gebhart/patrepeval huggingface dataset:
Understanding nature's design for a nanosyringe (2004)

Synthetic and natural peptide assemblies can possess transport or conductance activity across biomembranes through the formation of nanopores. The fundamental mechanisms of membrane insertion necessary for antimicrobial or synthetic pore formation are poorly understood. We observe a lipid-assisted mechanism for passive insertion into a model membrane from molecular dynamics simulations. The assembly used in the study, a generic nanotube functionalized with hydrophilic termini, is assisted in crossing the membrane core by transleaflet lipid flips. Lipid tails occlude a purely hydrophobic nanotube. The observed insertion mechanism requirements for hydrophobic-hydrophilic matching have implications for the design of synthetic channels and antibiotics.
Translational coupling in Bacillus subtilis of a heterologous Bacillus subtilis-Escherichia coli gene fusion (1985)

Translational coupling was demonstrated in a gene fusion in which the promoter and the N-terminal region of the Bacillus subtilis subtilisin (aprA) gene were fused to a promoterless Tn9-derived chloramphenicol acetyltransferase (CAT; EC 2.3.1.28) gene. Expression of this gene fusion results in the production of a native-sized CAT product, whereas the Tn9-derived CAT gene is usually not translated from its own ribosome binding site in B. subtilis (D. S. Goldfarb, R. L. Rodriguez, and R. H. Doi, Proc. Natl. Acad. Sci. USA 79:5886-5890, 1982). A 178-base-pair deletion, which removed part of the signal peptide and the propeptide of the aprA gene and created a translational stop codon 230 base pairs upstream of the CAT gene ribosome binding site, reduced expression of the CAT gene. A BamHI 10-mer linker insertion into this deletion site, which restored the reading frame and simultaneously removed the translation stop codon, restored CAT gene expression. The data indicate that expression of the CAT gene was dependent on translation of the truncated aprA gene into the ribosome binding site of the CAT gene.
Dorsal root entry zone lesions to control central pain in paraplegics (1981)

✓ Thirteen patients with intractable long-term pain following spinal cord injury and paraplegia were treated with dorsal root entry zone lesions placed at the level just above the transection. Pain relief of 50% or more was achieved in 11 of the 13 patients, with follow-up periods ranging from 5 to 38 months. A previous report showed that central pain from brachial plexus avulsion could be relieved by dorsal root entry zone lesions, and this technique has been extended to the central pain phenomena associated with spinal trauma and paraplegia.
Compression in Video and Audio (1995)

From the Publisher:
This book recognises the wide applications of compression by treating the subject from first principles without assuming any particular background for the reader.
Transformation of mouse fibroblasts with the oncogenes H‐ras or trk is associated with pronounced changes in drug sensitivity and metabolism (1993)

Malignant activation of oncogenes ras or trk is implicated in a number of solid tumors and leukemias. We determined the chemosensitivity profile of wild-type mouse NIH-3T3 fibroblasts, and that of NIH-3T3 lines transformed by the H-ras (S2-721) and trk (106-632) oncogenes, against 11 different drugs from various classes. Differences in sensitivity were related to drug accumulation and metabolism. Both ras- and trk-transformed cell lines were less sensitive to cisplatin (CDDP) and doxorubicin (DXR) than the wild type. NIH-3T3 transformants expressing H-ras were less sensitive than those expressing trk or the wild type to the indoloquinone EO9, methotrexate and arabino-furanosylcytosine. No clear difference in sensitivity was observed for vincristine, VP-16, or the new cytidine analog 2',2'-difluoro-deoxycytidine. In both ras- and trk-transformed cell lines sensitivity to 5FU was increased moderately, but sensitivity to 5'deoxy-5-fluorouridine (5'dFUR) was increased markedly. Only the trk-transformed line NIH-3T3 was more sensitive to 2'deoxy-5-fluorouridine. Expression of P-glycoprotein was not different between the 3 cell lines but DXR accumulation in both mutants was decreased, indicating a non-P-glycoprotein-associated difference in sensitivity. Conversion of 5'dFUR to 5FU (catalyzed by pyrimidine nucleoside phosphorylases) was 5-10 times higher in both mutants than in the wild type. The activity of the phosphoribosyl-transferase (direct conversion of 5FU to FUMP) was comparable, but the rate of conversion of 5FU to fluorouridine (FUR) was lower in the wild type, as well as that of 5FU to FUMP via FUR. In contrast, the activity of thymidylate synthase, the target enzyme for fluoropyrimidines, was higher in the wild-type cells. The concentrations of both purine and pyrimidine nucleotides were lower in cells expressing trk. In conclusion, transformation of cells with the H-ras or trk oncogenes can markedly influence sensitivity to several drugs and affect normal metabolism and that of several anti-cancer agents.
<title>Polarization and edge effects in photolithographic masks using three-dimensional rigorous simulation</title> (1994)

