gebhart/patrepeval huggingface dataset:
Formation of hydroxyl radicals from hydrogen peroxide in the presence of iron. Is haemoglobin a biological Fenton reagent? (1988)

The ability of oxyhaemoglobin and methaemoglobin to generate hydroxyl radicals (OH.) from H2O2 has been investigated using deoxyribose and phenylalanine as 'detector molecules' for OH.. An excess of H2O2 degrades methaemoglobin, releasing iron ions that react with H2O2 to form a species that appears to be OH.. Oxyhaemoglobin reacts with low concentrations of H2O2 to form a 'reactive species' that degrades deoxyribose but does not hydroxylate phenylalanine. This 'reactive species' is less amenable to scavenging by certain scavengers (salicylate, phenylalanine, arginine) than is OH., but it appears more reactive than OH. is to others (Hepes, urea). The ability of haemoglobin to generate not only this 'reactive species', but also OH. in the presence of H2O2 may account for the damaging effects of free haemoglobin in the brain, the eye, and at sites of inflammation.
Think globally, act locally: the making of a mouse mammary gland (1998)

On a phylogenetic scale of organ development the mammary gland is a recent acquisition. It was introduced 200 million years ago with the appearance of mammals to provide nourishment to the newborn in the form of milk. The mammary gland is characterized by a unique dependence on hormonal signals for terminal differentiation, which is attained only after pregnancy. At the time of birth, the anlage consists of a few rudimentary ducts in the vicinity of the nipple. Pronounced ductal outgrowth and branching commences at puberty, and in pregnancy an expanded lobulo-alveolar compartment develops. Functional differentiation of the secretory epithelium coincides with parturition and large amounts of milk are produced and secreted during lactation. After weaning of the young, the entire alveolar epithelial compartment is remodeled to resemble a virgin-like state. With each pregnancy, a new round of lobulo-alveolar development occurs. During the past 100 years, intensive efforts have been made to understand the endocrine control of mammopoiesis and lactogenesis. Classical research on endocrine ablated animals firmly established that ovarian steroids and pituitary peptide hormones are mandatory and sufficient for breast development and lactation. In 1900, Halban first established that mammary growth is controlled by the ovary (Halban 1900). He demonstrated that ovariectomy caused mammary regression, and that transplanted ovaries prevented the castration atrophy of mammary glands. Twenty-eight years later, Stricker and Grueter induced mammary development and milk secretion artificially in castrated virgin rabbits by injection of pituitary extract (Stricker and Grueter 1928). In 1933, Riddle, Bates, and Dykshorn purified the respective pituitary hormone (Riddle et al. 1933) and named it prolactin(PRL). In the last several years, the ability to delete genes from the mouse genome has allowed us to identify genetic components of mammary gland development. Molecular insight into the underlying genetic framework and signaling networks of the developing tissue has been gained through experimental manipulations of tissues from wild-type and knockout mice. Two distinct, yet braided, developmental concepts have unfolded. First, discrete signaling networks activated by systemic endocrine hormones induce mammopoiesis. Secondly, some of these signals are relayed through reciprocal interactions between the epithelium and the stroma. Table 1 contains those genes whose elimination from the mouse genome results in impaired mammary gland development. Among these genes are some of the ‘‘usual suspects’’ but also some previously unidentified players. Each mutation affects specific and distinct aspects of mammary development. These knockout mice not only confirmed the involvement of hormonal signaling but also provided tools to identify the tissue compartment that receives and executes these signals.
Enzyme behavior at surfaces. Site-specific variants of subtilisin BPN' with enhanced surface stability. (1994)

Enzyme adsorption and inactivation at the solid/liquid interface for subtilisin BPN' show a strong dependence on the nature of the solid surface. Adsorption of BPN' at the solid/liquid interface is considerably greater for a hydrophobic surface than for a hydrophilic one. Likewise, the rate of inactivation of the wild-type BPN' is over five times greater when equilibrated with a hydrophobic surface than with a hydrophilic surface. The rate data from these enzyme inactivation experiments performed at 50 degrees C are best fit by a second-order kinetic equation, suggesting a bimolecular pathway to inactivation. The role of increased surface adsorption on this bimolecular inactivation is discussed in terms of two different mechanisms. Several site-specific variants of subtilisin BPN' have been made in an attempt to alter the surface-inactivation of the wild-type enzyme. The extent of adsorption on the model surfaces is significantly lowered by certain lysine to phenylalanine changes in BPN'. Consequently, the surface autolytic stability shows a 4-fold improvement. The change in surface autolytic stability is achieved even though the basic kinetic parameters (kcat and KM) of the variant enzymes are not significantly different on a soluble substrate. The results provide insights into the use of mutagenesis to probe the mechanism of protein interactions with surfaces.
Mutations that improve the binding of yeast FLP recombinase to its substrate. (1988)

