gebhart/patrepeval huggingface dataset:
MODELING REGULATORY NETWORKS WITH WEIGHT MATRICES (1998)

Systematic gene expression analyses provide comprehensive information about the transcriptional response to different environmental and developmental conditions. With enough gene expression data points, computational biologists may eventually generate predictive computer models of transcription regulation. Such models will require computational methodologies consistent with the behavior of known biological systems that remain tractable. We represent regulatory relationships between genes as linear coefficients or weights, with the "net" regulation influence on a gene's expression being the mathematical summation of the independent regulatory inputs. Test regulatory networks generated with this approach display stable and cyclically stable gene expression levels, consistent with known biological systems. We include variables to model the effect of environmental conditions on transcription regulation and observed various alterations in gene expression patterns in response to environmental input. Finally, we use a derivation of this model system to predict the regulatory network from simulated input/output data sets and find that it accurately predicts all components of the model, even with noisy expression data.
Assessment of hepatic iron content using magnetic resonance imaging (2004)

Numerous studies over the past decade have shown that magnetic resonance imaging (MRI) has great potential for detecting and quantifying the distribution of iron in the body. With MRI, tissue iron is indirectly identified by the paramagnetic effects of iron on the shortening of water proton MR relaxation times. However, these effects are complex and involve a number of factors, such as tissue hydration, distribution of iron and water within the tissue, and the amount of iron loading within the iron storage molecules. A coherent understanding of how these factors influence the MRI signal is still lacking. The dependence on experimental conditions, such as magnet field strength, pulse sequences, and data acquisition parameters, further complicates iron quantification with MRI. To date, there is no generally accepted MRI approach available for clinical application. In this review, we first explain the basic MR relaxation mechanisms underlying the detection of iron with MRI. We then review the literature on empirical MRI studies of hepatic iron. Finally, we summarize the critical issues that need to be addressed to develop MRI techniques for non-invasive iron detection in the body.
An efficient computation of Euclidean distances using approximated look-up table (2000)

For fast vector quantization (VQ) encoding, we present in this paper a new method to speed up the calculation of the squared Euclidean distance between two vectors. We call it the approximated look-up table (ALUT) method. This method considers the frequency of each squared number that occurs in the equation of squared Euclidean distances, and generates a more practical table to store squared numbers. ALUT makes use of this table and some simple operations to speed up the calculation of squared Euclidean distances. From the VQ simulation results, we see that ALUT saves memory and produces better image quality compared with some other methods. It is a suitable method for VLSI implementation.
Activation of phospholipase D is tightly coupled to the phagocytosis of Mycobacterium tuberculosis or opsonized zymosan by human macrophages. (1996)

Phagocytosis of Mycobacterium tuberculosis by human mononuclear phagocytes is mediated primarily by complement receptors (CRs) but the transmembrane signaling mechanisms that regulate phagocytosis of the bacterium are unknown. We have analyzed the activation of phospholipase D (PLD) during phagocytosis of the virulent Erdman and attenuated H37Ra strains of M. tuberculosis by human monocyte-derived macrophages (MDMs), radiolabeled with [3H]-lyso-phosphatidylcholine. Phagocytosis of either Erdman or H37Ra M. tuberculosis in the presence of autologous non-immune serum was associated with a 2.5-3-fold increase in phosphatidic acid (PA). Definitive evidence for activation of PLD by M. tuberculosis was provided by markedly increased generation of the PLD-specific product phosphatidylethanol (PEt) (9.9-fold increases in [3H]-PEt for both Erdman and H37Ra strains compared to control, P < 0.001, n = 12), in the presence of 0.5% ethanol. Phagocytosis of opsonized zymosan (OZ), which is also mediated by CRs, was similarly associated with activation of PLD (12.2-fold increase in PEt, P < 0.001, n = 12). The competitive PLD inhibitor 2,3-diphosphoglycerate (2,3-DPG) produced concentration-dependent inhibition of PLD activity stimulated by either M. tuberculosis (-78 +/- 8%) or OZ (-73 +/- 6%). Inhibition of PLD by 2,3-DPG was associated with concentration-dependent reductions in phagocytosis of M. tuberculosis (-74 +/- 4%) and OZ (-68 +/- 5%). Addition of purified PLD from Streptomyces chromofuscus to 2,3-DPG-treated macrophages restored phagocytosis of M. tuberculosis to control levels. Inhibition of M. tuberculosis- or OZ-stimulated PA generation by ethanol was associated with concentration-dependent reductions in phagocytosis of both particles. Incubation of MDMs with either Erdman or H37Ra M. tuberculosis, or OZ, resulted in rapid (onset 1 min) and sustained (60 min) increases in the tyrosine phosphorylation (Tyr-P) of multiple MDM proteins. Prominent Tyr-P was noted in proteins of 150, 95, 72, 56, and 42 kD. The protein tyrosine kinase (PTK) inhibitors genistein and herbimycin A reduced M. tuberculosis-stimulated PLD activity by 66-84%. Inhibition of PLD activity by genistein or herbimycin A was associated with inhibition of phagocytosis of M. tuberculosis and OZ. These data demonstrate that PLD is activated during macrophage phagocytosis of M. tuberculosis or OZ, that PTKs are involved in this stimulation of PLD, and that the extent of phagocytosis of these particles is tightly coupled to activation of PLD.
Identification and Characterization of Protective T Cells in hsp65 DNA-Vaccinated and<i>Mycobacterium tuberculosis</i>-Infected Mice (1998)

