gebhart/patrepeval huggingface dataset:
Nonequilibrium hard-disk packings with controlled orientational order (2000)

This paper addresses one of the fundamental questions in the theory of hard-disk packings—how order within a system relates to packing density. The algorithm presented is a seed-based, growth protocol in which new disks are added sequentially to the surface of a growing cluster. The angular position of the new disk is chosen based on the minimization of an objective function designed to control order, as measured by the global bond-orientational order parameter ψ6, which varies between 0 and 1 (with 1 indicating perfect hexagonal close-packed order). Modifying the objective function allows the final packing fraction to be biased while maintaining tight control over ψ6. Inside of the range 0⩽ψ6⩽0.70, the targeted order parameter ψ6 is achieved to within two decimal places of accuracy. Furthermore, it is found that random structures (ψ6∼0.01) can be generated with packing fractions in the range 0.40⩽η⩽0.77. Interestingly, the algorithm can produce nonequilibrium hard-disk configurations that are considerably more disordered than those typical of the equilibrium fluid.
Fast Acquisition of Proton‐Detected HETCOR Solid‐State NMR Spectra of Quadrupolar Nuclei and Rapid Measurement of NH Bond Lengths by Frequency Selective HMQC and RESPDOR Pulse Sequences (2020)

Fast magic-angle spinning (MAS), frequency selective (FS) heteronuclear multiple quantum coherence (HMQC) experiments which function in an analogous manner to solution SOFAST HMQC NMR experiments, are demonstrated. Fast MAS enables efficient FS excitation of <sup>1</sup> H solid-state NMR signals. Selective excitation and observation preserves <sup>1</sup> H magnetization, leading to a significant shortening of the optimal inter-scan delay. Dipolar and scalar <sup>1</sup> H{<sup>14</sup> N} FS HMQC solid-state NMR experiments routinely provide 4- to 9-fold reductions in experiment times as compared to conventional <sup>1</sup> H{<sup>14</sup> N} HMQC solid-state NMR experiments. <sup>1</sup> H{<sup>14</sup> N} FS resonance-echo saturation-pulse double-resonance (RESPDOR) allowed dipolar dephasing curves to be obtained in minutes, enabling the rapid determination of NH dipolar coupling constants and internuclear distances. <sup>1</sup> H{<sup>14</sup> N} FS RESPDOR was used to assign multicomponent active pharmaceutical ingredients (APIs) as salts or cocrystals. FS HMQC also provided enhanced sensitivity for <sup>1</sup> H{<sup>17</sup> O} and <sup>1</sup> H{<sup>35</sup> Cl} HMQC experiments on <sup>17</sup> O-labeled Fmoc-alanine and histidine hydrochloride monohydrate, respectively. FS HMQC and FS RESPDOR experiments will provide access to valuable structural constraints from materials that are challenging to study due to unfavorable relaxation times or dilution of the nuclei of interest.
9 Tb/s Transmission Using 29 mW Optical Pump Power Per EDFA With 1.24 Tb/s/W Optical Power Efficiency Over 15,050 km (2021)

We transmit 143x32.6 GBd 8D-QPSK signal over 15,050 km with EDFAs consuming 29 mW of 980 nm-pump power. We experimentally achieve record optical power efficiency from 6.5 to 1.24 Tb&#x002F;s&#x002F;W with the corresponding optimum spectral efficiency from 2.4 to 2.0 b&#x002F;s&#x002F;Hz for transmission distances ranging from 6,020 to 15,050 km respectively. These results are enabled by: precisely tuned information spectral efficiency and EDFA output power based on our power efficiency model to maximize optical power efficiency; the use of coded modulation format with &lt;1.6 dB gap to Shannon limit and variable overhead FEC; the use of ultra-low loss fiber; more power efficient gain equalization with a single gain flattening filter per two EDFAs; and low back-to-back implementation penalty. We also confirmed the validity of our power efficiency model comparing the designed and measured OSNR evolution, achieved optical power efficiency and the corresponding spectral efficiency.
Involvement of Epigenetics and EMT-Related miRNA in Arsenic-Induced Neoplastic Transformation and Their Potential Clinical Use (2015)

