gebhart/patrepeval huggingface dataset:
DNA manipulation by means of insulator‐based dielectrophoresis employing direct current electric fields (2009)

Electrokinetic techniques offer a great potential for biological particle manipulation. Among these, dielectrophoresis (DEP) has been successfully utilized for the concentration of bioparticles. Traditionally, DEP is performed employing microelectrodes, an approach with attractive characteristics but expensive due to microelectrode fabrication costs. An alternative is insulator-based DEP, a method where non-uniform electric fields are created with arrays of insulating structures. This study presents the concentration of linear DNA particles (pET28b) employing a microchannel, with an array of cylindrical insulating structures and direct current electric fields. Results showed manipulation of DNA particles with a combination of electroosmotic, electrophoretic, and dielectrophoretic forces. Employing suspending media with conductivity of 104 muS/cm and pH of 11.15, under applied fields between 500 and 1500 V/cm, DNA particles were observed to be immobilized due to negative dielectrophoretic trapping. The observation of DNA aggregates that occurred at higher applied fields, and dispersed once the field was removed is also included. Finally, concentration factors varying from 8 to 24 times the feed concentration were measured at 2000 V/cm after concentration time-periods of 20-40 s. The results presented here demonstrate the potential of insulator-based DEP for DNA concentration, and open the possibility for fast DNA manipulation for laboratory and large-scale applications.
Scene Classification via a Gradient Boosting Random Convolutional Network Framework (2015)

Due to the recent advances in satellite sensors, a large amount of high-resolution remote sensing images is now being obtained each day. How to automatically recognize and analyze scenes from these satellite images effectively and efficiently has become a big challenge in the remote sensing field. Recently, a lot of work in scene classification has been proposed, focusing on deep neural networks, which learn hierarchical internal feature representations from image data sets and produce state-of-the-art performance. However, most methods, including the traditional shallow methods and deep neural networks, only concentrate on training a single model. Meanwhile, neural network ensembles have proved to be a powerful and practical tool for a number of different predictive tasks. Can we find a way to combine different deep neural networks effectively and efficiently for scene classification? In this paper, we propose a gradient boosting random convolutional network (GBRCN) framework for scene classification, which can effectively combine many deep neural networks. As far as we know, this is the first time that a deep ensemble framework has been proposed for scene classification. Moreover, in the experiments, the proposed method was applied to two challenging high-resolution data sets: 1) the UC Merced data set containing 21 different aerial scene categories with a submeter resolution and 2) a Sydney data set containing eight land-use categories with a 1.0-m spatial resolution. The proposed GBRCN framework outperformed the state-of-the-art methods with the UC Merced data set, including the traditional single convolutional network approach. For the Sydney data set, the proposed method again obtained the best accuracy, demonstrating that the proposed framework can provide more accurate classification results than the state-of-the-art methods.
Lasers in surgery and medicine (1984)

The first laser was only produced 23 years ago and in medicine and surgery lasers have already turned science fiction into science fact. Developments in laser technology are in progress, also with the development of finer glass fibres able to transmit all wavelengths. Two developments in the research phase are worthy of mention. First, the use of lasers to disobliterate blocked arteries and second, the revascularisation of the heart via channels drilled into the heart muscle by laser allowing blood to flow directly into the heart muscle from the ventricular cavities and so totally bypassing the coronary artery system. Lasers are already well established in medicine and surgery and more dramatic advances can be anticipated in the future.
Photoluminescence and Electronic Interaction of Anthracene Derivatives Adsorbed on Sidewalls of Single-Walled Carbon Nanotubes (2003)

Dye molecules (anthracene derivatives) are observed to strongly adsorb to single-walled carbon nanotubes (SWNTs). The adsorption coverage of anthracene molecules on SWNTs varied with the aromatic ring substituents. The observed red shifts of emission peaks of the absorptive adduct appear to depend on the energy level of the lowest unoccupied molecular orbital (LUMO) of the adsorbate, consistent with adsorption by a charge-transfer interaction, in which the SWNT is electron donor and anthracene is acceptor. The anthracene absorptive adducts can be displaced by adsorption of pyrene.
Biochemistry, molecular biology, and pharmacology of fatty acid synthase, an emerging therapeutic target and diagnosis/prognosis marker. (2010)

