gebhart/patrepeval huggingface dataset:
Immunologic responses during allergen-specific immunotherapy for respiratory allergy. (1988)

At present there is no absolute way to determine which patient will respond to immunotherapy and which will not. Even in treated patients who derive clinical benefit, there is no one "best" immunologic parameter to follow although the generation of allergen-specific IgG seems to correlate better with clinical improvement than the other parameters. Whether or not the measurement of allergen-specific IgG4 will prove to be a useful clinical parameter is still a controversial issue and is an area for active investigation. The reason that IgG4 becomes elevated selectively over time during immunotherapy is not clear nor is its function known in the immune response to allergen. It is of interest however that IgG4 does not fix complement and may therefore account for the absence of immune complex disease in patients treated over many years. The modification of allergens through denaturization so that they are less reactive with preformed IgG has resulted in potent preparations that induce a strong IgG response. These preparations permit flexibility in dosage and in frequency of administration as well as produce no greater side effects than aqueous extracts. While these preparations would be a decided advantage over existing extracts, recent information that is accumulating regarding T cell recognition of antigen opens the way for more precise targeting of our therapy. That is, determination of the antigenic epitopes that trigger helper T cells should permit the construction of peptides that can "block" T cell recognition and potentially lead to immunologic unresponsiveness.(ABSTRACT TRUNCATED AT 250 WORDS)
The Structure of β-Amino Derivatives of Nitroölefins<sup>1</sup> (1956)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Structure of β-Amino Derivatives of Nitroölefins1Jeremiah P. Freeman and William D. EmmonsCite this: J. Am. Chem. Soc. 1956, 78, 14, 3405–3408Publication Date (Print):July 1, 1956Publication History Published online1 May 2002Published inissue 1 July 1956https://pubs.acs.org/doi/10.1021/ja01595a039https://doi.org/10.1021/ja01595a039research-articleACS PublicationsRequest reuse permissionsArticle Views139Altmetric-Citations15LEARN 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
Generating detailed scene descriptions from range images (2005)

Techniques for extracting detailed, complete descriptions of polyhedral objects from light-stripe rangefinder data are described. The descriptions are in the form of 3D faces, edges, vertices, and their topology and geometry. A range image is first segmented into edge points. A line drawing is then obtained by fitting linear segments to the points in the image, and refining the segments to eliminate gaps. Faces are then generated from the line drawing. Interestingly, although the final description is in 3D. most of the processing is done in the 2D image space. This paper describes one part of a larger project whose goal is to obtain a full symbolic description of a scene from range data obtained from multiple viewpoints.
DBG2OLC: Efficient Assembly of Large Genomes Using the Compressed Overlap Graph (2015)

The highly anticipated transition to the third generation DNA sequencing (3rdGS) technology have reached a stalemate primarily due to the high error rates (15-45%), which make the assembly of long erroneous reads extremely challenging because existing software solutions for 3rdGS assembly are often overwhelmed by error correction tasks. We report three significant breakthroughs that push the envelope of genome assembly and offer an enabling software solution to overcome the current 3rdGS stalemate. Firstly, we take a counter-intuitive strategy and develop a base-level correction-free assembly algorithm, which resorts to data compression technology and the assembly was performed with the compressed reads. Magnitudes of compression lead to magnitudes of reduction in read lengths, enabling magnitudes of savings in computational time and memory space. We implement the new algorithm in a proof-of-concept software package DBG2OLC. Experiments with the 3rdGS data including PacBio and Oxford Nanopore show that our method is able to assemble large genomes magnitudes more efficiently than existing methods. For example, on a large PacBio human genome dataset we calculated the all-pair alignment of 54x erroneous long reads in 6 hours compared to the 405,000 CPU hours previously reported by Pacific Biosciences. Secondly, while maintaining comparable high quality assemblies, our approach requires significantly lower sequencing coverage (10x-20x) than existing assemblers, which translates to significant cost-cut for genome sequencing. Thirdly, our method is highly adaptive and is the only one to date that demonstrates ultra efficiencies not only for the 3rdGS PacBio and Nanapore sequences, but also for the latest NGS data.
Effect of Breathing, Pressure and Posture on Palatoglossal and Genioglossal Tone (1995)

