gebhart/patrepeval huggingface dataset:
Using NMRView to Visualize and Analyze the NMR Spectra of Macromolecules (2004)

Nuclear magnetic resonance (NMR) experiments on macromolecules can generate a tremendous amount of data that must be analyzed and correlated to generate conclusions about the structure and dynamics of the molecular system. NMRView is a computer program that is designed to be useful in visualizing and analyzing these data. NMRView works with various types of NMR datasets and can have multiple datasets and display windows opened simultaneously. Virtually all actions of the program can be controlled through the Tcl scripting language, and new graphical user interface components can be added with the Tk toolkit. NMR spectral peaks can be analyzed and assigned. A suite of tools exists within NMRView for assigning the data from triple-resonance experiments.
Biology of Animal Lectins (1993)

INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237 Biological Functions of Carbohydrates . . . . . . . . . . . . . . . . . . . . . . . . . . . 237 Classification of Animal Lectins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 239 Ca2+ -DEPENDENT (C-TYPE) LECTINS . . . . . . . . . . . . . . . . . . . . . . . . . . . 239 Type II Endocytic Receptors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 239 Macrophage Mannose Receptor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 243 Selectin Cell Adhesion Molecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 245 Collectins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 245 Proteoglycans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 249 Isolated Carbohydrate-Recognition Domains . . . . . . . . . . . . . . . . . . . . . . . 251 Mechanism of Carbohydrate Recognition . . . . . . . . . . . . . . . . . . . . . . . . . 252 SOLUBLE �-GALACTOSIDE-BINDING (S-TYPEl LECT1NS . . . . . . . . . . . . . 255 Organization of S-Type Lectins 255 L-14 Lectins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 256 L-30 Lectins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257 L-36 Lectins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257 OTHER GROUPS OF ANIMAL LECTINS . . . . . . . . . . . . . . . . . . . . . . . . . . 258 SUMMARY AND PERSPECTIVE 258
Characterization of a novel zinc binding site of protein kinase C inhibitor‐1 (1991)

The zinc-binding properties of an endogenous protein inhibitor of protein kinase C was studied. Equilibrium gel penetration revealed that 1 mol of this protein binds 0.97 mol of zinc with a dissociation constant of 4.3 microM. The site of zinc-binding, MVVNEGSDGGQSVYHVHLHVLGGR, was identified by a multi-step process consisting of tryptic digestion, fragment isolation, transfer to nitrocellulose, and hybridization with 65ZnCl2. Binding of 65ZnCl2 to selected synthetic fragments further localized the site of interaction to the sequence QSVYHVHLHVL. This region contains 3 closely positioned histidine residues and represents a novel zinc-binding site.
Change Detection in a 3-d World (2007)

This paper examines the problem of detecting changes in a 3-d scene from a sequence of images, taken by cameras with arbitrary but known pose. No prior knowledge of the state of normal appearance and geometry of object surfaces is assumed, and abnormal changes can occur in any image of the sequence. To the authors' knowledge, this paper is the first to address the change detection problem in such a general framework. Existing change detection algorithms that exploit multiple image viewpoints typically can detect only motion changes or assume a planar world geometry which cannot cope effectively with appearance changes due to occlusion and un-modeled 3-d scene geometry (ego-motion parallax). The approach presented here can manage the complications of unknown and sometimes changing world surfaces by maintaining a 3-d voxel-based model, where probability distributions for surface occupancy and image appearance are stored in each voxel. The probability distributions at each voxel are continuously updated as new images are received. The key question of convergence of this joint estimation problem is answered by a formal proof based on realistic assumptions about the nature of real world scenes. A series of experiments are presented that evaluate change detection accuracy under laboratory-controlled conditions as well as aerial reconnaissance scenarios.-
The Characterization of Transcutaneous Stimulating Electrodes (1976)

A simple mathematical model of a transcutaneous stimulating electrode molded from conductive elastomer is used to predict the current density pattern produced by such electrodes. A general method has been developed to determine experimentally the current distribution produced by this class of electrodes. Preliminary experimental results are qualitatively in agreement with predictions made from the model. The experimental method for the determination of current spread yields a valid assessment of electrode performance independent of the accuracy of the mathematical model.
Z-Selective and Syndioselective Ring-Opening Metathesis Polymerization (ROMP) Initiated by Monoaryloxidepyrrolide (MAP) Catalysts (2010)

