gebhart/patrepeval huggingface dataset:
Orientations of Liquid Crystals on Mechanically Rubbed Films of Bovine Serum Albumin: A Possible Substrate for Biomolecular Assays Based on Liquid Crystals (2000)

We report the uniform planar anchoring of thermotropic liquid crystals on films of bovine serum albumin (BSA) covalently immobilized on the surface of glass microscope slides and mechanically rubbed using a cloth. The azimuthal orientations of the liquid crystals were measured to be parallel to the direction of rubbing. Following immersion and removal of these rubbed films of BSA from aqueous solutions containing either BSA, fibrinogen, lysozyme, anti-FITC immunoglobulin G (IgG), or antistreptavidin IgG, we measured liquid crystals placed onto these surfaces to largely retain their uniform alignment. In contrast, following immersion of a rubbed film of BSA into an aqueous solution of anti-BSA IgG, we observed liquid crystals on these surfaces to assume nonuniform orientations. We conclude that specific binding of anti-BSA IgG to the film of rubbed BSA erased anisotropy induced within the film of BSA by rubbing. This result suggests that the spatial scale of anisotropy within the rubbed film of BSA is comparable to or smaller than the size of the IgG molecule. Because the anisotropy within a rubbed film of a protein can be erased by specific binding of a second protein, we believe these types of substrates (rubbed films of proteins) have the potential to be useful in a variety of label-free biomolecular assays where specific binding of a target species to its ligand can be imaged through observation of the optical appearance of liquid crystal placed onto the surface.
Determination of Sensory Thresholds of Selected Calcium Salts and Formulation of Calcium‐fortified Pocket‐type Flat Bread (2005)

ABSTRACT: Pita bread loaves were prepared from flours fortified with calcium carbonate, calcium sulfate, and tricalcium dicitrate at 8 ascending levels to provide ranges of 800 to 2500, 700 to 1500, and 400 to 2000 mg of added Ca/100 g flour, respectively. The detection thresholds of calcium salts in pita bread were determined by the 3‐alter‐native forced choice (3‐AFC) test and construction of dose‐response curves. Detection thresholds determined by calculating geometric mean of individual best estimate thresholds, using criterion of 50%‐above‐chance and probit analysis of 3‐AFC data, were in the middle region of calcium concentrations. Analysis of dose‐response curves yielded values for thresholds outside the range of surveyed calcium concentrations. The detection threshold of CaSO 4 (2724 mg/100 g) in pita bread was significantly higher (P &lt; 0.01) than those of calcium carbonate (1984 mg/100 g) and tricalcium dicitrate (2132 mg/100 g). Calcium‐fortified pita bread was similar ( P &lt; 0.01 ) to its regular counterpart when formulated to contain 1254.6, 1772.5, or 1155 mg/100 g of CaCO 3 , CaSO 4 , or tricalcium dicitrate, respectively. At the indicated levels of fortification, calcium‐fortified pita bread is expected to provide between 61% and 126.5% of the recommended daily intake for calcium for Middle Eastern populations.
Characterization of the apurinic endonuclease activity of Drosophila Rrp1 (1993)

Drosophila Rrp1 (Recombination repair protein 1) belongs to a family of DNA repair nucleases that includes Escherichia coli exonuclease III, Streptococcus pneumoniae exonuclease A, bovine BAP, mouse APEX endonuclease, and human APE. Within a 252 amino acid region, colinear homology is shared between all members. Rrp1 is unique in that it includes a 427 amino acid N-terminal region not related to any known sequence. The protein copurifies with an apurinic endonuclease and a double-stranded DNA 3'-exonuclease. In this study, a 5'-end-labeled 37 base pair oligonucleotide substrate containing a single apurinic site was used to characterize the endonuclease activity of Rrp1. This substrate is utilized efficiently by Rrp1: the specific activity observed is 1 x 10(5) units/mg. The abasic double-stranded DNA oligonucleotide is cleaved only at the abasic site to create a single-strand break. Strand breaks are not detected in the complementary strand, in the single-stranded DNA oligonucleotide, or in the base-paired control substrate. After endonucleolytic cleavage at the abasic site, exonucleolytic processing at the nick is slow and requires a molar excess of Rrp1, while exonuclease III degrades the nicked substrate more efficiently. The Rrp1 cleavage product comigrates with a DNaseI cleavage product, and the newly formed terminus supports DNA synthesis by DNA polymerase. Therefore, Rrp1 cleaves the phosphodiester backbone at one position 5' to the apurinic site and leaves a 3'-hydroxyl terminus. Rrp1 is a class II apurinic endonuclease and is likely to be important in DNA repair in Drosophila.
Boron Dipyridylmethene (DIPYR) Dyes: Shedding Light on Pyridine-Based Chromophores (2017)

