gebhart/patrepeval huggingface dataset:
A Reaction-Diffusion Model for Epidemic Routing in Sparsely Connected MANETs (2010)

We propose and investigate a deterministic traveling wave model for the progress of epidemic routing in disconnected mobile ad hoc networks. In epidemic routing, broadcast or unicast is achieved by exploiting mobility: message-carrying nodes "infect" non message-carrying nodes when they come within communication range of them. Early probabilistic analyses of epidemic routing follow a "well-mixed" model which ignores the spatial distribution of the infected nodes, and hence do not provide good performance estimates unless the node density is very low. More recent work has pointed out that the infection exhibits wave-like characteristics, but does not provide a detailed model of the wave propagation. In this paper, we model message propagation using a reaction-diffusion partial differential equation that has a traveling wave solution, and show that the performance predictions made by the model closely match simulations in regimes where the well- mixed model breaks down. In particular, we show that well-mixed models are generally overly optimistic in regard to the scaling of the message delivery delay with problem parameters such as communication range, node density, and total area. In contrast to prior work, our model provides insight into the spatial distribution of the "infection," and reveals that the performance is sensitive to the geometry of the deployment region, not just its area.
Optimization of a low concentration photovoltaic system (2014)

In this paper, we discuss optimization of a novel low-concentration photovoltaic system with the following properties: (1) static concentration without the need for tracking (2) thermal uniformity via Diffraction Efficiency Modulation (DEM), and (3) mass-fabricability and rollability. The approach leverages a unique combination of waveoptics modeling, multi-objective thermal-electro-optical optimization, and mass-fabricable, nano-manufacturing technology. We discuss various aspects of the optimization including a novel Helmholtz FD solver and thermal and electrical considerations.
Devices having high dielectric constant, ionically-polarizable materials (2023)

An electronic or electro-optic device has a first electrode, a second electrode spaced apart from the first electrode, and a dielectric layer disposed between the first and second electrodes. The dielectric layer has electrically insulating planar layers with intercalated ions therebetween such that the electrically insulating planar layers provide a barrier to impede movement of the intercalated ions to the first and second electrodes under an applied voltage while permitting a polarization of the dielectric layer while in operation.
Distributed Raman Amplification for Short-Reach Applications Including Passive Optical Networks (2019)

We study Raman Amplification for short-reach systems. The impact of system parameters, including feeder length and discrete losses are reported. Our measurements focus on the NG-PON2 upstream band, but are extensible to other optical bands, including O-band.
Design and implementation of the next generation electron beam resists for the production of EUVL photomasks (2018)

A new class of resist materials has been developed that is based on a family of heterometallic rings. The work is founded on a Monte Carlo simulation that utilizes a secondary and Auger electron generation model to design resist materials for high resolution electron beam lithography. The resist reduces the scattering of incident electrons to obtain line structures that have a width of 15 nm on a 40 nm pitch. This comes at the expense of lowering the sensitivity of the resist, which results in the need for large exposure doses. Low sensitivity can be dramatically improved by incorporating appropriate functional alkene groups around the metal-organic core, for example by replacing the pivalate component with a methacrylate molecule. This increases the resist sensitivity by a factor of 22.6 and demonstrates strong agreement between the Monte Carlo simulation and the experimental results. After the exposure and development processes, what remains of the resist material is a metal-oxide that is extremely resistant to silicon dry etch conditions; the etch selectivity has been measured to be 61:1.
Regulation of protein synthesis in Tetrahymena: isolation and characterization of polysomes by gel filtration and precipitation at pH 5.3 (1982)

