gebhart/patrepeval huggingface dataset:
Inhibition of serine proteases by peptidyl fluoromethyl ketones (1986)

We have synthesized peptidyl fluoromethyl ketones that are specific inhibitors of the serine proteases alpha-chymotrypsin and porcine pancreatic elastase. By analogy with the corresponding aldehydes it is assumed that the fluoromethyl ketones react with the gamma-OH group of the active site serine to form a stable hemiacetal [Lowe, G., & Nurse, D. (1977) J. Chem. Soc., Chem. Commun., 815; Chen, R., Gorenstein, D.G., Kennedy, W.P., Lowe, G., Nurse, D., & Schultz, R.M. (1979) Biochemistry 18, 921; Shah, D.O., Lai, K., & Gorenstein, D.G. (1984) J. Am. Chem. Soc. 106, 4272]. 19F NMR studies of the chymotrypsin-bound trifluoromethyl ketone inhibitors Ac-Leu-ambo-Phe-CF3 and Ac-ambo-Phe-CF3 clearly indicate that the carbonyl carbon is tetrahedral at the active site of the enzyme. The inhibitor is bound as either the stable hydrate or the hemiacetal, involving the active site serine. The effect of varying the number of amino acid residues in the peptidyl portion of the inhibitor and the number of fluorines in the fluoromethyl ketone moiety is examined. In the series of trifluoromethyl ketone elastase inhibitors, the lowering of Ki concomitant with the change from a dipeptide analogue to a tetrapeptide analogue (Ac-Pro-ambo-Ala-CF3, Ki = 3 X 10(-3) M; Ac-Ala-Ala-Pro-ambo-Ala-CF3, Ki = 0.34 X 10(-6) M) correlates well with the variation in V/K for hydrolysis of the corresponding amide substrates. This trend is indicative of the inhibitors acting as transition-state analogues [Bartlett, P.A., & Marlowe, C.K. (1983) Biochemistry 22, 4618; Thompson, R.C. (1973) Biochemistry 12, 47].(ABSTRACT TRUNCATED AT 250 WORDS)
Infrared Spectra of Metaborate Monomer and Trimer Ions (1964)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInfrared Spectra of Metaborate Monomer and Trimer IonsI. C. Hisatsune and Noelia Haddock SuarezCite this: Inorg. Chem. 1964, 3, 2, 168–174Publication Date (Print):February 1, 1964Publication History Published online1 May 2002Published inissue 1 February 1964https://pubs.acs.org/doi/10.1021/ic50012a003https://doi.org/10.1021/ic50012a003research-articleACS PublicationsRequest reuse permissionsArticle Views145Altmetric-Citations56LEARN 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-Alertsclose Get e-Alerts
Effect of Bipole Configuration on Atrial Electrograms During Atrial Fibrillation (1990)

Despite an increasing body of work on the nature of fibrillatory rhythms, and the application of different bipole configurations in antifibrillatory devices, little published work has assessed the effect of bipole configuration on the endocardial recordings of fibrillatory rhythms. To address this issue, a specially designed 6 Fr decapolar catheter was used to record intra-atrial electrograms during sustained atrial fibrillation in 15 patients. Simultaneous filtered (30-500 Hz) and unfiltered (0.05-5,000 Hz) recordings of atrial fibrillation were performed of four different bipole configurations: (a) 1-mm interelectrode spacing adjacent to the atrial wall; (b) 10-mm interelectrode spacing adjacent to the atrial wall; (c) 10-mm inter-electrode spacing 24 mm from the distal catheter tip; (d) 1-mm interelectrode spacing 24 mm from the distal catheter tip. One minute of such data was recorded, and each 4.27-second segment (x 14 segments) was analyzed for atrial rate, electrogram amplitude, amplitude probability density function (apdf), median frequency in the 2-9 Hz band, and electrogram morphology. Changes in bipole configuration resulted in profound changes in calculated atrial rate, amplitude, and apdf (P less than 0.001 by two-way ANOVA in each instance). Specifically, closer interbipole spacing and closer proximity to the atrial wall resulted in lower calculated atrial rates, higher electrogram amplitudes, and higher apdf values. In contrast, median frequency proved to be a more robust measure despite multiple configurations (P greater than 0.10 by two-way ANOVA). These changes significantly affected the predictive value of previously published detection criteria for rate (P less than 0.01) and apdf (P less than 0.00001). Bipole location also affected morphology, with locations adjacent to the atrial wall and with closer interbipole spacing having more discrete electrograms and greater apparent organization (P less than 0.0001). Further, when data segments from all patients and bipole configurations were grouped, rate and apdf were found to be strongly inversely correlated (r = -0.808). (r = -0.808).(ABSTRACT TRUNCATED AT 400 WORDS)
Molecular Morphology of Cyanobacterial Phycobilisomes (1982)

