gebhart/patrepeval huggingface dataset:
Plasmid content in Yersinia pestis strains of different origin (1990)

Plasmid content in 242 Yersinia pestis strains from various natural plague foci of the U.S.S.R. and other countries was studied. Of these strains, 172 (71%) were shown to carry three plasmids described previously of about 6, 45-50 and 60 MDa, respectively. Twenty strains (8%) from different foci harboured additional cryptic plasmids, most often of about 20 mDa in size. Plasmid pPst displayed considerable constancy of its molecular mass. On the contrary, size variations of pCad (45-49 MDa) and, especially, pFra (60-190 MDa) were found. Molecular mass of these plasmids correlated with the host strain origin.
Mutations in the Phosphatidylinositol-3-Kinase Pathway Predict for Antitumor Activity of the Inhibitor PX-866 whereas Oncogenic Ras Is a Dominant Predictor for Resistance (2008)

The novel phosphatidylinositol-3-kinase (PI3K) inhibitor PX-866 was tested against 13 experimental human tumor xenografts derived from cell lines of various tissue origins. Mutant PI3K (PIK3CA) and loss of PTEN activity were sufficient, but not necessary, as predictors of sensitivity to the antitumor activity of the PI3K inhibitor PX-866 in the presence of wild-type Ras, whereas mutant oncogenic Ras was a dominant determinant of resistance, even in tumors with coexisting mutations in PIK3CA. The level of activation of PI3K signaling measured by tumor phosphorylated Ser(473)-Akt was insufficient to predict in vivo antitumor response to PX-866. Reverse-phase protein array revealed that the Ras-dependent downstream targets c-Myc and cyclin B were elevated in cell lines resistant to PX-866 in vivo. Studies using an H-Ras construct to constitutively and preferentially activate the three best-defined downstream targets of Ras, i.e., Raf, RalGDS, and PI3K, showed that mutant Ras mediates resistance through its ability to use multiple pathways for tumorigenesis. The identification of Ras and downstream signaling pathways driving resistance to PI3K inhibition might serve as an important guide for patient selection as inhibitors enter clinical trials and for the development of rational combinations with other molecularly targeted agents.
The noisy-leaky integrator model implemented using pRAMs (2003)

The theory of the noisy-leaky integrator model of the neuron is presented, and its implementation using pRAMs (probabilistic RAMs) is discussed. Such a neuron is capable of storing temporal patterns of activity within it. With such an ability, a network can be expected to learn about the structure of its environment and thus to exhibit cognitive capacity. The architecture of a noisy-leaky integrator using pRAMs is described with its implementation using digital hardware. The refractory period and synaptic delay times may be modeled, and the level of noise in the system can be adjusted.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Molecular genetic characterization of XRCC4 function (1997)

XRCC4 is a generally expressed protein of 334 amino acids that is involved in the repair of DNA double-strand breaks and in V(D)J recombination, but its function is unknown. In this study, we have used a mutational approach and the yeast two-hybrid method to perform an initial characterization of this protein. We show that the XRCC4 protein is located in the nucleus. We also demonstrate that several potential phosphorylation sites are not required for XRCC4 function in a transient V(D)J recombination assay. In addition, we show that XRCC4 forms a homodimer in vivo with the homodimerization domain being located within amino acids 115-204. Finally, we define a core domain of XRCC4 that functions in V(D)J recombination and comprises amino acids 18-204. Potential functions of XRCC4 are discussed.
Linkage Studies of a Missouri Kindred with Autosomal Dominant Spondyloepimetaphyseal Dysplasia (SEMD) Indicate Genetic Heterogeneity (1997)

