gebhart/patrepeval huggingface dataset:
Melanoma differentiation associated gene-7/interleukin-24 reverses multidrug resistance in human colorectal cancer cells (2007)

Overexpression of the multidrug resistance 1 (MDR1) gene, encoding P-glycoprotein (P-gp), facilitates resistance to diverse chemotherapeutic drugs and current P-gp inhibitors display high toxicity. We studied the effects of melanoma differentiation associated gene-7/interleukin-24 (mda-7/IL-24), which exhibits cancer-specific apoptosis-inducing properties, in drug-sensitive (SW620) and drug-resistant (SW620/Dox) colorectal carcinoma cells. Adenovirus administered mda-7/IL-24, Ad.mda-7, effectively reversed resistance to doxorubicin-induced apoptosis in SW620/Dox cells by increased intracellular accumulation and decreased efflux of doxorubicin. Unexpectedly, P-gp-overexpressing cells (SW620/Dox) displayed increased apoptosis following Ad.mda-7 infection compared with parental SW620 cells, which correlated with more MDA-7/IL-24 protein in SW620/Dox than SW620 cell and potentially explains the increased sensitivity of P-gp-overexpressing cells to mda-7/IL-24. Transient overexpression of MDR1 in SW620 cells significantly increased apoptosis, decreased anchorage-independent growth, and increased MDA-7/IL-24 protein following Ad.mda-7 infection, whereas down-modulation of MDR1 in SW620/Dox cells by small interfering RNA decreased apoptosis following Ad.mda-7 infection. The increased mda-7/IL-24 sensitivity observed in SW620/Dox cells was partly due to increased reactive oxygen species generation and lower mitochondrial membrane potential. These findings confirm that mda-7/IL-24 is a potent MDR reversal agent, preferentially causing apoptosis in P-gp-overexpressing MDR cells, suggesting significant expanded clinical implications for the use of mda-7/IL-24 in treating neoplasms that have failed chemotherapy mediated by the P-gp MDR mechanism.
3-D mapping of body surface potentials (1987)

A new system has been developed in which the human body surface potentials are displayed in a 3-dimensional format using computer graphics. A wire-frame model of the human torso is constructed using geometrical data from several cross-sectional slices. The body surface potentials are measured and the isopotential lines drawn. By mapping the co-ordinates obtained with the isopotential line subroutine to the X, Y and Z torso arrays, a 3-dimensional representation of the depolarization wave travelling across the body surface can be displayed. The deviations from its normal path are clearly seen in the 2 clinical cardiac conditions presented (right bundle branch block and left ventricular premature beat). The increased realism and spatial resolution, as compared to ECG and the 2-dimensional contour map, lead to a clear understanding and interpretation of the underlying electrical phenomena of the heart while making a diagnosis or presenting experimental results.
An Electrolytic System that Uses Solid‐Supported Bases for in situ Generation of a Supporting Electrolyte from Acetic Acid Solvent. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Cucumber Production in California (2002)

The major production areas for fresh-market and pickling types of cucumbers (Cucumis sativus) in California are San Joaquin, San Diego, Ventura, San Benito, and Riverside Counties. In the nationwide market, California ranks second in fresh-market (slicing) cucumber production and fifth in pickling cucumber production. In the lower Sacramento Valley, planting begins in May for harvest from mid-August through mid-October. In Southern California, cucumbers are planted under plastic tunnels in January for harvest from mid-March through June. Fall production in Southern California is planted from March through August for harvest from May through November. The time from plant emergence to harvest is approximately 55 to 70 days depending on the selected variety.
Multi-Functional Characteristics of the Pseudomonas aeruginosa Type III Needle-Tip Protein, PcrV; Comparison to Orthologs in other Gram-negative Bacteria (2011)

