gebhart/patrepeval huggingface dataset:
Readthrough Strategies for Therapeutic Suppression of Nonsense Mutations in Inherited Metabolic Disease (2012)

Inherited metabolic diseases (IMDs) belong to the group of rare diseases due to their low individual prevalence. Most of them are inherited in autosomal recessive fashion and represent good candidates for novel therapeutical strategies aimed at recovering partial enzyme function as they lack an effective treatment, and small levels of enzymatic activity have been shown to be associated with improved outcome and milder phenotypes. Recently, a novel therapeutic approach for genetic diseases has emerged, based on the ability of aminoglycosides and other compounds in allowing translation to proceed through a premature termination codon introduced by a nonsense mutation, which frequently constitute a significant fraction of the mutant alleles in a population. In this review we summarize the essentials of what is known as suppression therapy, the different compounds that have been identified by high-throughput screens or developed using a medicinal chemistry approach and the preclinical and clinical trials that are being conducted in general and in the field of IMDs in particular. Several IMDs have shown to be good models for evaluating readthrough compounds using patients' cells carrying nonsense mutations, monitoring for an increase in functional recovery and/or enzyme activity. Overall, the positive results obtained indicate the feasibility of the approach for different diseases and although the levels of protein function reached are low, they may be enough to alleviate the consequences of the pathology. Nonsense suppression thus represents a potential therapy or supplementary treatment for a number of IMD patients encouraging further clinical trials with readthrough drugs with improved functionality and low toxicity.
Modified variable-threshold A/D converter (1990)

A modified variable-threshold A/D converter is presented. The proposed converter uses a single D/A converter with n different bit-resolutions instead of n D/A converters each with different bit-resolution in the conventional variable-threshold type. The necessary hardware for the new converter is less than that for the conventional one, which makes it suitable for monolithic integration.
Search for Microorganisms in Men with Urologic Chronic Pelvic Pain Syndrome: A Culture-Independent Analysis in the MAPP Research Network (2015)

Assessment of baseline culture-independent microbiological data from male subjects enrolled in the MAPP Network has identified overrepresentation of B. cenocepacia in urologic chronic pelvic pain syndrome. Future studies are planned to further evaluate microbiota associations with variable and changing urologic chronic pelvic pain syndrome symptom patterns.
Shielding Tests for Cables and Small Enclosures in the 1- to 10-GHz Range (1970)

Electromagnetic shielding tests in the 1- to 1O-GHz frequency range have been characterized by lack of repeatability and reliability. New test methods have been developed which correct most of the causes of erratic behavior and have been found to provide reasonably smooth curves when results are plotted against frequency. Study of the results obtained under various conditions of test indicates that the test procedures approach the desired goal of providing a measure of shielding effectiveness that is related only to the test item itself. The cable test procedures are usable with any type of shielded cable including multiple conductor cables with connectors not intended for RF usage. Cables may be tested in their final configuration without need for modification or removal of insulation, etc. Results are given for tests made under various conditions and are compared with results obtained previously with the triaxial test method. Evaluation of the test procedure for testing small shielded enclosures was performed by testing suitable boxes equipped with leakage openings that could be moved to various points on the surface of the box. The results indiate that the general effect on shielding of a particular type of opening remains much the same regardless of its location or orientation. Results are given for a number of opening designs under various conditions of test.
An Equation of State for Associating Fluids (1996)

An equation of state (EoS) suitable for describing associating fluids is presented. The equation combines the simplicity of a cubic equation of state (the Soave−Redlich−Kwong), which is used for the physical part and the theoretical background of the perturbation theory employed for the chemical (or association) part. The resulting EoS (Cubic Plus Association) is not cubic with respect to volume and contains five pure compound parameters which are determined using vapor pressures and saturated liquid densities. Excellent correlations of both vapor pressures and saturated liquid volumes are obtained for primary-alcohols (from methanol up to 1-tridecanol), phenol, tert-butyl alcohol, triethylene glycol, and water. Moreover, excellent prediction of saturated liquid volumes may be obtained from parameters which have been estimated by regressing only vapor pressures. Finally, we suggest a method for reducing the number of adjustable parameters for alcohols to three while maintaining the good correlation of vapor pressures and saturated liquid volumes. We investigate the possibility of using the homomorph approach for estimating the EoS parameters and explain the problems observed. The estimated pure compound parameters have been tested in the prediction of second virial coefficients with satisfactory results.
Expression of 17 Genes in <i>Clostridium thermocellum</i> ATCC 27405 during Fermentation of Cellulose or Cellobiose in Continuous Culture (2005)

