gebhart/patrepeval huggingface dataset:
OPM database and PPM web server: resources for positioning of proteins in membranes (2011)

The Orientations of Proteins in Membranes (OPM) database is a curated web resource that provides spatial positions of membrane-bound peptides and proteins of known three-dimensional structure in the lipid bilayer, together with their structural classification, topology and intracellular localization. OPM currently contains more than 1200 transmembrane and peripheral proteins and peptides from approximately 350 organisms that represent approximately 3800 Protein Data Bank entries. Proteins are classified into classes, superfamilies and families and assigned to 21 distinct membrane types. Spatial positions of proteins with respect to the lipid bilayer are optimized by the PPM 2.0 method that accounts for the hydrophobic, hydrogen bonding and electrostatic interactions of the proteins with the anisotropic water-lipid environment described by the dielectric constant and hydrogen-bonding profiles. The OPM database is freely accessible at http://opm.phar.umich.edu. Data can be sorted, searched or retrieved using the hierarchical classification, source organism, localization in different types of membranes. The database offers downloadable coordinates of proteins and peptides with membrane boundaries. A gallery of protein images and several visualization tools are provided. The database is supplemented by the PPM server (http://opm.phar.umich.edu/server.php) which can be used for calculating spatial positions in membranes of newly determined proteins structures or theoretical models.
Association of Intestinal Peptide Transport with a Protein Related to the Cadherin Superfamily (1994)

The first step in oral absorption of many medically important peptide-based drugs is mediated by an intestinal proton-dependent peptide transporter. This transporter facilitates the oral absorption of beta-lactam antibiotics and angiotensin-converting enzyme inhibitors from the intestine into enterocytes lining the luminal wall. A monoclonal antibody that blocked uptake of cephalexin was used to identify and clone a gene that encodes an approximately 92-kilodalton membrane protein that was associated with the acquisition of peptide transport activity by transport-deficient cells. The amino acid sequence deduced from the complementary DNA sequence of the cloned gene indicated that this transport-associated protein shares several conserved structural elements with the cadherin superfamily of calcium-dependent, cell-cell adhesion proteins.
Local induction of calcium phosphate formation on TiO2 coatings on titanium via surface treatment with a CO2 laser (2003)

Sol-gel-derived TiO(2) coatings are known to promote bonelike hydroxyapatite formation on their surfaces in vitro and in vivo. Hydroxyapatite integrates into bone tissue. In some clinical applications, the surface of an implant is simultaneously interfaced with soft and hard tissues, so it should match the properties of both. A new method is introduced for treating the coatings locally in a controlled manner. The local densification of sol-gel-derived titania coatings on titanium substrates with a CO(2) laser was studied in terms of the in vitro calcium phosphate-inducting properties. CO(2)-laser-treated multilayer coatings were compared with furnace-fired coatings prepared with the same recipe and previously shown to be bioactive. Additionally, local areas of furnace-fired multilayer coatings (previously shown to be bioactive in vitro) were further laser-treated to achieve various properties in the same implant. Topological surface properties were examined with atomic force microscopy. The formation of hydroxyapatite was studied with Fourier transform infrared and scanning electron microscopy energy-dispersive X-ray analysis. The results show that calcium phosphate formation can be adjusted locally by laser treatment. Calcium phosphate is a bonelike hydroxyapatite. The local treatment of sol-gel-derived coatings with a CO(2) laser is a promising technique for creating implants with various properties to interface different tissues and a possible way of coating implants that do not tolerate furnace firing.
A Highly Effective Nonpolar Isostere of Deoxyguanosine:  Synthesis, Structure, Stacking, and Base Pairing (2002)

