gebhart/patrepeval huggingface dataset:
The developing oligodendrocyte: key cellular target in brain injury in the premature infant (2011)

Brain injury in the premature infant, a problem of enormous importance, is associated with a high risk of neurodevelopmental disability. The major type of injury involves cerebral white matter and the principal cellular target is the developing oligodendrocyte. The specific phase of the oligodendroglial lineage affected has been defined from study of both human brain and experimental models. This premyelinating cell (pre-OL) is vulnerable because of a series of maturation-dependent events. The pathogenesis of pre-OL injury relates to operation of two upstream mechanisms, hypoxia-ischemia and systemic infection/inflammation, both of which are common occurrences in premature infants. The focus of this review and of our research over the past 15-20 years has been the cellular and molecular bases for the maturation-dependent vulnerability of the pre-OL to the action of the two upstream mechanisms. Three downstream mechanisms have been identified, i.e., microglial activation, excitotoxicity and free radical attack. The work in both experimental models and human brain has identified a remarkable confluence of maturation-dependent factors that render the pre-OL so exquisitely vulnerable to these downstream mechanisms. Most importantly, elucidation of these factors has led to delineation of a series of potential therapeutic interventions, which in experimental models show marked protective properties. The critical next step, i.e., clinical trials in the living infant, is now on the horizon.
Monitoring DNA Dynamics Using Spin-Labels with Different Independent Mobilities (1995)

The electron paramagnetic resonance (EPR) spectra of spin-labeled DNA duplexes, both bound to DEAE-Sephadex and free in solution, have been analyzed. The nitroxide spin-labels are covalently linked to a deoxyuridine residue using either a monoacetylene or diacetylene tether. This difference in tether length produces a dramatic difference in the independent mobility of the nitroxide relative to the DNA. In the case of the monoacetylene tether, the motion of the nitroxide has previously been shown to be tightly coupled to that of the DNA duplex. With the diacetylene tether, there is considerable independent motion of the probe. The diacetylene tether is intended to minimize the possibility of the nitroxide producing a perturbation of the dynamics of DNA. It is demonstrated here that, when coupled via the diacetylene tether, the nitroxide undergoes a rapid uniaxial rotation about the tether. A detailed analysis of the EPR spectrum of duplex DNA in solution, spin-labeled using the diacetylene tether, demonstrates that the motion of the nitroxide can be modeled in terms of this independent uniaxial rotation together with motion of the DNA which is consistent with the global tumbling of the duplex. As was previously found using the monoacetylene tether, there is no evidence of rapid, large-amplitude motions of the base pair in the EPR spectrum of a nitroxide coupled to duplex DNA via the diacetylene tether. This result confirms the small amplitudes of internal motion, local and collective, previously observed in duplex DNA with the monoacetylene-tethered nitroxide.
Grasp force control in two-finger grippers with pneumatic actuation (2002)

An experimental system has been proposed for force control in a two-finger gripper with an easy sensorization by using a commercial force sensor. A suitable model of the control scheme has been designed to control the grasping force. Experimental tests have been carried out at the Laboratory of Robotics and Mechatronics in Cassino and they are reported in the paper to show the practical feasibility of two-finger grippers with force controlled pneumatic actuation.
A fundamental limit on the performance of correlation based phase correction and flow estimation techniques (1994)

Cross correlation and similar operations are used in ultrasonic imaging to estimate blood or soft tissue motion in one or more dimensions and to measure echo arrival time differences for phase aberration correction. These estimates are subject to large errors known as false peaks and smaller magnitude errors known as jitter. While false peaks can sometimes be removed through nonlinear processing, jitter errors place a fundamental limit on the performance of delay estimation techniques. This paper applies the Cramer-Rao Lower Bound to derive analytical expressions which predict the magnitude of jitter for 1-D and 2-D problems using both radio frequency (RF) and envelope detected data. One-dimensional simulation results are presented which closely match theoretical predictions. These results indicate that for typical clinical conditions axial jitter for detected data is approximately five times greater than that for RF data. Lateral jitter is approximately ten times greater than axial jitter for RF data. Examples are presented which utilize these results to predict the performance of phase aberration correction and flow estimation systems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Mitochondrial DNA damage is more extensive and persists longer than nuclear DNA damage in human cells following oxidative stress (1997)

