gebhart/patrepeval huggingface dataset:
Detection of Intracellular Bacteria in the Buds of Scotch Pine ( Pinus sylvestris L.) by In Situ Hybridization (2000)

Bacterial isolates were obtained from pine (Pinus sylvestris L.) tissue cultures and identified as Methylobacterium extorquens and Pseudomonas synxantha. The existence of bacteria in pine buds was investigated by 16S rRNA in situ hybridization. Bacteria inhabited the buds of every tree examined, primarily colonizing the cells of scale primordia and resin ducts.
Asymmetric N–H Insertion Reaction with Chiral Aminoalcohol as Catalytic Core of Cinchona Alkaloids (2019)

In order to develop an efficient organocatalyst for the enantioselective N-H insertion reaction via carbene/carbenoid, the catalytic core of the cinchona alkaloids was investigated. According to our working hypothesis of an eight-membered ring transition state in the N-H insertion reaction, two pairs of enantiomers related to 2-amino-1-phenylethanol were investigated for their chiral inducing potential. Since both (1R,2S)-isomers gave the N-phenyl-1-phenylglycine derivative enriched in the R-form, while their enantiomers gave the S-form, the 2-amino-1-phenylethanol structure is concluded to be the catalytic core of the cinchona alkaloid in the enantioselective N-H insertion reaction via rhodium(II) carbenoid.
Basal ganglia-cortical connectivity underlies self-regulation of brain oscillations in humans (2022)

Brain-computer interfaces provide an artificial link by which the brain can directly interact with the environment. To achieve fine brain-computer interface control, participants must modulate the patterns of the cortical oscillations generated from the motor and somatosensory cortices. However, it remains unclear how humans regulate cortical oscillations, the controllability of which substantially varies across individuals. Here, we performed simultaneous electroencephalography (to assess brain-computer interface control) and functional magnetic resonance imaging (to measure brain activity) in healthy participants. Self-regulation of cortical oscillations induced activity in the basal ganglia-cortical network and the neurofeedback control network. Successful self-regulation correlated with striatal activity in the basal ganglia-cortical network, through which patterns of cortical oscillations were likely modulated. Moreover, basal ganglia-cortical network and neurofeedback control network connectivity correlated with strong and weak self-regulation, respectively. The findings indicate that the basal ganglia-cortical network is important for self-regulation, the understanding of which should help advance brain-computer interface technology.
High-Risk Human Papillomavirus E7 Alters Host DNA Methylome and Represses HLA-E Expression in Human Keratinocytes (2017)

ABSTRACT Human papillomavirus (HPV) infection distinctly alters methylation patterns in HPV-associated cancer. We have recently reported that HPV E7-dependent promoter hypermethylation leads to downregulation of the chemokine CXCL14 and suppression of antitumor immune responses. To investigate the extent of gene expression dysregulated by HPV E7-induced DNA methylation, we analyzed parallel global gene expression and DNA methylation using normal immortalized keratinocyte lines, NIKS, NIKS-16, NIKS-18, and NIKS-16ΔE7. We show that expression of the MHC class I genes is downregulated in HPV-positive keratinocytes in an E7-dependent manner. Methylome analysis revealed hypermethylation at a distal CpG island (CGI) near the HLA-E gene in NIKS-16 cells compared to either NIKS cells or NIKS-16ΔE7 cells, which lack E7 expression. The HLA-E CGI functions as an active promoter element which is dramatically repressed by DNA methylation. HLA-E protein expression on cell surface is downregulated by high-risk HPV16 and HPV18 E7 expression, but not by low-risk HPV6 and HPV11 E7 expression. Conversely, demethylation at the HLA-E CGI restores HLA-E protein expression in HPV-positive keratinocytes. Because HLA-E plays an important role in antiviral immunity by regulating natural killer and CD8 + T cells, epigenetic downregulation of HLA-E by high-risk HPV E7 may contribute to virus-induced immune evasion during HPV persistence.
Prediction of Salinity of Salty Crude Oil Using Arrhenius-Type Asymptotic Exponential Function and Vandermonde Matrix (2011)

