gebhart/patrepeval huggingface dataset:
Protein B of soluble methane monooxygenase from Methylococcus capsulatus (Bath). A novel regulatory protein of enzyme activity. (1985)

An understanding of the mechanism of biological methane oxidation has been hampered by the lack of purified proteins. We describe here a purification protocol for the previously uncharacterized protein B of the soluble methane monooxygenase from the obligate methanotroph Methylococcus capsulatus (Bath). Soluble methane monooxygenase is a multicomponent enzyme consisting of a hydroxylase component, protein A, a reductase component, protein C, and protein B. All three proteins are required for monooxygenase activity. Protein B proves to be a low molecular weight (16,000) single subunit protein devoid of prosthetic groups. The protein is a powerful regulator of soluble methane monooxygenase activity, possessing the capacity to convert the enzyme from an oxidase to an oxygenase. Proteins A and C together catalyze the reduction of molecular oxygen to water, a reaction prevented by protein B. The uncoupling of soluble methane monooxygenase in this manner displays a number of novel features. First, the product of the uncoupled reaction is water, and second, the uncoupling is independent of substrate. Free hydrogen peroxide is not an intermediate in the reduction of oxygen by the incomplete methane monooxygenase enzyme complex. Finally, electron transfer can occur between protein C and protein A in the absence of protein B and protein B prevents the steady-state transfer of electrons in the absence of an oxidizable substrate, such as methane. It is demonstrated that oxygen reduction occurs at the active site of the hydroxylase component, protein A. A unifying mechanism, describing the interaction of the three proteins of soluble methane monooxygenase, is proposed.
Forensic aspects of DNA-based human identity testing (2008)

The forensic applications of DNA-based human identity laboratory testing are often underappreciated. Molecular biology has seen an exponential improvement in the accuracy and statistical power provided by identity testing in the past decade. This technology, dependent upon an individual's unique DNA sequence, has cemented the use of DNA technology in the forensic laboratory. This paper will discuss the state of modern DNA-based identity testing, describe the technology used to perform this testing, and describe its use as it relates to forensic applications. We will also compare individual technologies, including polymerase chain reaction (PCR) and Southern Blotting, that are used to detect the molecular differences that make all individuals unique. An increasing reliance on DNA-based identity testing dictates that healthcare providers develop an understanding of the background, techniques, and guiding principles of this important forensic tool.
Evaluation of the Utility of Interphase Cytogenetics to Detect Residual Cells with a Malignant Genotype in Mixed Cell Populations: A Burkitt Lymphoma Model (1993)

Interphase cytogenetics has been used to detect tumor cells in the presence of a large excess of normal cells. Probes for fluorescence in situ hybridization were chosen to reveal a specific hybridization pattern in tumor cell nuclei as well as to provide an internal control for the assessment of the hybridization results. By enumerating mixtures of cytogenetically normal cells and tumor cells from a Burkitt lymphoma cell line, we were able to detect tumor cells at a frequency of one in 500. Normal cells could be differentiated from Burkitt lymphoma cells with a specificity of approximately 99.9%.
Coated Colloids: Preparation, Characterization, Assembly and Utilization (2002)

This chapter contains sections titled: Introduction Preparation and Characterization of Coated Colloids Layer-by-Layer Adsorption Colloid Precipitation Assembly and Utilization of Coated Colloids Mesoscopic Arrangement Enzymatic Catalysis Dispersions Thin Films Optical Properties Further Applications
Human Papillomavirus Vaccines and Prevention of Cervical Cancer (2004)

Cervical cancer and precancerous cervical lesions constitute a major problem in women's health. Every year 470,000 cases of cervical cancer are diagnosed worldwide, and about half the women afflicted will die. In the United States alone, approximately 14,000 cases of cervical cancer are diagnosed each year despite the availability of screening and access to high-quality gynecological care. With the confirmation that cervical cancer is caused by an infectious agent, human papillomavirus, the possibility of fighting this disease with either prophylactic or therapeutic vaccination arose. This review describes advances in vaccine development and very promising first results for prophylactic vaccination against cervical cancer.
Maximizing parallelism and minimizing synchronization with affine transforms (1997)

