gebhart/patrepeval huggingface dataset:
Loading-associated expression of TRIM72 and caveolin-3 in antigravitational soleus muscle in mice (2014)

Effects of mechanical loading on the expression level of tripartite motif-containing 72 (TRIM72) and caveolin-3 (Cav-3) in mouse soleus muscle were investigated. Mice were subjected to (1) continuous hindlimb suspension (HS) for 2 weeks followed by 1-week ambulation recovery or (2) functional overloading (FO) on the soleus by cutting the distal tendons of the plantaris and gastrocnemius muscles. Soleus muscle atrophy was induced by 2-week hindlimb suspension (HS). Reloading-associated regrowth of atrophied soleus muscle was observed by 1-week reloading following HS. HS also depressed the expression level of insulin receptor substrate-1 (IRS-1) mRNA, TRIM72, Cav-3, and phosphorylated Akt (p-Akt)/total Akt (t-Akt), but increased the phosphorylated level of p38 mitogen-activated protein kinase (p-p38MAPK) in soleus muscle. Thereafter, the expression level of MyoD mRNA, TRIM72 (mRNA, and protein), and Cav-3 was significantly increased and recovered to the basal level during 1-week reloading after HS. Although IRS-1 expression was also upregulated by reloading, the expression level was significantly lower than that before HS. Significant increase in p-Akt and phosphorylated p70 S6 kinase (p-p70S6K) was observed by 1-day reloading. On the other hand, 1-week functional overloading (FO) induced soleus muscle hypertrophy. In FO-associated hypertrophied soleus muscle, the expression level of IRS-1 mRNA, MyoD mRNA, TRIM72 mRNA, p-Akt, and p-p70S6K was increased, but the expression of Cav-3 and p-p38MAPK was decreased. FO had no effect on the protein expression level of TRIM72. These observations suggest that the loading-associated upregulation of TRIM72 protein in skeletal muscle may depress the regrowth of atrophied muscle via a partial suppression of IRS-1. In addition, downregulation of Cav-3 in skeletal muscle may depress overloading-induced muscle hypertrophy.
Minimum XPS core-level line widths of insulators, including silicate minerals (2004)

A monochromatic AlKα source and magnetic confinement charge compensation yield an As 3d line width of 0.52 eV for the bulk insulator As2S3 (orpiment) which is as narrow as the As 3d line width obtained for the semiconductor FeAsS (arsenopyrite). These results, and the XPS results for silicates, demonstrate that charge broadening of XPS spectra has been overcome for most insulators provided care is taken with sample preparation. XPS core level spectral investigations of these minerals now may be conducted at the same level of detail as have been conducted on semi-conductors and metals. The Si 2p spectrum of a non-conducting orthosilicate (Mg-rich olivine) displays a total line width of 1.36 eV compared to very high resolution synchrotron XPS line widths of 1.1 eV for an Si 2p spectrum of gaseous Si(OCH3)4, and 1.42 eV for the Si 2p peak of non-charging SiO2 thin-films grown on Si metal. These results demonstrate that Si 2p peak broadening of these silicates does not result from differential charging. Comparison of the Si 2p spectrum of Si in olivine which contains non-polymerized, independent SiO4 tetrahedra, with that of a gaseous analogue, Si(OCH3)4, also composed of non-polymerized Si atoms tetrahedrally bonded to O, provides insight into the cause of Si 2p peak broadening for olivine (and probably for all other silicates). The vibrational contributions to the Si 2p spectrum of Si(OCH3)4 were used to fit the Si 2p peak of olivine, with each vibrational contribution broadened to reflect the minimum line width of the XPS instrument. Although the Si 2p envelope resulting from this procedure yields a reasonable fit to the olivine Si 2p spectrum, additional minor vibrational contributions may be required to reproduce accurately the Si 2p spectrum of olivine. Continued development of the technique should allow determination of transition metal oxidation states and other chemical state properties of non-conductor Al-silicates
A Novel Trichomonas vaginalis Surface Protein Modulates Parasite Attachment via Protein:Host Cell Proteoglycan Interaction (2021)

