gebhart/patrepeval huggingface dataset:
Quantitative Bottom-Up Proteomics Depends on Digestion Conditions (2013)

Accurate quantification is a fundamental requirement in the fields of proteomics and biomarker discovery, and for clinical diagnostic assays. To demonstrate the extent of quantitative variability in measurable peptide concentrations due to differences among "typical" protein digestion protocols, the model protein, human serum albumin (HSA), was subjected to enzymatic digestion using 12 different sample preparation methods, and separately, was examined through a comprehensive timecourse of trypsinolysis. A variety of digestion conditions were explored including differences in digestion time, denaturant, source of enzyme, sample cleanup, and denaturation temperature, among others. Timecourse experiments compared differences in relative peptide concentrations for tryptic digestions ranging from 15 min to 48 h. A predigested stable isotope-labeled ((15)N) form of the full-length (HSA) protein, expressed in yeast was spiked into all samples prior to LC-MS analysis to compare yields of numerous varieties of tryptic peptides. Relative quantification was achieved by normalization of integrated extracted ion chromatograms (XICs) using liquid chromatography-tandem mass spectrometry (LC-MS/MS) by multiple-reaction monitoring (MRM) on a triple quadrupole (QQQ) MS. Related peptide fragmentation transitions, and multiple peptide charge states, were monitored for validation of quantitative results. Results demonstrate that protein concentration was shown to be unequal to tryptic peptide concentrations for most peptides, including so-called "proteotypic" peptides. Peptide release during digestion displayed complex kinetics dependent on digestion conditions and, by inference, from denatured protein structure. Hydrolysis rates at tryptic cleavage sites were also shown to be affected by differences in nearest and next-nearest amino acid residues. The data suggesting nonstoichiometry of enzymatic protein digestions emphasizes the often overlooked difficulties for routine absolute protein quantification, and highlights the need for use of suitable internal standards and isotope dilution techniques.
Trends in isothermal microcalorimetry (1997)

Isothermal microcalorimeters are of increasing importance in thermodynamics and as general ‘process monitors’. Recent developments in instrumentation and in experimental methods have been significant and several easy-to-use instruments are now commercially available. Important application areas include investigations of solute–solvent interactions and ligand binding processes, sorption processes, living cellular systems and the assessment of stabilities of technical products. The combination of isothermal calorimetry with different specific analytical techniques seems to be particularly promising.
Influence of tensile stress in steel cables on magnetic Barkhausen noise (1993)

The magnetic Barkhausen noise (BN) method can be applied for stress measurement in ferromagnetic steel cables. The cable is led through magnetizing and sensing coils, and the induced noise is amplified and measured. Seven-wire strands used in reinforced concrete steel rope used by cranes and zinc-coated steel rope are the cables tested. The BN changes with applied tensile stress in all these materials. As tensile stress increases, the magnitude of BN decreases and coercive force increases. The origin of this phenomenon is studied in relation to microstructure and X-ray diffraction (XRD) analysis. Based on the results, one utilization of BN for stress measurement is considered.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Molten-Salt-Cooled Advanced High-Temperature Reactor for Production of Hydrogen and Electricity (2003)

The molten-salt-cooled Advanced High-Temperature Reactor (AHTR) is a new reactor concept designed to provide very high-temperature (750 to 1000°C) heat to enable efficient low-cost thermochemical production of hydrogen (H2) or production of electricity. This paper provides an initial description and technical analysis of its key features. The proposed AHTR uses coated-particle graphite-matrix fuel similar to that used in high-temperature gas-cooled reactors (HTGRs), such as the General Atomics gas turbine-modular helium reactor. However, unlike the HTGRs, the AHTR uses a molten-salt coolant and a pool configuration, similar to that of the General Electric Super Power Reactor Inherently Safe Module (S-PRISM) liquid-metal reactor. Because the boiling points for molten fluoride salts are near ~1400°C, the reactor can operate at very high temperatures and atmospheric pressure. For thermochemical H2 production, the heat is delivered at the required near-constant high temperature and low pressure. For electricity production, a multireheat helium Brayton (gas-turbine) cycle, with efficiencies >50%, is used. The low-pressure molten-salt coolant, with its high heat capacity and natural circulation heat transfer capability, creates the potential for robust safety (including fully passive decay-heat removal) and improved economics with passive safety systems that allow higher power densities and scaling to large reactor sizes [>1000 MW(electric)].
A HIP Based Network Mobility Protocol (2007)

