gebhart/patrepeval huggingface dataset:
Comprehensive genomic characterization of squamous cell lung cancers (2019)

Lung squamous cell carcinoma is a common type of lung cancer, causing approximately 400,000 deaths per year worldwide. Genomic alterations in squamous cell lung cancers have not been comprehensively characterized, and no molecularly targeted agents have been specifically developed for its treatment. As part of The Cancer Genome Atlas, here we profile 178 lung squamous cell carcinomas to provide a comprehensive landscape of genomic and epigenomic alterations. We show that the tumour type is characterized by complex genomic alterations, with a mean of 360 exonic mutations, 165 genomic rearrangements, and 323 segments of copy number alteration per tumour. We find statistically recurrent mutations in 11 genes, including mutation of TP53 in nearly all specimens. Previously unreported loss-of-function mutations are seen in the HLA-A class I major histocompatibility gene. Significantly altered pathways included NFE2L2 and KEAP1 in 34%, squamous differentiation genes in 44%, phosphatidylinositol-3-OH kinase pathway genes in 47%, and CDKN2Aand RB1 in 72% of tumours. We identified a potential therapeutic target in most tumours, offering new avenues of investigation for the treatment of squamous cell lung cancers.
New Methods of Preparative Organic Chemistry. Transfer of Diazo Groups (1967)

Abstract When an arenesulfonyl azide, particularly p ‐toluenesulfonyl azide, reacts, in the presence of a base, with a compound containing an active methylene group, the two hydrogen atoms of the active methylene group are replaced by a diazo group to form a diazo compound and an arenesulfonamide. The method may be used for the synthesis of the diazo derivatives of cyclopentadienes, cyclohexadienes, 1,3‐dicarbonyl, 1,3‐disulfonyl, and 1,3‐ketosulfonyl compounds, ketones, carbonic acid esters, and β‐iminoketones. Secondary reactions can lead to azo compounds and heterocycles such as 1,2,3‐triazoles, 1,2,3‐thiadiazoles, and pyrazolin‐4‐ones. Azidinium salts react in the same way, but in this case an acidic reaction medium is necessary, a fact that is sometimes advantageous.
Fully integrated frequency and phase generation for a 6&#x2013;18GHz tunable multi-band phased-array receiver in CMOS (2008)

Fully integrated frequency-phase generators for a 6–18GHz wide-band phased-array receiver element are presented that generate 5–7GHz and 9–12GHz first LO signals with less than −95dBc/Hz phase noise at 100kHz offset. Second LO signals with digitally controllable four-quadrant phase- and amplitude spread with better than 3° resolution are generated and allow removal of systematic reference clock skew as well as accurate selection of the received signal phase. This frequency- and phase generation scheme was successfully demonstrated in a 6–18GHz receiver system configured as an electrical 4-element array.
Functional tagging of regulatory elements in the plant genome (1991)

In comparison with animals, relatively few plant genes have been identified that have been shown to be under organ-, tissue- or cell-type-specific regulation. In this paper, we describe how the beta-glucuronidase (GUS) reporter gene (gusA or uidA), fused to a weak promoter (a truncated (-90 bp) CaMV35S promoter), can be used to identify tissue-specific markers in transgenic tobacco plants. The rationale was that the expression of gusA would be determined primarily by position effect. Quantitative analysis revealed that, of 184 -90-gus transgenic plants, 73% exhibited gusA gene activation in leaf tissue, and the level of GUS enzyme activity varied over a 300-fold range within the population. In comparison, transformation with a promoterless gusA gene resulted in GUS expression in 78% of all plants analyzed (in leaf and/or root) and expression levels were three-fold or more lower. Qualitative GUS analysis of single locus -90-gus transformants revealed differential expression in diverse tissues. The spatial pattern of GUS activity was unique to individual transformants, was a reflection of differential gusA gene transcription, and was stably transmissible to progeny. Evidence for preferential expression in roots not only of the -90-gus, but also the promoterless gusA gene is presented. The value of the -90 bp promoter-gusA sequence, which is termed an 'interposon', as a tool both to identify native enhancer sequences in situ and to investigate position effects in plants, is discussed.
Role of dendritic cells in immunopathogenesis of human immunodeficiency virus infection (1997)

