gebhart/patrepeval huggingface dataset:
Single Cell Pico Force Microscopy: A Novel Tool for High Resolution Measurement of Cell Forces (2009)

Nearly all eukaryotic cells exert forces on their surroundings to generate and maintain tension within their cytoskeleton which is critical for normal cell function. In addition, cells exert forces on their surroundings to orient themselves within an organism, thus gaining information that influences cell fate and behavior, a process called mechanotransduction. In order to study mechanotransduction, a tool is needed that can observe the molecular level sensing events that trigger a decision by a cell as well as the ultimate response that occurs on the whole cell level. There are a number of optical techniques that are used to measure forces from adherent cells at the single cell level; some are good for measuring whole cell forces and some for measuring single molecule level forces, but none have the dynamic range necessary to span both regimes, which is critical for understanding mechanotransduction. To address this need, I have developed a Nano-ElectroMechanical Systems (NEMS) based tool, Single-Cell-Pico-Force-Microscopy (SCPFM), that measures forces exerted by adherent cells with macro-molecular level force sensitivity and sufficient dynamic range to monitor whole cell responses to stimuli with macro-molecular resolution. I have used SCPFM to measure force versus time data from a NIH-3T3 fibroblast as it is perturbed with Cytochalasin D (CD) and allowed to recover in growth media. Within the data there are three excellent examples of previously inaccessible molecular-mechanical processes that illustrate the immense potential of SCPFM to significantly enhance resolution of cell biology at the single cell level: 1) an initial contraction upon exposure to CD followed by the expected force drop, 2) small force oscillations, roughly 400pN peak-to-peak, with frequency that is monotonically dependent on the force being exerted by the lamellipodia, and 3) large, stable, quantized force steps of order 1nN are manifested when a cell’s cytoskeleton is perturbed with CD and allowed to recover in growth media. I propose two complimentary experimental efforts to undertake: a systematic effort to build a library of molecular-mechanical force signatures of various common cytoskeleton reactions and an effort to stimulate and observe compliance sensing and response in adherent cells.
Time‐resolved four‐wave mixing studies of excitons in GaN (2007)

Abstract Quantum beats in the time‐resolved four‐wave mixing (FWM) signals arising from GaN excitons are observed. Two different types of beats are investigated: beats between the A‐exciton (X A ) and B‐exciton (X B ) states; beats between the X A and A‐biexciton ((XX A )) states. The former exhibits oscillations along all directions in the delay‐ ( τ ) and real‐time ( t ) plane while the latter exhibits no beat in the direction parallel to the diagonal axis ( τ = t ). The results are well reproduced by a model calculation, showing good homogeneity of the sample.
X-Ray Raman Spectroscopy—A New Tool to Study Local Structure of Aromatic Hydrocarbons and Asphaltenes (2004)

Abstract Polycyclic aromatic hydrocarbons (PAHs) are essential components in numerous natural and man made organic compounds. In asphaltenes, knowledge of the electronic structure of both its aromatic and aliphatic components is of crucial importance, when trying to understand and predict its macroscopic properties. Theoretical studies of complex PAHs have led to simple rules to describe their π electron distribution, but systematic experimental support is still needed. A novel approach to directly probe carbon type in PAHs is described here, namely the technique of X-ray Raman spectroscopy (XRS). Conventional X-ray absorption spectroscopy (XAS) has been used for many years for element specific characterization of local structure and chemistry. However, in the soft X-ray region (relevant for light elements) its application to numerous carbonaceous systems including asphaltenes encounters problems. Most of the difficulties, including surface sensitivity and restricted sample environments, stem from the submicron path lengths of soft X-rays and/or electrons. XRS provides a means for obtaining the information content of soft X-ray absorption spectra while maintaining the experimental benefits of hard X-ray techniques (˜mm path length). In the XRS process an incident photon is inelastically scattered and part of its energy is transferred to excite an inner shell electron into an unoccupied state. Under the dipole approximation, the resulting features are identical to the corresponding XAS spectrum. In the past, the extremely low cross-section of XRS has made this technique impractical, but intense new X-ray facilities and improvements in X-ray optics have helped to advance this unique spectroscopic tool. We have applied XRS to a series of PAHs and several asphaltenes. The results directly support the simple ideas contained in the “sextet-double bond” description of PAHs. Furthermore, we show that XRS can probe the geometrry of aromatic ring systems in asphaltenes, as well as its ratio of aromatic and aliphatic constituents. Acknowledgments This research was partially supported by the National Institutes of Health, grants 44891-5, GM 44380, and GM-48145, and by the Department of Energy, Office of Biological and Environmental Research (SPC). The National Synchrotron Light Source and the Advanced Photon Source are supported by the Department of Energy, Office of Basic Energy Sciences. BioCAT is a National Institutes of Health-supported Research Center RR-08630. Notes aAsphaltene from two crude oil sources (Ven #20 and KUHM) were measured, they showed identical spectra.
Supplementary Figure 6 from Integrative Analysis of 1q23.3 Copy-Number Gain in Metastatic Urothelial Carcinoma (2023)

