gebhart/patrepeval huggingface dataset:
A ultra high field multi-element transceive volume array for small animal MRI (2008)

In this work, a dedicated, 9.4T shielded 8-element transceive volume-array for large rat MRI applications is designed and the prototype constructed. Angularly oriented radiating structured coil elements are used. It is shown that by orienting the radiating conductors of the coil element angularly, the RF penetration depth can be increased and the mutual coupling effect can be regulated to minimum. In addition, experimental results show that the prototype can produce homogenous B(1) field and is well suited for the Transmit SENSE application and the GRAPPA parallel imaging technique.
Tobacco-specific nitrosamines in European and USA cigarettes. (1990)

More than 170 types of commercial cigarettes from several European countries and the USA were analyzed for tobacco-specific nitrosamines (TSNA) in tobacco and mainstream smoke as well as for nitrate in tobacco. The cigarettes included filter and nonfilter cigarettes with different tar and nicotine yields. The observed range for N'-nitrosonornicotine (NNN) was from 4 to 1353 ng/cigarette in mainstream smoke and from 45 to 12454 ng/cigarette in tobacco. For 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) the values were between not detected (less than 4 ng/cigarette) and 1749 ng/cigarette in mainstream smoke and between not detected (less than 50 ng/cigarette) and 10745 ng/cigarette in tobacco. Nitrate levels ranged from 0.6 to 19.4 mg/cigarette. The TSNA levels for the cigarettes from the different countries investigated were in a similar range with the exception of few individual brands. The results demonstrated that there is no correlation between TSNA and tar deliveries in mainstream smoke. The TSNA deliveries in mainstream smoke depend on the amount or preformed TSNA in the actual tobacco composition, which is influenced by the nitrate level of the tobacco and the tobacco type. According to these results the tar delivery, although crucial, is not a sufficient index for the biological activity and the carcinogenic potential of cigarette smoke. Reduction of TSNA exposure can be achieved by selecting tobaccos with low levels of preformed TSNA in tobacco, which means a low nitrate content and reduction of the amount of Burley tobaccos and stems in blended cigarettes.
Biochemistry students' ideas about shape and charge in enzyme–substrate interactions (2014)

Biochemistry is a visual discipline that requires students to develop an understanding of numerous representations. However, there is very little known about what students actually understand about the representations that are used to communicate ideas in biochemistry. This study investigated biochemistry students' understanding of multiple representations of enzyme-substrate interactions through both student interviews (N = 25) and responses by a national sample (N = 707) to the Enzyme-Substrate Interactions Concept Inventory. This manuscript reports the findings regarding one category of misconceptions measured by the concept inventory, namely, students' understandings of shape and charge in the context of enzyme-substrate interactions. Students interpret molecular representations depicting such interactions by determining the complementarity between enzyme and substrate by focusing upon charge and hydrogen bonding, but with a disregard for stereochemistry.
Clinical and biochemical improvements in a patient with MNGIE following enzyme replacement (2013)

Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) is a rare autosomal recessive metabolic disorder caused by a deficiency of thymidine phosphorylase (TP, EC2.4.2.4) due to mutations in the nuclear gene TYMP . TP deficiency leads to plasma and tissue accumulations of thymidine and deoxyuridine which generate imbalances within the mitochondrial nucleotide pools, ultimately leading to mitochondrial dysfunction.1 MNGIE is characterized clinically by leukoencephalopathy, external ophthalmoplegia, peripheral polyneuropathy, cachexia, and enteric neuromyopathy manifesting as gastrointestinal dysmotility. The condition is relentlessly progressive, with patients usually dying from a combination of nutritional and neuromuscular failure at an average age of 37 years.2 Allogeneic hematopoietic stem cell transplantation (AHSCT) offers a permanent cure. Clinical and biochemical improvements following AHSCT have been reported but it carries a high mortality risk and is limited by matched donor availability.3 A consensus proposal for standardizing AHSCT recommends treatment of patients without irreversible end-stage disease and with an optimally matched donor; a majority of patients are ineligible and thus there is a critical requirement for an alternative treatment.4 Acknowledgment: The authors acknowledge Dr. Lynette Fairbanks, Purine Research Laboratory, St. Thomas' Hospital, London, and Michelle Levene, Clinical Sciences, St. George's University of London, for the biochemical analysis.
Using Ligand-Accelerated Catalysis to Repurpose Fluorogenic Reactions for Platinum or Copper (2020)

