gebhart/patrepeval huggingface dataset:
DNA "melting" proteins. I. Effects of bovine pancreatic ribonuclease binding on the conformation and stability of DNA. (1976)

Bovine pancreatic ribonuclease is a DNA "melting" protein, since it binds with greater overall affinity to the single-stranded than to the double-stranded form of natural and synthetic deoxyribose-containing polynucleotides. As such, the DNA-RNase system provides a simple model for the more complex and biologically relevant melting protein-nucleic acid systems. Aspects of the DNA-RNase interactions which are related to the quantitative assessment of this system as a melting protein model are investigated here. A boundary sedimentation velocity technique is used to measure thermodynamic parameters of the interaction; association constants (Kh and Kc) and site sizes (nh and nc) are determined for the interaction of ribonuclease with native (double helical) and denatured (random coil) DNA. It is shown that log Kh and log Kc are linear functions of log [Na+], binding decreasing with increasing Na+ concentration, with Kh about 2 orders of magnitude smaller than Kc at the ionic strengths studied, nh and nc are approximately 8 and approximately 11 nucleotide residues, respectively, indicating that potential binding sites overlap. Binding to both forms of DNA is non-cooperative. It is shown by CD and ultraviolet spectroscopy that the binding of RNase to single- and double-stranded DNA perturbs the conformations of these polynucleotide conformations very little relative to the unliganded structures. Hydrodynamic methods are used to show that RNase binds to native DNA without altering the overall solution structure of the latter; however conditons which permit binding to, and stabilization of, transiently exposed single-stranded sequences result in a collapse of the stiff native DNA structure. We demonstrate by melting transition studies that ribonuclease does bring about an equilibrium destabilization of native DNA and poly [d(A-T)] and, by applying a ligand-perturbed helic in equilibrium coil theory developed by McGhee (McGhee, J.D. (1976) Biopolymers 15, 1345-1375), it is shown that the extent of the observed destabilization is in semiquantitative accord with expectations based on the measured affinity constants and site sizes for RNase binding to both DNA conformations. Spectral methods are used to show that the relative stability of native DNA sequences of varying base composition is the same in the presence and absence of ribonuclease, strongly arguing that this "melting" ligand "traps" single-stranded sequences transiently exposed by thermal fluctuations. RNase also undergoes an order in equilibrium disorder conformational transition as a function of temperature (the denatured form of RNase stabilizes native DNA, while native RNase destabilizes the native double helix), and the coupled equilibria involved in these interacting conformational changes are interpreted and discussed as possible models of genome regulatory interactions.
Synchronization architecture and protocols for a multimedia news service application (1994)

We present a complete software control architecture for synchronizing multiple data streams generated from distributed media-storing database servers without the use of a global clock. Traffic prediction and scheduling is performed by the independent sources for the remote presentation. Certain compensation mechanisms at the receiver are also necessary because of the random network delays. A stream synchronization protocol (SSP) allows for synchronization recovery to preserve a high quality multimedia display at the receiver. SSP uses synchronization quality of service parameters to guarantee the simultaneous delivery of the different types of data streams. The various components of the architecture interact to provide real-time multimedia functions such as those found on VCRs.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
AffectiveWear (2015)

Facial expression is a powerful way for us to exchange information nonverbally. They can give us insights into how people feel and think. There are a number of works related to facial expression detection in computer vision. However, most works focus on camera-based systems installed in the environment. With this method, it is difficult to track user's face if user moves constantly. Moreover, user's facial expression can be recognized at only a limited place.
Time-referenced single-path multi-bit ΔΣ ADC using a VCO-based quantizer (2000)

In this paper, we present a single-path multi-bit delta-sigma analog-to-digital converter (/spl Delta//spl Sigma/ ADC) architecture that uses time as a reference for performing multi-bit digital-to-analog conversion in the feedback path. The architecture uses a voltage-controlled oscillator as a multi-bit quantizer. In the feedback path of the /spl Delta//spl Sigma/ ADC, the errors due to component mismatch are avoided by using a single-path for all the levels in a multi-bit digital-to-analog converter (DAC). The technique eliminates the need for feedback DAC architectures with static and dynamic component matching.
Regulation of Arabidopsis thaliana Em genes: role of ABI5 (2002)

