Miracle-dz/UniFAR-FTUs huggingface dataset:
Large scale molecular dynamics simulations of homogeneous nucleation.

We present results from large-scale molecular dynamics (MD) simulations of homogeneous vapor-to-liquid nucleation. The simulations contain between 1 × 10(9) and 8 × 10(9) Lennard-Jones (LJ) atoms, covering up to 1.2 μs (56 × 10(6) time-steps). They cover a wide range of supersaturation ratios, S ≃ 1.55-10(4), and temperatures from kT = 0.3 to 1. 0ε (where ε is the depth of the LJ potential, and k is the Boltzmann constant). We have resolved nucleation rates as low as 10(17) cm(-3) s(-1) (in the argon system), and critical cluster sizes as large as 100 atoms. Recent argon nucleation experiments probe nucleation rates in an overlapping range, making the first direct comparison between laboratory experiments and molecular dynamics simulations possible: We find very good agreement within the uncertainties, which are mainly due to the extrapolations of argon and LJ saturation curves to very low temperatures. The self-consistent, modified classical nucleation model of Girshick and Chiu [J. Chem. Phys. 93, 1273 (1990)] underestimates the nucleation rates by up to 9 orders of magnitudes at low temperatures, and at kT = 1. 0ε it overestimates them by up to 10(5). The predictions from a semi-phenomenological model by Laaksonen et al. [Phys. Rev. E 49, 5517 (1994)] are much closer to our MD results, but still differ by factors of up to 10(4) in some cases. At low temperatures, the classical theory predicts critical clusters sizes, which match the simulation results (using the first nucleation theorem) quite well, while the semi-phenomenological model slightly underestimates them. At kT = 1. 0ε, the critical sizes from both models are clearly too small. In our simulations the growth rates per encounter, which are often taken to be unity in nucleation models, lie in a range from 0.05 to 0.24. We devise a new, empirical nucleation model based on free energy functions derived from subcritical cluster abundances, and find that it performs well in estimating nucleation rates.
Pattern-Driven Colorization of 3D Surfaces

Colorization refers to the process of adding color to black and white images or videos. This paper extends the term to handle surfaces in three dimensions. This is important for applications in which the colors of an object need to be restored and no relevant image exists for texturing it. We focus on surfaces with patterns and propose a novel algorithm for adding colors to these surfaces. The user needs only to scribble a few color strokes on one instance of each pattern, and the system proceeds to automatically colorize the whole surface. For this scheme to work, we address not only the problem of colorization, but also the problem of pattern detection on surfaces.
SURFACE CONDITION EFFECTS ON CRITICAL CHLORIDE THRESHOLD OF STEEL REINFORCEMENT

Deicing and anti-icing salts and seawater are the main sources of chloride ions that cause the corrosion of steel reinforcement embedded in reinforced concrete (RC) bridge and marine structures. This article reports on a study undertaken to evaluate the influence of the steel reinforcement surface condition on the corrosion performance. In the study, the critical chloride threshold values of five uncoated steel reinforcement types (ASTM A 706, ASTM A 615, microcomposite, stainless steel 304, and stainless steel [SS] 316LN) with as-received and polished surface conditions were quantitatively determined using the accelerated chloride threshold (ACT) test procedure. Micrographs of the surfaces (characterizing the mill scale and surface topography) for all steel reinforcement types were obtained using both optical and scanning electron microscopy (SEM). Results showed that the mean critical chloride threshold values increased with the complete removal of the as-received surface and with surface polishing for the ASTM A 706, microcomposite, and stainless steel 304 reinforcements. In addition the mean critical chloride threshold values decreased with the complete removal of the as-received surface and with surface polishing of the ASTM A 615 and SS316LN steels. The authors conclude that removal of the mill scale on the microcomposite steel reinforcement showed a significant improvement in the critical chloride threshold and removal of this mill scale may be economically justified.
Pseudomonas aeruginosa Pyocyanin Activates NRF2-ARE-Mediated Transcriptional Response via the ROS-EGFR-PI3K-AKT/MEK-ERK MAP Kinase Signaling in Pulmonary Epithelial Cells

