gebhart/patrepeval huggingface dataset:
Molecular and functional analysis of genes required for expression of group IB K antigens in <i>Escherichia coli</i> : characterization of the <i>his‐</i>region containing gene clusters for multiple cell‐surface polysaccharides (1997)

Escherichia coli group I capsular K antigens are found in two forms on the cell surface. The K(LPS) form is linked to lipopolysaccharide lipid A core, whereas the high-molecular-weight capsular form is assembled independently of lipid A core. Subgroup IB K antigens are generally co-expressed with either the O8 or O9 antigen and, under the appropriate conditions, with the exopolysaccharide, colanic acid. To examine the relationships between the genetic loci and the synthetic pathways for these various cell-surface polymers, the gene cluster responsible for expression of a prototype group IB K antigen (serotype K40) was cloned and the flanking chromosomal regions characterized. Analysis of the six orfs within the cluster indicates features typical of Wzy (Rfc)-dependent O antigens. Synthesis of group IB K antigens is initiated by WecA (Rfe), a UDP-GlcNAc::undecaprenylphosphate GlcNAc-1-phosphate transferase, and the chain length of K40LPS is determined by the wzz gene product. The his-region of the E. coli O8:K40 prototype is almost exclusively devoted to the expression of three different surface polysaccharides. The rfbK40 cluster is located adjacent to the cps (colanic acid synthesis) and rfbO8 (O8 antigen synthesis) loci in the gene order: his-rfbO8/O9-wzz-ugd-gnd-rfbK40-galF-cps. Thus, rfbK40 is in the location occupied by other Wzy-dependent rfb gene clusters, and rfbO8/O9 represents an additional locus.
Marriage equality: No more delays (2016)

If we needed any more proof that Prime Minister Malcolm Turnbull's plebiscite on equal marriage is a spurious delaying tactic, we got it on August 21 when the media reported that the vote will now be pushed back to February next year, some 18 months after it was first proposed.
Tunable electroabsorption in gallium arsenide doping superlattices (1987)

Tuning of the optical absorption coefficient by electrical bias in doping superlattices (n-i-p-i crystals) is demonstrated for the first time by both photoconductivity and transmission measurements at room temperature. The absorption coefficient at 1.04 μm obtained from the photoconductivity measurement varies by a factor of 240 when the p-n junction bias is changed from 0.4 to −1.5 V. A change of transmission up to 22% at 0.89 μm wavelength through a 2.1-μm-thick n-i-p-i crystal is achieved by varying bias merely between 0.6 and −2.0 V. Moreover, the change of transmission is nearly linear with p-n junction bias.
Outstanding quality factors of bulk acoustic wave resonators at cryogenic temperature (2008)

International audience
Comparison of QAOA with Quantum and Simulated Annealing (2019)

We present a comparison between the Quantum Approximate Optimization Algorithm (QAOA) and two widely studied competing methods, Quantum Annealing (QA) and Simulated Annealing (SA). To achieve this, we define a class of optimization problems with respect to their spectral properties which are exactly solvable with QAOA. In this class, we identify instances for which QA and SA have an exponentially small probability to find the solution. Consequently, our results define a first demarcation line between QAOA, Simulated Annealing and Quantum Annealing, and highlight the fundamental differences between an interference-based search heuristic such as QAOA and heuristics that are based on thermal and quantum fluctuations like SA and QA respectively.
MOLECULAR MECHANISM OF HEMOLYTIC ANEMIA IN HOMOZYGOUS HEMOGLOBIN C DISEASE (1969)

