gebhart/patrepeval huggingface dataset:
Co-translational Degradation of Apolipoprotein B100 by the Proteasome Is Prevented by Microsomal Triglyceride Transfer Protein (1997)

We studied the effect of inhibition of microsomal triglyceride transfer protein (MTP) on apolipoprotein (apo) B100 translation and secretion using HepG2 cells. The MTP-mediated lipid transfer activity was reduced using a specific MTP inhibitor. ApoB100 translation was synchronized by treatment with puromycin prior to L-[35S]methionine pulse-chase labeling. During the first 4 min of chase, synthesis of apoB polypeptides the size of 100-200 kDa was insensitive to the inhibitor, suggesting that inhibition of MTP did not affect the initiation of apoB100 translation. After 15 min of chase, the 100-200-kDa species were chased into polypeptides larger than 320 kDa (i.e. apoB65 or 65% of full-length apoB100) in both control and inhibitor-treated cells. However, the amount of these polypeptides decreased (by 36% for apoB65-75, by 64% for apoB75-85, by 76% for apoB85-95, and by 77% for apoB100) upon MTP inhibition. No accumulation of smaller polypeptides was observed, but total immunoprecipitable apoB radioactivity was decreased suggesting that apoB could undergo co-translational degradation when MTP activity was reduced. Inhibitors of the multicatalytic proteinase complex (proteasome) such as lactacystin or MG-115 could prevent apoB co-translational degradation. Nevertheless, MG-115 could not avoid the MTP inhibitor decreasing apoB100 secretion but rather induced the accumulation of secretion-incompetent apoB100 in the cell. These results indicate that MTP activity is required during the elongation of apoB100 polypeptides, particularly at the sequences downstream of carboxyl terminus of apoB65. Co-translational degradation might constitute a more general mechanism of early quality control for large or complex proteins.
Synthesis and Structural Characterization of M(PMe<sub>3</sub>)<sub>3</sub>(O<sub>2</sub>CR)<sub>2</sub>(OH<sub>2</sub>)H<sub>2</sub> (M = Mo, W):  Aqua−Hydride Complexes of Molybdenum and Tungsten (2005)

Mo(PMe(3))(6) and W(PMe(3))(4)(eta(2)-CH(2)PMe(2))H undergo oxidative addition of the O-H bond of RCO(2)H to yield sequentially M(PMe(3))(4)(eta(2)-O(2)CR)H and M(PMe(3))(3)(eta(2)-O(2)CR)(eta(1)-O(2)CR)H(2) (M = Mo and R = Ph, Bu(t); M = W and R = Bu(t)). One of the oxygen donors of the bidentate carboxylate ligand may be displaced by H(2)O to give rare examples of aqua-dihydride complexes, M(PMe(3))(3)(eta(1)-O(2)CR)(2)(OH(2))H(2), in which the coordinated water molecule is hydrogen-bonded to both carboxylate ligands.
A simple, economical and reproducible protein extraction protocol for proteomics studies of soybean roots (2012)

Sample preparation is a critical step in two-dimensional gel electrophoresis (2-DE) of plant tissues. Here we describe a phenol/SDS procedure that, although greatly simplified, produced well-resolved and reproducible 2-DE profiles of protein extracts from soybean [Glycine max (L.) Merril] roots. Extractions were made in three replicates using both the original and simplified procedure. To evaluate the quality of the extracted proteins, ten spots were randomly selected and identified by mass spectrometry (MS). The 2-DE gels were equally well resolved, with no streaks or smears, and no significant differences were observed in protein yield, reproducibility, resolution or number of spots. Mass spectra of the ten selected spots were compared with database entries and allowed high-quality identification of proteins. The simplified protocol described here presents considerable savings of time and reagents without compromising the quality of 2-DE protein profiles and compatibility with MS analysis, and may facilitate the progress of proteomics studies of legume-rhizobia interactions.
Image decomposition via the combination of sparse representations and a variational approach (2005)