&lt;p&gt;PDF file - 38KB, Chromosomal Instability. Analysis testing for potential confounding of pathologic stage and tissue type on chromosomal instability. Figure S6: Fraction of genome altered (FGA, 1) in both cohorts.&lt;/p&gt;
Phrasal Parser software - Deliverable 3.1 (1997)

This deliverable describes the first year's effort towards developing robust and accurate phrasal parsers at Cambridge, Pisa, RXRC and Stuttgart.
SemEval-2020 Task 7: Assessing Humor in Edited News Headlines (2020)

This paper describes the SemEval-2020 shared task "Assessing Humor in Edited News Headlines." The task's dataset contains news headlines in which short edits were applied to make them funny, and the funniness of these edited headlines was rated using crowdsourcing. This task includes two subtasks, the first of which is to estimate the funniness of headlines on a humor scale in the interval 0-3. The second subtask is to predict, for a pair of edited versions of the same original headline, which is the funnier version. To date, this task is the most popular shared computational humor task, attracting 48 teams for the first subtask and 31 teams for the second.
Initial Cell Search Method Based on Two-Step Frequency Offset Estimation for Small Cells in Heterogeneous Networks (2016)

This paper proposes a fast initial cell search method based on two-step frequency offset estimation for a small cell in Long Term Evolution (LTE) heterogeneous networks using different frequency spectra. In the proposed cell search method, a set of user equipment (UE) first estimates the frequency offset of a received primary synchronization signal (PSS) from a macrocell and computes the frequency offset of a received PSS for a small cell in Step 1 assuming the same frequency error of a temperature compensated crystal oscillator (TCXO) of a UE. The UE detects the PSS received timing from the maximum PSS correlation after compensating for the frequency offset by using the estimated value in Step 1 for the small cell. In Step 2, the UE estimates the residual frequency offset by taking a partial correlation of the PSS from the small cell. The UE detects the best secondary synchronization signal (SSS) sequence by taking the SSS sequence correlation for the received signal after compensating for the frequency offset using the estimated value in Step 2. System- level simulation results show that the proposed cell search method achieves a fast initial cell search time within approximately 150 ms to satisfy the cell ID detection probability of 95% even for the carrier frequency of a small cell up to 6 and 11 GHz, assuming the free-running frequency error of the UE TCXO of 3 and 1 ppm, respectively.
Static secondary ion mass spectrometric investigation of the glow-discharge-treated surfaces (1994)

Previously, a nonfouling surface containing polyethylene oxide (PEO) has been developed using a glow discharge process. In this process, a PEO surfactant is first deposited on a hydrophobic polymer surface via a solvent evaporation method. Then the surfactant is crosslinked to the substrate surface by an argon RFGD treatment. A dramatic reduction of protein adsorption and platelet adhesion on the treated surface was observed only when treated with a low power (&lt;5 W) and short treatment time (30 s). In this study, a static secondary ion mass spectrometry (SSIMS) was used to investigate the possible structure changes of PEO chains in the glow-discharge-treated surfactants. Results from this study suggest that the increased protein adsorption and platelet adhesion at longer treatment times (&gt;30 s) are most likely due to degradation of PEO chains in the RFGD-treated surfactant (along with minor surface oxidation).
Time Resolved Imaging Solving FPGA Logic Fault Localization by Pattern Matching Technique (2012)