Exposure to toxicants leads to cumulative molecular changes that overtime increase a subject's risk of developing urothelial carcinoma. To assess the impact of arsenic exposure at a time progressive manner, we developed and characterized a cell culture model and tested a panel of miRNAs in urine samples from arsenic-exposed subjects, urothelial carcinoma patients, and controls. To prepare an in vitro model, we chronically exposed an immortalized normal human bladder cell line (HUC1) to arsenic. Growth of the HUC1 cells was increased in a time-dependent manner after arsenic treatment and cellular morphology was changed. In a soft agar assay, colonies were observed only in arsenic-treated cells, and the number of colonies gradually increased with longer periods of treatment. Similarly, invaded cells in an invasion assay were observed only in arsenic-treated cells. Withdrawal of arsenic treatment for 2.5 months did not reverse the tumorigenic properties of arsenic-treated cells. Western blot analysis demonstrated decreased PTEN and increased AKT and mTOR in arsenic-treated HUC1 cells. Levels of miR-200a, miR-200b, and miR-200c were downregulated in arsenic-exposed HUC1 cells by quantitative RT-PCR. Furthermore, in human urine, miR-200c and miR-205 were inversely associated with arsenic exposure (P = 0.005 and 0.009, respectively). Expression of miR-205 discriminated cancer cases from controls with high sensitivity and specificity (AUC = 0.845). Our study suggests that exposure to arsenic rapidly induces a multifaceted dedifferentiation program and miR-205 has potential to be used as a marker of arsenic exposure as well as a maker of early urothelial carcinoma detection.
Exposure and compositional factors that influence polarization induced birefringence in silica glass (2007)

Silica glass exhibits a permanent anisotropic response, referred to as polarization induced birefringence (PIB), when exposed to short wavelength, polarized light. The magnitude of the PIB has been empirically correlated with the OH content of the glass. Our recent studies pertaining to PIB have focused on careful characterization of PIB, with particular emphasis on understanding all of the contributions to the measured birefringence signal and finally extracting only that signal associated with birefringence arising from exposure to a polarized light beam. We will demonstrate that a critical contributor to the total birefringence signal is birefringence that comes from exposure beam inhomogeneities. After subtracting beam profile effects we are able to show that PIB is proportional to the OH content of the glass. Polarized infrared (IR) measurements were performed on glasses that developed PIB as a consequence of exposure to polarized 157-nm light. These studies reveal that there is preferential bleaching of a specific hydroxyl (OH) species in the glass with OH aligned parallel to the incident polarization undergoing more bleaching than those perpendicular. Further, we observe a very strong correlation between the measured PIB of these samples and the anisotropic bleaching. From these studies we propose a mechanism that can explain the role of hydroxyl in PIB.
Effect of Zeolite on Fischer–Tropsch Synthesis in the Presence of a Catalyst Based on Skeletal Cobalt (2020)

The joint effect of skeletal cobalt and zeolite on the main catalytic parameters of a pelletized composite catalyst has been studied. All samples contain 50 wt % fine metallic aluminum powder. The amounts of other components are as follows: 20–30 wt % binder (boehmite), 5–20 wt % Beta zeolite in the H form (SiO2/Al2O3 = 38), and 10–20 wt % fine skeletal cobalt. The reference catalyst does not contain any zeolite. All the catalysts exhibit activity in Fischer–Tropsch synthesis and secondary transformations, the intensity of which depends on the zeolite/cobalt ratio. The composition of the resulting hydrocarbons (HCs) varies over a wide range; in particular, the content of n-paraffins and olefins is 39–88 and 3–38%, respectively. The chain growth probability varies in a range of 0.65–0.83 depending on the zeolite/cobalt ratio and the synthesis conditions. It has been shown that the catalysts studied are superior advantage to other cobalt–zeolite catalysts in CO conversion, specific activity, productivity, and stability.
Angiotensin converting enzyme in kainic acid–injected striata (1978)

