gebhart/patrepeval huggingface dataset:
On the Precoder Design of Flat Fading MIMO Systems Equipped With MMSE Receivers: A Large-System Approach (2011)

This paper is devoted to the design of precoders maximizing the ergodic mutual information (EMI) of bi-correlated flat fading MIMO systems equipped with MMSE receivers. The channel state information and the second-order statistics of the channel are assumed available at the receiver side and at the transmitter side respectively. As the direct maximization of the EMI needs the use of nonattractive algorithms, it is proposed to optimize an approximation of the EMI, introduced recently, obtained when the number of transmit and receive antennas <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">t</i> and τ converge to ∞ at the same rate. It is established that the relative error between the actual EMI and its approximation is a <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">O</i> ( [ 1/( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">t</i> <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> )]) term. It is shown that the left singular eigenvectors of the optimum precoder coincide with the eigenvectors of the transmit covariance matrix, and its singular values are solution of a certain maximization problem. Numerical experiments show that the mutual information provided by this precoder is close from what is obtained by maximizing the true EMI, but that the algorithm maximizing the approximation is much less computationally intensive.
Specific Regions of Contact between Human T-cell Leukemia Virus Type I Tax Protein and DNA Identified by Photocross-linking (1998)

The human T-cell leukemia virus type I Tax protein forms a ternary complex on DNA in association with a host factor, the cyclic AMP response element-binding protein (CREB). An understanding of the precise geometry of this complex has been elusive. We have used photocross-linking to investigate Tax-DNA contacts. Our data show that Tax contacts the DNA at two symmetric positions 14 nucleotides apart on either side of the Tax responsive element. The presence of symmetric, widely separated regions of contact suggests that at least two molecules of Tax are present in the complex. Mapping the contacts onto a three-dimensional model of the CREB-DNA binary complex shows that they lie on the same face of the DNA near the regions where the N termini of the CREB bZIP domains enter the major groove. This location correlates well with previous evidence that CREB amino acid residues immediately N-terminal to the bZIP domain are crucial for the formation of the ternary complex. The limited number of cross-links observed suggests that contacts are primarily with the phosphate backbone and does not support the idea that a major structural element of the Tax protein inserts into the major or minor grooves of the DNA.
Matrix Metalloproteinase-3 Differences in Oral and Skin Fibroblasts (2007)

While skin wounds heal by scarring, wounds of oral mucosa show privileged healing with minimal scar formation. Our hypothesis was that phenotypic differences between oral and skin fibroblasts underlie these differences in healing. The aims of this study were to compare MMP-3 expression by oral and skin fibroblasts and investigate a role for MMP-3 in mediating collagen gel contraction. Oral fibroblasts induced significantly greater gel contraction than did paired skin cells. Inhibition of MMP activity significantly inhibited gel contraction by both cell types. Specific inhibition of MMP-3 activity reduced gel contraction by oral, but not skin, fibroblasts. Oral fibroblasts produced significantly higher levels of MMP-3 than did skin fibroblasts at all levels studied. TGF-beta1 and -beta3 isoforms stimulated MMP-3 expression at mRNA, protein, and activity levels by both fibroblast populations. Results suggest that increased MMP-3 production by oral fibroblasts may underlie the differences in wound-healing outcome seen in skin and oral mucosa.
Recognition by natural killer cells of N6‐isopentenyladenosine‐treated human glioma cell lines (2017)

