gebhart/patrepeval huggingface dataset:
Polypyrimidine tract-binding protein down-regulates fibroblast growth factor receptor 1 alpha-exon inclusion. (2003)

Exclusion of the alpha-exon by alternative RNA splicing of the fibroblast growth factor receptor 1 (FGFR1) primary transcript leads to the production of FGFR1beta. Glial cell transformation is associated with a progressive increase in FGFR1beta expression that coincides with a dramatic increase in the expression of the splicing factor polypyrimidine tract-binding protein (PTB). Cell-specific overexpression of PTB increased alpha-exon skipping, and a reduction in PTB increased alpha-exon inclusion. Targeted disruption of PTB interaction with FGFR1 precursor RNA in vivo by an antisense oligonucleotide also increased alpha-exon inclusion. These results suggest that PTB plays a direct role in alpha-exon splicing.
A transgenic insect cell line engineered to produce CMP-sialic acid and sialylated glycoproteins (2003)

We have previously engineered transgenic insect cell lines to express mammalian glycosyltransferases and showed that these cells can sialylate N-glycoproteins, despite the fact that they have little intracellular sialic acid and no detectable CMP-sialic acid. In the accompanying study, we presented evidence that these cell lines can salvage sialic acids for de novo glycoprotein sialylation from extracellular sialoglycoproteins, such as fetuin, found in fetal bovine serum. This finding led us to create a new transgenic insect cell line designed to synthesize its own sialic acid and CMP-sialic acid. SfSWT-1 cells, which encode five mammalian glycosyltransferases, were transformed with two additional mammalian genes that encode sialic acid synthase and CMP-sialic acid synthetase. The resulting cell line expressed all seven mammalian genes, produced CMP-sialic acid, and sialylated a recombinant glycoprotein when cultured in a serum-free growth medium supplemented with N-acetylmannosamine. Thus the addition of mammalian genes encoding two enzymes involved in CMP-sialic acid biosynthesis yielded a new transgenic insect cell line, SfSWT-3, that can sialylate recombinant glycoproteins in the absence of fetal bovine serum. This new cell line will be widely useful as an improved host for baculovirus-mediated recombinant glycoprotein production.
Activation of the extracellular signal‐regulated kinase 2 by metabotropic glutamate receptors (1999)

Activation of metabotropic glutamate receptors (mGluRs) leads to modulation of a variety of second messenger pathways probably including the mitogen-activated protein kinase (MAPK) extracellular signal-regulated protein kinases (ERK). MAPK play a key role in the control of cellular responses to changes in the external environment by regulating transcriptional activity and the phosphorylation state of several cytoplasmic targets. In this study, Chinese hamster ovary (CHO) cells permanently transfected with rat mGluR1a, mGluR2 and mGluR4 were employed as a model to examine the activation of MAPK by glutamate through mGluRs. All three mGluR subtypes rapidly stimulated ERK activation. In particular, mGluR1a and mGluR2 preferentially mediated phosphorylation and activation of ERK2 in a pertussis toxin (PTX)-sensitive and concentration-dependent manner. The activation was blocked completely by pretreatment with the antagonist (rs)-alpha-methyl-4-carboxyphenylglycine (MCPG) or with the MEK inhibitor PD098059. Furthermore, mGluR1a-mediated ERK activation was suppressed by the depletion of endogenous protein kinase C (PKC) activity and by the PKC inhibitors staurosporine and calphostin C, but not chelerythrine. When cAMP was elevated in mGluR2-expressing cells, by forskolin or dibutyryl-cAMP, slight elevation of ERK activity was observed. However, glutamate-stimulated ERK activation remained unaffected. In these cells, the phosphatidylinositol 3 kinase (PI3K) inhibitor wortmannin produced a significant, albeit only partial, inhibition of mGluR2-mediated ERK activation. These findings raise the possibility of a MAPK cascade involvement in glutamate-dependent neuronal plasticity mediated through stimulation of mGluRs.
Concealment of bit error and cell loss in inter-frame coded video transmission (2002)