1. Patency of the upper airway is critical to respiration. Although about half of patients with the sleep apnoea/hypopnoea syndrome obstruct their upper airway at the retropalatal level, the respiratory actions of the palatal muscles have been little studied. We have therefore tested the hypothesis that the nasopharyngeal dilator muscle palatoglossus is activated during inspiration and by negative pressure. 2. Using intramuscular wire electrodes inserted perorally, we have compared the response of palatoglossus and genioglossus to breathing, posture change and airway negative pressure in 10 normal awake subjects before and after topical anaesthesia. The results are expressed as a percentage of maximal electromyogram. Data were analysed by repeated-measures analysis of variance. 3. Inspiratory activity was exhibited by both genioglossus [inspiratory, 10% +/- 2% (SEM); expiratory, 6% +/- 1%, P = 0.001] and palatoglossus (inspiratory, 16% +/- 5%, expiratory, 10% +/- 3%, P = 0.016), but only genioglossus exhibited increased activity on lying (supine 10% +/- 2%, erect 6% +/- 1% maximum, P = 0.01). 4. One hundred milliseconds after negative pressure application, activity increased in both genioglossus (7% +/- 2% and 13% +/- 3% respectively, P = 0.02) and palatoglossus (8% +/- 2% and 23% +/- 6% respectively, P < 0.001). After lignocaine surface anaesthesia to the nose and pharynx both genioglossus and palatoglossus still increased their activity in response to negative upper airway pressure, the extent of the increase being decreased for palatoglossus (P = 0.02) but not for genioglossus. 5. Thus, palatoglossus has respiratory activity and is activated by negative upper airway pressure.
High Affinity InhA Inhibitors with Activity against Drug-Resistant Strains of <i>Mycobacterium tuberculosis</i> (2006)

Novel chemotherapeutics for treating multidrug-resistant (MDR) strains of Mycobacterium tuberculosis (MTB) are required to combat the spread of tuberculosis, a disease that kills more than 2 million people annually. Using structure-based drug design, we have developed a series of alkyl diphenyl ethers that are uncompetitive inhibitors of InhA, the enoyl reductase enzyme in the MTB fatty acid biosynthesis pathway. The most potent compound has a Ki' value of 1 nM for InhA and MIC99 values of 2-3 microg mL(-1) (6-10 microM) for both drug-sensitive and drug-resistant strains of MTB. Overexpression of InhA in MTB results in a 9-12-fold increase in MIC99, consistent with the belief that these compounds target InhA within the cell. In addition, transcriptional response studies reveal that the alkyl diphenyl ethers fail to upregulate a putative efflux pump and aromatic dioxygenase, detoxification mechanisms that are triggered by the lead compound triclosan. These diphenyl ether-based InhA inhibitors do not require activation by the mycobacterial KatG enzyme, thereby circumventing the normal mechanism of resistance to the front line drug isoniazid (INH) and thus accounting for their activity against INH-resistant strains of MTB.
Fiber-Optic Nitric Oxide-Selective Biosensors and Nanosensors (1998)

Fiber-optic biosensors that are selective for nitric oxide and do not respond to most potential interferents have been prepared with cytochromes c'. Both micro- and nanosensors have been prepared, and their response is fast (< 1 s), reversible, and linear up to 1 mM nitric oxide. The detection limit is 20 microM, making the sensor useful for some biological samples, such as the macrophages studied here. While sensors have been prepared based on the fluorescence of the cytochromes c', optodes with greatly enhanced signal-to-noise ratios have been made by labeling the cytochrome c' with a fluorescent dye. Comparisons of cytochromes c' from three species of bacteria as well as of two matrixes were performed and the optimum sensor configuration is described.
Correlations of the Basicity of His 57 with Transition State Analogue Binding, Substrate Reactivity, and the Strength of the Low-Barrier Hydrogen Bond in Chymotrypsin (1998)