We describe the preparation and structure of the deoxyribonucleoside of 4-fluoro-6-methylbenzimidazole, abbreviated dH (8), which acts as a close shape mimic of the nucleoside deoxyguanosine. The nucleoside is prepared from 2-fluoro-4-methylaniline in seven steps. The X-ray crystal structure reveals a (-sc) glycosidic orientation, an S conformation for the deoxyribose moiety, and quite close shape mimicry of guanine by the substituted benzimidazole. Conformational studies by (1)H NMR and (1)H-(1)H ROESY experiments reveal an S-type conformation and an anti glycosidic orientation in solution (D(2)O), essentially the same as that of deoxyguanosine. Base-stacking studies in a "dangling end" context reveal that the benzimidazole base mimic stacks more strongly than all four natural bases, and more strongly than its counterpart guanine by 1.1 kcal/mol. Base-pairing studies in a 12mer DNA duplex show that, like other nonpolar nucleoside isosteres, H is destabilizing and nonselective when paired opposite natural bases. However, when paired opposite another nonpolar isostere, difluorotoluene (F), a mimic of thymine, the pair exhibits stability approaching that of its natural analogue, a G-T (wobble) base pair. The nucleoside analogue dH will be useful in studies of protein-DNA interactions, and the H-F base pair will serve as a structurally and thermodynamically close mimic of G-T in studies of DNA mismatch repair enzymes.
Expression and Functional Analysis of Olfactory Receptorsa (1998)

The olfactory system recognizes and discriminates myriads of odorants of diverse molecular structure. This task is supposed to be accomplished by a large array of seven-transmembrane domain receptors encoded by a multigene family. Although circumstantial evidence suggests that the identified genes encode odorant receptors, unequivocal proof requires demonstration that the resulting proteins should be able to interact with odorous molecules and couple via G proteins onto second messenger cascades. This goal can be achieved by heterologous expression of receptor proteins in surrogate eucaryotic cells, although the task is complicated by the diversity of putative odorous ligands and the large size of the receptor family. Employing the baculovirus/Sf9 cell system it was found that receptor proteins can be expressed at high levels. Stimulating receptor-expressing Sf9 cells with a mixture of numerous odorous compounds elicited a significant and dose-dependent second messenger response, which was never observed in control cells. Assaying a large panel of odorous compounds, including representatives of different odor classes and compounds of different chemical classes revealed that distinct receptor subtypes respond to certain odorants but not to others. Graded responses to only a subset of odorants indicate that the heterologous expressed receptor types have a selective but relatively broad ligand specificity. The easily manipulated bacterial system was employed to produce olfactory receptor proteins in large quantities. It was solubilized from inclusion bodies and upon reconstitution in liposomes displayed specific interaction with odor ligands.
Evaluation and Comparison of Two Commercial Enzyme-Linked Immunosorbent Assay Kits for Detection of Antigenically Diverse Human Noroviruses in Stool Samples (2004)

Two recently commercialized enzyme-linked immunosorbent assay kits, the SRSV(II)-AD (Denka Seiken Co. Ltd., Tokyo, Japan) and IDEIA NLV (DakoCytomation Ltd., Ely, United Kingdom) kits, that detect human norovirus (HuNV) antigens in stool samples were evaluated to assess whether they could be used instead of reverse transcription-PCR (RT-PCR) for routine diagnosis. The sensitivities and specificities of the two kits were tested with a panel of 103 stool samples containing HuNVs of 4 and 10 genetic subgroups within genogroups I and II (GI and GII), respectively, and 39 stool samples containing other enteric viruses. The Denka kit had a high sensitivity (>70% for 10 of the 14 subgroups) but a specificity of only 69%, and the Dako kit had a low sensitivity (<30% for 6 GII subgroups) but a high specificity of 100%. Statistical analysis suggests that HuNVs of four subgroups (subgroups GII/2, GII/5, GII/6, and GII/n) are likely to elude detection by the Dako kit. The two kits also demonstrated differences in reactivities. While the Dako kit discriminated between the GI and GII antigens of HuNVs, the Denka kit cross-reacted with samples containing all GI and GII subgroups of HuNVs. Moreover, the Denka kit also reacted with samples containing human sapovirus (HuSV). We demonstrate that the cross-reactivity of the Denka kit is not due to specific reactions with HuNV and HuSV antigens. These results indicate that neither the Denka kit nor the Dako kit has all the performance characteristics required to replace the RT-PCR methods used to detect HuNVs.
Specific targeting of the IL-23 receptor, using a novel small peptide noncompetitive antagonist, decreases the inflammatory response (2014)