Immunization by intramuscular injection of plasmid DNA expressing mycobacterial 65-kDa heat shock protein (hsp65) protects mice against challenge with virulent Mycobacterium tuberculosis H37Rv. During infection or after immunization, CD4+/CD8- and CD8+/CD4- hsp65-reactive T cells increased equally in spleens. During infection, the majority of these cells were weakly CD44 positive (CD44(lo)) and produced interleukin 4 (IL-4) whereas after immunization the majority were highly CD44 positive (CD44(hi)) and produced gamma interferon (IFN-gamma). In adoptive transfer of protection to naive mice, the total CD8+/CD4- cell population purified from spleens of immunized mice was more protective than that from infected mice. When the cells were separated into CD4+/CD8- and CD8+/CD4- types and then into CD44(hi) and CD44(lo) types, CD44(lo) cells were essentially unable to transfer protection, the most protective CD44(hi) cells were CD8+/CD4-, and those from immunized mice were much more protective than those from infected mice. Thus, whereas the CD44(lo) IL-4-producing phenotype prevailed during infection, protection was associated with the CD8+/CD44(hi) IFN-gamma-producing phenotype that predominated after immunization. This conclusion was confirmed and extended by analysis of 16 hsp65-reactive T-cell clones from infected mice and 16 from immunized mice; the most protective clones, in addition, displayed antigen-specific cytotoxicity.
A 12 b 65 MSample/s CMOS ADC with 82 dB SFDR at 120 MHz (2002)

A recent trend in cellular basestation design is to digitize multiple channels with a single ADC, often at the intermediate frequency (IF). This requires an ADC with wide dynamic range, particularly SFDR above 80 dB and SNR better than 70 dB, even when sampling input frequencies above 70 MHz. This 12b, 65MSample/s (MSPS) ADC incorporates a wide-bandwidth, low-distortion input stage coupled with a digitally-calibrated, multibit pipeline architecture optimized for low power consumption.
Transient propagation dynamics of flowing plasmas accelerated by radio-frequency electric fields (2017)

Flowing plasmas are of significant interest due to their role in astrophysical phenomena and potential applications in magnetic-confined fusion and spacecraft propulsion. The acceleration of a charge-neutral plasma beam using the radio-frequency self-bias concept could be particularly useful for the development of neutralizer-free propulsion sources. However, the mechanisms that lead to space-charge compensation of the exhaust beam are unclear. Here, we spatially and temporally resolve the propagation of electrons in an accelerated plasma beam that is generated using the self-bias concept with phase-resolved optical emission spectroscopy. When combined with measurements of the extraction-grid voltage, ion and electron currents, and plasma potential, the pulsed-periodic propagation of electrons during the interval of sheath collapse at the grids is found to enable the compensation of space charge.
ChemInform Abstract: Synthetic Studies on the Fluorinated Analogues for the Putative Oxindole‐Type Metabolites of 5‐Halotryptamines. (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
Vision-based navigation of mobile robot with obstacle avoidance by single camera vision and ultrasonic sensing (2002)

