gebhart/patrepeval huggingface dataset:
Inhibition of angiogenesis by the cancer chemopreventive agent conjugated linoleic acid. (2002)

Dietary conjugated linoleic acid (CLA) has been shown previously to inhibit rat mammary carcinogenesis. In addition to direct effects on mammary epithelial cells,including decreased proliferation and induction of apoptosis, CLA may exert its effects indirectly by inhibiting the differentiation of mammary stromal cells to an endothelial cell type. Specifically, CLA was found to decrease the ability of mammary stromal cells to form complex anastomosing microcapillary networks in vitro on Engelbreth-Holm-Swarm-derived reconstituted basement membrane. This suggested that CLA might inhibit angiogenesis in vivo. To test this possibility, CD2/F(1) mice were placed on synthetic diets containing 0, 1, or 2% CLA for 6 weeks, before angiogenic challenge by s.c. injection with an angiogenic gel substrate (Matrigel pellet assay). After 7 days, the pellets from animals fed the control diet were infiltrated by abundant branching networks of blood vessels with patent lumen-containing RBCs. In contrast, pellets from the CLA-fed animals contained fewer infiltrating cells, which formed limited branching cellular networks, the majority of which had collapsed lumen and no RBCs. Both levels of dietary CLA showed similar effects, with the number of RBC-containing vessels per 20x field decreased to a third of that seen in control. Dietary CLA decreased serum levels of vascular endothelial growth factor (VEGF) and whole mammary gland levels of VEGF and its receptor Flk-1. Both cis-9, trans-11 and trans-10, cis-12 CLA isomers were effective in inhibiting angiogenesis in vitro in a dose-dependent fashion. The ability of CLA to inhibit angiogenesis may contribute to its efficacy as a chemopreventive agent.
Ribozyme Targeting of Steroid Receptor Co-Activators: A Therapeutic Approach to Breast Cancer (2000)

Abstract : The gene of the nuclear receptor co activator AIB 1 is amplified in breast cancer cell lines as well as in breast tumor tissue. AIB 1 mRNA is often highly expressed in primary breast tumors and is has been shown that AIB 1 enhances estrogen and progesterone dependent transcription in vitro. Therefore it has been postulated that AIB 1 contributes to the development of breast cancer. However, it is currently not known what the precise role of AIB 1 is in the development of breast cancer. Our strategy to address this question is to establish breast cancer cell lines in which we can regulate AIB 1 levels with ribozymes in order to determine the impact of reduced AIB 1 gene expression on the phenotype and angiogenic or invasive properties of breast cancer cells. During the first year we developed MCF-7 breast cancer cells in which we are able to downregulate AIB 1 protein levels by up to 90%. Furthermore, downregulation of AIB 1 levels reduced the ability of the progesterone receptor to fully activate a progesterone regulated test promoter. We anticipate that our study will give valuable insights into the biological significance of AIB 1 as well as its potential role as a therapeutic target in breast cancer.
A fractionally-spaced maximum-likelihood sequence estimation receiver in a multipath fading environment (1992)

A fractionally spaced maximum-likelihood sequence estimation (FS-MLSE) receiver is described. The FS-MLSE algorithm is effective in combating the intersymbol interference (ISI) in a multipath fading environment where the multipath delay spread is comparable to the transmitted symbol duration or only a fraction of it. The intermediate values (other than the symbol values) required by the FS-MLSE algorithm are obtained by interpolation from the symbol decisions and the Nyquist filter coefficients. Simulation results show that the FS-MLSE algorithm exhibits a significant performance improvement over the conventional symbol-spaced MLSE algorithm in a relatively short delay spread environment.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
742. Human Artificial Chromosome (HAC) Vector Provides Long-Term Therapeutic Transgene Expression in Normal Human Primary Fibroblasts (2005)

