gebhart/patrepeval huggingface dataset:
LY294002 Inhibits Intermediate Conductance Calcium-Activated Potassium (KCa3.1) Current in Human Glioblastoma Cells (2022)

Glioblastomas (GBs) are among the most common tumors with high malignancy and invasiveness of the central nervous system. Several alterations in protein kinase and ion channel activity are involved to maintain the malignancy. Among them, phosphatidylinositol 3-kinase (PI3K) activity and intermediate conductance calcium-activated potassium (KCa3.1) current are involved in several aspects of GB biology. By using the electrophysiological approach and noise analysis, we observed that KCa3.1 channel activity is LY294002-sensitive and Wortmannin-resistant in accordance with the involvement of PI3K class IIβ (PI3KC2β). This modulation was observed also during the endogenous activation of KCa3.1 current with histamine. The principal action of PI3KC2β regulation was the reduction of open probability in intracellular free calcium saturating concentration. An explanation based on the "three-gate" model of the KCa3.1 channel by PI3KC2β was proposed. Based on the roles of KCa3.1 and PI3KC2β in GB biology, a therapeutic implication was suggested to prevent chemo- and radioresistance mechanisms.
Characterization of Particle Number Setups for Measuring Brake Particle Emissions and Comparison with Exhaust Setups (2023)

The stringency of vehicle exhaust emissions regulations resulted in a significant decrease in exhaust particulate matter (PM) emissions over the years. Non-exhaust particles (i.e., from brakes and tyres) account for almost half or more of road transport-induced ambient PM. Even with the internal combustion engine ban in 2035, electrified vehicles will still emit PM from brake and tyre wear. Consequently, non-exhaust PM emissions cannot decrease significantly without any regulatory measures. Because independent research carried out under different methods is not readily comparable, a Global Technical Regulation (GTR), which sets the procedures and boundaries of testing brake wear particle emissions, is currently under development. This overview describes the particle number (PN) measurement setup based on the well-known exhaust emissions PN methodology. We provide the technical requirements and the expected maximum losses. In addition, we estimate the effect of particle losses on the differences between different setups for typical size distributions observed during brake testing. Finally, we compare brake testing PN specifications to those of exhaust PN.
Enhanced Electrocatalysis for the Reduction of Hydrogen Peroxide at New Multiwall Carbon Nanotube Grafted Polydiphenylamine Modified Electrode (2006)

Abstract A new modified electrode having multiwall carbon nanotube (MWNT) grafted with polydiphenylamine (PDPA) as electrocatalytic layer is fabricated. FESEM image of the modified electrode shows a different morphology indicating the grafting of PDPA over MWNT. This morphology is in quite contrast from the conventional bilayer MWNT/conducting polymer modified electrode. The multiwall carbon nanotube grafted polydiphenylamine (MWNT‐g‐PDPA‐ME) shows excellent electrocatalytic activity towards the reduction of hydrogen peroxide. The combined presence of MWNT and PDPA as a single unit provides better sensitivity than the bilayer configuration (MWNT/PDPA‐ME). This modified electrode shows accelerated electron transfer at the interface with minimized surface fouling and surface renewability. The advantages of MWNT‐g‐PDPA‐ME over the bilayer electrode are demonstrated with chronoamperometric studies. The amperometric response to H 2 O 2 obtained at −300 mV (vs. SCE) is rapid and highly sensitive as evident from the higher (2.83×10 −3 cm 3 mol −1 s −1 ) rate constant for the diffusion reduction process.
A<sub>2</sub>B-Miktoarm Glycopolymer Fibers and Their Interactions with Tenocytes (2017)

