gebhart/patrepeval huggingface dataset:
Purification and Functional Reconstitution of Monomeric μ-Opioid Receptors (2009)

Despite extensive characterization of the mu-opioid receptor (MOR), the biochemical properties of the isolated receptor remain unclear. In light of recent reports, we proposed that the monomeric form of MOR can activate G proteins and be subject to allosteric regulation. A mu-opioid receptor fused to yellow fluorescent protein (YMOR) was constructed and expressed in insect cells. YMOR binds ligands with high affinity, displays agonist-stimulated [(35)S]guanosine 5'-(gamma-thio)triphosphate binding to Galpha(i), and is allosterically regulated by coupled G(i) protein heterotrimer both in insect cell membranes and as purified protein reconstituted into a phospholipid bilayer in the form of high density lipoprotein particles. Single-particle imaging of fluorescently labeled receptor indicates that the reconstituted YMOR is monomeric. Moreover, single-molecule imaging of a Cy3-labeled agonist, [Lys(7), Cys(8)]dermorphin, illustrates a novel method for studying G protein-coupled receptor-ligand binding and suggests that one molecule of agonist binds per monomeric YMOR. Together these data support the notion that oligomerization of the mu-opioid receptor is not required for agonist and antagonist binding and that the monomeric receptor is the minimal functional unit in regard to G protein activation and strong allosteric regulation of agonist binding by G proteins.
Lithium influences differentiation and tissue-specific gene expression of mouse embryonic stem (ES) cells in vitro (2001)

The effects of lithium chloride (LiCl) on differentiation of mouse embryonic stem (ES) cells were investigated in order to evaluate the ES cell test (EST) used in a European Union validation study for screening of embryotoxic agents in vitro. We show that LiCl inhibited concentration-dependently the differentiation of ES cells into cardiac and myogenic cells. Whereas the inhibition of cardiac differentiation by high concentrations of LiCl was obvious at day 5 + 5, decreased skeletal muscle cell differentiation was observed only at day 5 + 8. Semi-quantitative RT-PCR analyses revealed significantly lower levels of mRNA encoding cardiac-specific alpha-myosin heavy chain and skeletal muscle-specific myoD. By morphological investigation, an influence of lithium on neuronal differentiation was not evident. However, mRNA levels of genes encoding synaptophysin and the 160 kDa neurofilament protein were increased by high LiCl concentrations, whereas mRNA levels of mash-1 and Engrailed-1 were decreased, suggesting a specific influence of lithium on neuronal differentiation. Furthermore, LiCl treatment resulted in a slight, but non-significant increase of beta-catenin levels in ES cell-derived embryoid bodies. Our results demonstrate that the ES cell test, EST may be suitable to detect inhibitory effects of test compounds especially on cardiac differentiation, whereas effects on neuronal cells would not be detected. Therefore, we propose that morphological analyses of cardiac differentiation alone are insufficient to detect embryotoxic effects. The assay of other cell lineages at different developmental stages, and expression analyses of tissue-specific genes should also be employed.
Hyperexcitability of Cultured Spinal Motoneurons From Presymptomatic ALS Mice (2004)

ALS (amyotrophic lateral sclerosis) is an adult-onset and deadly neurodegenerative disease characterized by a progressive and selective loss of motoneurons. Transgenic mice overexpressing a mutated human gene (G93A) coding for the enzyme SOD1 (Cu/Zn superoxide dismutase) develop a motoneuron disease resembling ALS in humans. In this generally accepted ALS model, we tested the electrophysiological properties of individual embryonic and neonatal spinal motoneurons in culture by measuring a wide range of electrical properties influencing motoneuron excitability during current clamp. There were no differences in the motoneuron resting potential, input conductance, action potential shape, or afterhyperpolarization between G93A and control motoneurons. The relationship between the motoneuron's firing frequency and injected current (f-I relation) was altered. The slope of the f-I relation and the maximal firing rate of the G93A motoneurons were much greater than in the control motoneurons. Differences in spontaneous synaptic input were excluded as a cause of increased excitability. This finding identifies a markedly elevated intrinsic electrical excitability in cultured embryonic and neonatal mutant G93A spinal motoneurons. We conclude that the observed intrinsic motoneuron hyperexcitability is induced by the SOD1 toxic gain-of-function through an aberration in the process of action potential generation. This hyperexcitability may play a crucial role in the pathogenesis of ALS as the motoneurons were cultured from presymptomatic mice.
Expression of CD44 in kidney after acute ischemic injury in rats (2000)

