gebhart/patrepeval huggingface dataset:
Power management for energy harvesting wireless sensors (2005)

The objective of this work was to demonstrate smart wireless sensing nodes capable of operation at extremely low power levels. These systems were designed to be compatible with energy harvesting systems using piezoelectric materials and/or solar cells. The wireless sensing nodes included a microprocessor, on-board memory, sensing means (1000 ohm foil strain gauge), sensor signal conditioning, 2.4 GHz IEEE 802.15.4 radio transceiver, and rechargeable battery. Extremely low power consumption sleep currents combined with periodic, timed wake-up was used to minimize the average power consumption. Furthermore, we deployed pulsed sensor excitation and microprocessor power control of the signal conditioning elements to minimize the sensors’ average contribution to power draw. By sleeping in between samples, we were able to demonstrate extremely low average power consumption. At 10 Hz, current consumption was 300 microamps at 3 VDC (900 microwatts); at 5 Hz: 400 microwatts, at 1 Hz: 90 microwatts. When the RF stage was not used, but data were logged to memory, consumption was further reduced. Piezoelectric strain energy harvesting systems delivered ~2000 microwatts under low level vibration conditions. Output power levels were also measured from two miniature solar cells; which provided a wide range of output power (~100 to 1400 microwatts), depending on the light type & distance from the source. In summary, system power consumption may be reduced by: 1) removing the load from the energy harvesting & storage elements while charging, 2) by using sleep modes in between samples, 3) pulsing excitation to the sensing and signal conditioning elements in between samples, and 4) by recording and/or averaging, rather than frequently transmitting, sensor data.
The proliferation arrest of primary tumor cells out-of-niche is associated with widespread downregulation of mitotic and transcriptional genes (2013)

In recording the changes acquired in gene expression profile during culture of fresh bone marrow samples from patients with multiple myeloma or acute myeloid leukemia, the most remarkable finding in both instances was widespread downregulation of mitotic and transcriptional genes (e.g. MKI67, CCNB1, ASPM, SGOL1, DLGAP5, CENPF, BUB1, KIF23, KIF18a, KIF11, KIF14, KIF4, NUF2, KIF1, AE2FB, TOP2A, NCAPG, TTK, CDC20, and AURKB), which could account for the ensuing proliferation arrest. Many of these genes were also underexpressed in leukemic cells from the blood or myeloma cells from an extramedullary site compared with their expression in the aspirates. Taken together, our results exhibited mitotic and transcriptional gene subsets where their expression appears to be coordinated and niche dependent. In addition, the genes induced during culture specified a variety of angiogenic factors (e.g. interleukin-8 and CXCL-5) and extracellular matrix proteins (e.g. osteopontin and fibronectin) probably released by the tumor cells while generating their favored microenvironment.
Salt effects on bacteriophage T7-I. (1987)

The thermal denaturation as a measure of the structural stability of the nucleoprotein in bacteriophage T7 has been studied in dependence of the ionic environment. Optical density and circular dichroism melting curves measured at wavelengths characterizing either the DNA or protein conformational changes were compared to identify different steps of the denaturation and to follow the effect of the ions. Monovalent salts strengthen the helical structure of intraphage DNA logarithmically in the way as they do in the case of isolated double-stranded DNA. Mg2+ and Ca2+ at very low concentrations stabilize the DNA helicity. Higher divalent ion concentrations decrease the stability of the double helix because of the repulsive ionic interactions. The high structural sensitivity of DNA in the presence of Mg2+ and Ca2+ in this "in situ" environment can be related to the biological role of these ions.
Image-based multi-scale modelling and validation of radio-frequency ablation in liver tumours (2011)

