gebhart/patrepeval huggingface dataset:
Method Development of Efficient Protein Extraction in Bone Tissue for Proteome Analysis (2007)

Exploring bone proteome is an important and challenging task for understanding the mechanisms of physiological/pathological process of bone tissue. However, classical methods of protein extraction for soft tissues and cells are not applicable for bone tissue. Therefore, method development of efficient protein extraction is critical for bone proteome analysis. We found in this study that the protein extraction efficiency was improved significantly when bone tissue was demineralized by hydrochloric acid (HCl). A sequential protein extraction method was developed for large-scale proteome analysis of bone tissue. The bone tissue was first demineralized by HCl solution and then extracted using three different lysis buffers. As large amounts of acid soluble proteins also presented in the HCl solution, besides collection of proteins in the extracted lysis buffers, the proteins in the demineralized HCl solution were also collected for proteome analysis. Automated 2D-LC-MS/MS analysis of the collected protein fractions resulted in the identification of 6202 unique peptides which matched 2479 unique proteins. The identified proteins revealed a broad diversity in the protein identity and function. More than 40 bone-specific proteins and 15 potential protein biomarkers previously reported were observed in this study. It was demonstrated that the developed extraction method of proteins in bone tissue, which was also the first large-scale proteomic study of bone, was very efficient for comprehensive analysis of bone proteome and might be helpful for clarifying the mechanisms of bone diseases.
Parallel finite element methods for modeling contact in geometrically nonlinear membrane structures (2002)

This dissertation involves finite element modeling of geometrically nonlinear membrane structures with emphasis on the development of parallel computational methods for (1) modeling contact phenomena in membrane structures, and (2) mesh updating in fluid structure interaction (FSI) simulations. ^ A parallel contact formulation for large displacement problems is successfully established based on an implicit time integration scheme and the penalty method. The implicit integration is well suited for structural analysis in which contact happens over a long duration. Efficient parallel communication schemes are developed for the implicit contact algorithms. A “lumping” algorithm is developed that overcomes the difficulty in incorporating contact stiffness in large displacement problems, and eliminates the ill-conditioning in structural stiffness matrix caused by the use of a large penalty parameter. Numerical simulations are conducted to verify the accuracy and efficiency of the new contact algorithms. ^ Using the new contact analysis formulation, three large-scale simulations involving contact phenomena in parachute systems are performed. The first involves contact between three parachutes used in a cluster. The second involves contact within a single parachute during inflation from a folded configuration. The third involves contact of an inflated canopy by a foreign object. The new parallel contact algorithms are numerically stable for these problems that involve dynamics of thin fabric structures and sustained contact over a large time period. ^ Several new strategies are developed for updating the fluid mesh in fluid-structure interaction simulations to accommodate large displacements of the structure. These strategies are based on a “pseudo-solid” model, in which the fluid mesh is treated as elastic solid subjected to prescribed motions by the structural model. The methods are applied to a two-dimensional model under different types of motion for verification. Compared to previous work, the approaches developed in this work are able to achieve efficient mesh moving with minimum element shape distortion and volume change. ^
Relationship Between Periodontal Disease in Pregnant Women and the Nutritional Condition of Their Newborns (2002)

These data suggest that PD in pregnant women could be a clinically significant risk factor for preterm deliveries and low birth weight. There was considerable variability in the results, and these preliminary findings need to be confirmed in larger studies.
Native mass spectrometry and ion mobility characterization of trastuzumab emtansine, a lysine‐linked antibody drug conjugate (2015)

