gebhart/patrepeval huggingface dataset:
Antibody Conjugated Oligonucleotides as a Platform for Cyclic Immunofluorescent Staining (2019)

Journal Article Antibody Conjugated Oligonucleotides as a Platform for Cyclic Immunofluorescent Staining Get access Nathan McMahon, Nathan McMahon Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA Corresponding author: mcmahonn@ohsu.edu Search for other works by this author on: Oxford Academic Google Scholar Jocelyn Jones, Jocelyn Jones Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA Search for other works by this author on: Oxford Academic Google Scholar Allison Solanki, Allison Solanki Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA Search for other works by this author on: Oxford Academic Google Scholar Jennifer Eng, Jennifer Eng Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA Search for other works by this author on: Oxford Academic Google Scholar Sunjong Kwon, Sunjong Kwon Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA Search for other works by this author on: Oxford Academic Google Scholar Young-Hwan Chang, Young-Hwan Chang Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USAComputational Biology Program, Oregon Health and Science University, Portland, OR, USA Search for other works by this author on: Oxford Academic Google Scholar Guillaume Thibault, Guillaume Thibault Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USAComputational Biology Program, Oregon Health and Science University, Portland, OR, USA Search for other works by this author on: Oxford Academic Google Scholar Koei Chin, Koei Chin Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USACenter for Spatial Systems Biomedicine, Oregon Health and Science University, Portland, OR, USA Search for other works by this author on: Oxford Academic Google Scholar Michel Nederlof, Michel Nederlof Quantitative Imaging Systems, Pittsburg, PA, USA Search for other works by this author on: Oxford Academic Google Scholar Joe Gray, Joe Gray Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USAKnight Cancer Institute, Oregon Health and Science University, Portland, OR, USACenter for Spatial Systems Biomedicine, Oregon Health and Science University, Portland, OR, USA Search for other works by this author on: Oxford Academic Google Scholar ... Show more Summer L Gibbs Summer L Gibbs Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USAKnight Cancer Institute, Oregon Health and Science University, Portland, OR, USACenter for Spatial Systems Biomedicine, Oregon Health and Science University, Portland, OR, USA Search for other works by this author on: Oxford Academic Google Scholar Microscopy and Microanalysis, Volume 25, Issue S2, 1 August 2019, Pages 1206–1207, https://doi.org/10.1017/S1431927619006767 Published: 01 August 2019
Dysfunction of the Islet Lysosomal System Conveys Impairment of Glucose-Induced Insulin Release in the Diabetic GK Rat* (1999)

Accumulated evidence links an important signal involved in glucose-stimulated insulin release to the activation of the islet lysosomal glycogenolytic enzyme acid glucan-1,4-alpha-glucosidase. We have analyzed the function of the lysosomal system/lysosomal enzyme activities in pancreatic islets of young (6-8 weeks), spontaneously diabetic, GK (Goto-Kakizaki) rats and Wistar control rats in relation to glucose-induced insulin release. The insulin secretory response to glucose was markedly impaired in the GK rat, but was restored by the adenylate cyclase activator forskolin. Islet activities of classical lysosomal enzymes, e.g.. acid phosphatase, N-acetyl-beta-D-glucosaminidase, beta-glucuronidase, and cathepsin D, were reduced by 20-35% in the GK rat compared with those in Wistar controls. In contrast, the activities of the lysosomal alpha-glucosidehydrolases, i.e.. acid glucan-1,4-alpha-glucosidase and acid alpha-glucosidase, were increased by 40-50%. Neutral alpha-glucosidase (endoplasmic reticulum) was unaffected. Comparative analysis of liver tissue showed that lysosomal enzyme activities were of the same magnitude in GK and Wistar rats. Notably, in Wistar rats, the activities of acid glucan-1,4-alpha-glucosidase and acid alpha-glucosidase were approximately 15-fold higher in islets than in liver. Other lysosomal enzymes did not display such a difference. Normalization of glycemia in GK rats by phlorizin administered for 9 days did not influence either the lysosomal alpha-glucosidehydrolase activities or other lysosomal enzyme activities in GK islets. Finally, the pseudotetrasaccharide acarbose, which accumulates in the lysosomal system, inhibited acid glucan-1,4-alpha-glucosidase activity in parallel with its inhibitory action on glucose-induced insulin release in intact Wistar islets, whereas no effect was recorded for either parameter in intact GK islets. In contrast, acarbose inhibited the enzyme activity equally in islet homogenates from both GK and Wistar rats, showing that the catalytic activity of the enzyme itself in disrupted cells was unaffected. We propose that dysfunction of the islet lysosomal/vacuolar system is an important defect impairing the transduction mechanisms for glucose-induced insulin release in the GK rat.
Erratum to: Scaling up strategies of the chronic respiratory disease programme of the European Innovation Partnership on Active and Healthy Ageing (Action Plan B3: Area 5) (2017)