The rigorous electromagnetic simulation program TEMPEST has been extended for analysis of three-dimensional problems, and is applied to study transmission through small contact holes and printability of 360 degree(s) phase quartz bump defects. REsults generated from the rigorous electromagnetic simulator TEMPEST can be fed into the simulator SPLAT for partial coherent imaging with arbitrary lens aberrations. Application of three-dimensional TEMPEST in small contact hole studies shows that transmission loss is about three times as much as the loss in space openings in 1X projection printing, and polarization effects can be more important than the orientation of a rectangular mask. The thin mask and scalar approximations are unacceptable as they predict no polarization effects and peak intensities that can be 2X larger than that predicted from TEMPEST. Also, 360 degree(s) phase quartz bump defects in chromeless phase-shifting masks do not produce intensity drop severe enough to cause undesired printing.
The string B-tree (1999)

We introduce a new text-indexing data structure, the String B-Tree , that can be seen as a link between some traditional external-memory and string-matching data structures. In a short phrase, it is a combination of B-trees and Patricia tries for internal-node indices that is made more effective by adding extra pointers to speed up search and update operations. Consequently, the String B-Tree overcomes the theoretical limitations of inverted files, B-trees, prefix B-trees, suffix arrays, compacted tries and suffix trees. String B-trees have the same worst-case performance as B-trees but they manage unbounded-length strings and perform much more powerful search operations such as the ones supported by suffix trees. String B-trees are also effective in main memory (RAM model) because they improve the online suffix tree search on a dynamic set of strings. They also can be successfully applied to database indexing and software duplication.
Tecnologia digital de informação e comunicação (TDIC): apropriação e uso pelos professores de serviço social (2019)

As Tecnologias Digitais de Informacao e Comunicacao (TDIC) permitem, hoje, ministrar uma aula de forma muito mais dinâmica, interativa e colaborativa do que no passado. Com os recursos atualmente disponiveis e possivel unir teoria e mundo vivido, colocar os alunos como participes da producao do conhecimento e agregar aos tradicionais recursos didaticos, os propiciados pelas TDIC. Este e um cenario ideal frente a um mundo cada vez mais digital, o qual tem proposto mudancas a Educacao e solicitado aos professores maior apropriacao e uso de tais tecnologias para os processos de ensino e aprendizagem. Frente a esta demanda, o artigo apresenta os resultados da pesquisa que buscou identificar as Tecnologias Digitais de Informacao e Comunicacao (TDIC) conhecidas pelos professores das graduacoes publicas presenciais em Servico Social no Estado do Parana, e os objetivos com os quais tem utilizado essas ferramentas em suas atividades de ensino. A pesquisa teve por base um questionario online aplicado em 2016, no qual foi utilizado o software LimeSurvey, e foi acessada por mais de 50% dos professores que compunham o universo da pesquisa. Os resultados apontam para um reduzido conhecimento sobre os possiveis recursos em TDIC, bem como uma apropriacao dessas tecnologias como “mais um recurso” para o ensino.
Association of prostate cancer risk with snps in regions containing androgen receptor binding sites captured by ChIP‐On‐chip analyses (2011)

The results to date provide novel statistical evidence suggesting an androgen-mediated mechanism by which some PCa associated SNPs act to influence PCa risk. However, these results are hypothesis generating and ultimately warrant testing through in-depth molecular analyses.
Discovery of a Novel and Potent Class of FabI-Directed Antibacterial Agents (2002)

