gebhart/patrepeval huggingface dataset:
Molecular characterization and analysis of the biosynthetic gene cluster for the azoxy antibiotic valanimycin (2002)

Streptomyces viridifaciens MG456-hF10 produces the antibiotic valanimycin, a naturally occurring azoxy compound. Valanimycin is known to be derived from valine and serine with the intermediacy of isobutylamine and isobutylhydroxylamine, but little is known about the stages in the pathway leading to the formation of the azoxy group. In previous studies, a cosmid containing S. viridifaciens DNA was isolated that conferred valanimycin production upon Strepto-myces lividans TK24. Subcloning of DNA from the valanimycin-producing cosmid has led to the identi-fication of a 22 kb segment of DNA sufficient to allow valanimycin production in S. lividans TK24. Sequencing of this DNA segment and the surrounding DNA revealed the presence of 20 genes. Gene disruption experiments defined the boundaries of the valanimycin gene cluster, which appears to contain 14 genes. The cluster includes an amino acid decar-boxylase gene (vlmD), a valanimycin resistance gene (vlmF ), at least two regulatory genes (vlmE, vlmI ), two genes encoding a flavin monooxygenase (vlmH, vlmR), a seryl tRNA synthetase gene (vlmL ) and seven genes of unknown function. Overproduction and characterization of VlmD demonstrated that it catalyses the decarboxylation of l-valine. An unusual feature of the valanimycin gene cluster is that four genes involved in branched amino acid biosynthesis are located near its 5' end.
Preparation and Optical Properties of Indium Tin Oxide/Epoxy Nanocomposites with Polyglycidyl Methacrylate Grafted Nanoparticles (2011)

Visibly highly transparent indium tin oxide (ITO)/epoxy nanocomposites were prepared by dispersing polyglycidyl methacrylate (PGMA) grafted ITO nanoparticles into a commercial epoxy resin. The oleic acid stabilized, highly crystalline, and near monodisperse ITO nanoparticles were synthesized via a nonaqueous synthetic route with multigram batch quantities. An azido-phosphate ligand was synthesized and used to exchange with oleic acid on the ITO surface. The azide terminal group allows for the grafting of epoxy resin compatible PGMA polymer chains via Cu(I) catalyzed alkyne-azide "click" chemistry. Transmission electron microscopy (TEM) observation shows that PGMA grafted ITO particles were homogeneously dispersed within the epoxy matrix. Optical properties of ITO/epoxy nanocomposites with different ITO concentrations were studied with an ultraviolet-visible-near-infrared (UV-vis-NIR) spectrometer. All the ITO/epoxy nanocomposites show more than 90% optical transparency in the visible light range and absorption of UV light from 300 to 400 nm. In the near-infrared region, ITO/epoxy nanocomposites demonstrate low transmittance and the infrared (IR) transmission cutoff wavelength of the composites shifts toward the lower wavelength with increased ITO concentration. The ITO/epoxy nanocomposites were applied onto both glass and plastic substrates as visibly transparent and UV/IR opaque optical coatings.
Evaluation of Constituents of Piper retrofractum Fruits on Neurotrophic Activity (2013)

Three new compounds, 1-3, together with 22 known compounds, were isolated from the fruits of Piper retrofractum. The structures of the new compounds were elucidated on the basis of spectroscopic data analysis and comparison with literature values. Compound 1 was found to enhance the neurite outgrowth of NGF-mediated PC12 cells at concentrations ranging from 0.1 to 10 μM.
Molecular cloning and regulation of expression of the genes for initiation factor 3 and two aminoacyl-tRNA synthetases (1982)

A 22-kilobase fragment of the Escherichia coli chromosome which contains the genes for translation initiation factor 3, phenylalanyl-tRNA synthetase, and threonyl-tRNA synthetase was cloned into plasmid pACYC184. The hybrid plasmid (designated pID1) complements a temperature-sensitive pheS lesion in E. coli NP37. pID1-transformed NP37 overproduce initiation factor 3 and phenylalanyl-tRNA synthetase. Gene expression from pID1 was studied in vitro in a coupled transcription-translation system and in minicells. The results suggest that the genes for initiation factor 3 and phenylalanyl- and threonyl-tRNA synthetase are regulated by different mechanisms.
Electrospray ion mobility spectrometry of intact viruses (2004)

