gebhart/patrepeval huggingface dataset:
Single-Shot Visualization of Evolving Laser Wakefields Using an All-Optical Streak Camera (2014)

We visualize ps-time-scale evolution of an electron density bubble--a wake structure created in atmospheric density plasma by an intense ultrashort laser pulse--from the phase "streak" that the bubble imprints onto a probe pulse that crosses its path obliquely. Phase streaks, recovered in one shot using frequency-domain interferometric techniques, reveal the formation, propagation, and coalescence of the bubble within a 3 mm long ionized helium gas target. 3D particle-in-cell simulations validate the observed density-dependent bubble evolution, and correlate it with the generation of a quasimonoenergetic ∼ 100 MeV electron beam. The results provide a basis for understanding optimized electron acceleration at a plasma density n(e) ≈ 2 × 10(19) cm(-3), inefficient acceleration at lower density, and dephasing limits at higher density.
Conformation of guanine.cntdot.8-oxoadenine base pairs in the crystal structure of d(CGCGAATT(O8A)GCG) (1992)

The structure of the synthetic deoxydodecamer d(CGCGAATT(O8A)GCG)2 (O8A = 8-oxoadenine) has been determined by single-crystal X-ray diffraction techniques. The oligonucleotide crystallizes in the orthorhombic space group P2(1)2(1)2(1) with cell dimensions of a = 25.48 A, b = 41.84 A, and c = 64.91 A. The refinement has converged with an R-factor of 0.151 for 1119 reflections in the resolution range 8.0-2.25 A. Sixty-seven solvent molecules were located during the course of the refinement. The B-DNA helix consists of ten Watson-Crick base pairs and two guanine-8-oxoadenine (G.O8A) base pairs. In order to achieve hydrogen-bonding complementarity between the two bases, an unusual G(anti).O8A-(syn) wobble conformation is adopted. It is proposed that the G.O8A mispairs are held together by a network of four interbase hydrogen bonds which are the result of the formation of two reverse three-center hydrogen-bonding systems. These involve one carbonyl oxygen lone pair interacting with two hydrogen atoms. In a departure from previous observations of the characteristics of purine-purine anti-syn base pairs, lambda 1 and lambda 2, the angles between the glycosidic bonds and the C1'-C1' vector, are symmetric. A reassessment of the other purine-purine mispairs suggests that similar three-center hydrogen bonds may occur and make a contribution to stabilizing other base pairings.
Conformation of thymosin β4 in water determined by NMR spectroscopy (1993)

The conformational preferences of a 43-amino-acid G-actin-binding peptide, thymosin beta 4, in water at 1, 4 and 14 degrees C, and at pH 3.0 and 6.5 were studied by NMR. NMR showed that thymosin beta 4 lacks a uniquely folded conformation in water. However, some preferential alpha-helical conformations of thymosin beta 4 can be observed in aqueous solutions. The segment at residues 5-16 showed characteristic interactions for conformations in both the beta-strand and alpha-helical regions of the phi-psi space, based on strong C alpha H(i)-NH(i+1) interactions and NH-NH, C alpha H(i)-NH(i+3), and C alpha H(i)-C beta H(i+3) interactions, respectively. At 1-4 degrees C, another segment at residues 31-37 also shows both beta and alpha conformations, forming however a less well-defined helix than the segment at residues 5-16. At 14 degrees C, the conformational population of the helix at positions 5-16 is shifted more towards the random and turn-like structures, whereas the segment at positions 31-37 becomes exclusively a random coil.
Evaluation of Acyl Coenzyme A Oxidase (Aox) Isozyme Function in the n -Alkane-Assimilating Yeast Yarrowia lipolytica (1999)

