gebhart/patrepeval huggingface dataset:
Hydroxychloroquine (HCQ) Modulates Autophagy and Oxidative DNA Damage Stress in Hepatocellular Carcinoma to Overcome Sorafenib Resistance via TLR9/SOD1/hsa-miR-30a-5p/Beclin-1 Axis (2021)

Sorafenib is used for treating advanced hepatocellular carcinoma (HCC), but some patients acquire sorafenib resistance. We investigated the mechanisms underlying acquired sorafenib resistance in HCC cells and targeted them to re-sensitize them to sorafenib. In silico analysis indicated that toll-like receptor (TLR)-9 was significantly overexpressed, and that miRNA (hsa-miR-30a-5p) was downregulated in sorafenib-resistant HCC cells, which modulated HCC cell proliferation, oxidative stress, and apoptosis. TLR9 overexpression increased HCC cell proliferation, whereas TLR9 inhibition from hydroxychloroquine (HCQ) decreased HCC cell proliferation, tumor growth, oxidative stress marker (SOD1), and the formation of autophagosome bodies (reduced ATG5 and Beclin-1 expression). Moreover, HCQ treatment reduced epithelial-mesenchymal transition, leading to decreased clonogenicity, migratory ability, and invasiveness. HCQ targeted and reduced the self-renewal capacity phenotype by inhibiting tumorsphere generation. Both in vitro and in vivo results demonstrated the synergistic effect of the HCQ-sorafenib combination on sorafenib-resistant HCC (Huh7-SR) cells, increasing their sensitivity to treatment by modulating TLR9, autophagy (ATG5 and Beclin-1), oxidative stress (SOD1), and apoptosis (c-caspase3) expression and thus overcoming the drug resistance. This study's findings indicate that TLR9 overexpression occurs in sorafenib-resistant HCC cells and that its downregulation aids HCC suppression. Moreover, HCQ treatment significantly increases sorafenib's effect on sorafenib-resistant HCC cells.
Annealing Optimization for Progressive Learning with Stochastic Approximation (2022)

In this work, we introduce a learning model designed to meet the needs of applications in which computational resources are limited, and robustness and interpretability are prioritized. Learning problems can be formulated as constrained stochastic optimization problems, with the constraints originating mainly from model assumptions that define a trade-off between complexity and performance. This trade-off is closely related to over-fitting, generalization capacity, and robustness to noise and adversarial attacks, and depends on both the structure and complexity of the model, as well as the properties of the optimization methods used. We develop an online prototype-based learning algorithm based on annealing optimization that is formulated as an online gradient-free stochastic approximation algorithm. The learning model can be viewed as an interpretable and progressively growing competitive-learning neural network model to be used for supervised, unsupervised, and reinforcement learning. The annealing nature of the algorithm contributes to minimal hyper-parameter tuning requirements, poor local minima prevention, and robustness with respect to the initial conditions. At the same time, it provides online control over the performance-complexity trade-off by progressively increasing the complexity of the learning model as needed, through an intuitive bifurcation phenomenon. Finally, the use of stochastic approximation enables the study of the convergence of the learning algorithm through mathematical tools from dynamical systems and control, and allows for its integration with reinforcement learning algorithms, constructing an adaptive state-action aggregation scheme.
The 1999 West Nile virus warning signal revisited (2021)

The 1999 unprecedented emergence of West Nile virus in the western hemisphere represented a health security warning intelligence failure. This paper reviews the timeline of warning signal recognition and associated missed opportunities to bridge strategic and tactical assessments. The complexity of signal evolution involving multiple public and private institutions and professional disciplines, coupled to inherent biases and shortfalls in interpretation, resulted in significant delays in warning communication and lost opportunity for preparedness and emergency response.
Supplementary Methods from A Threshold of Systemic MAGE-A Gene Expression Predicting Survival in Resected Non–Small Cell Lung Cancer (2023)

&lt;p&gt;Detailed description of method and study protocol&lt;/p&gt;
Inhibitory Kinetics and Mechanism of Flavonoids Extracted fromCotinus coggygriaScop. Against Glioblastoma Cancer (2016)

