gebhart/patrepeval huggingface dataset:
Effect of Delta variant on viral burden and vaccine effectiveness against new SARS-CoV-2 infections in the UK (2021)

The effectiveness of the BNT162b2 and ChAdOx1 vaccines against new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections requires continuous re-evaluation, given the increasingly dominant B.1.617.2 (Delta) variant. In this study, we investigated the effectiveness of these vaccines in a large, community-based survey of randomly selected households across the United Kingdom. We found that the effectiveness of BNT162b2 and ChAdOx1 against infections (new polymerase chain reaction (PCR)-positive cases) with symptoms or high viral burden is reduced with the B.1.617.2 variant (absolute difference of 10-13% for BNT162b2 and 16% for ChAdOx1) compared to the B.1.1.7 (Alpha) variant. The effectiveness of two doses remains at least as great as protection afforded by prior natural infection. The dynamics of immunity after second doses differed significantly between BNT162b2 and ChAdOx1, with greater initial effectiveness against new PCR-positive cases but faster declines in protection against high viral burden and symptomatic infection with BNT162b2. There was no evidence that effectiveness varied by dosing interval, but protection was higher in vaccinated individuals after a prior infection and in younger adults. With B.1.617.2, infections occurring after two vaccinations had similar peak viral burden as those in unvaccinated individuals. SARS-CoV-2 vaccination still reduces new infections, but effectiveness and attenuation of peak viral burden are reduced with B.1.617.2.
Comparison of Flavivirus Universal Primer Pairs and Development of a Rapid, Highly Sensitive Heminested Reverse Transcription-PCR Assay for Detection of Flaviviruses Targeted to a Conserved Region of the NS5 Gene Sequences (2001)

Arthropod-transmitted flaviviruses are responsible for considerable morbidity and mortality, causing severe encephalitic, hemorrhagic, and febrile illnesses in humans. Because there are no specific clinical symptoms for infection by a determined virus and because different arboviruses could be present in the same area, a genus diagnosis by PCR would be a useful first-line diagnostic method. The six published Flavivirus genus primer pairs localized in the NS1, NS3, NS5, and 3' NC regions were evaluated in terms of specificity and sensitivity with flaviviruses (including the main viruses pathogenic for humans) at a titer of 10(5) 50% tissue culture infectious doses (TCID(50)s) ml(-1) with a common identification step by agarose gel electrophoresis. Only one NS5 primer pair allowed the detection of all tested flaviviruses with the sensitivity limit of 10(5) TCID(50)s ml(-1). Using a heminested PCR with new primers designed in the same region after an alignment of 30 different flaviviruses, the sensitivity of reverse transcription-PCR was improved and allowed the detection of about 200 infectious doses ml(-1) with all of the tick- and mosquito-borne flaviviruses tested. It was confirmed that the sequenced amplified products in the NS5 region allowed predictability of flavivirus species by dendrogram, including the New York 99 West Nile strain. This technique was successfully performed with a cerebrospinal fluid sample from a patient hospitalized with West Nile virus encephalitis.
Postprandial remodeling of the gut microbiota in Burmese pythons (2010)

The vertebrate gut microbiota evolved in an environment typified by periodic fluctuations in nutrient availability, yet little is known about its responses to host feeding and fasting. As many model species (for example, mice) are adapted to lifestyles of frequent small meals, we turned to the Burmese python, a sit-and-wait foraging snake that consumes large prey at long intervals (>1 month), to examine the effects of a dynamic nutrient milieu on the gut microbiota. We used multiplexed 16S rRNA gene pyrosequencing to characterize bacterial communities harvested from the intestines of fasted and digesting snakes, and from their rodent meal. In this unprecedented survey of a reptilian host, we found that Bacteroidetes and Firmicutes numerically dominated the python gut. In the large intestine, fasting was associated with increased abundances of the genera Bacteroides, Rikenella, Synergistes and Akkermansia, and with reduced overall diversity. A marked postprandial shift in bacterial community configuration occurred. Between 12 h and 3 days after feeding, Firmicutes, including the taxa Clostridium, Lactobacillus and Peptostreptococcaceae, gradually outnumbered the fasting-dominant Bacteroidetes, and overall 'species'-level diversity increased significantly. Most lineages seemed to be indigenous to the python rather than ingested with the meal, but a dietary source of Lactobacillus could not be ruled out. Thus, the observed large-scale alterations of the gut microbiota that accompany the Burmese python's own dramatic physiological and morphological changes during feeding and fasting emphasize the need to consider both microbial and host cellular responses to nutrient flux. The Burmese python may provide a unique model for dissecting these interrelationships.
Incomplete Depletion and Rapid Regeneration of Foxp3+ Regulatory T Cells Following Anti-CD25 Treatment in Malaria-Infected Mice (2007)