The redox-active pyocyanin (PCN) secreted by the respiratory pathogen Pseudomonas aeruginosa generates reactive oxygen species (ROS) and causes oxidative stress to pulmonary epithelial cells. Nuclear factor (erythroid-derived 2)-like 2 (NRF2) confers protection against ROS-mediated cell death by inducing the expression of detoxifying enzymes and proteins via its binding to the cis-acting antioxidant response element (ARE). However, a clear relationship between NRF2 and PCN-mediated oxidative stress has not been established experimentally. In this study, we investigated the induction of NRF2-ARE response by PCN in the pulmonary epithelial cells. We analyzed the effect of PCN on NRF2 expression and nuclear translocation in cultured human airway epithelial cells, and in a mouse model of chronic PCN exposure. NRF2-dependent transcription of antioxidative enzymes was also assessed. Furthermore, we used inhibitors to examine the involvement of EGFR and its downstream signaling components that mediate NRF2-ARE-activation in response to PCN. PCN enhances the nuclear NRF2 accumulation and activates the transcription of ARE-mediated antioxidant genes. Furthermore, PCN activates NRF2 by inducing the EGFR-phosphoinositide-3-kinase (PI3K) signaling pathway and its main downstream effectors, AKT and MEK1/2-ERK1/2 MAP kinases. Inhibition of the EGFR-PI3K signaling markedly attenuates PCN-stimulated NRF2 accumulation in the nucleus. We demonstrate for the first time that PCN-mediated oxidative stress activates the EGFR-PI3K-AKT/MEK1/2-ERK1/2 MAP kinase signaling pathway, leading to nuclear NRF2 translocation and ARE responsiveness in pulmonary epithelial cells.
Using a preclinical mouse model of high-grade astrocytoma to optimize p53 restoration therapy

Significance Glioblastoma is the most common and aggressive form of brain cancer. GBM patients typically respond poorly to conventional therapies. The tumor-suppressor protein 53 pathway is disrupted in a majority of GBM cases. Using a mouse model that mimics the progression of human GBM, we evaluate and optimize the therapeutic efficacy of functional p53 restoration in gliomas. We show that the efficacy of p53 restoration therapy in the animal model as well as in human GBM cells is improved markedly by an episodic dosing regimen that circumvents the selective pressure for adaptive resistance when p53 function is chronically restored. Based on clinical presentation, glioblastoma (GBM) is stratified into primary and secondary types. The protein 53 (p53) pathway is functionally incapacitated in most GBMs by distinctive type-specific mechanisms. To model human gliomagenesis, we used a GFAP-HRasV12 mouse model crossed into the p53ERTAM background, such that either one or both copies of endogenous p53 is replaced by a conditional p53ERTAM allele. The p53ERTAM protein can be toggled reversibly in vivo between wild-type and inactive conformations by administration or withdrawal of 4-hydroxytamoxifen (4-OHT), respectively. Surprisingly, gliomas that develop in GFAP-HRasV12;p53+/KI mice abrogate the p53 pathway by mutating p19ARF/MDM2 while retaining wild-type p53 allele. Consequently, such tumors are unaffected by restoration of their p53ERTAM allele. By contrast, gliomas arising in GFAP-HRasV12;p53KI/KI mice develop in the absence of functional p53. Such tumors retain a functional p19ARF/MDM2-signaling pathway, and restoration of p53ERTAM allele triggers p53-tumor–suppressor activity. Congruently, growth inhibition upon normalization of mutant p53 by a small molecule, Prima-1, in human GBM cultures also requires p14ARF/MDM2 functionality. Notably, the antitumoral efficacy of p53 restoration in tumor-bearing GFAP-HRasV12;p53KI/KI animals depends on the duration and frequency of p53 restoration. Thus, intermittent exposure to p53ERTAM activity mitigated the selective pressure to inactivate the p19ARF/MDM2/p53 pathway as a means of resistance, extending progression-free survival. Our results suggest that intermittent dosing regimes of drugs that restore wild-type tumor-suppressor function onto mutant, inactive p53 proteins will prove to be more efficacious than traditional chronic dosing by similarly reducing adaptive resistance.
LOOKING FOR A PULSE: A SEARCH FOR ROTATIONALLY MODULATED RADIO EMISSION FROM THE HOT JUPITER, τ BOÖTIS b