A four-generation kindred (14 affected and 10 unaffected members) from Missouri, U.S.A. in which spondyloepimetaphyseal dysplasia (SEMD) had been inherited as an autosomal dominant disorder was investigated for linkage to 13 candidate loci: COL2AI, COL9AI, COL9A2, COL9A3, COL10A1, COL11A1, COL11A2, PSACH, FGFR3, decorin, CRTL1, COMP, and PTHRP. Mutations of COL2A1, COL9A2, COL10, and FGFR3 have been reported previously in the Strudwick type of SEMD, multiple epiphyseal dysplasia type 2 (EDM2), the Schmid type of metaphyseal dysplasia, and in achondroplasia, respectively, and the pseudoachondroplasia (PSACH) locus has been mapped to chromosome 19p12. In addition, mutations in COL9 and COL11A are associated with murine forms of degenerative joint disease and chondroplasia, respectively. The family proved informative for 12 of the 13 loci and was uninformative at the decorin locus. Linkage between this form of SEMD, designated the Missouri variant, SEMDMO, and the 12 informative candidate loci was excluded (LOD scores < -2.00 at theta = 0.005 to 0.15), thereby indicating further genetic heterogeneity in these inherited disorders of bone and cartilage development.
"The write stuff": security issues for customer network management of broadband data services (2002)

Customer network management (CNM) services are being offered for public, broadband, data services such as frame relay, switched multi-megabit data service (SMDS), and cell relay services. Customer network management for these public services is intended to extend the customer's capability to manage their communications network from the local area into the wide area. Security features such as access control and authentication are critical to both the CNM service provider and the customer. This is especially true when offering the "write" (i.e., modify) capability. SNMP version 2 (SNMPv2) promises a useful, yet challenging, set of security features for supporting the write capability. The paper describes the security issues associated with CNM and how SNMPv2 and other tools are used to tackle these issues.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
MICROBIAL PRODUCTION OF L-LYSINE (1969)

Some prototrophic revertants from a homoserine auxotroph of Brevibacterium flavum No. 2247 (ATCC No. 14067), which grew as rapidly as No. 2247 in a minimal glucose-salts medium produced large amounts of lysine, whereas No. 2247, the original strain, produced little. The cell growth in a minimal medium of revertant strain, S-20, which produced 23g of L-lysine monohydrochloride from 100g of glucose, was completely inhibited by the addition of 10μg/ml of L-methionine (or L-threonine) and recovered by the further addition of L-threonine (or L-methionine). It was concluded that much lower homoserine dehydrogenase activity of S-20 than that of No. 2247 was the primary result of the mutation, which might cause apparent increase in the sensitivity of the cell growth to inhibition by L-methionine (or L-threonine) and further production of lysine through lowering of the threonine pool inside the cell.Some of the threonine auxotrophs derived from such revertant strains as S-20 produced much larger amounts of lysine than the parental strains or simple threonine auxotrophs directly derived from No. 2247. The amount of lysine produced was nearly equal to that of homoserine auxotroph, H-1013, derived from No. 2247. By-production of homoserine was small in contrast with the simple threonine auxotrophs as expected. These threonine auxotrophs were still sensitive to higher concentration of L-threonine.
The Effect of Pectinase on the Bubble Fractionation of Invertase from α-Amylase (1997)

Fermentation broth normally contains many extracellular enzymes of industrial interest. To separate such enzymes on-line could be useful in reducing the cost of recovery as well as in keeping their yield at a maxi­mum level by minimizing enzyme degradation from broth proteases (either the desired enzymes or the proteases could be removed selec­tively or both removed together and then separated). Several large-scale separation methods are candidates for such on-line recovery such as ultrafiltration, precipitation, and two-phase partitioning. Another promising technique for on-line recovery is adsorptive bubble fractiona­tion, the subject of this study. Bubble fractionation, like ultrafiltration, does not require contaminating additives and can complement ultrafil­tration by preconcentrating the enzymes using the gases normally pre­sent in a fermentation process. A mixture of enzymes in an aqueous bubble solution can, in principle, be separated by adjusting the pH of that solution to the isoelectric point (pI) of each enzyme as long as the enzymes have different pls. The model system investigated here is com­prised of three enzyme separations and the problem is posed as the effect of pectinase (a charged enzyme) on the bubble fractionation of invertase (a relatively hydrophilic enzyme) from α-amylase (a relatively hydrophobic enzyme). The primary environmental variable studied, therefore, is the pH in the batch bubble fractionation column. Air was used as the carrier gas. This prototype mixture exemplifies an aerobic fungal fermentation process for producing enzymes. The enzyme concentration here is mea­sured as total protein concentration by the Coomassie Blue (Bradford) solution method (1), both as a function of time and column position for each batch run. Since, from a previous study (2), it was found that invertase and α-amylase in a two-enzyme system can be partially separated in favor of one vs the other at two different pHs (pH 5.0 and 9.0) with significant separation ratios, emphasis is placed on the effect of pecti­nase at these pHs. In this study, the addition of pectinase reduced the total separation ratio of the α-amylase-invertase mixture at both pHs.
Phase-dependent neuronal coding of objects in short-term memory (2009)

