gebhart/patrepeval huggingface dataset:
Expression of glucocorticoid receptor α- and β-isoforms in human cells and tissues (2002)

Alternative splicing of the human glucocorticoid receptor (GR) primary transcript generates two protein isoforms: GR-alpha and GR-beta. We investigated the expression of both GR isoforms in healthy human cells and tissues. GR-alpha mRNA abundance (x10(6) cDNA copies/microg total RNA) was as follows: brain (3.83 +/- 0.80) > skeletal muscle > macrophages > lung > kidney > liver > heart > eosinophils > peripheral blood mononuclear cells (PBMCs) > nasal mucosa > neutrophils > colon (0.33 +/- 0.04). GR-beta mRNA was much less expressed than GR-alpha mRNA. Its abundance (x10(3) cDNA copies/microg total RNA) was as follows: eosinophils (1.55 +/- 0.58) > PBMCs > liver > or = skeletal muscle > kidney > macrophages > lung > neutrophils > brain > or = nasal mucosa > heart (0.15 +/- 0.08). GR-beta mRNA was not found in colon. While GR-alpha protein was detected in all cells and tissues, GR-beta was not detected in any specimen. Our results suggest that, in physiological conditions, the default splicing pathway is the one leading to GR-alpha. The alternative splicing event leading to GR-beta is minimally activated.
Address and Message Sequences for the Nociceptin Receptor:  A Structure−Activity Study of Nociceptin-(1−13)-peptide amide (1997)

Nociceptin (NC) and some of its fragments as well as nociceptin-(1-13)-peptide amide [NC- (1-13)-NH2] and a series of its analogues were prepared and tested in the mouse vas deferens in an attempt to identify the sequences involved in the activation (message) and in the binding (address) of nociceptin to its receptor. The NC receptor that inhibits the electrically evoked twitches of the mouse vas deferens was demonstrated to be distinct from the delta opioid receptor, since naloxone and Dmt-Tic-OH (a selective delta opioid receptor antagonist) block the delta opioid receptor but have no effect on the nociceptin receptor. Results from structure-activity experiments suggest that (a) the entire sequence of NC may not be required for full biological activities, since NC(1-13)-NH2 is as active as NC; (b) fragments of NC have however to be amidated as in NC(1-13)-NH2 in order to be protected from degradation by proteases; (c) cationic residues (as Arg8,12, Lys9,13) appear to play a functional role, since their replacement with Ala in the sequence of NC(1-13)-NH2 leads to inactivity; (d) the N-terminal tetrapeptide Phe-Gly-Gly-Phe is essential for activity: its full length and flexibility appear to be required for NC receptor activation and/or occupation; (e) Phe4 and not Phe1 appears to be the residue involved in receptor activation, since the replacement of Phe1 with Leu has no effect, while that of Phe4 leads to inactivity. Results summarized in this paper indicate that the structural requirements of NC for occupation and activation of its receptor are different from that of opioids, particularly delta agonists.
The Biology of Chronic Myeloid Leukemia (1999)

Chronic myeloid leukemia (CML) is a clonal myeloproliferative expansion of transformed, primitive hematopoietic progenitor cells. It involves myeloid, monocytic, erythroid, megakaryocytic, B-lymphoid, and occasionally T-lymphoid lineages.1 CML was the first human disease in which a specific abnormality of the karyotype — the Philadelphia (Ph) chromosome — could be linked to pathogenetic events of leukemogenesis.2 It was among the first neoplastic diseases in which therapy with a biologic agent (interferon) was found to suppress the leukemic clone and prolong survival.3 Although heterogeneous, CML is the best-characterized leukemia at a molecular level, and studies in recent years have helped to define further . . .
Rapid and continuous magnetic separation in droplet microfluidic devices (2014)