Characterizing supramolecular interactions offers significant challenges using NMR or crystallographic techniques either because of size limitations or the difficulty in forming suitable crystals, while mass spectrometry is largely limited to low resolution mass information. Here we report gas phase measurements of intact virus particles using electrospray ion mobility spectrometry with an accuracy in radial measurements that were sufficient to differentiate closely related species. In addition, measured diameters indicate that iscosahedral virus particles retain their structure in the gas phase as well as undergoing a slight compaction in the absence of solvent. Analysis of the human pathogen adenovirus represents the largest and most sophisticated biomolecular complex detected in the gas phase to date. These results, on a diverse set of viral systems, suggest that ion mobility spectrometry may have broad applications for the analysis of biological complexes.
Coexisting photoluminescence of Si and Ge nanocrystals in Ge/Si thin film (2001)

Thin films of composite germanium/silicon (Ge/Si) were prepared by pulsed laser ablation alternately on Ge and Si materials on a rotary target, followed by vacuum deposition of the ablated materials on an ultraclean glass substrate. X-ray diffraction and atomic force microscopy phase analysis confirmed that the film structure consisted of a mixture of Si and Ge nanoparticles which could exist in two possible phases. Most of the particles are of less than 30 nm in diameter even after the sample was annealed at 500 °C for 6 h. With different excitation light of wavelengths 280 and 380 nm the composite film yielded independent photoluminescence emissions corresponding, respectively, to the Si and Ge nanoparticles which did not interfere with each other. These results demonstrate that there was very little interaction between the Si and Ge emissions arising from their coexisting mixture in the thin film, even after high temperature annealing of the film in the atmosphere. It opens up the possibility for application of the Si/Ge composite film in multiple function optoelectronic devices.
Proton Relaxation Times in Arterial Wall and Atheromatous Lesions in Man (1986)

The proton relaxation times of autopsy samples of arterial intima-media were measured with an NMR spectrometer and results correlated to the microscopically estimated lipid content of the vascular wall. The normal arterial intima-media contained two T1 relaxation components. The short T1 component (T1s) was 90 +/- 13 ms and its relative weight was 11%. The long T1 component (T1l) was 523 +/- 89 ms and relative weight 88%, respectively. The average T2 was 99 +/- 18 ms. In diseased vessels, a positive correlation was found between the lipid content of the vessel wall and the relaxation rate of the fast component. T1s of the intima-media was significantly shorter (P less than .01) in severe atheromatosis compared with vessels without fat deposition. The results suggest that atheromatous lesions should be best highlighted in spin-echo images by using short TR and TE to suppress the influence of T1l and to avoid (noncontrast contributing) T2 decay of the signal intensity.
The interaction of α2-macroglobulin with proteinases. Characteristics and specificity of the reaction, and a hypothesis concerning its molecular mechanism (1973)

1. alpha(2)-Macroglobulin is known to bind and inhibit a number of serine proteinases. We show that it binds thiol and carboxyl proteinases, and there is now reason to believe that alpha(2)-macroglobulin can bind essentially all proteinases. 2. Radiochemically labelled trypsin, chymotrypsin, cathepsin B1 and papain are bound by alpha(2)-macroglobulin in an approximately equimolar ratio. Equimolar binding was confirmed for trypsin by activesite titration. 3. Pretreatment of alpha(2)-macroglobulin with a saturating amount of one proteinase prevented the subsequent binding of another. We conclude that each molecule of alpha(2)-macroglobulin is able to react with one molecule of proteinase only. 4. alpha(2)-Macroglobulin did not react with exopeptidases, non-proteolytic hydrolases or inactive forms of endopeptidases. 5. The literature on binding and inhibition of proteinases by alpha(2)-macroglobulin is reviewed, and from consideration of this and our own work several general characteristics of the interaction can be discerned. 6. A model is proposed for the molecular mechanism of the interaction of alpha(2)-macroglobulin with proteinases. It is suggested that the enzyme cleaves a peptide bond in a sensitive region of the macroglobulin, and that this results in a conformational change in the alpha(2)-macroglobulin molecule that traps the enzyme irreversibly. Access of substrates to the active site of the enzyme becomes sterically hindered, causing inhibition that is most pronounced with large substrate molecules. 7. The possible physiological importance of the unique binding characteristics of alpha(2)-macroglobulin is discussed.
Clinical utility of circulating tumor DNA for molecular assessment in pancreatic cancer (2015)

