gebhart/patrepeval huggingface dataset:
The Cationic Amphipathic α-Helix of HIV-1 Viral Protein R (Vpr) Binds to Nucleic Acids, Permeabilizes Membranes, and Efficiently Transfects Cells (2003)

Viral protein R (Vpr) is a small protein of 96 amino acids that is conserved among the lentiviruses human immunodeficiency virus type 1 (HIV-1), HIV-2, and simian immunodeficiency virus. We recently sought to determine whether the karyophilic properties of Vpr, as well as its ability to bind nucleic acids, could be used to deliver DNA into cells. We have found that the C-terminal domain of Vpr-(52-96) is able to efficiently transfect various cell lines. Here, we show that the shortest active sequence for gene transfer corresponds to the domain that adopts a alpha-helix conformation. DNA binding studies and permeabilization assays performed on cells demonstrated that the peptides that are efficient in transfection condense plasmid DNA and are membranolytic. Electron microscopy studies and transfection experiments performed in the presence of inhibitors of the endocytic processes indicated that the major entry pathway of Vpr-DNA complexes is through endocytosis. Taken together, the results show that the cationic C-terminal alpha-helix of Vpr has DNA-condensing as well as membrane-destabilizing capabilities, both properties that are indispensable for efficient DNA transfection.
Demonstration by class I gene transfer that reduced susceptibility of human cells to natural killer cell‐mediated lysis is inversely correlated with HLA class I antigen expression (1989)

HLA antigen-loss mutants and class I gene transferents were used to analyze the influence of class I expression on natural killer (NK) cell-mediated lysis. Only HLA antigen-loss mutants that had lost expression of either HLA-A and HLA-B antigens (mutant .184) or of HLA-A, B and C antigens (mutant .221) were distinctly susceptible to NK-mediated lysis. Mutants with reduced expression of class II antigens but unaltered expression of class I antigens remained resistant to NK lysis. A direct demonstration of the effect of class I antigen expression on human cells was made by analyzing a variety of gene transferents of the HLA-A, B, C null mutant .221 expressing only one transferred HLA-A, B or C gene. These results specifically show that expression of class I antigens, with a possible preferential effect of HLA-B expression, reduces the susceptibility of mutant .221 to NK-mediated lysis.
Soil and crop management for sustainable slopeland farming in Indonesia (1996)

Soil and crop management for sustainable slopeland farming in Indonesia , Soil and crop management for sustainable slopeland farming in Indonesia , مرکز فناوری اطلاعات و اطلاع رسانی کشاورزی
Significance of Heat-Stable and Heat-Labile Enterotoxins in Porcine Colibacillosis in an Additive Model for Pathogenicity Studies (2006)

Although heat-stable (ST) and heat-labile (LT) enterotoxins produced by enterotoxigenic Escherichia coli (ETEC) have been documented as important factors associated with diarrheal diseases, investigations assessing the contributions of individual enterotoxins to the pathogenesis of E. coli infection have been limited. To address the individual roles of enterotoxins in the diarrheal disease caused by K88-positive ETEC in young pigs, enterotoxin-positive and -negative isogenic E. coli strains were constructed by using pBR322 to clone and express LT and STb. Four strains, K88+ astA, K88+ astA/pBR322, K88+ astA STb+, and K88+ astA LT+, were constructed and subsequently included in gnotobiotic piglet challenge studies, and their pathogenesis was assessed. The results indicated that all K88+ isogenic strains were able to colonize the small intestines of piglets exhibiting the K88 receptor. However, only LT- and STb-positive strains caused appreciable diarrhea. Piglets inoculated with the K88+ astA LT+ strain became dehydrated within 18 h, while those inoculated with the K88+ astA STb+ strain did not, although diarrhea developed in several piglets. The changes in the blood packed-cell volume and plasma total protein of gnotobiotic piglets inoculated with the LT-positive strains were significantly greater than those of pigs inoculated with the K88 astA/pBR322 strain (P = 0.012, P = 0.002). Immunochemistry image analysis also suggested that LT enhanced bacterial colonization in a gnotobiotic piglet model. This investigation suggested that LT is a major contributor to the virulence of K88+ ETEC and that isogenic constructs are a useful tool for studying the pathogenesis of ETEC infection.
A common precursor for hematopoietic and endothelial cells (1998)

