gebhart/patrepeval huggingface dataset:
Abstract 16736: The Long Intergenic Non-coding RNA Landscape in Human Macrophage Activation (2016)

Introduction: With remarkable plasticity and wide-ranging states of activation in response to environmental challenges, macrophages play a central role in pathogenesis of cardiometabolic diseases (CMDs). However, the long non-coding RNA landscape that regulates macrophage activation is poorly defined. Hypothesis: Comprehensive analysis of long intergenic non-coding RNA (lincRNA) expression profiles reveals novel macrophage lincRNA signature. Methods: We used deep RNA sequencing to assemble the lincRNA transcriptome in human macrophages (HMDM, N=6 subjects) at rest and also after stimulation with lipopolysaccharide and interferon-gamma for M1-like inflammatory activation, and interleukin-4 for M2-like anti-inflammatory activation (A). Results: Through de novo assembly, we identified 2,766 macrophage lincRNAs including 861 previously unannotated novel lincRNAs. The majority (86%) was non-syntenic, or syntenic but not annotated in mouse genomes (B). Many macrophage lincRNAs also demonstrated tissue-enriched transcription patterns (12 %) and enhancer-like chromatin signatures (62 %). Macrophage activation, particularly to the M1 phenotype, markedly altered the lincRNA expression profiles with 96 lincRNAs differentially expressed (fold-change > 2 and FDR Conclusion: In summary, high-resolution transcriptomics identified 100s of lincRNAs that form part of the cellular response in macrophage activation as well as specific macrophage lincRNAs associated with human CMDs.
Optical-field-induced current in dielectrics (2013)

The conductivity of a dielectric is reversibly increased by several orders of magnitude on a femtosecond timescale by exploiting the instantaneous electric field of intense few-cycle near-infrared laser pulses leading to measurable ultrafast electric currents.
Changes in MIF and thyroxine, in a clinically relevant large animal model of sepsis (2009)

Introduction Urokinase receptor (uPAR, CD87), a glycosylphosphatidylinositol-anchored protein, is considered to play an important role in inflammation and fibrinolysis. The Gram-negative bacterium Burkholderia pseudomallei is able to survive and replicate within leukocytes and causes melioidosis, an important cause of pneumonia-derived community-acquired sepsis in Southeast Asia. We here investigated the expression and function of uPAR both in patients with septic melioidosis and in a murine model of experimental melioidosis. Methods Using a translational approach we conducted a patient study in patients with culture-confirmed sepsis caused by B. pseudomallei, in vitro experiments using wild-type (WT) and uPAR knockout (KO) cells, and mouse studies using WT and uPAR KO mice inoculated with B. pseudomallei. Results uPAR mRNA and surface expression was increased in patients with septic melioidosis in/on both peripheral blood monocytes and granulocytes as well as in the pulmonary compartment during experimental pneumonia-derived melioidosis in mice. uPAR-deficient mice intranasally infected with B. pseudomallei showed an enhanced growth and dissemination of B. pseudomallei when compared with WT mice, corresponding with increased pulmonary and hepatic inflammation. uPAR KO mice demonstrated significantly reduced neutrophil migration towards the pulmonary compartment after inoculation with B. pseudomallei. Further in vitro experiments showed that uPARdeficient macrophages and granulocytes display a markedly impaired phagocytosis of B. pseudomallei. Additional studies showed that uPAR deficiency did not influence hemostatic and fibrinolytic responses during severe melioidosis. Conclusions These data suggest that uPAR is crucially involved in the host defense against sepsis caused by B. pseudomallei by facilitating the migration of neutrophils towards the primary site of infection and subsequently facilitating the phagocytosis of B. pseudomallei. P2 A comparison of acute lung inflammation in Klebsiella pneumoniae B5055-induced pneumonia and sepsis in BALB/c mice
Parental History of Diabetes in an Insulin-treated Diabetes Registry (1997)

