gebhart/patrepeval huggingface dataset:
Assessment of troglitazone induced liver toxicity in a dynamically perfused two-organ Micro-Bioreactor system (2013)

Background The ever-growing amount of new substances released to the market and the limited predictability of current in vitro test systems has led to an ample need for new substance testing solutions. Many drugs like troglitazone, that had to be removed from the market due to drug induced liver injury, show their toxic potential only after chronic long term exposure. But for long-term multiple dosing experiments, a controlled microenvironment is pivotal, as even minor alterations in extracellular conditions may greatly influence the cell physiology. Within our research program, we focused on the generation of a micro-engineered bioreactor, which can be dynamically perfused by an on-chip pump and combines at least two culture spaces for multi-organ applications. This circulatory systems better mimics the in vivo conditions of primary cell cultures and assures steadier, more quantifiable extracellular signaling to the cells.
SWEETPEA (1999)

Programmable Embodied Agents are portable, wireless, interactive devices embodying specific, differentiable, interactive characteristics. They take the form of identifiable characters who reside in the physical world and interact directly with users. They can act as an out-of-band communication channel between users, as proxies for system components or other users, or in a variety of other roles. Traditionally, research into such devices has been based on costly custom hardware. In this paper, we report on our explorations of the space of physical character-based interfaces built on recently available stock consumer hardware platforms, structured around an initial framework of applications.
Nucleation and crystallization of isotactic poly(propylene) droplets in an immiscible polystyrene matrix (2000)

In this work, isotactic poly(propylene) (iPP) was finely dispersed in immiscible atactic polystyrene (PS) matrices. When the dispersion obtained is fine enough (droplet size of approximately 1–2 μm), the iPP crystallizes in a fractionated fashion at temperatures between 104 and 42°C. By applying a self-nucleation procedure we were able to corroborate that what causes the fractionated crystallization in most droplets is the lack of highly active heterogeneous nuclei (i. e. those normally active at low supercoolings in the bulk polymer) in every droplet. When a sufficient amount of a compatibilizer is used to obtain very small particle sizes and more homogeneous dispersions, the iPP crystallizes exclusively at a low temperature exotherm that exhibits an onset at 51°C and peaks at 46°C. Wide-angle X-ray diffraction measurements indicated that both the iPP in the bulk and in dispersed droplets crystallized in the monoclinic α-phase, this evidence may rule out the possibility that the crystallization observed at 46°C is due to the formation of another crystal modification or a mesomorphic phase as previously suggested in literature. The results presented in this work indicate that this low temperature exotherm may represent the dynamic crystallization during cooling of heterogeneity-free droplets that nucleate homogeneously at temperatures close to 51°C.
1,2-Bis(methylsulfonyl)-1-(2-chloroethyl)-2-[[1-(4-nitrophenyl)ethoxy]carbonyl]hydrazine: An anticancer agent targeting hypoxic cells (2005)

To target malignant cells residing in hypoxic regions of solid tumors, we have designed and synthesized prodrugs generating the cytotoxic alkylating species 1,2-bis(methylsulfonyl)-1-(2-chloroethyl)hydrazine (90CE) after bioreductive activation. We postulate that one of these agents, 1,2-bis(methylsulfonyl)-1-(2-chloroethyl)-2-[[1-(4-nitrophenyl)ethoxy]carbonyl]hydrazine (KS119), requires enzymatic nitro reduction to produce 90CE, whereas another agent, 1,2-bis(methylsulfonyl)-1-(2-chloroethyl)-2-[(4-nitrobenzyloxy)carbonyl]hydrazine (PNBC), can also be activated by nucleophilic attack by thiols such as glutathione (GSH)/GST. We demonstrated that these agents selectively kill hypoxic EMT6 mouse mammary carcinoma and CHO cells. In hypoxia, 50 microM KS119 produced 5 logs of kill of EMT6 cells without discernable cytotoxicity in air; similar effects were observed with CHO cells. PNBC was less efficacious against hypoxic tumor cells and also had some toxicity to aerobic cells, presumably because of GST/thiol activation, making PNBC less interesting as a selective hypoxic-cell cytotoxin. BALB/c mice with established EMT6 solid tumors were used to demonstrate that KS119 could reach and kill hypoxic cells in solid tumors. To gain information on bioreductive enzymes involved in the activation of KS119, cytotoxicity was measured in CHO cell lines overexpressing NADH:cytochrome b5 reductase (NBR), NADPH:cytochrome P450 reductase (NPR), or NADPH: quinone oxidoreductase 1 (NQO1). Increased cytotoxicity occurred in cells overexpressing NBR and NPR, whereas overexpressed NQO1 had no effect. These findings were supported by enzymatic studies using purified NPR and xanthine oxidase to activate KS119. KS119 has significant potential as a hypoxia-selective tumor-cell cytotoxin and is unlikely to cause major toxicity to well oxygenated normal tissues.
Shape gradients for histogram segmentation using active contours (2003)

