gebhart/patrepeval huggingface dataset:
Correlated waves of actin filaments and PIP<sub>3</sub> in <i>Dictyostelium</i> cells (2008)

Chemotaxis-deficient amiB-null mutant Dictyostelium cells show two distinct movements: (1) they extend protrusions randomly without net displacements; (2) they migrate persistently and unidirectionally in a keratocyte-like manner. Here, we monitored the intracellular distribution of phosphatidylinositol (3,4,5)-trisphosphate (PIP(3)) to gain insight into roles PIP(3) plays in those spontaneous motilities. In keratocyte-like cells, PIP(3) showed convex distribution over the basal membrane, with no anterior enrichment. In stalled cells, as well as in wild type cells, PIP(3) repeated wave-like changes, including emergence, expansion and disappearance, on the basal membrane. The waves induced lamellipodia when they approached the cell edge, and the advancing speed of the waves was comparable to the migration speed of the keratocyte-like cells. LY294002, an inhibitor of PI3 kinase, abolished PIP(3) waves in stalled cells and stopped keratocyte-like cells. These results together suggested that keratocyte-like cells are "surfing" on the PIP(3) waves by coupling steady lamellipodial protrusions to the PIP(3) waves. Simultaneous live observation of actin filaments and PIP(3) in wild type or stalled amiB(-) cells indicated that the PIP(3) waves were correlated with wave-like distributions of actin filaments. Most notably, PIP(3) waves often followed actin waves, suggesting that PIP(3) induces local depolymerization of actin filaments. Consistent with this idea, cortical accumulation of PIP(3) was often correlated with local retraction of the periphery. We propose that the waves of PIP(3) and actin filaments are loosely coupled with each other and play important roles in generating spontaneous cell polarity.
Highly conserved sequencim in the 3′ untranslated region of mRNAs coding for homologous proteins in distantly related species (1985)

Comparison of the nucleotide sequence of mRNAs coding for several vertebrate actins revealed a high degree of sequence homology in the 3' untranslated region (3' UTR) between those mRNAs coding for homologous (isotypic) actins in different organisms but not between mRNAs coding for very similar isoforms differing in their function or tissue specificity. A similar pattern of sequence conservation in the 3' UTR is also found in several other genes. Furthermore, while there is a great variation in the size of the 3' UTR of mRNAs coding for different proteins, mRNA coding for isotypic proteins in distantly related organisms often have 3' UTR of similar size. The data suggest that the 3' UTR may play an important role in the regulation of expression of at least some genes at the transcriptional or posttranscriptional level.
New carbazole‐containing monomers and polymers (1979)

Abstract Five novel vinyl monomers, all of which contain 3‐substituted carbazolyl groups [i.e., N ‐(9‐ethyl‐3‐carbazolyl)‐maleimide, 9‐ethyl‐3‐carbazolyl acrylamide, 9‐ethyl‐3‐carbazolyl methacrylamide, 9‐ethyl‐3‐hydroxymethylcarbazolyl acrylate, and 9‐ethyl‐3‐hydroxymethylcarbazolyl methacrylate], and their corresponding polymers were synthesized. Two methods were used for the synthesis of the last two monomers.
<title>Glass substrates for AMLCD applications: properties and implications</title> (1997)

Since its introduction almost two years ago, Corning's code 1737 AMLCD substrate glass has received strong market support. Some of this was anticipated as this glass offers several obvious improvements over existing substrates; however, some came unexpectedly as AMLCD manufacturers discovered new attributes offered by this glass. Chief among these anticipated improvements were a higher glass strain point, translating into a substrate with greater thermal stability; a lower density, resulting in lower weight and less gravitational sag; improved chemical durability, allowing more aggressive etching conditions; and a coefficient of thermal expansion more closely matched to silicon, opening up the possibility of chip-on-glass. Some of the unanticipated benefits include greater strength and a natural tendency of the glass to get sodium from silica barriers layers. This paper will review the development of Code 1737 glass, outlining the benefits it brings to the technical, commercial, and manufacturing development of next generation AMLCD's.
Precision measurement of backscattering cross-sections as a function of frequency (1976)

