gebhart/patrepeval huggingface dataset:
Bioreactor expansion of human neural precursor cells in serum‐free media retains neurogenic potential (2009)

Human neural precursor cells (hNPCs), harvested from somatic tissue and grown in vitro, may serve as a source of cells for cell replacement strategies aimed at treating neurodegenerative disorders such as Parkinson's disease (PD), Huntington's disease (HD), and intractable spinal cord pain. A crucial element in a robust clinical production method for hNPCs is a serum-free growth medium that can support the rapid expansion of cells while retaining their multipotency. Here, we report the development of a cell growth medium (PPRF-h2) for the expansion of hNPCs, achieving an overall cell-fold expansion of 10(13) over a period of 140 days in stationary culture which is significantly greater than other literature results. More importantly, hNPC expansion could be scaled-up from stationary culture to suspension bioreactors using this medium. Serial subculturing of the cells in suspension bioreactors resulted in an overall cell-fold expansion of 7.8 x 10(13) after 140 days. These expanded cells maintained their multipotency including the capacity to generate large numbers of neurons (about 60%). In view of our previous studies regarding successful transplantation of the bioreactor-expanded hNPCs in animal models of neurological disorders, these results have demonstrated that PPRF-h2 (containing dehydroepiandrosterone, basic fibroblast growth factor and human leukemia inhibitory factor) can successfully facilitate the production of large quantities of hNPCs with potential to be used in the treatment of neurodegenerative disorders.
Liquid crystal lens with concentric electrodes and inter-electrode resistors (2014)

In this review, we provide an overview of recent efforts in designing high-quality tunable liquid crystal (LC) lenses with concentric electrodes. The design concepts are introduced, and details about fabrication and evaluation methods are given. Computational and experimental approaches are used to gain understanding of the fundamental limiting factors affecting the performance of LC lenses. In addition, directions for improvement of image quality, speed, optical power, and off-axis performance are proposed.
Combining type-analysis with points-to analysis for analyzing Java library source-code (2015)

The predominant work in static program analysis is focused on whole program analysis assuming that the whole program is present at analysis time and the only unknowns are program inputs. However, for library designers it is of paramount importance to perform semantic checks via static program analysis tools without the presence of an application. The literature offers only little research on partial program analysis for object-oriented programming languages including Java. Analyzing libraries statically requires novel abstractions for all possible applications that are not known a-priori. In this work, we present a static program analysis technique that reasons about the state of the library by approximating the behaviour of all possible applications. The key contribution is (1) the combination of type-analysis with points-to analysis and (2) the development of a most-general application (MGA) as a type, which represents the interaction of the library with all possible applications.
OFDM Signal Identification and Transmission Parameter Estimation for Cognitive Radio Applications (2007)

Methods for identification of orthogonal frequency division multiplexing (OFDM) signals and estimation of fundamental OFDM parameters are developed in this paper. Detected transmissions are classified as single-carrier or multi-carrier. In the case of multi-carrier transmission, OFDM symbol duration and cyclic prefix (CP) length are estimated blindly using characteristics of OFDM transmission. For estimation of symbol duration and CP length, cyclostationarity of OFDM signaling is explored by using a maximum likelihood (ML) estimator. The proposed algorithms can be used in cognitive radio for identifying various OFDM-based transmissions and for electronic surveillance to detect illegal or enemy signals.
A Systematic Approach to Uncover Security Flaws in GUI Logic (2007)

To achieve end-to-end security, traditional machine-to-machine security measures are insufficient if the integrity of the human-computer interface is compromised. GUI logic flaws are a category of software vulnerabilities that result from logic bugs in GUI design/implementation. Visual spoofing attacks that exploit these flaws can lure even security- conscious users to perform unintended actions. The focus of this paper is to formulate the problem of GUI logic flaws and to develop a methodology for uncovering them in software implementations. Specifically, based on an in-depth study of key subsets of Internet Explorer (IE) browser source code, we have developed a formal model for the browser GUI logic and have applied formal reasoning to uncover new spoofing scenarios, including nine for status bar spoofing and four for address bar spoofing. The IE development team has confirmed all these scenarios and has fixed most of them in their latest build. Through this work, we demonstrate that a crucial subset of visual spoofing vulnerabilities originate from GUI logic flaws, which have a well-defined mathematical meaning allowing a systematic analysis.
Development of Calcium Phosphate Glass-Ceramics for Surgical and Dental Use (1987)

