gebhart/patrepeval huggingface dataset:
Penetrating cation/fatty acid anion pair as a mitochondria-targeted protonophore (2009)

A unique phenomenon of mitochondria-targeted protonophores is described. It consists in a transmembrane H(+)-conducting fatty acid cycling mediated by penetrating cations such as 10-(6'-plastoquinonyl)decyltriphenylphosphonium (SkQ1) or dodecyltriphenylphosphonium (C(12)TPP). The phenomenon has been modeled by molecular dynamics and directly proved by experiments on bilayer planar phospholipid membrane, liposomes, isolated mitochondria, and yeast cells. In bilayer planar phospholipid membrane, the concerted action of penetrating cations and fatty acids is found to result in conversion of a pH gradient (DeltapH) to a membrane potential (Deltapsi) of the Nernstian value (about 60 mV Deltapsi at DeltapH = 1). A hydrophobic cation with localized charge (cetyltrimethylammonium) failed to substitute for hydrophobic cations with delocalized charge. In isolated mitochondria, SkQ1 and C(12)TPP, but not cetyltrimethylammonium, potentiated fatty acid-induced (i) uncoupling of respiration and phosphorylation, and (ii) inhibition of H(2)O(2) formation. In intact yeast cells, C(12)TPP stimulated respiration regardless of the extracellular pH value, whereas a nontargeted protonophorous uncoupler (trifluoromethoxycarbonylcyanide phenylhydrazone) stimulated respiration at pH 5 but not at pH 3. Hydrophobic penetrating cations might be promising to treat obesity, senescence, and some kinds of cancer that require mitochondrial hyperpolarization.
Mechanisms of protein solubilization in reverse micelles (1992)

Solubilization properties of alpha-chymotrypsin and alcohol dehydrogenase (LADH) in reverse micelles are reported for three different solubilization techniques. The solubilization properties for these two proteins depend on the method used for protein addition. The addition of a dry protein powder to a reverse-micelle-containing organic phase does not appreciably solubilize the protein until the diameter of the reverse micelle is similar to that of the protein. However, when an aqueous protein solution is injected an organic phase, protein solubilization is not strongly dependent on micelle size. For chymotrypsin, multiple protein occupancy occurs at large micelle size, with as many as 11 chymotrypsin molecules solubilized in one reverse micelle. The solubilization of chymotrypsin using a phase-transfer technique with a positively charged surfactant follows the expected trend based on protein-surfactant electrostatic interactions. When a negatively charged surfactants is used for phase transfer, at low pH the solubilization data do not fit this electrostatic interaction mechanism. In this case, protein-surfactant aggregation may be occurring at the aqueous-organic interface.
Reversible Cognitive Decline Accompanies Migraine and Cluster Headaches (2000)

Vascular headaches, including migraine, cluster, and migrainous transformation to chronic daily headaches, are disabling. During and shortly after headache intervals, difficulties are reported in concentration, comprehension, and communication, not accounted for by nausea, photophobia, or sonophobia. These interfere with interpersonal relations and performance at work with economic loss. The hypothesis tested and reported here is that cognitive impairments comprise an important part of vascular headache diatheses. One hundred ninety-six otherwise normative subjects suffering from migraine or cluster, but not tension-type, headaches (136 women, 63 men; mean age, 46 years) participated in an outpatient prospective trial. One hundred thirty-three patients had migraine without aura, 39 migraine with aura, 11 periodic cluster (by IHS criteria), and 13 had migrainous transformation into chronic daily headaches. Neuropsychological testing was compared with and without headaches, by combined Mini-Mental Status Examination (MMSE), Cognitive Capacity Screening Examination (CCSE), and Hamilton Depression Rating Scale (HDRS). During headache intervals, significant decline was measured in both CCSE and MMSE scores (P <. 001) without HDRS change in all types of vascular headache and independent of headache severity, which often improved, or associated physical symptoms. Cognitive decline was promptly relieved by serotonin agonists and sleep. Disorders of cerebral serotoninergic projection systems appear to cause these reversible cognitive impairments.
Optical antennas: Resonators for local field enhancement (2003)

