gebhart/patrepeval huggingface dataset:
Screening of Natural Products and Approved Oncology Drug Libraries for Activity against Clostridioides difficile (2020)

Clostridioides difficile is the most common cause of healthcare-associated diarrhea. Infection of the gastrointestinal tract with this Gram-positive, obligate anaerobe can lead to potentially life-threatening conditions in the antibiotic-treated populace. New therapeutics are urgently needed to treat this infection and prevent its recurrence. Here, we screened two libraries from the National Cancer Institute, namely, the natural product set III library (117 compounds) and the approved oncology drugs set V library (114 compounds), against C. difficile. In the two libraries screened, 17 compounds from the natural product set III library and 7 compounds from the approved oncology drugs set V library were found to exhibit anticlostridial activity. The most potent FDA-approved drugs (mitomycin C and mithramycin A) and a promising natural product (aureomycin) were further screened against 20 clinical isolates of C. difficile. The anticancer drugs, mitomycin C (MIC<sub>50</sub> = 0.25 μg/ml) and mithramycin A (MIC<sub>50</sub> = 0.015 μg/ml), and the naturally derived tetracycline derivative, aureomycin (MIC<sub>50</sub> = 0.06 μg/ml), exhibited potent activity against C. difficile strains. Mithramycin A and aureomycin were further found to inhibit toxin production by this pathogen. Given their efficacy, these compounds can provide a quick supplement to current treatment to address the unmet needs in treating C. difficile infection and preventing its recurrence.
Dihedral angle based dimensionality reduction for protein structural comparison (2005)

Structural comparison of proteins is considered as one of the highly focused research areas in the field of bioinformatics. Structural similarity estimation techniques using singular geometric parameters derived from spatial coordinates of protein structural atoms have been reported previously, but it is also ascertained that a single geometric parameter based structural estimation can result in misconstrued classification and functional interpretation. In this paper we propose a novel geometric parameters based comparison protocol that uses previously unexplored pair of dihedral angles NC/sub a/NC/sub a/ and NCNC for similarity search. An orthonormal transformation is employed on the two-dimensional distribution for feature extraction and selective feature-space is represented in an indexing schema later used for similarity calibration. The results demonstrate the success of this dimensionality reduction based similarity measure in performing a rapid and length-independent similarity analysis of the protein structures.
A lateral-resonant-tunneling universal quantum-dot cell (1993)

A lateral-resonant-tunneling quantum-dot cell is described which is configurable to span the complete range of three-input functions. The cell area could be of the order of 0.1 mu m2. This cell could enable large, edge-fed, cellular cascade arrays. These arrays could perform general logic functions.
Top-edge profile control for SU-8 structural photoresist (2004)

Profile control for SU-8 ultrathick photoresist has been examined specifically with respect to a "T-topping" phenomenon observed at the top edge. It has been confirmed that filtering ultraviolet (UV) radiation below 350 nm is successful in correcting this type of geometric defect. The effectiveness of a doped glass filter (Hoya UV-34) has been verified, and an alternative approach using a vapor-deposited thin-film coating has been presented. The thin-film filter demonstrates equal success in reducing the T-topping defect. This alternative approach furthermore offers advantages related to cost, design flexibility, robustness, and environmental impact. Modifying exposure dose and pre-bake temperature without any filter was observed to have minimal impact.
Chemical production and characterisation of activated carbon from waste 'coffee grounds' (2013)

Activated carbon was prepared from grounds-coffee in this study. Experimental results reveal that for the ratio (0, 1 : 0, 3) of coffee grounds to activating agents ( ZnCl2,H3PO4 ) has not noteworthy influence. The rise temperature and carbonisation time respectively, in the interval of 500–700°C and 15–60 minutes have a considerable impact on the adsorptive capacities of the final product. However, this improvement increases the amount of ash. The chemical studies show that the activated carbon samples contain large quantities of mineral ions, mostly calcium, sulphate and phosphate ions. The adsorption tests, attest of the suitability of the product use in the wastewater treatments.
Single crystal growth of Al<sub>13</sub>Co<sub>4</sub> and Al<sub>13</sub>Fe<sub>4</sub> from Al‐rich solutions by the Czochralski method (2008)

