gebhart/patrepeval huggingface dataset:
Divergent evolution of arrested development in the dauer stage of Caenorhabditis elegans and the infective stage of Heterodera glycines (2007)

Our results indicate that hallmark gene expression patterns and metabolism features are not shared in the developmentally arrested life stages of C. elegans and H. glycines, suggesting that developmental arrest in these two nematode species has undergone more divergent evolution than previously thought and pointing to the need for detailed genomic analyses of individual parasite species.
Designing Biomimetic, Dissipative Material Systems (2016)

Throughout human history, new materials have been the foundation of transformative technologies: from bronze, paper, and ceramics to steel, silicon, and polymers, each material has enabled far-reaching advances. Today, another new class of materials is emerging—one with both the potential to provide radically new functions and to challenge our notion of what constitutes a “material”. These materials would harvest, transduce, or dissipate energy to perform autonomous, dynamic functions that mimic the behaviors of living organisms. Herein, we discuss the challenges and benefits of creating “dissipative” materials that can potentially blur the boundaries between living and non-living matter.
Identification of surface acoustic impedances in a reverberant room using the FDTD method (2014)

In numerical room acoustic simulations the acoustic impedance of walls and boundaries is of fundamental importance for the correct physical and perceptual synthesis of a sound field. Acoustic impedances are usually measured in reverberation chambers as absorption coefficients. In this type of measurements the sound field is assumed to be diffuse, which is an ideal condition usually not met in real rooms. This paper proposes a different approach to obtain the acoustic impedances, where a numerical model of the room is tuned with measurements using nonlinear optimization. The finite difference time domain (FDTD) method is used to simulate a sound field of a room and an optimization problem is solved to recover the acoustic impedances per frequency octave band. Results show that the use of a time-domain numerical method is advantageous as compared to a frequency-domain method, by making the measurement set-up more practical and improving the optimization convergence.
Stereoelectronic Effects Impact Glycan Recognition (2020)

Recognition of distinct glycans is central to biology, and lectins mediate this function. Lectin glycan preferences are usually centered on specific monosaccharides. In contrast, human intelectin-1 (hItln-1, also known as Omentin-1) is a soluble lectin that binds a range of microbial sugars, including β-Dgalactofuranose (β-Galf), D-glycerol 1-phosphate, D-glycero-D-talo-oct-2-ulosonic acid (KO), and 3- deoxy-D-manno-oct-2-ulosonic acid (KDO). Though these saccharides differ dramatically in structure, they share a common feature—an exocyclic vicinal diol. How and whether such a small fragment is sufficient for recognition was unclear. We tested several glycans with this epitope and found that L-glycero-α-Dmanno- heptose and D-glycero-α-D-manno-heptose possess the critical diol motif yet bind weakly. To better understand hItln-1 recognition, we determined the structure of the hItln-1·KO complex using X-ray crystallography, and our 1.59-Å resolution structure enabled unambiguous assignment of the bound KO conformation. This carbohydrate conformation was present in &gt;97% of the KDO/KO structures in the Protein Data Bank. Bioinformatic analysis revealed that KO and KDO adopt a common conformation, while heptoses prefer different conformers. The preferred conformers of KO and KDO favor hItln-1 engagement, but those of the heptoses do not. Natural bond orbital (NBO) calculations suggest these observed conformations, including the side chain orientations, are stabilized by not only steric but also stereoelectronic effects. Thus, our data highlight a role for stereoelectronic effects in dictating the specificity of glycan recognition by proteins. Finally, our finding that hItln-1 avoids binding prevalent glycans with a terminal 1,2 diol (e.g., NeuAc, and L-glycero-α-D-manno-heptose) suggests the lectin has evolved to recognize distinct bacterial species.
Bates, Wiltzius, and Fredrickson reply (1994)

Received 10 September 1993DOI:https://doi.org/10.1103/PhysRevLett.72.2305©1994 American Physical Society
Electrical transport in n-type 4H silicon carbide (2001)

Free electron density and low field electron mobility of 4H–SiC in the temperature range of 35–900 K are examined experimentally and theoretically. Five samples produced by cold-wall atmospheric pressure chemical vapor deposition and doped with nitrogen from 3.5×1015 cm−3 to 7.5×1017 cm−3 are investigated using the electric conductivity and Hall measurements. A complete description of the electron density and mobility is presented taking into account inequivalent positions of cubic and hexagonal donor sites as well as valley-orbit splittings of the donor levels. A good agreement between experiment and theory is achieved for all samples and it is demonstrated that the scattering of electrons by neutral donors is a dominant mode in 4H–SiC at low temperatures. The deformation potential for the intravalley scattering by acoustic phonons and coupling constants for the intervalley scattering by acoustic and optic phonons are determined. The dependence of electron mobility on doping at constant temperatures 77 K, 292 K, and 600 K is experimentally established and successfully described. Parallel conductivity at low temperatures by an impurity band in the sample with 7.5×1017 cm−3 donors is evidenced.
A rehabilitation tool for functional balance using altered gravity and virtual reality (2007)

