gebhart/patrepeval huggingface dataset:
Use of the Percentage of Free Prostate-Specific Antigen to Enhance Differentiation of Prostate Cancer From Benign Prostatic Disease (1998)

Use of the percentage of free PSA can reduce unnecessary biopsies in patients undergoing evaluation for prostate cancer, with a minimal loss in sensitivity in detecting cancer. A cutoff of 25% or less free PSA is recommended for patients with PSA values between 4.0 and 10.0 ng/mL and a palpably benign gland, regardless of patient age or prostate size. To our knowledge, this study is the largest series to date evaluating the percentage of free PSA in a population representative of patients in whom the test would be used in clinical practice.
Intelligent autonomous systems : IAS-4 : Proceedings of the international Conference Karlsruhe, Germany March 27-30,1995 (1995)

This text presents the proceedings of a conference on intelligent autonomous systems. Papers contribute solutions to the task of designing autonomous systems that are capable of operating independently of a human in partially structured and unstructured environments. For specific application, these systems should also learn from their actions in order to improve and optimize planning and execution of new tasks. There are numerous disciplines that contribute to the design of autonomous systems, including computer sciences, physics, electronics, computer engineering and mechanical engineering. One of the most difficult tasks is system integration, where systems such sensors, vision systems, controllers and machine elements are tied together to a functional entity. The papers bound in these proceedings discuss the results of numerous research endeavours and present the state of the art to obtain autonomy.
Functional Genetic Elements for Controlling Gene Expression in Cupriavidus necator H16 (2018)

A robust and predictable control of gene expression plays an important role in synthetic biology and biotechnology applications. Development and quantitative evaluation of functional genetic elements, such as constitutive and inducible promoters as well as ribosome binding sites (RBSs), are required. In this study, we designed, built, and tested promoters and RBSs for controlling gene expression in the model lithoautotroph <i>Cupriavidus necator</i> H16. A series of variable-strength, insulated, constitutive promoters exhibiting predictable activity within a >700-fold dynamic range was compared to the native P <sub><i>phaC</i></sub> , with the majority of promoters displaying up to a 9-fold higher activity. Positively (AraC/P <sub><i>araBAD</i></sub> -l-arabinose and RhaRS/P <sub><i>rhaBAD</i></sub> -l-rhamnose) and negatively (AcuR/P <sub><i>acuRI</i></sub> -acrylate and CymR/P <sub><i>cmt</i></sub> -cumate) regulated inducible systems were evaluated. By supplying different concentrations of inducers, a >1,000-fold range of gene expression levels was achieved. Application of inducible systems for controlling expression of the isoprene synthase gene <i>ispS</i> led to isoprene yields that exhibited a significant correlation to the reporter protein synthesis levels. The impact of designed RBSs and other genetic elements, such as mRNA stem-loop structure and A/U-rich sequence, on gene expression was also evaluated. A second-order polynomial relationship was observed between the RBS activities and isoprene yields. This report presents quantitative data on regulatory genetic elements and expands the genetic toolbox of <i>C. necator</i><b>IMPORTANCE</b> This report provides tools for robust and predictable control of gene expression in the model lithoautotroph <i>C. necator</i> H16. To address a current need, we designed, built, and tested promoters and RBSs for controlling gene expression in <i>C. necator</i> H16. To answer a question on how existing and newly developed inducible systems compare, two positively (AraC/P <sub><i>araBAD</i></sub> -l-arabinose and RhaRS/P <sub><i>rhaBAD</i></sub> -l-rhamnose) and two negatively (AcuR/P <sub><i>acuRI</i></sub> -acrylate and CymR/P <sub><i>cmt</i></sub> -cumate) regulated inducible systems were quantitatively evaluated and their induction kinetics analyzed. To establish if gene expression can be further improved, the effect of genetic elements, such as mRNA stem-loop structure and A/U-rich sequence, on gene expression was evaluated. Using isoprene production as an example, the study investigated if and to what extent chemical compound yield correlates to the level of gene expression of product-synthesizing enzyme.
Pyocyanin Facilitates Extracellular DNA Binding to Pseudomonas aeruginosa Influencing Cell Surface Properties and Aggregation (2013)

