gebhart/patrepeval huggingface dataset:
Targeting surface-layer proteins with single-domain antibodies: a potential therapeutic approach against Clostridium difficile-associated disease (2015)

Clostridium difficile is a leading cause of death from gastrointestinal infections in North America. Antibiotic therapy is effective, but the high incidence of relapse and the rise in hypervirulent strains warrant the search for novel treatments. Surface layer proteins (SLPs) cover the entire C. difficile bacterial surface, are composed of high-molecular-weight (HMW) and low-molecular-weight (LMW) subunits, and mediate adherence to host cells. Passive and active immunization against SLPs has enhanced hamster survival, suggesting that antibody-mediated neutralization may be an effective therapeutic strategy. Here, we isolated a panel of SLP-specific single-domain antibodies (VHHs) using an immune llama phage display library and SLPs isolated from C. difficile hypervirulent strain QCD-32g58 (027 ribotype) as a target antigen. Binding studies revealed a number of VHHs that bound QCD-32g58 SLPs with high affinity (K D = 3-6 nM) and targeted epitopes located on the LMW subunit of the SLP. The VHHs demonstrated melting temperatures as high as 75 °C, and a few were resistant to the gastrointestinal protease pepsin at physiologically relevant concentrations. In addition, we demonstrated the binding specificity of the VHHs to the major C. difficile ribotypes by whole cell ELISA, where all VHHs were found to bind 001 and 027 ribotypes, and a subset of antibodies were found to be broadly cross-reactive in binding cells representative of 012, 017, 023, and 078 ribotypes. Finally, we showed that several of the VHHs inhibited C. difficile QCD-32g58 motility in vitro. Targeting SLPs with VHHs may be a viable therapeutic approach against C. difficile-associated disease.
Novel Polyaromatic Quinone Imines. 2. Synthesis of Model Compounds and Stereoregular Poly(quinone imines) from Disubstituted Anthraquinones (1996)

Novel poly(quinone diimines) from anthraquinones symmetrically disubstituted with solubilizing ethyleneoxy or long chain alkoxy groups have been synthesized and characterized. The disubstituted anthraquinones 1,5-bis(2-methoxyethoxy)anthraquinone (EO1AQ), 1,5-bis(2-(2-methoxyethoxy)ethoxy)anthraquinone (EO2AQ), 1,5-bis(2-(2-(2-methoxyethoxy)ethoxy)anthraquinone (EO2AQ), 1,5-bis(2-(2-2-methoxyethoxy)ethoxy)ethoxy)anthraquinone (EO3AQ), 1,5-bis(octyloxy)anthraquinone (15OOAQ), 2,6-bis(octyloxy)anthraquinone (26OOAQ), and 1,4-bis(octyloxy)anthraquinone (14OOAQ) were synthesized and condensed with aniline in the presence of titanium tetrachloride and 1,4-diazabicyclo[2.2.2]octane to give N,N‘-diphenyl-1,5-bis(2-methoxyethoxy)nanthraquinone 9,10-diimine (DEOnAQ, n = 1−3), N,N-diphenyl-1,5-bis(octyloxy)anthraquinone 9,10-diimine (15DOOAQ), and N,N‘-diphenyl-2,6-bis(octyloxy)anthraquinone 9,10-diimine (26DOOAQ), respectively, as model compounds for the polymers. The relative stereochemistry of these diimines was determined by 1H NMR spectroscopy. Polycondensation of the disubstituted anthraquinones with 4,4‘-thiodianiline (SDA) gave high molecular weight (Mw 30 000) poly(anthraquinone diimines) and large macrocycles. Polycondensation of 1,4-phenylenediamine (PDA) with EO2AQ gave high molecular weight (Mw 14 000) polyaromatic anthraquinone diimines. PDA gave molecular weights of Mw 5000−23 000 for the bis(octyloxy)-substituted anthraquinones. The molecular weights of polymerizations incorporating PDA are lowered due to steric interactions of successive repeat units and solubility constraints.
At what time is the cocktail party? A late locus of selective attention to natural speech (2012)

