gebhart/patrepeval huggingface dataset:
A palette of fluorescent proteins optimized for diverse cellular environments (2015)

To perform quantitative live cell imaging, investigators require fluorescent reporters that accurately report protein localization and levels, while minimally perturbing the cell. Yet, within the biochemically distinct environments of cellular organelles, popular fluorescent proteins (FPs), including EGFP, can be unreliable for quantitative imaging, resulting in the underestimation of protein levels and incorrect localization. Specifically, within the secretory pathway, significant populations of FPs misfold and fail to fluoresce due to non-native disulphide bond formation. Furthermore, transmembrane FP-fusion constructs can disrupt organelle architecture due to oligomerizing tendencies of numerous common FPs. Here, we describe a powerful set of bright and inert FPs optimized for use in multiple cellular compartments, especially oxidizing environments and biological membranes. Also, we provide new insights into the use of red FPs in the secretory pathway. Our monomeric 'oxFPs' finally resolve long-standing, underappreciated and important problems of cell biology and should be useful for a number of applications.
Endoplasmic reticulum stress enhances fibrotic remodeling in the lungs (2011)

Evidence of endoplasmic reticulum (ER) stress has been found in lungs of patients with familial and sporadic idiopathic pulmonary fibrosis. We tested whether ER stress causes or exacerbates lung fibrosis by (i) conditional expression of a mutant form of surfactant protein C (L188Q SFTPC) found in familial interstitial pneumonia and (ii) intratracheal treatment with the protein misfolding agent tunicamycin. We developed transgenic mice expressing L188Q SFTPC exclusively in type II alveolar epithelium by using the Tet-On system. Expression of L188Q SFTPC induced ER stress, as determined by increased expression of heavy-chain Ig binding protein (BiP) and splicing of X-box binding protein 1 (XBP1) mRNA, but no lung fibrosis was identified in the absence of a second profibrotic stimulus. After intratracheal bleomycin, L188Q SFTPC-expressing mice developed exaggerated lung fibrosis and reduced static lung compliance compared with controls. Bleomycin-treated L188Q SFTPC mice also demonstrated increased apoptosis of alveolar epithelial cells and greater numbers of fibroblasts in the lungs. With a complementary model, intratracheal tunicamycin treatment failed to induce lung remodeling yet resulted in augmentation of bleomycin-induced fibrosis. These data support the concept that ER stress produces a dysfunctional epithelial cell phenotype that facilitates fibrotic remodeling. ER stress pathways may serve as important therapeutic targets in idiopathic pulmonary fibrosis.
A Catalyst-Free Benzylic C–H Bond Olefination of Azaarenes for Direct Mannich-like Reactions (2011)

A highly efficient synthesis of trans-alkenylazaarene under catalyst-free conditions was developed via the addition of methylazaarenes to N-sulfonyl aldimines and a subsequent C-N elimination in situ. A one-pot procedure for this addition-elimination was also developed. The reaction could tolerate a broad substrate scope and give the corresponding alkenylazaarenes in high yields.
Fault-tolerance in parallel architectures with crosspoint switches (2002)

Based on an existing IBM/370 switch connected parallel processor (SCPP) prototype implementation, conceptual enhancements in the design for continuous availability are described. These enhancements include the user-specifiable two- to three-fold concurrent execution of processes on nonsynchronized processing units (PUs). The output produced by these processes is compared by software or hardware means. The asynchronism of the execution allows the detection of context-dependent software failures in addition to the detection of hardware errors. These design advances encompass novel hardware and software features aimed at achieving continuous system operation as well as superior information integrity at an improved cost/performance ratio, facilitating a proven crosspoint switch intercommunication mechanism of the SCPP.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Copper(II) Carboxylate Promoted Intramolecular Diamination of Terminal Alkenes:  Improved Reaction Conditions and Expanded Substrate Scope (2007)