This paper presents the first algorithm to find the optimal affine transform that maximizes the degree of parallelism while minimizing the degree of synchronization in a program with arbitrary loop nestings and affine data accesses. The problem is formulated without the use of imprecise data dependence abstractions such as data dependence vectors. The algorithm presented subsumes previously proposed program transformation algorithms that are based on unimodular transformations, loop fusion, fission, scaling, reindexing and/or statement reordering.
Heme oxygenase-1 induction by NRF2 requires inactivation of the transcriptional repressor BACH1 (2007)

Oxidative stress activates the transcription factor NRF2, which in turn binds cis-acting antioxidant response element (ARE) enhancers and induces expression of protective antioxidant genes. In contrast, the transcriptional repressor BACH1 binds ARE-like enhancers in cells naïve to oxidative stress and antagonizes NRF2 binding until it becomes inactivated by pro-oxidants. Here, we describe the dynamic roles of BACH1 and NRF2 in the transcription of the heme oxygenase-1 (HMOX1) gene. HMOX1 induction, elicited by arsenite-mediated oxidative stress, follows inactivation of BACH1 and precedes activation of NRF2. BACH1 repression is dominant over NRF2-mediated HMOX1 transcription and inactivation of BACH1 is a prerequisite for HMOX1 induction. In contrast, thioredoxin reductase 1 (TXNRD1) is regulated by NRF2 but not by BACH1. By comparing the expression levels of HMOX1 with TXNRD1, we show that nuclear accumulation of NRF2 is not necessary for HMOX1 induction; rather, BACH1 inactivation permits NRF2 already present in the nucleus at low basal levels to bind the HMOX1 promoter and elicit HMOX1 induction. Thus, BACH1 confers an additional level of regulation to ARE-dependent genes that reveals a new dimension to the oxidative stress response.
Subtiligase: a tool for semisynthesis of proteins. (1994)

A variant of subtilisin BPN', which we call subtiligase, has been used to ligate esterified peptides site-specifically onto the N termini of proteins or peptides in aqueous solution and in high yield. We have produced biotinylated or heavy-atom derivatives of methionyl-extended human growth hormone (Met-hGH) by ligating it onto synthetic peptides containing biotin or mercury. Polyethylene glycol (PEG)-modified atrial natriuretic peptide (ANP) was produced by ligating ANP onto peptides containing sites for PEG modification. We have established the N-terminal sequence requirements for efficient ligation onto proteins, using either synthetic substrates or pools of filamentous phage containing Met-hGH with random N-terminal sequences (substrate phage). To facilitate ligations involving proteins with highly structured or buried N termini, a more stable subtiligase was designed that effectively ligates peptides onto Met-hGH even in 4 M guanidine hydrochloride. The use of subtiligase should expand the possibilities for protein semisynthesis and rational protein design.
Comparison of camptothecin derivatives presently in clinical trials: genotoxic potency and mitotic recombination (2002)

The genotoxicity of camptothecin (CPT) and its clinical antineoplastic analogues irinotecan (CPT-11) and topotecan (TPT) were evaluated using the wing somatic mutation and recombination test (SMART) in Drosophila melanogaster. These compounds stabilize and trap the topoisomerase I-DNA complex, preventing the religation step of the breakage/rejoining reaction mediated by the enzyme. The standard version of the wing SMART was used to evaluate the three compounds and to compare the wing spots induced in marker-heterozygous and balancer-heterozygous flies. The results demonstrate that all compounds tested have a significant genotoxic effect in both genotypes analysed. At the same time, a comparison of the clone induction frequencies in marker-heterozygous and balancer-heterozygous flies shows that mitotic recombination is the prevalent mechanism through which the three compounds induce all categories of wing spots (78-93% recombination). TPT was the most genotoxic compound, probably because substitutions of amino groups for the 9-carbon of the CPT A ring leads to compounds with greater in vivo activity. CPT and CPT-11 induced, respectively, about 7 and 28 times fewer mutant clones per millimolar exposure unit than TPT.
Early Intervention for Young Children with Autism: Continuum-Based Behavioral Models (1999)