A significant amount of reactive oxygen species (ROS) is generated during mitochondrial oxidative phosphorylation. Several studies have suggested that mtDNA may accumulate more oxidative DNA damage relative to nuclear DNA. This study used quantitative PCR to examine the formation and repair of hydrogen peroxide-induced DNA damage in a 16.2-kb mitochondrial fragment and a 17.7-kb fragment flanking the beta-globin gene. Simian virus 40-transformed fibroblasts treated with 200 microM hydrogen peroxide for 15 or 60 min exhibited 3-fold more damage to the mitochondrial genome compared with the nuclear fragment. Following a 60-min treatment, damage to the nuclear fragment was completely repaired within 1.5 hr, whereas no DNA repair in the mitochondrion was observed. Mitochondrial function, as assayed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide reduction, also showed a sharp decline. These cells displayed arrested-cell growth, large increases in p21 protein levels, and morphological changes consistent with apoptosis. In contrast, when hydrogen peroxide treatments were limited to 15 min, mtDNA damage was repaired with similar kinetics as the nuclear fragment, mitochondrial function was restored, and cells resumed division within 12 hr. These results indicate that mtDNA is a critical cellular target for ROS. A model is presented in which chronic ROS exposure, found in several degenerative diseases associated with aging, leads to decreased mitochondrial function, increased mitochondrial-generated ROS, and persistent mitochondrial DNA damage. Thus persistent mitochondrial DNA damage may serve as a useful biomarker for ROS-associated diseases.
Truncation of Arabidopsis thaliana and Selaginella lepidophylla trehalose-6-phosphate synthase unlocks high catalytic activity and supports high trehalose levels on expression in yeast (2002)

Plants, such as Arabidopsis thaliana and Selaginella lepidophylla, contain genes homologous with the trehalose-6-phosphate synthase (TPS) genes of bacteria and fungi. Most plants do not accumulate trehalose with the desert resurrection plant S. lepidophylla, being a notable exception. Overexpression of the plant genes in a Saccharomyces cerevisiae tps1 mutant results in very low TPS-catalytic activity and trehalose accumulation. We show that truncation of the plant-specific N-terminal extension in the A. thaliana AtTPS1 and S. lepidophylla SlTPS1 homologues results in 10-40-fold higher TPS activity and 20-40-fold higher trehalose accumulation on expression in yeast. These results show that the plant TPS enzymes possess a high-potential catalytic activity. The growth defect of the tps1 strain on glucose was restored, however, the proper homoeostasis of glycolytic flux was not restored, indicating that the plant enzymes were unable to substitute for the yeast enzyme in the regulation of hexokinase activity. Further analysis of the N-terminus led to the identification of two conserved residues, which after mutagenesis result in strongly enhanced trehalose accumulation upon expression in yeast. The plant-specific N-terminal region may act as an inhibitory domain allowing modulation of TPS activity.
Purification and properties of Renilla reniformis luciferase (1977)

Luciferase from the anthozoan coelenterate Renilla reniformis (Renilla luciferin:oxygen 2-oxidoreductase (decarboxylating), EC 1.13.12.5.) catalyzes the bioluminescent oxidation of Renilla luciferin producing light (lambdaB 480 nm, QB 5.5%), oxyluciferin, and CO2 (Hori, K., Wampler, J.E., Matthews, J.C., and Cormier, M.J. (1973), Biochemistry 12, 4463). Using a combination of ion-exchange, molecular-sieve, sulfhydryl-exchange, and affinity chromatography, luciferase has been purified, approximately 12 000-fold with 24% recovery, to homogeneity as judged by analysis with disc and sodium dodecyl sulfate-polyacrylamide gel electrophoresis, gel filtration, and ultracentrifugation. Renilla luciferase is active as a nearly spherical single polypeptide chain monomer of 3.5 X 10(4) daltons having a specific activity of 1.8 X 10(15) hp s-1 mg-1 and a turnover number of 111 mumol min-1 mumol-1 of enzyme. This enzyme has a high content of aromatic and hydrophobic amino acids such that it has an epsilon280nm 0.1% of 2.1 and an average hydrophobicity of 1200 cal residue-1. The high average hydrophobicity of luciferase, which places it among the more hydrophobic proteins reported, is believed to account, at least in part, for its tendency to self-associate forming inactive dimers and higher molecular weight species.
Advances in vaccine delivery: transcutaneous immunisation (1999)

