gebhart/patrepeval huggingface dataset:
Resistance to Experimental Autoimmune Encephalomyelitis in Mice Lacking the Cc Chemokine Receptor (Ccr2) (2000)

Monocyte recruitment to the central nervous system (CNS) is a necessary step in the development of pathologic inflammatory lesions in experimental autoimmune encephalomyelitis (EAE), a murine model of multiple sclerosis. Monocyte chemoattractant protein (MCP)-1, a potent agonist for directed monocyte migration, has been implicated in the pathogenesis of EAE. Here we report that deficiency in CC chemokine receptor (CCR)2, the receptor for MCP-1, confers resistance to EAE induced with a peptide derived from myelin oligodendrocyte glycoprotein peptide 35-55 (MOGp35-55). CCR2(-/)- mice immunized with MOGp35-55 failed to develop mononuclear cell inflammatory infiltrates in the CNS and failed to increase CNS levels of the chemokines RANTES (regulated on activation, normal T cell expressed and secreted), MCP-1, and interferon (IFN)-inducible protein 10 (IP-10) as well the chemokine receptors CCR1, CCR2, and CCR5. Additionally, T cells from CCR2(-/)- immunized mice showed decreased antigen-induced proliferation and production of IFN-gamma compared with wild-type immunized controls, suggesting that CCR2 enhances the T helper cell type 1 immune response in EAE. These data indicate that CCR2 plays a necessary and nonredundant role in the pathogenesis of EAE.
Structure, DNA minor groove binding, and base pair specificity of alkyl- and aryl-linked bis(amidinobenzimidazoles) and bis(amidinoindoles) (1993)

A series of bis(amidinobenzimidazoles) and bis(amidinoindoles) with varied linking chains connecting the aromatic groups and various modifications to the basic amidino groups have been prepared. The calf thymus (CT) DNA and nucleic acid homopolymer [poly(dA).poly(dT),poly(dA-dT).poly-(dA-dT), and poly(dG-dC).poly(dG-dC)] binding properties of these compounds have been studied by thermal denaturation (delta Tm) and viscosity. The compounds show a greater affinity for poly(dA).poly(dT) and poly(dA-dT).poly(dA-dT) than for poly(dG-dC).poly(dG-dC). Viscometric titrations indicate that the compounds do not bind by intercalation. Molecular modeling studies and the biophysical data suggest that the molecules bind to the minor groove of CT DNA and homopolymers. Analysis of the shape of the molecules is consistent with this mode of nucleic acid binding. Compounds with an even number of methylenes connecting the benzimidazole rings have a higher affinity for DNA than those with an odd number of methylenes. Molecular modeling calculations that determine the radius of curvature of four defined groups in the molecule show that the shape of the molecule, as a function of chain length, affects the strength of nucleic acid binding. Electronic effects from cationic substituents as well as hydrogen bonding from the imidazole nitrogens also contribute to the nucleic acid affinity. The bis(amidinoindoles) show no structurally associated differential in nucleic acid base pair specificity or affinity.
Bounds on the maximum-likelihood decoding error probability of low-density parity-check codes (2001)

We derive both upper and lower bounds on the decoding error probability of maximum-likelihood (ML) decoded low-density parity-check (LDPC) codes. The results hold for any binary-input symmetric-output channel. Our results indicate that for various appropriately chosen ensembles of LDPC codes, reliable communication is possible up to channel capacity. However, the ensemble averaged decoding error probability decreases polynomially, and not exponentially. The lower and upper bounds coincide asymptotically, thus showing the tightness of the bounds. However, for ensembles with suitably chosen parameters, the error probability of almost all codes is exponentially decreasing, with an error exponent that can be set arbitrarily close to the standard random coding exponent.
Hysteroscopic Removal of Submucous Leiomyomas (1990)