Human fatty acid synthase (FASN) is a 270-kDa cytosolic dimeric enzyme that is responsible for palmitate synthesis. FASN is slowly emerging and rediscovered as a marker for diagnosis and prognosis of human cancers. Recent studies showed that FASN is an oncogene and inhibition of FASN effectively and selectively kill cancer cells. With recent publications of the FASN crystal structure and the new development of FASN inhibitors, targeting FASN opens a new window of opportunity for metabolically combating cancers. In this article, we will review critically the recent progresses in understanding the structure, function, and the role of FASN in cancers and pharmacologically targeting FASN for human cancer treatment.
Microvascular anastomoses performed in rats using a microsurgical telemanipulator (2000)

Complex procedures requiring a high degree of precision and dexterity can be performed using an electromechanical interface specifically designed for micromanipulation. Performance limitations are similar to those previously reported for remote surgical teleoperation, and most likely reflect incompletely characterized restrictions on multi-sensory information.
Raf induces NF-κB by membrane shuttle kinase MEKK1, a signaling pathway critical for transformation (2000)

NF-kappaB is regulated by inhibitor proteins (IkappaBs), which retain NF-kappaB in the cytoplasm. Signal-induced phosphorylation by the IkappaB-kinase complex containing the IkappaB-kinases 1 and 2 (IKK-1/2 or IKK-alpha/beta) and subsequent degradation of the IkappaB proteins are prerequisites for NF-kappaB activation. Many signals induce NF-kappaB, one of them being oncogenic Raf kinase. We investigated whether NF-kappaB induction is critical for Raf-mediated transformation. Here, we demonstrate that inhibition of NF-kappaB interferes with transformation by the Raf-oncogene, and we characterized the mechanism of NF-kappaB induction by activated Raf kinase and the tumor promoter phorbol 12-myristate 13-acetate (PMA). NF-kappaB activation by PMA and Raf critically depends on the IkappaB-kinase complex, most notably on IKK-2. A major signaling pathway induced by Raf is the mitogenic cytoplasmic kinase cascade. However, different inhibitors of this cascade do not affect PMA- and Raf-mediated NF-kappaB activation. Raf does not phosphorylate the IkappaB-kinase proteins directly. Raf rather synergizes with another membrane shuttle kinase MEKK1, and Raf-mediated activation of NF-kappaB is blocked by a dominant negative form of MEKK1. These results suggest that Raf induction of NF-kappaB is relayed by MEKK1, but not by the classical mitogenic cytoplasmic kinase cascade.
Triphenylphosphine-Catalyzed Isomerisation of Propargyl Bromide to 1-Bromopropadiene (1997)

Abstract Pure bromopropadiene, BrCH=C=CH2 has been obtained by isomerisation of propargyl bromide in the presence of catalytic amounts of triphenylphosphine.
Characterization of a New Metallo-β-Lactamase Gene, bla NDM-1 , and a Novel Erythromycin Esterase Gene Carried on a Unique Genetic Structure in Klebsiella pneumoniae Sequence Type 14 from India (2009)

A Swedish patient of Indian origin traveled to New Delhi, India, and acquired a urinary tract infection caused by a carbapenem-resistant Klebsiella pneumoniae strain that typed to the sequence type 14 complex. The isolate, Klebsiella pneumoniae 05-506, was shown to possess a metallo-beta-lactamase (MBL) but was negative for previously known MBL genes. Gene libraries and amplification of class 1 integrons revealed three resistance-conferring regions; the first contained bla(CMY-4) flanked by ISEcP1 and blc. The second region of 4.8 kb contained a complex class 1 integron with the gene cassettes arr-2, a new erythromycin esterase gene; ereC; aadA1; and cmlA7. An intact ISCR1 element was shown to be downstream from the qac/sul genes. The third region consisted of a new MBL gene, designated bla(NDM-1), flanked on one side by K. pneumoniae DNA and a truncated IS26 element on its other side. The last two regions lie adjacent to one another, and all three regions are found on a 180-kb region that is easily transferable to recipient strains and that confers resistance to all antibiotics except fluoroquinolones and colistin. NDM-1 shares very little identity with other MBLs, with the most similar MBLs being VIM-1/VIM-2, with which it has only 32.4% identity. As well as possessing unique residues near the active site, NDM-1 also has an additional insert between positions 162 and 166 not present in other MBLs. NDM-1 has a molecular mass of 28 kDa, is monomeric, and can hydrolyze all beta-lactams except aztreonam. Compared to VIM-2, NDM-1 displays tighter binding to most cephalosporins, in particular, cefuroxime, cefotaxime, and cephalothin (cefalotin), and also to the penicillins. NDM-1 does not bind to the carbapenems as tightly as IMP-1 or VIM-2 and turns over the carbapenems at a rate similar to that of VIM-2. In addition to K. pneumoniae 05-506, bla(NDM-1) was found on a 140-kb plasmid in an Escherichia coli strain isolated from the patient's feces, inferring the possibility of in vivo conjugation. The broad resistance carried on these plasmids is a further worrying development for India, which already has high levels of antibiotic resistance.
An adaptation of the interior point method for solving the global routing problem (1991)