Distinguishing between speakers and focusing attention on one speaker in multi-speaker environments is extremely important in everyday life. Exactly how the brain accomplishes this feat and, in particular, the precise temporal dynamics of this attentional deployment are as yet unknown. A long history of behavioral research using dichotic listening paradigms has debated whether selective attention to speech operates at an early stage of processing based on the physical characteristics of the stimulus or at a later stage during semantic processing. With its poor temporal resolution fMRI has contributed little to the debate, while EEG-ERP paradigms have been hampered by the need to average the EEG in response to discrete stimuli which are superimposed onto ongoing speech. This presents a number of problems, foremost among which is that early attention effects in the form of endogenously generated potentials can be so temporally broad as to mask later attention effects based on the higher level processing of the speech stream. Here we overcome this issue by utilizing the AESPA (auditory evoked spread spectrum analysis) method which allows us to extract temporally detailed responses to two concurrently presented speech streams in natural cocktail-party-like attentional conditions without the need for superimposed probes. We show attentional effects on exogenous stimulus processing in the 200-220 ms range in the left hemisphere. We discuss these effects within the context of research on auditory scene analysis and in terms of a flexible locus of attention that can be deployed at a particular processing stage depending on the task.
Applications of carbon film cold cathodes in vacuum electron devices (2002)

Carbon film cathodes have been shown to be very robust and stable in over 5,000 hours of testing in continuous operation at 0.2A/sqcm and capable of at least 2.OA/cm2 in pulsed operation. The primary evaluation vehicle is a metal ceramic diode that is constructed and processed with methods that are standard in the high vacuum tube industry. Some of the information presented was developed from X-ray and vacuum gauge tubes designed specifically to utilize carbon film emitters. Additional analytical measurements have been made to establish the work function, emittance, noise and stability at pressure levels above 10/sup -4/ Torr.
Long-range incommensurate magnetic order in a Dy-Y multilayer (1986)

A multilayer sample of Dy(47 A\r{})/Y(40 A\r{}), produced by molecular-beam-epitaxy techniques, is shown to order magnetically in an incommensurate helix that is coherent over several multilayer periods. The magnetic satellite peak has harmonics resulting from the multilayer modulation. The dc magnetic properties are suggestive of a metamagnet.
Alfalfa Mosaic Virus RNA. Determination of the Sequence Homology Between the Four RNA Species and a Comparison with the Four RNA Species of Cucumber Mosaic Virus (1978)

The method of Taylor et al. [Taylor, J. M., Illmensee, R & Summers, J. (1976) Biochim. Biophys. Acta, 442, 324--330 and Gould and Symons (1977) Nucleic Acids Res. 4, 3787--3802] has been used to transcribe complementary DNA probes from the four major RNAs of alfalfa mosaic virus (AMV). Analysis of the kinetics of hybridization of these probes in homologous and heterologous complementary DNA . RNA hybridization reactions has shown that the sequence of the smallest RNA (RNA 4), which contains the coat protein gene, is present within RNA 3 and located at the 3' end of this RNA species. RNAs 1 and 2 are unique RNA molecules with little or no sequence homology between them or RNAs 3 and 4. This latter observation contrasts with the situation that occurs in cucumber mosaic virus (CMV) as CMV RNAs 1--4 were shown to have a common nucleotide stretch of 200 bases at their 3' termini; the location of RNA 4 within RNA 3 of CMV was also shown to be at the 3' end of this RNA species.
Introduction to Protein Chemistry (1958)

Introduction to Protein Chemistry Get access Introduction to Protein Chemistry . Fox Sidney W. Foster Joseph F. . 459 pgs., illus. John Wiley and Sons, Inc. , New York . ( 1957 ) $9.50 Parkhurst A. Shore Parkhurst A. Shore National Institutes of Health Search for other works by this author on: Oxford Academic Google Scholar AIBS Bulletin, Volume 8, Issue 5, November 1958, Page 45, https://doi.org/10.2307/1292587 Published: 01 November 1958
Homoserine Kinase from <i>Escherichia coli</i> K12 (1976)

Homoserine kinase was purified to apparent homogeneity from a derepressed strain of Escherichia coli K12, using standard fractionation techniques. It is a dimer (Mr = 60000) composed of apparently identical polypeptide chains (Mr = 29000). Its amino acid composition and N-terminal sequence have been determined. L-Threonine is a competitive inhibitor of the substrate L-homoserine; this inhibition is straighforward and shows no sign of co-operativity. Evidence is presented that homoserine and threonine bind to the same site of this non-allosteric enzyme. The binding of homoserine and threonine can also be studied by difference spectroscopy; the latter studies reveal an unexpected effect of magnesium ions, which might be the basis for the unusual high Mg2+ requirement for optimal enzyme reaction.
Low-input Performance of Zoysiagrass (Zoysia spp.) Cultivars Maintained under Dense Tree Shade (2011)

