gebhart/patrepeval huggingface dataset:
Nuclear distribution of Drosophila DNA topoisomerase II is sensitive to both RNase and DNase (1995)

The nuclear distribution of Drosophila DNA topoisomerase II was determined by immunoblot analysis after nuclease digestion and cell fractionation. About 60% of DNA topoisomerase II could be removed from nuclei by RNase A, about 70% by DNase I, and about 90% by incubation with both enzymes together or with micrococcal nuclease. Nuclease treatment of nuclei did not affect the distribution of lamins Dm1 and Dm2 or other nuclear proteins similarly. Nuclease-mediated solubilization of DNA topoisomerase II from Drosophila nuclei was also dependent on NaCl concentration. Solubilization was not efficient below 100 mM NaCl. Sucrose velocity gradient ultracentrifugation demonstrated that DNA topoisomerase II solubilized from nuclei by either RNase A or DNase I migrated at about 9 S, as expected for the homodimer. Results of chemical crosslinking supported this observation. We conclude that DNA topoisomerase II has both RNA- and DNA-dependent anchorages in Drosophila embryo nuclei.
Polymorphic Worm Detection Using Structural Information of Executables (2005)

Abstract. Network worms are malicious programs that spread automatically across networks by exploiting vulnerabilities that affect a large number of hosts. Because of the speed at which worms spread to large computer populations, countermeasures based on human reaction time are not feasible. Therefore, recent research has focused on devising new techniques to detect and contain network worms without the need of human supervision. In particular, a number of approaches have been proposed to automatically derive signatures to detect network worms by analyzing a number of worm-related network streams. Most of these techniques, however, assume that the worm code does not change during the infection process. Unfortunately, worms can be polymorphic. That is, they can mutate as they spread across the network. To detect these types of worms, it is necessary to devise new techniques that are able to identify similarities between different mutations of a worm. This paper presents a novel technique based on the structural analysis of binary code that allows one to identify structural similarities between different worm mutations. The approach is based on the analysis of a worm’s control flow graph and introduces an original graph coloring technique that supports a more precise characterization of the worm’s structure. The technique has been used as a basis to implement a worm detection system that is resilient to many of the mechanisms used to evade approaches based on instruction sequences only.
Tunable isolator using variable capacitor for multi-band system (2013)

A novel tunable isolator for multi-standard mobile handsets has been successfully developed. A new circuit configuration for tuning operation frequency of the isolation is proposed. It shows that the isolation band is tuned widely by varying the variable capacitor value without increasing the insertion loss. A 1.5 × 0.9 × H0.4mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> Core-Isolator and a 0.5 × 0.5 × 0.2mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> (BaSr)TiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> (BST) variable capacitor have been fabricated on a PCB. By using this circuit, usable isolation band could be expanded to 698-915MHz, which is 6 times wider than conventional one. The developed isolator keeps other characteristics such as 0.6dB max of insertion loss, 12dB min of isolation and -60dBc level of ACLR (5MHz).
The Characterization of PLGA/Small Intestinal Submucosa Composites as Scaffolds for Intervertebral Disc (2007)

In order to application for the tissue engineered intervertebral disc (IVD), we designed the synthetic/natural hybrid scaffolds with poly(lactide-co-glycolide) (PLGA) and small intestine submucosa (SIS). SIS has been widely used as a biomaterial because SIS consists of various collagens and cytokines. SIS, however, possesses disadvantages such as their weak mechanical properties and uncontrolled degradation. Novel composite scaffolds of PLGA/SIS were manufactured by simple immersion method of PLGA scaffolds in SIS solution under vacuum. Then SIS was crosslinked. Also, PLGA scaffolds and SIS sponges were manufactured by solvent casting/salt leaching and freeze-dried methods, respectively. We evaluated pore structure, porosity, water absorption ability and cell viability of three types of scaffolds for the application of IVD.
Homozygous deletions within 9p21-p22 identify a small critical region of chromosomal loss in human malignant mesotheliomas. (1993)