The rapid growth of IP-based mobile telecommunication technologies in the past few years has revealed situations where not only a single node but an entire network moves and changes its point of attachment to the Internet. The main goal of any protocol supporting network mobility (NEMO) is to provide continuous, optimal and secure Internet access to all nodes and even recursively nested mobile subnetworks inside a moving network. This paper describes a Host Identity Protocol (HIP) extension called HIP-NEMO, based on hierarchical topology, signaling delegation and connection tracking to enable secure and efficient network mobility support in the HIP layer
Disk flutter and its impact on HDD servo performance (2001)

With rapid growth in storage density and spindle motor speed in hard disk drives (HDD's), disk flutter and its impact on drive performance is becoming a more and more important issue. In this study, vibrations of disks used in 3.5" hard disk drives with different thickness have been measured. A model has been developed to translate disk motion measured in vertical direction to actual head off-track motion. This model was constructed based on geometric modeling and FEM analysis of disk mode shapes. It was then validated by drive level position error signal (PES) measurements. Based on the model and flutter measurement, the TMR impact of the flutter after servo has been studied and the PES projection for drives with different spindle speeds have been carried out.
<i>The Calculus of Variations</i> (1963)

The simplest problem lagrangian derivatives canonical variables field theory Jacobi's condition the simplest problem in parametric form problems on a conditional extremum the direct method for nonparametric problems the Sturm-Liouville problem the direct method for a problem in parametric form two-demensional problems the generalized dirichlet problem for a linear equation of elliptic type S.N.Bernshtein's principle geodesic lines on a triaxial ellipsoid Poincare's theorem on periodic extremals E.Noether's theorem on invariant functionals.
<title>Erbium 3-um fiber laser in the power range for surgery</title> (1996)

The erbium 2.7-micrometer fluorozirconate fiber laser is investigated in computer simulations and experiments. An output power of 158 mW at 2.7 micrometer is achieved from an erbium- doped single-mode fiber cascade laser. The output power is limited only by the pump power available from the Ti:sapphire laser. The slope efficiency of 23.3% in the cascade-lasing regime is close to the calculated limit of 27%. It is shown that this cascade regime represents the most efficient system for the operation of an erbium 2.7-micrometer fluorozirconate fiber laser.
PEG-epirubicin Conjugates with High Drug Loading (2005)

PEG is used as a polymeric carrier for low molecular weight drugs, but limitations arise from the fact that only one or two hydroxyl residues are on each polymer. Therefore, the synthesis of dendrimeric structures, based on amino adipic acid or beta-glutamic acid, as a branching molecule, built on a PEG diol of Mw 10,000Da was investigated. The large polycyclic drug epirubicin molecule was chosen as a model to investigate the influence of structure branching and drug steric hindrance during coupling reactions. Several derivatives with increased numbers of drug molecules linked to each PEG chain were synthesized and their physical, chemical and biological properties were studied. The use of specific amino bicarboxylic acids (amino adipic acid or -glutamic acid), as the branching moiety for the dendrimer synthesis, allowed linking the hindered molecule epirubicin to multibranched PEG. Most drug loaded conjugates only dissolve in water following dissolution in DMSO. This solubility problem was solved by adding a hydrophilic peptide linker between the drug and the polymer. The conjugates, synthesized in good yield and purity, showed better stability than free epirubicin in different pH buffers and in plasma as well as prolonged residence time in blood. Dynamic light scattering investigation showed that these products have a high tendency to aggregate forming stable micelles.
Intrathecal IgM synthesis predicts the onset of new relapses and a worse disease course in MS (2002)

