gebhart/patrepeval huggingface dataset:
Mucus accumulation in the lungs precedes structural changes and infection in children with cystic fibrosis (2019)

Although destructive airway disease is evident in young children with cystic fibrosis (CF), little is known about the nature of the early CF lung environment triggering the disease. To elucidate early CF pulmonary pathophysiology, we performed mucus, inflammation, metabolomic, and microbiome analyses on bronchoalveolar lavage fluid (BALF) from 46 preschool children with CF enrolled in the Australian Respiratory Early Surveillance Team for Cystic Fibrosis (AREST CF) program and 16 non-CF disease controls. Total airway mucins were elevated in CF compared to non-CF BALF irrespective of infection, and higher densities of mucus flakes containing mucin 5B and mucin 5AC were observed in samples from CF patients. Total mucins and mucus flakes correlated with inflammation, hypoxia, and oxidative stress. Many CF BALFs appeared sterile by culture and molecular analyses, whereas other samples exhibiting bacterial taxa associated with the oral cavity. Children without computed tomography-defined structural lung disease exhibited elevated BALF mucus flakes and neutrophils, but little/no bacterial infection. Although CF mucus flakes appeared "permanent" because they did not dissolve in dilute BALF matrix, they could be solubilized by a previously unidentified reducing agent (P2062), but not <i>N</i>-acetylcysteine or deoxyribonuclease. These findings indicate that early CF lung disease is characterized by an increased mucus burden and inflammatory markers without infection or structural lung disease and suggest that mucolytic and anti-inflammatory agents should be explored as preventive therapy.
Tumor Angiogenesis Change Estimated by Using Diffuse Optical Spectroscopic Tomography: Demonstrated Correlation in Women Undergoing Neoadjuvant Chemotherapy for Invasive Breast Cancer? (2011)

http://radiology.rsna.org/lookup/suppl/doi:10.1148/radiol.11100699/-/DC1.
Enhanced learning-based imaging with thin-film luminescent concentrators (2014)

LumiConSense, a transparent, flexible, scalable, and disposable thin-film image sensor has the potential to lead to new human-computer interfaces that are unconstrained in shape and sensing-distance. In this article we make four new contributions: (1) A new real-time image reconstruction method that results in a significant enhancement of image quality compared to previous approaches; (2) the efficient combination of image reconstruction and shift-invariant linear image processing operations; (3) various hardware and software prototypes which, realize the above contributions, demonstrating the current potential of our sensor for real-time applications; and finally, (4) a further higher quality offline reconstruction algorithm.
Nematode-Bacterium Symbioses—Cooperation and Conflict Revealed in the “Omics” Age (2012)

Nematodes are ubiquitous organisms that have a significant global impact on ecosystems, economies, agriculture, and human health. The applied importance of nematodes and the experimental tractability of many species have promoted their use as models in various research areas, including developmental biology, evolutionary biology, ecology, and animal-bacterium interactions. Nematodes are particularly well suited for the investigation of host associations with bacteria because all nematodes have interacted with bacteria during their evolutionary history and engage in a variety of association types. Interactions between nematodes and bacteria can be positive (mutualistic) or negative (pathogenic/parasitic) and may be transient or stably maintained (symbiotic). Furthermore, since many mechanistic aspects of nematode-bacterium interactions are conserved, their study can provide broader insights into other types of associations, including those relevant to human diseases. Recently, genome-scale studies have been applied to diverse nematode-bacterial interactions and have helped reveal mechanisms of communication and exchange between the associated partners. In addition to providing specific information about the system under investigation, these studies also have helped inform our understanding of genome evolution, mutualism, and innate immunity. In this review we discuss the importance and diversity of nematodes, "omics"' studies in nematode-bacterial systems, and the wider implications of the findings.
Separation of contributions to spin valve interlayer exchange coupling field by temperature dependent coupling field measurements (2002)