We present a droplet microfluidic method to extract molecules of interest from a droplet in a rapid and continuous fashion. We accomplish this by first marginalizing functionalized super-paramagnetic beads within the droplet using a magnetic field, and then splitting the droplet into one droplet containing the majority of magnetic beads and one droplet containing the minority fraction. We quantitatively analysed the factors which affect the efficiency of marginalization and droplet splitting to optimize the enrichment of magnetic beads. We first characterized the interplay between the droplet velocity and the strength of the magnetic field and its effect on marginalization. We found that marginalization is optimal at the midline of the magnet and that marginalization is a good predictor of bead enrichment through splitting at low to moderate droplet velocities. Finally, we focused our efforts on manipulating the splitting profile to improve the enrichment provided by asymmetric splitting. We designed asymmetric splitting forks that employ capillary effects to preferentially extract the bead-rich regions of the droplets. Our strategy represents a framework to optimize magnetic bead enrichment methods tailored to the requirements of specific droplet-based applications. We anticipate that our separation technology is well suited for applications in single-cell genomics and proteomics. In particular, our method could be used to separate mRNA bound to poly-dT functionalized magnetic microparticles from single cell lysates to prepare single-cell cDNA libraries.
Epidemiology and Outcome of Mould Infections in Hematopoietic Stem Cell Transplant Recipients (2002)

Reports have focused on the emergence of moulds as pathogens in recipients of hematopoietic stem cell transplants. To review the incidence of and risks for mould infections, we examined the records of 5589 patients who underwent hematopoietic stem cell transplantation at the Fred Hutchinson Cancer Research Center (Seattle) from 1985 through 1999. After 1992, the incidence of invasive aspergillosis increased in allograft recipients and remained high through the 1990s. Infections with non-fumigatus Aspergillus species, Fusarium species, and Zygomycetes increased during the late 1990s, especially in patients who received multiple transplants. Although infection caused by Scedosporium species was common in patients who had neutropenia, infection caused by Zygomycetes typically occurred later after transplantation, when patients had graft-versus-host disease. The overall 1-year survival rate was equally poor (similar20%) for all patients with mould infections. The results of the present study demonstrate the changing epidemiology of mould infections, emphasizing the increasing importance of amphotericin B--resistant organisms and the differences in risks and outcome of infection with different filamentous fungi.
Synthesis and quantitative structure-activity relationships of some antibacterial 3-formylrifamycin SV N-(4-substituted phenyl)piperazinoacethydrazones (1978)

A series of 14 3-formylrifamycin SV N-(4-substituted phenyl)piperazinoacethydrazones has been synthesized and evaluated for their antimicrobial activity. The compounds were found active against Bacillus subtilis, Staphylococcus aureus, Mycobacterium phlei, and Mycobacterium tuberculosis but not as active as rifampin. The compounds also exhibited significant activity against Clostridium perfringens and in this bacterial system some were more active than rifampin. The QSAR showed that the activity against B. subtilis depended only on lipophilicity, and the regression equation was linear. A parabolic relationship between the antibacterial activity and lipophilicity of the compounds was found in Staph. aureus. Additionally, the activity was dependent upon the electronic and steric effects of the phenyl substituents. The sensitivity of M. phlei to the compounds was found to correlate well with a linear combination of hydrophobic, electronic, and steric parameters. No statistically significant correlation was possible between the physicochemical parameters studied and the activity of the compounds against C. perfringens and M. tuberculosis.
Ray tracing volume densities (1984)

This paper presents new algorithms to trace objects represented by densities within a volume grid, e.g. clouds, fog, flames, dust, particle systems. We develop the light scattering equations, discuss previous methods of solution, and present a new approximate solution to the full three-dimensional radiative scattering problem suitable for use in computer graphics. Additionally we review dynamical models for clouds used to make an animated movie.
Tyrosine phosphorylation of phospholipase C induced by membrane immunoglobulin in B lymphocytes. (1991)

Ligation of membrane IgM on B lymphocytes causes activation of a protein-tyrosine kinase(s) (PTK) and of phospholipase C (PLC). To determine whether these are elements of a common signal-transduction pathway, the effect of three PTK inhibitors on the rise in intracellular free Ca2+ concentration [( Ca2+]i) in human B-lymphoblastoid cell lines was assessed. Tyrphostin completely suppressed the increase in [Ca2+]i and the generation of inositol phosphates induced by ligation of membrane immunoglobulin (mIg) M. Herbimycin and genistein reduced by 30% and 50%, respectively, the rise in [Ca2+]i caused by optimal ligation of mIgM, and they abolished it in cells activated by suboptimal ligation of mIgM. Tyrphostin had no effect on the capacity of aluminum fluoride to increase [Ca2+]i. To determine whether a function of PTK is the phosphorylation of PLC, immunoprecipitates obtained with anti-phosphotyrosine from detergent lysates of B-lymphoblastoid cells were assayed for PLC activity. Ligation of mIgM increased immunoprecipitable PLC activity 2-fold by 90 sec and 4-fold by 30 min. Specific immunoprecipitation and Western blot analysis identified tyrosine phosphorylation of the gamma 1 isoform of PLC after 60 sec of stimulation. Activation of PLC in B cells by mIgM requires PTK function and is associated with tyrosine phosphorylation of PLC-gamma 1, suggesting a mechanism of PLC activation similar to that described for certain receptor PTKs.
Effects of Hydrogen on the Formation of Aligned Carbon Nanotubes by Chemical Vapor Deposition (2002)

Well-aligned carbon nanotubes with controllable properties were grown on porous silicon substrates by thermal chemical vapor deposition. The morphologies of the carbon nanotubes were varied with the introduction of H2 during the catalyst activation and/or carbon nanotube growth processes. It was found that H2 promotes the growth of carbon nanotubes while preventing the formation of spherical amorphous carbon particles. Without the introduction of H2 during the C2H2 thermal decomposition, aligned carbon nanotubes mixed with spherical carbon particles were formed on the substrate. However, with the introduction of H2, pure carbon nanotubes were synthesized. These nanotubes also had uniform diameters of 10-20 nm, which is much smaller than nanotubes synthesized without H2. The average growth rate of nanotubes was also affected by the introduction of hydrogen into the reaction chamber during nanotube growth. With the addition of hydrogen, the average growth rate changed from 78 nm/s to 145 nm/s. A possible growth mechanism, including the effect of a high ratio of H2 to C2H2, is suggested for the growth of these well-aligned carbon nanotubes with uniform diameters.
Temporal Coherent Control in Two-Photon Transitions: From Optical Interferences to Quantum Interferences (1997)

Temporal coherent control of an excited state wave packet is produced by a sequence of two identical ultrashort laser pulses. We show theoretically and experimentally in the case of the $(6s\ensuremath{-}7d)$ two-photon transition in Cs that optical and quantum interferences take place and are clearly distinguished.
Initial experience combining methotrexate with biologic agents for treating rheumatoid arthritis. (1996)

The combination of traditional disease modifying antirheumatic drugs such as methotrexate (MTX) with biologic agents for treating rheumatoid arthritis (RA) has thus far been limited. The combination of MTX and a depleting anti-CD4 monoclonal antibody (cM-T412) has been evaluated in phase I and II trials in patients with refractory RA. The potential of combining MTX with other biologic agents is reviewed.
4.-8. März 2019 (2019)

Hash tables are a core data structure in database systems, because they are fundamental for many database operators like hash-based join and aggregation. In recent years, the efficient vectorized implementation using SIMD (Single Instruction Multiple Data) instructions has attracted a lot of attention. Generally, all hash table implementations need to address what happens when collisions occur. In order to do that, the collisions have to be detected first. There are two types of collisions: (i) key duplicates and (ii) hash value duplicates. The second type is more complicated than the first type. In this paper, we investigate linear probing as a heavily applied hash table implementation and we present an extension of the state-of-the-art vectorized implementation with a hardware-supported duplicate or collision detection. For that, we use novel SIMD instructions which have been introduced with Intel’s SIMD instruction set extension AVX-512. As we are going to show, our approach outperforms the state-of-the-art vectorized version for the key handling, but introduces novel challenges for the value handling. We conclude the paper with some ideas how to tackle that challenge.
Construction of Recombinant Attenuated Salmonella enterica Serovar Typhimurium Vaccine Vector Strains for Safety in Newborn and Infant Mice (2010)

Recombinant bacterial vaccines must be safe, efficacious, and well tolerated, especially when administered to newborns and infants to prevent diseases of early childhood. Many means of attenuation have been shown to render vaccine strains susceptible to host defenses or unable to colonize lymphoid tissue effectively, thus decreasing their immunogenicity. We have constructed recombinant attenuated Salmonella vaccine strains that display high levels of attenuation while retaining the ability to induce high levels of immunogenicity and are well tolerated in high doses when administered to infant mice as young as 24 h old. The strains contain three means of regulated delayed attenuation, as well as a constellation of additional mutations that aid in enhancing safety, regulate antigen expression, and reduce disease symptoms commonly associated with Salmonella infection. The vaccine strains are well tolerated when orally administered to infant mice 24 h old at doses as high as 3.5 x 10(8) CFU.
A community-aware search engine (2004)