Abstract The activity of angiotensin converting enzyme is decreased in kainic acid–injected neostriata of rats, providing another biochemical similarity between this animal model and Huntington's chorea.
Dynamic DMF Binding in MOF-5 Enables the Formation of Metastable Cobalt-Substituted MOF-5 Analogues (2015)

Multinuclear solid-state nuclear magnetic resonance, mass spectrometry, first-principles molecular dynamics simulations, and other complementary evidence reveal that the coordination environment around the Zn2+ ions in MOF-5, one of the most iconic materials among metal–organic frameworks (MOFs), is not rigid. The Zn2+ ions bind solvent molecules, thereby increasing their coordination number, and dynamically dissociate from the framework itself. On average, one ion in each cluster has at least one coordinated N,N-dimethylformamide (DMF) molecule, such that the formula of as-synthesized MOF-5 is defined as Zn4O(BDC)3(DMF)x (x = 1–2). Understanding the dynamic behavior of MOF-5 leads to a rational low-temperature cation exchange approach for the synthesis of metastable Zn4–xCoxO(terephthalate)3 (x > 1) materials, which have not been accessible through typical high-temperature solvothermal routes thus far.
Graft formation and chain scission in blends of polyamide‐6 and ‐6.6 with maleic anhydride containing polymers (1998)

The in situ formation of a compatibilizer, consisting of a copolymer of PA grafted onto a maleic anhydride (MA) containing polymer, is essential for the morphology and properties of the corresponding PA blends. In this study four blends, containing PA-6 or PA-6.6 and EPDM-g-MA or poly(styrene-co-maleic anhydride) (SMA; 28 wt % MA), were prepared and characterized. Chemical analyses showed that the amount of PA graft is independent of the blend composition. Going from EPDM-g-MA to SMA the MA content of the original MA-containing polymer increases, which in the corresponding blends results in an increase in the number of PA grafts and a decrease in the length of the PA grafts. In the SMA blends the number averaged molecular weight of the grafted PA is only about 200 g/mol. It is postulated that the water molecule, released upon imide formation at the PA/(MA-containing polymer) interface, hydrolyses a PA amide group, resulting in a new amine end group, which in its turn reacts with the MA-containing polymer, etc. Differential scanning calorimetry shows that the degree of crystallinity of the PA phase is decreased only when the size of the PA phase between the MA-containing polymer domains approaches the PA crystalline lamellar thickness. © 1998 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 36: 179–188, 1998
Dictionary Optimization for Block-Sparse Representations (2012)

Recent work has demonstrated that using a carefully designed dictionary instead of a predefined one, can improve the sparsity in jointly representing a class of signals. This has motivated the derivation of learning methods for designing a dictionary which leads to the sparsest representation for a given set of signals. In some applications, the signals of interest can have further structure, so that they can be well approximated by a union of a small number of subspaces (e.g., face recognition and motion segmentation). This implies the existence of a dictionary which enables block-sparse representations of the input signals once its atoms are properly sorted into blocks. In this paper, we propose an algorithm for learning a block-sparsifying dictionary of a given set of signals. We do not require prior knowledge on the association of signals into groups (subspaces). Instead, we develop a method that automatically detects the underlying block structure given the maximal size of those groups. This is achieved by iteratively alternating between updating the block structure of the dictionary and updating the dictionary atoms to better fit the data. Our experiments show that for block-sparse data the proposed algorithm significantly improves the dictionary recovery ability and lowers the representation error compared to dictionary learning methods that do not employ block structure.
The swan genome and transcriptome: its not all black and white (2022)