Erratum to: Clinical and Translational Allergy (2016) 6:29 DOI 10.1186/s13601-016-0116-9&#13;\n&#13;\nIn this version of this article that was originally published [1], the name M. R. Khaitov was misspelled as M. R. Kaitov.
Organometallic Aspects of the Fischer‐Tropsch Synthesis (1982)

Abstract The Fischer‐Tropsch Synthesis counts among the industrial‐scale processes having a versatile and broad product range, and has for decades offered the most attractive possibility for the use of coal as a source of heating oil and fuels. This conceivably simple reaction, the catalytic hydrogenation of carbon monoxide, generally leads to simple hydrocarbons as well ( i.e. short chain olefins) that have been sought as chemical feedstocks since the oil crisis of the seventies, but fails to provide the large‐scale, economic process required, due in large part to the minimal selectivity of traditional Fischer‐Tropsch processes. In an effort to solve this problem current research in this sector is concerned not only with the optimization of old and the development of new catalytic systems, but also increasingly with the elucidation of numerous relevant reaction mechanisms. This article will discuss, from the viewpoint of an organometallic chemist, the significance of typical model reactions, both with regard to some fundamental aspects of synthesis gas chemistry, and in comparison with previous views concerning the mechanism of the Fischer‐Tropsch Synthesis. The importance of various unique classes of complexes that have been studied in the context of Fischer‐Tropsch chemistry is also evaluated with regard to their importance in the synthesis of hydrocarbons from carbon monoxide and hydrogen. It emerges that the primary steps of the reductive oligomerization of carbon monoxide are best described by the carbide/methylene mechanism, as originally proposed by Hans Fischer and Franz Tropsch .
Extending the application of subaperture finishing (2006)

Subaperture polishing technologies have radically changed the landscape of precision optics manufacturing and enabled the production of components with higher accuracies and increasingly difficult figure requirements. Magnetorheological Finishing (MRF<sup>&reg;</sup>), for example, is a proven, production-worthy, deterministic, subaperture finishing technology that has excelled at extending precision finishing well beyond the limitations of traditional polishing. Several recent MRF developments will be presented, including the post polishing of Single Point Diamond Turned (SPDT) surfaces, transmitted wavefront correction, and finishing of increasingly large apertures. The high precision finishing of challenging optics using a newly developed jet-based technology will also be discussed. A series of examples spanning a wide range of materials, geometries and specifications will be presented. Specific areas to be discussed include the finishing of optics less than 5 mm in diameter, which typically require a very labor-intensive, iterative process to finish, and the correction of steeply concave optics, such as domes, which are typically not well suited for sub-aperture polishing processes.
Aqueous Extracts of Corni Fructus Protect C2C12 Myoblasts from DNA Damage and Apoptosis Caused by Oxidative Stress (2021)

Abstract Background Although the various pharmacological effects of Corni Fructus are highly correlated with its antioxidant activity, the blocking effect against oxidative stress in muscle cells is not clear. The purpose of this study was to investigate the effect of aqueous extracts of Corni Fructus (CFE) against oxidative stress caused by hydrogen peroxide (H 2 O 2 ) in murine skeletal C2C12 myoblasts. Methods and results MTT assay for cell viability, DCF-DA staining for reactive oxygen species (ROS) production, Comet assay for DNA damage, annexin V-FITC and PI double staining for apoptosis, JC-1 staining and caspase assay for monitor mitochondrial integrity, and western blotting for related protein levels were conducted in H 2 O 2 oxidative stressed C2C12 cells. Our results showed that CFE pretreatment significantly ameliorated the loss of cell viability and inhibited apoptosis in H 2 O 2 -treated C2C12 cells in a concentration-dependent manner. DNA damage induced by H 2 O 2 was also markedly attenuated in the presence of CFE, which was associated with suppression of ROS generation. In addition, H 2 O 2 reduced mitochondrial membrane potential and caused downregulation of Bcl-2 and upregulation of Bax expression, although these were abrogated by CFE pretreatment. Moreover, CFE blocked H 2 O 2 -induced cytosolic release of cytochrome c , activation of caspase-9 and caspase-3, and degradation of poly (ADP-ribose) polymerase. Conclusion Taken together, the present results demonstrate that CFE could protect C2C12 cells from H 2 O 2 -induced damage by eliminating ROS generation, thereby blocking mitochondria-mediated apoptosis pathway. These results indicate that CFE has therapeutic potential for the prevention and treatment of oxidative stress-mediated myoblast injury.
Data-Efficient Communication Traffic Prediction With Deep Transfer Learning (2022)

Prediction of future traffic load is a crucial task to support the automatic Operations, Administration, and Management (OAM) of communication networks. Existing Machine Learning (ML) models require big data to accomplish this task. However, large data sets are not always available, due to the limited storage capacity and the high storage cost at Base Stations (BSs). To solve the problem, we leverage the spatial-temporal correlation among different BSs, which allows other BSs’ data to be used for the prediction of the target BS. One major challenge in realizing this idea is the imbalance of data amounts between neighbor BSs and a prediction target BS. If one simply aggregates the data from both neighbors and target, the target’s traffic features would be overwhelmed by the neighbors’ data. To address this challenge, we propose a Spatial-Temporal Transfer (STT) framework, which trains a base model with an aggregated data set from multiple BSs, and then carefully refines the base model to serve a target BS. To strike a perfect balance between general tendency and individual features, STT adopts an advanced transfer learning technique that exploits regularization on model parameters. Experiments show the efficiency of the proposed STT framework.
All-optical wavelength conversion for 20-Gb/s RZ format data (2000)

We have successfully demonstrated an all-optical wavelength conversion scheme for high-speed return-to-zero (RZ) format data input by using a semiconductor-optical-amplifier (SOA) converter incorporated with a stabilized asymmetric Mach-Zehnder interferometer (AMZI). A bit-error-rate penalty of the converted signals less than 1.2 dB compared to that of the back-to-back signals was achieved for the entire wavelength conversion range from 1530 to 1560 nm with an AMZI. In this scheme, the conversion speed faster than the carrier recombination rate of the SOAs was possible. Noninverted wavelength conversion of 20-Gb/s RZ format data signals has been achieved.
ChemInform Abstract: Synthesis of 4‐Aroyl‐((5‐phenyl‐2(2H)‐tetrazolyl)‐1‐oxoethyl)thiosemicarbazides and 4‐Aroyl‐5‐((5‐phenyl‐2(2H)‐tetrazolyl)methyl)‐1,2,4‐ (4H)‐triazole‐3‐thione. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Thickness and roughness dependence of DC modulation noise in thin film magnetic recording disk media (1990)

DC modulation noise was studied as a function of magnetic-layer thickness and surface roughness for longitudinal, low-noise, nominally 1000-Oe, plated CoP and CoNiZnP, thin-film magnetic recording disk media made from controlled fabrication runs. DC modulation noise is generated when a reverse longitudinal DC field is applied to a uniformly magnetized disk. A model which allows autocorrelation functions and noise spectra to be calculated and which agrees with measured noise data (with correlations greater than 0.99) was developed. Trends observed with measured data and the model indicate that inhomogeneities in the medium, and not surface roughness, are the dominant sources of noise.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A Uniform Treatment of Pragmatic Inferences in Simple and Complex Utterances and Sequences of Utterances (1995)