This paper describes a vision-based navigation method in an indoor environment for an autonomous mobile robot which can avoid obstacles. In this method, the self-localization of the robot is done with a mode-based vision system, and a non-stop navigation is realized by a retroactive position correction system. Stationary obstacles are avoided with single-camera vision and moving obstacles are detected with ultrasonic sensors. We report on experiments in a hallway using the YAMABICO robot.
Detection of apoptotic caspase activation in sera from patients with chronic HCV infection is associated with fibrotic liver injury (2004)

Chronic hepatitis C virus (HCV) infection is characterized by inflammatory liver damage and is associated with a high risk of development of cirrhosis and hepatocellular carcinoma. Although histological examination of liver biopsies is currently the gold standard for the detection of early liver damage, there is a strong need for better noninvasive methods. We recently demonstrated that the proapoptotic activation of caspases is considerably enhanced in histological sections from HCV-infected liver tissue, suggesting an important role of apoptosis in liver damage. Here, we investigated whether caspase activation is detectable also in sera from patients with chronic HCV infection. Using a novel enzyme-linked immunosorbent assay that selectively recognizes a proteolytic neoepitope of the caspase substrate cytokeratin-18, we demonstrate that caspase activity is markedly increased in the sera of HCV patients. Interestingly, while 27% of patients with chronic HCV infection showed normal aminotransferase levels despite inflammatory and fibrotic liver damage, more than 50% of those patients exhibited already elevated serum caspase activity. Moreover, 30% of patients with normal aminotransferase but elevated caspase activity revealed higher stages of fibrosis. In conclusion, compared with conventional surrogate markers such as aminotransferases, detection of caspase activity in serum might be a more sensitive method of detecting early liver injury. Thus, measurement of caspase activity might provide a novel diagnostic tool, especially for patients with normal aminotransferases but otherwise undiagnosed histologically active hepatitis and progressive fibrosis.
Single-walled carbon nanotubes for high-performance electronics (2013)

Single-walled carbon nanotubes (SWNT) could replace silicon in high-performance electronics with their exceptional electrical properties and intrinsic ultra-thin body. During the past five years, the major focus of this field is gradually shifting from proof-of-concept prototyping in academia to technology development in industry with emphasis on manufacturability and integration issues. This article reviews recent advances, starting with experimental and modeling works that evaluate the potential of adopting SWNTs in ultimately scaled transistors. Techniques to separate nanotubes according to their electronic types and assemble them into aligned arrays are then discussed, followed by a description of the engineering aspects in their implementation in integrated circuits and systems. A concluding discussion provides some perspectives on future challenges and research opportunities.
Chemopreventive Effect of Kava on 4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone plus Benzo[ <i>a</i> ]pyrene–Induced Lung Tumorigenesis in A/J Mice (2008)

Lung cancer is the leading cause of cancer death, and chemoprevention is a potential strategy to help control this disease. Epidemiologic survey indicates that kava may be chemopreventive for lung cancer, but there is a concern about its potential hepatotoxicity. In this study, we evaluated whether oral kava could prevent 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) plus benzo[a]pyrene (B[a]P)-induced lung tumorigenesis in A/J mice. We also studied the effect of kava to liver. At a dose of 10 mg/g diet, 30-week kava treatment (8 weeks concurrent with NNK and B[a]P treatment followed by 22 weeks post-carcinogen treatment) effectively reduced lung tumor multiplicity by 56%. Kava also reduced lung tumor multiplicity by 47% when administered concurrently with NNK and B[a]P for 8 weeks. Perhaps most importantly, kava reduced lung tumor multiplicity by 49% when administered after the final NNK and B[a]P treatment. These results show for the first time the chemopreventive potential of kava against lung tumorigenesis. Mechanistically, kava inhibited proliferation and enhanced apoptosis in lung tumors, as shown by a reduction in proliferating cell nuclear antigen (PCNA), an increase in caspase-3, and cleavage of poly(ADP-ribose) polymerase (PARP). Kava treatment also inhibited the activation of nuclear factor kappaBNF-kappaB, a potential upstream mechanism of kava chemoprevention. Although not rigorously evaluated in this study, our preliminary data were not suggestive of hepatotoxicity. Based on these results, further studies are warranted to explore the chemopreventive potential and safety of kava.
Vehicle Detection in Aerial Surveillance Using Dynamic Bayesian Networks (2011)

