gebhart/patrepeval huggingface dataset:
Nephrogenic Systemic Fibrosis (2008)

Summary For more than 10 years it has been believed that gadolinium‐based contrast agents in doses used for magnetic resonance imaging (MRI) are relatively safe with regard to acute non‐renal and renal adverse reactions and delayed reactions. However, recent observations have shown that it may not be the case in patients with reduced renal function as gadolinium‐based contrast agents may trigger the development of fibrosis in all parts of the body so‐called nephrogenic systemic fibrosis (NSF). Its primary predilection is the skin. Unrelated to the development of NSF, contrast‐induced nephropathy may occur after administration of gadolinium‐based contrast agents. The current review updates the recent developments regarding the severe delayed reaction. However, the fear of NSF should not lead to a denial of a well‐indicated enhanced MRI examination.
Efficiently supporting ad hoc queries in large datasets of time sequences (1997)

Ad hoc querying is difficult on very large datasets, since it is usually not possible to have the entire dataset on disk. While compression can be used to decrease the size of the dataset, compressed data is notoriously difficult to index or access.
ROLE OF ANIONIC PROTEINS IN KIDNEY STONE FORMATION: INTERACTION BETWEEN MODEL ANIONIC POLYPEPTIDES AND CALCIUM OXALATE CRYSTALS (2000)

The results suggest that a discrete number of protein molecules per crystal were required to direct crystallization toward COD, and that a characteristic size of polypeptide chain can be defined. The charge of the side group was not the sole determinant of this effect, as polyglutamic and polyaspartic acids behaved differently. Calcium oxalate crystal nucleation rates appeared to increase with Ox content.
Sequential Simplex Optimization: A Technique for Improving Quality and Productivity in Research, Development, and Manufacturing (1991)

The only book on the market devoted to sequential simplex optimization This book presents an easy-to-learn, effective optimization technique that can be applied immediately to many problems in the real world. The sequential simplex is an evolutionary operation (EVOP) technique that uses experimental results-it does not require a mathematical model. The authors present their subject with a level of detail and clarity that is refreshingly welcome in a technical text. The basics are presented first, followed by a detailed discussion of the fine points needed to get the most out of this optimization technique. Worksheets are provided and their use is illustrated with step-by-step worked examples. This makes the logic and calculations of the simplex algorithms easy to understand and follow. The text also provides more than 200 figures and over 500 references to sequential simplex applications, which allows rapid access to specific examples of the use of the technique in a wide range of applications. Sequential Simplex Optimization: A Technique for Improving Quality and Productivity in Research, Development, and Manufacturing is essential for any student or professional who desires to learn this innovative technique quickly and easily.
Virulence Properties of <i>Escherichia coli</i> 83972, a Prototype Strain Associated with Asymptomatic Bacteriuria (1999)

Little is known about bacteria associated with asymptomatic bacteriuria (ABU) with regard to urinary tract colonization mechanisms. In this study, virulence properties of Escherichia coli 83972, a strain that was isolated from a clinical ABU episode, were examined. The genetic potential for expression of P and type 1 pili was demonstrated, and DNA sequences related to type 1C and G (UCA) pilus genes were also detected. However, E. coli 83972 did not express D-mannose-resistant or D-mannose-sensitive hemagglutination after growth under standard conditions in vitro or upon isolation from the urine of colonized test subjects. Limited uroepithelial cell adherence was observed in vivo, and weak D-mannose-sensitive hemagglutination was detected after extended growth in urine in vitro.
Atomic force microscope observation of plasmid deoxyribose nucleic acid with restriction enzyme (1999)

We have observed plasmid deoxyribose nucleic acid (DNA), in real space images, before and after treating with restriction enzyme (Pvu II or Hinc II) using an atomic force microscope (AFM). The enzyme is recognized on DNA even in the absence of Mg2+ ions. In the presence of Mg2+, on the other hand, direct evidence was obtained that the enzyme could bind to circular plasmid DNA without cutting and cleaved it at the site corresponding to the specificity. Lengths of the DNA fragments observed by AFM were consistent with the values estimated by agarose gel electrophoresis. In addition, as substrates for the AFM observation, rutile TiO2(110) single crystal surface was found to be effective in expanding and fixing the DNA molecules as straight chains along the stepped surface.
Nonviral Direct Conversion of Primary Mouse Embryonic Fibroblasts to Neuronal Cells (2012)

