gebhart/patrepeval huggingface dataset:
Impact of Three Different Mutations in Ehrlichia chaffeensis in Altering the Global Gene Expression Patterns (2018)

The rickettsial pathogen Ehrlichia chaffeensis causes a tick-borne disease, human monocytic ehrlichiosis. Mutations within certain genomic locations of the pathogen aid in understanding the pathogenesis and in developing attenuated vaccines. Our previous studies demonstrated that mutations in different genomic sites in E. chaffeensis caused variable impacts on their growth and attenuation in vertebrate and tick hosts. Here, we assessed the effect of three mutations on transcriptional changes using RNA deep-sequencing technology. RNA sequencing aided in detecting 66-80% of the transcripts of wildtype and mutant E. chaffeensis. Mutation in an antiporter gene (ECH_0379) causing attenuated growth in vertebrate hosts resulted in the down regulation of many transcribed genes. Similarly, a mutation downstream to the ECH_0490 coding sequence resulted in minimal impact on the pathogen's in vivo growth, but caused major changes in its transcriptome. This mutation caused enhanced expression of several host stress response genes. Even though the ECH_0660 gene mutation caused the pathogen's rapid clearance in vertebrate hosts and aids in generating a protective response, there was minimal impact on the transcriptome. The transcriptomic data offer novel insights about the impact of mutations on global gene expression and how they may contribute to the pathogen's resistance and/or clearance from the host.
Surgical Repair of Achilles Tendon Ruptures Using Polypropylene Braid Augmentation (1994)

Surgical repair in fresh rupture of the Achilles tendon should be considered in active patients and athletes to restore their preinjury level of activity. Fifteen cases of Achilles tendon rupture underwent surgical repair using interpositional augmentation. This technique provides an immediate mechanical strength of the repair, avoiding the need for a postoperative plaster cast and allowing immediate motion of the ankle. No wound infection, scar adherence of the skin to the tendon, or rerupture of the tendon is present in this series. All patients were subjectively satisfied with the results and returned to their preinjury level of activity. Objectively, isokinetic assessment revealed no significant difference, as per t-test evaluation (P < .05), between the operated leg and the controlateral one.
Hardness, Toughness, and Scratchability of Germanium–Selenium Chalcogenide Glasses (2002)

Ge–Se chalcogenide glasses are characterized by relatively low hardness (0.39–2.35 GPa) and low fracture toughness (0.1–0.28 MPa·m 1/2 ). Actually, the hardness of chalcogen‐rich glasses is low enough so that the brittleness parameter, B = H / K c , is lower than that of silicate glasses. Whereas hardness and Young's modulus increase with increasing germanium contents, fracture toughness follows a trend similar to that of the density and exhibits a maximum for the Ge 20 Se 80 composition, which corresponds to the rigidity percolation threshold. Optical microscopy and atomic force microscopy observations suggest that the indentation deformation proceeds by a localized shear deformation phenomenon. Glasses in the chalcogen‐rich region behave viscoelastically at room temperature. As a consequence, an increase of the loading time results in a decrease of hardness and toughness.
Chirality of Methamphetamine and Amphetamine from Workplace Urine Samples (1994)

Several positive methamphetamine/amphetamine urine samples were reexamined to determine the chirality of the detected drug or drugs. (S)-N-(Trifluoroacetyl)prolyl derivatives were prepared and analyzed using GC/MS. In one case, pure d-isomers of methamphetamine and amphetamine were detected. In the remainder of the samples involving both drugs, skewed racemates were detected, with the l-isomer of methamphetamine and the d-isomer of amphetamine predominating slightly over their enantiomers. In samples involving amphetamine only, 50:50 mixtures of d- and l-isomers were detected. In no instance was pure i-methamphetamine (from a Vicks inhaler) detected.
Macrophage colony-stimulating factor receptor marks and regulates a fetal myeloid-primed B-cell progenitor in mice (2016)

