gebhart/patrepeval huggingface dataset:
Photoelectron distributions from femtosecond pump/probe excitation with chirped probe pulses (1998)

We calculate photoelectron distributions obtained from the two-photon pump/probe ionization of Na2. A first ultrashort pulse prepares a vibrational wave packet in the (2)1∑u+ electronic state. The dynamics is probed by time-delayed ionization caused by a chirped femtosecond laser pulse. Time-resolved photoelectron spectra are determined for different chirp parameters. It is shown that the spectra are very sensitive to the choice of the chirp. In particular the width can be selectively modified and the in- or outward motion of the wave packet can be distinguished by using an appropriately chirped electric field. An analytical expression for the photoelectron spectrum explains its dependence on the chirp parameter.
유아기 형제 갈등에 영향을 미치는 요인과 개입 프로그램의 효과 (2008)

The purpose of this study was to identify the importance of sibling relationships in early childhood, by examining the relationships between the variables in the children such as sex, age, temperament and attachment, with that of their parent`s intervention, and the sibling conflicts. The major findings were as follow: First, the sibling conflicts were related to the children`s temperament and attachment more than sibling`s sex, age and age deference. Second, the parent intervention was related to the sibling conflicts. Third, the intervention program had an effect on sibling conflicts.
Expressed protein ligation: A general method for protein engineering (1998)

A protein semisynthesis method-expressed protein ligation-is described that involves the chemoselective addition of a peptide to a recombinant protein. This method was used to ligate a phosphotyrosine peptide to the C terminus of the protein tyrosine kinase C-terminal Src kinase (Csk). By intercepting a thioester generated in the recombinant protein with an N-terminal cysteine containing synthetic peptide, near quantitative chemical ligation of the peptide to the protein was achieved. The semisynthetic tail-phosphorylated Csk showed evidence of an intramolecular phosphotyrosine-Src homology 2 interaction and an unexpected increase in catalytic phosphoryl transfer efficiency toward a physiologically relevant substrate compared with the non-tail-phosphorylated control. This work illustrates that expressed protein ligation is a simple and powerful new method in protein engineering to introduce sequences of unnatural amino acids, posttranslational modifications, and biophysical probes into proteins of any size.
TBX-3, the Gene Mutated in Ulnar-Mammary Syndrome, Is a Negative Regulator of p19 and Inhibits Senescence (2002)

Prolonged culturing of rodent cells in vitro activates p19(ARF) (named p14(ARF) in man), resulting in a p53-dependent proliferation arrest known as senescence. The p19(ARF)-Mdm2-p53 pathway also serves to protect primary cells against oncogenic transformation. We have used a genetic screen in mouse neuronal cells, conditionally immortalized by a temperature-sensitive mutant of SV40 large T antigen, to identify genes that allow bypass of senescence. Using retroviral cDNA expression libraries, we have identified TBX-3 as a potent inhibitor of senescence. TBX-3 is a T-box gene, which is found mutated in the human developmental disorder Ulnar-Mammary Syndrome. We have shown that TBX-3 potently represses expression of both mouse p19(ARF) and human p14(ARF). We have also shown here that point mutants of TBX-3, which are found in Ulnar-Mammary Syndrome, have lost the ability to inhibit senescence and fail to repress mouse p19(ARF) and human p14(ARF) expression. These data suggest that the hypoproliferative features of this genetic disorder may be caused, at least in part, by deregulated expression of p14(ARF).
Quantification of the Effects of Chain Length and Concentration on the Thermal Behavior of Elastin-like Polypeptides (2004)

At a specific temperature, elastin-like polypeptides (ELPs) undergo a sharp solubility transition that can be exploited in a variety of applications in biotechnology and medicine. The temperature of the transition varies with ELP sequence, molecular weight, and concentration. We present a single equation of three parameters that quantitatively predicts the transition temperature as a function of ELP length and concentration for an ELP of a fixed composition. This model should be useful both for the design of new ELP sequences that exhibit a desired transition temperature and for the selection of variables to trigger the phase transition of an ELP for a given application.
Thiol-mediated redox regulation of lymphocyte proliferation. Possible involvement of adult T cell leukemia-derived factor and glutathione in transferrin receptor expression. (1994)

