gebhart/patrepeval huggingface dataset:
Economically destabilizing electric power markets for profit (2002)

Electric generators and distributors, in many cases no longer vertically integrated with guaranteed customers and suppliers, are starting to compete to sell and buy electricity. It is not at all clear, though, that current wholesale electricity markets produce economically optimal or efficient results. In fact, anecdotal evidence to the contrary has continually arisen. The purpose of this article, then, is to introduce market analysts to the study of model agent driven power market auctions. In particular, scenarios are examined where some of the players attempt to profit by intentionally driving market prices and creating economic instabilities. A double auction market of electricity is modeled, and different scenarios for malicious activities from the sellers' side are considered. The results of simulating using genetic algorithms and the Roth/Erv leaning algorithm are summarized. It is shown that under commonly found circumstances some of the players can significantly influence the market for profit (their own). It is also noticed that structural market power exists when the uniform pricing algorithm is selected. It is also noticed that the buyers are very disadvantaged if they are not able to hide their valuation for the commodity.
SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks (2015)

The described approach fills a heretofore absent niche in workflows for large-scale biochemical kinetic model construction. In several applications the algorithm has already been demonstrated to be useful and scalable. SBMLsqueezer is platform independent and can be used as a stand-alone package, as an integrated plugin, or through a web interface, enabling flexible solutions and use-case scenarios.
Abstracts, Division of Biological Chemistry, 222nd National Meeting of the American Chemical Society, August 26−29, 2001 (2001)

ADVERTISEMENT RETURN TO ISSUEPREVCurrent Topics/Persp...Current Topics/PerspectivesAbstracts, Division of Biological Chemistry, 222nd National Meeting of the American Chemical Society, August 26−29, 2001Richard B. SilvermanCite this: Biochemistry 2001, 40, 29, 8607–8664Publication Date (Web):June 29, 2001Publication History Published online29 June 2001Published inissue 1 July 2001https://pubs.acs.org/doi/10.1021/bi0151420https://doi.org/10.1021/bi0151420review-articleACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views1448Altmetric-Citations1LEARN 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 SUBJECTS:Biochemistry,Chemical structure,Genetics,Monomers,Peptides and proteins Get e-Alerts
Instantaneous mapping of liquid crystal orientation using a polychromatic polarizing microscope (2022)

Polarizing microscopy brought about many advancements in the science of liquid crystals and other soft materials, including those of biological origin. Recent developments in optics and computer-based analysis enabled a new generation of quantitative polarizing microscopy which produces spatial maps of the optic axis. Unfortunately, most of the available approaches require a long acquisition time of multiple images which are then analyzed to produce the map. We describe a polychromatic polarizing microscope, which allows one to map the patterns of the optical axis in a single-shot exposure, thus enabling a fast temporal resolution. We present a comparative analysis of the new microscope with alternative techniques such as a conventional polarizing optical microscope and MicroImager of Hinds Instruments.
Human TRAV1-2-negative MR1-restricted T cells detect S. pyogenes and alternatives to MAIT riboflavin-based antigens (2016)

Mucosal-associated invariant T (MAIT) cells are thought to detect microbial antigens presented by the HLA-Ib molecule MR1 through the exclusive use of a TRAV1-2-containing TCRα. Here we use MR1 tetramer staining and ex vivo analysis with mycobacteria-infected MR1-deficient cells to demonstrate the presence of functional human MR1-restricted T cells that lack TRAV1-2. We characterize an MR1-restricted clone that expresses the TRAV12-2 TCRα, which lacks residues previously shown to be critical for MR1-antigen recognition. In contrast to TRAV1-2(+) MAIT cells, this TRAV12-2-expressing clone displays a distinct pattern of microbial recognition by detecting infection with the riboflavin auxotroph Streptococcus pyogenes. As known MAIT antigens are derived from riboflavin metabolites, this suggests that TRAV12-2(+) clone recognizes unique antigens. Thus, MR1-restricted T cells can discriminate between microbes in a TCR-dependent manner. We postulate that additional MR1-restricted T-cell subsets may play a unique role in defence against infection by broadening the recognition of microbial metabolites.
Effects of Temperature and Landfill Ageing on leaching and Degradation of Phtalates from a Poly(vinyl chloride) Carpet under Simulated Landfill Conditions (2008)