The role of dendritic cells (DC) in the pathogenesis of human immunodeficiency virus (HIV) disease has been a subject of considerable interest for several years. Initial studies focused on the infection, dysfunction, and depletion of DC in HIV-infected individuals. More recent studies have begun to identify the functional role of DC in the initiation and propagation of viral replication in T cells in HIV-infected individuals. This review discusses recent data regarding the role of DC in HIV disease with the aim of delineating basic immunopathogenic principles of infection and the development of therapeutic strategies.
Fast and accurate 3D gesture recognition interface (2002)

A video-based gesture recognition system can serve as a natural and accurate 3D user input device. We describe a two-camera system, that recognizes three gesture classes: two static and one dynamic. For one of these gestures (pointing), the system estimates five parameters of 3D pose: position and pointing direction. The recognition is robust, independent of the user and fast (60 Hz), and the estimated pose is very stable. We describe some of the interface applications that demonstrate the benefits of the system: control of a video game, piloting a virtual reality fly-through, and interaction with a 3D scene editor.
Renal Sympathetic Denervation in Patients With Treatment-Resistant Hypertension After Witnessed Intake of Medication Before Qualifying Ambulatory Blood Pressure (2013)

It is unknown whether the decline in blood pressure (BP) after renal denervation (RDN) is caused by denervation itself or concomitantly improved drug adherence. We aimed to investigate the BP lowering effect of RDN in true treatment-resistant hypertension by excluding patients with poor drug adherence. Patients with resistant hypertension (n=18) were referred for a thorough clinical and laboratory work-up. Treatment-resistant hypertension was defined as office systolic BP>140 mm Hg, despite maximally tolerated doses of ≥ 3 antihypertensive drugs, including a diuretic. In addition, ambulatory daytime systolic BP>135 mm Hg was required after witnessed intake of antihypertensive drugs to qualify. RDN (n=6) was performed with Symplicity Catheter System. The mean office and ambulatory BPs remained unchanged at 1, 3, and 6 months in the 6 patients, whereas there was no known change in antihypertensive medication. Two patients, however, had a fall in both office and ambulatory BPs. Our findings question whether BP falls in response to RDN in patients with true treatment-resistant hypertension. Additional research must aim to verify potential BP lowering effect and identify a priori responders to RDN before this invasive method can routinely be applied to patients with drug-resistant hypertension. Clinical Trial Registration- URL: http://www.clinicaltrials.gov. Unique identifier: NCT01673516.
Optical, magnetic and dielectric properties of non-liquid crystalline elastomers doped with magnetic colloids (2005)

Magnetic nanoparticles from magnetic colloidal suspensions were incorporated in the urethane/urea elastomer (PU/PBDO) by swelling fully crosslinked elastomer samples with a toluene and ferrofluid mixture. It is shown that ferrofluid grains can be efficiently incorporated into the matrix of elastomers. The dependence of the birefringence of both the pure and ferrofluid-doped elastomer samples on strain is linear. The ratio of birefringence to strain of the ferrofluid-doped samples is greater than that of the pure elastomer samples, indicating that ferrofluid grains are oriented by the strained polymer network. We propose that this strain-induced orientation is due to the shape anisotropy of the nanoparticles.
Trends in local wireless data networks (2002)

This paper starts with a review or historical trends in the field of wireless local area networks, including issues of regulation and standards. The most important technical issues for wireless LANs are also discussed. Trends in applications are described, including the vision of wireless local area networks moving beyond the "LAN extensions" that were the most important applications of first-generation wireless LAN products, and finding a market in the field of mobile computing. Then the paper presents two of the more important transmission-related issues of interest to mobile users; power usage and data rate. The tradeoff between power consumption and data rate is studied in the context of five transmission techniques that have been considered by wireless LAN standards bodies; direct sequence and frequency hopping spread spectrum, multicarrier modulation, decision-feedback equalization, and sectored antenna systems.
Transcriptional and post‐translation regulation of the Tiel receptor by fluid shear stress changes in vascular endothelial cells (2003)