We consider the problem of image segmentation using active contours through the minimization of an energy criterion involving both region and boundary functionals. These functionals are derived through a shape derivative approach instead of classical calculus of variation. The equations can be elegantly derived without converting the region integrals into boundary integrals. From the derivative, we deduce the evolution equation of an active contour that makes it evolve towards a minimum of the criterion. We focus more particularly on statistical features globally attached to the region and especially to the probability density functions of image features such as the color histogram of a region. A theoretical framework is set for the minimization of the distance between two histograms for matching or tracking purposes. An application of this framework to the segmentation of color histograms in video sequences is then proposed. We briefly describe our numerical scheme and show some experimental results.
Polymorphisms for the size of heterochromatic regions allow sex-independent quantification of post-BMT chimerism targeting metaphase and interphase cells. (1999)

The polymorphism for the size of the PCH of chromosome 9 uncovered by Sau3A-REISD allows accurate quantification of the hemopoietic chimerism after sex-matched BMT.
Parameters of Integral Circulant Graphs and Periodic Quantum Dynamics (2007)

The intention of the paper is to move a step towards a classification of network topologies that exhibit periodic quantum dynamics. We show that the evolution of a quantum system, whose hamiltonian is identical to the adjacency matrix of a circulant graph, is periodic if and only if all eigenvalues of the graph are integers (that is, the graph is integral). Motivated by this observation, we focus on relevant properties of integral circulant graphs. Specifically, we bound the number of vertices of integral circulant graphs in terms of their degree, characterize bipartiteness and give exact bounds for their diameter. Additionally, we prove that circulant graphs with odd order do not allow perfect state transfer.
Paraquat inhibits mixed-function oxidation by rat lung (1983)

The effect of paraquat on 7-ethoxycoumarin (7-EC)deethylation, an NADPH-dependent cytochrome P-450-linked reaction, was studied in isolated rat lungs. Control lungs oxidatively deethylated 7-EC at a constant rate, metabolizing 178 +/- 12 nmol/g dry wt in 50 min (n=3, mean +/- SE). When glucose was omitted from the perfusate, 7-EC deethylation was lower (85 +/- 17 nmol/g, P less than 0.05), and the rate progressively decreased, suggesting inadequate pentose shunt regeneration of NADPH. During perfusion with paraquat (10(-3) M), 7-EC metabolism was still lower (75 +/- 5 nmol/g in the presence of glucose and 18 +/- 4 nmol/g in the absence of glucose, P less than 0.05). Addition of lactate plus pyruvate partially restored 7-EC deethylase activity in control lungs but had no effect in lungs perfused with paraquat. Varying perfusate paraquat concentrations (10(-6) to 10(-3) M) inhibited 7-EC deethylation in a dose-dependent fashion (r = 0.79, P less than 0.02). Oxidative demethylation of p-nitroanisole, another cytochrome P-450-linked reaction, was similarly inhibited by paraquat. In contrast, microsomes isolated from paraquat-perfused lungs showed no inhibition of 7-EC metabolism (measured in the presence of an NADPH-regenerating system). We conclude that paraquat depletes NADPH in the isolated lung to a sufficient extent to impair mixed-function oxidation. Such NADPH depletion may play a role in the toxicity of paraquat.
Studies on antihemorrhagic substances in herbs classified as hemostatics in Chinese medicine. VI On the antihemorrhagic principle in Sophora japonica L. (1987)

