gebhart/patrepeval huggingface dataset:
TOUSLED Is a Nuclear Serine/Threonine Protein Kinase That Requires a Coiled-coil Region for Oligomerization and Catalytic Activity (1997)

The TOUSLED (TSL) gene is essential for the proper morphogenesis of leaves and flowers in Arabidopsis thaliana. Protein sequence analysis predicts TSL is composed of a carboxyl-terminal protein kinase catalytic domain and a large amino-terminal regulatory domain. TSL fusion proteins, expressed in and purified from yeast, were used to demonstrate TSL protein kinase activity in vitro. TSL trans-autophosphorylates on serine and threonine residues, and phosphorylates exogenous substrates. Using the yeast two-hybrid system, TSL was found to oligomerize via its NH2-terminal domain. A deletion series indicates that a region containing two alpha-helical segments predicted to participate in a coiled-coil structure is essential for oligomerization. TSL localizes to the nucleus in plant cells through an essential NH2-terminal nuclear localization signal; however, this signal is not necessary for protein kinase activity. Finally, deletion mutants demonstrate a strict correlation between catalytic activity and the ability to oligomerize, arguing that activation of the protein kinase requires interaction between TSL molecules.
Age-related changes in human dermal elastic fibres (1981)

Age-related changes in human dermal elastic fibres were studied by scanning (SEM) and transmission (TEM) electron microscopy. The SEM findings showed an increase in the complexity of shape and arrangement of the fibres including flattening and branching, an increase in the roughness of the surface, and a decrease in interfibrillar areas. The TEM findings showed a decrease in micro-fibrils and amorphous material, and an increase in electron dense inclusions followed by the appearance of vesicular structure.
Therapeutic Strategies for Triple-Negative Breast Cancer (2008)

Triple-negative breast cancer (TNBC) is a clinically relevant term referring to breast carcinomas that do not express the estrogen receptor, progesterone receptor, and human epidermal growth factor receptor type 2 and became operational after human epidermal growth factor receptor type 2 testing was introduced. This is a challenging disease to treat because of the absence of a specific target, but these tumors are sensitive to chemotherapy. An improved understanding of the biology of TNBC has led to evaluation of DNA-damaging chemotherapy drugs, specifically, platinum compounds, and several targeted agents, including poly(ADP-ribose) polymerase inhibitors, epidermal growth factor receptor inhibitors, angiogenesis inhibitors, microtubule inhibitors, Src inhibitors, checkpoint kinase I inhibitors, mammalian target of rapamycin inhibitors, androgen receptor blocker, tumor necrosis factor-related apoptosis-inducing ligand receptor agonists, and transforming growth factor-beta antagonists, that may lead to improved clinical outcomes. Ongoing clinical trials will further define the optimal chemotherapy regimen and most effective targeted therapeutic strategy for TNBC.
Receptor-Guided Alignment-Based Comparative 3D-QSAR Studies of Benzylidene Malonitrile Tyrphostins as EGFR and HER-2 Kinase Inhibitors (2003)

The overexpression and/or mutation of the epidermal growth factor receptor family of tyrosine kinases, namely EGFR and HER-2, have been implicated in poor prognosis of human solid tumors and are under investigation as molecular targets for cancer therapy. To gain insights into selectivity in the interaction of inhibitors at the ATP site of the two kinases, we have carried out docking, comparative molecular field analysis (CoMFA), and comparative molecular similarity analysis (CoMSIA) 3D-QSAR studies on 50 benzylidene malonitrile derivatives. Docking studies indicate different binding modes (A, B, C, D, and E) that are dependent on the R(1) substituent of the compounds. Binding modes A and B are favored by compounds having a hydroxyl substituent at R(1) whereas a methoxy substituent at R(1) results in compounds occupying binding modes, C, D, and E. The compounds preferred modes A, B, and C in the apo-enzyme whereas modes B, D, and E were preferred in the enzyme in complex with erlotinib. For 3D QSAR studies, based on the multiple binding modes obtained from the docking, four composite alignment strategies (I, II, III, IV) were employed and compared with alignment V, which is based on pairwise atom alignment of the common structural elements. Alignments I and II produced models with better predictive ability than those from alignments III and IV against an external test set. In the EGFR kinase results, alignments I and II produced comparable 3D-QSAR models with alignment II being slightly better than I, whereas in the HER-2 results, alignment I was better than alignment II in its predictive ability. It appears that differences in binding mode preferences at the ATP site might constitute a reason for the selectivity of the dihydroxy compounds as inhibitors of EGFR relative to HER-2. They are more likely to have multiple binding modes at the ATP site of EGFR, i.e., either modes A or B, than in the ATP site of HER-2 where they are possibly limited to only binding mode, A. Selectivity of the methoxy compounds on the other hand appears to depend on hydrogen bonding interactions involving the cyano group and residue 751 in the ATP site.
Characterization of a set of T7 RNA polymerase active site mutants. (1994)