ABSTRACT The Australian black swan ( Cygnus atratus ) is an iconic species with contrasting plumage to that of the closely related Northern Hemisphere white swans. The relative geographic isolation of the black swan may have resulted in a limited immune repertoire and increased susceptibility to infectious disease, notably infectious diseases from which Australia has been largely shielded. Indeed, unlike Mallard ducks and the mute swan ( Cygnus olor ), the black swan is extremely sensitive to severe highly pathogenic avian influenza (HPAI). Understanding this susceptibility has been impaired by the absence of any available swan genome and transcriptome information. Here, we generate the first chromosome-length annotated black and mute swan genomes annotated with transcriptome data, all using long-read based pipelines generated for vertebrate species. We used these genomes and transcriptomes, to show that unlike other wild waterfowl, black swans lack an expanded immune gene repertoire, lack a key viral pattern-recognition receptor in endothelial cells and mount a poorly controlled inflammatory response to HPAI. We also implicate genetic differences in SLC45A2 in the iconic plumage of the Australian black swan. Together, these data suggest that the immune system of the black swan is such that should any avian viral infection become established in its native habitat the survival of the black swan would be in significant peril.
Atomistic Wear in a Single Asperity Sliding Contact (2008)

Abrasive wear of sharp silicon tips sliding distances of up to 750 m on a polymeric surface is studied using atomic force microscopy. The data cannot be explained by conventional macroscopic wear models. We present a new model in which the barrier for breaking an atomic bond is lowered by the frictional stress acting on the contact. Quantitative agreement is obtained between the model and wear data for all load forces and sliding distances studied.
An Experimental and Numerical Investigation Into the Effects of Squealer Blade Tip Modifications on Aerodynamic Performance (2013)

Gas turbine blades using the so-called squealer tip configuration represent a majority of the high-pressure first stage blades in service. The squealer tip in its most basic format is simply a two-tooth labyrinth seal projecting from the blade tip towards the stationary shroud or casing. As with all blade tip configurations, the geometry is a compromise between aerodynamics, cooling, mechanical stress, durability, and repair. While many proposed blade tip innovations involve more complex geometries, this study seeks to determine if a simpler geometry, other than a flat tip, can provide equivalent aerodynamic performance with a reasonable chance of satisfying all other design factors. Using an annular sector blade cascade, total pressure loss surveys are measured with three blade tip geometries, the standard squealer tip, a single-sided suction side seal strip, and the single-sided strip with a pressure side winglet added. The same cascade is modeled numerically as a periodic passage for each of the geometries tested. Experiment and simulation both utilize all blade tip cooling flow injection locations and nominal magnitudes, as well as a constant tip clearance above the suction side seal strip. Experimental data show that the removal of the pressure side seal strip reduces the area-averaged total pressure loss slightly, while the addition of a winglet returns the performance to the baseline result. Numerical predictions indicate essentially equal performance for all geometries. The numerical results provide insight into the loss mechanisms of both the tip leakage flows and the coolant injection flows. This study, when combined with literature data on heat transfer and cooling, concludes that the simpler single-sided suction seal strip is better overall than the commonly employed squealer tip.
Studying complex metal-molecule interface with low temperature scanning tunneling microscope : from electronic structure to charge transport (2008)

A fundamental understanding of complex metal-organic interfaces is widely considered to be a milestone on the way to successful realization of molecular-based electronic devices. In the context of interface studies, local tunneling methods, based on the ability of the scanning tunneling microscope (STM) to resolve surface structure as well as surface electronic and vibrational properties with atomic scale resolution, are considered to be very helpful. However, the potential of such methods as applied to cases of complex organic adsorption have not yet been exhaustively tested. In this thesis, a well-studied model case of complex organic adsorption was selected in order to apply a number of local STM methods aiming at a detailed characterization of the interface structural, electronic, vibrational and transport properties on the scale of a single metal-molecule contact. The main objective is twofold: On the one hand a fundamental analysis of the complex metal-organic interfaces is performed, especially the relation between their electronic structure and charge transport properties. On the other hand, we aim a detailed test of various STM-based techniques applied to the realistic problem of complex adsorption and transport measurements. Given that the chosen interface system is the best studied case of complex organic adsorption showing the highest degree of order and at the same time demonstrating very rich phenomenology one may expect that the results obtained on such a system will clearly demonstrate the potential and limitations of the experimental techniques applied.
LURK: Server-Controlled TLS Delegation (2020)

The following topics are dealt with: security of data; data privacy; learning (artificial intelligence); telecommunication security; Internet; cryptography; mobile computing; computer network security; authorisation; Internet of Things.
Novel Heterocyclic Thyromimetics. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
ITS Self-Positioning System Using Radio Frequency Identification-Based Wide-Area Multilayer Scheduling to Monitor and Manage Development Traffic on a Highly Constrained Mountain Highway Corridor (2009)