Erythrocytes from a patient with homozygous hemoglobin C disease were subjected to gradual osmotic dehydration by incubation in hypertonic saline. Serial observations of these cells before and after 4 and 12 hr incubation were carried out by means of interference, Soret absorption, polarization microscopy, and the electron microscope employing the freeze-etching technique. Light microscopic studies showed a progressive contraction of cellular contents into central masses which, after 12 hr dehydration, formed birefringent intracellular hemoglobin crystals in 50-75% of the cells. Electron microscopic study of freeze-etched replicas of these cells at 0, 4, and 12 hr of dehydration reveals progressive aggregation, alignment, and crystallization of hemoglobin molecules. Molecular aggregation found in C-C cells prior to osmotic dehydration was not seen in normal erythrocytes. Aggregation and packing varied from cell to cell. Reticulocytes showed a loosely packed aggregate mesh-work; older cells showed variation of molecular packing, which appeared tightest in cells corresponding to microspherocytes. With further loss of intracellular water, aggregates coalesced into patterns of tighter molecular packing with small regions of alignment, and, finally, crystallization occurred. Hemoglobin molecules measuring 70 A in diameter were readily identified within the period patterns of intracellular crystals. These findings suggest that the hemoglobin C molecules within C-C erythrocytes exist in an aggregated state. As the cell ages, intracellular water is lost and intermolecular distance decreases, hemoglobin C molecules polymerize into intracellular crystals. This pathological behavior of hemoglobin C is associated with a charge alteration conferred by the substitution of beta-6-lysine for glutamic acid on the external surface in the A-helix region of the beta-chain of the molecule, possibly increasing intermolecular attraction. Molecular aggregation accounts for the increased rigidity of C-C cells which leads to accelerated membrane and water loss with resultant microspherocyte formation. The microspherocyte, with highest intracellular hemoglobin concentration, rapidly undergoes intracellular crystallization, and is sequestered and destroyed by reticuloendothelial elements.
Cell-Based Delivery Systems: Development of Encapsulated Cell Technology for Ophthalmic Applications (2006)

Encapsulated cell technology (ECT) was developed to treat diseases of the central nervous system and the eye. An intraocular implantable encapsulated cell unit prototype for chronic delivery of therapeutic agents has been developed to treat ophthalmic disorders. The ECT has promising applications to major types of ocular disorders such as retinal degeneration, ocular inflammation, and angiogenesis. Retinal vascular proliferation can occur in a number of different sites within the eye, and plays a role in many ocular diseases. To investigate whether ciliary neurotrophic factor delivered via mammalian cells was effective in photoreceptor protection, a short-term study using unencapsulated NTC-201 cells was carried out in a rapid retinal degeneration, transgenic rat retinitis pigmentosa model, S334ter-3. The rcd1 affected dogs carrying a mutation of the gene encoding the b-subunit of the rod cyclic GMP phosphodiesterase were provided by the Retinal Disease Studies Facility, which is a resource maintained by the NEI/NIH and the Foundation Fighting Blindness.
The log transformation is special (1995)

The logarithmic (log) transformation is a simple yet controversial step in the analysis of positive continuous data measured on an interval scale. Situations where a log transformation is indicated will be reviewed. This paper contends that the log transformation should not be classed with other transformations as it has particular advantages. Problems with using the data themselves to decide whether or not to transform will be discussed. It is recommended that log transformed analyses should frequently be preferred to untransformed analyses and that careful consideration should be given to use of a log transformation at the protocol design stage.
The plastic deformation of polycrystalline aggregates (1962)

Abstract For a number of metallic polycrystalline aggregates, it is shown experimentally that [sgrave]f, the flow stress at constant strain, is related to the grain diameter l by where [sgrave]0 and k are constants. This has the same form as the relationship between the lower yield point, when this occurs, and grain size. An explanation is given by an extension of Taylor's theory to allow for the resistance at the grain boundary to the formation of a slip band. Dislocation-locking and a small number of slip systems are shown to favour a strong grain-size dependence of [sgrave]f and this explains the variation of this dependence amongst the common metals and alloys.
Integrating metadata tools with the data services archive to provide Web-based management of large-scale scientific simulation data (2004)

A metadata tool system and a data service system are undergoing development and integration, at Sandia National Laboratories, to provide Web-based access to high-performance computing clusters and its associated simulation data. These clusters host a set of scalable post-processing applications for very large data manipulation, and the examination of results generated by high-fidelity simulations in support of the design to analysis process for ensuring safety and reliability of the nation's nuclear weapons stockpile. The primary subject of this work is the integration of metadata tools with a data service archiving capability, resulting in a service-oriented and Web-based architecture, which provides end users the ability from their desktops to manage and understand simulation results for very large, complex problems.
Acoustic radiation force enhances adhesion of microbubbles targeted to p-selectin (2005)