The separation of image content into semantic parts plays a vital role in applications such as compression, enhancement, restoration, and more. In recent years, several pioneering works suggested such a separation be based on variational formulation and others using independent component analysis and sparsity. This paper presents a novel method for separating images into texture and piecewise smooth (cartoon) parts, exploiting both the variational and the sparsity mechanisms. The method combines the basis pursuit denoising (BPDN) algorithm and the total-variation (TV) regularization scheme. The basic idea presented in this paper is the use of two appropriate dictionaries, one for the representation of textures and the other for the natural scene parts assumed to be piecewise smooth. Both dictionaries are chosen such that they lead to sparse representations over one type of image-content (either texture or piecewise smooth). The use of the BPDN with the two amalgamed dictionaries leads to the desired separation, along with noise removal as a by-product. As the need to choose proper dictionaries is generally hard, a TV regularization is employed to better direct the separation process and reduce ringing artifacts. We present a highly efficient numerical scheme to solve the combined optimization problem posed by our model and to show several experimental results that validate the algorithm's performance.
A 100-MHz ultrasonic transducer array using ZnO thin films (1995)

A 100-MHz ultrasonic linear transducer array made from a piezoelectric zinc oxide thin film on a sapphire substrate was developed and evaluated. Epitaxial, high-acoustic quality 10-/spl mu/m-thick ZnO film layers were produced by rf-magnetron sputter deposition onto a (111)-oriented gold film (with a chromium adhesion layer) that was vacuum-evaporated onto a (0001) sapphire surface. We found that, in well-oriented growth of gold, it is important to control the chromium sublayer thickness (less than 5 nm). An array was constructed by photolithography with an appropriate etch. V-shaped grooves between adjacent elements were formed by using an anisotropic etchant (HCl and HNO/sub 3/-based) that preferentially etched the c-plane of ZnO. Typical array elements were 90 /spl mu/m wide, 3.2 mm long, and 10 /spl mu/m thick, and the pitch of an array was typically 100 /spl mu/m. Our fine uniform array resulted in uniform ultrasonic response of individual elements throughout the array. For a 32-element array, the ultrasound beam in the azimuth plane in water could be electronically focused in the 100 MHz range to obtain a half-amplitude width of 60 /spl mu/m at the focal depth, agreeing well with theoretical predictions. Besides the use demonstrated with this present transducer, piezoelectric thin films should also lead to fabrication of various other kinds of ultrasonic transducers that can operate at high frequencies and should provide opportunities for miniaturizing transducers and making integrated ultrasonic devices.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Optimal Control of Multi-Stage Discrete Event Systems With Real-Time Constraints (2009)

We consider discrete event systems involving tasks with real-time constraints and seek to control processing times so as to minimize a cost function subject to each task meeting its own constraint. When tasks are processed over a single stage, it has been shown that there are structural properties of the optimal state trajectory that lead to very efficient solutions of such problems. When tasks are processed over multiple stages and are subject to end-to-end real-time constraints, these properties no longer hold and no obvious extensions are known. We consider such a multi-stage problem with not only stage-dependent but also task-dependent cost functions over all tasks at each stage and derive several new optimality properties. These properties lead to the idea of introducing ldquovirtualrdquo deadlines at each stage except the last one, thus partially decoupling the stages so that the known efficient solutions for single-stage problems can be used. We prove that a sequence of solutions to single-stage problems with virtual deadlines updated at each step converges to the global optimal solution of the multi-stage problem. This leads to a virtual deadline algorithm (VDA) which is scalable in the number of processed tasks. We illustrate the scalability and efficiency of the VDA through numerical examples.
An automatic climate probe system based on CAN bus architecture (2003)

A method of designing an automatic climate probe system based on CAN bus architecture and with good flexibility is introduced. The emphasis is on the hardware and software design of the system.
Alice in warningland: a large-scale field study of browser security warning effectiveness (2013)

