gebhart/patrepeval huggingface dataset:
Molecular modeling of organic and biomolecular systems using BOSS and MCPRO (2005)

Abstract An overview is provided of the capabilities for the current versions of the BOSS and MCPRO programs for molecular modeling of organic and biomolecular systems. Recent applications are noted, particularly for QM/MM studies of organic and enzymatic reactions and for protein‐ligand binding. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1689–1700, 2005
Serial Communications Programming in Windows95 with API Functions (2000)

这篇论文介绍这些功能的用法。它介绍怎么与他们一起编程序在 Windows95 由连续 porst 执行在一台计算机和另外的数字设备之间的连续通讯的技术。在 C++ 程序语言写的这种技术的应用程序的相关样品代码也被给。这种技术成功地被使用从一个频率监视器收到收音机噪音的数据。
Biologics in the treatment of rheumatoid arthritis and ankylosing spondylitis. (2010)

There are clear differences in the clinical picture and in the pathogenesis between rheumatoid arthritis (RA) and ankylosing spondylitis (AS). Biologic agents targeting TNF-alpha are efficacious in both diseases, with some tendency to work even better in spondyloarthritides (SpA) on a clinical basis. However, anti-TNF therapy was shown to inhibit radiographic progression in RA but not in AS. This is probably due to the outstanding difference in pathogenesis: while in RA osteodestructive lesions such as erosions predominate, AS patients will rather develop osteoproliferative changes such as syndesmophytes. There is some evidence that anti-TNF agents may show longterm efficacy and acceptable safety profiles over 5-10 years. There are some differences between the agents.Whether the recent developments of targeted therapies in RA with agents such as rituximab, abatacept and tocilizumab will also work for AS is unknown at present.
Functional mapping of harpin HrpZ of Pseudomonas syringae reveals the sites responsible for protein oligomerization, lipid interactions and plant defence induction (2010)

Harpin HrpZ is one of the most abundant proteins secreted through the pathogenesis-associated type III secretion system of the plant pathogen Pseudomonas syringae. HrpZ shows membrane-binding and pore-forming activities in vitro, suggesting that it could be targeted to the host cell plasma membrane. We studied the native molecular forms of HrpZ and found that it forms dimers and higher order oligomers. Lipid binding by HrpZ was tested with 15 different membrane lipids, with HrpZ interacting only with phosphatidic acid. Pore formation by HrpZ in artificial lipid vesicles was found to be dependent on the presence of phosphatidic acid. In addition, HrpZ was able to form pores in vesicles prepared from Arabidopsis thaliana plasma membrane, providing evidence for the suggested target of HrpZ in the host. To map the functions associated with HrpZ, we constructed a comprehensive series of deletions in the hrpZ gene derived from P. syringae pv. phaseolicola, and studied the mutant proteins. We found that oligomerization is mainly mediated by a region near the C-terminus of the protein, and that the same region is also essential for membrane pore formation. Phosphatidic acid binding seems to be mediated by two regions separate in the primary structure. Tobacco, a nonhost plant, recognizes, as a defence elicitor, a 24-amino-acid HrpZ fragment which resides in the region indispensable for the oligomerization and pore formation functions of HrpZ.
Sensitization of the Trigeminovascular Pathway: Perspective and Implications to Migraine Pathophysiology (2012)

Migraine headache is commonly associated with signs of exaggerated intracranial and extracranial mechanical sensitivities. Patients exhibiting signs of intracranial hypersensitivity testify that their headache throbs and that mundane physical activities that increase intracranial pressure (such as bending over or coughing) intensify the pain. Patients exhibiting signs of extracranial hypersensitivity testify that during migraine their facial skin hurts in response to otherwise innocuous activities such as combing, shaving, letting water run over their face in the shower, or wearing glasses or earrings (termed here cephalic cutaneous allodynia). Such patients often testify that during migraine their bodily skin is hypersensitive and that wearing tight cloth, bracelets, rings, necklaces and socks or using a heavy blanket can be uncomfortable and/or painful (termed her extracephalic cutaneous allodynia). This review summarizes the evidence that support the view that activation of the trigeminovascular pathway contribute to the headache phase of a migraine attack, that the development of throbbing in the initial phase of migraine is mediated by sensitization of peripheral trigeminovascular neurons that innervate the meninges, that the development of cephalic allodynia is propelled by sensitization of second-order trigeminovascular neurons in the spinal trigeminal nucleus which receive converging sensory input from the meninges as well as from the scalp and facial skin, and that the development of extracephalic allodynia is mediated by sensitization of third-order trigeminovascular neurons in the posterior thalamic nuclei which receive converging sensory input from the meninges, facial and body skin.
A Study of the Active Using of the Solar Energy by Using a Porous Media of Kirkuk city (2006)