The basicity of His 57-Nepsilon2 within the low-barrier hydrogen-bonded (LBHB) diad His 57-Asp 102 and the 1H NMR chemical shift of the LBHB proton in tetrahedral, hemiketal complexes of chymotrypsin with peptidyl trifluoromethyl ketones (peptidyl-TFKs) have been studied. The following results were obtained with various peptidyl-TFKs at 5 degrees C: N-Ac-Gly-DL-Phe-CF3, pKa = 11.1 and deltaLBHB = 18.7 ppm; N-Ac-L-Val-DL-Phe-CF3, pKa = 11.8 and deltaLBHB = 18.9 ppm; N-Ac-L-Leu-DL-Val-CF3, pKa = 10.3 and deltaLBHB = 18.9 ppm; and N-Ac-L-Leu-DL-naphthyl-CF3, pKa = 10.9 and deltaLBHB = 19.0 ppm. Results for peptidyl-TFKs with Phe in the P1 position and N-Ac, N-Ac-Gly, N-Ac-L-Val, and N-Ac-L-Leu in the P2 position were well correlated with literature values for inhibition constants Ki and kcat/Km for the corresponding peptidyl methyl esters. The plot of log Ki versus the apparent pKa of His 57-Nepsilon2 displayed a slope of -0.77, and that of log kcat/Km for peptidyl methyl esters versus the pKa of His 57-Nepsilon2 in corresponding peptidyl-TFK complexes gave a slope of 0.68. The slope of a plot of pKa versus deltaLBHB was 3.7, and that of log kcat/Km for peptidyl methyl ester substrates versus deltaLBHB for the corresponding peptidyl-TFK-chymotrypsin complexes was 2.7. A plot of log Ki versus deltaLBHB displayed a slope of -3.0. These plots indicated that the pKa of His 57 and substrate reactivity were correlated with increasing strength of the low-barrier hydrogen bond. The apparent pKa of His 57-Nepsilon2 for the chymotrypsin-N-Ac-L-Leu-DL-Phe-CF3 complex is 10.6 at 25 degrees C, whereas it is 12.0 at 5 degrees C [Cassidy, C. S., Lin, J. L., and Frey, P. A. (1997) Biochemistry 36, 4576-4584]. The apparent discrepancy is likely to be due to a temperature dependence in the cooperative ionization of His 57 in peptidyl-TFK complexes, which appears to be coupled to inhibitor dissociation, hydration and ionization of free peptidyl-TFK, ionization of Ile 16, and a conformational change.
The 9S RNA precursor of<i>Escherichia coli</i>5S RNA has three structural domains: implications for processing (1988)

The secondary structure of the 9S RNA precursor to ribosomal 5S RNA in Escherichia coli has been determined using chemical reagents and ribonucleases in combination with a reverse transcription procedure. The 9S RNA precursor was generated in vitro by T7 RNA polymerase, and the rrnB operon terminator, T1, was able to terminate the in vitro transcript. The secondary structure model exhibits three structural domains corresponding to a 5' region, a mature region and a terminator region. The mature domain is structurally identical to 5S RNA, and the ribosomal proteins L18 and L25 are able to bind to the precursor. The processing endoribonuclease RNase E cleaves between the structural domains. Moreover, an intramolecular refolding of the nascent transcript must take place if the current view of RNase III processing stems is correct.
Choline transport in Saccharomyces cerevisiae (1980)

Choline transport of Saccharomyces cerevisiae was measured by the filtration method with the use of glass microfiber paper. The uptake was time and temperature dependent. The kinetics of choline transport showed Michaelis behavior; an appearent Km for choline was 0.56 microM. N-Methylethanolamine, N,N-dimethylethanolamine, and beta-methylcholine were competitive inhibitors of choline transport, with Ki values of 40.1, 3.1, and 6.9 microM, respectively. Ethanolamine, phosphorylcholine, and various amino acids examined had no effect. Choline transport required metabolic energy; removal of glucose resulted in a great loss of transport activity, and the remaining activity was abolished by 2,4-dinitrophenol, carbonyl cyanide p-trifluoromethoxyphenyl hydrazone, arsenate, and cyanide. External Na+ was not required, and the transport was not effected by ionophores, valinomycin, and gramicidin D. These results indicate that S. cerevisiae possess an active choline transport system mediated by a specific carrier. This view is further supported by the isolation and characterization of a choline transport mutant. The choline transport activity in this mutant was very low, whereas the transport of L-leucine, L-methionine, D-glucose, and myo-inositol was normal. Together with the choline transport mutant, mutants defective in choline kinase were also isolated.
Distributed, game-based, intelligent tutoring systems &#x2014; The next step in computer based training? (2008)

