gebhart/patrepeval huggingface dataset:
Action of Biguanides, Phenols and Detergents on <i>Escherichia coli</i> and its Spheroplasts (1969)

Summary The bactericidal potency of groups of biguanides, phenols and detergents has been compared with that of the bis ‐biguanide, chlorhexidine, and related to measurable effects of the compounds on bacteria. Biguanides, like chlorhexidine, precipitated bacterial cytoplasm and also lysed spheroplasts over a limited concentration range: higher concentrations prevented lysis. Certain phenols and detergents which lysed spheroplasts did not precipitate cytoplasm. All the compounds released radioactivity from isotopically labelled bacteria; at suitable concentrations, biguanides released more radioactivity than chlorhexidine, but at higher concentrations the amount of radioactivity released was reduced. Bactericidal activity correlated with both the ability to lyse spheroplasts and to precipitate cytoplasm from solution. The findings support the hypothesis that damage to the cell wall alone does not kill bacteria but an increase in permeability allows entry of the bactericide. Action of compounds on the cell wall is discussed in relation to a model of its ultrastructure.
Mechanisms of electron field emission from diamond, diamond-like carbon, and nanostructured carbon (1999)

It is argued that the facile electron field emission from carbon systems occurs primarily because surface groups such as C–H can produce large changes in local electron affinity, so that electric fields from the anode can be focused toward unhydrogenated surface areas of high affinity, the fields ending on negative charges in an underlying depletion layer. The resulting downward band bending creates large surface fields which allow Fowler–Nordheim emission, while not exceeding the material’s breakdown field.
Analysis of polyethylene glycol modified superoxide dismutase by chromatographic, electrophoretic, light scattering, chemical and enzymatic methods. (1988)

Covalent conjugation of bovine erythrocyte superoxide dismutase (SOD) with activated polyethylene glycol (PEG) results in a mixture of modified species (PEG-SOD) with properties different from those of the native enzyme. The components of this mixture were resolved by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), isoelectric focusing, and chromatographic (size-exclusion, anion-exchange, cation-exchange and reverse-phase high performance liquid chromatography) techniques. Physicochemical properties such as apparent molecular weight, isoelectric point, relative hydrophobicity and relative cation-anion charge number were measured by electrophoretic and chromatographic procedures. Dispersity and apparent radius were examined by chromatographic and light scattering techniques. The extent of covalent modification and enzymatic activity change were measured by chemical and spectroscopic methods, showing that activity loss was not due to catalytic site modification. The properties of the PEG-modified form of the enzyme were compared with those of native SOD and showed that in addition to changing biological properties, PEG modification of proteins can result in a product with unexpectedly high heterogeneity and substantial changes in isoelectric point and hydrophobicity. Altered biological properties may therefore not merely be due to shielding of protein surface by PEG chains. Apparent properties of PEG modified proteins such as molecular weight were found to be highly method dependent, with poor agreement being shown among classical measurements.
Effect of Topical Cyclosporine Rinse on Oral Lichen Planus (1990)

As a topical preparation, cyclosporine may be useful in the treatment of oral lichen planus and possibly other cutaneous disorders.
&lt;title&gt;Quantum dot infrared photodetectors&lt;/title&gt; (2002)

InAs quantum dot infrared photodetectors based on bound-to- bound intraband transitions in undoped InAs quantum dots are reported. AlGaAs blocking layers were employed to achieve low dark current. The photoresponse peaked at 6.2 micrometers . At 77 K and -0.7 V bias the responsivity was 14 mA/W and the detectivity, D*, was 10<SUP>10</SUP> cmHz<SUP>1/2</SUP>/W. By introducing InGaAs cap layers, a QDIP with bias-controllable two-color characteristic was demonstrated.
DNA-Directed Protein Immobilization on Mixed Self-Assembled Monolayers via a Streptavidin Bridge (2004)

