gebhart/patrepeval huggingface dataset:
Mechanism of Anucleate Cell Production in the oriC-Deleted Mutants of Bacillus subtilis (1997)

We constructed oriC-deleted mutants of Bacillus subtilis by integrating the minimal replication region of plasmid pLS32 into the proA (115 degrees), spoIIIJ (360 degrees) and thrS (256 degrees) loci of the chromosome, respectively. All three mutants produced anucleate cells and the DNA/protein ratio was lower than that of the wild-type strain when grown in nutrient broth. However, when grown in minimal-glucose medium, the frequency of anucleate cells was reduced in all of them and the DNA/protein ratio was restored to normal. Especially, the oriC-deleted mutant in which the plasmid was integrated near oriC produced almost no anucleate cell. These results indicate that initiation frequency of chromosome replication from the integrated plasmid origin were reduced disproportionately to cell mass increase in rich medium, which in turn disrupted coordination between DNA replication cycle and cell division cycle. The locations of the plasmid origin relative to the natural oriC locus affected the production of anucleate cell remarkably, suggesting that partition mechanism of chromosome was also impaired by the translocation of its replication origin.
Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons (1991)

We demonstrate in this work that the surface tension, water-organic solvent, transfer-free energies and the thermodynamics of melting of linear alkanes provide fundamental insights into the nonpolar driving forces for protein folding and protein binding reactions. We first develop a model for the curvature dependence of the hydrophobic effect and find that the macroscopic concept of interfacial free energy is applicable at the molecular level. Application of a well-known relationship involving surface tension and adhesion energies reveals that dispersion forces play little or no net role in hydrophobic interactions; rather, the standard model of disruption of water structure (entropically driven at 25 degrees C) is correct. The hydrophobic interaction is found, in agreement with the classical picture, to provide a major driving force for protein folding. Analysis of the melting behavior of hydrocarbons reveals that close packing of the protein interior makes only a small free energy contribution to folding because the enthalpic gain resulting from increased dispersion interactions (relative to the liquid) is countered by the freezing of side chain motion. The identical effect should occur in association reactions, which may provide an enormous simplification in the evaluation of binding energies. Protein binding reactions, even between nearly planar or concave/convex interfaces, are found to have effective hydrophobicities considerably smaller than the prediction based on macroscopic surface tension. This is due to the formation of a concave collar region that usually accompanies complex formation. This effect may preclude the formation of complexes between convex surfaces.
Hypersensitivity to Aloe (1980)

Hypersensitivity, manifested by generalized nummular eczematous and papular dermatitis, and presumably by contact urticaria, developed in a 47-year-old man after four years of using oral and topical aloe. Patch tests for aloe were positive in this patient.
Pulsed and Steady Field Gradient NMR Diffusion Measurements in Polymers (1985)

Abstract Some twenty years after the development of the steady and pulsed gradient spin-echo NMR methods of measuring self-diffusion, these techniques are now maturing and experiencing a surge of interest, much of it concentrated on polymer systems. The methods are briefly reviewed here, together with the most important results in polymers, with particular concentration on work described within the last few years. The research is divisible into three categories: diffusion of diluent and penetrant molecules in rubbery high polymers, diffusion of polymer molecules in dilute and semidilute solutions with liquid solvents, and diffusion of macromolecules dissolved in concentrated solutions or melts of equivalent or different polymers of arbitrary molecular weight. The review includes the main theoretical interpretations of the experiments, particularly the free-volume theory in its various forms and power-law behaviors postulated by recent refinements of tube/reptation and scaling theory. This article represents an updated elaboration of an earlier review.
Mucosal Immunity Induced by Intramuscular Administration of Free Peptides In‐Line with PADRE: IgA Antibodies to the ELDKWA Epitope of HIV gp41 (2002)

