gebhart/patrepeval huggingface dataset:
Oriented and selective enzyme immobilization on functionalized silica carrier using the cationic binding module Zbasic2: Design of a heterogeneous D‐amino acid oxidase catalyst on porous glass (2012)

D-amino acid oxidase from Trigonopsis variabilis (TvDAO) is applied in industry for the synthesis of pharmaceutical intermediates. Because free TvDAO is extremely sensitive to exposure to gas-liquid interfaces, biocatalytic processing is usually performed with enzyme immobilizates that offer enhanced stability under bubble aeration. We herein present an "Immobilization by Design" approach that exploits engineered charge complementarity between enzyme and carrier to optimize key features of the immobilization of TvDAO. A fusion protein between TvDAO and the positively charged module Z(basic2) was generated, and a corresponding oppositely charged carrier was obtained by derivatization of mesoporous glass with 3-(trihydroxysilyl)-1-propane-sulfonic acid. Using 250 mM NaCl for charge screening at pH 7.0, the Z(basic2) fusion of TvDAO was immobilized directly from E. coli cell extract with almost absolute selectivity and full retention of catalytic effectiveness of the isolated enzyme in solution. Attachment of the homodimeric enzyme to the carrier was quasi-permanent in low-salt buffer but fully reversible upon elution with 5 M NaCl. Immobilized TvDAO was not sensitive to bubble aeration and received substantial (≥ tenfold) stabilization of the activity at 45°C as compared to free enzyme, suggesting immobilization via multisubunit oriented interaction of enzyme with the insoluble carrier. The Z(basic2) enzyme immobilizate was demonstrated to serve as re-usable heterogeneous catalyst for D-amino acid oxidation. Z(basic2) -mediated binding on a sulfonic acid group-containing glass carrier constitutes a generally useful strategy of enzyme immobilization that supports transition from case-specific empirical development to rational design.
Phloem Anatomy of Citrus Trees: Healthy vs. Greening-affected (2012)

Phloem cells from HLB-affected trees become obstructed with callose and P-protein plugs. The presence of these plugs is believed to hinder the translocation of photoassimilates (nitrogenous and reduced carbon compounds) to the root system. However, even with seemingly collapsed phloem tissue, citrus trees remain viable and produce fruit for some time, suggesting either incomplete plugging of phloem elements or the existence of alternative routes for photoassimilate transport. In this study, we examined the basic structure of phloem tissue from HLB-free and HLB-affected trees under light and scanning electron microscopy. To avoid any possible interference with callose induced by injury during sampling, we employed a freeze substitution technique. Sieve elements from HLB-free trees show sizable lateral pores to phloem and ray parenchyma. Early stage HLB-affected phloem cells contain dark electron dense material and jagged appearing cell walls. Eventually, these cells totally collapse into almost a solid cell-wall barrier. The large number of wall depressions all along the cortex, ray and vascular parenchyma with abundant pit fields, could be an essential anatomical feature necessary to support symplastic transport of photoassimlates in an HLB-compromised phloem system.
Application of laser ultrasound for surface acoustic wave microscopy (1998)

This paper discusses the approach we have taken to developing laser ultrasonics so that it can fufil many of the functions normaly associated with the scanning acoustic microscope. In particular, we discuss applications involving accurate measurement of surface acoustic wave velocity and imaging applications involving the scattering of surface acoustic waves (SAWs). We present some novel techniques for detection ofSAWs and show how computer-generated holography should be a valuable solution to improve the laser generation efficiency of SAWs.
Photodissociation Studies of Sulfur Oxides. (1996)

Abstract : The detailed reaction dynamics of several gas phase polyatomic systems has been established in this research at the Department of Chemistry at the University of Puerto Rico. Real time dynamics of sulfur monoxide photoelimination reactions have been studied by laser induced fluorescence spectroscopy of the nascent SO fragment on the B(3)sigma (-) - X(3)sigma(-) transition in the region of 237-310 nm. The following group of molecules has been studied: Sulfur dioxide (SO2), the thionyl halides (SOX2; where X=F,C1 or Br), dimethyl sulfoxide ((CH3)2SO), ethylene episulfoxide ((CH2)2SO), trimethylene sulfoxide ((CH2)3SO), tetramethylene sulfoxide ((CH2)4SO), and thionyl aniline (C6H5NSO!. In all of these experiments, the parent molecule is irradiated with an excimer laser (either 193 or 248 nm) and the energy disposal into the nascent SO photofragment is determined, and used as a mechanistic probe. A broad picture of sulfur monoxide photoelimination reactions emerges from this work. In a second area, the photophysics and photochemistry of the vinoxy radical were investigated. Fluorescence decay rates were determined in the presence of twelve collision partners: He, Ar, N2, O2, CO, H2, HCl, CO2, N2O, C2H4, SF6 and CH3OCH=CH2. The measured electronic quenching cross-sections vary from 0.01 - 66.5 A2. A vibrational level dependence was found for the radiative lifetimes. A kinetic model, consistent with all the experimental observations has been postulated. Several new transitions of the CH2CHO (B-X) transition have been discovered. Finally, a study of bimolecular reactions has been initiated. jg p2
A new platform technology RuVaCare, an extracorporeal anti-cancer vaccine is efficient in breaking immune barrier to target cancer cells (Conference Presentation) (2019)

