gebhart/patrepeval huggingface dataset:
Edgeless silicon sensors for Medipix-based large-area X-ray imaging detectors (2011)

Some X-ray imaging applications demand sensitive areas exceeding the active area of a single sensor. This requires a seamless tessellation of multiple detector modules with edgeless sensors. Our research is aimed at minimising the insensitive periphery that isolates the active area from the edge. Reduction of the edge-defect induced charge injection, caused by the deleterious effects of dicing, is an important step. We report on the electrical characterisation of 300 μm thick edgeless silicon p+-ν-n+ diodes, diced using deep reactive ion etching. Sensors with both n-type and p-type stop rings were fabricated in various edge topologies. Leakage currents in the active area are compared with those of sensors with a conventional design. As expected, we observe an inverse correlation between leakage-current density and both the edge distance and stop-ring width. From this correlation we determine a minimum acceptable edge distance of 50 μm. We also conclude that structures with a p-type stop ring show lower leakage currents and higher breakdown voltages than the ones with an n-type stop ring. <br/><br/>
High‐throughput DNA sequencing – concepts and limitations (2010)

Recent advances in DNA sequencing have revolutionized the field of genomics, making it possible for even single research groups to generate large amounts of sequence data very rapidly and at a substantially lower cost. These high-throughput sequencing technologies make deep transcriptome sequencing and transcript quantification, whole genome sequencing and resequencing available to many more researchers and projects. However, while the cost and time have been greatly reduced, the error profiles and limitations of the new platforms differ significantly from those of previous sequencing technologies. The selection of an appropriate sequencing platform for particular types of experiments is an important consideration, and requires a detailed understanding of the technologies available; including sources of error, error rate, as well as the speed and cost of sequencing. We review the relevant concepts and compare the issues raised by the current high-throughput DNA sequencing technologies. We analyze how future developments may overcome these limitations and what challenges remain.
Mass Spectrometry of Peptides (2024)

INTRODUCTION. PREFACE. SECTION I: IONIZATION METHODS. 252Cf PLASMA DESORPTION METHODS. Fundamental Aspects of Protein Mass Spectrometry Using 252-Californium Plasma Desorption. Plasma Desorption Mass Spectrometry of Peptides and Peptide Conjugates. The Analysis of Synthetic Peptides and Proteins. Analysis of Peptides and Proteins by Plasma Desorption Mass Spectrometry. LASER-INDUCED MULTIPHOTON IONIZATION. Laser-Induced Multiphoton Ionization of Peptides in Supersonic Beam/Mass Spectrometry. SECTION II: INSTRUMENTAL DEVELOPMENTS. MAGNETIC SECTOR INSTRUMENTS. The Molecular Weight Determination of Large Peptides by Magnetic Sector Mass Spectrometry. Four-Sector Tandem Mass Spectrometry of Peptides. QUADRUPOLE FOURIER TRANSFORM. Peptide Sequence Analysis by Triple Quadrupole and Quadrupole Fourier Transform Mass Spectrometry. TIME-OF-FLIGHT INSTRUMENTS. Correlation Measurements in a Reflecting Time-of-Flight Mass Spectrometer. SECTION III: ANALYSIS OF PEPTIDES. SAMPLE PREPARATION. Sample Preparation and Matrix Selection for Analysis of Peptides by FAB and Liquid SIMS. LC-MS ANALYSIS. On-Line Methods for Peptide Analysis by Continuous-Flow FABMS. ANALYSIS OF PROTEIN PRODUCTS. Investigation of Amino Acid Mutation by High Resolution Mass Spectrometry. The Mass Spectral Analysis of Hemoglobin Variants. PROTEIN CROSS-LINKAGES. Detection and Location of Disulfide Bonds in Proteins by Mass Spectrometry. PEPTIDE INTERACTIONS WITH METAL IONS. Tandem Mass Spectrometry for Determining the Amino Acid Sequence of Cyclic Peptides and for Assessing Interactions of Peptides and Metal Ions. PERMETHYLATED PEPTIDES. Analysis of Permethylated Peptides by Mass Spectrometry. NEUROPEPTIDES. Applications of Mass Spectrometry for Characterization of Neuropeptides. Peptide-Charting Applied to Studies of Precursor Processing in Endocrine Tissues. QUANTIFICATION OF NEUROPEPTIDES. Mass Spectrometry of Biologically Important Neuropeptides
RAP1 protein activates and silences transcription of mating-type genes in yeast. (1991)

