gebhart/patrepeval huggingface dataset:
Direct In-Gel Fluorescence Detection and Cellular Imaging of <i>O</i> -GlcNAc-Modified Proteins (2008)

We report an advanced chemoenzymatic strategy for the direct fluorescence detection, proteomic analysis, and cellular imaging of O-GlcNAc-modified proteins. O-GlcNAc residues are selectively labeled with fluorescent or biotin tags using an engineered galactosyltransferase enzyme and [3 + 2] azide-alkyne cycloaddition chemistry. We demonstrate that this approach can be used for direct in-gel detection and mass spectrometric identification of O-GlcNAc proteins, identifying 146 novel glycoproteins from the mammalian brain. Furthermore, we show that the method can be exploited to quantify dynamic changes in cellular O-GlcNAc levels and to image O-GlcNAc-glycosylated proteins within cells. As such, this strategy enables studies of O-GlcNAc glycosylation that were previously inaccessible and provides a new tool for uncovering the physiological functions of O-GlcNAc.
Quality assurance: Fundamental reproducibility tests for 3D treatment‐planning systems (2005)

The use of image-based 3D treatment planning has significantly increased the complexity of commercially available treatment-planning systems (TPSs). Medical physicists have traditionally focused their efforts on understanding the calculation algorithm; this is no longer possible. A quality assurance (QA) program for our 3D treatment-planning system (ADAC Pinnacle3) is presented. The program is consistent with the American Association of Physicists in Medicine Task Group 53 guidelines and balances the cost-versus-benefit equation confronted by the clinical physicist in a community cancer center environment. Fundamental reproducibility tests are presented as required for a community cancer center environment using conventional and 3D treatment planning. A series of nondosimetric tests, including digitizer accuracy, image acquisition and display, and hardcopy output, is presented. Dosimetric tests include verification of monitor units (MUs), standard isodoses, and clinical cases. The tests are outlined for the Pinnacle3 TPS but can be generalized to any TPS currently in use. The program tested accuracy and constancy through several hardware and software upgrades to our TPS. This paper gives valuable guidance and insight to other physicists attempting to approach TPS QA at fundamental and practical levels.
Performance Liquid Chromatography/Tandem Mass Spectrometry (2011)

A sensitive method was developed using ultra-high-performance liquid chromatography (UHPLC)/MS/MS with positive electrospray ionization for determining aflatoxin M1 (AFM1) in milk and milk powder. A 50 mL quantity of low-fat liquid milk containing 100 ng/L AFM1, was prepared using immunoaffinity columns with a mean recovery rate of 79% (n = 3). UHPLC columns (BEH C18, BEH HILIC, and HSS T3) greatly reduced the chromatographic time and lowered the instrumental detection limits (IDLs) 16 to 58 times compared to an HPLC column (Betabasic C18). The HSS T3 column was chosen because it provided a low IDL (0.11 pg) and the lowest ion suppression of signal intensity (63.4%) among the tested columns. Matrix-fortified calibration curves were used for quantification and showed good linearity (r > 0.997) at 0.05-500 ng/mL. The LOD was 0.18 ng/kg for milk and 2.08 nglkg for milk powder, based on the signal intensity of the confirmatory product ion (m/z 259.1), which was less abundant than the quantitative product ion (m/z 273.1). Certified reference materials of milk powder at three levels (<0.05, 0.111 +/- 0.018, and 0.44 +/- 0.06 microg/kg) were measured within a day and between days; the results were all close to the certified levels with low variations (RSDs < 15%), showing good precision and accuracy.
Immunological detection of aflatoxin B1-DNA adducts formed in vivo. (1988)

