gebhart/patrepeval huggingface dataset:
Peak Annotation and Verification Engine for Untargeted LC–MS Metabolomics (2018)

Untargeted metabolomics can detect more than 10 000 peaks in a single LC-MS run. The correspondence between these peaks and metabolites, however, remains unclear. Here, we introduce a Peak Annotation and Verification Engine (PAVE) for annotating untargeted microbial metabolomics data. The workflow involves growing cells in <sup>13</sup>C and <sup>15</sup>N isotope-labeled media to identify peaks from biological compounds and their carbon and nitrogen atom counts. Improved deisotoping and deadducting are enabled by algorithms that integrate positive mode, negative mode, and labeling data. To distinguish metabolites and their fragments, PAVE experimentally measures the response of each peak to weak in-source collision induced dissociation, which increases the peak intensity for fragments while decreasing it for their parent ions. The molecular formulas of the putative metabolites are then assigned based on database searching using both m/ z and C/N atom counts. Application of this procedure to Saccharomyces cerevisiae and Escherichia coli revealed that more than 80% of peaks do not label, i.e., are environmental contaminants. More than 70% of the biological peaks are isotopic variants, adducts, fragments, or mass spectrometry artifacts yielding ∼2000 apparent metabolites across the two organisms. About 650 match to a known metabolite formula based on m/ z and C/N atom counts, with 220 assigned structures based on MS/MS and/or retention time to match to authenticated standards. Thus, PAVE enables systematic annotation of LC-MS metabolomics data with only ∼4% of peaks annotated as apparent metabolites.
Theory and Application of a Micro-Scale Abrasive Wear Test (1997)

Abstract A micro-scale abrasion test has recently been developed that allows measurement of the wear resistance of the surface regions of a material. The typical penetration depth is less than 30 μm. The test uses a simple mechanical and optical system and involves rotating a hard steel sphere against a specimen in the presence of small abrasive particles. The method has been used to investigate the wear resistance of thin PVD coatings (1 to 5 µm), metallic glass ribbons, and paint films in addition to bulk samples of metals, ceramics, and glasses. The associated theory has been extended so that results may be obtained from any curved surface. This furthers its applicability to practical surface-engineered components such as twist drills, bearings, turbine blades, and biomedical prostheses. A detailed characterization of the experimental procedure has been undertaken to provide an understanding of the repeatability and sensitivity of the test. In a study of cutting-tool coatings, the wear resistance measured by this method has been shown to correlate with scratch test response and with the performance of coated end-mills in cutting tests.
Bioreducible Cross-Linked Hyaluronic Acid/Calcium Phosphate Hybrid Nanoparticles for Specific Delivery of siRNA in Melanoma Tumor Therapy (2017)

This study introduces a novel cross-linking strategy capable of successfully stabilizing CaP nanoparticles and stimuli-responsive small interfering RNA (siRNA) release. We synthesized a polysaccharide derivative thiolated hyaluronic acid (HA-SH), which was slightly modified but multifunctional and developed a smart redox-responsive delivery system. siRNA was efficaciously condensed by calcium phosphate (CaP) via electrostatic interaction to form a positively charged inner "core". Disulfide cross-linked HA (HA-ss-HA) was formed and played a role as an anionic outer "shell" to stabilize the CaP core. We demonstrated that the nanoparticles were stable both in the storage milieu and systemic circulation, thus overcoming the most serious disadvantage of CaP nanoparticles for gene delivery. Meanwhile, this smart system could selectively release siRNA into the cytosol by both a GSH-triggered disassembly and successful endosomal escape. Therefore, the hybrid delivery system achieved an 80% gene-silencing efficiency in vitro for both luciferase and Bcl2. Silencing of Bcl2 resulted in dramatic apoptosis of B16F10 cells. Besides, equipped with the tumor-targeting component HA, the nanoparticles significantly suppressed the growth of B16F10 xenograft tumor in mice. The anionic HA-ss-HA-equipped nanoparticles showed no apparent toxicity in vitro or in vivo, as well as showed a high transfection efficiency. Taken together, this redox-responsive, tumor-targeting smart anionic nanoparticle holds great promise for exploitation in functionalized siRNA delivery and tumor therapy.
4H-SiC Trench MOSFET With L-Shaped Gate (2016)