To confirm observations of an excess maternal transmission of Type 2 (non-insulin dependent) diabetes mellitus in a setting which minimizes potential biases and confounders, we explored the patterns of maternal and paternal diabetes in a cohort (n = 1775) of subjects with insulin-treated diabetes mellitus (ITDM) in Tasmania, Australia. In order to identify individuals with Type 1 diabetes or insulin-treated Type 2 diabetes, cases were classified into groups based on their age at diagnosis and subsequent time to commencement of insulin. Individuals initially diagnosed younger than age 30 (predominantly Type 1 diabetes cases) reported a similar percentage of mothers and fathers with diabetes, but individuals diagnosed at age 30 or older (predominantly insulin-treated Type 2 diabetes) reported a maternal excess of diabetes. Having an elevated body mass index was associated with a higher frequency of maternal diabetes, but not of paternal diabetes. Because both childhood-onset Type 1 diabetes and adult-onset insulin-treated Type 2 diabetes cases were subject to the same potential study biases, these results offer support for an excess maternal role in Type 2 diabetes transmission.
Facile Phase‐Separation Approach to Encapsulate Functionalized Polymers in Core–Shell Nanoparticles (2013)

Core–shell nanoparticles filled with a reactive hydrophobic azide‐terminated polyisobutylene are prepared by a combination of miniemulsion and solvent evaporation techniques. Successful encapsulation is achieved by the rational selection of the polymer pair that displays a large difference in solubility parameters ( δ ) and interfacial tensions with water ( γ polymer/water ). By labeling the two polymers with different fluorescent dyes, core–shell structures can be visualized by fluorescence microscopy. After extraction of the polymer present in the core, hollow morphologies are observed by transmission electronic microscopy. The encapsulation efficiency of the reactive polymer increases with decreasing surfactant concentration, with values as high as 90%. This study presents a simple and reaction‐free method to encapsulate reactive polymers. Considering the drawbacks of self‐healing agents with low molar mass, such as volatility and higher propensity for leakage from nanocapsules, the encapsulation of reactive polymers in nanocontainers is an interesting and new alternative for self‐healing materials. image
Crosstalk Between Dysfunctional Mitochondria and Inflammation in Glaucomatous Neurodegeneration (2021)

Mitochondrial dysfunction and excessive inflammatory responses are both sufficient to induce pathology in age-dependent neurodegenerations. However, emerging evidence indicates crosstalk between damaged mitochondrial and inflammatory signaling can exacerbate issues in chronic neurodegenerations. This review discusses evidence for the interaction between mitochondrial damage and inflammation, with a focus on glaucomatous neurodegeneration, and proposes that positive feedback resulting from this crosstalk drives pathology. Mitochondrial dysfunction exacerbates inflammatory signaling in multiple ways. Damaged mitochondrial DNA is a damage-associated molecular pattern, which activates the NLRP3 inflammasome; priming and activation of the NLRP3 inflammasome, and the resulting liberation of IL-1β and IL-18 via the gasdermin D pore, is a major pathway to enhance inflammatory responses. The rise in reactive oxygen species induced by mitochondrial damage also activates inflammatory pathways, while blockage of Complex enzymes is sufficient to increase inflammatory signaling. Impaired mitophagy contributes to inflammation as the inability to turnover mitochondria in a timely manner increases levels of ROS and damaged mtDNA, with the latter likely to stimulate the cGAS-STING pathway to increase interferon signaling. Mitochondrial associated ER membrane contacts and the mitochondria-associated adaptor molecule MAVS can activate NLRP3 inflammasome signaling. In addition to dysfunctional mitochondria increasing inflammation, the corollary also occurs, with inflammation reducing mitochondrial function and ATP production; the resulting downward spiral accelerates degeneration. Evidence from several preclinical models including the DBA/2J mouse, microbead injection and transient elevation of IOP, in addition to patient data, implicates both mitochondrial damage and inflammation in glaucomatous neurodegeneration. The pressure-dependent hypoxia and the resulting metabolic vulnerability is associated with mitochondrial damage and IL-1β release. Links between mitochondrial dysfunction and inflammation can occur in retinal ganglion cells, microglia cells and astrocytes. In summary, crosstalk between damaged mitochondria and increased inflammatory signaling enhances pathology in glaucomatous neurodegeneration, with implications for other complex age-dependent neurodegenerations like Alzheimer's and Parkinson's disease.
Dynamic monitoring of LLC lung metastasis development and prevention (2005)