Previous DNA analyses have demonstrated that 9p13-p22 is a frequent site of chromosomal loss in leukemia, glioma, melanoma, and lung and bladder carcinomas. Recent cytogenetic studies have revealed recurrent alterations of 9p in malignant mesothelioma (MM). We have performed gene dosage studies of 23 MM cell lines, using probes for several 9p21-p22 loci (IFNB, IFNA/IFNW, D9S3, D9S126, D9S169, and D9S171), to identify a common region of deletion. Homozygous and/or hemizygous deletions were identified in 19 (83%) cell lines. Homozygous losses (10 cell lines; 43%) occurred most often at the D9S171 and IFNA/IFNW loci. In 8 cell lines, 2 or more of the 9p loci examined were found to be homozygously lost; 2 others displayed homozygous losses only at the D9S171 locus. Results from our deletion mapping analysis suggest that D9S171 is located between IFNA/IFNW and D9S126. The data presented here indicate that allelic loss from 9p21-p22 is a common occurrence in MM and further delineate the location of a putative 9p tumor suppressor gene(s) to a region between IFNA/IFNW and D9S171. These MM cell lines may facilitate efforts to define an even smaller critically deleted region, leading to the eventual cloning and characterization of this gene.
The Effect of Splenectomy on Escherichia coli Sepsis and Its Treatment with Semisoluble Aminated Glucan (1987)

Rats were subjected to sham laparotomy or splenectomy and were challenged with either 0.2 X 10(9) Escherichia coli intravenously or 1 X 10(9) E. coli intraperitoneally. By means of quantitative blood culturing asplenic animals were shown to have a significantly impaired ability to clear the bacteria in both forms of challenge. Treatment with intraperitoneally injected semisoluble aminated glucan (SAG), known to have strong macrophage-stimulatory properties, compensated completely for the asplenic state. The substance protected against postsplenectomy sepsis both when given before and when given after removal of the spleen. This protective effect of SAG seemed to last at least 3 weeks.
Recent progress in structured light in order to solve the correspondence problem in stereovision (2002)

We present a summary of the most significant techniques, used in the last few years, concerning the coded structured light methods employed to get 3D information. In fact, depth perception is one of the most important subjects in computer vision. Stereovision is an attractive and widely used method, but, rather limited to make 3D surface maps, due to the correspondence problem. The correspondence problem can be improved using a method based on a structured light concept, projecting a given pattern on the measuring surfaces, although some relations between the projected pattern and the reflected one must be solved. This relationship can be directly found codifying the projected light, so that, each imaged region of the projected pattern carries the necessary information to solve the correspondence problem. We do not need to mention the numerous advantages in accurate obtention of 3D information for many research subjects, such as: robotics, autonomous navigation, shape analysis, and so on.
SR proteins are autoantigens in patients with systemic lupus erythematosus: Importance of phosphoepitopes (2000)

We have identified a novel set of autoantigens in SLE, the SR protein family of non-small nuclear RNP pre-messenger RNA splicing factors. Anti-SR autoantibodies are distinct from those which bind dsDNA. The identification of this new set of autoantigens and the observation that the auto-epitope(s) involves posttranslational modification offer new possibilities for understanding autoimmunity and its development.
Analysis of the resonantly photopumped Na-Ne x-ray-laser scheme (1991)

This paper analyzes the resonantly photopumped Na-Ne x-ray-laser scheme that has been studied experimentally on Z pinches for the last five years. By modeling as an x-ray source the Na Z-pinch output obtained on the Saturn generator experiments at Sandia National Laboratories, the time-dependent properties of the Ne lasant are studied. Our model yields a maximum gain, approximately 0.2 ${\mathrm{cm}}^{\mathrm{\ensuremath{-}}1}$, with a full width at half maximum duration of 18.5 ns, on the 4f\ensuremath{\rightarrow}3d transition at 231 \AA{} under the conditions of the Saturn experiments. We investigate the effects of varying parameters such as the ion density of the Ne lasant and the linewidth of the Na pump line. The impact of radiation trapping on the gain of the various laser lines is considered in a one-dimensional slab geometry.
ESR evidence for the formation of hydroxyl radicals during the reaction of vanadyl ions with hydrogen peroxide. (1989)

