gebhart/patrepeval huggingface dataset:
Characterizing Fluorine-Ion Implant Effects on Poly-Si Thin-Film Transistors With ${\hbox{Pr}}_{2}{\hbox{O}}_{3}$ Gate Dielectric (2008)

The fluorine ion implantation applied to the polycrystalline silicon thin-film transistors (poly-Si TFTs) with high-k Pr <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> as gate dielectric is investigated for the first time. Using the Pr <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> gate dielectric can obtain a high gate capacitance density and thin equivalent-oxide thickness, exhibiting a greatly enhancement in the driving capability of TFT device. Introducing fluorine ions into the poly-Si film by fluorine ion implantation technique can effectively passivate the trap states in the poly-Si film and at the Pr <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> /poly-Si interface to improve the device electrical properties. The Pr <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> TFTs fabricated on fluorine-implanted poly-Si film exhibit significantly improved electrical performances, including lower threshold voltage, steeper subthreshold swing, higher field-effect mobility, lower off-state leakage current, and higher on/off current ratio, as compared with the control poly-Si Pr <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> TFTs. Also, the incorporation of fluorine ions also improves the reliability of poly-Si Pr <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> TFTs against hot-carrier stressing, which is attributed to the formation of stronger Si-F bonds. Furthermore, superior threshold-voltage rolloff characteristic is also demonstrated in the fluorine-implanted poly-Si Pr <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> TFTs. Therefore, the proposed scheme is a promising technology for high-performance and high-reliability solid-phase crystallized poly-Si TFT.
Does the uncertainty in relative biological effectiveness affect patient treatment in proton therapy? (2021)

Clinical treatment with protons uses the concept of relative biological effectiveness (RBE) to convert the absorbed dose into an RBE-weighted dose that equals the dose for radiotherapy with photons causing the same biological effect. Currently, in proton therapy a constant RBE of 1.1 is generically used. However, empirical data indicate that the RBE is not constant, but increases at the distal edge of the proton beam. This increase in RBE is of concern, as the clinical impact is still unresolved, and clinical studies demonstrating a clinical effect of an increased RBE are emerging. Within the European Particle Therapy Network (EPTN) work package 6 on radiobiology and RBE, a workshop was held in February 2020 in Manchester with one day of discussion dedicated to the impact of proton RBE in a clinical context. Current data on RBE effects, patient outcome and modelling from experimental as well as clinical studies were presented and discussed. Furthermore, representatives from European clinical proton therapy centres, who were involved in patient treatment, laid out their current clinical practice on how to consider the risk of a variable RBE in their centres. In line with the workshop, this work considers the actual impact of RBE issues on patient care in proton therapy by reviewing preclinical data on the relation between linear energy transfer (LET) and RBE, current clinical data sets on RBE effects in patients, and applied clinical strategies to manage RBE uncertainties. A better understanding of the variability in RBE would allow development of proton treatments which are safer and more effective.
Analysis of the Human Cancer Glycome Identifies a Novel Group of Tumor-Associated N -Acetylglucosamine Glycan Antigens (2009)

The cell surface is covered by a dense layer of protein- and lipid-linked glycans. Although it has been known that distinct glycan structures are associated with cancer, the whole spectrum of cancer-associated glycans has remained undiscovered. In the present study, we analyzed the protein-linked cancer glycome by matrix-assisted laser desorption/ionization time-of-flight mass spectrometric glycan profiling of cancer patient tissue samples. In lung cancer, we detected accumulation of a novel group of tumor-associated glycans. These protein-linked glycans carried abnormal nonreducing terminal beta-N-acetyl-D-glucosamine (GlcNAc) residues. A similar phenomenon was also detected in structural analyses of tumor-derived glycosphingolipids. This showed that glycan biosynthesis may dramatically change in cancer and that direct glycome analysis can detect the resulting marker glycans. Based on the structural knowledge, we further devised a covalent labeling technique for the detection of GlcNAc-expressing tumors with a specific transferase enzyme. In normal tissues, terminal GlcNAc antigens are capped by galactosylation. Similarly to common cancer-associated glycan antigens T, Tn, and sialyl-Tn, the newly discovered GlcNAc antigens result from incomplete glycosylation. In conclusion, the identified terminal GlcNAc glycans should be recognized as a novel class of tumor markers.
Computational Modeling of Temporary Clay Stabilizers Supported by Performance Testing (2015)