The development of a fluorescent probe for a specific metal has required exquisite design, synthesis, and optimization of fluorogenic molecules endowed with chelating moieties with heteroatoms. These probes are generally chelation- or reactivity-based. Catalysis-based fluorescent probes have the potential to be more sensitive; however, catalytic methods with a biocompatible fluorescence turn-on switch are rare. Here, we have exploited ligand-accelerated metal catalysis to repurpose known fluorescent probes for different metals, a new approach in probe development. We used the cleavage of allylic and propargylic ethers as platforms that were previously designed for palladium. After a single experiment that combinatorially examined >800 reactions with two variables (metal and ligand) for each ether, we discovered a platinum- or copper-selective method with the ligand effect of specific phosphines. Both metal-ligand systems were previously unknown and afforded strong signals owing to catalytic turnover. The fluorometric technologies were applied to geological, pharmaceutical, serum, and live cell samples and were used to discover that platinum accumulates in lysosomes in cisplatin-resistant cells in a manner that appears to be independent of copper distribution. The use of ligand-accelerated catalysis may present a new blueprint for engineering metal selectivity in probe development.
Endothelial/Pericyte Interactions (2005)

Interactions between endothelial cells and mural cells (pericytes and vascular smooth muscle cells) in the blood vessel wall have recently come into focus as central processes in the regulation of vascular formation, stabilization, remodeling, and function. Failure of the interactions between the 2 cell types, as seen in numerous genetic mouse models, results in severe and often lethal cardiovascular defects. Abnormal interactions between the 2 cell types are also implicated in a number of human pathological conditions, including tumor angiogenesis, diabetic microangiopathy, ectopic tissue calcification, and stroke and dementia syndrome CADASIL. In the present review, we summarize current knowledge concerning the identity, characteristics, diversity, ontogeny, and plasticity of pericytes. We focus on the advancement in recent years of the understanding of intercellular communication between endothelial and mural cells with a focus on transforming growth factor beta, angiopoietins, platelet-derived growth factor, spingosine-1-phosphate, and Notch ligands and their respective receptors. We finally highlight recent important data contributing to the understanding of the role of pericytes in tumor angiogenesis, diabetic retinopathy, and hereditary lymphedema.
The catalytic domain of human immunodeficiency virus integrase: ordered active site in the F185H mutant (1996)

We solved the structure and traced the complete active site of the catalytic domain of the human immunodeficiency virus type 1 integrase (HIV-1 IN) with the F185H mutation. The only previously available crystal structure, the F185K mutant of this domain, lacks one of the catalytically important residues, E152, located in a stretch of 12 disordered residues [Dyda et al. (1994) Science 266, 1981-1986]. It is clear, however, that the active site of HIV-1 IN observed in either structure cannot correspond to that of the functional enzyme, since the cluster of three conserved carboxylic acids does not create a proper metal-binding site. The conformation of the loop was compared with two different conformations found in the catalytic domain of the related avian sarcoma virus integrase [Bujacz et al. (1995) J. Mol. Biol. 253, 333-346]. Flexibility of the active site region of integrases may be required in order for the enzyme to assume a functional conformation in the presence of substrate and/or cofactors.
Polydopamine-Coated, Nitrogen-Doped, Hollow Carbon–Sulfur Double-Layered Core–Shell Structure for Improving Lithium–Sulfur Batteries (2014)

