gebhart/patrepeval huggingface dataset:
The physical foundations of formation density logging (gamma-gamma) (1965)

Abstract The principal modes of interaction between gamma rays and atoms are reviewed. Special attention is paid to the need for using only Compton scattering in order to determine the electron density of a sample or earth formation and for eliminating chemical composition effects arising from low-energy photoelectric absorption. The nature of the so-called Z/A effect is discussed in relation to the conversion of electron density, the immediately measured quantity, into bulk density. Since gamma-ray diffusion results from repeated scattering in the formation, the Boltzmann transport equation is used as the framework for understanding empirical observations. The method-of-moments solution provides both an understanding of the spatial variation of the gamma-ray energy spectrum and also a basis for reducing the Boltzmann equation to the simple diffusion equation. A discussion is presented comparing experimental results with the diffusion solution for the point-source-at-plane-interface problem. The comparison confirms the validity of the mathematical and physical approximations made.
Experimental Visna in Icelandic Sheep: The Prototype Lentiviral Infection (1985)

A brief review of experimental infection of Icelandic sheep following intracerebral inoculation of neurotropic strains of visna virus is presented. In vivo replication of the virus is restricted, so that some cells carry the deoxyribonucleic acid provirus as an unexpressed genome. This cellular restriction plays a major role in the slow progression of the infection, abetted by neutralizing antibody in serum and spinal fluid. The latent provirus maintains the viral genome in the presence of an active immune response, since immune surveillance cannot recognize cells that are not synthesizing viral antigens. Infected Icelandic sheep experience two types of diseases of the central nervous system: a subclinical subacute encephalitis begins within weeks of infection in most sheep; and at irregular intervals from 0.5-8 years after infection, clinical paresis develops in the majority of Icelandic sheep and is accompanied by discrete focal demyelinating lesions in the spinal cord. The subacute encephalomyelitis is probably mediated by an antiviral cellular immune response, whereas the pathogenesis of the focal demyelinating lesions is still obscure. During persistent infection there is some selection for neutralization-resistant antigenic variants of the infecting serotype, and these are isolated at a frequency of approximately 15%. However, variants do not replace the infecting serotype, and antigenic drift does not appear essential for persistence of visna virus or for the occurrence of demyelinating lesions.
Fabrication of improved-quality seed crystals for growth of bulk silicon carbide (2011)

Sublimation epitaxy in a vacuum has been used to grow silicon carbide layers with a low defect concentration and with SiC wafers cut from single-crystal ingots produced by the modified Lely method serving as substrates. It is concluded on the basis of a comparative study of the distribution of structural defects in substrates and epitaxial layers that an isomorphic pair composed of an epitaxial layer and a single-crystal SiC substrate, which is a composite of materials produced by the same method (sublimation synthesis), but in different technological conditions, is promising for fabrication of improved-quality silicon carbide seed crystals.
Intercellular mobility and homing of an archaeal rDNA intron confers a selective advantage over intron- cells of Sulfolobus acidocaldarius. (1995)

Some intron-containing rRNA genes of archaea encode homing-type endonucleases, which facilitate intron insertion at homologous sites in intron- alleles. These archaeal rRNA genes, in contrast to their eukaryotic counterparts, are present in single copies per cell, which precludes intron homing within one cell. However, given the highly conserved nature of the sequences flanking the intron, homing may occur in intron- rRNA genes of other archaeal cells. To test whether this occurs, the intron-containing 23S rRNA gene of the archaeal hyperthermophile Desulfurococcus mobilis, carried on nonreplicating bacterial vectors, was electroporated into an intron- culture of Sulfolobus acidocaldarius. PCR experiments demonstrated that the intron underwent homing and spread through the culture. By using a double drug-resistant mutant of S. acidocaldarius, it was shown that spreading resulted partly from a selective advantage of intron+ cells and partly from intercellular mobility of the intron and homing.
Potentiometric Titrations and Nickel(II) Complexes of Four Topologically Constrained Tetraazamacrocycles (2001)