Experimental results on error concealment techniques to hide the video quality degradation due to bit errors and cell losses from the viewer's perception are presented. The impact of bit error and cell loss in a hybrid DPCM/DCT (differential pulse code modulation/discrete cosine transform) coding algorithm is described through three different video sequence simulations. Two effective schemes that conceal the information loss caused by bit errors and cell losses based on the information in the previous frame are presented. These error concealment techniques work very well in real-time playback as long as the location of bit error and cell loss is properly detected by the decoder. Impairments caused by a cell loss can be compensated for by simple replenishment in real-time playback. Although motion replenishment performs better in the case of uniformly slow motion, it requires that the network have a priority capability. Impairments due to undetected bit errors cannot be compensated for by any concealment algorithm.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Studies with enteroaggregative Escherichia coli in the gnotobiotic piglet gastroenteritis model (1992)

Two strains of enteroaggregative Escherichia coli of human origin fed to gnotobiotic piglets caused diarrhea or death in the majority of them. Histological examination revealed moderate hyperemia of the distal small intestine and cecum, swelling of small intestinal villi, and layers of aggregated bacteria stacked together in a mucus gel-like matrix overlying intact epithelium. These findings confirm that enteroaggregative E. coli strains produce distinctive intestinal lesions different from those caused by other major categories of diarrheagenic E. coli.
Genetic Risk Signatures of Opioid-Induced Respiratory Depression Following Pediatric Tonsillectomy (2014)

Background: Respiratory depression is a clinically and economically important but preventable complication of opioids. Genetic factors can help identify patients with high risk for respiratory depression. Methods: In this prospective genotype blinded clinical study, we evaluated the effect of a panel of variants in candidate genes on opioid-related respiratory depression in 347 children following tonsillectomy. Results: Using unsupervised hierarchical clustering and a combination of candidate genotypes and clinical variables, we identified several distinct clusters of patients at high risk (36-38%) and low risk (10-17%) of respiratory depression; the relative risk of respiratory depression for high versus low risk clusters was 2.1-3.8 (p = 0.003). Conclusion: Genetic risk predictions (genetic signatures) along with clinical risk factors effectively identify children at higher and lower risks of opioid-induced respiratory depression. Genetic signatures of respiratory depression offer strategies for improved clinical decision support to guide clinicians to balance the risks of opioid adverse effects with analgesia. Original submitted 9 July 2014; Revision submitted 19 September 2014.
The Src family of tyrosine protein kinases in hemopoietic signal transduction (1992)

The Src family of tyrosine protein kinases represent an expanding class of closely related intracellular enzymes that participate in the signal transduction pathways of a variety of surface receptors. One of the more surprising aspects of the information relating Src protein kinases to receptor signaling is the apparent diversity of receptor types with which the Src-related enzymes are reported to interact physically or functionally. Traditional biochemical and genetic approaches have yielded much information regarding the interactions between the Src tyrosine protein kinases and other cellular proteins in defined cell types, and emerging technologies, most notably homologous recombination in embryonal stem cells to achieve gene "knockouts," are providing new insights into the participation of the Src-related gene products in signal transduction and development.
Demonstrating Oxygen Loss and Associated Structural Reorganization in the Lithium Battery Cathode Li[Ni0.2Li0.2Mn0.6]O2 (2006)

The cathode in rechargeable lithium-ion batteries operates by conventional intercalation; Li+ is extracted from LiCoO2 on charging accompanied by oxidation of Co3+ to Co4+; the process is reversed on discharge. In contrast, Li+ may be extracted from Mn4+-based solids, e.g., Li2MnO3, without oxidation of Mn4+. A mechanism involving simultaneous Li and O removal is often proposed. Here, we demonstrate directly, by in situ differential electrochemical mass spectrometry (DEMS), that O2 is evolved from such Mn4+ -containing compounds, Li[Ni(0.2)Li(0.2)Mn(0.6)]O2, on charging and using powder neutron diffraction show that O loss from the surface is accompanied by diffusion of transition metal ions from surface to bulk where they occupy vacancies created by Li removal. The composition of the compound moves toward MO(2). Understanding such unconventional Li extraction is important because Li-Mn-Ni-O compounds, irrespective of whether they contain Co, can, after O loss, store 200 mAhg(-1) of charge compared with 140 mAhg(-1) for LiCoO(2).
Tomato Response to Starter Fertilizer, Polyethylene Mulch, and Level of Soil Phosphorus (1993)