In this work, interlayer exchange coupling fields of spin valve samples have been measured as a function of temperature, and fit to a temperature dependent combination of RKKY and Neel coupling fields. The RKKY coupling strength is assumed proportional to the form (T/T0)/sinh(T/T0), where T is temperature and T0 is characteristic temperature. [N. Persat and A. Dinia, Phys. Rev. B 56, 2676 (1997)] This allows the RKKY coupling and Neel coupling field to be separated quantitatively. The results of such an analysis on various CoFe/Cu/CoFe spin valve structures allow the extraction of a roughness parameter from the Neel model and the T0 parameter from the RKKY model. The measured roughness on the top surface was generally 2–3 times greater than the value obtained from the Neel analysis. The extracted T0 parameter was one order of magnitude smaller than that measured for bulk Cu by the de Hass–van Alphen effect. [N. Persat and A. Dinia, Phys. Rev. B. 56, 2676 (1997); B. Lengeler and W. R. Wampler, Phys. Rev. B 15, 5493 (1977)] Part of this reduction may be due to the 2D nature of the electron gas, as justified by an estimate of the 2D free electron Fermi energy calculation. However a factor of four difference remains, with the experimental value of T0 being around 100 K. This behavior, while not fully explained, is consistent with the measurements of other workers.
Role of Substrate in Au Nanoparticle Decoration by Electroless Deposition (2020)

Decoration of nanostructures is a promising way of improving performances of nanomaterials. In particular, decoration with Au nanoparticles is considerably efficient in sensing and catalysis applications. Here, the mechanism of decoration with Au nanoparticles by means of low-cost electroless deposition (ELD) is investigated on different substrates, demonstrating largely different outcomes. ELD solution with Au potassium cyanide and sodium hypophosphite, at constant temperature (80 °C) and pH (7.5), is used to decorate by immersion metal (Ni) or semiconductor (Si, NiO) substrates, as well as NiO nanowalls. All substrates were pre-treated with a hydrazine hydrate bath. Scanning electron microscopy and Rutherford backscattering spectrometry were used to quantitatively analyze the amount, shape and size of deposited Au. Au nanoparticle decoration by ELD is greatly affected by the substrates, leading to a fast film deposition onto metallic substrate, or to a slow cluster (50-200 nm sized) formation on semiconducting substrate. Size and density of resulting Au clusters strongly depend on substrate material and morphology. Au ELD is shown to proceed through a galvanic displacement on Ni substrate, and it can be modeled with a local cell mechanism widely affected by the substrate conductivity at surface. These data are presented and discussed, allowing for cheap and reproducible Au nanoparticle decoration on several substrates.
Detection of botnets using combined host- and network-level information (2010)

Bots are coordinated by a command and control (C&C) infrastructure to launch attacks that seriously threaten the Internet services and users. Most botnet-detection approaches function at the network level and require the analysis of packets' payloads, raising privacy concerns and incurring large computational overheads. Moreover, network traffic analysis alone can seldom provide a complete picture of botnets' behavior. By contrast, in-host detection approaches are useful to identify each bot's host-wide behavior, but are susceptible to the host-resident malware if used alone. To address these limitations, we consider both the coordination within a botnet and the malicious behavior each bot exhibits at the host level, and propose a C&C protocol-independent detection framework that combines host- and network-level information for making detection decisions. The framework is shown to be effective in detecting various types of botnets with low false-alarm rates.
Study on sequence component based fault phase selector during power swings (2010)

For digital distance relays, in order to get the correct measuring impedance, phase selector is widely used to identify the fault phases first. However, when a fault occurs at the line during power system swings, the traditional sequence component based phase selector might not identify the fault phase correctly, which leads to mal-operation of distance relays. Therefore, how to improve the existing sequence component based phase selector, especially at the condition of power system swings, is crucial. The relationship between the relative phase and amplitude of the sequence component of various asymmetric faults is analyzed. An improved asymmetric fault phase selector during power swings is proposed according to the corresponding relationship between the zero, negative sequence current components and the asymmetric fault types. The simulation results have shown the effectiveness of the method under power swings. Combining with fault component phase selector in no power swing, this method can perfectly solve the phase selection problem of transmission lines.
Effect of a Chemical Treatment Series on the Structure and Mechanical Properties of Abaca Fiber (<i>Musa textilis</i>) (2020)

