gebhart/patrepeval huggingface dataset:
Colonic Cl channel blockade by three classes of compounds (1991)

We compared the potency and inhibitory actions of three different classes of organic acids on a Cl channel derived from colonic enterocyte plasma membrane vesicles. Chloride channels were incorporated into planar lipid bilayer membranes to examine the effects of the anthranilic acids, diphenylamine 2-carboxylic acid (DPC) and 5-nitro-2-(3-phenylpropylamino)benzoic acid (NPPB), the indanyl alkanoic acids, 2-[(2-cyclopentyl-6,7-dichloro-2,3-dihydro-2-methyl-1-oxo-1H-inden -5-yl)oxy] acetic acid (IAA-94) and its stereoenantiomer IAA-95, and the disulfonic stilbene, 4,4'-dinitro-stilbene-2,2'-disulfonic acid (DNDS). Except for DNDS, each of the blockers was equipotent from both the outer membrane and the cytoplasmic side of the channel protein. The potency order from the outmembrane side was DNDS greater than IAA-94 = IAA-95 greater than NPPB much greater than DPC. In contrast, the potency order from the cytoplasmic side was IAA-94 = IAA-95 greater than NPPB greater than DNDS much greater than DPC. DPC and NPPB caused a concentration-dependent decrease in the single-channel conductance (fast block). DNDS, IAA-94, and IAA-95 caused a flickery-type block and a concentration-dependent decrease in open-channel probability. Kinetic analysis revealed that blockade could be explained by a linear closed-opened-blocked kinetic scheme. Similarities in the electrostatic potential maps of these open-channel blockers suggest they may bind to a single shared binding site within the channel protein.
Bulk density of solid polymer resins as a function of temperature and pressure (1990)

Abstract In a plasticating extruder, solid polymers are heated and are subjected to high pressures before they are melted and delivered to a die. In both the solids conveying and melting sections, these temperature and pressure increases will compact the unmelted polymer bed as it moves down the screw channel. Performance of the extruder depends in part on how well the screw design matches the compaction behavior of the resin for a given set of process conditions. The design of these screw sections, however, is often done based on past experience and with little knowledge of the resin compaction behavior. A much improved design would include screw performance prediction using variable bulk density and computer simulations. Computer simulations, however, are often performed using constant solid bulk density because of the lack of reliable density data as a function of both pressure and temperature. An instrument was developed for studying the compaction behavior of pellet and powder resins. Bulk densities and storage friction coefficients are reported for several important thermoplastic resins as a function of temperature and pressure. The bulk density data were fitted to a semi‐empirical model.
Measurement of the Spin Relaxation Time of Single Electrons in a Silicon Metal-Oxide-Semiconductor-Based Quantum Dot (2010)

We demonstrate direct detection of individual electron spin states, together with measurement of spin relaxation time (T1), in silicon metal-oxide-semiconductor-based quantum dots (QD). Excited state spectroscopy of the QD has been performed using a charge-sensing technique. T1 of single spin excited states has been done in the time domain by a pump-and-probe method. For an odd and an even number of electrons, we found a magnetic field dependent and invariant T1, respectively.
Multi-modal interaction in the age of information appliances (2002)

The coming millennium will be characterized by the availability of multiple information appliances that make ubiquitous information access an accepted fact of life. The ability to access and transform information via a multiplicity of appliances, each designed to suit the user's specific usage environment, requires the exploitation of all available input and output modalities to maximize the band-width of man-machine communication. There will be an increasingly strong demand for devices that present the same set of functionalities when accessing and manipulating the information, independently of the access device. The resulting uniform interface must be inherently multi-modal and dialog driven. This paper addresses the challenges of coordinated, synchronized multimodal user interaction that is inherent in designing user interfaces that work across these multiplicity of information appliances. Amongst the key issues to be addressed are the user's ability to interact in parallel with the same information via a multiplicity of appliances and user interfaces, and the need to present a unified, synchronized view of information across the various appliances that the user deploys to interact with information. We achieve such synchronized interactions and views by adopting the well-known Model, View, Controller (MVC) design paradigm and adapting it to conversational interactions. The resulting conversational MVC (CMVC) is to be considered as the key underlying principle of any conversational multi-modal application.
<title>Comparison between intrinsic and extrinsic contrast for malignancy detection using NIR mammography</title> (1999)