Electrospun biodegradable membranes have attracted great attention for a range of tissue engineering applications. Among them, poly(ε-caprolactone) (PCL) is one of the most widely used polymers, owing to its well-controlled biocompatibility and biodegradability. However, PCL also has a number of limitations, such as its hydrophobic nature and the lack of functional groups on its side chain, limiting its ability to interact with cells. Herein, we have designed and prepared a series of well-defined A<sub>2</sub>B-miktoarm copolymers with PCL and glycopolymer segments to address these limitations. Moreover, copolymers were electrospun to make membranes, which were studied in vitro to investigate cell affinity, toxicity, activity, and adhesion with these materials. The results indicate that incorporating glucose moieties into miktoarm polymers has improved the biocompatibility of the PCL while increasing the cellular interaction with the membrane material.
Multi-objective prioritization for data center vulnerability remediation (2022)

Nowadays, one of the most relevant challenges of a data center is to keep its information secure. To avoid data leaks and other security problems, data centers have to manage vulnerabilities, including determining the higher-risk vulnerabilities to prioritize. However, the current literature is scarce in the proposal of intelligent methods for the complex problem of vulnerabilities prioritization. Depending on the adopted metrics, the priority could shift, compromising simple sorting-based approaches and impairing the utilization of conflicting risk assessment metrics. Unlike the related work, this study proposes a multi-objective method that uses user-chosen vulnerabilities assessment metrics to output a complete list of these vulnerabilities ranked by their risk and overall impact in the context of an organization. The method includes a multi-objective large-scale optimization problem representation, a novel population initialization scheme, an expressive fitness function, a post-optimization process, and a custom way to select the best solution among the non-dominated ones. The dataset used in the experiments contains anonymized real-world information about database vulnerabilities obtained from a private organization. The experiments' results indicated that the proposed method can reduce the number of vulnerabilities needed to reach an organization's predefined security targets compared to the baselines simulating a security team's analysis. Multi-objective optimization achieved on average a 48,17% reduction in the vulnerabilities needed to reach the organization's target values compared to the baselines.
Suppression of Lipogenesis <i>via</i> Reactive Oxygen Species–AMPK Signaling for Treating Malignant and Proliferative Diseases (2017)

Gefitinib-resistant (G-R) nonsmall-cell lung cancer (NSCLC) and rheumatoid arthritis (RA) were studied as conditions representative of malignant and proliferative diseases, respectively. Strong lipogenic activity and high expression of sterol regulatory element-binding protein 1 (SREBP1) were found in both G-R NSCLC cells and synovial fibroblasts from RA patients (RASFs). Berberine (BBR), an effective suppressor of SREBP1 and lipogenesis regulated through reactive oxygen species (ROS)/AMPK pathway, selectively inhibited the growth of G-R NSCLC cells and RASFs but not that of normal cells. It effectively caused mitochondrial dysfunction, activated ROS/AMPK pathway, and finally suppressed cellular lipogenesis and cell proliferation. Addition of ROS blocker, AMPK inhibitor, and palmitic acid significantly reduced the effect of BBR. In an in vivo study, treatment of BBR led to significant inhibition of mouse tumor xenograft growth and remarkably slowed down the development of adjuvant-induced arthritis in rats. Innovation and Conclusion: Targeting ROS/AMPK/lipogenesis signaling pathway selectively inhibited the growth of G-R NSCLC cells and the progress of RASFs in vitro and in vivo, which provides a new avenue for treating malignancies and proliferative diseases. Antioxid. Redox Signal. 28, 339-357.
Comparative Quantification of Trail-Following Behavior in Pest Ants (2019)

A comparison of trail-following movement parameters of six major urban pest ants, <i>Nylanderia fulva</i> (Forel) (Hymenoptera: Formicidae), <i>Pheidole megacephala</i>, <i>Linepithema humile</i> (Mayr), <i>Solenopsis invicta</i> Buren, <i>Paratrechina longicornis</i> (Forel), and <i>Technomyrmex albipes</i> (Smith) demonstrated several differences in velocity of movement, amplitude of the deviations from a marked trail, percent fidelity to the trail, number of curves per unit of trail, and trail-following accuracy. <i>Paratrechina longicornis</i> and <i>N. fulva</i> had the largest deviations from the marked trails and moved three times faster (25-30 mm/s) along the trail than the slowest ant, <i>S. invicta</i> (< 10 mm/s), with other ants following between these extremes. Species differences in relation to going toward or returning from food were observed in a few cases, especially with <i>Pa. longicornis</i> for which velocity, amplitude, and trail fidelity differed between the foraging and return trails. Quantification of ant trail-following movement parameters can be useful in understanding the mechanics of ant movement and may be important in testing specific strategies and products that disrupt trail-following behavior.
Simple Evolutionary Optimization Can Rival Stochastic Gradient Descent in Neural Networks (2016)