The simultaneous detection of multiple analytes is an important consideration for the advancement of biosensor technology. Currently, few sensor systems possess the capability to accurately and precisely detect multiple antigens. This work presents a simple approach for the functionalization of sensor surfaces suitable for multichannel detection. This approach utilizes self-assembled monolayer (SAM) chemistry to create a nonfouling, functional sensor platform based on biotinylated single-stranded DNA immobilized via a streptavidin bridge to a mixed SAM of biotinylated alkanethiol and oligo(ethylene glycol). Nonspecific binding is minimized with the nonfouling background of the sensor surface. A usable protein chip is generated by applying protein-DNA conjugates which are directed to specific sites on the sensor chip surface by utilizing the specificity of DNA hybridization. The described platform is demonstrated in a custom-built surface plasmon resonance biosensor. The detection capabilities of a sensor using this protein array have been characterized using human chorionic gonadotropin (hCG). The platform shows a higher sensitivity in detection of hCG than that observed using biotinylated antibodies. Results also show excellent specificity in protein immobilization to the proper locations in the array. The vast number of possible DNA sequences combine with the selectivity of base-pairing makes this platform an excellent candidate for a sensor capable of multichannel protein detection.
Cumulant based stochastic optimal power flow (S-OPF) for variance optimization (2005)

This paper presents a cumulant method based solution for stochastic optimal power flow (S-OPF) including a variance minimization objective function. In this case, the objective of the problem is to minimize the variance of the active power generation at the slack bus by optimizing the decision variables given uncertainty in loading levels. Results using the proposed method are compared against Monte Carlo simulations to demonstrate accuracy of the results. Additionally, variances computed at the optimal point are compared against the variances computed at the minimum cost point to provide a measurement of the improvement by the optimization process. Two systems are tested consisting of 30 and 57 buses respectively. In general, variances computed using the proposed methodology are within 1% of those computed using 10,000 sample Monte Carlo simulations and the variances are between 3 and 11% narrower than those at the minimum cost solution.
Interaction of the Ribosomal Protein, L5, with Protein Phosphatase Type 1 (1995)

The two-hybrid system was used to screen for binding proteins of type 1 protein phosphatase. Two plasmids were constructed, one containing the cDNA of the delta isoform of the type 1 catalytic subunit and the other containing a chicken gizzard cDNA library. Yeast (Y190) were transformed with the plasmids and screened for interacting species. 35 positive clones were categorized into 19 gene groups. Most of these were not identified. One clone, however, contained a sequence identical to the C-terminal portion of the chicken ribosomal protein L5 and corresponded to nucleotide residues 606-975. L5 was isolated from rat liver ribosomes as the L5.5 S RNA complex. This activated phosphatase activity of a myosin-bound phosphatase and the isolated type 1 catalytic subunit using phosphorylated myosin light chains and phosphorylase alpha as substrates. In addition, it was found that phosphatase sedimented with ribosomal subunits containing L5 but did not sediment with those deficient in L5. These data indicate that L5 binds to the catalytic subunit of the type 1 protein phosphatase and may act as a target molecule for phosphatase in ribosomal function or other cell mechanisms.
Embedded microstructures for daylighting and seasonal thermal control (2012)

A novel concept for an advanced fenestration system was studied and samples were produced to demonstrate the feasibility. The resulting novel glazing will combine the functions of daylighting, glare protection, and seasonal thermal control. Coated microstructures provide redirection of the incident solar radiation, thus simultaneously reducing glare and projecting daylight deep into the room in the same manner as an anidolic mirror-based system. The solar gains are reduced for chosen angles corresponding to aestival elevations of the sun, thereby minimizing heating loads in winter and cooling loads in summer. A ray-tracing program developed especially for the study of laminar structures was used for the optimization of structures with the above mentioned goals. The chosen solution is based on reflective surfaces embedded in a polymer film that can be combined with a standard doubled glazed window. The fabrication of such structures required several steps. The fabrication of a metallic mould with a relative high aspect ratio and mirror polished surfaces is followed by the production of an intermediate Polydimethylsiloxane moulds that was subsequently used to replicate the structure with a UV curable polymer. Selected facets of these samples were then coated with a thin film of highly reflective material in a physical vapour deposition process. Finally, the structures were filled with the same polymer to integrated the mirrors.
Recent advances in diffuse optical imaging (2005)

