gebhart/patrepeval huggingface dataset:
Construction of a set of Saccharomyces cerevisiae vectors designed for recombinational cloning (2003)

The Gateway technology is becoming an increasingly popular method for cloning ORFs by recombination. It allows the transfer of any ORF flanked by specific recombination sites into any vectors harbouring the corresponding sites. Here we describe the construction of a set of 20 Saccharomyces cerevisiae Gateway compatible vectors. These plasmids bear an URA3 or TRP1 selection marker. They are designed for expression without tag sequence or for C- or N-terminal protein tagging with 3HA (haemagglutinin), 13MYC, 4TAP (tandem affinity purification) or GST (glutathione S-transferase) epitopes. The centromeric vectors allow expression of DNA sequence in yeast under tetracycline-regulatable promoters, while expression from the high copy vectors is driven by PGK promoter. To test their applicability, the genes encoding the RNA polymerase I subunit Rpa12p or the TFIIS transcription factor were cloned in these vectors. Their expression was demonstrated using Western blotting or complementation assays.
Surfactants and Polymers in Drug Delivery (2002)

This reference features the latest findings surrounding the physicochemical aspects of surfactant and polymer systems to facilitate the design and understanding of novel and advanced drug delivery formulations. It covers the basics of surfactant and polymer surface activity and self-assembly, the various types of structures formed by such compounds
Efficient interactive fuzzy keyword search (2009)

Traditional information systems return answers after a user submits a complete query. Users often feel "left in the dark" when they have limited knowledge about the underlying data, and have to use a try-and-see approach for finding information. A recent trend of supporting autocomplete in these systems is a first step towards solving this problem. In this paper, we study a new information-access paradigm, called "interactive, fuzzy search," in which the system searches the underlying data "on the fly" as the user types in query keywords. It extends autocomplete interfaces by (1) allowing keywords to appear in multiple attributes (in an arbitrary order) of the underlying data; and (2) finding relevant records that have keywords matching query keywords approximately. This framework allows users to explore data as they type, even in the presence of minor errors. We study research challenges in this framework for large amounts of data. Since each keystroke of the user could invoke a query on the backend, we need efficient algorithms to process each query within milliseconds. We develop various incremental-search algorithms using previously computed and cached results in order to achieve an interactive speed. We have deployed several real prototypes using these techniques. One of them has been deployed to support interactive search on the UC Irvine people directory, which has been used regularly and well received by users due to its friendly interface and high efficiency.
Reversal of Type 1 Diabetes in Mice by Brown Adipose Tissue Transplant (2012)

Current therapies for type 1 diabetes (T1D) involve insulin replacement or transplantation of insulin-secreting tissue, both of which suffer from numerous limitations and complications. Here, we show that subcutaneous transplants of embryonic brown adipose tissue (BAT) can correct T1D in streptozotocin-treated mice (both immune competent and immune deficient) with severely impaired glucose tolerance and significant loss of adipose tissue. BAT transplants result in euglycemia, normalized glucose tolerance, reduced tissue inflammation, and reversal of clinical diabetes markers such as polyuria, polydipsia, and polyphagia. These effects are independent of insulin but correlate with recovery of the animals' white adipose tissue. BAT transplants lead to significant increases in adiponectin and leptin, but with levels that are static and not responsive to glucose. Pharmacological blockade of the insulin receptor in BAT transplant mice leads to impaired glucose tolerance, similar to what is seen in nondiabetic animals, indicating that insulin receptor activity plays a role in the reversal of diabetes. One possible candidate for activating the insulin receptor is IGF-1, whose levels are also significantly elevated in BAT transplant mice. Thus, we propose that the combined action of multiple adipokines establishes a new equilibrium in the animal that allows for chronic glycemic control without insulin.
Treatment of canine atopic dermatitis: 2010 clinical practice guidelines from the International Task Force on Canine Atopic Dermatitis (2010)