Summary Production of wet crude because of a rise in the oil/water contact in many oil fields has been a growing field problem, and it has affected the quality of crudes. In almost all cases, salt is dissolved in the water that is dispersed in the crude oil and its separation is not simple because desalting is a critical operation because of the importance of meeting the specifications of acceptable quantities of salt and water in the treated oil. For these reasons, measurements of salt and water content in crude oils are very important in all oil-industry operations, including crude-oil production, processing, and transportation and refining. In this paper, we attempt to formulate a method that is easier than existing approaches, that is less complicated and requires fewer computations for accurate and rapid estimation of crude-oil salinity as a function of the quantity of brine that remains in the oil, its salinity (in vol% of sodium chloride concentration), and temperature, using an Arrhenius- type asymptotic exponential function and Vandermonde matrix. The proposed method predicts the salinity of salty crude oil for temperatures up to 373 K and sodium chloride concentrations up to 250,000 ppm (25% by volume). Estimations from the proposed correlation are found to be in excellent agreement with the reported data in the literature, with average absolute deviation being 0.3%. The proposed method is superior owing to its accuracy and clear numerical background based on the Vandermonde matrix, wherein the relevant coefficients can be retuned quickly for various cases. The tool developed in this study can be of immense practical value for engineers, providing a quick check on the salt content in the crude oil at various conditions without the necessity of any experimental measurements. In particular, petroleum and field engineers would find the proposed approach to be user friendly, with transparent calculations involving no complex expressions.
The light stress‐induced protein ELIP2 is a regulator of chlorophyll synthesis in Arabidopsis thaliana (2007)

The early light-induced proteins (ELIPs) belong to the multigenic family of pigment-binding light-harvesting complexes. ELIPs accumulate transiently and are believed to play a protective role in plants exposed to high levels of light. Constitutive expression of the ELIP2 gene in Arabidopsis resulted in a marked reduction of the pigment content of the chloroplasts, both in mature leaves and during greening of etiolated seedlings. The chlorophyll loss was associated with a decrease in the number of photosystems in the thylakoid membranes, but the photosystems present were fully assembled and functional. A detailed analysis of the chlorophyll-synthesizing pathway indicated that ELIP2 accumulation downregulated the level and activity of two important regulatory steps: 5-aminolevulinate synthesis and Mg-protoporphyrin IX (Mg-Proto IX) chelatase activity. The contents of glutamyl tRNA reductase and Mg chelatase subunits CHLH and CHLI were lowered in response to ELIP2 accumulation. In contrast, ferrochelatase activity was not affected and the inhibition of Heme synthesis was null or very moderate. As a result of reduced metabolic flow from 5-aminolevulinic acid, the steady state levels of various chlorophyll precursors (from protoporphyrin IX to protochlorophyllide) were strongly reduced in the ELIP2 overexpressors. Taken together, our results indicate that the physiological function of ELIPs could be related to the regulation of chlorophyll concentration in thylakoids. This seems to occur through an inhibition of the entire chlorophyll biosynthesis pathway from the initial precursor of tetrapyrroles, 5-aminolevulinic acid. We suggest that ELIPs work as chlorophyll sensors that modulate chlorophyll synthesis to prevent accumulation of free chlorophyll, and hence prevent photooxidative stress.
Hepatitis C Virus–Associated Fulminant Hepatic Failure (1996)

ULMINANT hepatic failure is a dramatic clinical syndrome characterized by massive necrosis of liver cells. Among patients with non-A, non-B fulminant hepatitis, antibodies against HCV (anti-HCV) or serum HCV RNA were found in 40 to 60 percent in Japan 5,6 and Taiwan, 7 but in only 2 percent (range, 0 to 12 percent) in Western countries, Whether these discrepancies reflect geographic differences in the epidemiology of HCV infection or the pathogenicity of the prevalent viral strains is not known. Furthermore, because of the dramatic course of fulminant hepatic failure, in most patients only a single serum sample, often obtained late in the course of the disease, was studied.
Tumor-Targeted Synergistic Blockade of MAPK and PI3K from a Layer-by-Layer Nanoparticle (2015)

