gebhart/patrepeval huggingface dataset:
Molecular analysis of the cryptic and functional phn operons for phosphonate use in Escherichia coli K-12 (1991)

We cloned the cryptic phn operon of a K-12 strain, phn(EcoK), and analyzed the nucleotide sequence of the phn region (11,672 bp). An mRNA start site upstream of the phnC gene was identified by S1 nuclease mapping. The pho regulon activator PhoB protects a pho box region near the mRNA start in DNase I footprinting and methylation protection experiments. The sequence of the cryptic phn(EcoK) operon was very similar to that of the functional phn operon of an Escherichia coli B strain, phn(EcoB) (C.-M. Chen, Q.-Z. Ye, Z. Zhu, B. L. Wanner, and C. T. Walsh, J. Biol. Chem. 265:4461-4471, 1990). The phnE(EcoK) gene has an 8-bp insertion, absent from the phnE(EcoB) gene, which causes a frameshift mutation. The spontaneous activation of the cryptic phn(EcoK) operon is accompanied by loss of this additional 8-bp insertion. Studies of the structure, regulation, and function of the phn region suggest that the phosphate starvation-inducible phn operon consists of 14 cistrons from phnC to phnP.
Yellow fever virus infection in Syrian golden hamsters: relationship between cytokine expression and pathologic changes. (2008)

Infection of primates by yellow fever virus (YFV) often results in severe multi-organ failure with marked histologic abnormalities. However, the role of host's immune response, particularly innate immunity, in disease process is unclear. In this study, we used a well established hamster model of yellow fever to examine the dynamic changes of cytokine expression and histopathology in the liver, spleen, kidney, and heart during the course of YFV infection. We observed that the levels of inflammatory cytokines (IFN-gamma, IL-2, TNF-alpha) in the liver were significantly reduced in the mid-stage of infection (8 days), but were elevated later (12 days). In contrast, IL-12p40 was elevated throughout the infection. The levels of IFN-gamma, IL-2, and TNF-alpha were increased in the spleen, kidney, and heart throughout the study period. For regulatory cytokines, IL-10 was significantly increased, and TGF-beta was reduced in the liver, spleen and heart in both early and mid-stages of infection, but was elevated in the kidney during the entire course of infection. In view of the pathologic changes, the observed cytokine profiles suggest that YFV has immunosuppressive effects, which contribute to liver damage in the mid-stage of infection, followed by an immunopathogenic mechanism that leads to disease progression during the late-stages of infection. Our findings support the hypothesis that organ injury by YFV is probably due to a combination of multiple factors, including direct viral injury and host innate immune responses.
<sup>13</sup>C NMR Studies of Vitamin C Transport and Its Redox Cycling in Human Erythrocytes (1998)

13C NMR spectra of labeled [1-13C]- and [2-13C]ascorbic acid were seen to contain resonances arising from the intra- and extracellular populations in suspensions of human erythrocytes; i.e., they displayed the "split-peak" phenomenon. This new observation enabled the ready determination of the location, whether inside or outside cells, of the redox reactions in which the vitamin C was involved and to monitor the transport of the compounds into and out of the cells. Thus, the membrane permeability of ascorbic acid and the apparent Vmax and KM for the reduction of dehydroascorbic acid were determined in a noninvasive manner. In contrast to other work, evidence was found of a transporter of dehydroascorbic acid which is different from the glucose transporter. This transport system also appeared to be involved in the simultaneous reduction of dehydroascorbic acid on its passage into the cells. A second reduction process appeared to occur extracellularly, by the passage of reducing equivalents through the plasma membrane, as occurs with the reduction of ferricyanide. Evidence is presented that the processes of vitamin C recycling rely on different cellular sources of reducing equivalents. Whereas the transport and reduction via the membrane appeared to be dependent on glycolysis (NADH), the reduction of intracellular dehydroascorbic acid, formed in the process of transmembrane electron transfer or by transport from the outside of the cell, is currently thought to depend on NADPH.
Materials adaptation: why leave it all to the teacher? (1989)