Pyocyanin is an electrochemically active metabolite produced by the human pathogen Pseudomonas aeruginosa. It is a recognized virulence factor and is involved in a variety of significant biological activities including gene expression, maintaining fitness of bacterial cells and biofilm formation. It is also recognized as an electron shuttle for bacterial respiration and as an antibacterial and antifungal agent. eDNA has also been demonstrated to be a major component in establishing P. aeruginosa biofilms. In this study we discovered that production of pyocyanin influences the binding of eDNA to P. aeruginosa PA14 cells, mediated through intercalation of pyocyanin with eDNA. P. aeruginosa cell surface properties including cell size (hydrodynamic diameter), hydrophobicity and attractive surface energies were influenced by eDNA in the presence of pyocyanin, affecting physico-chemical interactions and promoting aggregation. A ΔphzA-G PA14 mutant, deficient in pyocynain production, could not bind with eDNA resulting in a reduction in hydrodynamic diameter, a decrease in hydrophobicity, repulsive physico-chemical interactions and reduction in aggregation in comparison to the wildtype strain. Removal of eDNA by DNase I treatment on the PA14 wildtype strain resulted in significant reduction in aggregation, cell surface hydrophobicity and size and an increase in repulsive physico-chemical interactions, similar to the level of the ΔphzA-G mutant. The cell surface properties of the ΔphzA-G mutant were not affected by DNase I treatment. Based on these findings we propose that pyocyanin intercalation with eDNA promotes cell-to-cell interactions in P. aeruginosa cells by influencing their cell surface properties and physico-chemical interactions.
Genetic predisposition to multiple sclerosis as revealed by immunoprinting (1997)

This study was designed to examine the immunogenetic background predisposing to multiple sclerosis (MS). Three hundred fifty-eight clinically well-characterized MS patients from Germany were investigated and compared to 395 healthy control subjects. Each individual was genotyped for 22 polymorphic markers located within or close to immunorelevant candidate genes including HLA-DRB1*, T-cell receptor (TCR), cell interaction molecules, cytokines, and cytokine receptor genes. Altogether, approximately 17,000 genetic analyses were performed. Patients were grouped according to the course of MS-relapsing-remitting or chronic progressive. Most of the genetic markers were not associated with increased risk or their exact contribution was not clear (e.g., tumor necrosis factor). The relative risks for HLA-DRB1*15+ and DRB1*03+ individuals were 3.64 and 1.42, respectively. In both groups of patients, certain TCRB gene polymorphisms were risk factors. In DRB1*03+ individuals the relative risk was increased (> 22) when a specific TCRBV6S3 allele was also inherited. Furthermore, distinct linkage disequilibria of TCRBV6S1/TCRBV6S3 elements in patients and control subjects strongly suggested an additional risk factor in the TCRBV region for DRB1*15+ individuals. These findings are discussed with respect to the pathogenesis and rational approaches to the therapy of MS.
Autologous Transplantation of Bone Marrow Cells Improves Damaged Heart Function (1999)

Transplantation of BMCs induced angiogenesis. BMCs cultured with 5-aza differentiated into cardiac-like muscle cells in culture and in vivo in ventricular scar tissue and improved myocardial function.
High-frequency transformation of yeast by plasmids containing the cloned yeast ARG4 gene (1979)

