gebhart/patrepeval huggingface dataset:
An elongation factor-associating domain is inserted into human cysteinyl-tRNA synthetase by alternative splicing (2000)

The amino acid sequence of human cytoplasmic cysteinyl-tRNA synthetase (CRS) was examined by analyzing sequences of genomic and expressed sequence tag fragments. From theses analyses, a few interesting possibilities were suggested for the structure of human CRS. First, different isoforms of CRS may result from alternative splicing. Second, the largest one would comprise 831 amino acids. Third, a new exon was identified encoding an 83 amino acid domain that is homologous to parts of elongation factor-1 subunits as well as other proteins involved in protein synthesis. Northern blot analysis showed three different mRNAs for CRS (of approximately 3.0, 2.7 and 2.0 kb) from human testis while only the 2.7 kb mRNA was commonly detected in other tissues. Expression of the exon 2-containing transcript in testis was confirmed by RT-PCR and northern blotting. CRS containing the exon 2-encoded peptide retained catalytic activity comparable to that lacking this peptide. This peptide was responsible for the specific interaction of CRS with elongation factor-1gamma.
Real-time Imaging of Tumor-Cell Shedding and Trafficking in Lymphatic Channels (2007)

In the present report, we show real-time imaging of cancer cell trafficking in lymphatic vessels. Cancer cells labeled with both green fluorescent protein (GFP) in the nucleus and red fluorescent protein (RFP) in the cytoplasm or with GFP only or RFP only were injected into the inguinal lymph node of nude mice. The labeled cancer cells trafficked through lymphatic vessels where they were imaged via a skin flap in real time at the cellular level until they entered the axillary lymph node. The bright fluorescence of the cancer cells and the real-time microscopic imaging capability of the Olympus OV100 small-animal imaging system enabled imaging of the trafficking cancer cells in the lymphatics. Using this imaging strategy, two different cancer cell lines, one expressing GFP and the other expressing RFP, were simultaneously injected in the inguinal lymph node. Fluorescence imaging readily distinguished the two color-coded cell lines and their different abilities to survive in the lymphatic system. Using this imaging technology, we also investigated the role of pressure on tumor-cell shedding into lymphatic vessels. Pressure was generated by placing 25- and 250-g weights for 10 s on the bottom surface of a tumor-bearing footpad. Tumor cell fragments, single cells, and emboli shed from the footpad tumor were easily distinguished with the labeled cells and OV100 imaging system. Increasing pressure on the tumor increased the numbers of shed cells, fragments, and emboli. Pressure also deformed the shed emboli, increasing their maximum major axis. Imaging lymphatic trafficking of cancer cells can reveal critical steps of lymph node metastasis.
α-Synuclein O-GlcNAcylation alters aggregation and toxicity, revealing certain residues as potential inhibitors of Parkinson’s disease (2019)

A compelling link is emerging between the posttranslational modification O-GlcNAc and protein aggregation. A prime example is α-synuclein, which forms toxic aggregates that are associated with neurodegeneration in Parkinson's and related diseases. α-Synuclein has been shown to be O-GlcNAcylated at nine different positions in in vivo proteomics experiments from mouse and human tissues. This raises the possibility that O-GlcNAc may alter the aggregation of this protein and could be both an important biological mediator of neurodegeneration and also a therapeutic target. Here, we expand upon our previous research in this area through the chemical synthesis of six site-specifically O-GlcNAcylated variants of α-synuclein. We then use a variety of biochemical experiments to show that O-GlcNAc in general inhibits the aggregation of α-synuclein but can also alter the structure of α-synuclein aggregates in site-specific ways. Additionally, an α-synuclein protein bearing three O-GlcNAc modifications can inhibit the aggregation of unmodified protein. Primary cell culture experiments also show that several of the O-GlcNAc sites inhibit the toxicity of extracellular α-synuclein fibers that are likely culprits in the spread of Parkinson's disease. We also demonstrate that O-GlcNAcylation can inhibit the aggregation of an aggressive mutant of α-synuclein, indicating that therapies currently in development that increase this modification might be applied in animal models that rely on this mutant. Finally, we also show that the pan-selective antibody for O-GlcNAc does not generally recognize this modification on α-synuclein, potentially explaining why it remains understudied. These results support further development of O-GlcNAcylation tools and therapeutic strategies in neurodegenerative diseases.
Molecular Dynamics Simulation of the High Lithium Ion Conductor, La0.6i0.2TiO3. (1999)