Upright balance function can be improved following balance specific training performed in a supine position in an environment providing the perception of an upright position with respect to gravity. Future studies will implement this concept in patients.
Experimental chaos : 7th Experimental Chaos Conference, San Diego, California 26-29 August 2002 (2003)

Electronics, optics, and fluids have been strong fields for the application of nonlineardynamics. The trend over the years has been the growth of biophysics (especially neuroscience and cardiac dynamics), oceanography, and geophysics for the employment of the concepts and techniques of nonlinear dynamics. Topics include: electronics; optics; geophysics, oceanography, and meterology; hydrodynamics, turbulence, and plasmas; biophysics; neurophysiology; chemical chaos; interdisciplinary; as well as data analysis.
Multi-omics analysis of serial samples from metastatic TNBC patients on PARP inhibitor monotherapy provide insight into rational PARP inhibitor therapy combinations (2020)

Abstract Due to complexity of advanced epithelial cancers, it is necessary to implement patient specific combination therapies if we are to markedly improve patient outcomes. However, our ability to select and implement patient specific combination therapies based on dynamic molecular changes in the tumor and tumor ecosystem in response to therapy remains extremely limited. In a pilot study, we evaluated the feasibility of real-time deep analysis of serial tumor samples from triple negative breast cancer patients to identify mechanisms of resistance and treatment opportunities as they emerge under therapeutic stress engendered by poly-ADP-ribose polymerase (PARP) inhibitors (PARPi). Although PARP inhibition was consistently observed in all patients, deep molecular analysis of the tumor and its ecosystem revealed insights into potentially effective therapeutic PARPi combinations. In a BRCA-mutant basal breast cancer exceptional long-term survivor, we noted striking PARPi-induced tumor destruction accompanied by a marked infiltration of immune cells containing CD8 effector cells, consistent with pre-clinical evidence for association between STING mediated immune activation and benefit from PARPi and immunotherapy. Tumor cells in the exceptional responder underwent extensive protein network rewiring in response to PARP inhibition. In contrast, there were minimal changes in the ecosystem of a luminal androgen receptor (LAR) rapid progressor in response to PARPi likely due to indifference to the effects of PARP inhibition. In this rapid progressor, there was minimal evidence of immune activation or protein network rewiring in response to PARPi, despite PARP being inhibited, and no clinical benefit was noted for this participant. Together, deep real-time analysis of longitudinal biopsies identified a suite of PARPi-induced emergent changes including immune activation, DNA damage checkpoint activation, apoptosis and signaling pathways including RTK, PI3K-AKT and RAS-MAPK, that could be used to select patient specific combination therapies, based on tumor and immune state changes that are likely to benefit specific patients. Highlights Longitudinal analysis of serial tumor samples in real-time identifies adaptive mechanisms of resistance to PARPi therapies. Deep molecular analysis of the tumor reveals insights into potentially effective therapeutic PARPi combinations. Extensive protein network rewiring, microenvironment and immune state changes are assessable factors for patient specific combination therapies.
Optical Decoupling in a Loss-Modulated Dual-Cavity VCSEL (2007)

We have demonstrated the principle of optical decoupling in a loss-modulated VCSEL by use of a dual-cavity geometry. Adjusting detuning between cavities controls the decoupling amount. Flat (+/-3db) response up to 20 GHz is demonstrated.
A novel method for determining and improving the quality of a quadrupolar fiber gyro coil under temperature variations (2013)

We introduce a parameter called pointing error thermal sensitivity (PETS) for quantitatively determining the quality of a quadrupolar (QAD) fiber coil under radial temperature variations. We show both analytically and experimentally that the pointing error of a fiber gyro incorporating the fiber coil is linearly proportional to the final radial thermal gradient on the coil, with PETS as the proportional constant. We further show that PETS is linearly proportional to another parameter called effective asymmetric length of the coil. By thermally inducing different radial thermal gradients on the fiber coil and measuring the corresponding pointing errors in a gyroscopic measurement setup, we can confidently determine the PETS of the fiber coil and its associated effective asymmetric length caused by imperfections in coil winding. Consequently, we are able to precisely trim the coil to achieve best thermal performance.
Diastereoselective Synthesis of the Potent Antiviral Agent (-)-2'-Deoxy-3'-thiacytidine and Its Enantiomer (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDiastereoselective Synthesis of the Potent Antiviral Agent (-)-2'-Deoxy-3'-thiacytidine and Its EnantiomerHaolun Jin, M. Arshad Siddiqui, Colleen A. Evans, H. L. Allan Tse, Tarek S. Mansour, Michael D. Goodyear, Paul Ravenscroft, and Christopher D. BeelsCite this: J. Org. Chem. 1995, 60, 8, 2621–2623Publication Date (Print):April 1, 1995Publication History Published online1 May 2002Published inissue 1 April 1995https://pubs.acs.org/doi/10.1021/jo00113a050https://doi.org/10.1021/jo00113a050research-articleACS PublicationsRequest reuse permissionsArticle Views1001Altmetric-Citations48LEARN 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
Control-Oriented Physics-Based NOX Emission Model for a Diesel Engine With Exhaust Gas Recirculation (2020)