When yeast FLP recombinase is expressed from the phage lambda PR promoter in a Salmonella host, it cannot efficiently repress an operon controlled by an operator/promoter region that includes a synthetic, target FLP site. On the basis of this phenotype, we have identified four mutant FLP proteins that function as more efficient repressors of such an operon. At least two of these mutant FLP proteins bind better to the FLP site in vivo and in vitro. One mutant changes the presumed active site tyrosine residue of FLP protein to phenylalanine, is blocked in recombination, and binds the FLP site about five-fold better than the wild-type protein. A second mutant protein that functions as a more efficient repressor retains catalytic activity. We conclude that the eukaryotic yeast FLP recombinase, when expressed in a heterologous prokaryotic host, can function as a repressor, and that mutant FLP proteins that bind DNA more tightly may be selected as more efficient repressors.
The X-Space Formulation of the Magnetic Particle Imaging Process: 1-D Signal, Resolution, Bandwidth, SNR, SAR, and Magnetostimulation (2010)

The magnetic particle imaging (MPI) imaging process is a new method of medical imaging with great promise. In this paper we derive the 1-D MPI signal, resolution, bandwidth requirements, signal-to-noise ratio (SNR), specific absorption rate, and slew rate limitations. We conclude with experimental data measuring the point spread function for commercially available SPIO nanoparticles and a demonstration of the principles behind 1-D imaging using a static offset field. Despite arising from the nonlinear temporal response of a magnetic nanoparticle to a changing magnetic field, the imaging process is linear in the magnetization distribution and can be described as a convolution. Reconstruction in one dimension is exact and has a well-behaved quasi-Lorentzian point spread function.The spatial resolution improves cubically with increasing diameter of the SPIO domain, inverse to absolute temperature, linearly with saturation magnetization, and inversely with gradient. The band width requirements approach a megahertz for reasonable imaging parameters and millimeter scale resolutions, and the SNR increases with the scanning rate. The limit to SNR as we scale MPI to human sizes will be patient heating. SAR and magnetostimulation limits give us surprising relations between optimal scanning speeds and scanning frequency for different types of scanners.
The inter-α-inhibitor family: from structure to regulation (1996)

Inter-alpha-inhibitor (IalphaI) and related molecules, collectively referred to as the IalphaI family, are a group of plasma protease inhibitors. They display attractive features such as precursor polypeptides that give rise to mature chains with quite distinct fates and functions, and inter-chain glycosaminoglycan bonds within the various molecules. The discovery of an ever growing number of such molecules has raised pertinent questions about their pathophysiological functions. The knowledge of this family has long been structure-oriented, whereas the structure/function and structure/regulation relationships of the family members and their genes have been largely ignored. These relationships are now being elucidated in events such as gene transcription, precursor processing, changes in plasma protein levels in health and disease and binding capacities that involve hyaluronan as well as other plasma proteins as ligands. This review presents some recent progress made in these fields that paves the way for an understanding of the functions of IalphaI family members in vivo. Finally, given the wealth of heterogeneous, complicated and sometimes contradictory nomenclatures and acronyms currently in use for this family, a new, uniform, nomenclature is proposed for IalphaI family genes, precursor polypeptides and assembled proteins.
Quantitative Genetics of Transgenic Mice: Components of Phenotypic Variation in Body Weights and Weight Gains (1996)