Investigation of the role of regulatory T cells (Treg) in model systems is facilitated by their depletion using anti-CD25 Abs, but there has been considerable debate about the effectiveness of this strategy. In this study, we have compared the depletion and repopulation of CD4+CD25+Foxp3+ Treg in uninfected and malaria-infected mice using 7D4 and/or PC61 anti-CD25 Abs. We find that numbers and percentages of CD25(high) cells, but not Foxp3+ cells, are transiently reduced after 7D4 treatment, whereas treatment with PC61 alone or in combination with 7D4 (7D4 plus PC61) reduces but does not eliminate Foxp3+ cells for up to 2 wk. Importantly, all protocols fail to eliminate significant populations of CD25-Foxp3+ or CD25(low)Foxp3+ cells, which retain potent regulatory capacity. By adoptive transfer we show that repopulation of the spleen by CD25(high)Foxp3+ cells results from the re-expression of CD25 on peripheral populations of CD25-Foxp3+ but not from the conversion of peripheral Foxp3-) cells. CD25(high)Foxp3+ repopulation occurs more rapidly in 7D4-treated mice than in 7D4 plus PC61-treated mice, reflecting ongoing clearance of emergent CD25+Foxp3+ cells by persistent PC61 Ab. However, in 7D4 plus PC61-treated mice undergoing acute malaria infection, repopulation of the spleen by CD25+Foxp3+ cells occurs extremely rapidly, with malaria infection driving proliferation and CD25 expression in peripheral CD4+CD25-Foxp3+ cells and/or conversion of CD4+CD25-Foxp3- cells. Finally, we reveal an essential role for IL-2 for the re-expression of CD25 by Foxp3+ cells after anti-CD25 treatment and observe that TGF-beta is required, in the absence of CD25 and IL-2, to maintain splenic Foxp3+ cell numbers and a normal ratio of Treg:non-Treg cells.
Substrate requirements of hepatitis C virus serine proteinase for intermolecular polypeptide cleavage in Escherichia coli (1994)

Using as substrates a series of chimeric proteins containing various fragments of the hepatitis C virus precursor polyprotein between Escherichia coli maltose binding protein and dihydrofolate reductase, we analyzed the substrate requirements of hepatitis C viral serine proteinase (Cpro-2) for intermolecular polypeptide cleavage in E. coli. Cpro-2-dependent substrate cleavage was observed in E. coli cells simultaneously transformed with expression plasmids for the Cpro-2 molecule and substrate protein. The cleavage sites were estimated by determining the amino (N)-terminal amino acid sequences of dihydrofolate reductase-fused processed products purified partially by affinity chromatography from the lysates, indicating that cleavage occurred at sites identical to those observed in eukaryotic cells. Mutation analysis using the chimeric substrate indicated that the presence of cysteine and small uncharged residues at positions P1 and P1', respectively, of the putative cleavage site is necessary for cleavage and that acidic residues in the region upstream of the cleavage site are required for efficient cleavage.
Gas Solubility in Ionic Liquids (2013)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTGas Solubility in Ionic LiquidsZhigang Lei, Chengna Dai, and Biaohua Chen*View Author Information State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Box 266, Beijing, 100029, China*Phone: +86 10 64433695. E-mail: [email protected]Cite this: Chem. Rev. 2014, 114, 2, 1289–1326Publication Date (Web):November 6, 2013Publication History Received13 December 2012Published online6 November 2013Published inissue 22 January 2014https://pubs.acs.org/doi/10.1021/cr300497ahttps://doi.org/10.1021/cr300497areview-articleACS PublicationsCopyright © 2013 American Chemical SocietyRequest reuse permissionsArticle Views17093Altmetric-Citations847LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Anions,Bubbles,Gases,Saturation,Solubility Get e-Alerts
Cell adhesion mediated by CD4 and MHC class II proteins requires active cellular processes. (1993)