The antihemorrhagic principle of Sophora japaonica L. was isolated from the aqueous extract of dried buds by partition and Sephadex LH-20 column chromatography, and identified as quercetin [2- (3, 4- dihydroxyphenyl) -3, 5, 7 -trihydroxy-4H- 1-benzopyran-4- one].
[Vertebral artery loop and cervical pain]. (1985)

Diagnosis of a vertebral artery loop in the transverse canal, suggested by a CT scan image, is dependent mainly on results of angiography (preferably computer assisted and by the venous route). This lesion is a differential diagnosis of a neuroma, when the cervical intervertebral foramen is enlarged.
Individual lung blood flow during unilateral hypoxia: effects of inhaled nitric oxide (1998)

We hypothesized that the diversion of blood away from a hypoxic lung to the opposite oxygenated lung can be enhanced by inhaling nitric oxide (NO) into the oxygenated lung. We measured individual lung blood flow when 50 ppm NO was selectively inhaled to: a hyperoxic lung during contralateral hypoxia; a normoxic lung during bilateral normoxia; and a hyperoxic lung during bilateral hyperoxia. Twenty two patients with healthy lungs were studied during intravenous anaesthesia. The lungs were separately and synchronously ventilated. The relative perfusion of each lung was assessed by the inert gas elimination technique. Unilateral hypoxic (inspiratory oxygen fraction (FI,O2) 0.05) ventilation during contralateral hyperoxia reduced the perfusion of the hypoxic lung from a mean (SD) of 47 (9)% of cardiac output (Q'), to 30 (7)% (p<0.001) of Q'. NO inhalation to the hyperoxic lung increased its blood flow from 70 (7)% to 75 (6)% (p<0.05) of Q', and reduced the blood flow to the hypoxic lung to 25 (6)% (p<0.05). Unilateral NO inhalation during bilateral normoxia or hyperoxia had no effect on pulmonary blood flow distribution. Nitric oxide inhalation to a hyperoxic lung increases the perfusion to this lung by redistribution of blood flow if the opposite lung is hypoxic.
Maturational sequence of neuroblastoma revealed by molecular analysis on cDNA microarrays (2002)

Neuroblastoma (NB), one of the most common solid tumors among children, is histologically classified by the degree of maturation. To elucidate the mechanisms underlying its maturational sequence, we analyzed gene-expression profiles of 14 NB tumors on cDNA microarrays consisting of 23,040 genes. Computational analysis identified 78 genes whose expression levels were significantly different between differentiating NB tumors and poorly differentiated NB tumors. This group included genes associated with cell maturation and apoptosis. Among them we identified 15 that were up-regulated in Stage IV NB tumors; these included genes encoding cell adhesion molecules and cytoskeleton proteins. The set of genes we report here should contribute to a better understanding of NB tumor maturation and could lead to development of new therapeutic strategies.
The effects of gas mixtures on ion engine erosion and performance (1987)

Erosion measurements were performed on a modified J-series 30 cm ion engine operating on xenon propellant. Erosion data was obtained by measuring the trench depth etched into masked polished metal samples for test durations of up to 24 hours. The data indicates that erosion is greatest at the cathode side of the baffle, with tantalum being the material with the least erosion of all materials tested. There is a clear indication of a significant reduction in erosion of all materials tested when nitrogen is added to the propellant. The technique used in these experiments requires test samples which are extremely smooth and flat.
A Broadband Spectroscopic Sensor Probe (2008)

Abstract The electrical properties of many materials are closely related to their composition and to their moisture content in particular. For sensor development, characterising the response of a particular volume of material over a broad frequency range is desirable, since separate measurements could generate errors due to spatial variability. A coaxial probe has been designed for measurement of the permittivity of smooth and flat, solid or liquid samples over the frequency range from 1 Hz to 6 GHz. Although the probe is capable of a very wide frequency range, separate instruments are generally required, and here we focus on measurements above 1MHz. We demonstrate measurements in the frequency domain using a vector network analyser, and in the time domain using a broadband oscilloscope. For switching, we employed a coaxial switch and demonstrate how that is included within the instrument calibration. Calibration of the probe used three References: an open circuit, short circuit (indium foil) and a reference liquid, ideally chosen for a permittivity similar to that of the sample. The sample complex permittivity was calculated by a numerical model which used as inputs, the measured reflection coefficient and physical measurements of the probe geometry.
ChemInform Abstract: Ligating Properties of Platinum(II) Ions in Mixed‐Metal (Pt<sub>2</sub>M) Trimers (M: Cu(II), Ni(II), Co(II), Fe(II)). (1986)

