gebhart/patrepeval huggingface dataset:
Helix‐capping interaction in λ cro protein: A free energy simulation analysis (1994)

The stability mutant Tyr-26-->Asp was studied in the Cro protein from bacteriophage lambda using free energy molecular dynamics simulations. The mutant was calculated to be more stable than the wild type by 3.0 +/- 1.7 kcal/mol/monomer, in reasonable agreement with experiment (1.4 kcal/mol/monomer). Moreover, the aspartic acid in the mutant was found to form a capping interaction with the amino terminus of the third alpha-helix of Cro. The simulations were analyzed to understand better the source of the stability of this helix-capping interaction and to examine the results in light of previous explanations of stabilizing helix caps--namely, a model of local unsatisfied hydrogen bonds at the helix termini and the helix macrodipole model. Analysis of the simulations shows that the stabilizing effect of this charged helical cap is due both to favorable hydrogen bonds with backbone NH groups at the helix terminus and to favorable electrostatic interactions (but not hydrogen bonds) with their carbonyls (effectively the next row of local dipoles in the helix). However, electrostatic interactions are weak or negligible with backbone dipolar groups in the helix further away from the terminus. Moreover, the importance of other local electrostatic interactions with polar side chains near the helix terminus, which are neglected in most treatments of this effect, are shown to be important. Thus, the results support a model that is intermediate between the two previous explanations: both unsatisfied hydrogen bonds at the helix terminus and other, local preoriented dipolar groups stabilize the helix cap. These findings suggest that similar interactions with preoriented dipolar groups may be important for cooperativity in other charge-dipole interactions and may be employed to advantage for molecular design.
Quantitative, Label-Free Characterization of Stem Cell Differentiation at the Single-Cell Level by Broadband Coherent Anti-Stokes Raman Scattering Microscopy (2013)

We use broadband coherent anti-Stokes Raman scattering (BCARS) microscopy to characterize lineage commitment of individual human mesenchymal stem cells cultured in adipogenic, osteogenic, and basal culture media. We treat hyperspectral images obtained by BCARS in two independent ways, obtaining robust metrics for differentiation. In one approach, pixel counts corresponding to functional markers, lipids, and minerals, are used to classify individual cells as belonging to one of the three lineage groups: adipocytes, osteoblasts, and undifferentiated stem cells. In the second approach, we use multivariate analysis of Raman spectra averaged exclusively over cytosol regions of individual cells to classify the cells into the same three groups, with consistent results. The exceptionally high speed of spectral imaging with BCARS allows us to chemically map a large number of cells with high spatial resolution, revealing not only the phenotype of individual cells, but also population heterogeneity in the degree of phenotype commitment.
Data from Tumor Suppressor Functions of <i>ARLTS1</i> in Lung Cancers (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;i&gt;ARLTS1&lt;/i&gt; is a newly characterized tumor suppressor gene located at chromosome 13q14.3 and involved in the pathogenesis of various types of tumors: two single-nucleotide polymorphisms, one of them responsible for protein truncation, were found statistically associated with familial malignancies, whereas DNA hypermethylation and genomic deletions have been identified as a mechanism of &lt;i&gt;ARLTS1&lt;/i&gt; down-regulation in sporadic cancers. We found that in a large portion of lung carcinomas (37%) and in all analyzed lung cancer cell lines, &lt;i&gt;ARLTS1&lt;/i&gt; is strongly down-regulated due to DNA methylation in its promoter region. After its restoration by adenoviral transduction, &lt;i&gt;ARLTS1&lt;/i&gt;-negative A549 and H1299 cells underwent apoptosis and inhibition of cell growth. Furthermore, &lt;i&gt;ARLTS1&lt;/i&gt; reexpression significantly reduced the ability of A549 and H1299 to form tumors in nude mice. Finally, we identified ∼650 transcripts differentially expressed after restoration of &lt;i&gt;ARLTS1&lt;/i&gt; expression in A549 cells, suggesting that various pathways involved in cell survival, proliferation, signaling, and development mediate the effects of wild-type &lt;i&gt;ARLTS1&lt;/i&gt; in a lung cancer system. [Cancer Res 2007;67(16):7738–45]&lt;/p&gt;&lt;/div&gt;
A Lightweight Synchronization Mechanism for Concurrent Programming (2015)

