gebhart/patrepeval huggingface dataset:
In Vitro Packaging of UV Radiation-Damaged DNA from Bacteriophage T7 (1977)

When DNA from bacteriophage T7 is irradiated with UV light, the efficiency with which this DNA can be packaged in vitro to form viable phage particles is reduced. A comparison between irradiated DNA packaged in vitro and irradiated intact phage particles shows almost identical survival as a function of UV dose when Escherichia coli wild type or polA or uvrA mutants are used as the host. Although uvrA mutants perform less host cell reactivation, the polA strains are identical with wild type in their ability to support the growth of irradiated T7 phage or irradiated T7 DNA packaged in vitro into complete phage. An examination of in vitro repair performed by extracts of T7-infected E.coli suggests that T7 DNA polymerase may substitute for E. coli DNA polymerase I in the resynthesis step of excision repair. Also tested was the ability of a similar in vitro repair system that used extracts from uninfected cells to restore biological activity of irradiated DNA. When T7 DNA damaged by UV irradiation was treated with an endonuclease from Micrococcus luteus that is specific for pyrimidine dimers and then was incubated with an extract of uninfected E. coli capable of removing pyrimidine dimers and restoring the DNA of its original (whole genome size) molecular weight, this DNA showed a higher packaging efficiency than untreated DNA, thus demonstrating that the in vitro repair system partially restored the biological activity of UV-damaged DNA.
HIV-1 Genotypic Resistance Patterns Predict Response to saquinavir–ritonavir Therapy in Patients in Whom Previous Protease Inhibitor Therapy Had Failed (1999)

In patients in whom protease inhibitor-containing antiretroviral therapy fails, HIV-1 genotype is predictive of virologic response to subsequent therapy. This predictive capacity adds to that of standard clinical evaluation.
Changes in Endogenous Substrates of Isolated Rabbit Heart Mitochondria during Storage (1967)

Abstract Rabbit heart mitochondria were isolated in the presence of low concentrations (150 to 250 µm) of pyruvate-2- or -3-14C to label the endogenous substrates. Chromatographic analyses of protein-free filtrates of the mitochondria indicated that the principal labeled endogenous substrates were citrate, malate, glutamate, and alanine. During storage of the mitochondria under anoxic conditions at 0°, radioactive citrate disappeared while aspartate and succinate increased. Continual changes in the composition of the endogenous substrates occurred during storage. When air was supplied to the mitochondrial suspension, the changes were similar to, but more rapid than, those occurring under anoxic conditions. Under aerobic conditions, however, radioactive succinate did not appear. Changes in total citrate, alanine, glutamate, and aspartate paralleled the changes in their radioactivity. Although partially metabolized, the endogenous substrates were largely retained by the mitochondria during repeated washing. During storage, in addition to metabolism, partial loss of some substrates into the medium was evident. Possible relationships of the metabolism of the endogenous substrates to the metabolic properties of isolated mitochondria are discussed.
The human microbiome, asthma, and allergy (2015)

The human microbiome can be defined as the microorganisms that reside within and on our bodies and how they interact with the environment. Recent research suggests that numerous mutually beneficial interactions occur between a human and their microbiome, including those that are essential for good health. Modern microbiological detection techniques have contributed to new knowledge about microorganisms in their human environment. These findings reveal that the microbiomes of the lung and gut contribute to the pathogenesis of asthma and allergy. For example, evidence indicates that the microbiome of the gut regulates the activities of helper T cell subsets (Th1 and Th2) that affect the development of immune tolerance. Moreover, recent studies demonstrate differences between the lung microbiomes of healthy and asthmatic subjects. The hygiene and biodiversity hypotheses explain how exposure to microorganisms is associated with asthma and allergy. Although those living in developed countries are exposed to fewer and less diverse microorganisms compared with the inhabitants of developing countries, they are experiencing an increase in the incidence of asthma and allergies. Detailed analyses of the human microbiome, as are being conducted under the auspices of the Human Microbiome Project initiated in 2007, promise to contribute insights into the mechanisms and factors that cause asthma and allergy that may lead to the development of strategies to prevent and treat these diseases.
Partially coherent image processing by laser scanning (1975)