Abstract The electronic reflectance spectra in the range 500‐ 1500 nm of the trimers (Ia), (Ib) and (II) are analyzed by using a set of metalligand bonding parameters which produce calculated excited‐state energies in good agreement with the observed electronic spectra of the analogous Ni(‐II), Co(II), and Fe(II) complexes (Ic).
Visual Data Mining of Brain Cells (2002)

Little is known about the influence of morphological variablity on the physiological response of brain cells. It is assumed that variables such as the number of branching points in the cell tree-like structure, its area and the change in shape from soma to terminals may influence the neuron behavior differently under different electric stimulation. In laboratory experiments, it is difficult to separate the electrophysiological effects of biochemical differences (i. e., channel types and their distributions) from those of the morphological differences in a neuron&apos;s behavior. Therefore, wehaveused computer simulations of 3D neuroanatomical data of hippocampal cells while keeping the electrophysiological model constant across different neurons. This allowed us to look specifically at the morphological influence on the neuronal function. We have obtained neuroanatomical data (particularly, hippocampal pyramidal cells) from public electronic archives. Because of the amount of painstaking work to reconstruct the three-dimemsional structure of a neuron, these archives tend to be very small (ranging from 3 to 50 cells). Additionally, there is the possibility that different archives have significant morphological differences due to the reconstruction technique. Therefore, it is difficult to reach robust conclusions on the relationship between morphological parameters and electrophysiological output. However, we found that visual data mining techniques combined with computational neural modeling is a very effective wayto detect some structure in the data. There are, indeed, morphological variables that can be used to determine whether hippocampal pyramidal cells spike, burst, or have a plateau in response to a given level of input current.
E2F4 Is Required for Early Eye Patterning (2009)

Increasingly, studies reveal novel functions for cell cycle proteins during development. Here, we investigated the role of E2F4 in eye development. E2F4-deficient mouse embryos exhibit severe early eye patterning defects, which are evident from embryonic day 11.5 and characterized by aberrant shape of the optic cup, coloboma as well as abnormal eye pigmentation. Loss of E2F4 is associated with proximal-distal patterning defects in the optic vesicle. These defects are characterized by the expansion of optic stalk marker gene expression to the optic cup and reduced expression of ventral optic cup markers. These defects are associated with a split of Shh expression domain at the ventral midline of the forebrain and expansion of the Shh activity into the ventral optic cup. Despite these patterning defects, early neuronal differentiation and Shh expression in the retina are not affected by E2F4 deletion. Overall, the results of our studies show a novel role of E2F4 in the early eye development.
X-ray standing-wave investigations of valence electronic structure (2001)

We have examined the valence-electron emission from Cu, Ge, GaAs, InP, and NiO single crystals under the condition of strong x-ray Bragg reflection; i.e., in the presence of the spatially modulated x-ray standing-wave interference field that is produced by the superposition of the incident and reflected x-ray beams. These crystals span the entire metallic, covalent, and ionic range of solid-state bonding. It is demonstrated that the valence-electron emission is closely coupled to the atomic cores, even for electron states close to a metallic Fermi edge. Using the bond-orbital approximation, the x-ray standing-wave structure factor for valence-electron emission is derived in terms of the bond polarities and photoionization cross sections of the atoms within the crystalline unit cell and compared to experiment. Additionally, we demonstrated that by exploiting the spatial dependence of the electric-field intensity under Bragg condition, site specific valence electronic structure may be obtained. The technique is demonstrated for GaAs and NiO.
The Structure of the Cyclodextrin Complex. XI. Crystal Structure of Hexakis(2,3,6-tri-<i>O</i>-methyl)-α-cyclodextrin–<i>p</i>-Iodoaniline Monohydrate (1982)

