gebhart/patrepeval huggingface dataset:
Inhibition of HIV-1 integrase by small molecules: the potential for a new class of AIDS chemotherapeutics. (2001)

HIV-1 integrase, one of three constitutive viral enzymes required for replication, is an attractive target for chemotherapeutic intervention in the treatment of AIDS. Unlike the retroviral reverse transcriptase and protease enzymes, successful drug candidates based on the inhibition of integrase have yet to emerge despite the multitude of laboratories working on the problem. In vitro inhibition of integrase in the laboratory has not always led to antiviral activity in cell culture. Indeed, most compounds found from broad screening efforts have fallen into this category. Only recently have compounds that inhibit enzymatic function as well as exhibiting an antiviral effect as a result been discovered. The reasons why certain structural classes of compounds fail to have antiviral activity are only beginning to be understood. In the last two years a new class of compounds has emerged that do produce potent inhibition of viral growth in cell culture. Further work in this area may yet produce clinically useful antiviral agents.
QUIP: Quantitative User Interface Profiling (1999)

We introduce a usability evaluation system that provides automatic, quantitative analysis of usage trace data. A problem with existing usability evaluation techniques such as expert evaluation and walk-throughs is that the results are subjective and qualitative. Observational research leads to the most relevant results, but it can be expensive, and analysis of the results is tedious. In the system that we introduce, usage traces are automatically aggregated into a usage profile in which disparities between user and designer conceptual models are exposed graphically. Keywords User interface, usability, automated evaluation, profiling INTRODUCTION Some problems with usability evaluation techniques such as expert evaluation and walk-throughs are that they do not involve real users, and the results are subjective and qualitative. Objective and quantitative information based on real usage of an interface is better for the purposes of understanding usability defects and planning resource...
Selective effects of experimental glaucoma on axonal transport by retinal ganglion cells to the dorsal lateral geniculate nucleus. (1991)

Rapid-phase axonal transport to the dorsal lateral geniculate nucleus (dLGN) was determined autoradiographically in seven macaque monkey eyes with chronic intraocular pressure (IOP) elevation, in four eyes with an acute IOP elevation, and in three eyes with normal IOP. The monkeys with chronic IOP elevation showed a greater decrease in radioactive labeling of the magnocellular layers of the dLGN than the parvocellular layers by qualitative examination. Grain counts in selected specimens confirmed that transport to the magnocellular layers was less than to the parvocellular layers in monkeys with chronic IOP elevation. This selectivity was present in mildly damaged specimens and increased with greater ganglion cell loss. In monkeys with acute IOP elevation, qualitative evaluation suggested no consistent difference in transport among the dLGN layers; one animal in this group had less transport to the parvocellular than to the magnocellular layers by grain counts. Starting in early stages of the disease, chronic experimental glaucoma causes preferential damage to the ganglion cells that project to the magnocellular layers of the dLGN.
Impact of spatio-temporal correlation in cooperative spectrum sensing for mobile cognitive radio networks (2013)

Cooperative Spectrum Sensing (CSS) has been proposed as a solution to increase accuracy of spectrum sensing in a Cognitive Radio Network (CRN), but with a few exceptions the design and performance evaluation of CSS schemes has focused so far on static networks, neglecting the role and potential impact of terminals mobility, in conjunction with channel spatio-temporal correlation. This work addresses such issues by proposing a CSS scheme with a correlation-based nodes selection and by evaluating its performance in a realistic simulation environment using accurate models for signal propagation, degree of correlation among sensing measurements and mobility behaviour. The proposed scheme adopts the well known Moran's I statistical index, defined in 1950 by P.A.P. Moran, as the metric for determining the degree of correlation between Secondary Users (SUs), and selects a subset of SUs characterized by low correlation and high expected sensing performance in order to achieve satisfactory network sensing performance while reducing the overhead related to sensing in terms of bandwidth utilization and energy consumption. The proposed scheme is compared with an alternative solution, where all SUs participate in the sensing process, by means of computer simulations considering both static and mobile SUs under accurate models for channel correlation and mobility. Simulation results, while confirming that the proposed scheme achieves a reduction in the number of devices involved in sensing without significant performance loss, hint that the advantage guaranteed by SU mobility might be lower than what estimated by previous studies under simpler assumptions. © VDE Verlag GMBH.
Prediction of Alzheimer’s Disease Using the CSF Aβ42/Aβ40 Ratio in Patients with Mild Cognitive Impairment (2007)