De novo CD44 and ligand expression at wound margins accompanies cellular proliferation and migration that effect repair of injured mucosal and vascular endothelial tissues. To determine whether CD44 could play a role in recovery from acute ischemic renal injury, we characterized its renal expression and those of two of its ligands, hyaluronic acid and osteopontin. Although no expression is detectable in nonischemic kidneys, several mRNAs for CD44 are present within 1 day after injury. CD44 mRNA is expressed in proximal tubules undergoing repair. CD44 peptide is present in basal and lateral cell membranes. Hyaluronic acid is normally expressed in the interstitium of the renal papilla only. By 1 day postischemia, hyaluronic acid can be detected, in addition, in the interstitium surrounding regenerating tubules. Osteopontin, not normally expressed in the renal proximal tubule, is expressed in regenerating tubules by 3 days after induction of acute ischemic injury. Immunoreactive osteopontin peptide continues to be localized in those tubules still undergoing repair for as long as 7 days after the injury. Our data are consistent with a role for CD44-ligand interactions in the regenerating proximal tubule participating in the process of recovery after ischemic injury.
Microfluidic technologies for high-throughput screening applications (2003)

In this thesis, I present a strategy for the design and development of microfluidic devices for high-throughput screening applications, such as mutant enzyme libraries expressed in prokaryotic hosts, where a few point mutations at the DNA level translates to hundreds of thousands of enzyme variants. The work falls into three main sections. Section I addresses fundamental research in polymer chemistry, where I explore the suitability of several polymers for microfluidic applications, examining properties such as molding, fluorescence, solvent compatibility, and adhesion/sealing to glass substrates. Section II describes my development of a two-phase microfluidic device, in which I report on crossflow-based dynamic formation of picoliter-sized water droplets in a continuously flowing oil-surfactant stream. A predictive model describing the fluid dynamics of droplet formation in this model is presented as well as its applications in screening bacterial populations. Section III reports the development of multilayer soft lithography technology using silicone rubber to build addressable high-density microfluidic arrays with thousands of integrated mechanical valves. This technology, which introduces the concept of fluidic large scale integration, is presented as a high-throughput parallel method to analyze bacterial enzyme expression at the single cell level. The detection of enzymatic activity in these high-density microarrays is described, comparing a self-constructed solid-state laser apparatus with a modified scanner (Axon Industries) used for looking at DNA arrays.
Breast cancer diagnosis and screening. (2000)

Approximately 180,000 new cases of breast cancer are diagnosed annually, accounting for about 48,000 deaths per year in the United States. The screening guidelines for the diagnosis of breast cancer are continually changing. Because of increased awareness of the signs and symptoms of breast cancer and the use of screening mammograms, breast cancers are increasingly being diagnosed at earlier stages. Annual mammograms and clinical breast examinations are recommended for women older than 40 years. Women older than 20 years should be encouraged to do monthly breast self-examinations, and women between 20 and 39 years of age should have a clinical breast examination every three years. These guidelines are modified for women with risk factors, particularly those with a strong family history of breast cancer. Ultrasonographic studies are most useful to evaluate cystic breast masses. For solid masses, diagnostic biopsy techniques include fine-needle aspiration, core biopsy and excisional biopsy.
Flexizyme as a versatile tRNA acylation catalyst and the application for translation (2006)

Here we describe a de novo tRNA acylation system consisting of artificial ribozymes. This system, the flexizyme (Fx) system, allows for the preparation of acyl-tRNAs with almost no limitation on the use of a variety of amino/hydroxy acids and tRNAs. To demonstrate its utility, we have carried out protein synthesis involving site-specific incorporation of nonnatural amino and hydroxy acids via amber or programmed frame-shift suppressions. We have also demonstrated peptide synthesis involving multiple nonnatural amino acids via sense codon suppression. The combination of the Fx system and appropriate cell-free translation is a powerful and flexible tool for mRNA-encoded synthesis of nonnatural polypeptides.
Derivatization procedures to facilitatede novo sequencing of lysine-terminated tryptic peptides using postsource decay matrix-assisted laser desorption/ionization mass spectrometry (2000)