Embryonic stem cell-derived embryoid bodies contain a unique precursor population which, in response to vascular endothelial growth factor, gives rise to blast colonies in semi-solid medium. Upon transfer to liquid culture with appropriate cytokines, these blast colonies generate both hematopoietic and adherent, stromal-type cells. Cells within the adherent population display characteristics of endothelial lineage including the expression of CD31, flk-1, flt-1, tie-2, the capacity to take up acetylated LDL and the presence of cytoplasmic Weibel-Palade bodies. Mixing studies demonstrated that the hematopoietic and endothelial precursors within the blast colonies develop from the same cell, the blast colony-forming cell. Kinetic analysis showed that the blast colony-forming cell represents a transient cell population that develops early and is lost quickly during embryoid body development. These findings provide strong evidence that the blast colony-forming cell represents the long-hypothesized hemangioblast, the common precursor of the hematopoietic and endothelial lineages.
Toward Thermoplastic Lignin Polymers; Part II: Thermal & Polymer Characteristics of Kraft Lignin & Derivatives (2013)

This work focused on providing a molecular understanding of the way the polymeric properties of kraft lignin and its derivatives are affected by various thermal treatments. This information was then correlated with the polymeric properties of the materials (glass transition temperature (Tg), molecular weight characteristics, and thermal stability) for a series of selectively and progressively derivatized softwood kraft lignin samples. Softwood kraft lignin was highly susceptible to thermally induced reactions that caused its molecular characteristics to be severely altered with the concomitant formation of irreversible cross-linking. However, by fully methylating the phenolic OH groups from within the structure of softwood kraft lignin, the thermal stability of these materials was dramatically enhanced and their Tg reduced. While optimum thermal stability and melt re-cycling was observed with the fully methylated derivatives, fully oxypropylated phenolic substitution did not offer the same possibilities. The accumulated data is aimed at providing the foundations for a rational design of single component, lignin-based thermoplastic materials with reproducible polymeric properties when thermally processed in a number of manufacturing cycles.
Covalent assembly of a soluble T cell receptor-peptide-major histocompatibility class I complex. (1996)

We used stepwise photochemical cross-linking for specifically assembling soluble and covalent complexes made of a T-cell antigen receptor (TCR) and a class I molecule of the major histocompatibility complex (MHC) bound to an antigenic peptide. For that purpose, we have produced in myeloma cells a single-chain Fv construct of a TCR specific for a photoreactive H-2Kd-peptide complex. Photochemical cross-linking of this TCR single-chain Fv with a soluble form of the photoreactive H-2Kd-peptide ligand resulted in the formation of a ternary covalent complex. We have characterized the soluble ternary complex and showed that it reacted with antibodies specific for epitopes located either on the native TCR or on the Kd molecules. By preventing the fast dissociation kinetics observed with most T cell receptors, this approach provides a means of preparing soluble TCR-peptide-MHC complexes on large-scale levels.
TERE1, a novel gene affecting growth regulation in prostate carcinoma (2002)

Recently, we isolated a ubiquitously expressed gene designated TERE1, which has a significant effect on the growth regulation in bladder cancer. The TERE1 gene maps to chromosome 1p36.11-1p36.33 between the micro-satellite markers D1S2667 and D1S434, a chromosome locus that has been identified by loss of heterozygosity studies as a site of a putative tumor suppressor gene or genes for multiple tumor types including prostate carcinoma. The expression of the TERE1 transcript and protein was examined in a series of thirty microdissected prostate tumors by semi-quantitative RT/PCR and immunohistochemistry. There was a significant 61% decrease in the TERE1 transcript in prostate carcinoma (CaP) and a distinct loss of the TERE1 protein in metstatic prostate. Though a loss of heterozygosity at chromosome 1p36 was found in 25% of these prostate tumors, there appeared to be no TERE1 mutations present in these tumor samples. Induced TERE1 expression after transduction or transfection of TERE1 constructs into two prostate carcinoma (LNCaP and PC-3) cell lines significantly decreased proliferation up to 80% with a significant increase in the number of cells in G1. Serum factors but not DHT (dihydrotestosterone) appear to regulate the amount of TERE1 protein in the androgen responsive LNCaP cell line. Additionally, we have identified by microarray analysis various growth regulatory genes that are down-regulated or up-regulated in TERE1-transduced PC-3 cells. Altogether, these data suggest that TERE1 maybe significant in prostate cancer growth regulation and the down regulation or absence of TERE1 may be an important component of the phenotype of advanced disease.
An Antibody as Surrogate Receptor Reveals Determinants of Activity of an Innate Immune Peptide Antibiotic (2010)