Needle-free delivery of vaccines has become a global priority. Transcutaneous immunisation (TCI), topical application of vaccine antigens to the skin, can elicit systemic antibody and T-cell responses, suggesting that this new technique may provide a means for vaccination without needles. TCI requires the use of an adjuvant such as cholera toxin added to a vaccine antigen, such as diphtheria toxoid, to induce antibodies to diphtheria toxoid. The adjuvant and antigen are thought to target Langerhans cells, potent antigen-presenting cells found in the superficial layers of the skin. TCI appears to be a highly practical technique for delivery of vaccines that provides unique access to the immune system.
ChemInform Abstract: SYNTHESIS OF 3‐HYDROXY‐5‐METHYLISOXAZOLE AND 5‐SUBSTITUTED 4‐OXAZOLIN‐2‐ONE (1980)

Abstract Die aus Diketen (I) und den Hydroxylaminen (II) leicht zugänglichen Acetessigsäurehydroxylamide (III) cyclisieren unter Säurekatalyse zum 3‐Hydroxy‐5‐methylisoxazol (IV), die O‐Benzoylhydroxamsäuren (V) hingegen liefern basenkatalysiert die Oxazolone (VI), als Nebenprodukt wird bei Basenunterschuß das Phenacylcarbamoyloxazolon (VII) isoliert.
Visceral adipose tissue area is an independent risk factor for hepatic steatosis (2007)

Our results suggest that visceral abdominal adiposity is correlated with hepatic steatosis in healthy living liver donors.
Use of Sodium Bromate for Aromatic Bromination:  Research and Development (1999)

Sodium bromate is a powerful brominating agent for aromatic compounds that contain deactivating substituents. A bromination process, in which sodium bromate was utilized, was optimized on laboratory scale. Addition of a strong acid into a stirred aqueous solution, or slurry, of the substrate and bromate salt at 40−100°C, leads to the decomposition of the bromate ions and production of the active brominating species. Substrates such as nitrobenzene, benzoic acid, and benzaldehyde were brominated in high yields (85−98%) and specificity. The reaction is especially useful for the bromination of disubstituted benzenes, such as 4-nitrofluorobenzene or 4-fluorobenzoic acid. Several substrates, such as dinitrobenzenes or nitrobenzoic acids, did not undergo bromination at all. The main parameters of the reaction and some of its synthetic potential are discussed.
Multiple control elements in the TRP1 promoter of Saccharomyces cerevisiae. (1986)

The TRP1 promoter generates two groups of mRNAs, transcript I and transcript II. The difference in size between the largest and smallest mRNAs is about 200 base pairs. A series of one-sided and internal deletions were constructed in vitro throughout the TRP1 promoter, and the effect of each deletion on transcription was assessed by Northern blotting. We showed that 395 base pairs of the TRP1 promoter were sufficient for the normal transcription of all RNAs and that the promoter contained two control domains. The control domain for transcript I consisted of one positive element and one negative element, while the control domain for transcript II contained two positive elements. The negative element, mapped between -293 and -318, expression of transcript I. Two regions of transcript I. Two regions (-280 to -236 and -235 to -209) were required for accurate initiation of transcript I. Each region contained sequences homologous to known consensus sequences of the TATA box.
Serial Recombination during Circulation of Type 1 Wild-Vaccine Recombinant Polioviruses in China (2003)