Atopic dermatitis (AD) is a common chronic relapsing pruritic skin disease of dogs for which treatment has varied over time and geographical location. Recent high quality randomized controlled trials and systematic reviews have established which drugs are likely to offer consistent benefit. The International Task Force for Canine AD currently recommends a multi-faceted approach to treat dogs with AD. Acute flares should be treated with a combination of nonirritating baths and topical glucocorticoids, once an attempt has been made to identify and remove the suspected causes of the flare. Oral glucocorticoids and antimicrobial therapy must be added when needed. In dogs with chronic AD, a combination of interventions should be considered. Again, factors that trigger flares of AD must be identified and, if possible, avoided. Currently recognized flare factors include food, flea and environmental allergens, Staphylococcus bacteria and Malassezia yeast. Skin and coat hygiene and care must be improved by bathing with nonirritating shampoos and dietary supplementation with essential fatty acids. The severity of pruritus and skin lesions can be reduced with a combination of anti-inflammatory drugs. Currently, medications with good evidence of high efficacy include topical and oral glucocorticoids, and calcineurin inhibitors such as oral ciclosporin and topical tacrolimus. The dose and frequency of administration of these drugs should be tailored to each patient considering each drug's efficacy, adverse effects and cost. Allergen-specific immunotherapy should be offered, whenever feasible, in an attempt to prevent recurrence of clinical signs upon further exposure to environmental allergens to which the patient is hypersensitive.
Vocal detection in music with support vector machines (2008)

We propose a statistical learning approach for the automatic detection of vocal regions in a polyphonic musical signal. A support vector model, based on a large feature set, is employed to discriminate accompanied singing voice from pure instrumental regions. We propose a temporal smoothing of the posterior probabilities with a hidden Markov model that helps adapting the segmentation sequence to the precision of the manual annotation. Quantitative results on a copyright- free public musical corpus show a classification accuracy of 82%.
Medical Problem Solving (1990)

This essay reviews the origins, findings and influence of the monograph Medical Problem Solving: An Analysis of Clinical Reasoning. Majorfindings of the monograph are reviewed in the light of subsequent work and the results of selected studies of clinical cognition are related to the book's conclusions, thus sketching the growth of this field of research in the decade since publication. Several remaining methodologicalproblems and scholarly issues in the field are discussed, including: sampling cases and subjects, the definition of medical expertise, the role of verbal report in analyzing thinking, the level of clinical realism needed in research, and the relation of informationprocessing approaches to more quantitative approaches such as behavioral decision theory and social judgment theory.
Urate oxidase (rasburicase) for treatment of severe tophaceous gout (2005)

Gout is a clinical disorder caused by deposition of urate crystals in a joint leading to acute inflammatory response with acute pain. In severe and longstanding gout, the crystals accumulate in soft tissues such as cartilage, subcutaneous tissue or even veins leading to the development of tophi responsible for very large deposit formations and disability. Most cases of gout present with the sudden onset of severe acute arthritis in a peripheral joint in the leg. Urate oxidase, or uricase (EC 1.7.3.3), is a peroxisomal liver enzyme that catalyses the enzymatic oxidation of uric acid into the more water-soluble allantoin (Figure 1). Urate oxidase is an endogenous enzyme found in most mammals but not in humans. During primate evolution, the inactivation of the hominoid urate oxidase gene was caused by independent nonsense or frameshift mutations and has taken a two-step deterioration process, first in the promotor and second in the coding region [1]. Two nonsense mutations were found in the human urate oxidase gene, which confirms, at the molecular level, that the urate oxidase gene in humans is non-functional [2–3]. Because uric acid is a powerful scavenger of free radicals, it has been proposed that uric acid plays an important role in protection hominoids from oxidative damage and the prolonged live span [1,4]. Urate oxidase is used in humans for the control of increased serum uric acid in patients with acute tumour lysis syndrome after receiving chemotherapy. Rasburicase (SR 29142), a recombinant urate oxidase expressed in Saccharomyces cerevisiae, has been demonstrated to be superior to allopurinol in the control of uric acid in a randomized trial of paediatric and adult patients at risk of acute tumour lysis syndrome [5,6]. However, only few case reports address the potential role of urate oxidase for treatment of severe tophaceous gout. A French group treated three heart transplant patients with uncontrollable gout with non-recombinant urate oxidase and observed shrinking of tophi and improved mobility of the fingers in all three patients [7]. Phillips and co-workers used rasburicase for treatment of severe tophaceous gout refractory to high-dose allopurinol in a patient with end-stage renal disease and observed a regression of gout tophi [8]. The treatment was well tolerated in all reported patients and produced no adverse effects. We analysed efficacy and safety of rasburicase in the long-term control of hyperuricaemia in an adult kidney transplant patient with severe tophaceous gout.
Origins and control of polarization effects in single-mode fibers (1983)