The treatment of cancerous tumours in the liver remains clinically challenging, despite the wide range of treatment possibilities, including radio-frequency ablation (RFA), high-intensity focused ultrasound and resection, which are currently available. Each has its own advantages and disadvantages. For non- or minimally invasive modalities, such as RFA, considered here, it is difficult to monitor the treatment in vivo. This is particularly problematic in the liver, where large blood vessels act as heat sinks, dissipating delivered heat and shrinking the size of the lesion (the volume damaged by the heat treatment) locally; considerable experience is needed on the part of the clinician to optimize the heat treatment to prevent recurrence. In this paper, we outline our work towards developing a simulation tool kit that could be used both to optimize treatment protocols in advance and to train the less-experienced clinicians for RFA treatment of liver tumours. This tool is based on a comprehensive mathematical model of bio-heat transfer and cell death. We show how simulations of ablations in two pigs, based on individualized imaging data, compare directly with experimentally measured lesion sizes and discuss the likely sources of error and routes towards clinical implementation. This is the first time that such a 'loop' of mathematical modelling and experimental validation in vivo has been performed in this context, and such validation enables us to make quantitative estimates of error.
Greater than normal expression of the collagen-binding stress protein heat-shock protein-47 in the infarct zone in rats after experimentally-induced myocardial infarction (2000)

The present data demonstrated that an increase in expression of HSP47 is produced by spindle-shaped mesenchymal cells in the infarct zone. Expression of HSP47 mRNA was concurrent with the expression of collagen mRNA of types I and III. Hypoxia is one of the factors which induces expression of HSP47.
Self‐aspirating atmospheric pressure chemical ionization source for direct sampling of analytes on surfaces and in liquid solutions (2005)

A self-aspirating heated nebulizer probe is described and demonstrated for use in the direct analysis of analytes on surfaces and in liquid samples by atmospheric pressure chemical ionization (APCI) mass spectrometry. Functionality and performance of the probe as a self-aspirating APCI source is demonstrated using reserpine and progesterone as test compounds. The utility of the probe to sample analytes directly from surfaces was demonstrated first by scanning development lanes of a reversed-phase thin-layer chromatography plate in which a three-component dye mixture, viz., Fat Red 7B, Solvent Green 3, and Solvent Blue 35, was spotted and the components were separated. Development lanes were scanned by the sampling probe operated under computer control (x, y plane) while full-scan mass spectra were recorded using a quadrupole ion trap mass spectrometer. In addition, the ability to sample the surface of pharmaceutical tablets (viz., Extra Strength Tylenol and Evista tablets) and to detect the active ingredients (acetaminophen and raloxifene, respectively) selectively was demonstrated using tandem mass spectrometry (MS/MS). Finally, the capability to sample analyte solutions from the wells of a 384-well microtiter plate and to perform quantitative analyses using MS/MS detection was illustrated with cotinine standards spiked with cotinine-d3 as an internal standard.
Trans-Synaptic Spread of Tau Pathology In Vivo (2012)

Tauopathy in the brain of patients with Alzheimer's disease starts in the entorhinal cortex (EC) and spreads anatomically in a defined pattern. To test whether pathology initiating in the EC spreads through the brain along synaptically connected circuits, we have generated a transgenic mouse model that differentially expresses pathological human tau in the EC and we have examined the distribution of tau pathology at different timepoints. In relatively young mice (10-11 months old), human tau was present in some cell bodies, but it was mostly observed in axons within the superficial layers of the medial and lateral EC, and at the terminal zones of the perforant pathway. In old mice (>22 months old), intense human tau immunoreactivity was readily detected not only in neurons in the superficial layers of the EC, but also in the subiculum, a substantial number of hippocampal pyramidal neurons especially in CA1, and in dentate gyrus granule cells. Scattered immunoreactive neurons were also seen in the deeper layers of the EC and in perirhinal and secondary somatosensory cortex. Immunoreactivity with the conformation-specific tau antibody MC1 correlated with the accumulation of argyrophilic material seen in old, but not young mice. In old mice, axonal human tau immunoreactivity, especially at the endzones of the perforant pathway, was greatly reduced. Relocalization of tau from axons to somatodendritic compartments and propagation of tauopathy to regions outside of the EC correlated with mature tangle formation in neurons in the EC as revealed by thioflavin-S staining. Our data demonstrate propagation of pathology from the EC and support a trans-synaptic mechanism of spread along anatomically connected networks, between connected and vulnerable neurons. In general, the mouse recapitulates the tauopathy that defines the early stages of AD and provides a model for testing mechanisms and functional outcomes associated with disease progression.
Practical and Efficient Synthesis of Alkyl, Alkenyl and Aryl-alkyl α,α-Difluoro Esters as Precursors of Potential Inhibitors of the Pheromone Catabolism in Insects (2000)