Two monoclonal antibodies (6A10 and 12F5) were obtained after fusion of mouse P3X63-AG.8.653 myeloma cells with spleen cells isolated from BALB/c mice immunized with imidazole ring-opened aflatoxin B1 (AFB1)-DNA and characterized by competitive enzyme-linked immunosorbent assays. Both antibodies are highly specific for imidazole ring opened AFB1-DNA and show some cross-reactivity with AFB1-DNA and no cross-reactivity with 8,9-dihydro-8-(7-guanyl)-9-hydroxy-AFB1, AFB1 conjugated with bovine serum albumin, aflatoxin M1 conjugated with bovine serum albumin, AFB1, or aflatoxin G1. Antibody 6A10 was further characterized and showed no cross-reactivity with DNA modified by several other carcinogens. It could detect adducts with 4-fold higher sensitivity in highly modified DNA (2.5 adducts/100 nucleotides) than in low modified DNA (4 adducts/10(5) nucleotides). With low modified DNA the limit of sensitivity is 5 adducts/10(7) nucleotides. Antibody 6A10 reliably detected adducts formed in vivo in rats and mice treated with AFB1. In a pilot study, AFB1 adducts were detected in liver tissues from individuals living in areas with suspected exposure to AFB1. Monitoring adduct levels in human tissue may provide information not only on carcinogen exposure but also on the relationship among infection with hepatitis B virus, dietary exposure to aflatoxin B1, and liver cancer.
A new adaptive separable median filter for removing blocking effects (1993)

A novel adaptive separable median filter as a postfilter is presented for removing the blocking effects which generally originate from lower-bit-rate image transmission. This filter adaptively transforms from a traditional median filter to a low-pass filter progressively when the filter is close to the position of blocking effects. Simulation results demonstrate that this filter is extremely useful not only in removing the blocking effects, but also in maintaining the main advantages of the median filter such as edge preservation and noise reduction.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Studies of pendant-arm macrocyclic ligands. Part 5. Synthesis of two pyridine-containing penta-aza macrocycles with single pyrrolidinyl pendant arms and characterisation of their nickel(<scp>II</scp>) and copper(<scp>II</scp>) complexes. Crystal structure of perchlorato{7-[2′-(1″-pyrrolidinyl)ethyl]-3,7,11,17-tetra-azabicyclo[11.3.1]heptadeca-1(17),13,15-triene}nickel(<scp>II</scp>) perchlorate (1987)

Two new pyridine-containing penta-aza macrocyclic ligands, 7-[2′-(1″-pyrrolidinyl)ethyl]- and 7-[3′-(1″-pyrrolidinyl)propyl]-3,7,11,17-tetra-azabicyclo[11.3.1]heptadeca-1 (17),13,15-triene (L1 and L2 respectively) have been prepared, and their nickel(II) and copper(II) complexes of formulae [M(L1)(OClO3)][ClO4] and [M(HL)][ClO4]3(M = Ni or Cu, L = L1 or L2) have been isolated and characterised. In the octahedral complex [Ni(L1)(OClO3)][ClO4] the presence of a co-ordinated perchlorate group has been established by X-ray crystallography, and the macrocyclic ligand found to co-ordinate close to the corners of a square pyramid with the pendant pyrrolidinyl group at the apical position.
Thermodynamic anomalies and structural fluctuations in aqueous solutions of tertiary butyl alcohol (2013)

In this work, we discuss the connection between the anomalies of the thermodynamic properties, experimentally observed in tertiary butyl alcohol (TBA) and water solutions, and the molecular clustering in these solutions, as revealed by molecular dynamics (MD) simulations. These anomalies are observed in relatively dilute solutions of about 0.03 to 0.08 mole fraction of TBA and become more pronounced at low temperatures. MD simulations show that these solutions exhibit shortranged (order of 1 nm), shortlived (tens of picoseconds) "micelle-like" structural fluctuations in the same concentration range. We attribute the anomalies in the thermodynamic properties of aqueous TBA solutions to these structural fluctuations on the molecular scale.
EVALUATION OF DESIGN TOOLS FOR RAPID PROTOTYPING OF PARALLEL SIGNAL PROCESSING ALGORITHMS (1996)

Approved for public release; distribution unlimited Acknowledgments I would like to thank those who have helped me in this research. I thank my thesis advisor, Dr. Gary Lamont, for his effort to find an area of research which not only aligned with my experience, but also provided me the opportunity to investigate other areas previously unfamiliar to me. Dr. Lamont provided the right amount of suggestion, encouragement,and freedom for me to make the most out of the research experience. I thank my sponsor, Dr. Robert Ewing, for his insight into current Wright Laboratory signal processing needs and the accompanying motivation. I also would like to thank the members of my thesis committee. My topic has taken many twists and turns over the past year, and while I may have lost some along the way, each was helpful at different stages of the journey. The weary travelers of my thesis committee are Dr. Andrew Terzuoli, Lt.
Series resonant converter with third-order commutation network (1992)

