gebhart/patrepeval huggingface dataset:
Large scale statistical prediction of protein-protein interaction by potentially interacting domain (PID) pair. (2002)

Protein-protein interaction plays a critical role in biological processes. The identification of interacting proteins by computational methods can provide new leads in functional studies of uncharacterized proteins without performing extensive experiments. We developed a database for the potentially interacting domain pairs (PID) extracted from a dataset of experimentally identified interacting protein pairs (DIP: database of interacting proteins) with InterPro, an integrated database of protein families, domains and functional sites. In developing protein interaction databases and predictive methods, sensitive statistical scoring systems is critical to provide a reliability index for accurate functional analysis of interaction networks. We present a statistical scoring system, named "PID matrix score" as a measure of the interaction probability (interactability) between domains. This system provided a valuable tool for functional prediction of unknown proteins. For the evaluation of PID matrix, cross validation was performed with subsets of DIP data. The prediction system gives about 50% sensitivity and more than 98% specificity, which implies that the information for interacting proteins pairs could be enriched about 30 fold with the PID matrix. It is demonstrated that mapping of the genome-wide interaction network can be achieved by using the PID matrix.
The neuronal perceptron with DNA strand displacement (2018)

In the field of biologic computing and neural networks, DNA strand displacement technology performs well in computing, programming and information processing. In this paper, based on two-domain DNA strand displacement, the neural DNA perceptron is proposed to implement Boolean operations. Some operation instances are simulated by Visual DSD (DNA strand displacement) software in which details of simulation process were presented. Our results showed that the precision of the neural DNA perceptron is higher than that of a bio-sensor designed by Shi et al. Furthermore, extrapolating from the neural DNA perceptron, we presented a multi-bit numerical comparator to achieve multi-bit numerical comparisons, which received stable and intuitive simulation results. The neural DNA perceptron and the multi-bit numerical comparator are easy to operate and achieve satisfactory effects.
Predictive Abilities of Bayesian Regularization and Levenberg–Marquardt Algorithms in Artificial Neural Networks: A Comparative Empirical Study on Social Data (2016)

The objective of this study is to compare the predictive ability of Bayesian regularization with Levenberg–Marquardt Artificial Neural Networks. To examine the best architecture of neural networks, the model was tested with one-, two-, three-, four-, and five-neuron architectures, respectively. MATLAB (2011a) was used for analyzing the Bayesian regularization and Levenberg–Marquardt learning algorithms. It is concluded that the Bayesian regularization training algorithm shows better performance than the Levenberg–Marquardt algorithm. The advantage of a Bayesian regularization artificial neural network is its ability to reveal potentially complex relationships, meaning it can be used in quantitative studies to provide a robust model.
Are there <i>n</i> + 2 Points in <i>E<sup>n</sup></i> with Odd Integral Distances? (1974)

(1974). Are there n + 2 Points in En with Odd Integral Distances? The American Mathematical Monthly: Vol. 81, No. 1, pp. 21-25.
A Self-Sensing Piezoelectric Actuator for Collocated Control (1992)

A technique has been developed which allows a single piece of piezoelec tric material to concurrently sense and actuate in a closed loop system. The motivation behind the technique is that such a self-sensing actuator will be truly collocated and has applications in active and intelligent structures, such as vibration suppression. A theoreti cal basis for the self-sensing actuator is given in terms of the electromechanical consti tutive equations for a piezoelectric material. In a practical implementation of the self- sensing actuator an electrical bridge circuit is used to measure strain. The bridge circuit is capable of measuring either strain or time rate of strain in the actuator. The usefulness of the proposed device was experimentally verified by actively damping the vibration in a cantilever beam. A single piezoceramic element bonded to the base of the beam functioned both as a distributed moment actuator and strain sensor. Using a rate feedback control law, the first mode of vibration was suppressed, reducing the settling from 35 seconds to 2.5 seconds. Using a positive position feedback law the first two modes of vibration were suppressed; the first mode settling time was reduced from 35 to 0.3 sec onds and the second mode settling time was reduced from 7 seconds to 0.9 seconds.
Optimized cassettes for fluorescent protein tagging in <i>Saccharomyces cerevisiae</i> (2004)