We report the Z-selective and syndioselective polymerization of 2,3-bis(trifluoromethyl)bicyclo[2.2.1]hepta-2,5-diene (NBDF6) and 3-methyl-3-phenylcyclopropene (MPCP) by monoaryloxide monopyrrolide imido alkylidene (MAP) catalysts of Mo. The mechanism of polymerization with syn-Mo(NAd)(CHCMe(2)Ph)(Pyr)(OHIPT) (1; Ad = 1-adamantyl, OHIPT = O-2,6-(2,4,6-i-Pr(3)C(6)H(2))(2)C(6)H(3)) as the initiator is proposed to consist of addition of monomer to the syn initiator to yield a syn first insertion product and propagation via syn insertion products. In contrast, the mechanism of polymerization with syn-Mo(NAr)(CHCMe(2)Ph)(Pyr)(OTPP) (4; Ar = 2,6-i-Pr(2)C(6)H(3), OTPP = 2,3,5,6-Ph(4)C(6)H) as the initiator at -78 °C consists of addition of monomer to the syn initiator to yield an anti first insertion product and propagation via anti insertion products. Polymerizations of NBDF6 and MPCP at room temperature initiated by 4 led to polymers without a regular structure. We propose that the syndiotacticity of cis polymers is the consequence of the required inversion at the metal center with each insertion of monomer, i.e., stereogenic metal control of the polymer structure. We also propose that the two mechanisms for forming cis,syndiotactic polymers arise as a consequence of the relative steric bulk of the imido and phenoxide ligands.
Novel sulphonamide derivatives for the treatment of cancer (2000)

The sulphonamides constitute an important class of therapeutic agents in current medicinal science. After the discovery by Gerhard Domagk, of sulphamidochrysoidine (prontosil) as the first antibiotic sulpha-drug an active metabolite of the drug, sulphanilamide, was further derivatised in order to find compounds exhibiting superior antibacterial activity or different pharmacological effects. Diversification of the sulphanilamide structure led to the serial development of improved antibiotics, insulin-releasing hypoglycaemic drugs, carbonic anhydrase- (CA) inhibitory diuretics, anti-hypertensive drugs etc. It is of particular interest that various structurally novel sulphonamide derivatives have recently been reported to show substantial anti-tumour activity in vitro and/or in vivo. Although they have a common chemical motif of an aromatic/heterocyclic sulphonamide, there are a variety of mechanisms for their anti-tumour action, such as disruption of microtubule assembly, cell cycle arrest in the G1 phase, functional suppression of the transcriptional activator NF-Y, angiogenesis inhibition and carbonic anhydrase inhibition. Furthermore, some of these compounds selected via elaborate preclinical screenings are currently being evaluated in clinical trials. This review summarises recent patents and related papers which have disclosed novel classes of sulphonamide derivatives for the treatment of cancer.
Treatment. Disease-modifying therapies. (1988)

Many patients with systemic lupus can be treated effectively with antimalarials and nonsteroidal anti-inflammatory drugs without ever having to take systemic corticosteroids at all or for any significant length of time. On the other hand, some patients with life-threatening disease, active major organ disease, or intolerable corticosteroid toxicities should be given immunosuppressive drugs, plasmapheresis, and/or other therapies in addition to corticosteroids early in their disease course, before permanent, end-organ damage occurs and before the predictable serious and debilitating toxicities of prolonged, daily high-dose corticosteroids develop. Just as lupus patients now routinely undergo detailed serologic testing, it is conceivable that, in the future, routine determination of human leukocyte antigen (HLA) haplotypes45 and T-cell subsets88a will help define, at disease onset, those patients who are destined to have severe disease. Perhaps this knowledge, combined with a better understanding of the exact mechanisms of action of these disease-modifying therapies, will allow a more rational approach to the treatment of SLE.
Multiple signal transduction pathways lead to extracellular ATP‐stimulated mitogenesis in mammalian cells: I. Involvement of protein kinase C–dependent and –independent pathways (1991)

