gebhart/patrepeval huggingface dataset:
The use of anisotropic cell sheets to control orientation during the self-organization of 3D muscle tissue (2013)

In some parts of native tissues, the orientation of cells and/or extracellular matrixes is well organized. We know that because anisotropy produces important tissue functions, an appropriate anisotropy needs to be designed to biomimetically construct complex tissue. Here, we show the unique features of anisotropic myoblast sheets for organizing the three-dimensional (3D) orientation of myoblasts and myotubes. Utilizing a micropatterned thermoresponsive surface, human skeletal muscle myoblasts were aligned on the surface, and manipulated as a single anisotropic cell sheet by reducing the culture temperature. Consequently, layering of anisotropic myoblast sheets using gelatin gel allowed 3D myotube constructs to be built up with the desired anisotropy. We also discovered a surprising myoblast behavior. An anisotropic cell sheet placed on top of other cell sheets in fabricating thick tissue was able to change the cell orientation in several layered cell sheets underneath. This self-organization is believed to provide the uniqueness required in designing 3D cell orientation architecture for reconstructed muscle tissue.
Using the debugger as an integral part of teaching CS1 (2003)

Traditionally, using a debugger has had the connotation of finding and removing defects. In this paper and presentation, we explore the use of a modern integrated debugger as a program understanding tool for novice programming students in CS1. With the move to Java in the first course, instructors and students are faced with either ignoring the details of object-oriented concept or with explaining the concepts in a way that novices can understand. We show how the debugger can be used to depict the initial construction of an object, the object's inherited members, and polymorphic calls to the object's methods. Although each of these concepts can be difficult for beginning programmers, using the debugger to explicitly illustrate these concepts provides students with an opportunity for a much deeper understanding of their programs.
Immunochemical localization of myosin heavy chain isoforms and paramyosin in developmentally and structurally diverse muscle cell types of the nematode Caenorhabditis elegans. (1987)

The nematode Caenorhabditis elegans contains two major groups of muscle cells that exhibit organized sarcomeres: the body wall and pharyngeal muscles. Several additional groups of muscle cells of more limited mass and spatial distribution include the vulval muscles of hermaphrodites, the male sex muscles, the anal-intestinal muscles, and the gonadal sheath of the hermaphrodite. These muscle groups do not exhibit sarcomeres and therefore may be considered smooth. Each muscle cell has been shown to have a specific origin in embryonic cell lineages and differentiation, either embryonically or postembryonically (Sulston, J. E., and H. R. Horvitz. 1977. Dev. Biol. 56:110-156; Sulston, J. E., E. Schierenberg, J. White, and J. N. Thomson. 1983. Dev. Biol. 100:64-119). Each muscle type exhibits a unique combination of lineage and onset of differentiation at the cellular level. Biochemically characterized monoclonal antibodies to myosin heavy chains A, B, C, and D and to paramyosin have been used in immunochemical localization experiments. Paramyosin is detected by immunofluorescence in all muscle cells. Myosin heavy chains C and D are limited to the pharyngeal muscle cells, whereas myosin heavy chains A and B are localized not only within the sarcomeres of body wall muscle cells, as reported previously, but to the smooth muscle cells of the minor groups as well. Myosin heavy chains A and B and paramyosin proteins appear to be compatible with functionally and structurally distinct muscle cell types that arise by multiple developmental pathways.
Contribution of Stereotactic Brain Biopsies to the Diagnosis of Presenile Dementia (1990)

Precise diagnosis of presenile dementia is a great challenge. The only valuable classification of dementia is the neuropathological one. We present the first series of stereotactic biopsies in 28 presenile patients (18 males, age 39 less than or equal to 58 less than or equal to 69 years, and 10 females, age 23 less than or equal to 52 less than or equal to 66 years). The results demonstrate that the clinical and paraclinical diagnosis (including positron emission tomography scan, neuropsychological examinations, computed tomography scan, electroencephalogram) in only one third of all cases and only in 50% of the Alzheimer and Creutzfeld-Jakob cases. This is very important to be kept in mind when epidemiology or efficacy of drugs are investigated without any neuropathological confirmation.
Effect of carrier ionic properties on cellulase productivity by immobilized filamentous <i>Trichoderma reesei</i> (1994)