Evidence supports an important role for beta-amyloid (Abeta) in the pathogenesis of Alzheimer's disease (AD). Here, we investigate baseline levels of the 40- and 42-amino-acid-long Abeta peptides (Abeta40 and Abeta42) in cerebrospinal fluid (CSF) from a cohort of patients with mild cognitive impairment (MCI, n = 137) in relation to the final diagnosis after 4-6 years of follow-up time. CSF Abeta42 concentration at baseline and the Abeta42/Abeta40 ratio were significantly decreased in the MCI patients who developed AD as compared to cognitively stable MCI patients and MCI patients who developed other forms of dementia (p < 0.001). The baseline levels of Abeta40 were similar in all MCI groups but correlated with change in Mini Mental State Examination scores in converters to AD. The Abeta42/Abeta40 ratio was superior to Abeta42 concentration with regard to identifying incipient AD in MCI (p < 0.05). In conclusion, the data provide further support for the view that amyloid precursor protein metabolism is disturbed in early sporadic AD and points to the usefulness of the Abeta42/Abeta40 ratio as a predictive biomarker for AD.
Overexpression of legumain in tumors is significant for invasion/metastasis and a candidate enzymatic target for prodrug therapy. (2003)

Expression of legumain, a novel asparaginyl endopeptidase, in tumors was identified from gene expression profiling and tumor tissue array analysis. Legumain was demonstrated in membrane-associated vesicles concentrated at the invadopodia of tumor cells and on cell surfaces where it colocalized with integrins. Legumain was demonstrated to activate progelatinase A. Cells overexpressing legumain possessed increased migratory and invasive activity in vitro and adopted an invasive and metastatic phenotype in vivo, inferring significance of legumain in tumor invasion and metastasis. A prodrug strategy incorporating a legumain-cleavable peptide substrate onto doxorubicin was developed. The prototype compound, designated legubicin, exhibited reduced toxicity and was effectively tumoricidal in vivo in a murine colon carcinoma model.
An ATPase Depending an the Presence of Single‐Stranded DNA from Mouse Myeloma (1976)

An ATPase was purified from mouse myeloma MOPC 70E the activity of which depends on the presence of single-stranded DNA and divalent cations such as Mg2+, Mn2+, Ca2+, Ni2+ or Fe2+. The enzyme splits both ribonucleoside and deoxyribonucleoside triphosphates but preferentially ATP and dATP yielding nucleoside diphosphates and inorganic phosphate. The enzyme has an absolute requirement for single-stranded DNA. Alternating double-stranded polydeoxynucleotides are only slight effective, and native double-stranded DNA, single-stranded and double-stranded RNAs as well as DNA - RNA hybrids are ineffective in stimulating the ATPase. The enzyme has further characterized by sedimentation in a sucrose density gradient (s20, w = 5.5 S) and by isoelectric focussing in an ampholine pH gradient (pI = 6.5).
Multiple roles of cytochrome c oxidase in mammalian cells under action of red and IR‐A radiation (2010)

This article reviews the current knowledge in photobiology and photomedicine about the influence of monochromatic, quasimonochromatic, and bread-band radiation of red-to-near infrared (IR-A) part on solar spectrum upon mammalian cells and human skin. The role of cytochrome c oxidase as the photoacceptor and photosignal transducer is underlined and its photosensitivity at certain circumstances is discussed. The role of ATP as a critical signaling molecule is discussed.
A combined cell-free transcription-translation system fromSaccharomyces cerevisiaefor rapid and robust protein synthe (2014)

