gebhart/patrepeval huggingface dataset:
JARID1B is a histone H3 lysine 4 demethylase up-regulated in prostate cancer (2007)

Histone methylation is a dynamic process that participates in a diverse array of cellular processes and has been found to associate with cancer. Recently, several histone demethylases have been identified that catalyze the removal of methylation from histone H3 lysine residues. Through bioinformatic and biochemical analysis, we identified JARID1B as a H3K4 demethylase. Overexpression of JARID1B resulted in loss of tri-, di-, and monomethyl H3K4 but did not affect other histone lysine methylations. In vitro biochemical experiments demonstrated that JARID1B directly catalyzes the demethylation. The enzymatic activity requires the JmjC domain and uses Fe(II) and alpha-ketoglutarate as cofactors. Furthermore, we found that JARID1B is up-regulated in prostate cancer tissues, compared with benign prostate samples. We also demonstrated that JARID1B associates with androgen receptor and regulates its transcriptional activity. Thus, we identified JARID1B as a demethylase capable of removing three methyl groups from histone H3 lysine 4 and up-regulated in prostate cancer.
Determination of PvCOCO2 From the Exponential CO2 Rise During Rebreathing (1958)

It is shown theoretically that the CO2 time course during rebreathing involves two exponential terms, one of these terms being negligible after the first respiration. The validity of the exponential equation is shown experimentally. With the aid of this formula it is possible to compute the CO2 tension in the mixed venous blood. Rebreathing is preferred to breath holding as previously described by Dubois and Fenn, since rebreathing yields far more accurate results. The PvCOCO2 values computed from the rebreathing values were compared with values obtained by the Haldane method. The mean difference was not statistically significant. With the aid of this ‘exponential’ method for the determination of the PvCOCO2, the cardiac output was determined on the indirect Fick principle. The mean value of nine subjects under almost basal conditions was found to be 4.99 1/min. The variations on one and the same subject were less than 10%. Submitted on August 13, 1956
Ubiquitination and Degradation of ATF2 Are Dimerization Dependent (1999)

Ubiquitination and proteasome-dependent degradation are key determinants of the half-lives of many transcription factors. Homo- or heterodimerization of basic region-leucine zipper (bZIP) transcription factors is required for their transcriptional activities. Here we show that activating transcription factor 2 (ATF2) heterodimerization with specific bZIP proteins is an important determinant of the ubiquitination and proteasome-dependent degradation of ATF2. Depletion of c-Jun as one of the ATF2 heterodimer partners from the targeting proteins decreased the efficiency of ATF2 ubiquitination in vitro, whereas the addition of exogenously purified c-Jun restored it. Similarly, overexpression of c-Jun in 293T human embryo kidney cells increased ATF2 ubiquitination in vivo and reduced its half-life in a dose-dependent manner. Mutations of ATF2 that disrupt its dimerization inhibited ATF2 ubiquitination in vitro and in vivo. Conversely, removal of residues 150 to 248, as in a constitutively active ATF2 spliced form, enhanced ATF2 dimerization and transactivation, which coincided with increased ubiquitination and decreased stability. Our findings indicate the increased sensitivity of transcriptionally active dimers of ATF2 to ubiquitination and proteasome-dependent degradation. Based on these observations, we conclude that increased targeting of a transcriptionally active ATF2 form indicates the mechanism by which the magnitude and the duration of the cellular stress response are regulated.
Clinical protocol for pregnancy termination in bitches using prostaglandin F2 alpha. (1997)

Sixty-seven pregnant bitches were given atropine sulphate (0.025 mg kg-1), prifinium bromide (0.1 ml kg-1) and metopimazine (0.5 mg kg-1) and 15 min later 2.5 micrograms cloprostenol kg-1 s.c., three times at 48 h intervals (day 1, day 3, day 5). After one treatment, 53 of the 67 bitches had aborted, and after a second treatment, 62 of the 67 bitches had aborted. In 18 bitches, progesteronemia kinetics were followed-up: the first injection of cloprostenol resulted in a significant (P < 0.01) fall in progesteronemia. In 12 of the 18 bitches that had aborted following the first protocol, this rapid fall in progesterone was noteworthy as it decreased progesterone concentration on average from 17.07 +/- 8.20 ng ml-1 on day 1 to 1.31 +/- 0.34 ng ml-1 on day 3. The premedication administered 15 min before the injection of prostaglandins, prevented the appearance of side effects in 39 of the 67 bitches (58.2%).
TEAtime Adaptive-Computing Case-Study, Demonstration and Updated Results (2006)