We describe a class of image-processing optical systems, based on a laser scanner, whose output is an electronic video signal from a simple photodetector. We show that certain image-processing properties of these systems are exactly equivalent to the properties of conventional, partially coherent, image-processing optical systems. These systems are of interest when we want to combine optical image processing with further electronic processing. Some applications, such as electronic read out of phase-encoded images, are discussed.
Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation (2002)

The riboflavin biosynthesis in bacteria was analyzed using comparative analysis of genes, operons and regulatory elements. A model for regulation based on formation of alternative RNA structures involving the RFN elements is suggested. In Gram-positive bacteria including actinomycetes, Thermotoga, Thermus and Deinococcus, the riboflavin metabolism and transport genes are predicted to be regulated by transcriptional attenuation, whereas in most Gram-negative bacteria, the riboflavin biosynthesis genes seem to be regulated on the level of translation initiation. Several new candidate riboflavin transporters were identified (impX in Desulfitobacterium halfniense and Fusobacterium nucleatum; pnuX in several actinomycetes, including some Corynebacterium species and Strepto myces coelicolor; rfnT in Rhizobiaceae). Traces of a number of likely horizontal transfer events were found: the complete riboflavin operon with the upstream regulatory element was transferred to Haemophilus influenzae and Actinobacillus pleuropneumoniae from some Gram-positive bacterium; non-regulated riboflavin operon in Pyrococcus furiousus was likely transferred from Thermotoga; and the RFN element was inserted into the riboflavin operon of Pseudomonas aeruginosa from some other Pseudomonas species, where it had regulated the ribH2 gene.
Muscle NMDA receptors regulate the resting membrane potential through NO-synthase. (1995)

The early postdenervation depolarization of rat diaphragm muscle fibres (8-10 mV) is substantially smaller (3 mV) when muscle strips are bathed with 1 mM L-glutamate (GLU) or N-methyl-D-aspartate (NMDA). The effects of GLU and NMDA are not seen in the presence of aminophosphonovaleric acid (APV), a blocker of NMDA-subtype of glutamate receptors, 5 mM Mg2+ (which blocks NMDA-controlled ion channels) and L-nitroarginine methylester (NAME), an inhibitor of NO-synthase. This indicates that NMDA-subtype of GLU receptors might be involved in the regulation of the membrane potential in muscle fibres, most probably through the NO-synthase system.
Design of a specific phenyllactate dehydrogenase by peptide loop exchange on the Bacillus stearothermophilus lactate dehydrogenase framework (1992)

Restriction sites were introduced into the gene for Bacillus stearothermophilus lactate dehydrogenase which enabled a region of the gene to be excised which coded for a mobile surface loop of polypeptide (residues 98-110) which normally seals the active site vacuole from bulk solvent and is a major determinant of substrate specificity. Oligonucleotide-overlap extension (using the polymerase chain reaction) was used to obtain double-stranded DNA regions which coded for different length and sequence loops and which also contained the same restriction sites. The variable length and sequence loops were inserted into the cut gene and used to synthesize hydroxyacid dehydrogenases with altered substrate specificities. Loops which were longer and shorter than the original were made. The substrate specificities of enzymes with these new loops were considerably altered. For many poor enzyme-substrate pairs, the effect of fructose 1,6-bisphosphate on the steady-state kinetic parameters suggested that the substrate was mainly bound in a nonproductive mode. With one longer loop construction (BL1), activity with pyruvate was reduced one-million-fold but activity with phenylpyruvate was largely unaltered. A switch in specificity (kcat/KM) of 390,000-fold was achieved. The 1700:1 selectivity of enzyme BL1 for phenylpyruvate over pyruvate is that required in a phenyllactate dehydrogenase to be used in monitoring phenylpyruvate in the urine of patients with phenylketonuria consuming an apparently phenylalanine-free diet.
Hardware Design of a Binary Integer Decimal-based IEEE P754 Rounding Unit (2007)