To better confine the sulfur/polysulfides in the electrode of lithium-sulfur (Li/S) batteries and improve the cycling stability, we developed a double-layered core-shell structure of polymer-coated carbon-sulfur. Carbon-sulfur was first prepared through the impregnation of sulfur into hollow carbon spheres under heat treatment, followed by a coating polymerization to give a double-layered core-shell structure. From the study of scanning transmission electron microscopy (STEM) images, we demonstrated that the sulfur not only successfully penetrated through the porous carbon shell but also aggregated along the inner wall of the carbon shell, which, for the first time, provided visible and convincing evidence that sulfur preferred diffusing into the hollow carbon rather than aggregating in/on the porous wall of the carbon. Taking advantage of this structure, a stable capacity of 900 mA h g(-1) at 0.2 C after 150 cycles and 630 mA h g(-1) at 0.6 C after 600 cycles could be obtained in Li/S batteries. We also demonstrated the feasibility of full cells using the sulfur electrodes to couple with the silicon film electrodes, which exhibited significantly improved cycling stability and efficiency. The remarkable electrochemical performance could be attributed to the desirable confinement of sulfur through the unique double-layered core-shell architectures.
Strength, Power and Related Functional Ability of Healthy People Aged 65–89 Years (1994)

This cross-sectional study was designed to examine the effects of healthy ageing on muscle strength, power, and potentially related functional ability. Subjects were recruited through local and national newspapers and inclusion was based on strict health criteria, by questionnaire. Isometric knee extensor, isometric elbow flexor and handgrip strength, leg extensor power, timed rise from a low chair, lifting a weighted bag on to a surface, and stepping unaided on to boxes of different heights were measured in 50 men and 50 women, evenly distributed over the age range 65-89 years. The differences in isometric strength and leg extensor power over the age range were equivalent to 'losses' of 1-2% per annum and approximately 3 1/2% per annum, respectively. The decline of explosive power was faster than the decline of knee extensor strength in men (p = 0.0001), but not significantly so in women (p = 0.08). Power standardized for body weight influenced chair rise time and step height. Isometric knee extensor strength standardized for body weight influenced chair rise time.
Recursion relation generation of probability profiles for specific‐sequence macromolecules with long‐range correlations (1974)

Abstract The problem of calculating detailed probability profiles giving the probability of each unit in the chain to be in the ordered state (and all other average quantities as well including the fraction of strand association) for specific‐sequence macromolecules requiring statistical weights that correlate up to the total number of units in the chain (e.g., DNA, collagen) is formulated in terms of recursion relations for appropriate a priori and conditional probabilities, thus generalizing the approach of Lacombe and Simha for nearest‐neighbor correlations in specific sequence macromolecules. The technique allows the probability profiles for chains of thousands of units to be calculated in minutes making no approximation in the basic model.
Caveolin-1–Deficient Mice Have Increased Tumor Microvascular Permeability, Angiogenesis, and Growth (2007)

Caveolin-1 (Cav-1) is a major structural protein that is essential to the formation of the organelle, caveolae. Cav-1 knockout (KO) mice were observed to be completely devoid of caveolae yet they exhibit a hyperpermeable vasculature. Given the nature of the hyperpermeable Cav-1 KO endothelium, we sought to investigate if tumors grown in Cav-1 KO mice would be leaky and grow faster. Indeed, Lewis lung carcinoma cells implanted into Cav-1 KO mice had increased tumor vascular permeability, measured by Evans blue extravasation and fibrinogen deposition compared with tumors implanted into wild-type (WT) mice. Cav-1 KO mice also had significantly higher tumor growth rates, attributable to increased tumor angiogenesis and decreased tumor cell death. Furthermore, administration of an antipermeability peptide, cavtratin, was able to correct the tumor hyperpermeability as well as attenuate the increased tumor growth. Mechanistically, endothelial cells isolated from Cav-1 KO mice exhibited increased tyrosine phosphorylation on vascular endothelial growth factor (VEGF) receptor-2 (VEGFR-2) and decreased association with the adherens junction protein, VE-cadherin. Thus, the loss of Cav-1 increases tumor permeability and growth and that may relate to enhanced VEGF signaling due to lack of Cav-1 inhibition of VEGFR-2 or decreased VE-cadherin mediated VEGFR-2 phosphorylation.
Vertical transmission of human immunodeficiency virus (HIV) infection. Reactivity of maternal sera with glycoprotein 120 and 41 peptides from HIV type 1. (1992)