RAP1 is a sequence-specific DNA-binding protein essential for cell growth. The occurrence of RAP1-binding sites in many promoter regions, the mating-type gene silencer elements, and telomeres suggests that RAP1 has multiple functions in the cell. To assess its role in transcription, temperature-sensitive mutations in RAP1 were generated. Analysis of rap1ts strains provides evidence that RAP1 functions in both transcriptional activation and silencing of mating-type genes. Several observations indicate that rap1ts strains are defective in the expression of MAT alpha, whose upstream activation sequence (UAS) contains a RAP1-binding site. At nonpermissive temperatures, decreases in MAT alpha steady-state transcript levels can be detected in MAT alpha rap1ts strains. Furthermore, these strains are deficient in alpha-pheromone production and simultaneously express at least two alpha-specific genes. These phenotypes can be reversed by replacing the RAP1-binding site at MAT alpha with a binding site for the GAL4 transcriptional activator. Certain rap1ts alleles have an opposite effect on the silent mating-type locus HMR, which becomes partially derepressed at nonpermissive temperatures.
Evaluation of Pericranial Myofascial Nociception by Pressure Algometry. Reproducibility and Factors of Variation (1992)

Pressure pain detection threshold and pressure pain tolerance threshold were measured in the temples and on the fingers in 40 healthy volunteers, equally distributed as to sex and handedness. Lower pressure pain thresholds were found over the temporal muscle than in a neighbouring temporal location without interposed myofascial tissue (p less than 0.001), indicating that nociception from myofascial tissue contributes to the pressure pain threshold. Pressure pain tolerance was more reproducible within the individual subject but differed more between subjects than pressure pain detection. Pressure pain thresholds were higher on the fingers than in the temples (p less than 10(-5)) and, in general, thresholds were higher in males than in females (p = 0.02-0.09). Finally, pressure pain thresholds were lateralized in dextrals but not in sinistrals. The information that can be obtained from pressure pain detection and tolerance thresholds is discussed and examination of both threshold types is recommended in future studies.
Blood Transfusion in Elderly Patients with Acute Myocardial Infarction (2001)

Blood transfusion is associated with a lower short-term mortality rate among elderly patients with acute myocardial infarction if the hematocrit on admission is 30.0 percent or lower and may be effective in patients with a hematocrit as high as 33.0 percent on admission.
Dew nucleation and growth (2006)

Dew is the condensation of water vapor into liquid droplets on a substrate. It is characterized by an initial heterogeneous nucleation on a substrate and a further growth of droplets. The presence of a substrate that geometrically constrains the growth is the origin of the peculiarities and richness of the phenomenon. A key point is the drop interaction through drop fusion or coalescence, which leads to scaling in the growth and gives universality to the process. As a matter of fact, growth dynamics are only dependent on substrate and drop dimensionality. Coalescence events lead to temporal and spatio-temporal fluctuations in the substrate coverage, drop configuration, etc., which give rise to a very peculiar dynamics. When the substrate is a liquid or a liquid crystal, the drop pattern can exhibit special spatial order, such as crystalline, hexatic phases and fractal contours. Condensation on a solid substrate near its melting point can make the drop jump. The applications of monitoring dew formation are manifold. Examples can be found in medicine (sterilization process), agriculture (green houses) and hydrology (production of drinkable water).
FK506 is neuroprotective in a model of antiretroviral toxic neuropathy (2002)

Antiretroviral toxic neuropathy is the most common neurological complication of human immunodeficiency virus infection. This painful neuropathy not only affects the quality of life of human immunodeficiency virus-infected patients but also severely limits viral suppression strategies. We have developed an in vitro model of this toxic neuropathy to better understand the mechanism of neurotoxicity and to test potential neuroprotective compounds. We show that among the dideoxynucleosides, ddC appears to be the most neurotoxic, followed by ddI and then d4T. This reflects their potency in causing neuropathy. AZT, which does not cause a peripheral neuropathy in patients, does not cause significant neurotoxicity in our model. Furthermore, in this model, we show that the immunophilin ligand FK506 but not cyclosporin A prevents the development of neurotoxicity by ddC, as judged by amelioration of ddC-induced "neuritic pruning," neuronal mitochondrial depolarization, and neuronal necrotic death. This finding suggests a calcineurin-independent mechanism of neuroprotection. As calcineurin inhibition underlies the immunosuppressive properties of these clinically used immunophilin ligands, this holds promise for the neuroprotective efficacy of nonimmunosuppressive analogs of FK506 in the prevention or treatment of antiretroviral toxic neuropathy.
Fungal Elicitor-Mediated Responses in Pine Cell Cultures (1992)

