gebhart/patrepeval huggingface dataset:
Low-Carbon Sustainable Composites from Waste Phosphogypsum and Their Environmental Impacts (2021)

Phosphogypsum (PG) is an industrial waste from the production of phosphoric acid and phosphate fertilizer. Disposal and landfill of PG pose significant environmental problems due to its hazardous components. Although many researchers have explored the possibility of PG recycling, challenges still exist before it can be high-effectively reused. In particular, a great deal of recent attention has been attracted to explore using PG as raw material to manufacture sustainable composites. The impurities movement, recycling efficiency, and environmental impacts have to be further investigated. This review article summarized the state of the art of the purification process, application areas, and the environmental impacts of PG waste. The main challenges and potential application approaches were discussed. This article is focused on reviewing the details of the PG reusing which benefits the readers on learning the knowledge from previous efforts. The main challenges of reusing PG were discussed from the chemical, physical, and materials perspectives.
Cyclo‐oxygenase‐2 Plays a Critical Role in UV‐induced Skin Carcinogenesis<sup>†</sup> (2008)

Besides induction of DNA damage and p53 mutations, chronic exposure to UV irradiation leads to the constitutive up-regulation of cyclo-oxygenase-2 (COX-2) expression and to increased production of its primary product in skin, prostaglandin E2 (PGE2). COX-2 has also been shown to be constitutively overexpressed in mouse, as well as human, UV-induced skin cancers and premalignant lesions. UV exposure results in ligand-independent activation of the epidermal growth factor receptor and subsequent activation of mitogen-activated protein kinase and phosphatidylinositol 3-kinase/Akt pathways leading to transcriptional activation of the COX-2 gene. Use of COX-2-specific inhibitors and genetic manipulation of COX-2 expression have demonstrated that UV induction of COX-2 in the skin contributes to the induction of epidermal hyperplasia, edema, inflammation, and counters the induction of apoptosis after UV exposure. Likewise, inhibition of COX-2 activity or reduced expression in COX-2 knockout mice resulted in significantly reduced UV-induced tumorigenesis, while overexpression of COX-2 in transgenic mice enhanced UV-induced tumor development. A combination of signaling from the PGE2 EP1, EP2 and/or EP4 receptors mediates the effects of COX-2 overexpression. These studies demonstrate the crucial role of COX-2 in the development of UV-related nonmelanoma skin cancers.
<i>Nitrososphaera viennensis</i> , an ammonia oxidizing archaeon from soil (2011)

Genes of archaea encoding homologues of ammonia monooxygenases have been found on a widespread basis and in large amounts in almost all terrestrial and marine environments, indicating that ammonia oxidizing archaea (AOA) might play a major role in nitrification on Earth. However, only one pure isolate of this group from a marine environment has so far been obtained, demonstrating archaeal ammonia oxidation coupled with autotrophic growth similar to the bacterial counterparts. Here we describe the cultivation and isolation of an AOA from soil. It grows on ammonia or urea as an energy source and is capable of using higher ammonia concentrations than the marine isolate, Nitrosopumilus maritimus. Surprisingly, although it is able to grow chemolithoautotrophically, considerable growth rates of this strain are obtained only upon addition of low amounts of pyruvate or when grown in coculture with bacteria. Our findings expand the recognized metabolic spectrum of AOA and help explain controversial results obtained in the past on the activity and carbon assimilation of these globally distributed organisms.
Controlled Cortical Impact Traumatic Brain Injury in 3xTg-AD Mice Causes Acute Intra-Axonal Amyloid-  Accumulation and Independently Accelerates the Development of Tau Abnormalities (2011)