Protein farnesyltransferase from the eyes of Penaeus japonicus farnesylates predominantly H-ras-specific carboxyl termini, with the sequence CVLS, but not the K-ras-specific sequence CVIM or the protein geranylgeranyltransferase-specific sequence CAIL. The purified protein farnesyltransferase from shrimp was found by immunoblotting and polyacrylamide gel electrophoresis under denaturing conditions to consist of subunits of Mr 49,000 and Mr 48,000. Since the active protein farnesyltransferase was found to have a relative mass of 100,000, the purified enzyme was deduced to be a heterodimer. The enzyme had an optimal pH of 6 and a K(m) of 14 +/- 1 microM with the synthetic peptide RTRCVLSH as the substrate. The enzyme was activated by Mn+2 and Mg+2 but inhibited by Ca+2 ions.
TU‐F‐500‐01: Point and Counter Point Debate: Brachytherapy Is Better Than External Beam Therapy for Partial Breast Irradiation (2013)

Partial breast irradiation (PBI) by either brachytherapy or external beam (EB) therapy is frequently used for the treatment of certain populations of breast cancer patients. The claim that brachytherapy is better than EB for PBI is the Proposition debated here. Advantages claimed for brachytherapy for PBI include: • brachytherapy is associated with smaller treatment volumes, lower integral doses, and smaller doses/fraction to normal tissues • dosimetric parameters which affect toxicity have been thoroughly investigated for brachytherapy • brachytherapy is supported by over ten years of study with excellent local control and minimal toxicity • with brachytherapy, evidence‐based treatment planning guidelines have been published. Advantages claimed for EB therapy include: • all clinics have linacs, whereas not all have an HDR unit or LDR facilities • brachytherapy requires specific skills and training that not all radiation oncologists have • brachytherapy is an invasive procedure • a brachytherapy program requires greater effort and staff to commission and maintain • brachytherapy is performed BID, which is inconvenient to patients • not all patients are appropriate for brachytherapy treatment Arguing FOR the Proposition is Dorin Todor, Ph.D. Dr. Todor obtained his Ph.D. in Physics from Old Dominion University, Norfolk, VA followed by a one‐year Research Fellowship at Memorial Sloan Kettering Cancer Center, New York. Since then he has worked at the Virginia Commonwealth University where he is currently an Associate Professor. His major research interests include real‐time 3D HDR source position detection and tracking, and dual fusion imaging for intraoperative planning, execution and evaluation of brachytherapy implants. Arguing against the Proposition is Stewart Becker, Ph.D. Dr. Becker obtained his M.S. and Ph.D. degrees in Medical Physics from the University of Wisconsin, Madison after which he moved to the Department of Radiation Oncology, New York University Medical Center, where he is currently Senior Physicist and Assistant Professor. His major research interests include image‐guided radiotherapy, and whole and accelerated partial breast radiotherapy. Learning Objectives 1. To understand why brachytherapy might be better than external beam therapy for partial breast irradiation 2. To understand why external beam therapy might be better than brachytherapy for partial breast irradiation 3. To know how brachytherapy and external beam therapy differ when applied to partial breast irradiation
Ultrasonic Circular Cyclo Coagulation in patients with Primary Open-Angle Glaucoma: a Multicenter Clinical Trial (2013)

Purpose To evaluate the efficacy and safety of the Ultrasonic Circular Cyclo Coagulation (UC3) procedure in patients with primary open-angle glaucoma (POAG).



Methods Prospective multicenter clinical trial. 42 eyes of 42 patients with POAG, intraocular pressure (IOP) > 21 mmHg, an average of 1.65 failed previous surgeries and an average of 3.2 hypotensive medications were insonified with a probe comprising 6 piezoelectric transducers. 18 patients (group 1) were treated with a 4 seconds exposure time for each shot and 24 patients (group 2) with a 6 seconds exposure time. Follow-up visits were performed at 1 day, 1 week, 1, 2, 3, 6 and 12 months after.