Abstract Two types of glass-ceramics have been developed in the system of calcium phosphate without silica. The preparation conditions, crystallization processes, and some of physical properties are briefly reported. These glass-ceramics have high potential use for bone substitutes and dental materials such as dental crown, root and tooth.
Biosynthesis of Colabomycin E, a New Manumycin‐Family Metabolite, Involves an Unusual Chain‐Length Factor (2014)

Colabomycin E is a new member of the manumycin-type metabolites produced by the strain Streptomyces aureus SOK1/5-04 and identified by genetic screening from a library of streptomycete strains. The structures of colabomycin E and accompanying congeners were resolved. The entire biosynthetic gene cluster was cloned and expressed in Streptomyces lividans. Bioinformatic analysis and mutagenic studies identified components of the biosynthetic pathway that are involved in the formation of both polyketide chains. Recombinant polyketide synthases (PKSs) assembled from the components of colabomycin E and asukamycin biosynthetic routes catalyzing the biosynthesis of "lower" carbon chains were constructed and expressed in S. aureus SOK1/5-04 ΔcolC11-14 deletion mutant. Analysis of the metabolites produced by recombinant strains provided evidence that in both biosynthetic pathways the length of the lower carbon chain is controlled by an unusual chain-length factor supporting biosynthesis either of a triketide in asukamycin or of a tetraketide in colabomycin E. Biological activity assays indicated that colabomycin E significantly inhibited IL-1β release from THP-1 cells and might thus potentially act as an anti-inflammatory agent.
Title: Integration of an Inertial Navigation System and DP (2008)

The paper describes an architecture for the integration of an inertial navigation system (INS) into a dynamic positioning (DP) system. It discusses the major benefits of using INS for DP, and includes the results of sea-trials conducted to show these benefits. There are a number of possible benefits to using an INS as an input to the DP system. These benefits are dependent upon a range of factors including the operations being undertaken by the vessel, the ease of use and the quality of the equipment. One use of an INS is to supplement or clean-up measurements from an existing measurement system. By coupling the INS to a hydro-acoustic system the INS can help to reduce the noise on the measurements and fill-in for long update rates, for example, to prolong battery life for transponders.
Experimental Determination of the Multiplicity Deadtime Parameter (2008)

Definition, extraction, and application of dead-time parameters, in correlated neutron counting, are long standing, thorny issues. Traditionally, dead-time corrections have been estimated on the assumption of a simple paralyzing model, arising from the action of the discriminator in the charged amplifiers connected to the 3 He proportional counters, using a fixed dead-time. Various schemes exist to apply the paralyzable model to the multiplicity shift register histogram data. In principle, several methods could be used to estimate the dead-time parameter. The approach which is most widely applied involves measuring a series of Cf-252 sources spanning a wide dynamic range of counting rates. Ratios between the Singles, Doubles and Triples rates which ought to be independent of fissile mass are extracted. The dead-time is chosen so as to achieve the best independence in the ratios, characteristic of the fissioning system, over the counting range. These measurements can be quite laborious to conduct; require a set of Cf-252 sources matched in construction and isotopic composition; require long counts to achieve the requisite precision and involve a good deal of numerical analysis to interpret. In this work we present a simpler scheme which produces comparable values in a way that is easier to implement. In essence we place a near random neutron source, such as may be realized using Am/Li α-n sources, in the cavity and record the multiplicity histograms as one would for an assay. The variance to mean-squared is narrower than for a random counting experiment, however, as a result of the dead-time losses. A simple formula exists allowing the deadtime to be extracted from this measurement. In this paper, we present results for the traditional approach, the proposed approach and also a variation based on adjusting the total event rate by adding Am/Li sources to a single Cf-252 source fixed in position for the case of a pair of Passive Scrap Multiplicity Counters (PSMC’s). Excellent agreement is obtained. Because the variance to mean squared approach gives high precision in a single, short, measurement it lends itself to studying dead-time behaviors systematically as a function of shift register settings, operating voltage and preamplifier trim
Use of thin layer spectroelectrochemistry in the study of NADH regeneration by means of an hydrogenase (1991)