A novel 4H-SiC trench metal-oxide-semiconductor field-effect transistor (MOSFET) with an L-shaped gate (LSG) is proposed and studied via numerical simulations in this letter. Adoption of an additional LSG region that surrounds the bottom corner of the trench allows the peak electric field in the SiO2 dielectric to be significantly relieved by charge compensation, and the device breakdown voltage can be greatly enhanced without causing significant degradation of the output characteristics. In high-voltage blocking states, the electric field at the bottom corner of the trench is weakened, which leads to improved device performance. The peak electric field value in the SiO2 dielectric decreases by 32.3% when compared with that of a conventional 4H-SiC trench MOSFET, while the breakdown voltage increases by 80.4%.
Topography of the Photosystem I Core Proteins of the Cyanobacterium Synechocystis sp. PCC 6803 (1997)

PsaA and PsaB are homologous integral membrane proteins that form the heterodimeric core of photosystem I. Domain-specific antibodies were generated to examine the topography of PsaA and PsaB. The purified photosystem I complexes from the wild type strain of Synechocystis sp. PCC 6803 were treated with eight proteases to study the accessibility of cleavage sites in PsaA and PsaB. Proteolytic fragments were identified using the information from N-terminal amino acid sequencing, reactivity to antibodies, apparent mass, and specificity of proteases. The extramembrane loops of PsaA and PsaB differed in their accessibility to proteases, which indicated the folded structure of the loops or their shielding by the small subunits of photosystem I. NaI-treated and mutant photosystem I complexes were used to identify the extramembrane loops that were exposed in the absence of specific small subunits. The absence of PsaD exposed additional proteolytic sites in PsaB, whereas the absence of PsaE exposed sites in PsaA. These studies distinguish PsaA and PsaB in the structural model for photosystem I that has been proposed on the basis of x-ray diffraction studies (Krauss, N., Schubert, W.-D., Klukas, O., Fromme, P., Witt, H. T., and Saenger, W. (1996) Nat. Struct. Biol. 3, 965-973). Using osmotically shocked cells for protease treatments, the N terminus of PsaA was determined to be on the n side of the photosynthetic membranes. Based on these data and available published information, we propose a topological model for PsaA and PsaB.
A panel of ancestry informative markers for estimating individual biogeographical ancestry and admixture from four continents: utility and applications (2008)

Autosomal ancestry informative markers (AIMs) are useful for inferring individual biogeographical ancestry (I-BGA) and admixture. Ancestry estimates obtained from Y and mtDNA are useful for reconstructing population expansions and migrations in our recent past but individual genomic admixture estimates are useful to test for association of admixture with phenotypes, as covariate in association studies to control for stratification and, in forensics, to estimate certain overt phenotypes from ancestry. We have developed a panel of 176 autosomal AIMs that can effectively distinguish I-BGA and admixture proportions from four continental ancestral populations: Europeans, West Africans, Indigenous Americans, and East Asians. We present allele frequencies for these AIMs in all four ancestral populations and use them to assess the global apportionment of I-BGA and admixture diversity among some extant populations. We observed patterns of apportionment similar to those described previously using sex and autosomal markers, such as European admixture for African Americans (14.3%) and Mexicans (43.2%), European (65.5%) and East Asian affiliation (27%) for South Asians, and low levels of African admixture (2.8-10.8%) mirroring the distribution of Y E3b haplogroups among various Eurasian populations. Using simulation studies and pedigree analysis we show that I-BGA estimates obtained using this panel and a four-population model has a high degree of precision (average root mean square error [RMSE]=0.026). Using ancestry-phenotype associations we demonstrate that a large and informative AIM panel such as this can help reduce false-positive and false-negative associations between phenotypes and admixture proportions, which may result when using a smaller panel of less informative AIMs.
pH-dependent inhibition of mushroom tyrosinase by <i>N</i>-substituted <i>N</i>-nitrosohydroxylamines (2008)