Abstract Filamentous cells of Trichoderma reesei were immobilized by an adhesion method using carriers prepared by radition polymerization and the effects of the ionic properties of the carriers on cellulase productivity have been investigated. The cationic polymers were better than anionic polymers in the adhesion of the cells. Enzyme productivity was affected by the ionic property of the polymer, the concentration of the coating monomer and the hydrophobicity of the pre‐coating polymer.
Sequential resonance assignment and secondary structure determination of the Ascaris trypsin inhibitor, a member of a novel class of proteinase inhibitors (1990)

The solution conformation of the Ascaris trypsin inhibitor, a member of a novel class of proteinase inhibitors, has been investigated by nuclear magnetic resonance spectroscopy. Complete sequence-specific assignments of the 1H NMR spectrum have been obtained by using a number of two-dimensional techniques for identifying through-bond and through-space (less than 5-A) connectivities. Elements of regular secondary structure have been identified on the basis of a qualitative interpretation of the nuclear Overhauser enhancement, coupling constant, and amide exchange data. These are two beta-sheet regions. One double-stranded antiparallel beta-sheet comprises residues 11-14 (strand 1) and 37-39 (strand 2). The other triple-stranded sheet is formed by two antiparallel strands comprising residues 45-49 (strand 4) and 53-57 (strand 5) connected by a turn (residues 50-52), and a small strand consisting of residues 20-22 (strand 3) that is parallel to strand 4.
Synthesis and Anaphylactogenicity of Monohaptenic Carbohydrate Conjugates (1983)

Abstract Peptidic model conjugates carrying a single 2‐carboxy‐4,6‐dinitrophenyl haptenic group, and as carbohydrate moieties D ‐gluconoyl, β‐ D ‐mannopyranosyl, 2‐deoxy‐β‐ D ‐glucopyranos‐2‐yl, or lactobionoyl residues, including the pseudocarbohydrate residue 1,3,4,5‐tetrahydroxycyclohexane‐1‐carbonyl, were synthesized. Conjugates carrying the lactobionoyl of the bis(2‐deoxy‐β‐ D ‐glucopyranos‐2‐yl) moiety were anaphylactogenic in the guinea pig, passively sensitized against 2‐carboxy‐4,6‐dinitrophenyl antigen.
Molecular Distinction of Circulating Pregnancy-Associated Plasma Protein A in Myocardial Infarction and Pregnancy (2004)

Our results provide the first evidence that circulating ACS-related PAPP-A is different from circulating pregnancy-related PAPP-A in that it is not complexed with proMBP. These findings provide a solid foundation for the design of immunoassays to accurately measure atherosclerosis-associated plasma protein A in the circulation.
TDP‐43 is recruited to stress granules in conditions of oxidative insult (2009)

Transactive response DNA-binding protein 43 (TDP-43) forms abnormal ubiquitinated and phosphorylated inclusions in brain tissues from patients with amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration. TDP-43 is a DNA/RNA-binding protein involved in RNA processing, such as transcription, pre-mRNA splicing, mRNA stabilization and transport to dendrites. We found that in response to oxidative stress and to environmental insults of different types TDP-43 is capable to assemble into stress granules (SGs), ribonucleoprotein complexes where protein synthesis is temporarily arrested. We demonstrated that a specific aminoacidic interval (216-315) in the C-terminal region and the RNA-recognition motif 1 domain are both implicated in TDP-43 participation in SGs as their deletion prevented the recruitment of TDP-43 into SGs. Our data show that TDP-43 is a specific component of SGs and not of processing bodies, although we proved that TDP-43 is not necessary for SG formation, and its gene silencing does not impair cell survival during stress. The analysis of spinal cord tissue from ALS patients showed that SG markers are not entrapped in TDP-43 pathological inclusions. Although SGs were not evident in ALS brains, we speculate that an altered control of mRNA translation in stressful conditions may trigger motor neuron degeneration at early stages of the disease.
Water Transfers in Queensland (1994)