Electromagnetic field enhancement in optical antenna arrays is studied by simulation and experiment at midinfrared wavelengths. The optical antennas are designed to produce intense optical fields confined to subwavelength spatial dimensions when illuminated at the resonant wavelength. Finite difference time domain (FDTD) method simulations are made of the current, charge, and field distributions in the antennas. The influence of antenna shape, length, and sharpness upon the intensity of the optical fields produced is found. Optical antennas arrays are fabricated on transparent substrates by electron beam lithography. Far-field extinction spectroscopy carried out on the antenna arrays shows the dependence of the resonant wavelength on the antenna length and material. The FDTD calculated and experimentally measured extinction efficiencies of the optical antennas are found to be in good agreement.
Obstructive Sleep Apnea and the Recurrence of Atrial Fibrillation (2003)

Patients with untreated OSA have a higher recurrence of AF after cardioversion than patients without a polysomnographic diagnosis of sleep apnea. Appropriate treatment with CPAP in OSA patients is associated with lower recurrence of AF.
An Efficient Method for the Isolation of Peramine, an Insect Feeding Deterrent Produced by the Fungus Acremonium Lolii (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAn Efficient Method for the Isolation of Peramine, an Insect Feeding Deterrent Produced by the Fungus Acremonium LoliiDaryl D. Rowan and Brian A. TapperCite this: J. Nat. Prod. 1989, 52, 1, 193–195Publication Date (Print):January 1, 1989Publication History Published online1 July 2004Published inissue 1 January 1989https://pubs.acs.org/doi/10.1021/np50061a030https://doi.org/10.1021/np50061a030research-articleACS PublicationsRequest reuse permissionsArticle Views179Altmetric-Citations16LEARN 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
Medium optimization for lipid production through co‐fermentation of glucose and xylose by the oleaginous yeast <b><i>Lipomyces starkeyi</i></b> (2008)

Abstract Co‐fermentation of lignocellulose‐based carbohydrates is a potential solution to improve the economics of microbial lipid production. In the present paper, experiments were performed to optimize the media composition for lipid production by the oleaginous yeast Lipomyces starkeyi AS 2.1560 through co‐fermentation of glucose and xylose (2 : 1 wt/wt). Statistical screening of nine media variables was performed by a Plackett–Burman design. Three factors, namely mixed sugar, yeast extract and FeSO 4 , were found as significant components influencing cellular lipid accumulation. Further optimization was carried out using a Box–Behnken factorial design to study the effects of these three variables on lipid production. A mathematical model with the R 2 value at 96.66% was developed to show the effect of each medium composition and their interactions on the lipid production. The model estimated that a maximal lipid content of 61.0 wt‐% could be obtained when the concentrations of mixed sugar, yeast extract and FeSO 4 were at 73.3 g/L (glucose 48.9 g/L, xylose 24.4 g/L), 7.9 g/L and 4.0 mg/L, respectively. The predicted value was in good accordance with the experimental data of 61.5%. Compared with the initial media, the optimized media gave 1.59‐fold and 2.03‐fold increases for lipid content and lipid productivity, respectively.
Disjoint Pattern Enumeration for Custom Instructions Identification (2007)

Extensible processors allow addition of application-specific custom instructions to the core instruction set architecture. These custom instructions are selected through an analysis of the program's dataflow graphs. The characteristics of certain applications and the modern compiler optimization techniques (e.g., loop unrolling, region formation, etc.) have lead to substantially larger dataflow graphs. Hence, it is computationally expensive to automatically select the optimal set of custom instructions. Heuristic techniques are often employed to quickly search the design space. In order to leverage full potential of custom instructions, our previous work proposed an efficient algorithm for exact enumeration of all possible candidate instructions (or patterns) given the dataflow graphs. But the algorithm was restricted to connected computation patterns. In this paper, we describe an efficient algorithm to generate all feasible disjoint patterns starting with the set of feasible connected patterns. Compared to the state-of-the-art technique, our algorithm achieves orders of magnitude speedup while generating the identical set of candidate disjoint patterns.
Preproenkephalin mRNA expression in developing rat heart and in cultured ventricular cardiac muscle cells (1989)

