gebhart/patrepeval huggingface dataset:
Rhizosphere microbiome assemblage is affected by plant development (2013)

There is a concerted understanding of the ability of root exudates to influence the structure of rhizosphere microbial communities. However, our knowledge of the connection between plant development, root exudation and microbiome assemblage is limited. Here, we analyzed the structure of the rhizospheric bacterial community associated with Arabidopsis at four time points corresponding to distinct stages of plant development: seedling, vegetative, bolting and flowering. Overall, there were no significant differences in bacterial community structure, but we observed that the microbial community at the seedling stage was distinct from the other developmental time points. At a closer level, phylum such as Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria and specific genera within those phyla followed distinct patterns associated with plant development and root exudation. These results suggested that the plant can select a subset of microbes at different stages of development, presumably for specific functions. Accordingly, metatranscriptomics analysis of the rhizosphere microbiome revealed that 81 unique transcripts were significantly (P<0.05) expressed at different stages of plant development. For instance, genes involved in streptomycin synthesis were significantly induced at bolting and flowering stages, presumably for disease suppression. We surmise that plants secrete blends of compounds and specific phytochemicals in the root exudates that are differentially produced at distinct stages of development to help orchestrate rhizosphere microbiome assemblage.
Application possibilities with continuous YBCO loops made of HTS wire (2010)

In our previous experiments we have produced YBCO rings machined from bulks for superconducting applications. In this work we examine the arrangement of the continuous superconducting loop made of HTS wire for advanced applications. A Korean group of researchers led by Hee-Gyoun Lee produced 100% BSCCO loops from tape for the first time in 2006 [1]. In our solutions we use parallel and serial turns from perfect YBCO loops made from HTS wire. Production of multi-serial turns is not the same as the "wind and flip" [1] method. In our case the twisting of the YBCO wire along its longitudinal axis can be avoided. We check the quality of the perfect YBCO loops with the transformation of the DC magnetic field [2]. In the case of the AC application we describe a new arrangement of the self-limiting transformer with using these loops. This self-limiting transformer can be a voltage or current restricting system. The paper presents the results of our experiments and opens new advanced applications of perfect YBCO loops made of HTS wire focusing on the efficiency and importance of the Korean team in creating the perfect closed loop.
Functionalization of protein-based nanocages for drug delivery applications (2014)

Traditional drug delivery strategies involve drugs which are not targeted towards the desired tissue. This can lead to undesired side effects, as normal cells are affected by the drugs as well. Therefore, new systems are now being developed which combine targeting functionalities with encapsulation of drug cargo. Protein nanocages are highly promising drug delivery platforms due to their perfectly defined structures, biocompatibility, biodegradability and low toxicity. A variety of protein nanocages have been modified and functionalized for these types of applications. In this review, we aim to give an overview of different types of modifications of protein-based nanocontainers for drug delivery applications.
What dermatologists need to know about mast cell disease: a dermatopathologist's view. (1999)

Mast cell disease involves a group of conditions characterized by the infiltration of mast cells in the tissues and organs. Mast cell disease predominantly affects the skin, presenting in the form of urticaria pigmentosa. This concise review article defines mast cell disease. This paper presents a dermatopathologist's perspective on the diagnosis, management, and treatment of mast cell disease.
Stochastic Matrix Product States (2010)

The concept of stochastic matrix product states is introduced and a natural form for the states is derived. This allows us to define the analogue of Schmidt coefficients for steady states of nonequilibrium stochastic processes. We discuss a new measure for correlations which is analogous to entanglement entropy, the entropy cost S(C), and show that this measure quantifies the bond dimension needed to represent a steady state as a matrix product state. We illustrate these concepts on the basis of the asymmetric exclusion process.
Atomic Force Microscopy Study of the Effect of Antimicrobial Peptides on the Cell Envelope of <i>Escherichia coli</i> (2005)

