gebhart/patrepeval huggingface dataset:
Rapid and flexible online desalting using Nafion‐coated melamine sponge for mass spectrometry analysis (2022)

Flexible, low-cost, and efficient online desalting was achieved by the Nafion-coated sponge. A variety of molecules ranging from small molecules, peptides, proteins to oligosaccharides and DNAs can be desalted for MS analysis. The desalting by Nafion sponge has great potential for desalting applications that require customized fluidic design and rapid analysis.
Actin Cytoskeleton Remodeling Drives Breast Cancer Cell Escape from Natural Killer–Mediated Cytotoxicity (2018)

Elucidation of the underlying molecular mechanisms of immune evasion in cancer is critical for the development of immunotherapies aimed to restore and stimulate effective antitumor immunity. Here, we evaluate the role of the actin cytoskeleton in breast cancer cell resistance to cytotoxic natural killer (NK) cells. A significant fraction of breast cancer cells responded to NK-cell attack via a surprisingly rapid and massive accumulation of F-actin near the immunologic synapse, a process we termed "actin response." Live-cell imaging provided direct evidence that the actin response is associated with tumor cell resistance to NK-cell-mediated cell death. High-throughput imaging flow cytometry analyses showed that breast cancer cell lines highly resistant to NK cells were significantly enriched in actin response-competent cells as compared with susceptible cell lines. The actin response was not associated with a defect in NK-cell activation but correlated with reduced intracellular levels of the cytotoxic protease granzyme B and a lower rate of apoptosis in target cells. Inhibition of the actin response by knocking down CDC42 or N-WASP led to a significant increase in granzyme B levels in target cells and was sufficient to convert resistant breast cancer cell lines into a highly susceptible phenotype. The actin response and its protective effects were fully recapitulated using donor-derived primary NK cells as effector cells. Together, these findings establish the pivotal role of actin remodeling in breast cancer cell resistance to NK-cell-mediated killing.<b>Significance:</b> These findings establish the pivotal role of the actin cytoskeleton in driving breast cancer cell resistance to natural killer cells, a subset of cytotoxic lymphocytes with important roles in innate antitumor immunity. <i>Cancer Res; 78(19); 5631-43. ©2018 AACR</i>.
&lt;i&gt;Electroflotation of Escherichia coli Improves Detection Rates by Loop-mediated Isothermal Amplification&lt;/i&gt; (2017)

<abstract> <b><sc> Abstract.</sc></b> The power of portable molecular diagnostic systems for the detection of pathogenic microorganisms in food and environmental samples is largely limited by small assay volumes (typically 1-5 Î¼L), making direct detection of trace contamination (i.e. <10<sup>4</sup> CFU / mL) unreliable. To improve detection limits for pathogens dispersed on an ecological scale, we have developed a portable point-of-care (POC) sample preparation system using electroflotation (EF) to recover small quantities of these organisms from samples of hundreds of milliliters. Electrolysis reactions, supported on platinum-coated titanium electrodes, generate hydrogen and oxygen micro-bubbles that impel and displace suspended cells into a recovered concentrate. Samples were prepared by inoculating 380 mL of sterilized phosphate buffer (0.1 M, pH 6.6) with stock culture of Escherichia coli (E. coli) ATCC 25922 to final concentrations ranging from 10<sup>2</sup> to 10<sup>4 </sup>CFU/mL. Samples were subjected to 10, 15, and 20 minute durations of EF treatment under high and low turbulent mixing conditions. We used a loop mediated amplification (LAMP) assay with primers targeting a single-copy gene (glycerate kinase) in generic E. coli to evaluate the effects of EF treatment on concentration and recovery of detectable cell material. LAMP failed to detect E. coli in all untreated (control) samples at concentrations below 10<sup>4</sup> CFU/mL, but was able to detect E. coli in 10<sup>2</sup> CFU/mL samples subjected to various conditions of EF treatment. Two-way ANOVA showed significant differences in detection rates between EF treatment durations for both high (p=0.0019) and low turbulence (p=0.002). Dunnett‘s multiple comparison tests identified 5 process conditions resulting insignificant (p<0.05) differences in detection between treatments and the control.
Akt1–Mediated Skeletal Muscle Growth Attenuates Cardiac Dysfunction and Remodeling After Experimental Myocardial Infarction (2011)