Unmulched and polyethylene-mulched tomatoes (Lycopersicon esculentum Mill.) were grown with and without starter fertilizer (SF) in four field experiments. The fields varied as to residual P level and the amount of P incorporated before planting. No benefits from SF were obtained on a soil with high residual P that was moderately fertilized with P before transplanting or on a soil with low residual P that was heavily fertilized with P. A positive effect from SF was observed only when residual P was low and no P was broadcast, and this was true in mulched and umnulched plots. No significant SF by mulch interaction was obtained in these experiments even though mulching consistently increased shoot P concentrations and fruit yield. The mulch was beneficial even under conditions where unmulched tomato leaves contained 0.4 % P 3 weeks after transplanting, indicating that factors in addition to improved P nutrition are also involved in the mulch effect.
Retroviral vector with a CMV-IE/HIV-TAR hybrid LTR gives high basal expression levels and is up-regulated by HIV-1 Tat. (1995)

We have constructed a new retroviral vector by making modifications to the commonly used Moloney murine leukemia virus (MoMLV) based vector in the long terminal repeat (LTR). The changes include replacement of a portion of the U3 region of the MoMLV LTR with a hybrid regulatory element consisting of the human cytomegalovirus immediate-early enhancer/promoter (CMV-IE) together with the human immunodeficiency virus transactivation response element (HIV-TAR). Transfection of chloramphenicol acetyl transferase (CAT) reporter constructs into a variety of human cell lines showed that the hybrid LTR with the CMV-IE/HIV-TAR enhancer/promoter exhibited basal expression levels which were 10- to 50-fold higher than those obtained from the wild-type MoMLV-LTR enhancer/promoter. Expression from the recombinant LTR was further increased in the presence of the HIV-Tat protein, and surprisingly, Tat up-regulated transcription from both the HIV and the MoMLV TATA boxes. In contrast, a MoMLV enhancer/promoter containing only the HIV-TAR element in the LTR did not respond to Tat. When stably transfected into an amphotropic packaging cell line, the modified retroviral vector containing the hybrid LTR plus an extended packaging signal consistently gave higher titres of retrovirus than did the parental MoMLV based vector. Higher basal expression levels which can be further upregulated by Tat, together with more efficient virion production, suggests that the modified vector should be superior for anti-HIV gene therapy applications as well as for other more general applications in human gene therapy.
Shared fine specificity between T-cell receptors and an antibody recognizing a peptide/major histocompatibility class I complex. (1996)

Cytotoxic T cells recognize mosaic structures consisting of target peptides embedded within self-major histocompatibility complex (MHC) class I molecules. This structure has been described in great detail for several peptide-MHC complexes. In contrast, how T-cell receptors recognize peptide-MHC complexes have been less well characterized. We have used a complete set of singly substituted analogs of a mouse MHC class I, Kk-restricted peptide, influenza hemagglutinin (Ha)255-262, to address the binding specificity of this MHC molecule. Using the same peptide-MHC complexes we determined the fine specificity of two Ha255-262-specific, Kk-restricted T cells, and of a unique antibody, pSAN, specific for the same peptide-MHC complex. Independently, a model of the Ha255-262-Kk complex was generated through homology modeling and molecular mechanics refinement. The functional data and the model corroborated each other showing that peptide residues 1, 3, 4, 6, and 7 were exposed on the MHC surface and recognized by the T cells. Thus, the majority, and perhaps all, of the side chains of the non-primary anchor residues may be available for T-cell recognition, and contribute to the stringent specificity of T cells. A striking similarity between the specificity of the T cells and that of the pSAN antibody was found and most of the peptide residues, which could be recognized by the T cells, could also be recognized by the antibody.
The Three-Dimensional Structure of a Phosphorylcholine-Binding Mouse Immunoglobulin Fab and the Nature of the Antigen Binding Site (1974)

The structure of the Fab of McPC 603, a mouse myeloma protein with phosphorylcholine binding activity, has been determined to 3.1-A resoltuion. The four domains are found to be structurally similar with a well-defined double-layer structure. A large cavity exists at one end of the fragment, the walls of which are formed exclusively of hypervariable residues. Phosphorylcholine binds in this cavity and forms specific interactions with several well-defined amino-acid side chains of the protein. The hapten is bound asymmetrically and interacts more with the heavy chain than with the light chain.
Three distinct forms of type 2A protein phosphatase in human erythrocyte cytosol. (1988)

