gebhart/patrepeval huggingface dataset:
Genetic regulation onex vivodifferentiated natural killer cells from human umbilical cord blood CD34+cells (2012)

Natural killer (NK)-cells are a lymphocyte population playing a critical role in the immune surveillance against tumors and virally infected cells. The development of human hematopoietic stem cells (hHSC) into fully differentiated NK-cells pass through discrete stages of differentiation involving a variety of factors such as cytokines, membrane factors, and transcription factors (TFs). Because there is lack of studies in this field, we decided to perform an extended analysis of TFs during in vitro differentiation of NK-cells. At several points of differentiation, cells were characterized by their mRNA expression either for NK-cell cell markers, for a number of mature NK-cell receptors or a large panel of TFs. Our data suggests that some TFs (ID2, EGR-2 and T-BET) play a role in NK-cell commitment, differentiation and maturation. Although delayed on its expression, BLIMP1 also seems to be involved in differentiation and maturation of NK cells, but not in NK-cell commitment. E4BP4 and TOX are more related with initial stages of NK-cell commitment. PU.1, MEF, Ikaros, EGR-1, BCL11B and IRF-2 revealed less involvement in maturation and were more associated with NK-cell commitment and pNK cell production. GATA-3 showed a differential role during the ontogeny of NK-cells. We show that assessment of the transcripts present in the differentiating NK-cells demonstrated, a pattern of preserved and differential gene expression remarkably similar to that seen in mice except for E4BP4 that showed constant downregulation throughout the culture period. A thorough understanding of NK-cell developmental mechanisms is important as it may enable future therapeutic manipulation.
Engineering bilinear mode coupling in circuit QED: Theory and experiment (2019)

Photonic states of superconducting microwave cavities controlled by transmon ancillas provide a platform for encoding and manipulating quantum information. A key challenge in scaling up the platform is the requirement to communicate on demand the information between the cavities. It has been recently demonstrated that a tunable bilinear interaction between two cavities can be realized by coupling them to a bichromatically-driven transmon ancilla, which allows swapping and interfering the multi-photon states of the cavities [Gao et al., Phys. Rev. X 8, 021073(2018)]. Here, we explore both theoretically and experimentally the regime of relatively strong drives on the ancilla needed to achieve fast SWAP gates but which can also lead to undesired non-perturbative effects that lower the SWAP fidelity. We develop a theoretical formalism based on linear response theory that allows one to calculate the rate of ancilla-induced interaction, decay and frequency shift of the cavities in terms of a susceptibility matrix. We treat the drives non-perturbatively using Floquet theory, and find that the interference of the two drives can strongly alter the system dynamics even in the regime where the rotating wave approximation applies. We identify two major sources of infidelity due to ancilla decoherence. i) Ancilla dissipation and dephasing leads to incoherent hopping among Floquet states which occurs even when the ancilla is at zero temperature, resulting in a sudden change of the SWAP rate. ii) The cavities inherit finite decay from the relatively lossy ancilla through the inverse Purcell effect; the effect can be enhanced when the drive-induced AC Stark shift pushes certain ancilla transition frequencies to the vicinity of the cavity frequencies. The theoretical predictions agree quantitatively with the experimental results, paving the way for using the theory to design future experiments.
Immunological Barriers in the Nose and Paranasal Sinuses (1987)

This review deals mainly with lymphocyte subsets in the human nasal mucosa, and with the common cold. Lymphocytes have recently been characterized in biopsy specimens by an immuno-histochemical method (the avidin-biotin, monoclonal antibody peroxidase technique). In summary, the overall T:B cell ratio was 3:1 and that of T helper cells to T suppressor was 2.5:1; topographical differences within the nasal mucosa were identified. Non-specific defence systems, such as interferon, provide some protection against rhinovirus infection, but most important is the presence of specific antibodies against a given antigenic type of virus. Recent results have suggested that a rhinovirus infection does not cause a marked destruction of the epithelial lining, that it is spotty in the nasal mucosa, and that it is most prominent in the nasopharynx. Increased knowledge about the site of infection and how symptoms are produced is essential for a rational approach to the development of anti-viral therapy.
Genetic control of natural resistance to Mycobacterium bovis (BCG) in mice. (1981)