We review the current state-of-the-art of diffuse optical imaging, which is an emerging technique for functional imaging of biological tissue. It involves generating images using measurements of visible or near-infrared light scattered across large (greater than several centimetres) thicknesses of tissue. We discuss recent advances in experimental methods and instrumentation, and examine new theoretical techniques applied to modelling and image reconstruction. We review recent work on in vivo applications including imaging the breast and brain, and examine future challenges.
Reversible, Metal-Free Hydrogen Activation (2006)

Although reversible covalent activation of molecular hydrogen (H2) is a common reaction at transition metal centers, it has proven elusive in compounds of the lighter elements. We report that the compound (C6H2Me3)2PH(C6F4)BH(C6F5)2 (Me, methyl), which we derived through an unusual reaction involving dimesitylphosphine substitution at a para carbon of tris(pentafluorophenyl) borane, cleanly loses H2 at temperatures above 100 degrees C. Preliminary kinetic studies reveal this process to be first order. Remarkably, the dehydrogenated product (C6H2Me3)2P(C6F4)B(C6F5)2 is stable and reacts with 1 atmosphere of H2 at 25 degrees C to reform the starting complex. Deuteration studies were also carried out to probe the mechanism.
Topical Verapamil HCl, Topical Trifluoperazine, and Topical Magnesium Sulfate for the Treatment of Peyronie’s Disease— A Placebo-Controlled Pilot Study (2007)

Topical verapamil gel proved effective in eliminating pain on erection, decreasing the size of plaque, decreasing curvature, and improving erection quality in patients with Peyronie's Disease. Treatment results improved significantly after 9 months' treatment as compared with 3 months' treatment.
A 12b, 50 MS/s, Fully Differential Zero-Crossing Based Pipelined ADC (2009)

Zero-crossing based switch capacitor circuits have been introduced as alternatives to op-amp based circuits for eased design considerations and improved power efficiency. This work further improves the resolution, power efficiency, and robustness of previous zero-crossing based circuits (ZCBCs) and features a 90 nm CMOS, offset compensated, fully differential, zero-crossing based, 12b, 50 MS/s, pipelined ADC requiring no CMFB. The power consumption is 4.5 mW. The FOM is 88 fJ/step. Fully differential signaling is used to improve power supply rejection and power efficiency. A power efficient chopping offset compensation technique is presented. Reference voltage switching is improved to avoid gate boosted switches. Redundancy is used to reduce output range requirements for increased signal range. Two regenerative latch architectures used for bit decision comparison are analyzed and measured for offset, noise, and speed.
Rate-control snoop : a reliable transport protocol for heterogeneous networks with wired and wireless links (2004)

In this paper, a new reliable transport protocol called rate-control snoop is proposed for improving TCP performance over error-prone wireless links. It is implemented at a base station where it performs rate-based transmission control based on characteristics of a data path. The proposed protocol monitors every packet that passes through the path and asks the sender to reduce the transmission rate when packet losses are detected only at a wired link. The performance of the proposed protocol is evaluated by simulations and it shows better throughput than TCP Reno, TCP-Snoop, and end-to-end rate control TCP.
Synthesis of Organosulfur Compounds. VIII. Cyclization Products from the Modified Willgerodt-Kindler Reaction (1973)

In order to clarify in more detail the cyclization mechanism of thioanilide to benzothiazole under the modified Willgerodt-Kindler reaction conditions, 2-picoline (III) was heated with meta-substituted anilines (IV) in the presence of sulfur and the reaction also gave thioanilides and one of the two possible benzothiazoles. The latter was proved tohave the structure of 5-substituted 2-(2-pyridyl) benzothiazoles (VI) by independent synthesis.On the other hand, the expected two isomeric benzothiazoles (VI and VII) were obtained from the oxidative cyclization of thioanilides by the modified Jacobson reaction.
Preparation of (–)-(7R)-7-acetyl-7-hydroxy-4,4-dimethoxy-5,6,7,8-tetrahydro-naphthalen-1(4H)-one, a chiral<scp>AB</scp>-synthon for anthracycline synthesis (1981)