Cancer cell stress induced by cytotoxic agents promotes antitumor immune response. Here, we observed that N6-isopentenyladenosine (iPA), an isoprenoid modified adenosine with a well established anticancer activity, was able to induce a significant upregulation of cell surface expression of natural killer (NK) cell activating receptor NK Group 2 member D (NKG2D) ligands on glioma cells in vitro and xenografted in vivo. Specifically suboptimal doses of iPA (0.1 and 1 µM) control the selective upregulation of UL16-binding protein 2 on p53wt-expressing U343MG and that of MICA/B on p53mut-expressing U251MG cells. This event made the glioblastoma cells a potent target for NK cell-mediated recognition through a NKG2D restricted mechanism. p53 siRNA-mediated knock-down and pharmacological inhibition (pifithrin-α), profoundly prevented the iPA action in restoring the immunogenicity of U343MG cells through a mechanism that is dependent upon p53 status of malignancy. Furthermore, accordingly to the preferential recognition of senescent cells by NK cells, we found that iPA treatment was critical for glioma cells entry in premature senescence through the induction of S and G2/M phase arrest. Collectively, our results indicate that behind the well established cytotoxic and antiangiogenic effects, iPA can also display an immune-mediated antitumor activity. The indirect engagement of the innate immune system and its additional activity in primary derived patient's glioma cell model (GBM17 and GBM37), fully increase its translational relevance and led to the exploitation of the isoprenoid pathway for a valid therapeutic intervention in antiglioma research.
Photodiode Amplifiers: OP AMP Solutions (1995)

Table of contents
Photodiodes.The Basic Amplifier.Bandwidth and Stability.Wideband Photodiode Amplifiers.Noise.Noise Reduction.High-Gain Photodiode Amplifiers.Reducing Power-Supply Noise Coupling.Reducing External Noise Effects.Position-Sensing Photodiode Amplifiers.
Differential Inactivation of Interferons by a Protease from Human Granulocytes (1992)

Human leukocyte suspensions produced interferon-alpha (IFN-alpha) without induction during incubation at 37 degrees C. The highest titers were obtained at about 30 million cells/ml. The best yields, approximately 2 IU per 10(6) cells, were achieved in medium with or without albumin; serum inhibited the production. The uninduced IFN-alpha peaked at 24 h. The titers dropped on further incubation due to release of a protease from polymorphonuclear cells. The protease inactivated all tested human class I IFNs, but recombinant IFN-alpha 1 was clearly more resistant to the enzyme than rIFN-alpha 2. Human IFNs-gamma from different sources exhibited striking differences in their sensitivity to the protease. Glycosylated natural IFN-gamma from human leukocytes and glycosylated rIFN-gamma from CHO cells were relatively resistant, whereas unglycosylated rIFN-gamma from Escherichia coli was rapidly degraded by the protease. The protease was inhibited by PMSF and by greater than or equal to 1% human or fetal bovine serum but not by EDTA or less than or equal to 1% human albumin. Its optimum pH was between 7 and 8. It was resistant to treatment for 30 min at 56 degrees C.
The genetic network of prototypic planarian eye regeneration is Pax6 independent (2002)

We report the presence of two Pax6-related genes, Pax6A and Pax6B, which are highly conserved in two planarian species Dugesia japonica and Girardia tigrina (Platyhelminthes, Tricladida). Pax6A is more similar to other Pax6 proteins than Pax6B, which is the most divergent Pax6 described so far. The planarian Pax6 homologs do not show any clear orthology to the Drosophila duplicated Pax6 genes, eyeless and twin of eyeless, which suggests an independent Pax6 duplication in a triclad or platyhelminth ancestor. Pax6A is expressed in the central nervous system of intact planarians, labeling a subset of cells of both cephalic ganglia and nerve cords, and is activated during cephalic regeneration. Pax6B follows a similar pattern, but shows a lower level of expression. Pax6A and Pax6B transcripts are detected in visual cells only at the ultrastructural level, probably because a limited amount of transcripts is present in these cells. Inactivation of both Pax6A and Pax6B by RNA-mediated gene interference (RNAi) inhibits neither eye regeneration nor eye maintenance, suggesting that the genetic network that controls this process is not triggered by Pax6 in planarians.
A CONSTITUTIONAL BIBLIOGRAPHY (1996)

The literature on the United States Constitution and the Supreme Court of the United States would fill an entire library.What follows is a list of books which likely would be of interest to curious readers, both lawyers and nonlawyers alike, who want to learn more about the basic principles of the Constitution.Each book is listed only once, in the interest of space, so the careful user ought to peruse the entire list.
Monitoring Early Differentiation Events in Human Embryonic Stem Cells by Massively Parallel Signature Sequencing and Expressed Sequence Tag Scan (2004)