Abstract The performance of systematically substituted temporary clay stabilizers has significant correlation with performances predicted by computational modeling. The model binding energies of different clay stabilizers onto various bentonite crystalline faces were independently calculated and corresponded well with a standard bench-top performance method indicating a systematic approach in the development of temporary clay stabilization performance may be realized. Various clay stabilizers are employed when stimulation requiring aqueous based fluids is necessary in water sensitive formations. Typically, if swelling or migrating clays are present, temporary or permanent stabilizers are utilized. Low molecular weight temporary stabilizers as a rule perform above a critical level concentration, but as the stabilizers concentration diminishes in the fracturing fluid due to flowback, formation fluid displacement, or other mechanisms, the clay can swell reducing porosity and permeability. Permanent stabilizers are generally higher molecular weight and can adhere to single or multiple clay platelets thus dissolution of the stabilizer into the fluid is not favored and the beneficial anti-swell effect is of higher duration. It was discovered when using binding energies of substituted ammonium ions on a bentonite interlayer, the binding energies correlated well with performance testing. The binding energy of ammonium ions substituted with 0 to 4 methyl groups or choline were calculated on the 001 crystal face(s) of bentonite. Bentonite being a 2:1 swelling clay had its inter-crystalline space gapped at 8 to 20Å. Unique molecular ions were introduced to this space and the binding energies were calculated using a Monte Carlo Isothermal Adsorption method. Performance testing was then conducted using a low pressure Bariod fluid loss cell. A set concentration of sodium bentonite was blended into water a specific RPM and duration in the presence of the particular ammonium ion, placed in the cell and pressure was applied and leak off rate were measured. The resulting leak off rates were compared to the binding energy. The design of efficient temporary clay stabilizers can be directly linked to performance. Further, the duration of the stabilization may also be modeled in a way where experimentation would be difficult in flow through porous media.
Characterization of the local charge environment of a single quantum dot via resonance fluorescence (2016)

We study the photon-statistical behavior of resonance fluorescence from self-assembled InAs quantum dots (QDs) as a function of the density of free charge carriers introduced by an above band-gap laser. Second-order correlation measurements show bunching behavior that changes with above-band laser power and is absent in purely above-band excited emission. Resonant photoluminescence excitation spectra indicate that the QD experiences discrete spectral shifts and continuous drift due to changes in the local charge environment. These spectral changes, combined with the tunneling of charges from the environment to the QD, provide an explanation of the bunching observed in the correlations.
Proceedings of the 4th ACM international workshop on Contents protection and security (2006)

It is our great pleasure to welcome you to the ACM Workshop on Multimedia Content Protection and Security - MCPS 2006. New technologies offer convenient ways to distribute and consume digital media; yet these new technologies also make it relatively easy to quickly and flawlessly copy digital data, posing tremendous challenges to protecting intellectual property rights. The future brings consolidation of the technology and entertainment industries. New formats for high-definition optical media are being released (HD-DVD and Blu-Ray). New standards bodies have emerged where IT, Content Owners and Consumer Electronics have come together to fight piracy (or at the very least to raise the bar). Consumers will eventually be affected.The mission of this workshop is to provide researchers and practitioners with a venue to explore ways in which a combination of emerging standards, emerging media formats, innovative solutions and technologies can be used to address these new challenges and to identify new directions for future research and development. With the organizers' participation in emerging content protection standards (Advanced Access Content Protection) for high-definition content we are able to offer a unique opportunity to share with workshop participants these upcoming changes.With this being our first opportunity to organize such a workshop, we were quite pleased with the number and quality of the submissions. Overall the acceptance rate was 35% with the accepted papers covering a variety of topics, including digital rights management, content protection, and watermarking for various forms of media. In addition, the program includes two invited talks. The first is by Andrew G. Setos, President of Engineering, The Fox Group, on the relationship between content and technology. The second is by Frank Casanova, Director QuickTime Marketing, Apple Computer Inc., on digital media and Web 2.0.
ChemInform Abstract: Photochemical Synthesis of N‐Arylbenzophenanthridine Selective Estrogen Receptor Modulators (SERMs). (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
<title>Materials and modeling for organic light-emitting diodes</title> (1997)