IL-23 is part of the IL-12 family of cytokines and is composed of the p19 subunit specific to IL-23 and the p40 subunit shared with IL-12. IL-23 specifically contributes to the inflammatory process of multiple chronic inflammatory autoimmune disorders, including psoriasis, multiple sclerosis, inflammatory bowel disease, and rheumatoid arthritis. So far, one antibody targeting the shared p40 subunit of IL-12 and IL-23, Ustekinumab, is approved clinically to treat psoriasis. However, there are no treatments inhibiting specifically the IL-23 proinflammatory response. We have developed small IL-23R-specific antagonists by designing all D-peptides arising from flexible regions of IL-23R. Of these peptides, we selected 2305 (teeeqqly), since in addition to its soluble properties, it inhibited IL-23-induced STAT3 phosphorylation in spleen cells. Peptide 2305 specifically binds to IL-23R/IL-12Rβ1-expressing HEK-293 cells and not to cells devoid of the receptor. Peptide 2305 showed functional selectivity by modulating IL-23-induced gene expression in IL-23R/IL-12Rβ1-expressing cells and in Jurkat cells; 2305 does not inhibit IL-12-induced cytokine expression in IL-12Rβ-IL-12Rβ2-HEK-293 cells. Finally, compared with anti-p40 treatment, 2305 effectively and selectively inhibits IL-23-induced inflammation in three in vivo mouse models: IL-23-induced ear inflammation, anti-CD40-induced systemic inflammatory response, and collagen-induced arthritis. We, hereby, describe the discovery and characterization of a potent IL-23R small-peptide modulator, 2305 (teeeqqly), that is effective in vivo. 2305 may be more convenient, less cumbersome, less costly, and most importantly, more specific than current biologics for the treatment of inflammatory conditions, and conceivably complement the actual therapies for these chronic and debilitating inflammatory diseases.
Representation of interwoven surfaces in 2 1/2 D drawing (2006)

The state-of-the-art in computer drawing programs is based on a number of concepts that are over two decades old. One such concept is the use of layers for ordering the surfaces in a drawing from top to bottom. Unfortunately, the use of layers unnecessarily imposes a partial ordering on the depths of the surfaces and prevents the user from creating a large class of potential drawings, e.g., of Celtic knots and interwoven surfaces. In this paper we describe a novel approach which only requires local depth ordering of segments of the boundaries of surfaces in a drawing rather than a global depth relation between entire surfaces. Our program provides an intuitive user interface which allows a novice to create complex drawings of interwoven surfaces that would be difficult and time-consuming to create with standard drawing programs.
Cellular actions of beta-amyloid precursor protein and its soluble and fibrillogenic derivatives (1997)

beta-Amyloid precursor protein (beta-APP), the source of the fibrillogenic amyloid beta-peptide (A beta) that accumulates in the brain of victims of Alzheimer's disease, is a multifunctional protein that is widely expressed in the nervous system. beta-Amyloid precursor protein is axonally transported and accumulates in presynaptic terminals and growth cones. A secreted form of beta-APP (sAPP alpha) is released from neurons in response to electrical activity and may function in modulation of neuronal excitability, synaptic plasticity, neurite outgrowth, synaptogenesis, and cell survival. A signaling pathway involving guanosine 3',5'-cyclic monophosphate is activated by sAPP alpha and modulates the activities of potassium channels, N-methyl-D-aspartate receptors, and the transcription factor NF kappa B. Additional functions of beta-APP may include modulation of cell adhesion and regulation of proliferation of nonneuronal cells. Alternative enzymatic processing of beta-APP liberates A beta, which has a propensity to form amyloid fibrils; A beta can damage and kill neurons and increase their vulnerability to excitotoxicity. The mechanism involves generation of oxyradicals and impairment of membrane transport systems (e.g., ion-motive ATPases and glutamate and glucose transporters). Genetic mutations or age-related metabolic changes may promote neuronal degeneration in Alzheimer's disease by increasing production of A beta and/or decreasing levels of neuroprotective sAPP alpha.
Nitroazole Universal Bases in Peptide Nucleic Acids (1999)