In this study, a solar collector that uses porous media has been designed and constructed as an absorbing and storing heat surface. The solar collector is inclined of ( ) with the horizon. Heat has been absorbed from the collector by forced convection of air. A theoretical and experimental study was made for testing the performance of the collector in continuous operating of an air blower( from a.m to p.m) The highest instantaneous efficiency of the collector was about ( ), while the highest different between air input temperature and air output temperature from solar collector was about( ).
The Role of Cell Surface Attachment and Proteolysis in the Insulin-Like Growth Factor (IGF)-Independent Effects of IGF-Binding Protein-3 on Apoptosis in Breast Epithelial Cells (1999)

We have recently reported that insulin-like growth factor (IGF)-binding protein-3 (IGFBP-3) can significantly increase ceramide-induced apoptosis in an Hs578T breast carcinoma cell line in an IGF-independent manner. It was observed in that study that IGFBP-3 added to the cultures was proteolytically modified, generating a specific pattern of fragmentation. We have also previously reported that almost all of the IGFBP-3 outside the circulation in extravascular fluids is in a fragmented form, apparently due to the activity of a cation-dependent serine protease. The aim of this study was to investigate the role of proteolysis in the IGFBP-3 enhancement of C2-induced apoptosis.
Three-dimensional digital microfluidic manipulation of droplets in oil medium (2015)

We here develop a three-dimensional DMF (3D DMF) platform with patterned electrodes submerged in an oil medium to provide fundamental solutions to the technical limitations of 2D DMF platforms and water-air systems. 3D droplet manipulation on patterned electrodes is demonstrated by programmably controlling electrical signals. We also demonstrate the formation of precipitates on the 3D DMF platform through the reaction of different chemical samples. A droplet containing precipitates, hanging on the top electrode, can be manipulated without adhesion of precipitates to the solid surface. This method could be a good alternative strategy to alleviate the existing problems of 2D DMF systems such as cross-contamination and solute adsorption. In addition, we ascertain the feasibility of temperature-controlled chemical reaction on the 3D DMF platform by introducing a simple heating process. To demonstrate applicability of the 3D DMF system to 3D biological process, we examine the 3D manipulation of droplets containing mouse fibroblasts in the 3D DMF platform. Finally, we show detachment of droplets wrapped by a flexible thin film by adopting the electro-elasto-capillarity (EEC). The employment of the EEC may offer a strong potential in the development of 3D DMF platforms for drug encapsulation and actuation of microelectromechanical devices.
Inhibition of DNA repair with aphidicolin enhances sensitivity of targets to tumor necrosis factor. (1993)