While evolutionary algorithms (EAs) have long offered an alternative approach to optimization, in recent years backpropagation through stochastic gradient descent (SGD) has come to dominate the fields of neural network optimization and deep learning. One hypothesis for the absence of EAs in deep learning is that modern neural networks have become so high dimensional that evolution with its inexact gradient cannot match the exact gradient calculations of backpropagation. Furthermore, the evaluation of a single individual in evolution on the big data sets now prevalent in deep learning would present a prohibitive obstacle towards efficient optimization. This paper challenges these views, suggesting that EAs can be made to run significantly faster than previously thought by evaluating individuals only on a small number of training examples per generation. Surprisingly, using this approach with only a simple EA (called the limited evaluation EA or LEEA) is competitive with the performance of the state-of-the-art SGD variant RMSProp on several benchmarks with neural networks with over 1,000 weights. More investigation is warranted, but these initial results suggest the possibility that EAs could be the first viable training alternative for deep learning outside of SGD, thereby opening up deep learning to all the tools of evolutionary computation.
Models for Stationary Noise Propagation in Multi-sampled PWM Power Electronic Control Systems With Decimation (2023)

This article derives models for stationary noise propagation in multi-sampled control systems, taking decimation into account. It is explained how the decimation is either included deliberately, in case of multi-rate control, or inherently by the modulator, in case of multi-sampled pulsewidth modulation (MS-PWM). In the latter case, the decimation rate is determined by the switching frequency and the number of pulsewidth modulation (PWM) carriers. The proposed models are then used for digital filter design, with a goal of suppressing the decimation-related aliasing and attenuating noise, while considering the imposed impact on the dynamic response. The theory is verified in simulations and experimentally, confirming the assumed decimation mechanisms as well as the potentiality of MS-PWM to jointly enable high-bandwidth control and strong noise suppression. The experimental measurements are conducted on two hardware prototypes, comprising two-level and three-level dc–dc buck converters.
Abstract C121: Genomic characterization of invasive cervical cancer in Guatemala and Venezuela: Common activation of the PIK3CA pathway. (2013)

Abstract Cervical cancer represents the most dramatic cancer health disparity of women in the world, with over 270,000 deaths annually, concentrated in poor, rural, and indigenous populations. Guatemala and Venezuela are illustrative of this disparity as cervical cancer is the predominant cause of cancer cases and deaths in women. The average age of the subjects is 50, and smoking and oral contraceptive use is low. The affected women have an average of 6 children and adeno- or adenosquamous pathologies represent 25% of the tumors. To determine the genomic changes in invasive tumors, we initiated a prospective collection of invasive cervical cancer tissue. To determine the most frequently mutated genes we sequenced the exomes of 23 tumors in the Ion Torrent Proton and followed up with targeted sequencing of genes by Ampliseq in an additional 280 tumors. The exome sequence revealed potential driver mutations in several known cancer genes such as PTEN, PIK3CA, TSC1, SETD2, HRAS, PTCH, ARID1A, ARID4A and RB1. Targeted resequencing in a larger set of tumors of commonly mutated genes in the COSMIC database (PIK3CA, TP53, STK11, PTEN, KRAS, HRAS, and CDKN2A) revealed 40% mutation in PIK3CA and 11% in PTEN (a negative regulator of the PI kinase pathway). TP53 and STK11 were significantly mutated (10 and 8% of tumors, respectively) but HRAS, KRAS and CDKN2A at a very low level (0-2%). The PIK3CA mutations were concentrated in the known activating sites in the helical domain (E542K and E545K). To determine HPV stain types we amplified the HPV L1 gene found detectable in HPV in 96% of samples with HPV16 in 53%, HPV18 in 12%, HPV45 in 10% and HPV 26, 31, 33, 35, 39, 52, 56, 58, 67, 68, 69, and 73 in 0.8-4.9% of samples. In conclusion, invasive cervical cancers display frequent mutation of the helical domain of PIK3CA and activation of the PI kinase pathway, suggesting that targeted inhibition of this pathway may provide an avenue for therapy in this largely untreatable, common cancer. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):C121. Citation Format: Michael Dean, Eduardo Gharzouzi, Enrique Alvirez, Guillermo Villagran, Ushie Odey, Julie Sawitzke, Joe Boland, Hong Lou, Meredith Yeager. Genomic characterization of invasive cervical cancer in Guatemala and Venezuela: Common activation of the PIK3CA pathway. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr C121.
Spinal Cord Stimulation in Other Indications (2013)

