gebhart/patrepeval huggingface dataset:
Mechanism of Abietadiene Synthase Catalysis:  Stereochemistry and Stabilization of the Cryptic Pimarenyl Carbocation Intermediates (2002)

Abietadiene synthase (AS) catalyzes the complex cyclization-rearrangement of (E,E,E)-geranylgeranyl diphosphate (8, GGPP) to a mixture of abietadiene (1a), double bond isomers 2a-4a and pimaradienes 5a-7a as a key step in the biosynthesis of the abietane resin acid constituents (1b-4b) of conifer oleoresin. The reaction proceeds at two active sites by way of the intermediate, copalyl diphosphate (9). In the second site, a putative tricyclic pimaradiene or pimarenyl(+) carbocation intermediate of undefined C13 stereochemistry and annular double bond position is formed. Three 8-oxy-17-nor analogues of 9 (17 and 19a,b) and three isomeric 15,16-bisnorpimarenyl-N-methylamines (26a-c) were synthesized and evaluated as alternative substrates and/or inhibitors for recombinant AS from grand fir. The stereospecific cyclization of 8 alpha-hydroxy-17-nor CPP (19a) to 17-normanoyl oxide (20a) and the higher inhibitory potency of the norpimarenylamine 26a (K(i) = 0.1 nM) both suggest pimarenyl intermediates having the 13 beta methyl configuration and 8,14-double bond corresponding to sandaracopimaradiene (5a). The 2000-fold stimulation of inhibition by 26a in the presence of inorganic pyrophosphate indicates an important role for carbocation/OPP anion stabilization of the secondary sandaracopimaren-15-yl(+) ion. The failure of 8 beta-hydroxy-17-nor CPP (19b) to undergo enzymatic cyclization was taken as evidence that 9 is bound with a "coplanar" side chain conformation and that the S(N)' cyclization occurs on the 17 alpha face. The routing of the sandarcopimara-15-en-8-yl carbocation toward various diterpenes in biogenetic schemes is attributed to differing conformations of ring C and/or orientations of the C13 vinyl group in the active sites of the corresponding diterpene cyclases.
Distributed and Autonomous Resource and Power Allocation for Wireless Networks (2013)

In this paper, a distributed and autonomous technique for resource and power allocation in orthogonal frequency division multiple access (OFDMA) femto-cellular networks is presented. Here, resource blocks (RBs) and their corresponding transmit powers are assigned to the user(s) in each cell individually without explicit coordination between femto-base stations (FBSs). The “allocatability” of each resource is determined utilising only locally available information of the following quantities: the required rate of the user; the quality (i.e., strength) of the desired signal; the frequency-selective fading on each RB; and the level of interference incident on each RB. Using a fuzzy logic system, the time-averaged values of each of these inputs are combined to determine which RBs are most suitable to be allocated in a particular cell, i.e., which resources can be allocated such that the user requested rate(s) in that cell are satisfied. Fuzzy logic presents a completely novel, low-complexity methodology for inter-cell interference coordination (ICIC). A comprehensive study of this system in a femtocell environment is performed, yielding system performance improvements in terms of throughput, energy efficiency and coverage over state-of-the-art ICIC techniques.
Improving Post-Click User Engagement on Native Ads via Survival Analysis (2016)

In this paper we focus on estimating the post-click engagement on native ads by predicting the dwell time on the corresponding ad landing pages. To infer relationships between features of the ads and dwell time we resort to the application of survival analysis techniques, which allow us to estimate the distribution of the length of time that the user will spend on the ad. This information is then integrated into the ad ranking function with the goal of promoting the rank of ads that are likely to be clicked and consumed by users (dwell time greater than a given threshold). The online evaluation over live traffic shows that considering post-click engagement has a consistent positive effect on both CTR, decreases the number of bounces and increases the average dwell time, hence leading to a better user post-click experience.
Current Trends in Lower Urinary Tract Health Highlights From Annual Advances in Genitourinary Health: A Scientific Update (2006)