In order to identify new factors involved in Em (a class I Late Embryogenesis Abundant protein) gene expression, Arabidopsis mutants with an altered expression of an Em promoter GUS fusion construct and a modified accumulation of Em transcripts and proteins were isolated. Germination tests on ABA showed that the most affected mutant had a weak abi phenotype. Complementation tests further revealed this mutant to be a new abi5 allele, consequently named abi5-5. In addition to reducing the final level of Em transcripts in the dry seed, the abi5-5 mutation causes a delay in the accumulation of AtEm1 during seed development. An additional characteristic of the abi5-5 mutant, is the ability of its seeds to germinate at high concentrations of salt and mannitol. The abi5-5 mutation was characterized at the molecular level and was shown to result from a two base pair deletion in the coding sequence of the ABI 5 gene. The wild type and mutant recombinant proteins were produced in E. coli and were assayed for DNA-binding activity on their target promoters by electrophoretic mobility shift assay (EMSA). The ABI5 recombinant protein binds the ABRE sequence in the AtEm6 promoter as shown by Dnase footprinting. Among the ABRE-type sequences selected on both Em promoters, the G-box type AGACACGTGGCATGT element of the AtEm6 promoter shows the strongest binding by EMSA quantification.
Bioconjugation of hydrogen-bonded organic semiconductors with functional proteins (2015)

We report on bioconjugation strategies to functionalize hydrogen-bonded pigment semiconductors with proteins, and demonstrate hybrid bioelectronics devices operating under aqueous conditions.
Sketchpad a Man-Machine Graphical Communication System (1964)

The Sketchpad system makes it possible for a man and a computer to converse rapidly through the medium of line drawings. Heretofore, most interaction between man and computers has been slowed down by the need to reduce all communication to written statements that can be typed; in the past, we have been writing letters to rather than conferring with our computers. For many types of communication, such as describing the shape of a mechanical part or the connections of an electrical circuit, typed statements can prove cumbersome. The Sketchpad system, by eliminating typed statements (except for legends) in favor of line drawings, opens up a new area of man-machine communication.
Strongly non-linear optical ferroelectric liquid crystals for frequency doubling (1993)

Abstract From our research for novel non-linear optical (NLO) materials for frequency doublers and optical modulators we report on new ferroelectric liquid crystals, which for the first time, exhibit second order NLO coefficients (for example d 22 = 5 pm V−1, which are comparable to those of state of the art inorganic NLO materials. The novel compounds contain 5-amino-2-nitrophenyl groups attached close to the chiral centres. The switching behaviour of the new compounds, their spontaneous polarization, as well as their frequency doubling of Nd:YAG laser pulses in the S*c and in the glass state, are reported. Moreover their waveguiding properties are presented.
Watt-range, coherent, uniphase powers from phase-locked arrays of antiguided diode lasers (1991)

Twenty-element near-resonant AlGaAs/GaAs arrays of antiguides have been optimized for maximum intermodal discrimination and large Strehl ratio. It is found that 1000-μm-long devices with two intracavity Talbot-type spatial filters, and a 3 to 1 ratio between element core and interelement spacing provide the best results. The intermodal discrimination is discussed for both Talbot and uniform devices. For devices with two Talbot-type spatial filters, diffraction-limited-beam operation is obtained to 1 W pulsed power, and operation in a beam with lobewidth 1.5× diffraction limit is obtained to 2 W and 19× threshold. cw diffraction-limited-beam operation is obtained to 0.5 W, limited by thermal considerations. Uniform devices operate in beams with lobewidth ≊3× diffraction limit to 5 W and 45× threshold. At 5 W total output the coherent uniphase power is 1.6 W, and the coherent power in the main lobe is 0.94 W.
Living Radical Polymerization by the RAFT Process (2005)

