gebhart/patrepeval huggingface dataset:
MULTIPROTEIN-DNA COMPLEXES IN TRANSCRIPTIONAL REGULATION (1999)

Transcription in eukaryotes is frequently regulated by a mechanism termed combinatorial control, whereby several different proteins must bind DNA in concert to achieve appropriate regulation of the downstream gene. X-ray crystallographic studies of multiprotein complexes bound to DNA have been carried out to investigate the molecular determinants of complex assembly and DNA binding. This work has provided important insights into the specific protein-protein and protein-DNA interactions that govern the assembly of multiprotein regulatory complexes. The results of these studies are reviewed here, and the general insights into the mechanism of combinatorial gene regulation are discussed.
Shedding light on host niches: label-freein situdetection ofMycobacterium gordonaevia carotenoids in macrophages by Raman microspectroscopy (2014)

Macrophages are the primary habitat of pathogenic mycobacteria during infections. Current research about the host-pathogen interaction on the cellular level is still going on. The present study proves the potential of Raman microspectroscopy as a label-free and non-invasive method to investigate intracellular mycobacteria in situ. Therefore, macrophages were infected with Mycobacterium gordonae, a mycobacterium known to cause inflammation linked to intracellular survival in macrophages. Here, we show that Raman maps provided spatial and spectral information about the position of bacteria within determined cell margins of macrophages in two-dimensional scans and in three-dimensional image stacks. Simultaneously, the relative intracellular concentration and distributions of cellular constituents such as DNA, proteins and lipids provided phenotypic information about the infected macrophages. Locations of bacteria outside or close to the outer membrane of the macrophages were notably different in their spectral pattern compared with intracellular once. Furthermore, accumulations of bacteria inside of macrophages exhibit distinct spectral/molecular information because of the chemical composition of the intracellular microenvironment. The data show that the connection of microscopically and chemically gained information provided by Raman microspectroscopy offers a new analytical way to detect and to characterize the mycobacterial infection of macrophages.
Secondary Electron flash-a high performance, low power flash technology for 0.35 μm and below (2002)

This work presents recent results on Secondary Electron flash memory, and contrasts this approach to standard for scaled, low power mass storage applications.
Aligned single‐wall carbon nanotube polymer composites using an electric field (2006)

Abstract While high shear alignment has been shown to improve the mechanical properties of single‐wall carbon nanotube (SWNT)‐polymer composites, this method does not allow for control over the electrical and dielectric properties of the composite and often results in degradation of these properties. Here, we report a novel method to actively align SWNTs in a polymer matrix, which permits control over the degree of alignment of the SWNTs without the side effects of shear alignment. In this process, SWNTs were aligned via AC field‐induced dipolar interactions among the nanotubes in a liquid matrix followed by immobilization by photopolymerization under continued application of the electric field. Alignment of SWNTs was controlled as a function of magnitude, frequency, and application time of the applied electric field. The degree of SWNT alignment was assessed using optical microscopy and polarized Raman spectroscopy, and the morphology of the aligned nanocomposites was investigated by high‐resolution scanning electron microscopy. The structure of the field induced aligned SWNTs was intrinsically different from that of shear aligned SWNTs. In the present work, SWNTs are not only aligned along the field, but also migrate laterally to form thick, aligned SWNT percolative columns between the electrodes. The actively aligned SWNTs amplify the electrical and dielectric properties of the composite. All of these properties of the aligned nanocomposites exhibited anisotropic characteristics, which were controllable by tuning the applied field parameters. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 1751–1762, 2006
Learning local evidence for shading and reflectance (2002)