Pseudomonas aeruginosa possesses a type III secretion system (T3SS) to intoxicate host cells and evade innate immunity. This virulence-related machinery consists of a molecular syringe and needle assembled on the bacterial surface, which allows delivery of T3 effector proteins into infected cells. To accomplish a one-step effector translocation, a tip protein is required at the top end of the T3 needle structure. Strains lacking expression of the functional tip protein fail to intoxicate host cells. P. aeruginosa encodes a T3S that is highly homologous to the proteins encoded by Yersinia spp. The needle-tip proteins of Yersinia, LcrV, and P. aeruginosa, PcrV, share 37% identity and 65% similarity. Other known tip proteins are AcrV (Aeromonas), IpaD (Shigella), SipD (Salmonella), BipD (Burkholderia), EspA (EPEC, EHEC), Bsp22 (Bordetella), with additional proteins identified from various Gram-negative species, such as Vibrio and Bordetella. The tip proteins can serve as a protective antigen or may be critical for sensing host cells and evading innate immune responses. Recognition of the host microenvironment transcriptionally activates synthesis of T3SS components. The machinery appears to be mechanically controlled by the assemblage of specific junctions within the apparatus. These junctions include the tip and base of the T3 apparatus, the needle proteins and components within the bacterial cytoplasm. The tip proteins likely have chaperone functions for translocon proteins, allowing the proper assembly of translocation channels in the host membrane and completing vectorial delivery of effector proteins into the host cytoplasm. Multi-functional features of the needle-tip proteins appear to be intricately controlled. In this review, we highlight the functional aspects and complex controls of T3 needle-tip proteins with particular emphasis on PcrV and LcrV.
High Throughput Determination of Plant Height, Ground Cover, and Above-Ground Biomass in Wheat with LiDAR (2018)

Crop improvement efforts are targeting increased above-ground biomass and radiation-use efficiency as drivers for greater yield. Early ground cover and canopy height contribute to biomass production, but manual measurements of these traits, and in particular above-ground biomass, are slow and labor-intensive, more so when made at multiple developmental stages. These constraints limit the ability to capture these data in a temporal fashion, hampering insights that could be gained from multi-dimensional data. Here we demonstrate the capacity of Light Detection and Ranging (LiDAR), mounted on a lightweight, mobile, ground-based platform, for rapid multi-temporal and non-destructive estimation of canopy height, ground cover and above-ground biomass. Field validation of LiDAR measurements is presented. For canopy height, strong relationships with LiDAR (<i>r</i><sup>2</sup> of 0.99 and root mean square error of 0.017 m) were obtained. Ground cover was estimated from LiDAR using two methodologies: red reflectance image and canopy height. In contrast to NDVI, LiDAR was not affected by saturation at high ground cover, and the comparison of both LiDAR methodologies showed strong association (<i>r</i><sup>2</sup> = 0.92 and slope = 1.02) at ground cover above 0.8. For above-ground biomass, a dedicated field experiment was performed with destructive biomass sampled eight times across different developmental stages. Two methodologies are presented for the estimation of biomass from LiDAR: 3D voxel index (3DVI) and 3D profile index (3DPI). The parameters involved in the calculation of 3DVI and 3DPI were optimized for each sample event from tillering to maturity, as well as generalized for any developmental stage. Individual sample point predictions were strong while predictions across all eight sample events, provided the strongest association with biomass (<i>r</i><sup>2</sup> = 0.93 and <i>r</i><sup>2</sup> = 0.92) for 3DPI and 3DVI, respectively. Given these results, we believe that application of this system will provide new opportunities to deliver improved genotypes and agronomic interventions via more efficient and reliable phenotyping of these important traits in large experiments.
Pancreatic Beta Cell Culture: Preparation of Purified Monolayers (1975)

Procedures were developed for preparing partially purified beta cell monolayer cultures. Neonatal rat pancreases were dissociated with a trypsin-collagenase solution. Beta cells were separated from denser acinar cells by centrifuging the initial suspension in a two layer discontinous Ficoll gradient (20, 25%). Resultant cultures, highly enriched in beta cells, were further purified by incubation with cystine-free medium. This caused necrosis of the majority of fibroblastoid cells within two days, while beta cells were considerably less affected. The resultant cultures contained an average of 72% beta cells compared to 10% in untreated control cultures. Insulin release by purified monolayers remained responsive to changes in the glucose concentration of the culture medium.
Sulforaphane Attenuates Muscle Inflammation in Dystrophin-deficient mdx Mice via NF-E2-related Factor 2 (Nrf2)-mediated Inhibition of NF-κB Signaling Pathway (2015)