To improve the mucosal antibody response against a short amino acid (aa) sequence (ELDKWA) of HIV gp41, we have investigated a construction including this peptide in-line with the Pan DR epitope (PADRE). ELDKWA is a conserved peptide playing a key role in the pathogenicity of HIV transmission. PADRE is a non-natural peptide with multipotential immunogenic properties. The results show striking differences between mucosal and systemic immune systems, with a preferential response of the mucosal organs. In contrast with most mucosal immunizations, the intracellular response persists for over two months after the last injection. This strongly suggests that further investigations of conserved key epitopes from various pathogens may lead to safe and chemically defined mucosal vaccines with synthetic peptides. These candidate vaccines with free peptides may be suitable for mass campaigns even in developing countries.
Complement Protease MASP-1 Activates Human Endothelial Cells: PAR4 Activation Is a Link between Complement and Endothelial Function (2009)

Activation of the complement system can induce and enhance inflammatory reaction. Mannose-binding lectin-associated serine protease-1 (MASP-1) is an abundant protease of the complement lectin pathway; however, its physiological function is unclear. In this study, we demonstrate for the first time that MASP-1 is able to activate Ca(2+) signaling, NF-kappaB, and p38 MAPK pathways in cultured HUVECs. Activation was initiated by MASP-1 only; the related protease, MASP-2, had no such effect. The phenomenon was dependent on the proteolytic activity of MASP-1, suggesting modulation of endothelial cell function through a protease-activated receptor (PAR). Using synthetic peptide substrates representing the protease-sensitive regions of PARs, we were able to demonstrate that PAR4 is a target of MASP-1. The presence of functionally active PAR4 in HUVECs was demonstrated using PAR4 agonist peptide and mRNA quantification. Finally, we showed that the amount of membrane-bound intact PAR4 decreases after MASP-1 treatment. All of these results provide a novel link between the regulation of endothelial cell function and complement system activation, and they suggest that MASP-1-induced PAR4 activation could contribute to the development of the inflammatory reaction.
Geometrical percolation threshold of overlapping ellipsoids (1995)

A recurrent problem in materials science is the prediction of the percolation threshold of suspensions and composites containing complex-shaped constituents. We consider an idealized material built up from freely overlapping objects randomly placed in a matrix, and numerically compute the geometrical percolation threshold ${\mathit{p}}_{\mathit{c}}$ where the objects first form a continuous phase. Ellipsoids of revolution, ranging from the extreme oblate limit of platelike particles to the extreme prolate limit of needlelike particles, are used to study the influence of object shape on the value of ${\mathit{p}}_{\mathit{c}}$. The reciprocal threshold 1/${\mathit{p}}_{\mathit{c}}$ (${\mathit{p}}_{\mathit{c}}$ equals the critical volume fraction occupied by the overlapping ellipsoids) is found to scale linearly with the ratio of the larger ellipsoid dimension to the smaller dimension in both the needle and plate limits. Ratios of the estimates of ${\mathit{p}}_{\mathit{c}}$ are taken with other important functionals of object shape (surface area, mean radius of curvature, radius of gyration, electrostatic capacity, excluded volume, and intrinsic conductivity) in an attempt to obtain a universal description of ${\mathit{p}}_{\mathit{c}}$. Unfortunately, none of the possibilities considered proves to be invariant over the entire shape range, so that ${\mathit{p}}_{\mathit{c}}$ appears to be a rather unique functional of object shape. It is conjectured, based on the numerical evidence, that 1/${\mathit{p}}_{\mathit{c}}$ is minimal for a sphere of all objects having a finite volume.
Using SDI-12 with ST microelectronics MCU's (2015)

ST Microelectronics microcontrollers and processors are readily available, capable and economical processors. Unfortunately they lack a broad user base like similar offerings from Texas Instrument, Atmel, or Microchip. All of these devices could be useful in economical devices for remote sensing applications used with environmental sensing. With the increased need for environmental studies, and limited budgets, flexibility in hardware is very important. To that end, and in an effort to increase open support of ST devices, I am sharing my teams' experience in interfacing a common environmental sensor communication protocol (SDI-12) with ST devices.
Crystal Structure of an in Vitro Affinity- and Specificity-matured Anti-testosterone Fab in Complex with Testosterone (2002)