A linear-programming (LP) solution technique is applied to solve the global routing problem. Minimal spanning trees that were found in the subgrid by generating vertical and horizontal lines about the points of a given net and a modified interior point approach that reduces the number of arc constraints which were considered in the routing problem were used to reduce the problem site. An interior point algorithm approach is developed to solve the resulting LP problem. A FORTRAN code ROUTFAST is tested on several problems of varying arc capacities. ROUTFAST is compared with MINOS 5.0 which is a Simplex-based code on the same set of problems. ROUTFAST is at least 8-20 times faster than MINOS on the largest problems tested and seems to be getting faster as the problem size and arc capacity increases. Using a modification (ROUTLP) to solve four benchmark gate-array layout problems, ROUTFAST yielded competitive global routing results to TimberWolfSC Version 5.4 and in a fraction of TimberWolfSC's running time.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Absence of Evidence of Porcine Circovirus Infection in Piglets with Congenital Tremors (2003)

Porcine circovirus types 1 (PCV1) and 2 (PCV2) have been associated with congenital tremors (CTs) in piglets in the United States. In this study, central nervous system and nonneural tissues of 40 CT piglets from Spain, the United Kingdom, Ireland, and Sweden were investigated for the presence of PCV1 and PCV2 using in situ hybridization and immunohistochemical labeling on paraffin sections. The polymerase chain reaction for PCV2 was also carried out on sera from the Spanish CT cases. No evidence of circovirus nucleic acid or antigen was found in any CT piglet. Although these results do not support the hypothesis that PCV1 or PCV2 are linked to porcine CT, they cannot disprove it.
High-Q ring resonators in thin silicon-on-insulator (2004)

We have fabricated high-Q microrings from thin silicon-on-insulater SOI layers and measured Q values of 45 000 in these rings, which were then improved to 57 000 by adding a PMMA cladding. The optimal waveguide designs were calculated, and the waveguide losses were analyzed. These high-Q resonators are expected to lead to interesting devices for telecommunication filters and sources as well as optical refractive index sensing.
A FRET-Based Method for Probing the Conformational Behavior of an Intrinsically Disordered Repeat Domain fromBordetella pertussisAdenylate Cyclase (2009)

A better understanding of the conformational changes exhibited by intrinsically disordered proteins is necessary as we continue to unravel their myriad biological functions. In repeats in toxin (RTX) domains, calcium binding triggers the natively unstructured domain to adopt a beta roll structure. Here we present an in vitro Forster resonance energy transfer (FRET)-based method for the investigation of the conformational behavior of an RTX domain from the Bordetella pertussis adenylate cyclase consisting of nine repeat units. Equilibrium and stopped-flow FRET between fluorescent proteins, attached to the termini of the domain, were measured in an analysis of the end-to-end distance changes in the RTX domain. The method was complemented with circular dichroism spectroscopy, tryptophan fluorescence, and bis-ANS dye binding. High ionic strength was observed to decrease the calcium affinity of the RTX domain. A truncation and single amino acid mutations yielded insights into the structural determinants of beta roll formation. Mutating the conserved Asp residue in one of the nine repeats significantly reduced the affinity of the domains for calcium ions. Removal of the sequences flanking the repeat domain prevented folding, but replacing them with fluorescent proteins restored the conformational behavior, suggesting an entropic stabilization. The FRET-based method is a useful technique that complements other low-resolution techniques for investigating the dynamic conformational behavior of the RTX domain and other intrinsically disordered protein domains.
Comparison of Tear Sampling Techniques for Pharmacokinetic Analysis: Ofloxacin Concentrations in Rabbit Tears after Sampling with Schirmer Tear Strips, Capillary Tubes, or Surgical Sponges (2000)