The presence of oligoclonal IgM bands in CSF can be a prognostic marker in the early phases of MS.
Polyclonal hematopoietic reconstitution in leukemia patients at remission after suppression of specific gene rearrangements [see comments] (1993)

Clonality studies of hematopoietic reconstitution after remission were performed in 24 female patients (pts) with leukemias characterized by specific molecular markers. At diagnosis, 13 pts had promyelocytic leukemia (PML) retinoic acid receptor-alpha (RAR-alpha)-rearranged acute promyelocytic leukemia (APL), 8 Philadelphia positive (Ph′+) break-point cluster region (BCR+) chronic myeloid leukemia (CML), and 3 Ph′+ (BCR+) acute lymphoblastic leukemia (ALL). All pts were analyzed at presentation and after Southern blot suppression of specific rearrangements after various treatments, including conventional chemotherapy, autologous or allogeneic bone marrow transplant (BMT), all-trans retinoic acid, and alpha-2b interferon. DNA from BM samples collected at diagnosis and, during remission phases, were subjected to Southern blot analysis with the M27 beta probe to detect X chromosome methylation differences, and with BCR, in CML and ALL cases, or PML/RAR- a probes for gene rearrangements, in APL cases. Twenty-one of the 24 pts had polyclonal methylation patterns at remission, together with disappearance of the specific rearrangement, whereas 3 pts retained the same single unmethylated DXS255 allele detected at diagnosis despite no evidence of gene rearrangement. Concerning these 3 pts, such an apparently clonal pattern was also observed in one case in T lymphocytes and skin-derived DNA; in a second case in BM fibroblasts and T lymphocytes; and, in the third case, in blood mononuclear cells obtained from her healthy female BM donor. All these 3 pts are in unmaintained clinical and cytogenetic remission after more than 20 months off therapy. These data suggest that (1) polyclonal and presumably normal hematopoiesis occurs in APL, CML, and Ph′+ ALL pts once the major burden of leukemic cells carrying a specific rearrangement is suppressed by treatment; and (2) unbalanced X chromosome methylation patterns, or aberrant methylation of X chromosome regions may be observed in some cases, most likely reflecting constitutional features simulating a clonal picture.
Large restriction fragments containing poly-TG are highly polymorphic in a variety of vertebrates (1990)

Southern blots of genomic DNA from a variety of species digested by restriction endonucleases having a four-bp specificity, were probed with a bovine genomic clone consisting of seven tandem poly-TG stretches separated by a 29bp linker sequence. Highly variable DNA 'fingerprint' patterns were obtained in chicken, sheep, and horse, moderately variable DNA 'fingerprints' in mouse and man, and a monomorphic pattern in Drosophila. In chicken, horse and man a (TG)10 synthetic oligonucleotide probe gave results identical to those given by the bovine probe. Furthermore, in chicken the DNA fingerprint variation showed typical Mendelian inheritance and differed from the fingerprints obtained with Jeffreys 33.6 and M13 minisatellite probes. Thus, for a variety of vertebrate species, poly-TG-containing probes can uncover useful genetic variation.
Department Heads’ Self-Perception of their Leadership Styles at Jimma University, Ethiopia (2011)

The purpose of this study was to investigate the self-perception of department heads about their own leadership styles at Jimma University. The study employed descriptive survey method and used quantitative approach. Department heads were source of data. Using availability sampling technique, all 51 department heads in the university were included in the study. Accordingly, LEAD-Self instrument and Demographic Variables Survey questionnaires were employed to collect data. The data was analyzed using both descriptive and inferential statistics and finally examined using relevant literature. The result of this study showed that department heads perceived the leadership style ‘selling’ as their own predominant and ‘participating’ as their secondary leadership style. The study further revealed that the perception of department heads did not significantly vary across demographic variables such as work experience, level of education and disciplinary background. Finally, the researchers recommended that department heads, as leaders; need to vary their leadership style in order to fit into the situations. Specially, in higher education institutions, where majority of the teaching staff hold post graduate degree, deligative leadership style seems to be appropriate and department heads, therefore, need to exercise such kind of leadership style as needed. Moreover, the university is advised to arrange continuous and relevant training for department heads to make them capable of varying their leadership styles to fit into situations. In addition, since leadership styles can vary across situations and time, further research needs to be conducted if there may be differences in the leadership styles of department heads longitudinally.
Bayesian variable assessment (1998)