This article begins by discussing the background to the idea of learner involvement in syllabus design. It seems unlikely that full learner participation in decisions concerning content and methodology will be possible in most circumstances, but it is suggested here that learner creativity can be introduced in other ways, specifically in the area of materials adaptation. The article describes five principles which lie behind learner involvement in materials adaptation. These principles are then illustrated concretely by means of four extremely diverse opportunities for learner involvement in the adaptation process.
The molecular biology of von Willebrand disease (1999)

von Willebrand disease is the most common inherited bleeding disorder in humans, with the general population prevalence estimated to be as high as 1% in some studies. This condition exhibits extensive heterogeneity with over 20 distinct subtypes distinguished based on subtle clinical and laboratory differences in presentation. Recent research laboratory advances have shed considerable new light on the molecular basis of this disorder. Specific mutations within the von Willebrand factor gene have been identified in many of the qualitative variants of von Willebrand disease, providing important new insight into the structure and function of this central clotting protein. However, the complex genetic factors determining the clinical severity of type 1 von Willebrand disease, the most common variant, still remain largely unknown and are the subject of current investigation.
The Arabidopsis SUPERMAN Gene Mediates Asymmetric Growth of the Outer Integument of Ovules. (1995)

Arabidopsis superman (sup, also referred to as floral mutant10) mutants have previously been shown to have flowers with supernumerary stamens and reduced carpels as a result of ectopic expression of the floral homeotic gene APETALA3 (AP3). Here, we report that sup mutations also cause specific alterations in ovule development. Growth of the outer integument of wild-type ovules occurs almost exclusively on the abaxial side of the ovule, resulting in a bilaterally symmetrical hoodlike structure. In contrast, the outer integument of sup mutant ovules grows equally on all sides of the ovule, resulting in a nearly radially symmetrical tubular shape. Thus, one role of SUP is to suppress growth of the outer integument on the adaxial side of the ovule. Genetic analyses showed that the effects of sup mutations on ovule development are independent of the presence or absence of AP3 activity. Thus, SUP acts through different mechanisms in its early role in ensuring proper determination of carpel identity and in its later role in asymmetric suppression of outer integument growth.
Synthesis of <i>O</i>-Phosphoserine-Containing Peptides by Solution- and Solid-Phase Methods (1991)

The preparation of Ser(P)-containing peptides is described by the use of either (a) a 'global phosphite-triester phosphorylation' approach which uses dialkyl N,N- dialkylphosphoramidites or by (b) a more general approach which utilizes protected Boc- Ser(PO3R2)-OH derivatives in the Boc mode of solution or solid phase peptide synthesis. In the first approach, a protected Ser-containing peptide is synthesized and phosphorylated using dibenzyl or di-t-butyl N,N-diethylphosphoramidite/ 1H-tetrazole followed by oxidation of the resultant 'phosphite-triester' intermediate. The cleavage of benzyl phosphate groups is effected by hydrogenolysis while t-butyl phosphate groups are cleaved by mild acidolytic treatment. In the second and more efficient approach, various Boc-Ser(PO3R2)-OH derivatives are prepared from Boc-Ser-OH by a high yielding three step route using either the phosphorotriester or 'phosphite-triester' phosphorylation procedures. The benzyl derivative, Boc-Ser(PO3Bzl2)-OH, has been used for the synthesis of Ser(PO3Bzl2)-containing peptides followed by a final palladium-catalyzed deprotection step. However, this derivative has restricted use in peptide synthesis due to the susceptibility of benzyl phosphate groups to acidolytic treatments used for Boc-cleavage. The phenyl derivative, Boc-Ser(PO3Ph2)-OH, has been used for the synthesis of several complex Ser(PO3Ph2)-containing peptides with complete cleavage of the phenyl groups effected by platinum oxide-mediated hydrogenation. This derivative has also been used in solid phase methodology for the synthesis of various simple Ser(P)-containing peptides.
Fully Integrated, Multiport, Planar-Waveguide, Spectral Comparators and Multiplexers Based on Lithographic Holography (2005)