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Human artificial chromosomes (HACs) are segregating freely from host chromosomes through a set of cell divisions. Accordingly, the host genome is not disrupted and the expression of the transgene could be sustained for a prolonged period without suffering the effects of its surrounding sequence on the host genome. These are the ideal properties required for vectors in gene therapy, and therefore HACs are potentially useful to ensure both safety and duration of gene expression in therapeutic gene delivery. We constructed a novel human chromosome 21-derived HAC (21|[Delta]|pqHAC) vector, which devoid of most expressed genes by telomere truncation at the genomic regions proximal to the centromere in both p and q arms, and inserted human erythropoietin (EPO) gene, which is a growth factor for erythroid cells and widely used for the clinical treatment of anemia in renal insufficiency, into the HAC (EPO-21|[Delta]|pqHAC) as a model of therapeutic transgenes. Although low transfer efficiency of intact HACs to the cells has hampered the studies using normal human primary cells, the major targets for ex vivo gene therapy, we successfully demonstrated the introduction of EPO-21|[Delta]|pqHAC vector into normal primary human fibroblasts (hPFs) with micro cell-mediated chromosome transfer (MMCT). However, the mitotic stability of EPO-21|[Delta]|pqHAC vector in normal hPFs and the growth ability of the resultant hPF clones to obtain graft cells for transplantation remained to be elucidated. Here, we studied the hPF clones harboring the EPO-21|[Delta]|pqHAC vector cytogenetically and demonstrated that the structurally defined, extra artificial chromosome was highly maintained in normal hPFs under non-selective condition at a constant copy number mostly in a single copy per cell without accompanying aberration of host chromosomes. Mitotic-loss rates were determined, and the level of stability of EPO-21|[Delta]|pqHAC vector was comparable with those reported for the other top-down and bottom-up artificial chromosomes in human fibro-sarcoma cell line HT1080 cells. These hPF clones proliferated from a single colony up to 3.8x107 cells and then their growth stopped, suggesting that cell senescence occurred and the introduction of the EPO-21|[Delta]|pqHAC vector did not cause immortalization. We also showed the long-term expression of human epo gene in the hPFs carrying the EPO-21|[Delta]|pqHAC vector. In conclusion, this study shows the potential application of the 21|[Delta]|pqHAC vector in hormone-replacement gene therapy, which might ensure safety with no lesion of host chromosomes and provides long-term therapeutic transgene expression. This also implies that utilization of the HAC vector offers novel options for ex vivo gene therapy.
Children and Adults with Refractory Acute Graft-versus-Host Disease Respond to Treatment with the Mesenchymal Stromal Cell Preparation “MSC-FFM”—Outcome Report of 92 Patients (2019)

(1) Background: Refractory acute graft-versus-host disease (R-aGvHD) remains a leading cause of death after allogeneic stem cell transplantation. Survival rates of 15% after four years are currently achieved; deaths are only in part due to aGvHD itself, but mostly due to adverse effects of R-aGvHD treatment with immunosuppressive agents as these predispose patients to opportunistic infections and loss of graft-versus-leukemia surveillance resulting in relapse. Mesenchymal stromal cells (MSC) from different tissues and those generated by various protocols have been proposed as a remedy for R-aGvHD but the enthusiasm raised by initial reports has not been ubiquitously reproduced. (2) Methods: We previously reported on a unique MSC product, which was generated from pooled bone marrow mononuclear cells of multiple third-party donors. The products showed dose-to-dose equipotency and greater immunosuppressive capacity than individually expanded MSCs from the same donors. This product, MSC-FFM, has entered clinical routine in Germany where it is licensed with a national hospital exemption authorization. We previously reported satisfying initial clinical outcomes, which we are now updating. The data were collected in our post-approval pharmacovigilance program, i.e., this is not a clinical study and the data is high-level and non-monitored. (3) Results: Follow-up for 92 recipients of MSC-FFM was reported, 88 with GvHD ≥°III, one-third only steroid-refractory and two-thirds therapy resistant (refractory to steroids plus ≥2 additional lines of treatment). A median of three doses of MSC-FFM was administered without apparent toxicity. Overall response rates were 82% and 81% at the first and last evaluation, respectively. At six months, the estimated overall survival was 64%, while the cumulative incidence of death from underlying disease was 3%. (4) Conclusions: MSC-FFM promises to be a safe and efficient treatment for severe R-aGvHD.
Measuring unresolved surface features using imaging ellipsometric polarization signatures (2002)