Hot Jupiters have been proposed as a likely population of low-frequency radio sources due to electron cyclotron maser emission of similar nature to that detected from the auroral regions of magnetized solar system planets. Such emission will likely be confined to specific ranges of orbital/rotational phase due to a narrowly beamed radiation pattern. We report on GMRT 150 MHz radio observations of the hot Jupiter τ Boötis b, consisting of 40 hr carefully scheduled to maximize coverage of the planet's 79.5 hr orbital/rotational period in an effort to detect such rotationally modulated emission. The resulting image is the deepest yet published at these frequencies and leads to a 3σ upper limit on the flux density from the planet of 1.2 mJy, two orders of magnitude lower than predictions derived from scaling laws based on solar system planetary radio emission. This represents the most stringent upper limits for both quiescent and rotationally modulated radio emission from a hot Jupiter yet achieved and suggests that either (1) the magnetic dipole moment of τ Boötis b is insufficient to generate the surface field strengths of >50 G required for detection at 150 MHz or (2) Earth lies outside the beaming pattern of the radio emission from the planet.
Bovine Enteroviruses as Indicators of Fecal Contamination

ABSTRACT Surface waters frequently have been contaminated with human enteric viruses, and it is likely that animal enteric viruses have contaminated surface waters also. Bovine enteroviruses (BEV), found in cattle worldwide, usually cause asymptomatic infections and are excreted in the feces of infected animals in large numbers. In this study, the prevalence and genotype of BEV in a closed herd of cattle were evaluated and compared with BEV found in animals in the immediate environment and in environmental specimens. BEV was found in feces from 76% of cattle, 38% of white-tailed deer, and one of three Canada geese sharing the same pastures, as well as the water obtained from animal watering tanks, from the pasture, from streams running from the pasture to an adjacent river, and from the river, which emptied into the Chesapeake Bay. Furthermore, BEV was found in oysters collected from that river downstream from the farm. These findings suggest that BEV could be used as an indicator of fecal pollution originating from animals (cattle and/or deer). Partial sequence analysis of the viral genomes indicates that different viral variants coexist in the same area. The possibility of identifying the viral strains found in the animals and in the contaminated areas by sequencing the RNA genome, could provide a tool to find the origin of the contamination and should be useful for epidemiological and viral molecular evolution studies.
Inhibition of mTOR Radiosensitizes Soft Tissue Sarcoma and Tumor Vasculature

Purpose: The PI3K/Akt/mTOR prosurvival pathway is frequently up-regulated in soft tissue sarcoma. Mammalian target of rapamycin (mTOR) inhibitors, such as rapamycin, have recently shown clinical benefit in soft tissue sarcoma, and mTOR inhibition has also been associated with radiosensitization of carcinoma and endothelial cells. This study tested the hypothesis that rapamycin radiosensitizes soft tissue sarcoma and endothelial cells in vitro and in vivo through the inhibition of mTOR. Experimental Design: Colony formation assays were done to determine the radiosensitizing properties of rapamycin on three human soft tissue sarcoma cell lines (SK-LMS-1, SW-872, and HT-1080) and human dermal microvascular endothelial cells (HDMEC). The functional effects of rapamycin and radiation on the endothelial compartment were evaluated with microvascular sprouting assays. The in vivo radiosensitizing activity of rapamycin was assessed with s.c. SK-LMS-1 nude mice xenografts treated with concurrent daily rapamycin, radiation, or both for three weeks. Results:In vitro radiosensitization was shown in all three soft tissue sarcoma cell lines with minimally cytotoxic doses of rapamycin. SK-LMS-1 xenografts displayed significant tumor growth delay with rapamycin and radiation compared with either treatment alone. Radiation resulted in transient increased mTOR function, whereas rapamycin abolished this signaling in irradiated and unirradiated samples. In HDMEC, rapamycin and radiation reduced microvessel sprouting, but did not alter colony formation. Conclusions: Minimally cytotoxic concentrations of rapamycin inhibited the mTOR cascade in culture and in vivo while radiosensitizing soft tissue sarcoma, and produced synergistic effects with radiation on HDMEC microvessel formation. By targeting both tumor and endothelial compartments, rapamycin produced potent radiosensitization of soft tissue sarcoma xenografts. Clinical trials combining rapamycin and radiotherapy in soft tissue sarcoma are warranted.
Tau isoform‐specific modulation of kinesin‐driven microtubule gliding rates and trajectories as determined with tau‐stabilized microtubules