This proposal seeks to study the potential therapeutic modality of chemoprevention and anticancer effects and mechanisms of the flavonoids from Cotinus coggygria Scop. on glioblastoma cancer. In the current study, the total flavonoids (TFs) isolated from Cotinus coggygria Scop. var. cinerea Engl. (Cotinus coggygria Scop.) and the major flavonoids of Cotinus coggygria Scop. (CCFs) were identified, and the inhibitory kinetics of TF and CCF on glioblastoma cell lines were calculated. We also investigated whether TF or CCF regulated the apoptotic mechanism in cellular models of glio-blastoma cells. Finally, we evaluated whether treatment with TF or CCF suppressed tumor growth and inhibited migration in orthotopic mouse models of glioblastoma in vivo. In this study, the CCFs were identified as rutin, myricetin, and fisetin. TF and CCF remarkably inhibited cell proliferation and downregulated the PI3K/Akt and ERK signaling pathway in glioblastoma cell lines. Furthermore, the mitochondrial caspase-dependent cascade was regulated by TF and myricetin. In addition, TF and myricetin exhibited significant antitumor effects on glioblastoma in vivo. Taken together, these results suggest that phytochemical and biological data provide evidence for the active components in Cotinus coggygria, and that the TFs are responsible for the anticancer effects on glioblastoma cell growth via induction of apoptosis. In addition, the representative compound myricetin could provide a clinically relevant therapeutic opportunity. Therefore, our data strongly suggest that myricetin-deprived CCF can serve as a potent chemopreventive herbal medicine.
Abstract 4143: Enhancing adaptive immune responses with telomerase-mediated telomere targeting therapeutics in hepatocellular carcinoma (2023)

Abstract Hepatocellular carcinoma (HCC) is the most common primary malignant tumor of the liver and is the third leading cause of cancer-related deaths. In recent years, immune checkpoint inhibitors (ICIs) have improved treatment of solid tumors including HCC. However, due to low response rates with current standard of care immunotherapy and angiogenic inhibitors, there is an urgent need to develop new therapeutic strategies to improve the efficacy of immunotherapy against HCC. Our lab has shown that 6-thio-2’ deoxyguanosine (6-thio-dG), a telomerase-mediated telomere targeting agent, is incorporated into newly synthesized telomeres by telomerase and causes rapid telomere uncapping, thereby inducing telomere-associated DNA damage in cancer cells. These damaged DNA fragments can then lead to enhanced adaptive immune responses. In this study, we evaluated the therapeutic effects of 6-thio-dG in vitro and in vivo together with ICIs in liver tumors to determine whether combining immunotherapy with a telomere-targeting agent could serve as an effective strategy for HCC. To explore whether 6-thio-dG is effective in killing liver cancer cells, we ran cell viability and telomere dysfunction induced foci (TIF) assays to assess DNA damage on telomeres in vitro and compared tumor volumes of mice following 6-thio-dG monotherapy, immunotherapy, and sequential treatment of 6-thio-dG and immunotherapy in syngeneic mouse models. We observed that 6-thio-dG reduced cell viability and induced telomere dysfunction in a panel of human and mouse liver cancer cells. In addition, 6-thio-dG enhanced the therapeutic effect of immunotherapies in liver syngeneic mouse models. Overall, our findings show that the telomere-targeting anticancer agent 6-thio-dG inhibits HCC as a single monotherapy and/or sequential therapy together with immunotherapies. These results provide an experimental rationale for a potentially new immunochemotherapy strategy based on the administration of a telomere-targeting agent. Citation Format: Ann Marie Flusche, Jerry Shay, Ilgen Mender Ogunrinde. Enhancing adaptive immune responses with telomerase-mediated telomere targeting therapeutics in hepatocellular carcinoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4143.
Real-time imaging-guided microbubble mediated high intensity focused ultrasound heating in an ex-vivo machine-perfused pig liver (2018)