Uterine leiomyomas are benign neoplasms that, when symptomatic, may require surgical treatment. The most symptomatic leiomyomas are of the submucous variety, causing persistent or recurrent uterine bleeding. Fifty-nine women experiencing abnormal uterine bleeding, dysmenorrhea, and/or infertility were diagnosed to have submucous leiomyomas, and of these, 52 were treated by hysteroscopic removal. In all women treated, the symptoms disappeared or markedly decreased. Of 16 patients with associated infertility, 10 conceived and 8 of these delivered a viable infant vaginally. Two women had a spontaneous abortion at 6 weeks and 11 weeks gestation, respectively. Although hysteroscopic removal of submucous leiomyomas is feasible in some patients, specific criteria for patient selection are needed that will allow the hysteroscopist to avoid failures and prevent complications. Hysteroscopy offers the best diagnostic method to detect or confirm submucous leiomyomas and, in selected cases, provides a good surgical alternative for treatment.
Printed organic transistors for ultra-low-cost RFID applications (2005)

Printed electronics provides a potential pathway toward the realization of ultra-low-cost radio frequency identification (RFID) tags for item-level tracking of consumer goods. Here, we report on our progress in developing materials and processes for the realization of printed transistors for low-cost RFID applications. Using inkjet printing of novel conductors, dielectrics, and organic semiconductors, we have realized printed transistors with mobilities >10/sup -1/cm/sup 2//V-s. AC performance of these devices is adequate for 135-kHz RFID, and, with further optimization, 13.56-MHz RFID appears to be within reach. We review the performance of these devices, and discuss optimization strategies for achieving the ultimate performance goals requisite for realizing ultra-low-cost printed RFID.
Novel biotinylated nucleotide - analogs for labeling and colorimetric detection of DNA (1987)

A series of dATP and dCTP nucleotide analogs have been synthesized which are modified by attachment of aliphatic linkers containing a functional group to the amino-nitrogen at the hydrogen bonding positions of the bases, that is, at the 6-position of adenine and the 4-position of cytosine. These nucleotides are incorporated into DNA probes by standard nick-translation protocols. DNA probes labeled with biotin derivatives of these nucleotides are effectively hybridized to target DNA sequences and can be detected by a streptavidin and calf intestinal alkaline phosphatase conjugate with a sensitivity (0.25 pg DNA) sufficient for reproducible and rapid detection of single copy genes in a Southern blot of mammalian DNA. Also, a procedure has been developed to allow reprobing of nylon filters that have been hybridized with biotinylated probes and developed with the streptavidin/alkaline phosphatase conjugate and a standard dye system.
Immunologic and clinical effects of personalized selection of peptide vaccines in HLA-A2 positive patients with advanced cancer (2008)

3031 Background: Personalized selection of the right peptides for each patient could be a novel peptide-based immunotherapy for boosting anticancer immunity in many patients (pts). Here we describe immunologic and clinical effects of a personalized peptide vaccine for HLA-A2 positive advanced cancer pts who mostly failed the standard therapy. Methods: To evaluate safety and immune responses of vaccination, 74 HLA-A2 positive advanced cancer pts, including 27 hormone refractory prostate cancer (HRPC), 13 colon cancer (CC), 8 pancreatic cancer (PC), 6 gastric cancer (GC), 4 brain tumor (BT), and 16 other types of cancer (Others) pts were enrolled in a phase I/II clinical trial. Pre-vaccination peripheral blood mononuclear cells and/or plasma were measured for their CTL or IgG levels for each of the 14–20 candidate peptides which can induce HLA-A2-restricted CTL activity against cancer cells followed by weekly or bi-weekly subcutaneous administration of the top four peptides (3mg each) showing the strongest immune responses. The protocol was approved by each ethics committee. Results: Vaccination-related adverse events were mainly grade 1 or 2 skin reactions at the injection sites, and there were no severe adverse events except for rectal bleeding in a cervical cancer pt. In the post (6–8th)-vaccination samples, CTL responses were boosted in 46 of 70 pts tested, while IgG responses were boosted in 55 of 73 pts tested, respectively. Best clinical responses were 1 CR, 11 PR, 31 SD, and 31 PD. Objective responses were obtained in urologic and gynecologic cancers or brain tumors by vaccination in the thigh or upper back regions, respectively, suggesting that location of sentinel lymph node near to tumor site is a pivotal factor for tumor regression. Median survival times in all pts are 14.3 months: 25 months in HRPC, 9.7 in BT, 8 in GC, 7 in PC, 6 in CC, and 17 in Others, respectively. Conclusions: This personalized peptide vaccine could be recommended for further stages of clinical trials because of safety, boosting of immune responses, and potential clinical benefits. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Expert Testimony Other Remuneration GreenPeptide GreenPeptide GreenPeptide GreenPeptide
Theoretical Study on the Factors Controlling the Accessibility of Cationic Metal Centers in Zirconocene Polymerization Catalysts (2000)