No AccessJournal of UrologyIntroduction1 Mar 2006Current Trends in Lower Urinary Tract Health Highlights From Annual Advances in Genitourinary Health: A Scientific Update Jerry G. Blaivas, Arthur L. Burnett, and Alan J. Wein Jerry G. BlaivasJerry G. Blaivas Weill Medical College of Cornell University, New York, New York Financial interest and/or other relationship with Astellas (Yamanouchi), Pfizer, Novartis and Lilly. More articles by this author , Arthur L. BurnettArthur L. Burnett Johns Hopkins University School of Medicine, Baltimore, Maryland Financial interest and/or other relationship with Pfizer, Guilford Pharmaceuticals, Bayer/GlaxoSmithKline and Lilly/ICOS. More articles by this author , and Alan J. WeinAlan J. Wein University of Pennsylvania Health System, Philadelphia, Pennsylvania Financial interest and/or other relationship with ONO Pharmaceuticals, Pharmacia, Yamanouchi, Indevus, Theravance, Bard, Lilly, Pfizer, Novartis, BioXell and GlaxoSmithKline. More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(05)00314-9AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Current Trends in Lower Urinary Tract Health Highlights From Annual Advances in Genitourinary Health: A Scientific Update." The Journal of Urology, 175(3S), pp. S3–S4 © 2006 by American Urological AssociationFiguresReferencesRelatedDetails Volume 175Issue 3SMarch 2006Page: S3-S4 Advertisement Copyright & Permissions© 2006 by American Urological AssociationKeywordsdiagnosisdifferentialurogenital systemMetricsAuthor Information Jerry G. Blaivas Weill Medical College of Cornell University, New York, New York Financial interest and/or other relationship with Astellas (Yamanouchi), Pfizer, Novartis and Lilly. More articles by this author Arthur L. Burnett Johns Hopkins University School of Medicine, Baltimore, Maryland Financial interest and/or other relationship with Pfizer, Guilford Pharmaceuticals, Bayer/GlaxoSmithKline and Lilly/ICOS. More articles by this author Alan J. Wein University of Pennsylvania Health System, Philadelphia, Pennsylvania Financial interest and/or other relationship with ONO Pharmaceuticals, Pharmacia, Yamanouchi, Indevus, Theravance, Bard, Lilly, Pfizer, Novartis, BioXell and GlaxoSmithKline. More articles by this author Expand All Advertisement PDF downloadLoading ...
Exploring the primary electron acceptor (QA)‐site of the bacterial reaction center from Rhodobacter sphaeroides (2002)

The functional replacement of the primary ubiquinone (QA) in the photosynthetic reaction center (RC) from Rhodobacter sphaeroides with synthetic vitamin K derivatives has provided a powerful tool to investigate the electron transfer mechanism. To investigate the binding mode of these quinones to the QA binding site we have determined the binding free energy and charge recombination rate from QA(-) to D+ (kAD) of 29 different 1,4-naphthoquinone derivatives with systematically altered structures. The most striking result was that none of the eight tested compounds carrying methyl groups in both positions 5 and 8 of the aromatic ring exhibited functional binding. To understand the binding properties of these quinones on a molecular level, the structures of the reaction center-naphthoquinone complexes were predicted with ligand docking calculations. All protein--ligand structures show hydrogen bonds between the carbonyl oxygens of the quinone and AlaM260 and HisM219 as found for the native ubiquinone-10 in the X-ray structure. The center-to-center distance between the naphthoquinones at QA and the native ubiquinone-10 at QB (the secondary electron acceptor) is essentially the same, compared to the native structure. A detailed analysis of the docking calculations reveals that 5,8-disubstitution prohibits binding due to steric clashes of the 5-methyl group with the backbone atoms of AlaM260 and AlaM249. The experimentally determined binding free energies were reproduced with an rmsd of approximately 4 kJ x mol(-1) in most cases providing a valuable tool for the design of new artificial electron acceptors and inhibitors.
Identification of an Imino Group Indispensable for Cleavage by a Small Ribozyme (2009)