Abstract The crystal structure of hexakis(2,3,6-tri-O-methyl)-α-cyclodextrin–p-iodoaniline complex, C54H96O30·C6H6NI·H2O, was determined by the X-ray method. The crystal is monoclinic with the space group P21, Z=2, a=11.440(4), b=23.674(6), c=13.531(3) Å, and β=91.90(2)°. The structure was solved by the heavy atom method combined with the rigid-body least-squares technique and refined by the block-diagonal least-squares method to the final R-value of 0.11 for 2186 reflections (sinθ⁄λ&lt;0.49). Hexakis(2,3,6-tri-O-methyl)-α-cyclodextrin is in the shape of a truncated elliptical cone; these cones are stacked along the a axis to form a channel-type structure. The guest p-iodoaniline and water molecules are located in the channel. The iodophenyl group is inserted rather loosely from the base side of the truncated cone. The iodine atom is located at the center of the cavity, while the amino group outside the host cavity forms a hydrogen bond with the water molecule. The water molecule is also hydrogen bonded to the adjacent host molecule along the channel. The crystal is built up of columns of the host molecules, which are closely packed in the van der Waals contact.
Local accommodation in a lateral eyed bird facilitates seeing simultaneously in two different places in space (2010)

Many lateral eyed birds are bifoveate or have dual retinal specialisations corresponding with their lateral and frontal viewing modes. For example, the eye design in the pigeon, which is typical of many granivorous birds, incorporates an optic axis for lateral distant viewing and a frontal area in the temporal retina associated with close binocular viewing. In this paper we ask how these two separate visual axis are used to focus on objects, not only at different eccentricities, but also at different absolute distances. Using simultaneous infrared (IR) photoretinoscopy and IR keratometry, we find that the pigeons optical system can indeed simultaneously support differential refractive states on the lateral and frontal axis. Maps of the refractive error (RE) and corneal power in cyclopleged and anaesthetized pigeons, reveal small but antagonistic gradients in different sectors of the visual field. In particular, we find that at rest, the frontal field is relatively myopic and yet the cornea has less power in this sector. We studied how these RE and corneal power maps actively vary during a reaching behaviour. We found that during the saccadic like peck response, the optic axis is not focussed on the grain and has only 30% of the required accommodation power. In contrast, we calculate that the frontal axis does have adequate power to focus on the grain. Furthermore, at the last stationary head fixation position (which occurs at an eye-grain distance of 67mm, SD=3.9mm) before the final descent when the eyes begin to close, accommodation on the frontal axis can be supported wholly by the cornea, which allows dramatic RE changes (−13D, SD=7.7) without unduly effecting the refractive error on the optic axis (−2D, SD=1.7). We propose that the shape of the cornea facilitates this local accommodation mechanism and that this dual visual system can be simultaneously focussed at disparate distances in space.
The influence of surface currents on pattern-dependent charging and notching (1998)

Surface charge dissipation on insulator surfaces can reduce local charging potentials thereby preventing ion trajectory deflection at the bottom of trenches that leads to lateral sidewall etching (notching). We perform detailed Monte Carlo simulations of pattern-dependent charging during etching in high-density plasmas with the maximum sustainable surface electric field as a parameter. Significant notching occurs for a threshold electric field as low as 0.5 MV/cm or 50 V/μm, which is reasonable for the surface of good insulators. The results support pattern-dependent charging as the leading cause of notching and suggest that the problem will disappear as trench widths are reduced.
Somatostatin Analogs Inhibit Somatostatin Secretion from Cultured Hypothalamus Cells (1984)

The effect of somatostatin (SRIF) analogs on the secretion of radioimmunoassayable SRIF (SRIF-LI) was studied in the model system of fetal rat hypothalamus cells maintained in long-term, primary dispersed culture. These experiments exploited the biologic activity of certain synthetic SRIFs which cross-react poorly in our standard RIA for SRIF. Carbachol-stimulated SRIF-LI secretion was suppressed by [DTrp8]-SRIF-14, [DTrp22]-SRIF-28 and the octapeptide, des-AA1,2,4,5,12,13[DTrp8]-SRIF. Effective concentrations of synthetic analogs were at or below 1 nM. des-Trp8-SRIF-14, an analog inactive in all other SRIF biological assays, was similarly ineffective in this assay system at doses up to 10 nM. Following removal of peptide by washing, peptide-treated and control cells responded similarly to depolarization with high potassium buffer. The data demonstrate a direct action of SRIF analogs on the hypothalamus to suppress SRIF-LI release and are consistent with the possibility that an endogenous peptide participates in 'ultrashortloop' negative feedback control of its own secretion in the intact animal.