In this work we reconstruct and compare NIR images of the intrinsic and extrinsic distribution of the absorption coefficient in the breast. The NIR protocol followed involves optical imaging before and after the administration of the NIR contrast agent Infracyanine 25 or Cardiogreen¨ and runs in parallel with the MRI examination protocol, while the patient is located in the magnet. For imaging purposes we employ a time-resolved imager using two wavelengths at 780 and 830 nm. The tomographic needs are served with a perturbation analysis that solves the heterogeneous diffusion equation and creates the forward model. Inversion is performed using the algebraic reconstruction technique (ART). Coregistration with Gd-DTPA enhanced MR images allows for direct and unequivocal comparison between optical and MR images. We focus on the comparison between the use of intrinsic or extrinsic contrast to differentiate breast tissue types. The distribution of the NIR contrast agent yields very good coregistration with the MR contrast enhanced images and that it allows accurate quantification. Our results greatly exemplify the need for NIR contrast agents in optical mammography. Conversely imaging of the intrinsic coefficient is associated with more experimental uncertainties leading to less quantification accuracy.
ChemInform Abstract: Self‐Assembled Multiporphyrin Arrays Mediated by Self‐Complementary Quadruple Hydrogen Bond Motifs. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Thermal and photochemical promotion of silicon and silicon dioxide etching by carbonyl difluoride (1986)

Silicon (111) surfaces that were cleaned and characterized in ultrahigh vacuum were exposed to carbonyl difluoride. After adsorption of COF2, the silicon crystal was heated to 625 °C resulting in a surface etching reaction as evidenced by the desorption of silicon tetrafluoride. Si(111) surfaces covered with a native oxide layer were also exposed to carbonyl difluoride. Dissociation of COF2, using high fluences from the CO2 laser, caused etching of the SiO2 surface. Volatile SiF4(g) was detected by transmission Fourier transform infrared spectroscopy. Two mechanisms, for the thermally enhanced etching of silicon by COF2 and the photochemically promoted etching of silicon dioxide by COF2, are proposed.
<title>Automatic counting of FISH spots in interphase cells for prenatal characterization of aneuploidies</title> (1999)

Fluorescent In-Situ Hybridization (FISH) is becoming an accepted technique for identification of aneuploidies in interphase fetal cells obtained by either CVS (chorionic villus sampling) or amniocentesis. Currently the analysis is done manually by a skilled operator and is a lengthy and fatiguing process. Applied Imaging is developing an automated procedure for counting FISH spots in these samples. Spot counting involves slide preparation, probe hybridization, filter selection, FISH image acquisition, image analysis, operator verification, and analysis of count distributions. We concentrate on the tasks starting with image acquisition. The following topics are covered: selection of appropriate cells, acquisition and processing of Z-stacks of FISH images for presentation and spot counting, background removal, formation of segmentation tree and selection of spot markers, growing of spot markers by means of constrained watershed, detection of irregular spots and flagging them for the user, time and accuracy compared with manual method, and applicability to a clinical research setting.
Stability and kinetics of G-quadruplex structures (2008)

In this review, we give an overview of recent literature on the structure and stability of unimolecular G-rich quadruplex structures that are relevant to drug design and for in vivo function. The unifying theme in this review is energetics. The thermodynamic stability of quadruplexes has not been studied in the same detail as DNA and RNA duplexes, and there are important differences in the balance of forces between these classes of folded oligonucleotides. We provide an overview of the principles of stability and where available the experimental data that report on these principles. Significant gaps in the literature have been identified, that should be filled by a systematic study of well-defined quadruplexes not only to provide the basic understanding of stability both for design purposes, but also as it relates to in vivo occurrence of quadruplexes. Techniques that are commonly applied to the determination of the structure, stability and folding are discussed in terms of information content and limitations. Quadruplex structures fold and unfold comparatively slowly, and DNA unwinding events associated with transcription and replication may be operating far from equilibrium. The kinetics of formation and resolution of quadruplexes, and methodologies are discussed in the context of stability and their possible biological occurrence.
Measurement of thermal expansion coefficients of W, WSi, WN, and WSiN thin film metallizations (1990)

