gebhart/patrepeval huggingface dataset:
Synthesis of Muramyl Peptides Containing meso-Diaminopimelic Acid (2002)

Chain-extension of L-glutamate aldehyde 3 by means of the Wittig−Horner reaction furnished the desired C7 dicarboxylic acid derivative, which in turn, after C-C double bond hydrogenation and protecting group manipulation, afforded the 2,6-diaminopimelic acid derivatives (S,R)-9 and (S,S)-9, both with the desired orthogonal protecting group pattern. Synthesis of the muramic acid derivative 15 and attachment of an L-alanine residue furnished muramyl-L-alanine 18. The corresponding 1,6-anhydromuramic acid derivative 26 was obtained similarly. Treatment of these compounds with peptides 28−30 and with the 2,6-diaminopimelic acid containing di- and tripeptides 32a, 32b, and 35 gave the protected muramyl peptides 17, 37, 40, 42, 44, 46, and 49a and 49b, which, after deprotection, afforded the desired target molecules muramyl-L-alanine (38), muramyl-L-alanyl-D-glutamic acid (39), muramyl-L-alanyl-D-glutaminide (41), muramyl-L-alanyl-D-isoglutaminyl-L-lysine (43), muramyl-L-alanyl-D-isoglutaminyl-(2S,6R)-2,6-diaminopimelic acid (45), muramyl-L-alanylL-isoglutaminyl-(2S,6R)-2,6-diaminopimelinyl-D-alanine (47), 1,6-anhydromuramyl-L-alanyl-D-isoglutaminyl-(2S,6R)-2,6-diaminopimelic acid (50a), and 1,6-anhydromuramyl-L-alanyl-D-isoglutaminyl-(2S,6S)-2,6-diaminiopimelic acid (50b). (© Wiley-VCH Verlag GmbH, 69451 Weinheim, Germany, 2002)
Dissection of CR1, factor H, membrane cofactor protein, and factor B binding and functional sites in the third complement component (1996)

Previous studies have suggested that the residues 727-768 of human (Hu) C3 contain the binding sites for CR1, factor H, and factor B. Here, we have (1) characterized further some of the C3 structural requirements for its binding to CR1, H, and B, (2) investigated the functions associated with these C3-ligand interactions, and (3) studied the relationship of MCP-binding sites in C3 with those for CR1, H, and B. Hu C3 molecules in which residues 727-768 were deleted (designated C3delta727-768) or substituted with the corresponding segment of cobra venom factor, Xenopus, or trout C3 (chimeric C3s) were expressed in the baculovirus system and analyzed for their reactivity with C3-binding proteins. In contrast to wild-type iC3 which, in the presence of CR1, is cleaved by factor I to iC3b-a and C3c-a and C3dg, all chimeric C3s were cleaved only to iC3b-a. In addition, the cleavage of deleted (C3delta727-768) iC3 to iC3b-a by factor I in the presence of CR1 was significantly reduced, whereas it remained unaltered in the presence of MCP. Cleavage of iC3 to iC3b-a by factor I and H was similar in all expressed C3s except C3delta727-768, whose cleavage was significantly reduced. All of the expressed molecules except C3delta727-768 were capable of forming the fluid-phase alternative pathway C3 convertase, and all reacted with properdin. These results suggest that during cleavage of iC3 by factor I and CR1, or H, CR1 and H bind to at least two sites on C3 and that the MCP binding site(s) on C3b are different from those for CR1. They also indicate that some or all of the C3 residues that are directly involved in, or contribute to, the structure of one of the CR1 and H binding sites are located within residues 727-768. These studies also demonstrate that, although this segment of C3 may be involved in C3-factor B interaction, other residues in addition to 736EE (previously implicated in B binding) must also contribute significantly to this interaction.
Can A Denaturant Stabilize DNA? Pyridine Reverses DNA Denaturation in Acidic pH (2015)

The stability of DNA is highly dependent on the properties of the surrounding solvent, such as ionic strength, pH, and the presence of denaturants and osmolytes. Addition of pyridine is known to unfold DNA by replacing π-π stacking interactions between bases, stabilizing conformations in which the nucleotides are solvent exposed. We show here experimental and theoretical evidences that pyridine can change its role and in fact stabilize the DNA under acidic conditions. NMR spectroscopy and MD simulations demonstrate that the reversal in the denaturing role of pyridine is specific, and is related to its character as pseudo groove binder. The present study sheds light on the nature of DNA stability and on the relationship between DNA and solvent, with clear biotechnological implications.
Performance and capacity of distributed dynamic channel assignment and power control in shadow fading (2002)

The author presents a comprehensive study of dynamic channel assignment and power control (DCA/PC) algorithms which introduces a simple method to estimate the potential capacity of any such system. It is indicated that interference adaptation is the dominant source of gain in typical settings, compared to trunking efficiency. Simulation studies show that distributed DCA/PC algorithms can achieve much of the potential gain (capacity gains of 2-4 are observed where the potential gain is estimated to be about 5).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Moessbauer studies on oxo-bridged iron(III) porphines (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMoessbauer studies on oxo-bridged iron(III) porphinesManuel A. Torrens, Darel K. Straub, and L. M. EpsteinCite this: J. Am. Chem. Soc. 1972, 94, 12, 4160–4162Publication Date (Print):June 1, 1972Publication History Published online1 May 2002Published inissue 1 June 1972https://pubs.acs.org/doi/10.1021/ja00767a018https://doi.org/10.1021/ja00767a018research-articleACS PublicationsRequest reuse permissionsArticle Views316Altmetric-Citations44LEARN 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
Expanding Roles for CD4 T Cells and Their Subpopulations in Tumor Immunity and Therapy (2013)

The importance of CD4 T cells in orchestrating the immune system and their role in inducing effective T cell-mediated therapies for the treatment of patients with select established malignancies are undisputable. Through a complex and balanced array of direct and indirect mechanisms of cellular activation and regulation, this functionally diverse family of lymphocytes can potentially promote tumor eradication, long-term tumor immunity, and aid in establishing and/or rebalancing immune cell homeostasis through interaction with other immune cell populations within the highly dynamic tumor environment. However, recent studies have uncovered additional functions and roles for CD4 T cells, some of which are independent of other lymphocytes, that can not only influence and contribute to tumor immunity but paradoxically promote tumor growth and progression. Here, we review the recent advances in our understanding of the various CD4 T cell lineages and their signature cytokines in disease progression and/or regression. We discuss their direct and indirect mechanistic interplay among themselves and with other responding cells of the antitumor response, their potential roles and abilities for "plasticity" and memory cell generation within the hostile tumor environment, and their potentials in cancer treatment and immunotherapy.
Structural Dynamics with Parameter Uncertainties (1987)

The treatment of structural parameters as random variables has been the subject of structural dynamicists and designers for many years. Several problems have been involved during the last few decades and resulted in new theorems and interesting phenomena. This paper reviews a number of topics pertaining to structural dynamics with parameter uncertainties. These include direct problems such as random eigenvalues and random responses of discrete and continuous systems. The impact of these problems on related areas of interest such as sensitivity of structural performance to parameter variations, design optimization, and reliability analysis is also addressed. The paper includes the results of experimental investigations, the phenomenon of normal modes localization, and the effect of mistuning of turbomachinery blades on their flutter and forced response characteristics.
Development and Application of Fluorescence Polarization Assays in Drug Discovery (2003)

Fluorescence polarization technology has been used in basic research and commercial diagnostic assays for many decades, but has begun to be widely used in drug discovery only in the past six years. Originally, FP assays for drug discovery were developed for single-tube analytical instruments, but the technology was rapidly converted to high-throughput screening assays when commercial plate readers with equivalent sensitivity became available. This review will discuss fluorescence polarization assays in current use in drug discovery research as well as those in development that will likely be used in the near future. These assays include targets such as kinases, phosphatases, proteases, G-protein coupled receptors, and nuclear receptors.
Potential Role of WAF1/Cip1/p21 as a Mediator of TGF-β Cytoinhibitory Effect (1995)

Transforming growth factor-beta (TGF-beta) inhibits cell cycle progression of many types of human cells by arresting them in the G1 phase of the cell cycle. The arrest is mediated through interactions of various cyclin-dependent protein kinases (CDKs) and their inhibitors. We demonstrate that treatment with TGF-beta induces increased levels of WAF1/Cip1/p21, a potent inhibitor of various cyclin-CDK kinase activities, in two colon cancer cell lines (LS1034 and LS513), which are sensitive to TGF-beta-induced growth arrest. The induction in at least one of these cell lines (LS1034,p53-) is p53-independent. No WAF1 induction was observed after TGF-beta treatment in a third cell line (HT-29), which is completely insensitive to the cytoinhibitory effect of TGF-beta. In both LS513 and LS1034, WAF1 induction correlated with reduced cyclin E-associated kinase activity in vitro and suppression of the retinoblastoma susceptibility gene (Rb) protein phosphorylation in vivo. In addition, WAF1 was physically associated with cyclin E in the two sensitive cell lines. These results suggest that WAF1/Cip1/p21 is a mediator of cellular sensitivity to TGF-beta.
Infrared Thermography as a Measure of Emotion Response (2014)

