gebhart/patrepeval huggingface dataset:
An introduction to kinetic, constraint-based and Boolean modeling in systems biology (2010)

Mathematical modeling and model analysis of biochemical reaction networks are becoming important tools for biological research and for applications in medicine and bioprocess engineering. We will discuss the special role of mathematical modeling in biological research. In engineering applications, models are primarily means to accomplish a design task (e.g. controller design). In contrast, the goal of modeling in biology is often to coherently and comprehensively integrate and develop the knowledge of a biological system beyond the level of the conventional verbal or graphical descriptions. In this way, modeling supports biologists in exploring biochemical networks. This tutorial gives an overview over several available modeling techniques with respect to their area of application: Kinetic modeling provides a detailed, dynamic and quantitative model of cellular reaction networks. Constraint-based modeling is applicable to large metabolic networks and Boolean modeling is applicable to large signal transducing networks. This tutorial paper addresses researchers with an engineering background that start to make themselves familiar with modeling in systems biology.
Co-Expression of Tyrosine Hydroxylase and GTP Cyclohydrolase I in Arginine Vasopressin-Synthesizing Neurons of the Human Supraoptic Nucleus Demonstrated by Laser Microdissection and Real-Time PCR (2006)

Tyrosine hydroxylase (TH), the first and limiting enzyme for catecholamine synthesis, has been identified immunohistochemically (IHC) in human neurosecretory neurons where it is found to colocalize with vasopressin (AVP) or oxytocin. TH expression shows striking interindividual variability and appears to depend on neuronal activation. Since GTP cyclohydrolase I (GCHI), the first enzyme for tetrahydrobiopterin synthesis, the essential cofactor of TH, and aromatic L-amino acid decarboxylase (AADC) have so far not been detected in neurosecretory neurons, the functional role of TH in catecholamine synthesis is still questionable. Our purpose was to investigate in postmortem hypothalamus whether GCHI and AADC mRNAs are co-expressed with TH in human AVP-synthesizing neurons. Total RNA was extracted from laser microdissected TH-IHC-identified neurons as well as from dissected parts of the dorsolateral supraoptic nucleus (dl-SON) of 12 control subjects, i.e. without known neurological, psychiatric or endocrinological illness. GCHI, AADC and TH mRNA expression was determined by real-time PCR. Our results showed that GCHI mRNA is co-expressed with TH in almost all cases that had a considerable number of TH-immunoreactive (TH-IR) neurosecretory neurons. A positive correlation was found between TH-immunohistochemical intensity and the presence of GCHI mRNA. AADC mRNA expression was detected only in microdissected areas of dl-SON in 2 cases that showed an increased number of TH-IR neurons. The co-expression of GCHI with TH indicates that TH is indeed active in human neurosecretory neurons. The apparent limited expression of AADC indicates that dopamine might be produced in human neurosecretory neurons under activation of the hypothalamoneurohypophyseal system, although the possibility that L-dopa is the final product cannot be excluded.
Response to Journal Club (2014)

Department of Neurosurgery, Washington University School of Medicine, St. Louis, Missouri Correspondence: Eric C. Leuthardt, MD, Department of Neurosurgery, Washington University School of Medicine, Campus Box 8057, 660 South Euclid, St. Louis, MO 63130. E-mail: [email protected]
A Framework for the Analysis of Damaged Composite Materials Using the Homogenization Method (2003)

Article A Framework for the Analysis of Damaged Composite Materials Using the Homogenization Method was published on June 1, 2003 in the journal Journal of the Mechanical Behavior of Materials (volume 14, issue 2-3).
Quantitative sodium MRI of the human brain at 9.4 T provides assessment of tissue sodium concentration and cell volume fraction during normal aging (2015)