The ability to hold multiple objects in memory is fundamental to intelligent behavior, but its neural basis remains poorly understood. It has been suggested that multiple items may be held in memory by oscillatory activity across neuronal populations, but yet there is little direct evidence. Here, we show that neuronal information about two objects held in short-term memory is enhanced at specific phases of underlying oscillatory population activity. We recorded neuronal activity from the prefrontal cortices of monkeys remembering two visual objects over a brief interval. We found that during this memory interval prefrontal population activity was rhythmically synchronized at frequencies around 32 and 3 Hz and that spikes carried the most information about the memorized objects at specific phases. Further, according to their order of presentation, optimal encoding of the first presented object was significantly earlier in the 32 Hz cycle than that for the second object. Our results suggest that oscillatory neuronal synchronization mediates a phase-dependent coding of memorized objects in the prefrontal cortex. Encoding at distinct phases may play a role for disambiguating information about multiple objects in short-term memory.
Transduction of the Chinese hamster ovary aprt gene by herpes simplex virus (1984)

The Chinese hamster ovary adenine phosphoribosyl transferase gene (aprt) was reengineered to be flanked by sequences from the thymidine kinase (tk) gene of herpes simplex virus. This construct was cotransfected with DNA from herpes simplex virus type 1, and after 3 days, virus was harvested and Tk- plaques were selected after the virus was plated on Tk- cells in the presence of bromodeoxycytosine. Recombinant viruses were identified by dot-blot hybridization, and the arrangement of aprt and tk sequences were determined by Southern blot hybridization. Analysis of the recombinants revealed that acquisition of aprt sequences resulted from insertional inactivation of the tk locus as a consequence of homology-based recombination. Recombination was precise, as evidenced by the failure to detect plasmid sequences or the synthetic restriction endonuclease sites that bounded the mutant tk gene in the aprt-tk construct. Infection of Aprt- mouse or Chinese hamster ovary cells with UV-irradiated virus and selection in medium containing azaserine and adenine resulted in the survival of numerous colonies that stably express the aprt gene. Transformed cells synthesized an aprt mRNA that is identical to wild-type mRNA as determined by Northern blot and S1 nuclease analyses. Cells lytically infected with the recombinant virus do not appear to transcribe the aprt gene. Thus, infected cells differentiate between virus and foreign promoters even when a cellular gene is cis to the virus chromosome.
Compatibility of common MCM-D dielectric with scanning laser ablation via generation processes (1993)

The use of a scanning laser ablation-based via generation process for MCM-D substrate fabrication is described. The robustnesses of a variety of thin (1-5- mu m-thick) conformal metal masking layers were compared by static exposure in a computer controlled XeCl excimer laser exposure tool. The relative ablation rates of commercially available dielectric materials were compared for a range of fluences from 0 to 600 mJ/cm/sup 2/ using static excimer laser exposure. Based on process limits established by these static test results, generic scanning laser ablation (SLA) processing parameters were established which were successfully used for the fabrication of vias in low-stress, acetylene terminated, and fluorinated polyimides as well as benzocyclobutene (BCB) and polyphenylquinoxalines (PPQs). The extent of soot accumulation during SLA was dependent on the conformal metal masking layer used. Excessive accumulation of soot resulted in mask cracking around the vias. The use of helium as a process gas was found to reduce dramatically the amount of soot that accumulated and consequently to eliminate soot-related mask damage.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Reactive Oxygen Species are Involved in Nitric Oxide-Induced Apoptosis of Neurons (2001)