Phycobilisomes were isolated from several cyanobacteria following cell lysis with Triton X-100. They were purified by phosphate precipitation and hydrophobic-interaction chromatography. Their phycobiliprotein compositions were quantitatively determined by application of sets of simultaneous absorbance equations to gel chromatographic separations of the chromoproteins. Phycobilisomes purified from several cyanobacteria had characteristic elution times on agarose gel chromatography. Combining electron microscope observations of phycobilisome structure, phycobiliprotein composition, and agarose gel chromatography estimates of molecular weight permitted the calculation of many details of phycobilisome molecular structure. Complementary chromatic adaptation resulted in a change of phycobilisome composition and structure. The polypeptide compositions of phycobilisomes were examined by sodium dodecyl sulfate-agarose gel chromatography and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The phycobilisomes were composed of phycobilipeptides derived from the constituent phycobiliproteins. Higher molecular-weight phycobilipeptide aggregates were also observed. The dominant forces responsible for the maintenance of phycobilisome structure are concluded to be hydrophobic interactions.
Virtual Distributed Computing Environment (2000)

Abstract : The next generation of network-centric applications will utilize a large number of computing and storage systems that are connected by global high speed networks. We refer to the environment that provides transparent computing and communication services for large scale parallel and distributed applications as Metacomputing environment. In this report, we present the design and the experimental results with the Virtual Distribute Computing Environment (VDCE) and the Adaptive Distributed Virtual Computing Environment (ADViCE) being developed at the University of Arizona and Syracuse University.
A memory control chip for formatting data into blocks suitable for video coding applications (1989)

Most compression algorithms for motion television require large data storage, usually several television fields, and typically operate on blocks of data. A chip has been built to support both of these features. It generates, from a single clock source, all of the control and address signals required by standard off-the-shelf dynamic RAMs (DRAMs). This includes data packing and unpacking and automatic refresh when required. Counters are provided to address the data into and out of the memories of the form of blocks. The block sizes and field dimensions are programmable and are independent for both read and write operations. Thus, one set of counters can be programmed for sequentially scanned data coming from a camera or going to a television monitor, and other set of counters can be programmed for the block size employed in the compression hardware. Blocks of data can be accessed either continuously or one at a time. When data are read from the memories, a single pel-width pulse marks the start of valid data. Signals marking both end of the block and end of field have also been provided to ease system interfacing.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Kinetics and mechanism of the Bamberger cleavage of imidazole and of histidine derivatives by diethyl pyrocarbonate in aqueous solution (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTKinetics and mechanism of the Bamberger cleavage of imidazole and of histidine derivatives by diethyl pyrocarbonate in aqueous solutionM. E. Grace, M. J. Loosemore, M. L. Semmel, and R. F. PrattCite this: J. Am. Chem. Soc. 1980, 102, 22, 6784–6789Publication Date (Print):October 15, 1980Publication History Published online1 May 2002Published inissue 15 October 1980https://pubs.acs.org/doi/10.1021/ja00542a020https://doi.org/10.1021/ja00542a020research-articleACS PublicationsRequest reuse permissionsArticle Views688Altmetric-Citations22LEARN 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-Alertsclose Get e-Alerts
The expression analysis of ICOS‐L on activated T cells and immature dendritic cells as well as malignant B cells and Grave’s‐disease‐derived thyroid tissues by two novel mAbs against human ICOS‐L (2006)