Sodium ion homeostasis is a fundamental property of viable tissue, allowing the tissue sodium concentration to be modeled as the tissue cell volume fraction. The modern neuropathology literature using ex vivo tissue from selected brain regions indicates that human brain cell density remains constant during normal aging and attributes the volume loss that occurs with advancing age to changes in neuronal size and dendritic arborization. Quantitative sodium MRI performed with the enhanced sensitivity of ultrahigh‐field 9.4 T has been used to investigate tissue cell volume fraction during normal aging. This cross‐sectional study ( n = 49; 21–80 years) finds that the in vivo tissue cell volume fraction remains constant in all regions of the brain with advancing age in individuals who remain cognitively normal, extending the ex vivo literature reporting constant neuronal cell density across the normal adult age range. Cell volume fraction, as measured by quantitative sodium MRI, is decreased in diseases of cell loss, such as stroke, on a time scale of minutes to hours, and in response to treatment of brain tumors on a time scale of days to weeks. Neurodegenerative diseases often have prodromal periods of decades in which regional neuronal cell loss occurs prior to clinical presentation. If tissue cell volume fraction can detect such early pathology, this quantitative parameter may permit the objective measurement of preclinical disease progression. This current study in cognitively normal aging individuals provides the basis for the pursuance of investigations directed towards such neurodegenerative diseases. Copyright © 2015 John Wiley &amp; Sons, Ltd.
Robust DOA Estimation for Uncorrelated and Coherent Signals (2011)

A new direction of arrival (DOA) estimation method is introduced with arbitrary array geometry when uncorrelated and coherent signals coexist. The DOAs of uncorrelated signals are first estimated via subspace-based high resolution DOA estimation technique. Then a matrix that only contains the information of coherent signals can be formulated by eliminating the contribution of uncorrelated signals. Finally a subspace block sparse reconstruction approach is taken for DOA estimations of the coherent signals.
Evaluation of a fluorapatite-spinel ceramic as a bone implant (1981)

The objective of this study waa to produoe a oeramlo that oan be used as a hard tissue Implant. After inves­ tigation of several mixtures of trioalolum phosphate, oalolum fluoride, magnesium carbonate and alumina, a composite of fluorapatlte and spinel was selected as the ceramic material. The ability to prepare sound samples and the minimum solubility In tissue fluids were the main reasons for the selection of a composite with one mole of fluorapatlte to three moles of magnesium alumlnate spinel. The ceramic was tested to determine the effect of porosity on strength so that the optimmm coalajLnation of microstructure and mechanical properties could be obtained. The effect of the duration of stay in the physlologloal environment on the bending strength was determined after in vitro tests in Ringer's solution for porous and nonporous bars, and also after in vivo tests of non-perous subcutaneous implants. Porous bone bridges Implanted in dogs were studied in terms of bone ingrowth, Implant stabilization and tissue compatibility. Thin sections of tte bone-oeramlo interface were prepared and analyzed using optical micros­ copy with polarized transmitted llgh*»
On the fourth-order cumulants estimation for the HO blind separation of cyclostationary sources (2002)

Most of the HO blind source separation methods developed this last decade aim at blindly separating statistically independent sources, assumed stationary and ergodic. Nevertheless, in many situations such as in radiocommunications, the sources are non-stationary and very often (quasi)-cyclostationary (digital modulations). In these contexts, it is important to wonder if the performance of these HO blind source separation methods may be affected by the potential non-stationarity of the sources. The purpose of this paper is to bring some answers to this question through the behaviour analysis of the empirical fourth-order cumulant estimators in the presence of (quasi)-cyclostationary sources.
High-speed CW step-frequency coherent radar for dynamic monitoring of civil engineering structures (2004)

A high-speed coherent radar for dynamic testing of civil engineering structures is proposed. The radar operates a continuous-wave (CW) step-frequency in Ku-band, and the base-band signal is generated by direct digital synthesis. Vibration measurements carried out on a 200 m-long bridge forced by vehicular traffic are reported.
VLA-2 blockade in vivo by vatelizumab induces CD4+FoxP3+ regulatory T cells (2019)

