gebhart/patrepeval huggingface dataset:
Effect of chemical modification of recombinant human acetylcholinesterase by polyethylene glycol on its circulatory longevity (2001)

Post-translational modifications were recently shown to be responsible for the short circulatory mean residence time (MRT) of recombinant human acetylcholinesterase (rHuAChE) [Kronman, Velan, Marcus, Ordentlich, Reuveny and Shafferman (1995) Biochem. J. 311, 959–967; Chitlaru, Kronman, Zeevi, Kam, Harel, Ordentlich, Velan and Shafferman (1998) Biochem. J. 336, 647–658; Chitlaru, Kronman, Velan and Shafferman (2001) Biochem. J. 354, 613–625], which is one of the major obstacles to the fulfilment of its therapeutic potential as a bioscavenger. In the present study we demonstrate that the MRT of rHuAChE can be significantly increased by the controlled attachment of polyethylene glycol (PEG) side chains to lysine residues. Attachment of as many as four PEG molecules to monomeric rHuAChE had minimal effects, if any, on either the catalytic activity (Km = 0.09mM and kcat = 3.9×105min−1) or the reactivity of the modified enzyme towards active-centre inhibitors, such as edrophonium and di-isopropyl fluorophosphate, or to peripheral-site ligands, such as propidium, BW284C51 and even the bulky snake-venom toxin fasciculin-II. The increase in MRT of the PEG-modified monomeric enzyme is linearly dependent, in the tested range, on the number of attached PEG molecules, as well as on their size. It appears that even low level PEG-conjugation can overcome the deleterious effect of under-sialylation on the pharmacokinetic performance of rHuAChE. At the highest tested ratio of attached PEG-20000/rHuAChE (4:1), an MRT of over 2100min was attained, a value unmatched by any other known form of recombinant or native serum-derived AChE reported to date.
Controller design and optimal tuning of a wafer handling robot (2015)

Frog-leg robots have been widely used for handling silicon wafers inside the vacuum environment of semiconductor manufacturing machines. In order to enhance stiffness, frog-leg robots adopt a parallel structure. A main challenge of controlling wafer handling robot is avoiding vibration, which is the major cause of wafer sliding and particle contamination. This paper presents two control approaches to improve the performance of frog-leg robots. First, in addition to the basic tri-loop PID feedback controller, torque offset is injected to the input of the robot to compensate the robot's nonlinear dynamics. This reduces the following error and major vibration. The torque offset is calculated based on identified robot dynamics. Second, a test based optimization method is developed to tune the gains of the feedback controller. Wafer vibration is measured and analyzed to score the system performance. Comparison results show that the proposed control scheme gives much improved performance.
Decreased miR-199 augments visceral pain in patients with IBS through translational upregulation of TRPV1 (2015)

Decreased colonic miR-199a/b correlates with visceral pain in patients with IBS-D. Similarly, reduced miR-199a expression in rat DRG and colon tissue is associated with heightened visceral hypersensitivity. In vivo upregulation of miR-199a decreases visceral pain via inhibition of TRPV1 signalling. Thus, miR-199 precursors may be promising therapeutic candidates for the treatment in patients with visceral pain.
Cover Feature: Kinetic Resolution of Racemic 2‐Hydroxyarylketones by Asymmetric Esterification: Investigation of the Influence of the Co‐Base on the Selectivity (Asian J. Org. Chem. 2/2020) (2020)

“Koma” is a kind of spinning top toy. A spinning top is a popular play around the world and “Koma” playing is considered an auspicious activity in Japan. An axle attached to a circular and thick material is rotated by the motion of throwing with a string. If you use the right hand, the rotation mode will be clockwise. When using the left hand, the rotation mode is counterclockwise. The clockwise spinning top and the counterclockwise spinning top correspond to mirror images, and these enantiomers can be created separately via enantioselective synthesis. More information can be found in the Communication by Kenya Nakata, Isamu Shiina et al. on page 202 in Issue 2, 2020 (DOI: 10.1002/ajoc.201900702).
Exponential scaling of neural algorithms - a future beyond Moore's Law? (2017)

