gebhart/patrepeval huggingface dataset:
Gelatin‐embedded cell–polymer constructs for histological cryosectioning (2004)

Abstract Many tissue‐engineering strategies involve the delivery of cells via porous polymer scaffolds. Obtaining histological sections of the emerging tissue is often necessary to analyze numerous characteristics of the microscopic environment. However, difficulties arise upon applying standard histological techniques to cell‐seeded polymer scaffolds. This report describes a simple and reliable method for cryosectioning cell–polymer constructs embedded in gelatin. Solvent‐soluble (PLGA) and insoluble (PGA) scaffolds were cultured in vitro with preosteoblasts, followed by histological processing with paraffin, OCT, or gelatin. Although paraffin‐embedded PGA scaffolds withstood standard sectioning and rinsing steps, paraffin‐embedded PLGA scaffolds were partially dissolved during the clearing step. OCT‐embedded scaffolds produced sections that did not adhere well to slides, and most of the sample was lost during rinsing steps. In contrast, gelatin‐embedded scaffolds exhibited adequate structural integrity during cryosectioning, adhered well to the slides, retained the actual polymer morphology, and exhibited compatibility with common stains. © 2004 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater 72B: 79–85, 2005
Models and model building in intelligent process control systems (2002)

A novel approach to the intelligent control of cogeneration plants comprising multiple-aspect modeling and model interpretation is presented. The most important characteristics of this approach are the following: (1) models represent the plant as well as the control system; (2) the control system is derived from this representation; (3) processing of sensory input signals is done in the context of the models; (4) control actions are determined based on the basis of the actual state of the plant and the models. This system has demonstrated that not only are the capabilities of the control system enhanced, but the system development efforts are reduced dramatically as well.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Experimental approaches to kinetics of gas diffusion in hydrogenase (2008)

Hydrogenases, which catalyze H(2) to H(+) conversion as part of the bioenergetic metabolism of many microorganisms, are among the metalloenzymes for which a gas-substrate tunnel has been described by using crystallography and molecular dynamics. However, the correlation between protein structure and gas-diffusion kinetics is unexplored. Here, we introduce two quantitative methods for probing the rates of diffusion within hydrogenases. One uses protein film voltammetry to resolve the kinetics of binding and release of the competitive inhibitor CO; the other is based on interpreting the yield in the isotope exchange assay. We study structurally characterized mutants of a NiFe hydrogenase, and we show that two mutations, which significantly narrow the tunnel near the entrance of the catalytic center, decrease the rates of diffusion of CO and H(2) toward and from the active site by up to 2 orders of magnitude. This proves the existence of a functional channel, which matches the hydrophobic cavity found in the crystal. However, the changes in diffusion rates do not fully correlate with the obstruction induced by the mutation and deduced from the x-ray structures. Our results demonstrate the necessity of measuring diffusion rates and emphasize the role of side-chain dynamics in determining these.
Dynamics of Poly(propylene sulfide) Studied by Dynamic Mechanical Measurements and Dielectric Spectroscopy (1999)

Dynamical properties of bulk poly(propylene sulfide) (PPS) were investigated for a range of molar masses between 600 and 50 000 g/mol. The primary and secondary relaxation (α-relaxation and β-relaxation) were studied using dielectric spectroscopy. The local segmental relaxation (α-relaxation) and the chain backbone conformational relaxation were studied using dynamic mechanical measurements. The dynamical properties of PPS are compared to those of poly(propylene oxide) (PPO) and are shown to be very similar. However, the glass transition temperature of PPS decreases strongly for low molar masses, while for PPO it is almost independent of the molar mass down to 400 g/mol.
From Patient-Specific Mathematical Neuro-Oncology to Precision Medicine (2013)