This paper introduces read-log-update (RLU), a novel extension of the popular read-copyupdate (RCU) synchronization mechanism that supports scalability of concurrent code by allowing unsynchronized sequences of reads to execute concurrently with updates. RLU overcomes the major limitations of RCU by allowing, for the first time, concurrency of reads with multiple writers, and providing automation that eliminates most of the programming difficulty associated with RCU programming. At the core of the RLU design is a logging and coordination mechanism inspired by software transactional memory algorithms. In a collection of micro-benchmarks in both the kernel and user space, we show that RLU both simplifies the code and matches or improves on the performance of RCU. As an example of its power, we show how it readily scales the performance of a realworld application, Kyoto Cabinet, a truly difficult concurrent programming feat to attempt in general, and in particular with classic RCU.
Identification of structural factors that affect binding to cannabinoid receptor type 1 (2021)

Similar to the opioid system, the endocannabinoid system which regulates immune response, memory and nociceptive thresholds, cell communication, appetite, and metabolism, also modulates (via Cannabinoid receptor type 1 - CB1R) the rewarding effects of natural and synthetic cannabinoids. Although currently there is significant controversy concerning the (legal) use of cannabis, it has been established that prolonged consumption of a large variety of chemicals from the cannabinoid family can lead to the development of psychiatric and cardiovascular pathologies. In addition to (-)-Δ9-trans-tetrahydrocannabinol (Δ9-THC or simply THC), the main addictive component of cannabis, 43 other synthetic cannabimimetic agents are currently classified as Schedule I drugs and their use in the U.S. is illegal (DEA-DCT-DIR-032-18 [1]). In this study, three-dimensional spectrometric data-activity relationship (3D-SDAR) quantitative and categorical models aimed at better understanding the molecular mechanism of action and the structural features governing binding to CB1R were developed. The performance parameters for a consensus model constructed from composite PLS and KNN quantitative models achieved R2 of 0.703 for an external blind set and an accuracy of 0.846, sensitivity of 0.870, and specificity of 0.840 for binary classification. In addition to the classical A, B, C-tricyclic terpenoid system, other structural alerts were also discovered and reported. We also identified the presence of a hERG linked toxicophore in the molecular structures of a subset of diaryl-(piperidinyl)purines which are known to be selective and potent CB1R binders.
Ultrafast Laser Technology for X-Ray FEL Science (2019)

Ultrafast lasers are one of the enabling technologies for X-ray and XUV FEL facilities. The requirements for those facilities' daily operation and experiments place challenging demands on ultrafast lasers for timing distribution, the FEL electron source, for laser driven electron beam manipulation and for pump-probe experiments.
High hole lifetime (3.8 µs) in 4H-SiC diodeswith 5.5 kV blocking voltage (1999)

The hole lifetime τp in the n-base of 4H-SiC diodes with 5.5 kV blocking voltage has been measured in the temperature range 300–550 K. The τp increases monotonically in this temperature range from 0.6 to 3.8 µs. Forward current-voltage characteristics demonstrate a very high level of base modulation by minority carriers.
Cascadability of large-scale 3-D MEMS-based low-loss photonic cross-connects (2005)

The performance of cascaded low-loss (<3.5 dB) 256/spl times/256 three-dimensional microelectromechanical system (3-D MEMS) photonic cross-connects (PXCs) is experimentally investigated in a recirculating loop. After 60 transitions through the PXC, a power penalty of 1.7 dB is observed, which is attributed to the accumulation of the low polarization-dependent loss in the optical switch. The use of 3-D MEMS PXCs as a wavelength-selective switch (WSPXC) for transparent all-optical networks is also demonstrated. Measured Q-factors for all 16 100-GHz-spaced wavelengths at 10 Gb/s over eight spans of 75-km single-mode fiber and eight transitions through the WSPXC nodes are better than 17 dB.
Interplay among recovery time, signal, and noise: Series- and parallel-tuned circuits are not always the same (2000)

The quality factor, Q, of the magnetic resonance probe and the manner in which the probe is coupled to the spectrometer play important roles in the quality of the obtained experimental data, affecting the signal-to-noise ratio (SNR), the probe recovery time, radiation-damping, and the coupling between multiple coils. For example, high SNR often requires a high-Q probe, while a short recovery time to observe of broad signals generally requires low Q. Here, we discuss effecting a compromise between SNR and recovery time by adjusting the coupling of the probe and preamplifier by mismatching their impedances. Unlike the more common impedance-matched case, the conditions for optimum performance for parallel- and series-tuned probes are found to differ significantly. © 2000 John Wiley & Sons, Inc. Concepts Magn Reson 12: 125–136, 2000
Corrigendum: Methotrexate in Chronic Active Crohn's Disease: A Double-Blind, Randomized, Israeli Multicenter Trial (2015)

