gebhart/patrepeval huggingface dataset:
The human interferon system: characterization and classification after discovery of novel members. (2003)

The human interferon (IFN) system is the best characterized of all animal IFN systems. Until recently it is thought that all IFNs and IFN-related genes and proteins have been discovered. However, in the last three years, the discovery and characterization of IFNs including IFN-epsilon (IFN-epsilon), IFN-kappa (IFN-kappa) and a novel IFN-lambda (IFN-lambda) family, in particular, substantially changed this opinion. In this article, we attempt to review recent developments in the field of interferon discovery and present an overview of current classification of the human IFN system. Characterization of the constituent parts of the human IFN system including ligands, receptors and players involved in the signal transduction pathway are discussed.
The alpha effect. A review (1973)

Abstract Instances of high reactivity (as signaled by a positive Brönsted deviation) by nucleophiles bearing one or more unshared pairs of electrons on an atom adjacent to the nucleophilic center (the alpha effect) are surveyed in the context of possible explanations for this phenomenon. No single cause appears to account satisfactorily for all the data. However, four factors (ground‐state destabilization of the nucleophile, transition‐state stabilization, solvent effect differences for alpha and nonalpha nucleophiles, and product stability) may be involved in contributory roles. The response to proton basicity of a substrate is probably not related to its susceptibility to the alpha effect. Carbon electrophiles seem to be receptive to the alpha effect in the order digonal &gt; trigonal &gt; tetrahedral. The inconsistent behavior of alpha nucleophiles makes the prediction of alpha effects rather risky and confirms the complicated nature of nucleophilic substitutions.
CRP represses the CRISPR/Cas system in Escherichia coli: evidence that endogenous CRISPR spacers impede phage P1 replication (2014)

The CRISPR/Cas system is an important aspect in bacterial immunology. The anti-phage activity of the CRISPR system has been established using synthetic CRISPR spacers, but in vivo studies of endogenous CRISPR spacers are relatively scarce. Here, we showed that bacteriophage P1 titre in Escherichia coli decreased in the glucose-containing medium compared with that in the absence of glucose. This glucose effect of E. coli against phage P1 infection disappeared in cse3 deletion mutants. The effect on the susceptibility to phage P1 was associated with cAMP receptor protein (CRP)-mediated repression of cas genes transcription and crRNA maturation. Analysis of the regulatory element in the cse1 promoter region revealed a novel CRP binding site, which overlapped with a LeuO binding site. Furthermore, the limited sequence identity between endogenous spacers and the phage P1 genome was necessary and sufficient for CRISPR-mediated repression of phage P1 replication. Trans-expression of the third and seventh spacers in the CRISPR I region or third and sixth spacers in the CRISPR II region effectively reduced phage P1 titres in the CRISPR deletion mutants. These results demonstrate a novel regulatory mechanism for cas repression by CRP and provide evidence that endogenous spacers can repress phage P1 replication in E. coli.
Anti–de Sitter black holes, thermal phase transition, and holography in higher curvature gravity (2002)

We study anti--de Sitter black holes in the Einstein-Gauss-Bonnet and the generic ${R}^{2}$ gravity theories, evaluate different thermodynamic quantities, and also examine the possibilities of Hawking-Page--type thermal phase transitions in these theories. In the Einstein theory, with a possible cosmological term, one observes a Hawking-Page phase transition only if the event horizon is a hypersurface of positive constant curvature $(k=1).$ But, with the Gauss-Bonnet and/or the $(\mathrm{Riemann}{)}^{2}$ interaction terms, there may occur a similar phase transition for a horizon of negative constant curvature $(k=\ensuremath{-}1).$ We examine the finite coupling effects, and find that $N&gt;5$ could trigger a Hawking-Page phase transition in the latter theory. For the Gauss-Bonnet black holes, one relates the entropy of the black hole to a variation of the geometric property of the horizon based on the first law and Noether charge. With a $(\mathrm{Riemann}{)}^{2}$ term, however, we can do this only approximately, and the two results agree when ${r}_{H}\ensuremath{\gg}L,$ the size of the horizon is much bigger than the AdS curvature scale. We establish some relations between bulk data associated with the AdS black hole and boundary data defined on the horizon of the AdS geometry. Following a heuristic approach, we estimate the difference between Hubble entropy $({\mathcal{S}}_{H})$ and Bekenstein-Hawking entropy $({\mathcal{S}}_{\mathrm{BH}})$ with a $(\mathrm{Riemann}{)}^{2}$ term, which, for $k=0$ and $k=\ensuremath{-}1,$ implies ${\mathcal{S}}_{\mathrm{BH}}&lt;~{\mathcal{S}}_{H}.$
The spectrum of pediatric eosinophilic esophagitis beyond infancy: a clinical series of 30 children (2000)