Hybrid ColE1 plasmids, containing cloned DNA from the yeast ARG4 region [e.g., pYe(arg4)1], transform yeast arg4 mutants to ARG4(+) with a frequency of 10(-4) (about 10(3) transformants per mug of plasmid DNA) and can replicate autonomously without integrating into the yeast genome. The yeast transformants are genetically unstable when grown on nonselective medium, but can be readily grown and maintained on minimal medium lacking arginine. The existence of unintegrated replicating plasmid DNA in the yeast transformants was demonstrated by Southern gel hybridization and by transformation of Escherichia coli argH mutants with DNA preparations from yeast transformants and subsequent recovery of intact plasmid DNA from the bacterial transformants. Plasmid DNAs recovered from the E. coli-yeast-E. coli "shuttle" remain essentially unchanged, as judged by DNA restriction fragment patterns. Some plasmid mutations leading to increased efficiency of expression of the ARG4 gene in E. coli do not appear to affect expression of the cloned ARG4 gene in yeast. Appropriate derivatives of these ARG4 plasmids are of potential usefulness as vectors for cloning genes in yeast and for studying the mechanism of yeast DNA replication.
Texaphyrins: Synthesis and Applications (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTexaphyrins: Synthesis and ApplicationsJonathan L. Sessler, Gregory Hemmi, Tarak D. Mody, Toshiaki Murai, Anthony Burrell, and Stuart W. YoungCite this: Acc. Chem. Res. 1994, 27, 2, 43–50Publication Date (Print):February 1, 1994Publication History Published online1 May 2002Published inissue 1 February 1994https://pubs.acs.org/doi/10.1021/ar00038a002https://doi.org/10.1021/ar00038a002research-articleACS PublicationsRequest reuse permissionsArticle Views1547Altmetric-Citations237LEARN 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
Solid‐phase synthesis, conformational analysis and in vitro cleavage of synthetic human synaptobrevin II 1–93 by tetanus toxin L chain (1994)

A 93-residue peptide corresponding to the cytosolic domain of a human vesicle associated membrane protein (VAMP or synaptobrevin) has been prepared by solid-phase peptide synthesis in order to investigate the proteolytic activity of the tetanus toxin light chain (TeTx L chain). This protein has been recently reported to inactivate the neuronal rat synaptobrevin II by proteolysis. We show in this study that the synthetic human synaptobrevin II 1-93 (Syb II 1-93) as well as an N-terminus-shortened 69-residue peptide (Syb II 25-93) were cleaved selectively at the Gln76-Phe77 peptide bond by TeTx L chain while shorter peptides were not. A Michaelis constant Km = 192 +/- 2 microM and a catalytic constant kcat = 0.5 min-1 were found for the 93-residue peptide. A neutral optimum pH for the cleavage rate, an inhibition by preincubation of the toxin with well known nonspecific inhibitors of metallopeptidases as well as a zinc-dependent enzyme activity suggest that TeTx belongs to the zinc endopeptidase family. Moreover an activation by reducing agents and an inhibition by cysteine-modifying chemical reagents indicate a critical thiol dependency. Among several specific inhibitors of zinc endopeptidases tested, none could inhibit TeTx L chain even at high concentration. Structural studies by 600-MHz 1H-NMR showed that in water or dimethylsulfoxide the peptide Syb II 1-93 and shorter fragments did not present well defined conformations. Nevertheless protein-protein interactions have been shown for the peptides Syb II 1-93 and 25-93 but not for Syb II 51-93, a fragment not cleaved by TeTx L chain.
Excess Toxicity Associated with Docetaxel and Irinotecan in Patients with Metastatic, Gemcitabine-Refractory Pancreatic Cancer: Results of a Phase II Study (2008)

The combination of docetaxel and irinotecan given on a 21-day cycle is associated with excess toxicity in gemcitabine-refractory patients with advanced pancreatic cancer. Although select patients may benefit from treatment, the overall risk:benefit ratio is unfavorable, and other dosing regimens and therapeutic options should be explored in this setting.
The Use of Amniotic Membrane in Acute Massive Full-thickness Loss of the Abdominal Wall from Clostridial Myonecrosis (1979)

A patient who developed clostridial infection of the abdominal wall following laparotomy for small bowel perforation is described. Immediate debridement resulted in the loss of the entire abdominal wall. Dressing of the exposed viscera during the period of stabilization and prior to reconstruction was achieved using amniotic membranes.
Amphiphiles in aqueous solution: well beyond a soap bubble (2013)

Owing to their "dual" affinity, amphiphiles self-assemble in water to form different kinds of nanoscale multimolecular assemblies ranging from simple micelles and vesicles to highly organized fibers, helices and tubes. In this tutorial review the aggregates formed in water by head/tail amphiphiles are revisited and discussed from the point of view of supramolecular chemistry with a focus on their structure and recognition abilities. Their applications in materials chemistry, as soft templates for inorganic nanostructures, as well as in biological and medicinal chemistry are also illustrated. Special attention is paid to highlight intriguing aspects, for example the control of morphology and chirality, their modulation by experimental parameters and chiral symmetry breaking.
Larrabee: A Many-Core x86 Architecture for Visual Computing (2009)