Abstract From a designer point of view, the analysis of a failure root cause can quickly become a nightmare if the number of hypothesis provided by a simulation tool is too high. To help solving this kind of problem the use of physical probing measurement can reduce drastically the number of assumptions made by the simulation by invalidating certain hypotheses. The purpose of this paper is to add to the simulation a new source of information based on light emission to solve this kind of problem. Virtual logic diagram computation is able to provide several hypotheses of fault for a given node and data coming from Time Resolved Imaging (TRI) measurement allows extraction of transition pattern for a given node where the assumption has been established. The cross-referencing of this information aims at eliminating wrong hypotheses and making the simulation more reliable.
A Randomized Trial of Convalescent Plasma for COVID-19—Potentially Hopeful Signals (2020)

Ling Li, MD, PhD; Wei Zhang, MD; Yu Hu, MD, PhD; Xunliang Tong, MD, PhD; Shangen Zheng, MD; Juntao Yang, PhD; Yujie Kong, MD; Lili Ren, PhD; Qing Wei, MD; Heng Mei, MD, PhD; Caiying Hu, MD; Cuihua Tao, MD; Ru Yang, MD; Jue Wang, MD; Yongpei Yu, PhD; Yong Guo, PhD; Xiaoxiong Wu, MD; Zhihua Xu, MD; Li Zeng, MD; Nian Xiong, MD, PhD; Lifeng Chen, MD; Juan Wang, MD; Ning Man, MD; Yu Liu, PhD; Haixia Xu, MD; E. Deng, MS; Xuejun Zhang, MS; Chenyue Li, MD; Conghui Wang, PhD; Shisheng Su, PhD; Linqi Zhang, PhD; Jianwei Wang, PhD; Yanyun Wu, MD, PhD; Zhong Liu, MD, PhD
Arterial compliance and retinal vascular caliber in cerebrovascular disease (2007)

Reduced arterial wall compliance in large arterial beds is associated with retinal arteriolar narrowing, whereas reduced arterial wall compliance in small arterial beds is associated with retinal venular widening. These data may provide further insights into the effects of altered arterial stiffness on the cerebral microcirculation.
Skin Delivery of Caffeine Contained in Biofunctional Textiles (2010)

Biofunctional textiles are materials with new properties and added value. In this work, emphasis was placed on the release capacity of the active principle (caffeine) from the formulation or from the biofunctional textile. In addition, a new in vitro methodology of percutaneous absorption was designed to demonstrate the delivery of encapsulated caffeine from the biofunctional textile to the different skin layers. In the first step, permeation studies through a nylon membrane were performed and the release capacity of caffeine present in the samples was quantified. In the second step, it was possible to detect the presence of caffeine in the different layers of the skin, while maintaining a close contact between the biofunctional textile and the skin by using pressure during the percutaneous absorption test. The new system is satisfactory for measuring the pass of the active principle from the biofunctional textile to the different skin layers.
Application Of Nonparametric Detectors To Point Target Detection In Infrared Clutter Backgrounds (1989)

This paper presents the adaptation and performance evaluation of the Wilcoxon and Mann-Whitney nonparametric detectors for point targets in infrared clutter backgrounds. These detectors are designed to detect a level shift in a set of M samples containing interference which has an incompletely known distribution. We present a transformation based on the Walsh transformation which allows us to apply the Wilcoxon or Mann-Whitney detectors to the case of a target of small extent imbedded in a large number of background samples. We include the formulation of the two nonparametric detectors along with analytical approximations that can be used to calculate performance predictions in terms of probability of detection and false alarm. Last, we present simulation results comparing the nonparametric detectors with an adaptive linear detector. Performance comparisons are shown for simulations against scenes consisting of recorded infrared clutter video as well as a synthetic white noise scene.
Measurement of the dispersion stability of pristine and surface-modified multiwalled carbon nanotubes in various nonpolar and polar solvents (2007)