Drug discovery initiatives often depend critically on knowledge of ligand-receptor interactions. However, the identity or structure of the target receptor may not be known in every instance. The concept of receptor surrogate, a molecular environment mimic of natural receptor, may prove beneficial under such circumstances. Here, we demonstrate the potential of monoclonal antibodies (mAbs) to act as surrogate receptors for a class of innate immune peptide antibiotics, a strategy that can help comprehend their action mechanism and identify chemical entities crucial for activity. A panel of antibody surrogates was raised against indolicidin, a tryptophan-rich cationic broad spectrum antimicrobial peptide of innate immune origin. Employing an elegant combination of thermodynamics, crystallography, and molecular modeling, interactions of the peptide with a high affinity anti-indolicidin monoclonal antibody were analyzed and were used to identify a motif that contained almost the entire antibiotic activity of native indolicidin. The analysis clarified the interaction of the peptide with previously proposed targets such as bacterial cell membrane and DNA and could further be correlated with antimicrobial compounds whose actions involve varied other mechanisms. These features suggest a multipronged assault pathway for indolicidin. Remarkably, the anti-indolicidin mAb surrogate was able to isolate additional independent bactericidal sequences from a random peptide library, providing compelling evidence as to the physiological relevance of surrogate receptor concept and suggesting applications in receptor-based pharmacophore research.
Molecular characterization of Sin3 PAH-domain interactor specificity and identification of PAH partners (2006)

Sin3 is the central component of a multisubunit co-repressor complex. A number of DNA-binding proteins are targeted by the Sin3 complex to chromatin through association with its paired amphipathic helix (PAH) domains. Here, we performed a yeast two-hybrid screening using a peptide aptamer library and identified peptides that interact with either PAH1 or PAH2. Analysis of PAH2 interacting peptides uncovered motifs similar to previously characterized PAH2 interacting proteins, Mad, Ume6 and kruppel-like members, while analysis of PAH1 interacting peptides revealed an LXXLL motif. In addition, a tandem affinity purification (TAP)-tagging approach of Sin3b resulted in the isolation of known and novel interactors amongst which neural retina leucine (NRL) zipper. Strikingly, one of the identified PAH2 interacting peptide showed strong resemblance to the NRL region amino acids 125-150. Direct association between PAH2 and NRL was shown and NRL(125-150) mediated transcriptional repression in reporter assays. Finally, we reveal that PAH1 and PAH2 amino acids 7, 14 and 39 shown previously to be important for Mad-PAH2 interaction, also play an important role in the specificity of interaction between PAH1, PAH2 and identified aptamers. Our results provide novel insights into the molecular determinant of the specificity of PAH1 and PAH2 for their interacting partners.
Joint transceiver design for MIMO communications using geometric mean decomposition (2005)

In recent years, considerable attention has been paid to the joint optimal transceiver design for multi-input multi-output (MIMO) communication systems. In this paper, we propose a joint transceiver design that combines the geometric mean decomposition (GMD) with either the conventional zero-forcing VBLAST decoder or the more recent zero-forcing dirty paper precoder (ZFDP). Our scheme decomposes a MIMO channel into multiple identical parallel subchannels, which can make it rather convenient to design modulation/demodulation and coding/decoding schemes. Moreover, we prove that our scheme is asymptotically optimal for (moderately) high SNR in terms of both channel throughput and bit error rate (BER) performance. This desirable property is not shared by any other conventional schemes. We also consider the subchannel selection issues when some of the subchannels are too poor to be useful. Our scheme can also be combined with orthogonal frequency division multiplexing (OFDM) for intersymbol interference (ISI) suppression. The effectiveness of our approaches has been validated by both theoretical analyses and numerical simulations.
Stability of cocaine in saliva. (1988)