Oren, R; Moshkowitz, M; Odes, S; Becker, S; Keter, D; Pomeranz, I; Shirin, C; Reisfeld, I; Broide, E; Lavy, A; Fich, A; Eliakim, R; Patz, J; Villa, Y; Arber, N; Gilat, T
Probing Monotopic Phosphoglycosyl Transferases from Complex Cellular Milieu (2022)

Monotopic phosphoglycosyl transferase enzymes (monoPGTs) initiate the assembly of prokaryotic glycoconjugates essential for bacterial survival and proliferation. MonoPGTs belong to an expansive superfamily with a diverse and richly annotated sequence space; however, the biochemical roles of most monoPGTs in glycoconjugate biosynthesis pathways remain elusive. To better understand these critical enzymes, we have implemented activity-based protein profiling (ABPP) probes as protein-centric, membrane protein compatible tools that lay the groundwork for understanding the activity and regulation of the monoPGT superfamily from a cellular proteome. With straightforward gel-based readouts, we demonstrate robust, covalent labeling at the active site of various representative monoPGTs from cell membrane fractions using 3-phenyl-2H-azirine probes.
Sodium Stress in the Halophyte Thellungiella halophila and Transcriptional Changes in a thsos1‐RNA Interference Line (2007)

Abstract The plasma membrane Na + /H + ‐antiporter salt overly sensitive1 (SOS1) from the halophytic Arabidopsis ‐relative Thellungiella halophila (ThSOS1) shows conserved sequence and domain structure with the orthologous genes from Arabidopsis thaliana and other plants. When expression of ThSOS1 was reduced by RNA interference (RNAi), pronounced characteristics of salt‐sensitivity were observed. We were interested in monitoring altered transcriptional responses between Thellungiella wild type and thsos1‐4, a representative RNAi line with particular emphasis on root responses to salt stress at 350 mmol/L NaCl, a concentration that is only moderately stressful for mature wild type plants. Transcript profiling revealed several functional categories of genes that were differently affected in wild‐type and RNAi plants. Down‐regulation of SOS1 resulted in different gene expression even in the absence of stress. The pattern of gene induction in the RNAi plant under salt stress was similar to that of glycophytic Arabidopsis rather than that of wild type Thellungiella . The RNAi plants failed to down‐regulate functions that are normally reduced in wild type Thellungiella upon stress and did not up‐regulate functions that characterize the Thellungiella salt stress response. Metabolite changes observed in wild type Thellungiella after salt stress were less pronounced or absent in RNAi plants. Transcript and metabolite behavior suggested SOS1 functions including but also extending its established function as a sodium transporter. The down‐regulation of ThSOS1 converted the halophyte Thellungiella into a salt‐sensitive plant.
Distribution of magnetic moments in Co/Pt and Co/Pt/Ir/Pt multilayers detected by magnetic x-ray absorption (1993)

Circular magnetic x-ray dichroism (CMXD) was observed at the Pt and Ir L2,3 edges in the multilayered structures 25⋅(4 Å Co+30 Å Pt) and 25⋅(4 Å Co+11 Å Pt+8 Å Ir+11 Å Pt). The samples were prepared by sputtering and show a large perpendicular anisotropy. The magnetic absorption at the Pt and Ir L2,3 edges was measured in an external magnetic field of 0.15 T perpendicular to the surface. The results indicate a significant spin polarization of the Pt and Ir layers. By comparison with the corresponding CMXD signals of Pt and Ir impurities in a ferromagnetic iron host we estimated the local spin and orbital moments. The results show that the innermost three monolayers in both systems couple ferromagnetically to the Co layers with an average magnetic moment of about 0.01 μB.
Yb-Doped and Hybrid-Structured Solid Photonic Bandgap Fibers and Linearly-Polarized Fiber Lasers Oscillating above 1160nm (2011)