A qualitative and rapid measurement technique based on multiple light scattering was employed to analyze the dispersion stability of black multiwalled carbon nanotube (CNT) suspensions. Pristine and chemically oxidized CNTs were dispersed in various polar and nonpolar solvents. The change in the transmission of near-infrared light from the suspensions was periodically measured along the height of a sample cell at room temperature. Using this method, it was possible to obtain the variation of the dispersion stability within only a day. Pristine and surface-modified CNTs dispersed in nonpolar media aggregated within 2 h and sedimentation progressively proceeded with time. As the polar component of the solubility parameter and the solubility in water decreased, faster aggregation and severe sedimentation occurred and vice versa. When the CNTs were modified with carboxylic anion groups, the dispersibility in polar solvents was significantly enhanced due to the combination of polar–polar affinity and electrostatic repulsion, with the result that the transmission flux remained unchanged. The origin of electrostatic repulsion can be found from the increased zeta potential and conductivity of CNTs with carboxylic anion groups.
Application of Laser Peening Technology for Low-Pressure Turbine Blades (2020)

We found some damage at the forks of low-pressure turbine blades caused by random vibration and steam-flashback vibration at nuclear power plant. In this study, to improve fatigue property, we developed and examined laser peening technology for 12Cr stainless steel and material properties. Laser peening induces compressive residual stress on material surfaces. We fabricated fatigue specimens that simulate the stress concentration zone of the forks and applied laser peening to the specimen surfaces. The residual stress was measured by X-ray diffraction and compressive residual stress was formed on the peened surface. From the fatigue test results, the fatigue strength of the laser peened specimens improved about 40% more than the unpeened specimens.
New Bounds for Generalized Separating Hash Families (2007)

The main result of this paper is a necessary condition for generalized separating hash families. We extend previous methods used to obtain upper bounds for separating hash family types {w, w} and {w, w − 1} to the general case {w1, w2,..., wt} for t ≥ 2. 1
Study of Heat Transfer Distribution in a Channel with Inclined Target Surface Cooled by a Single Array of Staggered Impinging Jets (2009)

An experimental investigation has been carried out to study the heat transfer characteristics in a channel with a heated target surface inclined at an angle, cooled by a single array of staggered impinging jets. The work encompasses the effect of three feed channel aspect ratios (5, 7, 9) and three exit outflow orientations (coincident with the entry flow, opposed to the entry flow, and both), and three Reynolds numbers (9400, 14,400, 18,800) on heat transfer. Results show that increasing the Reynolds number increases the heat transfer on the inclined target surface. The outflow orientations affect significantly the local heat transfer charactracistrics, through influencing the jet flow together with the crossflow in the impingement channel. The outflow orientation coincident with the entry flow and the outflow from both sides show better averaged Nusselt number values compared to outflow orientation opposed to the entry flow. The inclined surface affects the local Nusselt number distribution especially for the outflow orientation opposing the entry flow at the narrow region of the impingement channel. In general, the feed channel aspect ratio does not affect the Nusselt number distribution, except for outflow coincident with the entry flow. The local Nusselt number for aspect ratio 9 has been found to be greater than the Nusselt number for aspect ratio 5 by 11%. Additionally, for a given jet-orifice plate with staggered holes, the heat transfer is almost the same throughout the target surface for the outflow exiting in both directions.
A multicentre randomised clinical endpoint study of parma 5 computer‐assisted oral anticoagulant dosage (2008)

To meet growing demand for oral anticoagulation worldwide there has been increased dependence on computer-assistance in dosage although the safety and effectiveness of any of the individual computer-assisted dosage programs has not previously been established. This randomised multicentre clinical end-point study assessed a new version of the PARMA 5 program. It compared PARMA 5 safety and effectiveness with manual dosage by experienced medical staff at 19 centres with a known interest in oral anticoagulation. Target recruitment was 8000 patient-years, randomised to medical staff or PARMA-5 assisted dosage. Safety and effectiveness of the PARMA 5 program was compared with manual dosage. A total of 10,421 patients were recruited (15,369 patient-years) in the 5-year study. International normalised ratio (INR) tests numbered 167,791 with manual and 160,078 with PARMA 5 dosage. With parma 5 there was overall a non-significant reduction in clinical events but in the 2542 patients with deep vein thrombosis/pulmonary embolism, clinical events were significantly reduced (P = 0.005). Success in achieving 'time in target INR range' was also significantly greater with PARMA 5 compared with the dosage by experienced medical staff. This study demonstrated the safety and effectiveness of PARMA 5-assisted dosage.
Calix[4]resorcinarene Derivatives as High‐Resolution Resist Materials for Supercritical CO2 Processing (2008)