Polymer light-emitting diodes, based for example on MEH-PPV, are known to be susceptible to oxidative degradation. This leads to loss of conjugation, i.e. lower carrier mobility and higher operating voltage, and to the formation of carbonyl species, i.e. to luminescence quenching. In-situ FTIR has revealed that ITO can act as the source of oxygen. In order to explore further the mechanism of oxidation and to provide guidance for its elimination, we have studied the behavior of MEH-PPV LEDs prepared with a variety of conducting polymer anodes including polyaniline and polythiophene derivatives cast from various solvents and with various molecular and polymeric dopants. In all cases examined, it is found that polymer anodes lead to significant improvement in lifetime over devices with ITO as the anode contact. Moreover, in contrast to the variability observed for ITO anodes, conducting polymers with polymers with polymeric dopants yield consistently good devices with power efficiencies of about 0.5 percent at 5 volts and brightness in excess of 1000 cd/m<SUP>2</SUP>. Anodes prepared with small molecule dopants are more variable and exhibit short term behavior which suggests interfacial electrochemistry. We describe the device characteristics in the context of a model of hole-dominated bipolar charge injection with Langevin recombination.
Improving image segmentation performance and quantitative analysis via a computer-aided grading methodology for optical coherence tomography retinal image analysis (2010)

We demonstrate quantitative analysis and error correction of optical coherence tomography (OCT) retinal images by using a custom-built, computer-aided grading methodology. A total of 60 Stratus OCT (Carl Zeiss Meditec, Dublin, California) B-scans collected from ten normal healthy eyes are analyzed by two independent graders. The average retinal thickness per macular region is compared with the automated Stratus OCT results. Intergrader and intragrader reproducibility is calculated by Bland-Altman plots of the mean difference between both gradings and by Pearson correlation coefficients. In addition, the correlation between Stratus OCT and our methodology-derived thickness is also presented. The mean thickness difference between Stratus OCT and our methodology is 6.53 microm and 26.71 microm when using the inner segment/outer segment (IS/OS) junction and outer segment/retinal pigment epithelium (OS/RPE) junction as the outer retinal border, respectively. Overall, the median of the thickness differences as a percentage of the mean thickness is less than 1% and 2% for the intragrader and intergrader reproducibility test, respectively. The measurement accuracy range of the OCT retinal image analysis (OCTRIMA) algorithm is between 0.27 and 1.47 microm and 0.6 and 1.76 microm for the intragrader and intergrader reproducibility tests, respectively. Pearson correlation coefficients demonstrate R(2)>0.98 for all Early Treatment Diabetic Retinopathy Study (ETDRS) regions. Our methodology facilitates a more robust and localized quantification of the retinal structure in normal healthy controls and patients with clinically significant intraretinal features.
The role of the PIK3CA gene in the development and aging of the brain (2021)

The CLOVES syndrome is an overgrowth disease arising from mosaic activating somatic mutations in the PIK3CA gene. These mutations occur during fetal development producing malformation and overgrowth of a variety of tissues. It has recently been shown that treatment with low doses of a selective inhibitor of Class I PI3K catalytic subunit p110α, the protein product of the PIK3CA gene, can yield dramatic therapeutic benefits for patients with CLOVES and PROS (a spectrum of PIK3CA-related overgrowth syndromes). To assess the long-term effects of moderate loses of p110α activity, we followed development and growth of mice with heterozygous loss of p110α (Pik3ca<sup>+/-</sup>) over their entire lifetimes, paying particular attention to effects on the brain. While homozygous deletion of the Pik3ca gene is known to result in early embryonic lethality, these Pik3ca<sup>+/-</sup> mice displayed a longer lifespan compared to their wild-type littermates. These mice appeared normal, exhibited no obvious behavioral abnormalities, and no body weight changes. However, their brains showed a significant reduction in size and weight. Notably, mice featuring deletion of one allele of Pik3ca only in the brain also showed gradually reduced brain size and weight. Mechanistically, either deletion of p110α or pharmacological inhibition of p110α activity reduced neurosphere size, but not numbers, in vitro, suggesting that p110α activity is critical for neuronal stem cells. The phenotypes observed in our two genetically engineered mouse models suggest that the sustained pharmacological inhibition of the PIK3CA activity in human patients might have both beneficial and harmful effects, and future treatments may need to be deployed in a way to avoid or minimize adverse effects.
Timing attacks against trusted path (2002)

Presents new attacks against a user workstation's trusted path mechanism. These timing attacks can cause a user's password to leak bits. The timing attacks can then be combined with network authentication protocol brute-force attacks against the remainder of the key space to obtain the user's password. We present several countermeasures against this attack. We also define a property of user systems (workstations) called Trojan horse non-persistence. Workstations that fail to have this properly are more vulnerable to the timing attack and other Trojan horse attacks.
On-Demand Dynamic Branch Prediction (2014)