Abstract Stringent NOX emission norm for heavy duty vehicles motivates the use of predictive models to reduce emissions of diesel engines by coordinating engine parameters and aftertreatment. In this paper, a physics-based control-oriented NOX model is presented to estimate the feedgas NOX for a diesel engine. This cycle-averaged NOX model is able to capture the impact of all major diesel engine control variables including the fuel injection timing, injection pressure, and injection rate, as well as the effect of cylinder charge dilution and intake pressure on the emissions. The impact of the cylinder charge dilution controlled by the engine exhaust gas recirculation (EGR) in the highly diluted diesel engine of this work is modeled using an adiabatic flame temperature predictor. The model structure is developed such that it can be embedded in an engine control unit without any need for an in-cylinder pressure sensor. In addition, details of this physics-based NOX model are presented along with a step-by-step model parameter identification procedure and experimental validation at both steady-state and transient conditions. Over a complete federal test procedure (FTP) cycle, on a cumulative basis the model prediction was more than 93% accurate.
Generation of Ball Possession Statistics in Soccer Using Minimum-Cost Flow Network (2019)

We present an automatic technique for calculating ball possession statistics from the video of a soccer match. The possession statistics is generated based on the number of valid passes made by an individual team. A valid pass is detected as a split or merge event of the ball with a player. A pass starts when the ball splits from a player. A pass ends when the ball merges with a player. We use a minimum-cost flow network to model number of valid passes in the soccer match. The ball and the players represent the nodes of the network. Each edge of the network is associated with a cost derived from the between-frame correspondences of the ball and the players. The total flow through the network is optimized to track the number of valid passes. Experimental results show that the accuracy of the proposed method is at least 4% better than that of a similar approach.
Naturally circulating dendritic cells to vaccinate cancer patients (2013)

Dendritic cell-based immunotherapy is a promising strategy against cancer that appears to be feasible, safe and to induce potent tumor-specific immune responses. The use of naturally circulating dendritic cells (DCs), rather than cultured monocyte-derived DCs, might constitute the next logical step to translate anticancer immune responses into long-lasting clinical benefits.
Preparation of triazamacrocycles containing only secondary amine functions using both tosyl and boc protecting groups (1996)

Abstract 1,8,15‐Triazacycloheneicosane ( 1 ); 1,9,17‐triazacyclotetracosane ( 2 ) and 1,10,19‐triazacycloheptacosane ( 3 ) were prepared by treating the appropriate N,N ‐bis(ω‐bromoalkyl)toluenesulfonamide 8–10 with the appropriate N,N ′‐ditosyl‐α,ω‐diaminoalkane 11–13 in dimethylformamide using sodium hydride as the base followed by phenol and 33% hydrobromic acid in acetic acid to remove the tosyl protecting groups. 2‐Allyloxymethyl‐4,11,18‐ triazaoxacycloheneicosane ( 4 ) was prepared in two ways. First, N,N′,N″‐ tritosylbis(hexamemylene)triamine ( 18 ) was treated with 2‐allyloxymethyl‐3‐oxa‐1,6‐hexanediol ditosylate ( 23 ) and cesium carbonate in dimethylformamide followed by sodium amalgam to remove the tosyl protecting groups. The second preparation of 4 was done by treating the tri‐BOC analog of 18 with 23 followed by hydrochloric acid in isopropyl alcohol to remove the BOC protecting groups. The overall yields of 4 using these two processes were very close.
Redundancy and ECC mechanisms to improve energy efficiency of on-die interconnects (2012)

We present a detailed analysis of the bandwidth requirements in a network-on-chip at high and low voltages. We propose mechanisms to maintain the functionality of a system-on-chip despite the presence of failures in the network-on-chip used to connect its components. Our mechanisms alleviate failures in the links and/or the connected buffers, and allow voltage scaling for the network. Our best mechanism allows reliable network operation well below 500 mV while reducing power by more than a factor of 5 and energy by 28% compared to a baseline without fault-tolerance mechanisms.
1065: Quality of Life among Men with Localized Prostate Cancer: A Two-Year Longitudinal Assessment (2004)