We review our recent work on Yb-doped and hybrid-structured solid photonic bandgap fibers (Yb-HS-SPBGFs) for linearly-polarized fiber lasers oscillating in the small gain wavelength range from 1160nm to 1200nm. The stack-and-draw or pit-in-jacket method is employed to fabricate two Yb-HS-SPBGFs. Both of the fiber shows optical filtering property for eliminating ASE in the large gain wavelength range from 1030nm to 1130nm and enough high birefringence for maintaining linear polarization, thanks to the photonic bandgap effect and the induced birefringence of the hybrid structure. The fiber attenuation of the Yb-HS-SPBGF fabricated by the pit-in-jacket method is much lower than that of the Yb-HS-SPBGF fabricated by stack-and-draw method. Linearly-polarized single stage fiber lasers using Yb-HS-SPBGFs are also demonstrated. Laser oscillation at 1180nm is confirmed without parasitic lasing in the fiber lasers. High output power and high slope efficiency in linearly-polarized single-cavity fiber laser using the low-loss Yb-HS-SPGF fabricated by the pit-in-jacket method are achieved. Narrow linewidth, high polarization extinction ratio and high beam quality are also confirmed, which are required for high-efficient frequency-doubling. A compact and high-power yellow-orange frequency-doubling laser would be realized by using a linearly-polarized single-cavity fiber laser employing a low-loss Yb-HS-SPBGF.
Procédé thermochimique de production de froid de forte puissance pour application mobile. Etude et caractérisation de la dynamique du système (2017)

A better cold chain logistics understanding and control is a major safety issue in deep freezing processes within -20°C/-30°C. Self-cooling solutions based on thermochemical systems appear very suitable for rapid cooling of isothermal containers and its temperature regulation for several hours. Different process concepts and configurations are presented to tackle this problem. Through their dynamic nodal modeling, involving thermodynamic management of one or various reactors, an analysis of their behaviors is performed to evaluate their relevance. A selection of the best performing configurations leads us to an industrial pre-design.To undertake quality measures, a diagnosis approach for possible reactors malfunctions is developed. The methodology is based on a comparison of experimental responses between tested reactor and reference one under the same operating conditions. A database of simulated faulty behaviors will allow the detection and identification of possible malfunctions of reactors coming from the production line.
Structures of Cu surfaces developing in benzotriazole solutions: Effect of pH (2017)

The effect of pH on layer formation onto clean Cu surfaces in benzotriazole (BTA) aqueous solutions was studied by in situ spectroscopic ellipsometry. The effect of H2O2 addition was also investigated. Time changes in the ellipsometric parameters Ψ and Δ, which correspond to the structural changes of the layers on Cu, were discussed. In acidic solutions, a BTA or a Cu–BTA complex layer grows directly on Cu. The out-diffusion of Cu is suppressed at the Cu layer interface. When H2O2 was mixed, the Cu surface is eroded in acidic solutions. In alkaline solutions, the BTA layer grows on the oxidized Cu layer, or no growth occurs, depending on the composition of the solutions. In neutral solutions, the Cu–BTA complex layer forms on Cu, and the uncovered part is oxidized in the presence of H2O2.
Supplementary Figures from Molecular Profiling Establishes Genetic Features Predictive of the Efficacy of the p110β Inhibitor KIN-193 (2023)

&lt;p&gt;Six supplementary figures and legends.&lt;/p&gt;
Characterization of deep acceptor level in as-grown ZnO thin film by molecular beam epitaxy (2014)

We report deep level transient spectroscopy results from ZnO layers grown on silicon by molecular beam epitaxy (MBE). The hot probe measurements reveal mixed conductivity in the as-grown ZnO layers, and the current—voltage (I—V) measurements demonstrate a good quality p-type Schottky device. A new deep acceptor level is observed in the ZnO layer having activation energy of 0.49 ±0.03 eV and capture cross-section of 8.57 × 10−18 cm2. Based on the results from Raman spectroscopy, photoluminescence, and secondary ion mass spectroscopy (SIMS) of the ZnO layer, the observed acceptor trap level is tentatively attributed to a nitrogen-zinc vacancy complex in ZnO.
Rate-Splitting for Max-Min Fair Multigroup Multicast Beamforming in\n Overloaded Systems (2017)