Ultrasound contrast microbubbles can be targeted to regions of intravascular pathology. However, the efficiency of microbubble attachment to molecular targets tends to be low, and adhesion in large, high-flow vessels has not been demonstrated. The efficacy of targeted contrast enhanced ultrasound imaging may be improved by increasing the fraction of free-flowing microbubbles that directly contact the vessel wall at the target site. Several studies have proven that low-intensity acoustic radiation can be used as a mechanism to force free-stream microbubbles toward a surface. In the current work, we present evidence that acoustic radiation increases the specific delivery of targeted microbubbles in vitro and in vivo. Lipid shell microbubbles bearing a monoclonal antibody as a targeting ligand were infused through a capillary flow chamber coated with the pro-inflammatory endothelial protein P-selectin. A 2.0 MHz ultrasonic pulse train was applied perpendicular to the flow direction, and microbubble accumulation was observed on the flow chamber surface opposite the transducer. We observed that acoustic pressures between 70 and 170 kPa improve microbubble adhesion up to 60-fold at microbubble concentrations between 0.25 and 75/spl times/10/sup 6/ mL/sup -1/. We found that adhesion was highly dependent upon microbubble concentration, and that acoustic pressure mediated the greatest enhancement in adhesion at concentrations within the clinical dosing range. Acoustic pressure enhanced adhesion to P-selectin nearly 80-fold at a wall shear rate of 1244 s/sup -1/, suggesting that this mechanism is appropriate for achieving targeted microbubble delivery in very fast-flow vessels. We examined microbubble adhesion in a murine model of microvascular inflammation using intravital microscopy, and observed a six-fold increase in targeted microbubble adhesion in inflamed venules with acoustic radiation.
Disseminated Intravascular Coagulation and Portal Hypertension Following Pancreatic Islet Autotransplantation (1980)

A patient undergoing subtotal pancreatectomy and intraportal islet tissue autotransplantation for chronic pancreatitis developed severe portal hypertension (49 cm of H(2)O) and acute disseminated intravascular coagulation (DIC). In an attempt to identify the cause of these problems, portal pressure and the activities of the coagulation and fibrinolytic systems were studied in dogs undergoing intraportal autotransplantation of islet tissue. Following intraportal injection of the pancreatic tissue in five control dogs, the portal pressure rose to a maximum of 43.2 cm of H(2)O +/- 2.4 and major coagulation abnormalities occurred. The mean hematocrit value fell to 18% +/- 8.6, the mean platelet count to 218,000 +/- 31,000, the mean plasma fibrinogen to 40 mg/dl +/- 18, and the mean euglobulin clot lysis time (ECLT) to 25 min +/- 4. Partial thromboplastin time (PTT) became prolonged (233 secs +/- 30) and significant quantities of fibrinogen-fibrin degradation products (FDP-fdp) (1:128 +/- 32) appeared. These changes indicate the development of DIC probably secondary to significant amounts of tissue thromboplastin detected in the tissue homogenate infused at time of autotransplantation. In a group of seven dogs in whom heparin and Trasylol (aprotinin) were added to the pancreatic tissue at the time of transplantation, portal pressure rose only to a peak of 28.3 cm of H(2)O +/- 3.6 and no significant abnormalities occurred in mean hematocrit value, plasma fibrinogen, platelet count or ECLT. Minor prolongation of PTT occurred secondary to the activity of heparin. FDP-fdp (1:16) were present transiently during tissue injection. Four patients in whom heparin and Trasylol were added to the pancreatic tissue at the time of autotransplantation developed only minor elevations of portal pressure (mean 15.5 cm of H(2)O) without intravascular coagulopathy.
Plenary lectures: Problems in neurosurgery — A rich environment for engineer (2012)

These plenary lectures discuss the following: problems in neurosurgery - a rich environment for engineer; building a brain machine interface: the neuroprosthetics grand challenge; micro and nano robotics system for single cell analysis; contact robotics: physical interaction in assistive and therapeutic technologies; neural adaptations to a brain machine interface; and heterogeneous networked robotic teams: bioinspired approaches.
About This Reverberation Business (1979)