We have evaluated the elongation rates, processivities, and abortive transcription characteristics of a set of T7 RNA polymerase mutants that map to the polymerase active site. The effects of these mutations on transcription are complex: they cause decreases in activity and processivity during both the processive and abortive phases of transcription and exhibit disproportionate decreases in activity and processivity on poly(dA).poly(dT) or poly(dT) versus poly(dG).poly(dC) templates. They also exhibit an increase in the proportion of slippage dependent poly(G) transcript synthesis during the initial stages of transcription. It is shown that these multiple, distinct effects on transcription can be attributed to decreases in the mutant enzymes' phosphodiester bond formation rates. Estimates of the decreases in these rates are derived from the measured transcript elongation rates and processivities of the mutant enzymes.
The purple pigments produced by acetylation of 2-(2-oxoindolin-3-yl)-glyoxylates in the presence of pyridine (1977)

The reaction of 2-(2-oxoindolin-3-yl)glyoxylates with acetic anhydride in the presence of pyridine gives insoluble purple pigments in which two molecules of the indoline have condensed with one molecule of acetic anhydride and for which a spirocyclobutene structure (13a) is suggested. The mode of formation of the pigments is discussed.
Crystal Structure of Macrophage Migration Inhibitory Factor Complexed with (E)-2-Fluoro-p-hydroxycinnamate at 1.8 Å Resolution:  Implications for Enzymatic Catalysis and Inhibition, (1999)

Macrophage migration inhibitory factor (MIF) exhibits dual activities. It acts as an immunoregulatory protein as well as a phenylpyruvate tautomerase. To understand better the relationship between these two activities and to elucidate the structural basis for the enzymatic activity, a crystal structure of a complex between murine MIF and (E)-2-fluoro-p-hydroxycinnamate, a competitive inhibitor of the tautomerase activity, has been determined to 1.8 A resolution. The structure is nearly superimposable on that of the free protein indicating that the presence of the inhibitor does not result in any major structural changes. The inhibitor also confirms the location of the active site in a hydrophobic cavity containing the amino-terminal proline. Within this cavity, the inhibitor interacts with residues from adjacent subunits. At the back of the cavity, the side-chain carbonyl oxygen of Asn-97' interacts with the phenolic hydroxyl group of the inhibitor while at the mouth of the cavity the ammonium group of Lys-32 interacts with a carboxylate oxygen. The other carboxylate oxygen of the inhibitor interacts with Pro-1. The hydroxyl group of Tyr-95' interacts weakly with the fluoro group on the inhibitor. The hydrophobic side chains of five active-site residues (Met-2, Ile-64, Met-101, Val-106, and Phe-113) and the phenyl moiety of Tyr-95' are responsible for the binding of the phenyl group. Further insight into the enzymatic activity of MIF was obtained by carrying out kinetic studies using the enol isomers of phenylpyruvate and (p-hydroxyphenyl)pyruvate. The results demonstrate that MIF processes the enol isomers more efficiently than the keto isomers primarily because of a decrease in Km. On the basis of these results, a mechanism is proposed for the MIF-catalyzed tautomerization reaction.
High-dose rituximab therapy in chronic lymphocytic leukemia. (2000)