Green fluorescent protein (GFP) has become an increasingly popular protein tag for determining protein localization and abundance. With the availability of GFP variants with altered fluorescence spectra, as well as GFP homologues from other organisms, multi-colour fluorescence with protein tags is now possible, as is measuring protein interactions using fluorescence resonance energy transfer (FRET). We have created a set of yeast tagging vectors containing codon-optimized variants of GFP, CFP (cyan), YFP (yellow), and Sapphire (a UV-excitable GFP). These codon-optimized tags are twice as detectable as unoptimized tags. We have also created a tagging vector containing the monomeric DsRed construct tdimer2, which is up to 15-fold more detectable than tags currently in use. These tags significantly improve the detection limits for live-cell fluorescence imaging in yeast, and provide sufficient distinguishable fluorophores for four-colour imaging.
Aromatic Cyclodehydration. XXXI.<sup>1</sup> New Polycyclic Aromatic Systems Containing the Quinolizinium Nucleus (1956)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAromatic Cyclodehydration. XXXI.1 New Polycyclic Aromatic Systems Containing the Quinolizinium NucleusC. K. Bradsher and Leo E. BeaversCite this: J. Am. Chem. Soc. 1956, 78, 11, 2459–2462Publication Date (Print):June 1, 1956Publication History Published online1 May 2002Published inissue 1 June 1956https://pubs.acs.org/doi/10.1021/ja01592a031https://doi.org/10.1021/ja01592a031research-articleACS PublicationsRequest reuse permissionsArticle Views127Altmetric-Citations22LEARN 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
Response and Remission Rates Following High-Frequency vs. Low-Frequency Repetitive Transcranial Magnetic Stimulation (rTMS) Over Right DLPFC for Treating Major Depressive Disorder (MDD): A Meta-Analysis of Randomized, Double-Blind Trials (2018)

<b>Background:</b> High-frequency (HF) repetitive transcranial magnetic stimulation (rTMS) over the left dorsolateral prefrontal cortex (L-DLPFC) is the most widely applied treatment protocol for major depressive disorder (MDD), while low-frequency (LF) rTMS over the right DLPFC (R-DLPFC) also exhibits similar, if not better, efficacy for MDD. Therefore, a meta-analysis is warranted to compare the efficacy of the two protocols for MDD. <b>Method:</b> We searched the literature from 1990 through to August 1, 2017 using MEDLINE, and the literature from 1995 through to August 1, 2017 using EMBASE, PsycINFO, the Cochrane Central Register of Controlled Trials (CENTRAL), SCOPUS, and ProQuest Dissertations and Theses (PQDT). We included randomized controlled trials (RCT) comparing the efficacy of HF rTMS over the L-DLPFC and LF rTMS over the R-DLPFC for MDD, which used response and/or remission rates as the primary endpoints, with and without sham-controlled. <b>Results:</b> (1) The meta-analysis of the response rates was based on 12 studies, including 361 patients with MDD (175 for HF (> 5 Hz) over the L-DLPFC, and 186 for LF (<5 Hz) over the R-DLPFC; odds ratio = 1.08; 95%, confidence interval = 0.88-1.34). (2) The meta-analysis of the remission rate was based on 5 studies, including 131 MDD patients (64 for HF over the L-DLPFC and 67 for LF over the R-DLPFC; odds ratio = 1.29; 95% confidence interval = 0.54-3.10). <b>Conclusion:</b> Both HF rTMS over the L-DLPFC and LF over the R-DLPFC demonstrated similar therapeutic efficacy for the treatment of patients with MDD. The results suggested that further investigation on treatment efficacy indicators before/during treatment is necessary and helpful for optimizing a personalized protocol for patients.
Changes in the Molecular Orientation and Tensile Properties of Uniaxially Drawn Cellulose Films (2006)