Although it is well established that unique B-cell lineages develop through distinct regulatory mechanisms during embryonic development, much less is understood about the differences between embryonic and adult B-cell progenitor cells, likely to underpin the genetics and biology of infant and childhood PreB acute lymphoblastic leukemia (PreB-ALL), initiated by distinct leukemia-initiating translocations during embryonic development. Herein, we establish that a distinct subset of the earliest CD19(+) B-cell progenitors emerging in the E13.5 mouse fetal liver express the colony-stimulating factor-1 receptor (CSF1R), previously thought to be expressed, and play a lineage-restricted role in development of myeloid lineages, and macrophages in particular. These early embryonic CSF1R(+)CD19(+) ProB cells also express multiple other myeloid genes and, in line with this, possess residual myeloid as well as B-cell, but not T-cell lineage potential. Notably, these CSF1R(+) myeloid-primed ProB cells are uniquely present in a narrow window of embryonic fetal liver hematopoiesis and do not persist in adult bone marrow. Moreover, analysis of CSF1R-deficient mice establishes a distinct role of CSF1R in fetal B-lymphopoiesis. CSF1R(+) myeloid-primed embryonic ProB cells are relevant for infant and childhood PreB-ALLs, which frequently have a bi-phenotypic B-myeloid phenotype, and in which CSF1R-rearrangements have recently been reported.
EFFECTS OF DRYING SHRINKAGE OF CONCRETE ON SHEAR BEHAVIOR OF REINFORCED CONCRETE BEAMS WITHOUT SHEAR REINFORCEMENT (2017)

せん断補強筋のないRCはりのせん断強度およびその寸法効果に及ぼすコンクリートの収縮の影響を明らかにすることを目的とし，乾燥収縮が-1000μを超える高収縮コンクリートと低収縮コンクリートを用いて，有効高さ(250mm，500mm，1000mm)，水結合材比(50%，35%)をパラメータとした曲げせん断載荷実験を行った．その結果，コンクリートの収縮によってRCはりのせん断強度が低下すること，コンクリートの収縮および強度増加によってせん断強度の寸法効果が大きくなることを確認した．また，収縮，強度，有効高さの連成作用を考慮したせん断耐荷機構を提示した．さらに，収縮の影響を考慮した等価引張鉄筋比を既存のせん断強度評価式に組み込むことにより，実測値を比較的高い精度で予測できることを確認した．
Supplementary Fig. S4D from Antitumor activity of a membrane lytic peptide cyclized with a linker sensitive to membrane type 1-matrix metalloproteinase (2023)

Supplementary Fig. S4D from Antitumor activity of a membrane lytic peptide cyclized with a linker sensitive to membrane type 1-matrix metalloproteinase
Comparative Analysis of 22 Coronavirus HKU1 Genomes Reveals a Novel Genotype and Evidence of Natural Recombination in Coronavirus HKU1 (2006)

We sequenced and compared the complete genomes of 22 strains of coronavirus HKU1 (CoV HKU1) obtained from nasopharyngeal aspirates of patients with respiratory tract infections over a 2-year period. Phylogenetic analysis of 24 putative proteins and polypeptides showed that the 22 CoV HKU1 strains fell into three clusters (genotype A, 13 strains; genotype B, 3 strains and genotype C, 6 strains). However, different phylogenetic relationships among the three clusters were observed in different regions of their genomes. From nsp4 to nsp6, the genotype A strains were clustered with the genotype B strains. For nsp7 and nsp8 and from nsp10 to nsp16, the genotype A strains were clustered with the genotype C strains. From hemagglutinin esterase (HE) to nucleocapsid (N), the genotype B strains were clustered closely with the genotype C strains. Bootscan analysis showed possible recombination between genotypes B and C from nucleotide positions 11,500 to 13,000, corresponding to the nsp6-nsp7 junction, giving rise to genotype A, and between genotypes A and B from nucleotide positions 21,500 to 22,500, corresponding to the nsp16-HE junction, giving rise to genotype C. Multiple alignments further narrowed the sites of crossover to a 143-bp region between nucleotide positions 11,750 and 11,892 and a 29-bp region between nucleotide positions 21,502 and 21,530. Genome analysis also revealed various numbers of tandem copies of a perfect 30-base acidic tandem repeat (ATR) which encodes NDDEDVVTGD and various numbers and sequences of imperfect repeats in the N terminus of nsp3 inside the acidic domain upstream of papain-like protease 1 among the 22 genomes. All 10 CoV HKU1 strains with incomplete imperfect repeats (1.4 and 4.4) belonged to genotype A. The present study represents the first evidence for natural recombination in coronavirus associated with human infection. Analysis of a single gene is not sufficient for the genotyping of CoV HKU1 strains but requires amplification and sequencing of at least two gene loci, one from nsp10 to nsp16 (e.g., pol or helicase) and another from HE to N (e.g., spike or N). Further studies will delineate whether the ATR is useful for the molecular typing of CoV HKU1.
Study of Distributed Detection Based on N-P Rule with Correlated Sensors (2006)