An efficient method for the synthesis of long chain alkyl, alkenyl and aryl-alkyl α,α-difluoro esters through reductive cleavage of the corresponding S-methyl dithiocarbonates with diphenylphosphine oxide and di-tert-butyl peroxide as initiator is reported. The α,α-difluoro esters 4a-j have been obained for the first time and in good overall yields. A limitation of the method is the presence of radical-sensitive functions, such as disubstituted double or triple bonds, in the substrate since the concomitant addition of the phosphonyl radical to the unsaturated carbons may induce isomerization of the double bond or polymerization. If stereomerically pure alkenyl α,α-difluoro esters are required, it is suggested to run the reductive cleavage on the S-methyl dithiocarbonate of the acetylenic precursor followed by stereoselective hydrogenation to the alkene.
Applying genotyping (TILLING) and phenotyping analyses to elucidate gene function in a chemically induced sorghum mutant population (2008)

TILLING as a reverse genetic approach has been successfully applied to sorghum. The diversity of the mutant phenotypes observed in the field, and the density of induced mutations calculated from TILLING indicate that this mutant population represents a useful resource for members of the sorghum research community. Moreover, TILLING has been demonstrated to be applicable for sorghum functional genomics by evaluating a small subset of the EMS-induced mutant lines.
Association of Src-like protein tyrosine kinases with the CD2 cell surface molecule in rat T lymphocytes and natural killer cells. (1992)

The cell surface molecule CD2 has a signaling role in the activation of T lymphocytes and natural killer cells. Because perturbation of CD2 leads to the appearance of tyrosine-phosphorylated proteins, we investigated the possibility that CD2 associates with cytoplasmic protein tyrosine kinases. As determined by in vitro kinase assays and phosphoamino acid analysis, protein tyrosine kinase activity coprecipitated with CD2 from rat T lymphocytes, T lymphoblasts, thymocytes, interleukin-2-activated natural killer cells, and RNK-16 cells (a rat natural killer cell line). In each case, both p56lck and p59fyn were identified in the CD2 immunoprecipitate. In the thymus, the association between CD2 and these kinases occurred predominately in a small subset of thymocytes that had the cell surface phenotype of mature T cells, indicating that the association is a regulated event and occurs late in T-cell ontogeny. The finding that CD2 is associated with p56lck and p59fyn in detergent lysates suggests that interactions with these Src-like protein kinases play a critical role in CD2-mediated signal transduction.
Collageneous matrix coatings on titanium implants modified with decorin and chondroitin sulfate: Characterization and influence on osteoblastic cells (2006)

Studies in developmental and cell biology have established the fact that responses of cells are influenced to a large degree by morphology and composition of the extracellular matrix. Goal of this work is to use this basic principle to improve the biological acceptance of implants by modifying the surfaces with components of the extracellular matrix (ECM), utilizing the natural self-assembly potential of collagen in combination with further ECM components in close analogy to the situation in vivo. Aiming at load-bearing applications in bone contact, collagen type I in combination with the proteoglycan decorin and the glycosaminoglycan chondroitin sulfate (CS) was used; fibrillogenesis, fibril morphology, and adsorption of differently composed fibrils onto titanium were assessed. Both decorin and CS could be integrated into the fibrils during fibrillogenesis, the amount bound respectively desorbed depending on the ionic strength of fibrillogenesis buffer. Including decorin always resulted in a significant decrease of fibril diameter, CS in only a slight decrease or even increase, depending on the collagen preparation used. No significant changes in adsorption to titanium could be detected. Osteoblastic cells showed different reactions for cytoskeletal arrangement and osteopontin expression depending on the composition of the ECM, with CS enhancing the osteoblast phenotype.
Subpopulations of Cytogenetically Abnormal Cells in Fibroblast Cultures Derived From Workers Exposed to Mineral Oil 2 (1978)