A highly selective, high affinity recombinant anti-testosterone Fab fragment has been generated by stepwise optimization of the complementarity-determining regions (CDRs) by random mutagenesis and phage display selection of a monoclonal antibody (3-C(4)F(5)). The best mutant (77 Fab) was obtained by evaluating the additivity effects of different independently selected CDR mutations. The 77 Fab contains 20 mutations and has about 40-fold increased affinity (K(d) = 3 x 10(-10) m) when compared with the wild-type (3-C(4)F(5)) Fab. To obtain structural insight into factors, which are needed to improve binding properties, we have determined the crystal structures of the mutant 77 Fab fragment with (2.15 A) and without testosterone (2.10 A) and compared these with previously determined wild-type structures. The overall testosterone binding of the 77 Fab is similar to that of the wild-type. The improved affinity and specificity of the 77 Fab fragment are due to more comprehensive packing of the testosterone with the protein, which is the result of small structural changes within the variable domains. Only one important binding site residue Glu-95 of the heavy chain CDR3 is mutated to alanine in the 77 Fab fragment. This mutation, originally selected from the phage library based on improved specificity, provides more free space for the testosterone D-ring. The light chain CDR1 of 77 Fab containing eight mutations has the most significant effect on the improved affinity, although it has no direct contact with the testosterone. The mutations of CDR-L1 cause a rearrangement in its conformation, leading to an overall fine reshaping of the binding site.
A Large Gene Cluster Encoding Several Magnetosome Proteins Is Conserved in Different Species of Magnetotactic Bacteria (2001)

In magnetotactic bacteria, a number of specific proteins are associated with the magnetosome membrane (MM) and may have a crucial role in magnetite biomineralization. We have cloned and sequenced the genes of several of these polypeptides in the magnetotactic bacterium Magnetospirillum gryphiswaldense that could be assigned to two different genomic regions. Except for mamA, none of these genes have been previously reported to be related to magnetosome formation. Homologous genes were found in the genome sequences of M. magnetotacticum and magnetic coccus strain MC-1. The MM proteins identified display homology to tetratricopeptide repeat proteins (MamA), cation diffusion facilitators (MamB), and HtrA-like serine proteases (MamE) or bear no similarity to known proteins (MamC and MamD). A major gene cluster containing several magnetosome genes (including mamA and mamB) was found to be conserved in all three of the strains investigated. The mamAB cluster also contains additional genes that have no known homologs in any nonmagnetic organism, suggesting a specific role in magnetosome formation.
Estrogen-androgen for hormone replacement. A review. (1997)

Although the literature includes relatively few clinical trials or well-controlled studies and is further limited by the subjective nature of outcomes, such as sexual and psychological function, the available data suggest that for many postmenopausal women, estrogen-androgen replacement may provide benefits beyond those provided by estrogen-only replacement therapy.
复杂系统的基础非线性动力学、统计物理学、信息和预报 (2008)

复杂性科学或复杂系统的研究现在已成为系统科学的前沿领域。它用统一的观点来研究物理科学、工程科学、环境科学、生命科学以及人文科学中带有共性的问题。作者认为，这个领域第一次突破是20世纪80年代末到90年代初，是非线性科学、统计物理学与数字仿真中的思想与工具相互作用的结果。
Diode-based additive manufacturing of metals using an optically-addressable light valve (2017)

Selective Laser Melting (SLM) of metal powder bed layers, whereby 3D metal objects can be printed from a digital file with unprecedented design flexibility, is spurring manufacturing innovations in medical, automotive, aerospace and textile industries. Because SLM is based on raster-scanning a laser beam over each layer, the process is relatively slow compared to most traditional manufacturing methods (hours to days), thus limiting wider spread use. Here we demonstrate the use of a large area, photolithographic method for 3D metal printing, using an optically-addressable light valve (OALV) as the photomask, to print entire layers of metal powder at once. An optical sheet of multiplexed ~5 kW, 20 ms laser diode and ~1 MW, 7 ns Q-switched laser pulses are used to selectively melt each layer. The patterning of near infrared light is accomplished by imaging 470 nm light onto the transmissive OALV, which consists of polarization-selective nematic liquid crystal sandwiched between a photoconductor and transparent conductor for switching.
Lessons From Initial Experience With the In Situ Saphenous Vein Graft (1984)