Abstract Czochralski growth of large metallic alloy single crystals of Al 13 Co 4 and Al 13 Fe 4 from Al‐rich solutions has been demonstrated for the first time. A detailed description of all decisive steps of the growth procedure is given with particular emphasis to seeding from a native phase as well as spontaneous nucleation if no seed crystal from a preceding experiment is available. Czochralski growth in a high‐temperature solution system requires much lower pulling rates compared to typical growth experiments from the melt and a time‐dependent temperature program to compensate the change of the liquidus temperature that results from the permanently increasing Al content of the liquid phase. With a given amount of the initial melt, the size of the Al 13 Co 4 crystals is limited by the rather narrow temperature range of the Al 13 Co 4 primary crystallization window, followed by Al 9 Co 2 phase crystallization. In the Al‐Fe system, despite the huge temperature range of equilibrium between Al 13 Fe 4 and its Al‐rich melt, Czochralski growth of Al 13 Fe 4 is restricted to higher temperatures due to the limited solubility that leads to mother liquid inclusions even at extremely low pulling rates. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Interactions of a Periplasmic Binding Protein with a Tetradentate Siderophore Mimic (2013)

Iron-bound structure: The ferric complex of a tetradentate siderophore mimic was synthesized and co-crystallized with the periplasmic binding protein CeuE of Campylobacter jejuni. In addition to electrostatic and hydrogen-bonding interactions between the binding pocket and the substrate, the structure showed direct coordination of two amino acid side chains to the Fe(III) center (orange, see figure).
Time series forecasting using neural networks vs. Box- Jenkins methodology (1991)

We discuss the results of a comparative study of the performance of neural networks and conventional methods in forecasting time series. Our work was initially inspired by previously published works that yielded inconsistent results about comparative performance. We have experimented with three time series of different complexity using different feed forward, backpropagation neural network models and the standard Box-Jenkins model. Our experiments demonstrate that for time series with long memory, both methods produced comparable results. However, for series with short memory, neural networks outper formed the Box-Jenkins model. We note that some of the comparable results arise since the neural network and time series model appear to be functionally similar models. We have found that for time series of different complexities there are optimal neural network topologies and parameters that enable them to learn more efficiently. Our initial conclusions are that neural networks are robust and provide good long-term forecasting. They are also parsimonious in their data requirements. Neural networks represent a promising alternative for forecasting, but there are problems deter mining the optimal topology and parameters for efficient learning.
Novel Technique for Measuring the Index Profile of Optical Fibers (1976)

A novel technique for measuring the refractive index profile of optical fibers is demonstrated, which offers substantial advantages over alternative methods. The method consists of illuminating a small area of the fiber core and measuring the total transmitted power. The transmission of leaky modes is accounted for in the manner reported previously by other authors. The index profiles of germanium-doped fibers obtained by this technique are compared to interferometric measurements. The resolution is shown to be limited by wave optics effects to about λ <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">o</inf> (4n√2Δ) <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−1</sup> , where Δ ≡ Δn/n. The distortion of the index profile as the wavelength varies and wave-optics effects are investigated.
Adaptive template-matching method for recognition of low-resolution license number (2010)

In this paper, we propose an adaptive template-matching method to recognize of low-resolution license number. The first step is to extract license plate from low-resolution image by manual. The license plate is divided into several blocks, and every block corresponds to a license character. Subsequently, we estimate the adaptive filter via pesudoinverse operation, and it is applied to template to generate filtered template which is similar to divided character. Eventually, the filtered template and the similarity measurement between the license character and the template are obtained. According to the similarity measurement, the proposed method can identify the license number. Moreover, our method outputs several possible resultants of license number recognition, it is helpful to police in image forensic. The advantage of our approach is that training process is unnecessary. The quantized rank histogram is measured to evaluate the recognition performance. The experiment results demonstrate that the proposed method is capable of coping with license number recognition in low-resolution images.
Development of Structure−Lipid Bilayer Permeability Relationships for Peptide-like Small Organic Molecules (2008)

