gebhart/patrepeval huggingface dataset:
Physiology and biochemistry of Drosophila learning mutants (1996)

Single gene mutants of Drosophila that are defective in learning/memory processes have increased substantially our understanding of the physiology, biochemistry, and anatomy underlying conditioned behaviors. Drosophila learning mutants can be separated into two general classes, those with structural defects in the brain and those without (conditioning mutants) any obvious brain alterations. From studies of brain structural mutants, two neuroanatomic areas have merged as important for normal conditioned behavior: the mushroom bodies and the central complex. Biochemical and molecular genetic studies of the conditioning mutants have implicated numerous types of molecules in learning, but the adenosine 3',5'-cyclic monophosphate (cAMP) second messenger pathway has emerged as especially important. Five different genes in this pathway, amnesiac (a product similar to adenylate cyclase activating peptides), dunce (cAMP phosophodiesterase), rutabaga (adenylyl cyclase), DCO (protein kinase A), and dCREB2 (cAMP-response element binding protein), have proven important for normal learning. The products of many of these learning mutants are enriched in mushroom bodies, which highlight the importance of mushroom bodies for normal learning and the cAMP second messenger cascade for the physiology of mushroom body cells in their role(s) underlying learning. Physiological studies of the mutants have demonstrated that plastic properties of synaptic transmission, including facilitation and posttetanic potentiation, are abnormal in the mutants. An appendix describing the currently used paradigms to test Drosophila behavior is included.
Hexylene- and Phenylene-Bridged Polysiloxane Network Materials (1995)

Hexylene- and phenylene-bridged polymethylsiloxane xerogels and aerogels were prepared by sol-gel polymerizations. The materials were prepared by the hydrolysis and condensation of 1, 6-bis(diethoxymethylsilyl)hexane 1 and 1, 4-bis(diethoxymethylsilyl) benzene 3 under acidic and basic conditions. The polymerizations afforded network polymers in the form of gels within several hours. The gels were dried to afford both xerogels and aerogels. The materials were characterized by solid state 29Si and 13C CP MAS NMR spectroscopy, nitrogen sorption porosimetry, thermal gravimetric analysis, and scanning electron microscopy.
Low-Level Monocyte Chemoattractant Protein-1 Stimulation of Monocytes Leads to Tumor Formation in Nontumorigenic Melanoma Cells (2001)

Tumors commonly produce chemokines for recruitment of host cells, but the biological significance of tumor-infiltrating inflammatory cells, such as monocytes/macrophages, for disease outcome is not clear. Here, we show that all of 30 melanoma cell lines secreted monocyte chemoattractant protein-1 (MCP-1), whereas normal melanocytes did not. When low MCP-1-producing melanoma cells from a biologically early, nontumorigenic stage were transduced to overexpress the MCP-1 gene, tumor formation depended on the level of chemokine secretion and monocyte infiltration; low-level MCP-1 secretion with modest monocyte infiltration resulted in tumor formation, whereas high secretion was associated with massive monocyte/macrophage infiltration into the tumor mass, leading to its destruction within a few days after injection into mice. Tumor growth stimulated by monocytes/macrophages was due to increased angiogenesis. Vessel formation in vitro was inhibited with mAbs against TNF-alpha, which, when secreted by cocultures of melanoma cells with human monocytes, induced endothelial cells under collagen gels to form branching, tubular structures. These studies demonstrate that the biological effects of tumor-derived MCP-1 are biphasic, depending on the level of secretion. This correlates with the degree of monocytic cell infiltration, which results in increased tumor vascularization and TNF-alpha production.
Prostaglandin E2 is a selective inducer of interleukin-12 p40 (IL-12p40) production and an inhibitor of bioactive IL-12p70 heterodimer (2001)