Akt1-mediated skeletal muscle growth attenuates cardiac remodeling after myocardial infarction and is associated with an increased capillary density in the heart. This improvement appears to be mediated by skeletal muscle to cardiac communication, leading to activation of eNOS-signaling in the heart.
The Effects of Common Anti-Inflammatory Drugs on the Healing Rat Patellar Tendon (2007)

Selective and nonselective cyclooxygenase (COX) inhibitors should be used judiciously in the acute period after injury or surgical repair at the bone-tendon junction.
Oval Flow Mode Between Two Corotating Disks With Stationary Shroud (2014)

The characteristic flow behavior, time-averaged velocity distributions, phase-resolved ensemble-averaged velocity profiles, and turbulence properties of the flow in the interdisk midplane between shrouded two corotating disks at the interdisk spacing to disk radius aspect ratio 0.2 and rotation Reynolds number 3.01 × 105 were experimentally studied by flow visualization method and particle image velocimetry (PIV). An oval core flow structure rotating at a frequency 60% of the disks rotating frequency was observed. Based on the analysis of relative velocities, the flow in the region outside the oval core flow structure consisted of two large vortex rings, which move circumferentially with the rotation motion of the oval flow core. Four characteristic flow regions—solid-body-rotation-like region, buffer region, vortex region, and shroud-influenced region—were identified in the flow field. The solid-body-rotation-like region, which was featured by its linear distribution of circumferential velocity and negligibly small radial velocity, was located within the inscribing radius of the oval flow core. The vortex region was located outside the circumscribing radius of the oval flow core. The buffer region existed between the solid-body-rotation-like region and the vortex region. In the buffer region, there existed a “node” point that the propagating circumferential velocity waves diminished. The circumferential random fluctuation intensity presented minimum values at the node point and high values in the solid-body-rotation-like region and shroud-influenced region due to the shear effect induced by the wall.
Hypoxia-Ischemia or Excitotoxin-Induced Tissue Plasminogen Activator- Dependent Gelatinase Activation in Mice Neonate Brain Microvessels (2013)

Hypoxia-ischemia (HI) and excitotoxicity are validated causes of neonatal brain injuries and tissue plasminogen activator (t-PA) participates in the processes through proteolytic and receptor-mediated pathways. Brain microvascular endothelial cells from neonates in culture, contain and release more t-PA and gelatinases upon glutamate challenge than adult cells. We have studied t-PA to gelatinase (MMP-2 and MMP-9) activity links in HI and excitotoxicity lesion models in 5 day-old pups in wild type and in t-PA or its inhibitor (PAI-1) genes inactivated mice. Gelatinolytic activities were detected in SDS-PAGE zymograms and by in situ fluorescent DQ-gelatin microscopic zymographies. HI was achieved by unilateral carotid ligature followed by a 40 min hypoxia (8%O₂). Excitotoxic lesions were produced by intra parenchymal cortical (i.c.) injections of 10 µg ibotenate (Ibo). Gel zymograms in WT cortex revealed progressive extinction of MMP-2 and MMP-9 activities near day 15 or day 8 respectively. MMP-2 expression was the same in all strains while MMP-9 activity was barely detectable in t-PA⁻/⁻ and enhanced in PAI-1⁻/⁻ mice. HI or Ibo produced activation of MMP-2 activities 6 hours post-insult, in cortices of WT mice but not in t-PA⁻/⁻ mice. In PAI-1⁻/⁻ mice, HI or vehicle i.c. injection increased MMP-2 and MMP-9 activities. In situ zymograms using DQ-gelatin revealed vessel associated gelatinolytic activity in lesioned areas in PAI-1⁻/⁻ and in WT mice. In WT brain slices incubated ex vivo, glutamate (200 µM) induced DQ-gelatin activation in vessels. The effect was not detected in t-PA⁻/⁻ mice, but was restored by concomitant exposure to recombinant t-PA (20 µg/mL). In summary, neonatal brain lesion paradigms and ex vivo excitotoxic glutamate evoked t-PA-dependent gelatinases activation in vessels. Both MMP-2 and MMP-9 activities appeared t-PA-dependent. The data suggest that vascular directed protease inhibition may have neuroprotection potential against neonatal brain injuries.
A simplified cell-based assay to identify coronavirus 3CL protease inhibitors (2020)