We address the important and unsolved problem of determining whether variations in image intensity are caused by changes in surface normal (shading) or reflectance (paint). A solution to this problem is necessary for machines to interpret images as people do and could have many applications. We take a learning-based approach. We generate a trainiiag set of synthetic images containing both surface normal and reflectance variations, and then label the variations at each position, scale, and orientation as to whether they are caused by shading or paint. The classification is done locally, using a feature vector of nonlinear filter responses. We fit a probability density model to the filter outputs using a mixture of factor analyzers. The resulting model indicates the probability based on local image evidence, that a pyramid coefficient at each orientation and scale is caused by shading or reflectance variations. Although the classification is done using a fixed lighting direction, we can solve for the correct lighting direction by rotating the image to the orientation, relative to the light source, that gives the most shape-like labelings. The labeling allows us to reconstruct two high passed images: one contains those parts of the input image caused by shading effects, while the other contains only those parts caused by reflectance changes. The resulting classifications compare well with human psychophysical performance on a test set of images, and show good results for test photographs.
QUANTITATIVE OPTICAL SPECTROSCOPY FOR TISSUE DIAGNOSIS (1996)

The interaction of light within tissue has been used to recognize disease since the mid-1800s. The recent developments of small light sources, detectors, and fiber optic probes provide opportunities to quantitatively measure these interactions, which yield information for diagnosis at the biochemical, structural, or (patho)physiological level within intact tissues. However, because of the strong scattering properties of tissues, the reemitted optical signal is often influenced by changes in biochemistry (as detected by these spectroscopic approaches) and by physiological and pathophysiological changes in tissue scattering. One challenge of biomedical optics is to uncouple the signals influenced by biochemistry, which themselves provide specificity for identifying diseased states, from those influenced by tissue scattering, which are typically unspecific to a pathology. In this review, we describe optical interactions pursued for biomedical applications (fluorescence, fluorescence lifetime, phosphorescence, and Raman from cells, cultures, and tissues) and then provide a descriptive framework for light interaction based upon tissue absorption and scattering properties. Finally, we review important endogenous and exogenous biological chromophores and describe current work to employ these signals for detection and diagnosis of disease.
CD5 and immunoglobulin V gene expression in B-cell lymphomas and chronic lymphocytic leukemia (1990)

We studied the expression of CD5 and immunoglobulin variable gene families in a panel of monoclonal Epstein-Barr virus (EBV) transformed lines, chronic lymphocytic leukemias (CLLs) and CD5+ and CD5- B-cell lymphomas. The CD5 gene expression was in all cases identical to that of T-cell malignancies. The utilization of the various VH and VK gene families was roughly proportional to the estimated gene family size in EBV lines obtained from adult healthy subjects. In contrast we found a statistically significant biased usage of VH6 in CLL and VH5 in CD5+ lymphomas as compared with EBV lines, and of VKIII in both CLL and CD5+ lymphomas as compared with EBV lines. Some differences in the variable gene usage were also noted when comparing CD5+ and CD5- lymphomas. These findings are analyzed in the context of possible mechanisms involved in the malignant transformation of CD5+ B cells.
N-Glycosylation of MDA-7/IL-24 Is Dispensable for Tumor Cell–Specific Apoptosis and “Bystander” Antitumor Activity (2006)

Biochemical and genetic mutation-based analyses confirm that the MDA-7/IL-24 protein can induce transformed cell-specific apoptosis through a mechanism involving endoplasmic reticulum (ER) stress-associated pathways. Covalent modifications by N-linked glycans in the ER contribute to the conformational maturation and biological functions of many proteins. Because MDA-7/IL-24 is a glycosylated protein, we investigated the role of glycosylation in mediating the specific biological and "bystander" antitumor activities of this cytokine. An adenovirus vector expressing a nonsecreted and nonglycosylated version of MDA-7/IL-24 protein was generated via deletion of its signal peptide and point mutations of its three N-glycosylated sites. In this study, we showed that this intracellular nonglycosylated protein was as effective as wild-type MDA-7/IL-24 protein in inducing apoptosis in multiple tumor cell lines. Both constructs (a) displayed transformed cell specificity and localization to the ER compartment, (b) mediated apoptosis through JAK/STAT-independent and p38(MAPK)-dependent pathways, (c) induced sustained ER stress as evidenced by expression of ER stress markers (BiP/GRP78, GRP94, XBP-1, and eIF2alpha), and (d) generated proteins that physically interacted with BiP/GRP78. Additionally, an expression construct containing the mda-7/IL-24 signal peptide linked to the mutated nonglycosylated mda-7/IL-24 gene retained the ability to induce bystander antitumor activity. These studies reveal that MDA-7/IL-24 glycosylation is not mandatory for inducing cell death or bystander activities in different cancer cells, providing new insights into the mechanism by which MDA-7/IL-24 induces apoptosis and ER stress.
Immunochemical Characterization of the Basement Membrane Glycoprotein Laminin (1979)