In out-of-order (OoO) processors, speculative execution with high branch prediction accuracy is employed to achieve good single thread performance. In these processors the branch prediction unit tables (BPU) are accessed in parallel with the instruction cache before it is known whether a fetch group contains branch instructions. For integer applications, we find 85 percent of BPU lookups are done for non-branch operations and of the remaining lookups, 42 percent are done for highly biased branches that can be predicted statically with high accuracy. We evaluate on-demand branch prediction (ODBP), a novel technique that uses compiler generated hints to identify those instructions that can be more accurately predicted statically to eliminate unnecessary BPU lookups. We evaluate an implementation of ODBP that combines static and dynamic branch prediction. For a four wide superscalar processor, ODBP delivers as much as 9 percent improvement in average energy-delay (ED) product, 7 percent core average energy saving, and 3 percent speedup. ODBP also enables the use of large BPU's for a given power budget.
A novel sansalvamide analogue inhibits pancreatic cancer cell proliferation via induction of macrophage inhibitory cytokine (MIC-1) (2006)

Proc Amer Assoc Cancer Res, Volume 47, 2006

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Introduction: Pancreatic cancer continues to be a devastating disease with a poor prognosis and survival. Novel therapeutics are currently under investigation. Sansalvamide A is a cyclic peptide from a marine fungus and has potent anti-proliferative activity in cancer cells. Macrophage inhibitory cytokine (MIC-1) is a member of the transforming growth factor beta superfamily and is associated with pro-apoptotic and anti-tumorigenic activities. In the present study, we investigated the growth-inhibitory effects of a novel brominated and methylated sansalvamide depsipeptide analogue on human pancreatic cancer cells and the role of MIC-1 in this growth inhibition. Methods: Human pancreatic cancer (ASPC-1) cells were treated with 10 μM sansalvamide analogue and cell counting was conducted at 24, 48 and 72 hours. Olignonucleotide microarray analysis was conducted to identify genes whose expression is markedly changed by the sansalvamide depsipeptide. Real-time RT-PCR was performed after 24 hours to confirm the time and concentration-dependent up-regulation of one particular gene, MIC-1. ASPC-1 cells were also pre-treated with actinomycin D (an inhibitor of transcription) to determine the role of transcription and message stability in sansalvamide analogue-induced MIC-1 expression. Results: The sansalvamide depsipeptide analogue significantly inhibited cell proliferation (93% decrease in cell number at 72 hours with 10μM, P<0.01). The sansalvamide depsipeptide analogue caused concentration and time-dependent induction of MIC-1 expression (5.1 fold increase at 3 hours, 14.0 fold increase at 6 hours, 10.3 fold increase at 12 hours and 6.3 fold increase at 24 hours with 10 μM, P <0.01 ). In cells pre-treated with actinomycin D, the sansalvamide depsipeptide analogue inhibits the induction of MIC-1, suggesting that a change in transcription is involved. Conclusions: The sansalvamide analogue induced growth inhibition and up-regulated MIC-1 gene expression at the transcriptional level in human pancreatic cancer cells. Furthermore, the growth inhibition is associated with increased expression of MIC-1.
Analysis of Lateral Tire Friction Dynamics (2007)

Tire friction model is a key part of the overall multi-body tire dynamics model. The LuGre dynamic tire friction model is analytically linearized for pure cornering conditions. The linearized model parameters are conveniently expressed as functions of static curve slope parameters. The linearized lateral force and self aligning torque sub-models are described by equivalent mechanical system. The linearized model and equivalent system parameters are analyzed for different slip angle and wheel center speed operating points. An example of application of linearized tire friction model to tire vibration analysis is presented as well.
ESTs, cDNA microarrays, and gene expression profiling: tools for dissecting plant physiology and development (2004)

Gene expression profiling holds tremendous promise for dissecting the regulatory mechanisms and transcriptional networks that underlie biological processes. Here we provide details of approaches used by others and ourselves for gene expression profiling in plants with emphasis on cDNA microarrays and discussion of both experimental design and downstream analysis. We focus on methods and techniques emphasizing fabrication of cDNA microarrays, fluorescent labeling, cDNA hybridization, experimental design, and data processing. We include specific examples that demonstrate how this technology can be used to further our understanding of plant physiology and development (specifically fruit development and ripening) and for comparative genomics by comparing transcriptome activity in tomato and pepper fruit.
A dataset of images and morphological profiles of 30 000 small-molecule treatments using the Cell Painting assay (2017)

Because computational algorithms and methods for handling single-cell morphological measurements are not yet routine, the dataset serves as a useful resource for the wider scientific community applying morphological (image-based) profiling. The dataset can be mined for many purposes, including small-molecule library enrichment and chemical mechanism-of-action studies, such as target identification. Integration with genetically perturbed datasets could enable identification of small-molecule mimetics of particular disease- or gene-related phenotypes that could be useful as probes or potential starting points for development of future therapeutics.