Integrin α2β1, also known as very late antigen (VLA)-2, is a collagen-binding molecule expressed constitutively on platelets. Vatelizumab, a monoclonal antibody targeting the α2 subunit (CD49b) of VLA-2, was recently investigated for its safety and efficacy during a Phase 2 clinical study in multiple sclerosis patients, as integrin-mediated collagen binding at the site of inflammation is central to a number of downstream pro-inflammatory events. In the course of this study, we could show that VLA-2 is expressed ex vivo on platelets, platelet-T-cell aggregates, as well as a small population of highly activated memory T cells. Even though the clinical trial did not meet its primary clinical end-point (reduction in the cumulative number of new contrast-enhancing lesions on magnetic resonance imaging (MRI)), we observed enhanced frequencies of regulatory T cells (TREG) following vatelizumab treatment. Elevated TREG frequencies might be explained by the inhibition of p38 mitogen-activated protein kinase (MAPK) signaling, which is critically involved in the polarization of T helper 17 (TH17) cells and is activated by the α2 integrin cytoplasmic domain. Our findings suggest that blockade of VLA-2 might be a way to safely shift the TH17/TREG balance by inducing TREGin vivo.
Facile growth of aluminum oxide thin film by chemical liquid deposition and its application in devices (2020)

Abstract Uniform and continuous Al 2 O 3 thin films were prepared by the chemical liquid deposition (CLD) method. The breakdown field strength of the amorphous CLD-Al 2 O 3 film is 1.74 MV/cm, making it could be used as a candidate dielectric film for electronic devices. It was further proposed to use the CLD-Al 2 O 3 film as an electron blocking layer in a triboelectric nanogenerator (TENG) for output performances enhancement. Output voltages and currents of about 200 V and 9 µA were obtained, respectively, which were 2.6 times and 3 times, respectively, higher than TENG device without an Al 2 O 3 . A colloidal condensation-based procedure controlled by adjusting the pH value of the solution was proposed to be the mechanism of CLD, which was confirmed by the Tyndall effect observed in the growth liquid. The results indicated that the CLD could serve as a low-cost, room temperature, nontoxic and facile new method for the growth of functional thin films for semiconductor device applications.
Novel design methodology of matching networks based on the use of symmetry operators (2009)

In this paper we present a novel design methodology of matching networks. The functionality of a matching network is two-fold: first to decouple the antennas of a particular antenna array and secondly to match the resultant ports. The benefits of using a matching network are several: the antenna elements of a particularly antenna array can be closely spaced thus producing compact array designs (but at the expenses of narrower bandwidth), and it can be shown that the produced set of radiation patterns/polarization are orthogonal among each other (assuming an ideal NLOS scenario), thus producing maximum diversity gains when employed in MIMO systems. Several methods to design matching networks exist in the literature. Most of these designs methods, do not provide a general procedure to derive such networks for any number of antenna elements, topologies or antenna spacing. Instead, the proposed methodology is valid for any number of antenna elements, array topology, and antenna spacing. It is based on the use of the Takagi factorization, which allows us to produce reciprocal lossless designs. To compute this factorization we make use of the symmetry operators Theory to simply derive these networks from a physical inspection of the symmetry properties of the antenna array.
An experimental study of CDDP-liposome microcapsule. (1991)

Modification of drug forms on and cancer agents followed the concept of drug delivery system is one of many attempts to obtain full efficacy of chemotherapy against cancer, and reduce its side-effects. In this paper, we made a basic research to give chemotherapy with cisplatin in liposome microcapsules an assured status in expecting the efficacy of blood vessel-embolism produced by the capsule itself, and gradual discharge of the agent from those capsules.
Adherence of mutans streptococci to other oral bacteria (1990)

Adherence of mutans streptococci to strains of Actinomyces viscosus, Streptococcus sanguis, and Streptococcus mitis immobilized on a nitrocellulose membrane was measured. Strains of Streptococcus mutans, S. sobrinus, and S. rattus bound in a lactose-independent manner to a variety of the actinomyces and streptococci. Most of these reactions could proceed in the presence of whole saliva although adherence of S. rattus BHT to the streptococci was inhibited by salivary molecules. In contrast, adherence of S. mutans 10449 and KPSK2 to A. viscosus, S. sanguis, and S. mitis was enhanced by salivary molecules. S. mutans KPSK2, S. sobrinus OMZ 176, and S. rattus FA-1 binding to A. viscosus NC3 and S. sanguis G9B exhibited saturation kinetics. Adherence to A. viscosus NC3 was of a higher avidity than adherence to S. sanguis G9B. Attachment of S. mutans KPSK2 to S. sanguis G9B and of S. mutans OMZ 176 to A. viscosus NC3 and S. sanguis G9B was inhibited by heat treatment of the mutans streptococci. Attachment of S. mutans KPSK2 to A. viscosus NC3 and of S. rattus FA-1 to A. viscosus NC3 and S. sanguis G9B was unaffected by heat. These observations suggest that the mutans streptococci can adhere to a variety of early plaque bacteria by several distinct mechanisms. Such interactions may be important in the colonization of tooth surfaces by the mutans streptococci.
Polarization engineering of III-nitride nanostructures for high-efficiency light emitting diodes (2008)

