gebhart/patrepeval huggingface dataset:
Mixed fungal populations and lignocellulosic tissue degradation in the bovine rumen (1987)

Anaerobic fungi in ruminal fluid from cows eating Bermuda grass hay plus a grain and minerals supplement were evaluated for diversity in sporangial morphotypes and colony growth patterns and for the degradation of various lignocelluloses. In selective cultures containing streptomycin and penicillin, an active population of ruminal fungi colonized leaf blades and degraded fiber at rates and extents almost equal to that of the total ruminal population. Three major sporangial morphotypes were consistently observed on leaf blades: oval, globose, and fusiform. Fungal colonies representing three distinct growth types consistently developed in anaerobic roll tubes inoculated with strained ruminal fluid. Sporangial morphotypes could not be matched to colony types due to multiple sporangial forms within a colony. Under identical growth conditions, one type exhibited a monocentric growth pattern, while two types exhibited polycentric growth patterns previously unreported in ruminal fungi. Mixed ruminal fungi in selective cultures or in digesta taken directly from the rumen produced a massive clearing of the sclerenchyma. Quantitation of tissue areas in cross sections by light microscopic techniques showed that fungal incubations resulted in significant (P = 0.05) increases in sclerenchyma degradation compared to whole ruminal fluid incubations. The mestome cell wall was at times penetrated and partially degraded by fungi; the colonization was less frequent and to a lesser degree than with the sclerenchyma. Conversely, ruminal bacteria were not observed to degrade the mestome sheath. Phenolic monomers at 1 mM concentrations did not stimulate to a significant (P = 0.05) extent the dry weight loss or fungal colonization of leaf blades; at 10 mM concentrations cinnamic and benzoic acids were toxic to ruminal fungi.
The5ESSSwitching System: Architectural Overview (1985)

This paper presents an overview of the 5ESS™ system architecture. The administrative, communications, and switching modules are described, together with an overall view of the software architecture. Operations and maintenance aspects and a short discussion of evolutionary trends are covered.
Utrophin A is essential in mediating the functional adaptations of mdx mouse muscle following chronic AMPK activation (2014)

Duchenne muscular dystrophy (DMD) is caused by the absence of dystrophin along muscle fibers. An attractive therapeutic avenue for DMD consists in the upregulation of utrophin A, a protein with high sequence identity and functional redundancy with dystrophin. Recent work has shown that pharmacological interventions that induce a muscle fiber shift toward a slower, more oxidative phenotype with increased expression of utrophin A confer morphological and functional improvements in mdx mice. Whether such improvements result from the increased expression of utrophin A per se or are linked to other beneficial adaptations associated with the slow, oxidative phenotype remain to be established. To address this central issue, we capitalized on the use of double knockout (dKO) mice, which are mdx mice also deficient in utrophin. We first compared expression of signaling molecules and markers of the slow, oxidative phenotype in muscles of mdx versus dKO mice and found that both strains exhibit similar phenotypes. Chronic activation of 5' adenosine monophosphate-activated protein kinase with 5-amino-4-imidazolecarboxamide riboside (AICAR) resulted in expression of a slower, more oxidative phenotype in both mdx and dKO mice. In mdx mice, this fiber type shift was accompanied by clear functional improvements that included reductions in central nucleation, IgM sarcoplasmic penetration and sarcolemmal damage resulting from eccentric contractions, as well as in increased grip strength. These important morphological and functional adaptations were not seen in AICAR-treated dKO mice. Our findings show the central role of utrophin A in mediating the functional benefits associated with expression of a slower, more oxidative phenotype in dystrophic animals.
Cascaded trellis-based rate-distortion control algorithm for MPEG-4 advanced audio coding (2006)