Bacterial enoyl-acyl carrier protein (ACP) reductase (FabI) catalyzes the final step in each elongation cycle of bacterial fatty acid biosynthesis and is an attractive target for the development of new antibacterial agents. High-throughput screening of the Staphylococcus aureus FabI enzyme identified a novel, weak inhibitor with no detectable antibacterial activity against S. aureus. Iterative medicinal chemistry and X-ray crystal structure-based design led to the identification of compound 4 [(E)-N-methyl-N-(2-methyl-1H-indol-3-ylmethyl)-3-(7-oxo-5,6,7,8-tetrahydro-1,8-naphthyridin-3-yl)acrylamide], which is 350-fold more potent than the original lead compound obtained by high-throughput screening in the FabI inhibition assay. Compound 4 has exquisite antistaphylococci activity, achieving MICs at which 90% of isolates are inhibited more than 500 times lower than those of nine currently available antibiotics against a panel of multidrug-resistant strains of S. aureus and Staphylococcus epidermidis. Furthermore, compound 4 exhibits excellent in vivo efficacy in an S. aureus infection model in rats. Biochemical and genetic approaches have confirmed that the mode of antibacterial action of compound 4 and related compounds is via inhibition of FabI. Compound 4 also exhibits weak FabK inhibitory activity, which may explain its antibacterial activity against Streptococcus pneumoniae and Enterococcus faecalis, which depend on FabK and both FabK and FabI, respectively, for their enoyl-ACP reductase function. These results show that compound 4 is representative of a new, totally synthetic series of antibacterial agents that has the potential to provide novel alternatives for the treatment of S. aureus infections that are resistant to our present armory of antibiotics.
Early Detection and Prognosis of Ovarian Cancer Using Serum YKL-40 (2004)

YKL-40 may represent a novel marker for the detection of early-stage ovarian cancer. YKL-40 levels in early-stage patients may also predict disease recurrence and survival. The utility of YKL-40 in detection of early-stage ovarian cancer deserves further investigation.
Use of hypomethylating agents in myelodysplastic syndromes. (2007)

Aberrant DNA methylation is one of the molecular hallmarks of cancer and leukemia. By repressing gene expression, it is considered a functional equivalent to the physical inactivation of tumor suppressor genes by deletions or mutations. To clinically exploit this process, compounds with DNA hypomethylating properties have been evaluated both in the laboratory and the clinic. Two such agents, 5-azacytidine and 5-aza-2'-deoxycytidine, are currently approved by the US Food and Drug Administration for the treatment of patients with myelodysplastic syndromes. Ongoing studies are evaluating alternative dosing schedules for these drugs and the activity and safety of this class of agent in combination with histone deacetylase inhibitors. Here we summarize the experience of hypomethylating agents in myelodysplastic syndromes.
Peptide Ligands of pp60c-src SH2 Domains:  A Thermodynamic and Structural Study (1997)

Thermodynamic measurements, structural determinations, and molecular computations were applied to a series of peptide ligands of the pp60(c-src) SH2 domain in an attempt to understand the critical binding determinants for this class of molecules. Isothermal titration calorimetry (ITC) measurements were combined with structural data derived from X-ray crystallographic studies on 12 peptide-SH2 domain complexes. The peptide ligands studied fall into two general classes: (1) dipeptides of the general framework N-acetylphosphotyrosine (or phosphotyrosine replacement)-Glu or methionine (or S-methylcysteine)-X, where X represents a hydrophobic amine, and (2) tetra- or pentapeptides of the general framework N-acetylphosphotyrosine-Glu-Glu-Ile-X, where X represents either Glu, Gln, or NH2. Dipeptide analogs which featured X as either hexanolamine or heptanolamine were able to pick up new hydrogen bonds involving their hydroxyl groups within a predominantly lipophilic surface cavity. However, due to internal strain as well as the solvent accessibility of the new hydrogen bonds formed, no net increase in binding affinity was observed. Phosphatase-resistant benzylmalonate and alpha,alpha-difluorobenzyl phosphonate analogs of phosphotyrosine retained some binding affinity for the pp60(c-src) SH2 domain but caused local structural perturbations in the phosphotyrosine-binding site. In the case where a reversible covalent thiohemiacetal was formed between a formylated phosphotyrosine analog and the thiol side chain of Cys-188, deltaS was 25.6 cal/(mol K) lower than for the nonformylated phosphotyrosine parent. Normal mode calculations show that the dramatic decrease in entropy observed for the covalent thiohemiacetal complex is due to the inability of the phosphotyrosine moiety to transform lost rotational and translational degrees of freedom into new vibrational modes.
Perforin and interferon-γ activities independently control tumor initiation, growth, and metastasis (2001)