Human CD4 is an accessory molecule found on the cell surface of a subset of T lymphocytes. We have previously shown by infection of simian fibroblasts with an SV40-CD4 recombinant virus that CD4 acts as an adhesion molecule by binding to human MHC class II Ag expressed on the surface of human B lymphocytes. This report confirms that human B lymphoblastoid cell lines expressing class II molecules at the cell surface can bind to Chinese hamster ovary cells that have been stably transfected with human CD4. This cellular adhesion is a late event, which is first detected after 2 h, but remains stable for up to 16 h. The association between CD4 and class II is energy dependent, as it is detected at 37 degrees C, but not at 4 degrees C or if either cell type is fixed with paraformaldehyde. ATP is required for the establishment and maintenance of stable CD4/class II-mediated cell conjugates. Cytoskeletal interactions also regulate CD4/class II adhesion as treatment with the microtubule and microfilament inhibitors colchicine, cytochalasin-D, and nocodazole rapidly dissociates even preformed cell conjugates. Our observations also indicate that the Ag-independent engagement of class II by CD4 induces homotypic clustering of human B cells. This effect is blocked by reagents directed against lymphocyte function-associated Ag-1 and may result from the induction of a high affinity phenotype of lymphocyte function-associated Ag-1 induced by class II signaling. Finally, we discuss the implications of CD4/class II-mediated adhesion and the role of CD4 in the regulation of T cell adhesion.
Biocatalysis at Extreme Temperatures (1992)

Enzymes are typically labile molecules and thus are adversely affected when exposed to any type of extreme conditions. As such, biocatalysis, in either a physiological or biotechnological sense, has usually constrained to a rather narrow range of temperature, pH, pressure, ionic strength and to an aqueous environment. In fact, given its physiological role, and the need at times to regulate enzymatic activity, this is appropriate. Unfortunately, the use of biological catalysts for technological purpose necessitates that enzymes be stable and functional in nonphysiological environments. The challenge then is to either isolate enzymes more suitable for a particular application or be able to modify existing enzymes systematically to improve their stability and/or function. While a number of thermostable enzymes have been studied previously, the focus here is on thermostable enzymes produced by high temperature microorganisms.
Preclinical review of anti-tumor necrosis factor monoclonal antibodies (1993)

Bacterial challenge induces the release of TNF (among other mediators), which exerts both physiologic and toxic effects that may ultimately lead to organ dysfunction and death. New anti-TNF therapies such as anti-TNF antibodies appear to attenuate the injurious effects of TNF and promote survival in otherwise lethal septic shock animal models, suggesting a similar benefit might be obtained in the treatment of human septic shock.
Room-temperature continuous-wave operation of 1.54-μm vertical-cavity lasers (1995)

We report on the room-temperature continuous-wave operation of vertical-cavity lasers operating at 1.54 μm. The devices use a 7 strain-compensated quantum-well active layer sandwiched between two Al(Ga)As-GaAs quarter-wave mirrors joined by wafer fusion. Five device sizes between 8 and 20 μm were found to operate continuously at room temperature (23/spl deg/C), The lowest room-temperature continuous-wave threshold current of 2.3 mA was measured on an 8-μm diameter device, while the highest continuous-wave operating temperature of 33/spl deg/C was measured on a 12-μm device.
Is transcutaneous electrical nerve stimulation effective in relieving postoperative pain after thoracotomy? (2009)