High intensity focused ultrasound (HIFU) is used clinically for the ablation of prostate and liver tumors. More recently, HIFU has been used in the brain for locally controlled thermal treatment of nonessential tremors. However, the thermal lesion location is restricted to a small area in the tissue due to geometric and boundary limitations (avoiding skin and bone burns). Bubble-enhanced heating (BEH) allows for the use of lower power and can generate spatially controlled thermal lesions in regions not currently accessible with conventional HIFU. We have studied BEH in vitro and in a machine perfused pig liver (MPL). The MPL presents a versatile platform for perfusion and BEH studies because it is clinically relevant and allows for delivery of microbubbles under ultrasound imaging. We first applied conventional HIFU and BEH in vitro, in an enclosure with acoustic windows contaiing glycerin and microbubbles while monitoring the temperature with a fine wire thermocouple. A focused 1 MHz transducer and various clinically approved microbubbles were used. Then we applied BEH on the MPL by introducing microbubbles under image guidance. With this initial study, we have observed that BEH has resulted in 5-10x energy reduction for the formation of a reference lesion in vitro, and 3-6x in the MPL.
LUMBAR PEDICLE SUBTRACTION OSTEOTOMY (2007)

The correction of lumbar kyphotic deformities requires careful preoperative clinical and radiographic evaluation. For patients with rigid deformities at locations where previous anterior spinal surgery was performed, pedicle subtraction osteotomy remains an attractive treatment option. This technique uses a single-stage posterior approach for removal of the posterior elements and a wedge of the vertebral body. Using this method, it is possible to introduce up to 35 degrees of lumbar lordosis and add up to 10 cm of posterior trunk translation. Patient satisfaction from correction of these deformities is frequently excellent, but a high degree of attention must be directed to avoid neural injuries and reduce intraoperative blood loss.
Pyrolysis Yields from Microwave-Assisted Heating of Solid Wastes (2012)

This paper continues previous work on pyrolysis processing of solid wastes for spacecraft and planetary surface applications. A domestic microwave oven was modified for use in this work for scoping studies in which the effects of sample composition, use of central microwave absorbers, and secondary pyrolysis of liquids were studied. Experiments were done with wheat straw and various formulations of a feces simulant. The microwave absorbers examined included activated carbon and char produced from previous experiments. The addition of a separate microwave-heated secondary pyrolysis zone was also examined as a means of reducing the liquid product yields. In general, the feces simulants had similar pyrolysis yields when compared to wheat straw for the char and total gas yields, but individual gas yields were different. For example, the feces simulants produced significantly more ethylene, larger amounts of methane, and smaller amounts of carbon oxides (CO + CO2). This can be largely explained by the differences in elemental compositions. A comparison was also made of the microwave-assisted pyrolysis of feces simulants of variable moisture contents (0-60 wt. %). The higher moisture contents (40-60 wt. %) result in a delay for the onset of pyrolysis and a higher energy demand per gram of sample, as might be expected. However, at lower moisture contents, such as the 20 wt. % water for the baseline sample, it was found that the overall energy demand appeared to be lower than for the dried sample, perhaps due to the more efficient absorption of microwave energy.
Development of Non-TSV Interposer (NTI) for High Electrical Performance Package (2016)

Nowadays, 2.5D and 3D stacked die technologies are under prosperous development for the benefit of transistor scaling and performance. However, with the trend of higher electrical performance, lower power consumption and cost effective demand, Non-TSV interposer (NTI) is one of the ways to meet the requirement. This paper introduces and demonstrates the NTI process flow, which includes chip-on-wafer (CoW) stacking, mold encapsulation, silicon removal and chip module-on-substrate (CMoS) etc. We successfully solved the high wafer warpage issue and epoxy material out-gassing problem through material selection and process condition change. As a result, all processes were processed without any handling and quality issue. New NTI chip module's warpage variation between room temperature and reflow's peak temperature is less than 35 um, which dramatically reduces the stress during CMoS process.
A molecular sensitization map of European children reveals exposome‐ and climate‐dependent sensitization profiles (2023)

We show regional, exposome- and climate-dependent differences in molecular IgE-reactivity profiles in Northern, Western/Central and Southern Europe which may form a molecular basis for precision medicine-based approaches for treatment and prevention of allergy.
PANEL: Will 3D-IC Remain a Technology of the Future Even in the Future (2013)