Transdifferentiation, where differentiated cells are reprogrammed into another lineage without going through an intermediate proliferative stem cell-like stage, is the next frontier of regenerative medicine. Wernig et al. first described the direct conversion of fibroblasts into functional induced neuronal cells (iNs). Subsequent reports of transdifferentiation into clinically relevant neuronal subtypes have further endorsed the prospect of autologous cell therapy for neurodegenerative disorders. So far, all published neuronal transdifferentiation protocols rely on lentiviruses, which likely precludes their clinical translation. Instead, we delivered plasmids encoding neuronal transcription factors (Brn2, Ascl1, Myt1l) to primary mouse embryonic fibroblasts with a bioreducible linear poly(amido amine). The low toxicity and high transfection efficiency of this gene carrier allowed repeated dosing to sustain high transgene expression levels. Serial 0.5 µg cm(-2) doses of reprogramming factors delivered at 48-hour intervals produced up to 7.6% Tuj1(+) (neuron-specific class III β-tubulin) cells, a subset of which expressed MAP2 (microtubule-associated protein 2), tau, and synaptophysin. A synapsin-red fluorescent protein (RFP) reporter helped to identify more mature, electrophysiologically active cells, with 24/26 patch-clamped RFP(+) cells firing action potentials. Some non-virally induced neuronal cells (NiNs) were observed firing multiple and spontaneous action potentials. This study demonstrates the feasibility of nonviral neuronal transdifferentiation, and may be amenable to other transdifferentiation processes.
dGTP triphosphohydrolase, a unique enzyme confined to members of the family Enterobacteriaceae (1991)

The enzyme dGTP triphosphohydrolase (dGTPase; EC 3.1.5.1) was assayed in partially purified extracts of several genera of bacteria, and it was found to be strictly confined to members of the family Enterobacteriaceae. Whereas 11 of 12 enteric bacteria had comparable activity for this enzyme, 8 of 8 nonenteric bacteria, including species in the very closely related genera Vibrio and Aeromonas, did not assay positively for this enzyme. When challenged with Escherichia coli anti-dGTPase antiserum, the active enzymes fell into three groups, retaining 0, approximately 50, or 100% of their original activity. A computer search has revealed an amino acid sequence in the E. coli enzyme which matches well with the single-stranded-DNA binding motif of Prasad and Chiu (J. Mol. Biol. 193:579-584, 1987) and may account for the enzyme's observed interaction with DNA. As far as we are aware, this is the only enzymatic activity so far reported to be present solely in the enteric bacteria.
Far field subwavelength focusing using optical eigenmodes (2011)

We report the focusing of light to generate a subdiffractive, subwavelength focal spot of full width half maximum 222 nm at an operating wavelength of 633 nm using an optical eigenmode approach. Crucially, the spot is created in the focal plane of a microscope objective thus yielding a practical working distance for applications. The optical eigenmode approach is implemented using an optimal superposition of Bessel beams on a spatial light modulator. The effects of partial coherence are also discussed. This far field method is a key advance toward the generation of subdiffractive optical features for imaging and lithographic purposes.
HOLOGRAPHIC PLASMA DIAGNOSTICS. (1968)

by studying the emission of Balmer-alpha photons and by using the available tokamak diagnostics (Thomson scattering, microwave/far-infrared interferometer, pyroelectric radiometer, hard x-ray detector).
Patterned wafer inspection using spatial filtering for the cluster environment (1992)

Automated-process tool clusters are becoming increasingly prevalent in advanced semiconductor manufacturing plants, necessitating integrated inspection of patterned semiconductor wafers for defects and particulates. Integrated inspection tools must be small, sensitive, inexpensive, and fast in order to be compatible with the cluster environment. We show that intensity spatial filtering, with some refinements, can provide the required sensitivity and speed in a small, inexpensive package. By using dark-field illumination and a nonrectangular azimuthal orientation (e.g., 45 degrees ) to the primarily rectangular pattern, we show that the strongest diffraction from the pattern can be made to bypass the optical system entirely. This technique alleviates stringent scatter and antireflection requirements on the optics, and it permits the use of off-the-shelf components.
Current Therapy 1980: Latest Approved Methods of Treatment for the Practicing Physician (1980)