Gliomas are notoriously aggressive, malignant brain tumors that have variable response to treatment. These patients often have poor prognosis, informed primarily by histopathology. Mathematical neuro-oncology (MNO) is a young and burgeoning field that leverages mathematical models to predict and quantify response to therapies. These mathematical models can form the basis of modern "precision medicine" approaches to tailor therapy in a patient-specific manner. Patient-specific models (PSMs) can be used to overcome imaging limitations, improve prognostic predictions, stratify patients, and assess treatment response in silico. The information gleaned from such models can aid in the construction and efficacy of clinical trials and treatment protocols, accelerating the pace of clinical research in the war on cancer. This review focuses on the growing translation of PSM to clinical neuro-oncology. It will also provide a forward-looking view on a new era of patient-specific MNO.
Acetohydroxy acid synthase I of Escherichia coli: purification and properties (1979)

Several properties of the three acetohydroxy acid synthases of Escherichia coli have been compared in crude extracts. The three enzymes can be readily distinguished from each other. Acetohydroxy acid synthase I, the product of the ilvB gene, has been purified to near homogeneity. The purification was made possible by the fact that the enzyme was maintained in buffers of a high ionic strength or in buffers containing glycerol. Density gradient centrifugation studies indicated that the enzyme exists as a dimer of subunits of similar (60,000) molecular weight in buffers containing glycerol with or without two of the cofactors. Mg2+ and thiamine diphosphate. When flavine adenine dinucleotide was added along with Mg2+ and thiamine diphosphate, an increase in the rate of sedimentation occurred that was thought to be due to a rapid tetramer-dimer interconversion. The addition of pyruvate, the substrate, along with the three cofactors, resulted in a further increase in sedimentation rate, due presumably to an increase in the tetramer-to-dimer ratio. The addition of valine to the complete system resulted in maintenance of the enzyme in the dimeric state concomitant with inhibition of enzyme activity.
Retrometabolism‐Based Drug Design and Targeting (2003)

Abstract Retrometabolic approaches represent systematic drug design methodologies that thoroughly integrate structure—activity and structure—metabolism relationships and are aimed to design safe compounds with an improved therapeutic index. They incorporate two major concepts aimed to design soft drugs and chemical delivery systems, respectively. Soft drugs are new, active therapeutic agents that undergo predictable metabolism to inactive metabolites after exerting their desired therapeutic effect. Chemical delivery systems are biologically inert molecules that provide enhanced and targeted delivery of an active drug to a particular organ or site through a designed sequential metabolism that involves several steps. The present comprehensive review includes an overview of the general retrometabolic drug design principles and provides a variety of specific examples to illustrate the concepts. If possible, the rationale for the design as well as the pharmacokinetic and pharmacodynamic properties of the new therapeutic agents are briefly summarized and compared to those of the other compounds used in the same field.
Gain temperature dependence of erbium-doped silica and fluoride fiber amplifiers in multichannel wavelength-multiplexed transmission systems (1997)

The temperature dependence of the gain of aluminosilica and fluoride based erbium-doped fiber amplifiers are theoretically and experimentally examined and compared. As expected from the larger temperature dependence of erbium-doped fluoride fibers (EDFB) cross sections, the single channel gain of EDFF amplifiers presents larger wavelength-dependent temperature sensitivity. The implications of this large and nonuniform temperature dependence of the gain on wavelength-division multiplexing (WDM) are theoretically analyzed and discussed.
Autolysis parallels activation of <i>μ</i>-calpain (1996)

The kinetics of autolysis and activation of mu-calpain were measured with microtubule-associated protein 2 (MAP2) as a very sensitive substrate. The initial rate of MAP2 hydrolysis was found to be a linear function of the autolysed 76 kDa form of mu-calpain large subunit at both 10 and 300 microM Ca2+, and both straight lines intersected the origin. This finding supports the view that native mu-calpain is an inactive proenzyme and that activation is accompanied by autolysis. The first-order rate constant of autolysis, K1(aut), was determined at different Ca2+ concentrations: the half-maximal value was at pCa2+ = 3.7 (197 microM Ca2+), whereas the maximal value was 1.52 s-1, at 30 degrees C. The Ca(2+)-induced activation process was then monitored by using our novel, continuous fluorimetric assay with labelled MAP2 as substrate. The first-order rate constant of activation, k1(act), was derived as the reciprocal of the lag phase ('transit time') at the initial part of the progress curve: half-maximum was at pCa2+ = 3.8 (158 microM Ca2+) and the maximum value was 2.15 s-1. The good agreement between the kinetic parameters of mu-calpain autolysis and activation is remarkable. We claim that this is the first kinetically correct determination of the rate constant of autolysis of mu-calpain. Pre-activated mu-calpain has a Ca2+ requirement that is almost three orders of magnitude smaller [half-maximal activation at pCa2+ = 6.22 (0.6 microM Ca2+)]. We cannot exclude the possibility that the activation process involves other mechanistic steps, e.g. the rapid dissociation of the mu-calpain heterodimer, but we state that in our conditions in vitro autolysis and activation run in close parallel.
Methotrexate intracellular disposition in acute lymphoblastic leukemia: a mathematical model of gamma-glutamyl hydrolase activity. (2002)