The TEAtime system described herein was prototyped and characterized in a matter of days after the TEAtime idea was conceived. This rapid-prototyping was only possible by using an FPGA. TEAtime (Timing Error Avoidance) is a microarchitectural/logic/analog design that allows any digital system to ‘maximize’ its performance under any given environmental, operating or manufacturing conditions [4, 6, 7]. It is a form of
Intravenous apoptotic cell infusion as a cell‐based therapy toward improving hematopoietic cell transplantation outcome (2010)

Allogeneic hematopoietic cell transplantation (AHCT) is an efficient therapy for different malignant and nonmalignant hematological diseases. However, the use of this therapeutic approach is still limited by some severe toxic side effects, mainly graft-versus-host disease (GvHD). Today, the risk of fatal GvHD restrains the wider application of AHCT to many patients in need of an effective therapy for their high-risk hematologic malignancies. Thus, new strategies, including cell-based therapy approaches, are required. We propose to use intravenous donor apoptotic leukocyte infusion to improve AHCT outcome. In experimental AHCT models, we demonstrated that intravenous apoptotic leukocyte infusion, simultaneously with allogeneic bone marrow grafts, favors hematopoietic engraftment, prevents allo-immunization, and delays acute GvHD onset. Here, we review the different mechanisms and the potential beneficial effects associated with the immunomodulatory properties of apoptotic cells in the AHCT setting.
Optimization of particle bombardment parameters for the genetic transformation of Brazilian maize inbred lines (2008)

The objective of this work was to develop a genetic transformation system for tropical maize genotypes via particle bombardment of immature zygotic embryos. Particle bombardment was carried out using a genetic construct with bar and uidA genes under control of CaMV35S promoter. The best conditions to transform maize tropical inbred lines L3 and L1345 were obtained when immature embryos were cultivated, prior to the bombardment, in higher osmolarity during 4 hours and bombarded at an acceleration helium gas pressure of 1,100 psi, two shots per plate, and a microcarrier flying distance of 6.6 cm. Transformation frequencies obtained using these conditions ranged from 0.9 to 2.31%. Integration of foreign genes into the genome of maize plants was confirmed by Southern blot analysis as well as bar and uidA gene expressions. The maize genetic transformation protocol developed in this work will possibly improve the efficiency to produce new transgenic tropical maize lines expressing desirable agronomic characteristics.
Balloon catheter injury to rabbit carotid artery. I. Changes in smooth muscle phenotype. (1989)

Stereology was used to investigate the changes in ultrastructure of smooth muscle cells during the formation of an experimental intimal thickening induced by injury with an inflated balloon catheter. The volume density of myofilaments in the cell cytoplasm was measured in smooth muscle cell-lined areas (which are freely permeable to Evans blue dye and, hence, stain blue) and in re-endothelialized areas (which remain white after injection of Evans blue) of the rabbit carotid artery. Two weeks after injury, the volume densities of myofilaments in the intimal smooth muscle cells in both white and blue areas were significantly less than that for control medial smooth muscle (67.9% +/- 3.6%; mean +/- SE), being 38.8% +/- 1.0% and 35.9 +/- 3.3%, respectively. By 6 weeks after injury, the volume density had increased significantly in both white (55.1% +/- 3.4%) and blue areas (53.5% +/- 3.0%), and these values did not change significantly by 18 weeks. The volume density of myofilaments in the luminal (lining) smooth muscle cells in the blue areas was significantly less than that of control medial cells and remained low (26.7% +/- 2.1%) up to 18 weeks after injury. The initial balloon-induced injury caused considerable damage to the smooth muscle cells in the media, and the remaining medial cells underwent similar changes in ultrastructure to the cells in the neointima. At 2 weeks, the cells had a low volume density of myofilaments (44.9% +/- 2.4%), which returned to a level not significantly different from the control artery by 6 weeks after injury. There were no differences in the estimates of the volume density of myofilaments between the inner and outer media of the injured arteries. These findings suggest that, after injury produced by a balloon catheter, the smooth muscle cells in both the media and the resultant intimal thickening undergo a reversible change in ultrastructure.
Situating the Banna: An Ethnographic Description of Ethnic Identification (2009)