This paper proposes what may be the step in computer based training, a distributed, game-based intelligent tutoring system, and discusses possible complications with creating such a system. Recent research has demonstrated a positive effect on learning by integrating intelligent tutoring systems within virtual worlds and video games as teaching aids. These systems cover many topics including reading and math for elementary students as well as computer programming, physics, and medicine for college level students. As well, there has been work demonstrating the positive outcomes of using web-based tutoring systems. While these systems have shown that computer based training is effective, none have investigated multi-user tutoring systems in which teams of players work together within a virtual world to solve more complex problems such as operating a multi- operator robot. Such a system could increase a students understanding of a subject by allowing them to discuss the problem in real time with the other players on their team.
Laparoscopic and robot assisted radical prostatectomy: establishment of a structured program and preliminary analysis of outcomes. (2002)

A structured approach minimizes complications during the establishment of laparoscopic radical prostatectomy program. Robotic assistance helps skilled "open" surgeons learn the technique of laparoscopic radical prostatectomy.
High-frequency A/S coupling for AP buried-landmine detection using laser Doppler vibrometers (2004)

The coupling of airborne sound into roadways and desert soils has been significantly investigated for the purposes of locating buried antitank (AT) landmines. However, there has been relatively little acoustic-to-seismic (A/S) coupling data collected for the purpose of buried antipersonnel (AP) landmine detection. A/S coupling landmine research has typically been accomplished with a low frequency sound source radiating pseudo-random noise in the frequency range 0f 80-300 Hz and a scanning single beam laser Doppler vibrometer (LDV) with a 10 cm beam spacing. The single beam LDV is operated in a serial data collection procedure resulting in long scan times. Recently, a data collection platform that uses 16 LDVs has been used to detect buried AT landmines. In the work reported here, this data collection platform is used to scan a significant number of AP landmines. For this purpose, the LDV beam spacing is reduced to 3 cm and the upper frequency of the sound source is increased to 2 KHz.
The impact of intra-die device parameter variations on path delays and on the design for yield of low voltage digital circuits (1997)

The yield of low voltage digital circuits is found to he sensitive to local gate delay variations due to uncorrelated intra-die parameter deviations. Caused by statistical deviations of the doping concentration they lead to more pronounced delay variations for minimum transistor sizes. Their influence on path delays in digital circuits is verified using a carry select adder test circuit fabricated in 0.5 and 0.35 /spl mu/m complementary metal-oxide-semiconductor (CMOS) technologies with two different threshold voltages. The increase of the path delay variations for smaller device dimensions and reduced supply voltages as well as the dependence on the path length is shown. It is found that circuits with a large number of critical paths and with a low logic depth are most sensitive to uncorrelated gate delay variations. Scenarios for future technologies show the increased impact of uncorrelated delay variations on digital design. A reduction of the maximal clock frequency of 10% is found for, for example, highly pipelined systems realized in a 0.18-/spl mu/m CMOS technology.
[Update on inhalation therapy in asthma and obstructive bronchopulmonary diseases]. (1994)