Even though a patient has a good immune system, tumors are shielded from it, because tumors grow by suppressing the host’s immune-response by various mechanisms. They are keeping their local microenvironment immune suppressed by producing immune suppressive cytokines like IL-10 and TGF-b, express immune checkpoint ligands like Programmed Death Ligand 1 (PDL1), and harbor immune suppressive cells like Tregs and MDSCs. To overcome these barriers a stronger anti-tumour immune-response is essential. We evaluated a whole cell vaccine with extracorporeal Rutherrin®-PDT treated cancer cells (RuVaCareTM) to break the suppressive barrier in the RG2-glioblastoma model. Rutherrin®-PDT induced strong immunogenic cell death (ICD) in glioblastoma cells in-vitro. RuVaCareTM supernatants showed significantly higher level of extracellular ATP, which is known to induce recruitment of antigen presenting cells (APCs) and their activation by eliciting an effective anti-tumour immune-response. Extracellular calreticulin (CRT) is one of the hallmarks of ICD; its expression went up in more than 85% cells undergoing Rutherrin®-PDT mediated cell death. There was a close to 10 times increase in expression of HSP 70 in RuVaCareTM. Immunostimulatory cytokines IFNa, IL-1b and GMCSF expression is high in the RuVaCareTM. In-vivo efficacy of the RuVaCare™ was evaluated in orthotopic RG2 rat glioblastoma model. There was a significant increase (~43% with 2-time vaccine and 87% in the 6-time vaccine) in survival in the RuVaCare™ vaccinated groups compared to unvaccinated controls. Increased intratumoral CD8+T-cell numbers are shown to be correlated with increased survival in glioblastoma rats, with RuVaCare™ there was a significant increase in the number of CD8+T-cells.
Self-Amplifying Pestivirus Replicon RNA Encoding Influenza Virus Nucleoprotein and Hemagglutinin Promote Humoral and Cellular Immune Responses in Pigs (2021)

Self-amplifying replicon RNA (RepRNA) promotes expansion of mRNA templates encoding genes of interest through their replicative nature, thus providing increased antigen payloads. RepRNA derived from the non-cytopathogenic classical swine fever virus (CSFV) targets monocytes and dendritic cells (DCs), potentially promoting prolonged antigen expression in the DCs, contrasting with cytopathogenic RepRNA. We engineered pestivirus RepRNA constructs encoding influenza virus H5N1 (A/chicken/Yamaguchi/7/2004) nucleoprotein (Rep-NP) or hemagglutinin (Rep-HA). The inherent RNase-sensitivity of RepRNA had to be circumvented to ensure efficient delivery to DCs for intracellular release and RepRNA translation; we have reported how only particular synthetic delivery vehicle formulations are appropriate. The question remained concerning RepRNA packaged in virus replicon particles (VRPs); we have now compared an efficient polyethylenimine (PEI)-based formulation (polyplex) with VRP-delivery as well as naked RepRNA co-administered with the potent bis-(3',5')-cyclic dimeric adenosine monophosphate (c-di-AMP) adjuvant. All formulations contained a Rep-HA/Rep-NP mix, to assess the breadth of both humoral and cell-mediated defences against the influenza virus antigens. Assessment employed pigs for their close immunological relationship to humans, and as natural hosts for influenza virus. Animals receiving the VRPs, as well as PEI-delivered RepRNA, displayed strong humoral and cellular responses against both HA and NP, but with VRPs proving to be more efficacious. In contrast, naked RepRNA plus c-di-AMP could induce only low-level immune responses, in one out of five pigs. In conclusion, RepRNA encoding different influenza virus antigens are efficacious for inducing both humoral and cellular immune defences in pigs. Comparisons showed that packaging within VRP remains the most efficacious for delivery leading to induction of immune defences; however, this technology necessitates employment of expensive complementing cell cultures, and VRPs do not target human cells. Therefore, choosing the appropriate synthetic delivery vehicle still offers potential for rapid vaccine design, particularly in the context of the current coronavirus pandemic.
Development of an inexpensive legume‐Rhizobium inoculation technology which may be used in aerial seeding (1994)

Abstract Encapsulation of seeds with alginate entrapped rhizobia (AER) bead has been developed as a new seed‐applied inoculum technique for utilizing legume‐ Rhizobium symbiosis for the management and protection of natural ecosystems. Alginate beads trapped water and immobilized rhizobia which ensured germination of seeds and nodulation of seedlings. Incorporation of a synthetic polymer, Jalshakti, in alginate beads did not enhance symbiotic nitrogen fixation but sufficient number of rhizobia remain viable in them even after 30 weeks of storage reflecting suitability of these materials as carriers for rhizobia. Plant cultures raised from these beads were similar to or even better than the inoculated controls in symbiotic parameters indicating the effectiveness of seed‐applied inoculum technique. Pelleting of seeds with these polymers after coating with gum arabic lead to substantial reduction in symbiotic association and viability of rhizobia. Experiments involving two legume‐ Rhizobium associations indicated that the encapsulation of seed with AER bead is a cheap, inexpensive and effective inoculation technique which may be used in aerial seeding.
The aged epidermal permeability barrier. Structural, functional, and lipid biochemical abnormalities in humans and a senescent murine model. (1995)