The polarization state of light in single-mode fibers is very sensitive to any perturbation which is not symmetric about the fiber axis. While this is a source of noise, drift, or signal fading in some applications, it can also be exploited in novel guided-wave devices. The basic birefringences that couple the two modes and change the polarization state along the fiber are reviewed. The three cases of uniform, phase-matched, and random coupling are considered. Polarization preservation in both low- and high-birefringence fibers is achieved by reducing this coupling. In addition to polarization-state changes, bireftingent fibers can quickly reduce the polarization degree of nonmonochromatic light if both modes are excited, a characteristic that greatly simplifies evaluation of the degree of polarization preservation in these fibers. Current evaluations of the birefringence and the polarization-holding ability of state-of-the-art fibers are discussed, and it is concluded that fibers with good polarization-holding properties are becoming available.
Human liver cathepsin L (1985)

Cathepsin L was purified to apparent homogeneity from human liver obtained post mortem. It was necessary to treat the homogenate at pH 4.2 and 37 degrees C to release active enzyme. The purification procedure involved ion-exchange chromatography on carboxymethyl-Sephadex and the Mono S column of a Pharmacia fast-protein-liquid-chromatography system. The enzyme was found to consist of two polypeptide chains of Mr 25 000 and 5000. The larger chain was shown to contain the active-site cysteine residue. Human cathepsin L proved to be similar to the rat and rabbit enzymes in regard to kinetic constants for the substrate benzyloxycarbonylphenylalanylarginine 7-(4-methyl)coumarylamide and rates of inactivation by the active-site-directed reagents benzyloxycarbonylphenylalanylphenylalanyldiazomethane and benzyloxycarbonylphenylalanylalanyldiazomethane. Thus clear characteristics of cathepsin L are now emerging, and these should simplify the identification of the enzyme in other tissues and species.
Effect of manufacturing defects on optical performance of discontinuous freeform lenses (2009)

Discontinuous freeform lens based secondary optics are essential to LED illumination systems. Surface roughness and smooth transition between two discrete sub-surfaces are two of the most common manufacturing defects existing in discontinuous freeform lenses. The effects of these two manufacturing defects on the optical performance of two discontinuous freeform lenses were investigated by comparing the experimental results with the numerical simulation results based on Monte Carlo ray trace method. The results demonstrated that manufacturing defects induced surface roughness had small effect on the light output efficiency and the shape of light pattern of the PMMA lens but significantly affected the uniformity of light pattern, which declined from 0.644 to 0.313. The smooth transition surfaces with deviation angle more than 60 degrees existing in the BK7 glass lens, not only reduced the uniformity of light pattern, but also reduced the light output efficiency from 96.9% to 91.0% and heavily deformed the shape of the light pattern. Comparing with the surface roughness, the smooth transition surface had a much more adverse effect on the optical performance of discontinuous freeform lenses. Three methods were suggested to improve the illumination performance according to the analysis and discussion.
Rearrangement and cleavage of [(aryloxy)methyl]silanes by organolithium reagents: conversion of phenols into benzylic alcohols (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRearrangement and cleavage of [(aryloxy)methyl]silanes by organolithium reagents: conversion of phenols into benzylic alcoholsJohn J. Eisch, James E. Galle, Andrzej Piotrowski, and Miin Rong TsaiCite this: J. Org. Chem. 1982, 47, 26, 5051–5056Publication Date (Print):December 1, 1982Publication History Published online1 May 2002Published inissue 1 December 1982https://pubs.acs.org/doi/10.1021/jo00147a002https://doi.org/10.1021/jo00147a002research-articleACS PublicationsRequest reuse permissionsArticle Views1471Altmetric-Citations26LEARN 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
Generation and Characterization of Monoclonal Antibodies Against the E6 and E7 Oncoproteins of HPV (2001)

Generation of three monoclonal antibodies (MAbs) to the major oncoproteins of human papillomavirus (HPV) was accomplished by an intense prime/boost regimen. Mice were primed with expression vectors expressing either the E6 or E7 oncoproteins of HPV-16 followed by boosting with a vaccinia virus construct and a replication-defective E1-deleted adenoviral recombinant of the human strain 5, and last, with baculovirus-derived HPV-16 E6 and E7 proteins in incomplete Freunds' adjuvant. Splenocytes were then fused with a myeloma cell line. The vaccination protocol generated one anti-E7 MAb of the IgM isotype and two anti-E6 MAbs of the IgG1 subisotype. The MAbs were tested for functionality in standard laboratory assays and found to detect the E6 and E7 proteins, respectively. The E7 MAb cross-reacted with the HPV-1a E7 oncoprotein. The binding sites of the MAbs were mapped to defined regions of each viral protein.
Hedgehog Secretion and Signal Transduction in Vertebrates (2012)

Signaling by the Hedgehog (Hh) family of secreted proteins is essential for proper embryonic patterning and development. Dysregulation of Hh signaling is associated with a variety of human diseases ranging from developmental disorders such as holoprosencephaly to certain forms of cancer, including medulloblastoma and basal cell carcinoma. Genetic studies in flies and mice have shaped our understanding of Hh signaling and revealed that nearly all core components of the pathway are highly conserved. Although many aspects of the Drosophila Hh pathway are conserved in vertebrates, mechanistic differences between the two species have begun to emerge. Perhaps the most striking divergence in vertebrate Hh signaling is its dependence on the primary cilium, a vestigial organelle that is largely absent in flies. This minireview will provide an overview of Hh signaling and present recent insights into vertebrate Hh secretion, receptor binding, and signal transduction.
Printing chemical libraries on microarrays for fluid phase nanoliter reactions (2003)

Chemical compounds within individual nanoliter droplets of glycerol were microarrayed onto glass slides at 400 spots/cm2. Using aerosol deposition, subsequent reagents and water were metered into each reaction center to rapidly assemble diverse multicomponent reactions without crosscontamination or the need for surface linkage. This proteomics technique allowed the kinetic profiling of protease mixtures, protease-substrate interactions, and high-throughput screening reactions. An inhibitor of caspases 2, 4, and 6 was identified by using a 352-compound combinatorial library microarrayed in quadruplicates on 100 slides and screened against caspases 2, 4, and 6, as well as thrombin and chymotrypsin. From one printing run that consumes <1 nanomole of each compound, large combinatorial libraries can be subjected to numerous separation-free homogeneous assays at volumes 103-104 smaller than current high-throughput methods.
Relative lung and systemic bioavailability of sodium cromoglycate inhaled products using urinary drug excretion post inhalation (2002)

The relative lung and systemic bioavailability of sodium cromoglycate following inhalation by different methods have been determined using a urinary excretion pharmacokinetic method. On three separate randomised study days, 7 days apart, subjects inhaled (i) 4x5 mg from an Intal metered dose inhaler (MDI), (ii) 4x5 mg from an MDI attached to a large volume spacer (MDI+SP) and (iii) 20 mg from an Intal Spinhaler (DPI). Urine samples were provided at 0, 0.5, 1, 2, 5 and 24 h post dose. The mean (S.D.) amount of sodium cromoglycate excreted in the urine during the first 30 min post inhalation was 38.1 (27.5), 222.3 (120.3) and 133.1 (92.2) microg following MDI, MDI+SP and DPI, respectively. The mean ratio (90% confidence interval) of these amounts excreted in the urine over the first 30 min for MDI+SP vs. MDI, DPI vs. MDI and MDI+SP vs. DPI was 801.0 (358.0, 1244; p<0.002)%, 457.0 (244.0, 670.0; p<0.02)% and 262.4 (110.2, 414.5)%, respectively. Similarly for the 24 h cumulative amount of sodium cromoglycate excreted over the 24 h post inhalation the ratios were 375.4 (232.9, 517.9; p<0.005)%, 287.5 (183.4, 391.6; p<0.02)% and 211.4 (88.3, 334.5)%, respectively. The results highlight better lung deposition of sodium cromoglycate from a metered dose inhaler attached to a large volume spacer.
The distinct expression patterns of claudin-10, -14, -17 and E-cadherin between adjacent non-neoplastic tissues and gastric cancer tissues (2013)

The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1475928069111326.
GaAs metal semiconductor metal photodetectors with low dark current and high responsivity at 850 nm (2002)

In this paper, we report on the fabrication a GaAs metal–semiconductor–metal photodetector with both low dark current and high responsivity at 850 nm. By using the Schottky contacts modified by a thin, n+-doped layer on the surface of the devices, the lowest dark current density of about 4.5 × 10−7 cm−2 was achieved. Besides, in the same devices, the responsivity resulting from a newly designed resonant-cavity-enhanced structure with a superlattice distributed Bragg reflector was about 0.34 A W−1 at 850 nm. The equivalent external quantum efficiency of the devices with equal finger spacing and finger width was about 48%. Our design is relatively easy and reproducible for both the sample growth and the device process.
A multicenter, double-blind, randomized, controlled phase III clinical trial of chicken type II collagen in rheumatoid arthritis (2009)

ChiCTR-TRC-00000093.
ChemInform Abstract: Halogens (F, Cl, Br, I, At) and Noble Gases (1989)

Abstract Review: (123 refs.
0461 Patterns of Tongue Thickness Changes in Obstructive Sleep Apnea Patients: A Whole-Night Simultaneous Ultrasound and Polysomnographic Study (2019)

Tongue deformation may play a critical role in the development of obstructive sleep apnea (OSA). We combined an ultrasound system with polysomnography (PSG) to simultaneously record changes in tongue thickness during a whole night’s sleep. Our ultrasound system included a custom-designed curvilinear transducer. The center frequency of the probe was 3 MHz, and it had 16 channels. We placed the probe in the submental midline sagittal plane. We designed a dedicated ultrasound device to automatically detect maximum tongue thickness at a recording rate of 1 Hz. The device synchronizes with the PSG and transmits the measured data to a computer for storage. The system receives an A-line signal from each channel, determines the depth of the air-mucosal interface as the tongue thickness, and then registers the maximum tongue thickness and its channel number. We generated a “SonoPSG” report for each patient, reporting on the mean or median maximum tongue thickness and the distribution of the registered channels in various sleep stages as well as during various respiratory events. In total, the study comprised 50 patients, including 15 without OSA, 7 with mild, 14 with moderate and 14 with severe OSA. We calculated the mean maximum tongue thickness during eupnea and respiratory events according to OSA severity. A mixed-model ANOVA demonstrated a significant difference between the groups. The distribution of the registered channels in eupnea and other respiratory events showed that when eupnea and snoring occurred, most registered channels were located in the second quartile of the tongue. However, when hypopnea or apnea occurred, most registered channels shifted posteriorly toward the third quartile of the tongue. With our novel ultrasound system, quantified tongue thickness results can be recorded during the whole night and synchronized with PSG. Future applications of our ultrasound system will involve an individualized treatment plan for each OSA patient, to verify treatment results, especially for those procedures targeting the tongue, and to investigate the pathophysiology of OSA. None