Inflammation is widely distributed in patients with Duchenne muscular dystrophy and ultimately leads to progressive deterioration of muscle function with chronic muscle damage, oxidative stress, and reduced oxidative capacity. NF-E2-related factor 2 (Nrf2) plays a critical role in defending against inflammation in different tissues via activation of phase II enzyme heme oxygenase-1 and inhibition of the NF-κB signaling pathway. However, the role of Nrf2 in the inflammation of dystrophic muscle remains unknown. To determine whether Nrf2 may counteract inflammation in dystrophic muscle, we treated 4-week-old male mdx mice with the Nrf2 activator sulforaphane (SFN) by gavage (2 mg/kg of body weight/day) for 4 weeks. The experimental results demonstrated that SFN treatment increased the expression of muscle phase II enzyme heme oxygenase-1 in an Nrf2-dependent manner. Inflammation in mice was reduced by SFN treatment as indicated by decreased infiltration of immune cells and expression of the inflammatory cytokine CD45 and proinflammatory cytokines tumor necrosis factor-α, interleukin-1β, and interleukin-6 in the skeletal muscles of mdx mice. In addition, SFN treatment also decreased the expression of NF-κB(p65) and phosphorylated IκB kinase-α as well as increased inhibitor of κB-α expression in mdx mice in an Nrf2-dependent manner. Collectively, these results show that SFN-induced Nrf2 can alleviate muscle inflammation in mdx mice by inhibiting the NF-κB signaling pathway.
Flash Storage Today (2008)

The past few years have been an exciting time for flash memory. The cost has fallen dramatically as fabrication has become more efficient and the market has grown; the density has improved with the advent of better processes and additional bits per cell; and flash has been adopted in a wide array of applications. The flash ecosystem has expanded and continues to expand especially for thumb drives, cameras, ruggedized laptops, and phones in the consumer space.
Mobile Robots Navigation in Indoor Environments Using Kinect Sensor (2012)

This paper presents the development of a perception system for indoor environments to allow autonomous navigation for surveillance mobile robots. The system is composed by two parts. The first part is a reactive navigation system in which a mobile robot moves avoiding obstacles in environment, using the distance sensor Kinect. The second part of this system uses a artificial neural network (ANN) to recognize different configurations of the environment, for example, path ahead, left path, right path and intersections. The ANN is trained using data captured by the Kinect sensor in indoor environments. This way, the robot becomes able to perform a topological navigation combining internal reactive behavior to avoid obstacles and the ANN to locate the robot in the environment, in a deliberative behavior. The topological map is represented by a graph which represents the configuration of the environment, where the hallways (path ahead) are the edges and locations (left path and intersection, for example) are the vertices. The system also works in the dark, which is a great advantage for surveillance systems. The experiments were performed with a Pioneer P3-AT robot equipped with a Kinect sensor in order to validate and evaluate this approach. The proposed method demonstrated to be a promising approach to autonomous mobile robots navigation.
Targeted Disruption of Carcinoembryonic Antigen-Related Cell Adhesion Molecule 1 Promotes Diet-Induced Hepatic Steatosis and Insulin Resistance (2009)

Carcinoembryonic antigen-related cell adhesion molecule 1 (CC1) is a cell adhesion molecule within the Ig superfamily. The Tyr-phosphorylated isoform of CC1 (CC1-L) plays an important metabolic role in the regulation of hepatic insulin clearance. In this report, we show that CC1-deficient (Cc1(-/-)) mice are prone to hepatic steatosis, as revealed by significantly elevated hepatic triglyceride and both total and esterified cholesterol levels compared with age-matched wild-type controls. Cc1(-/-) mice were also predisposed to lipid-induced hepatic steatosis and dysfunction as indicated by their greater susceptibility to store lipids and express elevated levels of enzymatic markers of liver damage after chronic feeding of a high-fat diet. Hepatic steatosis in the Cc1(-/-) mice was linked to a significant increase in the expression of key lipogenic (fatty acid synthase, acetyl CoA carboxylase) and cholesterol synthetic (3-hydroxy-3-methylglutaryl-coenzyme A reductase) enzymes under the control of sterol regulatory element binding proteins-1c and -2 transcription factors. Cc1(-/-) mice also exhibited impaired insulin clearance, glucose intolerance, liver insulin resistance, and elevated hepatic expression of the key gluconeogenic transcriptional activators peroxisome proliferator-activated receptor-gamma coactivator-1 and Forkhead box O1. Lack of CC1 also exacerbated both glucose intolerance and hepatic insulin resistance induced by high-fat feeding, but insulin clearance was not further deteriorated in the high-fat-fed Cc1(-/-) mice. In conclusion, our data indicate that CC1 is a key regulator of hepatic lipogenesis and that Cc1(-/-) mice are predisposed to liver steatosis, leading to hepatic insulin resistance and liver damage, particularly when chronically exposed to dietary fat.
Ultrashort Pulse Formation in a Short-Pulse-Stimulated Raman Oscillator (1971)