Alzheimer's disease (AD) is a neurodegenerative disorder characterized pathologically by progressive neuronal loss, extracellular plaques containing the amyloid-β (Aβ) peptides, and neurofibrillary tangles composed of hyperphosphorylated tau proteins. Aβ is thought to act upstream of tau, affecting its phosphorylation and therefore aggregation state. One of the major risk factors for AD is traumatic brain injury (TBI). Acute intra-axonal Aβ and diffuse extracellular plaques occur in ∼30% of human subjects after severe TBI. Intra-axonal accumulations of tau but not tangle-like pathologies have also been found in these patients. Whether and how these acute accumulations contribute to subsequent AD development is not known, and the interaction between Aβ and tau in the setting of TBI has not been investigated. Here, we report that controlled cortical impact TBI in 3xTg-AD mice resulted in intra-axonal Aβ accumulations and increased phospho-tau immunoreactivity at 24 h and up to 7 d after TBI. Given these findings, we investigated the relationship between Aβ and tau pathologies after trauma in this model by systemic treatment of Compound E to inhibit γ-secretase activity, a proteolytic process required for Aβ production. Compound E treatment successfully blocked posttraumatic Aβ accumulation in these injured mice at both time points. However, tau pathology was not affected. Our data support a causal role for TBI in acceleration of AD-related pathologies and suggest that TBI may independently affect Aβ and tau abnormalities. Future studies will be required to assess the behavioral and long-term neurodegenerative consequences of these pathologies.
Floxed exon (Flexon): A flexibly positioned stop cassette for recombinase-mediated conditional gene expression (2022)

Conditional gene expression is a powerful tool for genetic analysis of biological phenomena. In the widely used "lox-stop-lox" approach, insertion of a stop cassette consisting of a series of stop codons and polyadenylation signals flanked by <i>lox</i> sites into the 5' untranslated region (UTR) of a gene prevents expression until the cassette is excised by tissue-specific expression of Cre recombinase. Although lox-stop-lox and similar approaches using other site-specific recombinases have been successfully used in many experimental systems, this design has certain limitations. Here, we describe the Floxed exon (Flexon) approach, which uses a stop cassette composed of an artificial exon flanked by artificial introns, designed to cause premature termination of translation and nonsense-mediated decay of the mRNA and allowing for flexible placement into a gene. We demonstrate its efficacy in <i>Caenorhabditis elegans</i> by showing that, when promoters that cause weak and/or transient cell-specific expression are used to drive Cre in combination with a <i>gfp(flexon)</i> transgene, strong and sustained expression of green fluorescent protein (GFP) is obtained in specific lineages. We also demonstrate its efficacy in an endogenous gene context: we inserted a <i>flexon</i> into the Argonaute gene <i>rde-1</i> to abrogate RNA interference (RNAi), and restored RNAi tissue specifically by expression of Cre. Finally, we describe several potential additional applications of the Flexon approach, including more precise control of gene expression using intersectional methods, tissue-specific protein degradation, and generation of genetic mosaics. The Flexon approach should be feasible in any system where a site-specific recombination-based method may be applied.
First Demonstration of Airborne SAR With Nonlinear FM Chirp Waveforms (2016)

For synthetic aperture radar (SAR), a system impulse response with low sidelobes is very important because sidelobes may interfere with the nearby scatterers and contribute to multiplicative noise. It is well known that a nonlinear frequency-modulation (NLFM) chirp waveform can shape the signal's power spectral density and provide a radar matched filter output with lower sidelobes without loss of the signal-to-noise ratio when compared with the linear frequency-modulation chirp. These advantages make the NLFM waveform to be a promising candidate to improve the imaging quality for SAR. However, so far, to our knowledge, there is no real application of NLFM waveforms for SAR. This letter, for the first time, demonstrates the airborne SAR experiment using an NLFM waveform. In the underlying experiment, the construction of the NLFM signal is investigated and a modified range migration algorithm (RMA) is developed to adapt it for focusing the NLFM SAR data. Both simulation and experimental results exhibit the promising power of the NLFM chirp and show the accuracy of the proposed modified RMA.
The extracytoplasmic function sigma factors: role and regulation (1998)