We recently reported that extracellular ATP was mitogenic for Swiss 3T3, 3T6, and A431 cells (Huang et al.: Proc. Natl. Acad. Sci. USA, 86:7904-7908, 1989). Here we examined the possible involvement of activation of the protein kinase C (PKC) signal transduction pathway in the mechanism of action of extracellular ATP. A potent synergistic stimulation of DNA synthesis in quiescent cultures of 3T3 and 3T6 cells was observed when ATP was presented in combination with growth factors that activate PKC, such as bombesin, vasopressin, or tumor-promoting phorbol esters. This finding suggests that ATP and these mitogens do not act through a common mechanism. In contrast, ATP was unable to show synergism with phorbol esters in A431 cells. We discovered striking differences when we examined the kinetics of formation of diacylglycerol (DAG) stimulated by ATP among these cell lines. Thus, ATP stimulated a sustained biphasic increase of DAG in A431 cells, but only a rapid transient increase of DAG formation was observed in 3T3 and 3T6 cells. The breakdown of phosphatidylcholine was stimulated by ATP in A431 cells; however, a significantly reduced effect was displayed in 3T6 cells. Furthermore, we found that the diacylglycerol-kinase inhibitor, 1-monooleoylglycerol, greatly potentiated ATP-stimulated DNA synthesis in A431 cells. Finally, down-regulation of PKC by long-term exposure to phorbol dibutyrate (PDBu) prevented stimulation of DNA synthesis induced by bombesin, vasopressin, or phorbol esters in 3T3 or 3T6 cells, while it had no such effect on ATP-stimulated mitogenesis in the presence of insulin or epidermal growth factor. On the other hand, PDBu-mediated down-regulation of PKC partially inhibited [3H [thymidine incorporation stimulated by ATP in A431 cells. Taken together, we conclude that a protein kinase C-dependent pathway is partially involved in ATP-stimulated DNA synthesis in A431 cells, but a protein kinase C-independent pathway exists in 3T3 and 3T6 cells. Pertussis toxin (PTX) inhibited the sustained phase of DAG formation and the breakdown of phosphatidylcholine stimulated by ATP in A431 cells. This suggests involvement of a PTX-sensitive G protein.
Novel anti-inflammatory mechanisms ofN-Acetyl-Ser-Asp-Lys-Pro in hypertension-induced target organ damage (2008)

High blood pressure (HBP) is an important risk factor for cardiac, renal, and vascular dysfunction. Excess inflammation is the major pathogenic mechanism for HBP-induced target organ damage (TOD). N-acetyl-Ser-Asp-Lys-Pro (Ac-SDKP), a tetrapeptide specifically degraded by angiotensin converting enzyme (ACE), reduces inflammation, fibrosis, and TOD induced by HBP. Our hypothesis is that Ac-SDKP exerts its anti-inflammatory effects by inhibiting: 1) differentiation of bone marrow stem cells (BMSC) to macrophages, 2) activation and migration of macrophages, and 3) release of the proinflammatory cytokine TNF-α by activated macrophages. BMSC were freshly isolated and cultured in macrophage growth medium. Differentiation of murine BMSC to macrophages was analyzed by flow cytometry using F4/80 as a marker of macrophage maturation. Macrophage migration was measured in a modified Boyden chamber. TNF-α release by activated macrophages in culture was measured by ELISA. Myocardial macrophage activation in mice with ANG II-induced hypertension was studied by Western blotting of Mac-2 (galectin-3) protein. Interstitial collagen deposition was measured by picrosirius red staining. We found that Ac-SDKP (10 nM) reduced differentiation of cultured BMSC to mature macrophages by 24.5% [F4/80 positivity: 14.09 ± 1.06 mean fluorescent intensity for vehicle and 10.63 ± 0.35 for Ac-SDKP; P &lt; 0.05]. Ac-SDKP also decreased galectin-3 and macrophage colony-stimulating factor-dependent macrophage migration. In addition, Ac-SDKP decreased secretion of TNF-α by macrophages stimulated with bacterial LPS. In mice with ANG II-induced hypertension, Ac-SDKP reduced expression of galectin-3, a protein produced by infiltrating macrophages in the myocardium, and interstitial collagen deposition. In conclusion, this study demonstrates that part of the anti-inflammatory effect of Ac-SDKP is due to its direct effect on BMSC and macrophage, inhibiting their differentiation, activation, and cytokine release. These effects explain some of the anti-inflammatory and antifibrotic properties of Ac-SDKP in hypertension.
Synthesis, Properties, and Ambipolar Organic Field-Effect Transistor Performances of Symmetrically Cyanated Pentacene and Naphthacene as Air-Stable Acene Derivatives (2011)