Transgenic mice possessing an ovine growth hormone gene were used to study the effects of elevated growth hormone on quantitative genetic variation. Males hemizygous for the transgene were mated to wild-type females to produce half- and full-sib families in which approximately half the progeny were transgenic and half were wild type. Analyses of body weights at 3-10 weeks, and weight gains from 3 to 6, and 6 to 10 weeks produced estimates of the proportion of total variance due to additive genetic effects (h2) and common litter effects (c2), and the genetic correlation between transgenic and wild-type expression of each trait. At 10 weeks, body weight of transgenics exceeded that of wild types by 26 and 49% in males and females, respectively. Estimated genetic variances in the transgenic group were significantly greater than zero for body weights at most ages and for both measurements of gain. Common litter effects accounted for a similar proportion of variation in the wild-type and transgenic groups. Additive genetic correlations between wild-type and transgenic expression of body weights tended to decline with age, indicating that a partially different array of genes may have begun to affect body weight in the transgenic group.
Therapeutic Interference With Vascular Calcification—Lessons From Klotho-Hypomorphic Mice and Beyond (2018)

Medial vascular calcification, a major pathophysiological process associated with cardiovascular disease and mortality, involves osteo-/chondrogenic transdifferentiation of vascular smooth muscle cells (VSMCs). In chronic kidney disease (CKD), osteo-/chondrogenic transdifferentiation of VSMCs and, thus, vascular calcification is mainly driven by hyperphosphatemia, resulting from impaired elimination of phosphate by the diseased kidneys. Hyperphosphatemia with subsequent vascular calcification is a hallmark of klotho-hypomorphic mice, which are characterized by rapid development of multiple age-related disorders and early death. In those animals, hyperphosphatemia results from unrestrained formation of 1,25(OH)<sub>2</sub>D<sub>3</sub> with subsequent retention of calcium and phosphate. Analysis of klotho-hypomorphic mice and mice with vitamin D<sub>3</sub> overload uncovered several pathophysiological mechanisms participating in the orchestration of vascular calcification and several therapeutic opportunities to delay or even halt vascular calcification. The present brief review addresses the beneficial effects of bicarbonate, carbonic anhydrase inhibition, magnesium supplementation, mineralocorticoid receptor (MR) blockage, and ammonium salts. The case is made that bicarbonate is mainly effective by decreasing intestinal phosphate absorption, and that carbonic anhydrase inhibition leads to metabolic acidosis, which counteracts calcium-phosphate precipitation and VSMC transdifferentiation. Magnesium supplementation, MR blockage and ammonium salts are mainly effective by interference with osteo-/chondrogenic signaling in VSMCs. It should be pointed out that the, by far, most efficient substances are ammonium salts, which may virtually prevent vascular calcification. Future research will probably uncover further therapeutic options and, most importantly, reveal whether these observations in mice can be translated into treatment of patients suffering from vascular calcification, such as patients with CKD.
Nucleotide sequence of the erythromycin resistance gene of the conjugative transposon Tn1545 (1990)

Journal Article Nucleotide sequence of the erythromycin resistance gene of the conjugative transposon Tn1545 Get access Patrick Trieu-Cuot, Patrick Trieu-Cuot * Unité des Agents Antibactériens, CNRS UA 271, Institut Pasteur25 rue du Dr Roux, 75724 Paris Cedex 15, France *To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar Claire Poyart-Salmeron, Claire Poyart-Salmeron Unité des Agents Antibactériens, CNRS UA 271, Institut Pasteur25 rue du Dr Roux, 75724 Paris Cedex 15, France Search for other works by this author on: Oxford Academic PubMed Google Scholar Cécile Carlier, Cécile Carlier Unité des Agents Antibactériens, CNRS UA 271, Institut Pasteur25 rue du Dr Roux, 75724 Paris Cedex 15, France Search for other works by this author on: Oxford Academic PubMed Google Scholar Patrice Courvalin Patrice Courvalin Unité des Agents Antibactériens, CNRS UA 271, Institut Pasteur25 rue du Dr Roux, 75724 Paris Cedex 15, France Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 18, Issue 12, 25 June 1990, Page 3660, https://doi.org/10.1093/nar/18.12.3660 Published: 25 June 1990 Article history Received: 01 May 1990 Published: 25 June 1990
Noninvasive assessment of the hydration gradient across the cornea using confocal Raman spectroscopy. (1998)