Rituximab (Rituxan; Genentech, Inc, South San Francisco, CA and IDEC Pharmaceutical Corporation, San Diego, CA) is a chimeric monoclonal antibody that targets mature B cells in most lymphoid B-cell malignancies. Rituximab is approved by the US Food and Drug Administration for therapy for recurrent B-cell lymphoma. In initial clinical trials the activity in small lymphocytic lymphoma, the counterpart of chronic lymphocytic leukemia (CLL), was less than 20%. In an attempt to increase the level of rituximab activity in CLL, we conducted a phase I dose-escalation study to overcome both the lower CD20 antigen density on CLL cells compared with lymphoma cells and the shorter half-life of rituximab in small lymphocytic lymphoma. Cohorts of patients were treated with escalated doses on weeks 2, 3, and 4 after an initial rituximab dose of 375 mg/m2 on day 1. The maximum dose of rituximab evaluated was 2,250 mg/m2. There is clear evidence of a dose-response relationship. Severe toxicity (grades 3 and 4) noted following the first dose of therapy in variant forms of CLL, namely mantle cell lymphoma and prolymphocytic leukemia, was uncommon in typical CLL. No unusual toxicity was noted at higher doses. Further exploration of the dosing schedule of rituximab in CLL and development of combination therapies is necessary. This agent shows promise for interaction in combined chemoimmunotherapy strategies for front-line and relapsed patients with CLL.
Pretargeted radioimmunotherapy of mesothelin-expressing cancer using a tetravalent single-chain Fv-streptavidin fusion protein. (2005)

SS1scFvSA localized in the mesothelin-expressing tumor, resulting in a high accumulation of radiolabeled DOTA-biotin. The specific activity of DOTA-biotin had a significant effect on its tumor uptake. Therapeutic tumor doses were obtained without dose-limiting toxicity.
Clinical hypothermia temperatures increase complement activation and cell destruction via the classical pathway (2014)

In summary, therapeutic hypothermia temperatures increased antibody-initiated complement activation and eukaryotic cell destruction suggesting that the benefits of therapeutic hypothermia may be mediated via other mechanisms. Antibody-initiated complement activation has been shown to contribute to ischemia-reperfusion injury in several animal models, suggesting that for diseases with this mechanism hypothermia-enhanced complement activation may partially attenuate the benefits of therapeutic hypothermia.
Transforming growth factor-β inhibition of epithelial cell proliferation linked to the expression of a 53-kDa membrane receptor (1989)

Cells whose proliferation is blocked by transforming growth factor-beta (TGF-beta) express three distinct surface glycoproteins of 53, 73, and 300 kDa that bind TGF-beta with high affinity, but whose function is unknown. We have isolated two classes of chemically-induced Mv1Lu epithelial cell mutants resistant to growth inhibition by TGF-beta. Class R mutants have selectively lost expression of the 53-kDa (type I) TGF-beta-binding protein. They have also lost the ability to respond to TGF-beta with elevated fibronectin expression and cell flattening. Class S mutants bind normally but do not respond to TGF-beta. TGF-beta-resistant mutants retain a contact inhibited, nontransformed phenotype. The properties of S mutants suggest that they are defective in the TGF-beta signal transduction mechanism, while the results with R mutants identify the type I TGF-beta-binding protein as the receptor involved in mediating TGF-beta actions on cell adhesion and proliferation.
Serum proteome profiling detects myelodysplastic syndromes and identifies CXC chemokine ligands 4 and 7 as markers for advanced disease (2007)