ICOS-L, a newly identified member of B7 superfamily, plays an important role in immune responses. In this article, we report on two novel mouse anti-human ICOS-L monoclonal antibodies (mAbs) named as 11C4 and 12B11, whose specificities were verified by methods of flow cytometry, western blotting, and epitope competition assay. The two mAbs bound to distinct ICOS-L epitopes on B cells. Interestingly, mAb 11C4 could well recognize ICOS-L molecule on activated T cells and Jurkat cell lines, which is different from commercial anti-ICOS-L mAb (clone number MIH12) and the other mAb 12B11. In addition, we found that the expression of ICOS-L molecule was only detected on the surface of immature monocyte-derived dendritic cells (Mo-DCs) and was sharply decreased after induction of mature Mo-DCs activated by tumor necrosis factor-alpha or CD40. Furthermore, we showed that 11C4 could effectively suppress the maturation of Mo-DCs in vitro as evidenced by the low expression of CD80, CD86, CD83, and human leukocyte antigen-DR, which suggested that ICOS-L may be involved in the maturation of Mo-DCs. Using immunohistochemistry staining with mAb 11C4, the expression of ICOS-L was found in B lymphoma tissues and thyroid tissues from the Grave's disease but not in thyroid adenoma and normal thyroid tissues.
Serial Number Arithmetic (1996)

This memo defines serial number arithmetic, as used in the Domain Name System. The DNS has long relied upon serial number arithmetic, a concept which has never really been defined, certainly not in an IETF document, though which has been widely understood. This memo supplies the missing definition. It is intended to update RFC1034 and RFC1035.
Simulation of carbene chemistry and other problems in computer-assisted organic synthesis (1993)

Three projects were undertaken as part of the CAMEO program, which predicts the products of organic reactions given starting materials and conditions: (1) A module was written to simulate carbene reactions. Mechanistically and thermodynamically based, it can predict the behavior of a wide range of compounds it has never encountered, and suggests likely side products. It provides insight into the underlying processes through messages issued when mechanistic decisions are made. The principal stages are: (a) Optional carbene formation, incorporating all major preparative routes. (b) Perception of carbene philicity, selectivity and spin multiplicity. (c) Analysis, wherein a few fundamental mechanisms are essayed on all applicable atoms and bonds. Each resulting potential product is rated using a model from transition state theory. To the mechanism's base rank are added entropic and enthalpic adjustments for substituent effects. This allows neat incorporation of the effects of catalyst, carbene selectivity, temperature and intramolecularity. (d) Product evaluation and generation. (2) A package was developed to compose aesthetic structure diagrams from connection tables. There are three modes, ranging from neatening to complete redesign. Difficult mono-and bicyclic rings are drawn from stored templates. Suggestions are made for a template dictionary and for drawing complex systems not in it. An irregular polygon technique improves the appearance of bridged and polyfused rings. Techniques for combating atom overlap are included. When more than one molecule is present they are distributed evenly about the screen in two steps: (a) the molecules are located where they have the best opportunity for dispersion; (b) they are dynamically scattered using a force field-like approach. A function to assess aesthetic appearance was invented; it can decide if a redrawn structure is improved. (3) Symmetry is perceived by iterative partitioning. Stereochemistry, including that of "U" double bonds, is treated. To identify duplicate products, two methods of deriving a canonical connection table are available. One uses fast symmetry-driven partitioning; the other is a rigorous stereochemically-extended implementation of the Morgan algorithm. Additionally, the last chapter discusses innovations in graphics and a new non-graphics interface.
Identification of Imidazo-Pyrrolopyridines as Novel and Potent JAK1 Inhibitors (2012)