Spinal cord stimulation (SCS) had been tried in many other disabling conditions with variable outcome. This chapter summarizes other uses of SCS, apart from failed back surgery syndrome and complex regional pain syndrome. It illustrates the three off&hyphen;label indications of SCS: motor control, vasoactive applications and genitourinary effects. SCS for minimally conscious and vegetative state may be used before considering more invasive approaches such as deep brain stimulation (DBS). The newer and promising indications such as cerebral vasospasm have a potential of significant improvement in morbidity and mortality in a very difficult patient category, while other directions such as SCS for brain tumors are still in their infancy with a rather uncertain future.
Chemoinformatic Approach: The Case of Natural Products of Panama (2019)

Chemoinformatic analysis was used to characterize a compound database of natural products from Panama and other reference collections. Data mining allowed to compare drug-likeness properties with public and commercial software and to achieve a statistical analysis of the physicochemical properties. Visualization of the chemical space in 3D indicates a high structural similarity. Molecular flexibility and complexity were evaluated using 2D descriptors, whereas the molecular scaffold was obtained using the Murcko method, and these showed few differences between the explored data set. In this chapter, we also present and discuss an example of the application of the chemoinformatic approach using the concept of modeling the activity landscape to study the structure-activity relationships (SARs) of compounds with activity against Plasmodium falciparum.
Tyramide Amplification Methods for In Situ Hybridization (2001)

The relative insensitivity of in situ hybridization (ISH) has been cited as an important limiting factor in the potential applications of this technique (1). Therefore, a major initiative on the part of researchers who use molecular biologic techniques is the improvement of sensitivity of ISH. There are two means of achieving this: the amplification of target sequences and the amplification of signal (2). The former encompasses such techniques as in situ polymerase chain reaction (PCR) and in situ reverse transcriptase (RT)-PCR, and is not discussed in this review. The latter includes catalyzed reporter deposition, a major component of which is the use of labeled tyramide as a means of signal amplification. This technique, which has subsequently been adapted for use in ISH from its initial immunohistochemical applications, is a powerful tool for increasing sensitivity in molecular biologic testing. Through the use of tyramide signal amplificationTM (TSATM), the theoretical limits of ISH can be approached.
Opportunities and Barriers to Rural Telerobotic Surgical Health Care in 2021: Report and Research Agenda from a Stakeholder Workshop (2021)