To compensate for the poor output voltage regulation of the series resonant converter (SCR), a converter is derived by adding an inductor in parallel with the resonant capacitor of the conventional SCR. The resulting converter is called the LLC-SRC. This converter is analyzed via a two-dimensional state-plane diagram through a proper transformation of its state variables. Based on the analysis results, a set of characteristic curves is derived showing that the control characteristics and component stresses of the new converter are improved compared with those of a conventional SRC. Based on these curves, the design procedure for the LLC-SRC is formulated. The experimental results from the breadboard model were used to verify the theoretical work.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Abatement of perfluorocarbons with an inductively coupled plasma reactor (1999)

Preliminary tests using an inductively coupled plasma (ICP) reactor to abate C2F6, CF4, and CHF3 show promising results. In conjunction with this, some of the operating parameters, which need to be considered when trying to obtain maximum abatement efficiency, are explored. Near 100% destruction efficiency (DRE) for the persistently fluorinated compounds (PFCs) mentioned earlier has been achieved with O2 as the additive gas. Similarly, the abatement of CF4 with CH4 and/or CH4/O2 as the additive gas, has shown comparable results. For the non-CF4 PFCs, like C2F6 and CHF3, the formation of CF4 as an abatement by-product was monitored and shown that it can be controlled by varying the operating parameters of the ICP reactor. The trends in the DRE observed while manipulating the ICP operating parameters such as ICP power, residence time, amount/type of additive gas, and Ar dilution, show that there are trade offs which must be taken into account. A quadrupole mass spectrometer was used for analyzing the abatement effluents.
Identification of <i>CBL</i>, a proto‐oncogene at 11q23.3, as a novel <i>MLL</i> fusion partner in a patient with de novo acute myeloid leukemia (2003)

We have shown that the CBL gene at 11q23.3, telomeric to MLL, was fused to MLL in an adult patient with de novo acute myeloid leukemia (FAB-M1). Southern blot analysis indicated that the MLL rearrangement was involved in the chromosomal abnormality. cDNA panhandle polymerase chain reaction identified the fusion transcript, in which MLL exon 6 was fused in-frame with CBL exon 8. Long-distance PCR amplified the genomic junction region, which involved the fusion of the 3' portion of an Alu element in intron 6 of MLL with the 5' portion of an Alu element in intron 7 of CBL. The absence of extensive sequence similarity at both breakpoints of MLL and CBL indicated that the recombination was not generated through homologous recombination. MLL and CBL are located between STS markers D11S939 and D11S924. Analysis of the sequence demonstrated that the transcriptional orientation of both genes at 11q23.3 is from centromere to telomere. The results of Southern blotting in conjunction with fluorescence in situ hybridization suggest that the MLL-CBL fusion was the result of an interstitial deletion. CBL, a proto-oncogene, functions as a negative regulator of several receptor protein-tyrosine-kinase signaling pathways and as an adaptor protein in tyrosine phosphorylation-dependent signaling. CBL is the second gene at 11q23.3 found to fuse with MLL.
Mutator Gene of <i>Escherichia coli</i> B (1967)

An azaserine-resistant derivative of Escherichia coli B/UV, AZA/R(1), was found to carry a mutator gene. This gene, designated mutS1, was mapped by means of conjugation and P1kc-mediated transduction. The mutS1 gene was cotransduced with argB at a frequency of 2.4%; the gene order in this region of the chromosome is thy argB mutS1. To determine whether a relationship commonly exists between azaserine resistance and the mutator property, 12 additional azaserine-resistant derivatives of B/UV were developed and tested for the mutator phenotype. None of the twelve was a mutator strain. The level of azaserine resistance was not increased over that of the recipient parent when mutS1 was transduced to an azaserine-susceptible strain. Reversion studies indicated that mutS1 induced adenosine-ribosylthymine to guanosine-cytidine and guanosine-cytidine to adenosine-ribosylthymine transitions. Because such mutational changes are suppressible with deoxynucleosides when induced by base analogues, an attempt was made to suppress the mutator activity of mutS1 by the addition of deoxyribonucleosides to the medium. No suppression was found. Recombinants were prepared containing mutS1 and the Treffers mutator gene of E. coli K-12. The effect of the mutator genes appears to be additive.
Day case anaesthesia and memory (1979)