The interaction between the vascular endothelium and hemodynamic forces (and more specifically, fluid shear stress), induced by the flow of blood, plays a major role in vascular remodeling and in new blood vessels formation via a process termed arteriogenesis. Tie1 is an orphan tyrosine kinase receptor expressed almost exclusively in endothelial cells and is required for normal vascular development and maintenance. The present study demonstrates that Tie1 expression is rapidly down-regulated in endothelial cells exposed to shear stress, and more so to shear stress changes. This down-regulation is accompanied by a rapid cleavage of Tie1 and binding of the cleaved Tie1 45 kDa endodomain to Tie2. The rapid cleavage of Tie1 is followed by a transcriptional down-regulation in response to shear stress. The activity of the Tie1 promoter is suppressed by shear stress and by tumor necrosis factor alpha. Shear stress-induced transcriptional suppression of Tie1 is mediated by a negative shear stress response element, localized in a region of 250 bp within the promoter. The rapid down-regulation of Tie1 by shear stress changes and its rapid binding to Tie2 may be required for destabilization of endothelial cells in order to initiate the process of vascular restructuring.
Relationships and host range of human, canine, simian and porcine isolates of simian virus 5 (parainfluenza virus 5) (2004)

Sequence comparison of the V/P and F genes of 13 human, canine, porcine and simian isolates of simian virus 5 (SV5) revealed a surprising lack of sequence variation at both the nucleotide and amino acid levels (0-3%), even though the viruses were isolated over 30 years and originated from countries around the world. Furthermore, there were no clear distinguishing amino acid or nucleotide differences among the isolates that correlated completely with the species from which they were isolated. In addition, there was no evidence that the ability of the viruses to block interferon signalling by targeting STAT1 for degradation was confined to the species from which they were isolated. All isolates had an extended cytoplasmic tail in the F protein, compared with the original W3A and WR monkey isolates. Sequence analysis of viruses that were derived from human bone-marrow cells isolated in London in the 1980s revealed that, whilst they were related more closely to one another than to the other isolates, they all had identifying differences, suggesting that they were independent isolates. These results therefore support previous data suggesting that SV5 can infect humans persistently, although the relationship of SV5 to any human disease remains highly contentious. Given that SV5 has been isolated on multiple occasions from different species, it is proposed that the term simian virus 5 is inappropriate and suggested that the virus should be renamed parainfluenza virus 5.
Brown adipose tissue regulates glucose homeostasis and insulin sensitivity (2012)

Brown adipose tissue (BAT) is known to function in the dissipation of chemical energy in response to cold or excess feeding, and also has the capacity to modulate energy balance. To test the hypothesis that BAT is fundamental to the regulation of glucose homeostasis, we transplanted BAT from male donor mice into the visceral cavity of age- and sex-matched recipient mice. By 8-12 weeks following transplantation, recipient mice had improved glucose tolerance, increased insulin sensitivity, lower body weight, decreased fat mass, and a complete reversal of high-fat diet-induced insulin resistance. Increasing the quantity of BAT transplanted into recipient mice further improved the metabolic effects of transplantation. BAT transplantation increased insulin-stimulated glucose uptake in vivo into endogenous BAT, white adipose tissue (WAT), and heart muscle but, surprisingly, not skeletal muscle. The improved metabolic profile was lost when the BAT used for transplantation was obtained from Il6-knockout mice, demonstrating that BAT-derived IL-6 is required for the profound effects of BAT transplantation on glucose homeostasis and insulin sensitivity. These findings reveal a previously under-appreciated role for BAT in glucose metabolism.
Selective activation-induced apoptosis of peripheral T cells imposed by macrophages. A potential mechanism of antigen-specific peripheral lymphocyte deletion (1996)