Cellulose films were prepared by dissolving lyocell fibers in LiCl/N,N-dimethylacetamide solvent and subsequently coagulating and drying them under ambient conditions. To introduce preferred orientation, the films were uniaxially drawn under air-dry and rewetted conditions, respectively. Preferred orientation was determined by birefringence measurements and by wide-angle X-ray scattering. Mechanical properties were characterized by means of tensile tests with films conditioned to standard temperatures and humidity. Drawing resulted in the substantial reorientation of cellulose, whereby the molecular chains in the amorphous regions exhibited clearly stronger reorientation than the crystalline fraction. The average degree of orientation was comparable to orientation achieved in spun cellulose fibers. Wet-drawing resulted in improved tensile strength and modulus of elasticity but reduced elongation at break. The mechanical properties of wet-drawn films are competitive with regard to cellophane and melt-blown cellulose films, particularly considering their high modulus of elasticity of up to 26 GPa, which is also comparable to values obtained for industrially produced cellulose fibers.
A MEMS-Based Electrolytic Tilt Sensor (2006)

A MEMS-based tilt sensor has been realized using electrolytic solution, which is filled in a micromachined 400 mum-deep cavity and responsed relative to tilt angle due to the gravity. The device consists of anisotropically etched deep cavity to contain electrolytic solution and Au/NiCr metal electrodes to detect the electrical signal formed on non-planar surfaces from the substrate surface to the bottom of the cavity. The tilting motion of the device changes the immersed area of the electrodes in the electrolytic solution and the unbalanced ratio of the electrical signal is monitored by the change in its resistance. Potassium hydroxide (KOH) solution is chosen as the electrolyte due to the relatively high ionic conductance and it is diluted with methanol for an optimized concentration considering the viscosity. The fabricated electrolytic tilt sensor is excited by an alternating current to prevent electrolysis in the electrolyte-filled cavity and measured by Wheatstone bridge circuit. Experiments reveal that the resistance of KOH electrolyte is smallest at 5 wt% in its concentration and 800 Hz in the driving frequency. The tested Micro Electro Mechanical Systems (MEMS)-based electrolytic tilt sensor with KOH solution shows a resolution of approximately 50 mV per one degree of inclination angle change and operating angle range of plusmn60deg. The measured output characteristic of the fabricated MEMS-based electrolytic tilt sensor sustains comparison with other conventional electrolytic tilt sensors.
Insecticidal toxin from Bacillus thuringiensis is released from roots of transgenic Bt corn in vitro and in situ (2000)

The insecticidal toxin encoded by the cry1Ab gene from Bacillus thuringiensis was released in root exudates from transgenic Bt corn during 40 days of growth in soil amended to 0, 3, 6, 9, or 12% (v/v) with montmorillonite or kaolinite in a plant growth room and from plants grown to maturity in the field. The presence of the toxin in rhizosphere soil was determined by immunological and larvicidal assays. No toxin was detected in any soils from isogenic non-Bt corn or without plants. Persistence of the toxin was apparently the result of its binding on surface-active particles in the soils, which reduced the biodegradation of the toxin. The release of the toxin could enhance the control of insect pests or constitute a hazard to nontarget organisms, including the microbiota of soil, and increase the selection of toxin-resistant target insects.
SAR of Carbon‐Linked, 2‐Substituted Purines: Synthesis and Characterization of AP23451 as a novel Bone‐Targeted Inhibitor of Src Tyrosine Kinase With <i>In Vivo</i> Anti‐Resorptive Activity (2008)