To test whether DNA injury contributes to TNF-induced cytotoxicity, we attempted to enhance DNA injury by inhibiting its repair and then assessing effects on cytotoxicity. DNA repair, assayed as unscheduled DNA synthesis, was first detected in TNF-sensitive targets by 2-3 h of incubation with TNF. Targets resistant to TNF cytotoxicity did not demonstrate significant repair replication. Repair preceded the detection of TNF-induced DNA injury, which was subsequently demonstrated by a double-stranded DNA fragmentation assay, sedimentation of DNA in neutral and alkaline sucrose gradients, and gel electrophoresis of extracted DNA. This suggested that early during exposure to TNF, DNA repair proceeds more rapidly than strand breakage. To inhibit repair, nontoxic concentrations of aphidicolin (inhibitor of DNA polymerase-alpha) and dideoxythymidine (inhibitor of DNA polymerase-beta and gamma) were used. Aphidicolin inhibited repair and consistently sensitized to TNF cytotoxicity, decreasing the ID50 for TNF at least 10- to 50-fold. In contrast, dideoxythymidine had no effect on repair or cytotoxicity. Deoxycytidine, which competitively inhibits binding of aphidicolin to DNA polymerase, blocked the sensitization in a concentration-dependent fashion. In targets sensitized with aphidicolin, TNF-induced strand breakage was accelerated, being detected by 4 h of culture in the sucrose gradient assay. Sensitization to TNF was not due to a heightened activation of poly (ADP-ribose) polymerase. These results indicate that TNF-induced strand breakage participates in TNF-induced cytotoxicity and that the level of DNA repair plays a role in determining relative sensitivity of targets.
Positron Emission Tomography Scanning: Current and Future Applications (2002)

Whole-body positron emission tomography (PET) imaging with (18)F deoxyglucose (FDG) is a molecular imaging modality that detects metabolic alterations in tumor cells that are common to neoplastic cells. FDG-PET has recently been approved by the Health Care Finance Administration for Medicare reimbursement for diagnosing, staging, and restaging lung cancer, colorectal cancer, lymphoma, melanoma, head and neck cancer, and esophageal cancer. This review discusses the scientific evidence that led to the emergence of PET imaging as an accepted clinical tool in patients with solitary pulmonary nodules, lung cancer, colorectal cancer, melanoma, lymphoma, breast cancer, and other cancers. When possible, we compare the performance of PET to that of anatomical imaging. We discuss future clinical applications of this imaging modality.
Effect of induced fever on serum iron and ferritin concentrations in man (1977)

Previous reports have shown that endotoxin decreases serum iron in experimental animals. In this study fever was produced in nine female and nine male normal subjects in order to define the temporal and quantitative changes in serum iron and ferritin concentrations. Six volunteers were randomly given bacterial endotoxin (5 ng/kg) or saline intravenously and received the alternative compound a week later. Serial blood samples were drawn at 4-hr intervals for a 24-hr period, beginning when the compound was administered, for the determination of serum iron and ferritin concentrations. The same study was performed with intramuscular etiocholanolone (0.3 mg/kg) or the vehicle, propylene glycol, as a control, but the first blood sample was obtained 9 hr after the compound was given. In addition, blood samples were obtained at 12-hr intervals in six volunteers for 11 days after an intramuscular injection of etiocholanolone. The results showed a significant increase (p less than 0.005 for etiocholanolone, P less than 0.01 for endotoxin) in serum ferritin and a significant decrease (p less than 0.005 for etiocholanolone, p less than 0.001 for endotoxin) in serum iron for both pyrogenic compounds compared with the control compounds. However, the amount of fever and the changes in the iron parameters were greater with etiocholanolone. One episode of induced fever with etiocholanolone effected changes in serum ferritin and iron concentrations that lasted 10 days. Thus this study demonstrated that a single episode of fever in man produced rapid and prolonged changes in serum iron and ferritin concentrations.
Promoter hypermethylation of BNIP3 and prognosis in human colorectal cancer (2008)

15025 Background: Promoter hypermethylation plays an important role in the inactivation of tumor suppressor genes and apoptotic genes during tumorigenesis and tumor growth. BNIP3 is a proapoptotic member of the Bcl-2 family and expressed in hypoxic regions of tumors. In the present study, promoter hypermethylation of BNIP3 was investigated in colorectal cancer (CRC) specimen and compared to patient’s prognosis. Methods: Methylation status of 145 CRC specimens, all of which were formalin-fixed and paraffin embedded, were studied by methylation specific PCR. Patient characteristics: 52 female and 93 males, 64.5 years old in average, stage0:I:II:III:VI = 6:19:49:49:22. Results: Hypermethylation of BNIP3 was observed 54% of the specimens. Methylation status had no correlation with any clinicopathological factor. Patients with BNIP3 hypermethylated cancer showed significant poorer survival than those with unmethylated cancer in overall survival and disease specific survival (p=0.013 and 0.028, respectively. Log-rank test), but not in relapse free survival (p=0.315) Conclusions: Promoter hypermethylation of BNIP3 were supposed to be negative predictive and prognostic factors in patients with CRC. Possible reasons for poorer prognosis in hypermethylation group are speculated to be prevention of tumor apoptosis in the chemotherapy and resistance to hypoxia-induced cell death in human CRC. No significant financial relationships to disclose.
Michael Addition Polymerization of Trifunctional Amine and Acrylic Monomer: A Versatile Platform for Development of Biomaterials (2016)