The copper(II) carboxylate promoted diamination reaction has been improved by the use of the organic soluble copper(II) neodecanoate [Cu(ND)2]. Cu(ND)2 allowed the less-polar solvent dichloroethane (DCE) to be used, and as a consequence, decomposition of less-reactive substrates could be avoided. High diastereoselectivity was observed in the synthesis of 2,5-disubstituted pyrrolidines. Ureas, bis(anilines), and alpha-amido pyrroles derived from 2-allylaniline could also participate in the diamination reaction.
Synchronization and chaos (1983)

We believe that synchronization and chaos are closely related. Common intuition suggests that when a circuit is off synchronization the observed output, although not periodic, will be a sum of periodic (intermodulation) components. In fact, at least for a large class of systems we have studied, the output does not have this relatively simple form but is actually chaotic. This paper studies a simple but realistic model for a large class of triggered oscillators. Theory and experiments both confirm that the output shows the properties of sensitivity to initial conditions, nonperiodicity, broad spectrum, and complicated recurrence, that characterize chaotic motion.
Experimental Study of Carbon Dioxide Separation From Gas Mixture by Vortex Tube (2017)

Due to the global warming, climate treaty regulations and credits have been enhanced. As a result, the Carbon Capture & Storage (CCS) technologies have been emerged. In this study, it is presented that is separating the CO2 from Air by vortex generator. The vortex tube is a device to separate inlet gases to hotter and colder mixture than inlet by energy separation technology. In this study, the vortex tube is applied to CO2 gas separation from air that is investigated under atmospheric temperature. Prior to feasibility experiment, transient response shows that the temperature separation is settled down in 3000 seconds. Experimental parameters of gas separation are pressures and concentrations of CO2 that is mixed with air. Results show that CO2 gas separation is proportional to operating temperature. The percentage of CO2 gas separation is 7.4 % at 3barg and cold mass fraction of 0.6. The gas separation is also affected by inlet CO2 concentration.
LGS shear horizontal SAW devices for biosensor applications (2004)

Low cost, highly sensitive biosensors for the selective detection of pathogens in liquids are urgently needed. These sensors can play a major role in limiting the threat of hazardous microbial agents introduced into food and water supplies accidentally or through acts of terrorism. Surface acoustic wave (SAW) sensors utilizing the shear horizontal (SH) mode together with a nucleic acid recognition technique called rolling circle amplification (RCA) represent an attractive technology for this type of application due to reduced acoustic wave attenuation of the SH mode in aqueous environments when compared to generalized SAW. Langasite (LGS) offers high coupling for the SH SAW mode, temperature compensated SH SAW orientations, and high dielectric permittivity aqueous solutions. These properties have been discussed in a previous work by M. Pereira da Cunha et al. (2002). This paper reports on LGS SH SAW delay lines that have been designed and fabricated with a gold shorted delay path as the sensing area, in which biomolecule sensing is performed as a model for the RCA recognition layer. Proteins were sequentially bound to a cysteamine-modified gold surface. With each protein addition, marked changes in the delay line phase were recorded, indicating the functionality of the biosensor as a platform for the RCA layer.
Long chain fatty acid binding to human plasma albumin. (1975)

The binding of six physiologically important long chain fatty acids to defatted human plasma albumin was measured at 37 degrees in a calcium-free Krebs-Ringer phosphate buffer, pH 7.4. The data were analyzed in terms of multiple stepwise equilibria. With the saturated acids, the magnitude of the equilibrium (association) constants, Ki, increased as the chain length increased: laurate smaller than myristate smaller than palmitate smaller than stearate. Oleate was bound more tightly than stearate; by contrast, linoleate was bound less tightly than stearate. The equilibrium constants, K1 through K12, ranged from 2.4 times 10-6 - 3.5 times 10-3 m-1 for laurate to 2.6 times 10-8 - 3.5 times 10-5 m-1 for oleate. Successive values of Ki decrease for each of the acids, indicating that major cooperative binding effects do not occur over the physiological range of fatty acid concentrations. In no case could the Ki be segregated into distinct classes, suggesting that any grouping of albumin binding sites is somewhat arbitrary. The results were inconclusive concerning whether premicellar association of unbound fatty acid occurs. Although corrections for premicellar association produced very little change in the Ki values for myristate, they raised the Ki for palmitate and stearate by 300 to 700 per cent. A sigmoidal relationship was obtained when the logarithm of Ki was plotted against chain length for the saturated fatty acids containing 6 to 18 carbon atoms, indicating that the binding energy is not simply a statistical process dependent only on the fatty acid chain length. This selectivity that albumin contributes to the binding process may be due to varying degrees of configurational adaptability of its binding sites as the fatty acid increases in length.
Virus-Specific CD8+ T Cells in the Liver: Armed and Ready to Kill (2007)