A best evidence topic was constructed according to a structured protocol. The question addressed was whether the use of transcutaneous electrical nerve stimulation (TENS) is effective in reducing post-thoracotomy pain. Of the 74 papers found with a report search, nine prospective randomized controlled trials (RCT), among which three were double-blind, presented the best evidence to answer the clinical question. All investigated the effect of TENS as an adjunct therapy for relieving acute post-thoracotomy pain in patients undergoing thoracic surgery. The authors, journal, date and country of publication, study type, group studied, relevant outcomes and results of these papers are given. We conclude that a vast majority - seven of the nine retrieved studies - were in favor of TENS as an adjuvant to narcotic analgesics for improving outcome after thoracic surgery. Indeed, the interest and benefit has been shown not only in the treatment of acute post-thoracotomy pain (pain scores and narcotic requirements were consistently lower in the TENS group as opposed to the Placebo-TENS group), but also when used together with narcotic analgesics to reduce the duration of recovery room stay and to increase chest physical tolerance (better coughing attempts during chest physiotherapy) with positive effects on pulmonary ventilator function [forced expiratory volume in 1 s (FEV(1)) and/or forced vital capacity (FVC)]. Specifically, the TENS treatment was shown to be ineffective when used alone in severe post-thoracotomy pain (i.e. posterolateral thoracotomy incision), but useful as an adjunct to other medications in moderate post-thoracotomy pain (i.e. muscle sparing thoracotomy incision) and very effective as the sole pain-control treatment in patients experiencing mild post-thoracotomy pain (i.e. video-assisted thoracoscopy incision). Hence, current evidence shows TENS associated with postoperative medications to be safe and effective in alleviating postoperative pain and in improving patient recovery, thus enhancing the choice of available medical care and bettering outcome after thoracic surgery.
Electron and counterion diffusion constants in mixed-valent polymeric osmium bipyridine films (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTElectron and counterion diffusion constants in mixed-valent polymeric osmium bipyridine filmsNigel A. Surridge, Connie S. Sosnoff, R. Schmehl, John S. Facci, and Royce W. MurrayCite this: J. Phys. Chem. 1994, 98, 3, 917–923Publication Date (Print):January 1, 1994Publication History Published online1 May 2002Published inissue 1 January 1994https://pubs.acs.org/doi/10.1021/j100054a029https://doi.org/10.1021/j100054a029research-articleACS PublicationsRequest reuse permissionsArticle Views191Altmetric-Citations30LEARN 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 options Get e-Alerts
Comparative single‐turnover kinetic analyses of trans‐cleaving hammerhead ribozymes with naturally derived non‐conserved sequence motifs (2005)

trans-Cleaving hammerhead ribozyme variants were generated with mimicked non-conserved internal loop motifs derived from five structurally diverse natural cis-cleaving ribozymes. Most modified trans-cleaving variants showed enhanced single-turnover cleavage rates relative to minimal counterparts that lack tertiary interactions between internal loop motifs I and II, and relative to controls with sequence changes in loop I. The trans-cleaving ribozyme derived from the positive strand of peach latent mosaic viroid had the highest observed cleavage rate, suggesting a structurally optimized motif that facilitates rapid formation of the ribozyme catalytic center in a trans-reaction.
Intratumoral activation and enhanced chemotherapeutic effect of oxazaphosphorines following cytochrome P-450 gene transfer: development of a combined chemotherapy/cancer gene therapy strategy. (1995)