To identify genes that may be involved in the process of human embryonic stem cell (hESC) differentiation, we profiled gene expression by expressed sequenced tag (EST) enumeration and massively parallel signature sequencing (MPSS) using RNA samples from feeder-free cultures of undifferentiated (passages 40-50) and differentiated (day 14) H1, H7, and H9 lines. MPSS and EST scan analysis showed good concordance and identified a large number of genes that changed rapidly as cultures transition from a pluripotent to a differentiated state. These included known and unknown ES cell-specific genes as well as a large number of known genes that were altered as cells differentiate. A subset of genes that were either up- or down-regulated were selected and their differential expression confirmed by a variety of independent methods, including comparison of expression after further differentiation, publicly available databases, and direct assessments by reverse transcriptase (RT)-PCR and immunocytochemistry. The analysis identified markers unique to the hESC and embryoid bodies (hEBs) stage as well as signaling pathways that likely regulate differentiation. The data generated can be used to monitor the state of hESC isolated by different laboratories using independent methods and maintained under differing culture conditions.
Comparison of measured and computed portal dose for IMRT treatment (2006)

A new 2D array Seven 29T model (PTW, Freiburg), equipped with 729 vented plane-parallel ion chambers, projected for pretreatment verification of radiotherapy plans, was used as a detector for the transmitted or portal dose measurements below a Rando phantom. The dosimetric qualities of the 2D array make it attractive for measuring transmitted dose maps from step-and-shoot intensity-modulated radiotherapy (IMRT). It is well known that for step-and-shoot IMRT beams that use a small number of monitor units (MUs) per sequence, the early and recent electronic portal imaging devices (EPIDs) present a different response at X-ray start-up that affects the accuracy of the measured transmitted dose. The comparison of portal doses measured to those calculated by a commercial treatment-planning system (TPS) can verify correct dose delivery during treatment. This direct validation was tested by irradiating a simulated head tumor in a Rando anthropomorphic phantom by step-and-shoot IMRT beams. The absolute transmitted doses on a plane orthogonal to the beam central axis below the phantom were measured by the 2D array calibrated in terms of dose to water and compared with the computed portal dose extracted by custom software. In a previous paper, the comparison between the IMRT portal doses, computed by a commercial TPS and measured by a linear array that supplied a 1 mm spatial dose resolution, was carried out. The gamma-index analysis supplied an agreement of more than 95% of the dose point with acceptance criteria, in terms of dose difference, DeltaDmax, and distance agreement, deltadmax, equal to 4% and 4 mm, respectively. In this paper, we verify the possible use of the PTW 2D array for measurements of the transmitted doses during several fractions of head and neck tumor radiotherapy. There are two advantages in the use of this 2D array as a portal dose device for the IMRT quality assurance program: first is the ability to perform absolute dose comparisons for hundreds of measurement positions to verify the correct dose delivery in several fractions of the therapy; second is the efficiency in time to detect these kinds of dose distributions within the field of view area of the CT scanner.
The effect of the substrate on the extracellular neural activity recorded micromachined silicon microprobes (2005)

The influence of a highly-doped silicon substrate on the neural activity recorded by thin-film microelectrode arrays has been explored using top, back, and double-sided recording sites. Probes having shank widths from 25-50 microm and site spacings (in depth) from 20-40 microm were used. The realization of back-looking and double-sided sites requires one mask in addition to the normal 8-mask passive probe process. Back-looking sites record as well as top sites even though separated by only a few microns from the surrounding silicon substrate, indicating that the substrate acts as an insulator and does not shunt local current from the extracellular space. On wide substrates, back-looking sites can thus be used to ensure a spherical recording field. As the substrate width is scaled to dimensions of a few microns, it should leave the extracellular field relatively undisturbed while providing mechanical support and suppressing crosstalk.
Real-time PCR evaluation of cell-free DNA subjected to various storage and shipping conditions (2015)