Boron dipyrromethene (BODIPY) derivatives have found widespread utility as chromophores in fluorescent applications, but little is known about the photophysical properties of pyridine-based BODIPY analogues, dipyridylmethene dyes. Indeed, it has been reported that boron difluoride dipyridylmethene (DIPYR) is nonemissive, and that derivatives of DIPYR have modest, if any, luminescence. In this report, we explore this little-touched area of chemical space and investigate the photophysical properties of three simple DIPYR dyes: boron dipyridylmethene, boron diquinolylmethene, and boron diisoquinolylmethene. The three dyes strongly absorb in the blue-green part of the spectrum (λ<sub>em</sub> = 450-520 nm, ε = 2.9-11 × 10<sup>4</sup> M<sup>-1</sup> cm<sup>-1</sup>) and display green fluorescence with high quantum yields (Φ<sub>PL</sub> = 0.2, 0.8, and 0.8, respectively). Key photophysical properties in these systems were evaluated using a combination of TD-DFT and extended multiconfigurational quasidegenerate second-order perturbation theory (XMCQDPT2) methods and compared to experimental results, revealing that high quantum yields of the quinoline and isoquinoline derivatives are a result of the relative reordering of S<sub>1</sub> and T<sub>2</sub> state energies upon benzannulation of the parent structure. The intense absorption and high emission efficiency of the benzannulated derivatives make these compounds an intriguing class of dyes for further derivatization.
Enhanced production ofd(−)-lactic acid by mutants ofLactobacillus delbrueckii ATCC 9649 (1992)

Chemical mutagenesis with ethyl methanesulfonate (EMS) was used to develop strains ofLactobacillus delbrueckii (ATCC 9649) that tolerated increased lactic acid concentrations while continuously producing the acid. Three mutants (DP2, DP3 and DP4) were compared with wild-typeL. delbrueckii by standing fermentations with different glucose concentrations. All three mutants produced higher levels of lactic acid than the wild-type. In pH-controlled (pH 6.0) stirred-tank-batch fermentations, mutant DP3 in 12% glucose, 1% yeast extract/mineral salt/oleic acid medium produced lactic acid at a rate that was more than 2-times faster than the wild-type. Mutant DP3 also produced 77 g/l lactic acid compared with 58 g/l for the wild-type. Overall, compated with wild-type, the mutants DP2 and DP3 exhibited faster specific growth rates, shorter lag phases, greater lactic acid yields, tolerated higher lactic acid concentrations, and produced as much as 12% lactic acid in 12% glucose, 3% yeast extract/mineral salt/oleic acid medium which required an additional 9% glucose when the residual glucose concentration decreased to ≤3%. Mutant DP3 was stable for over 1.5 years (stored freeze dried). The strain development procedure was very successful; mutants with enhanced lactic acid-producing capacity were obtained each time the procedure was employed.
Concentration and wavelength dependence of the effective third-order susceptibility and optical limiting of C60in toluene solution (1995)

The optical limiting action of C60 in toluene solution is mainly due to reverse saturable absorption (RSA). It is shown that the formalism describing nonlinear optical response due to instantaneous two-photon absorption can be used in the case of sequential two-photon absorption, yielding effective values of the relevant parameters of optical nonlinearity due to RSA. The effective two-photon absorption parameter beta eff and the effective nonlinear refractive index parameter gamma eff', which are related respectively to the imaginary and real parts of the effective third-order susceptibility chi eff(3) were measured by the z-scan technique as a function of fullerene concentration and of incident laser intensity and wavelength over the 420-640 nm region. The concentration dependence of these parameters indicates that the solution is optically thin as far as the ground state of C60 is concerned, whereas the wavelength dependence confirms the applicability of the formalism used in the sequential two-photon absorption model. Comparisons are made with other z-scan results on C60.
Protein transport in organelles: Dual targeting of proteins to mitochondria and chloroplasts (2009)