Abstract : Several multiplexer layouts based on holographic Brag reflectors were designed and fabricated in a preliminary device water Fabrication results constitute. for the first time the successful application of HBRs to wavelength division multiplexing. Measured device performance indicates that the photolithographic fabrication process has reduced multiplexer designs to practice essentially perfectly. Device apodization and engineering of multiplexer spectral transfer functions based on partial writing and offsetting of diffractive contours is shown to function with high fidelity. A compact-footprint multiplexer based on overlay of several HBRs on the same area was demonstrated. A novel approach to the control and mitigation of waveguide birefringence has been devised successfully.
How schools avoid enrolling children with disabilities (2016)

Children with disabilities are frequently discriminated against in Australian schools. It's an issue that has been ongoing for years, with reports showing that little has improved since 2002. Exclusion practices dubbed as include advising parents to send their child to another school that could better support them; only allowing a child to attend a school on the days that funding is available; and asking parents to pay extra money so the school can employ support staff or purchase equipment. Although this happens across all school types, it tends to be more prominent in, and easier for, non-government or private schools. As these schools compete for enrolments and top exam results, there is a disincentive for them to take any risk that might dilute those results. Unlike public schools, private schools are not required to run open enrolment processes. Their charter is to provide schooling of choice, not to provide for everyone. Because of this, the exact size of the gatekeeping problem is unknown. While government schools receive some extra funding from the state to support children with learning difficulties and disabilities, private schools aren't entitled to this. This has led to the over-representation of students with a disability in government schools, particularly those in disadvantaged areas where parents have fewer options. Over time this leads to a significant burden within some schools, adding to teacher stress and negatively affecting their wellbeing. The concentration of students with additional support needs also impacts other students. The less diversity there is within schools, the less opportunity there is for students to learn from one another. This is the case for abled and disabled students alike.
3-Imidomethyloxazolidines (1960)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT3-ImidomethyloxazolidinesMAX J. KALMCite this: J. Org. Chem. 1960, 25, 11, 1929–1937Publication Date (Print):November 1, 1960Publication History Published online1 May 2002Published inissue 1 November 1960https://pubs.acs.org/doi/10.1021/jo01081a026https://doi.org/10.1021/jo01081a026research-articleACS PublicationsRequest reuse permissionsArticle Views181Altmetric-Citations10LEARN 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-Alertsclose Get e-Alerts
313 km transmission experiment at 1 Gbit/s using optical amplifiers and a low chirp laser (1988)

The use of four in-line semiconductor laser amplifiers is reported in an optical fibre transmission experiment. Using direct detection at 1 Gbit/s, a transmission distance of 313 km of non-dispersion-shifted fibre was achieved. This is 142 km longer than previous experiments at similar data rates, and is the first time optical amplifiers have been used to improve transmission distance for fibre-optic communication systems.
Performance of a Holographic Supernotch Filter (1993)

Results are presented of a comparative evaluation of a holographic supernotch filter (HSNF) and a holographic notch filter (HNF) as a Rayleigh line rejection filter for Raman spectroscopy. The filter permits acquisition of both Stokes and anti-Stokes spectra down to ±200 cm −1 shift from excitation simultaneously, without filter angle adjustment. With slight angle adjustment, spectra can be recorded as close as 41 cm −1 from the excitation line. Performance of the HSNF is evaluated by measuring the low-frequency Raman spectra of Tb 2 (MoO 4 ) 3 , water, and naphthalene.
The intracellular domain of CD44 promotes the fusion of macrophages (2005)

