gebhart/patrepeval huggingface dataset:
Osmanli Arşivleri İçerik-Bazli Sorgulama (İBS) Sistemi Content-Based Retrieval (CBR) System for Ottoman Archives (2006)

We propose a content-based retrieval (CBR) system for digital Ottoman archive documents. In this system, the symbols extracted from the documents are matched with the most similar one in the symbol library, which is created in a supervised manner. The users specify queries by marking a region on an example document and the system retrieves all documents that include the symbols found in the query region. A prototype of the system is currently available on the Web.
Fine-Tuning of Piezo1 Expression and Activity Ensures Efficient Myoblast Fusion during Skeletal Myogenesis (2022)

Mechanical stimuli, such as stretch and resistance training, are essential in regulating the growth and functioning of skeletal muscles. However, the molecular mechanisms involved in sensing mechanical stress during muscle formation remain unclear. Here, we investigated the role of the mechanosensitive ion channel Piezo1 during myogenic progression of both fast and slow muscle satellite cells. We found that Piezo1 level increases during myogenic differentiation and direct manipulation of Piezo1 in muscle stem cells alters the myogenic progression. Indeed, Piezo1 knockdown suppresses myoblast fusion, leading to smaller myotubes. Such an event is accompanied by significant downregulation of the fusogenic protein Myomaker. In parallel, while Piezo1 knockdown also lowers Ca2+ influx in response to stretch, Piezo1 activation increases Ca2+ influx in response to stretch and enhances myoblasts fusion. These findings may help understand molecular defects present in some muscle diseases. Our study shows that Piezo1 is essential for terminal muscle differentiation acting on myoblast fusion, suggesting that Piezo1 deregulation may have implications in muscle aging and degenerative diseases, including muscular dystrophies and neuromuscular disorders.
Natural Compounds with Potential to Modulate Cancer Therapies and Self-Reactive Immune Cells (2020)

Cancer-related deaths are approaching 10 million each year. Survival statistics for some cancers, such as ovarian cancer, have remained unchanged for decades, with women diagnosed at stage III or IV having over 80% chance of a lethal cancer recurrence after standard first-line treatment (reductive surgery and chemotherapy). New treatments and adjunct therapies are needed. In ovarian cancer, as in other cancers, the immune response, particularly cytotoxic (CD8<sup>+</sup>) T cells are correlated with a decreased risk of recurrence. As well as completely new antigen targets resulting from DNA mutations (neo-antigens), these T cells recognize cancer-associated overexpressed, re-expressed or modified self-proteins. However, there is concern that activation of self-reactive responses may also promote off-target pathology. This review considers the complex interplay between cancer-reactive and self-reactive immune cells and discusses the potential uses for various leading immunomodulatory compounds, derived from plant-based sources, as a cancer therapy option or to modulate potential autoimmune pathology. Along with reviewing well-studied compounds such as curcumin (from turmeric), epigallocatechin gallate (EGCG, from green tea) and resveratrol (from grapes and certain berries), it is proposed that compounds from novel sources, for example, native Australian plants, will provide a useful source for the fine modulation of cancer immunity in patients.
Parallel, Solution Phase Synthesis of Dihydropyridine Miticides Via a Versatile Multicomponent Reaction (2005)

A novel class of highly active dihydropyridine miticides was prepared using a multicomponent reaction process. The initial lead was rapidly optimized using solution phase parallel synthesis techniques and a positional scanning approach. Detailed structure-activity relationships were developed for the amino and carbonyl components of the molecule and used to select the best candidates for broad field testing. The chemistry, biology and toxicology of these compounds will be presented along with numerous structural variants of the reaction products.
Distributed consensus networks of neutral type (2015)

We propose and study a network of autonomous agents which evolve their state under a distributed consensus algorithm of non-linear neutral type. We provide sufficient conditions for convergence to a common consensus point, by means of a stability in variation argument and fixed point theory. Our approach provides both an estimation on the rate of convergence and an implicit expression for the consensus point.
Nanostructured Silicon Surfaces for Cost-Effective Photovoltaic Efficiency Improvements: LDRD Final Report (2003)

No abstract prepared.
The 22q11.2 region regulates presynaptic gene-products linked to schizophrenia (2022)