Phenylalanine ammonia-lyase (PAL, EC 4.3.1.5) is involved in the lignification of pine suspension cultures in response to an elicitor prepared from an ectomycorrhizal fungus. To elucidate the molecular basis of this response, PAL was purified to homogeneity from jack pine (Pinus banksiana) suspension cultures using anion-exchange and chromatofocussing fast protein liquid chromatography. Physical characterization of the enzyme revealed that pine PAL was similar to PAL from other plant sources. Pine PAL had a pH optimum of 8.8, an isoelectric point of 5.75, and a native molecular mass of 340 kilodaltons. The enzyme appears to be a tetramer composed of 77 kilodalton subunits. Chromatographic and western blot analyses were used to identify possible isoenzymic changes in pine PAL in response to elicitation and to determine the nature of the increase in PAL activity associated with inducible lignification in these cultures. Only one species of PAL was detected in P. banksiana cell cultures and increased quantities of this protein were correlated with the enhanced enzyme activity observed in elicited cultures. P. banksiana PAL was not feedback-inhibited by a wide range of phenolic compounds at micromolar concentrations, including the reaction product cinnamic acid. Our data suggest that a different set of metabolic and molecular controls must be in place for the regulation of PAL in pine.
Expression and functional role of dipeptidyl peptidase IV (CD26) on human natural killer cells. (1995)

The expression and functional role of dipeptidyl peptidase IV (DP IV, CD26, EC 3.4.14.5) was studied on human natural killer (NK) cells. Here we show that freshly isolated NK cells do express only low amounts of DP IV. However, after IL-2 stimulation of NK cells (70% purity) surface DP IV expression was significantly increased in a subpopulation (30%) of these cells. Specific DP IV inhibitors (Lys-[Z-(NO2)]-piperidide, Lys-[Z(NO2)]-thiazolidide) and polyclonal antibodies directed against the ectopeptidase suppressed DNA synthesis and cell cycle progression of NK cells. The natural cytotoxic activity of DP IV+ CD56+ cells was found unchanged in comparison to those of DP IV- CD56+ cells. DP IV inhibitors had no effect on the natural cytotoxicity of mononuclear cells. From these data we conclude that DP IV is involved in the regulation of proliferation of NK cells, whereas natural cytotoxicity seems to be regulated independently.
Simultaneous Gravel Packing and Filter-Cake Cleanup With Shunt Tubes in Openhole Completions: A Case History From the Gulf of Mexico (2002)

Summary A case history from the Gulf of Mexico is presented in this paper for drilling and completing a horizontal openhole well with simultaneous gravel-packing and filter-cake cleanup with shunt tube screens. The openhole section was 277 ft, deviated from 85 to 90°. The producing sand was normally pressured. The drill-in fluid and gravel-pack carrier/filter-cake removal fluid selection was based upon extensive laboratory testing consisting of cleanup, compatibility, and sand-suspension-capability tests. A reservoir drill-in fluid comprising brine, starch, biopolymer, and sized calcium carbonate was chosen for the project. A viscoelastic surfactant (VES) fluid in a chelating agent solution (CAS) containing an enzyme breaker to simultaneously attack both the starch and CaCO3 components of the filter cake was identified as the best carrier fluid for the gravel pack. Laboratory test results, field procedures, and production results are discussed in detail, along with the decision process that resulted in the selected drilling and completion plan.
The central part of the mouse immunoglobulin κ locus (1999)