Thermal expansion coefficients and biaxial elastic moduli of the sputtered W, WNx, WSi0.45, and WSi0.67N0.10 thin films, used as refractory gate in the self-aligned metal-semiconductor field effect transistors on GaAs, were determined by insitu stress measurements during heating and cooling of the films on GaAs and Si substrates in the temperature range of 20–450 °C. For the WNx films the average values of thermal expansion coefficients increased with the nitrogen content, and varied from 4.5×10−6 °C−1 for tungsten to 5.80×10−6 °C−1 for WN0.43. For the WSi0.45 and WSi0.67N0.10 films, the measured values of coefficients of thermal expansion (6.55×10−6 and 6.37×10−6 °C−1, respectively) were close to that of GaAs (6.40×10−6 °C−1, respectively). Thus by using these films as refractory gates, the stress-induced interdiffusion and interaction at the interface with GaAs can be substantially reduced.
IL-7 induces rapid clathrin-mediated internalization and JAK3-dependent degradation of IL-7Rα in T cells (2010)

Interleukin-7 (IL-7) is an essential cytokine for T-cell development and homeostasis. It is well established that IL-7 promotes the transcriptional down-regulation of IL7RA, leading to decreased IL-7Ralpha surface expression. However, it is currently unknown whether IL-7 regulates the intracellular trafficking and early turnover of its receptor on ligand binding. Here, we show that, in steady-state T cells, IL-7Ralpha is slowly internalized and degraded while a significant fraction recycles back to the surface. On IL-7 stimulation, there is rapid IL-7Ralpha endocytosis via clathrin-coated pits, decreased receptor recycling, and accelerated lysosome and proteasome-dependent degradation. In accordance, the half-life of IL-7Ralpha decreases from 24 hours to approximately 3 hours after IL-7 treatment. Interestingly, we further demonstrate that clathrin-dependent endocytosis is necessary for efficient IL-7 signal transduction. In turn, pretreatment of T cells with JAK3 or pan-JAK inhibitors suggests that IL-7Ralpha degradation depends on the activation of the IL-7 signaling effector JAK3. Overall, our findings indicate that IL-7 triggers rapid IL-7Ralpha endocytosis, which is required for IL-7-mediated signaling and subsequent receptor degradation.
Transcription control of ribulose bisphosphate carboxylase/oxygenase activase and adjacent genes in Anabaena species (1994)

The gene encoding ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) activase (rca) was uniformly localized downstream from the genes encoding the large and small subunits of RubisCO (rbcL and rbcS) in three strains of Anabaena species. However, two open reading frames (ORF1 and ORF2), situated between rbcS and rca in Anabaena sp. strain CA, were not found in the intergenic region of Anabaena variabilis and Anabaena sp. strain PCC 7120. During autotrophic growth of Anabaena cells, rca and rbc transcripts accumulated in the light and diminished in the dark; light-dependent expression of these genes was not affected by the nitrogen source and the concentration of exogenous CO2 supplied to the cells. When grown on fructose, rca- and rbc-specific transcripts accumulated in A. variabilis regardless of whether the cells were illuminated. Transcript levels, however, were much lower in dark-grown heterotrophic cultures than in photoheterotrophic cultures. In photoheterotrophic cultures, the expression of the rca and rbc genes was similar to that in cultures grown with CO2 as the sole source of carbon. Although the rbcL-rbcS and rca genes are linked and are in the same transcriptional orientation in Anabaena strains, hybridization of rbc and rca to distinct transcripts suggested that these genes are not cotranscribed, consistent with the results of primer extension and secondary structure analysis of the nucleotide sequence. Transcription from ORF1 and ORF2 was not detected under the conditions examined, and the function of these putative genes remains unknown.
A digital fiber-optic liquid level sensor (1987)