An ongoing challenge facing emotion researchers is finding appropriate measurement tools. Many of our theories focus on emotion in the context of dynamic interaction, yet many of our most relied-upon measures either interrupt or alter interaction. New research suggests that infrared thermography may be useful as a nonintrusive way to measure emotion. Here we discuss the viability of thermography for studying emotion response and advancing emotion theory.
Isolation of Endophytic Streptomyces Strains from Surface-Sterilized Roots (1992)

When the roots of 28 plant species were surface sterilized and incubated on agar medium, endophytic actinomycetes in the root cortex were observed by direct microscopic observation and pure culture techniques.
Degradation of BACE by the ubiquitin‐proteasome pathway (2004)

The amyloid beta protein (Abeta) is derived from beta-amyloid precursor protein (APP). Cleavage of APP by beta-secretase generates a C-terminal fragment (APPCTFbeta or C99), which is subsequently cleaved by gamma-secretase to produce Abeta. BACE (or BACE1), the major beta-secretase involved in cleaving APP, has been identified as a Type 1 membrane-associated aspartyl protease. In this study, we found that treatment with proteasome inhibitors resulted in an increase in APP C99 levels, suggesting that APP processing at the beta-secretase site may be affected by the ubiquitin-proteasome pathway. To investigate whether the degradation of BACE is mediated by the proteasome pathway, cells stably transfected with BACE were treated with lactacystin. We found that BACE protein degradation was inhibited by lactacystin in a time- and dose-dependent manner. Non-proteasome protease inhibitors had no effect on BACE degradation. BACE protein is ubiquitinated. Furthermore, lactacystin increased APP C99 production and Abeta generation. Our data demonstrate that the degradation of BACE proteins and APP processing are regulated by the ubiquitin-proteasome pathway.
The Influence of Hyperglycemia on Neurological Outcome in Patients with Severe Head Injury (2000)

Early hyperglycemia is a frequent component of the stress response to head injury, a significant indicator of its severity, and a reliable predictor of outcome.
Smoking and drinking can induce p15 methylation in the upper aerodigestive tract of healthy individuals and patients with head and neck squamous cell carcinoma (2004)

The results suggest that p15 gene methylation can be induced by chronic smoking and drinking and may play a role in the very early stages of carcinogenesis in HNSCC.
Detection and monitoring of hidden fatigue crack growth using a built-in piezoelectric sensor/actuator network: I. Diagnostics (2004)

A piezoelectric based built-in diagnostic technique has been developed for monitoring fatigue crack growth in metallic structures. The technique uses diagnostic signals, generated from nearby piezoelectric actuators built into the structures, to detect crack growth. It consists of three major components: diagnostic signal generation, signal processing and damage interpretation. In diagnostic signal generation, appropriate ultrasonic guided Lamb waves were selected for actuators to maximize receiving sensor measurements. In signal processing, methods were developed to select an individual mode for damage detection and maximize signal to noise ratio in recorded sensor signals. Finally, in damage interpretation, a physics based damage index was developed relating sensor measurements to crack growth size. Fatigue tests were performed on laboratory coupons with a notch to verify the proposed technique. The damage index measured from built-in piezoceramics on the coupons showed a good correlation with the actual fatigue crack growth obtained from visual inspection. Furthermore, parametric studies were also performed to characterize the sensitivity of sensor/actuator location for the proposed technique.
<title>Adaptive position estimation for an automated guided vehicle</title> (1993)

In a mobile robotic system, complexities in positioning arise due to the motion. An adaptive position estimation scheme has been developed for an automated guide vehicle (AGV) to overcome these complexities. The scheme's purpose is to minimize the position error--the difference between the estimated position and the actual position. The method to achieve this is to adapt the system model by incorporating a parameter vector and using a maximum likelihood algorithm to estimate the parameters after an accurate position determination is made. A simulation of the vehicle's guidance system was developed and the estimator tested on an oval-shaped path. Upon injecting biases into the system, initial position errors were 10 centimeters or more. After the estimator converged, the maximum final errors were on the order of 1 to 2 centimeters (prior to measurement update). After each measurement update, after the estimator had converged, errors were on the order of 1 to 2 millimeters.
Development of Load Prediction Equations of Office Buildings (2002)