The concept of polarization engineering of InGaN quantum wells are discussed as an approach for improving the radiative recombination rate of III-Nitride based active region. Two quantum wells were discussed as follow: 1) staggered InGaN quantum well, and 2) type-II InGaN-GaNAs quantum well. Staggered InGaN quantum wells (QW) grown by metalorganic chemical vapor deposition was demonstrated as improved active region for visible light emitters. Fermi's Golden Rule indicates that InGaN QW with step-function like In distribution leads to significantly improved radiative recombination rate and optical gain due to increased electron-hole wavefunction overlap, in comparison to that of conventional InGaN QW. Spontaneous emission spectra of both conventional and staggered InGaN QW were calculated based on energy dispersion and transition matrix element obtained by 6-band <i>&lt;b&gt;k&bull;p&lt;/b&gt;</i> formalism for wurtzite semiconductor, taking into account valence-band-states mixing, strain effects, and polarization-induced electric fields. The calculated spectra for the staggered InGaN QW showed enhancement of radiative recombination rate, which is in good agreement with photoluminescence and cathodoluminescence measurements at emission wavelength regime of 425-nm and 500-nm. Experimental results of light emitting diode (LED) structures at 450-nm utilizing staggered InGaN QW show improvement in output power much higher than what is predicted theoretically. In addition to the staggered InGaN QW, type-II InGaN-GaNAs QW was also investigated theoretically with potential of implementation for high efficiency LEDs.
Reversed Distribution of Calpains and Calpastatin in Human Pituitary Gland and Selective Localization of Calpastatin in Adrenocorticotropin-Producing Cells as Demonstrated by Immunohistochemistry* (1986)

The immunohistochemical distribution of Ca2+-dependent cysteine proteinases (calpains I and II) and their endogenous inhibitor calpastatin in normal and adenomatous human pituitary tissue was studied using specific antibodies. The distributions of calpain and calpastatin were dissimilar in human pituitary gland, i.e. ACTH-immunoreactive cells were strongly positive for calpastatin and negative for calpains. PRL-, GH-, FSH-, and TSH-producing cells were negative for calpastatin, but moderately positive for calpains, especially for calpain II, the high Ca2+-requiring form of the enzyme. Similar results were found in pituitary adenoma tissue. These findings indicate that each type of cells producing a specific hormone is equipped with a different balance of the enzyme-inhibitor system involved in the Ca2+-dependent degradation of intracellular proteins.
Bupropion Plasma Levels Intraindividual and Interindividual Variability (1989)

AbstractPlasma levels of bupropion and three of its metabolites were studied in eight patients. There is significant variation in steady-state plasma levels of bupropion and its metabolites, but little variability within individuals. The relevance of this finding to clinical usage is discussed.
On the Dynamics of Hawaiian Cloud Bands: Island Forcing (1988)

This study focuses on basic island scale forcing mechanisms for the formation and evolution of a band cloud typically present upwind of the island of Hawaii. By means of numerical experiments and verification of our results against observations and laboratory experiments reported in the literature, we show that the band cloud is a complex three-dimensional phenomenon which is inseparable from the airflow around the island. In particular, we demonstrate that the event needs to be analyzed in terms of the basic fluid dynamics of strongly stratified flow past a three-dimensional obstacle. The band cloud is found to arise primarily from the dynamic interaction of the trade winds with the island. The upwind surface flow forms a separation line with an associated stagnation point. A low-level convergence zone forms along this line, resulting in an updraft line. If the updrafts are strong enough, a band cloud forms. Formation and characteristics of such a system are mostly controlled by the environmental stability and strength of the trade wind. A simple criterion for the occurrence of a strong band cloud is offered in terms of the height of the island, trade-wind speed, environmental stability, and the lifted condensation and/or free convection level. A series of controlled experiments addresses questions on the role of the thermal forcing in the formation and evolution of the band cloud. In particular, we show that the band cloud is not primarily related to the diurnal cycle (as was anticipated in the literature), but that the diurnal effects are relatively weak modulations of the primary effects of a strongly fluid flow past the island. The possibility of vortex shedding in the lee of the island and its implications for the band cloud are also discussed.
Direct Catalytic Asymmetric α-Amination of Aldehydes (2002)