The (–)-(R)-dienone (13) was prepared in 10 steps from the known 8-hydroxy-5-methoxy-2, 3-dihydronaphthalen-1(4H)-one (2), and the chirality at C(7) in (13) corresponds to that found at C(9) in the naturally occurring anthracyclines related to daunomycin.
EB1089 inhibits the parathyroid hormone–related protein–enhanced bone metastasis and xenograft growth of human prostate cancer cells (2009)

Parathyroid hormone-related protein (PTHrP) plays a major role in prostate carcinoma progression and bone metastasis. Once prostate cancers become androgen-independent, treatment options become limited. Vitamin D analogues represent a potentially valuable class of agents in this clinical context. Using the prostate cancer cell line C4-2 as a model, we studied the effects of PTHrP and the noncalcemic vitamin D analogue EB1089 on markers of prostate cancer cell progression in vitro and in vivo. C4-2 is a second-generation androgen-independent LNCaP subline that metastasizes to the lymph nodes and bone when injected into nude mice and produces mixed lytic/blastic lesions, mimicking the in vivo situation. We report that PTHrP increases cell migration and invasion, and that a pathway via which EB1089 inhibits these processes is through down-regulation of PTHrP expression. PTHrP also increases anchorage-independent cell growth in vitro and xenograft growth in vivo; EB1089 reverses these effects. The in vivo PTHrP effects are accompanied by increased tumor cell proliferation and survival. Treatment with EB1089 reverses the proliferative but not the antiapoptotic effects of PTHrP. PTHrP also increases intratumor vessel density and vascular endothelial growth factor expression; EB1089 reverses these effects. Intracardially injected C4-2 cells produce predominantly osteoblastic lesions; PTHrP overexpression decreases the latency, increases the severity and alters the bone lesion profile to predominantly osteolytic. EB1089 largely reverses these PTHrP effects. A direct correlation between PTHrP immunoreactivity and increasing tumor grade is observed in human prostate cancer specimens. Thus, decreasing PTHrP production by treatment with vitamin D analogues may prove therapeutically beneficial for prostate cancer.
Capturing knowledge of user preferences (2001)

Tools for filtering the World Wide Web exist, but they are hampered by the difficulty of capturing user preferences in such a dynamic environment. We explore the acquisition of user profiles by unobtrusive monitoring of browsing behaviour and application of supervised machine-learning techniques coupled with an ontological representation to extract user preferences. A multi-class approach to paper classification is used, allowing the paper topic taxonomy to be utilised during profile construction. The Quickstep recommender system is presented and two empirical studies evaluate it in a real work setting, measuring the effectiveness of using a hierarchical topic ontology compared with an extendable flat list.
Phosphabicyclononane-Containing Ru Complexes:  Efficient Pre-Catalysts for Olefin Metathesis Reactions (2007)

The catalytic performances of three Phosphabicyclononane (Phoban)-containing ruthenium-based pre-catalysts have been evaluated for metathesis transformations. A wide screening of substrates in ring-closing metathesis reactions reveals the greater efficiency of pre-catalyst 4. Comparison of the catalytic activities of 4 with Grubbs' first-generation pre-catalyst illustrates the key role of the Phoban ligand. Additionally, a comparative study of three Phoban-containing pre-catalysts has been conducted for the self-metathesis of 1-octene at low catalyst loading (25-100 ppm).
Myoblast seeding in a collagen matrix evaluatedin vitro (1996)