Abstract Thin layer spectroelectrochemistry is used to show that it is possible to mediate the electrochemical reduction of NADH by means of an hydrogenase. This kind of cofactor regeneration is associated to three model reactions involving the reduction of pyruvate, acetoacetylCoA and ketoglutarate.
A novel epitope on the C-terminus of SmD1 is recognized by the majority of sera from patients with systemic lupus erythematosus. (1998)

The SmD1 protein is a specific target for the autoantibody response in SLE. To further analyze this reactivity epitope, mapping was performed with cellulose-bound 13-mer peptides overlapping 10 amino acids (aa). In this initial approach, 4 out of 15 SLE sera recognized more than five overlapping peptides of the SmD1 C-terminus. Therefore, longer oligopeptides of up to 37 aa of this region were generated and probed for as antigens by ELISA. For the SmD1 aa 83-119 polypeptide, there was a striking increase of reactivity with 70.0% positive reactions out of 167 SLE sera. In contrast, 105 healthy control sera were negative, and only 8.3% of sera from patients with other inflammatory diseases (n = 267) exhibited a response, which was of low level only. The anti-SmD183-119 reactivity was significantly higher in anti-dsDNA antibody positive vs. negative sera (P < 0.001) and correlated with disease activity. Four of five human monoclonal anti-dsDNA antibodies also reacted with SmD183-119. The specificity for SmD1 was demonstrated by inhibition experiments and immunization of rabbits with SmD183-119 inducing SmD1-specific antibodies. In conclusion, the SmD183-119 peptide was demonstrated to be an important and highly specific target of the autoimmune response in SLE. The high sensitivity of this ELISA probably depends on a conformational epitope, which appears not to be accessible in the full-size SmD1 protein.
The herpes simplex virus 1 protein kinase U <sub>S</sub> 3 is required for protection from apoptosis induced by the virus (1997)

An earlier report showed that a disabled mutant lacking both copies of the major regulatory gene (alpha4) of herpes simplex virus 1 induced DNA degradation characteristic of apoptosis in infected cells, whereas the wild-type virus protected cells from apoptosis induced by thermal shock. More extensive analyses of the disabled mutant revealed a second mutation which disabled US3, a viral gene encoding a protein kinase known to phosphorylate serine/threonine within a specific arginine-rich consensus sequence. Analyses of cells infected with a viral mutant carrying a wild-type alpha4 gene but from which the US3 gene had been deleted showed that it induced fragmentation of cellular DNA, whereas a recombinant virus in which the deleted sequences of the US3 gene had been restored did not cause the cellular DNA to fragment. These results point to the protein kinase encoded by the US3 gene as the principal viral product required to block apoptosis.
Structure-Based Design, Synthesis, and Biological Evaluation of Highly Selective and Potent G Protein-Coupled Receptor Kinase 2 Inhibitors (2016)

G protein-coupled receptors (GPCRs) are central to many physiological processes. Regulation of this superfamily of receptors is controlled by GPCR kinases (GRKs), some of which have been implicated in heart failure. GSK180736A, developed as a Rho-associated coiled-coil kinase 1 (ROCK1) inhibitor, was identified as an inhibitor of GRK2 and co-crystallized in the active site. Guided by its binding pose overlaid with the binding pose of a known potent GRK2 inhibitor, Takeda103A, a library of hybrid inhibitors was developed. This campaign produced several compounds possessing high potency and selectivity for GRK2 over other GRK subfamilies, PKA, and ROCK1. The most selective compound, 12n (CCG-224406), had an IC50 for GRK2 of 130 nM, >700-fold selectivity over other GRK subfamilies, and no detectable inhibition of ROCK1. Four of the new inhibitors were crystallized with GRK2 to give molecular insights into the binding and kinase selectivity of this class of inhibitors.
Molecular cloning and regulatory analysis of the cuticle‐degrading‐protease structural gene from the entomopathogenic fungus <i>Metarhizium anisopliae</i> (1992)