5,12-Dicyanonaphthacene and 6,13-dicyanopentacene have been synthesized for the first time. The LUMO and HOMO levels are deepened as predicted and fabricated organic field-effect transistors (OFETs) showed ambipolar responses with carrier mobilities of 10(-3) cm(2)/V·s.
Animal models of tuberculosis (2009)

There is a wide range of animal models of tuberculosis; which is fortunate, given that there is a wide range of complex biological phenomena to model. Nonetheless, the inadequacy of animal models is a chronic grievance amongst researchers, often expressed in the conclusion that the mouse is not a good model of human tuberculosis. There clearly are major differences between experimental infection of mice and natural infection of humans, but this overarching dogma is inconducive to fruitful research.
Histamine alters E-cadherin cell adhesion to increase human airway epithelial permeability (2003)

During the immediate response to an inhaled allergen, there is an increase in the paracellular permeability of the airway epithelium.1 Histamine is an important agonist released during the immediate response to inhaled allergen. We hypothesized that histamine would increase human airway epithelial paracellular permeability and that it would do this by interrupting E-cadherin-based cell adhesion. Histamine, applied to the basolateral surface, increased the paracellular permeability of cultured human airway epithelia, and this effect of histamine was blocked by the histamine receptor antagonist promethazine. ECV304 cells express a histamine receptor, N-cadherin, and elements of the tight junction, including claudins, but they do not express E-cadherin. Histamine increased the paracellular permeability of ECV304 cells transfected with a vector and expressing E-cadherin but not ECV304 cells expressing lac-Z in the same vector. L cells do not express the histamine receptor, cadherins, or claudins. Histamine decreased adhesion of L cells expressing the human histamine receptor and E-cadherin to an E-cadherin-Fc fusion protein. Histamine did not alter the adhesion to the E-cadherin fusion protein of L cells expressing either the histamine receptor or E-cadherin alone. When applied to the apical surface, adenovirus poorly infects airway epithelial cells because its receptor, CAR, is restricted to the basolateral surface of the cells. When histamine was applied to the basolateral surface of airway epithelial cells, infection of the cells by adenovirus increased by approximately one log. This effect of histamine was also blocked by promethazine. Histamine increases airway paracellular permeability and increases susceptibility of airway epithelial cells to infection by adenovirus by interrupting E-cadherin adhesion.
A NOVEL DIAGNOSTIC TEST FOR PROSTATE CANCER EMERGES FROM THE DETERMINATION OF α-METHYLACYL-COENZYME A RACEMASE IN PROSTATIC SECRETIONS (2004)

In this study the quantification of AMACR transcripts normalized to PSA transcripts in prostatic secretions was shown to be predictive of CaP. Therefore, our novel approach using quantitative reverse transcriptase-PCR to detect the AMACR-to-PSA transcript ratio shows promise as a noninvasive screening test for CaP. Furthermore, early results demonstrate a trend toward excluding patients with clinically insignificant disease that may not yet require aggressive treatment due to a low cancer burden.
Analyses of selected safety endpoints in phase 1 and late-phase clinical trials of anti-PD-1 and PD-L1 inhibitors: prediction of immune-related toxicities (2017)