Aged epidermis displays altered drug permeability, increased susceptibility to irritant contact dermatitis, and often severe xerosis, suggesting compromise of the aged epidermal barrier. To delineate the functional, structural, and lipid biochemical basis of epidermal aging, we compared barrier function in young (20-30 yr) vs aged (> 80 yr) human subjects, and in a murine model. Baseline transepidermal water loss in both aged humans and senescent mice was subnormal. However, the aged barrier was perturbed more readily with either acetone or tape stripping (18 +/- 2 strippings vs 31 +/- 5 strippings in aged vs young human subjects, respectively). Moreover, after either acetone treatment or tape stripping, the barrier recovered more slowly in aged than in young human subjects (50 and 80% recovery at 24 and 72 h, respectively, in young subjects vs 15% recovery at 24 h in aged subjects), followed by a further delay over the next 6 d. Similar differences in barrier recovery were seen in senescent vs young mice. Although the total lipid content was decreased in the stratum corneum of aged mice (approximately 30%), the distribution of ceramides (including ceramide 1), cholesterol, and free fatty acids was unchanged. Moreover, a normal complement of esterified, very long-chain fatty acids was present. Finally, stratum corneum lamellar bilayers displayed normal substructure and dimensions, but were focally decreased in number, with decreased secretion of lamellar body contents. Thus, assessment of barrier function in aged epidermis under basal conditions is misleading, since both barrier integrity and barrier repair are markedly abnormal. These functional changes can be attributed to a global deficiency in all key stratum corneum lipids, resulting in decreased lamellar bilayers in the stratum corneum interstices. This constellation of findings may explain the increased susceptibility of intrinsically aged skin to exogenous and environmental insults.
Conventional and Back-Illuminated Cobalt- and Iodine-Mediated Dye-Sensitized Solar Cells for Artificial and Solar Light Conversion (2022)

Dye-sensitized solar cells (DSSCs) are among the leading PV technologies for indoor applications. These devices need to be optimized for these illumination conditions since, as it will be demonstrated, the best devices under solar conditions do not originate from the best devices under artificial illumination. This work studies the impact of the photoanode thickness, its light-scattering properties, dye loading, distance from the photoelectrode to the counter electrode on the charge transfer, recombination, and photovoltaic response of cobalt (III/II) bipyridine ([Co(bpy)3] 3+/2+) and iodide/triiodide (I–/I3–) DSSCs under 1 Sun and artificial 1000 lx light illumination. The champion [Co(bpy)3] 3+/2+ device displayed a power conversion efficiency (PCE) of 11.0 and 32.0% under AM1.5G and 1000 lx, respectively. The best I–/I3– cells yielded 9.0% 1 Sun PCE and 23.1% of PCE under 1000 lx. Optimized [Co(bpy)3]3+/2+ and I–/I3– DSSCs demonstrated huge potential as efficient indoor-photovoltaics and can straightforwardly be used as back-illuminated devices to improve the output power under low illumination. Under 1000 lx room light, the champion cobalt DSSCs displayed a record PCE of 27.3% from the rear-side with 85.3% of retention ratio.
Corrosion Behavior of Ultra-high Strength Drilling Steel in Alkaline Brines Containing Hydrogen Sulfide at High Temperature (2019)

Presented by NETL at CORROSION 2016, 03/16
Anhydrocochlioquinone A, a New Antitumor Compound from Bipolaris oryzae. (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
ChemInform Abstract: Stereochemical Studies of Fluoride Ion‐Assisted Reductions of Ketones by Organosilicon Hydrides. (1985)

Abstract Die Silane (I) und die Ketone (II) reagieren in Gegenwart von Fluorid‐Ionen über die Silylether (III) zu den optisch aktiven Spaltprodukten (IV) und (V).
Genetically modified wine yeasts and risk assessment studies covering different steps within the wine making process (2010)

The use of gene technology to modify the genome of wine yeasts belonging to the species Saccharomyces cerevisiae began in the early 1990s. From a purely scientific point of view, many yeast constructs [genetically modified organisms (GMO)] have been made so far, covering more or less all stages of the wine making process in which microorganisms or commercial enzymes play a key role. The range of theoretical applications is summarised in this report. So far, only two wine-producing countries worldwide allow the use of engineered wine yeasts; the changing situation in Germany regarding consumers’ attitudes towards gene technology, and foodstuffs thus produced, will be outlined here. Experiments at the Geisenheim Research Center have highlighted the essential stages of the wine making process where yeasts are involved by using engineered wine yeasts in comparison with non-engineered yeast strains. