotoxin. The down-regulation of cytochrome oxidase activity by TTX was reverted to control levels by LED. LED alone also up-regulated enzyme activity. Thus, the results are consistent with our hypothesis that LED has a stimulating effect on cytochrome oxidase in neurons, even when they have been functionally silenced by TTX.
The butterfly satellite IMP for the wideband packet satellite network (1986)

Multiprocessor computer systems have proven effective as high performance switching nodes in packet switched data communications networks. They are well suited to performing the required queuing, routing, and scheduling tasks, and can scale upward to provide higher system throughput when combined with software that exploits the parallelism provided by the hardware. This paper describes the packet switch used in the DARPA Wideband Packet Satellite Network and the Butterfly™ Multiprocessor on which it is based.
Robust and Accurate Surface Measurement Using Structured Light (2008)

This paper proposes a robust and accurate method for measuring 3-D surfaces using a binocular system. To eliminate the effect caused by the distortion of projector lens, each structured light sheet is fitted to a conicoid. A curvilinear detector, which combines the zero-crossing detection algorithm with Steger's detector, is employed to detect the subpixel locations of the light stripes, thus preventing the Steger's curvilinear detector from failing to detect them in the endpoints of the stripes. The proposed coding method combines the information of the linked line with the gray code to avoid producing outliers caused by erroneous decoding and make the coding procedure more robust. Experiments showed that each structured light sheet fitted to a conicoid can effectively improve the measurement accuracy. The subpixel detection method can detect the exact subpixel locations of the stripes. Likewise, the encoding strategy results in the production of fewer outliers, while the reconstruction result becomes more perfect.
Tracking the inflammatory response in stroke in vivo by sensing the enzyme myeloperoxidase (2008)

Inflammation can extend ischemic brain injury and adversely affect outcome in experimental animal models. A key difficulty in translating animal studies to humans is the lack of a definitive method to confirm and track inflammation in the brain in vivo. Myeloperoxidase (MPO), a key inflammatory enzyme secreted by activated neutrophils and macrophages/microglia, can generate highly reactive oxygen species to cause additional damage in cerebral ischemia. We report here that a functional, enzyme-activatable MRI agent can accurately track the oxidative activity of MPO noninvasively in stroke in living animals. We found that MPO is widely distributed in ischemic tissues, correlates positively with infarct size, and is detected even 3 weeks postinfarction. The peak level of MPO activity, determined by activation of the MPO-sensing agent in vivo and confirmed by MPO activity and quantitative RT-PCR assays, occurred on day 3 after ischemia. Both neutrophils and macrophages/microglia contribute to secrete MPO in the ischemic brain, although neutrophils peak earlier (days 1-3) whereas macrophages/microglia are most abundant later (days 3-7). In contrast to the conventional MRI agent diethylenetriamine-pentatacetate gadolinium, which reports blood-brain barrier disruption, MPO imaging is able to additionally track MPO activity and confirm inflammation on the molecular level in vivo, information that was previously only possible to obtain on ex vivo brain sections and impossible to assess in living human patients. Our findings could allow efficient noninvasive serial screening of therapies targeting inflammation and the use of MPO imaging as an imaging biomarker to risk-stratify patients.
Human Plasma Gelsolin Binds Adenosine Triphosphate (1990)

Binding studies of human plasma gelsolin with ATP were done by equilibrium dialysis. Analysis of the binding data showed that plasma gelsolin had one class of ATP binding site with Kd = 2.8 x 10(-7) M, which saturated at an ATP/gelsolin ratio of 0.6. The bioluminescent assay for ATP with luciferin and firefly luciferase confirmed that the protein contained a nucleotide as ATP.
Nuclear Magnetic Resonance (2012)

As a spectroscopic method, nuclear magnetic resonance (NMR) has seen spectacular growth, both as a technique and in its applications. Today's applications of NMR span a wide range of scientific disciplines, from physics to biology to medicine. Each volume of Nuclear Magnetic Resonance comprises a combination of annual and biennial reports which together provide comprehensive coverage of the literature on this topic. This Specialist Periodical Report reflects the growing volume of published work involving NMR techniques and applications, in particular NMR of natural macromolecules, which is covered in two reports: NMR of Proteins and Nucleic Acids and NMR of Carbohydrates, Lipids and Membranes. In his foreword to the first volume, the then editor, Professor Robin Harris announced that the series would be a discussion on the phenomena of NMR and that articles will be critical surveys of the literature. This has certainly remained the case throughout the series, and in line with its predecessors, Volume 40 aims to provide a comprehensive coverage of the relevant NMR literature. For the current volume this relates to publications appearing between June 2009 and May 2010 (the nominal period of coverage in volume 1 was July 1970 to June 1971). Compared to the previous volume there are some new members of the reporting team. Theoretical Aspects of Spin-Spin Couplings are covered by J. Jazwinski, while E. Swiezewska and J.Wojcik provide an account of NMR of Carbohydrates, Lipids and Membranes.
Eosinophilic esophagitis: treatment in 2005 (2006)

This article reviews the past year's literature, concentrating on the pathophysiology, and treatment of eosinophilic esophagitis in both children and adults.
Solution-Based Analysis of Multiple Analytes by a Sensor Array:  Toward the Development of an “Electronic Tongue” (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTSolution-Based Analysis of Multiple Analytes by a Sensor Array: Toward the Development of an "Electronic Tongue"John J. Lavigne, Steve Savoy, Marvin B. Clevenger, Jason E. Ritchie, Bridget McDoniel, Seung-Jin Yoo, Eric V. Anslyn, John T. McDevitt, Jason B. Shear, and Dean NeikirkView Author Information Department of Chemistry and Biochemistry Department of Electrical Engineering The University of Texas at Austin Austin, Texas 78712 Cite this: J. Am. Chem. Soc. 1998, 120, 25, 6429–6430Publication Date (Web):June 11, 1998Publication History Received23 December 1997Published online11 June 1998Published inissue 1 July 1998https://pubs.acs.org/doi/10.1021/ja9743405https://doi.org/10.1021/ja9743405rapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views1443Altmetric-Citations182LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Color,Fluorescence,Mathematical methods,Neurophysiology,Sensors Get e-Alerts
Mechanism of homophilic binding mediated by the neural cell adhesion molecule NCAM. Evidence for isologous interaction. (1994)

We have previously shown that a decapeptide sequence between Lys-243 and Glu-252 (KYSFNYDGSE) in the third immunoglobulin (Ig)-like domain of chick neural cell adhesion molecule NCAM is directly involved in NCAM-to-NCAM binding. To identify the domain that interacts with this decapeptide sequence, the Ig-like domain 3 of NCAM was expressed in bacteria and the refolded protein was assayed for its NCAM binding activity. Covaspheres conjugated with domain 3 protein bound to a substratum coated with either NCAM or the domain 3 protein, suggesting that NCAM-NCAM binding is mediated by interactions between domain 3 sequences on apposing molecules. Further studies were carried out using a cell-to-substratum binding assay. Mouse L cells stably transformed with different deletion constructs of NCAM were assayed for their ability to attach to substratum coated with different peptide conjugates. The results indicated that a site in NCAM Ig-like domain 3 bound specifically to the decapeptide sequence. To identify this site, cells expressing mutant NCAMs with alterations in the amino acid sequence of the homophilic binding site were subjected to the same cell-to-substratum assay. Mutant NCAMs that had lost their homophilic binding activity also failed to attach to the peptide substrate. Taken together, these results suggest that the NCAM homophilic binding site interacts isologously with the same sequence on apposing molecules.