It is well known that sub-wavelength structures can modify the polarization of incident light. Due to the coupling of electric fields at the sub-wavelength boundary, the responses to TE and TM polarized light are different. This effect has been intensively investigated in optical data storage [1, 2], metrology [3-6] and artificial dielectric synthesis [7, 8]. In optical metrology applications, this effect can be used as a sensitive measure of the sub-wavelength structures. In this summary, we report a measurement technique capable of measuring unresolved isolated features using a high resolution imaging ellipsometer. The imaging ellipsometer technique has been reported in details in a separate publication [9]. Illustrated in Fig. 1, a high numerical aperture (NA=0.8) objective is used in the setup. The high NA illumination gives rise to both a good ellipsometric signal and high spatial resolution. The transmission axes of the polarizer and the analyzer are aligned with the x-axis and y-axis, respectively. The sample is placed at the focal plane of the objective. A fiber bundle with a narrow band filter (10 nm bandwidth with central wavelength at 633 nm) is used as the illumination source to form an image on the CCD. The condenser collimates the light from each point from the source. Since individual points from the source in the field-of-view of the condenser subtend very small angles with respect to the optical axis, we can analyze each image point in the same way as the on-axis point. For a ray from the on-axis point entering the pupil at position (θ, ϕ), where θ is the corresponding incident angle on the sample of this ray after the lens and ϕ is the azimuth angular position from the x-axis, it can be shown that the power contributed from this ray on the detector is:
A relative clutter metric (1998)

Clutter plays a very important role in the area of machine and human-in-the-loop target acquisition. A great deal of interest has recently been shown in assessing several different definitions of clutter. In spite of so many definitions available, no single clutter definition has been agreed on by the infrared community as being the best. We develop a new clutter metric, called relative clutter, which is based on factor analysis which is extensively used for statistical analysis. This relative clutter combines many definitions of clutter. Different methods for calculating the relative clutter based on the magnitude of the eigenvalues obtained from the correlation matrix are suggested. The relative clutter of many images is analyzed.
High range resolution radar signal classification a partitioned rough set approach (2002)

In automatic target recognition (ATR) systems there are advantages to developing classifiers based on a portion of the signal. A partitioning technique is introduced in this paper that allows rough set theory to be applied to real-world size problems. Rough set theory (RST) is an emerging concept for determining features and then classifiers from a training data set. RST guarantees that once the data has been labeled all possible classifiers (based on that labeling) can be generated. There are multiple classifiers for each signal partition and multiple partitions for each signal. Classifiers based on a single reduct (classifier) or one partition do not perform well enough to be useful. We fuse all the reducts from all the partitions into one classifier. This fusion of partitioned reducts yields a synergistic result that produces a classifier with a high probability of declaration and good probability of correct classification.
Single-mask fabrication of high-G piezoresistive accelerometers with extended temperature range (2007)

This paper presents a fabrication process in which all components of an in-plane piezoresistive accelerometer are fabricated simultaneously using a single mask.By dry-etching a silicon-on-insulator (SOI) wafer that has a specific resistivity, piezoresistors are defined and isolated from each other and from the bulk silicon without the pn-junctions normally required in piezoresistive sensors.In addition to simplifying the fabrication, the temperature range is also extended when compared to conventional piezoresistive accelerometers, due to the absence of pn-junctions.Singleaxis accelerometers, designed for an acceleration range of 1 G to 500 G with a sensitivity of 1 mV/G, were fabricated and tested, and linear output characteristics were demonstrated.The temperature performance was also characterized.The temperature coefficient of sensitivity (TCS) was 0.3%/℃ and the temperature coefficient of offset (TCO) was 20 mG/℃.
Design and synthesis of a helix heparin-binding peptide (1992)