Purpose: Cross-talk and feedback between the RAS/RAF/MEK/ERK and PI3K/AKT/mTOR cell signaling pathways is critical for tumor initiation, maintenance, and adaptive resistance to targeted therapy in a variety of solid tumors. Combined blockade of these pathways—horizontal blockade—is a promising therapeutic strategy; however, compounded dose-limiting toxicity of free small molecule inhibitor combinations is a significant barrier to its clinical application. Experimental Design: AZD6244 (selumetinib), an allosteric inhibitor of Mek1/2, and PX-866, a covalent inhibitor of PI3K, were co-encapsulated in a tumor-targeting nanoscale drug formulation—layer-by-layer (LbL) nanoparticles. Structure, size, and surface charge of the nanoscale formulations were characterized, in addition to in vitro cell entry, synergistic cell killing, and combined signal blockade. In vivo tumor targeting and therapy was investigated in breast tumor xenograft-bearing NCR nude mice by live animal fluorescence/bioluminescence imaging, Western blotting, serum cytokine analysis, and immunohistochemistry. Results: Combined MAPK and PI3K axis blockade from the nanoscale formulations (160 ± 20 nm, −40 ± 1 mV) was synergistically toxic toward triple-negative breast (MDA-MB-231) and RAS-mutant lung tumor cells (KP7B) in vitro, effects that were further enhanced upon encapsulation. In vivo, systemically administered LbL nanoparticles preferentially targeted subcutaneous MDA-MB-231 tumor xenografts, simultaneously blocked tumor-specific phosphorylation of the terminal kinases Erk and Akt, and elicited significant disease stabilization in the absence of dose-limiting hepatotoxic effects observed from the free drug combination. Mice receiving untargeted, but dual drug-loaded nanoparticles exhibited progressive disease. Conclusions: Tumor-targeting nanoscale drug formulations could provide a more safe and effective means to synergistically block MAPK and PI3K in the clinic.
A role for caspase 2 and PIDD in the process of p53-mediated apoptosis (2008)

When treated with some DNA-damaging agents, human tumor-derived H1299 cells expressing inducible versions of wild-type or mutant p53 with inactive transactivation domain I (p53(Q22/S23)) undergo apoptosis as evidenced by cytochrome c release, nuclear fragmentation, and sub-G1 DNA content. Apoptosis induced by p53(Q22/S23) is relatively slow, however, and key downstream effector caspases are not activated. Nevertheless, with either version of p53, caspase 2 activation is required for release of cytochrome c and cell death. Remarkably, although p53(Q22/S23) is known to be defective in transcriptional activation of numerous p53 target genes, it can induce expression of proapoptotic targets including PIDD and AIP1 at least to the same extent as wild-type p53. Furthermore, RNAi silencing of PIDD, previously shown to be required for caspase 2 activation, suppresses apoptosis by both wild-type p53 and p53(Q22/S23). Thus, the initial stage of DNA damage-facilitated, p53-mediated apoptosis occurs by a PIDD- and caspase 2-dependent mechanism, and p53's full transcriptional regulatory functions may be required only for events that are downstream of cytochrome c release.
Schematic overview of oligosaccharides, with survey on their major physiological effects and a focus on milk ones (2020)

While Biochemistry textbooks for University degree courses do not deal with oligosaccharides, this subject is now becoming essential in Biomedical Sciences for several reasons. Oligosaccharides are currently used in foods and beverages for their useful physicochemical and prebiotic qualities, albeit their excessive consumption may have side effects. They are also essential components of milk, where they exert a protective role on infants acting as stimulants for the development of immune system and gut microbiota. Oligosaccharides are seen as an alternative to improperly used antibiotics in the diet for monogastric animals and considered promising safe anti-parasite treatments in agriculture. Besides, they are widely used in both cosmetics and pharmaceutics. For these reasons, biotechnological research is hardworking on new enzymes able to synthesize them in a great variety. At the same time, oligosaccharides belong to the so-called FODMAP (Fermentable Oligo-, Di- and Monosaccharides And Polyols) group of compounds, whose decreased use in diet is beneficial to several syndromes of the digestive tract. The scope of this review is to give a general and schematic view of oligosaccharides. We describe the structure, source and use of several of the most known oligosaccharides, focusing on their health implications. Main groups in human milk and their substitutes in infant formulas are also reported. In the end some of the most recent studied oligosaccharides and their promising applications are discussed.
LONG TERM SPIRONOLACTONE AND THE ADRENAL CORTEX IN ESSENTIAL HYPERTENSION (1980)