For a scattering measurement setup comparisons are made between different modes of operation. In order to make the comparisons, a simple procedure is outlined so that a figure of merit characterizing a given mode can be found. Figures of merit are found for three modes of operation. The different modes of operation are characterized by the manner in which the test object signal is separated from undesired signals such as background and support scattered signals. The setup and the analysis of the measured signals in the different modes of operation are discussed in detail.
Exploring Lysine Riboswitch for Metabolic Flux Control and Improvement of <scp>l</scp>-Lysine Synthesis in <i>Corynebacterium glutamicum</i> (2015)

Riboswitch, a regulatory part of an mRNA molecule that can specifically bind a metabolite and regulate gene expression, is attractive for engineering biological systems, especially for the control of metabolic fluxes in industrial microorganisms. Here, we demonstrate the use of lysine riboswitch and intracellular l-lysine as a signal to control the competing but essential metabolic by-pathways of lysine biosynthesis. To this end, we first examined the natural lysine riboswitches of Eschericia coli (ECRS) and Bacillus subtilis (BSRS) to control the expression of citrate synthase (gltA) and thus the metabolic flux in the tricarboxylic acid (TCA) cycle in E. coli. ECRS and BSRS were then successfully used to control the gltA gene and TCA cycle activity in a lysine producing strain Corynebacterium glutamicum LP917, respectively. Compared with the strain LP917, the growth of both lysine riboswitch-gltA mutants was slower, suggesting a reduced TCA cycle activity. The lysine production was 63% higher in the mutant ECRS-gltA and 38% higher in the mutant BSRS-gltA, indicating a higher metabolic flux into the lysine synthesis pathway. This is the first report on using an amino acid riboswitch for improvement of lysine biosynthesis. The lysine riboswitches can be easily adapted to dynamically control other essential but competing metabolic pathways or even be engineered as an "on-switch" to enhance the metabolic fluxes of desired metabolic pathways.
Denaturation of <i>α</i> ‐lactalbumin and ubiquitin studied by electrospray and laser spray (2007)

Electrospray and laser spray mass spectra of human alpha-lactalbumin and bovine ubiquitin were studied, with an emphasis on the denaturation induced by laser spray. There were no remarkable differences in the electrospray and laser spray mass spectra for acidic and basic aqueous solutions of alpha-lactalbumin in positive and negative modes of operations. This originates from the fact that this protein is tightly folded with four disulfide bonds. For ubiquitin, however, denaturation was induced by laser spray for the positive mode of operation and the [M+nH](n+) with a maximum of n = 13 was observed, i.e., all the acidic amino acid residues are fully neutralized (protonated). In contrast, the laser-induced denaturation was not observed for the negative mode of operation, i.e., denaturation of ubiquitin is largely suppressed in the negatively charged liquid droplets. The marked difference observed in the positive and negative modes of operations for ubiquitin is ascribed to the difference in the susceptibility of side-chain/main-chain interactions in the positive-ion excess and in the negative-ion excess liquid droplets. That is, the interactions between the basic residues and main-chain amide carbonyl groups (-NH(3) (+)***O=C< or -NH(2)***O=C<) which play an important role in stabilizing the protein structures are not so affected in the negative mode of operation but are weakened in the positive mode of operation.
The effects of porcine somatotropin, gender and porcine stress syndrome on growth, carcass composition and pork quality (1997)