Awareness of the spectrum of eosinophilic esophagitis should promote optimal diagnosis and treatment of this elusive entity, both in children and in adults.
Anti-Inflammatories Inhibit Cancer Growth--But How? (2001)

CANCER RESEARCHAbout 15 years ago, evidence began accumulating that aspirin and related drugs, known as NSAIDs, hinder the development of colon cancer and perhaps other cancers as well. But researchers are deeply divided over how they exert this potentially beneficial effect--an important issue, because figuring out the mechanism could aid the design of better chemopreventive drugs. Consequently, on 8 January, the National Cancer Institute brought many of the leading researchers in the field together for a workshop aimed at examining the evidence on both sides.
Dye-Sensitized Solar Cells (2010)

A review on dye-sensitized solar cells (DSCs). Some brief notes on solar energy in general and DSC in particular are given, followed by a discussion of the operational principles of DSC (energetics and kinetics). Then, the development of material components and some specific exptl. techniques to characterize DSC are described. The current status of module development is also discussed, and finally a brief future outlook is given.
Noninvasive Induction of Muscle Fiber Hypertrophy and Hyperplasia: Effects of High-Intensity Focused Electromagnetic Field Evaluated in an In-Vivo Porcine Model: A Pilot Study (2019)

Histopathologic quantification showed significant structural muscle changes through a combination of fiber hypertrophy and hyperplasia. Control biopsies showed a lack of similar changes. The data correlate with findings of other HIFEM research and suggest that HIFEM could be used for noninvasive induction of muscle growth.
β-Arrestin-dependent Desensitization of Luteinizing Hormone/Choriogonadotropin Receptor Is Prevented by a Synthetic Peptide Corresponding to the Third Intracellular Loop of the Receptor (1999)

Desensitization is a ubiquitous response of guanine nucleotide-binding protein-coupled receptors (GPCRs) characterized by the waning of effector activity despite continued presence of agonist. Binding of an arrestin to the activated, often phosphorylated GPCR triggers desensitization. We reported for the luteinizing hormone/choriogonadotropin receptor (LH/CG R) that beta-arrestin tightly bound to porcine ovarian follicular membranes mediates agonist-dependent desensitization of LH/CG R-stimulated adenylyl cyclase (AC) activity (Mukherjee, S., Palczewski, K., Gurevich, V. V., Benovic, J. L., Banga, J. P., and Hunzicker-Dunn, M. (1999) Proc. Natl. Acad. Sci. U. S. A. 96, 493-498). We now show that addition of a synthetic peptide corresponding to the entire third intracellular loop (3i) of the LH/CG R completely and specifically reverses desensitization of AC activity, with an ED50 of 10 microM but does not modulate basal, hCG-stimulated, or forskolin-stimulated AC activities. beta-Arrestin binds selectively to the 3i peptide coupled to activated Sepharose. Desensitization of LH/CG R-stimulated AC activity is rescued when the 3i peptide is preincubated with exogenous beta-arrestin. These results show that endogenous beta-arrestin participates in cell-free desensitization of agonist-dependent LH/CG R-stimulated AC activity in follicular membranes by interacting directly with the 3i loop of the receptor, thereby preventing Gs activation.
An Area and Power Efficient Radiation Hardened by Design Flip-Flop (2006)