Results IOP was significantly reduced in both groups (p 20%) was achieved in 12 of 18 (67%) eyes of the group 1 and in 17 of 24 (71%) eyes of the group 2. Four patients were re-treated. No major intra- or post-operative complications occurred.



Conclusion UC3 seems to be an effective and well-tolerated method to reduce intraocular pressure in patients with POAG.



Commercial interest
Utility-maximizing event stream suppression (2013)

Complex Event Processing (CEP) has emerged as a technology for monitoring event streams in search of user specified event patterns. When a CEP system is deployed in sensitive environments the user may wish to mitigate leaks of private information while ensuring that useful nonsensitive patterns are still reported. In this paper we consider how to suppress events in a stream to reduce the disclosure of sensitive patterns while maximizing the detection of nonsensitive patterns. We first formally define the problem of utility-maximizing event suppression with privacy preferences, and analyze its computational hardness. We then design a suite of real-time solutions to solve this problem. Our first solution optimally solves the problem at the event-type level. The second solution, at the event-instance level, further optimizes the event-type level solution by exploiting runtime event distributions using advanced pattern match cardinality estimation techniques. Our user study and experimental evaluation over both real-world and synthetic event streams show that our algorithms are effective in maximizing utility yet still efficient enough to offer near real-time system responsiveness.
Multiscale Compressive Video Acquisition (2013)

A low cost SWIR video camera prototype was built by combing compressive sensing multi-scale video (CS-MUVI) acquisition framework with the single pixel camera (SPC). The performance of the system was demonstrated by our experimental results.
Crystal structure of a fungal polyglycine hydrolase using a RoseTTAFold model (2022)

Chitinase-modifying proteins (CMP) are a subclass of polyglycine hydrolases that are secreted by fungi in response to plant-fungal defense. These CMPs are responsible for inactivating plant chitinases through cleavage of their interdomain linker region. Our work focused on the structural investigation of a chitinase-modifying protein originating from Fusarium vanettenii. We used a combinatorial approach of in silico and in vitro methods to determine the structure solution. Previous attempts at homology modelling failed to generate a reasonable model, suggesting unique structural features. Owing to recent developments in structure prediction, we were able to generate a fulllength homology model using RoseTTAFold1 for our target protein. In combination with a native data set, we were able to solve the structure to 2.2 Angstroms. The structure solution revealed two distinct domains. The amino terminal domain revealed a putatively novel fold, thus explaining previous homology modelling difficulties, whereas the carboxyl terminal domain revealed a beta-lactamase-like region. Further work has focused on the crystallization of the catalytic mutant and co-crystallization of the substrate complex.
Synthesis and Characterization of Reactive End-Capped Poiymide Oligomers (1984)

Abstract A series of reactive, end-capped, polyimide oligomers has been prepared for possible use as planarizing coatings in the electronics industry. Thus, 1,3-bis(3-aminophenoxy)benzene was treated with various excess amounts of 2,2-bis(3,4-dicarboxyphenyl)hexafluoro-propane dianhydride in m-cresol containing toluene and isoquinoline. The resulting anhydride-terminated amic-acid oligomers were thermally imidized and then allowed to react with 3-aminophenylethyne, 1-phenyl-4-(3-aminophenyl)buta-1-ene-3-yne, 1-phenyl-4-(3-amino-phenyl)-1,3-butadiyne, 2-aminobiphenylene, or 1-phenyl-2-(3-amino-phenyl)ethyne. Thermal imidization of these intermediates produced the corresponding end-capped polyimide oligomers. The white oligomers were soluble in organic solvents, such as diglyme, and had glass transition temperatures (Tg's) between 95 and 145°C. The Tg of an ethynyl-terminated oligomer was reduced from 105 to 62°C upon the incorporation of 20 wt % of the reactive plasticizer bis[2-(3-ethynylphenoxy)ethyl]ether. The oligomers underwent exothermic polymerizations between 225 and 420°C. Their TGA thermograms showed 5% weight losses near 530°C in air.
Role of Lewis and Broensted acid sites in zeolites and amorphous aluminosilicates in the formation of the products of condensation in transformations of propane and propylene (1989)