Studies of interethnic warfare in Lower Omo Valley have explored relationships between identity and culture and between society and ecology. This paper is first to add eth­ nographic information about myth, clan classification, and interethnic warfare among Banna to academic discourse. It also clarifies how Banna people construct their ethnic identity: they identify themselves as members of Banna through a various forms of recognitipn and narra­ tives, but these everyday activities do not guarantee a discrete Banna land, language, and culture. Research has revealed that, contrary to group's assertion, Banna identity has no discrete unity. Appadurai (1996) theorized that locality is a phenomenological property of social life, which might be discovered through description of neighborhoods as the actually existing social forms in which locality, as a dimension or value, is variably realized.
Synthesis-Dependent First-Order Raman Scattering in SrTiO3Nanocubes at Room Temperature (2008)

Raman spectroscopy was used to demonstrate that the lattice dynamics of SrTiO3 (STO) nanoparticles strongly depends on their microstructure, which is in turn determined by the synthetic approach employed. First-order Raman modes are observed at room temperature in STO single-crystalline nanocubes with average edge lengths of 60 and 120 nm, obtained via sol-precipitation coupled with hydrothermal synthesis and a molten salt procedure, respectively. First-order Raman scattering arises from local loss of inversion symmetry caused by surface frozen dipoles, oxygen vacancies, and impurities incorporated into the host lattice. The presence of polar domains is suggested by the pronounced Fano asymmetry of the peak corresponding to the TO2 polar phonon, which does not vanish at room temperature. These noncentrosymmetric domains will likely influence the dielectric response of these nanoparticles.
Dosing and Monitoring NovoSeven® Treatment (1996)

The concept of using factor VIIa (FVIIa) to induce hemostasis in hemophilia is new and takes advantage of the normal tissue factor/FVII-dependent coagulation pathway which is enhanced by the administration of extra exogenous recombinant FVIIa. Since this is a pharmacological treatment and not a simple substitution therapy the current dosis recommendations are based on preclinical data (in vitro and in animals) as well as on clinical experience. It is concluded that the initial dose should be high enough to maintain a plasma level of FVII-coagulant activity (FVII:C) at > 6 U/ml for several hours corresponding roughly to a dose of 90-120 mu g/kg.
Segmental Recurrent Neural Networks (2015)

We introduce segmental recurrent neural networks (SRNNs) which define, given an input sequence, a joint probability distribution over segmentations of the input and labelings of the segments. Representations of the input segments (i.e., contiguous subsequences of the input) are computed by encoding their constituent tokens using bidirectional recurrent neural nets, and these "segment embeddings" are used to define compatibility scores with output labels. These local compatibility scores are integrated using a global semi-Markov conditional random field. Both fully supervised training -- in which segment boundaries and labels are observed -- as well as partially supervised training -- in which segment boundaries are latent -- are straightforward. Experiments on handwriting recognition and joint Chinese word segmentation/POS tagging show that, compared to models that do not explicitly represent segments such as BIO tagging schemes and connectionist temporal classification (CTC), SRNNs obtain substantially higher accuracies.
Two-dimensional optical phased array antenna on silicon-on-Insulator (2010)

Optical wireless links can offer a very large bandwidth and can act as a complementary technology to radiofrequency links. Optical components nowadays are however rather bulky. Therefore, we have investigated the potential of silicon photonics to fabricated integrated components for wireless optical communication. This paper presents a two-dimensional phased array antenna consisting of grating couplers that couple light off-chip. Wavelength steering of $0.24 degrees /nm is presented reducing the need of active phase modulators. The needed steering range is $1.5 degrees . The 3dB angular coverage range of these antennas is about $0.007pi sr with a directivity of more than 38dBi and antenna losses smaller than 3dB.
The Jak Family Tyrosine Kinase Jak3 Is Required for IL-2 Synthesis by Naive/Resting CD4+ T Cells (1999)