In this study, we attempted to explore the factors affecting the yield of cell-free fetal DNA (cffDNA) obtained from maternal blood samples, including the use of different types of collection tubes, the interval between sample processing, and sample shipping under extreme weather conditions. Blood samples were drawn into K3EDTA tubes and cell-stabilizing tubes (Streck blood collection tube, BCT) from women pregnant with male fetuses. Real time PCR was used to amplify a β-actin gene fragment to measure the total plasma cell-free DNA concentration, while an SRY gene fragment was used to quantify the cffDNA. The samples in the K3EDTA tubes revealed a decreased quantity of SRY after 5 days of transportation, with a median of 25.9 copies/mL (P < 0.01); however, the value remained stable at 33.4 copies/mL in the BCT tubes. We observed a statistically significant increase in stability of the amount of total DNA in the blood samples stored in K3EDTA tubes (P < 0.01) and transportated under extreme outdoor temperatures (-20°-0°C) than that of the control values. These results indicate that it could be possible to avoid the presence of excess maternal DNA in samples shipped under extreme weather conditions for no more than 2 days, by collecting the blood samples in BCT tubes.
Reservoir monitoring in oil sands: Developing a permanent cross‐well system (2011)

Geophysical cross‐well methods for reservoir monitoring of the SAGD process in oil sands have been evaluated and ranked by Statoil and Schlumberger in a joint research project. Modeling results indicate that seismic geophones and ERT electrodes are suitable for detecting changes in the reservoir caused by increased temperatures and steam replacing the oil. High temperatures and the need for electrically insulated casing have called for extensive testing of materials. After dealing with these challenges, a permanent cross‐well system has been developed. Two vertical observation wells have been drilled and permanently instrumented, and testing of the downhole sensors have been accomplished.
Action Research: A Brief Overview (2008)

This contribution outlines several variants of teacher / action research, describing some of the different "tools" and "intentions" of a number of prominent qualitative researchers. URN: urn:nbn:de:0114-fqs0001173
Bioengineering of noncoding RNAs for research agents and therapeutics (2016)

The discovery of functional small noncoding RNAs (ncRNAs), such as microRNAs and small interfering RNAs, in the control of human cellular processes has opened new avenues to develop RNA-based therapies for various diseases including viral infections and cancers. However, studying ncRNA functions and developing RNA-based therapeutics relies on access to large quantities of affordable ncRNA agents. Currently, synthetic RNAs account for the major source of agents for RNA research and development, yet carry artificial modifications on the ribose ring and phosphate backbone in sharp contrast to posttranscriptional modifications present on the nucleobases or unmodified natural RNA molecules produced within cells. Therefore, large efforts have been made in recent years to develop recombinant RNA techniques to cost-effectively produce biological RNA agents that may better capture the structure, function, and safety properties of natural RNAs. In this article, we summarize and compare current in vitro and in vivo methods for the production of RNA agents including chemical synthesis, in vitro transcription, and bioengineering approaches. We highlight the latest recombinant RNA approaches using transfer RNA (tRNA), ribosomal RNA (rRNA), and optimal ncRNA scaffold (OnRS), and discuss the applications of bioengineered ncRNA agents (BERAs) that should facilitate RNA research and development.
Structure and function of voltage‐gated sodium channels (1998)

1. Sodium channels mediate fast depolarization and conduct electrical impulses throughout nerve, muscle and heart. This paper reviews the links between sodium channel structure and function. 2. Sodium channels have a modular architecture, with distinct regions for the pore and the gates. The separation is far from absolute, however, with extensive interaction among the various parts of the channel. 3. At a molecular level, sodium channels are not static: they move extensively in the course of gating and ion translocation. 4. Sodium channels bind local anaesthetics and various toxins. In some cases, the relevant sites have been partially identified. 5. Sodium channels are subject to regulation at the levels of transcription, subunit interaction and post-translational modification (notably glycosylation and phosphorylation).
IL-7 Contributes to the Progression of Human T-cell Acute Lymphoblastic Leukemias (2011)