Guanidination of the epsilon-amino group of lysine-terminated tryptic peptides can be accomplished selectively in one step with O-methylisourea hydrogen sulfate. This reaction converts lysine residues into more basic homoarginine residues. It also protects the epsilon-amino groups against unwanted reaction with sulfonation reagents, which can then be used to selectively modify the N-termini of tryptic peptides. The combined reactions convert lysine-terminated tryptic peptides into modified peptides that are suitable for de novo sequencing by postsource decay matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. The guanidination reaction is very pH dependent. Product yields and reaction kinetics were studied in aqueous solution using either NaOH or diisopropylethylamine as the base. Methods are reported for derivatizing and sequencing lysine-terminated tryptic peptides at low pmole levels. The postsource decay (PSD) MALDI tandem mass spectra of a model peptide (VGGYGYGAK), the homoarginine analog and the sulfonated homoarginine analog are compared. These spectra show the influence that each chemical modification has on the peptide fragmentation pattern. Finally, we demonstrate that definitive protein identifications can be achieved by PSD MALDI sequencing of derivatized peptides obtained from solution digests of model proteins and from in-gel digests of 2D-gel separated proteins.
Application and analysis of a robust trajectory tracking controller for under-characterized autonomous vehicles (2008)

When developing path tracking controllers for autonomous vehicles the dynamic constraints of the vehicle are a critical factor. It is therefore necessary to ensure that all tracking trajectories produced by the controller are smooth and continuous. In this paper, a path tracking controller is proposed and implemented on an experimental autonomous vehicle. This tracking method decouples the low-level heading and steering control of the vehicle from the main tracking controller, therefore requiring less vehicle characterization. The results of this paper will show this method yields a RMS 0.25 m cross-track error with little to no vehicle characterization.
Characterization of New Cell Permeable C3-like Proteins That Inactivate Rho and Stimulate Neurite Outgrowth on Inhibitory Substrates (2002)

The activation state of Rho is an important determinant of axon growth and regeneration in neurons. Axons can extend neurites on growth inhibitory substrates when Rho is inactivated by C3-ADP-ribosyltransferase (C3). We found by Rho-GTP pull-down assay that inhibitory substrates activate Rho. To inactivate Rho, scrape-loading of C3 was necessary because it does not freely enter cells. To overcome the poor permeability of C3, we made and characterized five new recombinant C3-like chimeric proteins designed to cross the cell membrane by receptor-independent mechanisms. These proteins were constructed by the addition of short transport peptides to the carboxyl-terminal of C3 and tested using a bioassay measuring neurite outgrowth of PC-12 cells plated on growth inhibitory substrates. All five constructs stimulated neurite outgrowth but with different dose-response profiles. Biochemical properties of the chimeric proteins were examined using C3-05, the most effective construct tested. Gel shift assays showed that C3-05 retained the ability to ADP-ribosylate Rho. Western blots and immunocytochemistry were used to verify the presence of C3 inside treated cells. C3-05 was also effective at promoting neurite outgrowth in primary neuronal cultures, as well as causing the disassembly of actin stress fibers and focal adhesions complexes in fibroblasts. These studies demonstrate that the new C3-like proteins are effective in delivering biologically active C3 into different cell types, thereby, inactivating Rho.
Contrasting monaural and interaural spectral cues for human sound localization (2004)

A human psychoacoustical experiment is described that investigates the role of the monaural and interaural spectral cues in human sound localization. In particular, it focuses on the relative contribution of the monaural versus the interaural spectral cues towards resolving directions within a cone of confusion (i.e., directions with similar interaural time and level difference cues) in the auditory localization process. Broadband stimuli were presented in virtual space from 76 roughly equidistant locations around the listener. In the experimental conditions, a "false" flat spectrum was presented at the left eardrum. The sound spectrum at the right eardrum was then adjusted so that either the true right monaural spectrum or the true interaural spectrum was preserved. In both cases, the overall interaural time difference and overall interaural level difference were maintained at their natural values. With these virtual sound stimuli, the sound localization performance of four human subjects was examined. The localization performance results indicate that neither the preserved interaural spectral difference cue nor the preserved right monaural spectral cue was sufficient to maintain accurate elevation judgments in the presence of a flat monaural spectrum at the left eardrum. An explanation for the localization results is given in terms of the relative spectral information available for resolving directions within a cone of confusion.
Gas chromatographic quantification of fatty acid methyl esters: Flame ionization detection vs. Electron impact mass spectrometry (2005)