Heart muscle tissue has previously been reported to have the highest content of preproenkephalin (ppEnk) mRNA of any tissue in the adult rat. We have determined that it is present in the ventricular cardiac muscle cells of the heart and is developmentally regulated. The expression of ppEnk mRNA was observed to be low throughout the first 2 weeks of postnatal development and decreases substantially during week 3. Expression was again low by week 4, but by adulthood (approx. 3 months), it reached a maximum. ppEnk mRNA was actively expressed in primary cardiac muscle cell cultures prepared from both neonatal and adult rats. Its steady-state content in cell cultures was observed to be increased by cyclic AMP and 3-isobutyl-1-methylxanthine. The phorbol ester phorbol 12-myristate 13-acetate elicited a transient effect (i.e. an increase was observed at 4 h and a return to control values by 24 h). We speculate that enkephalin may play a multi-functional role in the differentiation of neonatal cardiac muscle cells and in the terminally differentiated adult heart cell. We demonstrate that the primary culture systems employed in this study will be useful models with which to explore both transcriptional and translational regulation of ppEnk mRNA in the heart.
Lack of lymphatic vascular specificity of vascular endothelial growth factor receptor 3 in 185 vascular tumors (1999)

The results of the current study show that although VEGFR-3 shows specificity toward lymphatics in normal tissues, this receptor is distributed extensively in benign and malignant vascular tumors and therefore can be considered a novel marker in the assessment of endothelial cell differentiation of vascular neoplasms.
Error correction of microchip synthesized genes using Surveyor nuclease (2011)

The development of economical and high-throughput gene synthesis technology has been hampered by the high occurrence of errors in the synthesized products, which requires expensive labor and time to correct. Here, we describe an error correction reaction (ECR), which employs Surveyor, a mismatch-specific DNA endonuclease, to remove errors from synthetic genes. In ECR reactions, errors are revealed as mismatches by re-annealing of the synthetic gene products. Mismatches are recognized and excised by a combination of mismatch-specific endonuclease and 3'→5' exonuclease activities in the reaction mixture. Finally, overlap extension polymerase chain reaction (OE-PCR) re-assembles the resulting fragments into intact genes. The process can be iterated for increased fidelity. With two iterations, we were able to reduce errors in synthetic genes by >16-fold, yielding a final error rate of ∼1 in 8700 bp.
ANTIMIC: a database of antimicrobial sequences (2003)

Antimicrobial peptides (AMPs) are important components of the innate immune system of many species. These peptides are found in eukaryotes, including mammals, amphibians, insects and plants, as well as in prokaryotes. Other than having pathogen-lytic properties, these peptides have other activities like antitumor activity, mitogen activity, or they may act as signaling molecules. Their short length, fast and efficient action against microbes and low toxicity to mammals have made them potential candidates as peptide drugs. In many cases they are effective against pathogens that are resistant to conventional antibiotics. They can serve as natural templates for the design of novel antimicrobial drugs. Although there are vast amounts of data on natural AMPs, they are not available through one central resource. We have developed a comprehensive database (ANTIMIC, http://research.i2r. a-star.edu.sg/Templar/DB/ANTIMIC/) of known and putative AMPs, which contains approximately 1700 of these peptides. The database is integrated with tools to facilitate efficient extraction of data and their analysis at molecular level, as well as search for new AMPs. These tools include BLAST, PDB structure viewer and the Antimic profile module.
Secure code distribution (1997)