Several synthetic N-substituted N-nitrosohydroxylamines were found to inhibit mushroom tyrosinase in a pH-dependent manner regardless of the N-substituent. The inhibitory activity, or pI(50) ( - log [IC(50), M]) value, linearly decreased as the pH of the media increased. The inhibitory activities of tested N-substituted N-nitrosohydroxylamines at pH 6.8 and 5.8 were found to be almost 10 times and 100 times greater than at pH 7.8, respectively. The types of inhibition were different at pH 6.8 and 5.8. These results suggest that the inhibitory effect of N-substituted N-nitrosohydroxylamines is caused by the non-ionized form of the inhibitor. Furthermore, the mechanism of inhibition depends on the interaction between the inhibitor and the active site of tyrosinase at different pH values.
Sensor Applications and Physiological Features in Drivers’ Drowsiness Detection: A Review (2018)

Drowsiness in drivers has become a serious cause of concern due to the occurrences of a large number of fatalities on the road each year. Lives of pedestrians and passengers are put to risk as drivers tend to fall asleep at the steering wheel. In the recent past, many researchers have paid attention to the problem of drowsiness detection since safe roads and safe driving are of paramount concern to all societies. This paper has led to the development of several novel and effective methods in detecting drivers' drowsiness. These include: 1) Vehicle based methods; 2) Behavioral methods; and 3) Physiological methods. Since wake-sleep is an intermediate state between two physiologically dissimilar states, physiological signals can define this transition more accurately when compared with approaches that fall in other categories. This paper focuses on the role of physiological signals in detecting driver's drowsiness level. The proposed methods measure the physiological signals by means of various sensors, which monitor the driver's physiological parameters on a continual basis. Multiple sensors can be embedded on the driver or in the vicinity of the driver to capture vital signs indicating the onset of drowsiness. The aim here is to provide an insightful review of all such key approaches that fall in this category. This paper conducts a detailed study in which key physiological parameters that relate to drowsiness are identified, described, and analyzed. Furthermore, the overall advantages and limitations of these physiological based schemes are also highlighted.
Atmospheric Deterioration of Clean Surface of Epitaxial (001)-YBaCuO Films Studied by Low-Energy Electron Diffraction (1991)

The effects of gas exposure on the clean surface of the epitaxial YBaCuO thin films were closely investigated using the low-energy electron diffraction (LEED) method. The clean surface was obtained by in-vacuum annealing at 500°C. Once the clean surface was exposed to air, even at room temperature, the LEED spots disappeared or sometimes became faint. To ensure the degradation mechanism of the YBaCuO clean surface, the specimens were exposed to pure O 2 and N 2 gases separately and measured by LEED. As a result, it was found that O 2 is very safe but N 2 serves as a poisonous gas for the YBaCuO clean surface.
The Clinical Significance of Changes in Genetic Heterogeneity of the Hypervariable Region 1 in Chronic Hepatitis C With Interferon Therapy (1996)