[formula: see text] The syntheses of PNA oligomers containing potential ambiguous nucleobase analogues, namely 3-nitropyrrole and 5-nitroindole, have been accomplished. Hybridization properties of these PNAs with complementary oligodeoxynucleotides were evaluated by thermal denaturation experiments. Both novel residues exhibited little variation in Tm (< or = 1.5 degrees C) when positioned against any of the four nucleoside bases. The capability to incorporate degenerate sites should further expand the utility of PNA in applications where precise sequence information is not available.
Influence of Preservation Solution on the Isolation and Culture of Human Hepatocytes from Liver Grafts (2005)

A major problem for the isolation and transplantation of hepatocytes is the lack of resources for obtaining viable hepatocytes. Improving this situation would enhance hepatic cell transplantation programs. Our objective was to evaluate the influence of the preservation solutions used during organ retrieval on the quality of hepatocytes isolated from liver tissue. We compared the results of the collagenase perfusion technique for isolation of hepatocytes in human livers flushed with University of Wisconsin (UW) and Celsior preservation solutions. Yield (number of viable cells per gram of tissue), cellular viability, efficiency of cells to attach to culture plates and form a monolayer, and drug metabolizing competence of the hepatocytes were measured. Successful isolation was achieved in 63% of the procedures using the UW solution and 100% of the procedures using the Celsior solution. In the UW group, significantly lower cell viability (38 +/- 41% vs. 79 +/- 14%, p < 0.05), yield of cells (4.0 +/- 5.2 x 10(6) vs. 8.2 +/- 5.6 x 10(6) cells/g, p < 0.05), and protein content at 24 h of culture (0.6 +/- 0.6 vs. 1.2 +/- 0.3 mg protein per plate, p < 0.05) than in Celsior solution were found. However, similar values of P450 activities were found in both groups. The more successful isolation, better yield, and higher cell viability obtained from human liver grafts preserved in Celsior solution, in comparison to UW solution, suggest Celsior solution as the most appropriate for preserving cadaveric hepatic tissue to be used for hepatocyte harvesting.
Immunocytochemical demonstration of vimentin in astrocytes and ependymal cells of developing and adult mouse nervous system (1981)

The occurrence of vimentin, a specific intermediate filament protein, has been studied by immunoflourescence microscopy in tissue of adult and embryonic brain as well as in cell cultures from nervous tissue. By double imminofluorescence labeling, the distribution of vimentin has been compared with that of subunit proteins of other types of intermediate filaments (glial fibrillary acidic [GFA] protein, neurofilament protein, prekeratin) and other cell-type specific markers (fibronectin, tetanus toxin receptor, 04 antigen). In adult brain tissue, vimentin is found not only in fibroblasts and cells of larger blood vessels but also in ependymal cells and astrocytes. In embryonic brain tissue, vimentin is detectable as early as embryonic day 11, the earliest stage tested, and is located in radial fibers spanning the neural tube, in ventricular cells, and in blood vessels. At all stages tested, oligodendrocytes and neurons do not express detectable amounts of vimentin. In primary cultures of early postnatal mouse cerebellum, a coincident location of vimentin and GFA protein is seen in astrocytes, and both types of filament proteins are included in the perinuclear aggregates formed upon exposure of the cells to colcemid. In cerebellar cell cultures of embryonic-day-13 mice, vimentin is seen in various cell types of epithelioid or fibroblastlike morphology but is absent from cells expressing tetanus toxin receptors. Among these embryonic, vimentin-positive cells, a certain cell type reacting neither with tetanus toxin nor with antibodies to fibronectin or GFA protein has been tentatively identified as precursor to more mature astrocytes. The results show that, in the neuroectoderm, vimentin is a specific marker for astrocytes and ependymal cells. It is expressed in the mouse in astrocytes and glial precursors well before the onset of GFA protein expression and might therefore serve as an early marker of glial differentiation. Our results show that vimentin and GFA protein coexist in one cell type not only in primary cultures in vitro but also in the intact tissue in situ.
MRI patterns of atrophy associated with progression to AD in amnestic mild cognitive impairment (2007)

