gebhart/patrepeval huggingface dataset:
Lectin-type oxidized LDL receptor-1 distinguishes population of human polymorphonuclear myeloid-derived suppressor cells in cancer patients (2016)

Polymorphonuclear myeloid-derived suppressor cells (PMN-MDSC) are important regulators of immune responses in cancer and have been directly implicated in promotion of tumor progression. However, the heterogeneity of these cells and lack of distinct markers hampers the progress in understanding of the biology and clinical importance of these cells. Using partial enrichment of PMN-MDSC with gradient centrifugation we determined that low density PMN-MDSC and high density neutrophils from the same cancer patients had a distinct gene profile. Most prominent changes were observed in the expression of genes associated with endoplasmic reticulum (ER) stress. Surprisingly, low-density lipoprotein (LDL) was one of the most increased regulators and its receptor oxidized LDL receptor 1 <i>OLR1</i> was one of the most overexpressed genes in PMN-MDSC. Lectin-type oxidized LDL receptor 1 (LOX-1) encoded by <i>OLR1</i> was practically undetectable in neutrophils in peripheral blood of healthy donors, whereas 5-15% of total neutrophils in cancer patients and 15-50% of neutrophils in tumor tissues were LOX-1<sup>+</sup>. In contrast to their LOX-1<sup>-</sup> counterparts, LOX-1<sup>+</sup> neutrophils had gene signature, potent immune suppressive activity, up-regulation of ER stress, and other biochemical characteristics of PMN-MDSC. Moreover, induction of ER stress in neutrophils from healthy donors up-regulated LOX-1 expression and converted these cells to suppressive PMN-MDSC. Thus, we identified a specific marker of human PMN-MDSC associated with ER stress and lipid metabolism, which provides new insight to the biology and potential therapeutic targeting of these cells.
The Placental Gene PEG10 Promotes Progression of Neuroendocrine Prostate Cancer (2015)

More potent targeting of the androgen receptor (AR) in advanced prostate cancer is driving an increased incidence of neuroendocrine prostate cancer (NEPC), an aggressive and treatment-resistant AR-negative variant. Its molecular pathogenesis remains poorly understood but appears to require TP53 and RB1 aberration. We modeled the development of NEPC from conventional prostatic adenocarcinoma using a patient-derived xenograft and found that the placental gene PEG10 is de-repressed during the adaptive response to AR interference and subsequently highly upregulated in clinical NEPC. We found that the AR and the E2F/RB pathway dynamically regulate distinct post-transcriptional and post-translational isoforms of PEG10 at distinct stages of NEPC development. In vitro, PEG10 promoted cell-cycle progression from G0/G1 in the context of TP53 loss and regulated Snail expression via TGF-β signaling to promote invasion. Taken together, these findings show the mechanistic relevance of RB1 and TP53 loss in NEPC and suggest PEG10 as a NEPC-specific target.
Porous Nanomaterials: Porous Nanomaterials for Ultrabroadband Omnidirectional Anti‐Reflection Surfaces with Applications in High Concentration Photovoltaics (Adv. Energy Mater. 7/2017) (2017)

In article number 1601992, Ralph G. Nuzzo, John A. Rogers, and co-workers demonstrate broadband anti-reflection coatings that rely on porous nanomaterials formed by self-assembly. The image shows the use of such coatings (orange) on an array of lenses within a concentration photovoltaics architecture, where photons are efficiently concentrated onto underlying triple-junction solar cells, leading to an efficiency enhancement of ≈8%.
Fabrication of nanoscale metal paths in oxide thin layers by noble-gas ion beams (2013)

We investigated the fabrication process of a nanostructure with alumina insulator layer and nanoscale Cu paths punching through an alumina layer inserted between magnetic multilayers. Ion-beam–assisted oxidation was applied to an AlCu layer, where ion beams with three kinds of noble gases of different mass, Ne, Ar and Xe, were compared. The heavy gas overcame the trade-off between the increasing purity of nanoscale Cu paths and the decreasing oxygen defects of the alumina. It is considered that the high mobility of surface atoms in the AlCu layer brought about by the heavy-gas ion beam promotes segregation of alumina and Cu.
Network Vector Quantization (2004)