4633 This study focuses on tumor cell survival and angiogenesis after tumor cell intravasation of vasculature. Dynamic monitoring was performed using the mouse lung metastasis model treated with platelet activation inhibitor (PGI2) and VEGFR inhibitor (SU5416). 3x105 DiI labeled LLC (Lewis lung carcinoma) cells were injected into the tail veins of C57BL6J mice to develop tumor metastasis in lung. The experimental animals were divided into control, PGI2 (100ug/mouse, once), and SU5416 (25mg/kg daily, for 5 days) groups. Lung, liver, and spleen frozen sections were cut and stained with DAPI at 15 min, 24 hours, 4 days, 8 days, 13 days and 15 days after injection of LLC cells for fluorescence microscopy assay. A similar experiment was performed (5 mice each group) and lung and liver were investigated at 15 days after injection of LLC cells for metastasis tumor colonies. A novel vivo and vitro combination technique was developed to test platelet active LLC cells binding on HUVEC capillary-like structures. The capability of VEGFR inhibitor (SU 5416) in blocking new vasculature development was tested in a mouse dorsal vascular window model. The dynamic monitoring shows that DiI labeled LLC cells accumulated in the lungs of all treatment groups (with slightly less accumulation in mice treated with PGI2). Very little DiI labeled LLC cells accumulated in liver and spleen at 15 min after injection. At the 24 hours and 4 days time points, DiI( red ) density was increasing in liver and spleen, but decreased at 8 day, 13 day, and 15 day time points. Meanwhile, DiI density in lung was changing with time, treatment, and tumor cell survival. Lung surface tumor colony counts show that there are 40-50 times more colonies in control lungs than SU5416 and combination groups, and the weights of lungs are also significantly different. Histology evidence is consistent with the above results. PGI2 significantly reduced LLC cell binding to HUVEC capillary-like structures (10 times lower). The dorsal window model with LLC cells showed that treatment with 5 doses of the VEGFR inhibitor SU5416 (3 mice) completely impeded angiogenesis compared to the control (3 mice). Conclusions: 1).The first several days are crucial in LLC cells developing metastasis in lung after intravasation. 2). VEGFR inhibitor (SU5416) can significantly prevent LLC cells from developing metastasis in lung. 3). Platelet activation inhibitor (PGI2) efficiently reduces LLC cell adhesion on endothelium (HUVEC). 4). VEGFR inhibitor (SU5416) is seemingly more effective than platelet activation inhibitor (PGI2) in impeding LLC lung metastasis formation after intravasation.
Targeting Valuable Chemical Commodities: Hydrazine‐mediated Diels‐Alder Aromatization of Biobased Furfurals (2022)

A hydrazine-mediated approach towards renewable aromatics production via Diels-Alder aromatization of readily available, biobased furfurals was explored as alterative to the more classical approaches that rely on reactive but uneconomical reduced dienes (e. g., 2,5-dimethylfuran). To enable cycloaddition chemistry with these otherwise unreactive formyl furans, substrate activation by N,N-dimethyl hydrazone formation was investigated. The choice of the reaction partner was key to the success of the transformation, and in this respect acrylic acid showed the most promising results in the synthesis of aromatics. This strategy allowed for selectivities up to 60 % for a complex transformation consisting of Diels-Alder cycloaddition, oxabridge opening, decarboxylation, and dehydration. Exploration of the furfural scope yielded generic structure-reactivity-stability relationships. The proposed methodology enabled the redox-efficient, operationally simple, and mild synthesis of renewable (p-disubstituted) aromatics of commercial importance under remarkably mild conditions.
ChemInform Abstract: HETEROCYCLIC DIENAMINES. I. REACTION OF FISCHER′S BASE WITH ACETYLENIC ESTERS (1977)

Abstract Die Fischer‐Base (I) reagiert mit Dimethyl‐acetylendicarboxylat in Abhängigkeit vom Lösungsmittel zu dem Indolinyliden‐dien (II) (in Methanol) oder zu einem Gemisch der Isomeren (II), (III) und (IV) (13 : 56 : 31 ; in Chloroform).
A Time-of-Flight 3-D Image Sensor With Concentric-Photogates Demodulation Pixels (2014)