In this paper, a few low-complexity and high-performance rate-distortion control algorithms for MPEG-4 Advanced Audio Coding (AAC) are proposed. One key element in producing good quality compressed audio particularly at medium and low rates is a high performance rate-distortion controller in the audio encoder. Although the trellis-based rate-distortion control algorithms previously proposed can achieve a praiseworthy performance, their computational complexity is extremely high. Therefore, for practical applications, it is very desirable to achieve a similar performance at a much lower complexity. Two types of techniques are proposed in this paper to reduce the computational burden of the trellis-based algorithms. One is splitting a very heavy calculation stage into two sequential steps with much less computation. The other is reducing the candidates in the trellis for parameter search. Together, when applicable, our approach achieves a similar coding performance (audio quality) but requires less than 1/1000 complexity in computation.
SPIKE: a database of highly curated human signaling pathways (2010)

The rapid accumulation of knowledge on biological signaling pathways and their regulatory mechanisms has highlighted the need for specific repositories that can store, organize and allow retrieval of pathway information in a way that will be useful for the research community. SPIKE (Signaling Pathways Integrated Knowledge Engine; http://www.cs.tau.ac.il/&~spike/) is a database for achieving this goal, containing highly curated interactions for particular human pathways, along with literature-referenced information on the nature of each interaction. To make database population and pathway comprehension straightforward, a simple yet informative data model is used, and pathways are laid out as maps that reflect the curator&rsquo;s understanding and make the utilization of the pathways easy. The database currently focuses primarily on pathways describing DNA damage response, cell cycle, programmed cell death and hearing related pathways. Pathways are regularly updated, and additional pathways are gradually added. The complete database and the individual maps are freely exportable in several formats. The database is accompanied by a stand-alone software tool for analysis and dynamic visualization of pathways.
The implications of patterns in HIV diversity for neutralizing antibody induction and susceptibility (2009)

HIV diversity is so extensive that vaccine design strategies may benefit by factoring in diversity from the earliest stages, even for vaccines that target relatively conserved regions.
Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization (2004)

A partition function calculation for RNA secondary structure is presented that uses a current set of nearest neighbor parameters for conformational free energy at 37 degrees C, including coaxial stacking. For a diverse database of RNA sequences, base pairs in the predicted minimum free energy structure that are predicted by the partition function to have high base pairing probability have a significantly higher positive predictive value for known base pairs. For example, the average positive predictive value, 65.8%, is increased to 91.0% when only base pairs with probability of 0.99 or above are considered. The quality of base pair predictions can also be increased by the addition of experimentally determined constraints, including enzymatic cleavage, flavin mono-nucleotide cleavage, and chemical modification. Predicted secondary structures can be color annotated to demonstrate pairs with high probability that are therefore well determined as compared to base pairs with lower probability of pairing.
An input shaping controller enabling cranes to move without sway (1997)

A gantry crane at the Savannah River Technology Center was retrofitted with an Input Shaping controller. The controller intercepts the operator`s pendant commands and modifies them in real time so that the crane is moved without residual sway in the suspended load. Mechanical components on the crane were modified to make the crane suitable for the anti-sway algorithm. This paper will describe the required mechanical modifications to the crane, as well as, a new form of Input Shaping that was developed for use on the crane. Experimental results are presented which demonstrate the effectiveness of the new process. Several practical considerations will be discussed including a novel (patent pending) approach for making small, accurate moves without residual oscillations.
Effect of Acid Treatment of Montmorillonite on “Support-Activator” Performance to Support Metallocene for Propylene Polymerization Catalyst (2016)

This work is focused on montmorillonite (MMT)-based “support-activators” (S-As) for the metallocene-catalyzed propylene polymerization. This catalyst was previously industrialized; however, for further technological advances, the activation mechanism is investigated. The chemical and morphological requirements of the S-A are surveyed using both commercially available raw clay minerals (non-acid-treated) and acid-treated clay minerals. The S-A possessing strong-acid sites (pKa < −8.2) gives a highly active catalyst. Acid treatment of MMT induces morphological changes as well as the formation of strong acid sites. Based on pore size distribution analysis and atomic force microscopy observations, it is concluded that the strong acid sites are located in the small pores around the edge of the clay mineral (not in the interlayer), where the structure is disordered by the acid treatment.
Reversible Formation of Molecular Junctions in 2D Nanoparticle Arrays (2006)