As many as fifty proteins have now been experimentally demonstrated to be targeted to both mitochondria and plastids, a phenomenon referred to as dual targeting. Although the first reported case of dual targeting of a protein was reported in 1995, there is still little understanding of the mechanism of dual targeting and any similarities or differences with respect to the targeting of location-specific proteins. This minireview summarizes dual targeting in terms of signals, passenger proteins, receptors, regulation, why proteins may need to be dual targeted and the future challenges that remain in this area.
A highly efficient mesoscopic solar cell based on CH3NH3PbI3−xClxfabricated via sequential solution deposition (2014)

A mixed halide perovskite of CH3NH3PbI(3-x)Cl(x) is synthesized via two-step sequential solution deposition by using a mixture of PbCl2 and PbI2 as the precursor to overcome the low solubility of pure PbCl2 with easy morphology control. 11.7% power conversion efficiency is achieved for the mesoscopic cell, much higher than the cell constructed via a spin-coating process.
Global and local genome mapping in Arabidopsis thaliana by using recombinant inbred lines and random amplified polymorphic DNAs. (1992)

A population of Arabidopsis thaliana recombinant inbred lines was constructed and used to develop a high-density genetic linkage map containing 252 random amplified polymorphic DNA markers and 60 previously mapped restriction fragment length polymorphisms. Linkage groups were correlated to the classical genetic map by inclusion of nine phenotypic markers in the mapping cross. We also applied a technique for local mapping that allows targeting of markers to a selected genome region by pooling DNA from recombinant inbred lines based on their genotype. We conclude that random amplified polymorphic DNAs, used in conjunction with a recombinant inbred population, can facilitate the genetic and physical characterization of the Arabidopsis genome and that this method is generally applicable to other organisms for which appropriate populations either are available or can be developed.
Formation of “air‐gap” structure at a GaN epilayer/substrate interface by using an InN interlayer (2003)

We propose a new technique for “air-gap” formation at a GaN/sapphire interface by using an InN interlayer. This is aimed to grow epitaxial GaN films with reduced stress and cracks. First, an InN interlayer of about 0.2 μm thick is grown at 600 °C in atmospheric pressure. Then a 30 nm-thick GaN buffer layer is grown on the InN layer at 550 °C. The substrate temperature is ramped up to 1000 °C in the NH3 flow, and finally a 1.5 μm-thick GaN epilayer is grown on the annealed GaN buffer layer using nitrogen carrier gas. Consequently, an “air-gap” structure is naturally formed close to the substrate surface. During the ramping period of substrate temperature, the InN layer decomposes due to its thermal instability and metallic In is formed. It is found that metallic In drops as a result of InN decomposition contribute to the air-gap formation. No cracks are found on the GaN surface and a reduced stress in the layer is confirmed by PL and Raman shift measurements. (© 2003 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
Selective Cloning of Cell Surface Proteins Involved in Organ Development: Epithelial Glycoprotein Is Involved in Normal Epithelial Differentiation (1999)

Coordinating the activities of neighboring cells during development in multicellular organisms requires complex cellular interactions involving secreted, cell surface, and extracellular matrix components. Although most cloning efforts have concentrated on secreted molecules, recent work has emphasized the importance of membranebound molecules during development. To identify developmental genes, we raised antibodies to normal embryonic pancreatic epithelial cell surface proteins. These antibodies were characterized and used to clone the genes coding for the proteins by a panning strategy. Using this approach, we cloned the rat homologue of the mouse epithelial glycoprotein (EGP). Our immunohistochemistry data, describing the expression of EGP during rat development, as well as our in vitro data, looking at the effect of the anti-EGP antibody and the extracellular domain of EGP on embryonic pancreatic epithelial cell number and volume, strongly suggest a role for EGP during pancreatic development.
Multidrug-Resistant Pseudomonas aeruginosa : Risk Factors and Clinical Impact (2005)