The first direct catalytic asymmetric alpha-amination of aldehydes is described herein. alpha-Unbranched aldehydes react in this novel proline-catalyzed reaction with dialkyl azodicarboxylates to give alpha-amino aldehydes in excellent yields and enantioselectivities.
The clinical physiology of water metabolism. Part I: The physiologic regulation of arginine vasopressin secretion and thirst. (1979)

Water balance is tightly regulated within a tolerance of less than 1 percent by a physiologic control system located in the hypothalamus. Body water homeostasis is achieved by balancing renal and nonrenal water losses with appropriate water intake. The major stimulus to thirst is increased osmolality of body fluids as perceived by osmoreceptors in the anteroventral hypothalamus. Hypovolemia also has an important effect on thirst which is mediated by arterial baroreceptors and by the renin-angiotensin system. Renal water loss is determined by the circulating level of the antidiuretic hormone, arginine vasopressin (AVP). AVP is synthesized in specialized neurosecretory cells located in the supraoptic and paraventricular nuclei in the hypothalamus and is transported in neurosecretory granules down elongated axons to the posterior pituitary. Depolarization of the neurosecretory neurons results in the exocytosis of the granules and the release of AVP and its carrier protein (neurophysin) into the circulation. AVP is secreted in response to a wide variety of stimuli. Change in body fluid osmolality is the most potent factor affecting AVP secretion, but hypovolemia, the renin-angiotensin system, hypoxia, hypercapnia, hyperthermia and pain also have important effects. Many drugs have been shown to stimulate the release of AVP as well. Small changes in plasma AVP concentration of from 0.5 to 4 muU per ml have major effects on urine osmolality and renal water handling.
Frequency stable superconducting resonator with buffer layers (1997)

The resonant frequency of a superconducting planar resonator is dependent on the material properties and thicknesses of the superconductors, the dielectric (substrate), and the buffer layers. In this article, we compute the first and second derivatives with respect to temperature of a wave velocity ratio (with respect to free space) for various combinations of material properties. The dependence of resonant frequency on the dielectric constant and thicknesses of the substrate and buffer layers is discussed. An example of YBCO thin films on rutile with sapphire buffer layers was computed. From this example, it may be concluded that, if a turning point can be realized at T=60 K and the temperature controlled to better than 0.1 mK, then frequency standards with stabilities of parts in 1015 should be attainable.
Evaluation of Proteolytic activity of commercial shampoo-A preliminary study (2014)

A shampoo is a cleaning aid for the hair and is counted amongst the foremost beauty products. Shampoo is a hair care product that is used for the removal of oils, skin particles, dandruff, environmental pollutants and other contaminant particles that gradually build up in hair. The goal of using shampoo is to remove the unwanted build up without stripping out so much sebum as to make hair unmanageable. Shampoo is generally made by combining a surfactant, most often sodium lauryl sulfate or sodium laureth sulfate, with a co-surfactant, most often cocamidopropyl betaine in water to form a thick, viscous liquid. Other essential ingredients include salt (sodium chloride), which is used to adjust the viscosity, a preservative and fragrance. Today's shampoo formulations are beyond the stage of pure cleaning of the hair. Additional benefits are expected, e.g. conditioning, smoothing of the hair surface, good health of hair, i.e, hair free of dandruff, dirt, grease and lice and all, its safety benefits are expected. As the scalp is one of the most highly permeable part of the body, products applied to the scalp go directly to the blood, without being filtered in any way. So it is very important to know and understand the effects of ingredients used in shampoo formulations. Proteolysis is the directed degradation (digestion) of proteins by cellular enzymes called proteases or by intramolecular digestion. In the present research represent the proteolysis effectiveness of shampoos based on synthetic ingredients.