Type 1 wild-vaccine recombinant polioviruses sharing a 367-nucleotide (nt) block of Sabin 1-derived sequence spanning the VP1 and 2A genes circulated widely in China from 1991 to 1993. We surveyed the sequence relationships among 34 wild-vaccine recombinants by comparing six genomic intervals: the conserved 5'-untranslated region (5'-UTR) (nt 186 to 639), the hypervariable portion of the 5'-UTR (nt 640 to 742), the VP4 and partial VP2 genes (nt 743 to 1176), the VP1 gene (nt 2480 to 3385), the 2A gene (nt 3386 to 3832), and the partial 3D gene (nt 6011 to 6544). The 5'-UTR, capsid (VP4-VP2 and VP1), and 2A sequence intervals had similar phylogenies. By contrast, the partial 3D sequences could be distributed into five divergent genetic classes. Most (25 of 34) of the wild-vaccine recombinant isolates showed no evidence of additional recombination beyond the initial wild-Sabin recombination event. Eight isolates from 1992 to 1993, however, appear to be derived from three independent additional recombination events, and one 1993 isolate was derived from two consecutive events. Complete genomic sequences of a representative isolate for each 3D sequence class demonstrated that these exchanges had occurred in the 2B, 2C, and 3D genes. The 3D gene sequences were not closely related to those of the Sabin strains or 53 diverse contemporary wild poliovirus isolates from China, but all were related to the 3D genes of species C enteroviruses. The appearance within approximately 2.5 years of five recombinant classes derived from a single ancestral infection illustrates the rapid emergence of new recombinants among circulating wild polioviruses.
Unidirectional Cre-mediated genetic inversion in mice using the mutant loxP pair lox66/lox71 (2003)

The Cre/loxP recombination system is a commonly used tool to alter the mouse genome in a conditional manner by deletion or inversion of loxP-flanked DNA segments. While Cre-mediated deletion is essentially unidirectional, inversion is reversible and therefore does not allow the stable alteration of gene function in cells that constitutively express Cre. Site-directed mutagenesis yielded a pair of asymmetric loxP sites (lox66 and lox71) that display a favorable forward reaction equilibrium. Here, we demonstrate that lox66/lox71 mediates efficient and predominantly unidirectional inversion of a switch substrate targeted to the mouse genome in combination with either inducible or cell type-specific cre-transgenes in vivo.
Efficient Assembly of Iminodicarboxamides by a “Truly” Four‐Component Reaction (2012)

Mix and match: Similar to a galaxy consisting of millions of stars, a multicomponent reaction (MCR) system can result in millions of compounds. The MCR of α-amino acids, oxo components, isocyanides, and amines leads to numerous and diverse compounds, thus having enormous potential for drug discovery or catalyst screening.
Tumor Necrosis Factor-α Confers Resistance to Hypoxic Injury in the Adult Mammalian Cardiac Myocyte (1998)

Taken together, the above observations demonstrate that TNF-alpha pretreatment confers resistance to hypoxic stress in the adult cardiac myocyte through a novel mechanism that appears to be different from but not necessarily exclusive of the protective response conferred by HSP 72 expression.
Light forces the pace: optical manipulation for biophotonics (2010)

The biomedical sciences have benefited immensely from photonics technologies in the last 50 years. This includes the application of minute forces that enable the trapping and manipulation of cells and single molecules. In terms of the area of biophotonics, optical manipulation has made a seminal contribution to our understanding of the dynamics of single molecules and the microrheology of cells. Here we present a review of optical manipulation, emphasizing its impact on the areas of single-molecule studies and single-cell biology, and indicating some of the key experiments in the fields.
Selective epitaxial silicon growth in the 650–1100 °C range in a reduced pressure chemical vapor deposition reactor using dichlorosilane (1989)

Selective epitaxial silicon layers have been grown in a reduced pressure (&amp;lt;2 Torr) reactor in the 650–1100 °C temperature range using only dichlorosilane (DCS) gas diluted in hydrogen. The growth rate plotted in Arrhenius coordinates (log G vs 1/T) shows an activation energy of 59 kcal/mol in the 650–800 °C range. A comparison is made between the DCS system and our previous results concerning the SiH4/HCl/H2 system.
Targeted Inactivation of the Isoprenylcysteine Carboxyl Methyltransferase Gene Causes Mislocalization of K-Ras in Mammalian Cells (2000)