In this paper, we develop pixels with concentric-photogates for applications in time-of-flight 3-D image sensors with single-tap architecture. The pixel uses a buried-channel device and features a reduced effective electron transit length, for the rapid transfer of a signal electron. A reduction in the interpixel irregularity of signal levels and a consequent increase in the demodulation signal amplitude are observed in the single-tap operation mode as opposed to the multitap operation mode. Specifically, we are able to achieve a demodulation contrast higher than 50% from 20 MHz modulation of an 850 nm light-emitting diode illumination. Finally, we construct a sensor composed of 198 <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$\,\times\,$</tex></formula> 108 concentric photogate pixels, each with a pitch of 28 <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$\mu{\rm m}$</tex></formula> , and use it to generate a 3-D image conveying gross distance information and detailed object features with a distance error of less than 1% over a range of 1 to 7 m.
Leading-Edge Profiles for the Reduction of Airfoil Interaction Noise (2019)

Airfoils operating in a turbulent flow are an efficient source of noise radiation by scattering vorticity into sound at the leading edge. Much work has been undertaken demonstrating the effectiveness by which serrations, or undulations, introduced onto the leading edge can substantially reduce broadband leading-edge interaction noise. However, most of this work is focused on sinusoidal leading-edge serration profiles. In this paper, a family of serration profiles is proposed that is capable of providing significantly greater noise reductions than single-wavelength serrations at optimal conditions. This new family of profiles will be shown to reduce interaction noise through a fundamentally different noise reduction mechanism than conventional single-wavelength profiles. Unlike single-wavelength profiles, which produce a single compact dominant source region per serration wavelength, these new profiles are designed to produce two or more dominant compact sources per serration wavelength of roughly the same source strength that are separated in the streamwise direction. Because these sources are arranged to be closer together than the turbulence length scale, they are highly coherent and, at certain frequencies, radiate exactly 180 deg out of phase, leading to very high levels of noise reduction in the far field. The experimental noise reduction spectra are first compared against an analytic model obtained as a solution of the acoustic wave equation using the Wiener–Hopf technique. This approach focuses solely on solving for an acoustic field, and not for any secondary vorticity induced by the edge. As such, this comparison, which shows disagreement, proves that secondary vorticity is a dominant mechanism for these new profiles. A simple supplementary analytical model has therefore been developed to explain this noise reduction mechanism for these new profiles, based on interference between sources distributed along the leading edge. Good qualitative agreement is obtained with the experimental results.
ChemInform Abstract: Asymmetric Synthesis of Bryostatin 2. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 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.
Asynchronous coded caching (2017)

Coded caching is a technique that promises huge reductions in network traffic in content-delivery networks. However, the original formulation and several subsequent contributions in the area, assume that the file requests from the users are synchronized, i.e., they arrive at the server at the same time. In this work we formulate and study the coded caching problem when the file requests from the users arrive at different times. We assume that each user also has a prescribed deadline by which they want their request to be completed. In the offline case, we assume that the server knows the arrival times before starting transmission and in the online case, the user requests are revealed to the server over time. We present a LP formulation for the offline case that minimizes the overall rate subject to constraint that each user meets his/her deadline. While the online case is much harder, we demonstrate that in the case when the server wishes to minimize the overall completion time, the online solution can be as good as the offline solution. Our simulation results indicate that in the presence of mild asynchronism, much of the benefit of coded caching can still be leveraged.
Resonant interaction of sound wave with internal solitons in the coastal zone (1991)

Naturally occurring internal solitary wave trains (solitons) have often been observed in the coastal zone, but no reported measurements of such solitary waves include low-frequency long-range sound propagation data. In this paper, the possibility that internal waves are responsible for the anomalous frequency response of shallow-water sound propagation observed in the summer is investigated. The observed transmission loss is strongly time dependent, anisotropic and sometimes exhibits an abnormally large attenuation over some frequency range. The parabolic equation (PE) model is used to numerically simulate the effect of internal wave packets on low-frequency sound propagation in shallow water when there is a strong thermocline. It is found that acoustic transmission loss is sensitive to the signal frequency and is a ‘‘resonancelike’’ function of the soliton wavelength and packet length. The strong interaction between acoustic waves and internal waves, together with the known characteristics of internal waves in the coastal zone, provides a plausible explanation for the observed anomalous sound propagation in the summer. By decomposing the acoustic field obtained from the PE code into normal modes, it is shown that the abnormally large transmission attenuation is caused by ‘‘acoustic mode-coupling’’ loss due to the interaction with the internal waves. It is also shown that the ‘‘resonancelike’’ behavior of transmission loss predicted by the PE analysis is consistent with mode coupling theory. As an inverse problem, low-frequency acoustic measurements could be a potential tool for remote-sensing of internal wave activity in the coastal zone.
Ultrasound Detection of Regional Oxidative Stress in Deep Tissues Using Novel Enzyme Loaded Nanoparticles (2017)