Clostridium thermocellum is a thermophilic, anaerobic, cellulolytic bacterium that produces ethanol and acetic acid as major fermentation end products. The effect of growth conditions on gene expression in C. thermocellum ATCC 27405 was studied using cells grown in continuous culture under cellobiose or cellulose limitation over a approximately 10-fold range of dilution rates (0.013 to 0.16 h(-1)). Fermentation product distribution displayed similar patterns in cellobiose- or cellulose-grown cultures, including substantial shifts in the proportion of ethanol and acetic acid with changes in growth rate. Expression of 17 genes involved or potentially involved in cellulose degradation, intracellular phosphorylation, catabolite repression, and fermentation end product formation was quantified by real-time PCR, with normalization to two calibrator genes (recA and the 16S rRNA gene) to determine relative expression. Thirteen genes displayed modest (fivefold or less) differences in expression with growth rate or substrate type: sdbA (cellulosomal scaffoldin-dockerin binding protein), cdp (cellodextrin phosphorylase), cbp (cellobiose phosphorylase), hydA (hydrogenase), ldh (lactate dehydrogenase), ack (acetate kinase), one putative type IV alcohol dehydrogenase, two putative cyclic AMP binding proteins, three putative Hpr-like proteins, and a putative Hpr serine kinase. By contrast, four genes displayed >10-fold-reduced levels of expression when grown on cellobiose at dilution rates of >0.05 h(-1): cipA (cellulosomal scaffolding protein), celS (exoglucanase), manA (mannanase), and a second type IV alcohol dehydrogenase. The data suggest that at least some cellulosomal components are transcriptionally regulated but that differences in expression with growth rate or among substrates do not directly account for observed changes in fermentation end product distribution.
Probability (2010)

This classic introduction to probability theory for beginning graduate students covers laws of large numbers, central limit theorems, random walks, martingales, Markov chains, ergodic theorems, and Brownian motion. It is a comprehensive treatment concentrating on the results that are the most useful for applications. Its philosophy is that the best way to learn probability is to see it in action, so there are 200 examples and 450 problems. The fourth edition begins with a short chapter on measure theory to orient readers new to the subject.
Geological seismography (1940)

My remarks pertain to the application of seismography to geological surveying. Captain Heck's paper is particularly pertinent, especially as it is an excellent summary of the real contributions which our Special Committees of the Union have made in such a significant phase of geophysics during the past three or four years. The points which I should like to emphasize are as follows: (1) Seismography is the earliest of geophysical techniques directly applied to the study of the composition and structure of the Earth. This has been recognized in most text‐books of general geology from the time of Sir Charles Lyell.
Comparison of the selective estrogen receptor modulator arzoxifene (LY353381) with tamoxifen on tumor growth and biomarker expression in an MCF-7 human breast cancer xenograft model. (2003)

Arzoxifene (ARZ) is a selective estrogen receptor (ER) modulator with greater bioavailability than raloxifene which is being developed as treatment for breast cancer. We have used an in vivo model of hormone-sensitive breast cancer to study the growth-inhibitory and pharmacodynamic effects of ARZ in comparison with the most widely used antiestrogen, tamoxifen (TAM). We compared the abilities of ARZ and TAM to antagonize the estrogen (E2)-dependent growth of MCF-7 human breast cancer xenografts in oophorectomized athymic mice. At four different time points over 28 days, we studied their time-related pharmacodynamic effects on biomarkers of tumor growth (cell proliferation/death measured by Ki-67 and apoptosis scores), cell cycle activity (cyclin D1 and p27(kip1)), and hormone-regulated gene expression (ERalpha, progesterone receptor, and pS2). Although maximal growth inhibition was seen after E2 withdrawal, ARZ and TAM induced significant and similar inhibition of E2-stimulated tumor growth. Inhibition of growth was reflected by changes in the tumor growth index (ratio posttreatment/pretreatment Ki-67/apoptosis scores). ARZ and TAM resulted in a significant (P < 0.001) increase in ER expression and reduction in progesterone receptor expression, whereas changes in cyclin D1 score were inversely related to p27(kip1) score. A significant but delayed biological effect was observed with a 10-fold lower dose of ARZ. These results show that ARZ is an effective antagonist of E2-stimulated breast cancer growth with similar growth-inhibitory and pharmacodynamic effects to TAM in this model.
Movement of mitochondria in the axons and dendrites of cultured hippocampal neurons (2000)

Mitochondria generate ATP and are involved in the regulation of cytoplasmic calcium levels. It is thought that local demand for mitochondria differs between axons and dendrites. Moreover, it has been suggested that the distribution of both energy need and calcium flux in dendrites changes with patterns of synaptic activation, whereas the distribution of these demands in axons is stable. The present study sought to determine whether there are differences in mitochondrial movements between axons and dendrites that may relate to differences in local mitochondrial demand. We labeled the mitochondria in cultured hippocampal neurons with a fluorescent dye and used time-lapse microscopy to examine their movements. In both axons and dendrites, approximately one-third of the mitochondria were in motion at any one time. In both domains, approximately 70% of the mitochondria moved in the anterograde direction, whereas the remainder moved in the retrograde direction. The velocity of the movements in each direction in each domain ranged from 0.1 microm/sec to approximately 2 microm/sec, and the means and distributions of the velocities were similar. Only one difference in the behavior of mitochondria between axons and dendrites emerged from this analysis. Mitochondria in axons were more likely to move with a consistently rapid velocity than were those in dendrites. As a result, mitochondria in axons tended to travel farther than mitochondria in dendrites. These results suggest that the transport of mitochondria in axons and dendrites is similar despite any differences in mitochondrial demand between the two domains.
Application of Gas Endarterectomy to Atherosclerotic Peripheral Vessels and Coronary Arteries (1967)

A new technique of endarterectomy is described. It uses carbon dioxide gas, under pressure, to dissect the diseased inner layers of blood-vessel wall from the more normal outer layer. It has been utilized in 89 patients. It remains to be seen what the 5- and 10-year patency rates will be. This must, in large degree, relate to the patient's vascular disease. Finally, we hope that a series of coronary endarterectomies can be done to indicate the applicability of the technique to coronary revascularization.
Gabor Transforms: Some New Properties on the Gabor (1998)

By using the discrete Gabor transform or expansion, the time domain sequences are mapped into the joint time-frequency domain matrices or vice versa. In many applications, it is more effective to process signals, i.e., two dimensional matrices, in the joint timefrequency domain than in the time or frequency domain alone. From the mathematical point of view, the processing of the discrete Gabor coefficients is no more than the matrix computation. So it is beneficial to understand the properties of the Gabor coefficient matrix. In this paper, we shall investigate the rank of the Gabor coefficient matrix of a one dimensional time domain signal, which is one of the most important matrix properties.
Hemoglobin connecticut (β21(b3) Asp→Gly): A hemoglobin variant with low oxygen affinity (1981)

Electrophoretic analysis of a hemolysate from a young man undergoing a routine physical examination revealed an abnormal hemoglobin with a mobility similar to Hb S on cellulose acetate (pH, 8.4). This new variant, designated Hb Connecticut, was found in three generations of a family of Polish descent. Several individuals possessing the variant exhibited mild anemia. Structural analysis of the abnormal beta-chain indicated that the amino acid substitution was at position 21 (B3), and involved the replacement of aspartic acid with glycine. Oxygen dissociation studies revealed low oxygen affinity. The alkaline Bohr effect and the degree of cooperativity were unchanged. Analysis of the crystal structure of the variant suggested that the low oxygen affinity was due to the possible disruption of salt bridges between aspartic acid 21(B3) and lysines 61(ES) and 65(E9), changes that could lead to steric interference in oxygen binding.
NoRM: No‐Reference Image Quality Metric for Realistic Image Synthesis (2012)