Alternative sigma factors provide a means of regulating gene expression in response to various extracellular changes. One such class of sigma factors appears to control a variety of functions, including expression of heat-shock genes in Escherichia coli, biosynthesis of alginates and carotenoids in Pseudomonas aeruginosa and Myxococcus xanthus, respectively, iron uptake in E. coli and Pseudomonas spp., nickel and cobalt efflux in Alcaligenes europhus, plant pathogenicity in Pseudomonas syringae and synthesis of outer membrane proteins in Photobacterium sp. strain SS9. Most of these activities deal with extracytoplasmic functions, and such sigmas have been designated as ECF sigma factors. They have also been characterized in Mycobacteria as well as gram-positive bacteria such as Streptomyces coelicolor and Bacillus subtilus and the archaea Sulpholobus acidocaldarius. ECF factors belong to a subfamily of the sigma 70 class, based on their sequence conservation and function across bacterial species. The promoter consensus sequences recognized by the ECF factors are also highly conserved. In most of the cases, the activity of these factors is modulated by a cognate inner membrane protein that has been shown, both in E. coli and in P. aeruginosa, to act as an anti-sigma activity. This inner membrane protein is presumed to serve as a sensor and signalling molecule, allowing an adaptive response to specific environmental change. Presumably, an on-and-off switch of the anti-sigma activity leads to the release of the sigma factor and thereby to the co-ordinate transcription of the specific regulon it governs.
An emerging coronavirus causing pneumonia outbreak in Wuhan, China: calling for developing therapeutic and prophylactic strategies (2020)

In December of 2019, an outbreak of pneumonia caused by an unknown aetiology occurred in Wuhan, China and most patients were linked to a single seafood market, which reportedly sold seafood and some live animals, including poultry, bats, marmots and other wild animals, suggesting that the pathogen may be transmitted from an animal to human. The pathogen was soon identified to be a novel coronavirus, 2019-nCoV denoted by WHO [1].
Freestanding Graphene Paper Supported Three-Dimensional Porous Graphene–Polyaniline Nanocomposite Synthesized by Inkjet Printing and in Flexible All-Solid-State Supercapacitor (2014)

Freestanding paper-like electrode materials have trigged significant research interest for their practical application in flexible and lightweight energy storage devices. In this work, we reported a new type of flexible nanohybrid paper electrode based on full inkjet printing synthesis of a freestanding graphene paper (GP) supported three-dimensional (3D) porous graphene hydrogel (GH)-polyaniline (PANI) nanocomposite, and explored its practical application in flexible all-solid-state supercapacitor (SC). The utilization of 3D porous GH scaffold to load nanostructured PANI dramatically enhances the electrical conductivity, the specific capacitance and the cycle stability of the GH-PANI nanocomposite. Additionally, GP can intimately interact with GH-PANI through π-π stacking to form a unique freestanding GP supported GH-PANI nanocomposite (GH-PANI/GP) with distinguishing mechanical, electrochemical and capacitive properties. These exceptional attributes, coupled with the merits of full inkjet printing strategy, lead to the formation of a high-performance binder-free paper electrode for flexible and lightweight SC application. The flexible all-solid-state symmetric SC based on GH-PANI/GP electrode and gel electrolyte exhibits remarkable mechanical flexibility, high cycling performance and acceptable energy density of 24.02 Wh kg(-1) at a power density of 400.33 W kg(-1). More importantly, the proposed simple and scale-up full inkjet printing procedure for the preparation of freestanding GP supported 3D porous GH-PANI nanocomposite is a modular approach to fabricate other graphene-based nanohybrid papers with tailorable properties and optimal components.
The Old Stoics (1994)

Abstract This chapter discusses the Stoic school, founded by Zeno in 301, which was succeeded in turn by Cleanthes and Chrysippus. The Stoics differed from Plato and Aristotle in denying that spiritual activity could account for the maintenance of the world. The two principles which are responsible for all things are causal and material, but even so, the causal principle acts corporeally, since whatever acts or is acted upon must be a body. Thus God is equated with corporeal substance, but this material was not passive like Peropatetic or neo-Platonic matter. Since the Stoic God was not located only in heaven but was immanent in the world, the stars were not supreme deities, and they play only a small role in the piety of some of the greatest Stoic philosophers, such as Epictetus and Marcus Aurelius. Yet, the Stoics are important since they also emphasize the religious importance of the heavens.
Total synthesis of a tyrosine suppressor tRNA gene. XV. Synthesis of the promoter region. (1979)