The self-reactive T cells that escape clonal deletion in the thymus must be suppressed by the less well characterized process of peripheral tolerance. In this study, we show that monocyte-derived macrophages (M phi) undergoing terminal differentiation in the presence of macrophage CSF (M-CSF) acquire the ability to selectively induce apoptosis of T cells in an activation-specific fashion. Lymphocytes were stimulated via the TCR using anti-CD3 cross-linking, staphylococcal superantigen, or allogeneic mixed-leukocyte cultures. T cells activated while in contact with M-CSF-derived M phi exited the resting G0 state and re-entered the cell cycle, but experienced a sustained arrest near the first G1/S transition, followed by progressive apoptosis. In contrast, lymphocytes that were not stimulated remained viable, and could later activate normally when removed from contact with M phi. Functionally, exposure of T cells to alloantigens presented by M-CSF-derived M phi resulted in a selective depletion of the alloresponsive T cell population, while preserving reactivity to other mitogens and to alloantigens from different donors. The ability of M phi to impose activation-induced apoptosis on lymphocytes was regulated developmentally, being absent in fresh monocytes, progressively acquired during differentiation in M-CSF, and abrogated if monocytes were exposed to IFN-gamma before differentiation. We speculate that this novel interaction may help to selectively delete autoreactive T cells that respond to self Ags presented by noninflammatory tissue M phi.
Sputum in Severe Exacerbations of Asthma: Kinetics of Inflammatory Indices After Prednisone Treatment (1997)

We have investigated the time-course of symptoms, forced expiratory volume in one second (FEV1), and the airway inflammatory changes in sputum selected from saliva and blood of 10 patients with severe exacerbation of asthma betwen presentation and after 1, 2, 3, 7, and 21 days of treatment. The sputum was induced by a modified standard protocol, and we examined its safety. The severe exacerbation of asthma was defined by the presence of nocturnal symptoms disturbing sleep and/or the need for inhaled short acting beta2-agonist > or = 8 puffs/d and an FEV1 after bronchodilator < 60% of predicted. The treatment consisted of additional prednisone 30 mg daily for 5 d followed by reduction to zero by day 10. Abnormal findings [median (interquartile range)] in spontaneous and induced sputum included low viability of cells [52.0 (34.0)%]; eosinophilia [20.0 (16.4)%]; many free eosinophil granules; and increased levels of fluid-phase ECP [1960 (9204) microg/L], fibrinogen [6045 (10720) microg/L], and IL-5 [160 (212) pg/ml]. Peripheral blood eosinophils [10.4 (7.6)%] and ECP levels [34.0 (35.0) microg/L] were increased. After treatment, symptoms, FEV1, blood eosinophilia, and serum ECP improved in the first 24 h. Sputum eosinophils and ECP did not improve until 48 h and fibrinogen not until 7 d. The improvement in sputum eosinophils and ECP levels was correlated with improvement of FEV1 and in fluid-phase IL-5. Thirty sputum inductions were performed safely in the majority with inhaled isotonic or 3% saline (23.3% or 63.3%, respectively) over a short duration (mean 8.4 min). The patients who had a fall in FEV1 of > or = 10% (10 occasions) after induction differed from those with a fall of < 10% only in the amount of inhaled beta2-agonist used by the patients in the preceding 24 h [8.0 (5.0) versus 4.0 (3.0) puffs/d, p = 0.01]. The results suggest that spontaneous or induced sputum can be used safely to follow the kinetics of effects of antiinflammatory treatment in a severe exacerbation of asthma. The clinical and blood indices improve before those in sputum, raising the possibility that examination of sputum is a better guide in these patients to follow the effects of treatment.
A recombinant vaccine expressed in the milk of transgenic mice protects Aotus monkeys from a lethal challenge with Plasmodium falciparum (2001)

Two strains of transgenic mice have been generated that secrete into their milk a malaria vaccine candidate, the 42-kDa C-terminal portion of Plasmodium falciparum merozoite surface protein 1 (MSP1(42)). One strain secretes an MSP1(42) with an amino acid sequence homologous to that of the FVO parasite line, the other an MSP1(42) where two putative N-linked glycosylation sites in the FVO sequence have been removed. Both forms of MSP1(42) were purified from whole milk to greater than 91% homogeneity at high yields. Both proteins are recognized by a panel of monoclonal antibodies and have identical N termini, but are clearly distinguishable by some biochemical properties. These two antigens were each emulsified with Freund's adjuvant and used to vaccinate Aotus nancymai monkeys, before challenge with the homologous P. falciparum FVO parasite line. Vaccination with a positive control molecule, a glycosylated form of MSP1(42) produced in the baculovirus expression system, successfully protected five of six monkeys. By contrast, vaccination with the glycosylated version of milk-derived MSP1(42) conferred no protection compared with an adjuvant control. Vaccination with the nonglycosylated, milk-derived MSP1(42) successfully protected the monkeys, with 4/5 animals able to control an otherwise lethal infection with P. falciparum compared with 1/7 control animals. Analysis of the different vaccines used suggested that the differing nature of the glycosylation patterns may have played a critical role in determining efficacy. This study demonstrates the potential for producing efficacious malarial vaccines in transgenic animals.
Food Increases the Bioavailability of Isotretinoin (1983)