Macrophages seed all tissues in which they have the ability, in specific and rare instances, to fuse with themselves and to differentiate into osteoclasts in bone or into giant cells in chronic inflammatory reactions. Although these cells play a central role in osteoporosis and in foreign body rejection, respectively, the molecular mechanism used by macrophages to fuse remains poorly understood. Macrophages might also fuse with somatic and tumor cells to promote tissue repair and metastasis, respectively. We reported that CD44 expression is highly induced in macrophages at the onset of fusion in which it plays a role. We report now that the intracellular domain of CD44 (CD44ICD) is cleaved in macrophages undergoing fusion and that presenilin inhibitors prevent the release of CD44ICD and fusion. We also show that CD44ICD promotes the fusion of tissue macrophages and bone marrow-derived macrophages. Finally, we report that CD44ICD is localized in the nucleus of macrophages in which it promotes the activation of NF-kappaB. These observations open avenues to study the role of CD44ICD in blood cells and tumors.
Quantifying Optical Microangiography Images Obtained from a Spectral Domain Optical Coherence Tomography System (2012)

The blood vessel morphology is known to correlate with several diseases, such as cancer, and is important for describing several tissue physiological processes, like angiogenesis. Therefore, a quantitative method for characterizing the angiography obtained from medical images would have several clinical applications. Optical microangiography (OMAG) is a method for obtaining three-dimensional images of blood vessels within a volume of tissue. In this study we propose to quantify OMAG images obtained with a spectral domain optical coherence tomography system. A technique for determining three measureable parameters (the fractal dimension, the vessel length fraction, and the vessel area density) is proposed and validated. Finally, the repeatability for acquiring OMAG images is determined, and a new method for analyzing small areas from these images is proposed.
Changes in functional connectivity of human MT/V5 with visual motion input (2004)

The neural basis of human mental function is characterized by interactions between brain regions. Temporal correlations in MR signals between areas may provide one method for investigating these interactions. This approach was used to examine functional connectivity in the motion processing system of the human brain. Correlations between MT/V5 and other brain regions were examined in a resting state (without visual stimulation) and in an active state produced by viewing moving concentric circles. A network of regions consistent with the known functional anatomy of visual processing was correlated with MT/V5 during rest. When subjects were viewing motion, a more limited network was correlated with MT/V5, suggesting MT/V5 was acting in concert with a smaller network specific to the task.
Synthesis of GABA<sub>A</sub>Receptor Agonists and Evaluation of their α-Subunit Selectivity and Orientation in the GABA Binding Site (2008)

Drugs used to treat various disorders target GABA A receptors. To develop alpha subunit selective compounds, we synthesized 5-(4-piperidyl)-3-isoxazolol (4-PIOL) derivatives. The 3-isoxazolol moiety was substituted by 1,3,5-oxadiazol-2-one, 1,3,5-oxadiazol-2-thione, and substituted 1,2,4-triazol-3-ol heterocycles with modifications to the basic piperidine substituent as well as substituents without basic nitrogen. Compounds were screened by [(3)H]muscimol binding and in patch-clamp experiments with heterologously expressed GABA A alpha ibeta 3gamma 2 receptors (i = 1-6). The effects of 5-aminomethyl-3 H-[1,3,4]oxadiazol-2-one 5d were comparable to GABA for all alpha subunit isoforms. 5-piperidin-4-yl-3 H-[1,3,4]oxadiazol-2-one 5a and 5-piperidin-4-yl-3 H-[1,3,4]oxadiazol-2-thione 6a were weak agonists at alpha 2-, alpha 3-, and alpha 5-containing receptors. When coapplied with GABA, they were antagonistic in alpha 2-, alpha 4-, and alpha 6-containing receptors and potentiated alpha 3-containing receptors. 6a protected GABA binding site cysteine-substitution mutants alpha 1F64C and alpha 1S68C from reacting with methanethiosulfonate-ethylsulfonate. 6a specifically covalently modified the alpha 1R66C thiol, in the GABA binding site, through its oxadiazolethione sulfur. These results demonstrate the feasibility of synthesizing alpha subtype selective GABA mimetic drugs.
Diagnosing Leukemia in Blood Smear Images Using an Ensemble of Classifiers and Pre-Trained Convolutional Neural Networks (2017)