Interleukin-12 p70 (IL-12p70) heterodimer, composed of p35 and p40 subunits, is a major Th1-driving cytokine, promoting cell-mediated immunity. In contrast, IL-12p40 homodimer, secreted by APC in the absence of p35 expression, and free p40 monomer do not mediate IL-12 activity but act as IL-12 antagonists. Here it is reported that prostaglandin E(2) (PGE(2)), an inflammatory mediator with a previously known Th2-driving function, dose-dependently enhances the IL-12p40 mRNA expression and the secretion of IL-12p40 protein in human tumor necrosis factor-alpha (TNFalpha)-stimulated immature dendritic cells (DCs). This effect is selective and is not accompanied by the induction of IL-12p35 expression or by secretion of IL-12p70 heterodimer. Inability of TNFalpha/PGE(2) to induce IL-12p70 was not compensated by interferon gamma (IFNgamma), which strongly enhanced the lipopolysaccharide (LPS)-induced IL-12p70 production. In addition to the selective induction of IL-12p40 in TNFalpha-stimulated DCs, PGE(2) inhibited the production of IL-12p70 and IL-12p40 in DCs stimulated with LPS or CD40 ligand. These data suggest an additional level of the Th2-promoting activity of PGE(2), via selective induction of IL-12p40. Selective induction of IL-12p40 and suppression of bioactive IL-12p70 may have negative impact on anticancer vaccination with PGE(2)-matured DCs. (Blood. 2001;97:3466-3469)
Radial Filtration of Drilling Muds (1940)

It is generally recognized that fluid is lost from rotary drilling muds topermeable strata during normal drilling operations; but that this fluid is thefiltrate from the mud, rather than the mud itself, has been shown by variousworkers. The presence of this filtrate in oil-bearing or gas-bearing strata isundesirable and harmful. The decreased permeability of the stratum to oileffected by the presence of water has been pointed out by severalinvestigators, and since, in the production of the reservoir fluid, thegreatest pressure drop occurs immediately adjacent to the borehole, it followsthat infiltered water is particularly objectionable in this region. Again, thisfiltrate tends to make electrical logs less reliable, since oil in theproximity of the borehole is probably flushed out to an appreciable extent bythe water Observation of side wall cores may be misleading for the same reason.Drill-stem tests in low-pressure areas may be of doubtful value where no oil isrecovered, unless sufficient time is allowed for production of water lost fromthe mud. The infiltered water may hinder drilling operations by softeningshales and causing sloughing; the "tight hole" occasioned by excessivedeposition of filter cake in the hole is a common occurrence. The filter cakeremaining on the face of the producing formation may itself sometimes bedetrimental to production. In view of these implications of the importance of filtration of mud, aninvestigation was undertaken to determine the factors involved in theinfiltration process, and to correlate these in such a manner that the valuesobtained in routine filter tests employing a conventional filter of the"wall-building tester" type, together with data on size of hole, drillpipe, and rate of mud circulation, could be used to estimate water loss anddistance of penetration of the filtrate into strata. Quantitative relations of filter-cake permeability, filtrate viscosity, andrate of filtration have been developed for filtration in the simple laboratoryfilter. T.P. 1112
Superconducting Proximity Effect and Majorana Fermions at the Surface of a Topological Insulator (2008)

We study the proximity effect between an s-wave superconductor and the surface states of a strong topological insulator. The resulting two-dimensional state resembles a spinless px+ipy superconductor, but does not break time reversal symmetry. This state supports Majorana bound states at vortices. We show that linear junctions between superconductors mediated by the topological insulator form a nonchiral one-dimensional wire for Majorana fermions, and that circuits formed from these junctions provide a method for creating, manipulating, and fusing Majorana bound states.
The Mouse/Human Chimeric Monoclonal Antibody cA2 Neutralizes TNF In Vitro and Protects Transgenic Mice from Cachexia and TNF Lethality In Vivo (1995)

The pleiotropic cytokine tumour necrosis factor-alpha (TNF) is thought to play a central role in infectious, inflammatory and autoimmune diseases. Critical to the understanding and management of TNF-associated pathology is the development of highly specific agents capable of modifying TNF activity. We evaluated the ability of a high affinity mouse/human chimeric anti-TNF monoclonal antibody (cA2) to neutralize the in vitro and in vivo biological effects of TNF. cA2 inhibited TNF-induced mitogenesis and IL-6 secretion by human fibroblasts, TNF-priming of human neutrophils, and the stimulation of human umbilical vein endothelial cells by TNF as measured by the expression of E-selectin, ICAM-1 and procoagulant activity. cA2 also specifically blocked TNF-induced adherence of human neutrophils to an endothelial cell monolayer. Receptor binding studies suggested that neutralization resulted from cA2 blocking of TNF binding to both p55 and p75 TNF receptors on the cells. In vivo, repeated administration of cA2 to transgenic mice that constitutively express human TNF reversed the cachectic phenotype and prevented subsequent mortality. These results demonstrated that cA2 effectively neutralized a broad range of TNF biological activities both in vitro and in vivo.
Cloning, Expression, and Sequence Analysis of the ORF4 Gene of the Porcine Reproductive and Respiratory Syndrome Virus MN-1b (1994)