We empirically assess whether browser security warnings are as ineffective as suggested by popular opinion and previous literature. We used Mozilla Firefox and Google Chrome’s in-browser telemetry to observe over 25 million warning impressions in situ. During our field study, users continued through a tenth of Mozilla Firefox’s malware and phishing warnings, a quarter of Google Chrome’s malware and phishing warnings, and a third of Mozilla Firefox’s SSL warnings. This demonstrates that security warnings can be effective in practice; security experts and system architects should not dismiss the goal of communicating security information to end users. We also find that user behavior varies across warnings. In contrast to the other warnings, users continued through 70.2% of Google Chrome’s SSL warnings. This indicates that the user experience of a warning can have a significant impact on user behavior. Based on our findings, we make recommendations for warning designers and researchers. 1
Comprehensive Expression Analysis of Time-dependent Genetic Responses in Yeast Cells to Low Temperature (2002)

We performed genome-wide expression analysis to determine genetic responses in Saccharomyces cerevisiae to a low temperature environment using a cDNA microarray. Approximately 25% of the genes in the yeast genome were found to be involved in the response of yeast to low temperature. This finding of a large number of genes being involved in the response to low temperature enabled us to give a functional interpretation to the genetic responses to the stimulus. Functional and clustering analyses of temporal changes in gene expression revealed that global states of the expressions of up-regulated genes could be characterized as having three phases (the early, middle, and late phases). In each phase, genes related to rRNA synthesis, ribosomal proteins, or several stress responses are time-dependently up-regulated, respectively. Through these phases, yeast cells may improve reduced efficiency of translation and enhance cell protection mechanisms to survive under a low temperature condition. Furthermore, these time-dependent regulations of these genes would be controlled by the cAMP-protein kinase A pathway. The results of our study provide a global description of transcriptional response for adaptation to low temperature in yeast cells.
Haptenation: Chemical Reactivity and Protein Binding (2011)

Low molecular weight chemical (LMW) allergens are commonly referred to as haptens. Haptens must complex with proteins to be recognized by the immune system. The majority of occupationally related haptens are reactive, electrophilic chemicals, or are metabolized to reactive metabolites that form covalent bonds with nucleophilic centers on proteins. Nonelectrophilic protein binding may occur through disulfide exchange, coordinate covalent binding onto metal ions on metalloproteins or of metal allergens, themselves, to the major histocompatibility complex. Recent chemical reactivity kinetic studies suggest that the rate of protein binding is a major determinant of allergenic potency; however, electrophilic strength does not seem to predict the ability of a hapten to skew the response between Th1 and Th2. Modern proteomic mass spectrometry methods that allow detailed delineation of potential differences in protein binding sites may be valuable in predicting if a chemical will stimulate an immediate or delayed hypersensitivity. Chemical aspects related to both reactivity and protein-specific binding are discussed.
<i>De novo</i> Design of Monomeric β-Hairpin and β-Sheet Peptides (2006)

Since the first report in 1993 (JACS 115, 5887-5888) of a peptide able to form a monomeric beta-hairpin structure in aqueous solution, the design of peptides forming either beta-hairpins (two-stranded antiparallel beta-sheets) or three-stranded antiparallel beta-sheets has become a field of intense interest. These studies have yielded great insights into the principles governing the stability and folding of beta-hairpins and antiparallel beta-sheets. This chapter reviews briefly those principles and describes a protocol for the de novo design of beta-sheet-forming peptides based on them. Criteria to select appropriate turn and strand residues and to avoid aggregation are provided. Because nuclear magnetic resonance is the most appropriate technique to check the success of new designs, the nuclear magnetic resonance parameters characteristic of beta-hairpins and three-stranded antiparallel beta-sheets are given.
Digital polymer motor for robotic applications (2004)

In this paper we present a packaged actuator to be applied for micro- and macro- robotic applications. The actuator is based on polymer dielectrics, and intrinsically has muscle-like characteristics capable of performing motions such as forward/backward/controllable compliance. The actuator is featured in several aspects such as simplicity and lightness in weight, cost-effectiveness, multiple DOF-actuation, and digital interface. In this paper, its basic concepts are briefly introduced and the issues about design, fabrication and applications are discussed.
Activation of K<sub>ATP</sub> channels by H<sub>2</sub>S in rat insulin‐secreting cells and the underlying mechanisms (2005)