We examined changes in the hypervariable region 1 of the hepatitis C virus (HCV) RNA that occurred with interferon therapy in 33 patients with chronic hepatitis C to assess the clinical significance of this region. The 33 patients had HCV genotype 1b and were classified into three groups based on serum aminotransferase levels during and after therapy with alpha interferon; long-term responders (n = 9), short-term responders (n = 11), and nonresponders (n = 13). Changes in the genetic heterogeneity of the hypervariable region 1 were determined by using nonisotopic polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP). HCV RNA levels were evaluated by reverse transcriptase PCR and branched DNA probe assays. Changes in sequences were determined by cloning and sequencing analysis. Before therapy, the long-term responders had significantly lower degrees of heterogeneity and lower viral levels than nonresponders. There were no significant differences between short-term and nonresponders. With interferon therapy, viral levels and degree of heterogeneity decreased to a greater extent among long-term and short-term responders than among nonresponders. Sequencing analysis showed that the three groups had similar clone numbers initially, but long-term responders had rather homogeneous viral populations, whereas short-term and nonresponders had heterogeneous populations, but that there were no nucleotide sequences or amino acid alignments that were specific for any group before, during, and 6 months after therapy. Approximately half of short-term and nonresponders received a second course of interferon 7 to 10 months after the initial therapy; all showed an identical response to the second course of therapy regardless of interim changes in the heterogeneity of hypervariable region 1. These findings suggest that (1) patients who were nonresponders or short-term responders had mixed viral populations that had differing sensitivities to interferon, (2) the changes in the hypervariable region 1 (HVR 1) did not affect responsiveness to interferon, and (3) the lower heterogeneity in the HVR 1 was associated with a long-term response to interferon only when the viral levels were low.
A game-theoretic framework for multimetric optimization of interconnect delay, power, and crosstalk noise during wire sizing (2004)

The continuous scaling of interconnect wires in deep submicron (DSM) circuits results in increased interconnect delay, power, and crosstalk noise. In this work, we develop a game-theoretic framework and multimetric optimization algorithms for the simultaneous optimization during wire sizing of (i) interconnect delay and crosstalk noise, and (ii) interconnect delay, power, and crosstalk noise. We formulate the wire sizing optimization problem as a normal form-game model and solve it using Nash equilibrium theory. Game theory allows the optimization of multiple metrics with conflicting objectives. This property is exploited in modeling the wire sizing problem while simultaneously optimizing various design parameters like interconnect delay, power, and crosstalk noise, which are conflicting in nature. The nets connecting the driving cell and the driven cell are divided into net segments. The net segments within a channel are modeled as players and the range of possible wire sizes forms the set of strategies. The payoff function is modeled (i) as the geometric mean of interconnect delay and crosstalk noise in the case of first formulation, and (ii) as the weighted sum of interconnect delay, power, and crosstalk noise in the second formulation. The net segments are optimized from the ones closest to the driven cell towards the ones at the driving cell. Complete information about the coupling effects among the nets is extracted after the detailed routing phase. The time and space complexities of the proposed wire sizing formulations are linear in terms of the number of net segments. Experimental results on several medium and large open-core designs indicate that the proposed algorithm for simultaneous optimization of interconnect delay and crosstalk noise yields an average reduction of 21.48% in interconnect delay and a 26.25% reduction in crosstalk noise without any area overhead, over and above the optimization from the Cadence place and route tools. It is shown through experimental results that the algorithm performs significantly better than simulated annealing and genetic search. Further, new simple but accurate models are developed for three parallel interconnect net segments. It is shown that these models yield the same level of accuracy with significantly better run times compared to the models reported in Chen et al. [2004]. A mathematical proof of existence for the Nash equilibrium solution for the proposed wire sizing formulation is also provided.
Detection of hepatitis C virus ribonucleic acid in the serum by amplification with polymerase chain reaction. (1990)