We present an automatic vehicle detection system for aerial surveillance in this paper. In this system, we escape from the stereotype and existing frameworks of vehicle detection in aerial surveillance, which are either region based or sliding window based. We design a pixelwise classification method for vehicle detection. The novelty lies in the fact that, in spite of performing pixelwise classification, relations among neighboring pixels in a region are preserved in the feature extraction process. We consider features including vehicle colors and local features. For vehicle color extraction, we utilize a color transform to separate vehicle colors and nonvehicle colors effectively. For edge detection, we apply moment preserving to adjust the thresholds of the Canny edge detector automatically, which increases the adaptability and the accuracy for detection in various aerial images. Afterward, a dynamic Bayesian network (DBN) is constructed for the classification purpose. We convert regional local features into quantitative observations that can be referenced when applying pixelwise classification via DBN. Experiments were conducted on a wide variety of aerial videos. The results demonstrate flexibility and good generalization abilities of the proposed method on a challenging data set with aerial surveillance images taken at different heights and under different camera angles.
Antitumor activity of palmitic acid found as a selective cytotoxic substance in a marine red alga. (2003)

In a previous report, we discussed an extract from a marine red alga, Amphiroa zonata, which shows selective cytotoxic activity to human leukemic cells, but no cytotoxicity to normal human dermal fibroblast (HDF) cells in vitro. In this study, we identified palmitic acid, a selective cytotoxic substance from the marine algal extract, and investigated its biological activities. At concentrations ranging from 12.5 to 50 micrograms/ml, palmitic acid shows selective cytotoxicity to human leukemic cells, but no cytotoxicity to normal HDF cells. Furthermore, palmitic acid induces apoptosis in the human leukemic cell line MOLT-4 at 50 micrograms/ml. Palmitic acid also shows in vivo antitumor activity in mice. One molecular target of palmitic acid in tumor cells is DNA topoisomerase I, however, interestingly, it does not affect DNA topoisomerase II, suggesting that palmitic acid may be a lead compound of anticancer drugs.
ZnS nanocrystal cytotoxicity is influenced by capping agent chemical structure and duration of time in suspension (2012)

As a result of their characteristic physical and optical properties, including their size, intense fluorescence, broad excitation, narrow emission and resistance to photobleaching, semiconductor nanocrystals are potentially useful for a variety of biological applications including molecular imaging, live-cell labeling, photodynamic therapy and targeted drug delivery. In this study, zinc sulfide (ZnS) semiconductor nanocrystals were synthesized in the 3 to 4 nm size range with selected capping agents intended to protect the nanocrystal core and increase its biological compatibility. We show that the biocompatibility of ZnS nanocrystals with primary murine splenocytes is influenced by the chemical structure of the outer capping agent on the nanocrystal. Additionally, the cytotoxicity of ZnS nanocrystals increases markedly as a function of time spent in suspension in phosphate-buffered saline (PBS). These data suggest that the potential therapeutic and/or biological use of ZnS nanocrystals is inherently dependent upon the proper choice of capping agent, as well as the conditions of nanocrystal preparation and storage.
Beyond the combinatorial limit in depth minimization for LUT-based FPGA designs (1993)