Hydroxyl radicals from the reaction of vanadyl ions (VO2+) with hydrogen peroxide (H2O2) in an acidic solution can be detected by an electron spin resonance (ESR) spectroscopy using water-soluble spin-traps, α-(4-pyridyl-1-oxide)-N__-tert-butylnitrone (POBN) and 5, 5-dimethyl-1-pyrroline N__--oxide (DMPO). Further, the fact that some hydroxyl radical scavengers suppressed or reduced the production of POBN-OH adducts affirms the formation of hydroxyl radicals at the initial step of the reaction between VO2+ and H2O2.
Crystal Structure of the Catalytic Subunit of Cyclic Adenosine Monophosphate-Dependent Protein Kinase (1991)

The crystal structure of the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase complexed with a 20-amino acid substrate analog inhibitor has been solved and partially refined at 2.7 A resolution to an R factor of 0.212. The magnesium adenosine triphosphate (MgATP) binding site was located by difference Fourier synthesis. The enzyme structure is bilobal with a deep cleft between the lobes. The cleft is filled by MgATP and a portion of the inhibitor peptide. The smaller lobe, consisting mostly of amino-terminal sequence, is associated with nucleotide binding, and its largely antiparallel beta sheet architecture constitutes an unusual nucleotide binding motif. The larger lobe is dominated by helical structure with a single beta sheet at the domain interface. This lobe is primarily involved in peptide binding and catalysis. Residues 40 through 280 constitute a conserved catalytic core that is shared by more than 100 protein kinases. Most of the invariant amino acids in this conserved catalytic core are clustered at the sites of nucleotide binding and catalysis.
lbnamed: A Load Balancing Name Server in Perl (1995)

Given a cluster of workstations, users have always wanted a way to login to the least-loaded workstation. This paper discusses an attempt to solve that problem using a load balancing name server. This name server also has the ability to serve other dynamic information as well, such as /etc/passwd information (a la Hesiod [2]). The prototype was written in Perl 4 [1], and recently converted to Perl 5. This paper describes the Perl 4 version first and then describes some of the interesting features in the Perl 5 version. This paper assumes the reader has a basic understanding of Perl, DNS, and BIND [3].
Sortases and the Art of Anchoring Proteins to the Envelopes of Gram-Positive Bacteria (2006)

The cell wall envelopes of gram-positive bacteria represent a surface organelle that not only functions as a cytoskeletal element but also promotes interactions between bacteria and their environment. Cell wall peptidoglycan is covalently and noncovalently decorated with teichoic acids, polysaccharides, and proteins. The sum of these molecular decorations provides bacterial envelopes with species- and strain-specific properties that are ultimately responsible for bacterial virulence, interactions with host immune systems, and the development of disease symptoms or successful outcomes of infections. Surface proteins typically carry two topogenic sequences, i.e., N-terminal signal peptides and C-terminal sorting signals. Sortases catalyze a transpeptidation reaction by first cleaving a surface protein substrate at the cell wall sorting signal. The resulting acyl enzyme intermediates between sortases and their substrates are then resolved by the nucleophilic attack of amino groups, typically provided by the cell wall cross bridges of peptidoglycan precursors. The surface protein linked to peptidoglycan is then incorporated into the envelope and displayed on the microbial surface. This review focuses on the mechanisms of surface protein anchoring to the cell wall envelope by sortases and the role that these enzymes play in bacterial physiology and pathogenesis.
RepeatsDB: a database of tandem repeat protein structures (2013)

RepeatsDB (http://repeatsdb.bio.unipd.it/) is a database of annotated tandem repeat protein structures. Tandem repeats pose a difficult problem for the analysis of protein structures, as the underlying sequence can be highly degenerate. Several repeat types haven been studied over the years, but their annotation was done in a case-by-case basis, thus making large-scale analysis difficult. We developed RepeatsDB to fill this gap. Using state-of-the-art repeat detection methods and manual curation, we systematically annotated the Protein Data Bank, predicting 10,745 repeat structures. In all, 2797 structures were classified according to a recently proposed classification schema, which was expanded to accommodate new findings. In addition, detailed annotations were performed in a subset of 321 proteins. These annotations feature information on start and end positions for the repeat regions and units. RepeatsDB is an ongoing effort to systematically classify and annotate structural protein repeats in a consistent way. It provides users with the possibility to access and download high-quality datasets either interactively or programmatically through web services.
Annealing‐Free High Efficiency and Large Area Polymer Solar Cells Fabricated by a Roller Painting Process (2010)