A radiation hardened by design flip-flop with high single event effect immunity is described. Circuit size and power are reduced by a combination of proven SEE hard techniques, i.e., a temporal latch master and DICE slave are used. Two shift register chains each comprised of 1920 flip-flops have been implemented in the IBM 0.13 mum bulk CMOS process. Measured SEE immunity in accelerated heavy ion testing, and power results are described. A threshold LET over 45 LET (MeV-cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2 </sup> /mg) at V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">DD</sub> =1.5 V is demonstrated. High layout density and the likely high LET failure mechanisms are described
An alternatively spliced form of Met receptor is tumorigenic (2006)

The Met tyrosine kinase receptor is a widely expressed molecule, which mediates pleiotropic cellular responses following activation by its ligand, hepatocyte growth factor/scatter factor (HGF/SF). Previously, one of the authors identified an alternatively spliced form of Met (Met-SM) that lacked a single exon of a 47-amino-acid segment in the juxtamembrane domain. Here we report that Met-SM is a potent transforming gene in NIH3T3 mouse fibroblast cells. Met-SM-transfected NIH3T3 cells show stronger foci-forming activity than wild type- Met-transfected ones. In addition, Met-SM-transfected NIH3T3 cells form colonies in soft agar and are tumorigenic in athymic nu/nu mice. Furthermore, HGF/SF significantly increases the focus-forming activity of Met-SM comparing to wild type Met. The amount of protein and of tyrosine kinase activity of Met-SM accumulates to a high level following HGF/SF treatment. The accumulation of Met-SM correlated well with its delayed ubiquitination and increased stability. These results are consistent with the important role of the juxtamembrane domain in protein stability of Met receptor and suggest that the alternatively-spliced form may contribute to the development and progression of human cancer.
Hemagglutinin Protein Is a Primary Target of the Measles Virus–Specific HLA‐A2–Restricted CD8+T Cell Response during Measles and after Vaccination (2007)

To characterize the measles virus (MV)-specific T cell responses important for evaluation of measles vaccines, human leukocyte antigen (HLA)-A2-positive and -negative adults immunized with measles-mumps-rubella vaccine were studied. Both groups developed increases in antibody and in interferon (IFN)- gamma -producing cells in response to pooled hemagglutinin (H) and fusion peptides. HLA-A2-binding peptides were predicted for all MV-encoded proteins and confirmed by T2 cell stabilization. Twenty-nine peptides were tested, and 19 (6 from H) stimulated increased IFN- gamma secretion in a majority of vaccinees. Peptide-loaded HLA-A2 tetramers or immunoglobulin dimers documented MV-specific CD8+ T cell responses after vaccination and during measles and confirmed new A2 epitopes in H (250-259 and 516-525 aa) and matrix (M; 50-58 aa) protein and previously described epitopes in H (30-38 aa), M (211-219 aa), and nonstructural protein C (84-92 aa). No single peptide dominated the response. We conclude that H is an important stimulus for CD8+ T cell as well as for antibody responses in HLA-A2-positive individuals.
A Photopolymerized Sealant for Corneal Lacerations (2002)

Our novel photocrosslinkable methacrylated hyaluronan polymer sealed 97% (37/38) of the experimental corneal lacerations. HA-MA may prove useful for sealing corneal lacerations in patients and for other sutureless ophthalmic surgical procedures.
Synthesis, processing, and secretion of recombinant human factor VIII expressed in mammalian cells. (1988)