Computational methods to estimate passive membrane permeability coefficients of organic molecules, including peptides, would be valuable in understanding various biological processes associated with molecular transport across cell membranes and in reducing the time required for screening developability properties of new drug candidates. This study explores the suitability of fragment-based linear free energy relationships (LFERs) to predict lipid bilayer permeability coefficients and decadiene/water partition coefficients of a set of 47 model permeants. The inclusion of mono-, di-, and tripeptides comprised of glycine, alanine, and sarcosine residues in the database presented added challenges due to the apparent lack of independence of the contribution of the backbone amide residue in peptides to the free energy of transfer (Delta(Delta G degrees ) -CONH-) from water to organic solvents or to the bilayer barrier domain. In order to elucidate the impact of neighboring group effects on Delta(Delta G degrees ) -CONH-, a series of RGZ glycine (G)-containing peptides having an additional -NHCH 2CO- residue compared to their RZ counterparts were synthesized, where R = acetyl (Ac-), 4-carboxymethylphenyl acetyl (CMPA-), or 4-methylphenyl acetyl (MPA-), and Z = -OH, -OMe, -NHMe, or -NMe 2. While variations in R had no significant impact on Delta(Delta G degrees ) -Gly-, significant effects of neighboring ( i + 1) Z substituents at the C-terminus were revealed both in studies of the relative transport of RGZ/RZ compound pairs across DOPC bilayers and partitioning between water and 1,9-decadiene (a bulk solvent with a similar chemical selectivity to the barrier domain of DOPC/eggPC bilayers). The proximity effects decline when the bulk solvent used in partitioning studies is 1-octanol, suggesting a possible role for intramolecular hydrogen bonding in the observed nonadditivity of Delta(Delta G degrees ) -CONH-. A new LFER for predicting decadiene/water partition coefficients was developed by including the contributions of polar fragments, total nonpolar surface area of nonpolar fragments, and correction factors to account for the effects of i + 1 substituents in peptides on the group contribution of the peptide backbone amide bond to the free energy of transfer. This LFER could be used to predict lipid bilayer permeability coefficients by including an additional term to account for the added influence of molecular size on bilayer permeability.
Identification of Ligand Analogues that Control c-di-GMP Riboswitches (2012)

Riboswitches for the bacterial second messenger c-di-GMP control the expression of genes involved in numerous cellular processes such as virulence, competence, biofilm formation, and flagella synthesis. Therefore, the two known c-di-GMP riboswitch classes represent promising targets for developing novel modulators of bacterial physiology. Here, we examine the binding characteristics of circular and linear c-di-GMP analogues for representatives of both class I and II c-di-GMP riboswitches derived from the pathogenic bacterium Vibrio choleae (class I) and Clostridium difficile (class II). Some compounds exhibit values for apparent dissociation constant (K(D)) below 1 μM and associate with riboswitch RNAs during transcription with a speed that is sufficient to influence riboswitch function. These findings are consistent with the published structural models for these riboswitches and suggest that large modifications at various positions on the ligand can be made to create novel compounds that target c-di-GMP riboswitches. Moreover, we demonstrate the potential of an engineered allosteric ribozyme for the rapid screening of chemical libraries for compounds that bind c-di-GMP riboswitches.
The impact of carboxyalkylation of branched polyethylenimine on effectiveness in small interfering RNA delivery (2010)

Carboxyalkylation of branched 25 kDa PEI resulted in polymers with strongly reduced cytotoxicity and improved silencing efficacy. Mechanistic studies demonstrated that the presence of a surplus of free carboxyalkylated polymer is responsible for the improved siRNA delivery.
Monoclonal Antibodies to Substance P: Production, Characterization of Their Fine Specificities, and Use in Immunocytochemistry (1987)