Over the last three decades, instructional methods derived from applied behavior analysis (ABA) have shown considerable promise for many young children with autism. The ABA approach establishes a priori that assessment and intervention methods must be based on generally accepted rules of scientific evidence. On one hand, the approach has produced a rich resource of conceptually consistent and scientifically validated techniques that can be applied in various combinations across many different contexts. On the other hand, this diversity has resulted in some confusion regarding the precise characteristics of ABA. In this article, the authors first describe many of the common programmatic and methodologic elements that form the foundation of the approach. A summary of the scope of the behavioral research is provided including greater detail on six studies that demonstrated large-scale interventions. Finally, the authors describe components of program models that share common elements of the ABA approach and use a broad continuum of traditional behavioral techniques. Some specific myths about the approach are simultaneously addressed.
Mechanism and role of PDZ domains in signaling complex assembly (2001)

PDZ domains are protein-protein recognition modules that play a central role in organizing diverse cell signaling assemblies. These domains specifically recognize short C-terminal peptide motifs, but can also recognize internal sequences that structurally mimic a terminus. PDZ domains can therefore be used in combination to bind an array of target proteins or to oligomerize into branched networks. Several PDZ-domain-containing proteins play an important role in the transport, localization and assembly of supramolecular signaling complexes. Examples of such PDZ-mediated assemblies exist in Drosophila photoreceptor cells and at mammalian synapses. The predominance of PDZ domains in metazoans indicates that this highly specialized scaffolding module probably evolved in response to the increased signaling needs of multicellular organisms.
State estimation and feedforward tremor suppression for a handheld micromanipulator with a Kalman filter (2011)

Active compensation of physiological tremor for handheld micromanipulators depends on fast control and actuation responses. Because of real-world latencies, real-time compensation is usually not completely effective at eliminating unwanted hand motion. By modeling tremor, more effective cancellation is possible by anticipating future hand motion. We propose a feedforward control strategy that utilizes tremor velocity from a state-estimating Kalman filter. We demonstrate that estimating hand motion in a feedforward controller overcomes real-world latencies in micromanipulator actuation. In hold-still tasks with a fully handheld micromanipulator, the proposed feedforward approach improves tremor rejection by over 50%.
Tissue Engineering Based on Cell Sheet Technology (2007)

Abstract Cell sheet technology enables novel approaches to tissue engineering without the use of biodegradable scaffolds. Cell sheet technology consists of a temperature‐responsive culture dish, which enables reversible cell adhesion to and detachment from the dish surface by controllable hydrophobicity of the surface. This allows for a non‐invasive harvest of cultured cells as an intact monolayer cell sheet including deposited extra cellular matrices. The monolayer cell sheet can be transplanted to host tissues without using biodegradable scaffolds and sutures. Thick tissue constructs and patterned cell sheets using two or more kinds of cell source are also developed by means of layered cell sheets in vitro. This Progress Report summarizes temperature‐controlled cell adhesion‐detachment behavior and applications of the cell sheet technology to regeneration of cornea, periodontal ligament, bladder epithelia, oesophageal epithelia, myocardium, and liver.
PROJECT MANAGEMENT IMPROVED MULTIWELL SHALLOW GAS DEVELOPMENT (1995)

Because of time and economic constraints, a multiwell shallow gas development project in southeastern Alberta required thorough pre-job planning and special drilling, cementing, and completions designs. The project took place during a period of peak industry activity, putting extra challenges on logistics and services.
Introducing a new section to Breast Cancer Research: Endocrinology and hormone therapy (2003)

Endocrine therapy is increasingly understood as the conceptual basis for the future treatment and prevention of breast cancer. Endocrine agents have considerably changed the approach to targeted treatment during the past two decades, and select endocrine agents have advanced the goal of preventing breast cancer. Progress has occurred because of a vigorous interaction between laboratory scientists and the clinical trials community. Breast Cancer Research is launching a new section on endocrinology and hormone therapy in order to invigorate this exchange and challenge our readers with novel concepts that might result in enhanced survival in breast cancer.
Which Polyphenolic Compounds Contribute to the Total Antioxidant Activities of Apple? (2005)