We study the fusion algorithms of distributed detection based on Neyman-Pearson criteria with correlated condition. We consider a parallel network structure that consists of a number of local sensors and a fusion center.Each sensor makes a binary deci- sion based on its own observation.The detections with known and unknown joint pdf are considered.In both cases,we give the theoreti- cal derivation of optimal fusion rules and corresponding solution.In the end,some useful conclusions are given based on the experi- ment.
Purification and in Vitro Reconstitution of the Essential Protein Components of an Aromatic Polyketide Synthase (1998)

A minimal set of proteins which catalyze the synthesis of aromatic polketides from malonyl CoA has been purified and partially characterized. Plasmid-encoded actinorhodin (act) ketosynthase/chain-length factor (KS/CLF) complex was purified from Streptomyces coelicolor CH999/pSEK38, and assayed with purified aromatic PKS holo-ACPs which were overproduced and purified from Escherichia coli and phosphopantetheinylated in vitro using purified E. coli holo-ACP synthase. When highly purified preparations of KS/CLF, and holo-ACP failed to catalyze polyketide biosynthesis, a fourth protein was sought and purified from the S. coelicolor CH999 host on the basis of its ability to complement KS, CLF, and holo-ACP in polyketide synthesis. N-terminal sequencing identified this protein as the fatty acid synthase (fabD) malonyl CoA:ACP transacylase (MAT), recruited from primary metabolism. A alpha2/beta2 structure was shown for the act KS/CLF complex, and three malonyl-enzyme biosynthetic intermediates were identified, defining an escorted path followed by malonyl groups en route from CoA to polyketide.
In-Situ ETEM Reveals Formation Mechanism of Single Pt Atom on Ru Nanoparticle Electrocatalysts for CO-Resilient Methanol Oxidation (2022)

Journal Article In-Situ ETEM Reveals Formation Mechanism of Single Pt Atom on Ru Nanoparticle Electrocatalysts for CO-Resilient Methanol Oxidation Get access Agus R Poerwoprajitno, Agus R Poerwoprajitno School of Chemistry, The University of New South Wales, Sydney, NSW, Australia Search for other works by this author on: Oxford Academic Google Scholar Lucy Gloag, Lucy Gloag School of Chemistry, The University of New South Wales, Sydney, NSW, Australia Search for other works by this author on: Oxford Academic Google Scholar John Watt, John Watt Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM, USA Corresponding author: watt@lanl.gov Search for other works by this author on: Oxford Academic Google Scholar Soshan Cheong, Soshan Cheong Mark Wainwright Analytical Centre, The University of New South Wales, Sydney, NSW, Australia Search for other works by this author on: Oxford Academic Google Scholar Benjamin K Miller, Benjamin K Miller Gatan Inc., Pleasanton, CA, USA Search for other works by this author on: Oxford Academic Google Scholar Dale L Huber, Dale L Huber Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM, USA Search for other works by this author on: Oxford Academic Google Scholar Richard D Tilley Richard D Tilley School of Chemistry, The University of New South Wales, Sydney, NSW, AustraliaMark Wainwright Analytical Centre, The University of New South Wales, Sydney, NSW, Australia Search for other works by this author on: Oxford Academic Google Scholar Microscopy and Microanalysis, Volume 28, Issue S1, 1 August 2022, Pages 130–131, https://doi.org/10.1017/S1431927622001428 Published: 01 August 2022
Diode-pumped Nd:YAG laser for precision laser machining (1996)

Results are presented on a high power, diode-pumped, pulsed Nd:YAG laser for precision laser machining. The laser is an unstable resonator with a graded reflectivity outcoupler, generating a beam with excellent beam quality. The gain medium is a single zig-zag slab, pumped symmetrically by diode arrays. The use of diode arrays minimizes the thermal loading on the slab, and the zig-zag path averages thermal distortions in the zig-zag dimension. Measurements of beam divergence as a function of diode duty-cycle will be presented. Available pulse formats will also be discussed. To date, the laser has produced 720 W at 20% diode duty-cycle with a stable cavity and 550 W at 20% duty cycle with an unstable cavity in close agreement with model predictions. The beam divergence has been measured to be 1.7 times diffraction-limited at 20% duty cycle. The laser has been operated with pulse lengths from 20 μs to 1 ms and is being used to obtain laser processing data, with some results shown.
Fabrication of petal-shaped masks for suppression of the on-axis Poisson spot in telescope systems (2016)