<i>Trichomonas vaginalis</i> is a highly prevalent, sexually transmitted parasite which adheres to mucosal epithelial cells to colonize the human urogenital tract. Despite adherence being crucial for this extracellular parasite to thrive within the host, relatively little is known about the mechanisms or key molecules involved in this process. Here, we have identified and characterized a <i>T. vaginalis</i> hypothetical protein, TVAG_157210 (TvAD1), as a surface protein that plays an integral role in parasite adherence to the host. Quantitative proteomics revealed TvAD1 to be ∼4-fold more abundant in parasites selected for increased adherence (MA parasites) than the isogenic parental (P) parasite line. <i>De novo</i> modeling suggested that TvAD1 binds <i>N</i>-acetylglucosamine (GlcNAc), a sugar comprising host glycosaminoglycans (GAGs). Adherence assays utilizing GAG-deficient cell lines determined that host GAGs, primarily heparan sulfate (HS), mediate adherence of MA parasites to host cells. TvAD1 knockout (KO) parasites, generated using CRISPR-Cas9, were found to be significantly reduced in host cell adherence, a phenotype that is rescued by overexpression of TvAD1 in KO parasites. In contrast, there was no significant difference in parasite adherence to GAG-deficient lines by KO parasites compared with wild-type, which is contrary to that observed for KO parasites overexpressing TvAD1. Isothermal titration calorimetric (ITC) analysis showed that TvAD1 binds to HS, indicating that TvAD1 mediates host cell adherence via HS interaction. In addition to characterizing the role of TvAD1 in parasite adherence, these studies reveal a role for host GAG molecules in <i>T. vaginalis</i> adherence.<b>IMPORTANCE</b> The ability of the sexually transmitted parasite <i>Trichomonas vaginalis</i> to adhere to its human host is critical for establishing and maintaining an infection. Yet how parasites adhere to host cells is poorly understood. In this study, we employed a novel adherence selection method to identify proteins involved in parasite adherence to the host. This method led to the identification of a protein, with no previously known function, that is more abundant in parasites with increased capacity to bind host cells. Bioinformatic modeling and biochemical analyses revealed that this protein binds a common component on the host cell surface proteoglycans. Subsequent creation of parasites that lack this protein directly demonstrated that the protein mediates parasite adherence via an interaction with host cell proteoglycans. These findings both demonstrate a role for this protein in <i>T. vaginalis</i> adherence to the host and shed light on host cell molecules that participate in parasite colonization.
2L-piRNA: A Two-Layer Ensemble Classifier for Identifying Piwi-Interacting RNAs and Their Function (2017)

Involved with important cellular or gene functions and implicated with many kinds of cancers, piRNAs, or piwi-interacting RNAs, are of small non-coding RNA with around 19-33 nt in length. Given a small non-coding RNA molecule, can we predict whether it is of piRNA according to its sequence information alone? Furthermore, there are two types of piRNA: one has the function of instructing target mRNA deadenylation, and the other does not. Can we discriminate one from the other? With the avalanche of RNA sequences emerging in the postgenomic age, it is urgent to address the two problems for both basic research and drug development. Unfortunately, to the best of our knowledge, so far no computational methods whatsoever could be used to deal with the second problem, let alone deal with the two problems together. Here, by incorporating the physicochemical properties of nucleotides into the pseudo K-tuple nucleotide composition (PseKNC), we proposed a powerful predictor called 2L-piRNA. It is a two-layer ensemble classifier, in which the first layer is for identifying whether a query RNA molecule is piRNA or non-piRNA, and the second layer for identifying whether a piRNA is with or without the function of instructing target mRNA deadenylation. Rigorous cross-validations have indicated that the success rates achieved by the proposed predictor are quite high. For the convenience of most biologists and drug development scientists, the web server for 2L-piRNA has been established at http://bioinformatics.hitsz.edu.cn/2L-piRNA/, by which users can easily get their desired results without the need to go through the mathematical details.
Gene theraphy of lysosomal storage disorders (1995)