Laminin was recently characterized as being a major non-collageneous protein of the basement membrane matrix produced by a mouse tumor. It was extracted from the tumor matrix with neutral buffer and purified under non-denaturing conditions. Rabbit and guinea pig antisera raised against laminin or a large pepsin fragment P1 of laminin showed strong binding to both laminin and peptide P1 but only a weak reaction with reduced and alkylated laminin. The major antigenic determinants of laminin were located in a disulfide knot, comprising one third of the molecule, which resisted degradation by pepsin or cyanogen bromide. Minor antigenic determinants shared by the native and reduced protein could also be identified. The data were interpreted as showing that laminin consists of conformationally rigid as well as more flexible domains. Absorption studies with mouse kidney homogenate indicated that authenic basement membranes contain a protein immunologically identical to laminin. Tissues from other species contain a related protein which exhibits partial cross-reaction with mouse laminin. Together with immunofluorescence data the findings demonstrate that laminin, like type IV collagen, occurs in most basement membranes of the body.
A Molecular Signature to Discriminate Dysplastic Nodules From Early Hepatocellular Carcinoma in HCV Cirrhosis (2006)

Molecular data based on gene transcriptional profiles of a 3-gene set allow a reliable diagnosis of early HCC. Immunostaining of GPC3 confirms the diagnosis of HCC.
Reversible inhibitors of the gastric (H+/K+)-ATPase. 1. 1-Aryl-4-methylpyrrolo[3,2-c]quinolines as conformationally restrained analogs of 4-(arylamino)quinolines (1990)

The 4-(arylamino)quinoline 4, previously described as an antiulcer compound, is shown to be an inhibitor of the gastric (H+/K+)-ATPase. It is postulated that 1-arylpyrrolo[3,2-c]quinolines 6 act as conformationally restrained analogues of 4. A series of derivatives of 6 has been prepared and shown to be potent inhibitors of the target enzyme in vitro. Substitution in the ortho position of the aryl ring is important for activity. Unsaturation in the 5-membered ring makes little difference, but introduction of heteroatoms into the same ring markedly reduces activity. In more detailed kinetic experiments, 15c and 4 both show reversible, K(+)-competitive binding to the enzyme, with submicromolar Ki values. The compounds appear to act at the lumenal face of the enzyme and to require protonation for activity. Several compounds in the series are shown to be potent inhibitors of pentagastrin-stimulated acid secretion in the rat.
The human circadian system adapts to prior photic history (2011)

Light is the most potent stimulus for synchronizing the endogenous circadian timing system to the 24 h day. The timing, intensity, duration, pattern and wavelength of light are known to modulate photic resetting of the circadian system and acute suppression of melatonin secretion. The effect of prior photic history on these processes, however, is not well understood. Although previous studies have shown that light history affects the suppression of melatonin in response to a subsequent light exposure, here we show for the first time that a very dim light history, as opposed to a typical indoor room illuminance, amplifies the phase-shifting response to a subsequent sub-saturating light stimulus by 60–70%. This greater efficacy provides evidence for dynamic adaptive changes in the sensitivity of circadian ocular photoreception. This plasticity has important implications for the optimization of light therapy for the treatment of circadian rhythm sleep disorders.
Diameter-Selective Solubilization of Single-Walled Carbon Nanotubes by Reversible Cyclic Peptides (2005)

We have utilized reversible cyclic peptides (RCPs)-peptides containing alternating l- and d-amino acids with N- and C-termini derivatized with thiol-containing groups allowing reversible peptide cyclization-to solubilize and noncovalently functionalize carbon single-walled nanotubes (SWNTs) in aqueous solution. Solubilization occurs through wrapping of RCPs around the circumference of a SWNT, followed by the formation of head-to-tail covalent bonds, yielding closed rings on the nanotubes. By controlling the length of the RCPs, we have demonstrated limited diameter-selective solubilization of the SWNTs as revealed by UV/vis/NIR and Raman spectroscopies, as well as atomic force microscopy.
Syntheses of chlorpromazine undecahydrododecaborate and nonahydrodecaborate-promising agents for neutron capture therapy of malignant melanoma. (1976)