Methotrexate (MTX) is an antifolate that is widely used for the treatment of childhood acute lymphoblastic leukemia (ALL) and a number of other malignant and nonmalignant diseases. Within cells, MTX is metabolized to more active methotrexate polyglutamates (MTXPG), and these polyglutamates are subsequently cleaved in lysosomes by gamma-glutamyl hydrolase (GGH). GGH is reported to act as either an endopeptidase or an exopeptidase, exhibiting species differences in these functions. To better define the in vivo functions of GGH in human leukemia cells, we characterized GGH activity with different MTXPG substrates (MTX with three to five glutamates) in human T- and B-lineage leukemia cell lines, and in primary leukemia cells from newly diagnosed patients with ALL. Parameters estimated from fitting a series of hypothetical mathematical models to the data revealed that the experimental data were best fit by a model where GGH simultaneously cleaved multiple glutamyl residues, with highest activity at cleaving the outermost or two outermost residues from a polyglutamate chain. The model also revealed that GGH has a higher affinity for longer chain polyglutamates. Together, these findings provide new insights to the intracellular disposition of MTX in human ALL cells, and provides a mechanism-based model for characterizing differences among patients and genetic subtypes of ALL.
Noninterferometric wide-field optical profilometry with nanometer depth resolution (2002)

Applying the principle of differential confocal microscopy to wide-field optically sectioning microscopy, we develop a noninterferometric optical profilometer without scanning mechanisms. Depth resolution of 2 nm is achieved with a power-regulated tungsten-halogen lamp as the light source and a 14-bit CCD camera as the detector. The effects of inhomogeneous surface reflectivity are removed from topographic measurements by arithmetic division. The whole system can be constructed on a single silicon chip for use as a miniaturized optical profiler.
Bayesian Optimization in Weakly Specified Search Space (2017)

Bayesian optimization (BO) has recently emerged as a powerful and flexible tool for hyper-parameter tuning and more generally for the efficient global optimization of expensive black-box functions. Systems implementing BO has successfully solved difficult problems in automatic design choices and machine learning hyper-parameters tunings. Many recent advances in the methodologies and theories underlying Bayesian optimization have extended the framework to new applications and provided greater insights into the behavior of these algorithms. Still, these established techniques always require a user-defined space to perform optimization. This pre-defined space specifies the ranges of hyper-parameter values. In many situations, however, it can be difficult to prescribe such spaces, as a prior knowledge is often unavailable. Setting these regions arbitrarily can lead to inefficient optimization - if a space is too large, we can miss the optimum with a limited budget, on the other hand, if a space is too small, it may not contain the optimum point that we want to get. The unknown search space problem is intractable to solve in practice. Therefore, in this paper, we narrow down to consider specifically the setting of "weakly specified" search space for Bayesian optimization. By weakly specified space, we mean that the pre-defined space is placed at a sufficiently good region so that the optimization can expand and reach to the optimum. However, this pre-defined space need not include the global optimum. We tackle this problem by proposing the filtering expansion strategy for Bayesian optimization. Our approach starts from the initial region and gradually expands the search space. Wedevelop an efficient algorithm for this strategy and derive its regret bound. These theoretical results are complemented by an extensive set of experiments on benchmark functions and tworeal-world applications which demonstrate the benefits of our proposed approach.
Review of the current status of tooth whitening with the walking bleach technique (2003)