Lysosomal storage disorders (LSD) result from deficiencies in enzymes normally implicated in the catabolism of macromolecules inside the lysosome. Many of these enzymes can reach the lysosome after being secreted in the extracellular medium and recaptured by specific cell surface receptors. This has suggested a rationale for therapeutic approaches in LSD, in which the missing enzyme is provided by an external source. Current therapies based on this concept, including the administration of purified enzyme and bone marrow transplantation, have been shown to result in clinical improvements in both animal models and patients. Although considerable difficulties must be surmounted, LSD present a favourable situation for gene therapy. The gene corresponding to the affected enzyme has been identified in most diseases and cDNAs are available. Low and unregulated levels of enzyme activity should be sufficient for correction. Importantly, a variety of gene transfer strategies can be carefully evaluated in animal models.
Trajectory Tracking Control for Four-Wheel Independent Drive Intelligent Vehicle Based on Model Predictive Control (2020)

For four-wheel independent drive intelligent vehicle, the Model Predictive Control (MPC) is adopted to design the trajectory tracking controller through active steering and four-wheel independent drive/brake. The control objective is to follow a desired trajectory while taking into account the control actuator constraints and vehicle dynamic stability constraints. To reduce the computational complexity, a linear time-varying model predictive controller is designed to linearize the nonlinear vehicle model locally at each sampling point. The co-simulation of CarSim/Simulink shows that the designed controller has high tracking accuracy on the basis of ensuring vehicle stability and strong robustness to vehicle velocity and road adhesion coefficient. The trajectory tracking accuracy based on MPC is better than that of the preview driver model (PDM).
Substitution mode of the amide fragment in some new N-[omega-[4-(2-methoxyphenyl)piperazin-1-yl]alkyl]pyrid-2(1H)-ones and their 5-HT1A/5-HT2A activity. (2002)

A series of omega-[4-(2-methoxyphenyl)piperazin-1-yl]alkyl derivatives with terminal pyrid-2(1H)-one fragments was synthesized and evaluated for their 5-HTIA and 5-HT2A activity. Enlargement of the aromatic amide system by its substitution with phenyl and/or p-methoxyphenyl in positions 4, 5 and/or 6, as well as modification of an aliphatic spacer allowed us to better understand structure-activity relationships in that group of compounds. The results of in vitro and in vivo experiments showed that only unsubstituted (1b) and monosubstituted (2b-4b) derivatives with the tetramethylene spacer demonstrated high 5-HTIA receptor affinity (Ki = 15-40 nM) and 5-HT1A/5-HT2A selectivity; they exhibited features of 5-HTIA antagonists. Those results suggested that the mode of substitution of the terminal amide moiety in the tested tetramethylene arylpiperazines was not significant for their 5-HTIA receptor activity. Conformational analysis calculations indicated that despite its great capacity for adaptation at 5-HTIA receptor site, an aryl substituent in position 4 in the pyrid-2(1H)-one ring destabilized the ligand-5-HT1A receptor complex formation in the case of trimethylene derivatives. Diarylsubstituted derivatives (5a-8a and 5b-8b) were characterized by a low 5-HT2A affinity (Ki > 446 nM) regardless of the spacer length, while those with the tetramethylene aliphatic chain had a higher 5-HT2A affinity than the remaining investigated compounds.
A three-phase to single-phase matrix converter for high-frequency induction heating (2009)

The paper describes a new three-phase to single-phase matrix converter featuring unity input power factor, very low input total harmonic distortion, and soft-switching over the full power range, for high frequency induction heating applications. A variable output pulse density modulation scheme has been proposed for stable operation of the converter, with the notable feature of requiring no on-line calculations for the synthesis of three-phase input current system. Practical issues in realising the converter, viz. line frequency synchronisation and output current circulation, are described. Good agreement between simulation and experimental results confirm the benefits of the proposed converter.
Phototunable photonic bandgap in a chiral liquid crystal laser device (2004)