Abstract Polymer solar cells are fabricated by a novel solution coating process, roller painting. The roller‐painted film – composed of poly(3‐hexylthiophene) (P3HT) and [6,6]‐phenyl‐C61‐butyric acid methyl ester (PCBM) – has a smoother surface than a spin‐coated film. Since the roller painting is accompanied by shear and normal stresses and is also a slow drying process, the process effectively induces crystallization of P3HT and PCBM. Both crystalline P3HT and PCBM in the roller‐painted active layer contribute to enhanced and balanced charge‐carrier mobility. Consequently, the roller‐painting process results in a higher power conversion efficiency (PCE) of 4.6%, as compared to that for spin coating (3.9%). Furthermore, annealing‐free polymer solar cells (PSCs) with high PCE are fabricated by the roller painting process with the addition of a small amount of octanedi‐1,8‐thiol. Since the addition of octanedi‐1,8‐thiol induces phase separation between P3HT and PCBM and the roller‐painting process induces crystallization of P3HT and PCBM, a PCE of roller‐painted PSCs of up to 3.8% is achieved without post‐annealing. A PCE of over 2.7% can also be achieved with 5 cm 2 of active area without post‐annealing.
Functioning of Cx43 Hemichannels Demonstrated by Single Channel Properties (2003)

It has been suggested that the opening of non-junctional connexin 43 (Cx43) hemichannels may play a role in cell physiology, but some workers doubt the reality of hemichannel openings. Here we show data on unitary conductance and voltage gating properties demonstrating that Cx43 hemichannels can open. Membrane depolarization > +60 mV induced single hemichannel currents in HeLa cells expressing Cx43 or Cx43 with enhanced green fluorescent protein attached to the carboxy terminal (Cx43-EGFP). The conductance of single hemichannels was approximately 220 pS, about twice that of the cell-cell channels. Cx43 and Cx43-EGFP hemichannels exhibited slow transitions (>5 ms) between closed and fully open states. Cx43 hemichannels also exhibited fast transitions (<1 ms) between the fully open state and a substate of approximately 75 pS. Similar gating was described for their respective cell-cell channels. No comparable single channel activity was detected in the parental (nontransfected cells) or HeLa cells expressing Cx43 fused at the amino terminal with EGFP (EGFP-Cx43). The latter chimera was inserted into the surface and formed plaques, but did not express functional hemichannels or cell-cell channels. These data convincingly demonstrate the opening of Cx43 hemichannels.
Femtosecond pulses in the focal region of lenses (1993)

A systematic theoretical and experimental study of focusing femtosecond light pulses by single lenses is presented. By evaluation of the diffraction integral the interplay of spherical and chromatic aberration is shown to determine the temporal as well as the spatial intensity distribution in the focal region of a lens. Conditions are derived under which the effect of spherical aberration dominates. Here a temporally unbroadened, in-focus pulse occurs while the spatial distribution is that expected from an annular lens aperture. If chromatic aberration is the major aberration, the in-focus pulses are considerably broadened. Both effects could clearly be measured with 100-fs pulses using a modified Michelson interferometer. In an intermediate parameter range both chromatic and spherical aberration contribute to the pulse broadening and to the spatial intensity pattern in a given plane in the focal region. From Fresnel diffraction we expect a weak-intensity distribution to precede the in-focus pulse on the axis. Another weak intensity peak is produced by the pulse traveling on axis. By measuring its separation from the main pulse in the marginal focal plane one can estiamte the aberration parameters.
Evaluation of heat-sensitive, neutrophil-toxic, and hemolytic activity of Haemophilus (Actinobacillus) pleuropneumoniae (1988)