Current search technologies work in a one size fits all fashion. Therefore, the answer to a query is independent of specific user information need. In this paper we describe a novel ranking technique for personalized search servicesthat combines content-based and community-based evidences. The community-based information is used in order to provide context for queries andis influenced by the current interaction of the user with the service. Ouralgorithm is evaluated using data derived from an actual service available on the Web an online bookstore. We show that the quality of content-based ranking strategies can be improved by the use of communityinformation as another evidential source of relevance. In our experiments the improvements reach up to 48% in terms of average precision.
Hyperalgesia due to nerve damage: role of nerve growth factor (1999)

The hypothesis that nerve growth factor (NGF) and brain-derived neurotrophic factor (BDNF) contribute to hyperalgesia resulting from nerve damage was tested in rats in which the sciatic nerve was partially transected on one side. Administration of antisera raised against NGF and BDNF relieved mechanical and thermal hyperalgesia in these animals. It has been suggested that NGF may elicit hyperalgesia by inducing mast cells to release algesic agents such as serotonin (5-HT). We found that degranulation of mast cells with compound 48/80 relieved mechanical and thermal hyperalgesia produced by nerve damage. We also found that local injection of the 5-HT2A and 5-HT3 receptor antagonists ketanserin and ICS 205-930 into the affected hind paw relieved mechanical hyperalgesia in a dose-dependent fashion. These findings support the idea that in this rat model of hyperalgesia due to peripheral nerve damage, NGF acts on mast cells to induce release of 5-HT, which sensitizes nociceptors. Hyperalgesia due to nerve injury and hyperalgesia due to inflammation may share some common features.
Anabolic effects of insulin-like growth factor-I (IGF-I) and an IGF-I variant in normal female rats (1993)

Administration of IGF-I over a 14-day period to growing female rats via s.c. implanted osmotic pumps led to an increased body weight gain, an improved N retention and a greater food conversion efficiency. The effects were dose-dependent, with the highest daily dose tested, 278 micrograms/day, producing 18-26% increases in these measurements. LR3IGF-I, a variant of human IGF-I that contains an amino terminal extension peptide as well as glutamate-3 replaced by arginine and exhibits very weak binding to IGF-binding proteins, was substantially more potent than the natural growth factor, in the 44 micrograms/day of this peptide produced similar effects to the high IGF-I dose. Organ weight and carcass composition measurements showed that the two IGF peptides generally maintained body proportions at those existing when the experiment began. Muscle protein synthesis and myofibrillar protein breakdown were both slightly increased by IGF treatment, so that the observed improvement in N retention could not be explained through protein accretion rates calculated from these measures. Infusion of human GH at a dose of 213 micrograms/day did not stimulate body growth. This investigation establishes that IGF peptides stimulate the growth of normal growing animals, with IGF-I variants that bind less well to IGF-binding proteins being more active than IGF-I.
Superior reductions in hepatic steatosis and fibrosis with co-administration of a glucagon-like peptide-1 receptor agonist and obeticholic acid in mice (2017)

Our data suggest a complementary or synergistic therapeutic effect of GLP-1R and FXR agonism in mouse models of metabolic disease and NASH.
Bacterial DNA induces NK cells to produce IFN-γ in vivo and increases the toxicity of lipopolysaccharides (1996)