This letter describes the phototunable photonic bandgap of cholesteric liquid crystal (CLC) doped with a fluorescent dye to generate the distributed feedback effect. Photoirradiation of the dye-doped CLC cell under UV light at 254 nm resulted in continuous changes in the chiral photonic bandgap from 550 to 720 nm due to photolysis reaction of the cholesteryl iodide embedded in the CLC host. We showed that the laser oscillation wavelength could be controlled in a wide wavelength range from 610 to 700 nm by photoassisted adjustment of CLC photonic bandgaps.
Ring‐Opening Copolymerization of Maleic Anhydride with Functional Epoxides: Poly(propylene fumarate) Analogues Capable of Post‐Polymerization Modification (2018)

Three functional epoxides were copolymerized with maleic anhydride to yield degradable poly(propylene fumarate) analogues. The polymers were modified post-polymerization and post-printing with either click-type addition reactions or UV deprotection to either attach bioactive species or increase the hydrophilicity. Successful dye attachment, induced wettability, and improved cell spreading show the viability of these analogues in biomaterials applications.
A Radial Basis Function Approach to a Color Image Classification Problem in a Real Time Industrial Application (1997)

In this thesis, we introduce a radial basis function network approach to solve a color image classification problem in a real time industrial application. Radial basis function networks are employed to classify the images of finished wooden parts in terms of their color and species. Other classification methods are also examined in this work. The minimum distance classifiers are presented since they have been employed by the previous research. We give brief definitions about color space, color texture, color quantization, color classification methods. We also give an intensive review of radial basis functions, regularization theory, regularized radial basis function networks, and generalized radial basis function networks. The centers of the radial basis functions are calculated by the k-means clustering algorithm. We examine the k-means algorithm in terms of starting criteria, the movement rule, and the updating rule. The dilations of the radial basis functions are calculated using a statistical method. Learning classifier systems are also employed to solve the same classification problem. Learning classifier systems learn the training samples completely whereas they are not successful to classify the test samples. Finally, we present some simulation results for both radial basis function network method and learning classifier systems method. A comparison is given between the results of each method. The results show that the best classification method examined in this work is the radial basis function network method.
<title>Guide to using field programmable gate arrays (FPGAs) for application-specific digital signal processing performance</title> (1996)

FPGAs have become a competitive alternative for high performance DSP applications, previously dominated by general purpose DSP and ASIC devices. This paper describes the benefits of using an FPGA as a DSP co-processor, as well as, a stand-alone DSP engine. Two case studies, a Viterbi decoder and a 16-tap FIR filter are used to illustrate how the FPGA can radically accelerate system performance and reduce component count in a DSP application. Finally, different implementation techniques for reducing hardware requirements and increasing performance are described in detail.
Recovery of Volatile Fatty Acids from Fermented Wastewater by Adsorption (2017)

Separation of volatile fatty acids (VFAs) from fermented wastewater is challenging, due to low VFA concentrations in mineral-rich streams. As a result, separation capacity and selectivity with traditional solvents and adsorbents are both compromised. In this study, using a complex artificial model solution mimicking real fermented wastewaters, it is shown that a simple and robust adsorption-based separation technique can retain a remarkable capacity and selectivity for VFAs. Four types of polystyrene-divinylbenzene-based resins (primary, secondary, and tertiary amine-functionalized, and nonfunctionalized) were examined as the adsorbents. The presence of chloride, sulfate, and phosphate salts resulted in coadsorption of their acidic forms HCl, H<sub>2</sub>SO<sub>4</sub>, and H<sub>3</sub>PO<sub>4</sub> on amine-functionalized adsorbents, and severely reduced the VFA capacity. With the nonfunctionalized adsorbent, almost no mineral acid coadsorption was observed. This together with a high total VFA capacity of up to 76 g/kg in equilibrium with the model solution containing a total VFA concentration of 1 wt % resulted in a very high selectivity for the VFAs. Nitrogen-stripping with various temperature profiles was applied to regenerate the adsorbent, and study the potential for fractionation of the VFAs during regeneration. Butyric acid (HBu) was obtained in mole fractions of up to 0.8 using a stepwise increase in the stripping temperature from 25 °C via 120 to 200 °C. During four successive adsorption-regeneration cycles, no reduction in the adsorption capacity was observed.
Random modulation cw lidar (1983)