Variable-selection regression methods are oriented towards selecting a single model as the vehicle for further inferences. The appropriate inference about variables not present in the selected model is unclear—the conclusion that they are unimportant and have no effect is unsatisfactory and may be misleading. Also, quite often, there will be a large number of subsets with nearly equal fit as measured by any of a number of regression criteria, making the selection of one subset all the more problematic. We propose that combining information across all models provides useful information that is usually ignored. Additionally, we feel the objective of the statistical analysis should not be to select a subset of variables for inclusion in a model, but to assess the role of each predictor variable in any relationship with the response. The term variable assessment we think is more descriptive of this objective. A single model is not desired necessarily, but an assessment of each variable. We develop a method for variable assessment that makes use of Bayesian modelselection methodology and combines information from all possible models. Exact implementation of the method would require fitting all possible regression models. However, using the Gibbs sampler approach to computations leads to substantial computational savings over fitting every possible model. Simulations suggest that combining information from all models, i.e., model averaging, has good statistical properties.
Aqueous Oxygen (1997)

Intra-arterial AO infusion was effective in these models for regional correction of hypoxemia and production of hyperoxemia.
Cellular predictive factors for the drug response of lung cancer. (2001)

The main objective of this study to analyze which of 31 cellular factors (resistance proteins, proliferative factors, apoptotic factors, angiogenic factors, proto-oncogenes) most accurately predict the resistance of non-small cell lung carcinomas. To this purpose, we used a short-term in vitro test that measures changes in the rate at which radioactive nucleic acid precursors are incorporated into tumor cells after the addition of doxorubicin to determine the response to doxorubicin in 94 non-small cell lung carcinomas. The results obtained by the short-term test were related to the various cellular factors which were in turn determined by immunohistochemistry and flow cytometry. A significant correlation was found between the data obtained by the short-term test and the expression of P-glycoprotein 170 (P = 0.00004), glutathione-S-transferase-pi (P = 0.0002), metallothionein (P = 0.0008), thymidylate synthase (P = 0.002), O6-methylguanine-DNA-methyltransferase (P = 0.008) and lung resistance-related protein (LRP, P = 0.03). There was only a weak correlation between heat shock proteins (HSP70) and no correlation between the expression of topoisomerase II or catalase and the short-term test results. To measure the proliferative activity, the following were determined: PCNA, cyclin A, cyclin D and cdk2. Only a weak relationship was found between the expression of cdk2 (P = 0.04) and PCNA (P = 0.05) and the doxorubicin response in vitro. Of the investigated pro-apoptotic factors (Fas/CD95, Fas ligand, caspase-3), only Fas/CD95 is significantly associated with the drug response (P = 0.007). The apoptotic index also reveals a significant correlation (P = 0.03). Angiogenesis, as measured by the microvessel density and the angiogenic factors, is inversely correlated to the resistance of non-small cell lung cancer. Platelet-derived endothelial cell growth factor (PD-ECGF) and vascular endothelial growth factor (VEGF) exhibit a significant relationship to the drug resistance (P = 0.0006 and P = 0.004, respectively). Of the investigated proto-oncogenes (Fos, Jun, ErbB-1, ErbB-2, Myc, Ras), only ErbB-2 is weakly associated with the in vitro short term test. In order to determine whether combining factors can result in improved predictive information, combinations of the factors (pairs, triplets) were analyzed. The systematic investigation of these combinations yields an improvement in the predictive information. With one factor up to 76.6% of the tumors, with two factors up to 85.4% and with three factors up to 89.5% of the tumors could be correctly diagnosed.
Reusable garbled gates for new fully homomorphic encryption service (2017)