It is unclear how the 22q11.2 deletion predisposes to psychiatric disease. To study this, we generated induced pluripotent stem cells from deletion carriers and controls and utilized CRISPR/Cas9 to introduce the heterozygous deletion into a control cell line. Here, we show that upon differentiation into neural progenitor cells, the deletion acted in trans to alter the abundance of transcripts associated with risk for neurodevelopmental disorders including autism. In excitatory neurons, altered transcripts encoded presynaptic factors and were associated with genetic risk for schizophrenia, including common and rare variants. To understand how the deletion contributed to these changes, we defined the minimal protein-protein interaction network that best explains gene expression alterations. We found that many genes in 22q11.2 interact in presynaptic, proteasome, and JUN/FOS transcriptional pathways. Our findings suggest that the 22q11.2 deletion impacts genes that may converge with psychiatric risk loci to influence disease manifestation in each deletion carrier.
The Mass Balance Technique of Managed Pressure Drilling, Reaching the Drilling Objectives Safely and Successfully Beyond the Conventional Limits of HPHT Deepwater Wells. (2011)

Abstract Managed Pressure Drilling (MPD) is an advanced form of primary well control usually employing a closed and pressurizable circulating drilling fluids (mud) system which facilitates drilling with precise management of the wellbore pressure profile. The primary objective of MPD is to optimize drilling processes by decreasing nonproductive time (NPT), mitigating drilling hazards and to enable the drilling of otherwise technically or economically un-drillable high-complexity prospects. Because MPD addresses NPT, the technology is of greatest potential benefit to offshore drilling programs where cost of dealing with drilling trouble zones is much higher than onshore. Although MPD was been safely and efficiently practiced from all types of offshore rigs and producing the desired results in the process, it is still considered a relatively "new" technology to the majority of offshore drillers. This impressive uptake in offshore MPD applications is due in part to a requirement to drill in greater water depths, through depleted zones or reservoirs and into narrow or relatively unknown equivalent mud weight (EMW) drilling windows. As evidenced by the greatly increased cost of drilling today's prospects, pre-salt drilling in deep water and HT/HP wells being good examples, it is easy to understand why many are concluding that most of the "easy" prospects have already been drilled. Those remaining are more likely to be "hydraulically challenged," requiring more precisely controlled management of the wellbore pressure profile to be drilled safely and efficiently. The following paper will explain interesting and important MPD topics related with the experience on:–Challenges associated with heaving from a micro-flux perspective, substantiated by high precision pressure sensors.–Kick/loss detection under heaving conditions detecting gains/losses within a micro-influx perspective.–Tactics to improve MPD operations in deepwater environments by the automation choke actuation systems and associated control algorithms.–Tactics for Safeguarding the Riser during MPD Operations.–Tactics for ascertaining the effectiveness of drilling with statically underbalanced mud to reduce/eliminate losses and maintain wellbore stability.
Gargle Lavage as a Safe and Sensitive Alternative to Swab Samples to Diagnose COVID-19: A Case Report in Japan (2020)

August) 893 itself [6]. This pandemic will pass, what will stay is the damage created by labeling people who are foreign as dangerous, by putting ourselves first and others last, and by having a very narrow scope of our sense of responsibility in the response to this pandemic. Now is not the time to have this "us against them mentality. " There can be strength in cross-collaboration at all levels to resolve this pandemic. Even in the setting of social distancing, families and communities can remain strong by staying virtually connected and by being creative around problem solving to make provision for food, shelter, and child care. But our sense of duty doesn't need to stop with us. Globally, there is a need to create an environment for shared learning regardless of ideology. This is necessary to inform public health responses but also to share knowledge and resources for the development of vaccines and therapeutics. As COVID-19 continues to spread to now also affect low-resource countries that, under regular circumstances, have very limited capacity for intensive care, I hope that we will not repeat the mistakes of the past as seen with the HIV epidemic where lifesaving drugs were only available in highresource countries, leaving impoverished nations with limited or no access to lifesustaining therapies. COVID-19 is not an Asian problem, it's not a European or even an American problem. It's a global problem that involves each of us and we should all be invested in coming up with solutions for ourselves, our neighbors, and for the world.
MRI-Based Digital Models Forecast Patient-Specific Treatment Responses to Neoadjuvant Chemotherapy in Triple-Negative Breast Cancer (2022)

Integrating MRI data with biologically based mathematical modeling successfully predicts breast cancer response to chemotherapy, suggesting digital twins could facilitate a paradigm shift from simply assessing response to predicting and optimizing therapeutic efficacy.
Ultra Clean Processing of Silicon Surfaces : Proceedings of the Fourth International Symposium on Ultra Clean Processing of Silicon Surfaces (UCPSS'98), held in Ostend, Belgium, September 21-23,1998 Vols. 65-66 Vols.65-66 (1999)

These proceedings try to cover all aspects of ultra-clean Si-technology: cleaning, contamination control, Si-surface chemistry and topography, and its relationship to device performance and process yield. New areas of concern included, cleaning at the interconnect level, resist strip and polymer removal (dry and wet), cleaning and contamination aspects of metallization, wafer backside cleaning and cleaning after Chemical-Mechanical-Polishing (CMP). Wet cleaning processes are still the dominant technology, despite the new results that have been obtained using dry cleaning processes. The conference also looked at the topic of ozonated DI-water as a replacement for hydrogen peroxide, or even sulfuric-based mixtures, which could potentially offer economical and environmental savings.
Solar spectral variations and their influence on concentrator solar cell performance (2013)

