gebhart/patrepeval huggingface dataset:
PROSTATE CANCER-SPECIFIC MORTALITY AFTER RADICAL PROSTATECTOMY FOR PATIENTS TREATED IN THE PROSTATE- SPECIFIC ANTIGEN ERA (2008)

You have accessJournal of Urology1 Apr 2008PROSTATE CANCER-SPECIFIC MORTALITY AFTER RADICAL PROSTATECTOMY FOR PATIENTS TREATED IN THE PROSTATE- SPECIFIC ANTIGEN ERA Andrew J Stephenson, Michael W Kattan, James A Eastham, Eric A Klein, Fernando J Bianco, Andrew J Vickers, Ofer Yossepowitch, and Peter T Scardino Andrew J StephensonAndrew J Stephenson , Michael W KattanMichael W Kattan , James A EasthamJames A Eastham , Eric A KleinEric A Klein , Fernando J BiancoFernando J Bianco , Andrew J VickersAndrew J Vickers , Ofer YossepowitchOfer Yossepowitch , and Peter T ScardinoPeter T Scardino View All Author Informationhttps://doi.org/10.1016/S0022-5347(08)61897-2AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "PROSTATE CANCER-SPECIFIC MORTALITY AFTER RADICAL PROSTATECTOMY FOR PATIENTS TREATED IN THE PROSTATE- SPECIFIC ANTIGEN ERA." The Journal of Urology, 179(4S), p. 649 © 2008 by American Urological AssociationFiguresReferencesRelatedDetails Volume 179Issue 4SApril 2008Page: 649 Advertisement Copyright & Permissions© 2008 by American Urological AssociationMetricsAuthor Information Andrew J Stephenson More articles by this author Michael W Kattan More articles by this author James A Eastham More articles by this author Eric A Klein More articles by this author Fernando J Bianco More articles by this author Andrew J Vickers More articles by this author Ofer Yossepowitch More articles by this author Peter T Scardino More articles by this author Expand All Advertisement PDF downloadLoading ...
Low-Complexity Iterative Estimators of Quasi Static Frequency Selective Channels (2007)

This paper proposes iterative estimators of quasi static frequency selective channels. Their properties (in terms of expectation and mean-squared estimation error) as well as complexity are discussed. Their average performance is also analytically approached. For the sake of low complexity, the derived estimators are either linear or affine in the vector of observations at the channel output. Such estimators are referred to as iterative because they use soft information on data symbols fed back by the soft-in/soft-out (SISO) channel decoder of a turbo equalizer. Because involved in this iterative process, they perform better at low signal-to-noise ratios (SNRs) than standard (i.e. non iterative) channel estimators using the same number of pilot symbols. Conversely, iterative estimators require a smaller number of pilot symbols to achieve the same performance as standard estimators.
Structural Investigation of NaCrO2 as a Positive Electrode for Rechargeable Sodium Battery Using Molten NaFSA-KFSA (2012)

Abstract not Available.
Modeling Between-Subject Variability in Subcutaneous Absorption of a Fast-Acting Insulin Analogue by a Nonlinear Mixed Effects Approach (2021)

Despite the great progress made in insulin preparation and titration, many patients with diabetes are still experiencing dangerous fluctuations in their blood glucose levels. This is mainly due to the large between- and within-subject variability, which considerably hampers insulin therapy, leading to defective dosing and timing of the administration process. In this work, we present a nonlinear mixed effects model describing the between-subject variability observed in the subcutaneous absorption of fast-acting insulin. A set of 14 different models was identified on a large and frequently-sampled database of lispro pharmacokinetic data, collected from 116 subjects with type 1 diabetes. The tested models were compared, and the best one was selected on the basis of the ability to fit the data, the precision of the estimated parameters, and parsimony criteria. The selected model was able to accurately describe the typical trend of plasma insulin kinetics, as well as the between-subject variability present in the absorption process, which was found to be related to the subject's body mass index. The model provided a deeper understanding of the insulin absorption process and can be incorporated into simulation platforms to test and develop new open- and closed-loop treatment strategies, allowing a step forward toward personalized insulin therapy.
Virtual execution environment for real-time TDL components (2007)