The Java Virtual Machine does not offer a way for code obtained from trusted sources to be granted extra rights. The article describes two approaches to authentification for code distribution: one extends the JVM to include a digital signature in applets; the other uses MIME encapsulation to take advantage of available security infrastructures. The signed-applet approach gives a programmer more flexibility because it addresses the security issues at a more fundamental level. However, signed-applet security mechanisms may vary for different code distribution schemes, making integration difficult. The MIME-based approach provides a unified security interface. It is more efficient in the sense that all classes can be encapsulated in one multipart attachment, and a single signature or verification operation will cover all classes. The approaches can also be combined and tailored to satisfy various requirements. Ultimately, operating systems must support the concept of a secure compartment so that separate resource management policies can be implemented for the secure compartment and the rest of the system.
Optical protection switches for trunk transmission systems (2003)

Two different types of optical matrix switches are presented for use as protection switches. One is an optoelectronic matrix switch using Si pin photodiodes. The first switch configuration offers two advantages for large matrix fabrication: high off-state output impedance and no electrical power requirement for establishing the off-state. The other is an optical-wavelength-division matrix switch, using an acoustooptic deflector, which requires minimal hardware for switching and realizes unlimited bandwidth. The switching speed, crosstalk, attainable matrix size, and optical source requirements are evaluated for both switches. Their protection system application schemes are clarified.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The Human Homologue of the Yeast Prt1 Protein Is an Integral Part of the Eukaryotic Initiation Factor 3 Complex and Interacts with p170 (1997)

Eukaryotic initiation factor 3 (eIF3) is a large multisubunit complex that stabilizes the ternary complex, eIF2 x GTP x tRNA(Met)i and promotes mRNA binding to the 40 S ribosomal subunit. eIF3 also functions as a ribosome subunit anti-association factor. The molecular mechanisms by which eIF3 exerts these functions are poorly understood. We describe here the cloning of the cDNA encoding the human homologue of the yeast eIF3 subunit Prt1. The human PRT1 cDNA encodes a protein of predicted molecular mass of 98.9 kDa that migrates at 116 kDa on SDS-polyacrylamide gels. Human and yeast Prt1 share 31% identity and 50% similarity at the amino acid level. The homology is distributed throughout the entire protein, except for the amino terminus, and is particularly high in the central portion of the protein, which contains a putative RNA recognition motif. hPrt1 is recognized by an antibody raised against eIF3, and an affinity-purified antibody to recombinant hPrt1 recognizes a protein migrating at 116 kDa in a purified eIF3 preparation. Far Western analysis shows that hPrt1 interacts directly with the p170 subunit of eIF3. Mapping studies identify the RNA recognition motif as the region required for association with p170. Taken together, these experiments demonstrate that hPrt1 is a component of eIF3. Our data, combined with those of Hershey and co-workers, suggest that mammalian eIF3 is composed of at least 10 subunits: p170, p116 (hPrt1), p110, p66, p48, p47, p44, p40, p36, and p35.
High-efficiency, low voltage resonant-cavity light-emittingdiodes operating around 650 nm (2000)

High efficiencies and low voltages for resonant-cavity light-emitting diodes operating close to 650 nm are reported. Peak external quantum efficiencies of 6% are obtained for a low current injection of ~1 mA, giving an optical power output of 0.1 mW. For higher current injection at 13 mA, 1 mW of power is produced with a slightly lower, but modest, efficiency of 4%. These record high efficiencies mean that high power performance previously achieved in RCLEDs at the inherently more efficient wavelength of 660 nm can now be replicated in 650 nm devices. Forward biased operating voltages are between 1.7 and 1.9 V for a current range of 0 – 60 mA.
Hybrid Rule Ordering in Classification Association Rule Mining. (2008)

Abstract. Classification Association Rule Mining (CARM) is an approach to classifier generation that builds an Association Rule Mining based classifier using Classification Association Rules (CARs). Regardless of which particular CARM algorithm is used, a similar set of CARs is always generated from data, and a classifier is usually presented as an ordered list of CARs, based on a selected rule ordering strategy. Hence to produce an accurate classifier, it is essential to develop a rational rule ordering mechanism. In the past decade, a number of rule ordering strategies have been introduced. Six major ones can be identified: Confidence Support &amp;amp; size-of-Antecedent (CSA), size-of-
Effects of the neurotrophin brain-derived neurotrophic factor in an experimental model of retinal detachment. (1999)