Lacombe breed pigs (72 gilts, 72 barrows) of three genotypes with respect to the porcine stress syndrome (normal, heterozygous, or homozygous for the halothane gene), were treated from 57 to 106 kg body weight with daily injections of 0.9% saline containing 0 or 3 mg of recombinant porcine somatotropin (pST) in a randomized block design. Pigs receiving pST had lower average daily feed intakes (ADF), greater average daily gains (ADG) and lower feed conversion efficiencies (FCE). Gilts relative to barrows had lower ADG, ADF and higher FCE. Gilts versus barrows and pigs treated with pST had reduced fat depths and greater loin depths at the 10th rib. Pigs homozygous for the halothane gene had reduced loin lean structure and color scores, greater light reflectance (L*), and lower soluble protein contents as expected, and these genotypic effects did not interact with pST treatment. Sex by pST treatment interactions (P < 0.05) were found for loin depth, moisture content, color score and L* values indicating barrows respond more favorably to pST treatment than gilts. Generally, pST treatment, gilts relative to barrows, and possession of the halothane gene increased carcass lean and reduced subcutaneous fat levels. Sex by pST treatment interactions were found for picnic lean (lower shoulder; P < 0.05), ham lean (P < 0.05), and total carcass lean (P = 0.09) further supporting the theory that barrows benefit more than gilts to pST treatment. No significant interactions were found between genotype and pST treatment for any qualitative muscle traits. Thus, pST treatment had no direct effect on meat quality and was not found to interact with the halothane gene. However, pST interactions with sex indicated barrows respond quantitatively and qualitatively more favorably than gilts to pST treatment. Key words: Somatotropin, porcine somatotropin, pork, porcine stress syndrome, stress, pigs, growth
High Load HCCI Operation Using Different Valving Strategies in a Naturally-Aspirated Gasoline HCCI Engine (2011)

<div class="section abstract"><div class="htmlview paragraph">Homogenous Charge Compression Ignition (HCCI) combustion offers significant efficiency improvements compared to conventional spark ignition engines. However, due to the nature of HCCI combustion, traditional HCCI combustion can be realized only in a limited operating range. In order to maximize fuel economy benefits the HCCI operating range needs to be extended to higher loads. One immediate benefit is to maximize the portion of the standard driving cycles (NEDC, FTP, etc.) that can be run with HCCI combustion, so that transitions between SI operation and HCCI operation can be avoided.</div><div class="htmlview paragraph">The HCCI operation at high load range is typically limited by a trade-off between combustion noise and combustion stability. In a previous research, we showed how to improve this trade-off using spark-assisted HCCI combustion strategy, and concluded that the HCCI high load operation is limited by the air availability due to a low lift cam when spark-assisted HCCI combustion was applied.</div><div class="htmlview paragraph">In this research different valving configurations were investigated to maximize the extension of high load limit of HCCI operation. Then two different valving strategies, such as Negative Valve Overlap (NVO) and Positive Valve Overlap (PVO), were compared to improve the efficiency of high load HCCI operation by controlling the amount of internal residual fraction and pumping loss.</div><div class="htmlview paragraph">When the NVO strategy was employed, as engine load increases, combustion phasing must be retarded to reduce combustion noise due to high amount of hot internal residuals. Retarded combustion phasing at high load HCCI operation is a key solution for the NVO strategy. On the other hand, when the PVO strategy was applied, optimal residual fraction can be achieved resulting in efficiency improvement due to optimal combustion phasing, lower pumping loss and less heat transfer loss. The high load limit was successfully extended to 10 bar IMEP<sub>g</sub> (Gross Indicated Mean Effective Pressure) while maintaining good efficiency and complying with emissions requirements.</div></div>
A Novel Synaptobrevin/VAMP Homologous Protein (VAMP5) Is Increased during In Vitro Myogenesis and Present in the Plasma Membrane (1998)

cDNA clones encoding a novel protein (VAMP5) homologous to synaptobrevins/VAMPs are detected during database searches. The predicted 102-amino acid VAMP5 harbors a 23-residue hydrophobic region near the carboxyl terminus and exhibits an overall amino acid identity of 33% with synaptobrevin/VAMP1 and 2 and cellubrevin. Northern blot analysis reveals that the mRNA for VAMP5 is preferentially expressed in the skeletal muscle and heart, whereas significantly lower levels are detected in several other tissues but not in the brain. During in vitro differentiation (myogenesis) of C2C12 myoblasts into myotubes, the mRNA level for VAMP5 is increased approximately 8- to 10-fold. Immunoblot analysis using antibodies specific for VAMP5 shows that the protein levels are also elevated approximately 6-fold during in vitro myogenesis of C2C12 cells. Indirect immunofluorescence microscopy and immunoelectron microscopy reveal that VAMP5 is associated with the plasma membrane as well as intracellular perinuclear and peripheral vesicular structures of myotubes. Epitope-tagged versions of VAMP5 are similarly targeted to the plasma membrane.
Size, power and false discovery rates (2007)