Abstract The novel high spin Ni2+ complexes of the topologically constrained tetraazamacrocycles (1–4) [4,11-dimethyl-1,4,8,11 - tetraazabicyclo[6.6.2]hexadecane (1); 4,10-dimethyl-1,4,7,10-tetraazabicyclo[6.5.2]pentadecane (2); 4,10-dimethyl-1,4,7,10-tetraazabicyclo[5.5.2]tetradecane (3); racemic-4,5,7,7,11,12,14,14-octamethyl-1,4,8,11-tetraazabicyclo[6.6.2]hexadecane (4)] show striking properties. Potentiometric titrations of the ligands 2 and 4 revealed them to be proton sponges, as reported earlier for 1 [1]. Ligand 3 is less basic, losing its last proton with a pK = 11.3(2). Despite high proton affinities, complexation reactions in the absence of protons successfully yielded Ni2+ complexes in all cases. The X-ray crystal structures of Ni(1)(acac)+, Ni(3)(acac)+ and Ni(1)(OH2)2 2+ demonstrate that the ligands enforce a distorted octahedral geometry on Ni2+ with two cis sites occupied by other ligands. Magnetic measurements and electronic spectroscopy on the corresponding Ni(L)Cl2 (L = 1–3) complexes reveal that all are high spin and six-coordinate with typical magnetic moments. In contrast, [Ni(4)Cl+] is five-coordinate with a slightly higher magnetic moment and its own characteristic electronic spectrum. The extra methyl groups on ligand 4 define a shallow cavity, sterically allowing only one chloride ligand to bind to the nickel(II) ion.
Chemical and Engineering Approaches To Enable Organic Field-Effect Transistors for Electronic Skin Applications (2011)

Skin is the body's largest organ and is responsible for the transduction of a vast amount of information. This conformable material simultaneously collects signals from external stimuli that translate into information such as pressure, pain, and temperature. The development of an electronic material, inspired by the complexity of this organ is a tremendous, unrealized engineering challenge. However, the advent of carbon-based electronics may offer a potential solution to this long-standing problem. In this Account, we describe the use of an organic field-effect transistor (OFET) architecture to transduce mechanical and chemical stimuli into electrical signals. In developing this mimic of human skin, we thought of the sensory elements of the OFET as analogous to the various layers and constituents of skin. In this fashion, each layer of the OFET can be optimized to carry out a specific recognition function. The separation of multimodal sensing among the components of the OFET may be considered a "divide and conquer" approach, where the electronic skin (e-skin) can take advantage of the optimized chemistry and materials properties of each layer. This design of a novel microstructured gate dielectric has led to unprecedented sensitivity for tactile pressure events. Typically, pressure-sensitive components within electronic configurations have suffered from a lack of sensitivity or long mechanical relaxation times often associated with elastomeric materials. Within our method, these components are directly compatible with OFETs and have achieved the highest reported sensitivity to date. Moreover, the tactile sensors operate on a time scale comparable with human skin, making them ideal candidates for integration as synthetic skin devices. The methodology is compatible with large-scale fabrication and employs simple, commercially available elastomers. The design of materials within the semiconductor layer has led to the incorporation of selectivity and sensitivity within gas-sensing devices and has enabled stable sensor operation within aqueous media. Furthermore, careful tuning of the chemical composition of the dielectric layer has provided a means to operate the sensor in real time within an aqueous environment and without the need for encapsulation layers. The integration of such devices as electronic mimics of skin will require the incorporation of biocompatible or biodegradable components. Toward this goal, OFETs may be fabricated with >99% biodegradable components by weight, and the devices are robust and stable, even in aqueous environments. Collectively, progress to date suggests that OFETs may be integrated within a single substrate to function as an electronic mimic of human skin, which could enable a large range of sensing-related applications from novel prosthetics to robotic surgery.
Molecular virology: a practical approach (1993)

Analysis of replication complexes of positive strand RNA plant viruses, Robert J. Hayes and Kenneth W. Buck molecular biology of influenza viruses and paramyxoviruses, Reay G. Paterson and Robert A. Lamb viral DNA replication, Nigel D. Stow and Ronald T. Hay analysis of viral sequence variation by PCR, Peter Simmonds and Shui-Wan Chan molecular analysis of immunodeficiency viruses, Thomas F. Schulz and Bruno Spire retroviral vectors, Andrew W. Stoker poliovirus antigen chimeras, David J. Evans Baculovirus expression vectors, Lorna M.D. Stewart and Robert D. Possee expression of genes by vaccinia virus vectors, Geoffrey L. Smith herpes simplex virus vectors, Frazer J. Rixon and John McLauchlan.
A gene trap approach in mouse embryonic stem cells: the lacZ reported is activated by splicing, reflects endogenous gene expression, and is mutagenic in mice. (1992)