The preparation of molecular junctions networks using self-assembly and microcontact printing of ligand-protected metallic nanoparticles is demonstrated. A subsequent in situ ligand-exchange reaction permits the interlinking of neighboring nanoparticles. The exchange process is shown to be reversible (see figure).
Ultra-high-yield growth of vertical single-walled carbon nanotubes: Hidden roles of hydrogen and oxygen (2005)

An oxygen-assisted hydrocarbon chemical vapor deposition method is developed to afford large-scale, highly reproducible, ultra-high-yield growth of vertical single-walled carbon nanotubes (V-SWNTs). It is revealed that reactive hydrogen species, inevitable in hydrocarbon-based growth, are damaging to the formation of sp(2)-like SWNTs in a diameter-dependent manner. The addition of oxygen scavenges H species and provides a powerful control over the C/H ratio to favor SWNT growth. The revelation of the roles played by hydrogen and oxygen leads to a unified and universal optimum-growth condition for SWNTs. Further, a versatile method is developed to form V-SWNT films on any substrate, lifting a major substrate-type limitation for aligned SWNTs.
Curved DNA: design, synthesis, and circularization. (1986)

Curved DNA molecules and unusually small circles have been obtained by ligation of synthetic 21-base precursors: (sequence in text). The ligation resulted in the formation of double-stranded oligo-(precursor)s possessing a strong 10.5-base-pair (bp) periodicity of the runs of adenines. Two-dimensional polyacrylamide gel electrophoresis of the ligation products showed two distinct families of spots: (i) noncircular oligo(precursor)s of 21 to 231 bp (1- to 11-mers) and (ii) four circles from 105 to 168 bp (eluted and analyzed by denaturing gel electrophoresis). The noncircular oligomers exhibited anomalously slow migration, as if they were as much as three times longer than they actually are. The amount of circular products peaked sharply at approximately equal to 126 bp, near which size the circles have been estimated to be nonconstrained both torsionally and in terms of bending. The nonconstrained circularization provides a technique for the direct measurement of the inherent curvature of DNA in solution. From the size of the circles, an estimate of 8.7 degrees is obtained for the absolute value of the AA X TT wedge angle (roll and tilt combined).
Phosphorylation of PHAS-I by mitogen-activated protein (MAP) kinase. Identification of a site phosphorylated by MAP kinase in vitro and in response to insulin in rat adipocytes. (1994)

PHAS-I is a heat- and acid-stable protein that is phosphorylated on Ser/Thr residues in response to insulin and growth factors. To investigate the phosphorylation of PHAS-I, the protein was expressed in bacteria and purified for use as substrate in protein kinase reactions in vitro. Recombinant PHAS-I was rapidly and stoichiometrically phosphorylated by mitogen-activated protein (MAP) kinase. At saturating MgATP, the Km and Vmax observed with PHAS-I were almost identical to those obtained with myelin basic protein, one of the best MAP kinase substrates. PHAS-I was also phosphorylated at a significant rate by casein kinase II and protein kinase C. To investigate sites of phosphorylation, PHAS-I was digested with collagenase and phosphopeptides were resolved by reverse phase high performance liquid chromatography. Almost all of the phosphate introduced by MAP kinase was recovered in the peptide, Leu-Met-Glu-Cys-Arg-Asn-Ser-Pro-Val-Ala-Lys-Thr. 32P was released in the seventh cycle of Edman degradation, identifying the Ser (Ser64) as the phosphorylated residue. Ser64 was also phosphorylated in response to insulin in rat adipocytes. We conclude that PHAS-I is a substrate for MAP kinase both in vivo and in vitro. As PHAS-I is one of the most prominent insulin-stimulated phosphoproteins in adipocytes, it may qualify as the major MAP kinase substrate in these cells.
Novel inhibitors targeted to methionine aminopeptidase 2 (MetAP2) strongly inhibit the growth of cancers in xenografted nude model (2004)