The determination of FAME by GC is among the most commonplace analyses in lipid research. Quantification of FAME by GC with FID has been effectively performed for some time, whereas detection with MS has been used chiefly for qualitative analysis of FAME. Nonetheless, the sensitivity and selectivity of MS methods advocate a quantitative role for GC-MS in FAME analysis-an approach that would be particularly advantageous for FAME determination in complex biological samples, where spectrometric confirmation of analytes is advisable. To assess the utility of GC-MS methods for FAME quantification, a comparative study of GC-FID and GC-MS methods has been conducted. FAME in prepared solutions as well as a biological standard reference material were analyzed by GC-FID and GC-MS methods using both ion trap and quadrupole MS systems. Quantification by MS, based on total ion counts and processing of selected ions, was investigated for FAME ionized by electron impact. Instrument precision, detection limits, calibration behavior, and response factors were investigated for each approach, and quantitative results obtained by each technique were compared. Although there were a number of characteristic differences between the MS methods and FID with respect to FAME analysis, the quantitative performance of GC-MS compared satisfactorily with that of GC-FID. The capacity to combine spectrometric examination and quantitative determination advances GC-MS as a powerful alternative to GC-FID for FAME analysis.
Neuropathology of ALS (1996)

<h3>Abstract</h3> To facilitate the process of tailor-making a deep neural network for exploring the dynamics of genomic DNA, we have developed a hands-on package called ezGeno that automates the search process of various parameters and network structure. ezGeno considers three different sets of search spaces, namely, the number of filters, dilation factors, and the connectivity between different layers. ezGeno can be applied to any kind of 1D genomic input such as genomic sequences, histone modifications, DNase feature data and so on. Combinations of multiple abovementioned 1D features are also applicable. Specifically, for the task of predicting TF binding using genomic sequences as the input, ezGeno can consistently return the best performing set of parameters and network structure, as well as highlight the important segments within the original sequences. For the task of predicting tissue-specific enhancer activity using both sequence and DNase feature data as the input, ezGeno also regularly outperforms the hand-designed models. In this study, we demonstrate that ezGeno is superior in efficiency and accuracy when compared to AutoKeras, a general open-source AutoML package. The average AUC of ezGeno is also consistently higher than the result of using a one-layer DeepBind model. With the flexibility of ezGeno, we expect that this package can provide future researchers not only support of model design in their analysis of genomic studies but also more insights into the regulatory landscape. <h3>Availability</h3> The ezGeno package can be freely accessed at https://github.com/ailabstw/ezGeno. <h3>Contact</h3> Dr. Chien-Yu Chen, chienyuchen@ntu.edu.tw
Conv-RAM: An energy-efficient SRAM with embedded convolution computation for low-power CNN-based machine learning applications (2018)

Convolutional neural networks (CNN) provide state-of-the-art results in a wide variety of machine learning (ML) applications, ranging from image classification to speech recognition. However, they are very computationally intensive and require huge amounts of storage. Recent work strived towards reducing the size of the CNNs: [1] proposes a binary-weight-network (BWN), where the filter weights (w <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">i</sub> 's) are ±1 (with a common scaling factor per filter: α). This leads to a significant reduction in the amount of storage required for the W <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">i</sub> 's, making it possible to store them entirely on-chip. However, in a conventional all-digital implementation [2, 3], reading the wj <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">i</sub> s and the partial sums from the embedded SRAMs require a lot of data movement per computation, which is energy-hungry. To reduce data-movement, and associated energy, we present an SRAM-embedded convolution architecture (Fig. 31.1.1), which does not require reading the w <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">i</sub> 's explicitly from the memory. Prior work on embedded ML classifiers have focused on 1b outputs [4] or a small number of output classes [5], both of which are not sufficient for CNNs. This work uses 7b inputs/outputs, which is sufficient to maintain good accuracy for most of the popular CNNs [1]. The convolution operation is implemented as voltage averaging (Fig. 31.1.1), since the wj's are binary, while the averaging factor (1/N) implements the weight-coefficient α (with a new scaling factor, M, implemented off-chip).
A Novel Family of Atherogenic Oxidized Phospholipids Promotes Macrophage Foam Cell Formation via the Scavenger Receptor CD36 and Is Enriched in Atherosclerotic Lesions (2002)