This paper presents a review of living radical polymerization achieved with thiocarbonylthio compounds [ZC(=S)SR] by a mechanism of reversible addition–fragmentation chain transfer (RAFT). Since we first introduced the technique in 1998, the number of papers and patents on the RAFT process has increased exponentially as the technique has proved to be one of the most versatile for the provision of polymers of well defined architecture. The factors influencing the effectiveness of RAFT agents and outcome of RAFT polymerization are detailed. With this insight, guidelines are presented on how to conduct RAFT and choose RAFT agents to achieve particular structures. A survey is provided of the current scope and applications of the RAFT process in the synthesis of well defined homo-, gradient, diblock, triblock, and star polymers, as well as more complex architectures including microgels and polymer brushes.
Restoration of ultraviolet-induced unscheduled DNA synthesis of xeroderma pigmentosum cells by the concomitant treatment with bacteriophage T4 endonuclease V and HVJ (Sendai virus). (1975)

Ultraviolet (UV)-induced unscheduled DNA synthesis of xeroderma pigmentosum cells, belonging to complementation groups A, B, C, D, and E, was restored to the normal level by concomitant treatment of the cells with T4 endonuclease V and UV-inactivated HVJ (Sendai virus). The present results suggest that (1) T4 endonuclease molecules were inserted effectively into the cells by the interaction of HVJ with the cell membranes, (2) the enzyme was functional on human chromosomal DNA which had been damaged by UV irradiation in the viable cells, (3) all the studied groups of xeroderma pigmentosum ("variant" was not tested) were defective in the first step (incision) of excision repair.
Epidermal Growth Factor Receptor Inhibitor–Associated Cutaneous Toxicities: An Evolving Paradigm in Clinical Management (2007)

Epidermal growth factor receptor inhibitors (EGFRIs) have demonstrated improved overall survival in patients with non-small cell lung cancer, pancreatic cancer, and colorectal cancer; however, their use is associated with dermatologic reactions of varying severity. The similar spectrum of events observed with monoclonal antibodies and tyrosine kinase inhibitors suggests such toxicities are a class effect. While such reactions do not necessarily require any alteration in EGFRI treatment, being best addressed through symptomatic treatment, there is limited evidence on which to base such therapies. In October 2006, at an international and interdisciplinary EGFRI dermatologic toxicity forum, the underlying mechanisms of these toxicities were discussed and commonly used therapeutic interventions were evaluated. Our aim was to reach a current consensus on management strategies. A three-tiered, EGFRI-focused toxicity grading system is suggested for the purposes of therapeutic decision making, and as a framework on which to build a stepwise approach to intervention. This approach to successful management is specifically tailored to accurately categorize dermatologic toxicity associated with EGFRIs, and can be easily applied by all health care professionals. The goal is to maximize quality of life in patients who are being treated with these agents--many of whom will be on these drugs for several months or even years.
α-Synuclein in Familial Alzheimer Disease (2001)

These data suggest that the epitope profiles of alpha-synuclein in LBs are similar, regardless of whether the biological trigger is related to synuclein or a different genetic pathway. These findings support the hypothesis that the mechanism of alpha-synuclein aggregation is the same within cell types but distinctive between cell types.
Haloperidol binding to monoclonal antibodies. Predictions of three-dimensional combining site structure via computer modeling. (1988)

The amino acid sequences of five monoclonal antibodies (designated mAbs A-E) which bind to the dopaminergic D-2 antagonist, haloperidol, with a variety of affinities (Kd = 4-810 nM), have been used to build theoretical, three-dimensional, computer models of the variable region combining sites. Physiocochemical interactions which have been previously determined from in vitro binding data have been used to orient the drug molecule within the combining site model. The results indicate that hydrophobic, aromatic, and ionic amino acids are involved in specific interactions with the antagonist molecule. For example, fluorescence quenching data suggests that a tryptophan residue is intimately involved in the binding of haloperidol by mAb A. Examination of the modeled structure reveals five tryptophans within the variable fragment, only one of which (H-50) is within the classical beta-barrel binding pocket and is readily accessible to the antigen. Haloperidol's relatively electron poor fluorophenyl ring system stacks with the electron-rich tryptophan ring system at a distance of 3.3 A and in so doing, places haloperidol's positively charged piperidinyl nitrogen atom within hydrogen bond distance of the negatively charged Glu-95 and Asp-100A residues of the H3 loop (Glu-H-95 and Asp-H-100A). This type of analysis for each antibody provides an interesting profile of changes in amino acid composition and hypervariable loop length which markedly effect binding affinity and specificity for a series of proteins which have similar combining site.
The Proto-oncoprotein Brx Activates Estrogen Receptor β by a p38 Mitogen-activated Protein Kinase Pathway (2001)