Antibody-drug conjugates (ADCs) are biochemotherapeutics consisting of a cytotoxic chemical drug linked covalently to a monoclonal antibody. Two main classes of ADCs, namely cysteine and lysine conjugates, are currently available on the market or involved in clinical trials. The complex structure and heterogeneity of ADCs makes their biophysical characterization challenging. For cysteine conjugates, hydrophobic interaction chromatography is the gold standard technique for studying drug distribution, the naked antibody content, and the average drug to antibody ratio (DAR). For lysine ADC conjugates on the other hand, which are not amenable to hydrophobic interaction chromatography because of their higher heterogeneity, denaturing mass spectrometry (MS) and UV/Vis spectroscopy are the most powerful approaches. We report here the use of native MS and ion mobility (IM-MS) for the characterization of trastuzumab emtansine (T-DM1, Kadcyla(®)). This lysine conjugate is currently being considered for the treatment of human epidermal growth factor receptor 2 (HER2)-positive breast cancer, and combines the anti-HER2 antibody trastuzumab (Herceptin(®)), with the cytotoxic microtubule-inhibiting maytansine derivative, DM1. We show that native MS combined with high-resolution measurements and/or charge reduction is beneficial in terms of the accurate values it provides of the average DAR and the drug load profiles. The use of spectral deconvolution is discussed in detail. We report furthermore the use of native IM-MS to directly determine DAR distribution profiles and average DAR values, as well as a molecular modeling investigation of positional isomers in T-DM1.
Ranging and processing mobile-satellite (1988)

A description and an analysis of a concept for a future satellite system for the cooperative surveillance and data link service of mobiles (e.g. aircraft, ships, and trucks) are presented. The system approach described, called Ranging and Processing Satellite (RAPSAT), is based on onboard processing and the use of crosslink communications (direct from one satellite to another) to provide data-link and cooperative surveillance functions. System architecture, multiple access, acquisition, and capacity are discussed and analyzed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A Design and Development of Novel Polymeric Prodrugs Prepared by Mechanochemical Solid-State Polymerization (2000)

The mechanochemical polymerization of solid-state monomer was first reported in 1959. Nevertheless, relatively little work has been done. We reported the first in-depth study of the mechanochemical polymerization of specially synthesized solid-state monomers, methacryloyl derivatives of bioactive compounds including detailed mechanistic implications. There are many advantages for this reaction. One of the most striking properties observed in the resulting polymers is that these polymeric prodrugs are of very low heterogeneity (narrow molecular weight distribution) which is of great value in pharmaceuticals for highly functionalized polymeric prodrugs. Thus, the present reaction provides a novel and simple methodology for the syntheses of highly functionalized polymeric prodrugs through a totally dry process. The nature of drug release from many kinds of polymeric prodrugs prepared by mechanochemical polymerization was also investigated. The rate of drug release from the polymeric prodrugs can be controlled by the property of comonomer and the structure of spacer between the main chain of polymer and drug. Several applications of polymeric prodrugs (chemoembolization and hybrid polymeric prodrugs) were also described. We have carried out the mechanochemical polymerization in the presence of pharmaceutical aids to exploit the features of this reaction. If one takes the physicochemical property of pharmaceutical aids into consideration, novel composite polymeric prodrugs possessing a variety of rates of drug release can be synthesized simultaneously with mixing.
Chemical Composition and Antimicrobial Activity of the Leaf Oil of<i>Amomum cannicarpum</i>(Wight) Bentham ex Baker (2006)

Abstract The essential oil obtained by hydrodistillation of the leaves of Amomum cannicarpum (Wight) Bentham ex Baker, (Family: Zingiberaceae) was analyzed by GC/FID and GC/MS. Individual components of the oil were identified by their mass spectra which were compared with published work. Twenty-nine compounds were identified, of which the major components were β-pinene (9.0%), caryophyllene oxide (6.6%), β-bisabolene (6.4%) and δ-cadinene (6.2%). The oil showed significant antimicrobial activity against certain Gram-positive and Gram-negative bacteria as well as against two fungi (Candida albicans and Aspergillus fumigatus).
Some observations on the assay of staphylococcal enterotoxin by the monkey-feeding test. (1953)

Abstract A wide variation in susceptibility was found in approximately 1,000 Macaca mulatta injected intragastrically with staphylococcal enterotoxin. The relative susceptibility of animals can be predicted to some degree on the basis of past response to enterotoxin. Graded dosage-response curves are not very satisfactory unless new animals are used. Unprovoked emesis has been observed on rare occasions. False positive vomiting reactions due to a dialyzable agent have been encountered in experimental preparations. These reactions were promptly detected by the use of proper controls.
Hadoop. TS: Large-Scale Time-Series Processing (2013)