The proliferative response of PBMC to PHA, Con A, OKT3 mAb and IL-2-dependent proliferation of PHA-blasts was examined in a thiol-free environment (cultured in a L-cystine- and GSH-free medium). [3H]TdR incorporation assay and cell cycle analysis revealed that stimulated PBMC could not enter the S phase when deprived of these thiol compounds. In thiol-free cultures, an increase in intracellular free Ca2+ concentration and IL-2R alpha-chain/p 55 (Tac) induction was still observed, whereas transferrin receptor induction was markedly reduced, suggesting that the proliferative response of mitogenically stimulated PBMC was arrested in the late G1 phase in which transferrin receptor is induced. In GSH-depleted cultures, a similar reduction of the proliferative response of PBMC and PHA-blasts was observed when the concentration of L-cystine was lowered, in a dose-dependent manner. Each reduction or loss of proliferative response was partially restored by supplementation of 2-ME or adult T cell leukemia-derived factor (ADF)/human thioredoxin which is considered to be an endogenous dithiol-reducing factor. L-Cystine transport analysis showed that mitogenically stimulated PBMC and PHA blasts incorporated L-cystine, whereas resting PBMC did not. Furthermore, ADF as well as 2-ME exhibited an enhancing activity on the L-cystine transport in PHA blasts. Together with the fact that L-cystine transport is a limiting step in glutathione synthesis, these findings suggest that GSH and ADF might cooperate in the thiol-mediated redox regulation process and might also play key roles in cell cycle (late G1 to S) progression of activated lymphocytes.
Ultrastructural localization of interferon receptors on the surfaces of cultured cells and erythrocytes (1982)

The bindings sites for interferon (IFN) on the limiting cell membranes of human and mouse fibroblasts and erythrocytes were revealed by an indirect immunoferritin technique. Mouse IFN-beta and human IFN-beta of high specific activity were used with the corresponding purified antibodies. Species-specific IFN binding was demonstrated by ferritin deposition on human erythrocytes and fibroblast membranes treated with human IFN and on mouse erythrocytes and fibroblast membranes treated with mouse IFN, but not on human erythrocytes or fibroblast membranes treated with mouse IFN. IFN binding sites on fibroblasts were located on regions of membranes between microvilli, whereas diphtheria toxin receptors were demonstrated mainly on microvilli. IFN binding altered the diphtheria toxin after IFN treatment. This reduced toxicity correlated with a decrease in the quantity of receptors for diphtheria toxin on the cell membrane. Thus, the species-specific binding of IFN appears to depend on membrane receptors in discrete regions of the limiting membrane which are present not only on functionally responsive fibroblasts but also on erythrocytes.
[N-Alkyl-(2-pyridyl)methanimine]copper(I) Complexes: Characterisation and Application as Catalysts for Atom-Transfer Polymerisation (1998)

The synthesis and characterisation of a series of novel bis(imine)copper(I) complexes and their use in atom-transfer polymerisation of methyl methacrylate is described. Several N-alkyl-(2-pyridyl)methanimines (alkyl = n-butyl, isobutyl, sec-butyl, n-propyl) and N-(n-propyl)-1-(2-pyridyl)ethanimine as ligands have been fully characterised. Three bis[N-alkyl-(2-pyridyl)methanimine]copper(I) complexes, [Cu{(C5H4N)CH=N(iBu)}2][BF4], [Cu{(C5H4N)C(CH3)=N(nPr)}2][PF6], and [Cu{(C5H4N)CH=N(sBu)}2][BF4] have been structurally characterised; all having a distorted tetrahedral arrangement of co-ordinating nitrogen atoms surrounding the metal centre. All of the catalysts were found to be effective atom-transfer polymerisation catalysts for the polymerisation of MMA in hydrocarbon solution. However, it was discovered that the performance of the catalysts containing n-alkyl substituents was superior to those containing branched alkyl substituents. The presence of branching in the alkyl substituent results in a reduction of reaction rate and a corresponding broadening of the polydispersity index.
Therapeutic vaccination using CD4+CD25+antigen-specific regulatory T cells (2004)