This is the latest edition of a compendium that has followed the same format for the past 32 years. Each year, the editor and consulting editors assign more than 280 diseases to a new panel of experts, none of whom covers more than one condition. Thus, each topic is new each year, giving the personal practices and preferences of the current authority. Emphasis may differ from the previous year, but a strong thread of recommendations is carried throughout. The average length of articles is 3 1/2 pages. Emphasis in each is primarily on treatment, including the general approach to management, drug therapy, surgery, and radiology. The old and the new are considered thoughtfully, and specific recommendations are usually given. Prevention is often emphasized. No references are cited. The breadth and depth of coverage are appropriate to the problems of the generalist or the specialist outside of his usual realm. It
Structural polymorphism of Alzheimer Aβ and other amyloid fibrils (2009)

Deposits of amyloid fibrils characterize a diverse group of human diseases that includes Alzheimer's disease, Creutzfeldt-Jakob disease and type II diabetes. Amyloid fibrils formed from different polypeptides contain a common cross-beta spine. Nevertheless, amyloid fibrils formed from the same polypeptide can occur in a range of structurally different morphologies. The heterogeneity of amyloid fibrils reflects different types of polymorphism: (i) variations in the protofilament number, (ii) variations in the protofilament arrangement and (iii) different polypeptide conformations. Amyloid fibril polymorphism implies that fibril formation can lead, for the same polypeptide sequence, to many different patterns of inter- or intra-residue interactions. This property differs significantly from native, monomeric protein folding reactions that produce, for one protein sequence, only one ordered conformation and only one set of inter-residue interactions.
Using Machine Learning for Vulnerability Detection and Classification (2018)

The work described in this paper aims at developing a machine learning based tool for automatic identification of vulnerabilities on programs (source, high level code), that uses an abstract syntax tree representation. It is based on FastScan, using code2seq approach. Fastscan is a recently developed system aimed capable of detecting vulnerabilities in source code using machine learning techniques. Nevertheless, FastScan is not able of identifying the vulnerability type. In the presented work the main goal is to go further and develop a method to identify specific types of vulnerabilities. As will be shown, the goal will be achieved by optimizing the model’s hyperparameters, changing the method of preprocessing the input data and developing an architecture that brings together multiple models to predict different specific vulnerabilities. The preliminary results obtained from the training stage, are very promising. The best f1 metric obtained is 93% resulting in a precision of 90% and accuracy of 85%, according to the performed tests and regarding a trained model to predict vulnerabilities of the injection type.
Long-chain Acyl-CoA Dehydrogenase Deficiency as a Cause of Pulmonary Surfactant Dysfunction (2014)

Long-chain acyl-CoA dehydrogenase (LCAD) is a mitochondrial fatty acid oxidation enzyme whose expression in humans is low or absent in organs known to utilize fatty acids for energy such as heart, muscle, and liver. This study demonstrates localization of LCAD to human alveolar type II pneumocytes, which synthesize and secrete pulmonary surfactant. The physiological role of LCAD and the fatty acid oxidation pathway in lung was subsequently studied using LCAD knock-out mice. Lung fatty acid oxidation was reduced in LCAD(-/-) mice. LCAD(-/-) mice demonstrated reduced pulmonary compliance, but histological examination of lung tissue revealed no obvious signs of inflammation or pathology. The changes in lung mechanics were found to be due to pulmonary surfactant dysfunction. Large aggregate surfactant isolated from LCAD(-/-) mouse lavage fluid had significantly reduced phospholipid content as well as alterations in the acyl chain composition of phosphatidylcholine and phosphatidylglycerol. LCAD(-/-) surfactant demonstrated functional abnormalities when subjected to dynamic compression-expansion cycling on a constrained drop surfactometer. Serum albumin, which has been shown to degrade and inactivate pulmonary surfactant, was significantly increased in LCAD(-/-) lavage fluid, suggesting increased epithelial permeability. Finally, we identified two cases of sudden unexplained infant death where no lung LCAD antigen was detectable. Both infants were homozygous for an amino acid changing polymorphism (K333Q). These findings for the first time identify the fatty acid oxidation pathway and LCAD in particular as factors contributing to the pathophysiology of pulmonary disease.
Voltage-Controlled Topotactic Phase Transition in Thin-Film SrCoO<sub><i>x</i></sub> Monitored by In Situ X-ray Diffraction (2015)