The synthesis, processing, and secretion of factor VIII expressed from heterologous genes introduced into Chinese hamster ovary cells has been studied. The results show factor VIII to be synthesized as a primary translation product of approximately 230 kDa that can be detected in the lumen of the endoplasmic reticulum. In this compartment, the majority of the factor VIII is in a complex with a resident protein of the endoplasmic reticulum, binding protein, and may never appear in the medium. Some factor VIII transits the endoplasmic reticulum to the Golgi apparatus, where it is cleaved to generate the mature heavy and light chains. In the absence of von Willebrand factor in the medium, the secreted heavy and light chains are unassociated and subsequently degraded. In the presence of von Willebrand factor in the medium, the heavy and light chains are secreted as a stable complex and activity accumulates linearly with time. The utilization and complexity of asparagine-linked carbohydrate present on the secreted recombinant-derived factor VIII and human plasma-derived factor VIII were compared and found to be very similar. In both cases, the asparagine-linked carbohydrate moieties on the heavy chain are primarily of the hybrid or complex-type. In contrast, the factor VIII from both sources contains a high-mannose type of asparagine-linked carbohydrate on the light chain.
Shale: an overlooked option for US nuclear waste disposal (2014)

Toss a dart at a map of the United States and, more often than not, it will land where shale can be found underground. A drab, relatively featureless sedimentary rock that historically attracted little interest, shale (as used here, the term includes clay and a range of clay-rich rocks) is entering Americans’ consciousness as a new source of gas and oil. But shale may also offer something entirely different—the ability to safely and permanently house high-level nuclear waste.
Potential antihistaminics: Tricyclic carboxylic acids derived from 6,11-dihydrodibenzo[b,e]thiepine and 4,9-dihydrothieno[2,3-c]-2-benzothiepine (1991)

Reaction of nitrile IVa with the Grignard’s reagent 1-methyl-4-piperidylmagnesium chloride gave carbinol XIb as product. Carbinols XIa and XIb were dehydrated and hydrolysed with dilute hydrochloric acid to give hydrochlorides of the tricyclic amino acids Vb and Vc . Isomeric compounds with a carboxyl group in position 9 of the tricyclic skeleton were obtained either by hydrolysis of the formely prepared nitrile VIIb (compound VIIIb ) or on reaction of bromoketone VIa with 1-methyl-4-piperidylmagnesium chloride, nucleophilic substitution of the bromine atom by the cyano group at the stage of carbinol XIIIb , and subsequent dehydration and hydrolysis of the cyano group, to give amino acid VIIIc . In the first case the synthesis of thiophene analogues XVIIIb and XVIIIc started from ketone XVa , which was brominated with bromine in acetic acid into position 2 of the tricyclic skeleton, followed by Grignard’s reaction with 3-dimethylaminopropylmagnesium chloride in tetrahydrofuran and hydrolysis to bromo derivative XVIb . In the second case derivative XVIc was obtained directly by bromination of hydrochloride XVc . Basic bromo derivatives XVIb and XVIc were reacted with butyllithium in tetrahydrofuran at –60°C to afford corresponding organometallic reagents which, when reacted with solid carbon dioxide, afforded the required amino acids XVIIIb and XVIIIc . Further, some other tricyclic nitriles were synthesized as potential intermediates. The prepared tricyclic amino acids Vb, Vc, VIIIb, VIIIc, XVIIIb and XVIIIc were tested both on animals and in assays of biochemical pharmacology. Some of them displayed considerable antihistaminic activity. The most interesting compound of this series, hydrochloride Vc (VUFB-17689) is a strong antihistaminic with distinctly suppressed sedative effects and it was therefore selected for a more detailed pharmacological testing.
A novel carrier frequency offset estimation scheme for OFDM systems utilizing correlation with a pilot symbol without null sub-carrier (2003)

The orthogonal frequency division multiplexing (OFDM) carrier frequency offset estimation scheme is investigated. The carrier frequency offset is detected by monitoring a certain pattern of the frequency domain power differences along the sub-carriers of the pilot symbol. The power differences are raised by inter sub-carrier interference (ICI). In order to estimate the carrier frequency offset effectively, the time domain filtering (windowing) is carried out. The carrier frequency offset estimation performances corresponding to the pre-determined sequences which are transmitted as a pilot symbol are evaluated by computer simulations. Peak-to-average power ratio characteristics are also investigated. The results show that the proposed scheme is effective even for the frequency selective fading channel.
High level expression of functional human IgMs in human PER.C6® cells (2009)