Journal Article Stability of cocaine in saliva. Get access E J Cone, E J Cone Addiction Research Center, Natl. Inst. on Drug Abuse, Baltimore, MD 21224 Search for other works by this author on: Oxford Academic Google Scholar S L Menchen S L Menchen Addiction Research Center, Natl. Inst. on Drug Abuse, Baltimore, MD 21224 Search for other works by this author on: Oxford Academic Google Scholar Clinical Chemistry, Volume 34, Issue 7, 1 July 1988, Page 1508, https://doi.org/10.1093/clinchem/34.7.1508 Published: 01 July 1988
Substituted 1,1-diphenyl-3-aminoprop-1-enes and 1,1-diphenyl-3-aminopropanes as potential antidepressant agents (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSubstituted 1,1-diphenyl-3-aminoprop-1-enes and 1,1-diphenyl-3-aminopropanes as potential antidepressant agentsRoy F. Maisey, Geraint Jones, A. R. Somerville, and Brian A. WhittleCite this: J. Med. Chem. 1971, 14, 2, 161–164Publication Date (Print):February 1, 1971Publication History Published online1 May 2002Published inissue 1 February 1971https://pubs.acs.org/doi/10.1021/jm00284a020https://doi.org/10.1021/jm00284a020research-articleACS PublicationsRequest reuse permissionsArticle Views143Altmetric-Citations22LEARN 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-Alertsclose Get e-Alerts
Light Harvesting by Phycobilisomes (1985)

Many bacterial clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated (Cas) systems employ the dual RNA–guided DNA endonuclease Cas9 to defend against invading phages and conjugative plasmids by introducing site-specific ...Read More
Miniaturized Antimicrobial Susceptibility Test by Combining Concentration Gradient Generation and Rapid Cell Culturing (2015)

Effective treatment of bacterial infection relies on timely diagnosis and proper prescription of antibiotic drugs. The antimicrobial susceptibility test (AST) is one of the most crucial experimental procedures, providing the baseline information for choosing effective antibiotic agents and their dosages. Conventional methods, however, require long incubation times or significant instrumentation costs to obtain test results. We propose a lab-on-a-chip approach to perform AST in a simple, economic, and rapid manner. Our assay platform miniaturizes the standard broth microdilution method on a microfluidic device (20 × 20 mm) that generates an antibiotic concentration gradient and delivers antibiotic-containing culture media to eight 30-nL chambers for cell culture. When tested with 20 μL samples of a model bacterial strain (E. coli ATCC 25922) treated with ampicillin or streptomycin, our method allows for the determination of minimum inhibitory concentrations consistent with the microdilution test in three hours, which is almost a factor of ten more rapid than the standard method.
Inhibition of TLR-4/MD-2 signaling by RP105/MD-1 (2005)

Activation of Toll-like receptor (TLR) signaling by microbial and host molecular signatures is critical to the induction of immune responses. Such signaling is, perforce, kept under tight control. We recently discovered a novel endogenous inhibitor of TLR-4 — RP105. Initially identified as a B-cell-specific molecule with a role in B-cell proliferation in response to RP105 mAb and LPS, RP105 is a TLR-4 homologue. Further, like TLR-4 whose surface expression and signaling depends upon co-expression of the secreted protein MD-2, surface expression of RP105 is dependent upon co-expression of the MD2 homologue, MD-1. Unlike the TLRs, however, RP105 lacks a signaling domain, having the apparent structure of a TLR inhibitor. Further, RP105 is not B-cell-specific; its expression directly mirrors that of TLR-4 on dendritic cells and macrophages. These considerations suggested a role for RP105 as a physiological inhibitor of TLR-4 signaling. Indeed, we have recently found that: (i) RP105 is a specific inhibitor of TLR-4 signaling in HEK293 cells; (ii) RP105/MD-1 interacts directly with TLR-4/MD-2, inhibiting the ability of this signaling complex to bind LPS; (iii) RP105 regulates TLR-4 signaling in dendritic cells and macrophages; and (iv) RP105 regulates in vivo responses to LPS.
Surfactants from oleic, erucic and petroselinic acid: Synthesis and properties (2010)