A new lidar scheme using a pseudorandom code modulated cw laser as a transmitting laser source (RM-CW lidar) is proposed and a demonstration of its use for aerosol measurement is shown. A formula for estimating the SNR values in RM-CW lidar was derived, and it was demonstrated that the observed SNR value was in good agreement with the calculation.
Detection of the <scp>F129L</scp> mutation in the cytochrome <i>b</i> gene in <i>Phakopsora pachyrhizi</i> (2015)

This is the first report of the occurrence of the F129L mutation in P. pachyrhizi. The practical relevance of this mutation for field efficacy of QoIs needs further investigation. © 2015 Society of Chemical Industry.
Synthetic Peptide-Based Vaccines and Antiviral Agents Including HIV/AIDS as a Model System (2023)

Vaccination, including vaccination against viral disease, has been one of the great triumphs of medicine in the past 200 years. Today, equipped with a maturing knowledge of immunity and of virus-host intreactions and with modem analytical tools of biochemistry and molecular and cell biology we face the challenge of developing preventive therapies that are safer, less expensive, easier to prepare and store, and are more effective than their earlier counterparts. In addition, new vaccines are under development for other viral diseases, for diseases which we are only now recognizing as virally based, and for diseases with which mankind has only recently been confronted, such as AIDS.
Long-term<i>C. elegans</i>immobilization enables high resolution developmental studies<i>in vivo</i> (2018)

Live-imaging of C. elegans is essential for the study of conserved cellular pathways (e.g. EGFR/Wnt signaling) and morphogenesis in vivo. However, the usefulness of live imaging as a research tool has been severely limited by the need to immobilize worms prior to and during imaging. Conventionally, immobilization is achieved by employing both physical and chemical interventions. These are known to significantly affect many physiological processes, and thus limit our understanding of dynamic developmental processes. Herein we present a novel, easy-to-use microfluidic platform for the long-term immobilization of viable, normally developing C. elegans, compatible with image acquisition at high resolution, thereby overcoming the limitations associated with conventional worm immobilization. The capabilities of the platform are demonstrated through the continuous assessment of anchor cell (AC) invasion and distal tip cell (DTC) migration in larval C. elegans and germ cell apoptosis in adult C. elegans in vivo for the first time.
From cilia and flagella to intracellular motility and back again: a review of a few aspects of microtubule‐based motility (1988)

Ciliary or flagellar movement is the model of microtubule-dependent motility, the best studied at the molecular level. It is based on the relative sliding of outer doublets of microtubules that are linked at their proximal end to the basal structure and interconnected by associated proteins, among which dynein ATPase is at the origin of the movement. It is regulated from inside and outside media by various diffusible factors such as Ca2+, cyclic adenosine monophosphate (cAMP), polypeptides and so on (see other conferences presented during this meeting). Other motility processes are based on microtubules: vesicle and organelle transport through the cytoplasm (axonal flow in neurons, pigment granule movements in fish chromatophores, movements of particles along heliozoan axopods, etc.) could be mediated by microtubule motors such as kinesin or MAP 1C. Kinesin and MAP 1C, like dynein, are proteins that bind to microtubules and show an ATPase activity associated with force production. They differ from each other by their structure, and biochemical and pharmacological properties. The movements of chromosomes during mitosis and meiosis have long been studied, but are still poorly understood at the molecular level; this topic will be discussed in the light of recent data. Other constituents of the cytoskeleton are certainly involved in cellular motility: actin microfilaments and their motor myosin, intermediate filaments, non-actin filaments, all organized around the Microtubule Organizing Center (MTOC). As more information becomes available, it seems increasingly obvious that these various networks are closely interconnected and that each component probably modulates, resists, or favors properties of its partners, contributing to cellular and intracellular motility.
The Electrostrictive Unimorph for Displacement Control (1982)

Rectangular unimorphs for displacement control have been fabricated using PMN-based electrostrictive ceramics instead of conventional piezoelectric ceramics. Bending response of the unimorph has been investigated under DC or AC applied voltage. The response has also been checked under mechanical load. The unimorph with 0.45PMN- 0.36PT-0.19BZN, which is the best choice at this moment, reveals a large displacement at the free end up to 20 µm under an applied cyclic voltage of 400 V with little hysteresis.