Targeted disruption of the pp60(src) (Src) gene has implicated this tyrosine kinase in osteoclast-mediated bone resorption and as a therapeutic target for the treatment of osteoporosis and other bone-related diseases. Here, we describe structure activity relationships of a novel series of carbon-linked, 2-substituted purines that led to the identification of AP23451 as a potent inhibitor of Src tyrosine kinase with antiresorptive activity in vivo. AP23451 features the use of an arylphosphinylmethylphosphinic acid moiety which confers bone-targeting properties to the molecule, thereby increasing local concentrations of the inhibitor to actively resorbing osteoclasts at the bone interface. AP23451 exhibited an IC50 = 68 nm against Src kinase; an X-ray crystal structure of the molecule complexed with Src detailed the molecular interactions responsible for its Src inhibition. In vivo, AP23451 demonstrated a dose-dependent decrease in PTH-induced hypercalcemia. Moreover, AP23517, a structurally and biochemically similar molecule with comparable activity (IC50 = 73 nm) except devoid of the bone-targeting element, demonstrated significantly reduced in vivo efficacy, suggesting that Src activity was necessary but not sufficient for in vivo activity in this series of compounds.
Analysis of real-time data transmission in the DLL of IEC/ISA fieldbus (2002)

Fieldbus provides real-time data communication among field devices in process control and factory automation systems. IEC and ISA recently approved the Committee Draft of the data link layer of fieldbus standard for use in industrial control systems. The data link layer of IEC/ISA fieldbus is operated on the basis of token-passing and scheduling mechanisms. In this paper, the authors analyze the performance characteristics of the IEC/ISA fieldbus, especially the capability of real-time data transmission. A discrete-event simulation model of the data link layer is developed. Using the simulation model, this paper identifies the network parameters that influence the performance of priority mechanism and real-time data transmission, and analyzes the delay performance of IEC/ISA fieldbus with respect to the change of the network parameters. The fieldbus simulation model also integrates a continuous-time simulation model of a control system as an application process. Using the simulation model, this paper investigates the effect of network-induced delay on the performance of a control system.
Palladium-Catalyzed Homocoupling and Cross-Coupling Reactions of Aryl Halides in Poly(ethylene glycol) (2006)

The direct coupling of aryl halides to prepare symmetrical and unsymmetrical biaryls were performed successfully in poly(ethylene glycol) (PEG) using Pd(OAc)2 as the catalyst in the absence of other additives or reductants. The selectivity toward biaryl depended on the amount of PEG used. Excessive PEGs induce the increase of hydrodehalogenation product, and the best selectivity to biaryl is obtained when the concentration of the hydroxyl group in PEG achieves 100 mol % relative to aryl halides. The catalyst system could be recycled and reused up to five times with no loss of catalytic activity.
Carcinoembryonic antigen and other tumor markers in tissue and serum or plasma of patients with primary mammary carcinoma (1978)

50 patients with primary breast cancer were studied to determine the CEA and HCG contents in their tumor cells before any treatment was initiated. Tumor cells were obtained by needle biopsy and each tumor cell population was stained by immunofluorescence. In 21 of the 50 patients, CEA containing cells were found in a frequency ranging from 5 to 80% of the tumor cell population. The results were confirmed by radioimmunoassay of tumor extracts. No apparent relation was seen to cytologic type or grade of differentiation. HCG was detected by IF in 4 tumors with an apocrine cytologic cell type. The level of CEA in plasma was determined before treatment and followed for 2-6 months in 72 patients. CEA was the only measured serum parameter that correlated initially with size and extent of the localized tumor. It was too low to be of use for monitoring primary disease, but should be of value in early detection of metastasis. Posttreatment a low or decreased plasma CEA was seen more often in patients who had had curative treatment than in those given palliative radiation. No raised serum HCG levels were found. Raised serum liver enzymes did not predict the extent of the primary tumor but may be an indication of distant spread. Tumor CEA content and CEA plasma concentration were correlated, although not very strongly. This means that CEA, although present in the tumor, is not always released in measurable amounts.
The Transmembrane Domains of the prM and E Proteins of Yellow Fever Virus Are Endoplasmic Reticulum Localization Signals (2004)