We have confirmed that the gene trap vector pGT4.5 creates spliced fusion transcripts with endogenous genes and prevents the synthesis of normal transcripts at the site of integration. cDNA was prepared to the lacZ fusion transcript in three ES cell lines to recover endogenous exon sequences upstream of lacZ. Each of the clones detected a unique-sized endogenous transcript, as well as the fusion transcript in the ES cell line from which the clone was derived. Sequence analysis of these clones and larger clones isolated from a random-primed cDNA library showed that the splice acceptor was used properly. For two insertions, the expression patterns of the lacZ reporter and the associated endogenous gene were compared in situ at three embryonic stages and were found to be similar. Three gene trap insertions were transmitted into the germ line, and abnormalities were observed with two of the three insertions in the homozygous state. RNA obtained from mice homozygous for the two mutant gene trap insertions was analyzed for normal endogenous transcripts and negligible amounts were detected, indicating that little splicing around the gene trap insertion occurred. This work demonstrates the capacity of the gene trap vector to generate lacZ fusion transcripts, to accurately report endogenous gene expression, and to mutate the endogenous gene at the site of integration.
Asynchronous Methods for Deep Reinforcement Learning (2016)

We propose a conceptually simple and lightweight framework for deep reinforcement learning that uses asynchronous gradient descent for optimization of deep neural network controllers. We present asynchronous variants of four standard reinforcement learning algorithms and show that parallel actor-learners have a stabilizing effect on training allowing all four methods to successfully train neural network controllers. The best performing method, an asynchronous variant of actor-critic, surpasses the current state-of-the-art on the Atari domain while training for half the time on a single multi-core CPU instead of a GPU. Furthermore, we show that asynchronous actor-critic succeeds on a wide variety of continuous motor control problems as well as on a new task of navigating random 3D mazes using a visual input.
Temperature-Induced Gelation Pluronic-g-Poly(acrylic acid) Graft Copolymers for Prolonged Drug Delivery to the Eye (1997)

Copolymers of PEO/PPO/PEO triblock polyethers (Pluronic® polyols) grafted onto a bioadhesive polymer backbone, polyacrylic acid (PAAc), exhibit unique, thermally-induced solution-to-gel phase transitions when their aqueous solutions are warmed. The bioadhesive, thermally-gelling properties of these graft copolymers makes them useful for prolonged delivery of drugs to mucosal surfaces, such as the surface of the eye. In vitro drug release from the graft copolymer matrices is prolonged significantly at 34 °C in PBS compared to homo-PAAc or physical mixtures of PAAc and Pluronic® polyols, especially when Pluronic® polyols with relatively long PPO segments are grafted.
The Emergence of Antigenic Variants is a Rare Event in Long-term Visna Virus Infection in vivo (1983)

Six sheep persistently infected with visna virus were studied for 4 1/2 to 5 3/4 years until they became ill. Virus was isolated at intervals from peripheral blood leukocytes and cerebrospinal fluid (CSF), and at the time of sacrifice from various parts of the brain and the lungs. Both brain and lungs showed lesions typical of advanced visna/maedi. All the sheep formed antibodies in sera and CSF. Virus isolates from each sheep were tested in neutralization tests against sera and CSF collected from the same animal. In one sheep all isolates were found to be identical to the inoculated virus by this test. In each of the other sheep an antigenic variant emerged from 1 to 3 years after inoculation and remained in circulation even after the formation of autologous antibodies. In one case a variant was isolated from the lungs, whereas in all cases the virus isolated from the brain was identical to the inoculated virus. The results show that antigenic variants are rare in visna and do not seem to have a role in the pathogenesis of the disease.
Ligation-Mediated PCR: Robotic Liquid Handling for DNA Damage and Repair (2002)