This study compared the precision and accuracy of 4 tear sampling methods. In vivo, albino rabbits were treated with single bilateral eye drops ofofloxacin 0.3% solution, 3 hr after which tear samples were collected using capillary tubes (CT), surgical sponges (SS), or tear strips for 15 sec (15sTS) or 60 sec (60sTS). In vitro, CT, SS, and tear strips were spiked with known volumes of ofloxacin solution in order to assess the bioanalytical accuracy of each technique. Ofloxacin levels were quantified by HPLC in all samples. Results showed that tear volumes and ofloxacin masses sampled in vivo depended on sampling method. Tear volume followed the rank order 60sTS > 15sTS > SS > CT. The volume collected by 60sTS exceeded precorneal tear volume. Ofloxacin mass followed the order 60sTS approximately 15sTS > SS > CT. Tear concentrations (mean +/- SD; N = 12) were 3.28 +/- 3.76 microg/g for 60sTS, 10.3 +/- 10.0 microg/g for 15sTS, 9.75 +/- 8.04 microg/g for SS, and 5.83 +/- 3.35 microg/g for CT. In vitro, SS, 15sTS, and 60sTS yielded accuracies of 103-107% and coefficients of variation (CV) < 9%. CT was only 85% accurate with a CV of 31%, indicating incomplete extraction during analysis. We concluded from this study that: 1) rabbit tear sampling by SS was rapid, easy, accurate, precise, and easily analyzable; 2) sampling by CT or 15sTS was accurate, but may require aggressive extraction (for CT) or be affected by tear flow rate (for 15sTS); and 3) tear sampling by 60sTS underestimated actual tear concentrations.
Effect of mannose chain length on targeting of glucocerebrosidase for enzyme replacement therapy of Gaucher disease (2007)

Recombinant human glucocerebrosidase (imiglucerase, Cerezyme) is used in enzyme replacement therapy for Gaucher disease. Complex oligosaccharides present on Chinese hamster ovary cell-expressed glucocerebrosidase (GCase) are enzymatically remodeled into a mannose core, facilitating mannose receptor-mediated uptake into macrophages. Alternative expression systems could be used to produce GCase containing larger oligomannose structures, offering the possibility of an improvement in targeting to macrophages. A secondary advantage of these expression systems would be to eliminate the need for carbohydrate remodeling. Here, multiple expression systems were used to produce GCase containing primarily terminal oligomannose, from Man2 to Man9. GCase from these multiple expression systems was compared to Cerezyme with respect to affinity for mannose receptor and serum mannose-binding lectin (MBL), macrophage uptake, and intracellular half-life. In vivo studies comparing clearance and targeting of Cerezyme and the Man9 form of GCase were carried out in a Gaucher mouse model (D409V/null). Mannose receptor binding, macrophage uptake, and in vivo targeting were similar for all forms of GCase. Increased MBL binding was observed for all forms of GCase having larger mannose structures than those of Cerezyme, which could influence pharmacokinetic behavior. These studies demonstrate that although alternative cell expression systems are effective for producing oligomannose-terminated glucocerebrosidase, there is no biochemical or pharmacological advantage in producing GCase with an increased number of mannose residues. The display of alternative carbohydrate structures on GCase expressed in these systems also runs the risk of undesirable consequences, such as an increase in MBL binding or a possible increase in immunogenicity due to the presentation of non-mammalian glycans.
Violent Reaction to Monoclonal Antibody Therapy Remains a Mystery (2006)

CAMBRIDGE, U.K.--
 On 13 March, six healthy volunteers in a clinical trial were injected with a superagonist, a drug meant to boost a type of T cell in the immune system, and soon all of them became violently ill. Exactly what triggered the reaction is not known. (Read more.)
Design and implementation of active error canceling in hand-held microsurgical instrument (2002)