Five hybrid clones secreting antibodies to the neuropeptide substance P have been obtained by somatic cell fusion of mouse myeloma cells with splenocytes from immunized mice of the Biozzi strain. To perform rapid and sensitive screening tests as well as to study the fine specificities of each monoclonal antibody, we developed a new enzyme immunoassay of substance P using acetylcholinesterase as label. All five monoclonal antibodies were directed to the C-terminal pentapeptide of substance P, especially to the Phe7 residue. They cross-reacted with neurokinin A and to some extent with neurokinin B but not with other nontachykinin mammalian peptides. One monoclonal antibody (SP 14) was used for immunocytochemical experiments in the rat spinal cord and spinal ganglion, both at the light and electron microscopic levels. A strong specific neurokinin-like immunoreactivity was observed in cell bodies, nerve fibers, and terminals, with a very low background staining. Finally, the affinities of several analogues of substance P for SP 14 monoclonal antibody were shown to be correlated with their biological activities, as measured by their hypotensive effects in vivo. These findings suggested a strong structural resemblance between the combining site of the antibody and that of the physiological substance P receptor.
Phylogenetic Diversity and Molecular Detection of Bacteria in Gull Feces (2008)

In spite of increasing public health concerns about the potential risks associated with swimming in waters contaminated with waterfowl feces, little is known about the composition of the gut microbial community of aquatic birds. To address this, a gull 16S rRNA gene clone library was developed and analyzed to determine the identities of fecal bacteria. Analysis of 282 16S rRNA gene clones demonstrated that the gull gut bacterial community is mostly composed of populations closely related to Bacilli (37%), Clostridia (17%), Gammaproteobacteria (11%), and Bacteriodetes (1%). Interestingly, a considerable number of sequences (i.e., 26%) were closely related to Catellicoccus marimammalium, a gram-positive, catalase-negative bacterium. To determine the occurrence of C. marimammalium in waterfowl, species-specific 16S rRNA gene PCR and real-time assays were developed and used to test fecal DNA extracts from different bird (n = 13) and mammal (n = 26) species. The results showed that both assays were specific to gull fecal DNA and that C. marimammalium was present in gull fecal samples collected from the five locations in North America (California, Georgia, Ohio, Wisconsin, and Toronto, Canada) tested. Additionally, 48 DNA extracts from waters collected from six sites in southern California, Great Lakes in Michigan, Lake Erie in Ohio, and Lake Ontario in Canada presumed to be impacted with gull feces were positive by the C. marimammalium assay. Due to the widespread presence of this species in gulls and environmental waters contaminated with gull feces, targeting this bacterial species might be useful for detecting gull fecal contamination in waterfowl-impacted waters.
Temporally and Regionally Disparate Differences in Plasmin Activity by Tranexamic Acid (2010)

Using a large animal model and in vivo microdialysis measurements of PLact, the unique findings from this study were 2-fold. First, TXA induced temporally distinct PLact profiles within the plasma and selected interstitial compartments. Second, TXA caused region-specific changes in PLact profiles. These temporal and regional differences in the effects of TXA may have important therapeutic considerations when managing fibrinolysis in the perioperative period.
Desenvolvimento de brinquedo de playground com referência no desenho animado “Doki” (2016)

No presente trabalho, visou-se desenvolver um brinquedo do tipo playground composto por elementos simbolicos presentes no desenho animado “Doki” e solucoes tecnicas utilizadas na producao pela empresa Xalingo S.A, uma das maiores empresas de jogos e brinquedos do pais. O referencial teorico abrangeu areas do conhecimento relativas ao design, semiotica, ergonomia aplicada a um produto infantil e processo industrial, tendo em vista as necessidades do projeto e sua adequacao para a possivel producao. A metodologia utilizada foi a de Lobach, complementada por Baxter, com o proposito de reunir informacoes para gerar melhores alternativas. Utilizando a linguagem do design e os elementos simbolicos presentes no desenho animado “Doki”, foi possivel atingir os objetivos propostos, principalmente quanto aos requisitos semioticos e ergonomicos, de forma e material. O resultado foi um playground atrativo e inovador que propicia o desenvolvimento infantil, a sociabilidade e a interacao durante a brincadeira.
[Therapeutic effect on murine asthma with sublingual use of Dermatophagoides farinae/chitosan nanoparticle vaccine]. (2011)