The estrogen receptors (ERs) are ligand-inducible transcription factors that play key roles in the control of growth and differentiation in reproductive tissues. We showed that the novel Dbl family proto-oncoprotein Brx enhances ligand-dependent activity of ERalpha via a Cdc42-dependent pathway. Brx also significantly enhances ligand-dependent activity of ERbeta. This enhancement is not affected by inhibition of p44/42 mitogen-activated protein kinase (MAPK) activation by PD98059. However, addition of the p38 MAPK inhibitor SB202190 abrogates the enhancement of ERbeta activity by Brx, showing that p38 MAPK activity is required for the enhancement of ERbeta function by Brx. In COS-7 cells, transfection of Brx leads to activation of endogenous p38 MAPK activity. Co-expression of the beta2 isoform of human p38 MAPK and a constitutively active form of the p38 MAPK kinase MKK6 (MKK6-EE) synergistically augments ligand-dependent activity of ERbeta. Our findings suggest that p38 MAPKs may be important regulators of ERbeta activity.
Reset-free integrated polarization controller using phase shifters (2005)

An endless, reset-free polarization controller implemented with planar lightwave circuits using phase shifters for tuning is proposed and demonstrated. By avoiding the need for tunable polarization mode converters, simple fabrication processes and a large range of material systems can be used, since neither the electrooptic effect nor a rotatable birefringence axis are necessary for device operation. The proof of concept is demonstrated by implementing the equivalent of a rotating waveplate using Ge-doped silica-on-silicon waveguides and thermooptic phase shifters. The polarization controller is shown to have excellent tolerance to fabrication variations. Fast thermooptic control (on the order of 10 kHz) is achieved using high-index-contrast (4%) waveguides.
Swt1, a Novel Yeast Protein, Functions in Transcription (2006)

The conserved TREX complex couples transcription to nuclear mRNA export. Here, we report that the uncharacterized open reading frame YOR166c genetically interacts with TREX complex components and encodes a novel protein named Swt1 for "synthetically lethal with TREX." Co-immunoprecipitation experiments show that Swt1 also interacts with the TREX complex biochemically. Consistent with a potential role in transcription as suggested by its interaction with TREX, Swt1 localizes mainly to the nucleus. Importantly, deletion of Swt1 leads to decreased transcription. Taken together, these data suggest that Swt1 functions in gene expression in conjunction with the TREX complex.
DNA methylation analysis of the promoter region of the human telomerase reverse transcriptase (hTERT) gene. (1999)

The promoter of the hTERT gene encoding the catalytic subunit of telomerase was recently cloned and has a dense CG-rich CpG island, suggesting a role for methylation in regulation of hTERT expression. In this study, we have initiated the analysis of the regulation of hTERT expression by examining the methylation status of up to 72 CpG sites extending from 500 bases upstream of the transcriptional start site of the hTERT gene into the first exon in 37 cell lines. These cell lines represent a variety of cell and tissue types, including normal, immortalized, and cancer cell lines from lung, breast, and other tissues. Using bisulfite genomic sequencing, we did not find a generalized pattern of site-specific or region-specific methylation that correlated with expression of the hTERT gene: most of the hTERT-negative normal cells and about one-third of the hTERT-expressing cell lines had the unmethylated/hypomethylated promoter, whereas the other hTERT-expressing cell lines showed partial or total methylation of the promoter. The promoter of one hTERT-negative fibroblast cell line, SUSM-1, was methylated at all sites examined. Treatment of SUSM-1 cells with the demethylating agent 5-aza-2'-deoxycytidine and the histone deacetylase inhibitor trichostatin A induced the cells to express hTERT, suggesting a potential role for DNA methylation and/or histone deacetylation in negative regulation of hTERT. This study indicates that there are multiple levels of regulation of hTERT expression in CpG island methylation-dependent and -independent manners.
Stay in-the-know regarding informed consent (2002)

Informed consent hinges on educating patients about their proposed treatments.
Primary Ovarian Leiomyomas: A Case Report and Review of the Literature (1999)