The fraction of ribosomes loaded on polysomes is about 95% in logarithmically growing Tetrahymena thermophila, and about 4% in starved cells. Cytoplasmic extracts from cells in these two physiological states were used to develop column chromatographic methods for the purification of polysomes. Bio-Gel A 1.5 m was found to separate total cytoplasmic ribosomes from many soluble proteins, including RNAse, with no detectable change in the polysome size distribution. Polysomes can be separated from monosomes and non-polysomal mRNA by chromatography on Bio-Gel A 15 m without size selection. These methods can easily be adapted to large scale preparations of polysomes, even from cells where a small fraction of the ribosomes is on polysomes. A method is described for reversible precipitation of polysomes and monosomes from dilute solutions at pH 5.3 which greatly facilitates polysome isolation. Hybridization of 3H-labeled polyU to RNA isolated from column fractions has been used to demonstrate that purification of EDTA released polysomal mRNA can be performed using the column chromatography procedures described here. These methods have been employed to demonstrate that most of the cytoplasmic mRNA in log-phase Tetrahymena is loaded onto polysomes while most of the mRNA is starved cells exists in a non-polysomal form.
Improving Run Life of Coiled-Tubing-Deployed ESP in Harsh Environment for Qatar's Al Karkara Field (2022)

Abstract Alternative deployed ESP Systems are strings that are deployed in the well on other than conventional tubulars. Coiled Tubing (CT) deployed Electric Submersible Pumps is one of the most common configurations and has been used successfully in Al Karkara field to reduce intervention cost. As part of a closed loop product improvement workflow, utilizing data from dismantle, inspection and failure analysis of equipment, design improvement were suggested and implemented to address root causes and maximize life in Al Karkara. As part of this work, the main challenges of the application as well as weaknesses identified on the different sections of the string are explained in detail. Moreover, the design and specification changes incorporated because of said observations are also covered, including improvements on the power cable, lower connector, multisensor, motor, bottom intake, and base protectors, among others. Through implementation of downhole equipment ESP upgrade and enhancing the operating philosophy, this improved the run life of Al Karkara field by more than 300%. With the industry shifting into a drastic reduction of total cost of ownership (TCO) approach and with the volatility of oil price, the rigless ESP deployment through coil tubing will help to eliminate the cost of a work over rig while reducing the deferred oil production. This paper showcases the ESP capabilities in this corrosive and high temperature environment.
Abstract B068: Inhibition of GSK-3: A novel therapeutic approach for breast cancer treatment (2013)

Abstract NF-kappaB is known to regulate human breast cancer progression, metastasis and chemoresistance. Glycogen Synthase Kinase-3beta (GSK-3beta), a serine/threonine protein kinase, is an essential positive regulator of NF-kappaB transcriptional activity and thereby GSK-3beta may represent a potential therapeutic target in human breast cancer. Our objectives were to determine the expression pattern of GSK-3beta in human breast cancer, to assess the effect of GSK-3 inhibition on breast cancer cell proliferation, survival and chemoresistance, and to evaluate our lead GSK-3 inhibitors alone and in combination with chemotherapeutic drugs for the targeted therapy of breast cancer. Using nuclear/cytosolic fractionation, Western immunoblotting and immunohistochemical staining, we observed aberrant nuclear accumulation of GSK-3beta in five breast cancer cell lines and in 7 of 8 primary human breast carcinomas and corresponding lymph node metastases whereas no detectable expression of GSK-3beta was found in benign breast tissue. Pharmacological inhibition of GSK-3 led to a decrease in proliferation and survival of breast cancer cells. Our in vitro comparison studies demonstrated that our lead GSK-3 inhibitor 9-ING-41 was significantly (30 times) more effective than GSK-3 inhibitor LY2090314 (Eli Lilly), currently in mid-stage clinical trials, in terms of growth inhibition of breast cancer cells. Inhibition of GSK-3 resulted in decreased expression of the NF-kappaB target genes Bcl-2 and XIAP and induction of apoptosis. Moreover, our lead GSK-3 inhibitor 9-ING-41 and doxorubicin acted synergistically to suppress growth of breast cancer cells. Our preliminary in vivo experiments demonstrated that monotherapy with our lead GSK-3 inhibitor 9-ING-41 (20 mg/kg) for 48 hours inhibited proliferation (as shown by BrDU assay) and induced apoptosis (as shown by TUNEL assay) in MDA-MB-468 orthotopic xenograft tumors. Moreover, in vivo toxicology study demonstrated that intravenous injections of 9-ING-41 did not adversely affect mouse complete blood counts or cause overt pathological changes in mouse organs. Our results identify GSK-3beta as a new potential drug target in breast cancer and suggest that inhibition of GSK-3 is a novel therapeutic approach to overcome NF-kappaB-mediated chemoresistance in breast cancer. Citation Format: Andrey Ugolkov, Irina Gaisina, Dmitry Malin, Peter Kulesza, Alan Kozikowski, Vincent Cryns, Andrew Mazar. Inhibition of GSK-3: A novel therapeutic approach for breast cancer treatment. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research: Genetics, Biology, and Clinical Applications; Oct 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2013;11(10 Suppl):Abstract nr B068.
A Roadmap Toward the Definition of Actionable Tumor-Specific Antigens (2020)