Myelodysplastic syndromes (MDS) are among the most frequent hematologic malignancies. Patients have a short survival and often progress to acute myeloid leukemia. The diagnosis of MDS can be difficult; there is a paucity of molecular markers, and the pathophysiology is largely unknown. Therefore, we conducted a multicenter study investigating whether serum proteome profiling may serve as a noninvasive platform to discover novel molecular markers for MDS. We generated serum proteome profiles from 218 individuals by MS and identified a profile that distinguishes MDS from non-MDS cytopenias in a learning sample set. This profile was validated by testing its ability to predict MDS in a first independent validation set and a second, prospectively collected, independent validation set run 5 months apart. Accuracy was 80.5% in the first and 79.0% in the second validation set. Peptide mass fingerprinting and quadrupole TOF MS identified two differential proteins: CXC chemokine ligands 4 (CXCL4) and 7 (CXCL7), both of which had significantly decreased serum levels in MDS, as confirmed with independent antibody assays. Western blot analyses of platelet lysates for these two platelet-derived molecules revealed a lack of CXCL4 and CXCL7 in MDS. Subtype analyses revealed that these two proteins have decreased serum levels in advanced MDS, suggesting the possibility of a concerted disturbance of transcription or translation of these chemokines in advanced MDS.
Misfit Strain Relaxation by Stacking Fault Generation in InGaN Quantum Wells Grown onm-Plane GaN (2009)

InGaN quantum wells, grown on non-polar m-plane GaN and emitting light at 560 nm, experience lattice mismatch strain relaxation by the generation of stacking faults. Each stacking fault terminates a basal plane from the substrate side, generating misfit dislocations that have a Burgers vector with a 1/2[0001] component. The structural and optical properties of such thin film structures are reported.
An improved Western blotting technique effectively reduces background (2002)

We have developed a simple method to dramatically improve Western blotting by use of water washing as well as altered buffer conditions. Our improved protocol reduces the cost and labor of Western blotting by shortening the washing time and uses less buffer and other reagents. This procedure does not significantly change existing protocols of Western blotting analysis; it simply contains a few modifications to the washing step and buffer conditions. Our improved technique may therefore have broad applications in various experimental conditions.
Therapeutic effects of histone deacetylase inhibitors in a murine asthma model (2016)

The results suggested that treatment with HDAC inhibitors can reduce airway inflammation, airway remodeling, and airway hyperresponsiveness in chronic allergic airway disease in mice.
Is “Middle-Schoolness” an Indicator of Excellence? (1989)

Realizing both the importance of ex cellence and the distinctiveness of level programs, the authors sought to determine if the way a school is organized for instruction and student life contributes to excellence. Believing that there might be a relationship between middle schoolness (the degree to which a school adheres to the school concept) and excellence, a national survey was con ducted. The purpose of the survey was to determine if there was indeed a difference in the degree of middle-schoolness be tween schools cited as excellent and a ran dom group of level schools. Sub stantial differences were found between the
Effect of Platelet-Associated Virus on Assays of HIV-1 in Plasma (1993)

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Pathological Changes Induced in Cerebrocortical Neurons by Phencyclidine and Related Drugs (1989)

Phencyclidine (PCP), a dissociative anesthetic and widely abused psychotomimetic drug, and MK-801, a potent PCP receptor ligand, have neuroprotective properties stemming from their ability to antagonize the excitotoxic actions of endogenous excitatory amino acids such as glutamate and aspartate. There is growing interest in the potential application of these compounds in the treatment of neurological disorders. However, there is an apparent neurotoxic effect of PCP and related agents (MK-801, tiletamine, and ketamine), which has heretofore been overlooked: these drugs induce acute pathomorphological changes in specific populations of brain neurons when administered subcutaneously to adult rats in relatively low doses. These findings raise new questions regarding the safety of these agents in the clinical management of neurodegenerative diseases and reinforce concerns about the potential risks associated with illicit use of PCP.
INFLAMMATION AND ATHEROSCLEROSIS (2006)

Atherosclerosis, the cause of myocardial infarction, stroke, and ischemic gangrene, is an inflammatory disease. The atherosclerotic process is initiated when cholesterol-containing low-density lipoproteins accumulate in the intima and activate the endothelium. Leukocyte adhesion molecules and chemokines promote recruitment of monocytes and T cells. Monocytes differentiate into macrophages and upregulate pattern recognition receptors, including scavenger receptors and toll-like receptors. Scavenger receptors mediate lipoprotein internalization, which leads to foam-cell formation. Toll-like receptors transmit activating signals that lead to the release of cytokines, proteases, and vasoactive molecules. T cells in lesions recognize local antigens and mount T helper-1 responses with secretion of pro-inflammatory cytokines that contribute to local inflammation and growth of the plaque. Intensified inflammatory activation may lead to local proteolysis, plaque rupture, and thrombus formation, which causes ischemia and infarction. Inflammatory markers are already used to monitor the disease process and anti-inflammatory therapy may be useful to control disease activity.
Differences in Dihydrotetrabenazine Isomer Concentrations Following Administration of Tetrabenazine and Valbenazine (2017)