The composition of the products of condensation formed from propylene and propane on crystalline and amorphous aluminosilicates containing acid sites of different natures was studied by IR spectroscopy. The method of IR spectroscopy in diffusely scattered light showed that the presence of Lewis acid sites causes the formation of strongly unsaturated hydrocarbon structures in the initial stages of coke formation.
Concise Total Synthesis of (−)‐Affinisine Oxindole, (+)‐Isoalstonisine, (+)‐Alstofoline, (−)‐Macrogentine, (+)‐Na‐Demethylalstonisine, (−)‐Alstonoxine A, and (+)‐Alstonisine (2017)

A highly enantio- and diastereoselective strategy to access any member of the sarpagine/macroline family of oxindole alkaloids via internal asymmetric induction was developed from readily available d-(+)-tryptophan. At the center of this approach was the diastereospecific generation of the spiro[pyrrolidine-3,3'-oxindole] moiety at an early stage via a tert-butyl hypochlorite-promoted oxidative rearrangement of a chiral tetrahydro-β-carboline derivative. This key branching point determined the spatial configuration at the C-7 spiro center to be entirely 7R or 7S. Other key stereospecific processes were the asymmetric Pictet-Spengler reaction and Dieckmann cyclization, which were scalable to the 600 and 150 gram levels, respectively. Execution of this approach resulted in first enantiospecific total synthesis of (+)-isoalstonisine and (-)-macrogentine from the chitosenine series (7R), as well as (+)-alstonisine, (+)-alstofoline, (-)-alstonoxine A and (+)-N<sub>a</sub> -demethylalstonisine from the alstonisine series (7S).
Applications of Cayley graphs, bilinearity, and higher-order residues to cryptology (2004)

First, we focus on the discrete-logarithm problem, showing an algorithm that works in optimal time (up to logarithmic factors) and uses only a small amount of space. Our algorithm is a modification of the classic Pollard rho algorithm, introducing explicit randomization of the parameters for the updating steps of the algorithm. In proving that the algorithm works as claimed, we see several intermediate and related results of independent interest. 
Next, we present the concept of hierarchical identity-based encryption (HIBE) schemes. An IBE scheme is one in which any string can be used as a public key (e.g., the recipient's e-mail address); private keys are distributed by one central authority. An HIBE scheme is the hierarchical analogue of an IBE; among its many advantages those that come from splitting the key-distribution burden as well as those that come from escrow-related applications. We present an example of an HIBE scheme, give security definitions, and mention some of the applications of HIBE schemes. 
Finally, we describe some cryptologic applications of the rth-power-residue symbol (a higher-order analogue of the Jacobi symbol). We present an encryption scheme in which recipients only need an rth root of unity to decrypt. By simply changing the value of r and distributing roots to a new group, controlling who receives such roots, the set of decrypters can be changed without generating a new modulus (N = pq). We present other applications of the system as well as another application of the rth-power-residue symbol: how to speed up the elliptic curve method for factoring numbers of the form N = pqr.
Pharmacokinetic interaction studies between felbamate and vigabatrin. (1995)

To assess the possible occurrence of pharmacokinetic interactions between the antiepileptic agents felbamate and vigabatrin, two randomized, double-blind, placebo-controlled, crossover studies were conducted in healthy male volunteers. In Study I, 18 subjects received oral vigabatrin 1000 mg every 12 h for two 8 days periods with felbamate 1200 mg every 12 h or placebo. In Study II, 18 other volunteers were administered oral felbamate 1200 mg every 12 h for two 8 days periods with vigabatrin 1000 mg every 12 h or placebo. On the eighth day of each treatment period, blood and urine samples were collected over 12 h for determination of the active S(+)- and inactive R(-)-vigabatrin enantiomer concentrations (Study I) or felbamate concentrations (Study II). In Study I, the pharmacokinetic parameters of R(-)-vigabatrin were similar during co-administration with felbamate or placebo. Felbamate produced a 13% increase in AUC(0.12 h) and an 8% increase in urinary excretion of S(+)-vigabatrin. Although these changes were statistically significant, their magnitude was small. In Study II, the pharmacokinetic parameters of felbamate were similar during concurrent administration with vigabatrin or placebo. These data indicate that there are no clinically relevant pharmacokinetic interactions between felbamate and vigabatrin in man.
Genomes in Focus: Development and Applications of CRISPR‐Cas9 Imaging Technologies (2017)