Internal bleaching procedures such as the walking bleach technique can be used for whitening of discoloured root-filled teeth. The walking bleach technique is performed by application of a paste consisting of sodium perborate-(tetrahydrate) and distilled water (3% H2O2), respectively, in the pulp chamber. Following a critical review of the scientific literature, heating of the mixture is contra-indicated as the risk of external cervical resorption and the formation of chemical radicals is increased by application of heat. An intracoronal dressing using 30% H2O2 should not be used in order to reduce the risk of inducing cervical resorption. This review provides advice based on the current literature and discusses how the walking bleach technique can lead to successful whitening of non-vital root-filled teeth without the risks of side-effects.
Lightweight CO{sub 2}-resistant cements for geothermal well completions (1994)

Alkali metal catalyzed reactions between CO{sub 2}-containing brines and portland cement-based well cements can result in rapid strength reductions, increased permeability and casing corrosion, reduced well life, increased costs, and environmental concerns. Materials formed by acid-base reactions between calcium aluminate compounds and phosphate-containing solutions yield high strength, low permeability and CO{sub 2}-resistant cements when cured in hydrothermal environments. The cementing formulations are pumpable for several hours at temperatures up to 150C, thereby making their use for well completions technically feasible. When this cementing matrix was exposed in an autoclave containing Na{sub 2}CO{sub 3}-saturated brine for 120 days, < 0.4 wt% CaCO{sub 3} was produced. A conventional portland cement-based well completion material will form {approx} 10 wt% CaCO{sub 3} after only 7 days exposure. Addition of hollow aluminosilicate microspheres to the uncured matrix constituents yields slurries with densities as low as {approx} 1.2 g/cc which cure to produce materials with properties meeting the criteria for well cementing. Laboratory characterization is nearing completion, engineering scale-up is underway, and plans for field testing in a variety of geothermal fluids are being made.
Integrated ZnO nanotips on GaN light emitting diodes for enhanced emission efficiency (2007)

Enhancement of light extraction from an integrated ZnO nanotips/GaN light emitting diode (LED) is demonstrated. The device is composed of a GaN LED with a Ga-doped ZnO (GZO) transparent conductive layer and ZnO nanotips grown on GZO for light extraction. The light output power of a ZnO nanotips/GZO/GaN LED exhibits 1.7 times enhancement, in comparison with a conventional Ni∕Au p-metal LED. The higher emission efficiency is attributed to the enhanced light transmission and scattering in the ZnO∕GaN multilayer.
Oh! Pascal! (1982)

From the Publisher:
Welcome to the third edition of Oh! Pascal! Like its predecessors, Oh! Pascal! is an introduction to problem solving and programming. It requires absolutely no background in computing and remains, I hope, interesting enough to be read before the lecture instead of just before the exam. I had a lot of fun putting Oh! Pascal! together, and I think that you'll like working with it over the next few months.
Receiver Design for Optical PPM Systems (1978)

An optimum receiver structure for optical PPM systemics is considered and from this a simple sub-optimum receiver is proposed which offers significant SNR improvement relative to existing design approaches and yet requires few circuit changes. Receivers incorporating either p-i-n or avalanche photodiodes and FET or BJT preamplifiers are analyzed. The optimization technique relies on matching the frequency response of the receiver to that of the incident optical pulse and setting the avalanche gain and threshold detector at optimum levels. For a FET preamplifier the SNR improvement is 10.8 dB with a p-i-n photodiode and 4.7 dB with an avalanche photodiode. For a BJT preamplifier the SNR improvement is 3.1 dB and 2.3 dB with the p-i-n and avalanche diodes, respectively.
High Performance Team Management (1989)

Successful management not only actively promotes team spirit, but installs the mechanisms and the means to develop team skills and to enhance team roles. Today′s managers are challenged to make a transition from the traditional way of operating or doing business, to experimenting with new styles of organising and managing.
Visual enhancement of Cone‐beam CT by use of CycleGAN (2019)

Our method produces visually PlanCT-like images from CBCT images while preserving anatomical structures.
Identification of an essential tyrosine residue in the catalytic site of a chitinase isolated from Zea mays that is selectively modified during inactivation with 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide. (1992)