The proposed noninvasive confocal Raman spectroscopic technique has the potential to assess the axial corneal water gradient with a degree of sensitivity and reproducibility.
Dynamic optimization of readsize in hypermedia servers (2003)

While disk scheduling techniques for continuous media (CM) servers are mostly designed to maximize the number of concurrent CM data streams, considerably less attention has been paid to discrete media (DM) data throughput. DM data throughput is vital to systems that need to support the heterogeneity and variety of data found in interactive hypermedia and digital library applications. Therefore, a server's ability in delivering a high DM data throughput without degrading its CM data throughput deserves more attention. A new technique is introduced to optimize the use of disk bandwidth at run-time and redirect the saved bandwidth to service DM requests. Based on a new cost model of disk access incurred in CM service, we formulate strategies to moderate the size of disk reads at run-time. Through experimental evaluations, these strategies are found to improve the efficiency of disk accesses and the DM data throughput of a hypermedia server without jeopardizing the throughput and quality of CM service.
Group of peptides that act synergistically with hydrophobic antibiotics against gram-negative enteric bacteria (1996)

A synthetic peptide, KFFKFFKFFK [corrected], consisting of cationic lysine residues and hydrophobic phenylalanine residues was found to sensitize gram-negative bacteria to hydrophobic and amphipathic antibiotics. At a concentration of 3 micrograms/ml, it decreased the MIC of rifampin for smooth, encapsulated Escherichia coli by a factor of 300. Other susceptible bacterial species included Enterobacter cloacae, Klebsiella pneumoniae, and Salmonella typhimurium, but Pseudomonas aeruginosa was resistant. Similar results were obtained with another synthetic peptide, IKFLKFLKFLK [corrected]. The fractional inhibitory concentration indices for the synergism of these peptides with rifampin, erythromycin, fusidic acid, and novobiocin were very close to those determined for the previously characterized potent outer-membrane-disorganizing agents polymyxin B nonapeptide and deacylpolymyxin B. KFFKFFKFFK [corrected] had direct activity against the gram-positive organism Micrococcus strain ML36, was strongly hemolytic, and was as active on polymyxin-resistant E. coli mutants as on their parent. These three attributes made KFFKFFKFFK [corrected] different from polymyxin derivatives and similar to cationic detergents, such as cetylpyridinium chloride. However, whereas the MIC of cetylpyridinium chloride for E. coli is low (0.5 to 4 micrograms/ml), that of KFFKFFKFFK [corrected] is much higher (30 to 100 micrograms/ml). Other groups of synthetic peptides studied included polymyxin-like peptides with an intrachain disulfide bridge. Their synergism with antibiotics was less marked. Still other peptides, including KEKEKEKEKE and KKKKKKFLFL, lacked any synergism with the probe antibiotics.
The Effect of the Mouse MutationClaw Pawon Myelination and Nodal Frequency in Sciatic Nerves (1998)

Despite the biophysical and clinical importance of differentiating nodal and internodal axolemma, very little is known about the process. We chose to study myelination and node of Ranvier formation in the hypomyelinating mouse mutant claw paw ( clp ). The phenotype of clp is delayed myelination in the peripheral nervous system. The specific defect is unknown but is thought to arise from a breakdown in the complex signaling mechanism between axon and Schwann cell. Myelination was assessed in sciatic nerve cross sections from adult and postnatal day 14 (P14) heterozygous and homozygous clp mice. Antibodies to P0, myelin-associated glycoprotein (MAG), and neural cell adhesion molecule were used to assess the stage of myelination. P14 homozygous clp mice showed an atypical staining pattern of immature myelin, which resolved into a relatively normal pattern by adulthood. Sodium channel clustering and node of Ranvier frequency were studied in whole-mount sciatic nerves with sodium channel and MAG antibodies. P14 homozygous clp nerves again showed an atypical, immature pattern with diffuse sodium channel clusters suggesting nodal formation was delayed. In the adult, homozygous clp sciatic nerves displayed dramatically shortened internodal distances. The data from this study support the hypotheses that node of Ranvier formation begins with the onset of myelination and that the number and location of nodes of Ranvier in the sciatic nerve are determined by myelinating Schwann cells.
Mode-Locked Ultrashort Pulse Generation from On-Chip Normal Dispersion Microresonators (2015)