Influenza A virus infection of C57BL/6 mice is a well-characterized model for studying CD8+ T cell-mediated immunity. Analysis of primary and secondary responses showed that the liver is highly enriched for CD8+ T cells specific for the immunodominant H2D(b)NP(366-374) (D(b)NP(366)) epitope. Functional analysis established that these liver-derived virus-specific CD8+ T cells are fully competent cytotoxic effectors and IFN-gamma secretors. In addition, flow cytometric analysis of early apoptotic cells showed that these influenza-specific CD8+ T cells from liver are as viable as those in the spleen, bronchoalveolar lavage, mediastinal lymph nodes, or lung. Moreover, cytokine profiles of the influenza-specific CD8+ T cells recovered from different sites were consistent with the bronchoalveolar lavage, rather than liver population, being the most susceptible to activation-induced cell death. Importantly, adoptively transferred influenza virus-specific CD8+ T cells from the liver survived and were readily recalled after virus challenge. Together, these results show clearly that the liver is not a "graveyard" for influenza virus-specific CD8+ T cells.
Demonstration of all-optical demultiplexing of a multilevel soliton signal employing soliton decomposition and self-frequency shift (1997)

We report an experimental demonstration of an all optical demultiplexing a burst of 4/spl times/10-Gb/s multilevel TDM soliton signal using the soliton effect pulse compression and soliton self-frequency shift in a silica fiber.
A direct comparative framework of customer satisfaction: An application to Internet search engines (2004)

Traditionally, satisfaction evaluations have been studied in the expectancy-disconfirmation paradigm in which customers compare firm performance to expectations. The current customer-satisfaction framework incorporates competitive comparisons indirectly through expectations. However, in markets in which competing alternatives are often primed in the evaluation context (e.g., product and retailer information presented in Bizrate.com), customers may directly compare performance and satisfaction across competing alternatives. In this article, we develop a direct comparative framework (DCF) of customer satisfaction. To make our DCF managerially useful, we also develop an operational model that managers can use to draw strategic insights based on customers’ satisfaction evaluations. We demonstrate our framework and operational model by applying them to the Internet search-engine market.
Dual Regulation of EDG1/S1P1 Receptor Phosphorylation and Internalization by Protein Kinase C and G-protein-coupled Receptor Kinase 2 (2002)

Here we demonstrate that phosphorylation of the sphingosine 1-phosphate (SSP) receptor "endothelial differentiation gene 1" (EDG1 or S1P(1)) receptor is increased in response to either SSP or phorbol 12-myristate 13-acetate (PMA) exposure but not lysophosphatidic acid. Phosphoamino acid analysis demonstrated that SSP stimulated the accumulation of phosphoserine and phosphothreonine but not phosphotyrosine. An inhibitor of PMA-stimulated EDG1 phosphorylation failed to block SSP-stimulated phosphorylation. Additionally, removal of 12 amino acids from the carboxyl terminus of EDG1 specifically reduced SSP- but not PMA-stimulated phosphorylation, suggesting that SSP and PMA increase EDG1 phosphorylation via distinct mechanisms. In vitro assays revealed that G-protein-coupled receptor kinase 2 may be at least partially responsible for SSP-stimulated EDG1 phosphorylation observed in intact cells. In addition, phosphorylation by PMA and SSP were associated with a loss of EDG1 from the cell surface by distinct mechanisms. Removal of 12 residues from the carboxyl terminus of EDG1 completely inhibited SSP-mediated internalization, suggesting that this domain dictates susceptibility to receptor internalization while retaining sensitivity to SSP-stimulated phosphorylation. Thus, we conclude that (a) EDG1 phosphorylation and internalization are controlled via independent mechanisms by agonist occupation of the receptor and protein kinase C activation, and (b) although determinants within the receptor's carboxyl-terminal tail conferring EDG1 sensitivity to agonist-mediated internalization and G-protein-coupled receptor kinase phosphorylation exhibit a degree of overlap, the two phenomena are separable.
Fortescue William Millett (1915)