Collagens may be used as biomaterials for soft tissue reconstruction, e.g., the abdominal wall. We previously developed a biocompatible dermal sheep collagen (DSC), which in an abdominal wall reconstruction model showed controlled biodegradation and functioned as a matrix for in-growth of fibroblasts but not of muscle. It was hypothesized that regeneration of muscle via DSC may be possible by seeding of muscle cells. Using a syringe, mouse C2C12 myoblasts were seeded in DSC disks and incubated in methylcellulose-based growth medium, changed at 24 h into differentiation medium. An estimated 85% of the cells were well distributed, especially in the top half of the DSC disks. Some 15% of the cells ended up on top. At 4 h, all cells showed a spherical morphology, sometimes with clear adhesion plaques. At 24 h, cells on the top started to form a "capsule" with well-spread cells. Underneath the capsule, of the remaining 85% of the cells, approximately 30% showed adhesion and spreading on/in between collagen bundles. At day 3 after the addition of differentiation medium, the spread cells showed first indications of myotube formation. At day 7, myotube formation had proceeded, while extracellular matrix, i.e., collagen and elastin, had been deposited. This study shows that myoblast seeding into DSC is feasible, resulting in a reasonable cell distribution and survival of 45% of the cells. The surviving cells are able to differentiate into myotubes and form an extracellular matrix.
Site-Specific Characterization of <scp>d</scp>-Amino Acid Containing Peptide Epimers by Ion Mobility Spectrometry (2013)

Traditionally, the d-amino acid containing peptide (DAACP) candidate can be discovered by observing the differences of biological activity and chromatographic retention time between the synthetic peptides and naturally occurring peptides. However, it is difficult to determine the exact position of d-amino acid in the DAACP candidates. Herein, we developed a novel site-specific strategy to rapidly and precisely localize d-amino acids in peptides by ion mobility spectrometry (IMS) analysis of mass spectrometry (MS)-generated epimeric fragment ions. Briefly, the d/l-peptide epimers were separated by online reversed-phase liquid chromatography and fragmented by collision-induced dissociation (CID), followed by IMS analysis. The epimeric fragment ions resulting from d/l-peptide epimers exhibit conformational differences, thus showing different mobilities in IMS. The arrival time shift between the epimeric fragment ions was used as criteria to localize the d-amino acid substitution. The utility of this strategy was demonstrated by analysis of peptide epimers with different molecular sizes, [d-Trp]-melanocyte-stimulating hormone, [d-Ala]-deltorphin, [d-Phe]-achatin-I, and their counterparts that contain all-l amino acids. Furthermore, the crustacean hyperglycemia hormones (CHHs, 8.5 kDa) were isolated from the American lobster Homarus americanus and identified by integration of MS-based bottom-up and top-down sequencing approaches. The IMS data acquired using our novel site-specific strategy localized the site of isomerization of l- to d-Phe at the third residue of the CHHs from the N-terminus. Collectively, this study demonstrates a new method for discovery of DAACPs using IMS technique with the ability to localize d-amino acid residues.
A monomeric red fluorescent protein (2002)

All coelenterate fluorescent proteins cloned to date display some form of quaternary structure, including the weak tendency of Aequorea green fluorescent protein (GFP) to dimerize, the obligate dimerization of Renilla GFP, and the obligate tetramerization of the red fluorescent protein from Discosoma (DsRed). Although the weak dimerization of Aequorea GFP has not impeded its acceptance as an indispensable tool of cell biology, the obligate tetramerization of DsRed has greatly hindered its use as a genetically encoded fusion tag. We present here the stepwise evolution of DsRed to a dimer and then either to a genetic fusion of two copies of the protein, i.e., a tandem dimer, or to a true monomer designated mRFP1 (monomeric red fluorescent protein). Each subunit interface was disrupted by insertion of arginines, which initially crippled the resulting protein, but red fluorescence could be rescued by random and directed mutagenesis totaling 17 substitutions in the dimer and 33 in mRFP1. Fusions of the gap junction protein connexin43 to mRFP1 formed fully functional junctions, whereas analogous fusions to the tetramer and dimer failed. Although mRFP1 has somewhat lower extinction coefficient, quantum yield, and photostability than DsRed, mRFP1 matures >10 times faster, so that it shows similar brightness in living cells. In addition, the excitation and emission peaks of mRFP1, 584 and 607 nm, are approximately 25 nm red-shifted from DsRed, which should confer greater tissue penetration and spectral separation from autofluorescence and other fluorescent proteins.