A fiber-optic liquid level sensor is presented which directly outputs digitally encoded liquid level information. The sensor operates on selective coupling at the liquid surface between a source waveguide and an array of digitally masked receiving waveguides. The receiving waveguides carry optical "high/low" signals to a remote detector and discriminator circuit. The sensor is capable of liquid level resolution of ± 2 mm over a range of up to several meters. A 40-cm-long prototype sensor has demonstrated an optical signal-to-noise ratio of 10-20 dB for several different transparent and semi-transparent liquids. The digital nature of the sensor provides good isolation from drift and the effect of tilt, source intensity fluctuations, and variations in liquid characteristics. Optical fibers are the only connections to the liquid tank, providing complete electrical isolation. The associated electronics are relatively simple and inexpensive.
Learning about objects through action - initial steps towards artificial cognition (2004)

Within the field of Neuro Robotics we are driven primarily by the desire to understand how humans and animals live and grow and solve every day's problems. To this aim we adopted a "learn by doing" approach by building artificial systems, e.g. robots that not only look like human beings but also represent a model of some brain process. They should, ideally, behave and interact like human beings (being situated). The main emphasis in robotics has been on systems that act as a reaction to an external stimulus (e.g. tracking, reaching), rather than as a result of an internal drive to explore or "understand" the environment. We think it is now appropriate to try to move from acting, in the sense explained above, to "understanding". As a starting point we addressed the problem of learning about the effects and consequences of self-generated actions. How does the robot learn how to pull an object toward itself or to push it away? How does the robot learn that spherical objects roll while a cube only slides if pushed? Interacting with objects is important because it implicitly explores object representation, event understanding, and can provide definition of object-hood that could not be grasped with a mere passive observation of the world. Further, learning to understand what one's own body can do is an essential step toward learning by imitation. In this view two actions are similar not only if their kinematics and dynamics are similar but rather if the effects on the external world are the same. Along this line of research we discuss some recent experiments performed at the AI-Lab at MIT and at the LIRA-Lab at the University of Genova on COG and Babybot respectively. We show how the humanoid robots can learn how to poke and prod objects to obtain a consistently repeatable effect (e.g. sliding in a given direction), to help visual segmentation, and to interpret a poking action performed by a human manipulator.
Functional Nanocomposites Prepared by Self-Assembly and Polymerization of Diacetylene Surfactants and Silicic Acid (2003)

Conjugated polymer/silica nanocomposites with hexagonal, cubic, or lamellar mesoscopic order were synthesized by self-assembly using polymerizable amphiphilic diacetylene molecules as both structure-directing agents and monomers. The self-assembly procedure is rapid and incorporates the organic monomers uniformly within a highly ordered, inorganic environment. By tailoring the size of the oligo(ethylene glycol) headgroup of the diacetylene-containing surfactant, we varied the resulting self-assembled mesophases of the composite material. The nanostructured inorganic host altered the diacetylene polymerization behavior, and the resulting nanocomposites show unique thermo-, mechano-, and solvatochromic properties. Polymerization of the incorporated surfactants resulted in polydiacetylene (PDA)/silica nanocomposites that were optically transparent and mechanically robust. Molecular modeling and quantum calculations and (13)C spin-lattice relaxation times (T(1)) of the PDA/silica nanocomposites indicated that the surfactant monomers can be uniformly organized into precise spatial arrangements prior to polymerization. Nanoindentation and gas transport experiments showed that these nanocomposite films have increased hardness and reduced permeability as compared to pure PDA. Our work demonstrates polymerizable surfactant/silica self-assembly to be an efficient, general approach to the formation of nanostructured conjugated polymers. The nanostructured inorganic framework serves to protect, stabilize, and orient the polymer, mediate its performance, and provide sufficient mechanical and chemical stability to enable integration of conjugated polymers into devices and microsystems.
H Infinity State Feedback Control for the Stabilization of the Three Euler Angles of Helicopter Based on LMI (2008)