Michael addition polymerizations of amines and acrylic monomers are versatile approaches to biomaterials for various applications. A combinatorial library of poly(β-amino ester)s and diverse poly(amido amine)s from diamines and diacrylates or bis(acrylamide)s have been reported, respectively. Furthermore, novel linear and hyperbranched polymers from Michael addition polymerizations of trifunctional amines and acrylic monomers significantly enrich this category of biomaterials. In this Review, we focus on the biomaterials from Michael addition polymerizations of trifunctional amines and acrylic monomers. First we discuss how the polymerization mechanisms, which are determined by the reactivity sequence of the three types of amines of trifunctional amines, i.e., secondary (2°) amines (original), primary (1°) amines, and 2° amines (formed), are affected by the chemistry of monomers, reaction temperature, and solvent. Then we update how to design and synthesize linear and hyperbranched polymers based on the understanding of polymerization mechanisms. Linear polymers containing 2° amines in the backbones can be obtained from polymerizations of diacrylates or bis(acrylamide)s with equimolar trifunctional amine, and several approaches, e.g., 2A<sub>2</sub>+BB'B″, A<sub>3</sub>+2BB'B', A<sub>2</sub>+BB'B″, to hyperbranched polymers are developed. Further through molecular design of monomers, conjugation of functional species to 2° amines in the backbones of linear polymers and the abundant terminal groups of hyperbranched polymers, the amphiphilicity of polymers can be adjusted, and additional stimuli, e.g., thermal, redox, reactive oxidation species (ROS), and light, responses can be integrated with the intrinsic pH response. Finally we discuss the applications of the polymers for gene/drug delivery and bioimaging through exploring their self-assemblies in various motifs, e.g., micelles, polyplexes particles/nanorings and hydrogels. Redox-responsive hyperbranched polymers can display 300 times higher in vitro gene transfection efficiency and provide a higher in vivo siRNA efficacy than PEI. Also redox-responsive micelle carriers can improve the efficacy of anticancer drug and the bioimaging contrast. Further molecular design and optimization of this category of polymers together with in vivo studies should provide safe and efficient biomaterials for clinical applications.
Pauses, Transition Relevance, and Speaker Change (1992)

Journal Article Pauses, Transition Relevance, and Speaker Change Get access W.Ray Thomason, W.Ray Thomason Assistant Instructor 1Speech Communication at the University of Texas at Austin Search for other works by this author on: Oxford Academic Google Scholar Robert Hopper Robert Hopper Charles Sapp Professor of Communication 1Speech Communication at the University of Texas at Austin Search for other works by this author on: Oxford Academic Google Scholar Human Communication Research, Volume 18, Issue 3, March 1992, Pages 429–444, https://doi.org/10.1111/j.1468-2958.1992.tb00559.x Published: 17 March 2006
Cloning and Characterization of Mouse RIP140, a Corepressor for Nuclear Orphan Receptor TR2 (1998)