We have identified five acyl coenzyme A (CoA) oxidase isozymes (Aox1 through Aox5) in the n-alkane-assimilating yeast Yarrowia lipolytica, encoded by the POX1 through POX5 genes. The physiological function of these oxidases has been investigated by gene disruption. Single, double, triple, and quadruple disruptants were constructed. Global Aox activity was determined as a function of time after induction and of substrate chain length. Single null mutations did not affect growth but affected the chain length preference of acyl-CoA oxidase activity, as evidenced by a chain length specificity for Aox2 and Aox3. Aox2 was shown to be a long-chain acyl-CoA oxidase and Aox3 was found to be active against short-chain fatty acids, whereas Aox5 was active against molecules of all chain lengths. Mutations in Aox4 and Aox5 resulted in an increase in total Aox activity. The growth of mutant strains was analyzed. In the presence of POX1 only, strains did not grow on fatty acids, whereas POX4 alone elicited partial growth, and the growth of the double POX2-POX3-deleted mutant was normal excepted on plates containing oleic acid as the carbon source. The amounts of Aox protein detected by Western blotting paralleled the Aox activity levels, demonstrating the regulation of Aox in cells according to the POX genotype.
Molecular Characterization of Waldenstrom's Macroglobulinemia Reveals Frequent Occurrence of Two B-Cell Clones Having Distinct IgH VDJ Sequences (2007)

The existence of two B-cell clones having distinct VDJ sequences is common in WM, suggesting that frequent transformation events may occur. In two cases, the partner clones had distinct tissue distributions in either blood or bone marrow, were of different immunoglobulin isotypes, and in one case exhibited differential response to therapy. The contributions of each clone are unknown. Their presence suggests that WM may involve a background of molecular and cellular events leading to emergence of one or more malignant clones.
Laterally coupled BAW filter using two acoustic modes (2013)

We study the use of the second-order thickness shear (TS <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> ) plate wave mode in a solidly-mounted, laterally acoustically coupled bulk acoustic wave filter to form a wider passband. Typically, the first-order thickness-extensional (TE1) mode is used to create the coupled even and odd mode resonances that build up the filter passband. An unwanted response can arise due to the TS <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> mode. By designing the dispersion of the thin-film reflector stack appropriately, the TS <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> mode can be brought close to TE1 so that both plate wave modes contribute to the passband. Measurement results for filter with varied structure parameters (electrode width, gap width, number of electrodes) are presented. For a 31-electrode filter with electrode width 9 μm, gap width 1.5 μm, and electrode length 200 μm, a total of 6 standing-wave resonances can be identified in the passband. The resonances span a frequency range of 230 MHz at 2 GHz (11.5%).
Maintenance of Laboratory Strains of Obligately Anaerobic Rumen Bacteria (1982)

Cultures of rumen bacteria can be stored at -20 degrees C for at least 2 years in a liquid medium containing 20% glycerol. Thawing, sampling, and refreezing do not significantly affect viability.
Transposition of the Tol2 Element, an Ac-Like Element From the Japanese Medaka Fish Oryzias latipes, in Mouse Embryonic Stem Cells (2004)

Abstract The Tol2 transposable element of the Japanese medaka fish belongs to the hAT family of transposons including hobo of Drosophila, Ac of maize, and Tam3 of snapdragon. To date, Tol2 is the only natural transposon in vertebrates that has ever been shown to encode a fully functional transposase. It has not been known, however, whether Tol2 can transpose in vertebrates other than fish. We report here transposition of Tol2 in mouse embryonic stem (ES) cells. We constructed a transposon donor plasmid containing a nonautonomous Tol2 element with the neomycin resistance gene and a helper plasmid capable of expressing the transposase and introduced the donor plasmid with various amounts of the helper plasmid by electroporation into mouse ES cells. The number of G418-resistant ES colonies increased as the amount of helper plasmid was increased, in a dose-dependent manner, indicating that the transposase activity elevated the integration efficiency. These G418-resistant ES colonies were cloned and the structure of the junction of the integrated Tol2 element and the genomic DNA was analyzed by inverse PCR. In those clones, Tol2 was surrounded by mouse genomic sequences and an 8-bp direct repeat was created adjacent to both ends of Tol2, indicating that Tol2 was integrated in the genome through transposition. The Tol2 transposon system is thus active in mouse as well as in fish. We propose that it should be used as a genetic tool to develop novel gene transfer, transgenesis, and mutagenesis methods in mammals.
Towards Democratizing Relational Data Visualization (2019)