Inhibition of angiogenesis is emerging as a promising strategy for the treatment of cancer. In our study reported here, the effects of 4 highly potent methionine aminopeptidase 2 (MetAP2) inhibitors, IDR-803, IDR-804, IDR-805 and CKD-732 (designed by structure-based molecular modeling), on angiogenesis and tumor growth were assessed. Concentrations of these inhibitors as low as 2.5 nM were able to inhibit the growth of human umbilical vein endothelial cells (HUVEC) by as much as 50%, arresting growth in the G1 stage of mitosis. An intracellular accumulation of p21(WAF1/Cip1) protein was also observed. Furthermore, at higher concentrations (25 nM) of these 4 MetAP2 inhibitors, a significant induction of apoptosis was apparent in the same HUVEC cultures. As a result of these findings, the possible anticancer effects of these inhibitors were examined, utilizing the SNU-398 hepatoma cell line. Interestingly, pretreatment with these inhibitors led to an increased number of apoptotic cells of up to 60% or more, compared to untreated controls. Moreover, utilizing an in vivo xenografted murine model, these inhibitors suppressed the growth of engrafted tumor. In conclusion, these 4 inhibitory compounds potently exert an antiangiogenic effect to inhibit the growth of cancers in vivo and could potentially be useful for the treatment of a variety of cancers.
Desipramine enhances opiate postoperative analgesia (1986)

In a double-blind, placebo-controlled study the analgesic efficacy of the combination of a tricyclic antidepressant and morphine was investigated. One of two tricyclic antidepressants (either amitriptyline, a relatively selective serotonin uptake inhibitor or desipramine, a relatively selective noradrenaline uptake inhibitor) or a placebo, was given for 1 week prior to surgery, followed by a single postoperative dose of morphine. Desipramine, but not amitriptyline, both increased and prolonged morphine analgesia. Neither tricyclic antidepressant reduced dental postoperative pain in the absence of morphine. We propose that desipramine enhances opiate analgesia by enhancing a noradrenergic component that contributes to endogenous opioid-mediated analgesia systems.
Structures and characterization of digoxin- and bufalin-bound Na + ,K + -ATPase compared with the ouabain-bound complex (2015)

Cardiotonic steroids (CTSs) are specific and potent inhibitors of the Na(+),K(+)-ATPase, with highest affinity to the phosphoenzyme (E2P) forms. CTSs are comprised of a steroid core, which can be glycosylated, and a varying number of substituents, including a five- or six-membered lactone. These functionalities have specific influence on the binding properties. We report crystal structures of the Na(+),K(+)-ATPase in the E2P form in complex with bufalin (a nonglycosylated CTS with a six-membered lactone) and digoxin (a trisaccharide-conjugated CTS with a five-membered lactone) and compare their characteristics and binding kinetics with the previously described E2P-ouabain complex to derive specific details and the general mechanism of CTS binding and inhibition. CTSs block the extracellular cation exchange pathway, and cation-binding sites I and II are differently occupied: A single Mg(2+) is bound in site II of the digoxin and ouabain complexes, whereas both sites are occupied by K(+) in the E2P-bufalin complex. In all complexes, αM4 adopts a wound form, characteristic for the E2P state and favorable for high-affinity CTS binding. We conclude that the occupants of the cation-binding site and the type of the lactone substituent determine the arrangement of αM4 and hypothesize that winding/unwinding of αM4 represents a trigger for high-affinity CTS binding. We find that the level of glycosylation affects the depth of CTS binding and that the steroid core substituents fine tune the configuration of transmembrane helices αM1-2.
An in vitro mechanical and histological study of acute stretching on rabbit tibial nerve (1990)