The influence of the ligand structure of zirconocene polymerization catalysts on the accessibility of the active reaction center was studied by an ab initio Hartree−Fock method. The variations in the accessibility were elucidated by comparing molecular structures and relative stabilities of 54 bridged zirconocene catalysts with 19 different bridging units, 18 ancillary Cp‘ ligands, and 18 ligand substituents. Ligand variations gave rise to various steric and electronic effects affecting both the nature and the concentration of active metal centers in the system, such as steric blocking or shielding of the metal center, and stabilization or destabilization of the active cationic species. Comparisons to experimental work demonstrated clear correlations between accessibility of the active reaction center and observed polymerization activity. Furthermore, interactions between the Lewis acidic aluminum centers and Lewis basic functionalities were observed. The consequences of such interactions are discussed.
Peptide and small molecule inhibitors of HECT-type ubiquitin ligases (2014)

The human genome encodes several hundred E3 ubiquitin ligases containing RING domains, and around 28 containing HECT domains. These enzymes catalyze the transfer of ubiquitin from E2 enzyme thioesters to a huge range of substrates and play crucial roles in many cellular functions. This makes them attractive potential therapeutic targets. However, they have proven difficult to inhibit: very few good inhibitors exist for RING domain ligases, and none have been described for HECT ligases. Here we show that bicyclic peptides isolated by phage display [Heinis C, Rutherford T, Freund S, Winter G (2009) Nat Chem Biol. 5(7):502-507] can target the E2 binding sites on the HECT domains of Smurf2, Nedd4, Mule/Huwe1, and WWP1, and thus act as specific inhibitors of these enzymes in vitro. By screening for displacement of one of these peptides from Smurf2, we were able to identify a small molecule, heclin (HECT ligase inhibitor), which inhibits several HECT ligases in tissue culture cells. In vitro, heclin does not block E2 binding but causes a conformational change that results in oxidation of the active site Cys. This demonstrates that HECT domains are potentially druggable and provides molecules that may be of experimental use. Heclin kills HEK293 cells growing in culture, consistent with an essential role for HECT ligase activity in mammalian cells.
The Repairability of Oxidative Free Radical Mediated Damage to DNA: A Review (1988)

Many DNA repair enzyme activities are present in both prokaryotic and eukaryotic organisms. Among these are DNA exo- and endonucleases and DNA glycosylases which remove oxidatively damaged portions of the DNA molecule, thereby initiating excision-repair. The existence of these enzymes may be taken as evidence that cellular DNA is continuously subject to endogenous oxidative stress. Many of the lesions introduced by ionizing and ultraviolet radiation are identical to those introduced into DNA by reactive oxygen species generated by activated white cells, and are substrates for the repair enzymes. The chemical nature of the lesions, their biologic effects, and the mechanism of their repairability are described.
Progress toward the evolution of an organism with an expanded genetic code (1999)

Several significant steps have been completed toward a general method for the site-specific incorporation of unnatural amino acids into proteins in vivo. An "orthogonal" suppressor tRNA was derived from Saccharomyces cerevisiae tRNA2Gln. This yeast orthogonal tRNA is not a substrate in vitro or in vivo for any Escherichia coli aminoacyl-tRNA synthetase, including E. coli glutaminyl-tRNA synthetase (GlnRS), yet functions with the E. coli translational machinery. Importantly, S. cerevisiae GlnRS aminoacylates the yeast orthogonal tRNA in vitro and in E. coli, but does not charge E. coli tRNAGln. This yeast-derived suppressor tRNA together with yeast GlnRS thus represents a completely orthogonal tRNA/synthetase pair in E. coli suitable for the delivery of unnatural amino acids into proteins in vivo. A general method was developed to select for mutant aminoacyl-tRNA synthetases capable of charging any ribosomally accepted molecule onto an orthogonal suppressor tRNA. Finally, a rapid nonradioactive screen for unnatural amino acid uptake was developed and applied to a collection of 138 amino acids. The majority of glutamine and glutamic acid analogs under examination were found to be uptaken by E. coli. Implications of these results are discussed.
MATERNAL CELL CONTAMINATION IN UNCULTURED AMNIOTIC FLUID (1996)