Hepatitis C virus (HCV) RNA was detected in the sera of patients with non-A, non-B chronic liver disease by polymerase chain reaction (PCR). RNA was extracted from the serum, reverse transcribed to cDNA, and amplified by PCR. With this method, 30 patients with non-A, non-B chronic liver disease and 10 healthy subjects were tested. HCV RNA was detected in 13 of 16 (81%) anti-HCV-positive patients and also in 7 of 14 (50%) anti-HCV-negative patients, but in none of 10 anti-HCV-negative healthy subjects. Specificity of this method was confirmed by direct sequencing of amplified cDNA segment. The nucleotide sequences (37 nucleotides) obtained from 15 patients showed only 68-78% homology compared with the prototype HCV nucleotide sequence. In addition, of 15 nucleotide sequences, there were 12 different types. But the translated amino acid sequences (12 amino acids) showed 83-100% homology compared with the prototype HCV amino acid sequence. These data suggest the majority of anti-HCV-positive patients are carriers of HCV. But to detect all the viremic patients, the anti-HCV antibody testing may be insufficient. Direct detection of HCV RNA may be useful in the study of virus replication and its association with various liver diseases.
Genetic diversity of flagellins of <i>Pseudomonas aeruginosa</i> (1996)

Physical genome analysis of the virulence-associated fliC locus in 20 Pseudomonas aeruginosa strains by mapping and sequencing revealed groups of heterologous a-type (1164 bp; 1185 bp) and highly conserved b-type (1467 bp) flagellin genes. Whereas only two synonymous nucleotide substitutions were detected in eight b-type fliC sequences, the 12 a-type sequences exhibited 57 nucleotide substitutions, of which 39 occurred within a variable central region. Although a-type and b-type flagellins differ by 35% in their primary structure, they share strong homology in their predicted features, implying that the polymorphic proteins fold into similar structures during polymerization of the flagella.
Fast Rebuilding B+-Trees for Index Recovery (2006)

Rebuilding an index is an essential step for database recovery. Fast recovery of the index is a necessary condition for fast database recovery. The B+-Tree is the most popular index structure in database systems. In this paper, we present a fast B+-Tree rebuilding algorithm called Max-PL. The main idea of Max-PL is that at first it constructs a B+-Tree index structure using the pre-stored max keys of the leaf nodes, and then inserts the keys and data pointers into the index. The algorithm employs a pipelining mechanism for reading the data records and inserting the keys into the index. It also exploits parallelisms in several phases to boost the overall performance. We analyze the time complexity and space requirement of the algorithm, and perform the experimental study to compare its performance to other B+-Trees rebuilding algorithms; Sequential Insertion and Batch-Construction. The results show that our algorithm runs on average at least 670% faster than Sequential Insertion and 200% faster than Batch-Construction.
Fluorescein-based pImarkers for capillary isoelectric focusing with laser-induced fluorescence detection (2002)

We prepared a series of low-molecular-mass fluorescent ampholytes with narrow pI range. These fluorescein-based ampholytes are detection compatible with argon laser-induced fluorescence (LIF) detection. The selected properties, important for their routine use as fluorescent pI markers, were examined. The pI values of new fluorescein-based pI markers were determined by capillary isoelectric focusing (CIEF) using currently available low-molecular-mass pI markers for CIEF with photometric detection. The examples of CIEF with fluorometric detection of new compounds together with fluorescein isothiocyanate (FITC) derivatized proteins are presented.
Homologous recombination repair intermediates promote efficient de novo telomere addition at DNA double-strand breaks (2019)

The healing of broken chromosomes by de novo telomere addition, while a normal developmental process in some organisms, has the potential to cause extensive loss of heterozygosity, genetic disease, or cell death. However, it is unclear how de novo telomere addition (dnTA) is regulated at DNA double-strand breaks (DSBs). Here, using a non-essential minichromosome in fission yeast, we identify roles for the HR factors Rqh1 helicase, in concert with Rad55, in suppressing dnTA at or near a DSB. We find the frequency of dnTA in rqh1Δ rad55Δ cells is reduced following loss of Exo1, Swi5 or Rad51. Strikingly, in the absence of the distal homologous chromosome arm dnTA is further increased, with nearly half of the breaks being healed in rqh1Δ rad55Δ or rqh1Δ exo1Δ cells. These findings provide new insights into the genetic context of highly efficient dnTA within HR intermediates, and how such events are normally suppressed to maintain genome stability.