Existing embedded software development methodologies can hardly cope with platform changes such as CPU upgrades, different RTOS or distributed systems. The timing definition language (TDL) enables the development of deterministic real-time components regardless of the deployment platform. The proposed virtual execution environment enables parallel execution and deterministic run-time composition of real-time TDL components with data dependencies. We focus on embedded code generation and the virtual machine that controls the execution of TDL components and their interaction patterns.
Electrical-Optical High Speed Serial Server Scalability Link (2007)

Increased demand for performance has driven a significant increase in the data rate and the complexity of today's high speed systems and interconnect. While skin effects and dielectric loss are significant sources of limitation of current high-speed digital communication (Broomall and Van Deusen, 1997), equalization at the transmitter, receiver, and interconnect has extended the range and performance of copper links. Electrical copper links are typically used to interconnect multiple processor subsystems to build symmetric multi-processor (SMP) systems, as well as to connect input/output (I/O) subsystems across relative long distances. During the electrical design and validation of a highly scalable, modular SMP server (Brown and Dhawan, 2002) with data rates of 3.2 GT/s (GigaTransfers per second) and higher, a test vehicle was designed and built. The goal was to characterize and contrast an all-copper external cable and a copper-to-optical interconnect technology, and to understand how to achieve the overall system design goals from the perspective of link performance, electrical challenges, and physical design constraints. Key design parameters have been modeled and correlated with laboratory measurements such as AC coupling capacitor selection and layout optimization, via stub, back-drilling, and signal launch effects. Modeling techniques and correlation challenges are discussed in this paper.
Effects of cell size and tissue electrical conductivity on damage of plant tissues by pulsed electric field (2011)

International audience
Role of in-line defect sampling methodology in yield management (2002)

This paper presents a comprehensive methodology for yield management based on in-line defect inspection. Using the data from fabs we demonstrate algorithms for computing the sampling plan in terms of the number of lots and wafers per lot to sample at different process steps. In making those computations we take into account in-line defect based yield estimation techniques and simulation based sensitivity selection. The in-line defect data presented in this paper are obtained using KLA 21XX wafer inspection systems from fabs across the world.
A Scalable Model Specialization Framework for Training and Inference using Submodels and its Application to Speech Model Personalization (2022)

Model fine-tuning and adaptation have become a common approach for model specialization for downstream tasks or domains. Fine-tuning the entire model or a subset of the parameters using light-weight adaptation has shown considerable success across different specialization tasks. Fine-tuning a model for a large number of domains typically requires starting a new training job for every domain posing scaling limitations. Once these models are trained, deploying them also poses significant scalability challenges for inference for real-time applications. In this paper, building upon prior light-weight adaptation techniques, we propose a modular framework that enables us to substantially improve scalability for model training and inference. We introduce Submodels that can be quickly and dynamically loaded for on-the-fly inference. We also propose multiple approaches for training those Submodels in parallel using an embedding space in the same training job. We test our framework on an extreme use-case which is speech model personalization for atypical speech, requiring a Submodel for each user. We obtain 128x Submodel throughput with a fixed computation budget without a loss of accuracy. We also show that learning a speaker-embedding space can scale further and reduce the amount of personalization training data required per speaker.
Spectral and structural comparison between bright and dim green fluorescent proteins in Amphioxus (2014)

The cephalochordate Amphioxus naturally co-expresses fluorescent proteins (FPs) with different brightness, which thus offers the rare opportunity to identify FP molecular feature/s that are associated with greater/lower intensity of fluorescence. Here, we describe the spectral and structural characteristics of green FP (bfloGFPa1) with perfect (100%) quantum efficiency yielding to unprecedentedly-high brightness, and compare them to those of co-expressed bfloGFPc1 showing extremely-dim brightness due to low (0.1%) quantum efficiency. This direct comparison of structure-function relationship indicated that in the bright bfloGFPa1, a Tyrosine (Tyr159) promotes a ring flipping of a Tryptophan (Trp157) that in turn allows a cis-trans transformation of a Proline (Pro55). Consequently, the FP chromophore is pushed up, which comes with a slight tilt and increased stability. FPs are continuously engineered for improved biochemical and/or photonic properties, and this study provides new insight to the challenge of establishing a clear mechanistic understanding between chromophore structural environment and brightness level.
Optimal Rate and Beam-Width Control in Wireless Ad-Hoc Networks with Directional Antennas (2007)