Microbial products released during bacterial infection induce cytokine-mediated inflammatory responses that can be protective, but excessive release of inflammatory cytokines may promote development of the sepsis syndrome. We examined the ability of bacterial DNA to induce in vivo cytokine release and to potentiate the toxicity of LPS. Intravenous treatment of mice with Escherichia coli (EC) DNA, but not calf thymus (CT) DNA, induced a rapid (within 4 h) dose-dependent increase in serum IFN-gamma and splenic IFN-gamma-forming cells. Over 90% of splenic IFN-gamma-producing cells were identified by surface phenotype as NK cells. Mice also mounted an IFN-gamma response following challenge with 20-base oligonucleotide that contained an internal CG motif (but did not respond to a control oligonucleotide). Treatment of mice with EC DNA followed by a sublethal LPS challenge resulted in a 3-fold increase in the peak serum level of TNF-alpha and a 10-fold increase in the peak level of IL-6 compared with mice that received CT DNA followed by LPS. Mice treated with EC DNA followed by LPS showed 75% mortality, compared with no deaths in mice treated with CT DNA followed by LPS. EC DNA/LPS treatment of mice with disrupted IFN-gamma genes resulted in a 5% mortality while 59% of similarly treated +/+ mice died. Thus, bacterial DNA induces in vivo release of IFN-gamma which, in turn, is associated with an increase in LPS-induced TNF-alpha and IL-6 release, and with increased sensitivity to the toxic effects of LPS.
Local absorption of zinc from wounds treated with different concentrations of zinc sulphate (1978)

In the present study it was shown in rats that zinc is absorbed from excisional wounds treated with zinc sulphate. Systemic toxic effects were observed in the group treated with 20% zinc sulphate. Local toxic effects were seen in wounds treated with 0.2%, 2% and 20% zinc sulphate. An inhibitory effect of zinc on the migration of granulocytes was suggested on the basis of microscopic observation. In the operated groups which were not treated with zinc and the group treated with 0.02% zinc sulphate a decline was observed in the concentration of zinc in serum. The zinc concentration in serum increased in proportion to the zinc sulphate concentration (0.2%, 2% and 20%) applied to the wounds, while the copper concentration decreased in the groups treated with 2% and 20% zinc sulphate. In all operated groups an increase in zinc and copper concentrations was observed in liver. This was most pronounced in groups treated with higher concentrations of zinc sulphate (0.2%, 2% and 20%). The groups treated with higher concentrations of zinc sulphate also had higher pancreas zinc concentrations than the remaining groups.
Repertoire cloning of lupus anti-DNA autoantibodies. (1996)

To investigate the autoantibody repertoire associated with SLE, we have created phage display IgG Fab libraries from two clinically active SLE patients and from the healthy identical twin of one of these patients. The libraries from the lupus discordant twins were found to both include unusually large representations of the V(H)5 gene family. By panning with DNA, the SLE libraries each yielded IgG anti-double-stranded (ds) DNA autoantibodies, which are characteristic of lupus disease. These included a V(H)5 autoantibody from the affected twin, that has a targeted cluster of mutations that potentially improves binding affinity. The recovered IgG anti-dsDNA autoantibodies expressed the same idiotypes associated with the in vivo IgG anti-dsDNA response of the respective SLE donor. Heavy-light chain shuffling experiments demonstrated a case in which the in vitro creation of anti-dsDNA binding activity required restrictive pairing of a heavy chain with Vlambda light chains similar to those in circulating anti-dsDNA autoantibodies. By contrast, IgG anti-ds autoantibodies could not be recovered from the library from the healthy twin, or from shuffled libraries with heavy chains from the healthy twin. These repertoire analyses illustrate how inheritance and somatic processes interplay to produce lupus-associated IgG autoantibodies.
Identification of CX 3CR1 (1998)

Fractalkine is a multimodular human leukocyte chemoattractant protein and a member of the chemokine superfamily. Unlike other human chemokines, the chemokine domain of fractalkine has three amino acids between two conserved cysteines, referred to as the CX3C motif. Both plasma membrane-associated and shed forms of fractalkine have been identified. Here, we show that the recombinant 76-amino acid chemokine domain of fractalkine is a potent and highly specific chemotactic agonist at a human orphan receptor previously named V28 or alternatively CMKBRL1 (chemokine beta receptor-like 1), which was shown previously to be expressed in neutrophils, monocytes, T lymphocytes, and several solid organs, including brain. CMKBRL1/V28 also functioned with CD4 as a coreceptor for the envelope protein from a primary isolate of HIV-1 in a cell-cell fusion assay, and fusion was potently and specifically inhibited by fractalkine. Thus CMKBRL1/V28 is a specific receptor for fractalkine, and we propose to rename it CX3CR1 (CX3C chemokine receptor 1), according to an accepted nomenclature system.