Modern scientific technology has provided a new class of large-scale simultaneous inference problems, with thousands of hypothesis tests to consider at the same time. Microarrays epitomize this type of technology, but similar situations arise in proteomics, spectroscopy, imaging, and social science surveys. This paper uses false discovery rate methods to carry out both size and power calculations on large-scale problems. A simple empirical Bayes approach allows the false discovery rate (fdr) analysis to proceed with a minimum of frequentist or Bayesian modeling assumptions. Closed-form accuracy formulas are derived for estimated false discovery rates, and used to compare different methodologies: local or tail-area fdr’s, theoretical, permutation, or empirical null hypothesis estimates. Two microarray data sets as well as simulations are used to evaluate the methodology, the power diagnostics showing why nonnull cases might easily fail to appear on a list of “significant” discoveries.
Monascin and Ankaflavin Act as Novel Hypolipidemic and High-Density Lipoprotein Cholesterol-Raising Agents in Red Mold Dioscorea (2010)

Monascus-fermented red mold dioscorea (RMD) has been proven to possess greater hypolipidemic effect than red mold rice (RMR) even though they include equal levels of cholesterol-lowering agent monacolin K. However, higher concentrations of yellow pigments (monascin and ankaflavin) were found in RMD than in RMR. In this study, purified monascin and ankaflavin were administered to hyperlipidemic hamsters for 8 weeks, respectively, to test whether these two compounds were novel hypolipidemic ingredients. In the statistical results, monascin and ankaflavin showed significant effect on lowering cholesterol, triglyceride, and low-density lipoprotein cholesterol levels in serum, as well as aorta lipid plaque (p < 0.05). Importantly, monascin and ankaflavin, unlike monacolin K, were able to perform up-regulation rather than down-regulation on high-density lipoprotein cholesterol (HDL-C) levels in serum. This finding not only explained why RMD showed greater hypolipidemic and HDL-C-raising effect than RMR but also proved that monascin and ankaflavin would act as novel and potent hypolipidemic ingredients.
The Integrated Sounding System: Description and Preliminary Observations from TOGA COARE (1994)

An Integrated Sounding System (ISS) that combines state-of-the-art remote and in situ sensors into a single transportable facility has been developed jointly by the National Center for Atmospheric Research (NCAR) and the Aeronomy Laboratory of the National Oceanic and Atmospheric Administration (NOAA/AL). The instrumentation for each ISS includes a 915-MHz wind profiler, a Radio Acoustic Sounding System (RASS), an Omega-based NAVAID sounding system, and an enhanced surface meteorological station. The general philosophy behind the ISS is that the integration of various measurement systems overcomes each system's respective limitations while taking advantage of its positive attributes. The individual observing systems within the ISS provide high-level data products to a central workstation that manages and integrates these measurements. The ISS software package performs a wide range of functions: real-time data acquisition, database support, and graphical displays; data archival and communications; and operational and posttime analysis. The first deployment of the ISS consists of six sites in the western tropical Pacific—four land-based deployments and two ship-based deployments. The sites serve the Coupled Ocean-Atmosphere Response Experiment (COARE) of the Tropical Ocean and Global Atmosphere (TOGA) program and TOGA's enhanced atmospheric monitoring effort. Examples of ISS data taken during this deployment are shown in order to demonstrate the capabilities of this new sounding system and to demonstrate the performance of these in situ and remote sensing instruments in a moist tropical environment. In particular, a strong convective outflow with a pronounced impact of the atmospheric boundary layer and heat fluxes from the ocean surface was examined with a shipboard ISS. If these strong outflows commonly occur, they may prove to be an important component of the surface energy budget of the western tropical Pacific.
Overexpression of a Profilin (GhPFN2) Promotes the Progression of Developmental Phases in Cotton Fibers (2010)