The search for tumor-specific antigens (TSAs) has considerably accelerated during the past decade due to the improvement of proteogenomic detection methods. This provides new opportunities for the development of novel antitumoral immunotherapies to mount an efficient T cell response against one or multiple types of tumors. While the identification of mutated antigens originating from coding exons has provided relatively few TSA candidates, the possibility of enlarging the repertoire of targetable TSAs by looking at antigens arising from non-canonical open reading frames opens up interesting avenues for cancer immunotherapy. In this review, we outline the potential sources of TSAs and the mechanisms responsible for their expression strictly in cancer cells. In line with the heterogeneity of cancer, we propose that discrete families of TSAs may be enriched in specific cancer types.
Film Dynamics and Lubricant Depletion by Droplets Moving on Lubricated Surfaces (2018)

A description of how droplets moving across a surface drive the depletion of infused liquid-repelling lubricant paves the way for broader adoption of liquid-infused repellant surfaces in a wide range of industries.
Gestational weight gain prediction using privacy preserving federated learning (2021)

Gestational weight gain prediction in expecting women is associated with multiple risks. Manageable interventions can be devised if the weight gain can be predicted as early as possible. However, training the model to predict such weight gain requires access to centrally stored privacy sensitive weight data. Federated learning can help mitigate this problem by sending local copies of trained models instead of raw data and aggregate them at the central server. In this paper, we present a privacy preserving federated learning approach where the participating users collaboratively learn and update the global model. Furthermore, we show that this model updation can be done incrementally without having the need to store the local updates eternally. Our proposed model achieves a mean absolute error of 4.455 kgs whilst preserving privacy against 2.572 kgs achieved in a centralised approach utilising individual training data until day 140.Clinical relevance- Privacy preserving training of machine learning algorithm for early gestational weight gain prediction with minor tradeoff to performance.
Is that really a question? : Going beyond factoid questions in NLP (2021)

Research in NLP has mainly focused on factoid questions, with the goal of finding quick and reliable ways of matching a query to an answer. However, human discourse involves more than that: it contains non-canonical questions deployed to achieve specific communicative goals. In this paper, we investigate this under-studied aspect of NLP by introducing a targeted task, creating an appropriate corpus for the task and providing baseline models of diverse nature. With this, we are also able to generate useful insights on the task and open the way for future research in this direction.
Supplementary Figure 1 from Altered Runx1 Subnuclear Targeting Enhances Myeloid Cell Proliferation and Blocks Differentiation by Activating a miR-24/MKP-7/MAPK Network (2023)

Supplementary Figure 1 from Altered Runx1 Subnuclear Targeting Enhances Myeloid Cell Proliferation and Blocks Differentiation by Activating a miR-24/MKP-7/MAPK Network
Using the Catherine Bergego Scale (CBS) in Rehabilitation of Spatial Neglect: Kessler-CBS Process (P02.033) (2012)