We describe generation of stable mode-locked pulse trains from on-chip normal dispersion microresonators. The excitation of hyperparametric oscillation is facilitated by the local dispersion disruptions induced by mode interactions. The system is then driven from hyperparametric oscillation to the mode-locked state with over 200 nm spectral width by controlled pump power and detuning. With the continuous-wave-driven nonlinearity, the pulses sit on a pedestal, akin to a cavity soliton. We identify the importance of pump detuning and wavelength-dependent quality factors in stabilizing and shaping the pulse structure, to achieve a single pulse inside the cavity. We examine the mode-locking dynamics by numerically solving the master equation and provide analytic solutions under appropriate approximations.
Construction and Analysis of Photolyase Mutants of Pseudomonas aeruginosa and Pseudomonas syringae : Contribution of Photoreactivation, Nucleotide Excision Repair, and Mutagenic DNA Repair to Cell Survival and Mutability following Exposure to UV-B Radiation (2001)

Based on nucleotide sequence homology with the Escherichia coli photolyase gene (phr), the phr sequence of Pseudomonas aeruginosa PAO1 was identified from the genome sequence, amplified by PCR, cloned, and shown to complement a known phr mutation following expression in Escherichia coli SY2. Stable, insertional phr mutants containing a tetracycline resistance gene cassette were constructed in P. aeruginosa PAO1 and P. syringae pv. syringae FF5 by homologous recombination and sucrose-mediated counterselection. These mutants showed a decrease in survival compared to the wild type of as much as 19-fold after irradiation at UV-B doses of 1,000 to 1,550 J m(-2) followed by a recovery period under photoreactivating conditions. A phr uvrA mutant of P. aeruginosa PAO1 was markedly sensitive to UV-B irradiation exhibiting a decrease in survival of 6 orders of magnitude following a UV-B dose of 250 J m(-2). Complementation of the phr mutations in P. aeruginosa PAO1 and P. syringae pv. syringae FF5 using the cloned phr gene from strain PAO1 resulted in a restoration of survival following UV-B irradiation and recovery under photoreactivating conditions. The UV-B survival of the phr mutants could also be complemented by the P. syringae mutagenic DNA repair determinant rulAB. Assays for increases in the frequency of spontaneous rifampin-resistant mutants in UV-B-irradiated strains containing rulAB indicated that significant UV-B mutability (up to a 51-fold increase compared to a nonirradiated control strain) occurred even in the wild-type PAO1 background in which rulAB only enhanced the UV-B survival by 2-fold under photoreactivating conditions. The frequency of occurrence of spontaneous nalidixic acid-resistant mutants in the PAO1 uvrA and uvrA phr backgrounds complemented with rulAB were 3.8 x 10(-5) and 2.1 x 10(-3), respectively, following a UV-B dose of 1,550 J m(-2). The construction and characterization of phr mutants in the present study will facilitate the determination of the roles of light and dark repair systems in organisms exposed to solar radiation in their natural habitats.
A Convenient Photocatalytic Fluorination of Unactivated CH Bonds (2014)

Fluorination reactions are essential to modern medicinal chemistry, thus providing a means to block site-selective metabolic degradation of drugs and access radiotracers for positron emission tomography imaging. Despite current sophistication in fluorination reagents and processes, the fluorination of unactivated CH bonds remains a significant challenge. Reported herein is a convenient and economic process for direct fluorination of unactivated CH bonds that exploits the hydrogen abstracting ability of a decatungstate photocatalyst in combination with the mild fluorine atom transfer reagent N-fluorobenzenesulfonimide. This operationally straightforward reaction provides direct access to a wide range of fluorinated organic molecules, including structurally complex natural products, acyl fluorides, and fluorinated amino acid derivatives.
Commonly Used Biodegradation Techniques for Drilling Fluid Chemicals, Are They Appropriate? (1995)

ABSTRACT In order to assess the suitability of commonly used biodegradation techniques to simulate the environmental behaviour of pseudo oil-based fluids in the sea, a comprehensive study has been conducted. More than 40 biodegradation experiments, using different techniques, have been performed on one particular synthetic base fluid (an acetal). The results are compared to large scale simulation tests and a seabed survey in an attempt to identify the biodegradation method that most closely resembles the natural biodegradation process.