Autoimmune disease results from the dysregulation of basic tolerogenic processes designed to control self/non-self-discrimination. Approaches to treat autoimmunity have focused historically on potent immunosuppressives that block the activation and expansion of antigen-specific T cells before they differentiate into pathogenic T cell responses. These therapies are very efficient in reducing clonal expansion and altering early signaling pathways. However, once the pathogenic responses are established (i.e., autoimmunity), the interventions are less effective on activated and differentiated T cell subsets (including memory T cells) or acting in the presence of an inflammatory milieu to abort immune responses at the target tissue and systemically. Moreover, the current immunotherapies require continuous use because they do not redirect the immune system to a state of tolerance. The continuous treatment leads to long-term toxicities and can profoundly suppress protective immune responses targeted at viruses, bacteria, and other pathogens. Over the past decade, there have been tremendous advances in our understanding of the basic processes that control immune tolerance. Among the most exciting has been the identification of a professional regulatory T cell subset that has shown enormous potential in suppressing pathologic immune responses in autoimmune diseases, transplantation, and graft vs. host disease. In this review, we summarize current efforts to induce and maintain tolerance in the autoimmune diabetes setting by using therapeutic vaccination with CD4(+)CD25(+) regulatory T cells. Emphasis will be placed on approaches to exploit regulatory T cells either directly or through the use of anti-CD3 immunotherapy.
Probing protein–chromophore interactions in Cph1 phytochrome by mutagenesis (2006)

We have investigated mutants of phytochrome Cph1 from the cyanobacterium Synechocystis PCC6803 in order to study chromophore-protein interactions. Cph1Delta2, the 514-residue N-terminal sensor module produced as a recombinant His6-tagged apoprotein in Escherichia coli, autoassembles in vitro to form a holoprotein photochemically indistinguishable from the full-length product. We generated 12 site-directed mutants of Cph1Delta2, focusing on conserved residues which might be involved in chromophore-protein autoassembly and photoconversion. Folding, phycocyanobilin-binding and Pr-->Pfr photoconversion were analysed using CD and UV-visible spectroscopy. MALDI-TOF-MS confirmed C259 as the chromophore attachment site. C259L is unable to attach the chromophore covalently but still autoassembles to form a red-shifted photochromic holoprotein. H260Q shows UV-visible properties similar to the wild-type at pH 7.0 but both Pr and Pfr (reversibly) bleach at pH 9.0, indicating that the imidazole side chain buffers chromophore protonation. Mutations at E189 disturbed folding but the residue is not essential for chromophore-protein autoassembly. In D207A, whereas red irradiation of the ground state leads to bleaching of the red Pr band as in the wild-type, a Pfr-like peak does not arise, implicating D207 as a proton donor for a deprotonated intermediate prior to Pfr. UV-Vis spectra of both H260Q under alkaline conditions and D207A point to a particular significance of protonation in the Pfr state, possibly implying proton migration (release and re-uptake) during Pr-->Pfr photoconversion. The findings are discussed in relation to the recently published 3D structure of a bacteriophytochrome fragment.
A Novel Porcine Model for Future Studies of Cell-enriched Fat Grafting (2018)

The Göttingen minipig is a feasible and cost-effective, large animal model for future translational studies of cell-enriched fat grafting.
A virus-directed enzyme prodrug therapy approach to purging neuroblastoma cells from hematopoietic cells using adenovirus encoding rabbit carboxylesterase and CPT-11. (2001)

Tumor cells that contaminate hematopoietic cell preparations contribute to the relapse of neuroblastoma patients who receive autologous stem cell rescue as a component of therapy. Therefore, effective purging methods are needed. This study details in vitro experiments to develop a viral-directed enzyme prodrug purging method that specifically targets neuroblastoma cells. The approach uses an adenovirus to deliver the cDNA encoding a rabbit liver carboxylesterase that efficiently activates the prodrug irinotecan,7-ethyl-10-[4-(1-piperidino)-1-piperidino]carbonyloxycamptothecin (CPT-11). The data show that an adenoviral multiplicity of infection of 50 transduces 100% of cultured neuroblastoma cells and primary tumor cells, irrespective of the level of tumor cell line contamination. Exposure of neuroblastoma cell lines or of mixtures of these cell lines with CD34(+) cells at a ratio of 10:90 to replication-deficient AdRSVrCE for 24 h and subsequent exposure of cells to 1-5 microM CPT-11 for 4 h increased the toxicity of CPT-11 to three neuroblastoma cell lines (SJNB-1, NB-1691, and SK-N-SH) from approximately 20-50-fold and eradicated their clonogenic potential. Also, after "purging," RNA for neuroblastoma cell markers (tyrosine hydroxylase, synaptophysin, and N-MYC) was undetectable by reverse transcription-PCR. In contrast, the purging protocol did not affect the number or type of colonies formed by CD34(+) cells in an in vitro progenitor cell assay. No bystander effect on CD34(+) cells was observed. The method described is being investigated for its potential clinical utility, particularly its efficacy for use with patients having relatively high tumor burdens, because no published methods have been shown to be efficacious when the tumor burden exceeds 1%.
High Resolution Crystal Structure of Human β-Glucuronidase Reveals Structural Basis of Lysosome Targeting (2013)