Ultra-high-resolution lithography resists based on calix[4] resorcinarene derivatives are shown to be compatible with supercritica l CO2 processing upon the incorporation of specific functionali ties, as illustrated by the inset to the figure. The compounds show high glass-transition temperatures, excellent solubility in supercritical CO2, and good film forming properties, enabling the patterning of line/space features as small as 70 nm (depicted in the figure).
Inhibitory effect of magnetic iron‐oxide nanoparticles on the pattern of expression of lanosterol 14 α ‐demethylase ( ERG11 ) in fluconazole‐resistant colonising isolate of Candida albicans (2020)

Fluconazole-resistant <i>Candida albicans</i> is a big scary reality. The authors assessed the antifungal effects of magnetic iron-oxide nanoparticles on fluconazole-resistant colonising isolate of <i>C. albicans</i> and determined the expression of <i>ERG11</i> gene, protein sequence similarity and ergosterol content. <i>C. albicans</i> isolates were characterised and fluconazole resistance is recognised using World Health Organization's WHONET software. Susceptibility testing of magnetic iron-oxide nanoparticles against fluconazole-resistant colonising isolate of <i>C. albicans</i> was performed according to Clinical and Laboratory Standards Institute guidelines. The expression patterns of <i>ERG11</i> and protein sequence similarity were investigated. Ergosterol quantification has been used to gauge the antifungal activity of magnetic iron-oxide nanoparticles. The findings indicated that 93% of <i>C. albicans</i> isolates were resistant to fluconazole. Magnetic iron-oxide nanoparticles were presented activity against fluconazole-resistant colonising isolate of <i>C. albicans</i> with minimum inhibitory concentration at 250-500 µg/ml. The expression level of <i>ERG11</i> gene was downregulated in fluconazole-resistant colonising isolate of <i>C. albicans</i>. The results revealed no differences in fluconazole-resistant colonising isolate of <i>C. albicans</i> by comparison with ERG11 reference sequences. Moreover, significant reduction was noted in ergosterol content. The findings shed a novel light on the application of magnetic iron-oxide nanoparticles in fighting against resistant <i>C. albicans</i>.
Abstract 17059: Genetic Ablation of c-kit Impairs Cardiac Stem Cell Function, Leading to Attenuated Cardiomyogenesis and Accelerated Myocardial Aging (2013)

The objective of this study was to determine whether defects in c-kit receptor tyrosine activity attenuate cardiac stem cell (CSC) growth, interfering with myocyte renewal and promoting myocardial ...
Predictors of functional benefit of hepatitis C therapy in a ‘real-life’ cohort (2018)

Our data may contribute to the discussion of potential risks and benefits of antiviral therapy with individual patients infected with HCV and with advanced liver disease.
Molecular basis of RNA polymerase promoter specificity switch revealed through studies ofThermusbacteriophage transcription regulator (2014)

Transcription initiation is the central point of gene expression regulation. Understanding of molecular mechanism of transcription regulation requires, ultimately, the structural understanding of consequences of transcription factors binding to DNA-dependent RNA polymerase (RNAP), the enzyme of transcription. We recently determined a structure of a complex between transcription factor gp39 encoded by a <i>Thermus</i> bacteriophage and <i>Thermus</i> RNAP holoenzyme. In this addendum to the original publication, we highlight structural insights that explain the ability of gp39 to act as an RNAP specificity switch which inhibits transcription initiation from a major class of bacterial promoters, while allowing transcription from a minor promoter class to continue.