The regions of loss observed in subjects with amnestic mild cognitive impairment (aMCI) who progressed to Alzheimer disease (AD) within 18 months of the MRI are typical of subjects with AD. The lack of gray matter loss in subjects with aMCI who remained clinically stable for their entire observed clinical course is consistent with the notion that patterns of atrophy on MRI at baseline map well onto the subsequent clinical course.
Design, formulation, and optimization of media. (1995)

The fundamental knowledge available about the microorganism, substrates, and process represent the basis on which a rational approach for the design and formulation of media for microbial processes can be attempted. In this respect, it is necessary to analyze critically the main objective to be optimized (yield, productivity, quality of final product, etc.). The first step of medium development is concerned with the decision to be taken about the adequate components to be used, followed by the calculation of their concentrations. After medium preparation and experimentation, the application of the most appropriate statistical optimization methodology will make it possible to attain the optimal medium. Medium design and formulation for plant cell processes are still carried out on an empirical basis owing to the lack of fundamental knowledge. However, some general guidelines can be given for growth and production media considering the experimental evidence available about the functions and influence of the medium components for promoting growth and product formation. Adequate manipulation of the carbon, nitrogen, and phosphorus sources and phytohormones and the inclusion of precursors and elicitors in the medium represent the best strategy for improving medium development for plant cell processes. The development of cost-effective medium supplies for mammalian cell culture production of proteins is a key element for a commercially successful process. Medium development is a task that requires experience, time, and resources in its solutions, which may be several. An optimal formulation is elusive because there will always be room for improvement, but through systematic, comprehensive work, practical combinations of nutrients, factors, and feeding schedules can be developed in a reasonable time. A properly developed formulation can bring the burden of the medium below 10% of the total cost of a mammalian cell process.
Superconductivity above 90 K in the square-planar compound systemABa2Cu3O6+xwithA=Y, La, Nd, Sm, Eu, Gd, Ho, Er and Lu (1987)

We have found superconductivity in the 90-K range in A${\mathrm{Ba}}_{2}$${\mathrm{Cu}}_{3}$${\mathrm{O}}_{6+\mathrm{x}}$ with A=La, Nd, Sm, Eu, Gd, Ho, Er, and Lu in addition to Y. The results suggest that the unique square planar Cu atoms, each surrounded by four or six oxygen atoms, are crucial to the superconductivity of oxides in general. In particular, the high ${\mathrm{T}}_{\mathrm{c}}$ in A${\mathrm{Ba}}_{2}$${\mathrm{Cu}}_{3}$${\mathrm{O}}_{6+\mathrm{x}}$ is attributed mainly to the quasi two-dimensional assembly of the ${\mathrm{CuO}}_{2}$-Ba-${\mathrm{CuO}}_{2+\mathrm{x}}$-Ba-${\mathrm{CuO}}_{2}$ layers sandwiched between two A layers, with particular emphasis in the ${\mathrm{CuO}}_{2+\mathrm{x}}$ layers. Higher-${\mathrm{T}}_{\mathrm{c}}$ oxides are predicted for compounds with bigger assemblies of ${\mathrm{CuO}}_{2}$ layers coupled by Ba-layers.
XML and DB2 (2002)

The eXtensible Markup Language (XML) is a key technology that facilitates both information exchange and e-business transactions. Starting with DB2 UDB Net.Data VI, an application can generate XML documents from SQL queries against DB2 or any ODBC compliant databases. Today DB2 UDB XML Extender not only serves as a repository for both XML documents and their Document Type Definitions (DTDs), but also provides data management functionalities such as data integrity, security, recoverability and manageability. The user has the option to store the entire document as an XML user-defined column or to decompose the document into multiple tables and columns. Fast search via indices is provided for both XML elements and attributes. Section search can be done against the content of the document. Query syntax adheres to W3C standards such as Extensive Stylesheet Language Transformation (XSLT) and XML Path Language (XPath) specifications. The user can retrieve the entire document or extract XML elements and attributes dynamically in an SQL query. In addition, XML Extender provides a stored procedure to generate XML documents from existing data. Together with Net.Data, one can browse the content of the XML documents via the Internet.