Cytotoxic and hemolytic activity of Haemophilus (Actinobacillus) pleuropneumoniae serotype 1 strain CM5 was investigated because of the potential role as a virulence determinant. Viable bacteria were toxic for porcine and bovine neutrophils, whereas bacteria killed by heat treatment at 60 C for 1 hour were not. Similarly, bacteria-free culture supernatant was cytotoxic and hemolytic in assays that used porcine neutrophils and erythrocytes, whereas supernatant treated at 60 C for 1 hour had no activity. Erythrocytes from various species were susceptible to the hemolytic activity of bacteria-free culture supernatant, with ovine and bovine erythrocytes being most sensitive. The neutrophil-toxic and hemolytic activity of bacteria-free culture supernatant was inhibited by cholesterol and oxygen and abolished after trypsin digestion. The neutrophil-toxic and hemolytic activity was preserved during storage at or less than 4 C, but was lost rapidly at 56 C or 80 C. Neutralizing antibodies were demonstrated in serum of pigs and rabbits immunized with 10-fold concentrated culture supernatant of strain CM5 and in field pigs that had recovered from natural infection with H pleuropneumoniae serotype 1. Bacteria-free culture supernatants of 18 strains, including H pleuropneumoniae serotypes 1 through 10, Actinobacillus suis, and Haemophilus taxon minor group, were tested for heat-sensitive, neutrophil-toxic, and hemolytic activity. Fifteen strains were neutrophil toxic, but only 10 of these were hemolytic. Haemophilus pleuropneumoniae, serotype 1, strain VLS557; serotype 5, strain K17; and Haemophilus taxon minor group strain 33PN were neither cytotoxic nor hemolytic.
Clospore: A Liquid Medium for Producing High Titers of Semi-purified Spores of Clostridium difficile (2011)

Clostridium difficile continues to cause infections in healthcare and other settings. Its spores survive well indoors and require sporicidal chemicals for infection control. However, proper testing of disinfectants is impeded due to difficulties in obtaining viable spores of high enough quality and titers to meet current regulations for sporicidal claims. A new liquid medium (Clospore) has been developed, based on a systematic review of the compositions of 20 other available media. C. difficile spores grown in the new medium and treated with a mixture of lysozyme and trypsin yielded final suspensions with > 10(9) CFU/mL of viable spores, with a purity of > 91% as tested by spore-staining and phase-contrast microscopy. The spores showed a biological decay rate of about 0.1 log10/month when dried on metal disks and stored indoors (air temperature 23 +/- 2 degrees C; relative humidity 52.76 +/- 15.08%). Heating the purified spore suspensions to 70 degrees C for 10 min to inactivate any vegetative cells showed no spore activation or inactivation. The spores could be stored for at least 14 months either refrigerated (4 degrees C) or frozen (-20 or -80 degrees C) in 50% (v/v) ethanol with virtually no loss in viability. The resistance of the enzyme-treated spores to three levels of sodium hypochlorite (1000, 3000, and 5000 ppm), using a standardized quantitative carrier test, was almost identical to that of the spores concentrated by centrifugation alone. The described procedure has been successfully applied to four standard (ATCC) and six clinical strains of C. difficile.
Electronic cigarettes and nicotine clinical pharmacology (2014)

Knowledge about e-cigarette nicotine pharmacology remains limited. Because a user's e-cigarette experience may significantly impact nicotine delivery, future nicotine pharmacokinetic and pharmacodynamic studies should be conducted in experienced users to accurately assess the products' impact on public health.
Chemoimmunotherapy with hyper‐CVAD plus rituximab for the treatment of adult Burkitt and Burkitt‐type lymphoma or acute lymphoblastic leukemia (2006)

The addition of rituximab to hyper-CVAD may improve outcome in adult BL or B-ALL, particularly in elderly patients.
Cimbiosys: a platform for content-based partial replication (2009)

Increasingly people manage and share information across a wide variety of computing devices from cell phones to Internet services. Selective replication of content is essential because devices, especially portable ones, have limited resources for storage and communication. Cimbiosys is a novel replication platform that permits each device to define its own content-based filtering criteria and to share updates directly with other devices. In the face of fluid network connectivity, redefinable content filters, and changing content, Cimbiosys ensures two properties not achieved by previous systems. First, every device eventually stores exactly those items whose latest version matches its filter. Second, every device represents its replication-specific metadata in a compact form, with state proportional to the number of devices rather than the number of items. Such compact representation results in low data synchronization overhead, which permits ad hoc replication between newly encountered devices and frequent replication between established partners, even over low bandwidth wireless networks. 1