Topotactic phase transition of functional oxides induced by changes in oxygen nonstoichiometry can largely alter multiple physical and chemical properties, including electrical conductivity, magnetic state, oxygen diffusivity, and electrocatalytic reactivity. For tuning these properties reversibly, feasible means to control oxygen nonstoichiometry-dependent phase transitions in functional oxides are needed. This paper describes the use of electrochemical potential to induce phase transition in strontium cobaltites, SrCoOx (SCO) between the brownmillerite (BM) phase, SrCoO₂.₅, and the perovskite (P) phase, SrCoO₃₋δ. To monitor the structural evolution of SCO, in situ X-ray diffraction (XRD) was performed on an electrochemical cell having (001) oriented thin-film SrCoOx as the working electrode on a single crystal (001) yttria-stabilized zirconia electrolyte in air. In order to change the effective pO₂ in SCO and trigger the phase transition from BM to P, external electrical biases of up to 200 mV were applied across the SCO film. The phase transition from BM to P phase could be triggered at a bias as low as 30 mV, corresponding to an effective pO₂ of 1 atm at 500 °C. The phase transition was fully reversible and the epitaxial film quality was maintained after reversible phase transitions. These results demonstrate the use of electrical bias to obtain fast and easily accessible switching between different phases as well as distinct physical and chemical properties of functional oxides as exemplified here for SCO.
[Clinical experience of a case applying temporal approach to zygomatic arch fracture]. (1989)

The technique of temporal approach was originally introduced by Gillies (1927) for reduction of the zygomatic arch and zygomatic complex fracture. We reported a case of zygomatic arch fracture which was treated by temporal approach in a 36-year-old woman. She rode on a motorcycle and fell down on the ground, so she injured the right zygomatic region. Roentgenograms revealed right zygomatic arch and maxillary fracture. We performed a reconstructive operation for the right zygomatic arch fracture with temporal approach and fixated using an acrylic resin splint for 2 weeks. At 7 months after this operation, depression of the zygomatic region was improved and paralysis in the cheek and upper lip region gradually disappeared.
Nanoparticle Phosphors Synthesized by Inductively Controlled Plasma Process for Plasma Based Display (2008)

Optimized volume production of nanoscale phosphor powders synthesized by radio frequency (RF) plasma process was developed for the application to plasma display panels. The nano powders were synthesized by feeding the both solid and liquid type precursors, and nanoparticle phosphors were characterized in terms of particle size, shape, and photoluminescence (PL) intensities. Computer simulation was performed in advance to determine the process parameters, and nano phosphors were evaluated by comparing with current commercial micron-sized phosphor powders. Practical feeding of both solid and liquid type precursor was proved to be effective for volume production.The developed process showed a potential as a production method for red, blue and green phosphor although the PL intensity still needs further improvement.
NFATc1 Regulates PD-1 Expression upon T Cell Activation (2008)

PD-1 is a transmembrane protein involved in the regulation of immunological tolerance. Multiple studies have reported an association between high levels of PD-1 expressed on T cell surfaces and exhaustion in lymphocyte populations when challenged by chronic viral infections, such as HIV. By using model systems consisting of murine EL4 cells, which constitutively express PD-1, and primary murine CD8 T cells that express PD-1 upon T cell stimulation, we have identified two tissue-specific hypersensitive sites at the 5' CR of the PD-1 locus. Gene reporter assays in CD8 T cells have shown that one of these sites has robust transcriptional activity in response to cell stimulation. Cell treatment with the calcineurin inhibitor cyclosporine A or a NFAT-specific inhibitor led to a sharp reduction in PD-1 expression in the constitutive and inducible systems. Furthermore, analysis of this region by chromatin immunoprecipitation assay revealed NFATc1 binding associated with gene activation in EL4 and primary CD8 T cells. Mutation of the NFATc1 binding site in PD-1 reporter constructs resulted in a complete loss of promoter activity. Together, these results demonstrate that PD-1 gene regulation occurs in part via the recruitment of NFATc1 to a novel regulatory element at the pdcd1 locus and provides the molecular mechanism responsible for the induction of PD-1 in response to T cell stimulation.
Transient Transgenic Expression of Gamma Interferon Promotes<i>Legionella pneumophila</i>Clearance in Immunocompetent Hosts (2001)