Objective: To introduce the Kessler-CBS Process, a detailed item-by-item instruction for reliably administering a validated functional neglect assessment to stroke survivors. Background Spatial neglect is a debilitating post-stroke neurocognitive disorder, associated with longer hospitalization and worse rehabilitation outcomes. However, clinicians have difficulty reliably identifying affected survivors, even when using validated neglect assessment procedures. CBS is the only published tool assessing performance in personal, peri-personal (within arm9s reach) and extra-personal spaces, as well as in both perceptual and motor domains. Our team at the Kessler Foundation Research Center has used the CBS in our rehabilitation research on spatial neglect since 2008. However, we encountered implementation obstacles in reliably administering and scoring this instrument, and thus developed the K-CBS Process to standardize spatial neglect diagnosis and enhance stroke care. Design/Methods: Rehabilitation researchers, physiatrists, and occupational therapists (OTs) drafted a detailed manual for using and scoring the CBS, reviewed videos of the actual CBS administration by OTs, and refined the manual in four iterative cycles over three years. The K-CBS Process constrained key features of examiners9 structured observations. Results: The K-CBS Process uses two forms: Form A contains the table of the scale and instructions for calculating the final score and assigning the severity of spatial neglect; Form B provides item by item instructions for how to make observations. Conclusions: Research confirms the validity and value of the CBS as an outcome measure, and it has the unique attribute of potentially separating function in different brain-behavior networks supporting different spatial processing stages. The Kessler-CBS Process may improve the CBS, making it more reliable for detecting spatial neglect and its functional consequences, and may help clinicians to assign neglect treatments. Routinely identifying post-stroke spatial neglect fulfills national post-stroke rehabilitation guidelines and may enhance the quality of care and improve rehabilitation outcomes for these patients. Supported by: The Kessler Foundation and the NIH/NINDS (K02 NS 047099-05, R01 NS 055808-02, PI: Barrett). Disclosure: Dr. Chen has nothing to disclose. Dr. Hreha has nothing to disclose. Dr. Fortis has nothing to disclose. Dr. Goedert has nothing to disclose. Dr. Barrett has received personal compensation for activities with WebMD. Dr. Barrett has received research support from the Kessler Foundation, NIH, O9Brien Technologies, Pfizer/Eisai, and the Wallerstein Foundation for Geriatric Improvement.
Variation in sex steroid methyl transferases associated with androgen deprivation therapy (ADT) efficacy in advanced prostate cancer. (2011)

4647 Background: The association of germline variation in genes regulating hormonal pathways with duration of treatment response in advanced prostate cancer patients receiving ADT was evaluated, focusing on genes in the androgen biosynthesis (the C4 Δ; C5 Δ; C21 CYP pathways and the alternate “backdoor pathway”) and metabolism pathways. Methods: We successfully genotyped 747 single nucleotide polymorphisms (SNPs) from 84 genes in a cohort of 304 patients with advanced prostate cancer who progressed on ADT. Tagging SNPs with a minor allele frequency (MAF) of >5% and r2 ≥0.8 were selected from HapMap, NIEHS and Seattle SNP databases. The primary endpoint was time to ADT failure, and we conducted a gene-level test (principal components), along with individual SNP level tests adjusted for patient age and Gleason score. To account for multiple testing, we calculated the false discovery rate (FDR), and FDRs of 0.10 were considered noteworthy. Results: The median age of the cohort at ADT failure was 72 years (range 65-78 years), and the overall median time to ADT failure was 3.21 years (IQ (25-75): 1.54-6.20 years). At the gene level, TRMT11 (tRNA methyltransferase 11 homologue) showed the strongest association with time to ADT failure (p<0.0008; adjusted p-value for FDR-0.068). Two of four TRMT11 tag SNPs were associated with time to ADT failure. The first was the intronic SNP rs1268121 (A>G) with a MAF of 15%, for which there was a positive association of median time to ADT failure with the number of variant alleles (p=0.023): 3.1 years for 0, 4.1 years for 1, and 5.9 years for 2 variant alleles. The second was the SNP rs6900796 (A>G) in the 3’ untranscribed region with a MAF of 49%, for which the median time to ADT failure was 2.6 years for 0, 2.5 years for 1, and 3.8 years for 2 variant alleles (p=0.023). Four additional genes showed an association with ADT response at the p<0.10 level, including LOC390956, PRMT3, SLC7A6OS, and WBSCR22, although all FDRs were >0.95. Conclusions: Variation in TRMT11 was associated with time to ADT failure. Confirmation of these findings in an independent cohort is needed.
Moving Electrons Purposefully through Single Molecules and Nanostructures: A Tribute to the Science of Professor Nongjian Tao (1963–2020) (2020)