Because of the growing importance of decimal floating-point (DFP) arithmetic, specifications for it were recently added to the draft revision of the IEEE 754 Standard (IEEE P754). In this paper, we present a hardware design for a rounding unit for 64-bit DFP numbers (decimal 64) that use the IEEE P754 binary encoding of DFP numbers, which is widely known as the Binary Integer Decimal (BID) encoding. We summarize the technique used for rounding, present the theory and design of the BID rounding unit, and evaluate its critical path delay, latency, and area for combinational and pipelined designs. Over 86% of the rounding unit's area is due to a 55-bit by 54-bit binary multiplier, which can be shared with a double-precision binary floating-point multiplier. To our knowledge, this is the first hardware design for rounding IEEE P754 BID-encoded DFP numbers.
IL8-CXCR2 pathway inhibition as a therapeutic strategy against MDS and AML stem cells (2015)

Acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS) are associated with disease-initiating stem cells that are not eliminated by conventional therapies. Novel therapeutic targets against preleukemic stem cells need to be identified for potentially curative strategies. We conducted parallel transcriptional analysis of highly fractionated stem and progenitor populations in MDS, AML, and control samples and found interleukin 8 (IL8) to be consistently overexpressed in patient samples. The receptor for IL8, CXCR2, was also significantly increased in MDS CD34(+) cells from a large clinical cohort and was predictive of increased transfusion dependence. High CXCR2 expression was also an adverse prognostic factor in The Cancer Genome Atlas AML cohort, further pointing to the critical role of the IL8-CXCR2 axis in AML/MDS. Functionally, CXCR2 inhibition by knockdown and pharmacologic approaches led to a significant reduction in proliferation in several leukemic cell lines and primary MDS/AML samples via induction of G0/G1 cell cycle arrest. Importantly, inhibition of CXCR2 selectively inhibited immature hematopoietic stem cells from MDS/AML samples without an effect on healthy controls. CXCR2 knockdown also impaired leukemic growth in vivo. Together, these studies demonstrate that the IL8 receptor CXCR2 is an adverse prognostic factor in MDS/AML and is a potential therapeutic target against immature leukemic stem cell-enriched cell fractions in MDS and AML.
Synthesis and Characterization of One-Dimensional MgO Nanostructures (2006)

Magnesium oxide (MgO) nanowire arrays, nanoribbons, two- and three-dimensional network like nanostructures were prepared by the simple thermal evaporation of Mg powder with and without using catalyst at a relatively low temperature. The non-catalytic approaches favor the formation of network like nanoforms whereas the catalytic approaches favors the formation of one-dimensional nanowire arrays and quasi one-dimensional nanoribbons depending on the temperature and vapor concentrations of the growth site. The diameter and length of the MgO network like columns varied within 40-50 nm and approximately 200 nm respectively. The MgO nanowires produced by the catalytic approach had diameter within 20-30 nm and length approximately 2 microm. Whereas the widths of the nanoribbons varied within 50-100 nm and their length were of the order of a few hundred micrometers. The nanoforms were single crystalline and cubic in phase. The products were characterized by the X-ray diffraction study, energy dispersive analysis of X-ray study, scanning and transmission electron microscopy, and photoluminescence measurements to explore the structural, compositional, morphological, and physical properties of the MgO nanoforms.
Facile reduction of ethyl thiol esters to aldehydes: application to a total synthesis of (+)-neothramycin A methyl ether (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFacile reduction of ethyl thiol esters to aldehydes: application to a total synthesis of (+)-neothramycin A methyl etherTohru Fukuyama, Shao Cheng Lin, and Leping LiCite this: J. Am. Chem. Soc. 1990, 112, 19, 7050–7051Publication Date (Print):September 1, 1990Publication History Published online1 May 2002Published inissue 1 September 1990https://pubs.acs.org/doi/10.1021/ja00175a043https://doi.org/10.1021/ja00175a043research-articleACS PublicationsRequest reuse permissionsArticle Views5512Altmetric-Citations275LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Single-cell RNA sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis (2020)