The paper describes a computational framework for time-series analysis. It allows rapid prototyping of new algorithms, since all components are re-usable. Generic data structures represent different types of time series, e. g. event and interevent time series, and define reliable interfaces to existing big data. Standalone applications, highly scalable MapReduce programs, and User Defined Functions for Hadoop-based analysis frameworks are the major modes of operation. Efficient implementations of univariate and bivariate analysis algorithms are provided for, e. g., long-term correlation, crosscorrelation and event synchronization analysis on large data sets.
Phosphoprotein inhibitor CPI-17 specificity depends on allosteric regulation of protein phosphatase-1 by regulatory subunits (2004)

Inhibition of myosin phosphatase is critical for agonist-induced contractility of vascular smooth muscle. The protein CPI-17 is a phosphorylation-dependent inhibitor of myosin phosphatase and, in response to agonists, Thr-38 is phosphorylated by protein kinase C, producing a >1,000-fold increase in inhibitory potency. Here, we addressed how CPI-17 could selectively inhibit myosin phosphatase among other protein phosphatase-1 (PP1) holoenzymes. PP1 in cell lysates was separated by sequential affinity chromatography into at least two fractions, one bound specifically to thiophospho-CPI-17, and another bound specifically to inhibitor-2. The MYPT1 regulatory subunit of myosin phosphatase was concentrated only in the fraction bound to thiophospho-CPI-17. This binding was eliminated by addition of excess microcystin-LR to the lysate, showing that binding at the active site of PP1 is required. Phospho-CPI-17 failed to inhibit glycogen-bound PP1 from skeletal muscle, composed primarily of PP1 with the striated muscle glycogen-targeting subunit (G(M)) regulatory subunit. Phospho-CPI-17 was dephosphorylated during assay of glycogen-bound PP1, not MYPT1-associated PP1, even though these two holoenzymes have the same PP1 catalytic subunit. Phosphorylation of CPI-17 in rabbit arteries was enhanced by calyculin A but not okadaic acid or fostriecin, consistent with PP1-mediated dephosphorylation. We propose that CPI-17 binds at the PP1 active site where it is dephosphorylated, but association of MYPT1 with PP1C allosterically retards this hydrolysis, resulting in formation of a complex of MYPT1.PP1C.P-CPI-17, leading to an increase in smooth muscle contraction.
Identification of candidate antigen in Whipple's disease using a serological proteomic approach (2006)

Whipple's disease (WD) is a chronic multisystemic infection, caused by Tropheryma whipplei, a Gram-positive rod. Recently, a reliable method has been developed for cultivating T. whipplei in vitro. This together with the availability of complete genome sequence of T. whipplei prompted us to initiate proteome analysis of T. whipplei. The objective of the present study was to identify candidate proteins for serological diagnosis of WD. Immunoreactivities of sera collected from 18 patients with WD were compared with those of 24 control subjects who did not have WD. For this, we used 2-DE, immunoblotting, and MS. In total, we identified 23 candidate antigenic proteins. These included a subset of six proteins, each of which was found significantly more frequently in cases as compared to their controls. The remaining 17 proteins were found exclusively in cases. The methods we used in the current study enabled us to identify candidate antigens that, in our view, might be useful for serological diagnosis of WD.
Reduction of hydroxy-functionalised carbaboranyl carboxylic acids and ketones by organolithium reagents (2015)

While the reaction of carbaboranyl carboxylic acids and ketones with organolithium reagents generally leads to cleavage of the exo-polyhedral C-C bond, introduction of a hydroxyl group at the second carbon atom of the cluster enables the reduction of the carbonyl compounds to tertiary alcohols. The proposed mechanism involving the formation of dimeric contact ion pairs was supported by X-ray crystallography and theoretical calculations.
NiFe Plated Biaxial MEMS Scanner for 2-D Imaging (2007)

A two-axis microelectromechanical systems micromirror actuator is developed for retinal scanning display and imaging applications. The device operation makes use of magnetostatic torque produced by the combination of a flux generating custom-made high-frequency electrocoil and the NiFe layer deposited on the movable part. Modeling of the actuation in the magnetic domain, as well as the experimental characterization of the mechanical part is described. The device is capable of full optical scan angles of 88deg (at 100-mA root-mean-square coil current) and 1.8deg for slow and fast-scan directions, respectively. In combination with a mirror size of 1.5 mm, resulting thetas <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">opt</sub> middotD products are 132degmiddotmm and 2.7degmiddotmm for slow and fast axis, respectively. Atmospheric operation of the device is enabled due to high mechanical quality factors of the order of 3000
Age-Dependent Exacerbation of White Matter Stroke Outcomes (2013)