Dermatophagoides farinae (Der f)/chitosan nanoparticle vaccine has therapeutic effect on murine asthma.
Gauging for Position - a Computer Simulation (1977)

In manufacturing industry the checking of a set of grouped features for position on a component is a common inspection operation involving, usually, the use of an appropriately designed solid receiver gauge. This paper describes the development of a computer simulation of a receiver gauge which can be used to check the position of any group of 'n' holes and, in the case of rejection, develop a rework strategy. The programme can cater for inspection of grouped features where the specification is regardless of feature size (RFS) or has been limited by the use of the maximum material modifier (MMC). Two case studies illustrating the use of this simulated gauge are presented and the results discussed.
Inactivation of a<i>Serpula (Treponema) hyodysenteriae</i>hemolysin gene by homologous recombination: Importance of this hemolysin in pathogenesis of<i>S. hyodysenteriae</i>in mice (1992)

The role of Serpula hyodysenteriae hemolysin in the pathogenesis of swine dysentery was studied. The inactivation of a gene, tly, encoding a hemolysin, and the virulence of a tly− mutant in mice is reported. We obtained chromosomal integration of the distrupted tly gene via homologous recombination in a S. hyodysenteriae wild-type strain following electroporation. A plasmid construct, in which the tly gene was disrupted by a kanamycin-resistance gene, was used for the electroporation. The mutants obtained had reduced hemolysis indicating that the tly encoded hemolysin is not the only hemolysin produced by S. hyodysenteriae. Mice infected with the tly− mutant had fewer cecal lesions than mice infected with the wild-type S. hyodysenteriae. From these results it was concluded that the tly encoded hemolysin may be an important virulence factor, but not the only one. It was demonstrated that gene transfer to spirochaetes can be achieved through electroporation.
A Low Voltage Low 1/f Noise CMOS Bandgap Reference (2005)

For a low voltage bandgap reference design, there is a tradeoff between the supply voltage and the performance of the bandgap reference in terms of untrimmed accuracy and 1/f noise performance. In this paper, the application of chopper stabilizing technique is proposed to address this tradeoff. Over five times of improvement in untrimmed accuracy and 1/f noise performance were demonstrated through a low voltage bandgap reference fabricated in a 0.8 /spl mu/m CMOS process.
A fully integrated photolithography workcell (2003)

A photolithography workcell that allows all operations on a wafer lot, from resist coat through to inspection, to be executed by a single operator is described. The workcells are based on 5* steppers and in-line coat and develop tracks. Operation of the cell is heavily based on automation software, with a single operator-interface terminal to all subequipment and process control databases. A key benefit of the workcell is the environment in which a single operator has ownership for all aspects of the photolithographic process. Feedback on process quality is available by inspection 12 min after a lot has started. Key results from the workcell are: (1) rework rate reduced from 11% to less than 2%; (2) feedback time on a lot reduced from 8 h to 15 min; and (3) average active time of work-in-progress in the photo area reduced from 24 h to 8 h.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Relative activation energies and frequency factors for competing fragmentations of oxetane molecular ions (1975)

Abstract A pair of substituted oxetane mass spectral decompositions exhibit regioselective ring cracking, and single and double hydrogen rearrangement cleavages involving substituent methyl groups. Analysis of ion abundances as a function of ionizing energy provides estimates of relative activation energies and frequency factors for these fragmentations.
Single-electron spectroscopy in a coupled triple-dot system: Role of interdot electron-electron interactions (2000)

We report on low-temperature single electron tunneling measurements of a coupled triple-dot system with tunable gate fabricated on a silicon-on-insulator structure. Conductance peak positions have been measured as a function of the interdot tunneling constant. We observe one peak at small values of the tunneling constant, and, as the tunneling constant increases, we find that this peak splits into several peaks with uneven spacings. This observed behavior of the conductance peak positions has been modeled by a three-site extended Hubbard model with interdot electron-electron interactions.