The problem of data visualization is to transform data into a visual context such that people can easily understand the significance of data. Nowadays, data visualization becomes especially important, because it is the de facto standard for modern business intelligence and successful data science. This tutorial will cover three specific topics: visualization languages define how the users can interact with various visualization systems; efficient data visualization processes the data and produces visualizations based on well-specified user queries; smart data visualization recommends data visualizations based on underspecified user queries. In this tutorial, we will go logically through these prior art, paying particular attentions on problems that may attract the interest from the database community.
The HLA-A,B "negative" mutant cell line C1R expresses a novel HLA-B35 allele, which also has a point mutation in the translation initiation codon (1992)

The HLA-A,B negative mutant cell line C1R is widely used as a transfection recipient in functional studies of class I MHC genes. It was derived from a normal B cell line, Hmy2, by three rounds of mutagenesis and immunoselection with anti-HLA mAb. Serology characterizes C1R to be negative for the HLA-A2, A3, B35, Bw62, and Cw3 Ag of the parental cell line while retaining expression of HLA-Cw4. We find, however, that CTL specific for HLA-B35 lyse C1R cells, suggesting that expression of HLA-B35 is also retained. To resolve this paradox we examined the expression of HLA-A,B,C genes and proteins in C1R cells. The results are consistent with deletion of the HLA-A3, Bw62, Cw3 haplotype and retention of the HLA-A2, B35, Cw4 haplotype in C1R. Although present, the HLA-A2 gene appears not to be transcribed. As expected, the HLA-Cw4 gene is transcribed and the protein expressed at normal levels. Transcription of the HLA-B35 gene is also normal and comparable to that of HLA-Cw4. However, expression of the HLA-B35 protein is reduced to a few percent of the parental level. Comparison of the nucleotide sequence of B35 alleles from C1R and Hmy2 revealed that reduced translation in C1R is caused by a point mutation (ATG to TTG) in the translation initiation codon. The HLA-B35 allele from C1R and Hmy2 represents a novel subtype, B*3503, differing from B*3501 by replacement of serine by phenylalanine at the peptide binding position 116. This study shows cell surface levels of a class I molecule which are insensitive to lysis by antibody and complement can be readily recognized by alloreactive T cells, further illustrating the relative sensitivity of Ag recognition by T cells.
Concepción: una ciudad para la imaginación (2002)

Si todos los ciudadanos soñáramos vivir en la mejor urbe del país, no hay duda que pensaríamos cómo mejorarla, cómo hacerla más atractiva. Todos los días vivimos la ciudad, pero no nos damos cuenta como influye en nuestras vidas, en el diario quehacer, en nuestras relaciones, en nuestros hijos, en el trabajo. Recorremos sus rincones, sus barrios, el centro, sin percatarnos, a veces, el desagrado o agrado que nos entrega. Cuando tenemos un inconveniente, atraso en la movilización, una calle inundada, un taco interminable por falta de calles alternativas, no poder estacionar cerca de donde deseamos, no encontrar >una dirección por falta de señalización adecuada, recibir los gases y el ruido de las máquinas de transporte urbano, entonces sí pensamos en que las autoridades no han arreglado esto o lo otro. Culpamos a quienes dirigen los servicios locales. La verdad es que todos somos culpables. Tenemos la ciudad que merecemos, pues no hemos hecho nada por mejorarla, por exigir que se solucionen sus defectos graves, por colaborar, desde el espacio que ocupamos, embelleciéndolo, dándole importancia a nuestro entorno inmediato.
Predicting completion times of batch query workloads using interaction-aware models and simulation (2011)

A question that database administrators (DBAs) routinely need to answer is how long a batch query workload will take to complete. This question arises, for example, while planning the execution of different report-generation workloads to fit within available time windows. To answer this question accurately, we need to take into account that the typical workload in a database system consists of mixes of concurrent queries. Interactions among different queries in these mixes need to be modeled, rather than the conventional approach of considering each query separately. This paper presents a new approach for estimating workload completion times that takes the significant impact of query interactions into account. This approach builds performance models using an experiment-driven technique, by sampling the space of possible query mixes and fitting statistical models to the observed performance at these samples. No prior assumptions are made about the internal workings of the database system or the cause of query interactions, making the models robust and portable. We show that a careful choice of sampling and statistical modeling strategies can result in accurate models, and we present a novel interaction-aware workload simulator that uses these models to estimate workload completion times. An experimental evaluation with complex TPC-H queries on IBM DB2 shows that this approach consistently predicts workload completion times with less than 20% error.
Tumor necrosis factor and CD11/CD18 (beta 2) integrins act synergistically to lower cAMP in human neutrophils. (1990)