Age has a profound effect on the outcome of WMS, with more prolonged cell death and oxidative damage, increased inflammation, greater secondary white matter atrophy, and a worse behavioral effect in aged versus young-adult mice.
Quantitation of Flavonoid Constituents in <i>Citrus</i> Fruits (1999)

Twenty-four flavonoids have been determined in 66 Citrus species and near-citrus relatives, grown in the same field and year, by means of reversed phase high-performance liquid chromatography analysis. Statistical methods have been applied to find relations among the species. The F ratios of 21 flavonoids obtained by applying ANOVA analysis are significant, indicating that a classification of the species using these variables is reasonable to pursue. Principal component analysis revealed that the distributions of Citrus species belonging to different classes were largely in accordance with Tanaka's classification system.
Applied Spectroscopy: A Compact Reference for Practitioners (1998)

The Practical Basics of Spectrometry: J. Workman, Optical Spectrometers. J. Workman, UV-VIS-NIR Spectrometry. J. Coates, IR Spectrometry: Sample Preparation and Spectrum Acquisition. J. Duckworth,Spectroscopic Quantitative Analysis. J. Duckworth, Spectroscopic Qualitative Analysis. Reflectance Measurements of Solids: A. Springsteen, Reflectance Spectroscopy: An Overview of Classification and Techniques. J. Workman, Spectroscopy of Solids. A. Springsteen, Standards for Reflectance Measurements. K.A. Snail and L.M. Hanssen, Accurate Measurements of Spectral Reflectance: Directional Hemispherical and Hemispherical Directional Reflectance Measurements Using Conic Mirror Reflectometers. S. McCall, The Bi-directional Reflectance Distribution Function. Practical Application of Spectroscopic Measurement: E.W. Ciurczak, Selecting a Spectroscopic Method by Industrial Application. J. Murray Stewart,Color and Solar Transmittance Measurements. S. White, Optical Spectroscopy of New Materials. J.F. Cordaro, Spectroscopy of Ceramics. E. Ciurczak, Spectroscopy Using Flowing Systems for Chemical, Pharmaceutical, and Biomedical Applications. S. Ghosh, Textile Application of Molecular Spectroscopy. J.M. Stewart, Solar Measurements. Glossary. Appendix.
Real-time scheduling of multiple segment tasks (2002)

The authors study the problem of on-line non-preemptive scheduling of multiple segment real-time tasks. Task segments alternate between using CPU and I/O resources. A task model is proposed which encompasses a wider class of tasks than models proposed earlier. Instead of developing new scheduling algorithms, the authors develop a class of slack distribution policies which use varying degrees of information about task structure and device utilization to budget task slack. Slack distribution policies are shown to improve the performance of all scheduling algorithms studied. Two key observations are: slack distribution is helpful beyond a certain threshold of task arrival rate, and algorithms which normally perform poorly are helped to a greater degree by slack distribution. A study of various scheduling algorithms for a constant value function reveals that all of them favor tasks with a large number of small segments to tasks with a small number of large segments. It is shown that the Moore ordering algorithm is not optimal for multiple segment tasks.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Feasibility of intercalated graphite railgun armatures (1990)

Graphite intercalation compounds may provide an excellent material for the fabrication of electro-magnetic railgun armatures. As a pulse of power is fed into the armature the intercalate could be excited into the plasma state around the edges of the armature, while the bulk of the current would be carried through the graphite block. Such an armature would have the desirable characteristics of both diffuse plasma armatures and bulk conduction armatures. In addition, the highly anisotropic nature of these materials could enable the electrical and thermal conductivity to be tailored to meet the specific requirements of electromagnetic railgun armatures. Preliminary investigations were performed in an attempt to determine the feasibility of using graphite intercalation compounds as railgun armatures. Issues of fabrication, resistivity, stability, and electrical current spreading are addressed for the case of highly oriented pyrolytic graphite.
A Mitochondrion-Targeted Antioxidant Ameliorates Isoflurane-Induced Cognitive Deficits in Aging Mice (2015)