The macrophage scavenger receptor CD36 plays an important role in binding and uptake of oxidized forms of low-density lipoprotein (LDL), foam cell formation, and lesion development during atherosclerosis. The structural basis of CD36-lipoprotein ligand recognition is an area of intense interest. In a companion article we reported the characterization of a structurally conserved family of oxidized choline glycerophospholipids (oxPC(CD36)) that serve as novel high affinity ligands for cells stably transfected with CD36, mediating recognition of multiple oxidized forms of LDL (Podrez, E. A., Poliakov, E., Shen, Z., Zhang, R., Deng, Y., Sun, M., Finton, P., Shan, L., Gugiu, B., Fox, P. L., Hoff, H. F., Salomon, R. G., and Hazen, S. L. (July 8, 2002) J. Biol. Chem. 277, 10.1074/jbc.M203318200). Here we use macrophages from wild-type and CD36 null mice to demonstrate that CD36 is the major receptor on macrophages mediating recognition of oxPC(CD36) species when presented (+/- plasma) in pure form, within PC bilayers in small unilamellar vesicles, and within liposomes generated from lipid extracts of native LDL. We also show that oxPC(CD36) promote CD36-dependent recognition when present at only a few molecules per particle, resulting in macrophage binding, uptake, metabolism, cholesterol accumulation, and foam cell formation. Finally, using high performance liquid chromatography with on-line electrospray ionization tandem mass spectrometry (LC/ESI/MS/MS), we demonstrate that oxPC(CD36) are generated in vivo and are enriched in atherosclerotic lesions. Collectively, our data suggest that formation of this novel family of oxidized phospholipids participates in CD36-mediated recognition of oxidized lipoproteins and foam cell formation in vivo.
교직 은퇴 후 스포츠 활동에 열중하는 전직 교사의 사중고(四重苦) 극복 방안 연구 (2015)

본 연구는 74세 한 체육인의 은퇴 전 스포츠 활동이 그의 삶에 어떠한 가치로 존재하여 영향을 미쳤는지를 이해하며, 은퇴 이후 연장된 스포츠 활동에 열중하는 삶이 사중고를 어떻게 해소하고 극복할 수 있게 했는지에 대한 방안을 논의하는데 있다. 이와 같은 목적을 달성하기 위해 생애사적 연구방법을 활용하였다. 자료 수집은 심층 면담, 참여 관찰, 현장 노트 및 녹음, 사진유도 면담을 통해 이루어졌으며, 자료 분석을 통한 결론은 다음과 같다. 첫째, 은퇴 전의 스포츠 활동은 연구 참여자의 삶 속에서 다양한 형태의 가치로 존재하였다. 둘째, 은퇴 이후의 스포츠 활동은 사중고를 일정 부분 극복하는 데 도움을 주었다. 셋째, 시니어계층에게 제안할 수 있는 스포츠 활동 참여 유형의 네 가지는, 스포츠 여가생활 유형, 시니어스포츠대회 선수생활 유형, 스포츠 지도자 유형, 재능기부 자원봉사 유형이다. 넷째, 행복한 노년기를 위한 개인적인 준비로는 생활습관의 관리, 스포츠 여가경영능력 배양, 스포츠 지도자 자격증 취득, 시니어스포츠대회에 참가, 재능기부 자원봉사 등이 있다. 국가적인 준비로는 시니어스포츠 활성화, 경제활동 및 사회발전에 참여하는 기회제공, 노인복지예산 확대 및 법제도의 점진적 개선이 필요하다. 사회적 준비로는 노인에 대한 사회인식의 변화로, 노인을 ``무능한 존재``에서 ``필요한 존재``로 사회인식을 개선하는 것이다.
N19 Polyepitope as a Carrier for Enhanced Immunogenicity and Protective Efficacy of Meningococcal Conjugate Vaccines (2004)

N19, a string of human universal CD4 T-cell epitopes from various pathogen-derived antigens, was shown to exert a stronger carrier effect than CRM197 for the induction of anti-group C Neisseria meningitidis capsular polysaccharide (MenC), after immunization of mice with various dosages of N19-MenC or CRM-MenC conjugate vaccines. After two immunizations, the N19-based construct induced anti-MenC antibody and protective bactericidal antibody titers higher than those induced by three doses of the CRM-MenC conjugate and required lower amounts of conjugate. N19-based conjugates are superior to CRM-based conjugates to induce protective immune responses to MenC conjugates.