The paper discusses the transfer of water entitlements in Queensland, with a particular emphasis on groundwater. In Queensland water entitlements have traditionally been tied to the land, and have been allocated as required by existing legislation. The use of groundwater is controlled through a licensing system that operates in declared areas of the state. In some of these areas, restrictions on the availability of new entitlements create the potential for a transfer market. By regulating the transfer market, the distribution of the extraction points could be altered to improve the performance of the aquifer. The Department of Primary Industries is developing new Natural Resource Management Legislation and in doing so is exploring the option of transferable property rights in relation to both surface and groundwater.
In vivo Characterization of the Effects of Abscisic Acid and Drying Protocols Associated with the Acquisition of Desiccation Tolerance in Alfalfa (Medicago sativa L.) Somatic Embryos (2002)

Although somatic embryos of alfalfa (Medicago sativa L.) had acquired some tolerance to desiccation at the cotyledonary stage of development (22 d after plating), additional culturing in 20 microm abscisic acid (ABA) for 8 d induced greater desiccation tolerance, as determined by increased germination. Compared with fast drying, slow drying of the ABA-treated embryos improved desiccation tolerance. However, slow drying of non-ABA-treated embryos led to the complete loss of germination capacity, while some fast-dried embryos survived. An electron paramagnetic resonance spin probe technique and in vivo Fourier transform infrared microspectroscopy revealed that cellular membrane integrity and a-helical protein secondary structure were maintained during drying in embryos cultured in media enriched with 20 microM ABA, but not in embryos cultured in the absence of ABA. Slow-dried, non-ABA-treated embryos had low oligosaccharide to sucrose ratios, an increased proportion of beta-sheet protein secondary structures and broad membrane phase transitions extending over a temperature range of more than 60 degrees C, suggestive of irreversible phase separations. The spin probe study showed evidence of imbibitional damage, which could be alleviated by prehydration in humid air. These observations emphasize the importance of appropriate drying and prehydration protocols for the survival and storage of somatic embryos. It is suggested that ABA also plays a role in suppressing metabolism, thus increasing the level of desiccation tolerance; this is particularly evident under stressful conditions such as slow drying.
Synthesis of a dithia-18-crown-6-tetracarboxylic acid (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of a dithia-18-crown-6-tetracarboxylic acidAshok Anantanarayan, Philip J. Dutton, Thomas M. Fyles, and Maurice J. PitreCite this: J. Org. Chem. 1986, 51, 5, 752–755Publication Date (Print):March 1, 1986Publication History Published online1 May 2002Published inissue 1 March 1986https://pubs.acs.org/doi/10.1021/jo00355a037https://doi.org/10.1021/jo00355a037research-articleACS PublicationsRequest reuse permissionsArticle Views434Altmetric-Citations10LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
On the Power of the Randomized Iterate (2011)