Twenty healthy male subjects received 80 mg (2 X 40 mg SEG capsules) oral isotretinoin separated by two-week washout periods in an open randomized crossover design. Isotretinoin was administered during a complete fast, 1 hour after a standard breakfast, with a standard breakfast, or 1 hour before a standard breakfast. Blood samples were obtained at specific times over a 72-hour period. Isotretinoin blood concentrations were determined by a specific HPLC method. The relative bioavailability (AUC) of isotretinoin was found to be approximately 1.5 to 2 times greater when the dose was administered 1 hour before, concomitantly with, or 1 hour after a meal than when it was given during a complete fast. In addition, because the Cmax value is lower when the dose is administered with food rather than 1 hour after a meal, coadministration of isotretinoin with food may be the best method of administration.
Pulse Compression (2005)

Abstract Three‐wave interaction in a nonlinear medium can be used to efficiently compress transform‐limited laser pulses with the additional option of shifting the center light frequency. After introducing the general mechanism together with a simple numerical model, we derive a more extensive and complete numerical model to study pulse compression of long (ps) and ultrashort (fs) pulses. A comparison between theory and experiment is given, and limitations of the models are established.
Preparation and characterization of glycerol-based cleavable surfactants and derived vesicles (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPreparation and characterization of glycerol-based cleavable surfactants and derived vesiclesDavid A. Jaeger, Janusz Jamrozik, Timothy G. Golich, Malgorzata Wegrzyn Clennan, and Jamshid MohebalianCite this: J. Am. Chem. Soc. 1989, 111, 8, 3001–3006Publication Date (Print):April 1, 1989Publication History Published online1 May 2002Published inissue 1 April 1989https://doi.org/10.1021/ja00190a038RIGHTS & PERMISSIONSArticle Views409Altmetric-Citations43LEARN 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 InReddit PDF (763 KB) Get e-Alerts Get e-Alerts
Reduced free IGF-I and increased IGFBP-3 proteolysis in Turner syndrome: modulation by female sex steroids (2001)

The bioactivity of the growth hormone-insulin-like growth factor (IGF) system is reduced in Turner syndrome and may explain the reduction seen in final height. We compared levels of free and total IGF-I, immunoreactive and Western ligand blot IGF-binding protein (IGFBP)-3, and IGFBP-3 proteolysis in women with Turner syndrome (n = 23) before (T(B)) and during 6 mo treatment with 17beta-estradiol and norethisterone. An age-matched group of controls (n = 24) was included. Total IGF-I and immunoreactive levels of IGFBP-3 were comparable in T(B) and controls, whereas free IGF-I (P = 0.02) in T(B) was less than in controls. Western ligand blotting (WLB)-IGFBP-3 was significantly lower in T(B) than in controls (P = 0.0005). Accordingly, IGFBP-3 proteolysis was greater in Turner syndrome (P = 0.001). Female sex steroid treatment increased WLB-IGFBP-3 (P = 0.0005), whereas immunoreactive IGFBP-3 and IGFBP-3 proteolysis were normalized (P = 0.004). Free IGF-I remained unchanged (P = 0.8), with a tendency toward a decrease in total IGF-I (P = 0.1). In conclusion, despite normal total IGF-I and immunoreactive IGFBP-3, free serum IGF-I is less and IGFBP-3 proteolysis is greater in Turner syndrome than in controls. During sex steroid treatment, IGFBP-3 proteolysis normalized, without any change in free IGF-I.