The Jak family tyrosine kinase, Jak3, is involved in signaling through cytokine receptors using the common gamma-chain. Mice deficient in Jak3 have mature T cells, all of which have an activated/memory cell phenotype but are unresponsive to in vitro stimulation. Due to this activated phenotype, it has been impossible to determine whether Jak3 plays a role in the responsiveness of naive/resting T cells. To circumvent this difficulty, we generated naive/resting Jak3-negative T cells by two genetic approaches. After stimulation, these cells failed to produce significant amounts of IL-2. Although no signaling defect could be detected, we did find that naive/resting Jak3-negative T cells have substantially reduced levels of the transcription factor NF-AT1 and moderately reduced levels of c-Jun and c-Fos. On the basis of these data, we propose that Jak3-dependent cytokine signals may be required to maintain the normal levels of basal transcription factors required for immediate responsiveness to Ag activation.
Upregulation of MAGE-A1, MAGE-A3, NY-ESO-1 and MHC Molecules on Neuroblastoma Cells Following Exposure to Decitabine and Interferon-γ (2010)

Abstract Abstract 5179 MAGE-A1, MAGE-A3, and NY-ESO-1 are cancer-testis (CT) antigens expressed on a number of malignant solid tumors, including neuroblastoma (NB), but many tumor cell lines down-regulate the expression of CT antigens as well as major histocompatibility (MHC) antigens, precluding recognition by antigen specific T cells. If expression of cancer antigens as well as MHC molecules could be enhanced pharmacologically, the efficacy of CT antigen specific immunotherapy could be improved. DNA methylation is an epigenetic mechanism used by cells to decrease the expression of several genes, including tumor suppressor genes. Decitabine (5-aza-2′-deoxycytidine, DAC) is a potent inhibitor of DNA methylation, and the doses associated with the demethylating action of this drug are much lower than those required for cytotoxicit. We have demonstrated that the expression of MAGE-A1, MAGE-A3, and NY-ESO-1 can be upregulated on neuroblastoma cells following exposure to the DAC. When these cell lines are cultured in the presence of DAC at concentrations similar to levels achieved with clinical administration, we were able to achieve expression of NY-ESO-1, MAGE-A1, or MAGE-A3 in 11/11 neuroblastoma cell lines. Concentrations of 1uM DAC were associated with strongest expression of these antigens, which was optimal after 72 hours of drug exposure. Culture of NB cell lines with IFN-γ was also associated with an increased expression of either MHC Class I or II by cytofluorometry, and Class I upregulated in 10/11 of these cell lines, although to varying degrees. MAGE-A1, MAGE-A3, and NY-ESO-1 specific CTL were cultured from volunteer donors by stimulating peripheral blood mononuclear cells with dendritic cells pulsed with overlapping peptide mixes derived from full length proteins, and these CTL lysed HLA partially matched, DAC treated neuroblastoma as well as glioblastoma cell lines. These studies confirm that DAC and IFN-γ can be used to increase the expression of CT antigens and MHC molecules on neuroblastoma cells, and pre-treatment with these agents makes tumor cell lines more susceptible to CTL mediated killing. Disclosures: No relevant conflicts of interest to declare.
A novel herpes simplex virus glycoprotein, gL, forms a complex with glycoprotein H (gH) and affects normal folding and surface expression of gH (1992)