The investigation of in vivo DNA repair in mammalian cells at nucleotide resolution requires the quantification of break frequencies less than one per kilobase. By optimizing several parameters of the ligation-mediated PCR technique, we find that the required sensitivity can be achieved. We also report details of a one-day procedure that can be performed either with or without a robotic liquid handling workstation. The use of near-infrared fluorescent-labeled primers with detection by a LI-COR DNA sequencer provides for safe, nonradioactive detection, similar in sensitivity to the use of 32P-labeled primers but with the additional advantage that high-quality digitized data are obtained directly. Multiplexing can be performed; that is, more than one sequence can be analyzed in a single reaction, and multiple reactions can be processed robotically. Primer sets for exons 5-8 of the tumor suppressor gene, p53, were designed for simultaneous thermal cycling. The improved procedure with infrared detection was used to monitor low-frequency damage (<1 break/kb) and/or repair of UVB, UVC, and chemical methylation. Quantitative data on the linearity of response and reproducibility are described. The coefficient of variation for technical replicates was typically 10%. The methods described here will permit high sample throughput for the detection of DNA damage and repair as well as in vivo protein footprints.
Clinical and molecular features of mitochondrial DNA depletion syndromes (2008)

Mitochondrial DNA depletion syndromes (MDSs) form a group of autosomal recessive disorders characterized by profoundly decreased mitochondrial DNA copy numbers in affected tissues. Three main clinical presentations are known: myopathic, encephalomyopathic and hepatocerebral. The first is associated with mutations in thymidine kinase 2 (TK2) and p53-induced ribonucleotide reductase B subunit (RRM2B); the second with mutations in succinate synthase A (SUCLA2) and B (SUCLG1); the third with mutations in Twinkle (PEO1), pol-gammaA (POLG1), deoxyguanosine kinase (DGUOK) and MPV17 (MPV17). In this work, we review the MDS-associated phenotypes and present our own experience of 32 MDS patients, with the aim of defining the mutation frequency of the known genes, the clinical spectrum of the diseases, and the genotype-phenotype correlations. Five of our patients carried previously unreported mutations in one of the eight MDS genes.
Antioxidant and Anti‐inflammatory Activities of Methanol Extracts of Tremella fuciformis and Its Major Phenolic Acids (2014)

Methanol extract subfractions of the edible white jelly mushroom (Tremella fuciformis), were assessed for the following antioxidant properties: ABTS(+) radical scavenging activity, 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging activity, and inhibitory activity of human low-density lipoprotein (LDL) oxidation. Among the subfractions tested, the chloroform subfraction exhibited the strongest antioxidant activity, with the highest total phenolic content (66.31 μg CAE/mg extract) and flavonoids content (5.12 μg QE/mg extract). The ABTS(+) radical scavenging activity of the chloroform subfraction was 7.89 μmol trolox/mg extract, which was the highest among all subfractions. This subfraction also showed the highest DPPH radical scavenging activity and inhibitory activity of LDL oxidation. In addition, the chloroform subfraction demonstrated anti-inflammatory activity through inhibition of nitric oxide production and inducible nitric oxide synthase expression in RAW 264.7 cells. Major phenolic acids from the mushroom extract were identified as 4-hydroxybenzoic acid (323 mg/kg dry weight of mushroom), gentisic acid (174 mg/kg dry weight of mushroom), and 4-coumaric acid (30 mg/kg dry weight of mushroom).
Systematic review: faecal microbiota transplantation in the management of inflammatory bowel disease (2012)

Whilst the available evidence is limited and weak, it suggests that faecal microbiota transplantation has the potential to be an effective and safe treatment for IBD, at least when standard treatments have failed. Well-designed randomised controlled trials are required to investigate these findings.
Sudden Coronary Death (1995)

Acute changes in coronary plaque morphology (thrombus, plaque disruption, or both) were found in 57% of cases of sudden coronary death. In hearts with myocardial scars and no acute infarction, active coronary lesions were identified in 46% of cases. Neither myocardial infarction (acute or healed) nor an active coronary lesion was present in 19% of hearts.
Construction of poxviruses as cloning vectors: insertion of the thymidine kinase gene from herpes simplex virus into the DNA of infectious vaccinia virus. (1982)