We present an integrated approach to synthesis and mapping to go beyond the combinatorial limit set up by the depth-optimal FlowMap algorithm. The new algorithm, named FlowSYN, uses the global combinatorial optimization techniques to guide the Boolean synthesis process during depth minimization. The combinatorial optimization is achieved by computing a series of minimum cuts of fixed heights in a network based on fast network flow computation, and the Boolean optimization is achieved by efficient OBDD-based implementation of functional decomposition. The experimental results show that FlowSYN improves FlowMap in terms of both the depth and the number of LUTs in the mapping solutions. Moreover, FlowSYN also outperforms the existing FPGA synthesis algorithms for depth minimization.
Modification of a whole room indirect calorimeter for measurement of rapid changes in energy expenditure (1994)

Whole room indirect calorimeters are among the most accurate devices for measurement of human energy expenditure and have provided useful data about determinants of total daily energy expenditure. However, a limitation of whole room indirect calorimeters has been the inability to detect acute (usually < 10-15 min) changes in energy expenditure. This precludes using these devices to study the acute effects of food, drugs, or exercise on energy expenditure. We describe modifications made to our whole room indirect calorimeter (respiratory chamber) to allow accurate measurement of energy expenditure over time periods as short as 1 min. The modifications involve changes in the system design and use of signal processing techniques. With these modifications, we can measure energy expenditure in 1-min intervals throughout the day. This allows accurate study of the acute effects of food, exercise, or drugs on energy expenditure in subjects moving freely inside the respiratory chamber. The ability to use respiratory chambers for these types of studies should improve our understanding of how body weight is regulated.
Overexpression of Erg11p by the Regulatable <i>GAL1</i> Promoter Confers Fluconazole Resistance in <i>Saccharomyces cerevisiae</i> (1999)

The contribution of the dosage of target enzyme P-450 14alpha-demethylase (14alphaDM) to fluconazole resistance in both Candida albicans and Saccharomyces cerevisiae remains unclear. Here, we show that overexpression of Saccharomyces P-450 14alphaDM in S. cerevisiae, under the control of the regulatable promoter GAL1, results in azole resistance.
Photoacoustic Imaging of Mesenchymal Stem Cells in Living Mice <i>via</i> Silica-Coated Gold Nanorods (2012)

Improved imaging modalities are critically needed for optimizing stem cell therapy. Techniques with real-time content to guide and quantitate cell implantation are especially important in applications such as musculoskeletal regenerative medicine. Here, we report the use of silica-coated gold nanorods as a contrast agent for photoacoustic imaging and quantitation of mesenchymal stem cells in rodent muscle tissue. The silica coating increased the uptake of gold into the cell more than 5-fold, yet no toxicity or proliferation changes were observed in cells loaded with this contrast agent. Pluripotency of the cells was retained, and secretome analysis indicated that only IL-6 was disregulated more than 2-fold from a pool of 26 cytokines. The low background of the technique allowed imaging of down to 100,000 cells in vivo. The spatial resolution is 340 μm, and the temporal resolution is 0.2 s, which is at least an order of magnitude below existing cell imaging approaches. This approach has significant advantages over traditional cell imaging techniques like positron emission tomography and magnetic resonance imaging including real time monitoring of stem cell therapy.
Ground stations for aeronautical and space laser communications at German Aerospace Center (2015)

Free-space laser communications are subject of current research and development in many research and industrial bodies. Long distance air-ground and space-ground can be implemented in future communication networks as feeder, backbone and backhaul links for various air- and space-based scenarios. The Institute of Communications and Navigation of the German Aerospace Center (DLR) operates two ground stations to investigate the communication channel and system: the Optical Ground Station Oberpfaffenhofen and the Transportable Optical Ground Station. The first one is a fixed installation and operated as experimental station with focus on channel measurements and tests of new developments. Various measurement devices, communication receivers and optical setups may easily be installed for different objectives. The facility is described with its dome installation, telescope setup and infrastructure. Past and current deployment in several projects is described and selected measurement achievements presented. The second ground station is developed for semi-operational use and demonstration purposes. Based on experience with the experimental ground station, this one is developed with higher level of integration and system robustness. The focus application is the space-ground and air-ground downlink of payload data from Earth observation missions. Therefore, it is also designed to be easily transportable for worldwide deployment. The system is explained and main components are discussed. The characteristics of both ground stations are presented and discussed. Further advancements in the equipment and capability are also presented.