The observation that approximately 70% of HIV-infected pregnant women do not transmit infection vertically suggests that antibody therapy may be effective in the prevention of transmission of HIV infection from mother to child. Currently, there is an incomplete understanding of the processes involved in vertical transmission of HIV infection. The elucidation of the serological basis of maternal immunity as it relates to protection from vertical transmission is the goal of this study. We have screened 20 maternal sera from HIV+ individuals of known vertical transmission status for reactivity with 31 peptides spanning the entire envelope glycoprotein of HIV-1. Of interest was reactivity to regions outside of the V3 loop of gp120. The findings have been examined in relationship to transmission status, as well as to in vitro anti-HIV-1 biological activity. Our results indicate that lack of vertical transmission is correlated with high viral neutralization activity, but not with antisyncytial activity nor with binding to the V3 peptides examined in this study. Also, the transmission group bound to fewer gp41 peptides when compared with the nontransmission group, suggesting that immune responses to gp41 may be important in preventing transmission. These findings may provide insights into the design of passive immunotherapies.
Site-directed mutagenesis of histidine-13 and histidine-114 of human angiogenin. Alanine derivatives inhibit angiogenin-induced angiogenesis (1989)

The roles of His-13 and His-114 in the ribonucleolytic and angiogenic activities of human angiogenin have been investigated by site-directed mutagenesis. Replacement of either residue by alanine (H13A and H114A) decreases enzymatic activity toward tRNA by at least 10,000-fold and virtually abolishes 10,000-fold and virtually abolishes angiogenic activity in the chick embryo chorioallantoic membrane assay. Both the H13A and H114A mutant proteins compete effectively with angiogenin in the latter assay; only a 5-fold molar excess of H13A over unmodified protein is required for complete inhibition. The His----Ala substitutions, however, do not have any significant effect on the interaction of angiogenin with human placental ribonuclease inhibitor, an extremely potent inhibitor of angiogenin (Ki approximately 7 x 10(-16 M) previously shown to interact with another active-site residue, Lys-40. The effects of more conservative replacements-glutamine at position 13 and asparagine at position 114--were also examined. While the enzymatic activity of the H114N mutant was at least 3300-fold less than for the unmodified protein, the H13Q derivative had only 300-fold reduced activity toward tRNA and cytidylyl(3'----5') adenosine. Both substitutions substantially decreased angiogenic activity. The parallel effects on ribonucleolytic and biological activities observed with all four mutant proteins provide strong evidence that the latter activity of angiogenin is dependent on a functional enzymatic active site. The capacity of the H13A and H114A derivatives to compete with angiogenin in the chorioallantoic membrane assay suggests several additional features of the biological mode of action of this protein.
New Disinfection and Sterilization Methods (2001)

New disinfection methods include a persistent antimicrobial coating that can be applied to inanimate and animate objects (Surfacine), a high-level disinfectant with reduced exposure time (ortho-phthalaldehyde), and an antimicrobial agent that can be applied to animate and inanimate objects (superoxidized water). New sterilization methods include a chemical sterilization process for endoscopes that integrates cleaning (Endoclens), a rapid (4-hour) readout biological indicator for ethylene oxide sterilization (Attest), and a hydrogen peroxide plasma sterilizer that has a shorter cycle time and improved efficacy (Sterrad 50).
Crossveinless 2 contains cysteine-rich domains and is required for high levels of BMP-like activity during the formation of the cross veins in Drosophila (2000)

The BMP-like signaling mediated by the ligands Dpp and Gbb is required to reinforce the development of most veins in the Drosophila wing. However, the formation of the cross veins is especially sensitive to reductions in BMP-like signaling. We show here that the formation of the definitive cross veins occurs after the initial specification of the longitudinal veins in a process that requires localized BMP-like activity. Since Dpp and Gbb levels are not detectably higher in the early phases of cross vein development, other factors apparently account for this localized activity. Our evidence suggests that the product of the crossveinless 2 gene is a novel member of the BMP-like signaling pathway required to potentiate Gbb of Dpp signaling in the cross veins. crossveinless 2 is expressed at higher levels in the developing cross veins and is necessary for local BMP-like activity. The Crossveinless 2 protein contains a putative signal or transmembrane sequence, and a partial Von Willebrand Factor D domain similar to those known to regulate the formation of intramolecular and intermolecular bonds. It also contains five cysteine-rich domains, similar to the cysteine-rich domains found in Chordin, Short Gastrulation and Procollagen that are known to bind BMP-like ligands. These features strongly suggest that Crossveinless 2 acts extracelluarly or in the secretory pathway to directly potentiate Dpp or Gbb signaling.
Molecular Mechanisms of Gating and Drug Block of Sodium Channels (2001)