The influences of the antibacterial magainin 2 and PGLa from the African clawed frog (Xenopus laevis) and the hemolytic bee venom melittin on Escherichia coli as the target cell were studied by atomic force microscopy (AFM). Nanometer-scale images of the effects of the peptides on this gram-negative bacterium's cell envelope were obtained in situ without the use of fixing agents. These high-resolution AFM images of the surviving and intact target cells before and after peptide treatment showed distinct changes in cell envelope morphology as a consequence of peptide action. Although all three peptides are lytic to E. coli, it is clear from this AFM study that each peptide causes distinct morphological changes in the outer membrane and in some cases the inner membrane, probably as a consequence of different mechanisms of action.
THE EFFECTS OF γ-GLUTAMYLCYSTEINE ETHYL ESTER, A PRODRUG OF GLUTATHIONE, ON ISCHEMIA-REPERFUSION-INDUCED LIVER INJURY IN RATS (1992)

This study was designed to clarify the effects of changes in liver tissue glutathione (GSH) concentration on postischemic liver injury together with the effects of gamma-glutamylcysteine ethyl ester (GCE), a prodrug of GSH, and GSH. Rats were pretreated with GSH (50 mg/kg, i.v.), or GCE (50 mg/kg, i.v.), or untreated. In each rat, liver was isolated, and liver mitochondria were prepared after 2 h of ischemia or 1 h of reperfusion following 2 h of ischemia. Mitochondrial function was measured polarographically. Liver adenine nucleotide concentrations were also determined using high-performance liquid chromatography. Liver tissue GSH, an oxidized form of glutathione (GSSG) concentrations, and activities of GSH peroxidase and GSSG reductase were determined enzymatically. Liver hypoxanthine and xanthine concentrations were determined by HPLC. Liver tissue concentration of lipid peroxide was measured. Leakages of aspartate aminotransferase (AST), alanine aminotransferase (ALT), lactate dehydrogenase (LDH), and adenine nucleotides into the hepatic vein after reperfusion were also measured. Administration of GCE improved the recovery of mitochondrial function and maintained tissue GSH concentration concomitantly. Increases in liver lipid peroxide concentration after reperfusion, and leakage of liver cell enzymes and adenine nucleotides were mitigated by administration of GCE. Administration of GSH itself failed to maintain tissue GSH concentration and had no protective effects. From these results, it is concluded that in the postischemic process, free radical formation might be enhanced, and the radical scavenging system deteriorated. To enhance the radical scavenging system is a possible maneuver to prevent radical-related cell damage associated with reperfusion, because pharmacological reduction of breakdown of ATP to hypoxanthine and xanthine seems to be difficult. GCE maintained liver GSH concentrations and mitigated postischemic liver injury, concomitantly. Clinical use of GCE might be recommended.
Effect of IL-12 on T-cell immune responses in patients with chronic HCV infectionNote (2000)

As the host's immune responses may determine the outcome of hepatitis C virus (HCV) infection, and interleukin (IL)-12 plays an essential role in host defense against infectious diseases, we studied the antigen-specific and non-specific cellular immune responses in patients with chronic HCV infection. A proliferative response to phytohemagglutinin (PHA) was found in all 20 patients. Of the 20, 8 (40%) displayed a lymphocyte proliferation in response to HCV antigen c22, 2 (10%) to c33, 6 (30%) to c100-3, and 1 (5%) to NS5. The addition of rhIL-12 to cultures of peripheral blood mononuclear cells (PBMC) stimulated with PHA significantly enhanced the proliferative responses in normal controls as well as in HCV-infected subjects. The increased proliferation was also observed in HCV-infected patients when PBMC were co-cultured with HCV antigens c22 and c100-3 in the presence of rhIL-12. The production of interferon gamma (IFNgamma), IL-2, IL-4 and IL-10 was observed in 7 (58.3%), 5 (41.7%), 3 (25.0%) and 5 (41.7%) HCV-infected individuals stimulated with c22, and in 4 (33.3%), 2 (16.7%), 2 (16.7%) and 2 (16.7%) with c100-3, respectively. All HCV-infected individuals had increased production of cytokines IFNgamma, IL-2, IL-4 and IL-10 in supernatants of PBMC after stimulation with PHA. IL-12 significantly augmented Th1 cytokine production in HCV-infected individuals stimulated with PHA and with HCV antigens. In conclusion, deficient cellular immune responses are present in HCV-infected patients and IL-12 can enhance the immune responses in these patients.
Mapping of a human T‐lymphotropic virus type I gag protein epitope that cross‐reacts with anti‐<i>Plasmodium falciparum</i> antibodies (1995)