Mice of 12 inbred strains infected i.v. with Mycobacterium bovis (BCG) exhibited 2 distinct patterns of response as determined by the degree of BCG burden in the spleens of animals at 3 wk after infection with 10(4) viable bacilli: susceptible (C57BL/6J and related sublines, BALB/c and DBA/1J) and resistant (A/J, C3H/HeCr, DBA/2J, CBA/J, C57Br, AKR). Mendelian analysis of this trait on segregating backcross and F2 populations derived from the mating of resistant and susceptible progenitors was compatible with the hypothesis that resistance to BCG is controlled by a single, dominant, autosomal gene, which is being given the designation Bcg. The product of the Bcg gene was found to influence the early phase of host response resulting in the genetic advantage of the resistant host being demonstrable as early as 24 hr after infection.
Synthesis of a novel histidine analogue and its efficient incorporation into a protein in vivo (2003)

Proteins containing unnatural amino acids have immense potential in biotechnology and medicine. We prepared several histidine analogues including a novel histidine analogue, beta-(1,2,3-triazol-4-yl)-DL-alanine. These histidine analogues were assayed for translational activity in histidine-auxotrophic Escherichia coli strain UTH780. We observed that several histidine analogues, including our novel histidine analogue, were efficiently incorporated into the protein in vivo; however, other analogues were rejected. These results suggest that the hydrogen atom at a specific position seriously affects incorporation.
Large-Scale Evolution of Image Classifiers (2017)

Neural networks have proven effective at solving difficult problems but designing their architectures can be challenging, even for image classification problems alone. Our goal is to minimize human participation, so we employ evolutionary algorithms to discover such networks automatically. Despite significant computational requirements, we show that it is now possible to evolve models with accuracies within the range of those published in the last year. Specifically, we employ simple evolutionary techniques at unprecedented scales to discover models for the CIFAR-10 and CIFAR-100 datasets, starting from trivial initial conditions and reaching accuracies of 94.6% (95.6% for ensemble) and 77.0%, respectively. To do this, we use novel and intuitive mutation operators that navigate large search spaces; we stress that no human participation is required once evolution starts and that the output is a fully-trained model. Throughout this work, we place special emphasis on the repeatability of results, the variability in the outcomes and the computational requirements.
Atrial fibrillation : mechanisms and management (1992)

Pathology of atrial fibrillation - insights from autopsy studies, J.T. Lie and Rodney H. Falk histology of the normal and diseased atrium, Saroja Bharati and Maurice Lev experimental observations in atrial fibrillation, Michiel J. Janse and Maurits A. Allessie role of the atrioventricular node in atrial fibrillation, Frits L. Meijler and Fred H. Wittkampf epidemiology of atrial fibrillation, William B. Kannel and Philip A. Wolf atrial fibrillation in the absence of overt cardiac disease, Richard A. Leather and Charles R. Kerr neural aspects of paroxysmal atrial fibrillation, Phillippe Coumel atrial fibrillation following cardiac surgery, Michael S. Lauer and Kim A. Eagle exercise hemodynamics of atrial fibrillation, J. Edwin Atwood echocardiography in atrial fibrillation, Charles Pollick electrical conversion of atrial fibrillation, Rodney H. Falk and Philip J. Podrid oral antiarrhythmic drugs used for atrial fibrillation - clinical pharmacology, Philip J. Podrid pharmacologic therapy for reversion of atrial fibrillation and maintenance of sinus rhythm, Therese Fuchs and Philip J. Podrid control of the ventricular rate in atrial fibrillation, Rodney H. Falk proarrhythmic responses to atrial antiarrhythmic therapy, Rodney H. Falk anticoagulant therapy for atrial fibrillation, Palle Peterson clinical electrophysiology of the normal and diseased human atria, Ross J. Simpson, Jr atrial fibrillation in Wolff-Parkinson-White syndrome, H.J.J. Wellens et al the use of pacemakers in atrial fibrillation, Arhtur Pollack and Rodney H. Falk catheter ablation in atrial fibrillation, Marten Rosenqvist and Melvin M. Scheinman surgical management of symptomatc atrial fibrillation, James W. Leitch et al management of atrial fibrillation - an overview, Philip J. Podrid and Rodney H. Falk.
A mutant of Escherichia coli defective in the first step of endotoxin biosynthesis. (1990)