The hairpin ribozyme is a small, noncoding RNA (ncRNA) that catalyzes a site-specific phosphodiester bond cleavage reaction. Prior biochemical and structural analyses pinpointed the amidine moiety of base Ade38 as a key functional group in catalysis, but base changes designed to probe function resulted in localized misfolding of the active site. To define the requirements for chemical activity using a conservative modification, we synthesized and incorporated N1-deazaadenosine into the full-length ribozyme construct. This single-atom variant severely impairs activity, although the active-site fold remains intact in the accompanying crystal structures. The results demonstrate the essentiality of the imino moiety as well as the importance of its interaction with the substrate in the precatalytic and transition-state conformations. This work demonstrates the efficacy of single-atom approaches in the analysis of ncRNA structure-function relationships.
A Low Complexity Moving Average Nested GMP Model for Digital Predistortion of Broadband Power Amplifiers (2022)

In this paper, a low complexity moving average nested generalized memory polynomial model (MAN-GMP) is proposed for digital predistortion (DPD) of broadband power amplifiers (PAs). As the signal bandwidth increases drastically, the strong nonlinear distortions, especially those induced by the memory effect, are generated from the highly efficient PAs. To compensate for the strong memory effect, a moving average nested envelope memory polynomial (MAN-EMP) model is derived from an accuracy-enhanced GMP model, which offers reduced complexity while suffering from degraded modeling accuracy. The MAN-GMP model is further proposed to improve the modeling accuracy by connecting several memory branches of the MAN-EMP model in parallel. An iterative algorithm is designed to extract the model coefficients efficiently through only one or two iterations. Experimental measurements are carried out on two sub-7 GHz broadband GaN Doherty PAs with up to 200 MHz bandwidth OFDM signals to benchmark the proposed MAN-GMP model against the GMP, the parallel-LUT-MP-EMP (PLUME), the augmented complexity-reduced GMP (ACR-GMP), the generalized twin-nonlinear two-box (GTNTB), and the enhanced Wiener models. The experimental results show that the MAN-GMP model can effectively compensate for the nonlinear distortion of broadband PAs with significant complexity reduction.
[P4–225]: HIPPOCAMPAL TEXTURE PREDICTS RATE OF COGNITIVE DECLINE IN MILD COGNITIVE IMPAIRMENT (2017)

Recent advances in Alzheimer disease neuroimaging enable the identification of individuals with underlying hippocampal atrophy, amyloid plaque, and tau burden. However, whether all such individuals will have similar rates of cognitive decline and progress towards clinical dementia is unknown. Novel neuroimaging markers including hippocampal texture could complement current neuroimaging biomarkers and assist in better stratification of individuals most at risk towards cognitive decline. Baseline, one and two-year MRI scans of subjects with healthy Control (HC), MCI and Alzheimer dementia (AD) at baseline from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database were used to compute baseline hippocampal texture and one and two-year hippocampal atrophy rates. We demarcated tertiles of hippocampal texture and characterized the relationship between each tertile and it s corresponding hippocampal atrophy rates over one and two years. Using a multivariate linear model, with positive baseline hippocampal texture value as a fixed factor, we determined the change in clinical dementia rating- sum of boxes (CDR-SB) scores over Year-2 and Year-3 with age, sex, education, APOEε4 gene status and baseline MMSE score as covariates. Hippocampal texture values were highest in AD and lowest in HC. Baseline hippocampal texture negatively correlated with two-year hippocampal atrophy across HC, MCI and AD groups and positively correlated with two and three year CDR-SB change in MCI group alone. Among MCI, the rate of CDR-SB decline at two and three years could be predicted based on positive or negative values of hippocampal texture alone.
State of charge balancing after hot swap for cascaded H-bridge multilevel converters (2017)

In battery supplied multilevel converters it is a common problem to maintain the energy balance between the energy storage placed in different modules. Large unbalance between the state-of-charge (SoC) appears when a damaged battery module is exchanged, and with high probability the newly inserted battery module has different SoC than the other modules. In case the unbalance is large it takes long time to equalize the modules SoC. In this paper a method to minimize the time used for the balancing is proposed. The proposed method is an extension of the nearest level control with sorting and selection based balancing, thus, it can be implemented as an addition to the nearest level control method.
Targeted protein degradation: from small molecules to complex organelles—a Keystone Symposia report (2022)