The proteinaceous insect cuticle is an effective barrier against most microbes, but entomopathogenic fungi can breach it using extracellular proteases. We report here the isolation and characterization of a cDNA clone of the cuticle-degrading protease (Pr1) of Metarhizium anisopliae. The cDNA sequence revealed that Pr1 is synthesized as a large precursor (40.3 kDa) containing a signal peptide, a propeptide and the mature protein predicted to have a molecular mass of 28.6 kDa. The primary structure of Pr1 has extensive similarity with enzymes of the subtilisin subclass of serine endopeptidases and the serine, histidine and aspartate components of the active site in subtilisins are preserved. Proteinase K demonstrated the closest sequence similarity to Pr1 (61%) but Pr1 was twofold more effective than proteinase K at degrading isolated cuticles of Manduca sexta and 33-fold more effective at degrading structural proteins bound to the cuticle by covalent bonds. We postulate that the additional positively charged residues on the surface of the Pr1 molecule, as determined using proteinase K, may facilitate electrostatic binding to cuticle proteins which is a prerequisite for activity. Northern-blot analysis of RNA and nuclear run-on assays demonstrated transcriptional control of the expression of Pr1 during nutrient deprivation and during the formation of infection structures. Southern-blot analysis demonstrated that genes with significant homologies to Metarhizium Pr1 were present in the entomopathogens Aspergillus flavus and Verticillium lecanii but not Zoophthora (= Erynia) radicans.
Hybrid retrospective-cost-based adaptive control using concurrent parameter estimation (2010)

We present an adaptive control methodology that requires no plant modeling information. The method is based on a cumulative retrospective cost adaptive control algorithm, which is a direct adaptive control algorithm for stabilization, disturbance rejection, and command following when partial plant modeling information is available, specifically, the first nonzero Markov parameter, the relative degree, and estimates of nonminimum-phase zeros. The same adaptive algorithm is used online to estimate the required modeling information. By merging these processes into a single architecture, the resulting hybrid adaptive control algorithm requires no prior modeling information. The method is demonstrated on several illustrative disturbance rejection and command following problems, where the plant can be either minimum or nonminimum phase, and stable or unstable.
Mixed-order compositing for 3D paintings (2011)

We present a method for rendering 3D paintings by compositing brush strokes embedded in space. The challenge in compositing 3D brush strokes is reconciling conflicts between their z -order in 3D and the order in which the strokes were painted, while maintaining temporal and spatial coherence. Our algorithm smoothly transitions between compositing closer strokes over those farther away and compositing strokes painted later over those painted earlier. It is efficient, running in O ( n log n ) time, and simple to implement. We demonstrate its effectiveness on a variety of 3D paintings.
Sustainable Green Lightweight Concrete Containing Plastic-Based Green Lightweight Aggregate (2021)