In view of recent evidence that spironolactone may inhibit synthesis of corticosteroids by a direct effect on the adrenal cortex, adrenocortical function was studied in eight patients with essential hypertension who had been treated with spironolactone from 3 months to 14 years. Their 24 h renal excretion of adrenocorticoid metabolites and the responses of cortisol, aldosterone and 18-hydroxy-11 -deoxycorticosterone (18-OH-DOC) to an incremental infusion of tetracosactrin (1-24 ACTH) were compared with those in eight patients with recently diagnosed essential hypertension who had received no spironolactone. The spironolactone-treated group had a significantly higher excretion of aldosterone, whilst the excretion of other adrenocorticoid metabolites did not differ. The same group also required less tetracosactrin to stimulate a detectable rise of plasma cortisol and 18-OH-DOC, they had greater plasma 18-OH-DOC responses at all infusion rates and, at the lowest infusion rates, had greater aldosterone responses. These results indicate that long-term spironolactone therapy does not inhibit adrenocortical function and may have some stimulatory effects.
Preparation and properties of bio-based polycarbonate/clay nanocomposites (2011)

1,4:3,6-Dianhydro-D-sorbitol (isosorbide)-based polycarbonate (ISPC)/clay nanocomposites have been prepared by mixing ISPC with an organophilic clay in a solvent. The organophilic clay Cloisite 30B provided the best results. In these ISPC/clay nanocomposites, the silicate layers of the clay were exfoliated and dispersed uniformly in the ISPC polymers. The storage moduli (E′) of these ISPC/clay nanocomposites were also higher than that of neat ISPC.
Sizing Stress Corrosion Cracking Using Laser Ultrasonics (2008)

Managing Stress Corrosion Cracking (SCC) damaged pipe has been a formidable challenge to the pipeline industry. Development of a practical solution for measurement and evaluation of SCC has been marred by the complexity of crack shapes, their distribution within a crack colony, and the lack of non-destructive technology capable of reliably measuring the crack depths. Laser Ultrasonics is an inspection technology wherein lasers are used for generation and detection of ultrasonic waves in the pipeline steel to be inspected. Unlike conventional ultrasonic testing, Laser Ultrasonics has a large frequency bandwidth and a tiny (∼0.5mm) footprint. These characteristics make it ideally suited for application as a depth sizing tool for closely-spaced cracks in a colony. It has been conclusively proved that laser ultrasonic inspection using the time of flight diffraction (TOFD) technique can reliably and accurately measure the depth of naturally occurring SCC and potentially other cracks and seam weld anomalies. This presentation describes the results of this co-sponsored project, including recent full scale demonstrations where a laser ultrasonic measurement subsystem has been built onto a prototype scanner.
Randomised controlled trial comparing oral and intravenous rehydration therapy in children with diarrhoea. (1991)

Rehydration by mouth or nasogastric tube is a safe and effective treatment for moderately dehydrated children with gastroenteritis.
Electrospun poly(methyl methacrylate) fibrous mat showing piezoelectric properties (2018)

A piezoelectric effect, such as actuation behavior with voltage application, could be observed from a poly(methyl methacrylate) (PMMA) fibrous mat fabricated by electrospinning. This fibrous mat increased or decreased its thickness in accordance with the polarity of the applied voltage, which appears to be an inverse piezoelectric effect. The appearance dT constant was as large as 8.5 nm/V owing to the softness of the fibrous structure, and the coupling constant KT = 0.31 indicated its efficient piezoelectric property. This piezoelectric behavior was repeatedly observed to be stable at room temperature. In addition, the polarization components of the fibrous mat, which are considered to be the origin of its piezoelectric effect, and its relaxation behavior were confirmed from the results of thermally stimulated current measurements.
Elevated miR-155 Promotes Inflammation in Cystic Fibrosis by Driving Hyperexpression of Interleukin-8 (2011)