The ability of neutrophils (PMN) to undergo a prolonged respiratory burst in response to cytokines such as tumor necrosis factor-alpha (TNF) depends on expression of CD11/CD18 (beta 2) integrins and interaction with matrix protein-coated surfaces (Nathan, C., S. Srimal, C. Farber, E. Sanchez, L. Kabbash, A. Asch, J. Gailit, and S. D. Wright. 1989. J. Cell Biol. 109:1341-1349). We tested the hypothesis that changes in cAMP mediate the joint action of cytokines and integrins. When plated on FBS- or fibrinogen-coated surfaces, PMN responded to TNF with a sustained fall in intracellular cAMP. This did not occur without TNF; in suspended PMN; in PMN treated with anti-CD18 mAb; or in PMN genetically deficient in beta 2 integrins. A preceding fall in cAMP appeared essential for TNF to induce a respiratory burst, because drugs that elevate cAMP blocked the burst if added any time before, but not after, its onset. Adenosine analogues and cytochalasins also block the TNF-induced respiratory burst if added before, but not after, its onset. Both also blocked the TNF-induced fall in cAMP. The effect of cytochalasins led us to examine the relationship between cAMP and actin reorganization. The same conditions that led to a sustained fall in cAMP led at the same time to cell spreading and the assembly of actin filaments. As with the respiratory burst, cAMP-elevating agents inhibited TNF-induced cell spreading and actin filament assembly if added before, but not after, spreading began. Thus, occupation of TNF receptors and engagement of CD18 integrins interact synergistically in PMN to promote a fall in cAMP. The fall in cAMP is closely related to cell spreading and actin reorganization. These changes are necessary for TNF to induce a prolonged respiratory burst. We conclude that integrins can act jointly with cytokines to affect cell shape and function through alterations in the level of a second messenger, cAMP.
(n, m) Structural Assignments and Chirality Dependence in Single-Wall Carbon Nanotube Raman Scattering (2001)

Raman spectra were obtained from thin bundles containing just a few single-wall carbon nanotubes (SWNTs). These spectra exhibit new characteristics absent in the ensemble Raman measurements. A large variation in the radial breathing mode (RBM) Stokes to anti-Stokes Raman intensity ratio was observed for different metallic tubes and can be understood with a simple resonant Raman analysis. An (n, m) structural assignment for many tubes at 632 nm laser excitation was tentatively achieved on the basis of the RBM frequency and the Stokes to anti-Stokes Raman ratio. The (9, 9) armchair tube fits the simple model poorly. The varying relative intensities of different components observed in the tangential G-band Raman modes provide convincing evidence for a recently predicted chirality dependence of Raman scattering. A new Raman feature at 1417 cm-1 was assigned to achiral tubes.
Morphologic Characteristics of the Left Atrial Appendage, Roof, and Septum: Implications for the Ablation of Atrial Fibrillation (2006)

Considerable variations of LAA and LA roof morphologies were demonstrated. Peculiar structures, including roof pouches and septal ridges, were delineated by CT imaging. These findings were important for determining the strategy of AF ablation and avoiding the procedure-related complications.
JBits: Java based interface for reconfigurable computing (1999)

The JBits ™ software is a set of Java ™ classes which provide an Application Programming Interface (API) to access the Xilinx FPGA bitstream. The interface operates on either bitstreams generated by Xilinx design tools, or on bitstreams read back from actual hardware. This permits all configurable resources like Look-up tables, routing and the flip-flops in the FPGA to be individually configured under software control. The API has been used to construct complete circuits and to modify existing circuits. In addition, the object-oriented support in the Java programming language has permitted a small library of parameterizable, object oriented macro circuits or Cores to be implemented. Finally, this API may be used as a base to construct other tools. This includes traditional design tools for performing tasks such as circuit placement and routing, as well as application specific tools to perform more narrowly defined tasks. The circuits developed can be downloaded on to the Xilinx hardware and probed using BoardScope. BoardScope is a graphical and interactive hardware debug tool for Xilinx FPGAs. It enables a user to look inside the chips and see the internal states and circuit configurations while the hardware is operating. The data is sampled using the readback capabilities of the FPGAs, and then graphically displayed. The interface to the hardware is provided by XHWIF, the Xilinx standard HardWare InterFace for FPGA based
Expression of hypoxia-inducible factor 1 and 2 in choroidal neovascular membranes associated with age-related macular degeneration (2007)