Nowadays the environment and its natural resources face many issues, related to the depletion of natural resources beside the increase in environmental pollution resulted from uncontrolled plastic waste disposal. Therefore, it is important to find effective and feasible solutions to utilize these wastes, such as using them to produce environmentally friendly green concrete. In this study, plastic-based green lightweight aggregates (PGLAs) containing PET plastic waste and by product additives were developed, and their subsequent physical and mechanical properties were compared with those of reference aggregates. Then, green lightweight aggregate concrete mixes (GLACs) were produced at 100% replacement of normal weight and lightweight coarse aggregate with developed PGLAs; and their fresh, hardened, microscopic and durability-related properties were compared to those of control mixes. Study results revealed that the unit weight of PGLAs were 21% to 29% less than that of normal coarse aggregate. Additionally, PGLAs had low water absorption that varied between 1.2% and 1.6%. The developed aggregates had 45% higher strength compared to that of lightweight coarse aggregate. Study results confirmed that structural green lightweight aggregate concretes (GLACs), that satisfied the dry density, compressive and splitting tensile strength requirements specified in ASTM C330, were feasibly produced. Finally, GLACs had low-to-moderate chloride penetration in accordance with ASTM C1202, thus it can be used in those areas exposed to the risk of chloride attack.
A syndrome-based LDPC decoder with very low error floor (2011)

This work improves the performance of LDPC decoders that implement iterative algorithms dominated by oscillatory behavior - such as offset Min-Sum algorithm - in cases of unsuccessful decoding of received words. The proposed LDPC decoder is applied on the decoding procedure of an LDPC algorithm by selecting the one of the N different estimated codewords (each produced at an iteration of the decoder) that corresponds to the syndrome with the minimum number of unsatisfied check constraints, as the output of the decoder. This method provides a decoder that achieves a notable performance improvement in the error floor region of operation for the offset Min-Sum decoding algorithm, with an insignificant increase of the hardware complexity.
Gene Encoding a Trehalose Phosphorylase from<i>Thermoanaerobacter brockii</i>ATCC 35047 (2002)

A gene encoding a trehalose phosphorylase was cloned from Thermoanaerobacter brockii ATCC 35047. The gene encodes a polypeptide of 774 amino acid residues. The deduced amino acid sequence was homologous to bacterial maltose phosphorylases and a trehalose 6-phosphate phosphorylase catalyzing anomer-inverting reactions. On the other hand, no homology was found between the T. brockii enzyme and an anomer-retaining trehalose phosphorylase from Grifola frondosa.
Fusion of block adaptive and vector quantizer for efficient SAR data compression (2002)

The paper proposes a new approach for efficient SAR raw data compression which consists of first compressing the raw data with the block adaptive quantizer (BAQ) and then performing a compression with vector quantizer (VQ) algorithm. This combination is computationally efficient since only one small codebook is needed for the coding which is independent from the data set. A signal-to-distortion ratio better than 12 dB and 6 dB is achieved for a data rate of 2 and 1 bit/sample, respectively.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Dominant-Negative Inhibition of Prion Formation Diminished by Deletion Mutagenesis of the Prion Protein (2000)

Polymorphic basic residues near the C terminus of the prion protein (PrP) in humans and sheep appear to protect against prion disease. In heterozygotes, inhibition of prion formation appears to be dominant negative and has been simulated in cultured cells persistently infected with scrapie prions. The results of nuclear magnetic resonance and mutagenesis studies indicate that specific substitutions at the C-terminal residues 167, 171, 214, and 218 of PrP(C) act as dominant-negative, inhibitors of PrP(Sc) formation (K. Kaneko et al., Proc. Natl. Acad. Sci. USA 94:10069-10074, 1997). Trafficking of substituted PrP(C) to caveaola-like domains or rafts by the glycolipid anchor was required for the dominant-negative phenotype; interestingly, amino acid replacements at multiple sites were less effective than single-residue substitutions. To elucidate which domains of PrP(C) are responsible for dominant-negative inhibition of PrP(Sc) formation, we analyzed whether N-terminally truncated PrP(Q218K) molecules exhibited dominant-negative effects in the conversion of full-length PrP(C) to PrP(Sc). We found that the C-terminal domain of PrP is not sufficient to impede the conversion of the full-length PrP(C) molecule and that N-terminally truncated molecules (with residues 23 to 88 and 23 to 120 deleted) have reduced dominant-negative activity. Whether the N-terminal region of PrP acts by stabilizing the C-terminal domain of the molecule or by modulating the binding of PrP(C) to an auxiliary molecule that participates in PrP(Sc) formation remains to be established.