Human β-glucuronidase (GUS) cleaves β-D-glucuronic acid residues from the non-reducing termini of glycosaminoglycan and its deficiency leads to mucopolysaccharidosis type VII (MPSVII). Here we report a high resolution crystal structure of human GUS at 1.7 Å resolution and present an extensive analysis of the structural features, unifying recent findings in the field of lysosome targeting and glycosyl hydrolases. The structure revealed several new details including a new glycan chain at Asn272, in addition to that previously observed at Asn173, and coordination of the glycan chain at Asn173 with Lys197 of the lysosomal targeting motif which is essential for phosphotransferase recognition. Analysis of the high resolution structure not only provided new insights into the structural basis for lysosomal targeting but showed significant differences between human GUS, which is medically important in its own right, and E. coli GUS, which can be selectively inhibited in the human gut to prevent prodrug activation and is also widely used as a reporter gene by plant biologists. Despite these differences, both human and E. coli GUS share a high structure homology in all three domains with most of the glycosyl hydrolases, suggesting that they all evolved from a common ancestral gene.
Involvement of SMRT Corepressor in Transcriptional Repression by the Vitamin D Receptor (2008)

To repress the expression of target genes, the unliganded nuclear receptor generally recruits the silencing mediator of retinoid and thyroid hormone receptor (SMRT)/nuclear receptor corepressor via its direct association with the conserved motif within bipartite nuclear receptor-interaction domains (IDs) of the corepressor. Here, we investigated the involvement of the SMRT corepressor in transcriptional repression by the unliganded vitamin D receptor (VDR). Using small interference RNA against SMRT in human embryonic kidney 293 cells, we demonstrated that SMRT is involved in the repression of the VDR-target genes, osteocalcin and vitamin D(3) 24-hydroxylase in vivo. Consistent with this, VDR and SMRT are recruited to the vitamin D response element of the endogenous osteocalcin promoter in the absence of 1alpha,25-(OH)(2)D(3) in chromatin immunoprecipitation assays. To address the involvement of the VDR-specific interaction of SMRT in this repression, we identified the molecular determinants of the interaction between VDR and SMRT. Interestingly, VDR specifically interacts with ID1 of the SMRT/nuclear receptor corepressor and that ID1 is required for their stable interaction. We also identified specific residues in the SMRT-ID1 that are required for VDR binding, using the one- plus two-hybrid system, a novel genetic selection method for specific missense mutations that disrupt protein-protein interactions. These mutational studies revealed that VDR interaction requires a wide range of the residues within and outside the extended helix motif of SMRT-ID1. Notably, SMRT mutants defective in the VDR interaction were also defective in the repression of endogenous VDR-target genes, indicating that the SMRT corepressor is directly involved in the VDR-mediated repression in vivo via an ID1-specific interaction with the VDR.
Symptomatic Occult Hydrocephalus with Normal Cerebrospinal-Fluid Pressure (1965)

THE term hydrocephalus refers to distention of the cerebral ventricles, usually as the result of obstruction somewhere along the pathway of the cerebrospinal-fluid circulation. Occult indicates that enlargement of the ventricles has occurred after union of the cranial sutures, and hence the head remains of normal size. Hydrocephalus is said to be noncommunicating or obstructive if the blockade of circulation is in the ventricular system and communicating or nonobstructive if there is a normal patency of the pathways from the ventricular system to the lumbar subarachnoid space. Its causes are numerous and include tumors encroaching on the ventricles, carcinomatosis of . . .
Fate in water of a recombinantEscherichia coli K-12 strain used in the commercial production of bovine somatotropin (1992)