Cell-free protein synthesis (CFPS) provides a valuable platform for understanding, using, and expanding the capabilities of the translation apparatus. For example, high-throughput CFPS is helping to address the increasing discrepancy between genome sequence data and their translation products. Here, we report the development of a combined cell-free transcription-translation (Tx/Tl) system from Saccharomyces cerevisiae that is suitable for such efforts. First, we show the ability to enable translation initiation in a cap-independent manner. The performance of various genetic elements was assessed, including 5'-UTR, 3'-UTR, and length of poly(A) tail. A specific vector harboring the 5'-UTR fragment of the Ω sequence from the tobacco mosaic virus and a poly(A) tail of 50 nucleotides led to optimal performance. Second, we developed a simple, two-step polymerase chain reaction (PCR) method for high-throughput production of linear templates for yeast CFPS. This procedure allows all functional elements needed for Tx/Tl to be added to an open-reading frame directly by overlap extension PCR. Our two-step PCR method was successfully applied to three reporter proteins: luciferase, green fluorescence protein, and chloramphenicol acetyl transferase, yielding 7 to 12.5 μg mL-1 active protein after 1.5-h batch reactions. Surprisingly, the linear templates outperformed plasmid DNA by up to 60%. Hence, the presented CFPS method has the potential to rapidly prepare tens to thousands of DNA templates without time-consuming cloning work. Further, it holds promise for fast and convenient optimization of expression constructs, study of internal ribosome entry site, and production of protein libraries for genome-scale studies. See accompanying commentary by Russ and Dueber DOI: 10.1002/biot.201400071.
Inhibition of hyaluronan is protective against renal ischaemia-reperfusion injury (2013)

Our results demonstrate that HA plays a significant role in the pathogenesis of IRI, perhaps in part through reduced expression of CD44. The suppression of HA accumulation during IR may protect renal function against ischaemic insults.
Recent developments and current status of gene therapy using viral vectors in the United Kingdom: Table 1 (2004)

Viral vectors remain the vehicles of choice for gene transfer in clinical trials of gene therapy in the United Kingdom and worldwide. In the United Kingdom alone, 88 clinical trials are registered with the Gene Therapy Advisory Committee (GTAC, www.advisorybodies.doh.gov.uk/genetics/gtac).

Although notable successes have been achieved in some inherited diseases, viral vectors have not been without their problems. We review the adverse events encountered to date and describe lessons that can be learnt from them to improve vector biology and pharmacology in order to make gene therapy with viral vectors a viable treatment for the future.

We searched Medline and Google, using the terms “gene therapy” and “viral vectors.” We also studied the websites www.wiley.co.uk/genmed/clinical and www.advisorybodies.doh.gov.uk/genetics/gtac for information on ongoing trials using viral vectors in the United Kingdom.

In April 2002 the BBC online news service in the United Kingdom carried an emotive headline: “Bubble boy saved by gene therapy.”1 The 18 month old infant featured had a rare immune disorder, X linked severe combined immunodeficiency (X-SCID), caused by a defective gene on the X chromosome. This gene encodes the common γC chain, an essential component of five cytokine receptors, all of which are necessary for the development of T cells and natural killer cells. Without the γC chain, mature T cells and natural killer cells are completely absent, whereas B cells are usually present in normal or increased numbers. X-SCID is fatal during the first year of life because of severe recurrent infections. As a result, much of the child's short life is spent in a sterile plastic bubble, a barrier to potentially life threatening infectious organisms. A collaboration of scientists from London, Paris, and Milan used a retroviral vector to introduce a functional copy of the defective gene into bone marrow stem cells taken from …
Thienamycin, a new .BETA.-lactam antibiotic. I. Discovery, taxonomy, isolation and physical properties. (1979)