In this paper, we propose a novel way to provide a fully homomorphic encryption service, namely by using garbled circuits. From a high level perspective, garbled circuits and fully homomorphic encryption, both aim at implementing complex computation on ciphertexts. We define a new cryptographic primitive named reusable garbled gate, which comes from the area of garbled circuits, then based on this new primitive we show that it is very easy to construct a fully homomorphic encryption. However, the instantiation of reusable garbled gates is rather difficult, in fact, we can only instantiate this new primitive based on indistinguishable obfuscation. Furthermore, reusable garbled gates can be a core component for constructing the reusable garbled circuits, which can reduce the communication complexity of them from O(n) to O(1). We believe that reusable garbled gates promise a new way to provide fully homomorphic encryption and reusable garbled circuits service fast.
A MODFET-based optoelectronic integrated circuit receiver for optical interconnects (1993)

The design, fabrication, and characterization of a 0.85- mu m sensitive photoreceiver is described. The monolithically integrated optoelectronic receiver is based on pseudomorphic InGaAs on GaAs modulation-doped field-effect transistors (MODFETs) and metal-semiconductor-metal (MSM) photodetectors. High-performance quarter-micrometer MODFETs with f/sub t/'s of approximately 70 GHz are utilized in a two-stage transimpedance amplifier. An asymmetric and a symmetric amplifier design are compared. The symmetric design is found to provide the desired zero DC offset voltage for a variety of supply voltages. Excess MSM-detector dark current and low-frequency internal gain are greatly reduced through the use of a silicon passivation layer and/or AlGaAs cap layer. Receiver transimpedances between 100 and 5000 Omega are obtained by varying the bias on an active feedback resistor. The parasitic capacitances of this common-gate feedback FET are studied. A transimpedance amplifier bandwidth as high as 14 GHz and an overall photoreceiver bandwidth of 11 GHz are measured.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
New therapeutic approaches for Pompe disease: enzyme replacement therapy and beyond. (2014)

Pompe disease is an autosomal recessive disorder of glycogen metabolism caused by a deficiency of the lysosomal enzyme acid alpha-glucosidase (GAA). Prior to 2006, therapy was palliative. Severely affected infants with Pompe succumbed to cardiomyopathy or respiratory failure by one year of age. Enzyme replacement therapy (ERT) with alglucosidase alfa (Genzyme, Cambridge, MA, USA) is currently the only approved treatment for Pompe disease which has improved overall survival, ventilator-free survival, cardiomyopathy, and motor development in infants. In patients with late onset Pompe disease, ERT has resulted in disease course stabilization with motor and pulmonary improvements. Factors impacting outcome include age at start of ERT, muscle fiber type, underlying genotype and a multidisciplinary approach to care. This article highlights the lessons learned from infants and adults treated with ERT, limitations of ERT, and the development of adjunctive and alternative therapies, including immune modulation, upregulation of receptor expression, diet and exercise, second-generation recombinant ERT, chaperone therapy, substrate reduction therapy and gene therapy.
Bloch-wave engineering for high-Q, small-V microcavities (2003)

The overall decay rate of the mode in an optical microcavity formed by a defect surrounded by two Bragg mirrors in a monomode waveguide is driven by two mechanisms, the desired coupling to a guided mode and the detrimental coupling to radiation modes. We propose two approaches fully compatible with planar fabrication, which allow to increase the cavity Q's by several orders of magnitude while keeping constant the mode volume V of the cavity. The first approach consists of engineering the mirror to taper the guided mode into the mirror Bloch mode, thus decreasing losses. The second approach is less intuitive and relies on a recycling mechanism of the radiation losses. The study is supported by computational results obtained for two-dimensional silicon-on-insulator geometries, but the results apply as well to other related geometries like three-dimensional photonic-wire cavities.