This study investigates the relationships between the composition, cell wall microstructure, and mechanical properties of the abaca fiber. Raw abaca fibers have undergone a series of sequential chemical treatments (acetone/methanol, boiling water, EDTA, HCl, NaClO 2 , and NaOH) to selectively remove certain non-cellulosic components (NCCs) in the fiber, such as waxes, water-soluble fragments, pectin, and lignin in a step-by-step manner. Changes in composition, morphology, and mechanical properties were observed using FTIR spectroscopy and ion chromatography, digital microscope and SEM, and tensile tests, respectively. The raw fiber was composed of 23% NCCs, 18% hemicellulose, and 58% cellulose, and exhibited a 17.4 GPa Young’s modulus and a 444 MPa tensile strength. Furthermore, the raw abaca fibers demonstrated a linear tensile graph without yielding, and a planar fracture surface without fiber pull-outs, thus suggesting a highly elastic but brittle nature. At the end of the alkali treatment, the fibrillated fiber was 83% cellulose, yet the stiffness and strength dropped to 7.3 GPa and 55 MPa, respectively, as more components were removed, and microfibril relaxation and realignment have occurred. Load-bearing cellulose and hemicellulose accounted for 42% and 36% of the stiffness, respectively, due to –OH groups capable of hydrogen bonding. 63% of the strength was due to thenative NCC matrices, which contribute a significant role within the cell wall’s load-transfer activities.
Human Dental Pulp‐Derived Mesenchymal Stem Cell Potential to Differentiate into Smooth Muscle‐Like Cells In Vitro (2021)

Previous studies have shown that mesenchymal stem cells (MSCs) derived from various tissue sources can be differentiated into smooth muscle-like cells (SMLCs) in vitro. In this paper, dental pulp-derived mesenchymal stem cells (DPSCs) were evaluated for their differentiation ability towards smooth muscle-like cells (SMLCs) under the effect of widely used cytokines (TGF-<i>β</i>1 and PDGF-BB) with special focus on different culturing environments. For this purpose, both the commercially used culturing plates (Norm-c) and 0.1% gelatin-precoated (Gel-c) plates were used. Isolated cells displayed plastic adherence, pluripotency and cell surface marker profiling, and adipogenic and osteogenic differentiation potential with lineage specific marker expression. Differentiated cells induced under different culturing plates showed successful differentiation into SMLCs by positively expressing smooth muscle cell (SMC) specific markers both at the mRNA and protein levels. Gelatin coating could substantially enhance DPSC differentiation potential than Norm-c-induced cells. However, the absence of mature marker MHY-11 by immunostaining results from all treatment groups further indicated the development of immature and synthetic SMLCs. Finally, it was concluded that DPSC differentiation ability into SMLCs can be enhanced under cytokine treatment as well as by altering the cellular niche by precoating the culturing plates with suitable substrates. However, to get fully functional, contractile, and mature SMLCs, still many different cytokine cocktail combinations and more suitable coating substrates will be needed.
Electronic structures of diplatinum complexes (2017)

The unusual photophys. properties of d8d8 complexes have intrigued inorg. chemists for many years. Nilay&#13;\nHazari and I (with other good friends) worked on dipalladium electronic structures during the time he was in&#13;\nthe Bercaw-Labinger group at Caltech. In my lecture in his honor, I will discuss the latest developments in the&#13;\nfield, with emphasis on work by Jay Winkler and Yan Choi Lam on diplatinum photophysics, and by Bryan&#13;\nHunter, Tania Darnton, Mike Hill, Tony Vlcek, and Standa Zalis on rare (unique) 6p-sigma-bonded complexes.
Ultrasensitive Protein Detection Technologies for Extracellular Vesicle Measurements (2023)