Single-cell RNA sequencing provides new insights into pathologic epithelial and mesenchymal remodeling in the human lung.
Functional gamma chain-associated T cell receptors on cerebrospinal fluid-derived natural killer-like T cell clones. (1987)

We have derived 33 independent T cell clones from the cerebrospinal fluid (CSF) of a patient with subacute sclerosing panencephalitis using a single T cell cloning method. 6% (2 of 33) of these clones express the T cell receptor gamma (TCR-gamma) protein and are called CSF TCR-gamma clones. Phenotypic analyses of the CSF TCR-gamma clones indicate that they are WT-31-, CD3+, CD4-, and CD8-. The TCR-gamma protein exists on the cell surface as part of an 85-kD disulphide-linked dimer noncovalently associated with the CD3 polypeptides. The CSF TCR-gamma clones have NK-like activity that can be inhibited by anti-CD3 mAbs. Both CSF TCR-gamma clones proliferated in response to anti-CD3 mAbs coupled to Sepharose beads and/or IL-2. Furthermore, stimulation of one of these clones with anti-CD3 mAbs results in a rapid rise in intracellular calcium. These data suggest that T cells bearing the CD3-TCR-gamma protein complex are functional and play a role in the human immune response.
Strategies for controlling biofouling in membrane filtration systems: challenges and opportunities (2010)

Biofouling is a critical problem in many membrane filtration processes. This review highlights the emerging strategies for polymer membrane modifications using organic and inorganic additives and surface modification to mitigate foulant deposition and biofilm formation. Constraints and opportunities for future implementation in membrane systems are outlined from the perspectives of water and wastewater treatment applications.
Accurate, Large Minibatch SGD: Training ImageNet in 1 Hour (2017)

Deep learning thrives with large neural networks and large datasets. However, larger networks and larger datasets result in longer training times that impede research and development progress. Distributed synchronous SGD offers a potential solution to this problem by dividing SGD minibatches over a pool of parallel workers. Yet to make this scheme efficient, the per-worker workload must be large, which implies nontrivial growth in the SGD minibatch size. In this paper, we empirically show that on the ImageNet dataset large minibatches cause optimization difficulties, but when these are addressed the trained networks exhibit good generalization. Specifically, we show no loss of accuracy when training with large minibatch sizes up to 8192 images. To achieve this result, we adopt a hyper-parameter-free linear scaling rule for adjusting learning rates as a function of minibatch size and develop a new warmup scheme that overcomes optimization challenges early in training. With these simple techniques, our Caffe2-based system trains ResNet-50 with a minibatch size of 8192 on 256 GPUs in one hour, while matching small minibatch accuracy. Using commodity hardware, our implementation achieves ~90% scaling efficiency when moving from 8 to 256 GPUs. Our findings enable training visual recognition models on internet-scale data with high efficiency.
A liquid drop on an air cushion as an analogue of Leidenfrost boiling (1986)

The paper describes the phenomenon of drop suspension above an air-blown porous surface, which is similar to the well-known levitation of a drop evaporating above a hot plate (‘spheroidal state’ or the Leidenfrost phenomenon). It has been shown that the basis of this similarity is the close analogy between the hydrodynamic mechanisms of drop suspension. Together with the viscous mechanism, the effect of gas- or heat-flow choking under the drop plays an important role here. The latter conditions the threshold character of the above phenomena. A mathematical model of cool- and hot-drop suspension is offered which does not contain any a priori assumptions about the drop form and can be applied to the critical range of parameters. An approximation has also been considered in which the bottom of the drop is assumed to be flat, which allows us to carry out an analysis within a wide range of parameters. The simplest version of this approximation is a disk model, where the problems considered are found to be similar. This version allows analytical solution. The model developed has been verified in a ‘cool’ experiment. The theoretical and experimental data have been shown to be in qualitative (and in some respects in quantitative) agreement.
Molecular-based optical devices (2003)