A policy of preference for the in situ saphenous vein was adopted for all patients requiring bypass grafting below the knee. In an initial series of 25 operations, technical complications occurred in eight cases (32%), including venographic extravasation, vein injury during valve lysis, and early graft occlusions due to incomplete valve lysis and routing under tension past the hamstring tendons. Early loss of tibial outflow vessels occurred twice, with retrieval of embolic debris possibly shed from the graft. In spite of these events, at an average follow-up of ten months, 21 grafts were open (84% patency). Two occlusions occurred in patients who suffered operative complications, and another graft was lost after rethrombosis of a donor axillobifemoral prosthesis. Acceptable patency in spite of technical mishaps early in my experience encourages continued efforts to master the in situ method.
Adeno-associated viral vectors engineered for macrolide-adjustable transgene expression In mammalian cells and mice (2007)

Capitalizing on established safety features and a track record of high transduction efficiencies of mammalian cells, adeno- associated virus type 2 were successfully engineered to provide new powerful tools for macrolide-adjustable transgene expression in mammalian cells as well as in mice.
Expression of survivin in CIN and invasive squamous cell carcinoma of uterine cervix. (2002)

Survivin is a novel member of the inhibitors of apotosis proteins (IAP). To evaluate the possible role of survivin in tumorigenesis of CIN (cervical intraepithelial neoplasia) and invasive squamous cervical carcinoma of the uterine cervix (SCC), the expression of survivin was studied.In 41 CIN and SCC tissues, the expression of survivin, Fas-ligand, Fas and bcl-2 was studied by immunohistochemistry. Survivin expression tended to increase along with tumor progression; low-grade squamous intra-epithelial lesions (HSIL, CIN I), 66.7%, high-grade squamous epithelial lesions (HSIL, CIN II and III), 87.5% and SCC, 100% with a statistical significance (p<0.019). Alteration of Fas-ligand, Fas and bcl-2 expression was detected in 12.5%-25% of HSIL and in 7.7%-30.8% of SCC but no abnormal expression was found in LSIL.Survivin expression seems to be more closely related to the progression of CIN and SCC compared to Fas-ligand, Fas and bcl-2.
Purification, Characterisation and cDNA Cloning of an Antimicrobial Peptide from Macadamia Integrifolia (1997)

An antimicrobial peptide with no significant amino acid sequence similarity to previously described peptides has been isolated from the nut kernels of Macadcamia integrifolia. The peptide, termed MiAMP1, is highly basic with an estimated pI of 10.1, a mass of 8.1 kDa and contains 76 amino acids including 6 cysteine residues. A cDNA clone containing the entire coding region corresponding to the peptide was obtained. The deduced amino acid sequence of the cDNA indicated a 26-amino-acid signal peptide at the N-terminus of the preprotein. Purified MiAMP1 inhibited the growth of a variety of fungal, oomycete and gram-positive bacterial phytopathogens in vitro. Some pathogens exhibited close to 100% inhibition in less than 1 microM peptide (5 microg/ml). Antimicrobial activity was diminished against most, but not all, microbes in the presence of calcium and potassium chloride salts (1 mM and 50 mM, respectively). MiAMP1 was active against bakers yeast, was inactive against Escherichia coli and was non-toxic to plant and mammalian cells. Analysis of genomic DNA indicated that MiAMP1 was encoded on a single copy gene containing no introns. The MiAMP1 gene may prove useful in genetic manipulations to increase disease resistance in transgenic plants.
ChemInform Abstract: Monoterpene‐Based Chiral β‐Amino Acid Derivatives Prepared from Natural Sources: Syntheses and Applications (2011)

Abstract Review: 46 refs.
Oral use ofLactobacillus rhamnosusGR-1 andL. fermentumRC-14 significantly alters vaginal flora: randomized, placebo-controlled trial in 64 healthy women (2003)