Extracellular vesicles (EVs) are nanoscopic, heterogenous, lipid-rich particles that carry a multitude of cargo biomolecules including proteins, nucleic acids, and metabolites. Although historically EVs were regarded as cellular debris with no intrinsic value, growing understanding of EV biogenesis has led to the realization that EVs facilitate intercellular communication and are sources of liquid biomarkers. EVs can be isolated and analyzed from a wide variety of accessible biofluids for biomarker discovery and diagnostic applications. There is a diversity of EVs from different biological compartments (e.g., cells and tissues), and some of these EVs are present at extremely low concentrations. Consequently, a challenge in the field is to find appropriate markers that enable selective isolation of these rare EVs. Many conventional protein detection technologies have limited sensitivity to detect low abundance biomarkers in EVs, limiting their use in EV research. Advances in ultrasensitive detection technologies are needed to harness the potential of EVs for clinical application. This Perspective highlights current EV research focusing on ultrasensitive detection technologies, their limitations, and areas of potential growth in the future.
Visualizing dynamic microvillar search and stabilization during ligand detection by T cells (2017)

During immune surveillance, T cells survey the surface of antigen-presenting cells. In searching for peptide-loaded major histocompatibility complexes (pMHCs), they must solve a classic trade-off between speed and sensitivity. It has long been supposed that microvilli on T cells act as sensory organs to enable search, but their strategy has been unknown. We used lattice light-sheet and quantum dot-enabled synaptic contact mapping microscopy to show that anomalous diffusion and fractal organization of microvilli survey the majority of opposing surfaces within 1 minute. Individual dwell times were long enough to discriminate pMHC half-lives and T cell receptor (TCR) accumulation selectively stabilized microvilli. Stabilization was independent of tyrosine kinase signaling and the actin cytoskeleton, suggesting selection for avid TCR microclusters. This work defines the efficient cellular search process against which ligand detection takes place.
Evaluation of the Climate Impact Reduction Potential of the Water-Enhanced Turbofan (WET) Concept (2021)

Aviation faces increasing pressure not only to reduce fuel burn, and; therefore, CO2 emissions, but also to provide technical solutions for an overall climate impact minimization. To combine both, a concept for the enhancement of an aircraft engine by steam injection with inflight water recovery is being developed. The so-called Water-Enhanced Turbofan (WET) concept promises a significant reduction of CO2 emissions, NOx emissions, and contrail formation. Representative missions for an A320-type aircraft using the proposed new engine were calculated. Applying a first-order one-dimensional climate assessment prospects the reduction of more than half of the Global Warming Potential over one hundred years, compared to an evolutionarily improved aero-engine. If CO2-neutrally produced sustainable aviation fuels are used, climate impact could be reduced by 93% compared to today’s aircraft. The evaluation is a first estimate of effects based on preliminary design studies and should provide a starting point for discussion in the scientific community, implying the need for research, especially on the formation mechanisms and radiation properties of potential contrails from the comparatively cold exhaust gases of the WET engine.
Traps, events, emulation, and enforcement (2008)

We question current trends that attempt to leverage virtualization techniques to achieve security goals. We suggest that the security role of a virtual machine centers on being a policy interpreter rather than a resource provider. These two roles (security reference monitor and resource emulator) are currently conflated within the context of virtual machines and VMMs. We believe that this ``double-duty'' leads to both a significant performance impact as well as a bloated virtualization layer. Increased complexity reduces confidence that the code is elementary enough to verify or trust from a security perspective. Ironically, as more security-related functionality is shoved into a VM platform, the system becomes less trustworthy as it becomes increasingly trusted.
Optical characterization of Ge-on-Si laser gain media (2011)

Tensile strained Ge films with P concentrations as high as 3.4 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">19</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> are grown using UHVCVD. Photoluminescence measurements reveal significant direct band gap narrowing, enhanced photoemission, and optical bleaching.
Conservation and divergence of meiotic DNA double strand break forming mechanisms in Arabidopsis thaliana (2021)