It has been suggested by dermatologists that boron compounds of chlorpromazine are promising agents for neutron capture therapy of malignant melanoma. The compounds are desired to have a high boron content, good stability, and sufficient solubility in water. To fulfil these requirements, chlorpromazine undecahydrododecaborate and nonahydrodecaborate have been synthesized starting from 2-chloro-10 (3-bromopropyl) phenothiazine and ammonioundecahydrododecaborate or 2-ammoniononahydrodecaborate, respectively.
An Efficient Algorithm for Exploiting Multiple Arithmetic Units (1967)

This paper describes the methods employed in the floating-point area of the System/360 Model 91 to exploit the existence of multiple execution units. Basic to these techniques is a simple common data busing and register tagging scheme which permits simultaneous execution of independent instructions while preserving the essential precedences inherent in the instruction stream. The common data bus improves performance by efficiently utilizing the execution units without requiring specially optimized code. Instead, the hardware, by ‘looking ahead’ about eight instructions, automatically optimizes the program execution on a local basis. The application of these techniques is not limited to floating-point arithmetic or System/360 architecture. It may be used in almost any computer having multiple execution units and one or more ‘accumulators.’ Both of the execution units, as well as the associated storage buffers, multiple accumulators and input/output buses, are extensively checked.
Preparation and evaluation of chitosan-calcium-gellan gum beads for controlled release of protein (2013)

The bead system composed of chitosan and calcium-gellan gum was prepared through a combination of ionotropic gelation and polyelectrolyte complexation for oral protein delivery. The characteristics of beads were investigated by scanning electron microscopy, Fourier transform infrared spectroscopy, differential scanning calorimetry, X-ray diffraction, release studies, and swelling measurements. It was found that chitosan endowed the calcium-gellan gum beads a dense surface and the crystal structure of polymers was disrupted after being combined together. The encapsulation efficiency of protein was in the range of 65–85 %. Higher gellan gum concentration combined with vacuum dryness significantly retarded protein fast release at pH 1.2 and achieved sustained release at pH 6.8, whereas providing efficient release at pH 7.4. The protein release was mainly attributed to Fickian diffusion mechanism in the process of swelling. The chitosan-calcium-gellan gum beads have the potential to act as a new carrier for controlled release of protein-based functional ingredients.
A system for computer music performance (1990)

A computer music performance system (CMPS) is a computer system connected to input devices (including musical keyboards or other instruments) and to graphic and audio output devices. A human performer generates input events using the input devices. The CMPS responds to these events by computing and performing sequences of output actions whose intended timing is determined algorithmically. Because of the need for accurate timing of output actions, the scheduling requirements of a CMPS differ from those of general-purpose or conventional real-time systems. This paper describes the scheduling facilities of FORMULA, a CMPS used by many musicians. In addition to providing accurate timing of output action sequences, FORMULA provides other basic functions useful in musical applications: (1) per-process virtual time systems with independent relationships to real time; (2) process grouping mechanisms and language-level control structures with time-related semantics, and (3) integrated scheduling of tasks (such as compiling and editing) whose real-time constraints are less stringent than those of output action computations.
New Functions for PI3K in the Control of Cell Division (2007)

Although cell lipids were initially envisioned as structural components of the cell, their essential contribution to initiation and regulation of cell responses is now clearly established. Among the different lipids that regulate cell responses, those produced by class I phosphoinositide 3-kinase (PI3K), phosphatidylinositol (3,4)P(2) (PIP(2)) and phosphatidylinositol (3,4,5)P(3) (PIP(3)), have concentrated much attention in recent years. PIP(2) and PIP(3) are involved in cell division and survival control, and mutations in the PI3K pathway are linked to autoimmunity and cancer. Here we discuss two novel observations: a PI3K function in the late-G(1) phase of the cell cycle and the contribution of the p85 PI3K regulatory subunit in the control of cytokinesis.
Nonsteroidal Anti-Inflammatory Drugs-The Clinical Dilemmas (1992)