The fate in water of Escherichia coli K-12 strain LBB269, both plasmid-free and carrying the recombinant plasmid pBGH1, was studied. E. coli K-12 strain LBB269 (pBGH1) is a nalidixic acid resistant derivative of W3110G (pBGH1), the microorganism used by Monsanto Company for the commercial production of bovine somatotropin. Water samples were obtained from the Missouri River and from the Monsanto Life Sciences Research Center aqueous waste basin. Strains LBB269 and LBB269 (pBGH1) were grown in fermentation vessel under bovine somatotropin (BST) production conditions, and inoculated into the water samples. The inoculated water samples were incubated at 26 degrees C, and the number of viable E. coli cells was determined as a function of time. In sterile water from both sources, the two strains remained at a constant level for at least 28 days; LBB269 (pBGH1) remained at a constant level in sterile water for at least 300 days. In non-sterile water from both sources, the two strains declined from an initial concentration of about 3.0 x 10(6) cells per ml to less than 10 cells per ml in 147 h. The study conditions did not adversely affect the populations of indigenous microorganisms. The selective loss of strains LBB269 and LBB269 (pBGH1) demonstrates that these E. coli strains do not survive in environmental sources of water. In addition, it was observed that the presence of pBGH1 had essentially no effect on the disappearance of strain LBB269 from either source of water.
Shape Memory Assisted Self-Healing Coating (2013)

In this communication, we report the preparation and characterization of new shape memory assisted self-healing (SMASH) coatings. The coatings feature a phase-separated morphology with electrospun thermoplastic poly(ε-caprolactone) (PCL) fibers randomly distributed in a shape memory epoxy matrix. Mechanical damage to the coating can be self-healed via heating, which simultaneously triggers two events: (1) the shape recovery of the matrix to bring the crack surfaces in spatial proximity, and (2) the melting and flow of the PCL fibers to rebond the crack. In controlled healing experiments, damaged coatings not only heal structurally, but also functionally by almost completely restoring the corrosion resistance. We envision the wide applicability of the SMASH concept in designing the next-generation self-healing materials.
Transcarboxylase: One of Nature's Early Nanomachines (2004)

The enzyme transcarboxylase (TC) catalyzes an unusual reaction; TC transfers a carboxylate group from methylmalonyl-CoA to pyruvate to form oxaloacetate and propionyl-CoA. Remarkably, to perform this task in Propionii bacteria Nature has created a large assembly made up of 30 polypeptides that totals 1.2 million daltons. In this nanomachine the catalytic machinery is repeated 6-12 times over using ordered arrays of replicated subunits. The latter are sites of the half reactions. On the so-called 12S subunit a biotin cofactor accepts carboxylate, - CO2- , from methylmalonyl-CoA. The carboxylated-biotin then translocates to a second subunit, the 5S, to deliver the carboxylate to pyruvate. We have not yet characterized the intact nanomachine, however, using a battery of biophysical techniques, we have been able to derive novel,and sometimes unexpected, structural and mechanistic insights into the 12S and 5S subunits. Similar insights have been obtained for the small 1.3S subunit that acts as the biotin carrier linking the 12S and 5S forms. Interestingly, some of these insights gained for the 12S and 5S subunits carry over to related mammalian enzymes such as human propionyl-CoA carboxylase and human pyruvate carboxylase, respectively, to provide a rationale for their malfunction in disease-related mutations.
Pulsatile perfusion system for ex vivo investigation of biochemical pathways in intact vascular tissue (1996)

We have constructed and performed initial validation of an innovative perfusion system that allows exposure of intact segments of vascular tissue to realistic physiological and hemodynamic environments ex vivo. Computer-controlled opening and closing of an in-line gate valve allows generation of arterial pressure waveforms. The control algorithm predicted resultant pressure waveforms with a high degree of accuracy (Pearson correlation coefficient > 0.97). To document vascular homeostasis ex vivo, vasomotor bioassays and morphological studies were performed. The bioassays consisted of injecting epinephrine (2 x 10(-3) mg/ml) into the perfusion system followed by acetylcholine (100 microM) while concurrently measuring vessel diameter with a laser micrometer, significant vasomotion was measured for canine carotid arteries (n = 4) bioassayed after 1, 24, and 48 h of perfusion (P < 0.03). Additionally, human saphenous vein segments were perfused for 24 h (n = 4) and viewed with laser confocal scanning microscopy and transmission electron microscopy; photomicrographs show typical vascular morphology. We conclude that the vascular perfusion system described herein is well suited for investigating the response of intact vascular tissue to hemodynamic variables.
The Grounded Condenser Antenna Radiation Formula (1931)

Exact formulas for the wave function and vertical electric field at the surface of the ground are derived for a vertical dipole of zero height.