Two type 2A protein phosphatases, phosphatases I (Mr = 180,000) and III (Mr = 177,000), were purified to near homogeneity from human erythrocyte cytosol. Phosphatase I was composed of alpha (34 kDa), beta (63 kDa), and delta (74 kDa) subunits in a ratio of 1:1:1. Phosphatase III comprised alpha, beta, and gamma (53 kDa) subunits in the same ratio. Heparin-Sepharose column chromatography converted most of phosphatase I and 20% of phosphatase III into alpha 1 beta 1 which were indistinguishable from phosphatase IV (Usui, H., Kinohara, N., Yoshikawa, K., Imazu, M., Imaoka, T., and Takeda, M. (1983) J. Biol. Chem. 258, 10455-10463). The catalytic subunit alpha and the beta subunit of phosphatases I, III, and IV displayed identical V8 and papain peptide maps, respectively, while the peptide maps of the alpha, beta, gamma, and delta subunits were clearly distinct. The molar ratio of phosphatases I, III, and IV in erythrocyte cytosol was estimated to be 6:1:14. Comparison of molecular activities of alpha, alpha 1 beta 1, alpha 1 beta 1 delta 1, and alpha 1 beta 1 gamma 1 revealed that beta suppressed phosphorylase and P-H2B histone phosphatase activities of alpha but stimulated the P-H1 histone phosphatase activity, and delta suppressed all the phosphatase activities of alpha 1 beta 1. The gamma subunit stimulated the P-histone phosphatase activity of alpha 1 beta 1 but inhibited the phosphorylase and P-spectrin phosphatase activities. The beta subunit increased the Mg2+ or Mn2+ requirement for P-H2B histone phosphatase activity of alpha, an effect which was counteracted by delta. The effects of heparin, H1 histone, protamine, and polylysine on the phosphorylase phosphatase activity of phosphatases I, III, IV, and alpha were described and discussed in connection with the functions of the subunits.
Semipolar $({\hbox{20}}\bar{{\hbox{2}}}\bar{{\hbox{1}}})$ InGaN/GaN Light-Emitting Diodes for High-Efficiency Solid-State Lighting (2013)

This work examines the effects of polarization-related electric fields on the energy band diagrams, wavelength shift, wave function overlap, and efficiency droop for InGaN quantum wells on various crystal orientations, including polar (0001) ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</i> -plane), semipolar (202̅1̅), semipolar (202̅1̅), and nonpolar (101̅0̅) ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</i> -plane). Based on simulations, we show that the semipolar (202̅1̅) orientation exhibits excellent potential for the development of high-efficiency, low-droop light-emitting diodes (LEDs). We then present recent advancements in crystal growth, optical performance, and thermal performance of semipolar (202̅1̅) LEDs. Finally, we demonstrate a low-droop, high-efficiency single-quantum-well blue semipolar (202̅1̅) LED with an external quantum efficiency of more than 50% at 100 A/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
CRISPR/cas9, a novel genomic tool to knock down microRNA in vitro and in vivo (2016)

MicroRNAs are small and non-coding RNA molecules with the master role in regulation of gene expression at post-transcriptional/translational levels. Many methods have been developed for microRNA loss-of-function study, such as antisense inhibitors and sponges; however, the robustness, specificity, and stability of these traditional strategies are not highly satisfied. CRISPR/cas9 system is emerging as a novel genome editing tool in biology/medicine research, but its indication in microRNA research has not been studied exclusively. In this study, we clone CRISPR/cas9 constructs with single-guide RNAs specifically targeting biogenesis processing sites of selected microRNAs; and we find that CRISPR/cas9 can robustly and specifically reduce the expression of these microRNAs up to 96%. CRISPR/cas9 also shows an exclusive benefit in control of crossing off-target effect on microRNAs in the same family or with highly conserved sequences. More significantly, for the first time, we demonstrate the long term stability of microRNA knockdown phenotype by CRISPR/cas9 in both in vitro and in vivo models.
Target Therapy for Colorectal Cancer (2006)