Targeted protein degradation is critical for proper cellular function and development. Protein degradation pathways, such as the ubiquitin proteasomes system, autophagy, and endosome-lysosome pathway, must be tightly regulated to ensure proper elimination of misfolded and aggregated proteins and regulate changing protein levels during cellular differentiation, while ensuring that normal proteins remain unscathed. Protein degradation pathways have also garnered interest as a means to selectively eliminate target proteins that may be difficult to inhibit via other mechanisms. On June 7 and 8, 2021, several experts in protein degradation pathways met virtually for the Keystone eSymposium "Targeting protein degradation: from small molecules to complex organelles." The event brought together researchers working in different protein degradation pathways in an effort to begin to develop a holistic, integrated vision of protein degradation that incorporates all the major pathways to understand how changes in them can lead to disease pathology and, alternatively, how they can be leveraged for novel therapeutics.
Classification of respiratory signals by linear analysis (2009)

The aim of this study is the classification of wheeze and non-wheeze epochs within respiratory sound signals acquired from patients with asthma and COPD. Since a wheeze signal, having a sinusoidal waveform, has a different behavior in time and frequency domains from that of a non-wheeze signal, the features selected for classification are kurtosis, Renyi entropy, f(50)/ f(90) ratio and mean-crossing irregularity. Upon calculation of these features for each wheeze and non-wheeze portion, the whole data scattered as two classes in four dimensional feature space is projected using Fisher Discriminant Analysis (FDA) onto the single dimensional space that separates the two classes best. Observing that the two classes are visually well separated in this new space, Neyman-Pearson hypothesis testing is applied. Finally, the correct classification rate is %95.1 for the training set, and leave-one-out approach pursuing the above methodology yields a success rate of %93.5 for the test set.
Selective Exploration of Commercial Documents in Web Search (2016)

Implicit user feedback is known to be a strong signal of user preferences in web search. Hence, solving the exploration-exploitation dilemma [5] became an important direction of improvement of ranking algorithms in the last years. In this poster, in the case of commercial queries, we consider a new negative effect of exploration on the user utility -- distracting and confusing users by shifting well-known documents from their common positions -- and propose an approach to take it into account within Multi-Armed Bandit algorithms, usually applied to solve the dilemma.
Gene Copy-Number Variation in Haploid and Diploid Strains of the Yeast Saccharomyces cerevisiae (2013)

The increasing ability to sequence and compare multiple individual genomes within a species has highlighted the fact that copy-number variation (CNV) is a substantial and underappreciated source of genetic diversity. Chromosome-scale mutations occur at rates orders of magnitude higher than base substitutions, yet our understanding of the mechanisms leading to CNVs has been lagging. We examined CNV in a region of chromosome 5 (chr5) in haploid and diploid strains of Saccharomyces cerevisiae. We optimized a CNV detection assay based on a reporter cassette containing the SFA1 and CUP1 genes that confer gene dosage-dependent tolerance to formaldehyde and copper, respectively. This optimized reporter allowed the selection of low-order gene amplification events, going from one copy to two copies in haploids and from two to three copies in diploids. In haploid strains, most events involved tandem segmental duplications mediated by nonallelic homologous recombination between flanking direct repeats, primarily Ty1 elements. In diploids, most events involved the formation of a recurrent nonreciprocal translocation between a chr5 Ty1 element and another Ty1 repeat on chr13. In addition to amplification events, a subset of clones displaying elevated resistance to formaldehyde had point mutations within the SFA1 coding sequence. These mutations were all dominant and are proposed to result in hyperactive forms of the formaldehyde dehydrogenase enzyme.
Caching and multicasting in DBS systems (2003)

The use of Caching and multicasting has been studied extensively in the context of terrestrial networks. However the use of these technologies in a Direct Broadcast Satellite (DBS) system remains unclear. In this paper we discuss possible choices of caching and multicasting schemes, motivated by current applications in the terrestrial Internet, that could be considered for a DBS system. We examine their advantages and disadvantages as well as the tradeoffs involved in combinations of different approaches. We also propose some uses of these technologies and describe an architecture that enhances the performance and efficiency of a DBS system.
Large-area Crystalline Microcolumnar LaBr<inf>3</inf>:Ce for high-resolution gamma ray imaging (2011)