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Spinous Process Strength (2000)

Specimens with a bone mineral density in the range of 0.263-0.997 g/cm2 failed at a mean load of 339 N when the load was applied through the spinous process hook of a flexible fixation device.
<i>In silico</i>prediction of drug therapy in catecholaminergic polymorphic ventricular tachycardia (2015)

The mechanism of therapeutic efficacy of flecainide for catecholaminergic polymorphic ventricular tachycardia (CPVT) is unclear. Model predictions suggest that Na(+) channel effects are insufficient to explain flecainide efficacy in CPVT. This study represents a first step toward predicting therapeutic mechanisms of drug efficacy in the setting of CPVT and then using these mechanisms to guide modelling and simulation to predict alternative drug therapies. Catecholaminergic polymorphic ventricular tachycardia (CPVT) is an inherited arrhythmia syndrome characterized by fatal ventricular arrhythmias in structurally normal hearts during β-adrenergic stimulation. Current treatment strategies include β-blockade, flecainide and ICD implementation--none of which is fully effective and each comes with associated risk. Recently, flecainide has gained considerable interest in CPVT treatment, but its mechanism of action for therapeutic efficacy is unclear. In this study, we performed in silico mutagenesis to construct a CPVT model and then used a computational modelling and simulation approach to make predictions of drug mechanisms and efficacy in the setting of CPVT. Experiments were carried out to validate model results. Our simulations revealed that Na(+) channel effects are insufficient to explain flecainide efficacy in CPVT. The pure Na(+) channel blocker lidocaine and the antianginal ranolazine were additionally tested and also found to be ineffective. When we tested lower dose combination therapy with flecainide, β-blockade and CaMKII inhibition, our model predicted superior therapeutic efficacy than with flecainide monotherapy. Simulations indicate a polytherapeutic approach may mitigate side-effects and proarrhythmic potential plaguing CPVT pharmacological management today. Importantly, our prediction of a novel polytherapy for CPVT was confirmed experimentally. Our simulations suggest that flecainide therapeutic efficacy in CPVT is unlikely to derive from primary interactions with the Na(+) channel, and benefit may be gained from an alternative multi-drug regimen.
FUNDAMENTALS OF PLANARIAN REGENERATION (2004)

The principles underlying regeneration in planarians have been explored for over 100 years through surgical manipulations and cellular observations. Planarian regeneration involves the generation of new tissue at the wound site via cell proliferation (blastema formation), and the remodeling of pre-existing tissues to restore symmetry and proportion (morphallaxis). Because blastemas do not replace all tissues following most types of injuries, both blastema formation and morphallaxis are needed for complete regeneration. Here we discuss a proliferative cell population, the neoblasts, that is central to the regenerative capacities of planarians. Neoblasts may be a totipotent stem-cell population capable of generating essentially every cell type in the adult animal, including themselves. The population properties of the neoblasts and their descendants still await careful elucidation. We identify the types of structures produced by blastemas on a variety of wound surfaces, the principles guiding the reorganization of pre-existing tissues, and the manner in which scale and cell number proportions between body regions are restored during regeneration.
Enhanced capacity in CDMA systems with alternate frequency planning (2002)

CDMA is a very attractive technique for PCS because of its potentially large capacity and well-known ability to resolve multipath fading. The next step will be to enhance the performance of CDMA system efficiently and optimally. Two new frequency planning schemes are proposed. One uses a frequency reuse factor of 3 and the other uses a cell partitioning. To show the advantages of two new frequency planning schemes, the capacity of CDMA systems is compared. First of all, the capacity of the current CDMA system is analyzed with the consideration of power control. Then, the performance of the CDMA systems using new frequency planning schemes is obtained. The results show that the current frequency reuse factor of 1 is not always optimal, even though it is the simplest frequency planning to deploy. The new frequency planning schemes provide more capacity and are more adaptive in the cases of non-uniformly distributed traffic loads.
Testing an Energy-Dispersive Counting-Mode Detector With Hard X-Rays From a Synchrotron Source (2008)