Natural IgM antibodies play an important role in the body's defense mechanisms against transformed cells in the human body and are currently being exploited both in prognoses of malignant lesions and in the therapy of cancer patients. However, despite growing interest and clinical promise, thus far the IgM class of antibodies has failed to gain widespread commercial interest as these are considered to be difficult to produce recombinantly. IgMs are polymeric and have a relatively large mass. In addition, IgM molecules are heavily glycosylated and, when produced in non-human cell lines, they may contain non-human glycan structures which may be potentially immunogenic. Clearly, production systems capable of expressing human recombinant IgM antibodies are needed. We have successfully used PER.C6 cells-a human cell line-to generate three separate human recombinant monoclonal IgMs in suspension cultures in protein-free medium. All three of the IgMs were constructed with joining (J) chain and were expressed in the pentameric form. One of the IgMs was also expressed as a hexamer without J chain. Clones with cell specific productivities greater than 20 pg/cell/day were generated, which led to yields of 0.5 g/L to 2g/L in fed-batch production. All the IgMs expressed were biologically active as shown in binding and cytotoxicity assays. These studies demonstrate the potential of PER.C6 cells for the production of high levels of functional recombinant IgM and other polymeric molecules, using a straightforward and rapid stable cell line generation method.
Methods for Sampling of Airborne Viruses (2008)

To better understand the underlying mechanisms of aerovirology, accurate sampling of airborne viruses is fundamental. The sampling instruments commonly used in aerobiology have also been used to recover viruses suspended in the air. We reviewed over 100 papers to evaluate the methods currently used for viral aerosol sampling. Differentiating infections caused by direct contact from those caused by airborne dissemination can be a very demanding task given the wide variety of sources of viral aerosols. While epidemiological data can help to determine the source of the contamination, direct data obtained from air samples can provide very useful information for risk assessment purposes. Many types of samplers have been used over the years, including liquid impingers, solid impactors, filters, electrostatic precipitators, and many others. The efficiencies of these samplers depend on a variety of environmental and methodological factors that can affect the integrity of the virus structure. The aerodynamic size distribution of the aerosol also has a direct effect on sampler efficiency. Viral aerosols can be studied under controlled laboratory conditions, using biological or nonbiological tracers and surrogate viruses, which are also discussed in this review. Lastly, general recommendations are made regarding future studies on the sampling of airborne viruses.
A Mine-free Central America: How Can We Improve on Success? (2010)

Since 1991, the Organization of American States has worked to eliminate the threat of anti-personnel landmines in the Americas. In 2010, the OAS Mine Action Program marked a major milestone toward that goal as Nicaragua completed its national demining plan to establish a once war-torn Central America as a mine-safe region. Notwithstanding the success of these efforts, it is important to understand what could have been done better to achieve mine-clearance goals more efficiently and effectively and how these lessons might be applied to other programs.
Overcoming resistance to tyrosine kinase inhibitors: Lessons learned from cancer cells treated with EGFR antagonists (2009)

Tyrosine kinase inhibitors (TKIs) are effective anti-cancer therapies but resistance to these agents eventually develops. Several models of resistance to TKIs have been studied including resistance to EGFR inhibitors. Recent studies in EGFR-dependent A431 cells found upregulation of the IGF1R pathway as a mechanism to overcome blockade of EGFR. This was associated with amplification of IGF1R signaling and recovery of downstream PI3K-AKT activation. This work adds to a growing body of cell lines in culture that have provided insights into mechanisms of resistance that can be interrogated in primary tumors in patients. In this review, these model systems and their applicability to human cancers, as well as strategies to identify and overcome resistance to TKIs, are discussed.