A glycoprotein encoded by the UL1 gene of herpes simplex virus type 1 (HSV-1) was detected in infected cells with antipeptide sera. The UL1 gene has previously been implicated in virus-induced cell fusion (S. Little and P. A. Schaffer, Virology 112:686-697, 1981). Two protein species, a 30-kDa precursor form and a 40-kDa mature form of the glycoprotein, both of which were modified with N-linked oligosaccharides, were observed. This novel glycoprotein is the 10th HSV-1 glycoprotein to be described and was named glycoprotein L (gL). A complex was formed between gL and gH, a glycoprotein known to be essential for entry of HSV-1 into cells and for virus-induced cell fusion. Previously, it had been reported that gH expressed in the absence of other viral proteins was antigenically abnormal, not processed, and not expressed at the cell surface (U.A. Gompels and A. C. Minson, J. Gen. Virol. 63:4744-4755, 1989; A. J. Forrester, V. Sullivan, A. Simmons, B. A. Blacklaws, G. L. Smith, A. A. Nash, and A. C. Minson, J. Gen. Virol. 72:369-375, 1991). However, gH coexpressed with gL by using vaccinia virus recombinants was antigenically normal, processed normally, and transported to the cell surface. Similarly, gL was dependent on gH for proper posttranslational processing and cell surface expression. These results suggest that it is a hetero-oligomer of gH and gL which is incorporated into virions and transported to the cell surface and which acts during entry of virus into cells.
Camel Single-domain Antibodies as Modular Building Units in Bispecific and Bivalent Antibody Constructs (2001)

Single-domain antibodies against various antigens are isolated from the unique heavy-chain antibodies of immunized camels and llamas. These minimal sized binders are very robust and bind the antigen with high affinity in a monomeric state. We evaluated the feasibility to produce soluble, functional bispecific and bivalent antibodies in Escherichia coli with camel single-domain antibody fragments as building blocks. Two single-domain antibody fragments were tethered by the structural upper hinge of a natural antibody to generate bispecific molecules. This linker was chosen for its protease resistance in serum and its natural flexibility to reorient the upstream and downstream located domains. The expression levels, ease of purification, and the solubility of the recombinant proteins were comparable with those of the constituent monomers. The individual moieties fully retain the binding capacity and the binding characteristics within the recombinant bispecific constructs. The easy generation steps and the biophysical properties of these bispecific and bivalent constructs based on camel single-domain antibody fragments makes them particularly attractive for use in therapeutic or diagnostic programs.
Complementation of a bovine papilloma virus low-copy-number mutant: evidence for a temporal requirement of the complementing gene. (1986)

We identified a bovine papilloma virus function encoded by the E6/E7 gene, which is required for both BPV high-copy-number replication and maintenance of transformation of cultured cells. A cDNA copy of this gene was isolated and expressed from a retrovirus vector. We found that complete complementation of a BPV low-copy-number mutant (dl576) by the cDNA encoding the E6/E7 gene was temporally dependent. When both the E6/E7 cDNA and dl576 were introduced together into cells, wild-type replication and stable transformation resulted. In contrast, introduction of the complementing cDNA into cells already carrying dl576 led to only partial amplification of the resident mutant DNA accompanied by a restoration of the transformed phenotype. These results, along with other findings, suggest that the establishment of BPV plasmid replication occurs in two stages: an initial amplification of the incoming DNA followed by stable homeostatic replication which maintains the existing copy number.
Broadly Neutralizing Antibodies Present New Prospects to Counter Highly Antigenically Diverse Viruses (2012)

Certain human pathogens avoid elimination by our immune system by rapidly mutating the surface protein sites targeted by antibody responses, and consequently they tend to be problematic for vaccine development. The behavior described is prominent for a subset of viruses--the highly antigenically diverse viruses--which include HIV, influenza, and hepatitis C viruses. However, these viruses do harbor highly conserved exposed sites, usually associated with function, which can be targeted by broadly neutralizing antibodies. Until recently, not many such antibodies were known, but advances in the field have enabled increasing numbers to be identified. Molecular characterizations of the antibodies and, most importantly, of the sites of vulnerability that they recognize give hope for the discovery of new vaccines and drugs.
Oxide-field dependence of the NMOS hot-carrier degradation rate and its impact on AC-lifetime prediction (2002)

This study presents a general relationship between the NMOS hot-carrier degradation rate n and the oxide-electric field at the drain E/sub ox/, which is valid over a wide range of stress-bias conditions and device parameters. Physical mechanisms for this oxide-field dependence are explored. It is also shown that failure to account for the oxide-field dependence of n and the inherent non-linearity of the degradation time dependence can result in significant overestimation of the predicted AC lifetime.