Based on relative abundance and potency, [+]-β-HTBZ appears to be the primary contributor to VMAT2 inhibition by TBZ, a finding in contrast with the generally held assertion that [+]-α-HTBZ is the major contributor. [-]-α-HTBZ, the other abundant TBZ metabolite, has much lower VMAT2 inhibitory potency than [+]-β-HTBZ, but increased affinity for other CNS targets, which may contribute to off-target effects of TBZ. In contrast, pharmacological activity for VBZ is derived primarily from [+]-α-HTBZ. Individual HTBZ isomer concentrations provide a more clinically relevant endpoint for assessing on- and off-target effects of TBZ than total isomer concentrations.
Cyclin Dependent Kinase 9 Inhibitors for Cancer Therapy (2016)

Cyclin dependent kinase (CDK) inhibitors have been the topic of intense research for nearly 2 decades due to their widely varied and critical functions within the cell. Recently CDK9 has emerged as a druggable target for the development of cancer therapeutics. CDK9 plays a crucial role in transcription regulation; specifically, CDK9 mediated transcriptional regulation of short-lived antiapoptotic proteins is critical for the survival of transformed cells. Focused chemical libraries based on a plethora of scaffolds have resulted in mixed success with regard to the development of selective CDK9 inhibitors. Here we review the regulation of CDK9, its cellular functions, and common core structures used to target CDK9, along with their selectivity profile and efficacy in vitro and in vivo.
Outcomes and Prognostic Factors in Recurrent Glioma Patients Enrolled Onto Phase II Clinical Trials (1999)

Histology is a dominant factor in determining outcome in patients with recurrent glioma enrolled onto phase II trials. Future trials should be designed with separate histology strata.
Reactivity of common functional groups with urethanes: Models for reactive compatibilization of thermoplastic polyurethane blends (2002)

Abstract Two model urethane compounds, dibutyl 4,4′‐methylenebis(phenyl carbamate) (BMB) and dioctyl 4,4′‐methylenebis(phenyl carbamate) (OMO) were prepared by capping 4,4′‐methylenebis(phenyl isocyanate) with n ‐butanol and n ‐octanol, respectively. The reactions of the two model urethane compounds with several small monofunctional compounds as well as two model poly(ethylene glycols) were carried out with neat mixtures at elevated temperatures. The ranking of reactivity of the functional groups with the urethanes was determined as follows—primary amine &gt; secondary amine ≫ hydroxyl ∼ acid ∼ anhydride ≫ epoxide. Nuclear magnetic resonance spectroscopy (NMR) was used for the quantitative analysis. Fourier transform infrared spectroscopy was used to complement the NMR analysis. Conversions of carbamate in each reaction were monitored over time at constant temperature (200 °C). The reactions between OMO and primary amine were conducted at 170, 180, 190, and 200 °C and best described with a second‐order bimolecular reaction model. The rate constant was estimated to be 1.8 × 10 −3 L · mol −1 · s −1 and activation energy 115 kJ · mol −1 . © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 2310–2328, 2002
Interference effects in femtosecond spectroscopy (2002)

This article aims to provide a short synopsis of interference effects connected with ultrafast laser pulses, where 'ultrafast' is defined as ca. 100 fs or faster. The discussion is divided into three parts: the first shows how interference between waves is responsible for generation of light pulses in the femtosecond and attosecond time domains; the second describes characterization of ultrafast pulses by different interferometric techniques, including diffraction of femtosecond light by a double slit; and the final section discusses selected measurements of interference phenomena created and probed with femtosecond time resolution, with an emphasis on experiments in atomic physics. The article attempts to illustrate how wave-like interference is a unifying concept that pervades much of physics on a femtosecond time-scale.