Cotton fiber development at the stages of elongation and secondary wall synthesis determines the traits of fiber length and strength. To date, the mechanisms controlling the progression of these two phases remain elusive. In this work, the function of a fiber-preferential actin-binding protein (GhPFN2) was characterized by cytological and molecular studies on the fibers of transgenic green-colored cotton (Gossypium hirsutum) through three successive generations. Overexpression of GhPFN2 caused pre-terminated cell elongation, resulting in a marked decrease in the length of mature fibers. Cytoskeleton staining and quantitative assay revealed that thicker and more abundant F-actin bundles formed during the elongation stage in GhPFN2-overexpressing fibers. Accompanying this alteration, the developmental reorientation of transverse microtubules to the oblique direction was advanced by 2 d at the period of transition from elongation to secondary wall deposition. Birefringence and reverse transcription-PCR analyses showed that earlier onset of secondary wall synthesis occurred in parallel. These data demonstrate that formation of the higher actin structure plays a determinant role in the progression of developmental phases in cotton fibers, and that GhPFN2 acts as a critical modulator in this process. Such a function of the actin cytoskeleton in cell phase conversion may be common to other secondary wall-containing plant cells.
Ruthenium(II)‐Catalyzed Oppenauer‐Type Oxidation of Secondary Alcohols (1996)

Abstract Highly efficient ruthenium‐catalyzed Oppenauer‐type oxidations of secondary alcohols to ketones have been developed. The catalytic system consists of [(PPh 3 ) 3 RuCl 2 ] ( 1 ) and K 2 CO 3 or [(C 4 Ph 4 COHOCC 4 Ph 4 )(μ‐H)(CO) 4 Ru 2 ] ( 2 ) in refluxing acetone. The catalytic reaction is of high efficiency and permits a catalyst: substrate ratio of 1:1000 at 56 °C. In some cases the initial turnover rate exceeds 1500 h ‐1 . The reaction was found to be general and compatible with double bonds and oxidation‐sensitive aromatics. With some allylic alcohols, isomerization to saturated ketones took place. The reaction proceeds by ruthenium‐catalyzed dehydrogenation of the alcohol and subsequent hydrogen transfer to acetone. No primary kinetic isotope effect was observed for the catalytic reaction when α‐deuterated 1‐phenylethanol was employed as substrate ( k H / k D =1.1); this shows that β‐hydride elimination from a ruthenium alkoxide intermediate is not the rate‐limiting step.
A kinetic-based sigmoidal model for the polymerase chain reaction and its application to high-capacity absolute quantitative real-time PCR (2008)

Called "linear regression of efficiency" or LRE, this novel kinetic approach confers the ability to conduct high-capacity absolute quantification with unprecedented quality control capabilities. The computational simplicity and recursive nature of LRE quantification also makes it amenable to software implementation, as demonstrated by a prototypic Java program that automates data analysis. This in turn introduces the prospect of conducting absolute quantification with little additional effort beyond that required for the preparation of the amplification reactions.
Comparison of Protein Extraction Solutions for Rice Starch Isolation and Effects of Residual Protein Content on Starch Pasting Properties (1999)

Protein extraction solutions such as aqueous solutions of sodium hydroxide (0.1 and 0.2 %), sodium lauryl sulfate (SLS, 1.2 %) containing sodium sulfite (0.12 %), and dodecylbenzene sulfonate (DoBS, 1.2 %) containing sodium sulfite (0.12 %) were compared in their protein removal efficiencies during isolation of starch from a rice flour (Ilpumbyo, a nonwaxy Korean rice variety). In addition, the pasting properties of the isolated starch was compared. More than 80 % of the flour protein was extracted in 1 h by stirring the dispersion (1:3, w/v) at room temperature. Repeating the extractions (1 or 2 h for each step) with fresh solution significantly increased the protein removal efficiency. When the extraction in 0.2 % NaOH was repeated four times (1 h for each step) at 25°C, the residual protein content in the isolated rice starch was 0.9 % (DB), equivalent to 86 % removal of the rice protein. Raising the extraction temperature slightly increased the protein solubility, but starch loss also became significant. Among the solutions, DoBS was most effective in removing rice protein whereas SLS was least. The residual protein content had a critical role in determining the pasting characteristics of the isolated starch, showing a negative correlation to the peak viscosity of the starch paste, but a positive correlation to the pasting temperature.
Plasma brain natriuretic peptide concentrations in patients undergoing pulmonary vein isolation (2006)

Raised plasma BNP concentrations decreased after successful segmental ostial PVI in patients with AF.