If asked “who needs faster planes?” the vast majority of the 2.75 billion airline passengers (source: IATA 2011) would say that they do need faster planes, and that they need them right now. Still, the commercial aircrafts cruising speed has remained the same - 800 km/hour - over the last 50+ years, and after the sad end of the Concorde project, neither Airbus nor Boeing are seriously working on the topic. Along the same lines, when asked “who needs 3D-IC?”, most IC designers say that they desperately need 3D-IC to keep advancing electronic products performance, whilst addressing the needs of higher bandwidth, lower cost, heterogeneous integration, and power constraints. Still, 3D-IC continues to be the technology of the future. What are the road blocks towards 3D-IC adoption? Is it process technology, foundry or OSAT commercial offering, or EDA, or the business economics that is holding 3D-IC on the ground? In the introductory presentation of this panel session, LETI Patrick Leduc will illustrate the state-of-the-art of commercial, mainstream 3D-IC. EPFL Professor Giovanni de Micheli will then moderate an industry and research panel, to understand what are the key factors preventing 3D-IC from becoming the technology of today.
A Coupled Hydrodynamic-Wave Model for Simulating Wave and Tidally-Driven 2D Circulation in Inlets (2002)

This study focuses on modeling the 2D, depth-averaged circulation of an ideal inlet that is driven by waves and tides using a coupled hydrodynamic-wave model. The circulation of an ideal inlet, consisting of a shallow bay of constant depth connected by a relatively narrow inlet to a sloping coastal shelf region, is studied. Circulation within the inlet is examined during the flood, slack, and ebb phases of the tidal cycle. The ideal inlet is also simulated with only wave forcing to better understand the effect of wave-current interaction on the circulation. The influence of the various forcings on bay/inlet circulation is further investigated by the introduction of Lagrangian tracers. Wave-current interaction is simulated by iteratively coupling the depth-integrated ADCIRC-2DDI hydrodynamic model to the 2D phase-averaged spectral wave model SWAN. ADCIRC-2DDI is a fully developed, 2-dimensional, finite element, barotropic hydrodynamic model capable of including wind, wave, and tidal forcing as well as river flux into the domain. The iterative hydrodynamic-wave model coupling is captured through the following approach. First, radiation stress gradients, determined from the SWAN wave field, serve as a surface stress forcing for ADCIRC. Elevations and currents, computed from ADCIRC, are subsequently input into the SWAN model at each iteration. The surface stress is then recalculated using the new wave field. Between these iterations the ADCIRC model is run for some appropriately small time interval during which the wave field is held constant.
Effects of cationic liposome‐DNA complexes on pulmonary surfactant function in vitro and in vivo (1997)

Cationic liposome-DNA complexes are being evaluated as potential gene therapy agents for the lung. Cations have strong effects on the biophysical functions of lung surfactant. Therefore, we assessed whether cationic liposomes [composed of N-(1-(2,3-dioleyloxy) propyl)-N,N,N-trimethyl-ammonium chloride and dioleylphosphatidylethanolamine] with or without DNA affect behavior of four types of surfactant in vitro. Experiments were carried out using a modified Wilhelmy surface balance. The ability of surfactants that contain protein and anionic lipids to lower surface tension was inhibited in the presence of cationic liposomes. Inactivation was less when DNA was preincubated with cationic liposomes. Surfactant that contained neither protein nor anionic lipids was not inactivated. Mechanical properties of the lung were studied to assess in vivo surfactant function after intratracheal instillation of a cationic liposome-DNA complex into adult rats. Pressure-volume deflation curves were shifted by 18% compared with those from normal (untreated) animals, but this effect was transient and not different from that observed in animals who received a similar volume of saline. These findings indicate that cationic liposomes alone may have deleterious effects on behavior of some surfactants possibly by disrupting charge interactions between negatively charged phospholipids and surfactant proteins. When DNA is added to liposomes before exposure to surfactants, the adverse charge interactions may be obviated by charge neutralization of liposomes by DNA.
Interventional Musculoskeletal Procedures Performed by Using MR Imaging Guidance with a Vertically Open MR Unit: Assessment of Techniques and Applicability (2002)

With use of a vertically open MR unit, MR-guided interventional procedures involving bone, soft tissue, intervertebral disks, and joints are safe and sufficiently rapid for use in clinical practice.
Application of high current density ions from PW-PS laser pulse nonlinear force driven plasma blocks for X-ray lasers (2004)