At the present state of analysis the central part of the kappa locus comprises four contigs of together 1.2 Mb and contains 55 Vkappa genes. It is flanked by the 3' part of the locus with 22 Vkappa genes in 0.4 Mb (T. Kirschbaum et al., Eur. J. Immunol. 1998. 28: 1458-1466) and the 5' part with 63 Vkappa genes in six contigs of together 1.5 Mb (F. Röschenthaler et al., accompanying report). The 5' and the central regions have one large contig in common. A part of the central region is linked to the 3' region resulting in a 1.1-Mb contig. The structure of the contigs was established mainly by the analysis of overlapping cosmid clones derived from genomic DNA and yeast and bacterial artificial chromosomes (YACs and BACs) and by PCR techniques. Pulsed-field gel electrophoresis of YAC digests indicated that three gaps between the contigs of the central region are 10-40 kb in size, comprising together about 90 kb. Internal duplications in this part of the locus and rearranged YACs were the major problems of the structural work. Structural details are to be found on the Internet at http://www.med.uni-muenchen.de/biochemie/zach au/kappa.htm. In a concluding section of the report the mouse kappa locus is compared to the human one and some aspects of the evolution of the kappa locus are discussed.
Acyl CoA profiles of transgenic plants that accumulate medium‐chain fatty acids indicate inefficient storage lipid synthesis in developing oilseeds (2002)

Several Brassica napus lines transformed with genes responsible for the synthesis of medium- or long-chain fatty acids were examined to determine limiting factor(s) for the subsequent accumulation of these fatty acids in seed lipids. Examination of a decanoic acid (10:0) accumulating line revealed a disproportionately high concentration of 10:0 CoA during seed development compared to long-chain acyl CoAs isolated from the same tissues, suggesting that poor incorporation of 10:0 CoA into seed lipids limits 10:0 fatty acid accumulation. This relationship was also seen for dodecanoyl (12:0) CoA and fatty acid in a high 12:0 line, but not for octadecanoic (18:0) CoA and fatty acid in a high 18:0 line. Comparison of 10:0 CoA and fatty acid proportions from seeds at different developmental stages for transgenic B. napus and Cuphea hookeriana, the source plant for the medium-chain thioesterase and 3-ketoacyl-ACP synthase transgenes, revealed that C. hookeriana incorporates 10:0 CoA into seed lipids more efficiently than transgenic B. napus. Furthermore, beta-oxidation and glyoxylate cycle activities were not increased above wild type levels during seed development in the 8:0/10:0 line, suggesting that lipid catabolism was not being induced in response to the elevated 10:0 CoA concentrations. Taken together, these data suggest that transgenic plants that are engineered to synthesize medium-chain fatty acids may lack the necessary mechanisms, such as specific acyltransferases, to incorporate these fatty acids efficiently into seed lipids.
Optimizing public-key encryption for wireless clients (2003)

Providing acceptable levels of security imposes significant computational requirements on wireless clients, servers, and network elements. These requirements are often beyond the modest processing capabilities and energy (battery) resources available on wireless clients. The relatively small sizes of wireless data transactions imply that public-key encryption algorithms dominate the security processing requirements. We propose techniques to improve the computational efficiency of public-key encryption algorithms. We focus on the modular exponentiation based encryption/decryption employed in many popular public-key algorithms. We study an extensive suite of algorithmic optimizations to the basic modular exponentiation algorithm and new advanced techniques. The proposed algorithmic optimizations lead to an "algorithm design space", across which performance varies significantly (over an order-of-magnitude). We evaluated the proposed algorithmic optimization techniques by obtaining processing times for the SSL (secure sockets layer) handshake protocol on a state-of-the-art embedded processor by using the optimal algorithm configuration and a popular conventional algorithm configuration. The results demonstrate that the optimum algorithm configuration leads to a 5.7/spl times/ improvement in SSL handshake protocol processing times. The proposed techniques are complementary to, and can be applied in conjunction with, improvements in security mechanisms and protocols, new hardware architectures, and improvements in silicon technologies.
Mapping of a Gene for Parkinson's Disease to Chromosome 4q21-q23 (1996)

Parkinson's disease (PD) is the second most common neurodegenerative disorder after Alzheimer's disease, affecting approximately 1 percent of the population over age 50. Recent studies have confirmed significant familial aggregation of PD and a large number of large multicase families have been documented. Genetic markers on chromosome 4q21-q23 were found to be linked to the PD phenotype in a large kindred with autosomal dominant PD, with a Zmax = 6.00 for marker D4S2380. This finding will facilitate identification of the gene and research on the pathogenesis of PD.
Niacin Reduces Atherosclerosis Development in APOE*3Leiden.CETP Mice Mainly by Reducing NonHDL-Cholesterol (2013)