Fibroblast cultures were grown from skin biopsy specimens from individuals with a high risk of cancer due to occupational exposure to mineral oil. A high frequency of chromosomally abnormal fibroblast subpopulations was found in cultures derived from tissue that had been exposed to the carcinogen, but these aberrant clonal populations were also present in control lines from the same individuals. Abnormal clones formed a greater proportion of the total cell population in the lines derived from the oil-exposed tissue compared with the control lines after a comparable time in culture. This difference in clone size may be a consequence of the in vivo exposure to mineral oil or other environmental agents.
Identification of a sperm protein 17 CTL epitope restricted by HLA‐A1 (2003)

Sperm protein 17 (Sp17) is a novel cancer-testis antigen. We previously reported the successful generation of Sp17-specific HLA-A1-restricted cytotoxic T-lymphocytes (CTLs) from the peripheral blood of a healthy donor using a recombinant Sp17 protein. These CTLs were able to kill not only target cells pulsed with the recombinant protein but also fresh Sp17+ tumor cells. In the present study, we have identified a nonapeptide sequence within the Sp17 protein that is predicted to have a high binding affinity for the HLA-A1 molecules. We generated the synthetic nonapeptide and successfully propagated a peptide-specific CTL line. We confirmed that peptide Sp17(103-111) (ILDSSEEDK) contains an Sp17 CTL epitope restricted by HLA-A1 and identified amino acid residues 104, 107, 109 and 110 as crucial for the CTL lysis. Our findings therefore provide the tool for the characterization of CD8 T-cell function in vivo and generation of epitope-specific treatment strategies.
Encapsulated Scale Inhibitor for Use in Fracturing Treatments (1995)

Abstract This paper describes the development and testing of a solid, encapsulated scale inhibitor for use in fracturing treatments. Data from laboratory and field tests are reported. Laboratory testing with a continuous flow apparatus has yielded inhibitor release rates under dynamic conditions. The inhibitor was tested to determine the minimum inhibitor concentration required to inhibit the formation of CaCO3, CaSO4, and BaSO4 scales in brine. Laboratory data were used to determine the parameters of a mathematical model to predict the long-term release rate of the inhibitor. Data from a treated well are compared with predictions of the model. Release-rate testing in a continuous-flow apparatus shows that an encapsulated solid derivative of a phosphonate inhibitor has a sustained release profile. Temperature (100° to 225°F) and brine strength have a small effect on the release-rate profile. Coating the solid derivative makes it compatible with metal-crosslinked fracturing fluids. The coating has a short-term effect on the release-rate profile. The composition of the solid derivative has the greatest effect on its long-term release-rate profile. A comparison between the mathematical model proposed to describe the long-term release rate of the inhibitor and actual data collected from a treated well shows a large discrepancy, likely because most of the inhibitor is not in contact with the water being produced from this well.
Vaccination promotes TH1-like inflammation and survival in chronic Pseudomonas aeruginosa pneumonia. A new prophylactic principle. (1997)