segments as a characteristic OCT finding in IPT. 8 9 Interestingly, experimental disruption of Muller cell metabolism induces photoreceptor dysmorphogenesis. 10 Although speculative, Muller cell abnormalities may secondarily affect photoreceptors in eyes with IPT, leading to the deep capillary proliferation.
Variations in Three-Dimensional Cancellous Bone Architecture of the Proximal Femur in Female Hip Fractures and in Controls (2000)

Cubes of cancellous bone were obtained from proximal femora of women with hip fractures (n = 26) and from female cadaveric controls (n = 32) to compare architecture and mechanics between groups. Specimens were scanned on a microcomputed tomography system. Stereologic algorithms and model-based estimates were applied to the data to characterize the three-dimensional cancellous microstructure. Cubes were mechanically tested to failure to obtain mechanical properties. Specimens from control subjects had significantly higher bone volume fraction, trabecular number, and connectivity than specimens from patients with hip fractures; no difference in trabecular thickness was observed between groups. Both maximum modulus and ultimate stress were significantly higher in the control than in the fracture group, consistent with the higher bone volume found in the control group. No statistical differences in any of these architectural or mechanical variables were found when groups were matched for bone volume. Specimens from both patients with hip fractures and controls demonstrated strong relationships between trabecular number and bone volume fraction that were statistically equivalent, suggesting that for a given bone mass, both groups have the same overall number of trabeculae. However, there was an architectural difference between fracture and control groups in terms of the three-dimensional spatial arrangement of trabeculae. Fracture specimens had a significantly more anisotropic (oriented) structure than control specimens, with proportionately fewer trabecular elements transverse to the primary load axis, even when matched for bone volume. Relationships between mechanical and architectural parameters were significantly different between groups, suggesting that fracture and control groups have different structure-mechanics relationships, which we hypothesize may be a consequence of the altered three-dimensional structure between groups.
Prevention of patient bacterial contamination of anaesthesia-circle-systems: A clinical study of the contamination risk and performance of different heat and moisture exchangers with electret filter (HMEF) (1997)

The microbiological contamination of 250 breathing system tubes after use in anaesthesia circle systems with reduced fresh gas flow was investigated. The lungs of 50 patients were ventilated without any filtering device between the endotracheal tube and the Y-piece. A total of 51, 49 and 100 patients, respectively, were given different types of heat and moisture exchanger with electret filters (HMEF). With no filtering device the tubing system was contaminated by microorganisms originating from the patient's tracheal secretion in 13% of the patients. In contrast, no bacterial migration into the tubing system was detected when any of the investigated HMEF-devices were used. We therefore conclude that heat and moisture exchangers with electret filters prevent contamination of the anaesthesia breathing system with microorganisms from the patients airways.
The role of the Wnt signaling pathway in incretin hormone production and function (2012)

Glucose metabolism is tightly controlled by multiple hormones and neurotransmitters in response to nutritional, environmental, and emotional changes. In addition to insulin and glucagon produced by pancreatic islets, two incretin hormones, namely glucagon-like peptide-1 (GLP-1) and gastric inhibitory polypeptide (GIP, also known as glucose-dependent insulinotropic peptide), also play important roles in blood glucose homeostasis. The incretin hormones mainly exert their regulatory effects via their corresponding receptors, which are expressed in pancreatic islets as well as many other extra-pancreatic organs. Recent studies have shown that the genes which encode these two incretin hormones can be regulated by the effectors of the Wnt signaling pathway, including TCF7L2, a transcription factor identified recently by extensive genome wide association studies as an important type 2 diabetes risk gene. Interestingly, TCF7L2 and β-catenin (β-cat), another effector of Wnt signaling pathway, may also mediate the function of the incretin hormones as well as the expression of their receptors in pancreatic β-cells. In this review, we have introduced the incretin hormones and the Wnt signaling pathway, summarized recent findings in the field, and provided our perspectives.