The antioxidant activities of eight apple cultivars were studied by using the ferric reducing/antioxidant power (FRAP), the beta-carotene-linoleic acid model system (beta-CLAMS), and the photochemiluminescent (PCL) assays. The antioxidant activity of apples is highly correlated to the total phenolic content (TPC) measured by the Folin-Ciocalteu method and the total polyphenolic index (TPI) obtained by HPLC. Extracts of the peel and flesh were analyzed and assayed separately. The FRAP activities of both peel and flesh extracts correlate well with the TPC (r = 0.95 and 0.99, respectively) and the TPI (r = 0.82 and 0.99, respectively). Similar results were found in the beta-CLAMS activities, showing correlation coefficients of r = 0.90 and 0.91 with the TPC for the peel and flesh extracts and of r = 0.90 and 0.84 with the TPI for the peel and flesh extracts, respectively. The antioxidant activity measured by the PCL assay was not correlated with TPC or TPI due to the lack of integratable lag phase in this method with the flavan-3-ols/procyanidins. Among the five major polyphenolic groups, flavan-3-ols/procyanidins had the highest positive correlation with the FRAP and beta-CLAMS activities: r = 0.84 and 0.88 for the peel extracts, respectively; and r = 0.98 and 0.87 for the flesh extracts, respectively. At individual compound level, epicatechin and procyanidin B2 were the major contributors to the antioxidant activity of apple. Hydroxycinnamic acids may have a significant role in the flesh.
Directed evolution of a (βα) 8 -barrel enzyme to catalyze related reactions in two different metabolic pathways (2000)

Enzymes participating in different metabolic pathways often have similar catalytic mechanisms and structures, suggesting their evolution from a common ancestral precursor enzyme. We sought to create a precursor-like enzyme for N'-[(5'-phosphoribosyl)formimino]-5-aminoimidazole-4-carboxamide ribonucleotide (ProFAR) isomerase (HisA; EC ) and phosphoribosylanthranilate (PRA) isomerase (TrpF; EC ), which catalyze similar reactions in the biosynthesis of the amino acids histidine and tryptophan and have a similar (betaalpha)(8)-barrel structure. Using random mutagenesis and selection, we generated several HisA variants that catalyze the TrpF reaction both in vivo and in vitro, and one of these variants retained significant HisA activity. A more detailed analysis revealed that a single amino acid exchange could establish TrpF activity on the HisA scaffold. These findings suggest that HisA and TrpF may have evolved from an ancestral enzyme of broader substrate specificity and underscore that (betaalpha)(8)-barrel enzymes are very suitable for the design of new catalytic activities.
Methods for strand-specific DNA detection with cationic conjugated polymers suitable for incorporation into DNA chips and microarrays (2005)

A strand-specific DNA sensory method is described based on surface-bound peptide nucleic acids and water-soluble cationic conjugated polymers. The main transduction mechanism operates by taking advantage of the net increase in negative charge at the peptide nucleic acid surface that occurs upon single-stranded DNA hybridization. Electrostatic forces cause the oppositely charged cationic conjugated polymer to bind selectively to the "complementary" surfaces. This approach circumvents the current need to label the probe or target strands. The polymer used in these assays is poly[9,9'-bis(6''-N,N,N-trimethylammonium)hexyl)fluorene-co-alt-4,7-(2,1,3-benzothiadiazole) dibromide], which was specifically designed and synthesized to be compatible with excitation sources used in commonly used DNA microarray readers. Furthermore, the utility of poly[9,9'-bis(6''-N,N,N-trimethylammonium)-hexyl)fluorene-co-alt-4,7-(2,1,3-benzothiadiazole) dibromide] has been demonstrated in homogenous and solid-state assays that involve fluorescence resonance energy transfer to a reporter dye (Cy5) and that can benefit from the light harvesting properties observed in water-soluble conjugated polymers.
A 42 to 47-GHz, 8-bit I/Q digital-to-RF converter with 21-dBm P<inf>sat</inf> and 16% PAE in 45-nm SOI CMOS (2013)

A novel stacked FET digital-to-RF converter is implemented in 45-nm SOI CMOS, which shares DC current through an I/Q digital-to-analog converter (DAC), I/Q mixer, and stacked-FET PA to provide high output power. The proposed architecture transmits at 1.25 Gbps for QPSK at 45GHz. This transmitter exhibits a 21.3-dBm saturated output power, while achieving a peak PAE of 16%. The circuit occupies 0.3 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> including pads, while the PAE and P <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">sat</sub> remains above 13% and 18 dBm from 42 to 47 GHz.
High-Field Electrical Transport in Single-Wall Carbon Nanotubes (2000)