Elaboration of heparin-protein-binding interactions is necessary to understand how heparin modulates protein function. The heparin-binding domain of some proteins is postulated to be a helix structure which presents a surface of high positive charge density. Thus, a synthetic 19-residue peptide designed to be alpha-helical in character was synthesized, and its interaction with heparin was studied. The peptide was shown to be 75% helix by circular dichroism (CD) spectrometry in neutral pH buffer (at 2 degrees C); helicity increased to nearly 85% under high ionic strength conditions or to nearly 100% in 75% ethanol. Increasing the temperature of the solution caused a change in the spectral envelope consistent with a coil transition of the peptide. The midpoint of the transition (i.e., the temperature at which the helix content was determined to be 50%) was 25 degrees C, and the determined van't Hoff enthalpy change (delta HvH) was 3.2 kcal/mol of peptide. By CD, heparin increases the helix content of the peptide to 100% and increases the apparent thermal stability of the peptide by about 1 kcal/mol. The melting point for the helix/coil transition of the heparin-peptide complex was 50 degrees C. The thermal coefficient of the transition (approximately 300 deg.cm2.dmol-1.degree C-1) was essentially the same for the peptide alone or the peptide-heparin complex. Dissociation of the complex under high ionic strength conditions was also observed in the CD experiment. Biological assays showed less heparin-binding activity than expected (micromolar KD values), but this was attributed to the absence of critical lysyl residues in the peptide.(ABSTRACT TRUNCATED AT 250 WORDS)
SOS3 Function in Plant Salt Tolerance Requires N-Myristoylation and Calcium Binding (2000)

The salt tolerance gene SOS3 (for salt overly sensitive3) of Arabidopsis is predicted to encode a calcium binding protein with an N-myristoylation signature sequence. Here, we examine the myristoylation and calcium binding properties of SOS3 and their functional significance in plant tolerance to salt. Treatment of young Arabidopsis seedlings with the myristoylation inhibitor 2-hydroxymyristic acid caused the swelling of root tips, mimicking the phenotype of the salt-hypersensitive mutant sos3-1. In vitro translation assays with reticulocyte showed that the SOS3 protein was myristoylated. Targeted mutagenesis of the N-terminal glycine-2 to alanine prevented the myristoylation of SOS3. The functional significance of SOS3 myristoylation was examined by expressing the wild-type myristoylated SOS3 and the mutated nonmyristoylated SOS3 in the sos3-1 mutant. Expression of the myristoylated but not the nonmyristoylated SOS3 complemented the salt-hypersensitive phenotype of sos3-1 plants. No significant difference in membrane association was observed between the myristoylated and nonmyristoylated SOS3. Gel mobility shift and (45)Ca(2)+ overlay assays demonstrated that SOS3 is a unique calcium binding protein and that the sos3-1 mutation substantially reduced the capacity of SOS3 to bind calcium. The resulting mutant SOS3 protein was not able to interact with the SOS2 protein kinase and was less capable of activating it. Together, these results strongly suggest that both N-myristoylation and calcium binding are required for SOS3 function in plant salt tolerance.
Localized harmonic motion imaging: theory, simulations and experiments (2003)