You have accessJournal of UrologyDiscussed Poster, Monday, May 10, 2004, 1:00 - 5:00 pm1 Apr 20041065: Quality of Life among Men with Localized Prostate Cancer: A Two-Year Longitudinal Assessment Michael A. Diefenbach, Robert G. Uzzo, Eric Horwitz, Richard E. Greenberg, Alan Pollack, Susan Raysor, and Jenevie Dorsey Michael A. DiefenbachMichael A. Diefenbach More articles by this author , Robert G. UzzoRobert G. Uzzo More articles by this author , Eric HorwitzEric Horwitz More articles by this author , Richard E. GreenbergRichard E. Greenberg More articles by this author , Alan PollackAlan Pollack More articles by this author , Susan RaysorSusan Raysor More articles by this author , and Jenevie DorseyJenevie Dorsey More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(18)38302-2AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "1065: Quality of Life among Men with Localized Prostate Cancer: A Two-Year Longitudinal Assessment." The Journal of Urology, 171(4S), p. 281 © 2016 by American Urological AssociationFiguresReferencesRelatedDetails Volume 171Issue 4SApril 2004Page: 281 Advertisement Copyright & Permissions© 2016 by American Urological AssociationMetricsAuthor Information Michael A. Diefenbach More articles by this author Robert G. Uzzo More articles by this author Eric Horwitz More articles by this author Richard E. Greenberg More articles by this author Alan Pollack More articles by this author Susan Raysor More articles by this author Jenevie Dorsey More articles by this author Expand All Advertisement Loading ...
Comparative phenotype and BTNL2 polymorphism in familial and sporadic sarcoidosis in the French SARCFAM cohort (2014)

Familial clustering and epidemiologic studies suggest a genetic susceptibility to sarcoidosis that may be associated with a difference in phenotype. The objective of the study was to compare the phenotype and the polymorphisms of the BTNL2 gene in familial and sporadic sarcoidosis. The cohort included 485 patients with histologically proved sarcoidosis (274 women, 211 men), with 267 sporadic cases (SC), and 218 familial cases (FC) from 142 families with at least two first-degree relatives with documented sarcoidosis. The clinical phenotype was studied retrospectively, and the polymorphisms of the BTNL2 gene were analysed. The sex ratio and ethnicity (77% Caucasian, 20% African/Caribbean and 3% from Asia) did not differ between FC and SC. The mean age at diagnosis was 38+1.9 yr in FC and 43+1.9 in SC (p=0.001). At the date of diagnosis the number of affected organs was significantly greater in FC than in SC (OR=1.29, p=0.01). The mean clinical severity score (range, 0-106) based on the number of affected organs and the clinical/biological manifestations was 17.2 at baseline, with no difference between FC and SC. Löfgren syndrome was present in 57 patients. Radiological stages were I (41%), II (41%), III (12.33%) and IV (5.4%), respectively. A total of 333 patients were treated, with no difference between groups. The frequency of the rs 2076530 polymorphism in BTNL2 was similar in FC and SC. In conclusion, familial sarcoidosis differs from sporadic disease only by earlier onset and higher number of affected organs. SARCFAM is an interesting tool for a study on natural history and the identification of new genetic loci in this disease.
A DNA Aptamer That Inhibits the Aberrant Signaling of Fibroblast Growth Factor Receptor in Cancer Cells (2021)

Growth factor receptors are activated through dimerization by the binding of their ligands and play pivotal roles in normal cell function. However, the aberrant activity of the receptors has been associated with cancer malignancy. One of the main causes of the aberrant receptor activation is the overexpression of receptors and the resultant formation of unliganded receptor dimers, which can be activated in the absence of external ligand molecules. Thus, the unliganded receptor dimer is a promising target to inhibit aberrant signaling in cancer. Here, we report an aptamer that specifically binds to fibroblast growth factor receptor 2b and inhibits the aberrant receptor activation and signaling. Our investigation suggests that this aptamer inhibits the formation of the receptor dimer occurring in the absence of external ligand molecules. This work presents a new inhibitory function of aptamers and the possibility of oligonucleotide-based therapeutics for cancer.
Deep-recessed GaN HEMTs using selective etch technology exhibiting high microwave performance without surface passivation (2007)

A selective dry etch technology of GaN over AlGaN using BCl <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> /SF <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sub> has been applied to passivation-free deep-recessed GaN HEMTs, significantly reducing the effects of growth and process variations on the device performance, improving reproducibility and manufacturability. The effects of Si delta-doping density on the gate leakage, breakdown voltage and dispersion were investigated. Excellent microwave power performances were achieved without SiN <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> passivation. 6 W/mm with PAE of 72% at V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</sub> = 30 V and 11.6 W/mm with PAE of 63% at V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</sub> =50 V were demonstrated at 4 GHz, while 5 W/mm with PAE of 63% at V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</sub> = 28 V and 10.5 W/mm with PAE of 53% at V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</sub> =48 V were obtained at 10 GHz.