Abstract Most surfactants are based on C 12 and C 14 chains from fatty acids and contain alkanols obtained from ethylene. Readily available fatty acids with C 18 and C 22 chains are barely used due to their lower water solubility and less suitable structure for micelle formation. To overcome these deficiencies, we attached polar groups to terminal and/or internal positions of oleic, petroselinic and erucic acid. Internal diols were prepared by epoxidation and acid‐catalyzed ring opening or by bishydroxylation with catalytic amounts of osmium tetroxide. Terminal alcohols were prepared by reduction of the methyl esters. For the synthesis of the non‐ionic surfactants, the alcohols were reacted with the p ‐toluenesulfonates of di‐, tri‐ and tetraethyleneglycols or the epoxide ring was opened with the corresponding oligoethyleneglycols. This way, ethoxylates free of homologues were obtained. Sodium sulfate surfactants were prepared by reacting the mono‐, di‐ and triols with different equivalents of chlorosulfonic acid. From the purified products, the spectroscopic and the surfactant properties were determined. The latter are in many cases equal or better than those of commercial ionic and non‐ionic surfactants based on C 12 and C 14 carbon chains.
Novel therapeutic approaches for multiple myeloma (2003)

Multiple myeloma (MM) affects 15,000 new patients annually in the US, with 50,000 total patients, and remains incurable. Our preliminary in vitro and animal studies suggest a role for MM-host interactions in regulating MM cell growth, drug resistance, and migration in the bone marrow. Importantly, treatment strategies which target mechanisms whereby MM cells grow and survive in the bone marrow, including thalidomide and its potent immunomodulatory derivatives and proteasome inhibitor PS-341, can overcome classical drug resistance in preclinical and early clinical studies.
A repeating 11‐mer amino acid motif and plant desiccation (1993)

Among the proteins that accumulate as plant seeds desiccate are several protein families that are composed principally of a tandemly repeated 11-mer amino acid motif. Proteins containing the same motif accumulate in the desiccating leaves of a desiccation-tolerant plant species. This motif is characterized by apolar residues in positions 1, 2, 5 and 9, and charged or amide residues in positions 3, 6, 7, 8 and 11. An alpha helical arrangement of the 11-mer repeating unit gives an amphiphilic helix whose hydrophobic stripe twists in a right-handed fashion around the helix. Should these proteins dimerize via binding of their hydrophobic faces, a right-handed coiled coil would be formed. Such a structure has not previously been observed. A conceivable function for these proteins in ion sequestration in the desiccated state is proposed.
Laminin-coated poly(L-lactide) filaments induce robust neurite growth while providing directional orientation (2000)

Cellular channels during development and after peripheral nerve injury are thought to provide guidance cues to growing axons. In tissue culture where these cues are absent, neurites from dorsal root ganglion neurons grow with a radial distribution. To induce directional axonal growth and to enhance the rate of axonal growth after injury, we have designed microfilaments of poly(L-lactide). We demonstrate that dorsal root ganglia grown on these filaments in vitro extend longitudinally oriented neurites in a manner similar to native peripheral nerves. The extent of neurite growth was significantly higher on laminin-coated filaments compared with uncoated and poly-L-lysine-coated filaments. As high as 5.8 +/- 0.2 mm growth was observed on laminin-coated filaments compared with 2.0 +/- 0.2 mm on uncoated and 2.2 +/- 0.3 mm on poly-L-lysine-coated filaments within 8 days. Schwann cells were found to grow on all types of filaments. They were, however, absent in the leading edges of growth on laminin-coated filaments. Photolysis of Schwann cells caused a significant reduction in the neurite length on all types of filaments. Laminin-coated filaments, however, induced significantly longer neurites compared with uncoated and/or poly-L-lysine-coated filaments even in the absence of Schwann cells. Our results suggest that laminin-coated poly(L-lactide) filaments are suitable for inducing directional and enhanced axonal growth. Implants designed by arranging these microfilaments into bundles should aid regenerating axons by providing guidance cues and channels to organize matrix deposition, cell migration, axon growth, and improve functional recovery.