Abstract Synthetically generating images and video frames of complex 3D scenes using some photo‐realistic rendering software is often prone to artifacts and requires expert knowledge to tune the parameters. The manual work required for detecting and preventing artifacts can be automated through objective quality evaluation of synthetic images. Most practical objective quality assessment methods of natural images rely on a ground‐truth reference, which is often not available in rendering applications. While general purpose no‐reference image quality assessment is a difficult problem, we show in a subjective study that the performance of a dedicated no‐reference metric as presented in this paper can match the state‐of‐the‐art metrics that do require a reference. This level of predictive power is achieved exploiting information about the underlying synthetic scene (e.g., 3D surfaces, textures) instead of merely considering color, and training our learning framework with typical rendering artifacts. We show that our method successfully detects various non‐trivial types of artifacts such as noise and clamping bias due to insufficient virtual point light sources, and shadow map discretization artifacts. We also briefly discuss an inpainting method for automatic correction of detected artifacts.
A delicate balance between rejection and BK polyomavirus associated nephropathy; A retrospective cohort study in renal transplant recipients (2017)

In conclusion, this study shows that immunosuppressive treatment with Tac and MPA compared to CsA and MPA is associated with a lower incidence of BPAR, but at the cost of an increased risk of developing BKPyVAN in the first two years post-transplant.
Estimating Anomality of the Video Sequences for Surveillance Using 1-Class SVM (2008)

We have proposed a method to detect and quantitatively extract anomalies from surveillance videos. Using our method, anomalies are detected as patterns based on spatio-temporal features that are outliers in new feature space. Conventional anomaly detection methods use features such as tracks or local spatio-temporal features, both of which provide insufficient timing information. Using our method, the principal components of spatio-temporal features of change are extracted from the frames of video sequences of several seconds duration. This enables anomalies based on movement irregularity, both position and speed, to be determined and thus permits the automatic detection of anomal events in sequences of constant length without regard to their start and end. We used a 1-class SVM, which is a non-supervised outlier detection method. The output from the SVM indicates the distance between the outlier and the concentrated base pattern. We demonstrated that the anomalies extracted using our method subjectively matched perceived irregularities in the pattern of movements. Our method is useful in surveillance services because the captured images can be shown in the order of anomality, which significantly reduces the time needed.
Pharmacokinetics, Biodistribution and Therapeutic Efficacy of Doxorubicin Encapsulated in Stealth® Liposomes (Doxil®) (1994)

Doxil® (Stealth® liposomal doxorubicin HCl) Injection is doxorubicin HCl incorporated into long circulating liposomes that contain surface-grafted polyoxyethylene chains. These surface-grafted polymer chains reduce the interaction of the liposomes with the mononuclear phagocytic system, accounting for the long circulation and altered biodistribution of Stealth liposomes. They also reduce adhesion of the liposomes to cells, blood vessel walls and other surfaces and result in increased vascular permeability of Stealth liposomes compared to conventional liposomes of equal size. Efficacy studies in several tumor models, including human xenograft models, have demonstrated that Doxil is more effective than unencapsulated doxorubicin (Adriamycin) or doxorubicin encapsulated in non-coated conventional liposomes. Doxil exhibits altered plasma pharmacokinetics, with a longer plasma half-life, large AUC and markedly smaller volume of distribution than Adriamycin. Tissue levels of doxorubicin are generally lower in Doxil-treated animals than in animals that receive an equivalent dose of Adriamycin, and Doxil is less cardiotoxic, myelotoxic and nephrotoxic than Adriamycin. Phase I and II studies evaluating the efficacy of Doxil in AIDS-related Kaposi sarcoma have been encouraging, with evidence of increased delivery of drug to the lesions and an overall good response to therapy. The increased efficacy of Doxil is believed to be related to its increased extravasation through the leaky tumor vasculature and its accumulation in tumor tissue.
<title>Script determination in document images</title> (1995)