Studies in Palawan, Philippines, and Irian Jaya, Indonesia, showed that indeterminate human T-lymphotropic virus type I (HTLV-I) Western blot immunoreactivity is due to cross-reacting anti-Plasmodium falciparum antibodies. To further define this immunoreactivity, mapping studies were conducted using the HTLV-I p19 protein to identify the precise epitope that reacts with these antibodies. Anti-P. falciparum antibody-positive sera from Palawan, Philippines, and Irian Jaya, Indonesia, were studied using overlapping synthetic peptides. Immunoreactivity was localized to residues 108-120 of p19. Further analysis of the sera with 5 biotinylated synthetic peptides showed that the cross-reactive epitope consists of the sequence PDSDPQI (amino acid residues 110-116), which was shown to be homologous to a 7 amino acid sequence on the Exp-1 protein of the P. falciparum blood stage parasite. This is the first study that identifies a specific HTLV-I protein epitope that cross-reacts with malaria antibodies.
Deactivation of PT-ZSM-5 for selective reduction of NO (1995)

Recent reports suggest the use of Pt-ZSM-5 with hydrocarbons to reduce NO selectively under oxidizing conditions and our laboratories, among others are investigating the use of Pt-zeolites to reduce NOx in the emission of Diesel or gasoline lean-burn vehicles. Here we consider the activity of Pt-ZSM-5, both as a fresh catalyst and after deactivation, and characterize a troubling aspect of catalyst deactivation. In severely deactivated materials, TEM reveals a film to have formed over Pt metal; we suggest this film is siliceous material derived from the zeolite and that an important mode of catalyst deactivation is due to geometric site blockage by this film.
<i>Caenorhabditis elegans</i> as an emerging model for studying the basic biology of obesity (2009)

The health problem of obesity and its related disorders highlights the need for understanding the components and pathways that regulate lipid metabolism. Because energy balance is maintained by a complex regulatory network, the use of a powerful genetic model like C. elegans can complement studies on mammalian physiology by offering new opportunities to identify genes and dissect complicated regulatory circuits. Many of the components that are central to governing human metabolism are conserved in the worm. Although the study of lipid metabolism in C. elegans is still relatively young, much progress has already been made in tracing out genetic pathways that regulate fat storage and in developing assays to explore different aspects of metabolic regulation and food sensation. This model system holds great promise for helping tease apart the complicated network of genes that maintain a proper energy balance.
Specific Gamma-Ray Dose Constants with Current Emission Data (2019)

The specific gamma-ray dose constant represents the gamma effective dose rate due to a point source of unit activity of a given nuclide at 1 m. New tabulations of specific gamma-ray dose constants have been made using current gamma emission data from the SCALE 6.2.3 software package and International Commission on Radiological Protection Publication 107, combined with the effective dose per fluence conversion coefficients (antero-posterior orientation) of International Commission on Radiological Protection Publication 116. SCALE data cover 1,264 nuclides, and International Commission on Radiological Protection Publication 107 data include 1,192 nuclides, with only 777 nuclides in common between the two sets.
Cell surface accessibility of GLUT4 glucose transporters in insulin-stimulated rat adipose cells. Modulation by isoprenaline and adenosine (1992)