Molecular dynamics (MD) simulation was carried out on the high Li ion conductor, La0.6Li0.2TiO3, using the partially ionic model (PIM). MD simulation of the Li ion conductivity with the variation of mobile ion size under high pressure revealed that this compound had the optimum lattice size for Li ion conduction and that the skeletal lattice was too small for Li+ ion to show the highest conductivity.
Improved bounds on object support from autocorrelation support and application to phase retrieval (1990)

New methods are described for determining tighter upper bounds on the support of an object, given the support of its autocorrelation. These upper bounds are shown, in a digital experiment, to be useful as object-support constraints used with the iterative transform algorithm for solving the phase-retrieval problem.
Atomic Force Microscope Based Kelvin Probe Measurements:  Application to an Electrochemical Reaction (1997)

An atomic force microscope (AFM) was utilized as a Kelvin probe to determine work functions of several metals and semiconductors quantitatively. Most of the experimental data show excellent agreement with published values measured by photoemission. Variations in work functions as low as 5 mV could be detected with a typical lateral resolution of 20 nm. This method allowed us to analyze and explain the energetics of an electrochemical reaction on the surface of WSe2, which could be in situ induced and controlled by an externally applied voltage between AFM tip and sample. Thus it could be exploited for etching nanostructures.
Design of a SPDM-like robotic manipulator system for Space Station on orbit replaceable unit ground testing - an overview of the system architecture (2002)

Space Station is an international joint development project sponsored by the United States, Canada, Europe, and Japan. The Canadian designed special purpose dexterous manipulator (SPDM) is scheduled to maintain the Space Station and perform the on orbit replaceable unit (ORU) removal/insertion tasks. Johnson Space Center (JSC) of National Aeronautics and Space Administration (NASA) has been assigned as the lead center to integrate all Space Station sub-systems and to perform the ground testing of Space Station ORUs for robotic compatibilities. The Track Task robotic testing facility for ORUs was established for this purpose. The facility consists of a pair of hydraulic manipulators, special end-effectors and tools, video sub-system, multiprocessors controller, and the display and control workstation. This paper discusses the design and implementation of this facility.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A Planar Attributes Model Based on Multi Level Security Policy (2004)

Security model is the foundation for meeting the security needs of information systems. Classical security models can only meet either confidentiality or integrity. None of model could resolve both of security requirements simultaneously. This paper presents a planar attributes model based on multi level security policy. In the model, the trusted subjects must accord with the least privilege principle. The concepts of confidence level and trusted level as labels of subjects and objects for constraining subjects accessing to objects are briefly described. This paper details a formal description and verification on the model which provides both the confidentiality and integrity for the system. It also explain the model in informal language briefly to help understand. Lastly, some open issues about model implementation are discussed, and the future direction of the model is pointed out. This model will be beneficial to be successful applied to constructing security systems in practices.
Serial propagation and purification of chicken Anaemia agent in mdcc‐MSB1 cell line (1987)

The TK-5803 strain of an agent which induces chicken anaemia was propagated and titrated in cultures of the MDCC-MSB1 cell line. When the isolates (tentatively designated MSBI-TK-5803 strain) from the original material were inoculated into 1-day-old susceptible chicks, they showed a severe pathogenicity, inducing anaemia with aplasia of the bone marrow and atrophy of the lymphoid organs. On density gradient separation, the peak of their infectivity titre appeared at a density of 1.35 to 1.36 g/cm(3) and numerous virus particles were demonstrated in the same fraction. The agent was resistant to heating for 30 min at 60 degrees C and 50% chloroform for 15 min at 4 degrees C, and passed through a 25 nm membrane filter, but it was completely inactivated after heating for 30 min at 70 degrees C or more. The purified virus particles were spherical or hexagonal in shape and 19.1 +/- 0.2 nm in diameter.
The Combination of Ionizing Radiation and Peripheral Vaccination Produces Long-term Survival of Mice Bearing Established Invasive GL261 Gliomas (2006)