With redox-sensitive fluorescene probes DCFH-DA and DHR123, the formation of cytosolic and intramitochondrial reactive oxygen species (ROS) inside immature rat cerebellar granule cells during the apoptosis induced by nitric oxide donor S-nitroso-N-acetyl-pennicillamine (SNAP) was monitoredby laser confocal scanning microscopy. The cytosolic and intramitochondrial ROS increase significantly after 0.5mmol/L SNAP treatment for 1 h. Pre-treatment with the nitric oxide scavenger hemoglobin can effectively inhibit the formation of cytosolic and intramitochondrial ROS and protect neurons from apoptosis. Adding glutathione can also protect neurons from apoptosis, and the cytotoxity of nitric oxide increases significantly while the synthesis of glutathione is inhibited. The results indicated that ROS might be involved in NO-induced apoptosis in neural cells and glutathione might be the endogenesis antioxidant to protect neurons from oxidative injury.
X-ray scatter data for diagnostic radiology (1978)

Using electrochemical and in situ luminescence measurements we show that ferricyanide ions are reduced at n-type ZnSe electrodes by hole injection into the valence band of the semiconductor. At negative potentials the holes recombine with electrons and electroluminescence is observed. At the open-circuit potential, the injected holes are used for the oxidation and dissolution of the semiconductor. This electroless etching reaction is under mixed diffusion/kinetic control at 20°C, but becomes diffusion controlled at higher temperature. U7 - Export Date: 2 August 2010 U7 - Source: Scopus
Effects of obesity, energy restriction and neutering on the faecal microbiota of cats (2017)

Surveys report that 25-57 % of cats are overweight or obese. The most evinced cause is neutering. Weight loss often fails; thus, new strategies are needed. Obesity has been associated with altered gut bacterial populations and increases in microbial dietary energy extraction, body weight and adiposity. This study aimed to determine whether alterations in intestinal bacteria were associated with obesity, energy restriction and neutering by characterising faecal microbiota using 16S rRNA gene sequencing in eight lean intact, eight lean neutered and eight obese neutered cats before and after 6 weeks of energy restriction. Lean neutered cats had a bacterial profile similar to obese rodents and humans, with a greater abundance (P<0·05) of Firmicutes and lower abundance (P<0·05) of Bacteroidetes compared with the other groups. The greater abundance of Firmicutes in lean neutered cats was due to a bloom in Peptostreptococcaceae. Obese cats had an 18 % reduction in fat mass after energy restriction (P<0·05). Energy reduction was concurrent with significant shifts in two low-abundance bacterial genera and trends in four additional genera. The greatest change was a reduction in the Firmicutes genus, Sarcina, from 4·54 to 0·65 % abundance after energy restriction. The short duration of energy restriction may explain why few bacterial changes were observed in the obese cats. Additional work is needed to understand how neutering, obesity and weight loss are related to changes in feline microbiota and how these microbial shifts affect host physiology.
The Effective Fine-Structure Constant of Freestanding Graphene Measured in Graphite (2010)

Electrons in graphene behave like Dirac fermions, permitting phenomena from high-energy physics to be studied in a solid-state setting. A key question is whether or not these fermions are critically influenced by Coulomb correlations. We performed inelastic x-ray scattering experiments on crystals of graphite and applied reconstruction algorithms to image the dynamical screening of charge in a freestanding graphene sheet. We found that the polarizability of the Dirac fermions is amplified by excitonic effects, improving screening of interactions between quasiparticles. The strength of interactions is characterized by a scale-dependent, effective fine-structure constant, α(g)* (k,ω), the value of which approaches 0.14 ± 0.092 ~ 1/7 at low energy and large distances. This value is substantially smaller than the nominal α(g) = 2.2, suggesting that, on the whole, graphene is more weakly interacting than previously believed.
High-Intensity Focused Ultrasound for <i>ex Vivo</i> Kidney Tissue Ablation: Influence of Generator Power and Pulse Duration (2004)