By use of polynucleotide kinase and polynucleotide ligase, the 10 deoxyoligonucleotide segments, whose syntheses have been described in accompanying papers, have been joined to form the 62-nucleotide-long DNA corresponding to the promoter region of an Escherichia coli suppressor tRNA gene. The following sequence in the joining reactions was used to obtain error-free and optimal yields of the products: 1) joining of Segment P-1 to P-3 in the presence of Segment P-2; 2) joining of Segments P-4 to P-7 to form Duplex [P4-7]; 3) joining of Segments P-8 to P-10 to Duplex [P4-7] to form Duplex [P4-10]; and finally, 4) joining of P-(1 + 3) and P-2 to Duplex [P4-10] to form the total promoter Duplex [P].
Oxidative stress-mediated TXNIP loss causes RPE dysfunction (2019)

The disruption of the retinal pigment epithelium (RPE), for example, through oxidative damage, is a common factor underlying age-related macular degeneration (AMD). Aberrant autophagy also contributes to AMD pathology, as autophagy maintains RPE homeostasis to ensure blood-retinal barrier (BRB) integrity and protect photoreceptors. Thioredoxin-interacting protein (TXNIP) promotes cellular oxidative stress by inhibiting thioredoxin reducing capacity and is in turn inversely regulated by reactive oxygen species levels; however, its role in oxidative stress-induced RPE cell dysfunction and the mechanistic link between TXNIP and autophagy are largely unknown. Here, we observed that TXNIP expression was rapidly downregulated in RPE cells under oxidative stress and that RPE cell proliferation was decreased. TXNIP knockdown demonstrated that the suppression of proliferation resulted from TXNIP depletion-induced autophagic flux, causing increased p53 activation via nuclear localization, which in turn enhanced AMPK phosphorylation and activation. Moreover, TXNIP downregulation further negatively impacted BRB integrity by disrupting RPE cell tight junctions and enhancing cell motility by phosphorylating, and thereby activating, Src kinase. Finally, we also revealed that TXNIP knockdown upregulated HIF-1α, leading to the enhanced secretion of VEGF from RPE cells and the stimulation of angiogenesis in cocultured human retinal microvascular endothelial cells. This suggests that the exposure of RPE cells to sustained oxidative stress may promote choroidal neovascularization, another AMD pathology. Together, these findings reveal three distinct mechanisms by which TXNIP downregulation disrupts RPE cell function and thereby exacerbates AMD pathogenesis. Accordingly, reinforcing or restoring BRB integrity by targeting TXNIP may serve as an effective therapeutic strategy for preventing or attenuating photoreceptor damage in AMD.
Early Colonic Damage and Invasion of Campylobacter jejuni in Experimentally Challenged Infant Macaca mulatta (1993)

Experimental challenge studies with Campylobacter jejuni were conducted in 3.5-month-old infant Macaca mulatta. One infant monkey (92-1) was challenged with 2.7 x 10(10) cfu of strain 78-37. A second infant was infected intentionally by natural transmission. The infants developed diarrhea 32 h after challenge of infant 92-1. Electron microscopic observations indicate that cell invasion is the primary mechanism of colon damage and diarrheal disease caused by C. jejuni. Intracellular C. jejuni were located in membrane-bound vacuoles and were free in the cytoplasm. Damaged epithelial cells exhibited premature apoptosis and were exfoliated into the lumen of the colon. C. jejuni were also located extracellularly in the mucosa and submucosa. Some cells had dilated endoplasmic reticulum, indicating possible alteration in ion and water transport.
Phosphate modified ceria as a Brønsted acidic/redox multifunctional catalyst (2017)

Modification of the surface of ceria with phosphates leads to acid/redox active materials that can serve as non-innocent supports for Pd-catalyzed hydrogenolysis of lignin model compounds.
Lasofoxifene (CP-336,156) Protects Against the Age-Related Changes in Bone Mass, Bone Strength, and Total Serum Cholesterol in Intact Aged Male Rats (2001)