Ionizing radiation can be successfully combined with peripheral vaccination for the treatment of established high-grade gliomas.
The Enzymatic Activity of CEM15/Apobec-3G Is Essential for the Regulation of the Infectivity of HIV-1 Virion but Not a Sole Determinant of Its Antiviral Activity (2003)

Human immunodeficiency virus, type 1 (HIV-1) Vif protein plays an essential role in the regulation of the infectivity of HIV-1 virion. Vif functions to counteract an anti-HIV-1 cellular factor in non-permissive cells, CEM15/Apobec-3G, which shares a cytidine deaminase motif. CEM15/Apobec-3G deaminates dC to dU in the minus strand DNA of HIV-1, resulting in G to A hypermutation in the plus strand DNA. In this study, we have done the mutagenesis analysis on two cytidine deaminase motifs in CEM15/Apobec-3G and examined their antiviral functions as well as the DNA editing activity. Point mutations in the C-terminal active site such as E259Q and C291A almost completely abrogated the antiviral function, while those in the N-terminal active site such as E67Q and C100A retained this activity to a lesser extent as compared with that of the wild type. The DNA editing activities of E67Q and E259Q mutants were both retained but impaired to the same extent. This indicates that the enzymatic activity of this protein is essential but not a sole determinant of the antiviral activity. Furthermore, all the deletion mutants tested in this study lost the antiviral activity because of the loss of the activity for dimerization, suggesting that the entire protein structure is necessary for the antiviral function.
Value of High-Density Lipoprotein (HDL) Subpopulations in Predicting Recurrent Cardiovascular Events in the Veterans Affairs HDL Intervention Trial (2005)

An altered HDL subpopulation profile marked with low alpha-1 and alpha-2 levels and a high alpha-3 level in coronary heart disease patients indicated an elevated risk for new CVD events. Moreover, alpha-1 and alpha-2 levels were superior to HDL-C levels in risk assessment in patients with low HDL-C in VA-HIT.
Modeling Tyrosinase Monooxygenase Activity. Spectroscopic and Magnetic Investigations of Products Due to Reactions between Copper(I) Complexes of Xylyl-Based Dinucleating Ligands and Dioxygen:  Aromatic Ring Hydroxylation and Irreversible Oxidation Products (1998)

A full account of a chemical system possessing features that mimic the reactivity aspects of tyrosinase is presented. Using dinucleating ligands with a m-xylyl spacer three new dicopper(I) complexes have been synthesized and their reactivity with dioxygen investigated. The six-membered chelate ring forming ligands provide only two nitrogen coordinations to each copper. The complexes [Cu(I)(2)L(CH(3)CN)(2)]X(2) (X = ClO(4)(-) (1a), SbF(6)(-) (1b)) and [Cu(I)(2)(L-NO(2))(CH(3)CN)(2)][SbF(6)](2) (1c) [L = alpha,alpha'-bis[N-methyl-N-(2-pyridylethyl)amino]-m-xylene; L-NO(2) = para-nitro derivative of L] have been characterized by IR and (1)H NMR spectroscopy. The reaction of O(2) with 1a-c in CH(2)Cl(2) or THF is instantaneous and causes stoichiometric xylyl hydroxylation reactions producing phenol products. Thus 1a produces phenoxo-/hydroxo-bridged product [Cu(II)(2)(L-O)(OH)][ClO(4)](2) (2a). The existence of putative peroxo-dicopper(II) species could not be detected even at -80 degrees C. A trend is observed for the extent of aromatic ring hydroxylation (298 K): CH(3)CN approximately DMF > CH(3)OH >> CH(2)Cl(2). Cyclic voltammetric experiment of 1a in DMF reveals an appreciably low redox potential (E(1/2) = -0.26 V vs SCE) for the Cu(II)(2)/Cu(I)(2) redox process. Variable-temperature (25-300 K) magnetic susceptibility measurements establish that the copper(II) centers in 2a and the dihydroxo-bridged complex [Cu(II)(2)L'(OH)(2)][ClO(4)](2) (2b) [formed due to an impurity (L') present during the synthesis of L following Method A; L' = bis[alpha,alpha'-bis(N-methyl-N-(2-pyridylethyl)amino)-m-xylene]methylamine] are antiferromagnetically coupled, with 2a considerably more coupled than 2b. Reaction of 1a with O(2) in CH(2)Cl(2) (298 K) produces an additional unhydroxylated product of composition [Cu(II)(2)L(OH)(OH(2))][ClO(4)](3).2H(2)O.0.5HCl (3a). In agreement with its proposed hydroxo-/aquo-bridged structure, 3a is weakly antiferromagnetically coupled. In CH(3)CN solution, 3a rearranges to generate a doubly hydroxo-bridged species [Cu(II)(2)L(OH)(2)](2+). Using a solution-generated dicopper(I) complex of a closely similar ligand (L' ') providing five-membered chelate ring, the reactivity toward dioxygen was also investigated. It produces only an irreversibly oxidized product of composition Cu(II)(2)L' '(OH)(ClO(4))(3)(H(2)O)(2) (3b) (L' ' = alpha,alpha'-bis[N-methyl-N-(2-pyridylmethyl)amino]-m-xylene). For 3b the copper(II) centers are almost uncoupled.
Blood coagulation alterations and thromboembolism in Crohn's disease. (1983)