Although there was variability in the treated retinas, most of the animals receiving BDNF had well-organized outer segments that were longer than those in vehicle-treated controls. Immunocytochemistry revealed that treated retinas had consistently less opsin redistribution to the plasma membrane, less phosducin upregulation, and fewer calbindin D-labeled horizontal cell processes. BDNF did not reduce overall cell death in the detachments or death of photoreceptors by apoptosis. However, it significantly reduced the proliferative response of Miller cells and the extent of upregulation of GFAP. CONCLUSIONS. The results suggest that BDNF may aid in the recovery of the retina after reattachment by maintaining the surviving photoreceptor cells, by reducing the gliotic effects in Müller cells, and perhaps by promoting outer segment regeneration.
14-3-3σ Expression Is an Independent Prognostic Parameter for Poor Survival in Colorectal Carcinoma Patients (2005)

These results provide evidence that 14-3-3sigma expression increases during carcinoma progression in a subset of colorectal carcinoma. The overexpression of this antigen identifies patients at high risk. It is tempting to suggest that 14-3-3sigma overexpression either promotes tumor proliferation and/or prevents apoptotic signal transduction in colorectal carcinoma. Thus, targeting 14-3-3sigma might be a new therapeutic strategy in colorectal carcinoma.
Monte Carlo localization for mobile robots (2003)

To navigate reliably in indoor environments, a mobile robot must know where it is. Thus, reliable position estimation is a key problem in mobile robotics. We believe that probabilistic approaches are among the most promising candidates to providing a comprehensive and real-time solution to the robot localization problem. However, current methods still face considerable hurdles. In particular the problems encountered are closely related to the type of representation used to represent probability densities over the robot's state space. Earlier work on Bayesian filtering with particle-based density representations opened up a new approach for mobile robot localization based on these principles. We introduce the Monte Carlo localization method, where we represent the probability density involved by maintaining a set of samples that are randomly drawn from it. By using a sampling-based representation we obtain a localization method that can represent arbitrary distributions. We show experimentally that the resulting method is able to efficiently localize a mobile robot without knowledge of its starting location. It is faster, more accurate and less memory-intensive than earlier grid-based methods,.
Conformational instability of the N‐ and C‐terminal lobes of porcine pepsin in neutral and alkaline solutions (1993)

Pepsin contains, in a single chain, two conformationally homologous lobes that are thought to have been evolutionarily derived by gene duplication and fusion. We have demonstrated that the individual recombinant lobes are capable of independent folding and reconstitution into a two-chain pepsin or a two-chain pepsinogen (Lin, X., et al., 1992, J. Biol. Chem. 267, 17257-17263). Pepsin spontaneously inactivates in neutral or alkaline solutions. We have shown in this study that the enzymic activity of the alkaline-inactivated pepsin was regenerated by the addition of the recombinant N-terminal lobe but not by the C-terminal lobe. These results indicate that alkaline inactivation of pepsin is due to a selective denaturation of its N-terminal lobe. A complex between recombinant N-terminal lobe of pepsinogen and alkaline-denatured pepsin has been isolated. This complex is structurally similar to a two-chain pepsinogen, but it contains an extension of a denatured pepsin N-terminal lobe. Acidification of the complex is accompanied by a cleavage in the pro region and proteolysis of the denatured N-terminal lobe. The structural components that are responsible for the alkaline instability of the N-terminal lobe are likely to be carboxyl groups with abnormally high pKa values. The electrostatic potentials of 23 net carboxyl groups in the N-terminal domain (as compared to 19 in the C-terminal domain) of pepsin were calculated based on the energetics of interacting charges in the tertiary structure of the domain. The groups most probably causing the alkaline denaturation are Asp11, Asp159, Glu4, Glu13, and Asp118.(ABSTRACT TRUNCATED AT 250 WORDS)