After isoprenylation and endoproteolytic processing, the Ras proteins are methylated at the carboxyl-terminal isoprenylcysteine. The importance of isoprenylation for targeting of Ras proteins to the plasma membrane is well established, but the importance of carboxyl methylation, which is carried out by isoprenylcysteine carboxyl methyltransferase (Icmt), is less certain. We used gene targeting to produce homozygous Icmt knockout embryonic stem cells (Icmt-/-). Lysates from Icmt-/- cells lacked the ability to methylate farnesyl-K-Ras4B or small-molecule Icmt substrates such as N-acetyl-S-geranylgeranyl-L-cysteine. To assess the impact of absent Icmt activity on the localization of K-Ras within cells, wild-type and Icmt-/- cells were transfected with a green fluorescent protein (GFP)-K-Ras fusion construct. As expected, virtually all of the GFP-K-Ras fusion in wild-type cells was localized along the plasma membrane. In contrast, a large fraction of the fusion in Icmt-/- cells was trapped within the cytoplasm, and fluorescence at the plasma membrane was reduced. Also, cell fractionation/Western blot studies revealed that a smaller fraction of the K-Ras in Icmt-/- cells was associated with the membranes. We conclude that carboxyl methylation of the isoprenylcysteine is important for proper K-Ras localization in mammalian cells.
pH Control of Transport through a Porous Membrane Self-Assembled with a Poly(acrylic acid) Loop Brush (2001)

Side chains of poly(acrylic acid) (PAA) were conjugated with cysteamines for self-assembly on a gold-coated membrane. The self-assembly of the cysteamine-modified PAA on the membrane was monitored by surface plasmon resonance spectroscopy. It was found that the amount of assembled polyelectrolytes significantly depended on the concentration of the polyelectrolytes, the content of cysteamine in the polyelectrolyte, solution pH, and ionic strength. Transport through porous membranes gold-coated and subsequently self-assembled with the polyelectrolyte was investigated. Water permeability through the membrane was reversibly regulated by pH and ionic strength. The permeability was high at low pH and low at high pH, and an increase in ionic strength increased the permeability at high pH. It was suggested that at low pH the polyelectrolyte was protonated which caused the brushes to shrink and opened the pores. At high pH, the opposite process took place. The ionic strength reduced the electrostatic repulsion between the ionized polyelectrolytes that shrank the opening of the pores. These phenomena depended on the state of the self-assembled polyelectrolytes. Filtration of water solutions of ionic (oligodeoxyribonucleotide) and nonionic (poly(ethylene glycol)) polymers through the modified membrane was also studied. pH-responsive permeability depended on the molecular weight of the solutes.
REVIEWS (1990)

REVIEWS Get access LINCOLN B. FULLER, Turned to Account: The Forms and Functions of Criminal Biography in Late Seventeenth- and Early Eighteenth-century England, Cambridge University Press, 1988. ISBN 0-521-32672-9. £30. RUTH HARRIS RUTH HARRIS Search for other works by this author on: Oxford Academic Google Scholar History Workshop Journal, Volume 29, Issue 1, Spring 1990, Pages 154–155, https://doi.org/10.1093/hwj/29.1.154 Published: 01 March 1990
Mechanisms of Endocrine Resistance in Breast Cancer (2010)

The estrogen receptor (ER) pathway plays a pivotal role in breast cancer development and progression. Endocrine therapy to block the ER pathway is highly effective, but its usefulness is limited by common intrinsic and acquired resistance. Multiple mechanisms responsible for endocrine resistance have been proposed and include deregulation of various components of the ER pathway itself, alterations in cell cycle and cell survival signaling molecules, and the activation of escape pathways that can provide tumors with alternative proliferative and survival stimuli. Among these, increased expression or signaling of growth factor receptor pathways, especially the EGFR/HER2 pathway, has been associated with both experimental and clinical endocrine therapy resistance. New treatment combinations targeting both ER and growth factor receptor signaling to block the crosstalk between these pathways and eliminate escape routes have been proven highly effective in preclinical models. Results of recent clinical studies, while partly supporting this approach, also highlight the need to better identify a priori the patients whose tumors are most likely to benefit from these specific cotargeting strategies.