H2S is an important gasotransmitter, generated in mammalian cells from L-cysteine metabolism. As it stimulates K(ATP) channels in vascular smooth muscle cells, H2S may also function as an endogenous opener of K(ATP) channels in INS-1E cells, an insulin-secreting cell line. In the present study, K(ATP) channel currents in INS-1E cells were recorded using the whole-cell and single-channel recording configurations of the patch-clamp technique. K(ATP) channels in INS-1E cells have a single-channel conductance of 78 pS. These channels were activated by diazoxide and inhibited by gliclazide. ATP (3 mm) in the pipette solution inhibited K(ATP) channels in INS-1E cells. Significant amount of H2S was produced from INS-1E cells in which the expression of cystathinonie gamma-lyase (CSE) was confirmed. After INS-1E cells were transfected with CSE-targeted short interfering RNA (CSE-siRNA) or treated with DL-propargylglycine (PPG; 1-5 mm) to inhibit CSE, endogenous production of H2S was abolished. Increase in extracellular glucose concentration significantly decreased endogenous production of H2S in INS-1E cells, and increased insulin secretion. After transfection of INS-1E cells with adenovirus containing the CSE gene (Ad-CSE) to overexpress CSE, high glucose-stimulated insulin secretion was virtually abolished. Basal K(ATP) channel currents were significantly reduced after incubating INS-1E cells with a high glucose concentration (16 mm) or lowering endogenous H2S level by CSE-siRNA transfection. Under these conditions, exogenously applied H2S significantly increased whole-cell K(ATP) channel currents at concentrations equal to or lower than 100 microm. H2S (100 microm) markedly increased open probability by more than 2-fold of single K(ATP) channels (inside-out recording) in native INS-1E cells (n = 4, P < 0.05). Single-channel conductance and ATP sensitivity of K(ATP) channels were not changed by H2S. In conclusion, endogenous H2S production from INS-1E cells varies with in vivo conditions, which significantly affects insulin secretion from INS-1E cells. H2S stimulates K(ATP) channels in INS-1E cells, independent of activation of cytosolic second messengers, which may underlie H2S-inhibited insulin secretion from these cells. Interaction among H2S, glucose and the K(ATP) channel may constitute an important and novel mechanism for the fine control of insulin secretion from pancreatic beta-cells.
COMPANHIA SENHORAS DO CERRADO: SUBJETIVIDADE E SAÚDE NO PROCESSO DE ENVELHECER (2014)

Este trabalho, com base na Epistemologia Qualitativa, objetivou compreender como a subjetividade é produzida na vivência do teatro e como ela repercute no processo de envelhecimento do sujeito. Teve como participante uma senhora de 91 anos pertencente à Cia de Teatro Senhoras do Cerrado, da Secretaria Municipal de Assistência Social da cidade de Goiânia. Para a construção das informações, trabalhou-se com a participante em um processo de conversação sobre a sua vivência da interpretação de temas e poesias no teatro. Textos de diferentes autores e a arte dramática foram os instrumentos mediadores que proporcionaram a visibilidade da qualidade de vida da pesquisada, e possibilitaram a ela uma abertura para a criatividade, a construção de novos sentidos e significados de sua vida. Percebeu-se, também, como a Cia de Teatro fortaleceu o papel social da integrante frente às possíveis mudanças de paradigmas preconceituosos da sociedade em relação à pessoa idosa por meio das apresentações públicas. A pesquisada ao longo dos 15 anos na Cia de Teatro Senhoras do Cerrado pôde desenvolver vários sentidos subjetivos de envelhecimento saudável, como a autonomia, reconhecimento de suas limitações, possibilidades, feminilidade e finitude. Constatou-se que o teatro e a interpretação podem ser agentes transformadores da realidade da pessoa favorecendo o seu enfrentamento real da velhice, sem máscaras . A arte dramática permite que a pessoa demonstre suas dificuldades, suas mazelas, seus declínios, mas, acima de tudo, se perceba como um sujeito em desenvolvimento, que pode enfrentar suas limitações e acreditar nas suas possibilidades. Essas constatações apontam a necessidade de dar continuidade a pesquisas sobre intervenções como esta, uma forma diferente de ação da Psicologia tradicional, utilizando-se da arte poética e dramática, na busca de um sujeito completo, sem polarização de saúde e doença. .
Microbes as Menaces, Mates & Marvels (2012)