Chitinase isolated from Zea mays seeds is inactivated by 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) in the absence of exogenous nucleophiles. Oligomers of N-acetylglucosamine,N,N',N",N"'-tetra-N-acetylchitotetraose (GlcNAc4), and to a lesser extent, N,N',N"-tri-N-acetylchitotriose (GlcNAc3) and N,N'-di-N-acetylchitobiose (GlcNAc2) provide partial protection against inactivation by the reagent. An examination of the concentration dependence of the protection afforded by GlcNAc4 revealed direct competition between the substrate analog and the reagent for the same binding sites on the enzyme. Isolation and Edman degradation of a "new" tryptic fragment, observed after inactivation of chitinase with EDC, revealed the sequence G-P-L-Q-I-S-W-N-*-N-Y-G-P-A-G-R, where the asterisk represents a cycle in which no amino acid was detected, presumably as a consequence of derivatization with EDC. In basic chitinases from dicotyledonous plants such as Arabidopsis thaliana, Phaseolis vulgaris (bean), Nicotiana tabacum (tobacco), and Solanum tuberosum (potato), as well as in the chitinase isolated from the monocotyledonous plant Hordeum vulgare (barley), this position is invariably occupied by a tyrosine. However, in the Oryza sativa (rice) basic chitinase, this position is occupied by a phenylalanine. The following additional evidence supports identification of this residue as tyrosine in Z. mays chitinase. (a) Inactivation of chitinase with EDC is reversible by treatment with hydroxylamine. (b) Liquid secondary ion mass spectrometric analysis of the isolated derivatized peptide revealed the presence of a molecular ion with a mass to charge ratio consistent with the peptide containing a derivatized tyrosine residue. These results provide evidence for an essential tyrosine residue at or near the catalytic site of chitinase that is selectively modified during inactivation with EDC.
A Secure Improved Multi-signature Scheme (2006)

The multisignature scheme is a signature scheme; in which plural signer jointly generate a signature for a message or several messages. Reentry, based on RSA and discrete logarithm with composite modulus, Huang and Chang proposed two multisignature schemes with distinguished signing authority and claimed that their schemes can resist forgery attack. Unfortunately, in this works, we show that their schemes are universally forgeable by security analysis on Huang-Chang multi-signature schemes. Given a multisignature of a certain document, arbitrary one can forge a multisignature on the document. To overcome the weakness of the schemes, we proposed an improved scheme and show that the scheme is proven secure in random oracle model.
Evolution of mitochondrial uncoupling proteins: novel invertebrate UCP homologues suggest early evolutionary divergence of the UCP family (2004)

Current hypothesis about the evolution of uncoupling proteins (UCPs) proposed by suggests that UCP4 is the earliest form of UCP ancestral to all other UCP orthologues. However, this hypothesis is difficult to reconcile with a narrow tissue distribution of UCP4 (which is a brain-specific isoform), suggesting highly specialized rather than anfcestral function for this protein. We searched for UCP2, UCP3, and UCP5 homologues in invertebrate genomes using amplification with degenerate primers designed against UCP2-specific conserved sequences and/or BLASTP search with stringent ad hoc criteria to distinguish between homologues and orthologues of different UCPs. Our study identified invertebrate UCP homologues similar to UCP2 and 3 (which we termed UCP6) and an invertebrate homologue of UCP5. Phylogenetic analysis indicates that there are at least three clades of UCPs in invertebrates, which are closely related to vertebrate UCP1-3, UCP4, and UCP5, respectively, and shows early evolutionary divergence of UCPs, which pre-dates the divergence of protostomes and deuterostomes. It also suggests that the newly identified UCP6 proteins from invertebrates are ancestral to the vertebrate UCP1, UCP2, and UCP3, and that divergence of these three vertebrate orthologues occurred late in evolution of the vertebrates. This study refutes the hypothesis of Hanak and Jezek (2001) that UCP4 is an ancestral form for all UCPs, and shows early evolutionary diversification of this protein family, which corresponds to their proposed functional diversity in regulation of proton leak, antioxidant defense and apoptosis.