A therapeutic rationale is proposed for the treatment of inflammatory diseases, such as rheumatoid arthritis (RA), by specific targeting of the JAK1 pathway. Examination of the preferred binding conformation of clinically effective, pan-JAK inhibitor 1 led to identification of a novel, tricyclic hinge binding scaffold 3. Exploration of SAR through a series of cycloamino and cycloalkylamino analogues demonstrated this template to be highly tolerant of substitution, with a predisposition to moderate selectivity for the JAK1 isoform over JAK2. This study culminated in the identification of subnanomolar JAK1 inhibitors such as 22 and 49, having excellent cell potency, good rat pharmacokinetic characteristics, and excellent kinase selectivity. Determination of the binding modes of the series in JAK1 and JAK2 by X-ray crystallography supported the design of analogues to enhance affinity and selectivity.
Self-focusing and nonlinear periodic beams in parabolic index optical fibres (2004)

The existence of exact nonlinear and periodic propagation modes in graded index nonlinear optical fibres that reproduce the periodic self-imaging property of the linear propagation regime is analytically proved. The stability of these periodically focused modes, which are constructed as self-similar solutions of the fibre nonlinear eigenmodes, is studied by means of standard linear stability analysis and numerical beam propagation. Self-similar solutions constructed from the fundamental nonlinear fibre mode are found to be linearly stable, whereas symmetry-breaking instabilities are found for higher-order nonlinear modes.
Biomarker-focused multi-drug combination therapy and repurposing trial in mdx mice (2021)

Duchenne muscular dystrophy is initiated by dystrophin deficiency, but downstream pathophysiological pathways such as membrane instability, NFĸB activation, mitochondrial dysfunction, and induction of TGFβ fibrosis pathways are thought to drive the disability. Dystrophin replacement strategies are hopeful for addressing upstream dystrophin deficiency; however, all methods to date use semi-functional dystrophin proteins that are likely to trigger downstream pathways. Thus, combination therapies that can target multiple downstream pathways are important in treating DMD, even for dystrophin-replacement strategies. We sought to define blood pharmacodynamic biomarkers of drug response in the mdx mouse model of Duchenne muscular dystrophy using a series of repurposed drugs. Four-week-old mdx mice were treated for four weeks with four different drugs singly and in combination: vehicle, prednisolone, vamorolone, rituximab, β-aminoisobutyric acid (BAIBA) (11 treatment groups; n = 6/group). Blood was collected via cardiac puncture at study termination, and proteomic profiling was carried out using SOMAscan aptamer panels (1,310 proteins assayed). Prednisolone was tested alone and in combination with other drugs. It was found to have a good concordance of prednisolone-responsive biomarkers (56 increased by prednisolone, 39 decreased) focused on NFκB and TGFβ cascades. Vamorolone shared 45 (80%) of increased biomarkers and 13 (33%) of decreased biomarkers with prednisolone. Comparison of published human corticosteroid-responsive biomarkers to our mdx data showed 14% (3/22) concordance between mouse and human. Rituximab showed fewer drug-associated biomarkers, with the most significant being human IgG. On the other hand, BAIBA treatment (high and low dose) showed a drug-associated increase in 40 serum proteins and decreased 5 serum proteins. Our results suggest that a biomarker approach could be employed for assessing drug combinations in both mouse and human studies.
The contradiction between channel estimation and PAPR performance in cyclic shift PTS (2012)