The presence of a bright (Poisson) spot in the geometrical shadow of circular/spherical shapes has been known for the past two centuries. A broad class of telescopes that involve simultaneous transmit and receive require suppression of the reflected light from the secondary mirror on the detector. For instance, the on-axis design of optical telescope for the evolved Laser Interferometric Space Antenna (eLISA), a re-scoped version of the baseline LISA mission concept, requires suppression of reflected laser light from the secondary mirror on the detector. In the past few years, the hypergaussian functions with petal-shaped realization have been shown to significantly suppress intensity along the optical axis. This work reports on fabrication of a series of petal-shaped masks using a variety of techniques such as 3D printing, photolithography, and wire Electro Discharge Machining. These masks are designed and fabricated to operate in the range of Fresnel numbers between 4 and 120. This paper discusses the challenges, successes, and failures of each fabrication technique and the optical performance of typical masks with suggestions for potential follow up work.
Inhibitors of NLRP3 Inflammasome in Ischemic Heart Disease: Focus on Functional and Redox Aspects (2023)

Myocardial ischemia-reperfusion injury (MIRI) is caused by several mechanisms, including the production of reactive oxygen species (ROS), altered cellular osmolarity, and inflammatory response. Calcium overload, altered oxygen levels, and mitochondrial ROS are also involved in these MIRI processes, resulting in the irreversible opening of the mitochondrial permeability transition pore (mPTP). These mechanisms and processes are associated with NLRP3 inflammasome priming and activation, which can also induce cell death by pyroptosis through the up-regulation of the caspase-1 pathway and IL-18 release. In addition, endothelial dysfunction, both in the presence and absence of MIRI, is also accompanied by altered oxygen levels, decreased nitric oxide production, and ROS overproduction, resulting in the expression of adhesion molecules and leukocyte infiltration in which the NLRP3 inflammasome plays a central role, thus contributing, through endothelial dysfunction, to the alteration of coronary flow, typical of ischemic heart disease. Given the intricate interrelationship between ROS and NLRP3, ROS inhibitors can reduce NLRP3 inflammasome activation, while NLRP3 inhibitors can reduce oxidative stress and inflammation. NLRP3 inhibitors have been intensively studied as anti-inflammatory agents in basic cardiovascular sciences. In this review, we analyze the interrelation between ROS and NLRP3 in ischemic heart disease and the effects of some NLRP3 inhibitors as possible therapeutic agents in this disease condition. All compounds considered in this review need larger studies to confirm their appropriate use in clinical scenarios as anti-ischemic drugs.
In-Plane rotation analysis by two-wavelength electronic speckle interferometry (1999)

A simple method is presented for the measurement of in-plane rotation (angle and sign) of an object by use of the conventional in-plane sensitive electronic speckle pattern interferometry technique combined with the two-wavelength laser diode method. The advantage of this method is that it can be used to measure the angle of rotation in a simple way by determination of fringe tilt. The experimental setup is described, and results are presented.
Characterization of Glutamate-1-Semialdehyde Aminotransferase and Its Activity Throughout Tomato Fruit Development and Ripening (1998)

Glutamate-1-semialdehyde aminotransferase (GSAT) is a key enzyme in the regulation of chlorophyll biosynthesis and a plausible site to regulate chlorophyll loss during fruit development via a decrease in its activity. The primary objective of this research was to characterize GSAT from tomato fruit by varying substrate concentration and pH and to measure GSAT in various organs of the tomato plant. A secondary objective was to measure GSAT activity and chlorophyll concentration at 5-day intervals from 10 d to 60 d postanthesis during tomato fruit development and ripening. An optimum pH of 7.0 was found, and a maximum velocity (Vmax) of 2.3 nmol·g –1 of tissue and a Km of 119 mmol·L –1 were calculated for GSAT. Activity among organs was greatest at 3.84 nmol·g –1 tissue in leaves of 4-week-old seedlings, 1.67 nmol·g –1 tissue in fruits 15 days postanthesis, and below 0.70 nmol·g –1 tissue in roots, stems, and overripe fruits (65 d postanthesis). During fruit development, GSAT activity was greatest at 10 d postanthesis and declined to day 25. Activity increased from day 25 to a peak at day 40 and then decreased again during ripening to 60 d postanthesis. Total chlorophyll and chlorophyll a concentrations in tomato fruit declined throughout development and ripening with the greatest decrease between 10 d and 25 d postanthesis. Thus, GSAT activity may contribute to the control of chlorophyll concentration in tomato fruit from 10 to 25 d postanthesis when chlorophyll loss mirrors the decline in GSAT activity.
Dual Fluorescent Labeling Method to Visualize Plasmid DNA Degradation (2008)