Although the brain has long been considered a potential inspiration for future computing, Moore's Law - the scaling property that has seen revolutions in technologies ranging from supercomputers to smart phones - has largely been driven by advances in materials science. As the ability to miniaturize transistors is coming to an end, there is increasing attention on new approaches to computation, including renewed enthusiasm around the potential of neural computation. This paper describes how recent advances in neurotechnologies, many of which have been aided by computing's rapid progression over recent decades, are now reigniting this opportunity to bring neural computation insights into broader computing applications. As we understand more about the brain, our ability to motivate new computing paradigms with continue to progress. These new approaches to computing, which we are already seeing in techniques such as deep learning and neuromorphic hardware, will themselves improve our ability to learn about the brain and accordingly can be projected to give rise to even further insights. This paper will describe how this positive feedback has the potential to change the complexion of how computing sciences and neurosciences interact, and suggests that the next form of exponential scaling in computing may emerge from our progressive understanding of the brain.
Peroxidase-Catalyzed Oxidative Polymerization of Bisphenols (2001)

Oxidative polymerization of bisphenolic monomers has been performed using peroxidase as catalyst in an aqueous organic solvent. Peroxidase induced the polymerization of an industrial product, bisphenol F, consisting of 2,2'-, 2,4'-, and 4,4'-dihydroxydiphenylmethanes. Under the selected conditions, the quantitative formation of the polymer was observed. Among the isomers, 2,4'- and 4,4'-dihydroxydiphenylmethanes were polymerized to give the polymer in high yields, whereas no polymerization of the 2,2'-isomer occurred. These data suggest that the radical transfer reaction between a phenoxy radical of the enzymatically polymerizable monomer and the enzymatically nonpolymerizable monomer frequently took place during the polymerization. Various 4,4'-dihydroxyphenyl compounds were also polymerized by peroxidase catalyst. The polymerization behaviors, and solubility and thermal properties of the resulting polymers strongly depended on the bridge structure as well as the enzyme origin. Polymers from dihydroxydiphenylmethanes showed relatively high thermal stability.
Abstract 4338: Response to neoadjuvant targeted therapy in operable head and neck cancer confers survival benefit (2023)

Abstract Purpose: Neoadjuvant targeted therapy provides a brief, preoperative ‘window of opportunity’ that can be exploited to individualize cancer care based on treatment response. We investigated whether response to neoadjuvant therapy during the preoperative window confers survival benefit in patients with operable head and neck squamous cell carcinoma (HNSCC). Patients and Methods: A pooled analysis of treatment naïve patients with operable HNSCC enrolled in one of three clinical trials from 2009-2020 (NCT00779389, NCT01218048, NCT02473731). Neoadjuvant regimens consisted of EGFR inhibitors (n=83) or anti-ErbB3 antibody therapy (n=9) within 28 days of surgery. Clinical to pathologic stage migration was compared to disease-free survival (DFS) and overall survival (OS) while adjusting for confounding factors using multivariable Cox regression. Circulating tumor markers validated in other solid tumor models were analyzed. Results: 92 of 118 patients were analyzed; all patients underwent surgery following neoadjuvant therapy. Clinical to pathologic downstaging was more frequent in patients undergoing neoadjuvant targeted therapy compared to a historic cohort without neoadjuvant therapy (P=0.048). Patients with pathologic downstage migration had the highest OS (89.5%, 95% CI 75.7-100) compared to those with no stage change (58%, 95% CI 46.2-69.8) or upstage (40%, 95% CI 9.6-70.4, P=0.003). On multivariable analysis, downstage migration remained a positive prognostic factor for OS (hazard ratio 0.22, 95% CI 0.05-0.90) while adjusting for measured confounders. Downstage migration correlated with decreased circulating tumor markers, SOX17 and TAC1 (P=0.0078). Conclusion: Brief neoadjuvant therapy achieved pathologic downstaging in a subset of patients and was associated with significantly better DFS and OS as well as decreased circulating methylated SOX17 and TAC1. Citation Format: Marco Antonio Mascarella, Tolani Olonisakin, Purva Rumde, Varun Vendra, Melonie Nance, Seungwon Kim, Mark Kubik, Shaum Sridharan, Robert Ferris, Moon Fenton, Daniel Clayburgh, James Ohr, Malabika Sen, Sonali Joyce, James Herman, Jennifer Grandis, Dan Zandberg, Umamaheswar Duvvuri. Response to neoadjuvant targeted therapy in operable head and neck cancer confers survival benefit. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4338.
Mid-infrared Continuous-wave Optical Parametric Oscillator with a Fan-out Grating MgO:PPLN Operating Up to 5.3 µm (2019)