We describe a mammalian cell-based assay capable of identifying coronavirus 3CL protease (3CLpro) inhibitors without requiring the use of live virus. By enabling the facile testing of compounds across a range of coronavirus 3CLpro enzymes, including the one from SARS-CoV-2, we are able to quickly identify compounds with broad or narrow spectra of activity. We further demonstrate the utility of our approach by performing a curated compound screen along with structure-activity profiling of a series of small molecules to identify compounds with antiviral activity. Throughout these studies, we observed concordance between data emerging from this assay and from live virus assays. By democratizing the testing of 3CL inhibitors to enable screening in the majority of laboratories rather than the few with extensive biosafety infrastructure, we hope to expedite the search for coronavirus 3CL protease inhibitors, to address the current epidemic and future ones that will inevitably arise.
Next generation telemedicine platforms to screen and triage (2019)

Visual impairment is a growing problem worldwide.1 By 2040, it is estimated that 288 million patients will have some forms of AMD,2 119 million with glaucoma cases,3 and 422 millions with DR.4 With ageing populations globally, most eye health services will struggle to manage these eye diseases with existing manpower and infrastructure, and face significant financial constraints.5 

In this setting, new models of care with digital health technologies and platforms are urgently needed.5 Conventionally, eye care service delivery can be conducted via routine, mobile and teleophthalmology settings. With the advancement in technology and telecommunication networks, numerous novel digital health solutions and service models can streamline and automate critical aspects of the screening and monitoring processes,6 including secure telemedicine platforms that can be coupled with automated algorithms using artificial intelligence and big data analytics.6 These measures not only help screen and triage patients with new eye diseases, but can also monitor stable patients who do not require management in tertiary eye care settings.

Telemedicine can be broadly divided into two types—synchronous and asynchronous models. The synchronous model usually requires good internet connectivity that enables real-time consultations between patients and physicians via a telemedicine platform. This model is useful for emergency rooms consultations in rural hospital settings where ophthalmology services are limited. Local emergency physicians could use telemedicine platforms to present their patients’ history and ocular examination, enabling ophthalmologists or specialists to help triage the urgency of referrals or …
Fungal Influence on Plant Tolerance to Stress (2012)

This chapter contains sections titled: Temperature Tolerance Salt-Stress Tolerance Habitat-Adapted Symbiosis Drought-Stress Tolerance Mechanisms of Symbiotically Conferred Stress Tolerance Mitigating Impacts of Climate Change Acknowledgments References
Expression and Characterization of PGD<sub>2</sub> Receptors in Chronic Rhinosinusitis: Modulation of DP and CRTH2 by PGD<sub>2</sub> (2008)

These results suggest that distinct expression of DP and CRTH2 is associated with the pathophysiology of CRS, including NP formation, and the expression of these receptors may be regulated by h-PGDS and PGD(2).
Optical Transport of 100G Ethernet Serial Formats (2007)

We review the electronic generation and transmission of recently demonstrated serial transport technologies at 100 Gb/s, including binary and multi-level formats.
Post‐genomic vaccine development (2006)

For over a century, vaccines were developed according to Pasteur's principles of isolating, inactivating and injecting the causative agent of an infectious disease. The availability of a complete microbial genome sequence in 1995 marked the beginning of a genomic era that has allowed scientists to change the paradigm and approach vaccine development starting from genomic information, a process named reverse vaccinology. This can be considered as one of the most powerful examples of how genomic information can be used to develop therapeutic interventions, which were difficult or impossible to tackle with conventional approaches. As the genomic era progressed, it became apparent that multi-strain genome analysis is fundamental to the design of universal vaccines. In the post-genomic era, the next challenge of the vaccine biologist will be the merging of the vaccinology with structural biology.
Pore-scale Spectral Induced Polarization (SIP) signatures associated with FeS biomineral transformations (2007)