Perforin (pfp) and interferon-gamma (IFN-gamma) together in C57BL/6 (B6) and BALB/c mouse strains provided optimal protection in 3 separate tumor models controlled by innate immunity. Using experimental (B6, RM-1 prostate carcinoma) and spontaneous (BALB/c, DA3 mammary carcinoma) models of metastatic cancer, mice deficient in both pfp and IFN-gamma were significantly less proficient than pfp- or IFN-gamma-deficient mice in preventing metastasis of tumor cells to the lung. Pfp and IFN-gamma-deficient mice were as susceptible as mice depleted of natural killer (NK) cells in both tumor metastasis models, and IFN-gamma appeared to play an early role in protection from metastasis. Previous experiments in a model of fibrosarcoma induced by the chemical carcinogen methylcholanthrene indicated an important role for NK1.1(+) T cells. Herein, both pfp and IFN-gamma played critical and independent roles in providing the host with protection equivalent to that mediated by NK1.1(+) T cells. Further analysis demonstrated that IFN-gamma, but not pfp, controlled the growth rate of sarcomas arising in these mice. Thus, this is the first study to demonstrate that host IFN-gamma and direct cytotoxicity mediated by cytotoxic lymphocytes expressing pfp independently contribute antitumor effector functions that together control the initiation, growth, and spread of tumors in mice.
Mechanism Inspired Development of Rationally Designed Dihydrofolate Reductase Inhibitors as Anticancer Agents (2012)

On the basis of structural analysis of dihydrofolate reductase (DHFR) (cocrystallized separately with NADPH, dihydrofolate and NADPH, trimethoprim), compounds 2 and 3 were optimized for inhibition of DHFR. Appreciable tumor growth inhibitory activities of compounds 2 and 3 over 60 human tumor cell lines were recorded. Combination of syringaldehyde and indole moieties in these two compounds was rationalized by the synthesis of compounds 4-7, 10, and 11, which were found to have less tumor growth inhibitory activities than compounds 2 and 3. Further, UV-vis and NMR spectral investigations showed significant interactions of compounds 2 and 3 with DHFR and inhibition of its catalytic activity was observed in the presence of these compounds. Therefore, modification of trimethoprim, an antibacterial drug with no tumor growth inhibition, led to the development of compounds 2 and 3 having appreciable anticancer activities that seem to be due to inhibition of DHFR.
Direct Sequencing of PCR Products with DNA-Binding Proteins (2003)

The polymerase chain reaction (PCR) has become widely established as a powerful core molecular biology technique because of its ability of produce large amounts of specific target DNA from limited template sources (). Numerous applications based on the PCR have also been developed, including site-directed mutagenesis, in vitro expression, and nucleotide sequencing (,). The combination of PCR amplification and direct sequencing of products is a highly desirable procedure that, in many cases, obviates the need for complex and time consuming cloning protocols (). However, there appears to be no one universally accepted method for direct PCR sequencing ().
Structural Analysis of Plant Genes (1986)

Crop loss due to soil salinization is an increasing threat to agriculture worldwide. This review provides an overview of cellular and physiological mechanisms in plant responses to salt. We place cellular responses in a time- and tissue-dependent context ...Read More
Neural net backlash compensation with Hebbian tuning by dynamic inversion (2002)

A neural network compensation scheme is presented for the class of nonlinear systems with backlash nonlinearity. The compensator uses the backstepping technique with neural networks (NN) for inverting the backlash nonlinearity in the feedforward path. Instead of a derivative, which cannot be implemented, a filtered derivative is used. Full rigorous stability proofs are given using filtered derivative. Compared with adaptive backstepping control schemes, we do not require the unknown parameters to be linear parametrizable. No regression matrices are needed. The technique provides a general procedure for using NN to determine the dynamic preinverse of an invertible dynamical system. A modified Hebbian algorithm is presented for NN tuning which yields a stable closed-loop system. Using this method yields a relatively simple adaptation structure and offers computational advantages over gradient descent based algorithms.
Molecular mechanisms responsible for the drug-induced posttranscriptional modulation of ribonucleotide reductase levels in a hydroxyurea-resistant mouse L cell line (1988)