We consider two of the most fundamental theorems in cryptography. The first, due to Håstad et al. [SIAM J. Comput., 28 (1999), pp. 1364–1396] is that pseudorandom generators can be constructed from any one-way function. The second, due to Yao [Proceedings of the $23$rd Annual Symposium on Foundations of Computer Science (FOCS), 1982, pp. 80–91], states that the existence of weak one-way functions implies the existence of full-fledged one-way functions. These powerful plausibility results shape our understanding of hardness and randomness in cryptography, but unfortunately their proofs are not as tight (i.e., security preserving) as one may desire. This work revisits a technique that we call the randomized iterate, introduced by Goldreich, Krawczyk, and Luby [SIAM J. Comput., 22 (1993), pp. 1163–1175]. This technique was used by Goldreich, Krawczyk, and Luby [SIAM J. Comput., 22 (1993), pp. 1163–1175] to give a construction of pseudorandom generators from regular one-way functions. We simplify and strengthen this technique in order to obtain a similar construction, where the seed length of the resulting generators is as short as $\Theta(n \log n)$ (rather than $\Theta(n^3)$ achieved by Goldreich, Krawczyk, and Luby [SIAM J. Comput., 22 (1993), pp. 1163–1175]). Our technique has the potential of implying seed length $\Theta(n)$, and the only bottleneck for such a result are the parameters of current generators against bounded-space computations. We give a construction with similar parameters for security amplification of regular one-way functions. This improves upon the construction of Goldreich et al. [Proceedings of the $31$st Annual Symposium on Foundations of Computer Science, (FOCS), 1990, pp. 318–326] in that the construction does not need to “know" the regularity parameter of the functions (in terms of security, the two reductions are incomparable). In addition, we use the randomized iterate to show a construction of a pseudorandom generator based on an exponentially hard one-way function that has a seed length of only $\Theta(n^2)$. This improves a recent result of Holenstein [Proceedings of the Theory of Cryptography, Third Theory of Cryptography Conference (TCC), 2006] that shows a construction with seed length $\Theta(n^5)$ based on such one-way functions. Finally, we show that the randomized iterate may even be useful in the general context of Håstad et al. [SIAM J. Comput., 28 (1999), pp. 1364–1396]. In particular, we use the randomized iterate to replace the basic building block of the Håstad et al. [SIAM J. Comput., 28 (1999), pp. 1364–1396] construction. Interestingly, this modification improves efficiency by an $\Theta(n^2)$ factor and reduces the seed length to $\Theta(n^7)$ (which also implies improvement in the security of the construction).
Evaluation of methylphosphonates as analogs for detecting phosphate contacts in RNA–protein complexes (2001)

The well-studied interaction between the MS2 coat protein and its cognate hairpin was used to test the utility of the methylphosphonate linkage as a phosphate analog. A nitrocellulose filter binding assay was used to measure the change in binding affinity upon introduction of a single methylphosphonate stereoisomer at 13 different positions in the RNA hairpin. Comparing these data to the available crystal structure of the complex shows that all phosphates that are in proximity to the protein show a weaker binding affinity when substituted with a phosphorothioate and control positions show no change. However, in two cases, a methylphosphonate isomer either increased or decreased the binding affinity where no interaction can be detected in the crystal structure. It is possible that methylphosphonate substitutions at these positions affect the structure or flexibility of the hairpin. The utility of the methylphosphonate substitution is compared to phosphate ethylation and phosphorothioate substitution experiments previously performed on the same system.
SYLON-DREAM: a multi-level network synthesizer (2003)

SYLON-DREAM, a logic network synthesizer which consists of SYLON-DREAM-INI for designing initial networks and SYLON-DREAM-MIN for further optimization, is presented. Unlike the networks designed by other approaches, those designed by SYLON-DREAM consist of MOS cells satisfying given constraints on the maximum number of series and parallel transistors. Such networks can be easily realized by a cell generator or mapped to the gates in existing cell libraries.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Development of a Turning Mid Turbine Frame With Embedded Design—Part I: Design and Steady Measurements (2013)