Porcine reproductive and respiratory syndrome virus (PRRSV) MN-1b strain open reading frame 4 (ORF4) has been cloned, sequenced, and expressed in Escherichia coli. The homologies of nucleotide and amino acid sequences between MN-1b (US isolate) and LV (European isolate) are 69% and 64%, respectively. The data also showed that ORF4 of MN-1b is 36 bases shorter than that of LV. Western blot analysis of expressed recombinant ORF4 protein reacted with 65% (26/40) of PRRSV-infected pig sera tested. These results demonstrated that ORF4 of PRRSV may not be a well-conserved region.
A newly recognized pathway for the negative regulation of mast cell-dependent hypersensitivity and inflammation mediated by an endogenous cell surface receptor of the gp49 family (1997)

Mast cells are constitutively present at the portals between self and nonself, and contain a large and diverse complement of proinflammatory mediators. These characteristics suggest that the activation of mast cells must be carefully regulated in vivo. Regulation of pathologic and physiologic mast cell activation has been traditionally associated simply with the presence or absence of an activating signal. We examine here evidence supporting a new paradigm: mast cell homeostasis may result from inhibition of activation mediated by receptors on the surface of mast cells, typified by a member of the gp49 family.
Glycoengineering of the methylotrophic yeast Hansenula polymorpha for the production of glycoproteins with trimannosyl core N‐glycan by blocking core oligosaccharide assembly (2008)

The initial lipid-linked oligosaccharide Glc(3)Man(9)GlcNAc(2)-dolichyl pyrophosphate (Dol-PP) for N-glycan is synthesized and assembled at the membrane of the endoplasmic reticulum (ER) and subsequently transferred to a nascent polypeptide by the oligosaccharide transferase complex. We have identified an ALG3 homolog (HpALG3) coding for a dolichyl-phosphate-mannose dependent alpha-1,3-mannosyltransferase in the methylotrophic yeast Hansenula polymorpha. The detailed analysis of glycan structure by linkage-specific mannosidase digestion showed that HpALG3 is responsible for the conversion of Man5GlcNAc(2)-Dol-PP to Man(6)GlcNAc(2)-Dol-PP, the first step to attach a mannose to the lipid-linked oligosaccharide in the ER. The N-glycosylation pathway of H. polymorpha has been remodeled by deleting the HpALG3 gene in the Hpoch1 null mutant strain blocked in the yeast-specific outer mannose chain synthesis and by introducing an ER-targeted Aspergillus saitoi alpha-1,2-mannosidase gene. This glycoengineered H. polymorpha strain produced glycoproteins mainly containing trimannosyl core N-glycan (Man(3)GlcNAc(2)), which is the common core backbone of various human-type N-glycans. The results demonstrate the high potential of H. polymorpha to be developed as an efficient expression system for the production of glycoproteins with humanized glycans.
Methionine Aminopeptidase-2 as a Selective Target of Myofibroblasts in Pulmonary Fibrosis (2007)

Idiopathic pulmonary fibrosis (IPF) is a progressive, scarring lung disease characterized by fibroblast accumulation and deposition of collagen. Factors that promote growth and/or survival of fibroblasts are potential therapeutic targets. Methionine aminopeptidase 2 (MetAP2), a member of the aminopeptidase family of proteases, has been implicated in cell proliferation in a variety of cell types, but its expression and function in the lung is not known. By immunohistochemistry, MetAP2 was expressed in many cell types, including fibroblasts, in IPF lungs. Fumagillin, an irreversible inhibitor of the enzymatic activity of MetAP2, attenuated collagen deposition in the bleomycin model of acute lung injury in mice. Treatment with fumagillin caused a selective reduction in the numbers of bromodeoxyuridine (BrdU)-positive myofibroblasts, but not type II alveolar epithelial cells, macrophages, or B- and T-lymphocytes in the lungs of bleomycin-treated mice. Incubation of primary rat lung fibroblasts with either fumagillin or with short interfering RNA that targeted MetAP2 led to reduced proliferation, as assessed by incorporation of BrdU. The profibrotic growth factor, platelet-derived growth factor, increased expression of MetAP2 in rat lung fibroblasts. We propose that MetAP2 plays a role in the proliferation of fibroblasts and myofibroblasts in fibrotic lung diseases and may serve as a novel pharmacologic target in IPF.
Evolution of Function in the Crotonase Superfamily:  The Stereochemical Course of the Reaction Catalyzed by 2-Ketocyclohexanecarboxyl-CoA Hydrolase (2004)