The Larrabee many-core visual computing architecture uses multiple in-order x86 cores augmented by wide vector processor units, together with some fixed-function logic. This increases the architecture's programmability as compared to standard GPUs. The article describes the Larrabee architecture, a software renderer optimized for it, and other highly parallel applications. The article analyzes performance through scalability studies based on real-world workloads.
Vascular Endothelial Growth Factor Levels in Immunodepleted Plasma of Cancer Patients As a Possible Pharmacodynamic Marker for Bevacizumab Activity (2007)

United States airport high-tech fingerprint identification equipment was unable to identify her fingerprints. As a result, the very first time she returned to the United States from Spain, she was retained at customs for several hours. The second time, an oncol-ogy clinical report had to be faxed to allow her to enter the United States. To our knowledge, this is the first report of a drug-related fingerprint misidentification.
The Release of Enzymes by Osmotic Shock from Escherichia coli in Exponential Phase (1966)

A number of degradative enzymes are specifically released from exponentially growing Escherichia coli by osmotic shock.They include alkaline phosphatase, cyclic phosphodiesterase, 5'-nucleotidase, acid phosphatase, and the ribonucleic acidinhibited endonuclease that is active with deoxyribonucleic acid.Small amounts of RNase are also set free, but some 16 control enzymes are found to remain within the cell.Only about 4% of the cellular protein is released into the shock medium.The procedure for osmotic shock has been modified in order to obtain about 80% viability with exponential cells, with good release of enzymes.In the first stage, cells are exposed to 20% sucrose-1 X 10 -4 M EDTA.In the second stage, the pellet of sucrose-treated cells is rapidly dispersed in cold 5 X 10 -4 M MgC 1 2, which causes the enzymes to be liberated.At least 90% of the DNA endonuclease and 50% of the latent ribonuclease are released from exponentially growing E. coli when as much as 2 X 10 -2 M MgC1 2 is used in the procedure for osmotic shock.
The effects of dentifrice systems on oral malodor. (1998)

Chronic oral malodor is a serious concern for about one-fifth of the North American population, and a field of emerging research interest. The present three studies, one involving gas chromatography and two employing odor judge assessment, examined the efficacy of baking soda and other toothpastes in reducing breath odor. The most common cause of oral malodor is elevated levels of volatile sulfur compounds (VSC's), primarily hydrogen sulfide (H2S) and methyl mercaptan (CH3SH), in the breath. Gas chromatography, an accurate means of measuring breath VSC, was employed to evaluate the breath levels of VSC in 11 men after brushing with baking soda-containing dentifrices with or without the addition of Zn++. Dentifrices with either Zn++ or a concentration of baking soda 20% or greater significantly reduced VSC levels. The addition of Zn++ to baking soda dentifrices enhanced the anti-odor effects. In the first organoleptic study, dentifrices containing 20% baking soda and 30% baking soda demonstrated significantly greater ability to reduce breath odor than a standard sodium fluoride/silica dentifrice. The subjects' baseline mouth odor evaluations, initially rated as strong, declined after brushing with the baking soda toothpastes to a barely detectable level at one hour, then rising to a faint level at two hours and moderate levels at three hours. In the second organoleptic study, a dentifrice containing 65% baking soda demonstrated significantly greater ability to reduce breath odor than a standard sodium fluoride/silica tartar control dentifrice, but did not differ significantly from a standard dentifrice containing 0.76% sodium monofluorophosphate in a dicalcium phosphate dihydrate base. The results of these studies indicate that dentifrices containing 20% or more baking soda can confer a significant odor-reducing benefit for time periods up to three hours.
Learning GNU Emacs (2nd ed.) (1996)