A train of picosecond pulses was used to pump a stimulated Raman oscillator designed such that the generated Stokes pulse was amplified by successive pump pulses. In this way partial group velocity matching could be achieved and significant time narrowing of the Stokes pulse realized. With benzene as the Raman active material, a minimum Stokes-pulse duration of ≃ 0.3 psec was recorded.
Acetic Acid Separation from Anaerobically Treated Palm Oil Mill Effluent by Ion Exchange Resins for the Production of Polyhydroxyalkanoate by<i>Alcaligenes eutrophus</i> (1997)

Separation of acetic acid from palm oil mill effluent (POME) to increase its concentration by an anion exchange resin was examined as a preliminary study for its recovery from POME that had been anaerobically treated by sludge from a palm oil mill. This paper concerns the acetic acid thus separated for producing bacterial polyhydroxyalkanoate (PHA) by Alcaligenes eutrophus. It was found that sludge particles in POME strongly inhibited the adsorption of acetic acid on the anion exchange resin. Removing the sludge particles from the POME facilitated the separation of acetic acid from the POME efficiently. The concentrated acetic acid thus obtained from anaerobically treated POME could be used as a substrate in the fed-batch production of polyhydroxyalkanoate by Alcaligenes eutrophus.
MicroRNA-140 plays dual roles in both cartilage development and homeostasis (2010)

Osteoarthritis (OA), the most prevalent aging-related joint disease, is characterized by insufficient extracellular matrix synthesis and articular cartilage degradation, mediated by several proteinases, including Adamts-5. miR-140 is one of a very limited number of noncoding microRNAs (miRNAs) specifically expressed in cartilage; however, its role in development and/or tissue maintenance is largely uncharacterized. To examine miR-140 function in tissue development and homeostasis, we generated a mouse line through a targeted deletion of miR-140. miR-140(-/-) mice manifested a mild skeletal phenotype with a short stature, although the structure of the articular joint cartilage appeared grossly normal in 1-mo-old miR-140(-/-) mice. Interestingly, miR-140(-/-) mice showed age-related OA-like changes characterized by proteoglycan loss and fibrillation of articular cartilage. Conversely, transgenic (TG) mice overexpressing miR-140 in cartilage were resistant to antigen-induced arthritis. OA-like changes in miR-140-deficient mice can be attributed, in part, to elevated Adamts-5 expression, regulated directly by miR-140. We show that miR-140 regulates cartilage development and homeostasis, and its loss contributes to the development of age-related OA-like changes.
Physical, biochemical, and immunological characterization of a thermostable amidase from Klebsiella pneumoniae NCTR 1 (1996)

An amidase capable of degrading acrylamide and aliphatic amides was purified to apparent homogeneity from Klebsiella pneumoniae NCTR 1. The enzyme is a monomer with an apparent molecular weight of 62,000. The pH and temperature optima of the enzyme were 7.0 and 65 degrees C, respectively. The purified amidase contained 11 5,5-dithiobis(2-nitrobenzoate) (DTNB)-titratable sulfhydryl (SH) groups. In the native enzyme 1.0 SH group readily reacted with DTNB with no detectable loss of activity. Titration of the next 3.0 SH groups with DTNB resulted in a loss of activity of more than 70%. The remaining seven inaccessible SH groups could be titrated only in the presence of 8 M guanidine hydrochloride. Titration of SH groups was strongly inhibited by carboxymethylation and KMnO4, suggesting the presence of SH groups at the active site(s). Inductively coupled plasma-atomic emission spectrometry analysis indicated that the native amidase contains 0.33 mol of cobalt and 0.33 mol of iron per mol of the native enzyme. Polyclonal antiserum against K. pneumoniae amidase was raised in rabbits, and immunochemical comparisons were made with amidases from Rhodococcus sp., Mycobacterium smegmatis, Pseudomonas chlororaphis B23, and Methylophilus methylotrophus. The antiserum immunoprecipitated and immunoreacted with the amidases of K. pneumoniae and P. chlororaphis B23. The antiserum failed to immunoreact or immunoprecipitate with other amidases.
Scattering from structures formed by resonant elements (1998)