Ribonucleotide reductase, which catalyzes the formation of deoxyribonucleotides from ribonucleoside diphosphate precursors, is the rate-limiting enzyme in DNA synthesis. The enzyme consists of two nonidentical subunits called M1 and M2, both of which are required for activity. Hydroxyurea, a specific inhibitor of DNA synthesis, acts by destroying the unique tyrosyl free radical of protein M2. Previously, we have described a mouse L cell line which exhibited a stable resistance to high concentrations of hydroxyurea. This mutant cell line contains elevated quantities of both proteins M1 and M2 as a result of corresponding increases in the levels of mRNAs for both subunits. Interestingly, both M1 and M2 protein levels were further elevated when mutant cells were cultured in the presence of hydroxyurea, and this elevation was not accompanied by increases in their corresponding mRNAs. These results indicated that hydroxyurea can modulate ribonucleotide reductase expression posttranscriptionally. In this report, we show that the level of both subunits of ribonucleotide reductase responds to hydroxyurea in a drug concentration dependent manner. Furthermore, results from kinetic studies indicate that protein M2 levels rise much more rapidly than protein M1. Pulse-chase experiments indicated that the half-lives of both the M1 and M2 polypeptides are increased by approximately 2-fold when the mutant cells are cultured in the presence of hydroxyurea. We also present evidence indicating that exposure of these cells to hydroxyurea leads to a relatively slow but specific increase in the rate of biosynthesis of both proteins M1 and M2, as assayed by pulse labeling.(ABSTRACT TRUNCATED AT 250 WORDS)
New steroids by Simmons-Smith methylenation and subsequent rearrangement (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNew steroids by Simmons-Smith methylenation and subsequent rearrangementGuenter Neef, Gerhard Cleve, Eckhard Ottow, Arne Seeger, and Rudolf WiechertCite this: J. Org. Chem. 1987, 52, 18, 4143–4146Publication Date (Print):September 1, 1987Publication History Published online1 May 2002Published inissue 1 September 1987https://pubs.acs.org/doi/10.1021/jo00227a045https://doi.org/10.1021/jo00227a045research-articleACS PublicationsRequest reuse permissionsArticle Views420Altmetric-Citations30LEARN 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
Photoluminescence and photoconductivity measurements on band-edge offsets in strained molecular-beam-epitaxy-grownInxGa1−xAs/GaAs quantum wells (1988)

Structure has been observed in the photoluminescence and photoconductivity spectra of ${\mathrm{In}}_{\mathrm{x}}$${\mathrm{Ga}}_{1\mathrm{\ensuremath{-}}\mathrm{x}}$As/GaAs (x\ensuremath{\le}1) strained quantum wells grown by molecular-beam epitaxy onto GaAs(001)-oriented substrates. Features in the spectra at energies larger than the energy gap of ${\mathrm{In}}_{\mathrm{x}}$${\mathrm{Ga}}_{1\mathrm{\ensuremath{-}}\mathrm{x}}$As are interpreted as the allowed excitonic transitions between electron and hole subbands (including the strain-split-off valence band) in ${\mathrm{In}}_{\mathrm{x}}$${\mathrm{Ga}}_{1\mathrm{\ensuremath{-}}\mathrm{x}}$As. The spectra were analyzed with the conduction-band offset and the energy gap of ${\mathrm{In}}_{\mathrm{x}}$${\mathrm{Ga}}_{1\mathrm{\ensuremath{-}}\mathrm{x}}$As as adjustable parameters. No strain relaxation in quantum wells with thickness smaller than the critical one was observed. The strain-split-off valence subband in ${\mathrm{In}}_{\mathrm{x}}$${\mathrm{Ga}}_{1\mathrm{\ensuremath{-}}\mathrm{x}}$As is found to be below the valence band of unstrained GaAs. The ratio of the conduction-band offset to the energy-gap discontinuity was determined to be 0.83\ifmmode\pm\else\textpm\fi{}0.06.