A new beta-lactam antibiotic, named thienamycin, was discovered in culture broths of Streptomyces MA4297. The producing organism, subsequently determined to be a hitherto unrecognized species, is designated Streptomyces cattleya (NRRL 8057). The antibiotic was isolated by adsorption on Dowex 50, passage through Dowex 1, further chromatography on Dowex 50 and Bio-Gel P2, and final purification and desalting on XAD-2. Thienamycin is zwitterionic, has the elemental composition C11H16N2O4S (M.W. = 272.18) and possesses a distinctive UV absorption (lambda max = 297 nm, epsilon = 7,900). Its beta-lactam is unusually sensitive to hydrolysis above pH8 and to reaction with nucleophiles such as hydroxylamine, cysteine and, to a lesser degree, the primary amine of the antibiotic itself. The latter reaction results in accelerated inactivation at high antibiotic concentrations.
Vaccination with Allergen-IL-18 Fusion DNA Protects Against, and Reverses Established, Airway Hyperreactivity in a Murine Asthma Model (2001)

Vaccination with naked DNA encoding a specific allergen has been shown previously to prevent, but not reverse, the development of allergen-induced airway hyperresponsiveness (AHR). To enhance the effectiveness of DNA vaccine therapies and make possible the treatment of established AHR, we developed a DNA vaccination plasmid containing OVA cDNA fused to IL-18 cDNA. Vaccination of naive mice either with this fusion DNA construct or with an OVA cDNA-containing plasmid protected the mice from the subsequent induction of AHR. Protection from AHR correlated with increased IFN-gamma production and reduced OVA-specific IgE production. The protection appeared to be mediated by IFN-gamma and CD8(+) cells because treatment of mice with neutralizing anti-IFN-gamma mAb or with depleting anti-CD8 mAb abolished the protective effect. Moreover, vaccination of mice with preexisting AHR with the OVA-IL-18 fusion DNA, but not with the OVA cDNA plasmid, reversed established AHR, reduced allergen-specific IL-4, and increased allergen-specific IFN-gamma production. Thus, combining IL-18 cDNA with OVA cDNA resulted in a vaccine construct that protected against the development of AHR, and that was unique among cDNA constructs in its capacity to reverse established AHR.
Dimensional Measurement of Objects in Single Images Independent from Restrictive Camera Parameters (2011)

Recent advances in microelectronics have produced new generations of digital cameras with variable focal lengths and pixel sizes which facilitate automatic and high-quality imaging. However, without knowing the values of these critical camera parameters, it is difficult to measure objects in images using existing algorithms. This work investigates this important problem aiming at dimensional measurements (e.g., diameter, length, width and height) of regularly shaped physical objects in a single 2-D image free from restrictive camera parameters. Traditionally, such measurements usually require determinations of the poses of a certain reference feature, i.e., the location and orientation of the feature relative to the camera, in order to establish a geometric model for the dimensional calculation. Points or lines associated with certain shapes (including triangles and rectangles) are often used as reference features for the pose estimation. However, with only a single image as the input, these methods assume the availability of 3-D spatial relationships of the points or lines, which limits the applications of these methods to practical problems where this knowledge is unavailable or difficult to estimate, such as in the problem of image-based food portion size estimation in dietary assessment. In addition to points and lines, the circle has also been used as a reference feature because it has a single elliptic perspective projection in images. However, almost all the existing approaches treat the parameters of focal length and pixel size as the necessary prior information. Here, we propose a new approach to dimensional estimation based on single image input using the circular reference feature and a pin-hole model without considering camera distortion. Without knowing the focal length and pixel size, our approach provides a closed-form solution for the orientation estimation of the circular feature. With additional information provided, such as the size of the circular reference feature, analytical solutions are provided for physical length estimation between an arbitrary pair of points on the reference plane. Studies using both synthetic and actual objects have been conducted to evaluate this new method, which exhibited satisfactory results. This method has also been applied to the measurement of food dimensions based on digital pictures of foods in circular dining plates.
Wireless Insufflation of the Gastrointestinal Tract (2012)