We have constructed recombinant vaccinia viruses containing the thymidine kinase gene from herpes simplex virus. The gene was inserted into the genome of a variant of vaccinia virus that had undergone spontaneous deletion as well as into the 120-megadalton genome of the large prototypic vaccinia variant. This was accomplished via in vivo recombination by cotransfection of eukaryotic tissue culture cells with cloned BamHI-digested thymidine kinase gene from herpes simplex virus containing flanking vaccinia virus DNA sequences and infectious rescuing vaccinia virus. Pure populations of the recombinant viruses were obtained by replica filter techniques or by growth of the recombinant virus in biochemically selective medium. The herpes simplex virus thymidine kinase gene, as an insert in vaccinia virus, is transcribed in vivo and in vitro, and the fidelity of in vivo transcription into a functional gene product was detected by the phosphorylation of 5-[125I]iodo-2'-deoxycytidine.
Dynamic Electrophysiological Behavior of Human Atria During Paroxysmal Atrial Fibrillation (1995)

The analysis of the FF intervals demonstrates a strict correlation with atrial functional refractoriness. The self-termination of atrial fibrillation is related to a prolongation of the functional refractoriness (mean FF), whereas a shortening of both functional and effective refractoriness (fifth percentile) is associated with atrial fibrillation persistence. The provoked shortening of the mean FF at the stimulation site is consistent with the presence of a gap of excitability during atrial fibrillation in the human atria.
Helical-scan computed tomography using cone-beam projections (2002)

A fast data-acquisition method for 3-D X-ray computed tomography is proposed. The method continuously rotates a cone-beam X-ray source and a 2-D detector constructed by stacking 1-D circular detector arrays for the fan-beam computed tomography. Simultaneously, a patient is translated in the field of view of the X-ray source. This method is called helical-san, because it provides cone-beam projections measured by moving an X-ray source on a helix surrounding the patient. An approximate convolution backprojection image reconstruction algorithm for the helical-scan is developed by extending L.A. Feldkamp's (1984) cone-beam reconstruction algorithm, for the circular-scan. How one should choose geometrical parameters of the data-acquisition system is discussed. Furthermore, the performance of the proposed method is analyzed by evaluating the point spread function of the reconstruction algorithm.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Testing the effects of FSHD candidate gene expression in vertebrate muscle development. (2010)

The genetic lesion leading to facioscapulohumeral muscular dystrophy (FSHD) is a dominant deletion at the 4q35 locus. The generally accepted disease model involves an epigenetic dysregulation in the region resulting in the upregulation of one or more proximal genes whose overexpression specifically affects skeletal muscle. However, multiple FSHD candidate genes have been proposed without clear consensus. Using Xenopus laevis as a model for vertebrate development our lab has studied the effects of overexpression of the FSHD candidate gene ortholog, frg1 (FSHD region gene 1), showing that increased levels of frg1 systemically led specifically to an abnormal musculature and increased angiogenesis, the two most prominent clinical features of FSHD. Here we studied the overexpression effects of three other promising FSHD candidate genes, DUX4, DUX4c, and PITX1 using the same model system and methods for direct comparison. Expression of even very low levels of either DUX4 or pitx1 early in development led to massive cellular loss and severely abnormal development. These abnormalities were not muscle specific. In contrast, elevated levels of DUX4c resulted in no detectable adverse affects on muscle and DUX4c levels did not alter the expression of myogenic regulators. This data supports a model for DUX4 and PITX1 in FSHD only as pro-apoptotic factors if their expression in FSHD is confined to cells within the myogenic pathway; neither could account for the vascular pathology prevalent in FSHD. Taken together, increased frg1 expression alone leads to a phenotype that most closely resembles the pathophysiology observed in FSHD patients.
Intelligent dialogue based on statistical models of clinical decision‐making (1986)

The independence Bayesian model has been used widely in computer programs designed to support clinical decision-making. A reasoning strategy has been developed to enable these programs to conduct clinically pertinent dialogue and explain their reasoning. It has been implemented in a program for the diagnosis of acute abdominal pain based on the Bayesian model of de Dombal et al. Several features of the dialogue design have been adopted from artificial intelligence research, including shared initiative and critiquing. The program adopts a flexible goal-driven strategy, attempting to confirm the clinician's diagnosis or rule out the likeliest alternative. Symptoms and signs are selected in order of their expected weights of evidence in favour of the hypothesized disease.