The use of CPA laser pulses of less than 50 fs duration and power above 30 TW may permit conditions for x-ray lasers where in solid state dense heavy nuclei materials Kshell electrons are emitted by irradiation of 5 MeV protons with subsequent transition of L-shell electrons into the K-shell level. Alternatively, if the L-shell emission dominates, M-L-x-ray laser operation may be interesting. The CPA laser pulses are used to produce plane plasma blocks of several wave length thickness where space charge neutral 5 MeV proton beams of 10 11 Amps/cm 2 current densities are moving co-axially into the heavy nuclei material.
Cascaded hybrid analog modulated linear LED driver for DC distribution system (2017)

DC grids are becoming popular due to higher efficiency and simple solar integration architecture. DC grids enable implementation of simple structures like compact linear LED drivers. But due to variations in LED characteristics from one batch to another batch (variation in manufacturing process) and use of dimming to control light output, implementation of compact linear LED drivers results in loss of efficiency. To overcome the problem of variations in LED voltage, cumbersome binning process may be employed. But with aging or/and temperature variation, this implementation does not result in satisfactory solution. In the proposed model, low cost small compact boost converter is serially connected with analog modulated/unmodulated linear LED driver. In the proposed driver, mini-boost driver of one-tenth capacity is employed in series with linear driver for providing variable constant current to facilitate wide dimming range.
ChemInform Abstract: Efficient C—B Bond Formation Promoted by N‐Heterocyclic Carbenes: Synthesis of Tertiary and Quaternary B‐Substituted Carbons Through Metal‐Free Catalytic Boron Conjugate Additions to Cyclic and Acyclic α,β‐Unsaturated Carbonyls. (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
Storage requirement estimation for optimized design of data intensive applications (2004)

A novel storage requirement estimation methodology is presented for use in the early system design phases when the data transfer ordering is only partially fixed. At that stage, none of the existing estimation tools are adequate, as they either assume a fully specified execution order or ignore it completely. A prototype CAD tool has been developed that includes major parts of the storage requirement estimation and optimization methodology. Using representative application demonstrators, we show how our techniques and tool can effectively guide the designer to achieve a transformed specification with low storage requirement.
Monte Carlo simulations of pure liquid substituted benzenes with OPLS potential functions (1993)

Abstract Intermolecular potential functions have been developed for use in computer simulations of substituted benzenes. Previously reported optimized potentials for liquid simulations (OPLS) for benzene and organic functional groups were merged and tested in Monte Carlo statistical mechanics simulations for the pure liquids of toluene, m ‐cresol, anisole, aniline, and benzonitrile at 25°C at 1 atm. The merged potential functions yielded acceptable thermodynamic results for the liquids except in the case of aniline, for which the error in the heat of vaporization was 12%. This was remedied by enhancing the polarity of the model to be more consistent with the observed dipole moment of aniline. Overall, the average errors in computed heats of vaporization and densities were then 2 and 1%, respectively. The structures of the liquids were characterized through energy and radial distribution functions. For m ‐cresol and aniline, the molecules participate in averages of 1.6 and 1.4 hydrogen bonds, respectively. Condensed phase effects on the torsional energies for anisole, m ‐cresol, and aniline were found to be small; m ‐cresol has a slightly enhanced tendency to be nonplanar in the liquid than in the gas phase, while anisole shows the opposite pattern. © 1993 John Wiley &amp; Sons, Inc.
Refined localization of the asparagine synthetase gene (ASNS) to chromosome 7, region q21.3, and characterization of the somatic cell hybrid line 4AF/106/K015 (1994)

We have mapped the asparagine synthetase gene (ASNS) to 7q21.3 by fluorescence in situ hybridization. While this study refined the localization of the gene, it also revealed a rearrangement in a somatic cell hybrid line which was used in previous ASNS mapping. Using additional probes from other regions of human chromosome 7, we showed that this cell line (4AF/106/KO15) contained a rearranged chromosome 7 in which a segment of the long arm was apparently duplicated and inserted into the short arm. Caution should be used therefore when interpreting data obtained from this cell line for gene mapping studies.