We have developed techniques for distinguishing which language is represented in an image of text. This work is restricted to an important subset of the world's languages, using techniques that should be applicable across even more comprehensive samples. The method first classifies the script into two broad classes: European and Asian. This classification is based on the spatial relationships of fiducial points related to the upward concavities in character structures. Script identification within the Asian class, (Japanese, Chinese, Korean) is performed by analysis of the optical density distribution of the text images.
Matrix Metalloproteinases (MMP-2 and MMP-9) of the Oral Cavity: Cellular Origin and Relationship to Periodontal Status (1994)

Proteolytic enzymes released by the host cells are associated with the tissue destruction in periodontal diseases. Matrix metalloproteinases (MMPs) have the primary role in this process, since, in concert, they can degrade most of the extracellular matrix components. In the present study, we investigated MMP-2 and MMP-9 in oral fluids of healthy subjects and periodontitis patients and the contributions of different oral cells to the enzyme production. The enzymograms revealed that the main gelatinase in oral rinses, crevicular fluid, and whole saliva migrated at 92 kDa. Activity was also detected at 200 kDa and 130 kDa and minor activity at 86 kDa, 72 kDa, and 40 kDa. Traces of gelatinolytic activity were also detected in pure parotid secretions. The 92-kDa enzyme was identified to MMP-9 and the 200-kDa gelatinase to MMP-2, by means of specific anti-72-kDa antiserum. Gingival keratinocytes produced mainly MMP-9, while gingival and granulation tissue fibroblasts expressed MMP-2. Glandular tissue contained mainly MMP-9, and mRNA for MMP-9 was also found in acinar epithelial cells. Periodontitis patients had significantly higher levels of MMP-9 than healthy subjects. Also, MMP-2 was elevated in periodontitis patients. Periodontal treatment reduced the amount of gelatinases dramatically. This study shows that gelatinases are produced by various cells in the oral cavity. The amount of gelatinases is elevated during periodontal disease, while conventional periodontal treatment efficiently reduces the levels these enzymes. We suggest that MMP-2 and MMP-9 could participate in tissue destruction in periodontitis.
Annexin-II, DNA, and Histones Serve as Factor H Ligands on the Surface of Apoptotic Cells (2009)

Apoptotic cells are opsonized by complement components such as C1q and C3b, which increases their susceptibility to phagocytosis. Soluble complement inhibitors such as factor H (fH) also recognize apoptotic cells to minimize the pro-inflammatory effects of downstream complement activation. We used four radiolabeled protein constructs that span different regions of the 20 complement control protein (CCP) modules that make up fH and found that fragments comprising CCPs 6-8, CCPs 8-15, and CCPs 19-20 but not CCPs 1-4, bound to apoptotic Jurkat T cells. There are four possible ligand types on apoptotic cells that could recruit fH: proteins, carbohydrates, lipids, and DNA. We found that CCPs 6-8 of fH bind to annexin-II, a trypsin-insensitive protein that becomes exposed on surfaces of apoptotic cells. The second ligand of fH, which interacts with CCPs 6-8 and 19-20, is DNA. Confocal microscopy showed co-localization of fH with antibodies specific for DNA. fH also binds to histones devoid of DNA, and CCPs 1-4, 6-8, and 8-15 mediate this interaction. Treatment of apoptotic cells with neuraminidase, chondroitinase, heparitinase, and heparinase did not change fH binding. Treatment of apoptotic cells with phospholipase A(2) dramatically increased both binding of fH and cell-surface DNA. We also excluded the possibility that fH interacts with lysophospholipids using surface plasmon resonance and flow cytometry with lipid-coated beads. Identification of annexin-II as one of the fH ligands on apoptotic cells together with the fact that autoantibodies against annexin-II are found in systemic lupus erythematosus provides further insight into understanding the pathogenesis of this disease.