The authors measured Spectral Induced Polarization (SIP) signatures in sand columns during (1) FeS biomineralization produced by sulfate reducing bacteria (D. vulgaris) under anaerboci conditions, and (2) subsequent biomineral dissolution upon return to an aerobic state. The low-frequency (0.1-10 Hz peak) relaxations produced during biomineralization can be modeled with a Cole-Cole formulation, from which the evolution of the polarization magnitude and relaxation length scale can be estimated. They find that the modeled time constant is consistent with the polarizable elements being biomineral encrused pores. Evolution of the model parameters is consistent with FeS surface area increases and pore-size reduction during biomineral growth, and subsequent biomineral dissolution (FeS surface area decreases and pore expansion) upon return to the aerobic state. They conclude that SIP signatures are diagnostic of pore-scale geometrical changes associated with FeS biomineralization by sulfate reducing bacteria.
Role of Terrestrial Wild Birds in Ecology of Influenza A Virus (H5N1) (2007)

House sparrows, European starlings, and Carneux pigeons were inoculated with 4 influenza A (H5N1) viruses isolated from different avian species. We monitored viral replication, death after infection, and transmission to uninfected contact birds of the same species. Sparrows were susceptible to severe infection; 66%-100% of birds died within 4-7 days. High levels of virus were detected from oropharyngeal and cloacal swabs and in organs of deceased sparrows. Inoculation of starlings caused no deaths, despite high levels of virus shedding evident in oropharyngeal swabs. Least susceptible were pigeons, which had no deaths and very low levels of virus in oropharyngeal and cloacal swabs. Transmission to contact birds did not occur frequently: only A/common magpie/Hong Kong/645/2006 virus was shown to transmit to 1 starling. In summary, recent influenza (H5N1) viruses are pathogenic for small terrestrial bird species but the rate of intraspecies transmission in these hosts is very low.
Rock phase control by using high power laser for production enhancements (2003)

This study is part of a more extensive research effort by Gas Technology Institute to apply high power laser technology in well construction and completion techniques for the oil and gas industry. It has been demonstrated that by altering laser parameters, including power and duration, changes in rock properties and phase behavior can be controlled. This paper presents the results and analysis of high power laser interactions, including the Mid-infrared Advanced Chemical Laser (MIRACL), Chemical Oxygen Iodine Laser (COIL) and carbon dioxide lasers in limestone, sandstone and shale samples. When laser energy was allowed to melt minerals within the rock matrix, an impermeable barrier with ceramic-like characteristics was created that may provide in-situ fluid flow control and wellbore stability. A porous ceramic barrier could also be created on demand through the application of a high velocity purging system for applications in unconsolidated rock formations, preventing sand production and tunnel collapse, critical concerns in well completion and production operations.
Differential binding of retinol analogs to two homologous cellular retinol-binding proteins. (1993)

A comparative study of the interactions of rat cellular retinol-binding protein (CRBP) and cellular retinol-binding protein II (CRBP II) with a number of synthetic phenyl-substituted analogs of all-trans-retinol was performed using fluorescence and nuclear magnetic resonance analysis. These studies indicate that CRBP II is more sensitive to modifications of the ring moiety than CRBP. Removal of the two methyl substituents on the ring which are ortho to the polyene chain abolishes binding to CRBP II. Conformational analysis of the ligands indicates that these two methyl groups influence the planarity of the ligand. The identification of monospecific ligands may prove useful for studying the physiological roles of these two proteins.
Progress in direct-drive inertial confinement fusion research at the laboratory for laser energetics (2006)

Direct-drive inertial confinement fusion (ICF) is expected to demonstrate high gain on the National Ignition Facility (NIF) in the next decade and is a leading candidate for inertial fusion energy production. The demonstration of high areal densities in hydrodynamically scaled cryogenic DT or D2 implosions with neutron yields that are a significant fraction of the “clean” 1-D predictions will validate the ignition-equivalent direct-drive target performance on the OMEGA laser at the Laboratory for Laser Energetics (LLE). This paper highlights the recent experimental and theoretical progress leading toward achieving this validation in the next few years. The NIF will initially be configured for X-ray drive and with no beams placed at the target equator to provide a symmetric irradiation of a direct-drive capsule. LLE is developing the “polar-direct-drive” (PDD) approach that repoints beams toward the target equator. Initial 2-D simulations have shown ignition. A unique “Saturn-like” plastic ring around the equator refracts the laser light incident near the equator toward the target, improving the drive uniformity. LLE is currently constructing the multibeam, 2.6-kJ/beam, petawatt laser system OMEGA EP. Integrated fast-ignition experiments, combining the OMEGA EP and OMEGA Laser Systems, will begin in FY08.
OS1207 Fabrication of Porous Aluminum by Friction Powder Sintering Process and Increasing in Size of Porous Aluminum by Multi-Pass Process (2014)