Using low-resistance electrical contacts, we have measured the intrinsic high-field transport properties of metallic single-wall carbon nanotubes. Individual nanotubes appear to be able to carry currents with a density exceeding 10(9) A/cm(2). As the bias voltage is increased, the conductance drops dramatically due to scattering of electrons. We show that the current-voltage characteristics can be explained by considering optical or zone-boundary phonon emission as the dominant scattering mechanism at high field.
Natural products. Antitubulin effect of congeners of N-acetylcolchinyl methyl ether: synthesis of optically active 5-acetamidodeaminocolchinyl methyl ether and of demethoxy analogues of deaminocolchinyl methyl ether (1992)

Trimethoxy-substituted dihydrodibenzocycloheptenes 4–7, required for a structure–activity study measuring the inhibition of tubulin polymerization in vitro, were synthesized by four different routes: (1) Synthesis of 4 was achieved from 2,3-dimethoxybenzaldehyde via biphenyl aldehyde 17, chain lengthening to propionic acid 20, acid-catalyzed cyclization toward ketone 21, and removal of the carbonyl group. (2) Compound 5 was obtained by eliminating the sterically most hindered methoxy group in 25 or 26 by metal reduction in alcohol. (3) Compound 6 was prepared from biphenyl aldehyde 34 obtained by Grignard reaction on oxazoline 32. (4) Compound 7 was obtained by reductive deoxygenation of the tetrazolyl ether derivative of N-acetylcolchinol 41. The key role of the aromatic oxygen atoms in colchicine and allo congeners as points of interaction with the colchicine binding site on tubulin was demonstrated by the lack of inhibitory activity of compounds 4–7. Optically active 5-acetamide 8a,b isomers of N-acetylcolchinyl methyl ether 2 were obtained after chemical resolution of amine 47. The absolute configuration of the optical isomers 47a,b and 8a,b was determined by 1 H NMR and CD measurements. These compounds were found inactive as inhibitors of tubulin polymerization.
Expression of antigenic determinants of the hemagglutinin gene of a human influenza virus in Escherichia coli. (1981)

Antigenic determinants of influenza virus hemagglutinin were expressed in Escherichia coli. DNA coding for presequences of hemagglutinin were removed and an ATG codon was placed before DNA coding for mature hemagglutinin. A number of expression plasmids were constructed in which various segments of this reconstructed hemagglutinin DNA were fused to DNA coding for bacterial beta-galactosidase. The fusion proteins exhibited specific binding to antiviral antibodies. This binding could be competitively inhibited by excess viral hemagglutinin, demonstrating that these fusion proteins contained antigenic determinants of hemagglutinin.
BIBLIOGRAPHISCHE NOTIZEN UND MITTEILUNGEN. Nachträge zu den Jahrgängen 89 (1996) und 90 (1997) (1998)

Article BIBLIOGRAPHISCHE NOTIZEN UND MITTEILUNGEN. Nachträge zu den Jahrgängen 89 (1996) und 90 (1997) was published on January 1, 1998 in the journal Byzantinische Zeitschrift (volume 89-90, issue s3).
Synthesis and antiherpes virus activity of phosphate and phosphonate derivatives of 9-[(1,3-dihydroxy-2-propoxy)methyl]guanine (1986)

A series of phosphate esters of 9-[(1,3-dihydroxy-2-propoxy)methyl]guanine (DHPG, 1) were synthesized and evaluated for antiherpes virus activity. The cyclic phosphate esters were made by a new, efficient method utilizing stannic chloride as a solubilizing agent. Monophosphate 2 and bisphosphate 4 showed comparable activity to DHPG and probably acted as prodrugs of DHPG. On the other hand, the cyclic phosphate of DHPG 3 was taken up by cells and bypassed the virus-specified thymidine kinase. As a result, 3 was active against DHPG-resistant HSV mutants that lacked the viral-specified thymidine kinase and was more toxic than DHPG to uninfected cells. The phosphonate 5, the least toxic of the derivatives tested, was only marginally active against HSV but showed substantial activity against human cytomegalovirus in vitro.
Orbital lesions in the Southeastern United States (1996)

The authors reviewed 312 orbital lesions accessioned in the Southeastern United States. Biographical data was recorded when available and the histopathology of each specimen was examined. The results were compared to four previous reviews of orbital lesions in Northern North America. No geographical variation in the occurrence of orbital tumors was observed.