<b><i>Background:</i></b> There are well-recognized challenges to delivering specialty health care in rural settings. These challenges are particularly evident for specialized surgical health care due to the lack of trained operators in rural communities. Telerobotic surgery could have a significant impact on the rural-urban health care gap, but thus far, the promise of this method of health care delivery has gone unrealized. With the increasing adoption of telehealth over the past year, along with the maturation of telecommunication and robotic technologies over the past 2 decades, a reappraisal of the opportunities and barriers to widespread implementation of telerobotic surgery is warranted. Here we report the outcome of a rural telerobotic stakeholder workshop to explore modern-day issues critical to the advancement of telerobotic surgical health care. <b><i>Materials and Methods:</i></b> We assembled a multidisciplinary stakeholder panel to participate in a 2-day Rural Telerobotic Surgery Stakeholder Workshop. Participants had diverse expertise, including specialty surgeons, technology experts, and representatives of the broader telerobotic health care ecosystem, including economists, lawyers, regulatory consultants, public health advocates, rural hospital administrators, nurses, and payers. The research team reviewed transcripts from the workshop with themes identified and research questions generated based on stakeholder comments and feedback. <b><i>Results:</i></b> Stakeholder discussions fell into four general themes, including (1) operating room team interactions, (2) education and training, (3) network and security, and (4) economic issues. The research team then identified several research questions within each of these themes and provided specific research strategies to address these questions. <b><i>Conclusions:</i></b> There are still important unanswered questions regarding the implementation and adoption of rural telerobotic surgery. Based on stakeholder feedback, we have developed a research agenda along with suggested strategies to address outstanding research questions. The successful execution of these research opportunities will fill critical gaps in our understanding of how to advance the widespread adoption of rural telerobotic health care.
Role of Polymorphonuclear Myeloid‐Derived Suppressor Cells and Neutrophils in Ischemic Stroke (2023)

Background Immune cells play a vital role in the pathology of ischemic stroke. Neutrophils and polymorphonuclear myeloid-derived suppressor cells share a similar phenotype and have attracted increasing attention in immune regulation research, yet their dynamics in ischemic stroke remain elusive. Methods and Results Mice were randomly divided into 2 groups and intraperitoneally treated with anti-Ly6G (lymphocyte antigen 6 complex locus G) monoclonal antibody or saline. Distal middle cerebral artery occlusion and transient middle cerebral artery occlusion were applied to induce experimental stroke, and mice mortality was recorded until 28 days after stroke. Green fluorescent nissl staining was used to measure infarct volume. Cylinder and foot fault tests were used to evaluate neurological deficits. Immunofluorescence staining was conducted to confirm Ly6G neutralization and detect activated neutrophils and CD11b<sup>+</sup>Ly6G<sup>+</sup> cells. Fluorescence-activated cell sorting was performed to evaluate polymorphonuclear myeloid-derived suppressor cell accumulation in brains and spleens after stroke. Anti-Ly6G antibody successfully depleted Ly6G expression in mice cortex but did not alter cortical physiological vasculature. Prophylactic anti-Ly6G antibody treatment ameliorated ischemic stroke outcomes in the subacute phase. Moreover, using immunofluorescence staining, we found that anti-Ly6G antibody suppressed activated neutrophil infiltration into parenchyma and decreased neutrophil extracellular trap formation in penumbra after stroke. Additionally, prophylactic anti-Ly6G antibody treatment reduced polymorphonuclear myeloid-derived suppressor cell accumulation in the ischemic hemisphere. Conclusions Our study suggested a protective effect of prophylactic anti-Ly6G antibody administration against ischemic stroke by reducing activated neutrophil infiltration and neutrophil extracellular trap formation in parenchyma and suppressing polymorphonuclear myeloid-derived suppressor cell accumulation in the brain. This study may provide a novel therapeutic approach for ischemic stroke.
Molecular Recognition (2016)

In the past, aggregation and self-assembly have been associated principally with micellar and colloidal systems of molecules; however, with the advent of supramolecular chemistry, molecular self-assembly has been opened to a much wider understanding that has facilitated access to a variety of different shapes and sizes, along with the construction of new and fascinating molecular topologies. This document aims at defining more than 150 terms related to aggregation and self-assembly in the particular case of macromolecules. The list is restricted to the most commonly encountered terms.
Consumer-grade polyurethane foam functions as a large and selective absorption sink for bisphenol A in aqueous media (2015)

Consumer-grade polyurethane foam functions as a large absorption sink for BPA, showing superior uptake rates and selectivity to conventional adsorbents.