A 3-year study was conducted to evaluate the comparative performance of zoysiagrass ( Zoysia spp .) cultivars for shaded environments in which inputs are minimized. Included in the study were commercial cultivars Diamond, Cavalier, Royal, Shadow Turf, Zorro, Zeon, Jamur, Crowne, Palisades, and Meyer. In July 2006, grass plugs were planted in a shade nursery comprised of live oak trees providing 89% shade. From 2007 to 2009, turf plots were periodically evaluated for quality, density, color, vertical canopy height, and extent of lateral spread. Overall turfgrass quality was noticeably reduced by the heavily shaded environment; however, some cultivars attained acceptable levels during midsummer periods. A turf performance index (TPI) was generated for ranking the cultivars that represented the number of times an entry occurred in the top statistical group across all parameters and rating dates. ‘Royal’, ‘Zorro’, and ‘Shadow Turf’ were the cultivars ranking in the top statistical grouping most often throughout the study. The results suggest that Z. matrellas may be better adapted than Z. japonicas for heavily shaded environments where inputs are conserved.
A Conical Beam Ship Array Antenna with Infinitely Variable Control of the Elevation Angle (1974)

Studies on a ship terminal for a maritime satellite system have shown that a shipboard antenna with a 6 - 8 dB gain would have an optimum in costs. Therefore the DFVLR - Institut fur Flugfunk und Mikrowellen decided to design an experimental shipboard antenna system meeting these datas. The first model of the antenna system was tested by the ESRO-Balloon-Simulation-Experiment during Sept./Oct. 1973 in the English Channel.
DETERMINATION OF MASS PROPERTIES OF POLYGONAL CSG OBJECTS IN PARALLEL (1991)

A parallel algorithm for determining the mass properties of objects represented in the Constructive Solid Geometry (CSG) scheme that uses polygons as primitives is presented. The algorithm exploits the fact that integration of local information around the vertices of the evaluated polygon is sufficient for the determination of its mass properties, i.e., determination of the edges and the complete topology of the evaluated polygon is not necessary. This reduces interprocessor communication and makes it suitable for parallel processing. The algorithm uses data parallelism, spatial partitioning and parallel sorting for parallelization. Tuple-sets on which simple operations have to be performed are identified. The elements of tuple-sets are distributed among the processors for parallelization. The uniform grid spatial partitioning technique is used to generate sub-problems that can be done in parallel and to reduce the cardinality of some of the tuple-sets generated in the algorithm. Parallel sorting is used to sort the tuple-sets between the data-parallel phases of the algorithm.
Detection of viruses with molecularly imprinted polymers integrated on a microfluidic biochip using contact-less dielectric microsensors (2009)

Rapid detection of viral contamination remains a pressing issue in various fields related to human health including clinical diagnostics, the monitoring of food-borne pathogens, the detection of biological warfare agents as well as in viral clearance studies for biopharmaceutical products. The majority of currently available assays for virus detection are expensive, time-consuming, and labor-intensive. In the present work we report the creation of a novel micro total analysis system (microTAS) capable of continuously monitoring viral contamination with high sensitivity and selectivity. The specific interaction between shape and surface chemistry between molecular imprinted polymer (MIP) and virus resulted in the elimination of non-specific interaction in the present sensor configuration. The additional integration of the blank (non-imprinted) polymer further allowed for the identification of non-specific adsorption events. The novel combination of microfluidics containing integrated native polymer and MIP with contact-less dielectric microsensors is evaluated using the Tobacco Mosaic Virus (TMV) and the Human Rhinovirus serotype 2 (HRV2). Results show that viral binding and dissociation events can be readily detected using contact-less bioimpedance spectroscopy optimized for specific frequencies. In the present study optimum sensor performance was achieved at 203 kHz within the applied frequency range of 5-500 kHz. Complete removal of the virus from the MIP and device reusability is successfully demonstrated following a 50-fold increase in fluid velocity. Evaluation of the microfluidic biochip revealed that microchip technology is ideally suited to detect a broader range of viral contaminations with high sensitivity by selectively adjusting microfluidic conditions, sensor geometries and choice of MIP polymeric material.
Cleavage of the bacteriophage P1 packaging site (pac) is regulated by adenine methylation. (1990)