The presence of maternal cells in uncultured amniotic fluid may result in error in the interpretation of prenatal tests such as direct DNA analysis and rapid aneuploidy detection by fluorescence in situ hybridization (FISH). Using simultaneous dual colour X and Y FISH, we assessed maternal cell contamination in uncultured amniotic fluids from 500 women carrying male fetuses. The presence of maternal cells was correlated with the amount of blood present in the amniotic fluid as defined by visual examination of the cell pellet after centrifugation. The overall rate of maternal cell contamination in uncultured amniotic fluid as identified using X and Y-specific probes was 21.4 per cent, compared with 0.2 per cent in cultured fluid. Sixteen per cent of slightly bloody and 55 per cent of moderately bloody uncultured fluids had at least 20 per cent maternal cells and were classified as uninformative according to our protocol for rapid aneuploidy detection. Maternal and fetal cells could not be distinguished based on morphological characteristics alone.
Efficient and Sequence-Specific DNA-Templated Polymerization of Peptide Nucleic Acid Aldehydes (2003)

On the basis of the distance-dependence of DNA-templated reductive amination reactions and of recent findings of D. Lynn and co-workers, we developed DNA-templated polymerizations of synthetic peptide nucleic acid (PNA) aldehydes. The coupling reactions proceed in a highly efficient and sequence-specific manner, even in the presence of mixtures of PNA aldehydes of different sequence. Synthetic peptide nucleic acid polymers containing as many as 40 PNA units (representing 10 consecutive coupling reactions) were formed efficiently. The ease of preparing PNAs containing tailor-made functional groups together with these findings raises the possibility of evolving synthetic sequence-defined polymers by iterated cycles of translation, selection, PCR amplification, and diversification previously available only to biological macromolecules.
A performance evaluation of storing XML data in relational database management systems (2001)

XML is an emerging standard for the representation and exchange of Internet data. Along with document type definition (DTD), XML permits the execution of a collection of queries, using XPath to identify data in XML documents. In this paper we examine how XML data can be stored and queried using a standard relational database management system (RDBMS). For this, we propose a technique for automatic mapping from an XML document to relations within the RDBMS. We demonstrate that our novel approach preserves the nested structure of the XML documents. By hiding database details we devise a seamless, transparent framework for user access to XML data. In order to achieve this, we propose a novel mechanism for translating an XPath query into an SQL statement. Furthermore, we propose efficient techniques for the construction of an XML document on the fly from the result set of the SQL statement. We also present findings in terms of query response time on the comparative performance of different techniques for the construction of an XML document on the fly.
The Molecular Basis of Shoot Responses of Maize Seedlings to Trichoderma harzianum T22 Inoculation of the Root: A Proteomic Approach (2008)

Trichoderma spp. are effective biocontrol agents for several soil-borne plant pathogens, and some are also known for their abilities to enhance systemic resistance to plant diseases and overall plant growth. Root colonization with Trichoderma harzianum Rifai strain 22 (T22) induces large changes in the proteome of shoots of maize (Zea mays) seedlings, even though T22 is present only on roots. We chose a proteomic approach to analyze those changes and identify pathways and genes that are involved in these processes. We used two-dimensional gel electrophoresis to identify proteins that are differentially expressed in response to colonization of maize plants with T22. Up- or down-regulated spots were subjected to tryptic digestion followed by identification using matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry and nanospray ion-trap tandem mass spectrometry. We identified 91 out of 114 up-regulated and 30 out of 50 down-regulated proteins in the shoots. Classification of these revealed that a large portion of the up-regulated proteins are involved in carbohydrate metabolism and some were photosynthesis or stress related. Increased photosynthesis should have resulted in increased starch accumulation in seedlings and did indeed occur. In addition, numerous proteins induced in response to Trichoderma were those involved in stress and defense responses. Other processes that were up-regulated were amino acid metabolism, cell wall metabolism, and genetic information processing. Conversely, while the proteins involved in the pathways noted above were generally up-regulated, proteins involved in other processes such as secondary metabolism and protein biosynthesis were generally not affected. Up-regulation of carbohydrate metabolism and resistance responses may correspond to the enhanced growth response and induced resistance, respectively, conferred by the Trichoderma inoculation.
Using the Domain Name System To Store Arbitrary String Attributes (1993)