Two simple anaesthetic techniques were administered to forty healthy women undergoing minor gynaecological surgery. There was a significantly shorter immediate recovery period following the use of a fentanyl and methohexitone technique. Memory function testing revealed an impairment of the ability to retain new information following anaesthesia. This returned to normal within 3 hr.
Review—Surface Coatings for Cathodes in Lithium Ion Batteries: From Crystal Structures to Electrochemical Performance (2022)

Lithium ion batteries (LIBs) have dominated the energy industry due to their unmatchable properties that include a high energy density, a compact design, and an ability to meet a number of required performance characteristics in comparison to other rechargeable systems. Both government agencies and industries are performing intensive research on Li-ion batteries for building an energy-sustainable economy. LIBs are single entities that consist of both organic and inorganic materials with features covering multiple length scales. Two vital parameters for LIBs are their stable and safe operation. Critical insights should be made for understanding the structure to property relationships and the behavior of components under the working condition of LIBs. Since, the cathode serves as a central component of LIBs, the overall cell performance is significantly affected by the chemical and physical properties of the cathode. Cathodes tend to react with the electrolytes and, hence, to undergo surface modifications accompanied by degradation. These side-reactions result in an erosion of battery performance, thereby causing a reduced battery life and power capacity. Recently, techniques for preparing surface coatings on cathode materials have been widely implemented as a measure to improve their stability, to enhance their electrochemical performance, and to prevent detrimental surface reactions between the electrode materials and electrolyte. This review will cover different types of surface coatings for cathode materials, as well as a comparison of the changes in electrochemical performance between those materials with and without an applied coating. In addition, a brief outlook is included for different cathode materials and their coatings.
Optimization of the Supply Voltage System in Interleaved Converters Using Intercell Transformers (2007)

Interleaved power converters are now used in many different conversion systems involving various topologies (series or parallel) and related to different fields or loads. This paper deals with interleaved parallel commutation cells using coupling transformers with a possibly high number of cells. The first part of the paper is a reminder of the basics of magnetic couplers addressing monolithic as well as distributed implementations. The limits associated with the conventional supply of such couplers (supply voltages forming a direct polyphase system) are described. In the second part of the paper, an optimized voltage supply improving the performances of the system is introduced. Experimental results obtained on a seven-cells test bench validate the approach
The Potential of Bone Marrow-Derived Cells to Differentiate to Glomerular Mesangial Cells (2001)

Bone marrow stem cells (BMC) develop into hematopoietic and mesenchymal lineages but have not been known to differentiate into glomerular cells. To investigate whether such differentiation is possible, a search was made for donor glomerular cells in lethally irradiated C57BL/6j (B6) mice given transplants of BMC from syngeneic mice transgenic for green fluorescence protein (GFP) ([GFP-->B6] mice). After the recipients of donor BMC manifested GFP-positive cells in their glomeruli, the numbers of such cells increased markedly, in a time-dependent manner, from 2 wk to 24 wk after bone marrow transplantation. Immunohistochemical analyses revealed that most GFP-positive cells in the glomeruli were neither macrophages nor T cells. With the use of a laser-scanning confocal microscope, GFP-positive cells were observed within the mesangium of [GFP-->B6] mice. Furthermore, indirect immunofluorescence assays demonstrated that desmin-positive cells in the glomeruli of these chimeric mice were also positive for GFP. Among glomerular cells isolated from [GFP-->B6] mice 24 wk after bone marrow transplantation and then cultured, the majority of cells (approximately 84%) stained for desmin and approximately 60% of the desmin-positive cells expressed GFP. In addition, these GFP-positive cells in the cultures contracted in response to angiotensin II stimulation. These results suggest that bone marrow-derived cells may have the potential to differentiate into glomerular mesangial cells.
Sub-epithelial gas breakthrough during femtosecond laser flap creation for LASIK (2007)

The incidence of flap-related complications associated with the use of motorized microkeratomes for creating corneal flap during LASIK is around 5%. For the femtosecond laser there have been previous reports of cavitation bubbles migrating to the anterior chamber resulting in poor tracking during subsequent excimer laser ablation. Vertical subepithelial gas breakthrough during femtosecond laser flap creation is rare and a PubMed search revealed no previous report of this complication. Vertical gas breakthrough occurs between the dissection plane and the subepithelial space resulting in escape of gas bubbles in to the subepithelial space. The cause is unknown but a thin flap or a focal break in the Bowman's membrane may contribute to this complication.
A microfluidic platform for quantitative analysis of cancer angiogenesis and intravasation (2014)