We present an algorithm for designing locally optimal vector quantizers for general networks. We discuss the algorithm's implementation and compare the performance of the resulting "network vector quantizers" to traditional vector quantizers (VQs) and to rate-distortion (R-D) bounds where available. While some special cases of network codes (e.g., multiresolution (MR) and multiple description (MD) codes) have been studied in the literature, we here present a unifying approach that both includes these existing solutions as special cases and provides solutions to previously unsolved examples.
Defining Th1 and Th2 Immune Responses in a Reciprocal Cytokine Environment In Vivo (2004)

The ability of committed Th1 and Th2 cells to function in altered cytokine environments is a central issue in autoimmune and immune-mediated diseases. Therefore, it is of interest to study the ability of Th1 or Th2 cells to expand and produce cytokine reciprocal environments in vivo. Using STAT4- and STAT6-deficient mice, we studied the expansion and cytokine production of Ag-specific Th1 or Th2 cells after transfer into Th1, Th2, or wild-type recipients. Our data show that these Th1 or Th2 cells proliferated and clonally expanded normally, regardless of the in vivo cytokine environment. These data have implications for the treatment of immune-mediated diseases by immunomodulatory agents that alter the cytokine milieu in vivo.
Application of the Barton photochemical reaction in the synthesis of 1-dethia-3-aza-1-carba-2-oxacephem: a novel agent against resistant pathogenic microorganisms (2003)

Racemic 7-(phenylacetamido)-1-dethia-3-aza-1-carba-2-oxacephem 3 was synthesized and found to possess antibacterial activity against Staphylococcus aureus FDA 209P, Escherichia coli ATCC 39188, Pseudomonas aeruginosa 1101-75 and Klebsiella pneumoniae NCTC 418 as well as the beta-lactamase producing organisms E. coli A9675 and P. aeruginosa 18S-H and the methicillin-resistant organism S. aureus 95. Formation of the carbacephem 3 originated from the Barton photochemical reaction in the conversion of 8 to 10. Intramolecular cyclization of syn-oximino beta-lactam 10 afforded 7-azido-2-oxa-3-azacephem 11, which was reduced and acylated to 12. Enzymatic removal of the methyl group from 12 gave the target molecule 3.
Overexpression of Human Catalase Inhibits Proliferation and Promotes Apoptosis in Vascular Smooth Muscle Cells (1999)

The role of reactive oxygen species, such as superoxide anions (O(2). (-)) and hydrogen peroxide (H(2)O(2)), in modulating vascular smooth muscle cell proliferation and viability is controversial. To investigate the role of endogenously produced H(2)O(2), rat aortic smooth muscle cells were infected with adenoviral vectors containing cDNA for human catalase (AdCat) or a control gene, beta-galactosidase (AdLacZ). Infection with AdCat resulted in dose-dependent increases in intracellular catalase protein, which was predominantly localized to peroxisomes. After infection with 100 multiplicity of infection (MOI) of AdCat, cellular catalase activity was increased by 50- to 100-fold, and intracellular H(2)O(2) concentration was reduced, as compared with control. Infection with AdCat reduced [(3)H]thymidine uptake, an index of DNA synthesis, in cells maintained in medium supplemented with 2% serum (0.37+/-0.09 disintegrations per minute per cell [AdLacZ] versus 0.22+/-0.08 disintegrations per minute per cell [AdCat], P<0.05). Five days after infection with 100 MOI of AdCat, cell numbers were reduced as compared with noninfected or AdLacZ-infected cells (157 780+/-8413 [AdCat], P<0.05 versus 233 700+/-3032 [noninfected] or 222 410+/-5332 [AdLacZ]). Furthermore, the number of apoptotic cells was increased 5-fold after infection with 100 MOI of AdCat as compared with control. Infection with AdCat resulted in induction of cyclooxygenase (COX)-2, and treatment with a COX-2 inhibitor overcame the AdCat-induced reduction in cell numbers. These findings indicate that overexpression of catalase inhibited smooth muscle proliferation while increasing the rate of apoptosis, possibly through a COX-2-dependent mechanism. Our results suggest that endogenously produced H(2)O(2) importantly modulates survival and proliferation of vascular smooth muscle cells.
From Conventional to Microfluidic: Progress in Extracellular Vesicle Separation and Individual Characterization (2022)