The H∞ state feedback control for the stabilization of the three Euler angles of helicopter is studied. The little perturbation model of helicopter is introduced. The proper generalized control variables are chosen and the generalized control object is established. The H∞ state feedback algorithm is developed based on the Iterative Linear Matrix Inequality (LMI) approach and the digital simulation is finished. The simulation results demonstrate the effectiveness of the H∞ state feedback controller.
High-affinity Cyclic Peptide Matriptase Inhibitors (2013)

These results provide a solid basis for the design of selective peptide inhibitors of matriptase with therapeutic potential. The type II transmembrane serine protease matriptase is a key activator of multiple signaling pathways associated with cell proliferation and modification of the extracellular matrix. Deregulated matriptase activity correlates with a number of diseases, including cancer and hence highly selective matriptase inhibitors may have therapeutic potential. The plant-derived cyclic peptide, sunflower trypsin inhibitor-1 (SFTI-1), is a promising drug scaffold with potent matriptase inhibitory activity. In the current study we have analyzed the structure-activity relationships of SFTI-1 and Momordica cochinchinensis trypsin inhibitor-II (MCoTI-II), a structurally divergent trypsin inhibitor from Momordica cochinchinensis that also contains a cyclic backbone. We show that MCoTI-II is a significantly more potent matriptase inhibitor than SFTI-1 and that all alanine mutants of both peptides, generated using positional scanning mutagenesis, have decreased trypsin affinity, whereas several mutations either maintain or result in enhanced matriptase inhibitory activity. These intriguing results were used to design one of the most potent matriptase inhibitors known to date with a 290 pm equilibrium dissociation constant, and provide the first indication on how to modulate affinity for matriptase over trypsin in cyclic peptides. This information might be useful for the design of more selective and therapeutically relevant inhibitors of matriptase.
Update in New Anabolic Therapies for Osteoporosis (2010)

Skeletal anabolic agents enhance bone formation, which is determined by the number and function of osteoblasts. Cell number is controlled by factors that regulate the replication, differentiation, and death of cells of the osteoblastic lineage, whereas cell function is controlled by signals acting on the mature osteoblast. Bone morphogenetic proteins (BMP) and Wnt induce the differentiation of mesenchymal cells toward osteoblasts, and IGF-I enhances the function of mature osteoblasts. The activity of BMP, Wnt, and IGF-I is controlled by proteins that, by binding to the growth factor or to its receptors, can antagonize its effects. Changes in the expression or binding affinity of these extracellular antagonists can be associated with increased or decreased bone formation and bone mass. Novel approaches to anabolic therapies for osteoporosis may include the use of factors with anabolic properties, or the neutralization of a growth factor antagonist. Selected approaches include the use of neutralizing antibodies to Wnt antagonists, the enhancement of BMP signaling by proteasome inhibitors, or the use of activin soluble receptors, IGF-I, or PTH analogs. An anabolic agent needs to be targeted specifically to the skeleton to avoid unwanted nonskeletal effects and ensure safety. Clinical trials are being conducted to test the long-term effectiveness and safety of novel bone anabolic agents.
HPLC Determination of Pheophorbide a and Pyropheophorbide a in Dried Laver Product Implicated in Food Poisoning (2005)

In an outbreak of food poisoning involving a dried purple laver product (called nori), four persons had allergic-like symptoms such as inflammation and red rash on their face, mouth and belly. The causative nori was extracted and smeared on the arm-skin of five volunteers. Three out of five volunteers had a slight allergic reaction after 5 to 30 min when they were exposed to sunlight. The levels of the chlorophyll derivatives, pheophorbide a and pyropheophorbide a, measured by HPLC were 851-906 and 5,460-5,624 microg/g, respectively, in the causative samples. Judging from the high contents of pyropheophorbide a and pheophorbide a and the symptoms of patients and volunteers, the causative agents were concluded to be the photosensitizers pyropheophorbide a and pheophorbide a.