Exploration of a novel and highly time- and cost-efficient approach to produce important lanthanide halide scintillators is being carried out, at RMD. These materials include LaBr <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> :Ce, LaBr <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> :Pr and LaCl <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> :Ce, in large physical sizes and production volumes, in both existing formats and new light-conserving morphologies required for demanding spectroscopic and imaging applications. Synthesis of such structures is accomplished using hot wall evaporation technique, which not only provides us with the control over film stoichiometry required to achieve efficient scintillation, but also permits the control of film morphology to tailor light propagation within the structure. This technique permits fabrication of thick films that can simultaneously provide the high absorption efficiency and high spatial resolution required for small-animal SPECT imaging and other medical and non-medical applications. Here we report on the growth of LaBr <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> :Ce scintillator films in our Crystalline Microcolumnar Structure™ (CMS™) form, which preserves response uniformity over the (often large) area of the film, and transparency throughout its thickness. Specifically, we have repeatedly produced LaBr <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> :Ce films measuring 6 cm in diameter (limited only by the size of the vapor deposition system used in this development) and approaching 2 cm in thickness, with densely packed microcolumns averaging ~25 μm in diameter. These films show bright light emissions comparable to their crystalline counterparts, and energy resolution of ~9% at 122 keV ( <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">57</sup> Co emission). Imaging data acquired using the University of Arizona Bazooka SPECT detector incorporating our CMS LaBr <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> :Ce film demonstrated ~125 μm spatial resolution at 122 keV, which is consistent with the measured intrinsic spatial resolution of 3 line-pair(LP)/mm of the film used, as determined at RMD using X-ray techniques.
Outcomes of Primary Total Knee Arthroplasty in Patients With Hematopoietic Stem Cell Transplantation (2017)

Patients who have undergone hematopoietic stem cell transplantation to treat underlying bone marrow pathology represent a unique and potentially high-risk patient population for total knee arthroplasty (TKA). This study retrospectively reviewed 15 TKA procedures performed on 11 patients with a history of hematopoietic stem cell transplantation. The authors analyzed patient survivorship; clinical outcomes, including complications; and implant survivorship. Mean follow-up was 5 years (range, 2-10 years). Patient survivorship free from mortality was 91% (95% confidence interval, 76%-100%) and 55% (95% confidence interval, 25%-85%) at 2 and 5 years, respectively. Patients who underwent hematopoietic stem cell transplantation for multiple myeloma had a significantly higher 5-year mortality rate (100%) compared with patients who had an underlying diagnosis of non-Hodgkin's lymphoma (0%) (P=.008). Mean Knee Society Score improved to 83 postoperatively (P<.001). Two patients (13%) had postoperative wound healing complications that did not lead to periprosthetic joint infection; however, an additional patient (7%) underwent revision surgery at 5 years for periprosthetic joint infection. Estimated implant survivorship without revision was 80% (95% confidence interval, 60%-100%) at 5 years. Elective primary TKA does not appear to affect survivorship in patients with a history of hematopoietic stem cell transplantation. These patients have modest clinical outcomes, higher complication rates as a result of delayed wound healing, and poorer implant survivorship compared with historical control subjects. [Orthopedics. 2017; 40(5):e774-e778.].
The effect of media background on reading and writing in perpendicular recording (2002)

The effect of stray fields from the recording layer on the reading and writing process has been studied for a perpendicular recording system. The system consists of a single pole writer with a wide return pole, a conventional spin-valve reader and a double layer recording medium. A writer- and reader-induced asymmetry is observed in the recording process for a dc erased background. The asymmetry is interpreted as stray fields of the dc background giving rise to reader saturation and an offset in the current driven inductive write field.
Search for squarks and gluinos in final states with jets and missing transverse momentum using 36  fb−1 of s=13  TeV pp collision data with the ATLAS detector (2018)

Search for squarks and gluinos in final states with jets and missing transverse momentum using 36 fb -1 of ffiffi s p = 13 TeV pp collision data with the ATLAS detector M. Aaboud et al.