Extracellular vesicles (EVs) are nanoscale membrane vesicles, which contain a wide variety of cargo such as proteins, miRNAs, and lipids. A growing body of evidence suggests that EVs are promising biomarkers for disease diagnosis and therapeutic strategies. Although the excellent clinical value, their use in personalized healthcare practice is not yet feasible due to their highly heterogeneous nature. Taking the difficulty of isolation and the small size of EVs into account, the characterization of EVs at a single-particle level is both imperative and challenging. In a bid to address this critical point, more research has been directed into a microfluidic platform because of its inherent advantages in sensitivity, specificity, and throughput. This review discusses the biogenesis and heterogeneity of EVs and takes a broad view of state-of-the-art advances in microfluidics-based EV research, including not only EV separation, but also the single EV characterization of biophysical detection and biochemical analysis. To highlight the advantages of microfluidic techniques, conventional technologies are included for comparison. The current status of artificial intelligence (AI) for single EV characterization is then presented. Furthermore, the challenges and prospects of microfluidics and its combination with AI applications in single EV characterization are also discussed. In the foreseeable future, recent breakthroughs in microfluidic platforms are expected to pave the way for single EV analysis and improve applications for precision medicine.
End Effects and Geometric Compensation in a Linear Permanent Magnet Synchronous Generator with Buried Topology (2020)

Electricity production from ocean waves with different design topologies is a topic of big research interest. Many of such topologies are based on submerged linear generators which inherently introduce end forces. In this paper, the detent force is investigated for two different winding patterns using Maxwell stress tensor in a finite element software. Induced voltage is also investigated for active stator area and the unequal contributions due to stator ends. Two ways of overcoming the end forces are further investigated: The first method reduces the magnetic flux difference when the translator is surrounded by stator and air, respectively. The second aims at countering the end forces at both ends for full active stator area. The first investigated end effect compensation decreased the end effects but increased the attraction forces. The second end effect compensation decreased the end forces during full active stator area with little effect on the attraction forces.
Nanosphere Lithography:  Effect of Substrate on the Localized Surface Plasmon Resonance Spectrum of Silver Nanoparticles (2001)

In this paper, we explore the optical contributions of the substrate to the localized surface plasmon resonance (LSPR) spectrum of surface confined Ag nanoparticles produced by nanosphere lithography (NSL). We present optical extinction spectra of Ag nanoparticles fabricated on the following substrates: fused silica, borosilicate optical glass, mica, and SF-10─a high refractive index specialty glass. For all the experiments discussed here, the Ag nanoparticles were approximately 100 nm in in-plane width and 25 nm in out-of-plane height. In a controlled N2 environment, the wavelength corresponding to the extinction maximum, λmax, shifts to the red with increasing refractive index of the substrate, nsubstrate. The sensitivity factor, Δλmax/Δnsubstrate, was measured to be 87 nm per refractive index unit (RIU). Experimental extinction spectra were modeled using the discrete dipole approximation (DDA). The DDA theory qualitatively predicts the experimentally observed trend that λmax is linearly dependent on nsubstrate; however, the theory overestimates the sensitivity by approximately a factor of 2. The sensitivity of the LSPR to the refractive index of bulk external solvent, nexternal, was also examined for each of the four substrates listed above. For all the cases, the change in λmax in response to bulk external solvent was linearly dependent upon nexternal. Values of the sensitivity factors, Δλmax/Δnexternal, ranged from 206 nm RIU-1 for mica to 258 nm RIU-1 for SF-10, a difference of only 25%. From the results presented here, we conclude that there is no systematic dependence, or at most a weak dependence, which correlates the bulk solvent sensitivity of the LSPR to nsubstrate. The DDA theory overestimates the LSPR sensitivity to bulk external environment, but the ratio of solvent to substrate sensitivity factors is correct within experimental uncertainty. This ratio has a value of approximately 2, which indicates that there is greater sensitivity in the optical response to the solvent than to the substrate. This ratio is within 10% of the ratio of areas of the particles that are exposed to solvent and substrate. We suggest that chemical interactions at the interfaces between the nanoparticle and the substrate and/or the nanoparticle and the bulk environment contribute significantly to the observed difference between experimental and theoretical sensitivity factors.
Prediction-Based Reachability for Collision Avoidance in Autonomous Driving (2021)