Presents the development and. initial experimental results of the first prototype of Micron, an active hand-held instrument to sense and compensate physiological tremor and other unwanted movement during vitreoretinal microsurgery. The instrument incorporates six inertial sensors, allowing the motion of the tip to be computed. The motion captured is processed to discriminate between desired and undesired components of motion. Tremor canceling is implemented via the weighted-frequency Fourier linear combiner (WFLC) algorithm, and compensation of non-tremorous error via a neural network technique is being investigated. The instrument tip is attached to a three-degree-of-freedom parallel manipulator with piezoelectric actuation. The actuators move the tool tip in opposition to the tremor, thereby suppressing the erroneous motion. Motion canceling experiments with oscillatory motions in the frequency band of physiological tremor show that Micron is able to reduce error amplitude by 45.3% in 1-D tests and 37.2% in 3-D tests.
Audio and video signatures for synchronization (2008)

We propose a framework based on signatures extracted from audio and video streams for automatically measuring and maintaining synchronization between the two streams. The audio signature is based on projections of a coarse representation of the spectrogram onto random vectors. The video signature is based on projections of a coarse representation of the difference image between two consecutive frames onto random vectors. The time alignment present at the signature generator between the two streams is recorded by combining audio and video signatures into a combined synchronization signature. At the detector after video and audio streams go through different processing operations, we extract the signatures again. The signatures extracted before and after processing from the audio and the video are compared independently using a Hamming distance based correlator to estimate the relative misalignment introduced due to processing in each of the streams. Then, the estimated relative misalignment between the audio and video streams is used to preserve the same alignment between the streams that was present before processing. Our experimental results show that we can achieve > 93.0% accuracy in synchronization.
Heck Reaction versus Free Radical Reaction for the Synthesis of Spiro[indoline-2,4′-piperidines] (1998)

Spiro[indoline-2,4′-piperidines] can be prepared from 2-bromoaniline by using a Heck reaction or a free radical reaction as the key step. The radical process produces better yields of spiro[indoline-2,4′-piperidines] than the Heck process.
Titanium nitride for transparent conductors (1994)

The transparency of thin films of the electroconductive titanium nitride was demonstrated. Titanium nitride has a high hardness and a high resistance against corrosion, and it is electroconductive. Its color is gold, and it is usually not transparent. Materials can be transparent if they are much thinner than the wavelength of visible light. Formerly, there was no technique available to form such a thin TiN film which is also electroconductive, because very thin TiN crystals grow as small islands. However, by using the dynamic ion beam mixing technique, we succeeded in forming continuous, transparent, and conductive TiN films.
The limits of expert performance using hierarchic marking menus (1993)

A marking menu allows a user to perform a menu selection by either popping-up a radial (or pie) menu, or by making a straight mark in the direction of the desired menu item without popping-up the menu. A hierarchic marking menu uses hierarchic radial menus and “zig-zag” marks to select from the hierarchy. This paper experimentally investigates the bounds on how many items can be in each level, and how deep the hierarchy can be, before using a marking to select an item becomes too slow or prone to errors.
The Complete Amino Acid Sequence of Low Molecular Mass Urokinase from Human Urine (1982)

The sequence of all 253 amino acids of the heavy (B-) chain of human urinary urokinase was determined. The fragmentation strategy employed included cyanogen bromide cleavage of S-carboxymethylated B-chain at Met and/or Trp residues, cleavage of acid-labile Asp-Pro bonds, and the use of the specific endoproteinases Lys-C and Arg-C for generation of overlapping fragments. For sequence determination automated solid- or liquid-phase techniques of Edman degradation were used. The amino acid sequence obtained substantiates the serine protease character of the B-chain of urokinase: a considerable homology with other serine proteinases, especially with the B-chain of human plasmin, was proved. The pertinent active site amino acids were localized: His-46, Asp-97, and Ser-198. A carbohydrate side chain, containing at least 4 glucosamine and 2 galactosamine residues, was demonstrated to be fixed at asparagine in position 144. The sequence data presented, together with the sequence of the second (A1-) chain of low molecular mass urokinase which was reported by us in an earlier communication, complete the knowledge of the whole primary structure of an active form of human urinary urokinase.