The packaging of bacteriophage PI DNA is initiated when the phage packaging site (pac) is recognized and cleaved and continues until the phage head is full. We have previously shown that pac is a 162-base-pair segment of P1 DNA that contains seven DNA adenine methyltransferase methylation sites (5'-GATC). We show here that cleavage of pac is methylation sensitive. Both in vivo and in vitro experiments indicate that methylated pac is cleavable, whereas unmethylated pac is not. Moreover, DNA isolated from P1 phage and containing an uncut pac site was a poor substrate for in vitro cleavage until it was methylated by the Escherichia coli DNA adenine methyltransferase. Comparison of that uncut pac DNA with other viral DNA fragments by digestion with methylation-sensitive restriction enzymes indicated that the uncut pac DNA was preferentially undermethylated. In contrast, virion DNA containing a cut pac site was not undermethylated. We believe these results indicate that pac cleavage is regulated by adenine methylation during the phage lytic cycle.
Luminal Heterodimeric Amino Acid Transporter Defective in Cystinuria (1999)

Mutations of the glycoprotein rBAT cause cystinuria type I, an autosomal recessive failure of dibasic amino acid transport (b(0,+) type) across luminal membranes of intestine and kidney cells. Here we identify the permease-like protein b(0,+)AT as the catalytic subunit that associates by a disulfide bond with rBAT to form a hetero-oligomeric b(0,+) amino acid transporter complex. We demonstrate its b(0,+)-type amino acid transport kinetics using a heterodimeric fusion construct and show its luminal brush border localization in kidney proximal tubule. These biochemical, transport, and localization characteristics as well as the chromosomal localization on 19q support the notion that the b(0,+)AT protein is the product of the gene defective in non-type I cystinuria.
The Promoter of the <i>Vicia faba</i> L. Leghemoglobin Gene <i>VfLb29</i> Is Specifically Activated in the Infected Cells of Root Nodules and in the Arbuscule-Containing Cells of Mycorrhizal Roots from Different Legume and Nonlegume Plants (2004)

The VfLb29 leghemoglobin gene promoter was polymerase chain reaction-amplified from a Vicia faba genomic library and was fused to the gusAint coding region. Expression of the chimeric gene was analyzed in transgenic hairy roots of the legumes V. faba, V. hirsuta, and Medicago truncatula as well as in transgenic Nicotiana tabacum plants. The VfLb29 promoter was found to be specifically active not only in the infected cells of the nitrogen-fixing zone of root nodules but also in arbuscule-containing cells of transgenic V. faba and M. truncatula roots colonized by the endomycorrhizal fungus Glomus intraradices. In addition to these two legumes, specific expression in arbuscule-containing cells was also observed in the nonlegume N. tabacum. All studies were done in comparison to the V. faba leghemoglobin gene promoter VfLb3 that as VfLb29 was expressed in the infected cells of root nodules but showed no activity in endomycorrhiza. An activation of the VfLb29 promoter due to hypoxia in metabolically active tissues was excluded. The conserved activation in arbuscule-containing cells of legumes and the nonlegume N. tabacum suggests a conserved trigger for this promoter in legume and nonlegume endomycorrhiza symbioses.
MMI-reflector: A novel on-chip reflector for photonic integrated circuits (2009)

Abstract We present a novel, compact, on-chip multi-mode interference (MMI) reflector, with near-100 % theoretical reflection. We measured 78±10 % reflection for an InP-based MMI-reflector fabricated with a single etch step with inductively coupled plasma (ICP) etching technique.
Cranial electrotherapy stimulation treatment of cognitive brain dysfunction in chemical dependence. (1984)

In a double-blind random assignment study, nomifensine was compared to imipramine in a population of depressed male inpatients (N = 36; ages 22-56 years). Nomifensine and imipramine in doses of 100-150 mg/day were found to be comparable over the 4-week treatment period on the Hamilton Depression Rating Scale and Clinical Global Impressions. The Self-Rating Symptom Scale showed differences favoring nomifensine for the Depression factor at Days 3, 7, and 10. In extensive laboratory analyses, no clinically important changes were seen within or between groups. Although differences were not significant, more discomforting side effects--specifically, anticholinergic, nervousness/restlessness, and sedation--were seen in the imipramine than the nomifensine group. These results indicate that nomifensine compares favorably with imipramine in the treatment of depressed inpatients.
Biomedical and Environmental Applications of Chitosan-based Nanomaterials (2011)

Being naturally abundant resources and having many interesting physicochemical and biological properties, chitin/chitosan have been found useful in many fields. This paper describes the strategy to design a multifunctional, chitosan based nanomaterials and their biomedical and environmental applications. Different physicochemical methods including FESEM/TEM, PPMS were used to characterize the obtained nanomaterials. For each application, a series of specific characterizing methods were used for evaluating the applicability/capacity of materials.
Interface between End-Functionalized PEO Oligomers and a Silica Nanoparticle Studied by Molecular Dynamics Simulations (2004)