When music is performed in a concert hall, a torrent of echos from the various different surfaces in the room strikes the ear, producing the impression of space to the listener. This effect can vary in evoked subjective response from great annoyance or even incomprehensibility, in the case of speech presented in a highly reverberant auditorium, to sheer ecstasy, in the case of late romantic music in the Vienna Grosser Musikvereinsaal. Most music is heard these days either in the comfort of one's home (or car), or in a university auditorium, both of which have generally short reverberation times. For this reason, most recordings of music already have some amount of reverberation added before distribution either by a natural process (i.e. recordings made in concert halls) or by artificial processes (plate or spring reverberators). Computer music is an especially fertile ground for artificial reverberation in that it is rarely, if ever, performed in highly reverberant concert halls. The use of the computer for the simulation of this reverberation also allows the composer another degree of freedom, namely to tailor the reverberation to the particular aural effect he wishes to present, allowing, for instance, each individual sound in the piece to carry an entirely different spatial aspect, if desired. In this paper, we review some of the work that has been done in the production of artificial reverberation by computer, and we present the fruits of our own labors along this line, both in the attempted simulation of the concert hall environment by computer and in the proliferation of different circuits for the realization of simulated room reverberation.
NMR measurements of Na+ and cellular energy in ischemic rat heart: role of Na(+)-H+ exchange (1993)

Interleaved 23Na- and 31P-nuclear magnetic resonance (NMR) spectra were continuously collected on perfused rat hearts subjected to low-flow ischemia (30 min, 10% flow) or zero-flow ischemia (21 min) followed by reperfusion. During untreated low-flow and zero-flow ischemia, intracellular Na+ (Nai+) increased by 53 +/- 11 (+/- SE) and 78 +/- 8%, respectively, and remained elevated for zero-flow hearts. However, during both low- and zero-flow ischemia, Nai+ did not increase in hearts treated with the Na(+)-H+ exchange inhibitor, 5-(N-ethyl-N-isopropyl)amiloride (EIPA). The pH decreases during ischemia were unchanged. EIPA treatment reduced ATP depletion during ischemia. During reperfusion from zero-flow ischemia, EIPA-treated hearts displayed more rapid and extensive recoveries of phosphocreatine and ATP. Recovery of left ventricular developed pressure was improved for zero-flow hearts treated with EIPA during the ischemic period exclusively (104 +/- 13%) compared with untreated hearts (36 +/- 21%). These data indicate that Na(+)-H+ exchange is an important mechanism for Nai+ accumulation, but not for pH regulation, during myocardial ischemia. Additionally, Nai+ homeostasis plays an important role in the postischemic recovery of cellular energy and ventricular function.
Real-Time Bidirectional Pyrophosphorolysis-Activated Polymerization for Quantitative Detection of Somatic Mutations (2014)

Detection of somatic mutations for targeted therapy is increasingly used in clinical settings. However, due to the difficulties of detecting rare mutations in excess of wild-type DNA, current methods often lack high sensitivity, require multiple procedural steps, or fail to be quantitative. We developed real-time bidirectional pyrophosphorolysis-activated polymerization (real-time Bi-PAP) that allows quantitative detection of somatic mutations. We applied the method to quantify seven mutations at codons 12 and 13 in KRAS, and 2 mutations (L858R, and T790M) in EGFR in clinical samples. The real-time Bi-PAP could detect 0.01% mutation in the presence of 100 ng template DNA. Of the 34 samples from the colon cancer patients, real-time Bi-PAP detected 14 KRAS mutant samples whereas the traditional real-time allele-specific PCR missed two samples with mutation abundance <1% and DNA sequencing missed nine samples with mutation abundance <10%. The detection results of the two EGFR mutations in 45 non-small cell lung cancer samples further supported the applicability of the real-time Bi-PAP. The real-time Bi-PAP also proved to be more efficient than the real-time allele-specific PCR in the detection of templates prepared from formalin-fixed paraffin-embedded samples. Thus, real-time Bi-PAP can be used for rapid and accurate quantification of somatic mutations. This flexible approach could be widely used for somatic mutation detection in clinical settings.
Preparation and characterization of biodegradable agar/poly(butylene adipate‐ <i>co</i> ‐terephatalate) composites (2009)