Peripheral nerves are often mechanically stretched in association with trauma to extremities, resulting in varying degrees of impairment of nerve function. However, little is known about the biomechanical properties of peripheral nerves and limits of stretching that the nerve may undergo before structural changes occur. Also, the injury pattern of nerves under stretching is poorly understood. In the present study, fresh rabbit tibial nerves (n = 18) were harvested. Nine nerves were stretched to failure in an INSTRON materials testing machine at a rate of 1 cm/min (strain rate of 0.5%/s). Load-deformation and stress-strain curves were determined. Histological examination by light microscopy of the stretched nerves as well as six normal control nerves and three clamped nonstretched control nerves was performed. The results show that the rabbit tibial nerves have an in situ strain of 11.0 +/- 1.5% and exhibit a nonlinear stress-strain relationship. After 20% strain, the curve becomes linear up to failure. The ultimate strain and tensile strength of the nerves were 38.5 +/- 2.0% and 11.7 +/- 0.7 MPa, respectively. At failure, the load dropped suddenly, but the specimens remained grossly intact. Histological analysis of the stretched nerves showed multiple ruptures of perineurial sheaths when compared to controls.
Cloning and expression of a Serpula (Treponema) hyodysenteriae hemolysin gene (1992)

Serpula (Treponema) hyodysenteriae, the etiologic agent of swine dysentery, produces a hemolysin which is thought to be an important factor in the pathogenesis of the disease. We report the cloning, sequencing, and expression of a hemolysin gene (tly) from S. hyodysenteriae B204. A pUC19 gene bank of strain B204 was constructed in the Escherichia coli K-12 strain DH5 alpha, and hemolytic recombinants were identified by plating the library on blood agar plates. From the hemolytic recombinants, a 1.5-kb DNA fragment could be isolated that contained information necessary for the production of a hemolysin/cytotoxin in E. coli. Nucleotide sequence determination of this 1.5-kb fragment showed that it contained an open reading frame capable of encoding a 26.9-kDa protein. The recombinant hemolysin was easily released from E. coli by osmotic shock. As with the native hemolysin, the recombinant hemolysin is EDTA insensitive, thermolabile, and cytotoxic for several eukaryotic cell lines. Southern blot hybridization showed that the cloned S. hyodysenteriae hemolysin gene tly is present in all pathogenic strains of S. hyodysenteriae tested and absent in the nonpathogenic, weakly hemolytic spirochete S. innocens.
The G-box: a ubiquitous regulatory DNA element in plants bound by the GBF family of bZIP proteins (1995)

The G-box (CACGTG) is a ubiquitous, cis-acting DNA regulatory element found in plant genomes. Proteins known as G-box factors (GBFs) bind to G-boxes in a context-specific manner, mediating a wide variety of gene expression patterns. We suggest that, as for many biological systems, different combinations of these common elements can lead to diversity and specificity in the regulation of plant gene expression.
A 200-MHz IF BiCMOS signal component separator for linear LINC transmitters (2000)

The linear amplification with nonlinear components (LINC) transmitter is an architecture that provides linear amplification using nonlinear but power efficient amplifiers. The signal component separator (SCS) is a crucial signal processing function of LINC. It forms two constant-amplitude phase-modulated signal components from the input signal. Due to the nonlinear signal processing involved, digital signal processing (DSP) implementation of the SCS at baseband has so far been assumed to be the best choice although it suffers from matching, bandwidth and power consumption problems. In this paper a new SCS architecture based on analog integrated circuit techniques is presented to avoid the disadvantages in a DSP based realization. A 200-MHz IF SCS chip using the proposed architecture was designed and fabricated in a 0.8 /spl mu/m BiCMOS process. An experimental LINC transmitter was built with the SCS chip, nonlinear amplifiers and a power combiner. Test results showed that spurious levels around -50 dBc could be obtained with a /spl pi//4-shifted DQPSK modulated North American Digital Cellular (NADC) signal. This implies a high degree of linearity in the implemented LINC transmitter.
Cultivation of Lednice (Yaba 1) virus in goose, duck, and chick embryo cells. (1976)

Lednice (Yaba 1) virus was found to multiply in primary cultures of goose, duck and chick embryo cells. The size of inoculum and age of embryos used for preparation of primary cultures was decisive for the amount of multiplied virus. One strain (110) of Lednice virus showed reduced ability to induce a cytopathic effect in the first passage in chick embryo cells. Virus multiplication in all three kinds of cells was confirmed by immunofluorescence.