In the past decade, the median duration of survival among patients with advanced colorectal cancer has increased from 12 months to about 18 months, primarily as a results of the introduction of irinotecan and oxaliplatin. Advances in the understanding of the molecular mechanisms underlying the development and progression of cancer have resulted in the discovery of new therapeutic interventions that target specific molecular abnormalities. Their specificity, and therefore their potential to bind preferentially and modify tumor-specific targets, sparing normal tissues and causing fewer side-effects compared to conventional cytotoxic agents, makes them an attractive therapeutic option. The future of this approach for the treatment of solid tumors is promising
Fischer Indolization of Ethyl Pyruvate 2-(2-(Trifluoromethyl)phenyl)-phenylhydrazone and New Insight into the Mechanism of the Goldberg Reaction. (Fischer Indolization and Its Related Compounds. XXVI) (1995)

The Fischer indolization of ethyl pyruvate 2-[2-(trifluoromethyl)phenyl]phenylhydrazone (5) gave two indolic products, ethyl 7-(trifluoromethyl)-1-phenylindole-2-carboxylate (12) as a minor product and ethyl 1-[2-(trifluoromethyl)phenyl]indole-2-carboxylate (13) as a major product. This result shows that the Fischer indolization occurred on the more electron-rich phenyl group. In the Goldberg reaction to prepare 13 from ethyl indole-2-carboxylate (15) and o- (21) or m-bromo-α, α, α-trifluotoluene (23), it was found that Goldberg reaction proceeds via a benzyne mechanism, at least in part, in a sterically crowded situation.
First assessment at home of amyotrophic lateral sclerosis (ALS) patients by a nutrition network in the French region of Limousin (2012)

Malnutrition is associated with poor survival among patients with amyotrophic lateral sclerosis (ALS). This study aimed to evaluate nutritional assessment by a network during first consultations in patients' homes. Patients identified by the regional ALS centre gave their informed consent. Assessment included functional, nutritional issues, evaluation of the need for help, whether personal or the use of aids, and noted any dietary supplementation and modification of the texture of food. Forty patients were seen a mean of 7.4 months after diagnosis; 52.5% had bulbar disease, 7.5% were malnourished; 29.4 ± 10.1 kcal/kg/day were consumed and protein intake was 1.3 ± 0.5 g/kg/day. Thirty-five percent of patients were anorexic, 43.8% reported taste disorders, and 70% had dysphagia, significantly associated with salivary stasis. Only 30% of dysphagic patients ate texture-modified food, and 90% of patients with problems drinking liquids did not use a thickener. In conclusion, assessment at home by a nutritional network can be conducted promptly. Malnutrition is rare in early disease, despite the fact that patients' diets are often low in energy and dysphagia is common. Unexpected taste disorders are detected. Dysphagia is very common but inadequately addressed. Consequently, home assessment by the network led several beneficial interventions.
A Comprehensive Review of Clinical Trials on EGFR Inhibitors Such as Cetuximab and Panitumumab as Monotherapy and in Combination for Treatment of Metastatic Colorectal Cancer. (2015)

Metastatic colorectal cancer is the fourth most common cause of death due to cancer after those of lung, stomach, and liver. Anti epidermal growth factor receptor drugs as a targeting therapy seem to be good candidates for curing metastatic colorectal cancer. Two available anti epidermal growth factor receptor monoclonal antibodies are cetuximab and panitumumab which have been approved for metastatic colorectal cancer treatment. Through the available literature on NCBI and clinical trials, 31 clinical trials in which cetuximab or panitumumab as monotherapy or in combination with chemotherapy were used for the treatment of metastatic colorectal cancer patients in different line settings and 12 clinical trials in which bevacizumab was used for being compared with anti epidermal growth factor receptor monoclonal antibodies or chemotherapy were chosen for reviewing and comparing the results of overall survival, progression free survival and adverse effects. Cetuximab and panitumumab are well accepted for the treatment of mCRC patients at all stages in different line settings. Although cetuximab administration in metastatic colorectal cancer patients is mostly associated with better overall survival and panitumumab results in better progression free survival, to confirm the superiority of each of them in the treatment protocol of epidermal growth factor receptor monoclonal antibodies, more clinical trials with larger sample size are needed. Through current available data from clinical studies, it can be concluded that the best treatment outcome is achieved by a combination of anti epidermal growth factor receptor monoclonal antibodies with conventional chemotherapy.