In the current meiotic recombination initiation model, the SPO11 catalytic subunits associate with MTOPVIB to form a Topoisomerase VI-like complex that generates DNA double strand breaks (DSBs). Four additional proteins, PRD1/AtMEI1, PRD2/AtMEI4, PRD3/AtMER2 and the plant specific DFO are required for meiotic DSB formation. Here we show that (i) MTOPVIB and PRD1 provide the link between the catalytic sub-complex and the other DSB proteins, (ii) PRD3/AtMER2, while localized to the axis, does not assemble a canonical pre-DSB complex but establishes a direct link between the DSB-forming and resection machineries, (iii) DFO controls MTOPVIB foci formation and is part of a divergent RMM-like complex including PHS1/AtREC114 and PRD2/AtMEI4 but not PRD3/AtMER2, (iv) PHS1/AtREC114 is absolutely unnecessary for DSB formation despite having a conserved position within the DSB protein network and (v) MTOPVIB and PRD2/AtMEI4 interact directly with chromosome axis proteins to anchor the meiotic DSB machinery to the axis.
Supplementary Table S1 from The Master Neural Transcription Factor BRN2 Is an Androgen Receptor–Suppressed Driver of Neuroendocrine Differentiation in Prostate Cancer (2023)

&lt;p&gt;RNAseq of ENZ-resistant cells.&lt;/p&gt;
Corrosion characteristics of an automotive coolant formulation dispersed with nanomaterials (2019)

Abstract This paper summarizes the anti-corrosive and anti-erosive properties of water-ethylene glycol based commercial coolant dispersed with nanomaterials. Multiwalled carbon nanotubes (MWCNTs), silver nanoparticles (Ag) and nanosized alumina particles (Al 2 O 3 ) are dispersed in 0.5% weight in automotive coolants and tested for anti-corrosive properties as per ASTM standards. Prior to dispersion, the nanomaterials are surface modified to get good stability in coolant solutions. The corrosion resistance is measured in terms of weight loss of materials that is commonly used in automotive systems. It is found that oxidized MWCNTs are suitable to automotive systems while silver and Al 2 O 3 nanoparticles are found to be deleterious in nature.
Eotaxin Levels in Pleural Effusions. Comparison with Monocyte Chemoattractant Protein-1 and IL-8. (2000)

Results suggest that eotaxin contributes to the migration of eosinophils in pleural inflammation. Taken together with the correlation between IL-8 and neutrophils, it appears that the predominant type of pleural inflammatory infiltrate is controlled, at least in part, by the subgroup of chemokines expressed in the pleural space.
Pivotal role of 5-lipoxygenase in the activation of human eosinophils: platelet-activating factor and interleukin-5 induce CD69 on eosinophils through the 5-lipoxygenase pathway (2001)

CD69 is an activation-related cell surface molecule on human eosinophils. It has been reported that interleukin (IL)-5, but not platelet-activating factor (PAF), can induce CD69 on human eosinophils in vitro. In this study, PAF induced CD69 intensely on eosinophils from patients with hypereosinophilic syndrome (HES), while only weakly on those from normal donors. Because HES eosinophils contain abundant cytosolic phospholipase A2 (cPLA2) and 5-lipoxygenase (5-LO), we examined the roles of several enzymes involved in the metabolism of arachidonic acid in the PAF- or IL-5-induced CD69 expression on eosinophils. The CD69 expression induced by PAF and IL-5 on HES eosinophils and that by IL-5 on normal eosinophils were both inhibited by AA861 and MK-886, inhibitors of 5-LO activity. In addition, AACOCF3, a selective cPLA2 inhibitor, inhibited IL-5-induced CD69 expression on normal eosinophils, although it hardly affected either IL-5- or PAF-induced CD69 expression on HES eosinophils. Moreover, PAF alone induced CD69 only weakly on normal eosinophils, but exogenous arachidonic acid remarkably enhanced PAF-induced CD69 expression on them. These findings suggest that IL-5 activates both cPLA2 and 5-LO but PAF activates only 5-LO. It is suggested that 5-LO plays a critical role in the induction of CD69 on eosinophils.
ChemInform Abstract: Synthesis of a New Fluorescent Small Molecule Probe and Its Use for in vivo Lipid Imaging. (2011)

Abstract The compound (III), named LipidGreen, stains lipid droplets in 3T3L1 pre‐adipocyte cell lines and fat deposits in zebrafish.