The efficiency of nonviral vectors for gene delivery may be enhanced by understanding the key barriers that limit the translocation of the therapeutic DNA into the nucleus. One such barrier is the instability of DNA in the cytoplasm. In this work, we have developed a method to dual-label plasmid DNA to be utilized as a tool to elucidate DNA instability during its trafficking in the intracellular microenvironment. Plasmid DNA containing rhodamine and maleimide groups linked using peptide nucleic acid (PNA) linkers was utilized for conjugation. Covalent conjugation of the maleimide group with a second fluorophore, fluorescein, did not alter the electrophoretic mobility or the structural integrity of the DNA, as confirmed by gel electrophoresis. The intact DNA was visualized as a single color (yellow) due to the close proximity of the green and red fluorophores. DNA degradation was simulated using restriction endonucleases (BamH1 and PflMI) to cut the DNA at two or more sites resulting in color separation. Confocal time-lapse imaging was utilized to follow DNA stability upon incubation of Lipofectamine2000/dual-labeled DNA complexes in CHO-K1 cells. Yellow fluorescent voxels were seen in the cell cytoplasm indicating the presence of intact DNA. Red and green fluorescent voxels were also seen in a few cells, suggesting separation of the fluorophores and probable DNA degradation. The methodology developed in this report provides a new tracking tool for investigators to explore DNA degradation at the molecular level inside single cell.
Parameter of Nonlinearity in Fluids. III. Values of Sound Velocity in Liquid Metals (1967)

The speed of sound is reported for liquid metals (mercury, indium, bismuth, sodium, and tin) as a function of pressure (0 to 150 atm) and temperature (up to 100°K above the melting point). The result and data are used to obtain expressions for the derivatives of the sound speed with respect to temperature and pressure. These coefficients are then used to determine the parameter of nonlinearity in terms of the ratio B/A of the first two coefficients of the adiabatic expansion of pressure in terms of the density.
Quantification of Multiple DNA Adducts Formed through Oxidative Stress Using Liquid Chromatography and Electrospray Tandem Mass Spectrometry (2002)

Damage to DNA can arise through covalent modification of bases by reaction with oxidants and products of lipid peroxidation derived through normal aerobic metabolism. Such premutagenic lesions, including 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dG), pyrimido[1,2alpha]purine-10(3H)one-2'-deoxyribose (M1-dG), etheno-2'-deoxyadenosine (epsilon-dA), and etheno-2'-deoxycytidine (epsilon-dC), are believed to be important in the development of human cancers related to diet, disease states, and lifestyle. We report the development of a method for concurrent quantification of these four adducts in DNA hydrolysates of 100 microg or less using on-line sample preparation coupled with liquid chromatography and tandem mass spectrometry. The sensitive detection permitted adduct quantification at levels below one adduct in 10(8) normal nucleotides and measurement of these adducts in DNA from untreated rodent liver and normal human liver samples. This methodology should prove useful in hypothesis-driven studies of cancer etiology in laboratory animals and humans.
Yeast two-hybrid interactions between Arabidopsis lyrata S Receptor Kinase and the ARC1 E3 ligase (2016)

Here we describe protein-protein interactions between signaling components in the conserved self-incompatibility pathway from Brassica spp. and Arabidopsis lyrata. Previously, we had demonstrated that ARC1 is necessary in A. lyrata for the rejection of self-pollen by the self-incompatibility pathway. The results described here demonstrate that A. lyrata ARC1 interacts with A. lyrata S Receptor Kinase (SRK1) in the yeast 2-hybrid system. A. lyrata ARC1 also interacted with B. napus SRK910 illustrating that interactions in this pathway are conserved across species. Finally, we discuss how the more widely occurring interactions between SRK and ARC1-related family members may be modulated in vivo by expression and subcellular localization patterns resulting in a particular response.
Vaginal high-risk human papillomavirus infection in a cross-sectional study among women of six different ethnicities in Amsterdam, the Netherlands: the HELIUS study (2016)

We found an overall higher hrHPV prevalence and higher sexual risk behaviour in the native Dutch population. Further research is needed to unravel the complex problem concerning cervical cancer disparities, such as differences in participation in the cervical cancer screening programme, or differences in clearance and persistence of hrHPV.