The ongoing lung tissue damage in chronically Pseudomonas aeruginosa infected cystic fibrosis (CF) patients has been shown to be caused by elastase liberated from polymorphonuclear leukocytes (PMN), which dominate the chronic inflammation in these patients. Most CF patients, however, contract the chronic lung infection with P. aeruginosa after a one-year period (median) of intermittent colonization. Therefore, prevention of the onset of the chronic infection or prevention of the dominance of the inflammation by PMNs would be important goals for a vaccine strategy against P. aeruginosa in CF. In a rat model of acute P. aeruginosa pneumonia we studied whether it was possible to improve the initial bacterial clearance and diminish the inflammatory response by vaccination prior to challenge with free, live P. aeruginosa. The vaccines studied were PAO 579 sonicate, O-polysaccharide toxin A (TA) conjugate, depolymerized alginate (3064) TA conjugate (D-ALG TA), or P. aeruginosa alginate (6680 + 8839). The vaccines could, however, not improve the very efficient natural clearance of P. aeruginosa from the lungs of the rats. In a rat model of chronic P. aeruginosa lung infection we found that none of the vaccines could prevent chronic lung inflammation. After challenge, however, none of the rats immunized with D-ALG TA died in contrast to the other vaccine groups combined (p = 0.03). In addition, the inflammatory response changed from an acute type inflammation dominated by PMNs as in CF patients to a chronic type inflammation dominated by mononuclear leukocytes. This response was achieved within the first week after challenge in D-ALG TA immunized rats; in the controls, the inflammation was still acute 4 weeks after challenge. Rats immunized with D-ALG TA had a significantly reduced severity of the macroscopic lung inflammation compared to the other vaccination groups (p = 0.009). The same effect could be obtained by IFN-gamma treatment (p = 0.004). The chronic P. aeruginosa lung infection was established in two inbred mice strains C3H/HeN, known as TH1 responders, and Balb/c, known as TH2 responders. The mortality due to the infection was significantly lower in C3H/HeN mice compared to Balb/c mice (p < 0.0003). P. aerurinosa was cleared more efficiently by C3H/HeN mice and significantly more C3H/HeN mice showed normal lung histopathology than Balb/c mice (p < 0.025). Supernatants from Concanavalin A stimulated spleen cells from C3H/HeN mice contained three times higher IFN-gamma concentration but only half as high interleukin-4 concentration than those of Balb/c mice. These findings suggest that change from the TH2-like response seen in CF patients towards a TH1 response might improve their prognosis.
The HAT2 gene, a member of the HD‐Zip gene family, isolated as an auxin inducible gene by DNA microarray screening, affects auxin response in Arabidopsis (2002)

The plant hormone, auxin, regulates many aspects of growth and development. Despite its importance, the molecular mechanisms underlying the action of auxin are largely unknown. To gain a more comprehensive understanding of the primary responses to auxin, we analyzed the expression of genes in Arabidopsis seedlings treated with indole-3-acetic acid (IAA) for 15 min. We identified a single gene that is downregulated early, and 29 genes that are upregulated early. Several types of typical transcription factors are identified as early upregulated genes, suggesting that auxin signals are mediated by a master set of diverse transcriptional regulators. Of the genes that responded to auxin, the expression of the homeobox gene, HAT2, was induced rapidly. Furthermore, we show that the expression of HAT2 is induced by auxin, but not by other phytohormones. To analyze the function of HAT2 in the plant's response to auxin, we generated 35S::HAT2 transgenic plants. These produced long hypocotyls, epinastic cotyledons, long petioles, and small leaves, which are characteristic of the phenotypes of the auxin-overproducing mutants, superroot1 (sur1) and superroot2 (sur2). On the other hand, 35S::HAT2 plants showed reduced lateral root elongation, and reduced auxin sensitivity compared to wild-type plants. Together with the results of RNA blotting and biochemical analyses, these findings suggest that HAT2 plays opposite roles in the shoot and root tissues in regulating auxin-mediated morphogenesis.
Long MDS codes for optimal repair bandwidth (2012)

MDS codes are erasure-correcting codes that can correct the maximum number of erasures given the number of redundancy or parity symbols. If an MDS code has r parities and no more than r erasures occur, then by transmitting all the remaining data in the code one can recover the original information. However, it was shown that in order to recover a single symbol erasure, only a fraction of 1/r of the information needs to be transmitted. This fraction is called the repair bandwidth (fraction). Explicit code constructions were given in previous works. If we view each symbol in the code as a vector or a column, then the code forms a 2D array and such codes are especially widely used in storage systems. In this paper, we ask the following question: given the length of the column l, can we construct high-rate MDS array codes with optimal repair bandwidth of 1/r, whose code length is as long as possible? In this paper, we give code constructions such that the code length is (r + l)log <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">r</sub> l.