Primary ovarian leiomyomas are uncommon benign tumors that are usually asymptomatic. Distinguishing them from other ovarian tumors is important in order to render the appropriate prognosis and treatment. The authors describe a 6 × 7 cm primary ovarian leiomyoma in a 45-year-old woman that was surgically managed. The histologie and immunohistochemical characteristics and pathogenesis are presented. (J GYNECOL SURG 15:55, 1999)
Evaluation of commercially supplied silver coated Teflon for spacecraft temperature control usage (1974)

A series of tests are described which were performed to evaluate the acceptability of a commercially supplied silver backed teflon thermal control coating relative to teflon previously coated at GSFC. Optical measurements made on numerous samples indicate that the commercial material possesses an average solar absorptance of 0.085, an emittance of 0.76 and an average alpha/epsilon equal to 0.112, all of which are equivalent to the GSFC coated teflon. The emittance of the protective inconel backing was found to be 0.037. The coating is shown to have good adhesion at the Ag-teflon interface and exposure to UV irradiation uncovered no coating irregularities. Temperature cycling over the range -135 C to +200 C produced crazing in the evaporated Ag layer as expected but no delamination was observed. The suitability of Mystik no. 7366 and 3M no. 467 adhesives as bonding agents for the metallized polymer is demonstrated. Various problems associated with production reproducibility and selection of a proper bonding process are discussed.
Oxidation of Some Sulfated Carbohydrates: Kinetics and Mechanism of Oxidation of Chondroitin-4-Sulfate by Alkaline Permanganate with Novel Synthesis of Coordination Biopolymer Precursor (2013)

The kinetics of oxidation of chondroitin-4-sulfate as sulfated carbohydrates by alkaline permanganate has been investigated spectrophotometrically. The oxidation reaction was found to proceed through two-distinct stages. The first stage was found to be relatively fast involving the formation of unstable green [CS, MnVIO42-] and blue [CS, MnVO43-] biopolymeric coordination intermediates at wavelengths of 610 and 730 nm, respectively. The second stage was corresponding to a slow decomposition of such intermediates to give rise to keto-acid derivative and soluble-colloidal manganese (IV) as final oxidation products. The oxidation reaction was found to be base-catalyzed. The kinetic parameters have been evaluated and a tentative oxidation reaction mechanism in good consistent with the kinetic results was suggested and discussed. Novel keto-acid derivative has been synthesized. The reaction product was characterized and identified by elemental analysis and spectral data.
Late and Long-lasting Response in an Adult Chronic Idiopathic Thrombocytopenic Purpura after Extended Course of Rituximab (2003)

"Late and Long-lasting Response in an Adult Chronic Idiopathic Thrombocytopenic Purpura after Extended Course of Rituximab." Leukemia & Lymphoma, 44(3), pp. 561–562KeywordsRituximabChronic Idiopathic Thrombocytopenic PurpuraMonoclonal AntibodyPrednisone
The UDP-N-acetylglucosamine:Dolichol Phosphate-N-acetylglucosamine-phosphotransferase Gene as a New Selection Marker for Potato Transformation (2013)

Here we describe the generation of potato plants that constitutively overexpressed, UDP-N-acetylglucosamine:dolichol phosphate-N-acetylglucosamine-phosphotransferase (GPT). Such transgenic plants can be formed in a medium with tunicamycin at 9.8 ± 0.28% efficiency, similar to the 9.4 ± 1.10 for the bialaphos resistance gene (Bar) gene. This study indicated that GPT transformation was very stable with high reproducibility, and that growth and tuber production in the GPT-transformed plants were stronger than in the wild-type plants.
Parylene flexible neural probes integrated with microfluidic channels (2005)

The fluidic channel in the flexible probe has three functions: (i) to inject chemicals into the tissues, (ii) to measure the neural activities from the tissues, and (iii) to improve the mechanical stiffness of the probe by filling the channel with a solid material. A 10-microm-thick microfluidic channel was embedded into the probe by using sacrificial photoresist patterns. Polyethylene glycol (PEG), which is solid at room temperature and dissolves when in contact with water, was used to fill the channel and increase the stiffness of the probe before insertion into the tissue. The impedance of the electrode inside the fluidic channel was around 100 kOmega at 1 kHz when the channel was filled with saline solution. We were able to insert the probe into a rat's brain and measure the neural signals with the electrode.