We report on a continuous-wave (cw) optical parametric oscillator (OPO) optimized for mid-infrared emission above 5.0 µm. The OPO is based on a magnesium-oxide-doped periodically poled LiNbO3 (MgO:PPLN) crystal with a fan-out grating design. A linear two-mirror cavity resonating both at the pump and signal wavelengths is stabilized to the pump laser by using the modified Pound-Drever-Hall (PDH) method. The idler wavelength is continuously tunable from 4.7 µm up to 5.3 µm by varying the poling period of the fan-out grating crystal. Pumped by a diode-pumped solid state (DPSS) laser with a power of 1.1 W at 1064 nm, the maximum idler output power is measured to be 5.3 mW at 4.8 µm. The output power above 5.0 µm is reduced to the hundreds of µW level due to increased absorption in the crystal, but is stable and strong enough to be measured with a conventional detector.
Gas Pipeline Compression System Design (2013)

Natural gas is a major world energy source. World natural gas reserves are estimated at 155 trillion cubic meters, 6112 TCF [1]. About 72% of the world's natural gas reserves are found in the Middle East and the former Soviet Union.
Supplementary Figure 2 from An Epithelial–Mesenchymal Transition Gene Signature Predicts Resistance to EGFR and PI3K Inhibitors and Identifies Axl as a Therapeutic Target for Overcoming EGFR Inhibitor Resistance (2023)

&lt;p&gt;PDF file - 96K, Structure of pyrrolopyrimidine AXL inhibitor SGI-7079&lt;/p&gt;
Communication Channel Estimation and Waveform Design: Time Delay Estimation on Parallel, Flat Fading Channels (2010)

Abstract : A review of performance bounds for time-delay estimation (TDE) is presented, including a discussion of current trends. Then the problem of waveform design for TDE using frequency-hopping (FH) waveforms is analyzed to study the effects of fading and diversity on TDE over parallel channels with flat, Rayleigh fading. The authors present the maximum likelihood estimator (MLE), the Cramer-Rao bound (CRB), and the Ziv-Zakai bound (ZZB) on TDE for several different approaches to modeling the fading channels. Computer simulations of the mean-squared error (MSE) of the MLEs indicate that the ZZB provides a significantly tighter bound than the CRB, and the ZZB exhibits a SNR-threshold region that agrees with the MLE performance.
Phase I I T rial o f I ntratumoral A dministration o f O NYX- 015, a R eplication-Sele ctive A denovirus, i n P atients W ith Refractory H ead a nd N eck C ancer (2001)

Purpose: To determine the safety, humoral immune response replication, and activity of multiple intratumoral injections of ONYX-015 (replication selective adenovirus) in patients with recurrent squamous cell carcinoma of the head and neck (SCCHN). Patients and Methods: This phase II trial enrolled patients with SCCHN who had recurrence/relapse after prior conventional treatment. Patients received ONYX015 at a dose of 2 3 10 11 particles via intratumoral injection for either 5 consecutive days (standard) or twice daily for 2 consecutive weeks (hyperfractionated) during a 21-day cycle. Patients were monitored for tumor response, toxicity, and antibody formation. Results: Forty patients (30 standard and 10 hyperfractionated) received 533 injections of ONYX-015. Standard treatment resulted in 14% partial to complete regression, 41% stable disease, and 45% progressive disease rates. Hyperfractionated treatment resulted in 10% complete response, 62% stable disease, and 29% progressive disease rates. Treatment-related toxicity included mild to moderate fever (67% overall) and injection site pain (47% on the standard regimen, 80% on the hyperfractionated regimen). Detectable circulating ONYX-015 genome suggestive of intratumoral replication was identified in 41% of tested patients on days 5 and 6 of cycle 1; 9% of patients had evidence of viral replication 10 days after injection during cycle 1, and no patients had evidence of replication > 22 days after injection. Conclusion: ONYX-015 can be safely administered via intratumoral injection to patients with recurrent/ refractory SCCHN. ONYX-015 viremia is transient. Evidence of modest antitumoral activity is suggested. J Clin Oncol 19:289-298. © 2001 by American Society of Clinical Oncology.
Enhanced Performance & Functionality of Tunable Delay Lines (2012)

Abstract : We demonstrated dramatic enhancements in the performance and functionality of tunable optical delay lines. We used tunable wavelength conversion combined with inter-channel chromatic dispersion and intra-channel dispersion compensation to achieve continuously tunable optical delays. Extremely long delays at very high bit-rates were demonstrated with minimal data distortion. We demonstrated delays for different data modulation formats, including on-off-keying and spectrally efficient DQPSK (differential -quadrature-phase-shift-keying .We used: (i) low dispersion slope, highly nonlinear fiber to achieve wide-bandwidth wavelength conversion based on four-wave mixing and (ii) a highly dispersive element with low dispersion slope to introduce a large linear change in time delay as a function of wavelength. Since the dispersive element also introduces data-destroying intra-channel chromatic dispersion, we made use of spectrally efficient DQPSK which increased the tolerance to all orders of dispersion. We demonstrated that tunable optical delays can potentially be used in a dynamic, reconfigurable, and heterogeneous optical system.
Development of Time Varying Kalman Smoother for Extracting Fetal ECG using Independent Component Analysis : Preliminary Study (2012)