Abstract A series of biocomposites were developed by reinforcing agar particles from red marine plant Gelidium robustum into poly(butylene adipate‐ co ‐terephatalate) (PBAT) using extrusion and injection molding technique. The effect of different content of agar (0, 10, 20, 30, and 40 wt%) on the physico‐mechanical properties of the biocomposite was evaluated. The dynamic mechanical behavior of the composites was studied to determine the storage and loss modulus. The incorporation of agar particles into PBAT enhanced the tensile strength and modulus with a reduced percentage of elongation at break. A reduction in the mechanical loss factor (tan δ) was noticed with the addition of agar particles into PBAT. A reverse trend was noticed for storage and loss modulus. The thermogravimetric analysis revealed that the degradation temperature of PBAT‐agar composites lies in between that of their individual components (agar and PBAT). An increase in melting ( T m ) and crystallization ( T c ) temperature of the biocomposites were noticed as agar particle content increased. The rheological study carried out by dynamic frequency experiments demonstrated that viscosity is increased with the presence of agar particles. The morphology of the biocomposites was analyzed using scanning electron microscope. POLYM. ENG. SCI., 2009. © 2009 Society of Plastics Engineers
QUALITATIVE SURVEY OF RNA CODEWORDS (1962)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
265. Reactions of unsaturated compounds. Part VII. The mechanism of the formation of unsaturated alcohols from olefins by the action of organic per-acids (1948)

W. J. Hickinbottom, J. Chem. Soc., 1948, 1331 DOI: 10.1039/JR9480001331
Infectious Diseases of Children (1993)

Surprise and delight were the reactions of this reviewer on noting the publication of the ninth edition of<i>Infectious Diseases of Children</i>. Seven years had elapsed since the previous revision, a longer gestation than any of its predecessors. I had incorrectly surmised that the proliferation of medical literature, especially of infectious disease texts and journals, had led to the demise of this oft-cited comparison. How wonderful to be proven wrong! Thirty-four years ago, the stated purpose of this book was "to provide a concise and handy description of certain common infectious diseases of children." The same goals have been delineated and achieved in this new edition, albeit now in the format of a multiauthored compendium. The text has been completely reorganized and updated, and important new diseases and new information about old diseases have been added. Topics discussed in the 36 chapters range from the acquired immunodeficiency syndrome, infections in
Perylene, pyrromethene and grafted rhodamine-doped xerogels for tunable solid state laser (1994)

Organic dye molecules have been widely used in solution as amplifying media in tunable lasers. The possibility of trapping these molecules in a solid state matrix may lead to a new field of application outside the laboratory. Many types of matrices can be used. We present results with new hybrid organic/inorganic xerogels prepared by hydrolysis-condensation of the methyl- or vinyl-triethoxysilane precursor under acid-catalyzed hydrolysis and basic-catalyzed condensation. Organic methyl or vinyl groups attached to the silica network provide a favorable environment to dye fluorescence. We have studied the effect induced by using different basic catalysts: N-(2-aminoethyl)-3-aminopropyltrimethoxysilane and 3- aminopropyltriethoxysilane are found to lead to the best matrix characteristics. Perylenes and pyrromethenes were chosen because of their thermal- and photo-stability. After gelation, 10 mm thick samples, polished to a surface roughness of about 4 nm, are placed in a plano- concave cavity as gain media and pumped by a frequency doubled nanosecond Q:switched Nd:YAG laser. Efficiency is the greatest with a pyrromethene 597 doped sample: more than 6 mJ output energy for a 10 mJ pump energy (2 J/cm<SUP>2</SUP> fluence) leading to a slope efficiency of 63%. The lifetime of the laser emission when the same point of the sample is sequentially used is also an important characteristic. Best results are obtained with perylene red dye: for a pump energy of 0.7 mJ at 1 Hz repetition rate, the output energy is still 50% of the initial value (0.1 mJ) after 80,000 shots. For a pyrromethene 597 doped MTEOS sample, it appears that the measured lifetimes are independent of the operating frequency in the 0.2 - 20 Hz range, indicating a reasonable heat conductivity for this type of matrix. We have also studied tunability by adding a grating or prism to the cavity: a typical tunability of over 50 nm or more is obtained with many of these dyes. Finally we report laser activity obtained with rhodamine B doped xerogels in which the dye molecules were covalently bonded to the silica network in order to stabilize the organic molecule structure.