In this paper we study optimal transmission strategies in wireless ad-hoc networks using directional antennas. Each node is capable of adjusting its transmission rate as well as its transmission and reception beam-widths. We explore the different tradeoffs involved in optimizing the performance. Specifically we look at the problem of optimally allocating the transmission rate given specific transmission and reception beam-widths. We then use those results to find the optimum beam-widths for maximizing the average throughput-distance. We illustrate this two stage optimization algorithm by numerical examples. We show that even when the transmission rate is chosen optimally, a bad choice of beam-width can degrade the performance by over 50%.
Chiral Indenes and Group‐4 Metallocene Dichlorides Containing α‐ and β‐Pinenyl‐Derived Ligand Substituents: Synthesis and Catalytic Applications in Polymerization and Carboalumination Reactions (2005)

Abstract The synthesis and characterization of chiral bis(indenyl)zirconium dichlorides containing β‐pinenyl‐derived ligand substituents is reported. Unbridged metallocene complexeshaving the {[(1 S ,2 S ,5 S )‐6,6‐dimethylbicyclo[3.1.1]hept‐2‐yl]methyl}dimethylsilyl substituent in both 1‐ and 2‐positions of the indenyl moiety were prepared and isolated in moderate to low yields by reaction of the corresponding indenyllithium salts with ZrCl 4 followed by work‐up and crystallization procedures. The corresponding tetrahydroindenyl complexes were obtained in excellent yields by catalytic hydrogenation of the indenyl six‐membered rings. In a complementary approach, a synthetic route to α‐pinenyl‐substituted indenyl ligand analogues was briefly evaluated, which however, suffered from low yields. Selected β‐pinenyl‐substituted indenyl complexes were scanned as catalysts for the dehydropolymerization of phenylsilane upon activation with n BuLi, for polymerization of ethylene and propylene upon activation with methylaluminoxane (MAO) as well as for enantioselective carboalumination of 1‐octene with triethyl‐ and trimethylaluminum. The bis(indenyl) complexes catalyzed the carboalumination reaction, albeit only low yields (8–16 %) and low enantioselectivities ( ee = 0.5–10 %) were obtained. The 2‐substituted bis(indenyl)zirconocene/MAO catalyst system produced atactic low‐molecular weight polypropylene with low polymerization activity whereas both 1‐ and 2‐substituted complexes showed high activities in ethylene polymerization producing polyethylenes with high molecular weights ( M w &gt; 440000). (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2005)
Influence of Ageing on Sealability of Elastomeric O‐Rings (2017)

Summary At BAM, which is the federal institute for materials research and testing in Germany, it is one of our tasks to evaluate the safety of casks designed for transport and/or storage of radioactive material. This includes the assessment of the service lifetime of elastomeric seals that are part of the container lid system with regard to the requirements for long‐term safety (40 years and more) of the containers. Therefore, we started an accelerated ageing programme with selected rubbers often used for seals (HNBR, EPDM and FKM) which are aged at four different temperatures (75 °C, 100 °C, 125 °C and 150 °C) up to 1.5 years. In order to assess sealability, O‐rings are aged in compression by 25% (corresponding to the compression during service) between plates as well as in flanges that allow leakage rate measurements. For comparison, uncompressed O‐rings are aged as well. Further methods characterising seal performance are compression stress relaxation (CSR) reflecting the loss of sealing force of a compressed seal over time, and compression set (CS) which represents the recovery behaviour of a seal after release from compression. Additionally, hardness is measured for information about the change of mechanical properties. The experimental results indicate that while hardness, CSR and CS show considerable degradation effects, the leakage rate stays relatively constant or even decreases until shrinkage combined with the loss of resilience of the aged seal leads to leakage. This demonstrates that static leakage rate, which is the only available direct seal performance criterion, has only limited sensitivity towards the degradation of the seal material. CS data is extrapolated using time‐temperature shifts and Arrhenius graphs. An exemplary CS of 50% would be reached after approx. 1.2, 17 and 29 years at 60 °C for HNBR, EPDM and FKM respectively.
5212Impaired function of brown adipose tissue is involved in the pathologies of pressure overload-induced heart failure (2018)