The purpose of this study was to evaluate if long-term (6 months) treatment with lasofoxifene (LAS), a new selective estrogen receptor modulator (SERM), can protect against age-related changes in bone mass and bone strength in intact aged male rats. Sprague-Dawley male rats at 15 months of age were treated (daily oral gavage) with either vehicle (n = 12) or LAS at 0.01 mg/kg per day (n = 12) or 0.1 mg/kg per day (n = 11) for 6 months. A group of 15 rats was necropsied at 15 months of age and served as basal controls. No significant change was found in body weight between basal and vehicle controls. However, an age-related increase in fat body mass (+42%) and decrease in lean body mass (-8.5%) was observed in controls. Compared with vehicle controls, LAS at both doses significantly decreased body weight and fat body mass but did not affect lean body mass. No significant difference was found in prostate wet weight among all groups. Total serum cholesterol was significantly decreased in all LAS-treated rats compared with both the basal and the vehicle controls. Both doses of LAS treatment completely prevented the age-related increase in serum osteocalcin. Peripheral quantitative computerized tomography (pQCT) analysis at the distal femoral metaphysis indicated that the age-related decrease in total density, trabecular density, and cortical thickness was completely prevented by treatment with LAS at 0.01 mg/kg per day or 0.1 mg/kg per day. Histomorphometric analysis of proximal tibial cancellous bone showed an age-related decrease in trabecular bone volume (TBV; -46%), trabecular number (Tb.N), wall thickness (W.Th), mineral apposition rate, and bone formation rate-tissue area referent. Moreover, an age-related increase in trabecular separation (Tb.Sp) and eroded surface was observed. LAS at 0.01 mg/kg per day or 0.1 mg/kg per day completely prevented these age-related changes in bone mass, bone structure, and bone turnover. Similarly, the age-related decrease in TBV and trabecular thickness (Tb.Th) and the age-related increase in osteoclast number (Oc.N) and osteoclast surface (Oc.S) in the third lumbar vertebral cancellous bone were completely prevented by treatment with LAS at both doses. Further, LAS at both doses completely prevented the age-related decrease in ultimate strength (-47%) and stiffness (-37%) of the fifth lumbar vertebral body. These results show that treatment with LAS for 6 months in male rats completely prevents the age-related decreases in bone mass and bone strength by inhibiting the increased bone resorption and bone turnover associated with aging. Further, LAS reduced total serum cholesterol and did not affect the prostate weight in these rats. Our data support the potential use of a SERM for protecting against the age-related changes in bone and serum cholesterol in elderly men.
Ornithonyssus bacoti infestation and elimination from a mouse colony. (2005)

Skin lesions, consisting of nonspecific bites with intense pruritus and excoriation of the skin, were found on personnel working in an animal colony primarily housing mice. The tropical rat mite, Ornithonyssus bacoti, was diagnosed from mites trapped on insect-monitoring sticky traps and collected from mouse cages in the colony. Because these mites do not live on mice but only come to feed when the animals are in their nest, an initial attempt was made to eliminate the mites with a thorough cleaning of the facility. Clidox foam was applied to the entire room with a foaming machine. Then the mice were transferred into the sanitized cages in the cleaned room. The numbers of mites were reduced to the point that they were no longer noticed in the colony, but the mites returned within 2 weeks. The mites were successfully eliminated with the use of permethrin-impregnated cotton balls in the mouse cages for 8 weeks and treatment of the premises. Treatment of the premises included spraying floors and walls of all rooms housing mice and adjacent hallways in the colony with pyrethrin spray by a commercial pest control company. To prevent one room of rabbits from maintaining the infestation, they were treated weekly with an organic pyrethrin dust. Insect sticky traps have remained negative for mites for more than 3 years after treatment.
A Printed and Flexible Field‐Effect Transistor Device with Nanoscale Zinc Oxide as Active Semiconductor Material (2008)

A family of single-source precursors for low temperature processing of uniform, transparent, and adherent ZnO thin films on various substrates is studied. They decompose cleanly under very mild processing conditions of 150 °C. The resulting ZnO thin films exhibit promising semiconducting properties when printed in a field-effect transistor (FET) device structure. This class of precursor compounds is compatible with existing printing technologies and allows printing of semiconductors on flexible polymer substrates under mild conditions.