Fully atomistic molecular dynamics (MD) simulations have been carried out on a series of bulk melt pure PEO oligomers and PEO oligomer−silica systems, which differed by their macromolecular end groups. A realistic hybrid model of a silica nanoparticle combining an ionic core as well as the fine-tuning of the surface thickness and number of OH groups per unit surface area was used. The PEO oligomers were decorrelated in all systems under study in order to prevent any artifacts related to the preparation procedure. Significant changes were found to occur in the immediate vicinity of the interface with flattened PEO backbones arranged in densily packed shells and stabilized by the added PEO−silica interactions. Their conformations were also more coiled in order to better adapt to the surface structure. While methyl end groups did not show special characteristics other than their steric effect, hydroxyl end groups had a much higher affinity for the surface and tended to position themselves perpendicular to the surface, thus forming dynamic hydrogen-bonding complexes between the hydroxyl oxygens and the silanol hydrogens. The range of influence of the nanoparticle was evident for structural properties only up to two or three molecular layers, 10−15 Å, but was approximately twice that for dynamical ones.
Assessment of the properties of poly(L-lactic acid) sheets produced with differing amounts of postconsumer recycled poly(L-lactic acid) (2012)

The properties of sheet containing mechanically recycled postconsumer poly(L-lactic acid) bottle flakes blended with virgin poly(L-lactic acid) resin were assessed. Poly(L-lactic acid) bottles were flaked, cleaned, blended with virgin resin and then extruded and thermoformed into trays. The molecular weight, physical, optical, thermal and mechanical properties of the sheet containing 0, 20, 40, 60, 80 and 100 wt.% poly(L-lactic acid) recycled content were evaluated. The best cleaning conditions were found by using a mixed-level fractional factorial design. Cleaning conditions of 15 min, at 85°C, 1 wt.% NaOH and 0.3 wt.% surfactant were adopted for cleaning the poly(L-lactic acid) flakes. Cast-extruded virgin poly(L-lactic acid) sheet had superior mechanical and optical properties than recycled poly(L-lactic acid) sheet. Recycled poly(L-lactic acid) sheets were darker and absorbed more ultraviolet light in the 260 to 285 nm range when 20% or more recycled content was added. At 40% poly(L-lactic acid) recycled content, the sheet had increased blue and red tones and the mechanical properties in the cross-machine direction decreased. At 60% poly(L-lactic acid) recycled content or above, reduction of weight average molecular weight, tensile strength and tensile strength at yield in the machine direction were found. At 80% poly(L-lactic acid) recycled content, the melting temperature and modulus of elasticity in the machine direction decreased. All sheet samples were successfully thermoformed into trays showing the potential to use post-consumer poly(L-lactic acid) flakes in the production of poly(L-lactic acid) containers.
Charge Separation in a Ruthenium-Quencher Conjugate Bound to DNA (2007)

A novel tris heteroleptic dipyridophenazine complex of ruthenium(II), [{Ru(phen)(dppz)(bpy'-his)}{Ru(NH3)5}]5+, containing a covalently tethered ruthenium pentammine quencher coordinated through a bridging histidine has been synthesized and characterized spectroscopically and biochemically in a DNA environment and in organic solvent. Steady-state and time-resolved luminescence measurements indicate that the tethered Ru complex is quenched relative to the parent complexes [Ru(phen)(dppz)(bpy')]2+ and [Ru(phen)(dppz)(bpy'-his)]2+ in DNA and acetonitrile, consistent with intramolecular photoinduced electron transfer. Intercalated into guanine-containing DNA, [{Ru(phen)(dppz)(bpy'-his)}{Ru(NH3)5}]5+, upon excitation and intramolecular quenching, is capable of injecting charge into the duplex based upon the EPR detection of guanine radicals. DNA-mediated charge transport is also indicated using a kinetically fast cyclopropylamine-substituted base as an electron hole trap. Guanine damage is not observed, however, in measurements using the guanine radical as the kinetically slower hole trap, indicating that back electron-transfer reactions are competitive with guanine oxidation. Moreover, transient absorption measurements reveal a novel photophysical reaction pathway for [{Ru(phen)(dppz)(bpy'-his)}{Ru(NH3)5}]5+ in the presence of DNA that is competitive with the intramolecular flash-quench process. These results illustrate the remarkably rich redox chemistry that can occur within a bimolecular ruthenium complex intercalated in duplex DNA.