Voltage-gated Na+ channels are composed of an alpha subunit of 260 kDa associated with beta subunits of 33-36 kDa. Alpha subunits have four homologous domains (I to IV) containing six transmembrane alpha helices (S1-S6). The S4 segments serve as voltage sensors and move outward to initiate activation. The S5 and S6 segments and the short membrane-associated loops between them form the pore. Fast inactivation is mediated by closure of an inactivation gate formed by the intracellular loop between domains III and IV. The 3-D structure of the inactivation gate has been determined bv NMR spectroscopy, revealing the conformation of the pore-blocking IFM motif. Peptide scorpion toxins that alter gating of Na+ channels bind to the extracellular ends of the IIS4 and IVS4 segments, trap them in either an activated or non-activated position, and thereby selectively alter channel activation or inactivation. Voltage sensor-trapping may be a general mechanism of toxin action on voltage-gated ion channels. Local anaesthetics block the pore of Na+ channels by binding to a receptor site in segment S6 in domains III and IV. Anticonvulsants and antiarrhythmic drugs also interact with this site. A high-affinity Na+ channel blocker has recently been developed with this site as its target. The emerging knowledge of the molecular mechanisms of Na+ channel gating and drug block may allow development of novel therapeutics for epilepsy, cardiac arrhythmia and persistent pain syndromes.
Vascular Imaging of Solid Tumors in Rats with a Radioactive Arsenic-Labeled Antibody that Binds Exposed Phosphatidylserine (2008)

These results show that radioarsenic-labeled bavituximab has potential as a new tool for imaging the vasculature of solid tumors.
<title>VisualGREP: a systematic method to compare and retrieve video sequences</title> (1997)

In this paper, we consider the problem of similarity between video sequences. Three basic questions are raised and (partially) answered. Firstly, at what temporal duration can video sequences be compared? The frame, shot, scene and video levels are identified. Secondly, given some image or video feature, what are the requirements on its distance measure and how can it be 'easily' transformed into the visual similarity desired by the inquirer? Thirdly, how can video sequences be compared at different levels? A general approach based on either a set or sequence representation with variable degrees of aggregation is proposed and applied recursively over the different levels of temporal resolution. It allows the inquirer to fully control the importance of temporal ordering and duration. Promising experimental results are presented.
Dogged Learning for Robots (2007)

Ubiquitous robots need the ability to adapt their behaviour to the changing situations and demands they will encounter during their lifetimes. In particular, non-technical users must be able to modify a robot's behaviour to enable it to perform new, previously unknown tasks. Learning from demonstration is a viable means to transfer a desired control policy onto a robot and mixed-initiative control provides a method for smooth transitioning between learning and acting. We present a learning system (dogged learning) that combines learning from demonstration and mixed initiative control to enable lifelong learning for unknown tasks. We have implemented dogged learning on a Sony Aibo and successfully taught it behaviours such as mimicry and ball seeking
Enteral siRNA delivery technique for therapeutic gene silencing in the liver via the lymphatic route (2015)

An efficient targeting delivery technology is needed for functional oligonucleotides to exert their potential effect on the target gene without an adverse effect in vivo. Development of enteral delivery systems for nucleic acids is a major challenge because of their large molecular size and instability. Here, we describe a new enteral delivery technique that enables small interfering RNA (siRNA) selectively delivered to the liver to silence its target Apolipoprotein B gene expression. A nuclease-resistant synthetic siRNA was conjugated with α-tochopherol and administered as lipid nanoparticle to the large intestine of the mice in a postprandial state. The selective transport into the liver, effective gene silence, and consequently significant reduction in serum low density lipoprotein-cholesterol level, were demonstrated. The chylomicron-mediated pathway via the lymphatic route was suggested as major mechanism. This unique approach may provide a basis for developing oral and rectal delivery systems for nucleic acids targeting liver.