A comparative study is performed to quantify the difference in efficiency and spectral sensitivity between a tandem junction and its spectrum splitting parallel junction counterpart. Direct normal solar spectra in a representative sunny site, Tucson, Arizona are calculated using the SPCTRAL2 model at 15-minute intervals throughout a year with real-time meteorological data input. The corresponding efficiencies of the two junctions under 500X concentration at cell temperatures deduced from thermal modeling with real-time ambient temperatures are computed. Both junction structures comprise the same materials, InGaP, GaAs and Ge, and are each optimized to the AM1.5D standard spectrum and cell temperature of 25 C, under which the parallel junction achieves a 1.0% absolute (and 2.5% relative) higher efficiency than the tandem junction. The two junctions are compared for their hourly, daily, and yearly average efficiencies. It is found that the yearly average efficiency of the parallel junction is 2.65% absolute (and 7.31% relative) higher than that of the tandem junction.
Detection of Acyl-CoA Derivatized with Butylamide for <i>in vitro</i> Fatty Acid Desaturase Assay (2016)

Membrane-bound fatty acid desaturases acting on acyl-CoA contribute to the biosynthesis of unsaturated fatty acids, such as arachidonic acid and docosahexaenoic acid in higher organisms. We propose a simplified method for measuring the desaturase activity that combines the in vitro reaction by desaturase-expressing yeast cell homogenate and the detection of acyl-CoA product as butylamide derivatives by gas chromatography. To set up the in vitro reaction, we traced the in vivo activity of rat liver ∆6 fatty acid desaturase (D6d) expressed in the yeast, Saccharomyces cerevisiae, and determined the time taken for the D6d activity to reach its maximum level. The cell homogenate of yeast expressing the maximum D6d activity was made to react in vitro with linoleoyl-CoA to generate the D6d product, γlinolenoyl-CoA. This product was successfully detected as a peak corresponding to γ-linolenoyl butylamide on gas chromatography. This procedure, with low background expression, using non-labeled acyl-CoA as substrate, will contribute toward developing a simple in vitro desaturase assay. It will also help in elucidating the functions of membrane-bound fatty acid desaturases with various substrate specificities and regioselectivities.
Counterion Effects on Ion Mobility and Mobile Ion Concentration of Doped Polyphosphazene and Polyphosphazene Ionomers (2007)

A physical model of electrode polarization is applied to dielectric (impedance) data from two poly(methoxyethoxy−ethoxy phenoxyphosphazene) systems with nearly identical chemical structures, one composed of an ionomer with a single mobile cation and the other composed of a salt-doped polymer with mobile cation and mobile anion. Quantitative comparison of the ion mobility and mobile ion concentration, based on chemical structure, is achieved. Both conductivity and ion mobility are reduced to common curves by normalizing T with Tg, indicating that Tg of the polymer matrix is a major factor controlling ion diffusion. Even with the use of normalized temperature, both the mobility of ions and the mobile ion concentration in the doped polymers are ∼10 times larger than those in the ionomers. These factors arise from faster diffusion of the anion and the local environment surrounding ion pairs. Also, Arrhenius and VFT parameters associated with mobile ion concentration and ion mobility, respectively, reveal differences in activation energies between ionomer and doped polymer that are due to interactions between the ion pairs and polymer segments.
Evaluation of an oral telomerase activator for early age-related macular degeneration - a pilot study (2016)

Purpose: Telomere attrition and corresponding cellular senescence of the retinal pigment epithelium contribute to the changes of age-related macular degeneration. Activation of the enzyme telomerase can add telomeric DNA to retinal pigment epithelium chromosomal ends and has been proposed as a treatment for age-related macular degeneration. We report the use of a small molecule, oral telomerase activator (TA)-65 in early macular degeneration. This study, focusing on early macular degeneration, provides a model for the use of TAs in age-related disease. Method: Thirty-eight (38) patients were randomly assigned to a 1-year, double-blinded, placebo-controlled interventional study with arms for oral TA-65 or placebo. Macular functions via micro-perimetry were the primary measured outcomes. Results: The macular function in the arm receiving the TA-65 showed significant improvement relative to the placebo control. The improvement was manifest at 6 months and was maintained at 1 year: macular threshold sensitivity (measured as average dB [logarithmic decibel scale of light attenuation]) improved 0.97 dB compared to placebo ( P -value 0.02) and percent reduced thresholds lessened 8.2% compared to the placebo arm ( P -value 0.04). Conclusion: The oral TA significantly improved the macular function of treatment subjects compared to controls. Although this study was a pilot and a larger study is being planned, it is noteworthy in that it is, to our knowledge, the first randomized placebo-controlled study of a TA supplement. Keywords: drusen, macular degeneration, micro-perimetry, senescence, telomerase activation, telomere
Microwave filters with flat time delay both in passband and stopband (1975)