Cystic Fibrosis (CF) is characterized by a massive proinflammatory phenotype in the lung arising from profound expression of inflammatory genes, including interleukin-8 (IL-8). We have previously reported that IL-8 mRNA is stabilized in CF lung epithelial cells, resulting in concomitant hyperexpression of IL-8 protein. However, the mechanistic link between mutations in CFTR and acquisition of the proinflammatory phenotype in the CF airway has remained elusive. We hypothesized that specific microRNAs (miRNAs) might mediate this linkage. To identify the potential link, we screened an miRNA library for differential expression in ΔF508-CFTR and wild type CFTR lung epithelial cell lines. Of 22 differentially and significantly expressed miRNAs, we found that expression of miR-155 was more than 5-fold elevated in CF IB3-1 lung epithelial cells in culture, compared with control IB3-1/S9 cells. Clinically, miR-155 was also highly expressed in CF lung epithelial cells and circulating CF neutrophils biopsied from CF patients. We report here that high levels of miR-155 specifically reduced levels of SHIP1, thereby promoting PI3K/Akt activation. However, overexpressing SHIP1 or inhibition of PI3K in CF cells suppressed IL-8 expression. Finally, we found that phospho-Akt levels were elevated in CF lung epithelial cells and were specifically lowered by either antagomir-155 or elevated expression of SHIP1. We therefore suggest that elevated miR-155 contributes to the proinflammatory expression of IL-8 in CF lung epithelial cells by lowering SHIP1 expression and thereby activating the PI3K/Akt signaling pathway. These data suggest that miR-155 may play an important role in the activation of IL-8-dependent inflammation in CF.
Mechanical Design of Compact Vertical and Horizontal Linear Nanopositioning Flexure Stages With Centimeter-Level Travel Range for X-Ray Beamline Instrumentation (2017)

Nanopositioning techniques present an important capability to support the state-of-the-art x-ray instrumentation research for the APS operations and upgrade project. To overcome the performance limitations of precision ball-bearing-based or roller-bearing-based linear stage systems, compact vertical and horizontal linear nanopositioning flexure stages have been designed and developed at the APS with centimeter-level travel range and nanometer-level resolution for x-ray beamline instrumentation. Using improved deformation compensated linear guiding mechanisms [*,**], the APS T8-55 vertical linear flexure stage and T8-56 horizontal linear flexure stage are initially designed as a pair of sample scanning stages for a hard x-ray scanning microscope at the APS sector 2. Due to their unique repeatable nanopositioning performance over the centimeter-level travel range, these stages are also suitable for many photon beam lines optics with repeatable and stable nanopositioning requirements. The mechanical design and finite element analyses of the APS T8-55 and T8-56 flexural stages, as well as its initial mechanical test results with laser interferometer are described in this paper.
Deep Neural Networks are Easily Fooled: High Confidence Predictions for Unrecognizable Images (2014)

Deep neural networks (DNNs) have recently been achieving state-of-the-art performance on a variety of pattern-recognition tasks, most notably visual classification problems. Given that DNNs are now able to classify objects in images with near-human-level performance, questions naturally arise as to what differences remain between computer and human vision. A recent study revealed that changing an image (e.g. of a lion) in a way imperceptible to humans can cause a DNN to label the image as something else entirely (e.g. mislabeling a lion a library). Here we show a related result: it is easy to produce images that are completely unrecognizable to humans, but that state-of-the-art DNNs believe to be recognizable objects with 99.99% confidence (e.g. labeling with certainty that white noise static is a lion). Specifically, we take convolutional neural networks trained to perform well on either the ImageNet or MNIST datasets and then find images with evolutionary algorithms or gradient ascent that DNNs label with high confidence as belonging to each dataset class. It is possible to produce images totally unrecognizable to human eyes that DNNs believe with near certainty are familiar objects, which we call "fooling images" (more generally, fooling examples). Our results shed light on interesting differences between human vision and current DNNs, and raise questions about the generality of DNN computer vision.
Management of chronic insomnia in the elderly. (2001)

Insomnia is a common complaint in the elderly. It is not a disease in and of itself, but a symptom of an underlying problem with the potential for medical, psychological, and functional complications. Approximately one half the persons aged 65 years and older experience insomnia. However, few mention their sleep problems to their primary care providers. Because of the prevalence of insomnia in the elderly and the potential for complications, it is important for primary health care providers to understand the cause, assessment, and management of chronic insomnia. Both pharmacologic and behavioral therapies are effective in the treatment of insomnia. Early recognition and treatment may increase the quality of life for the elderly insomniac.