The conventional understanding of microbes as causative agents of disease has led us to fear them and to consider them our deadly enemies. Much less appreciated are the central roles microbes play in shaping the environment and in maintaining plant, animal, and human health. All metazoan organisms – organisms that we can see with the naked eye – exist in lifelong partnerships with vast microbial communities. These “microbiomes” supply metazoans with essential life processes that are not encoded in nonmicrobial genomes. Recent work in microbiology has revealed that microbes, like metazoans, have specific body plans and sensory systems, that they can communicate with each other, and that they orchestrate collective behaviors. Investigations of these ancient yet enduring processes are uncovering the fundamental design principles of life. Microbes are also storehouses of new molecules, biochemical pathways, and materials with medical, industrial, and agricultural relevance. Scientists are harnessing these microbial products in efforts to confront humanity's most pressing problems. This essay explores the wonder, complexity, power, and utility of microbes in the twenty-first century.
18-LB: Increased Acidosis and Free-Radical Production Causes Recurrent Hypoglycemia–Induced Increase in Post-ischemic ER Stress in Treated Diabetic Rats (2020)

Cerebral ischemia is a serious complication of diabetes. Treatment of diabetes causes recurrent hypoglycemia (RH). Prior RH exposure increases ischemic brain damage in insulin-treated diabetic (ITD) rats. However, the mechanism of this injury is not well understood. We showed that ischemic acidosis increases reactive oxygen species (ROS) production in RH-exposed ITD (ITD + RH) rats. As enhanced acidosis and ROS production in normal subjects activate PERK, we hypothesized that increased ischemic acidosis and ROS production in RH-exposed ITD rats activate PERK. Therefore, we determined if the administration of tris-(hydroxymethyl)-aminomethane (THAM; an alkalizing agent) and N-acetylcysteine (NAC; an antioxidant) decrease RH-induced post-ischemic PERK activation in ITD + RH rats. Wistar rats were treated with insulin 2-3 weeks after streptozotocin induced diabetes. After 2 weeks, hyperinsulinemic hypoglycemia was induced for 3 hours for 5 days. Following groups were employed: (I) ITD + vehicle (Veh) (n = 6); (II) ITD + RH + Veh (n = 7); (III) ITD + RH + THAM (0.3 M, 3 ml/kg/hr, i.v.) (n = 6); and (IV) ITD + RH + NAC (150 mg/kg, i.v.) (n = 6). Transient global cerebral ischemia was induced by bilateral carotid artery occlusion with hypotension a day after RH. THAM/Veh was infused from 15 min before to 88 minutes after ischemia. NAC/Veh was administered 5 min before and 12 h after ischemia. Based on Western blot analysis, pPERK to total PERK ratio in the ITD + RH + THAM and ITD + RH + NAC groups were significantly lower by 32% and 26%, respectively, when compared with ITD + RH + Veh group. CHOP levels in the ITD + RH + THAM and ITD + RH + NAC group were lower by 38% and 63%, respectively, when compared with ITD + RH + Veh group. Therefore, ischemic acidosis and ROS production may mediate RH-induced ischemic activation of PERK. Understanding the ischemic damage in RH-exposed ITD rats may help identify new treatments for diabetes induced increase in ischemic injury. Disclosure A.K. Rehni: None. S. Cho: None. K.R. Dave: None. Funding National Institutes of Health (NS073779); American Heart Association (18POST34070061)