Understanding the mechanism behind cancer metastasis is a major challenge in cancer biology. Several in vitro models have been developed to mimic a cancer microenvironment by engineering cancer-endothelial cell (EC) and cancer-stromal cell interactions. It has been challenging to realistically mimic angiogenesis, intravasation, and extravasation using macro-scale approaches but recent progress in microfluidics technology has begun to yield promising results. We present a metastasis chip that produce microvessels, where EC and stromal cells can be patterned in close proximity to tumor cells. The vessels are formed following a natural morphogenic process and have smooth boundaries with proper cell-cell junctions. The engineered microvessels are perfusable and have well-defined openings toward inlet and outlet channels. The ability to introduce cancer cells into different locations bordering to the microvessel wall allowed generation and maintenance of appropriate spatial gradients of growth factors and attractants. Cancer angiogenesis and its inhibition by anti-vascular endothelial growth factor (bevacizumab) treatment were successfully reproduced in the metastasis chip. Cancer intravasation and its modulation by treatment of tumor necrosis factor-α were also modeled. Compared to other models, the unique design of the metastasis chip that engineers a clear EC-cancer interface allows precise imaging and quantification of angiogenic response as well as tumor cell trans-endothelial migration. The metastasis chip presented here has potential applications in the investigation of fundamental cancer biology as well as in drug screening.
Functional Comparison of the Two <i>Bacillus anthracis</i> Glutamate Racemases (2007)

Glutamate racemase activity in Bacillus anthracis is of significant interest with respect to chemotherapeutic drug design, because L-glutamate stereoisomerization to D-glutamate is predicted to be closely associated with peptidoglycan and capsule biosynthesis, which are important for growth and virulence, respectively. In contrast to most bacteria, which harbor a single glutamate racemase gene, the genomic sequence of B. anthracis predicts two genes encoding glutamate racemases, racE1 and racE2. To evaluate whether racE1 and racE2 encode functional glutamate racemases, we cloned and expressed racE1 and racE2 in Escherichia coli. Size exclusion chromatography of the two purified recombinant proteins suggested differences in their quaternary structures, as RacE1 eluted primarily as a monomer, while RacE2 demonstrated characteristics of a higher-order species. Analysis of purified recombinant RacE1 and RacE2 revealed that the two proteins catalyze the reversible stereoisomerization of L-glutamate and D-glutamate with similar, but not identical, steady-state kinetic properties. Analysis of the pH dependence of L-glutamate stereoisomerization suggested that RacE1 and RacE2 both possess two titratable active site residues important for catalysis. Moreover, directed mutagenesis of predicted active site residues resulted in complete attenuation of the enzymatic activities of both RacE1 and RacE2. Homology modeling of RacE1 and RacE2 revealed potential differences within the active site pocket that might affect the design of inhibitory pharmacophores. These results suggest that racE1 and racE2 encode functional glutamate racemases with similar, but not identical, active site features.
GAS ACCRETION IS DOMINATED BY WARM IONIZED GAS IN MILKY WAY MASS GALAXIES AT<i>z</i>∼ 0 (2012)

We perform high-resolution hydrodynamic simulations of a Milky Way-mass galaxy in a fully cosmological setting using the adaptive mesh refinement code, Enzo, and study the kinematics of gas in the simulated galactic halo. We find that the gas inflow occurs mostly along filamentary structures in the halo. The warm-hot (10^5 K < T < 10^6 K) and hot (T > 10^6 K) ionized gases are found to dominate the overall mass accretion in the system (with dM/dt = 3-5 M_solar/yr) over a large range of distances, extending from the virial radius to the vicinity of the disk. Most of the inflowing gas (by mass) does not cool, and the small fraction that manages to cool does so primarily close to the galaxy (R <~ 20 kpc), perhaps comprising the neutral gas that may be detectable as, e.g., high-velocity clouds. The neutral clouds are embedded within larger, accreting filamentary flows, and represent only a small fraction of the total mass inflow rate. The inflowing gas has relatively low metallicity (Z/Z_solar < 0.2). The outer layers of the filamentary inflows are heated due to compression as they approach the disk. In addition to the inflow, we find high-velocity, metal-enriched outflows of hot gas driven by supernova feedback. Our results are consistent with observations of halo gas at low z.