The immature flavivirus particle contains two envelope proteins, prM and E, that are associated as a heterodimer. Virion morphogenesis of the flaviviruses occurs in association with endoplasmic reticulum (ER) membranes, suggesting that there should be accumulation of the virion components in this compartment. This also implies that ER localization signals must be present in the flavivirus envelope proteins. In this work, we looked for potential subcellular localization signals in the yellow fever virus envelope proteins. Confocal immunofluorescence analysis of the subcellular localization of the E protein in yellow fever virus-infected cells indicated that this protein accumulates in the ER. Similar results were obtained with cells expressing only prM and E. Chimeric proteins containing the ectodomain of CD4 or CD8 fused to the transmembrane domains of prM or E were constructed, and their subcellular localization was studied by confocal immunofluorescence and by analyzing the maturation of their associated glycans. Although a small fraction was detected in the ER-to-Golgi intermediate and Golgi compartments, these chimeric proteins were located mainly in the ER. The C termini of prM and E form two antiparallel transmembrane alpha-helices. Interestingly, the first transmembrane passage contains enough information for ER localization. Taken altogether, these data indicate that, besides their role as membrane anchors, the transmembrane domains of yellow fever virus envelope proteins are ER retention signals. In addition, our data show that the mechanisms of ER retention of the flavivirus and hepacivirus envelope proteins are different.
Synthesis of 2-Substituted Furanonaphthoquinones Using Directed Metalation and Cross Coupling Reactions (1998)

Abstract A synthetic method for the preparation of C-2 substituted furanonaphthoquinones from ortholithium-benzamide and the 2-furan-carboxaldehyde derivative is described. Four 2-alkyl-furanonaphthoquinones and the 2-phenyl-substituted were prepared via phathalide. This route has been shown to be general application to the synthesis of furanonaphthoquinones.
Consistency of the monocular EKF-SLAM algorithm for 3 different landmark parametrizations (2010)

6 pages
Cathepsin B to cysteine proteinase inhibitor balance in metastatic cell subpopulations isolated from murine tumors. (1990)

Our laboratories have previously demonstrated that the malignancy of human and animal tumors is associated with increases in cathepsin B activity, due in part to increases in cathepsin B-specific RNA transcripts and in part to decreased regulation by the endogenous low molecular weight cysteine proteinase inhibitors (CPIs). In this study we have extended these observations to tumor cell subpopulations of B16 amelanotic melanoma (B16a) and Lewis lung carcinoma (3LL) isolated by centrifugal elutriation. B16a subpopulations exhibited a 10-fold differential in lung colonization potential, whereas 3LL subpopulations exhibited no differential. In the B16a subpopulations, cathepsin B activities, total cellular and plasma membrane-associated, corresponded positively (4- and 10-fold increase, respectively) with their lung colonization potentials. CPI activities, total cellular and plasma membrane-associated, corresponded inversely (2- and 5-fold decrease, respectively) with the lung colonization potential of the B16a subpopulations. In the 3LL subpopulations, neither cathepsin B nor CPI activities changed. In the plasma membrane fractions of all 3LL subpopulations the ratio of cathepsin B activity to CPI activity was less than 1, whereas in the plasma membrane fractions of all B16a subpopulations the ratio was 1 or greater. In the plasma membrane fractions of the B16a subpopulations of higher lung colonization potential the ratios were 2.5 and 7, indicating that the levels of endogenous CPIs in these fractions may not be sufficient to regulate cathepsin B activity. Cathepsin B mRNA levels were not increased in the B16a subpopulations expressing increased cathepsin B activity. Thus increased cathepsin B activity in these subpopulations was apparently due not to increased synthesis but to decreased regulation by the endogenous CPIs. These results suggest that membrane-associated cathepsin B and CPIs may both play a role in the expression of the experimental metastatic phenotype.
Optimized Backflushing Process for Fibrous Media in Engine Oil Filtration and Enhancement by Ultrasound (2013)

Abstract Filter media that are made of metal fiber fleece have been qualified as a very suitable method to clean engine oils from fine particles in large diesel application. However, regeneration by backflushing of these densely packed depth filtration media is a great challenge. In experimental studies, the principles of successful hydrodynamic backflushing could be identified. Furthermore, the auxiliary effects of medium‐ and high‐power ultrasound on this process were investigated and could be qualified. Ideal process parameters for the general aim of freeing filter media from clogging particle fractions whilst using minimized amounts of flushing medium can be derived. This generates input parameters for an optimized apparatus design in real‐scale application.