Physicians using nonsteroidal anti-inflammatory drugs (NSAIDs) are concerned that effective anti-inflammatory doses cause few gastrointestinal side effects. Among the causes of discontinuing therapy, upper gastrointestinal symptoms and the development of 'ulcer' complications are major concerns; endoscopic findings in asymptomatic users are not. Initial symptoms, poorly correlated with endoscopic findings, are relieved by anti-ulcer drugs and ameliorate with time of NSAID use in most patients. Symptoms accompanied by epigastric tenderness, or unrelieved by H2 antagonists, or resulting in cessation of NSAID therapy are more predictive of underlying ulcers. Complications probably arise in several ways, including as hemorrhages due to interference with platelet function, and as complications due to exacerbations of underlying ulcer disease or of ulcers caused by the NSAIDs. Pathogenesis and effective prophylaxis (yet to be established) may therefore vary in different patients, a clinical dilemma.
Fluorescence Excitation Emission Matrices of Human Tissue: A System for in vivo Measurement and Method of Data Analysis (1999)

We describe a system capable of measuring spatially resolved reflectance spectra from 380 to 950 nm and fluorescence excitation emission matrices from 330 to 500 nm excitation and 380 to 700 nm emission in vivo. System performance was compared to that of a standard scanning spectrofluorimeter. This “FastEEM” system was used to interrogate human normal and neoplastic oral cavity mucosa in vivo. Measurements were made through a fiber-optic probe and require 4 min total measurement time. We present a method based on autocorrelation vectors to identify excitation and emission wavelengths where the spectra of normal and pathologic tissues differ most. The FastEEM system provides a tool with which to study the relative diagnostic ability of changes in absorption, scattering, and fluorescence properties of tissue.
Proximity-Induced Superconductivity in DNA (2001)

Conductivity measurements on double-stranded DNA molecules deposited by a combing process across a submicron slit between rhenium/carbon metallic contacts reveal conduction to be ohmic between room temperature and 1 kelvin. The resistance per molecule is less than 100 kilohm and varies weakly with temperature. Below the superconducting transition temperature (1 kelvin) of the contacts, proximity-induced superconductivity is observed. These results imply that DNA molecules can be conducting down to millikelvin temperature and that phase coherence is maintained over several hundred nanometers.
Engineering three-dimensional hybrid supercapacitors and microsupercapacitors for high-performance integrated energy storage (2015)

Supercapacitors now play an important role in the progress of hybrid and electric vehicles, consumer electronics, and military and space applications. There is a growing demand in developing hybrid supercapacitor systems to overcome the energy density limitations of the current generation of carbon-based supercapacitors. Here, we demonstrate 3D high-performance hybrid supercapacitors and microsupercapacitors based on graphene and MnO2 by rationally designing the electrode microstructure and combining active materials with electrolytes that operate at high voltages. This results in hybrid electrodes with ultrahigh volumetric capacitance of over 1,100 F/cm(3). This corresponds to a specific capacitance of the constituent MnO2 of 1,145 F/g, which is close to the theoretical value of 1,380 F/g. The energy density of the full device varies between 22 and 42 Wh/l depending on the device configuration, which is superior to those of commercially available double-layer supercapacitors, pseudocapacitors, lithium-ion capacitors, and hybrid supercapacitors tested under the same conditions and is comparable to that of lead acid batteries. These hybrid supercapacitors use aqueous electrolytes and are assembled in air without the need for expensive "dry rooms" required for building today's supercapacitors. Furthermore, we demonstrate a simple technique for the fabrication of supercapacitor arrays for high-voltage applications. These arrays can be integrated with solar cells for efficient energy harvesting and storage systems.
Admission Resistin Levels Predict Peripancreatic Necrosis and Clinical Severity in Acute Pancreatitis (2010)

Admission resistin concentration serves as an early predictive marker of peripancreatic necrosis and clinical severity in acute pancreatitis. Resistin may have potential for clinical use as a new and diagnostic serum marker.