Significant changes have occurred in aerosol therapy in the last few years. New devices have been developed to facilitate the administration of bronchodilator or anti-inflammatory drugs into the airways. Metered-dose inhaler with or without a spacer or powder devices are now considered the ideal mode of administration of aerosolized medications in the regular treatment of child or adult asthma as well as in COPD. In mild to moderate acute asthma, bronchodilators are ideally administered with a metered dose inhaler with a spacer device, nebulisation being required in only a minority of patients. Powder devices such as the Turbuhaler may also be useful in acute asthma but inspiratory flow should be sufficient, and their usefulness in this context remains to be better determined. In severe acute asthma or in patients unable to properly use the other inhalation devices, nebulisation can be used, with oxygen in the case of acute asthma. In patients requiring mechanical ventilation, administration of bronchodilators can be done with a metered-dose inhaler with a spacer device specifically designed for this purpose: it will replace nebulisation in most cases. In young children and infants unable to use spacer devices with a mouthpiece (< 5 years), wet nebulisation is still used during acute attacks of asthma. In these circumstances, the use of metered-dose inhalers with a spacer and mask are probably appropriate in some children but further studies are required to recommend their use.
Ca2+-permeable mechanosensitive channels MCA1 and MCA2 mediate cold-induced cytosolic Ca2+ increase and cold tolerance in Arabidopsis (2018)

Cold shock triggers an immediate rise in the cytosolic free calcium concentration ([Ca<sup>2+</sup>]<sub>cyt</sub>) in Arabidopsis thaliana and this cold-induced elevation of [Ca<sup>2+</sup>]<sub>cyt</sub> is inhibited by lanthanum or EGTA. It is suggested that intracellular calcium mainly contributes to the cold-induced [Ca<sup>2+</sup>]<sub>cyt</sub> response by entering into the cytosol. Two calcium-permeable mechanosensitive channels, MCA1 and MCA2 (mid1-complementing activity), have been identified in Arabidopsis. Here, we demonstrate that MCA1 and MCA2 are involved in a cold-induced increase in [Ca<sup>2+</sup>]<sub>cyt</sub>. The cold-induced [Ca<sup>2+</sup>]<sub>cyt</sub> increase in mca1 and mca2 mutants was markedly lower than that in wild types. The mca1 mca2 double mutant exhibited chilling and freezing sensitivity, compared to wild-type plants. Expression of At5g61820, At3g51660, and At4g15490, which are not regulated by the CBF/DREB1s transcription factor, was down-regulated in mca1 mca2. These results suggest that MCA1 and MCA2 are involved in the cold-induced elevation of [Ca<sup>2+</sup>]<sub>cyt</sub>, cold tolerance, and CBF/DREB1-independent cold signaling.
T-Cell Vaccination Alters the Course of Murine Herpesvirus 68 Infection and the Establishment of Viral Latency in Mice (1999)

Diseases caused by gammaherpesviruses such as Epstein-Barr virus are a major health concern, and there is significant interest in developing vaccines against this class of viral infections. However, the requirements for effective control of gammaherpesvirus infection are only poorly understood. The recent development of the murine herpesvirus MHV-68 model provides an experimental tool to dissect the immune response to gammaherpesvirus infections. In this study, we investigated the impact of priming T cells specific for class I- and class II-restricted epitopes on the acute phase of the infection and the subsequent establishment of latency and infectious mononucleosis. The data show that vaccination with either major histocompatibility complex class I- or class II-restricted T-cell epitopes derived from lytic cycle proteins significantly reduced lung viral titers during the acute infection. Moreover, the peak level of latently infected spleen cells was significantly reduced following vaccination with immunodominant CD8(+) T-cell epitopes. However, this vaccination approach did not prevent the long-term establishment of latency or the development of the infectious mononucleosis-like syndrome in infected mice. Thus, the virus is able to establish latency efficiently despite strong immunological control of the lytic infection.
Pharmacology of Sclerotherapy (2010)

Sclerotherapy is the therapeutic use of sclerosants in the controlled destruction of undesired target tissues. Sclerosants have been used in vascular and nonvascular settings, both as primary and adjunctive therapy. Effective sclerotherapy requires a conceptual understanding of key questions about the process being treated, including the method of delivery, the presence of flow, and the required contact time to initiate sclerosis. However, beyond technique and delivery, practical and safe application of sclerotherapy requires an understanding of the uses, limitations, dosing, and side effects of sclerosants used during interventional radiology procedures. Agents discussed here include detergents and surfactants [ethanol, Sotradecol(®) (Bioniche Pharma, Pointe Claire, Quebec and Angiodynamics, Latham, NY), ethanolamine oleate], hypertonics (saline, glucose), and a review of several other types that are used less frequently.