Pancreatic ductal adenocarcinoma (PDAC) remains one of the most lethal malignancies. The genomic landscape of the PDAC genome features four frequently mutated genes (KRAS, CDKN2A, TP53, and SMAD4) and dozens of candidate driver genes altered at low frequency, including potential clinical targets. Circulating cell-free DNA (cfDNA) is a promising resource to detect and monitor molecular characteristics of tumors. In the present study, we determined the mutational status of KRAS in plasma cfDNA using multiplex picoliter-droplet digital PCR in 259 patients with PDAC. We constructed a novel modified SureSelect-KAPA-Illumina platform and an original panel of 60 genes. We then performed targeted deep sequencing of cfDNA and matched germline DNA samples in 48 patients who had ≥1% mutant allele frequencies of KRAS in plasma cfDNA. Importantly, potentially targetable somatic mutations were identified in 14 of 48 patients (29.2%) examined by targeted deep sequencing of cfDNA. We also analyzed somatic copy number alterations based on the targeted sequencing data using our in-house algorithm, and potentially targetable amplifications were detected. Assessment of mutations and copy number alterations in plasma cfDNA may provide a prognostic and diagnostic tool to assist decisions regarding optimal therapeutic strategies for PDAC patients.
Randomised double-blind comparative study of dexmedetomidine and tramadol for post-spinal anaesthesia shivering (2014)

We conclude that although both drugs are effective, the time taken for cessation of shivering is less with dexmedetomidine when compared to tramadol. Moreover, dexmedetomidine has negligible adverse effects, whereas tramadol is associated with significant nausea and vomiting.
Priority-Based Geometric Constraint Satisfaction (2007)

A well-constrained geometric system seldom occurs in practice, especially at the sketch-based initial conceptual design stage. Usually, it is either under- or overconstrained because design is a progressive process and it is difficult for a designer to specify all involved constraints in a consistent way. This paper presents a priority-based graph-reduction solution, in which each constraint is assigned with a priority to guide the reduction of a geometric constraint graph. The advantage of this method lies in its ability to find the optimal solutions to a geometric constraint system automatically, without requiring interactive intervention from users.
Holographic Polymer‐Dispersed Liquid Crystals: Materials, Formation, and Applications (2008)

By combining polymer‐dispersed liquid crystal (PDLC) and holography, holographic PDLC (H‐PDLC) has emerged as a new composite material for switchable or tunable optical devices. Generally, H‐PDLC structures are created in a liquid crystal cell filled with polymer‐dispersed liquid crystal materials by recording the interference pattern generated by two or more coherent laser beams which is a fast and single‐step fabrication. With a relatively ideal phase separation between liquid crystals and polymers, periodic refractive index profile is formed in the cell and thus light can be diffracted. Under a suitable electric field, the light diffraction behavior disappears due to the index matching between liquid crystals and polymers. H‐PDLCs show a fast switching time due to the small size of the liquid crystal droplets. So far, H‐PDLCs have been applied in many promising applications in photonics, such as flat panel displays, switchable gratings, switchable lasers, switchable microlenses, and switchable photonic crystals. In this paper, we review the current state‐of‐the‐art of H‐PDLCs including the materials used to date, the grating formation dynamics and simulations, the optimization of electro‐optical properties, the photonic applications, and the issues existed in H‐PDLCs.
Controlling DNA Capture and Propagation through Artificial Nanopores (2007)