Urogenital infections afflict an estimated one billion people each year. The size of this problem and the increased prevalence of multi-drug resistant pathogens make it imperative that alternative remedies be found. A randomized, placebo-controlled trial of 64 healthy women given daily oral capsules of Lactobacillus rhamnosus GR-1 and Lactobacillus fermentum RC-14 for 60 days showed no adverse effects. Microscopy analysis showed restoration from asymptomatic bacterial vaginosis microflora to a normal lactobacilli colonized microflora in 37% women during lactobacilli treatment compared to 13% on placebo (P=0.02). Lactobacilli were detected in more women in the lactobacilli-treated group than in the placebo group at 28 day (P=0.08) and 60 day (P=0.05) test points. Culture findings confirmed a significant increase in vaginal lactobacilli at day 28 and 60, a significant depletion in yeast at day 28 and a significant reduction in coliforms at day 28, 60 and 90 for lactobacilli-treated subjects versus controls. The combination of probiotic L. rhamnosus GR-1 and L. fermentum RC-14 is not only safe for daily use in healthy women, but it can reduce colonization of the vagina by potential pathogenic bacteria and yeast.
ChemInform Abstract: Chemical Regulations of Epigenetic Modifications: Opportunities for New Cancer Therapy (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Suspended heated silicon platform for rapid thermal control of surface reactions with application to carbon nanotube synthesis (2007)

Rapid continuous thermal control of chemical reactions such as those for chemical vapor deposition (CVD) growth of nanotubes and nanowires cannot be studied using traditional reactors such as tube furnaces, which have large thermal masses. We present the design, modeling, and verification of a simple, low-cost reactor based on resistive heating of a suspended silicon platform. This system achieves slew rates exceeding 100 degrees C/s, enabling studies of rapid heating and thermal cycling. Moreover, the reaction surface is available for optical monitoring. A first-generation CVD apparatus encapsulates the heated silicon platform inside a sealed quartz tube, and initial experiments demonstrate growth of films of tangled single-wall and aligned multiwall carbon nanotubes using this system. The reactor can be straightforwardly scaled to larger or smaller substrate sizes and may be extended for a wide variety of reactions, for performing in situ reaction diagnostics, for chip-scale growth of nanostructures, and for rapid thermal processing of microelectronic and micromechanical devices.
ChemInform Abstract: NMR STUDIES OF NICKEL HYDRIDES: THE INTRAMOLECULAR REARRANGEMENT OF THE HYDRIDOTRIS(TRI‐P‐TOLYL PHOSPHITE)NICKEL(II) ION (1985)

Abstract Die 1 H‐, "P‐ und zH‐NMR‐spektroskopische Untersuchung der Reaktion des Ni(O)‐Komplexes Ni[P(p‐MeC6H4)3]4 mit starken Säuren zeigt die Bildung fünf‐ und vierfach koordinierter Ni‐Hydride, deren Bildungsmechanismus erörtert wird.
INVESTIGATION OF XEROSTOMIA IN PATIENTS WITH RHEUMATOID ARTHRITIS (1998)

The authors investigated the prevalence of xerostomia in a group of 604 subjects participating in a rheumatoid arthritis, or RA, study to explore the relationship of reduced salivary flow symptoms and demographic, clinical and medical characteristics. Forty-three percent of these subjects exhibited one or more severe xerostomia symptoms. Separate analyses revealed that the subjects who had the most physical disease symptoms were at greater risk of having reduced salivary flow. The study's results suggest that patients with RA should be screened for xerostomia symptoms so appropriate clinical interventions can be initiated.
Confocal Microscopy for Intracellular Co-Localization of Proteins (2004)

Confocal laser scanning microscopy is the best method to visualize intracellular co-localization of proteins in intact cells. Because of the point scan/pinhole detection system, light contribution from the neighborhood of the scanning spot in the specimen can be eliminated, allowing high Z-axis resolution. Fluorescence detection by sensitive photomultiplier tubes allows the usage of filters with a narrow bandpath, resulting in minimal cross-talk (overlap) between two spectra. This is particularly important in demonstrating co-localization of proteins with multicolor labeling. Here, the methods outlining the detection of transiently expressed tagged proteins and the detection of endogenous proteins are described. Ideally, the intracellular co-localization of two endogenous proteins should be demonstrated. However, when antibodies raised against the protein of interest are unavailable for immunofluorescence or the available cell lines do not express the protein of interest sufficiently enough for immunofluorescence, an alternative method is to transfect cells with expression plasmids that encode tagged proteins and stain the cells with anti-tag antibodies. However, it should be noted that the tagging of proteins of interest or their overexpression could potentially alter the intracellular localization or the function of the target protein.