Insulin-stimulated glucose transport activity in rat adipocytes is inhibited by isoprenaline and enhanced by adenosine. Both of these effects occur without corresponding changes in the subcellular distribution of the GLUT4 glucose transporter isoform. In this paper, we have utilized the impermeant, exofacial bis-mannose glucose transporter-specific photolabel, 2-N-4-(1-azi-2,2,2-trifluoroethyl)benzoyl-1,3-bis-(D-mannos- 4-yloxy)-2-propylamine (ATB-BMPA) [Clark & Holman (1990) Biochem. J. 269, 615-622], to examine the cell surface accessibility of GLUT4 glucose transporters under these conditions. Compared with cells treated with insulin alone, adenosine in the presence of insulin increased the accessibility of GLUT4 to the extracellular photolabel by approximately 25%, consistent with its enhancement of insulin-stimulated glucose transport activity; the plasma membrane concentration of GLUT4 as assessed by Western blotting was unchanged. Conversely, isoprenaline, in the absence of adenosine, promoted a time-dependent (t1/2 approximately 2 min) decrease in the accessibility of insulin-stimulated cell surface GLUT4 of > 50%, which directly correlated with the observed inhibition of transport activity; the plasma membrane concentration of GLUT4 decreased by 0-15%. Photolabelling the corresponding plasma membranes revealed that these alterations in the ability of the photolabel to bind to GLUT4 are transient, as the levels of both photolabel incorporation and plasma membrane glucose transport activity were consistent with the observed GLUT4 concentration. These data suggest that insulin-stimulated GLUT4 glucose transporters can exist in two distinct states within the adipocyte plasma membrane, one which is functional and accessible to extracellular substrate, and one which is non-functional and unable to bind extracellular substrate. These effects are only observed in the intact adipocyte and are not retained in plasma membranes isolated from these cells when analysed for their ability to transport glucose or bind photolabel.
Relative retention times (RRTs) on two common gas chromatographic stationary phases and lowresolution mass spectrometric relative response factors (RRFs) for 87 polychlorinated dibenzofurans (2003)

Relative retention times (RRTs) on two common gas chromatographic stationary phases and lowresolution mass spectrometric relative response factors (RRFs) for 87 polychlorinated dibenzofurans
High Purity Isotopically Enriched<sup>29</sup>Si and<sup>30</sup>Si Single Crystals: Isotope Separation, Purification, and Growth (2003)

We report the successful isotope separation and bulk single crystal growth of 29Si and 30Si stable isotopes. The isotopic enrichments of the 29Si and 30Si single crystals determined by mass spectrometry are 99.23% and 99.74%, respectively. Both crystals have the electrically active net-impurity concentration less than 1015 cm-3. Thanks to the result of this work and the 28Si crystals we grew previously, high quality single crystals of every stable Si isotope (28Si, 29Si, and 30Si) have been made available for a wide variety of basic research and industrial applications.
2,3,7,8-Tetrachlorodibenzo- <i>p</i> -Dioxin Kills Immature Thymocytes by Ca <sup>2+</sup> -Mediated Endonuclease Activation (1988)

Suspensions of thymocytes from young rats were incubated with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), which resulted in a sustained increase in cytosolic free Ca2+ concentration followed by DNA fragmentation and loss of cell viability. Both the Ca2+ increase and DNA fragmentation were prevented in cells treated with the inhibitor of protein synthesis, cycloheximide, and DNA fragmentation and cell killing were not detected when cells were incubated in a "Ca2+-free" medium or pretreated with high concentrations of the calcium probe, quin-2 tetraacetoxymethyl ester. These results indicate that TCDD can kill immature thymocytes by initiating a suicide process similar to that previously described for glucocorticoid hormones.
On phase correction in tomographic research (2020)

Under consideration is the problem of improving the contrast of the image obtained by processing tomographic projections with phase distortion. The study is based on the wellknown intensity transfer equation. Unlike other works, this equation is solved in a bounded region of variation of the tomographic parameters. In a domain, a boundary value problem is posed for the intensity transfer equation which is then specialized for a three-dimensional parallel tomographic scheme. The case of two-dimensional tomography is also considered, together with the corresponding boundary value problem for the intensity transfer equation. We propose numerical methods for solving the boundary value problems of phase correction. The results are given of the numerical experiments on correction of tomographic projections and reconstruction of the structure of the objects under study (in particular, a slice of a geological sample) by using piecewise uniform regularization.
Immunogenicity of Mutations Induced by Nucleoside Reverse Transcriptase Inhibitors for Human Immunodeficiency Virus Type 1-Specific Cytotoxic T Cells (2000)