Electrochemistry intersected nanoscience 25 years ago when it became possible to control the flow of electrons through single molecules and nanostructures. Many surprises and a wealth of understanding were generated by these experiments. Professor Nongjian Tao was among the pioneering scientists who created the methods and technologies for advancing this new frontier. Achieving a deeper understanding of charge transport in molecules and low-dimensional materials was the first priority of his experiments, but he also succeeded in discovering applications in chemical sensing and biosensing for these novel nanoscopic systems. In parallel with this work, the investigation of a range of phenomena using novel optical microscopic methods was a passion of his and his students. This article is a review and an appreciation of some of his many contributions with a view to the future.
III-V Compound Avalanche Photodiodes on Silicon (2019)

We demonstrate the first III-V avalanche photodiodes grown directly on silicon by heteroepitaxy. The InGaAs/InAlAs APD exhibits gain > 20, low dark current, quantum efficiency > 40%, and low excess noise (k value ~0.2).
Experimental and Numerical Analysis on the Seizure of a Carbon-Filled PTFE Central Groove Journal Bearing during Start-Up Period (2018)

During the start-up period, if the journals bearing bushing and shaft materials have different heat conductivities, the thermal expansion of the shaft might be more rapid than that of the bushing. This reduces the radial clearance between the bearing components and generates higher shear stresses in the lubricating fluid, which can lead to bearing seizure, resulting in the deterioration of the journal bearing. (1) First, we present an experimental case study of the seizure of a central groove journal bearing with a carbon-filled polytetrafluoroethylene (PTFE) bushing and a steel shaft; (2) Then, a static thermoelastohydrodynamic (TEHD) simulation is compared to Cristea’s experiments (Cristea, A.-F., 2012); (3) Then, a pseudo-transient TEHD simulation is performed in order to numerically predict the observed phenomena on the test rig; (4) Finally, the evolution of the oil flow rate and the bushing temperatures during the start-up period determined with the pseudo-transient TEHD modelling are compared to the experimental data of the test rig. The pressure field is determined with the thermohydrodynamic (THD) Elrod’s modelling, with Vijayaraghvan’s robust solver algorithm. The pseudo-transient temperature field in the bearing components as well as the thermal and mechanical deformations are calculated with a commercial software.
XPS Studies of Chemically Modified Banana Fibers (2006)

Banana fibers obtained from the sheath of the banana plant (Musa Sapientum) whose major constituent is cellulose were modified using various chemical agents in order to improve their compatibility with the polymer matrix. The change in the surface composition of the raw and chemically modified fiber was investigated using various techniques such as solvatochromism, electrokinetic measurements, and XPS. Surface characterization by XPS showed the presence of numerous elements on the surface of the fiber. Investigation of the surface after alkali treatment on the other hand showed the removal of most of the elements. Silane treatment was found to introduce a considerable amount of silicon on the surface of the fiber. The [O]/[C] ratio was found to decrease in all cases except for the fluorinated and vinyl silane treated fibers. Detailed investigation of the deconvoluted C 1s spectra revealed the change in the percentage atomic concentration of the various elements on the fiber surface. The dissolution of the various surface components by alkali treatment, which was earlier revealed by SEM, was further confirmed by XPS. The XPS results were found to perfectly agree with the solvatochromic and electrokinetic measurements.
Effects of culture supernatant from Lactobacillus pentosus strain S-PT84 on autonomic nerve activity in rats. (2012)

Intestinal administration of various lactobacilli has been reported to affect autonomic neurotransmission, blood pressure, blood glucose, and body weight in rats, however, the mechanisms of action of the lactobacilli remain to be clarified. Therefore, the effect of the culture supernatant of Lactobacillus pentosus strain S-PT84 on the autonomic nerve activity in urethane-anesthetized rats was investigated. Intraduodenal injection of the low-molecular-weight (LMW) fraction (molecules less than 10,000 Da) of the S-PT84 culture supernatant elevated the brown adipose tissue sympathetic nerve activity and reduced the gastric vagal nerve activity. Moreover, intraoral administration of this LMW fraction increased the body temperature of rats above the interscapular brown adipose tissue. These results suggest that the LMW fraction of the S-PT84 culture supernatant affects the autonomic nerve activity and thermogenesis, and that the change in thermogenesis may be caused by the change in the sympathetic nerve activity of brown adipose tissue.