Drawing appropriate defeasible inferences has been proven to be one of the most pervasive puzzles of natural language processing and a recurrent problem in pragmatics. This paper provides a theoretical framework, called ``stratified logic'', that can accommodate defeasible pragmatic inferences. The framework yields an algorithm that computes the conversational, conventional, scalar, clausal, and normal state implicatures; and the presuppositions that are associated with utterances. The algorithm applies equally to simple and complex utterances and sequences of utterances.
The XCAT science portal (2001)

The design and prototype implementation of the XCAT Grid Science Portal is described in this paper. The portal lets grid application programmers easily script complex distributed computations and package these applications with simple interfaces for others to use. Each application is packaged as a "notebook" which consists of web pages and editable parameterized scripts. The portal is a workstation-based specialized "personal" web server, capable of executing the application scripts and launching remote grid applications for the user. The portal server can receive event streams published by the application and grid resource information published by Network Weather Service (NWS) [32] or Autopilot [15] sensors. Notebooks can be "published" and stored in web based archives for others to retrieve and modify. The XCAT Grid Science Portal has been tested with various applications, including the distributed simulation of chemical processes in semiconductor manufacturing and collaboratory support for X-ray crystallographers.
Ethylene Induced a High Accumulation of Dietary Isoflavones and Expression of Isoflavonoid Biosynthetic Genes in Soybean (Glycine max) Leaves (2016)

Dietary isoflavones, daidzein and genistein are of huge interest in the nutraceutical field due to their practical application to postmenopause complications. This study is the first report an efficient method to prepare isoflavone rich soybean leaves (soyleaves) which is an edible food stuff in Asian countries. The preharvest treatment of ethylene highly stimulated the level of isoflavone in soyleaves. Annotation and quantification of metabolites were determined by UPLC-Q-TOF-MS and HPLC. Phenolic metabolites of soyleaves are mostly kaempferol glycosides, but not dietary isoflavones. The accumulated isoflavones by ethylene treatment were determined to be daidzin 1, genistin 2, malonyldaidzin 3 and malonylgenistin 4, which were easily hydrolyzed to daidzein and genistein by β-glucosidase. Total content of dietary isoflavones was increased up to 13854 μg/g. The most suitable condition was estimated to be 250 μg/g ethylene or 200 μg/g ethephon (ethylene donor) treatment at the R3 growth stage. The ratio of daidzein and genistein glycosides was approximately 5 to 3. The accumulated isoflavonoid biosynthesis pathway genes were identified within the transcriptome of soyleaves tissues at 1 day after treatment of ethephon. The quantitative RT-PCR analysis of these genes indicated significantly higher expression of CHS, CHI, IFS, HID, IF7GT, and IF7MaT compared to control leaves. These findings suggest that ethylene activates a set of structural genes involved in isoflavonoid biosynthesis, thereby leading to enhanced production of isoflavones in soybean plants.
Mutagenic and Nonmutagenic Bypass of DNA Lesions byDrosophila DNA Polymerases dpolη and dpolι (2001)

cDNA sequences were identified and isolated that encode Drosophila homologues of human Rad30A and Rad30B called drad30A and drad30B. Here we show that the C-terminal-truncated forms of the drad30A and drad30B gene products, designated dpoletaDeltaC and dpoliotaDeltaC, respectively, exhibit DNA polymerase activity. dpoletaDeltaC and dpoliotaDeltaC efficiently bypass a cis-syn-cyclobutane thymine-thymine (TT) dimer in a mostly error-free manner. dpoletaDeltaC shows limited ability to bypass a 6-4-photoproduct ((6-4)PP) at thymine-thymine (TT-(6-4)PP) or at thymine-cytosine (TC-(6-4)PP) in an error-prone manner. dpoliotaDeltaC scarcely bypasses these lesions. Thus, the fidelity of translesion synthesis depends on the identity of the lesion and on the polymerase. The human XPV gene product, hpoleta, bypasses cis-syn-cyclobutane thymine-thymine dimer efficiently in a mostly error-free manner but does not bypass TT-(6-4)PP, whereas Escherichia coli DNA polymerase V (UmuD'(2)C complex) bypasses both lesions, especially TT-(6-4)PP, in an error-prone manner (Tang, M., Pham, P., Shen, X., Taylor, J. S., O'Donnell, M., Woodgate, R., and Goodman, M. F. (2000) Nature 404, 1014-1018). Both dpoletaDeltaC and DNA polymerase V preferentially incorporate GA opposite TT-(6-4)PP. The chemical structure of the lesions and the similarity in the nucleotides incorporated suggest that structural information in the altered bases contribute to nucleotide selection during incorporation opposite these lesions by these polymerases.
Automated search of natively folded protein fragments for high‐throughput structure determination in structural genomics (2000)