This paper describes a multi-layer ITS self-positioning system using GEN-2 smart RFID tags, smart phones and smartcards, as well as real time image and ID recognition. The hardware in the physical layer integrates digital beacons along heavy flow of mixed traffic in a severely constrained (marginal capacity and environmentally sensitive) access corridor with a control layer which schedules construction traffic (300 trucks per day over a period of ten years). Trucks, drivers and even cargo content are managed by a control center which provides scheduling commands, visual and ID monitoring, and real time incident avoidance. The second layer is modeled as a G/G/c class queuing system with semi-deterministic control provided by fusion of positioning data with event management, congestion control and visual feedback. Bidirectional control for flow from two holding hubs with multi-service (c>1) endpoints is demonstrated. The technology involves driver/time schedule registration, security monitoring and ordered recovery from stop/go orders via driver smartcard ID, truck GEN-2 RFID tag and software that matches ID to visual and command sequence. The system was developed primarily to monitor compliance with a mandatory traffic budget for a development within a constrained mountain highway corridor, but design function was expanded to optimize just-in-time delivery for construction materials, manage access to large development sites, and manage of incident impacts to construction traffic. A third internet-based layer with parallel real time access for both the local governmental jurisdiction and the private system manage is designed to provide transparency required to validate compliance to development traffic budgets.
Cyclin-G-associated kinase modifies -synuclein expression levels and toxicity in Parkinson's disease: results from the GenePD Study (2011)

Although family history is a well-established risk factor for Parkinson's disease (PD), fewer than 5% of PD cases can be attributed to known genetic mutations. The etiology for the remainder of PD cases is unclear; however, neuronal accumulation of the protein α-synuclein is common to nearly all patients, implicating pathways that influence α-synuclein in PD pathogenesis. We report a genome-wide significant association (P = 3.97 × 10(-8)) between a polymorphism, rs1564282, in the cyclin-G-associated kinase (GAK) gene and increased PD risk, with a meta-analysis odds ratio of 1.48. This association result is based on the meta-analysis of three publicly available PD case-control genome-wide association study and genotyping from a new, independent Italian cohort. Microarray expression analysis of post-mortem frontal cortex from PD and control brains demonstrates a significant association between rs1564282 and higher α-synuclein expression, a known cause of early onset PD. Functional knockdown of GAK in cell culture causes a significant increase in toxicity when α-synuclein is over-expressed. Furthermore, knockdown of GAK in rat primary neurons expressing the A53T mutation of α-synuclein, a well-established model for PD, decreases cell viability. These observations provide evidence that GAK is associated with PD risk and suggest that GAK and α-synuclein interact in a pathway involved in PD pathogenesis. The GAK protein, a serine/threonine kinase, belongs to a family of proteins commonly targeted for drug development. This, combined with GAK's observed relationship to the levels of α-synuclein expression and toxicity, suggests that the protein is an attractive therapeutic target for the treatment of PD.
BiPMAP: A Toolbox for Predictions of Perceived Motion Artifacts on Modern Displays (2022)

Presenting dynamic scenes without incurring motion artifacts visible to observers requires sustained effort from the display industry. A tool that predicts motion artifacts and simulates artifact elimination through optimizing the display configuration is highly desired to guide the design and manufacture of modern displays. Despite the popular demands, there is no such tool available in the market. In this study, we deliver an interactive toolkit, Binocular Perceived Motion Artifact Predictor (BiPMAP), as an executable file with GPU acceleration. BiPMAP accounts for an extensive collection of user-defined parameters and directly visualizes a variety of motion artifacts by presenting the perceived continuous and sampled moving stimuli side-by-side. For accurate artifact predictions, BiPMAP utilizes a novel model of the human contrast sensitivity function to effectively imitate the frequency modulation of the human visual system. In addition, BiPMAP is capable of deriving various in-plane motion artifacts for 2D displays and depth distortion in 3D stereoscopic displays.