Oxidative stress is a powerful tool that is critical to immune mediated responses in healthy individuals, yet additionally plays a crucial role in development of cancer, inflammatory pathologies, and tissue ischemia. Despite this, there remain relatively few molecular tools to study oxidative stress, particularly in living mammals. To develop an intravenously injectable probe capable of labeling sites of oxidative stress in vivo, 200 nm catalase synthetic hollow enzyme loaded nanospheres (catSHELS) are designed and fabricated using a versatile enzyme nanoencapsulation method. catSHELS catalyze H<sub>2</sub> O<sub>2</sub> to water and oxygen producing microbubbles that can be detected and imaged using a clinical ultrasound system. catSHELS are optimized in vitro to maximize ultrasound signal and their functionality is demonstrated in rat ischemic renal injury model. Ischemic oxidative injury is induced in a single kidney of normal rats by clamping the renal artery for 1 h followed by 2 h of reperfusion. Imaging of both kidneys is performed following the intravenous bolus injection of 10<sup>12</sup> catSHELS of the optimized formulation. There is significant increase in ultrasound signal of the injured kidney relative to controls. This method offers a novel intravenous approach to detect oxidative stress in deep tissues in living animals.
Embryo growth, testa permeability, and endosperm weakening are major targets for the environmentally regulated inhibition of Lepidium sativum seed germination by myrigalone A (2012)

Myrigalone A (MyA) is a rare flavonoid in fruit leachates of Myrica gale, a deciduous shrub adapted to flood-prone habitats. As a putative allelochemical it inhibits seed germination and seedling growth. Using Lepidium sativum as a model target species, experiments were conducted to investigate how environmental cues modulate MyA's interference with key processes of seed germination. Time course analyses of L. sativum testa and endosperm rupture under different light conditions and water potentials were combined with quantifying testa permeability, endosperm weakening, tissue-specific gibberellin (GA) and abscisic acid (ABA) contents, as well as embryo growth and apoplastic superoxide production important for cell expansion growth. Lepidium sativum testa permeability and early water uptake by imbibition is enhanced by MyA. During late germination, MyA inhibits endosperm weakening and embryo growth, both processes required for endosperm rupture. Inhibition of embryo cell expansion by MyA depends on environmental cues, which is evident from the light-modulated severity of the MyA-mediated inhibition of apoplastic superoxide accumulation. Several important key weakening and growth processes during early and late germination are targets for MyA. These effects are modulated by light conditions and ambient water potential. It is speculated that MyA is a soil seed bank-destroying allelochemical that secures the persistence of M. gale in its flood-prone environment.
Control of PS-b-PMMA directed self-assembly registration by laser induced millisecond thermal annealing (2014)

Directed self-assembly of PS-b-PMMA during laser spike annealing at peak temperatures of 300-800&deg;C for dwells of 1- 10 ms has been explored. The enhanced mobility of polymer chains at these temperatures improves registration compared to conventional thermal anneals. PS-b-PMMA films (forming 15 nm line/space standing lamellae) were cast on chemically patterned substrates with a copolymer neutral layer and annealed by laser and hot-plate (2 minutes 250&deg;C). Annealing by hot plate or multiple laser scans resulted in well-aligned features over micron length scales. By laser annealing multiple times, defectivity can be reduced by ~60%. However, laser annealing for only 10 ms before performing a hot plate anneal reduced defectivity by ~80%. Additionally, defects are more often localized as dislocation pairs rather than regions perpendicular to the underlying directing pattern resulting in far greater total alignment.