Using localized mutagenesis of whole cells, we have isolated a temperature-sensitive UDP-N-acetylglucosamine acyltransferase mutant of Escherichia coli that loses all detectable acyltransferase activity and quickly dies after a shift from 30 to 42 degrees C. Acyltransferase activity and temperature resistance are restored by transforming the mutant with a hybrid plasmid containing the E. coli gene for UDP-GlcNAc acyltransferase (lpxA). In addition, a new assay has been developed for quantitating the amount of lipid A (the active component of endotoxin) in E. coli and related Gram-negative strains. Cells are labeled with 32Pi and extracted with chloroform/methanol/water (1:2:0.8, v/v) to remove glycerophospholipids. The residue is then hydrolyzed with 0.2 M HCl to liberate the "monophosphoryl" lipid A degradation products (Qureshi, N., Cotter, R. J. and Takayama, K. (1986) J. Microbiol. Methods 5, 65-77), each of which bears a single phosphate residue at position 4'. The amount of lipid A is normalized to the total amount of labeled glycerophospholipid present in the cells. The steady state ratio of lipid A to glycerophospholipid in wild-type cells is approximately 0.12. The lipid A content of the acyltransferase mutant is reduced 2-3-fold, and the rate of lipid A synthesis is reduced 10-fold when compared to wild-type after 60 min at 42 degrees C. These results provide physiological evidence that UDP-N-acetylglucosamine acyltransferase is the major committed step for lipid A biosynthesis in E. coli and that lipid A is an essential molecule.
AccMon: Automatically Detecting Memory-Related Bugs via Program Counter-Based Invariants (2005)

This paper makes two contributions to architectural support for software debugging. First, it proposes a novel statistics-based, on-the-fly bug detection method called PC-based invariant detection. The idea is based on the observation that, in most programs, a given memory location is typically accessed by only a few instructions. Therefore, by capturing the invariant of the set of PCs that normally access a given variable, we can detect accesses by outlier instructions, which are often caused by memory corruption, buffer overflow, stack smashing or other memory-related bugs. Since this method is statistics-based, it can detect bugs that do not violate any programming rules and that, therefore, are likely to be missed by many existing tools. The second contribution is a novel architectural extension called the Check Look-aside Buffer (CLB). The CLB uses a Bloom filter to reduce monitoring overheads in the recently-proposed iWatcher architectural framework for software debugging. The CLB significantly reduces the overhead of PC-based invariant debugging. We demonstrate a PC-based invariant detection tool called AccMon that leverages architectural, run-time system and compiler support. Our experimental results with seven buggy applications and a total of ten bugs, show that AccMon can detect all ten bugs with few false alarms (0 for five applications and 2-8 for two applications) and with low overhead (0.24-2.88 times). Several existing tools evaluated, including Purify, CCured and value-based invariant detection tools, fail to detect some of the bugs. In addition, Purify's overhead is one order of magnitude higher than AccMon's. Finally, we show that the CLB is very effective at reducing overhead.
Current best treatment for non-alcoholic fatty liver disease (2003)