The discovery of the CRISPR-Cas9 endonuclease has enabled facile genome editing in living cells and organisms. Catalytically inactive Cas9 (dCas9) retains the ability to bind DNA in an RNA-guided fashion, and has additionally been explored as a tool for transcriptional modulation, epigenetic editing, and genome imaging. This Review highlights recent progress and challenges in the development of dCas9 for imaging genomic loci. The emergence and maturation of this technology offers the potential to answer mechanistic questions about chromosome dynamics and three-dimensional genome organization in vivo.
Rapamycin does not prevent increases in myofibrillar or mitochondrial protein synthesis following endurance exercise (2015)

The present study aimed to investigate the role of the mechanistic target of rapamycin complex 1 (mTORC1) in the regulation of myofibrillar (MyoPS) and mitochondrial (MitoPS) protein synthesis following endurance exercise. Forty-two female C57BL/6 mice performed 1 h of treadmill running (18 m min(-1) ; 5° grade), 1 h after i.p. administration of rapamycin (1.5 mg · kg(-1) ) or vehicle. To quantify skeletal muscle protein fractional synthesis rates, a flooding dose (50 mg · kg(-1) ) of l-[ring-(13) C6 ]phenylalanine was administered via i.p. injection. Blood and gastrocnemius muscle were collected in non-exercised control mice, as well as at 0.5, 3 and 6 h after completing exercise (n = 4 per time point). Skeletal muscle MyoPS and MitoPS were determined by measuring isotope incorporation in their respective protein pools. Activation of the mTORC1-signalling cascade was measured via direct kinase activity assay and immunoblotting, whereas genes related to mitochondrial biogenesis were measured via a quantitative RT-PCR. MyoPS increased rapidly in the vehicle group post-exercise and remained elevated for 6 h, whereas this response was transiently blunted (30 min post-exercise) by rapamycin. By contrast, MitoPS was unaffected by rapamycin, and was increased over the entire post-exercise recovery period in both groups (P < 0.05). Despite rapid increases in both MyoPS and MitoPS, mTORC1 activation was suppressed in both groups post-exercise for the entire 6 h recovery period. Peroxisome proliferator activated receptor-γ coactivator-1α, pyruvate dehydrogenase kinase 4 and mitochondrial transcription factor A mRNA increased post-exercise (P < 0.05) and this response was augmented by rapamycin (P < 0.05). Collectively, these data suggest that endurance exercise stimulates MyoPS and MitoPS in skeletal muscle independently of mTORC1 activation.
Role of xanthine oxidase and granulocytes in ischemia-reperfusion injury (1988)

In this lecture, evidence is presented to support the following hypothesis regarding the roles of xanthine oxidase-derived oxidants and granulocytes in ischemia-reperfusion-induced microvascular injury. During the ischemic period, ATP is catabolized to yield hypoxanthine. The hypoxic stress also triggers the conversion of NAD-reducing xanthine dehydrogenase to the oxygen radical-producing xanthine oxidase. During reperfusion, molecular oxygen is reintroduced into the tissue where it reacts with hypoxanthine and xanthine oxidase to produce a burst of superoxide anion and hydrogen peroxide. In the presence of iron, superoxide anion and hydrogen peroxide react via the Haber-Weiss reaction to form hydroxyl radicals. This highly reactive and cytotoxic radical then initiates lipid peroxidation of cell membrane components and the subsequent release of substances that attract, activate, and promote the adherence of granulocytes to microvascular endothelium. The adherent granulocytes then cause further endothelial cell injury via the release of superoxide and various proteases.