GNU Emacs is the most popular and widespread of the Emacs family of editors. It is also the most powerful and flexible. Unlike all other text editors, GNU Emacs is a complete working environment -- you can stay within Emacs all day without leaving. This book tells you how to get started with the GNU Emacs editor. It will also grow with you: as you become more proficient, this book will help you learn how to use Emacs more effectively. It takes you from basic Emacs usage (simple text editing) to moderately complicated customization and programming. The second edition of Learning GNU Emacs describes all of the new features of GNU Emacs 19.30, including fonts and colors, pull-down menus, scroll bars, enhanced X Window support, and correct bindings for most standard keys. GNUS, a Usenet newsreader, and ange-ftp mode, a transparent interface to the file transfer protocol, are also described. Learning GNU Emacs, second edition, covers: Using Emacs as an Internet Toolkit (to use electronic mail and Usenet news, telnet to other computers, retrieve files using FTP, browse the World Wide Web, and author Web documents)Emacs' rich, comprehensive online help facilitiesHow to edit files with EmacsUsing Emacs as a shell environmentHow to take advantage of built-in formatting featuresHow to use multiple buffers, Emacs windows, and X WindowsCustomizing EmacsThe Emacs interface to the X Window System, which allows you to use a mouse and pop-up menusWhys and hows of writing macros to circumvent repetitious tasksEmacs as a programming environmentThe basics of Emacs LISPHow to get Emacs The book is aimed at new Emacs users, whether or not they are programmers. Also useful for readers switching from other Emacs implementations to GNU Emacs.
Inhibition of HIV-1 by modification of a host membrane protease (1995)

While it is clear that CD4 is the receptor for the gp120 envelope protein of HIV-1, substantial evidence suggests that other host cell proteins are required for successful membrane fusion. Studies were initiated to examine the potential for a protein receptor which has an elastase-like character to participate in fusion of HIV-1 with permissive host cells. A synthetic elastase inhibitor was shown to significantly reduce HIV-1 infectivity when present during, but not after, the initial contact between virus and cells. A human T cell elastase-like membrane component was purified and shown to be lipid-associated. By competitive inhibition, the purified protein was shown to bind gp160 within the HIV-1 fusion domain. The binding parameters of whole T cell membrane extract, with a hydrophobic pentapeptide representative of the fusion domain, suggested an elastase-like protein is the single, secondary T cell receptor for HIV-1 (K = 1 x 10(3) M-1). The pentapeptide interacted with porcine and human (epithelial and polymorphonuclear leukocyte), but not murine, elastase isoforms, suggesting its participation in the permissiveness of host cells to infection.
The contribution of melanin to microbial pathogenesis (2003)

Melanins are enigmatic pigments that are produced by a wide variety of microorganisms including several species of pathogenic bacteria, fungi and helminths. The study of melanin is difficult because these pigments defy complete biochemical and structural analysis. Nevertheless, the availability of new reagents in the form of monoclonal antibodies and melanin-binding peptides, combined with the application of various physical techniques, has provided insights into the process of melanization. Melanization is important in microbial pathogenesis because it has been associated with virulence in many microorganisms. Melanin appears to contribute to virulence by reducing the susceptibility of melanized microbes to host defence mechanisms. However, the interaction of melanized microbes and the host is complex and includes immune responses to melanin-related antigens. Production of melanin has also been linked to protection against environmental insults. Interference with melanization is a potential strategy for antimicrobial drug and pesticide development. The process of melanization poses fascinating problems in cell biology and provides a type of pathogenic strategy that is common to highly diverse pathogens.
Androgen‐dependent expression of FcγRIIB2 by thyrocytes from patients with autoimmune Graves' disease: a possible molecular clue for sex dependence of autoimmune disease (2002)

Thyrocyte expression of HLA class I and class II antigens and related accessory molecules would convert these epithelial cells into functional antigen-presenting cells. Here we show that whereas normal thyrocytes express FcRn, Graves' disease thyrocytes also express FcgammaRIIB2. We further find that expression of FcgammaRIIB2, but not FcRn, is repressed by dihydrotestosterone. By mediating the uptake and transport of autoantibodies, we suggest that these IgG Fc receptors contribute in various ways to the onset and/or progression of autoimmune thyroid diseases. The androgen-mediated decrease of FcgammaRIIB2 expression in Graves' disease thyrocytes also provides a rationale for the predominant susceptibility of women to develop an autoimmune thyroid disease. Our findings open up a new prospect to autoimmunity, linking the role of the target organ to the sex dependence in autoimmune disease.