The impact of drug resistance mutations induced by nucleoside reverse transcriptase (RT) inhibitors (NRTI) on cytotoxic T-lymphocyte (CTL) recognition of human immunodeficiency virus type 1 strain LAI (HIV-1(LAI)) RT was addressed in 35 treated or untreated patients. Two HIV-1(LAI) RT regions encompassing mutation M41L, L74V, M184V, and T215Y/F were recognized in 75 and 83% mutated and in 33 and 42% unmutated samples, respectively. A total of 41 new CTL epitopes overlapping these mutations were predicted. Mutations enhanced HLA-binding scores of 17 epitopes, decreased scores of 5, and had no effect in 19. Four predicted epitopes containing mutations 41, 74, and 184 were tested and recognized by CD8 cells from mutated or unmutated samples, with frequencies up to 270 gamma interferon spot-forming cells per 10(6) peripheral blood mononuclear cells. Therefore, RT mutations induced by NRTI can increase the immunogenicity of RT for CTL and might allow a better immune control of resistant viruses in vivo, suggesting that specific immune therapy might help prevent these mutations.
Information integration: A new generation of information technology (2002)

The explosion of the Internet and e-business in recent years has caused a secondary explosion in the amounts and types of information available to enterprise applications. Industry analysts predict that more data will be generated in the next three years than in all of recorded history. Because the adoption of Internet-based business transaction models has significantly outpaced the development of tools and technologies to deal with the information explosion, many businesses find their systems breaking under the sheer volume and diversity of data being directed at them. The challenge facing businesses today is information integration. Enterprise applications must interact with databases, application servers, content management systems, data warehouses, workflow systems, search engines, message queues, Web crawlers, mining and analysis packages, and other enterprise integration applications. They must use a variety of programming interfaces and understand a variety of languages and formats. They must extract and combine data in multiple formats generated by multiple delivery mechanisms. Clearly, the boundaries that have traditionally existed between database management systems, content management systems, midtier caches, data warehouses, and other data management systems are blurring, and there is a great need for a platform that provides a unified view of all of these services and the data they deliver.
High Precision Ion Beam Milling with Time of Flight Compensation (2008)

Abstract Advanced semiconductor process technologies demand that patterns are milled precisely and without beam overshoot, which could damage adjacent transistors or expose neighboring interconnects. As mill box size becomes small enough and contains fewer pixels, the probability of the beam landing accurately at any given pixel for the prescribed pixel time becomes low. This has forced operators to employ higher than desired pixel times in order to preserve pattern acuity at the expense of optimized gas enhancement. In this article, the authors demonstrate the ability to machine and fill 50nm vias in advanced semiconductor process technologies. This capability is enabled directly by time of flight (ToF) operations. ToF compensation provides a significant advantage for patterning accuracy in advanced circuit edit applications. It enables FIB operators to use drastically shorter dwell times and pixel rates to enhance gas milling and deposition activities.
Image Segmentation Using Deep Learning: A Survey (2021)

Image segmentation is a key task in computer vision and image processing with important applications such as scene understanding, medical image analysis, robotic perception, video surveillance, augmented reality, and image compression, among others, and numerous segmentation algorithms are found in the literature. Against this backdrop, the broad success of deep learning (DL) has prompted the development of new image segmentation approaches leveraging DL models. We provide a comprehensive review of this recent literature, covering the spectrum of pioneering efforts in semantic and instance segmentation, including convolutional pixel-labeling networks, encoder-decoder architectures, multiscale and pyramid-based approaches, recurrent networks, visual attention models, and generative models in adversarial settings. We investigate the relationships, strengths, and challenges of these DL-based segmentation models, examine the widely used datasets, compare performances, and discuss promising research directions.
Enzyme-immobilized SiO2–Si electrode: Fast interfacial electron transfer with preserved enzymatic activity (2005)

The enzyme, glucose oxidase (GOx), is immobilized using electrostatic interaction on the native oxide of heavily doped n-type silicon. Voltammetric measurement shows that the immobilized GOx gives rise to a very fast enzyme-silicon interfacial electron transfer rate constant of 7.9s−1. The measurement also suggests that the enzyme retains its native conformation when immobilized on the silicon surface. The preserved native conformation of GOx is further confirmed by testing the enzymatic activity of the immobilized GOx using glucose. The GOx-immobilized silicon is shown to behave as a glucose sensor that detects glucose with concentrations as low as 50μM.