Partial transmit sequence (PTS) scheme is one of the most popular peak-to-average power ratio (PAPR) reduction schemes for orthogonal frequency division multiplexing (OFDM) systems. In term of PAPR performance, the cyclic shift on time-domain PTS is better than conventional PTS (C-PTS), and the receiver can detect the phase rotations without using side information (SI). But, In order to detect the phase rotation factors the receiver must obtain channel response before detecting. In this paper, we discuss the contradiction between channel estimation and PAPR performance in cyclic shift PTS method. Simulation shows that it is difficult to have both good PAPR and bit error rate (BER) performance while using pilots to estimate channel response in cyclic shift PTS method.
Nitrogen Glycosylation Reactions Involving Pyrimidine and Purine Nucleoside Bases with Furanoside Sugars (1995)

Different approaches for the synthesis of nucleoside analogs (potential HIV inhibitors) are described. Starting from a suitably substituted furanose ring, it is demonstrated that a high facial stereocontrol of the glycosylation reaction can be effected. Different reaction conditions including Lewis acid promoted, SN2 displacement and some enzymatic methodologies for the stereoselective synthesis of these compounds are reviewed.
Secondary axis induction by heterospecific organizers in zebrafish (1996)

To investigate the inductive activities of the vertebrate organizer, we transplanted the chicken organizer (Hensen's node) into zebrafish gastrula and analyzed resulting secondary axes. Grafted Hensen's node did not differentiate or participate in the secondary axis. It also did not induce a secondary notochord or expression of the genes normally expressed by the fish organizer including no tail, axial, goosecoid. Nevertheless, it recruited fish cells to organize a variety of tissues: the dorsal portion of the central nervous system including Rohon-Beard sensory neurons, otic vesicles, dorsal pigment stripe, dorsal fin, somites, heart, and pronephric ducts. Enlarged neural plate induced by the organizer was shown by the expression pattern of dlx3 and msxB genes, which demarcates the early presumptive neural tissue. In addition, Hensen's node of an earlier stage chicken embryo displayed differential movement in zebrafish from that of a later stage. This might reflect unknown differences in properties between the organizer at two different developmental stages related to its normal organizer activity. To create a model system to study the molecular mechanisms of the organizer, we next transplanted genetically modified mouse cells into zebrafish embryos. We found that Wnt3A-transfected NIH3T3 cells are much more potent in inducing a secondary axis than NIH3T3 cells alone. These results suggest that formation of a variety of tissues are controlled by signalling from the organizer itself with no requirement of participation of the organizer-derived tissues. Additionally, the activities of the organizer may involve a function of Wnt-family genes.
Measurement of central corneal thickness and pre-corneal tear film thickness of rabbits using the Scheimpflug system. (2013)

GSA can be used to measure CCT and analyze central tear film thickness of rabbits with the help of fluorescein.
ChemInform Abstract: Guanidination of a Peptide Side Chain Amino Group on a Solid Support. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Site-directed RNA editing: recent advances and open challenges (2021)

RNA editing by cytosine and adenosine deaminases changes the identity of the edited bases. While cytosines are converted to uracils, adenines are converted to inosines. If coding regions of mRNAs are affected, the coding potential of the RNA can be changed, depending on the codon affected. The recoding potential of nucleotide deaminases has recently gained attention for their ability to correct genetic mutations by either reverting the mutation itself or by manipulating processing steps such as RNA splicing. In contrast to CRISPR-based DNA-editing approaches, RNA editing events are transient in nature, therefore reducing the risk of long-lasting inadvertent side-effects. Moreover, some RNA-based therapeutics are already FDA approved and their use in targeting multiple cells or organs to restore genetic function has already been shown. In this review, we provide an overview on the current status and technical differences of site-directed RNA-editing approaches. We also discuss advantages and challenges of individual approaches.
Effects of E-selectin and P-selectin blockade on neutrophil sequestration in tissues and neutrophil oxidative burst in burned rats (1996)

Burn injury in rats results in accumulation of neutrophils in multiple tissues. Neutrophil deposition in the lungs and liver is blocked by administration of the E/P-selectin blocking antibody, CY-1747. Since sequestration of metabolically active neutrophils may induce tissue injury, therapies that block postburn leukosequestration may improve clinical outcomes by limiting remote tissue injury.