Electrophorescing biopolymers across nanopores modulates the ionic current through the pore, revealing the polymer's diameter, length, and conformation. The rapidity of polymer translocation ( approximately 30,000 bp/ms) in this geometry greatly limits the information that can be obtained for each base. Here we show that the translocation speed of lambda-DNA through artificial nanopores can be reduced using optical tweezers. DNAs coupled to optically trapped beads were presented to nanopores. DNAs initially placed up to several micrometers from the pore could be captured. Subsequently, the optical tweezers reduced translocation speeds to 150 bp/ms, about 200-fold slower than free DNA. Moreover, the optical tweezers allowed us to "floss" single polymers back and forth through the pore. The combination of controlled sample presentation, greatly slowed translocation speeds, and repeated electrophoresis of single DNAs removes several barriers to using artificial nanopores for sequencing, haplotyping, and characterization of protein-DNA interactions.
γ-AApeptide-based small-molecule ligands that inhibit Aβ aggregation (2013)

We report the design, synthesis, characterization and evaluation of a novel class of γ-AApeptide one-bead-one-compound (OBOC) library, from which a small γ-AApeptide was identified to effectively prevent and disassemble Aβ aggregation.
Muscle glycogenosis (1990)

This review describes clinical, biochemical and genetic features of the four inborn errors affecting muscle glycogen breakdown, namely deficiencies of phosphorylase, phosphorylase kinase, amylo-1,6-glucosidase and acid alpha-glucosidase. They are characterized by a wide spectrum of clinical manifestation, affecting age of onset, clinical features, progress of disease and tissue involvement. Biochemically, variability of all four enzyme deficiencies is evident in terms of differences in residual enzyme present in tissues, and in the presence or absence of enzyme protein. Genetic heterogeneity, which has been documented in each of the enzyme deficiencies, manifests itself in terms of the presence, absence, quantity or size of mRNA. In phosphorylase deficiency heterogeneity has also been documented at the DNA level. In acid maltase deficiency nine mutant phenotypes have been described affecting various stages of lysosomal enzyme processing.
Frequency-selective MEMS for miniaturized communication devices (2002)

With Q's in the tens to hundreds of thousands, micromachined vibrating resonators are proposed as IC-compatible tanks for use in the low phase noise oscillators and highly selective filters of communications subsystems. To date, LF oscillators have been fully integrated using merged CMOS+microstructure technologies, and bandpass filters consisting of spring-coupled micromechanical resonators have been demonstrated in the HF range. In particular, two-resonator micromechanical bandpass filters have been demonstrated with frequencies up to 14.5 MHz, percent bandwidths on the order of 0.2%, and insertion losses less than 1 dB. Higher-order three-resonator filters with frequencies near 455 kHz have also been achieved, with equally impressive insertion losses for 0.09% bandwidths, and with more than 64 dB of passband rejection. Evidence suggests that the ultimate frequency range of this high-Q tank technology depends upon material limitations, as well as design constraints-in particular, to the degree of electromechanical coupling achievable in micro-scale resonators.
A Novel Fuzzy Pain Demand Index Derived From Patient-Controlled Analgesia for Postoperative Pain (2007)

A multilayer hierarchical structure for an intelligent analysis system is described in this paper. Four levels (patients', measurement, Web-based, and interpreting) are used to collect massive amounts from clinical information and analyze it with both traditional and artificial intelligent methods. To support this, a novel fuzzy pain demand (FPD) index derived from the interval of each bolus of patient-controlled analgesia (PCA) is designed and documented in a large-scale clinical survey. The FPD index is modeled according to a fuzzy modeling algorithm to interpret the self-titration of the drug delivery. A total of 255 patients receiving intravenous PCA using morphine (1 mg/ml) tested this index by offline analysis from this system. We found the FPD index modeled from a fuzzy modeling algorithm to interpret the self-titration of the drug delivery can show the patients' dynamic demand and past efforts to overcome the postoperative pain. Moreover, it could become an online system to monitor patients' demand or intent to treat their pain so these factors could be entered into a patient's chart along with temperature, blood pressure, pulse, and respiration rates when medical practitioners check the patients.
DNA Integrity Assay: A Plasma-Based Screening Tool for the Detection of Prostate Cancer (2006)