A brief overview is presented of recent advances in the investigation of materials for the development of all-optical logic devices using nonlinear, bistable and threshold materials. The emphasis is on organic materials because of their flexibility, processability, and strong potential for future growth. These materials make possible the development of novel architectures capable of rapid parallel information processing and suitable for applications such as artificial intelligence, neural networks, and pattern recognition.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Synthesis of Virus Deoxyribonucleic Acid During Abortive Infection of Simian Cells by Human Adenoviruses (1966)

Rapp, Fred (Baylor University College of Medicine, Houston, Tex.), Lawrence A. Feldman, and Manley Mandel. Synthesis of virus deoxyribonucleic acid during abortive infection of simian cells by human adenoviruses. J. Bacteriol. 92:931-936. 1966.-Inoculation of green monkey kidney cells (GMK) with adenovirus types 2 or 12, under conditions where neither infectious virus was synthesized, resulted in an increase in the uptake of H(3)-thymidine into deoxyribonucleic acid (DNA). Extraction of the DNA from infected cells, followed by identification by isopycnic analysis in CsCl gradients, revealed the presence of virus DNA. Cells infected with adenovirus type 2 yielded DNA giving bands with peak densities of 1.699 g/ml [GMK DNA with 40 moles% guanine + cytosine (GC)] and 1.714 g/ml (adenovirus type 2 DNA with 55 moles% GC). Cells infected with adenovirus type 12 also yielded the GMK DNA and a band at 1.706 g/ml (adenovirus type 12 DNA with 47 moles% GC). The rate of synthesis of adenovirus type 2 DNA in KB cells (productive cycle) and in GMK cells infected only with adenovirus (nonproductive cycle) or with adenovirus and simian virus 40 (adeno-productive cycle) was not significantly different.
Structural, functional, and subunit assembly properties of hemoglobin Attleboro [.alpha.138 (H21) Ser .fwdarw. Pro] a variant possessing a site mutation at a critical C-terminal residue (1990)

Hemoglobin Attleboro, a new alpha-chain variant with a substitution of proline for serine at position 138 (H21), was found to be a noncooperative high-affinity hemoglobin (P50 = 0.26 mmHg at pH 7 and 20 degrees C) which lacked an alkaline Bohr effect. Addition of 2,3-diphosphoglycerate (DPG) or inositol hexaphosphate (IHP) led to a decrease in oxygen affinity but to no alteration in either Bohr effect or cooperativity. Ligand binding kinetics studies revealed an overall rate of oxygen dissociation at pH 7.0 and 20 degrees C that was 2.7-fold slower than that for Hb A. At pH 8.5, the kinetic profile was identical with that at pH 7, confirming the absence of a Bohr effect for this variant hemoglobin. Measurement of the rate of oxygen dissociation with carbon monoxide replacement indicated a lack of cooperativity. Sedimentation velocity experiments yielded s20,w values of 2.8 and 4.3 for 65 microM solutions of oxyhemoglobins Attleboro and A, respectively (indicating an enhancement in the oxy dimer population of this variant). Studies of the carbon monoxide combination of this variant revealed an association rate 20-fold faster than that for Hb A; only in the presence of a 1000-fold molar excess of IHP was there a significant reduction in the overall rate. Rapid-scan and traditional stopped-flow experiments conducted in the Soret Soret region demonstrated an alteration in the structure and rate of assembly of the deoxy tetramer of Hb Attleboro relative to that of Hb A. The abnormal properties of this hemoglobin variant can be attributed to major perturbations in the C-terminal region.
THE USE OF PREFABRICATED POLYETHYLENE PLATE FOR CRANIOPLASTY (1970)

Surgical Service (Neurosurgery), Veterans Administration Hospital, and State University of New York, Downstate Medical Center, Brooklyn
Shallow water analogy for a ballistic field effect transistor: New mechanism of plasma wave generation by dc current (1993)

We demonstrate that electrons in a ballistic field effect transistor behave as a fluid similar to shallow water. Phenomena similar to wave and soliton propagation, hydraulic jump, and others should take place in this electron fluid. We show that a relatively slow electron flow should be unstable because of plasma wave amplification due to the reflection from the device boundaries. This provides a new mechanism for the generation of tunable far infrared electromagnetic radiation.