In this paper, we consider the problem of achieving max-min fairness amongst\nmultiple co-channel multicast groups through transmit beamforming. We\nexplicitly focus on overloaded scenarios in which the number of transmitting\nantennas is insufficient to neutralize all inter-group interference. Such\nscenarios are becoming increasingly relevant in the light of growing\nlow-latency content delivery demands, and also commonly appear in multibeam\nsatellite systems. We derive performance limits of classical beamforming\nstrategies using DoF analysis unveiling their limitations; for example, rates\nsaturate in overloaded scenarios due to inter-group interference. To tackle\ninterference, we propose a strategy based on degraded beamforming and\nsuccessive interference cancellation. While the degraded strategy resolves the\nrate-saturation issue, this comes at a price of sacrificing all spatial\nmultiplexing gains. This motivates the development of a unifying strategy that\ncombines the benefits of the two previous strategies. We propose a beamforming\nstrategy based on rate-splitting (RS) which divides the messages intended to\neach group into a degraded part and a designated part, and transmits a\nsuperposition of both degraded and designated beamformed streams. The\nsuperiority of the proposed strategy is demonstrated through DoF analysis.\nFinally, we solve the RS beamforming design problem and demonstrate significant\nperformance gains through simulations.\n
Generalized Blind Mismatch Correction for Two-Channel Time-Interleaved A-to-D Converters (2007)

Calibration of sub-converter mismatches is a challenging task for high-performance time-interleaved analog-to-digital converters (TIADC). Presently known blind correction methods can remove static gain and sampling time mismatches. However, actual subconverters significantly deviate from a simple gain-timing model, and the resulting modeling error strictly limits maximum output signal-to-noise ratio achievable. Generalized mismatch modeling is, therefore, necessary to break the limitation of gain-timing model. In this paper, we propose a blind method for correcting generalized mismatch errors for M=2 TIADC, which is the first in the literature to the authors' knowledge. Cyclostationary spectral analysis shows that unique identification is possible in most practical cases. Simulation results show significant performance improvement by the proposed generalized correction method.
A novel potential therapy for vascular diseases: blood‐derived stem/progenitor cells specifically activated by dendritic cells (2014)

These observations provide preliminary evidence that alternatively activated dendritic cells can promote the generation of EPC-enriched stem/progenitor cells within a 1-day culture. The resulting product BGC101 has the potential for treatment of various vascular conditions such as coronary heart disease, stroke and peripheral ischemia.
Strategies to Identify and Edit Improvements in Synthetic Genome Segments Episomally (2022)

ABSTRACT Genome engineering projects often utilize bacterial artificial chromosomes (BACs) to carry multi-kilobase DNA segments on low copy number vectors. However, DNA synthesis and amplification have the potential to impose mutations on the contained DNA segments that can in turn reduce or prevent viability of the final strain. Here, we describe improvements to a multiplex automated genome engineering (MAGE) protocol to improve recombineering frequency and multiplexability. This protocol was applied to ‘recoding’ an Escherichia coli strain to swap out seven codons to synonymous alternatives genome-wide. Ten 44,402 to 47,179 bp de novo synthesized BAC-contained DNA segments from the recoded strain were unable to complement deletion of the corresponding 33 to 61 wild type genes using a single antibiotic resistance marker. Next-Generation Sequencing was used to identify 1-7 non-recoding mutations in essential genes per segment, and MAGE in turn proved a useful strategy to repair these mutations on the BAC-contained recoded segment when both the recoded and wild type copies of the mutated genes had to exist by necessity during the repair process. This strategy could be adapted to mutation identification and repair for other large-scale genome engineering projects, or for incorporation of small genetic engineering sites for quick protocol adjustments.
Development of a reversible helical electromagnetic launcher (2014)

The first-ever reversible helical electromagnetic launcher (HEML) to both accelerate and decelerate a projectile is presented and discussed. The reversible HEML is a hollow-projectile geometry with a barrel length of 750 mm and a bore diameter of 40 mm. Power for the reversible HEML is provided by a 3-module capacitive pulse forming network (PFN) that has a total energy storage of 1 MJ. Projectile mass is approximately 700 grams. The largest measured acceleration is 8000 m/s <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> immediately followed by a deceleration pulse of 15,000 m/s <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . Pulse lengths for the acceleration and deceleration pulses varied from 5 ms to a maximum of 14.5 ms. An uncertainty analysis and repeatability study was also done with regard to the measured results. Opportunities for improvement in this new proven technology are also explored.