Leukemia is a worldwide disease. In this paper we demonstrate that it is possible to build an automated, efficient and rapid leukemia diagnosis system. We demonstrate that it is possible to improve the precision of current techniques from the literature using the description power of well-known Convolutional Neural Networks (CNNs). We extract features from a blood smear image using pre-trained CNNs in order to obtain an unique image description. Many feature selection techniques were evaluated and we chose PCA to select the features that are in the final descriptor. To classify the images on healthy and pathological we created an ensemble of classifiers with three individual classification algorithms (Support Vector Machine, Multilayer Perceptron and Random Forest). In the tests we obtained an accuracy rate of 100%. Besides the high accuracy rate, the tests showed that our approach requires less processing time than the methods analyzed in this paper, considering the fact that our approach does not use segmentation to obtain specific cell regions from the blood smear image.
Enabling and scaling matrix computations on heterogeneous multi-core and multi-GPU systems (2012)

We present a new approach to utilizing all CPU cores and all GPUs on heterogeneous multicore and multi-GPU systems to support dense matrix computations efficiently. The main idea is that we treat a heterogeneous system as a distributed-memory machine, and use a heterogeneous multi-level block cyclic distribution method to allocate data to the host and multiple GPUs to minimize communication. We design heterogeneous algorithms with hybrid tiles to accommodate the processor heterogeneity, and introduce an auto-tuning method to determine the hybrid tile sizes to attain both high performance and load balancing. We have also implemented a new runtime system and applied it to the Cholesky and QR factorizations. Our approach is designed for achieving four objectives: a high degree of parallelism, minimized synchronization, minimized communication, and load balancing. Our experiments on a compute node (with two Intel Westmere hexa-core CPUs and three Nvidia Fermi GPUs), as well as on up to 100 compute nodes on the Keeneland system, demonstrate great scalability, good load balancing, and efficiency of our approach.
A Numerical Characterization of Particle Beam Collimation by an Aerodynamic Lens-Nozzle System: Part I. An Individual Lens or Nozzle (2002)

Particle beams have traditionally been produced by supersonic expansion of a particle-laden gas through a single nozzle to vacuum. However, it has been shown that, by passing the particle-laden gas through a series of axi-symmetric subsonic contractions and expansions (an aerodynamic lens system) prior to the supersonic expansion to vacuum through a single nozzle, beam divergence can be significantly reduced. In this paper, particle motion in expansions of a gas-particle suspension through either a single lens or a single nozzle have been investigated numerically. Since the single aerodynamic lens and the isolated nozzle are the elementary components of any aerodynamic lens-nozzle inlet system, a fundamental understanding of these components is essential for designing an inlet system with the desired sampling rate, collimation, and transmission properties. If a gas undergoes subsonic contraction and expansion through an orifice, the associated particles would follow the fluid streamlines if the particles were inertialess. However, real particles may either experience a displacement toward the axis of symmetry or may impact on the front surface of the lens. The first of these effects leads to collimation of the particles near the axis, but the second effect leads to particle loss. It is found that the maximum particle displacement occurs at a particle Stokes number, St, near unity and significant impact loss also begins at St ; 1. The lens dimensionless geometry and the Reynolds number of the flow are other important parameters. When a gas containing suspended particles undergoes supersonic expansion through a nozzle to vacuum from the lens working pressure (∼300 Pa), it is found that particle beam divergence is a function of Reynolds number, nozzle geometry, and particle Stokes number. More specifically, it is found that a stepped nozzle generally helps to reduce beam divergence and that particle velocity scales with the speed of sound.
Framing and multiple-PLP structures for LDM-based next generation terrestrial broadcasting systems (2015)

In this paper, we present framing and multiple-physical layer pipe (PLP) structures for layered division multiplexing (LDM)-based next generation terrestrial broadcasting systems. As a framing structure, single-layer frames and multi-layer frames can be simultaneously transmitted by a time division multiplexing (TDM) approach. In addition to a conventional multiple-PLP strategy, which is basically time-divisioned, layer-divisioned multiple-PLP strategies are introduced in order to implement low complexity and high efficiency LDM systems. In the case that the cells of upper layer and lower layer are super-imposed, a practical consideration of lower layer cell indication is addressed. Performance analysis is given when multiple PLPs are serviced with different TDM and LDM configurations.