While detecting 69.9% of those with prostate cancer, DIA maintained an overall specificity of 68.2% to 92%, a range favorably comparable to that currently accepted for PSA (60-70%). The variability in specificity between control groups is likely explained by the established 19% to 30% detection of prostate cancer on subsequent biopsies associated with control group 3. DIA detected 63% of the prostate cancers undetected by currently accepted PSA ranges.
PointWeb: Enhancing Local Neighborhood Features for Point Cloud Processing (2019)

This paper presents PointWeb, a new approach to extract contextual features from local neighborhood in a point cloud. Unlike previous work, we densely connect each point with every other in a local neighborhood, aiming to specify feature of each point based on the local region characteristics for better representing the region. A novel module, namely Adaptive Feature Adjustment (AFA) module, is presented to find the interaction between points. For each local region, an impact map carrying element-wise impact between point pairs is applied to the feature difference map. Each feature is then pulled or pushed by other features in the same region according to the adaptively learned impact indicators. The adjusted features are well encoded with region information, and thus benefit the point cloud recognition tasks, such as point cloud segmentation and classification. Experimental results show that our model outperforms the state-of-the-arts on both semantic segmentation and shape classification datasets.
Results from the Piano Tutor Project (1993)

The Piano Tutor combines an expert system and multimedia technology to form an interactive piano teaching system. Important elements of the Piano Tutor are: (1) the use of score-following software to interpret student performances, (2) the use of extensive multimedia to create a natural dialog with the student, (3) an expert system to analyze student mistakes and give pertinent multimedia feedback, and (4) the use of Instructional Design theory to develop an extensive curriculum that can be tailored automatically to individual student needs. Results from a preliminary assessment of the Piano Tutor are presented.
Polarisation-independent optical amplifier with buried facets (1989)

A polarisation-insensitive GaInAsP/InP laser amplifier with thick active layer and buried facets has been fabricated. The TE and TM gains are equal to within 1 dB at all drive current and wavelengths.
An Integrated Approach to the Teaching and Learning of Science and Mathematics Utilizing Technology � The Teachers' Perspective (2014)

The concept and importance of curriculum integration in Science and Mathematics has come to the fore in the recent years (Czerniak, 2007). Ireland's Science and Mathematics performance is well documented and extensively reported in the media and elsewhere (e.g. Expert Group on Future Skills Needs, 2008; Task Force on the Physical Sciences, 2002). Concern primarily lies with the post-primary students' underperformance in science and mathematics, coupled with a failure to make a successful transition to third level scientifically and mathematically orientated undergraduate courses. The aim of this study was to design, develop, implement and evaluate an integrated approach to the teaching and learning of Science and Mathematics in second level schools in Ireland. This was undertaken through the integration of a handheld graphic calculator known as ‘TI-Nspire’ into first year classes (age 12 -13 year olds) of science and mathematics. This integration was assisted by the development and implementation of a unit of learning on distance, speed and time, with specific lesson plans which integrated the teaching and learning of both subjects by utilising the TI-Nspire. The methodology of this research project was an exploratory year-long case study of three second level schools in Ireland and their implementation of the unit of learning in their respective schools. This paper focuses on the teachers' perspective of the integration of mathematics and science teaching and learning utilising technology. The study was qualitative in nature and was evaluated through a teacher's perspective where a teacher focuses on group interviews and independent lesson observations. The key finding emerging from the data is that the integration of mathematics and science was lost in coping with the technology demands required in implementing the unit of learning.
369. Polyene acids. Part VII. Half methyl esters and amides of the muconic acids (1953)

J. A. Elvidge, R. P. Linstead and P. Sims, J. Chem. Soc., 1953, 1793 DOI: 10.1039/JR9530001793