Porous aluminum (Al) was fabricated by a tool traversing friction powder compaction process with the sintering and dissolution process. In this process, a mixture of Al powder and NaCl as spacer particle was the starting material. After the powder mixture was placed in a mold, sintering was conducted only by the traversing of a rotating tool. Namely, no external heat source was used in fabrication of porous Al except for the friction heat generated by the traversing of the tool. In this study, increasing in size of porous aluminum was conducted by applying multi-pass process. Fabricated porous Al had a length and width equal to the tool traversing area. By a X-ray computing tomography observation, fabricated porous Al had uniform pore distribution. In a compression test, it was found that fabricated porous Al had almost the same mechanical properties, regardless of the position in the tool traversing area.
Trial Watch: Peptide-based anticancer vaccines (2015)

Malignant cells express antigens that can be harnessed to elicit anticancer immune responses. One approach to achieve such goal consists in the administration of tumor-associated antigens (TAAs) or peptides thereof as recombinant proteins in the presence of adequate adjuvants. Throughout the past decade, peptide vaccines have been shown to mediate antineoplastic effects in various murine tumor models, especially when administered in the context of potent immunostimulatory regimens. In spite of multiple limitations, first of all the fact that anticancer vaccines are often employed as therapeutic (rather than prophylactic) agents, this immunotherapeutic paradigm has been intensively investigated in clinical scenarios, with promising results. Currently, both experimentalists and clinicians are focusing their efforts on the identification of so-called tumor rejection antigens, i.e., TAAs that can elicit an immune response leading to disease eradication, as well as to combinatorial immunostimulatory interventions with superior adjuvant activity in patients. Here, we summarize the latest advances in the development of peptide vaccines for cancer therapy.
In Vitro Nimesulide Studies toward Understanding Idiosyncratic Hepatotoxicity: Diiminoquinone Formation and Conjugation (2008)

Nimesulide is a nonsteroidal anti-inflammatory drug (NSAID) marketed in more than 50 countries. This drug has caused rare and idiosyncratic but severe hepatotoxicity. The mechanisms associated with and factors responsible for this toxicity remain unknown. One of the nimesulide metabolites identified in human urine is 4-amino-2-phenoxy-methanesulfonanilide (M1). In the current study, we demonstrate that M1 is a stable metabolite that is highly susceptible to facile oxidation by cytochrome P450 enzymes (P450s) to form a reactive diiminoquinone intermediate (M2). Direct detection of M2 was difficult by LC-MS. However, its formation was confirmed indirectly by identification of N-acetyl-cysteine (NAC) adducts of M2. The formation of diiminoquinone M2 was P450 mediated with 2C19 and 1A2 as the two principal P450 enzymes catalyzing M1 oxidation. M1 metabolism irreversibly inhibited 2C19 but activated 1A2 in a time-dependent manner. P450 2C19 exclusively mediated further metabolism of M1 to the amino hydroxynimesulide M3 and its diiminoquinone M4. Similar to M2, M4 is also reactive and can be observed indirectly as its NAC adduct. Nucleophilic addition to diiminoquinone M2 occurs with low regioselectivity, yielding three adducts (the peak area ratio 1:0.08:12). The three regioisomers have the same m/z for [M + H](+), presumably due to nucleophilic addition at the three possible electrophilic sites (C-3, -5, and -6 positions of the sulfonaniline ring). The primary adduct, R, was derived from the attack of the nucleophile at the C-5 position of the sulfonaniline ring and was determined by MS/MS and (1)H and (13)C NMR analyses. The structural assignments were confirmed by chemical synthesis of the adduct R. M2 demonstrated its electrophilic reactivity by selectively alkylating human serum albumin (HSA) at the only free thiol, Cys-34. This suggests the possibility that other proteins may undergo a similar conjugation to form irreversible adducts. Under oxidizing conditions in the presence of cumene hydroperoxide (CHP), the formation of M2 was enhanced, indicating that oxidative stress may accelerate the production of reactive diiminoquinone species (M2 and M4).
Real-Time PCR Quantification of AT1 and AT2 Angiotensin Receptor mRNA Expression in the Developing Rat Kidney (2003)

The ratio of AT2 to AT1 gene expression modulates Ang II action in the developing kidney.