The mouse homologue of the human receptor-interacting protein 140 (RIP140) was isolated from a mouse embryonic cDNA library in yeast two-hybrid screening experiments by using the ligand binding domain (LBD) of nuclear orphan receptor TR2 as the bait. The receptor-interacting domains of mouse RIP140 were mapped to the regions containing the LXXLL motif (where L is leucine and X is any amino acid), and the RIP140-interacting domain of TR2 was mapped to its C-terminal 10- to 20-amino-acid sequence, a putative activation function 2 (AF-2) region. In a GAL4 reporter system and a reporter driven by the proximal region of the TR2 promoter, RIP140 functioned as a corepressor for both a GAL4 DNA binding domain (BD)–TR2 fusion and the wild-type receptor. When tethered to the BD of GAL4, RIP140 exerted a trans-repressive effect on the GAL4 reporter. In addition, RIP140 suppressed the retinoic acid (RA) receptor-mediated RA induction in a dose-dependent manner. Finally, it was demonstrated that in the presence of RIP140, a cytosolic, green fluorescent protein-tagged TR2 LBD translocated into the nucleus, and TR2 and RIP140 were coimmunoprecipitated from the cell extract, indicating that the interaction between RIP140 and the LBD of TR2 occurred in vivo. The potential biological role of RIP140 in TR2-modulated transcriptional activity is discussed.
Design of fiber amplifier based communication systems using a Volterra series approach (2002)

Using the Volterra series transfer function of the complete fiber optic communication system, the optimum dispersion management scheme is determined to minimize the effects of fiber dispersion, nonlinearities and spontaneous noise from the amplifiers.
Improvement in bioreactor productivities using free radicals: HOCl‐induced overproduction of xanthan gum from Xanthomonas campestris and its mechanism (2001)

Free-radical induction has been employed as a novel strategy to improve bioreactor productivity and, more specifically, the quality and productivity of xanthan gum from Xanthomonas campestris cultures. A 210% increase in xanthan yield and a 20% increase in viscosity (quality) resulted from HOCl (oxidant) treatment. The acetate mass fraction in xanthan gum decreased by 42% and its pyruvate mass fraction increased by 63% as a result of HOCl treatment. The growth rate was almost unaffected by HOCl treatment. A hypothesis to explain the mechanism of xanthan gum overproduction by free-radical induction has been formulated. The significant aspects of the hypothesis, such as SoxS protein binding to the promoter region of the gum gene and the consequent increase in mRNA concentrations, have been experimentally verified. © 2001 John Wiley & Sons, Inc. Biotechnol Bioeng 72: 62–68, 2001.
Variable transcriptional activity and ligand binding of mutant beta 1 3,5,3'-triiodothyronine receptors from four families with generalized resistance to thyroid hormone. (1992)

Mutations in the gene encoding the human beta 1 T3 receptor (hTR beta 1) have been associated with generalized resistance to thyroid hormone (GRTH). We measured the T3-binding affinity and transcriptional regulatory capacity of the mutant hTR beta 1 from four unrelated kindreds with GRTH. These mutations are contained in different functional regions of the ligand-binding domain. The T3 affinity of the mutant receptors correlated well with the degree of impairment of their trans-activating function in a transient cotransfection system in HeLa cells; two mutant receptors with undetectable ligand affinity showed no transcriptional activity, whereas the two other mutants characterized by a 2- and 5-fold reduction in T3 affinity required 5- and 15-fold higher T3 concentrations for half-maximal activity in the cotransfection assay, respectively. All of the mutant hTR beta 1s were able to inhibit the function of transfected normal hTR beta 1 and endogenous retinoic acid receptor in activating a palindromic positive T3 response element (TRE). In the partially functional mutants this dominant negative effect could be completely reversed by increased T3 concentrations. The dominant negative potency did not depend on the type of TRE used; mutant hTR beta 1s were able to inhibit normal receptor function to the same degree on a dimer-permissive palindromic TRE as on a nondimer-permissive inverted repeat of two identical half-sites separated by five spacer bases. However, the dominant negative potency was dependent on the absolute amount of receptor expression vector transfected. The expression of normal and mutant hTR beta 1 was assessed by immunocytochemistry. The hTR beta 1 protein levels in HeLa cells paralleled the amount of transfected expression vector. Moreover, all the mutant receptors were properly expressed in the nuclei of the transfected cells. These data suggest that different mutations in the ligand-binding domain of the human hTR beta 1 result in a variable degree of functional impairment, which may partially explain the phenotypic differences between kindreds with GRTH. Our findings suggest that competition for binding to the TRE and possibly the binding of limiting accessory factors may be more important in mediating the dominant negative effect than the formation of normal/mutant T3 receptor dimers.