Safety is an important topic in autonomous driving since any collision may cause serious injury to people and damage to property. Hamilton-Jacobi (HJ) Reachability is a formal method that verifies safety in multi-agent interaction and provides a safety controller for collision avoidance. However, due to the worst-case assumption on the car&#x2019;s future behaviours, reachability might result in too much conservatism such that the normal operation of the vehicle is badly hindered. In this paper, we leverage the power of trajectory prediction and propose a prediction-based reachability framework to compute safety controllers. Instead of always assuming the worst case, we cluster the car&#x2019;s behaviors into multiple driving modes, e.g. left turn or right turn. Under each mode, a reachability-based safety controller is designed based on a less conservative action set. For online implementation, we first utilize the trajectory prediction and our proposed mode classifier to predict the possible modes, and then deploy the corresponding safety controller. Through simulations in a T-intersection and an 8-way roundabout, we demonstrate that our prediction-based reachability method largely avoids collision between two interacting cars and reduces the conservatism that the safety controller brings to the car&#x2019;s original operation.
Noise-enhanced coupling between two oscillators with long-term plasticity (2016)

Spike timing-dependent plasticity is a fundamental adaptation mechanism of the nervous system. It induces structural changes of synaptic connectivity by regulation of coupling strengths between individual cells depending on their spiking behavior. As a biophysical process its functioning is constantly subjected to natural fluctuations. We study theoretically the influence of noise on a microscopic level by considering only two coupled neurons. Adopting a phase description for the neurons we derive a two-dimensional system which describes the averaged dynamics of the coupling strengths. We show that a multistability of several coupling configurations is possible, where some configurations are not found in systems without noise. Intriguingly, it is possible that a strong bidirectional coupling, which is not present in the noise-free situation, can be stabilized by the noise. This means that increased noise, which is normally expected to desynchronize the neurons, can be the reason for an antagonistic response of the system, which organizes itself into a state of stronger coupling and counteracts the impact of noise. This mechanism, as well as a high potential for multistability, is also demonstrated numerically for a coupled pair of Hodgkin-Huxley neurons.
Evaluation of short folded dipole antennas as receive elements of ultra‐high‐field human head array (2019)

Purpose To improve the receive (Rx) performance of a human head transceiver (TxRx) array at 9.4T without compromising its transmit (Tx) performance, a novel 16‐element array was developed, constructed, and tested. Methods We designed and constructed a phased array, which consists of 8 TxRx surface loops placed in a single row and circumscribing a head, and 8 Rx‐only short folded dipole antennas. Dipoles were positioned along the central axis of each transceiver loop perpendicular to its surface. We evaluated the effect of Rx dipoles on the Tx efficiency of the array and maximum local specific absorption rate (SAR) as compared to the array of 8 surface loops only. We also compared the new array to a 16‐channel array of the same size consisting of 8 TxRx surface loops and 8 Rx‐only vertical loops in terms of Tx efficiency, SAR, and signal‐to‐noise ratio (SNR). Results The new array improves both peripheral (up to 2 times) and central (1.17 times) SNR as compared to the 16‐element array of the same geometry consisting of 8 TxRx surface loops and 8 Rx‐only vertical loops. We demonstrated that an addition of actively detuned Rx‐only dipole elements produces only a small decrease (~7%) of the transmit field and a small increase (&lt;7%) of the maximum local SAR. Conclusion As a proof of concept, we developed and constructed a prototype of a 9.4T (400 MHz) head array consisting of 8 TxRx surface loops and 8 Rx‐only short optimized folded dipoles. We demonstrated that at ultra‐high field, dipoles outperformed Rx‐only vertical loops in vivo.
Gene Content and Diversity of the Loci Encoding Biosynthesis of Capsular Polysaccharides of the 15 Serovar Reference Strains of Haemophilus parasuis (2013)