The present study was undertaken in view of the higher incidence of thromboembolism in patients with Crohn's disease. The blood coagulation system was studied in 12 patients previously operated for Crohn's disease (8 cases of ileitis, 4 cases of colitis) and followed as out-patients. In 75% of cases, the disease was in an inactive stage. Eight patients showed slight lipid malabsorption. Serum levels of fibrinogen, platelets and factor V were shown to be significantly increased (p less than 0.001) as compared to controls. Prothrombin time and factors II, VII and X were shown to be decreased, while factors VIII and IX and antithrombin III were not significantly altered. Thrombocytosis and hyperfibrinogenemia, as reported in literature, seem to determine a condition of blood hypercoagulability, playing therefore a primary pathogenetic role in the genesis of thromboembolism in patients with Crohn's disease.
Plasma gonadotropin levels during early stages of ovarian tumorigenesis in mice of the W x -W u genotype. (1973)

Summary The ovaries of (C57BL/6J × C3H/HeJ) F 1 - W x /W v mice contain few oocytes at birth, rapidly lose the follicular apparatus, and develop a 95% incidence of bilateral complex tubular adenomas by 5 months of age. Plasma levels of the pituitary gonadotropic hormones, luteinizing hormone and follicle-stimulating hormone, determined by radioimmunoassay, were significantly elevated between 30 and 210 days of age in W x /W v mice in comparison with congenic +/+ controls. Both hormones were increased at least 4-fold throughout the period except for luteinizing hormone, which was increased 2-fold at 30 days. Ovariectomy at 60 days of age induced the same maximum levels of luteinizing and follicle-stimulating hormones within 2 weeks in females of both genotypes. These findings provide quantitative confirmation of the hypothesis that prolonged stimulation by gonadotropic hormones induces ovarian tumors.
Comparison of Mammographically Guided Breast Biopsy Techniques (1999)

Although sensitivities and specificities of SC bx and Mbx are good, 20% to 25% of patients will require an open biopsy because a definitive diagnosis could not be reached. This does not occur with the ABBI excisional biopsy specimen. The positive margin rates and residual tumor rates are comparable between the ABBI and WL bx. The ABBI avoids operating room and reexcision costs; therefore, in appropriately selected patients, this appears to be the most efficient method of biopsy.
Independent pathways of p53 induction by cisplatin and X-rays in a cisplatin-resistant ovarian tumor cell line. (1998)