Several techniques have been developed in an effort to estimate mechanical properties of tissues. These techniques typically estimate static or harmonic motion resulting from an externally or internally applied mechanical stimulus. In this paper, we discuss the advantages of utilizing a new technique that performs RF signal tracking in order to estimate the localized oscillatory motion resulting from the harmonic radiation force produced by two focused ultrasound transducer elements with overlapping beams oscillating at distinct frequencies. Four agar gels were utilized in order to determine the effect of stiffness on the motion amplitude. Estimates of the displacement relative to the initial position (i.e., at the onset of the application of the radiation force) were obtained during the application of the radiation force that oscillated at frequencies ranging between 200 Hz and 800 Hz. In the simulations, an exponential decrease of the displacement amplitude with stiffness was observed at all frequencies investigated. An M-mode version to depict both the spatial and temporal variation of the locally induced displacement was used. In experiments with gels of different stiffness, the resulting amplitude of the harmonic displacement estimated oscillated at the same frequencies and an exponential decrease of the displacement amplitude with get stiffness was also observed. In tissue experiments, the results showed that the method is feasible in tissues and that FUS ablation can be detected. These preliminary results demonstrate the feasibility of imaging localized harmonic motion as induced by an oscillatory ultrasound radiation force. Due to the highly localized and harmonic nature of the estimated response, this technique may be proven highly suitable for accurate estimation of the elastic modulus variation in tissues due to disease.
CHAPTER 14. Improving Photosynthetic Solar Energy Conversion Efficiency: the Truncated Light-harvesting Antenna (TLA) Concept (2018)

Application of the Truncated Light-harvesting Antenna (TLA) concept in photosynthesis entails a determined genetic engineering effort to minimize the light-harvesting antenna size of the photosystems in order to increase solar energy conversion efficiencies and the photosynthetic productivity of cyanobacteria and microalgae in mass cultures under bright sunlight cultivation conditions. Evidence in the literature supports the notion that TLA technology can significantly improve sunlight-to-product (e.g., biomass or hydrogen) energy conversion efficiencies. Approaches to generate TLA-strains in cyanobacteria and microalgae and their functional properties are summarized and discussed in this chapter. TLA-cyanobacteria were generated upon genetic deletion of the cpc operon, encoding phycocyanin and associated components of the phycobilisome peripheral rods. In the case of microalgae, recent advances on the assembly mechanism for the peripheral chlorophyll a-b light-harvesting complex enabled application of genes and proteins of the chloroplast Signal-Recognition Particle (CpSRP) pathway toward the attainment of green microalgal TLA-strains. These advances have expanded the molecular tool box by which to generated TLA-microalgae and, recently, TLA-diatoms. Substantial mechanistic and functional differences between the CpSRP pathway in microalgae and higher plants are outlined and discussed, showing that the CpSRP pathway cannot be equally applied for TLA strain generation in green microalgae and higher plants. The recent application of TLA-technology in green microalgae and cyanobacteria showed an interim increase in the sunlight-to-biomass energy conversion efficiency in the range of 1.5-1.6-fold over that measured with the corresponding wild type. However, it was estimated that the theoretically maximum potential of the TLA technology is an improvement in the solar-to-biomass energy conversion efficiency of microalgae by up to 3-fold over what can be achieved with wild type strains. In summary, current TLA-technology has shown significant improvement in the sunlight-to-biomass or sunlight-to-H2 energy conversion efficiency. Nonetheless, there is room for further improvement in solar energy conversion efficiency and yields, moving the process of photosynthesis from the current best 2-3% solar-to-biomass measured with green microalgae up to the theoretical maximum of 8-10% for the process of photosynthesis.
In-situ Monitoring of Cavity Filling in Nanoimprints by Capacitance (2006)

This report deals with the feasibility of carrying out in-situ monitoring of cavity filling in nanoimprints using capacitance measurements with a capacitance circuit built-in on the mold body. A finite element model valid for the numerical description of a parallel-plate capacitor has been developed, and simulations were carried out to predict the influence of cavity filling on capacitance values. On the other hand, in order to measure the continuous variations in capacitance of a parallel-plate capacitor during the course of imprinting, a series of experiments have been performed isothermally, and the capacitance values have been measured at various imprinting stages. The correlation between capacitance values and replicated polymer heights was studied. The preliminary results presented indicate that capacitance measurement is a feasible tool for the monitoring of cavity filling in nanoimprints.