Pseudomonas aeruginosa, a leading nosocomial pathogen, may become multidrug resistant (MDR). Its rate of occurrence, the individual risk factors among affected patients, and the clinical impact of infection are undetermined. We conducted an epidemiologic evaluation and molecular typing using pulsed-field gel electrophoresis (PFGE) of 36 isolates for 82 patients with MDR P. aeruginosa and 82 controls matched by ward, length of hospital stay, and calendar time. A matched case-control study identified individual risk factors for having MDR P. aeruginosa, and a retrospective matched-cohort study examined clinical outcomes of such infections. The 36 isolates belonged to 12 PFGE clones. Two clones dominated, with one originating in an intensive care unit (ICU). Cases and controls had similar demographic characteristics and numbers of comorbid conditions. A multivariate model identified ICU stay, being bedridden, having high invasive devices scores, and being treated with broad-spectrum cephalosporins and with aminoglycosides as significant risk factors for isolating MDR P. aeruginosa. Having a malignant disease was a protective factor (odds ratio [OR] = 0.2; P = 0.03). MDR P. aeruginosa was associated with severe outcomes compared to controls, including increased mortality (OR = 4.4; P = 0.04), hospital stay (hazard ratio, 2; P = 0.001), and requirement for procedures (OR = 5.4; P = 0.001). The survivors functioned more poorly at discharge than the controls, and more of the survivors were discharged to rehabilitation centers or chronic care facilities. The epidemiology of MDR P. aeruginosa is complex. Critically ill patients that require intensive care and are treated with multiple antibiotic agents are at high risk. MDR P. aeruginosa infections are associated with severe adverse clinical outcomes.
Molecular insights into DNA interference by CRISPR-associated nuclease-helicase Cas3 (2014)

Mobile genetic elements in bacteria are neutralized by a system based on clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins. Type I CRISPR-Cas systems use a "Cascade" ribonucleoprotein complex to guide RNA specifically to complementary sequence in invader double-stranded DNA (dsDNA), a process called "interference." After target recognition by Cascade, formation of an R-loop triggers recruitment of a Cas3 nuclease-helicase, completing the interference process by destroying the invader dsDNA. To elucidate the molecular mechanism of CRISPR interference, we analyzed crystal structures of Cas3 from the bacterium Thermobaculum terrenum, with and without a bound ATP analog. The structures reveal a histidine-aspartate (HD)-type nuclease domain fused to superfamily-2 (SF2) helicase domains and a distinct C-terminal domain. Binding of ATP analog at the interface of the SF2 helicase RecA-like domains rearranges a motif V with implications for the enzyme mechanism. The HD-nucleolytic site contains two metal ions that are positioned at the end of a proposed nucleic acid-binding tunnel running through the SF2 helicase structure. This structural alignment suggests a mechanism for 3' to 5' nucleolytic processing of the displaced strand of invader DNA that is coordinated with ATP-dependent 3' to 5' translocation of Cas3 along DNA. In agreement with biochemical studies, the presented Cas3 structures reveal important mechanistic details on the neutralization of genetic invaders by type I CRISPR-Cas systems.
Pituitary actions of ligands of the TGF-β family: activins and inhibins (2006)

Activins, as members of the transforming growth factor-beta superfamily, control and orchestrate many physiological processes and are vital for the development, growth and functional integrity of most tissues, including the pituitary. Activins produced by pituitary cells work in conjunction with central, peripheral, and other local factors to influence the function of gonadotropes and maintain a normal reproductive axis. Follistatin, also produced by the pituitary, acts as a local buffer to bind activin and modulate its bioactivity. On the other hand, inhibins of gonadal origin provide an endocrine feedback signal to antagonize activin signaling in cells that express the inhibin co-receptor, betaglycan, such as gonadotropes. This review highlights the pituitary roles of activin and the mechanisms through which these actions are modulated by inhibin and follistatin.
Structural and Kinetic Characterization of an Acyl Transferase Ribozyme (1998)

We have previously isolated, by in vitro selection, an acyl-transferase ribozyme that is capable of transferring a biotinylated methionyl group from the 3' end of a hexanucleotide substrate to its own 5'-hydroxyl. Comparison of the sequences of a family of evolved derivatives of this ribozyme allowed us to generate a model of the secondary structure of the ribozyme. The predicted secondary structure was extensively tested and confirmed by single-mutant and compensatory double-mutant analyses. The role of the template domain in aligning the acyl-donor oligonucleotide and acyl-acceptor region of the ribozyme was confirmed in a similar manner. The significance of different domains of the ribozyme structure and the importance of two tandem G:U wobble base pairs in the template domain were studied by kinetic characterization of mutant ribozymes. The wobble base pairs contribute to the catalytic rate enhancement, but only in the context of the complete ribozyme; the ribozyme in turn alters the metal binding properties of this site. Competitive inhibition experiments with unacylated substrate oligonucleotide are consistent with the ribozyme acting to stabilize substrate binding to the template, while negative interactions with the aminoacyl portion of the substrate destabilize binding.
Aptamers Overview: Selection, Features and Applications (2015)