We have utilized tau‐assembled and tau‐stabilized microtubules (MTs), in the absence of taxol, to investigate the effects of tau isoforms with three and four MT binding repeats upon kinesin‐driven MT gliding. MTs were assembled in the presence of either 3‐repeat tau (3R tau) or 4‐repeat tau (4R tau) at tau:tubulin dimer molar ratios that approximate those found in neurons. MTs assembled with 3R tau glided at 31.1 μm/min versus 25.8 μm/min for 4R tau, a statistically significant 17% difference. Importantly, the gliding rates for either isoform did not change over a fourfold range of tau concentrations. Further, tau‐assembled MTs underwent minimal dynamic instability behavior while gliding and moved with linear trajectories. In contrast, MTs assembled with taxol in the absence of tau displayed curved gliding trajectories. Interestingly, addition of 4R tau to taxol‐stabilized MTs restored linear gliding, while addition of 3R tau did not. The data are consistent with the ideas that (i) 3R and 4R tau‐assembled MTs possess at least some isoform‐specific features that impact upon kinesin translocation, (ii) tau‐assembled MTs possess different structural features than do taxol‐assembled MTs, and (iii) some features of tau‐assembled MTs can be masked by prior assembly by taxol. The differences in kinesin‐driven gliding between 3R and 4R tau suggest important features of tau function related to the normal shift in tau isoform composition that occurs during neural development as well as in neurodegeneration caused by altered expression ratios of otherwise normal tau isoforms. © 2010 Wiley‐Liss, Inc.
Decoder-Complexity-Aware Encoding of Motion Compensation for Multiple Heterogeneous Receivers

For mobile multimedia systems, advances in battery technology have been much slower than those in memory, graphics, and processing power, making power consumption a major concern in mobile systems. The computational complexity of video codecs, which consists of CPU operations and memory accesses, is one of the main factors affecting power consumption. In this article, we propose a method that achieves near-optimal video quality while respecting user-defined bounds on the complexity needed to decode a video. We specifically focus on the motion compensation process, including motion vector prediction and interpolation, because it is the single largest component of computation-based power consumption. We start by formulating a scenario with a single receiver as a rate-distortion optimization problem and we develop an efficient decoder-complexity-aware video encoding method to solve it. Then we extend our approach to handle multiple heterogeneous receivers, each with a different complexity requirement. We test our method experimentally using the H.264 standard for the single receiver scenario and the H.264 SVC extension for the multiple receiver scenario. Our experimental results show that our method can achieve up to 97% of the optimal solution value in the single receiver scenario, and an average of 97% of the optimal solution value in the multiple receiver scenario. Furthermore, our tests with actual power measurements show a power saving of up to 23% at the decoder when the complexity threshold is halved in the encoder.
A Continuous Enzyme-Coupled Assay for Triphosphohydrolase Activity of HIV-1 Restriction Factor SAMHD1

ABSTRACT The development of deoxynucleoside triphosphate (dNTP)-based drugs requires a quantitative understanding of any inhibition, activation, or hydrolysis by off-target cellular enzymes. SAMHD1 is a regulatory dNTP-triphosphohydrolase that inhibits HIV-1 replication in human myeloid cells. We describe here an enzyme-coupled assay for quantifying the activation, inhibition, and hydrolysis of dNTPs, nucleotide analogues, and nucleotide analogue inhibitors by triphosphohydrolase enzymes. The assay facilitates mechanistic studies of triphosphohydrolase enzymes and the quantification of off-target effects of nucleotide-based antiviral and chemotherapeutic agents.
Crystal structure of trans-1-{2-[4-(dimethylamino)phenyl]ethyl}-4-[2-(pyren-1-yl)ethyl]cyclohexane

The title compound, C34H37N, is a pyrene derivative in which the pyrene ring system is linked to an ethylcyclohexane unit which, in turn, carries a [4-(dimethylamino)phenyl]ethyl substituent in the para position. The central cyclohexane ring has a chair conformation, with the exocyclic C—C bonds in equatorial orientations. The benzene ring is inclined to the mean plane of the pyrene ring system [maximum deviation = 0.038 (4) Å] by 14.84 (15)°. In the crystal, molecules are linked by C—H⋯π interactions, forming chains propagating along [010]. The crystal was refined as a non-merohedral twin [domain ratio = 0.9989 (4):0.0011 (4)].
Antero-medial portal vs. transtibial techniques for drilling femoral tunnel in ACL reconstruction using 4-strand hamstring tendon: A cross-sectional study with 1-year follow-up