The basic science of diabetes and the metabolic syndrome 1077 tracking echocardiography in diabetic and control mice of both strains (6 mice per group). Then, the animals were euthanized and LV specimens were collected to determine cardiac miRNA expression by RT-quantitative PCR-based profiling approach (Exiqon miRCURY LNA Universal RT-qPCR Array Panel I+II). Results: A dysregulation of 140 miRNAs was observed in the WT diabetic hearts as compared to control mice. 57 of them were upregulated and 83 downregulated by more than 2.0-fold (p<0.05). Ingenuity Pathway Analysis revealed that dysregulated miRNAs were implicated in myocardial signalling networks triggering cell death, hypertrophy as well as metabolic and inflammatory responses. Interestingly enough, JunD was identified as a significant upstream regulator of these miRNA changes (p<0.001). Moreover, LV function was preserved in JunDTg as compared to WT mice. Accordingly, in diabetic JunDTg mice the dysregulation of 33 miRNAs involved in apoptosis (miR-1a, miR-138, miR-675), fibrosis (miR-30a, miR-126a, miR-138, miR-192, miR-196a), hypertrophy (miR-1a), inflammation (miR-30a, miR-126a, miR-135a, miR-138, miR-140, miR-675) and oxidative stress (miR-146b, miR-148a) did not take place. Conclusions: Our study shows for the first time that AP-1 transcription factor JunD contributes to protect against diabetes-induced myocardial dysfunction by preserving the miRNA landscape.
From Amherst (Massachusetts, USA) to Padua (Italy) and back again: Louis A. Carpino's scientifically productive journey (2020)

Abstract In this work, we studied and discussed a relevant aspect of peptide science, strictly related to the scientific production of Prof. Louis A. Carpino who passed away in early 2019. Specifically, we carried out a statistical survey on the significant 3D‐structural parameters (bond lengths, bond angles, and torsion angles) of the currently extensively used 9‐fluorenylmethyloxycarbonyl (Fmoc) α‐amino protecting group introduced by Carpino in peptide synthesis. In this compilation, we considered all 131 X‐ray diffraction structures available in the literature on amino acid / linear peptide derivatives and Fmoc‐labeled amines. Both Fmoc secondary and tertiary urethane functionalities were examined and separately analyzed.
Host Immune Defense Peptide LL-37 Activates Caspase-Independent Apoptosis and Suppresses Colon Cancer (2012)

Cathelicidins are a family of bacteriocidal polypeptides secreted by macrophages and polymorphonuclear leukocytes (PMN). LL-37, the only human cathelicidin, has been implicated in tumorigenesis, but there has been limited investigation of its expression and function in cancer. Here, we report that LL-37 activates a p53-mediated, caspase-independent apoptotic cascade that contributes to suppression of colon cancer. LL-37 was expressed strongly in normal colon mucosa but downregulated in colon cancer tissues, where in both settings its expression correlated with terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling-positive apoptotic cells. Exposure of colon cancer cells to LL-37 induced phosphatidylserine externalization and DNA fragmentation in a manner independent of caspase activation. Apoptogenic function was mediated by nuclear translocation of the proapoptotic factors, apoptosis-inducing factor (AIF) and endonuclease G (EndoG), through p53-dependent upregulation of Bax and Bak and downregulation of Bcl-2 via a pertussis toxin-sensitive G-protein-coupled receptor (GPCR) pathway. Correspondingly, colonic mucosa of cathelicidin-deficient mice exhibited reduced expression of p53, Bax, and Bak and increased expression of Bcl-2 together with a lower basal level of apoptosis. Cathelicidin-deficient mice exhibited an increased susceptibility to azoxymethane-induced colon tumorigenesis, establishing pathophysiologic relevance in colon cancer. Collectively, our findings show that LL-37 activates a GPCR-p53-Bax/Bak/Bcl-2 signaling cascade that triggers AIF/EndoG-mediated apoptosis in colon cancer cells.
Neutralization of Omicron BA.1, BA.2, and BA.3 SARS-CoV-2 by 3 doses of BNT162b2 vaccine (2022)