태아심박의 모니터링은 태아의 안녕을 평가하기 위해 중요한 정보이다. 비관혈적인 태아심전도는 산모의 복부 신호로부터 추출될 수 있다. 따라서 산모 복부의 혼합 신호로부터 태아심전도를 추출하기 위해 많은 유망한 신호처리 방법들이 개발되어 왔다. 그러나 비관혈적인 태아심전도는 안정적인 신호 측정법이 부족하고 신호처리 방법의 어려움으로 여전히 임상에서 널리 적용되지 못하고 있다. 태아심전도를 추출하는 신호처리 결과는 가우시안 백색잡음에 의해 신호대잡음비가 낮아질 수 있다. 본 논문에서는 태아심전도에서 시간에 따라 변하는 백색잡음 신호를 제거하여 신호대잡음비를 높이기 위한 방법으로 시변 칼만 평활기를 제안하였고 그 가능성을 확인하였다. Wiener 과정을 시스템 모델로 설정하고 백색잡음 크기에 따라 공분산 행렬을 수정하였으며, 이를 통해 칼만 이득을 변화시켜 평활화 정도를 가변시킬 수 있도록 설계하였다. 5채널 태아심전도 모델을 이용하여 백색잡음의 크기에 따른 최적 공분산 행렬 값을 구하였고, 모의실험을 통해 제안된 방법의 가능성을 확인할 수 있었다.
Effect of a non-hygroscopic surfactant coating upon fluorescein absorption from the respiratory tract. (1987)

The influence of a hydrophobic coating upon the absorption of fluorescein from the canine respiratory tract has been evaluated. Lauric acid was adsorbed onto the surface of micronized disodium fluorescein powder suspended in non-aqueous solutions of the fatty acid. A 0.24 g lauric acid coating for each gram of dye was sufficient to prevent hygroscopic growth in a 40 sec period at 37 C at 97% relative humidity. When this powder was aerosolized and administered by inhalation to Beagle dogs, fluorescein absorption proceeded at similar rates to that of the uncoated dye.
Busy period, congestion analysis and loss probability in fluid queues (2020)

International audience
Endosymbiont DNA in Endobacteria-Free Filarial Nematodes Indicates Ancient Horizontal Genetic Transfer (2010)

These results strongly suggest that the last common ancestor of extant filarial nematodes was infected with Wolbachia and that this former endosymbiont contributed to their genome evolution. Horizontally transferred Wolbachia DNA may explain the ability of some filarial species to live and reproduce without the endosymbiont while other species cannot.
Robot Assisted Pyeloplasty in the Infant—Lessons Learned (2006)

Robot assisted pyeloplasty is a safe and effective option in the surgical treatment of infant ureteropelvic junction obstruction. Further long-term studies are needed to confirm the usefulness of robotics in minimally invasive pediatric surgery.
Molecular dynamics simulations of vibrational lifetimes in amorphous silicon (1998)

Abstract Recent theoretical and time resolved Raman studies disagree on the lifetime of high energy vibrational modes in amorphous silicon. The latter suggests that the lifetime increases with increasing frequency and is of the order of 10 ns for the highest frequency modes, while the former predicts a picosecond timescale that follows the two-phonon density of states. Here we present the results of molecular dynamics simulations which are complementary to the perturbative calculations. At different temperatures, kinetic energy is put into selected modes of vibration in 216 and 4096 atom systems with periodic boundary conditions and the Stillinger—Weber potential. The lifetime of medium and high frequency modes is found to be of the order of 1 ops at 5, 10 and 30 K, in qualitative agreement with the perturbative calculations.
Deep Learning for Joint MIMO Detection and Channel Decoding (2019)

We propose a deep-learning approach for the joint MIMO detection and channel decoding problem. Conventional MIMO receivers adopt a model-based approach for MIMO detection and channel decoding in linear or iterative manners. However, due to the complex MIMO signal model, the optimal solution to the joint MIMO detection and channel decoding problem (i.e., the maximum likelihood decoding of the transmitted codewords from the received MIMO signals) is computationally infeasible. As a practical measure, the current model-based MIMO receivers all use suboptimal MIMO decoding methods with affordable computational complexities. This work applies the latest advances in deep learning for the design of MIMO receivers. In particular, we leverage deep neural networks (DNN) with supervised training to solve the joint MIMO detection and channel decoding problem. We show that DNN can be trained to give much better decoding performance than conventional MIMO receivers do. Our simulations show that a DNN implementation consisting of seven hidden layers can outperform conventional model-based linear or iterative receivers. This performance improvement points to a new direction for future MIMO receiver design.
Grain Refinement of AZ31 and AZ61 Mg Alloys through Room Temperature Processing by UP-Scaled High-Pressure Torsion (2019)