While the Domain Name System (DNS) [2,3] is generally used to store predefined types of information (e.g., addresses of hosts), it is possible to use it to store information that has not been previously classified.
Evidence for the direct involvement of the rhinovirus canyon in receptor binding. (1988)

Evidence is presented that indicates a deep crevice located on the surface of human rhinovirus type 14 is involved in virion attachment to cellular receptors. By using mutagenesis of an infectious cDNA clone, 11 mutants were created by single amino acid substitutions or insertions at positions 103, 155, 220, 223, and 273 of the structural protein VP1. Seven of the recovered mutants had a small plaque phenotype and exhibited binding affinities significantly lower than wild-type virus. One mutant, in which glycine replaced proline at amino acid position 155, showed a greatly enhanced binding affinity. Single-cycle growth kinetics suggested that 5 of the mutants had delayed growth cycles due to intracellular deficiencies apart from receptor binding.
Fibrosis and angiogenesis (2000)

Research during the past few years has contributed vastly to a better understanding of fibrosis and angiogenesis. Although studies to understand the molecular processes associated with fibrosis and angiogenesis were performed independently of each other, some common parallels have emerged. Translation of these observations into potential therapeutic possibilities needs further exploration.
Structural and Functional Characterization of an Essential RTX Subdomain of Bordetella pertussis Adenylate Cyclase Toxin (2006)

The adenylate cyclase toxin (CyaA) is one of the major virulence factors of Bordetella pertussis, the causative agent of whooping cough. CyaA is able to invade eukaryotic cells by a unique mechanism that consists in a calcium-dependent, direct translocation of the CyaA catalytic domain across the plasma membrane of the target cells. CyaA possesses a series of a glycine- and aspartate-rich nonapeptide repeats (residues 1006-1613) of the prototype GGXG(N/D)DX(L/I/F)X (where X represents any amino acid) that are characteristic of the RTX (repeat in toxin) family of bacterial cytolysins. These repeats are arranged in a tandem fashion and may fold into a characteristic parallel beta-helix or beta-roll motif that constitutes a novel type of calcium binding structure, as revealed by the three-dimensional structure of the Pseudomonas aeruginosa alkaline protease. Here we have characterized the structure-function relationships of various fragments from the CyaA RTX subdomain. Our results indicate that the RTX functional unit includes both the tandem repeated nonapeptide motifs and the adjacent polypeptide segments, which are essential for the folding and calcium responsiveness of the RTX module. Upon calcium binding to the RTX repeats, a conformational rearrangement of the adjacent non-RTX sequences may act as a critical molecular switch to trigger the CyaA entry into target cells.
Physical map of the Saccharomyces cerevisiae genome at 110-kilobase resolution. (1991)

A physical map of the Saccharomyces cerevisiae genome is presented. It was derived by mapping the sites for two restriction endonucleases, SfiI and NotI, each of which recognizes an 8-bp sequence. DNA-DNA hybridization probes for genetically mapped genes and probes that span particular SfiI and NotI sites were used to construct a map that contains 131 physical landmarks--32 chromosome ends, 61 SfiI sites and 38 NotI sites. These landmarks are distributed throughout the non-rDNA component of the yeast genome, which comprises 12.5 Mbp of DNA. The physical map suggests that those genes that can be detected and mapped by standard genetic methods are distributed rather uniformly over the full physical extent of the yeast genome. The map has immediate applications to the mapping of genes for which single-copy DNA-DNA hybridization probes are available.
Au@ZIF-8: CO Oxidation over Gold Nanoparticles Deposited to Metal−Organic Framework (2009)

Gold nanoparticles (NPs) were deposited to a zeolite-type metal-organic framework (MOF) by a simple solid grinding method. A catalyst, Au@ZIF-8, represents the first example of an active catalyst in CO oxidation by using a MOF as a novel support for noble metal NPs. The catalytic activity for CO oxidation is improved along with increasing Au loadings, and the highest catalytic activity is obtained for 5.0 wt % Au@ZIF-8, which presents half conversion of CO at approximately 170 degrees C. Gold NPs are close to being monodisperse and have no aggregation during catalytic reaction, and the catalytic activity is reproducible.