The objective of this study is to evaluate the design parameters and to develop the cooling and heating load prediction equations of office buildings. The building load calculation simulation was carried out using the DOE-2.1E program. The results of the simulation were used as data for multiple regression analysis which could develop the load prediction equations.
Structural Details on the Binding of Antihypertensive Drugs Captopril and Enalaprilat to Human Testicular Angiotensin I-Converting Enzyme , (2004)

Angiotensin converting enzyme (ACE) plays a critical role in the circulating or endocrine renin-angiotensin system (RAS) as well as the local regulation that exists in tissues such as the myocardium and skeletal muscle. Here we report the high-resolution crystal structures of testis ACE (tACE) in complex with the first successfully designed ACE inhibitor captopril and enalaprilat, the Phe-Ala-Pro analogue. We have compared these structures with the recently reported structure of a tACE-lisinopril complex [Natesh et al. (2003) Nature 421, 551-554]. The analyses reveal that all three inhibitors make direct interactions with the catalytic Zn(2+) ion at the active site of the enzyme: the thiol group of captopril and the carboxylate group of enalaprilat and lisinopril. Subtle differences are also observed at other regions of the binding pocket. These are compared with N-domain models and discussed with reference to published biochemical data. The chloride coordination geometries of the three structures are discussed and compared with other ACE analogues. It is anticipated that the molecular details provided by these structures will be used to improve the binding and/or the design of new, more potent domain-specific inhibitors of ACE that could serve as new generation antihypertensive drugs.
Gene Expression Platform for Synthetic Biology in the Human Pathogen Streptococcus pneumoniae (2014)

The human pathogen Streptococcus pneumoniae (pneumococcus) is a bacterium that owes its success to complex gene expression regulation patterns on both the cellular and the population level. Expression of virulence factors enables a mostly hazard-free presence of the commensal, in balance with the host and niche competitors. Under specific circumstances, changes in this expression can result in a more aggressive behavior and the reversion to the invasive form as pathogen. These triggering conditions are very difficult to study due to the fact that environmental cues are often unknown or barely possible to simulate outside the host (in vitro). An alternative way of investigating expression patterns is found in synthetic biology approaches of reconstructing regulatory networks that mimic an observed behavior with orthogonal components. Here, we created a genetic platform suitable for synthetic biology approaches in S. pneumoniae and characterized a set of standardized promoters and reporters. We show that our system allows for fast and easy cloning with the BglBrick system and that reliable and robust gene expression after integration into the S. pneumoniae genome is achieved. In addition, the cloning system was extended to allow for direct linker-based assembly of ribosome binding sites, peptide tags, and fusion proteins, and we called this new generally applicable standard "BglFusion". The gene expression platform and the methods described in this study pave the way for employing synthetic biology approaches in S. pneumoniae.
Pathway Engineering in Secondary Metabolite-Producing Actinomycetes (1994)

Actinomycetes represent the microbial group richest in production of variable secondary metabolites. These mostly bioactive molecules are the end products of complex multistep biosynthetic pathways. Recent progress in the molecular genetics and biochemistry of the biosynthetic capacities of actinomycetes enables first attempts to redesign these pathways in a directed fashion. However, in contrast to several examples of designed biochemical improvement of primary metabolic processes in microorganisms, none of the products or strains derived from pathway engineering in actinomycetes discussed herein have reached pilot or production scale. The main reasons for this slow progress are the complicated pathways themselves, their complex regulation during the actinomycete cell cycle, and their uniqueness, as most pathways and products are specific for a strain rather than for a given species or larger taxonomic group. However, the modular use of a minimum of very similar enzymes and their conversion of similar intermediates to form the building blocks for the production of a maximum of divergent end products gives hope for the future application of these genetic models for the redesign of complex pathways for modified or new natural products. Several strategies that can be followed to reach this aim are discussed, mainly for the variable 6-deoxyhexose metabolism as an ubiquitously applicable example.
Molecular Basis of T Cell Inactivation by CTLA-4 (1998)

CTLA-4, a negative regulator of T cell function, was found to associate with the T cell receptor (TCR) complex zeta chain in primary T cells. The association of TCRzeta with CTLA-4, reconstituted in 293 transfectants, was enhanced by p56(lck)-induced tyrosine phosphorylation. Coexpression of the CTLA-4-associated tyrosine phosphatase, SHP-2, resulted in dephosphorylation of TCRzeta bound to CTLA-4 and abolished the p56(lck)-inducible TCRzeta-CTLA-4 interaction. Thus, CTLA-4 inhibits TCR signal transduction by binding to TCRzeta and inhibiting tyrosine phosphorylation after T cell activation. These findings have broad implications for the negative regulation of T cell function and T cell tolerance.