The paper presents a new setup for the two-stage two-spool facility located at the Institute for Thermal Turbomachinery and Machine Dynamics (ITTM) of Graz University of Technology. The rig was designed in order to simulate the flow behavior of a transonic turbine followed by a counter-rotating low pressure (LP) stage like the spools of a modern high bypass aeroengine. The meridional flow path of the machine is characterized by a diffusing S-shaped duct between the two rotors. The role of turning struts placed into the mid turbine frame is to lead the flow towards the LP rotor with appropriate swirl. Experimental and numerical investigations performed on the setup over the last years, which were used as baseline for this paper, showed that wide chord vanes induce large wakes and extended secondary flows at the LP rotor inlet flow. Moreover, unsteady interactions between the two turbines were observed downstream of the LP rotor. In order to increase the uniformity and to decrease the unsteady content of the flow at the inlet of the LP rotor, the mid turbine frame was redesigned with two zero-lifting splitters embedded into the strut passage. In this first part of the paper the design process of the splitters and its critical points are presented, while the time-averaged field is discussed by means of five-hole probe measurements and oil flow visualizations. The comparison between the baseline case and the embedded design configuration shows that the new design is able to reduce the flow gradients downstream of the turning struts, providing a more suitable inlet condition for the low pressure rotor. The improvement in the flow field uniformity is also observed downstream of the turbine and it is, consequently, reflected in an enhancement of the LP turbine performance. In the second part of this paper the influence of the embedded design on the time-resolved field is investigated.
Uplink overhead analysis and outage protection for multi-carrier LTE-Advanced systems (2009)

In a multi-component carrier LTE-Advanced system, a user can simultaneously be scheduled on all component carriers (CCs). For the base station to perform radio channel aware packet scheduling, each user ideally has to feedback information corresponding to all CCs. This results in a potentially high amount of uplink overhead. Furthermore, a user in a power limited situation may experience outage because of insufficient power for the required feedback. In this paper we first propose several techniques at different layers for the overhead reduction, as well as protecting the users from being in the outage situation. Afterwards, we show how these techniques can be integrated in a LTE-Advanced system. A weighted proportional fair scheduler is also proposed to maintain good performance with a reduced amount of overhead. Extensive simulation results are presented in the end for analyzing the proper trade-off between performance and overhead reduction and outage protection.
A Multilevel State Estimation Paradigm for Smart Grids (2011)

The main objective of this paper is to describe a multilevel framework that facilitates seamless integration of existing state estimators (SEs) that are designed to function at different levels of modeling hierarchy in order to accomplish very large-scale monitoring of interconnected power systems. This has been a major challenge for decades as power systems grew pretty much independently in different areas, which had to operate in an interconnected and synchronized fashion. The paper initially provides a brief historical perspective which also explains the existing state estimation paradigm. This is followed by a review of the recent technological and regulatory drivers that are responsible for the new developments in the energy management functions. The paper then shows that a common theoretical framework can be used to implement a hierarchical scheme by which even very large-scale power systems can be efficiently and accurately monitored. This is illustrated for substation level, transmission system level as well as for a level between different transmission system operators in a given power system. Finally, the paper describes the use and benefits of phasor measurements when incorporated at these different levels of the proposed infrastructure. Numerical examples are included to illustrate performance of the proposed multilevel schemes.
<i>Chlamydomonas reinhardtii</i> Phosphoribulokinase (1990)

The sequence and kinetic properties of phosphoribulokinase purified from Chlamydomonas reinhardtii were determined and compared with the spinach (Spinacea oleracea) enzyme. Chlamydomonas phosphoribulokinase was purified to apparent homogeneity, with a specific activity of 410 micromoles per minute per milligram. Polyclonal antibodies to the purified protein were used to isolate a Chlamydomonas cDNA clone, which, upon sequencing, was found to contain the entire coding region. The transit peptide cleavage site was determined by Edman analysis of the mature protein. The precursor protein consists of a 31 amino acid transit peptide and a 344 amino acid mature polypeptide. The mature polypeptide has a calculated molecular weight of 38.5 kilodaltons and a pl of 5.75. The V(max) of the purified enzyme was 465 micromoles per minute per milligram, with apparent K(m) values of 62 micromolar ATP and 56 micromolar ribulose 5-phosphate. Immunoblot analysis indicated antigenic similarity and a similar subunit size for the enzyme from five higher plant species and Chlamydomonas. Southern blot analysis of Chlamydomonas genomic DNA indicated the presence of a single phosphoribulokinase gene. Comparison of the mature proteins from Chlamydomonas and spinach revealed 86 amino acid differences in primary structure (25% of the total) without a major difference in kinetic properties. The transit peptides of the spinach and Chlamydomonas proteins possessed little sequence homology.