This study presents application of an up-scaled high-pressure torsion (HPT) process to AZ31 and AZ61 Mg alloys for ultrafine grain refinement. Disks with 30 mm diameter were processed at room temperature under 6 to 7 GPa using the up-scaled HPT facility with a maximum capacity of 5 MN (500 ton). Microstructural evolution was evaluated by hardness measurement and microscopy observations including tensile testing. The grain size was well refined to ∼150 nm and ∼100 nm at the saturated state for the AZ31 and AZ61 alloys, respectively. Superplastic elongations of ∼520% and ∼550% were then attained in the corresponding alloys when tested in tension at elevated temperatures because of the grain boundary sliding controlled by grain boundary diffusion. Upsizing of the disk sample makes for a chance to extract the tensile specimens at different radial distance within the same disk and therefore the effect of the equivalent strain on the superplastic elongations was effectively evaluated.
Stereospecificity of Ketoreductase Domains of the 6-Deoxyerythronolide B Synthase (2007)

6-Deoxyerythronolide B synthase (DEBS) is a modular polyketide synthase (PKS) responsible for the biosynthesis of 6-dEB (1), the parent aglycone of the broad spectrum macrolide antibiotic erythromycin. Individual DEBS modules, which contain the catalytic domains necessary for each step of polyketide chain elongation and chemical modification, can be deconstructed into constituent domains. To better understand the intrinsic stereospecificity of the ketoreductase (KR) domains, an in vitro reconstituted system has been developed involving combinations of ketosynthase (KS)-acyl transferase (AT) didomains with acyl-carrier protein (ACP) and KR domains from different DEBS modules. Incubations with (2S,3R)-2-methyl-3-hydroxypentanoic acid N-acetylcysteamine thioester (2) and methylmalonyl-CoA plus NADPH result in formation of a reduced, ACP-bound triketide that is converted to the corresponding triketide lactone 4 by either base- or enzyme-catalyzed hydrolysis/cyclization. A sensitive and robust GC-MS technique has been developed to assign the stereochemistry of the resulting triketide lactones, on the basis of direct comparison with synthetic standards of each of the four possible diasteromers 4a-4d. Using the [KS][AT] didomains from either DEBS module 3 or module 6 in combination with KR domains from modules 2 or 6 gave in all cases exclusively (2R,3S,4R,5R)-3,5-dihydroxy-2,4-dimethyl-n-heptanoic acid-delta-lactone (4a). The same product was also generated by a chimeric module in which [KS3][AT3] was fused to [KR5][ACP5] and the DEBS thioesterase [TE] domain. Reductive quenching of the ACP-bound 2-methyl-3-ketoacyl triketide intermediate with sodium borohydride confirmed that in each case the triketide intermediate carried only an unepimerized d-2-methyl group. The results confirm the predicted stereospecificity of the individual KR domains, while revealing an unexpected configurational stability of the ACP-bound 2-methyl-3-ketoacyl thioester intermediate. The methodology should be applicable to the study of any combination of heterologous [KS][AT] and [KR] domains.
Immunization with a Plasmid DNA Vaccine Encoding the N-Terminus of Insulin-like Growth Factor Binding Protein-2 in Advanced Ovarian Cancer Leads to High-level Type I Immune Responses (2021)

IGFBP-2 N-terminus Th1 selective vaccination safely induces type I T cells without evidence of regulatory responses.
Microwave‐Assisted Beckmann Rearrangement: Convenient Synthesis of 1,3‐Diaza‐bicyclo[3.2.2]nonane (2006)

Abstract Small heterocyclic amines such as 1,3‐diaza‐bicyclo[3.2.2]nonane are known to be key components of biologically active molecules. A convenient synthesis of this compound utilizing a key Beckmann rearrangement of (Z)‐1‐aza‐bicyclo[2.2.2]octan‐3‐one oxime (6) with conc. H2SO4 under microwave irradiation was achieved. The desired compound (1) was obtained in 20% yield overall. Keywords: 1‐Aza‐bicyclo[2.2.2]octan‐3‐one oximeBeckmann rearrangement1,3‐diaza‐bicyclo[3.2.2]nonanemicrowave‐assisted organic synthesis