Structural genomic projects envision almost routine protein structure determinations, which are currently imaginable only for small proteins with molecular weights below 25,000 Da. For larger proteins, structural insight can be obtained by breaking them into small segments of amino acid sequences that can fold into native structures, even when isolated from the rest of the protein. Such segments are autonomously folding units (AFU) and have sizes suitable for fast structural analyses. Here, we propose to expand an intuitive procedure often employed for identifying biologically important domains to an automatic method for detecting putative folded protein fragments. The procedure is based on the recognition that large proteins can be regarded as a combination of independent domains conserved among diverse organisms. We thus have developed a program that reorganizes the output of BLAST searches and detects regions with a large number of similar sequences. To automate the detection process, it is reduced to a simple geometrical problem of recognizing rectangular shaped elevations in a graph that plots the number of similar sequences at each residue of a query sequence. We used our program to quantitatively corroborate the premise that segments with conserved sequences correspond to domains that fold into native structures. We applied our program to a test data set composed of 99 amino acid sequences containing 150 segments with structures listed in the Protein Data Bank, and thus known to fold into native structures. Overall, the fragments identified by our program have an almost 50% probability of forming a native structure, and comparable results are observed with sequences containing domain linkers classified in SCOP. Furthermore, we verified that our program identifies AFU in libraries from various organisms, and we found a significant number of AFU candidates for structural analysis, covering an estimated 5 to 20% of the genomic databases. Altogether, these results argue that methods based on sequence similarity can be useful for dissecting large proteins into small autonomously folding domains, and such methods may provide an efficient support to structural genomics projects.
Polyionic regulation of cartilage development: Promotion of chondrogenesis in vitro by polylysine is associated with altered glycosaminoglycan biosynthesis and distribution (1992)

The development of cartilage nodules in cultures of chick limb bud mesenchyme (Hamburger-Hamilton stages 23/24) is significantly promoted when the culture medium is supplemented with (poly-L-lysine (PL) (M(r) greater than or equal to 14K) (San Antonio and Tuan, 1986. Dev. Biol. 115: 313). Here we present findings consistent with the hypothesis that PL may promote chondrogenesis by interacting electrostatically with sulfated glycosaminoglycans (GAGs): (1) poly-L-ornithine, poly-L-histidine, poly-D,L-lysine, and lysine-containing heteropolypeptides stimulate chondrogenesis in proportion to their contents of cationic residues; (2) the effects of PL are diminished when limb mesenchyme cultures are supplemented with exogenous GAGs, including heparin, dermatan sulfate, and chondroitin sulfate; (3) in high density cultures of limb bud mesenchyme, the release of sulfated macromolecules, but not of proteins in general, into the culture medium was significantly inhibited by PL (398K M(r)) treatment, and a net increase in total GAG content of the PL-treated cultures was observed; and (4) in monolayer cultures of cells derived from other chick embryonic tissues, including liver, skeletal muscle, and calvaria, PL treatment promoted the cell layer-associated retention of sulfated GAG. These effects were not observed using the nonstimulatory, low M(r) PL (4K). Based on the above findings and those from previous studies, it is proposed that PL may promote chondrogenesis by interacting electrostatically with cartilage GAGs, thus trapping the extracellular matrix around the newly emerging cartilage nodules and thereby stabilizing their growth and differentiation.