Members of the mechanistically diverse enoyl-CoA hydratase (crotonase) superfamily catalyze reactions that involve stabilization of an enolate anion derived from an acyl thioester of coenzyme A. 2-Ketocyclohexanecarboxyl-CoA hydrolase (BadI), found in a pathway for anaerobic degradation of benzoate by Rhodopseudomonas palustris, is a member of the crotonase superfamily that catalyzes a reverse Dieckmann reaction in which the substrate is hydrolyzed to pimelyl-CoA. The substrate is the configurationally labile 2S-ketocyclohexanecarboxyl-CoA, and in 2H2O solvent hydrogen is incorporated into the 2-proS position of the pimelyl-CoA product. Therefore, the stereochemical course of the BadI-catalyzed reaction is inversion. This information is important for understanding the roles of active-site functional groups in the active site of BadI as well as in the active sites of the homologous 1,4-dihydroxynaphthoyl-CoA synthases that catalyze a forward Dieckmann reaction.
An algorithm for designing rings for survivable fiber networks (1991)

The authors present an algorithm for routing fiber around a ring in a network, when the network nodes, links, connectivity, and which offices are to be used on that ring together are known. The algorithm aids automated survivable network planning. The algorithm was programmed in C, and run on a SPARC-station. Under certain conditions, the problem degenerates to the traveling salesman problem, and the ring routing algorithm degenerates to the nearest neighbor method of solving that problem.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Immunodominant Tuberculosis CD8 Antigens Preferentially Restricted by HLA-B (2007)

CD8(+) T cells are essential for host defense to intracellular bacterial pathogens such as Mycobacterium tuberculosis (Mtb), Salmonella species, and Listeria monocytogenes, yet the repertoire and dominance pattern of human CD8 antigens for these pathogens remains poorly characterized. Tuberculosis (TB), the disease caused by Mtb infection, remains one of the leading causes of infectious morbidity and mortality worldwide and is the most frequent opportunistic infection in individuals with HIV/AIDS. Therefore, we undertook this study to define immunodominant CD8 Mtb antigens. First, using IFN-gamma ELISPOT and synthetic peptide arrays as a source of antigen, we measured ex vivo frequencies of CD8(+) T cells recognizing known immunodominant CD4(+) T cell antigens in persons with latent tuberculosis infection. In addition, limiting dilution was used to generate panels of Mtb-specific T cell clones. Using the peptide arrays, we identified the antigenic specificity of the majority of T cell clones, defining several new epitopes. In all cases, peptide representing the minimal epitope bound to the major histocompatibility complex (MHC)-restricting allele with high affinity, and in all but one case the restricting allele was an HLA-B allele. Furthermore, individuals from whom the T cell clone was isolated harbored high ex vivo frequency CD8(+) T cell responses specific for the epitope, and in individuals tested, the epitope represented the single immunodominant response within the CD8 antigen. We conclude that Mtb-specific CD8(+) T cells are found in high frequency in infected individuals and are restricted predominantly by HLA-B alleles, and that synthetic peptide arrays can be used to define epitope specificities without prior bias as to MHC binding affinity. These findings provide an improved understanding of immunodominance in humans and may contribute to a development of an effective TB vaccine and improved immunodiagnostics.
Neuroblastoma Killing Properties of Vδ2 and Vδ2-Negative γδT Cells Following Expansion by Artificial Antigen-Presenting Cells (2014)

In conclusion, we have demonstrated that polyclonal-expanded populations of γδT cells are capable of both antibody-dependent and -independent effector functions in neuroblastoma.
Binding sites for vascular endothelial growth factor are localized on endothelial cells in adult rat tissues. (1992)