The p53 tumor suppressor gene is critical in regulating cell proliferation following DNA damage, and disruption of p53 protein function by mutation has been implicated as a factor responsible for resistance of tumor cells to chemotherapeutic agents. Our studies were initiated by asking whether the translational product of the p53 gene is associated with cisplatin resistance in the 2780CP human ovarian tumor model. We have demonstrated by single-strand conformation polymorphism analysis and sequencing that p53 in parental cisplatin-sensitive A2780 cells was wild type. In 2780CP cells, however, a mutation was found in exon 5 at codon 172 (Val to Phe). Interestingly, exposure to X-rays resulted in p53 induction in both A2780 and 2780CP tumor models. The p53 increases by the ionizing radiation were accompanied by concomitant increases in levels of the p53-regulated p21Waf1/Cip1 protein and led to arrest of cells in G1 phase of the cell cycle. A yeast functional assay confirmed that p53 in A2780 was wild type, but, more importantly, it provided evidence that the p53 mutation in 2780CP cells was temperature sensitive and heterozygous. These experiments demonstrate that sensitive and resistant cells have normal p53 functions, despite the presence of p53 mutation in the 2780CP model. In parallel investigations using the Western technique, exposure of A2780 cells to clinically relevant concentrations of cisplatin (1-20 microM) resulted in time- and dose-dependent increases in p53, together with coordinate increases in p21Waf1/Cip1. In contrast, cisplatin did not induce these proteins in 2780CP cells to any significant degree. The results indicate that a defect exists in the signal transduction pathway for p53 induction following cisplatin-induced DNA damage in 2780CP cells, and this may represent a significant mechanism of cisplatin resistance. Furthermore, induction of p53 in 2780CP cells by X-rays, but not cisplatin, strongly suggests that independent pathways are involved in p53 regulation for the two DNA-damaging agents.
Elucidating glycosaminoglycan–protein–protein interactions using carbohydrate microarray and computational approaches (2011)

Glycosaminoglycan polysaccharides play critical roles in many cellular processes, ranging from viral invasion and angiogenesis to spinal cord injury. Their diverse biological activities are derived from an ability to regulate a remarkable number of proteins. However, few methods exist for the rapid identification of glycosaminoglycan-protein interactions and for studying the potential of glycosaminoglycans to assemble multimeric protein complexes. Here, we report a multidisciplinary approach that combines new carbohydrate microarray and computational modeling methodologies to elucidate glycosaminoglycan-protein interactions. The approach was validated through the study of known protein partners for heparan and chondroitin sulfate, including fibroblast growth factor 2 (FGF2) and its receptor FGFR1, the malarial protein VAR2CSA, and tumor necrosis factor-α (TNF-α). We also applied the approach to identify previously undescribed interactions between a specific sulfated epitope on chondroitin sulfate, CS-E, and the neurotrophins, a critical family of growth factors involved in the development, maintenance, and survival of the vertebrate nervous system. Our studies show for the first time that CS is capable of assembling multimeric signaling complexes and modulating neurotrophin signaling pathways. In addition, we identify a contiguous CS-E-binding site by computational modeling that suggests a potential mechanism to explain how CS may promote neurotrophin-tyrosine receptor kinase (Trk) complex formation and neurotrophin signaling. Together, our combined microarray and computational modeling methodologies provide a general, facile means to identify new glycosaminoglycan-protein-protein interactions, as well as a molecular-level understanding of those complexes.
Severe acute respiratory syndrome coronavirus (SARS-CoV)-2 infection induces dysregulation of immunity: <i>in silico</i> gene expression analysis (2021)

Highly pathogenic coronaviruses (CoVs) induce acute respiratory distress syndrome, and the severe acute respiratory syndrome coronavirus (SARS-CoV)-2 has caused a pandemic since late 2019. The diversity of clinical manifestations after SARS-CoV-2 infection results in great challenges to diagnose CoV disease 2019 (COVID-19). There is a growing body of published research on this topic; however, effective medications are still undergoing a long process of being assessed. In the search for potential genetic targets for this infection, we applied a holistic bioinformatics approach to study alterations of gene signatures between SARS-CoV-2-infected cells and mock-infected controls. Two different kinds of lung epithelial cells, A549 with angiotensin-converting enzyme 2 (ACE2) overexpression and normal human bronchial epithelial (NHBE) cells, were infected with SARS-CoV-2. We performed bioinformatics analyses of RNA-sequencing in this study. Through a Venn diagram, Database for Annotation, Visualization and Integrated Discovery, Gene Ontology, Ingenuity Pathway Analysis, and Gene Set Enrichment Analysis, the pathways and networks were constructed from commonly upregulated genes in SARS-CoV-2-infected lung epithelial cells. Genes associated with immune-related pathways, responses of host cells after intracellular infection, steroid hormone biosynthesis, receptor signaling, and the complement system were enriched. Dysregulation of the immune system and malfunction of interferon contribute to a failure to kill SARS-CoV-2 and exacerbate respiratory distress in severely ill patients. Current findings from this study provide a comprehensive investigation of SARS-CoV-2 infection using high-throughput technology.