The importance of microenvironmental factors for driving progression in leukemia has been debated. Previous evidence has pointed to interleukin-7 (IL-7), a fundamental cytokine to normal T-cell development and homeostasis, as an important determinant of the viability and proliferation of T-cell acute lymphoblastic leukemia (T-ALL) cells in vitro. In this study, we report that IL-7 is also a critical determinant of T-ALL progression. T-ALL cell lines and primary T-ALL samples initiated leukemia more slowly when engrafted to immunocompromised Rag2(-/-)IL2rg(-/-) mice lacking IL-7. This effect was not related to reduced engraftment or homing of transplanted cells to the bone marrow. Instead, IL-7 deficiency diminished expansion of leukemia cells in the bone marrow and delayed leukemia-associated death of transplanted mice. Moreover, infiltration of different organs by T-ALL cells, which characterizes patients with advanced disease, was more heterogeneous and generally less efficient in IL-7-deficient mice. Leukemia progression was associated with increased Bcl-2 expression and cell viability, reduced p27(Kip1) expression, and decreased cell-cycle progression. Clinical measurements of IL-7 plasma levels and IL-7 receptor (IL-7R) expression in T-ALL patients versus healthy controls confirmed that IL-7 stimulates human leukemia cells. Our results establish that IL-7 contributes to the progression of human T-cell leukemia, and they offer preclinical validation of the concept that targeting IL-7/IL-7R signaling in the tumor microenvironment could elicit therapeutic effects in T-ALL.
Electrochemical processes in a wire-in-a-capillary bulk-loaded, nano-electrospray emitter (2001)

Experiments are described that illustrate solvent oxidation, emitter electrode corrosion, and analyte oxidation in positive ion mode nano-electrospray mass spectrometry using a wire-in-a-capillary, bulk-loaded nano-electrospray emitter geometry. Time-lapsed color photography of pH and metal specific indicator solutions within operating nano-electrospray emitters, as well as temporal changes in the ions observed in the nano-electrospray mass spectra, are used to probe these reactions, judge their magnitude, and study the time dependent changes in solution composition and gas-phase ion signal brought about as a result of these electrochemical reactions. The significance of these observations for analytical applications of nano-electrospray mass spectrometry are discussed.
Material Properties That Predict Preservative Uptake for Silicone Hydrogel Contact Lenses (2012)

The current grouping system for testing contact lens-solution interactions separates all silicone hydrogels from conventional hydrogel contact lenses. However, not all silicone hydrogel lenses interact similarly with the same contact lens solution. Based upon the results of our research, we propose that the same material characteristics used to group conventional hydrogel lenses, water content and ionic charge, can also be used to predict uptake of hydrophilic preservatives for silicone hydrogel lenses. In addition, the hydrophobicity of silicone hydrogel contact lenses, although not investigated here, is a unique contact lens material property that should be evaluated for the uptake of relatively hydrophobic preservatives and tear components.
Foamy virus vectors (1996)

Human foamy virus (HFV) is a retrovirus of the spumavirus family. We have constructed vectors based on HFV that encode neomycin phosphotransferase and alkaline phosphatase. These vectors are able to transduce a wide variety of vertebrate cells by integration of the vector genome. Unlike vectors based on murine leukemia virus, HFV vectors are not inactivated by human serum, and they transduce stationary-phase cultures more efficiently than murine leukemia virus vectors. These properties, as well as their large packaging capacity, make HFV vectors promising gene transfer vehicles.
An Overview of Severe Acute Respiratory Syndrome–Coronavirus (SARS-CoV) 3CL Protease Inhibitors: Peptidomimetics and Small Molecule Chemotherapy (2016)

Severe acute respiratory syndrome (SARS) is caused by a newly emerged coronavirus that infected more than 8000 individuals and resulted in more than 800 (10-15%) fatalities in 2003. The causative agent of SARS has been identified as a novel human coronavirus (SARS-CoV), and its viral protease, SARS-CoV 3CL(pro), has been shown to be essential for replication and has hence been recognized as a potent drug target for SARS infection. Currently, there is no effective treatment for this epidemic despite the intensive research that has been undertaken since 2003 (over 3500 publications). This perspective focuses on the status of various efficacious anti-SARS-CoV 3CL(pro) chemotherapies discovered during the last 12 years (2003-2015) from all sources, including laboratory synthetic methods, natural products, and virtual screening. We describe here mainly peptidomimetic and small molecule inhibitors of SARS-CoV 3CL(pro). Attempts have been made to provide a complete description of the structural features and binding modes of these inhibitors under many conditions.