A counting-mode line detector has been evaluated at a synchrotron radiation source in order to assess its performance for imaging applications. The x-ray detector is based on 3 mm thick CdZnTe arrays with 1 mm pixel pitch and multi-threshold counting electronics. Data readout has been performed in threshold scan mode to provide maximum energy dispersion. The acquired energy spectra are interpreted regarding the characteristics of a periodic source and pulse pile-up in the detector. In particular, energy response and rate behavior of single-photon and double-photon events are investigated. Count rate dynamics are studied up to incident rates of . A further subject of the investigation is the variance of the observed counting rate. Linearity in the energy domain is tested between 40 keV and 140 keV.
Post genome analysis of Campylobacter jejuni (2001)

Completion of the Campylobacter jejuni NCTC11168 genome sequence offers unrivalled opportunities to understand the molecular basis of virulence for this major pathogen. Among the many novel features revealed by the genome sequence are at least 24 hypervariable sequences mostly found in genes encoding surface structures. Variation in the length of poly G/C tracts in genes containing these hypervariable sequences is frequently found in other mucosal pathogens and is likely to play a key role in enabling C. jejuni to evade the host immune response. Additionally, a novel capsule locus and three sialylation pathways were identified which may be important in the pathogenesis of both uncomplicated diarrhoeal disease and neurological sequelae of infection. The availability of the C. jejuni genome sequence data has coincided with important technological advances in bioinformatics, gene mutagenesis, proteome analysis and DNA microarrays. A C. jejuni DNA microarray holds great promise for transcriptome and comparative genome analysis. Given the range of disease associated with C. jejuni infection, combined with the diverse genotypic and phenotypic properties of clinical and environmental isolates, a Campylobacter DNA microarray will be particularly useful in determining correlates of pathogenicity and in deciphering the epidemiology of the organism. Post genome studies will liberate our understanding of C. jejuni from the piecemeal study of individual genes or operons towards a comprehensive analysis of the entire gene and protein complement. Armed with this wealth of new information, the opportunities to develop improved intervention strategies to reduce C. jejuni in the food chain will be enormous.
Spatio-temporal synchronization of periodic movements by style-phase adaptation: Application to biped walking (2012)

In this paper, we propose a framework for generating coordinated periodic movements of robotic systems with external inputs. We developed an adaptive pattern generator model that is composed of a two-factor observation model with a style parameter and phase dynamics with a phase variable. The style parameter controls the spatial patterns of the generated trajectories, and the phase variable controls its temporal profiles. To validate the effectiveness of our proposed method, we applied it to a simulated humanoid model to perform biped walking behaviors coordinated with observed walking patterns and the environment. The robot successfully performed stable biped walking behaviors even when the style of the observed walking pattern and the period were suddenly changed.
EyePhone: A mobile EOG-based Human-Computer Interface for assistive healthcare (2013)

Human-Computer Interfaces (HCI) allow effective interactions between human being and computers, which is of particular significance to people with disabilities or temporary mobility impairment. In this paper, we propose the EyePhone framework, a mobile HCI that allows users to control mobile phones through intentional eye or facial movements. A proof-of-concept prototype is developed based on a wearable electroencephalograph (EEG) headset and an Android smartphone. Specifically, a graphical window can receive and display continuous EEG data acquired from the headset; a mouse emulator can allow users to move a cursor around the smartphone screen by moving their heads and eyes; and an emergency dialer can allow users to make an emergency phone call through a certain pattern of eye/facial movements. The launching and switching of each functional module are also implemented through predefined head movement patterns, in order to achieve a true “hands-free” environment. The efficacy and efficiency of the proposed EyePhone system is evaluated based on experiments in a variety of scenarios (e.g., sitting, standing, and walking).