Cyclophosphamide and its isomer ifosfamide are cell cycle-nonspecific alkylating agents that undergo bioactivation catalyzed by liver cytochrome P-450 enzymes. The therapeutic efficacy of these oxazaphosphorine anticancer drugs is limited by host toxicity resulting from the systemic distribution of activated drug metabolites formed in the liver. Since tumor cells ordinarily do not have the capacity to activate oxazaphosphorines, we examined whether introduction into tumor cells of a cDNA encoding CYP2B1, a major catalyst of oxazaphosphorine activation, sensitizes the cells to the cytotoxic effects of cyclophosphamide and ifosfamide. Here we show that 9L gliosarcoma cells stably transfected with a cDNA encoding rat CYP2B1 are highly sensitive to cyclophosphamide and ifosfamide cytotoxicity as compared to parental 9L cells or 9L cells transfected with an Escherichia coli beta-galactosidase gene. The CYP2B1 enzyme inhibitor metyrapone protects the CYP2B1-expressing 9L cells from oxazaphosphorine cytotoxicity, demonstrating that the chemosensitivity of these cells is a direct consequence of intracellular prodrug activation. Moreover, CYP2B1-expressing 9L cells potentiate the cytotoxic effects of cyclophosphamide and ifosfamide toward cocultured CYP2B1-negative 9L tumor cells. This "bystander effect" does not require cell-cell contact, and therefore may have the therapeutic advantage of distributing cytotoxic drug metabolites to a wide area within a solid tumor mass. In vivo experiments using Fischer 344 rats implanted s.c. with CYP2B1-expressing 9L tumor cells demonstrated that intratumoral expression of the CYP2B1 gene provides a substantial therapeutic advantage over that provided by liver cytochrome P-450-dependent drug activation alone; cyclophosphamide treatment resulted in complete growth inhibition of CYP2B1-positive tumors, whereas only a modest growth delay effect was obtained with CYP2B1-negative tumors. These studies establish that drug-activating CYP genes may be useful for the development of novel combined chemotherapy/gene therapy strategies for cancer treatment utilizing established cancer chemotherapeutic agents.
A GaAs MMIC transceiver for 2.45 GHz wireless commercial products (2002)

Recent availability of unlicensed frequency bands (FCC part 15.247 and International Standards) has stimulated development of wireless products ranging from wireless LAN, PBX to data collection devices. This paper describes development and performance characteristics of an advanced MMIC transceiver that provides half duplex conversion between 2.4 GHz and 915 MHz. The chip is mounted in a 28-lead cofired ceramic package suitable for surface mount assembly. The highly integrated chip minimizes external components and can be readily implemented into miniature, low profile products such as the PCMCIA format.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Comparison of rice and whey protein osolate digestion rate and amino acid absorption (2013)

Background Athletes have a choice of different animal (e.g. whey, casein, egg, beef, fish) or plant protein (e.g. soy, rice, pea, hemp) sources, which differ in numerous ways such as the presence of allergens (lactose, soy), cholesterol, saturated fats, digestion rate (fast, intermediate, or slow absorption of amino acids), or the relative amount of individual amino acids. While digestibility of rice protein isolate (RPI) in rats has been shown to be inferior to animal protein (87% vs. 97% for casein), administration of 48 grams of RPI following resistance exercise decreased fat-mass and increased lean body mass, skeletal muscle hypertrophy, power and strength comparable to whey protein isolate (WPI). This study sought to investigate the amino acid rate of appearance in the blood of 48 grams of RPI compared to 48 grams of WPI.
Systematic study of the splitting kinetic of H/He co-implanted substrate (2003)

In this paper, we proposed the results of a systematic study of coimplantation of hydrogen and helium. Systematic SIMS and TEM analysis have been done.
Spectral linear prediction: Properties and applications (1975)

Linear prediction (LP) is presented as a spectral modeling technique in which the signal spectrum is modeled by an all-pole spectrum. The method allows for arbitrary spectral shaping in the frequency domain, and for modeling of continuous as well as discrete spectra (such as filter bank spectra). In addition, using the method of selective linear, prediction, all-pole modeling is applied to selected portions of the spectrum, with applications to speech recognition and speech compression. LP is compared with traditional analysis-by-synthesis (AbS) techniques for spectral modeling. It is found that linear prediction offers computational advantages over AbS, as well as better modeling properties if the variations of the signal spectrum from the desired spectral model are large. For relatively smooth spectra and for filter bank spectra, AbS is judged to give better results. Finally, a sub-optimal solution to the problem of all-zero modeling using LP is given.