Treatment of patients with non-alcoholic fatty liver disease (NAFLD) has typically been focused on the management of associated conditions such as obesity, diabetes mellitus and hyperlipidaemia. NAFLD associated with obesity may be resolved by weight reduction, although the benefits of weight loss have been inconsistent. Improving insulin sensitivity with lifestyle modifications or medications usually improves glucose and lipid levels in patients with diabetes and hyperlipidaemia. Improving insulin sensitivity is expected to improve the liver disease but in many diabetic/hyperlipidaemic patients with NAFLD, the appropriate control of glucose and lipid levels is not always accompanied by improvement of the liver condition. Results of pilot studies evaluating ursodeoxycholic acid, gemfibrozil, betaine, N-acetylcysteine, alphatocopherol, metformin and thiazolidinedione derivatives suggest that these medications may be of potential benefit. This article reviews the treatment modalities currently available for patients with NAFLD, including emerging data from clinical trials evaluating promising medications as well as possibilities for the future.
Association of Biomolecular Systems via Pulsed Field Gradient NMR Self-Diffusion Measurements (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAssociation of Biomolecular Systems via Pulsed Field Gradient NMR Self-Diffusion MeasurementsAmanda S. Altieri, Denise P. Hinton, and R. Andrew ByrdCite this: J. Am. Chem. Soc. 1995, 117, 28, 7566–7567Publication Date (Print):July 1, 1995Publication History Published online1 May 2002Published inissue 1 July 1995https://pubs.acs.org/doi/10.1021/ja00133a039https://doi.org/10.1021/ja00133a039research-articleACS PublicationsRequest reuse permissionsArticle Views1581Altmetric-Citations412LEARN 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 (2)»Supporting Information Supporting Information Get e-Alerts
Effects of composition and polymerization conditions on crosslinked polymer supports based on N‐acrylyl pyrrolidine and N,N‐dimethyl acrylamide for peptide synthesis (1983)

Abstract Poly( N ‐acrylyl pyrrolidine‐co‐ N , N ′‐bis(acrylyl) 1,2‐diaminoethane‐co‐ N ‐Acrylyl 1,6‐diamino hexane HCl) with 2,5,8,11,12,15, and 20% degrees of crosslinking (DC) and poly‐( N , N ′‐dimethylacrylaminde‐co‐ N , N ′‐bis(acrylyl) 1,2‐diaminoethane‐co‐ N ‐acrylyl 1,6‐diamino hexane HCl) with 2,5,10, and 15% DC have been synthesized in an entirely beaded form by reverse‐phase suspension polymerization. The monomer‐to‐water ratio was kept constant for all these polymers. With the exception of 2% crosslinked resins in the PAP and PDMA groups, all the resins exhibited favorable swelling properties in solvents normally used for peptide synthesis and the percent incorporation of the first amino acid residue was close to 100 for DC of up to 20%. This is explained as due to the flexible and polar characteristics of the crosslinking agent, N , N ′‐bis(acrylyl) 1,2‐diaminoethane. Between 5 and 20% DC the degree of swelling of the resins changes only slightly with increasing DC. This effect of DC on the swelling and percent incorporation of the first amino acid residue is more favorable for peptide synthesis than in the case of divinyl benzene crosslinked poly(styrene).
Gene Expression Profiling of Progressive Papillary Noninvasive Carcinomas of the Urinary Bladder (2005)

Gene expression profiling revealed novel genes with potential clinical utility to select patients that are more likely to develop aggressive disease.
On-chip continuous monitoring of motile microorganisms on an ePetri platform (2012)

Self-imaging Petri dish platforms with microscopy resolution, which we term 'ePetri', can significantly streamline cell cultures and/or other longitudinal biological studies. In this paper, we demonstrate high-resolution imaging and long-term culture of motile microorganisms in a specialized ePetri platform by taking advantage of the inherent motion. By applying a super-resolution algorithm to a set of low-resolution images of the microorganisms as they move across the sensing area of a complementary metal oxide semiconductor (CMOS) image sensor chip, we can render an improved-resolution image of the microorganisms. We perform a longitudinal study of Euglena gracilis cultured in an ePetri platform, and image-based analysis on the motion and morphology of the cells. As a miniaturized and automated culture monitoring platform, this ePetri technology can greatly improve studies and experiments with motile microorganisms.
Simian immunodeficiency virus DNA vaccine trial in macaques (1996)