Background and Purpose: The therapeutic application of noninvasive tissue ablation by high-intensity focused ultrasound (HIFU) requires precise physical definition of the focal size and determination of control parameters. The objective of this study was to measure the extent of ex-vivo porcine kidney tissue ablation at variable generator parameters and to identify parameters to control lesion size. Materials and Methods: The ultrasound waves generated by a cylindrical piezoceramic element (1.04 MHz) were focused at a depth of 100 mm using a parabolic reflector (diameter 100 mm). A needle hydrophone was used to measure the field distribution of the sound pressure. The morphology and extent of tissue necrosis were examined at generator powers of up to 400 W (Pel) and single pulse durations of as long as 8 seconds. Results: The two-dimensional field distribution resulted in an approximately ellipsoidal focus of 32 × 4 mm (–6 dB). A sharp demarcation between coagulation necrosis and intact tissue was observed. Lesion size was controlled by both the variation of generator power and the pulse duration. At a constant pulse duration of 2 seconds, a generator power of 100 W remained below the threshold doses for inducing a reproducible lesion. An increase in power to as high as 400 W induced lesions with average dimensions of as much as 11.2 × 3 mm. At constant total energy (generator power × pulse duration), lesion size increased at higher generator power. Conclusions: This ultrasound generator can induce defined and reproducible necrosis in ex-vivo kidney tissue. Lesion size can be controlled by adjusting the generator power and pulse duration. Generator power, in particular, turned out to be a suitable control parameter for obtaining a lesion of a defined size.
Linking the Visions (2000)

It is a major tendency of legal studies in our time to focus upon questions of general social policy, with argument centered on which theory or methodology ought to determine such matters. My own attention has been differently focused, on the nature and quality of legal thoughts itself, and of legal expression. It is to these matters that the work I do with the humanities – literature, classics, philosophy, and translation – many speaks.
High-frequency, spin-label EPR of nonaxial lipid ordering and motion in cholesterol-containing membranes (1998)

The EPR spectra of spin-labeled lipid chains in fully hydrated bilayer membranes of dimyristoyl phosphatidylcholine containing 40 mol % of cholesterol have been studied in the liquid-ordered phase at a microwave radiation frequency of 94 GHz. At such high field strengths, the spectra should be optimally sensitive to lateral chain ordering that is expected in the formation of in-plane domains. The high-field EPR spectra from random dispersions of the cholesterol-containing membranes display very little axial averaging of the nitroxide g-tensor anisotropy for lipids spin labeled toward the carboxyl end of the sn-2 chain (down to the 8-C atom). For these positions of labeling, anisotropic 14N-hyperfine splittings are resolved in the gzz and gyy regions of the nonaxial EPR spectra. For positions of labeling further down the lipid chain, toward the terminal methyl group, the axial averaging of the spectral features systematically increases and is complete at the 14-C atom position. Concomitantly, the time-averaged <Azz> element of the 14N-hyperfine tensor decreases, indicating that the axial rotation at the terminal methyl end of the chains arises from correlated torsional motions about the bonds of the chain backbone, the dynamics of which also give rise to a differential line broadening of the 14N-hyperfine manifolds in the gzz region of the spectrum. These results provide an indication of the way in which lateral ordering of lipid chains in membranes is induced by cholesterol.
Probability of error for diversity combining in DS CDMA systems with synchronization errors (1998)

Abstract An efficient series that is used to calculate the probability of error for a BPSK modulated DS CDMA system with chip timing and carrier phase errors in a slowly fading, multipath channel is derived. The receiver is assumed to be a coherent RAKE receiver. Three types of diversity schemes are considered: selection diversity, equal gain diversity combining and maximal ratio diversity combining. The error probability derivation does not resort to the widely used Gaussian approximation for the intersymbol interference and multiple access interference and is very accurate. The derived series for probability of error calculations is used to assess the reduction in the system capacity due to different levels of synchronization errors. For all three diversity combining schemes considered, the degradation in the system performance is expressed as an effective reduction in the system processing gain. Systems of 1.25 MHz, 5 MHz and 10 MHz are considered for different number of diversity branches and it is shown that the percentage reduction in the system capacity due to synchronization errors is approximately the same for all these systems.