Niacin decreases atherosclerosis development mainly by reducing nonHDL-cholesterol with modest HDL-cholesterol-raising and additional anti-inflammatory effects. The additive effect of niacin on top of simvastatin is mostly dependent on its nonHDL-cholesterol-lowering capacities. These data suggest that clinical beneficial effects of niacin are largely dependent on its ability to lower LDL-cholesterol on top of concomitant lipid-lowering therapy.
Crystal Structure of the Ribonuclease H Domain of HIV-1 Reverse Transcriptase (1991)

The crystal structure of the ribonuclease (RNase) H domain of HIV-1 reverse transcriptase (RT) has been determined at a resolution of 2.4 A and refined to a crystallographic R factor of 0.20. The protein folds into a five-stranded mixed beta sheet flanked by an asymmetric distribution of four alpha helices. Two divalent metal cations bind in the active site surrounded by a cluster of four conserved acidic amino acid residues. The overall structure is similar in most respects to the RNase H from Escherichia coli. Structural features characteristic of the retroviral protein suggest how it may interface with the DNA polymerase domain of p66 in the mature RT heterodimer. These features also offer insights into why the isolated RNase H domain is catalytically inactive but when combined in vitro with the isolated p51 domain of RT RNase H activity can be reconstituted. Surprisingly, the peptide bond cleaved by HIV-1 protease near the polymerase-RNase H junction of p66 is completely inaccessible to solvent in the structure reported here. This suggests that the homodimeric p66-p66 precursor of mature RT is asymmetric with one of the two RNase H domains at least partially unfolded.
Learning-Induced Physiological Memory in Adult Primary Auditory Cortex: Receptive Field Plasticity, Model, and Mechanisms (1998)

It is well established that the functional organization of adult sensory cortices, including the auditory cortex, can be modified by deafferentation, sensory deprivation, or selective sensory stimulation. This paper reviews evidence establishing that the adult primary auditory cortex develops physiological plasticity during learning. Determination of frequency receptive fields before and at various times following aversive classical conditioning and instrumental avoidance learning in the guinea pig reveals increased neuronal responses to the pure tone frequency used as a conditioned stimulus (CS). In contrast, responses to the pretraining best frequency and other non-CS frequencies are decreased. These opposite changes are often sufficient to shift cellular tuning toward or even to the frequency of the CS. Learning-induced receptive field (RF) plasticity (i) is associative (requires pairing tone and shock), (ii) highly specific to the CS frequency (e.g., limited to this frequency +/- a small fraction of an octave), (iii) discriminative (specific increased response to a reinforced CS+ frequency but decreased response to a nonreinforced CS- frequency), (iv) develops extremely rapidly (within 5 trials, the fewest trials tested), and (v) is retained indefinitely (tested to 8 weeks). Moreover, RF plasticity is robust and not due to arousal, but can be expressed in the deeply anesthetized subject. Because learning- induced RF plasticity has the major characteristics of associative memory, it is therefore referred to as "physiological memory". We developed a model of RF plasticity based on convergence in the auditory cortex of nucleus basalis cholinergic effects acting at muscarinic receptors, with lemniscal and nonlemniscal frequency information from the ventral and magnocellular divisions of the medial geniculate nucleus, respectively. In the model, the specificity of RF plasticity is dependent on Hebbian rules of covariance. This aspect was confirmed in vivo using microstimulation techniques. Further, the model predicts that pairing a tone with activation of the nucleus basalis is sufficient to induce RF plasticity similar to that obtained in behavioral learning. This prediction has been confirmed. Additional tests of the model are described. RF plasticity is thought to translate the acquired significance of sound into an increased frequency representation of behaviorally important stimuli.
Melt Extrusion and Spray Drying of Carbamazepine and Dipyridamole with Polyvinylpyrrolidone/Vinyl Acetate Copolymers (2008)

Consideration must be given to the characteristics of the polymer when selecting for glass solution formulation. Although a number of process parameters can be varied for melt extrusion and spray drying, their ability to overcome fundamental differences in the physical parameters discussed is limited.