An exact method is presented to find a new class of parametrical polynomials which provides <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">(n - m)</tex> zero derivatives of relative delay at <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">p = 0</tex> and <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</tex> zero derivatives about <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">p = \infty</tex> . Explicit expressions of the polynomials for <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n = 2,3,4,5</tex> , and <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</tex> (and for <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0 \leq m \leq n</tex> ) are derived from a linear second-order differential equation. Among the possible applications of these polynomials we show their interest in equalizing a class of microwave filters and for design of multiplexing systems.
Preventing Patients with Crohnʼs Disease from Discontinuing Infliximab: A Dynamic Survival Model (2012)

Purpose: Infliximab (IFX) treatment has been shown in the literature to have a low rate of persistence, although there has been limited information on causes for discontinuation of IFX therapy. We reviewed charts and utilized dynamic modeling to predict the effect of a variety of interventions on the ability for patients to continue IFX in the community setting. Methods: Records of all 120 Crohn's disease patients treated with IFX at the NorthShore University HealthSystem from March 17th 2003 to September 1st 2010 were reviewed. Nine categories of reasons for discontinued treatment were found: 1) ongoing disease activity (13.3%), 2) acute infusion reactions (9.2%), 3) complications of therapy (9.17%), 4) chronic infusion reactions (6.67%), 5) health insurance reasons (5.83%), 6) patient intolerance (5.00%), 7) surgery (4.17%), 8) patient lost to follow up (4.17%), and 9) patient improved (0.83%). Reasons 1, 2, 4, and 5 were deemed points of intervention. Dose increases or changing medication could improve reason 1, premedication or changing medication could improve reasons 2 and 4, while attention to insurance could improve reason 5. We created a model to simulate IFX therapy persistence using STELLA (isee, Hanover, NH). Rates of discontinuation and timing of these occurrences used in model were determined from the collected data and simulated with Weibull distributions. Data was expressed as a Kaplan-Meyer survival analysis to show the instantaneous percent of people on the drug where infliximab persistence, represented as “survival”. We then simulated various degrees of improvement of the four previously described points of intervention and their effect on survival curves. Results: Intervention produced little effect of persistence of therapy. For example, with a 25% reduction in reasons 1, 2, 4, and 5, no improvement in overall persistence was seen (Figure 1). With a 90% reduction in all infusion reactions, only a 3-10% increase in IFX persistence is seen over 5 year period.Figure: No Caption available.Conclusion: Dynamic modeling is a constructive method for characterizing the effects of interventions to improve IFX therapy for Crohn's disease. Although improvement in persistence of IFX therapy can be achieved with aggressive interventions, marked enhancement of multiple factors are required to produce relatively small changes in the high discontinuation rate seen within the community setting.Table: Effect of changes in rate of infusion reactions on IFX persistence
A transgenic mouse model expressing an ERα folding biosensor reveals the effects of Bisphenol A on estrogen receptor signaling (2016)

Estrogen receptor-α (ERα) plays an important role in normal and abnormal physiology of the human reproductive system by interacting with the endogenous ligand estradiol (E2). However, other ligands, either analogous or dissimilar to E2, also bind to ERα. This may create unintentional activation of ER signaling in reproductive tissues that can lead to cancer development. We developed a transgenic mouse model that constitutively expresses a firefly luciferase (FLuc) split reporter complementation biosensor (NFLuc-ER-LBD<sub>G521T</sub>-CFLuc) to simultaneously evaluate the dynamics and potency of ligands that bind to ERα. We first validated this model using various ER ligands, including Raloxifene, Diethylstilbestrol, E2, and 4-hydroxytamoxifen, by employing FLuc-based optical bioluminescence imaging of living mice. We then used the model to investigate the carcinogenic property of Bisphenol A (BPA), an environmental estrogen, by long-term exposure at full and half environmental doses. We showed significant carcinogenic effects on female animals while revealing activated downstream ER signaling as measured by bioluminescence imaging. BPA induced tumor-like outgrowths in female transgenic mice, histopathologically confirmed to be neoplastic and epithelial in origin. This transgenic mouse model expressing an ERα folding-biosensor is useful in evaluation of estrogenic ligands and their downstream effects, and in studying environmental estrogen induced carcinogenesis in vivo.