Apatamer technology has been around for a quarter of a century and the field had matured enough to start seeing real applications, especially in the medical field. Since their discovery, aptamers rapidly emerged as key players in many fields, such as diagnostics, drug discovery, food science, drug delivery and therapeutics. Because of their synthetic nature, aptamers are evolving at an exponential rate gaining from the newest advances in chemistry, nanotechnology, biology and medicine. This review is meant to give an overview of the aptamer field, by including general aspects of aptamer identification and applications as well as highlighting certain features that contribute to their quick deployment in the biomedical field.
Highly tumor-reactive, internalizing, mouse monoclonal antibodies to Le(y)-related cell surface antigens. (1990)

Two monoclonal antibodies, designated BR64 (IgG1) and BR96 (IgG3), were generated that, according to immunohistology, bind selectively to carcinomas of the colon, breast, ovary, and lung. They have no or very low reactivity with normal human tissues, except for the fact that BR64 strains capillaries in the hearts from certain normal donors and that both monoclonal antibodies stain some epithelial cells from the gastrointestinal system, including stomach. Preliminary studies indicate that at least a portion of the epitope recognized by BR64 and BR96 is a Le(y) carbohydrate chain. Both monoclonal antibodies can be "internalized" by antigen-positive tumor cells, since immunoconjugates with ricin A-chain are cytotoxic. BR96 has the additional properties of being cytotoxic by itself, and it can mediate antibody-dependent cellular cytotoxicity and complement dependent cytotoxicity.
A SELF-MICROEMULSIFYING DRUG DELIVERY SYSTEM (SMEDDS) (2010)

The oral delivery of lipophilic drugs presents a major challenge because of the low aqueous solubility of such compounds. Selfmicroemulsifying drug delivery systems (SMEDDSs) have gained exposure for their ability to increase solubility and bioavailability of poorly soluble drugs. SMEDDS, which are isotropic mixtures of oils, surfactants, solvents and co-solvents/surfactants, can be used for the design of formulations in order to improve the oral absorption of highly lipophilic drug compounds. SMEDDS can be orally administered in soft or hard gelatin capsules and form fine relatively stable oil-in-water (o/w) emulsions upon aqueous dilution owing to the gentle agitation of the gastrointestinal fluids. The efficiency of oral absorption of the drug compound from the SMEDDS depends on many formulation−related parameters, such as surfactant concentraƟon, oil/surfactant raƟo, polarity of the emulsion, droplet size and charge, all of which in essence determine the self-emulsification ability. Thus, only very specific pharmaceutical excipient combinations will lead to efficient self-microemulsifying systems. Although many studies have been carried out, there are few drug products on the pharmaceutical market formulated as SMEDDS confirming the difficulty of formulating hydrophobic drug compounds into such formulations. Significant improvement in the oral bioavailability of these drug compounds has been demonstrated for each case. The fact that almost 40% of the new drug compounds are hydrophobic in nature implies that studies with SMEDDS will continue, and more drug compounds formulated as SMEDDS will reach the pharmaceutical market in the future.
Experimental Electrochemistry for Chemists (1974)

The goal of this book is to outline the basic principles and modern methodology of electrochemistry, in such away that the uninitiated may gain sufficient background to use electrochemical methods for the study of chemical systems. Thus chemical problems that are amenable to an electrochemical approach are introduced as representative examples. We hope by this approach to give the reader the necessary background to assess intelligently the most appropriate electrochemical technique for the study of a specific chemical problem.
Monoclonal antibodies specific for simian virus 40 tumor antigens (1981)

Thirty hybridomas that secrete immunoglobulins against the simian virus 40 tumor antigens were isolated and cloned. Of these, 28 produced antibodies which bound to simian virus 40 large-T, and 2 produced antibodies which bound to the host 53,000-dalton protein. As in previous work, large-T antigen was found to have at least one determinant that it shared with small-t antigen and to have a minimum of six unique determinants. Several of the monoclonal antibodies from the L series hybridomas recognized determinants that were present on a subset of the large-T antigen from simian virus 40-transformed mouse cells. These monoclonal antibodies should be useful in studies of the structure and function of the simian virus 40 tumor antigens.