An experimental vaccine consisting of five DNA plasmids expressing different combinations and forms of simian immunodeficiency virus-macaque (SIVmac) proteins has been evaluated for the ability to protect against a highly pathogenic uncloned SIVmac251 challenge. One vaccine plasmid encoded nonreplicating SIVmac239 virus particles. The other four plasmids encoded secreted forms of the envelope glycoproteins of two T-cell-tropic relatives (SIVmac239 and SIVmac251) and one monocyte/macrophage-tropic relative (SIVmac316) of the uncloned challenge virus. Rhesus macaques were inoculated with DNA at 1 and 3, 11 and 13, and 21 and 23 weeks. Four macaques were inoculated intravenously, intramuscularly, and by gene gun inoculations. Three received only gene gun inoculations. Two control monkeys were inoculated with control plasmids by all three routes of inoculation. Neutralizing antibody titers of 1:216 to 1:768 were present in all of the vaccinated monkeys after the second cluster of inoculations. These titers were transient, were not boosted by the third cluster of inoculations, and had fallen to 1:24 to 1:72 by the time of challenge. Cytotoxic T-cell activity for Env was also raised in all of the vaccinated animals. The temporal appearance of cytotoxic T cells was similar to that of antibody. However, while antibody responses fell with time, cytotoxic T-cell responses persisted. The SIVmac251 challenge was administered intravenously at 2 weeks following the last immunization. The DNA immunizations did not prevent infection or protect against CD4+ cell loss. Long-term chronic levels of infection were similar in the vaccinated and control animals, with 1 in 10,000 to 1 in 100,000 peripheral blood cells carrying infectious virus. However, viral loads were reduced to the chronic level over a shorter period of time in the vaccinated groups (6 weeks) than in the control group (12 weeks). Thus, the DNA vaccine raised both neutralizing antibody and cytotoxic T-lymphocyte responses and provided some attenuation of the acute phase of infection, but it did not prevent the loss of CD4+ cells.
Chemical synthesis of (22E)-3α,6β,7β-trihydroxy-5β-chol-22-en-24-oic acid and its taurine and glycine conjugates (2004)

A method for the synthesis of Delta(22)-beta-muricholic acid (Delta(22)-beta-MCA), (22E)-3 alpha,6 beta,7 beta-trihydroxy-5 beta-chol-22-en-24-oic acid, and its taurine and glycine conjugates (Delta(22)-beta-muricholyltaurine and Delta(22)-beta-muricholylglycine) is described. The key intermediate, 3 alpha,6 beta,7 beta-triformyloxy-23,24-dinor-5 beta-cholan-22-al, was prepared from beta-muricholic acid (beta-MCA) via the 24-nor-22-ene and 24-nor-22,23-diol derivatives. Wittig reaction of the aldehyde with (carbomethoxymethylene) triphenylphosphorane and subsequent hydrolysis gave (unconjugated) Delta(22)-beta-MCA. Condensation reaction of the unconjugated acid with taurine or glycine methyl ester using diethylphosphorocyanide yielded the naturally occurring taurine or glycine conjugate (N-acylamidate) of Delta(22)-beta-MCA. These synthetic reference compounds are now available for investigation of the metabolism of beta-MCA by bacterial and hepatic enzymes in the rat and should also be useful as substrates for reductive deuteration or tritiation to give the 22,23-(2)H or (3)H-beta-MCA.
Intravenous vincristine infusion: Phase I trial (1981)

In an attempt to sustain potentially cytotoxic concentrations of vincristine in man, a five-day continuous infusion of vincristine after an initial intravenous bolus injection was administered to 30 patients with refractory malignancies. Three dosage levels were explored (0.5 mg/m2, 0.75 mg/m2, and 1.0 mg/m2 daily for five days). Neurologic and hematologic toxicity were severe at the high dose level, whereas mild to moderate toxicity occurred at the 0.5 and 0.75 mg/m2 dose levels. Objective responses were noted in 11 patients (37%) with the following malignancies: non-Hodgkin's lymphoma (4), acute non-lymphoblastic leukemia (2), chronic granulocytic leukemia in blast crisis (1), carcinoma of the breast (3), and small cell carcinoma of the lung (1). Responses were observed at each infusion dose level. Nine of the 11 responders had previously progressed while receiving conventional intravenous bolus injection of vincristine. These data suggest that the clinical usefulness of vincristine may be enhanced by the use of infusion techniques. A maximum daily dose of 0.5 mg/m2 given for five days is recommended for future trials of intravenous vincristine infusion.
The Urea Reduction Ratio and Serum Albumin Concentration as Predictors of Mortality in Patients Undergoing Hemodialysis (1993)

Low urea reduction ratios during dialysis are associated with increased odds ratios for death. These risks are worsened by inadequate nutrition.