Isoflurane possesses neurotoxicity and can induce cognitive deficits, particularly in aging mammals. Mitochondrial reactive oxygen species (mtROS) have been linked to the early pathogenesis of this disorder. However, the role of mtROS remains to be evaluated due to a lack of targeted method to treat mtROS. Here, we determined in aging mice the effects of the mitochondrion-targeted antioxidant SS-31, on cognitive deficits induced by isoflurane, a general inhalation anesthetic. We further investigated the possible mechanisms underlying the effects of SS-31 on hippocampal neuro-inflammation and apoptosis. The results showed that isoflurane induced hippocampus-dependent memory deficit, which was associated with mitochondrial dysfunction including reduced ATP contents, increased ROS levels, and mitochondrial swelling. Treatment with SS-31 significantly ameliorated isoflurane-induced cognitive deficits through the improvement of mitochondrial integrity and function. Mechanistically, SS-31 treatment suppressed pro-inflammatory responses by decreasing the levels of NF-κB, NLRP3, caspase 1, IL-1β, and TNF-α; and inhibited the apoptotic pathway by decreasing the Bax/Bcl-2 ratio, reducing the release of cytochrome C, and blocking the cleavage of caspase 3. Our results indicate that isoflurane-induced cognitive deficits may be attenuated by mitochondrion-targeted antioxidants, such as SS-31. Therefore, SS-31 may have therapeutic potentials in preventing injuries from oxidative stresses that contribute to anesthetic-induced neurotoxicity.
Preserved endothelium-dependent vasodilation at the vasospastic site in patients with variant angina. (1992)

Endothelial dysfunction has been implicated as a cause of coronary vasospasm in patients with variant angina. This study aimed to determine if endothelium-dependent vasodilation evoked with substance P (SP) was altered at the spastic site where vasospasm was induced by acetylcholine (ACH) in patients with variant angina. It has been shown that SP evokes endothelium-dependent vasodilation with no direct effect on vascular smooth muscle in excised human coronary arteries. SP and ACH were infused into the coronary arteries in nine patients with variant angina in whom coronary arteriograms showed normal or mild atherosclerotic lesions. The vasomotor responses of coronary arteries were assessed by quantitative arteriography. ACH at a high dose (100 micrograms/min) provoked coronary vasospasm associated with anginal attack in all patients. In contrast, SP at graded doses (13.5, 40, and 135 ng/min) caused the dose-dependent and comparable increases in the coronary diameter at the spastic and control sites. ACH at a low dose (10 micrograms/min) also caused comparable vasodilation at the spastic and control sites in patients with normal coronary arteries. Coronary vasodilating responses to SP were comparable in patients with variant angina and those with atypical chest pain. The results indicate that endothelium-dependent vasodilation evoked with SP and ACH at the low dose was present at the vasospastic site in patients with variant angina. These findings suggest that the ACH-induced coronary vasospasm in patients with variant angina results from hyperreactivity of vascular smooth muscle to ACH but not from endothelial dysfunction.
A Low-Power Quadrature VCO Using Current-Reused Technique and Back-Gate Coupling (2007)

A novel quadrature voltage controlled oscillator (QVCO) using current-reused tech- nique and back-gate coupling is presented. The QVCO realized with LC-tank is demonstrated in a 0.18um RF CMOS 1P6M process. Using the current-reused technique e-ciently reduces the power dissipation. However, by stacking switching transistors in series like a cascade, the architecture cannot perform well in phase noise. Through an improved circuit schematic with back-gate coupling, the phase noise of the circuit can be lowered. As a result of reducing four transistors in the circuit, the total power dissipation can be cut down even more. The simulation shows the phase noise is around i107dBc/Hz at 1MHz ofiset and the output frequency tuning range of the fabricated QVCO is 600kHz ranging from 5.15 to 5.75GHz for 802.11a. The circuit draws only 1.5mA from a 1.8-V supply. Compared with the recent works, the proposed topologies show a better phase noise performance and can be adopted for low-power applications.