Summary Background Antero-medial portal (AMP) and trans-tibial (TT) techniques are the most widely used methods for drilling femoral tunnel in ACL reconstructions; yet, debate continues about the preferred method. This study seeks to compare these 2 techniques in patients with ACL tears. Material/Methods In this comparative study, all cases of isolated ACL reconstruction using 4-strand hamstring tendon in 2006–2010 were evaluated for eligibility. Of 266 patients, 124 cases (60 TT and 64 AMP), with the mean age of 28.48±8.3, met the inclusion criteria. Both groups were compared in 8 follow-ups from the point of view of time of: return to post-surgical activities (including walking without crutches, normal life activity, jogging, and exercising), maximum range of passive movements, knee instability (Lachman test), functional condition (subjective IKDC and Lysholm knee scores), therapeutic outcomes, and patient’s satisfaction with treatment (VAS). Results AMP technique significantly accelerates patients’ return to activity. AMP patients achieved full range of motion much sooner than TT cases (P<0.0001). After 1-year follow-up, S-IKDC scores were 94.8±3.9 and 89.2±4.1 and S-LKS scores were 96.1±3 and 92.2±4.1 for AMP and TT groups, respectively (P<0.0001). Knee stability was similar in both groups on Lachman test (P=0.25). AMP group patients (VAS mean score: 9.78±0.4) had greater satisfaction compared to TT group patients (VAS mean score: 9.53±0.5) (P=0.003). Conclusions AMP technique leads to reduction in time to return to routine activities, better therapeutic outcomes and higher satisfaction rates.
Viral Vascular Endothelial Growth Factor Plays a Critical Role in Orf Virus Infection

ABSTRACT Infection by the parapoxvirus orf virus causes proliferative skin lesions in which extensive capillary proliferation and dilation are prominent histological features. This infective phenotype may be linked to a unique virus-encoded factor, a distinctive new member of the vascular endothelial growth factor (VEGF) family of molecules. We constructed a recombinant orf virus in which the VEGF-like gene was disrupted and show that inactivation of this gene resulted in the loss of three VEGF activities expressed by the parent virus: mitogenesis of vascular endothelial cells, induction of vascular permeability, and activation of VEGF receptor 2. We used the recombinant orf virus to assess the contribution of the viral VEGF to the vascular response seen during orf virus infection of skin. Our results demonstrate that the viral VEGF, while recognizing a unique profile of the known VEGF receptors (receptor 2 and neuropilin 1), is able to stimulate a striking proliferation of blood vessels in the dermis underlying the site of infection. Furthermore, the data demonstrate that the viral VEGF participates in promoting a distinctive pattern of epidermal proliferation. Loss of a functional viral VEGF resulted in lesions with markedly reduced clinical indications of infection. However, viral replication in the early stages of infection was not impaired, and only at later times did it appear that replication of the recombinant virus might be reduced.
Towards an integrated materials characterization toolbox

The material characterization toolbox has recently experienced a number of parallel revolutionary advances, foreshadowing a time in the near future when material scientists can quantify material structure evolution across spatial and temporal space simultaneously. This will provide insight to reaction dynamics in four-dimensions, spanning multiple orders of magnitude in both temporal and spatial space. This study presents the authors’ viewpoint on the material characterization field, reviewing its recent past, evaluating its present capabilities, and proposing directions for its future development. Electron microscopy; atom probe tomography; x-ray, neutron and electron tomography; serial sectioning tomography; and diffraction-based analysis methods are reviewed, and opportunities for their future development are highlighted. Advances in surface probe microscopy have been reviewed recently and, therefore, are not included [D.A. Bonnell et al.: Rev. Modern Phys. in Review]. In this study particular attention is paid to studies that have pioneered the synergetic use of multiple techniques to provide complementary views of a single structure or process; several of these studies represent the state-of-the-art in characterization and suggest a trajectory for the continued development of the field. Based on this review, a set of grand challenges for characterization science is identified, including suggestions for instrumentation advances, scientific problems in microstructure analysis, and complex structure evolution problems involving material damage. The future of microstructural characterization is proposed to be one not only where individual techniques are pushed to their limits, but where the community devises strategies of technique synergy to address complex multiscale problems in materials science and engineering.