Vascular endothelial growth factor (VEGF) is a secreted heparin-binding mitogen; its growth-promoting activity is limited to vascular endothelial cells in vitro and VEGF also stimulates angiogenesis in vivo. To identify target cells for VEGF and investigate the potential physiological role of this factor, iodinated recombinant human VEGF (125I-rhVEGF) was used for in vitro ligand autoradiography on tissue sections from adult rats. 125I-rhVEGF exhibited saturable, displaceable binding to a single class of sites with high affinity and low capacity in all tissues and organs examined. Colocalization of 125I-rhVEGF binding with Factor VIII-like immunoreactivity demonstrated binding sites associated with vascular endothelial cells of both fenestrated and nonfenestrated microvessels and the endothelium of large vessels, while no displaceable binding was evident on nonendothelial cells. Specific binding was associated with quiescent as well as proliferating vessels. These findings support the hypothesis that VEGF plays a specific role in both the maintenance and in the induction of growth of vascular endothelial cells.
Phase Determination by Multiple-Wavelength X-Ray Diffraction: Crystal Structure of a Basic "Blue" Copper Protein from Cucumbers (1988)

A novel x-ray diffraction technique, multiple-wavelength anomalous dispersion (MAD) phasing, has been applied to the de novo determination of an unknown protein structure, that of the "blue" copper protein isolated from cucumber seedlings. This method makes use of crystallographic phases determined from measurements made at several wavelengths and has recently been made technically feasible through the use of intense, polychromatic synchrotron radiation together with accurate data collection from multiwire electronic area detectors. In contrast with all of the conventional methods of solving protein structures, which require either multiple isomorphous derivatives or coordinates of a similar structure for molecular replacement, this technique allows direct solution of the classical "phase problem" in x-ray crystallography. MAD phase assignment should be particularly useful for determining structures of small to medium-sized metalloproteins for which isomorphous derivatives are difficult or impossible to make. The structure of this particular protein provides new insights into the spectroscopic and redox properties of blue copper proteins, an important class of metalloproteins widely distributed in nature.
Synthesis and Characterization of a Reactive Vinyl-Functionalized MCM-41:  Probing the Internal Pore Structure by a Bromination Reaction (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTSynthesis and Characterization of a Reactive Vinyl-Functionalized MCM-41: Probing the Internal Pore Structure by a Bromination ReactionMyong H. Lim, Christopher F. Blanford, and Andreas SteinView Author Information Department of Chemistry, University of Minnesota 207 Pleasant Street SE Minneapolis, Minnesota 55455-0431 Cite this: J. Am. Chem. Soc. 1997, 119, 17, 4090–4091Publication Date (Web):April 30, 1997Publication History Received8 November 1996Published online30 April 1997Published inissue 1 April 1997https://pubs.acs.org/doi/10.1021/ja9638824https://doi.org/10.1021/ja9638824rapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views2945Altmetric-Citations347LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Extraction,Halogenation,Hybrid materials,Porous materials,Vinyl Get e-Alerts
Phase Transformation, Coalescence, and Twinning of Monodisperse FePt Nanocrystals (2001)

The phase transformation, coalescence, and twin structure of thermally annealed 6 nm FePt nanocrystals under high vacuum on an amorphous carbon surface have been investigated. A1-FePt phase to L10−FePt phase transformation occurs at 530 °C. The multilayered nanocrystal assemblies coalesce to form larger grains at 600 °C. These coalesced nanocrystals do not form a single grained structure; instead, twinning becomes a characteristic structure feature. The surface of the coalescent grains consists of {111} and (001) facets.
Immunization Against Bovine Papillomavirus Infection (2007)

The two large open reading frames denoted L1 and L2 in the non-transforming region of the bovine papillomavirus type 1 (BPV-1) genome have been molecularly cloned to expression in Escherichia coli. Antisera against the E. coli-derived L1 and L2 protein reacted with BPV-1 in both enzyme-linked immunosorbent assays and immunoprecipitation reactions. Neutralization of BPV-induced transformation of mouse C127 cells was demonstrated most consistently with antisera against the L1 protein. E. coli-derived L1 protein protected calves against BPV-1 challenge after vaccination.