A two-dimensional (2-D) structure, formed by a finite number of resonant elements, has been considered in this paper, and its scattering characteristics have been analyzed in detail over a wide frequency band including the resonance region. The elements of the structure comprise perfectly conducting thin cylinders with longitudinal slots, it has been demonstrated that the scattered field of such an array exhibits rather remarkable properties at resonance frequencies. For instance, the strong coupling between the elements in the resonance region manifests itself into superdirective radiation in the far field and this is a common attribute of scatterers formed by coupled resonant elements.
A One-Time Password System (1996)

This document specifies an Internet standards track protocol for the Internet community, and requests discussion and suggestions for improvements.
Structure-Guided Engineering of a Pacific Blue Fluorophore Ligase for Specific Protein Imaging in Living Cells (2011)

Mutation of a gatekeeper residue, tryptophan 37, in E. coli lipoic acid ligase (LplA), expands substrate specificity such that unnatural probes much larger than lipoic acid can be recognized. This approach, however, has not been successful for anionic substrates. An example is the blue fluorophore Pacific Blue, which is isosteric to 7-hydroxycoumarin and yet not recognized by the latter's ligase ((W37V)LplA) or any tryptophan 37 point mutant. Here we report the results of a structure-guided, two-residue screening matrix to discover an LplA double mutant, (E20G/W37T)LplA, that ligates Pacific Blue as efficiently as (W37V)LplA ligates 7-hydroxycoumarin. The utility of this Pacific Blue ligase for specific labeling of recombinant proteins inside living cells, on the cell surface, and inside acidic endosomes is demonstrated.
Regulation of restrictocin production in Aspergillus restrictus (1992)

The production of restrictocin (a cytotoxin that specifically cleaves ribosomal RNA) by cultures of Aspergillus restrictus grown in liquid medium was investigated. The function of restrictocin, the method of its accumulation and the mode of resistance to restrictocin in A. restrictus are unknown. Previous studies have indicated that restrictocin accumulates in the medium with culture age. These observations have been extended in this study by cloning the cDNA of the res gene and using this cDNA clone to probe the onset of messenger RNA synthesis in the cells. The results of the Northern analysis were compared to the production and accumulation of restrictocin and morphological differentiation of the cells in culture. Restrictocin was found in the medium at the same time that mRNA was detected in the cells. This suggests that the leader sequence encoded by the cDNA provides an efficient secretion system for the protein. Both the protein and the mRNA were detected coincident with the formation of differentiated cell structures. These structures develop into conidiophores with one layer of sterigmata and conidia forming from the sterigmata. These results suggest that restrictocin is either involved in the process of conidiation or is coordinately regulated with differentiation leading to conidiation.
Homeotic genes controlling flower development in <i>Antirrhinum</i> (1991)

The chronic blockade of neuromuscular activity is known to promote the survival of developing motoneurons in vivo in the chick, mouse and rat embryo. Increased survival in this situation may reflect an activity-dependent mechanism for the regulation of trophic factor production by target cells. To test this notion, we have examined motoneuron survival in vivo and choline acetyltransferase (ChAT) development in vitro following treatment of chick embryos and rat spinal cord cultures with partially purified skeletal muscle extracts derived from normally active, chronically paralyzed and aneural embryos, and from denervated postnatal chickens. Extracts from active and paralyzed chick embryos were equally effective in promoting motoneuron survival and ChAT activity. Aneural embryonic muscle extracts were slightly less effective in promoting motoneurons survival in vivo, but were not significantly different from control extracts in the in vitro ChAT assay. Denervated postnatal muscle extracts, however, were more effective in enhancing both motoneuron survival and ChAT activity. These data indicate that: (1) the promotion of motoneuron survival in vivo by activity blockade may not be mediated by an up-regulation of trophic factor synthesis in target cells; (2) postnatal innervation may regulate the production of putative muscle-derived neurotrophic factors; and (3) the synthesis or availability of trophic agents may be regulated differently in embryonic and postnatal muscle.