Haemophilus parasuis is the causative agent of Glässer's disease, a systemic disease of pigs, and is also associated with pneumonia. H. parasuis can be classified into 15 different serovars. Here we report, from the 15 serotyping reference strains, the DNA sequences of the loci containing genes for the biosynthesis of the group 1 capsular polysaccharides, which are potential virulence factors of this bacterium. We contend that these loci contain genes for polysaccharide capsule structures, and not a lipopolysaccharide O antigen, supported by the fact that they contain genes such as wza, wzb, and wzc, which are associated with the export of polysaccharide capsules in the current capsule classification system. A conserved region at the 3' end of the locus, containing the wza, ptp, wzs, and iscR genes, is consistent with the characteristic export region 1 of the model group 1 capsule locus. A potential serovar-specific region (region 2) has been found by comparing the predicted coding sequences (CDSs) in all 15 loci for synteny and homology. The region is unique to each reference strain with the exception of those in serovars 5 and 12, which are identical in terms of gene content. The identification and characterization of this locus among the 15 serovars is the first step in understanding the genetic, molecular, and structural bases of serovar specificity in this poorly studied but important pathogen and opens up the possibility of developing an improved molecular serotyping system, which would greatly assist diagnosis and control of Glässer's disease.
Potassium Hydrogen Fluoride (2012)

[7789-29-9] KHF2 (MW 78.1)





InChI = 1S/F2H.K/c1-3-2;/q-1;+1



InChIKey = FLCWRBFUWAZYGV-UHFFFAOYSA-N



(fluorinating agent; used in the synthesis of trifluoroborates from various organoborons; fluorinating reagent for ring opening of epoxides and cyclopropanes)



Physical Data: mp 239 °C.



Solubility: soluble in water, DMF.



Form Supplied in: commercially available white solid.



Analysis of Reagent Purity: mp, 19F NMR.



Toxicity Data: highly toxic, corrosive, do not store in glass.
New strategies for multiphase catalysis using supercritical carbon dioxide (2004)

The work reported in this thesis deals with the development of an effective strategy for the recycling of a multipurpose catalyst. An immobilized metal complex acts as a "catalyst cartridge" applicable in a variety of catalytic reactions without using any volatile organic solvents but only carbon dioxide. In this case carbon dioxide has the function of mobile phase, increases the reactivity, dissolves reagents in the catalytic phase and allows products isolation in a solvent and metal free manner. As mobile phase, supercritical or simply compressed carbon dioxide would allow an efficient separation of products from the metal complex so that the "cartridge" can be used again either for the same reaction with a different substrate, or as a greater challenge for a completely different reaction. In line with these challenges, two new approaches toward multiphase catalysis were explored. Carbon dioxide was used in combination with ionic liquids in one case, and in combination with poly(ethylene glycol) modified phosphine ligands in the other for a variety of metal catalyzed reactions.
Abstract 1239: Characterization of the response of human T cells to an agonist human anti-CD27 mAb. (2013)

Abstract CD27, a member of the tumor necrosis factor receptor super family (TNFRSF), is constitutively expressed on the majority of mature T cells, memory B cells, and a portion of NK cells. Previously we have reported antitumor and immunological properties of the fully human anti-CD27 mAb 1F5 in huCD27 transgenic mouse models. Here we report the 1F5-induced immune modulation of isolated human T cells. In vitro activation of peripheral blood-derived T cells from different healthy volunteers with mAb 1F5 showed that crosslinking of CD27 in the presence of CD3 stimulation (OKT3 mAb) was essential to elicit proliferation and a broad spectrum of cytokine release. Analysis of this response on a multiplex cytokine array system revealed a Th1-biased cytokine profile (IFNγ, IL-2 and TNFα). Interestingly, IL-13 was the only major Th2 cytokine that was detected in large amounts. Furthermore, activation of isolated CD4+ and CD8+ T cells showed both subsets contributed to the IL-13 secretion with higher secretion amounts detected in the CD4+ T cell cultures. Altogether, the data suggest an agonistic role for 1F5 characterized predominantly by a defined antigen-receptor coupled Th1 effector response. IL-13, which appears later after stimulation may represent immune regulatory modulation as has been described in activation of the related 4-1BB co-stimulation pathway. Transcriptional profiling by microarray RNA hybridization is underway to map specific and global gene expression changes following 1F5 modulation of T cells. Citation Format: Karuna Sundarapandiyan, Laura Vitale, Biwei Zhao, Thomas O'Neill, Henry Marsh, Venky Ramakrishna, Tibor Keler. Characterization of the response of human T cells to an agonist human anti-CD27 mAb. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1239. doi:10.1158/1538-7445.AM2013-1239