Despite clear patient experience advantages, low specificity rates have thus far prevented swallowable capsule endoscopes from replacing traditional endoscopy for diagnosis of colon disease. One explanation for this is that capsule endoscopes lack the ability to provide insufflation, which traditional endoscopes use to distend the intestine for a clear view of the internal wall. To provide a means of insufflation from a wireless capsule platform, in this paper we use biocompatible effervescent chemical reactions to convert liquids and powders carried onboard a capsule into gas. We experimentally evaluate the quantity of gas needed to enhance capsule visualization and locomotion, and determine how much gas can be generated from a given volume of reactants. These experiments motivate the design of a wireless insufflation capsule, which is evaluated in ex vivo experiments. These experiments illustrate the feasibility of enhancing visualization and locomotion of endoscopic capsules through wireless insufflation.
Verknüpfung von Zuckern mit Aminosäureestern lipophiler Alkohole zu grenzflächenaktiven Zuckerderivaten (1962)

Article Verknüpfung von Zuckern mit Aminosäureestern lipophiler Alkohole zu grenzflächenaktiven Zuckerderivaten was published on January 1, 1962 in the journal Biological Chemistry (volume 330, issue Jahresband).
Inulin-type fructans modulate gastrointestinal peptides involved in appetite regulation (glucagon-like peptide-1 and ghrelin) in rats (2004)

The hypothesis tested in the present study is that dietary fructans are able to modulate gastrointestinal peptides involved in the control of food intake, namely glucagon-like peptide (GLP)-1 (7-36) amide and ghrelin. After 3 weeks of treatment with a standard diet (control) or the same diet enriched with 100 g fructans varying in their degrees of polymerization (oligofructose (OFS), Synergy 1 (Syn) or long chain inulin)/kg, male Wistar rats were deprived of food for 8 h before sample collection. Dietary energy intake throughout the experiment was significantly lower (P<0.05) in fructans-fed rats than in control rats, leading to a significant decrease (P<0.01) in epidydimal fat mass at the end of the treatment in OFS- and Syn-treated rats. GLP-1 (7-36) amide concentration in portal vein serum was higher in OFS- and Syn-fed than in control rats. Both GLP-1 (7-36) amide concentration and proglucagon mRNA concentrations were significantly greater (P<0.05) in the proximal colonic mucosa of fructans-fed rats v. controls. Normally active ghrelin concentration in plasma increases during food deprivation and rapidly falls during a meal. In the present study, after 8 h of food deprivation, active ghrelin in the plasma remained significantly lower (P<0.05) in OFS and Syn-fed than in control rats. These results are in accordance with the modifications of dietary intake and fat-mass development in short-chain fructans-treated rats and demonstrate the potential modulation of GLP-1 (7-36) amide and ghrelin by fermentable fibres such as fructans, which are rapidly and extensively fermented in the proximal part of the colon.
Selection using a one-eyed cursor in a fish tank VR environment (1997)

This study investigates the use of a 2D cursor presented to one eye for target selection in Fish Tank VR and other stereo environments. It is argued that 2D selection of 3D objects should be less difficult than 3D selection. Vision research concerning binocular rivalry and the tendency we have to project images onto surfaces suggests that this mode of viewing will not seem particularly unnatural. A Fitt's Law experiment was done to directly compare target acquisition with a one-eyed 2D cursor and target acquisition using a 3D cursor. In both cases we used the same input device (Polhemus Fastrak) so that the device lag and gain parameters were exactly matched. The results show a large improvement in target acquisition time using the 2D cursor. The practical implications of this is that the 2D selection method using a one-eyed cursor in preferable to the 3D selection method. Theoretical implications relate to methods for extending Fitts' Law from the one-dimensional task for which it was designed to 2D and 3D tasks. We conclude that the existing approaches to this problem are not adequate.