// Ricardo Costa 1 , Rubens B. Costa 1 , Sarah M. Talamantes 2 , Irene Helenoswki 3 , Benedito A. Carneiro 1 , Young Kwang Chae 1 , William J. Gradishar 1 , Razelle Kurzrock 4 and Francis J. Giles 1 1 Division of Hematology Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA 2 Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA 3 Northwestern University Department of Preventive Medicine, Chicago, Illinois, USA 4 Center for Personalized Cancer Therapy, Moores Cancer Center, University of California at San Diego, La Jolla, California, USA Correspondence to: Ricardo Costa, email: ricardo.costa@northwestern.edu Keywords: anti-PD-1 antibodies, toxicity, clinical trial, solid tumors Received: March 29, 2017&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Accepted: May 31, 2017&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Published: June 29, 2017 ABSTRACT Purpose: Anti-PD1 and PD-L1 antibodies are associated with immune-related adverse effects (irAEs). This analysis aims to assess the discrepancies between frequencies of irAEs observed in phase 1 trials with those seen in late-phase trials and to evolve the field of drug development. Methods: PubMed search was conducted for articles published until December of 2016. Trials needed to have at least one of the study arms consisting of nivolumab, pembrolizumab or atezolizumab monotherapy. Trials were matched based on compound used and similarity of populations. All toxicities were reported as frequencies and percentages. P -values to assess differences between matches and non-matches of phase 1 and late-phase trials and between early and late-phase trials themselves were obtained via Fisher&rsquo;s exact test. Odds ratios were obtained via logistic regression. Results: Our search yielded 15 late-phase and 10 matching phase 1 trials; n = 4823 and n = 1650, respectively. The most common AEs seen in phase 1 trials were also observed in late-phase trials except for phase 1 trials (median n = 118) with &lt; 118 patients ( P = 0.048). Rash, pruritus, and diarrhea were the most frequently irAEs reported. Only colitis was more frequent in late-phase studies ( P = 0.045). Conclusion: Toxicities of anti-PD-1 and PD-L1 observed in phase 1 trials and late-phase trials are similar. There is positive correlation between phase 1 trial sample size and concordance of toxicity frequencies seen in late-phase studies. In conclusion, current immunotherapy phase 1 trials are appropriate in assessing safety profile of anti-PD-1 and PD-L1 antibodies.
Effects of reactor severity on the gas-phase pyrolysis of cellulose- and kraft lignin-derived volatile matter (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEffects of reactor severity on the gas-phase pyrolysis of cellulose- and kraft lignin-derived volatile matterMichael Jerry Antal Jr.Cite this: Ind. Eng. Chem. Prod. Res. Dev. 1983, 22, 2, 366–375Publication Date (Print):June 1, 1983Publication History Published online1 May 2002Published inissue 1 June 1983https://pubs.acs.org/doi/10.1021/i300010a039https://doi.org/10.1021/i300010a039research-articleACS PublicationsRequest reuse permissionsArticle Views820Altmetric-Citations139LEARN 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 options Get e-Alerts
Automatic gender identification optimised for language independence (2002)

In this paper 63 automatic gender identification (AGI) systems based on the fusion of multiple knowledge sources using a linear classifier (LC) are tested on speakers of 11 languages present in the OGI speech corpus. It is found that training the LC with multiple languages can improve the accuracy of the AGI system.
Modulation of red blood cell population dynamics is a fundamental homeostatic response to disease (2015)

Increased red blood cell (RBC) volume variation (RDW) has recently been shown to predict a wide range of mortality and morbidity: death due to cardiovascular disease, cancer, infection, renal disease, and more; complications in heart failure and coronary artery disease, advanced stage and worse prognosis in many cancers, poor outcomes in autoimmune disease, and many more. The mechanisms by which all of these diseases lead to increased RDW are unknown. Here we use a semi-mechanistic mathematical model of in vivo RBC population dynamics to dissect the factors controlling RDW and show that elevated RDW results largely from a slight reduction in the in vivo rate of RBC turnover. RBCs become smaller as they age, and a slight reduction in the rate of RBC turnover allows smaller cells to continue circulating, expanding the low-volume tail of the RBC population's volume distribution, and thereby increasing RDW. Our results show that mildly extended RBC lifespan is a previously unrecognized homeostatic adaptation common to a very wide range of pathologic states, likely compensating for subtle reductions in erythropoietic output. A mathematical model-based estimate of the clearance rate may provide a novel early-warning biomarker for a wide range of morbidity and mortality.
Lipoic acid increases glucose uptake by skeletal muscles of obese‐diabetic ob/ob mice (2002)

The results suggest that alpha-lipoic acid can increase glucose uptake by a range of normal muscle types and improve the response to insulin by insulin-resistant skeletal muscles of ob/ob mice.