Abstract The newly emerged Omicron SARS-CoV-2 has 3 distinct sublineages: BA.1, BA.2, and BA.3. BA.1 accounts for the initial surge and is being replaced by BA.2, whereas BA.3 is at a low prevalence at this time. Here we report the neutralization of BNT162b2-vaccinated sera (collected at 1 month after dose 3) against the three Omicron sublineages. To facilitate the neutralization testing, we engineered the complete BA.1, BA.2, or BA.3 spike into an mNeonGreen USA-WA1/2020 SRAS-CoV-2. All BNT162b2-vaccinated sera neutralized USA-WA1/2020, BA.1-, BA.2-, and BA.3-spike SARS-CoV-2s with titers of &gt;20; the neutralization geometric mean titers (GMTs) against the four viruses were 1211, 336, 300, and 190, respectively. Thus, the BA.1-, BA.2-, and BA.3-spike SARS-CoV-2s were 3.6-, 4.0-, and 6.4-fold less efficiently neutralized than the USA-WA1/2020, respectively. Our data have implications in vaccine strategy and understanding the biology of Omicron sublineages.
Semiconductor quantum dot lasers epitaxially grown on silicon with low linewidth enhancement factor (2018)

This work reports on the ultra-low linewidth enhancement factor (αH-factor) of semiconductor quantum dot lasers epitaxially grown on silicon. Owing to the low density of threading dislocations and resultant high gain, an αH value of 0.13 that is rather independent of the temperature range (288 K–308 K) is measured. Above the laser threshold, the linewidth enhancement factor does not increase extensively with the bias current which is very promising for the realization of future integrated circuits including high performance laser sources.
Applications of fast fourier transform (FFT) in noninvasive physiological measurements in sport science. (1988)

Applications of fast fourier transform (FFT) in noninvasive physiological measurements in sport science.
Abstract B039: BIO-PROTAC: Application of cell penetrating scFv to treat undruggable KRAS mutant cancer (2023)

Abstract Activation of mutations in RAS has been found in high ratio in human cancers, inducing downstream critical effectors corresponding tumorigenesis. In recent years, RAS-RAF-ERK1/2 pathway is known as a crucial target for the anti-cancer drug development because of high prevalence of ERK activation in human cancers. The attempts in direct targeting to activated RAS, which is GTP bound, has been somewhat successful in the treatment of certain type of cancer, however, still beset by the resistance. Our aim is to develop inhibitor that cell-penetrating scFv (single-chain variable fragment) which targets mutated KRAS (mKBscFv; mutated KRAS binding scFv). The Fv fragment is the smallest unit composed of the variable region of heavy chain and light chain in an immunoglobulin molecule, that has a function of antigen-binding activity. The scFv can specifically bind to an antigen, thereby reducing side effects of non-specific binding seen in chemical drugs. However, due to the lack of cell penetrating ability of scFv, a delivery carrier is often required. In this study, the mKBscFv was measured binding affinity toward wild type KRAS and mutated KRAS using surface plasmon resonance (SPR). The scFv has higher affinity to mutated KRAS than wild type KRAS. A cell-penetrating peptide (CPP) was developed for drug delivery and was expressed at the C-terminus of mKBscFv for transferring cells. The mKBscFv-CPP was tagged with His tag to express in CHO cells, which was purified by FPLC. The purity of mKBscFv-CPP was confirmed by SDS PAGE and immunoblotting. The mKBscFv-CPP treated KRAS mutated cancer cells decreased cell viability in a concentration-dependent manner, and decreased expression of mutated GTP-bound KRAS. In addition to the bioactivity of the mKBscFv, it has further advantage as a proteolysis-targeting chimera (PROTAC). The plasmid DNA was prepared by adding a VHL-expressing sequence to the C-terminus of mKBscFv (mKBscFv-Vh). This gene was transfected into KRAS mutated cancer cells to express the protein, and as a result mutated GTP-bound KRAS was reduced. A CPP peptide domain was added to the C-terminus of this gene to express it as a protein in CHO cells. The mutated GTP-bound KRAS was reduced by mKBscFv-Vh-CPP in KRAS mutated cacner cells. Taken together, mKBscFv that binds to mutated KRAS was developed, and it can be expected to become a new protein anticancer drug effective against mutated KRAS-mediated cancer cells by fusing cell penetrating peptide and PROTAC technology. Citation Format: Gookjin Yoon, Beom Soo Jo, Dong Woo Lee, Jinwook Yang, Min-Ho Park, Sanghui Seok, Jue Yeon Lee, Chong Pyoung Chung, Yoon Shin Park, Yoon Jeong Park. BIO-PROTAC: Application of cell penetrating scFv to treat undruggable KRAS mutant cancer [abstract]. In: Proceedings of the AACR Special Conference: Targeting RAS; 2023 Mar 5-8; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Res 2023;21(5_Suppl):Abstract nr B039.