Gamma interferon (IFN-gamma) and T1-phenotype immune responses are important components of host defense against a variety of intracellular pathogens, including Legionella pneumophila. The benefit of intrapulmonary adenovirus-mediated IFN-gamma gene therapy was investigated in a nonlethal murine model of experimental L. pneumophila pneumonia. Intratracheal (i.t.) administration of 10(6) CFU of L. pneumophila induced the expression of T1 phenotype cytokines, such as IFN-gamma and interleukin-12 (IL-12). Natural killer cells were identified as the major cellular source of IFN-gamma. To determine if enhanced expression of IFN-gamma in the lung could promote pulmonary clearance of L. pneumophila, we i.t. administered 5 x 10(8) PFU of a recombinant adenovirus vector containing the murine IFN-gamma cDNA (AdmIFN-gamma) concomitant with L. pneumophila. We observed a 10-fold decrease in lung bacterial CFU at day 2 in the AdmIFN-gamma-treated group compared to controls (P < 0.01). Alveolar macrophages isolated from AdmIFN-gamma-treated animals displayed enhanced killing of intracellular L. pneumophila organisms ex vivo. Similar improvements in bacterial clearance were observed with i.t. recombinant IFN-gamma treatment. The transient transgenic expression of IL-12, a known inducer of IFN-gamma and promoter of T1-type immune responses, resulted in more modest improvement in bacterial clearance (sixfold reduction; P < 0.05). These results demonstrate that, even in immunocompetent hosts, exogenous administration or transient transgenic expression of IFN-gamma, and to a lesser extent IL-12, may be of potential therapeutic benefit in the treatment of patients with Legionella pneumonia.
Preparation of 5-Substituted 2-Mercapto-1-methylimidazoles. Direct Metalation of 2-Mercapto-1-methylimidazole (1990)

2-Mercapto-1-methylimidazole (1) is directly metalated with tert- butyllithium in tetrahydrofuran to give the 5, S-dianion 2. Reaction of the dianion 2 with a series of electrophiles gives regioselectively 5-substituted 2-mercapto-1-methylimidazoles 4, 5 and 7.
Structure‐activity studies of N,N‐dialkyl and cycloalkyl carbamate esters of dimethylethanolamine and choline with nicotinic and muscarinic cholinergic properties (1994)

Abstract Structure‐activity studies were performed on a series of newly synthesized N‐sub‐stituted carbamate esters of choline and dimethylethanolamine which exhibited either or both nicotinic and muscarinic cholinergic properties. Substitutions on the carbamyl N consisted of varying lengths of dialkyls, diphenyl, and various heterocycles. The compounds were evaluated for their nicotinic and muscarinic receptor binding properties in rat brain membranes, their effect on muscarinic receptor‐activated phosphoinositide (PI) turnover in rat cortical slices, and for muscarinic receptor‐mediated intracelluar Ca release in a mouse adrenal carcinoma cell line transfected with an m1 muscarinic cholinergic receptor gene. N,N‐diethylcarbamylcholine had the highest affinity for nicotinic cholinergic receptors; the K i value of 1 × 10 −9 M approached that of nicotine and being 1/5 that for the dimethyl analogue. With increasing chain length of the dialkyl substituents the nicotinic affinity progressively decreased, while muscarinic affinity increased. N,N‐diphenylcarbamylcholine had a K i value of 1 × 10 −7 M for nicotinic receptors and exhibited nicotinic antagonist activity. Contrary to the results with [ 3 H]‐N‐methylcarbamylcholine binding, the tertiary derivatives exhibited higher K i values for [ 3 H]‐3‐quinuclidinyl benzilate binding than the quarternaries; the tertiary dibutyl and diphenyl had the highest affinities with K i values of 4 × 10 −7 M. The inhibition of muscarinic receptor‐mediated PI turnover and release of intracellular calcium were related to the muscarinic antagonist potency of the compounds. © 1994 Wiley‐Liss, Inc.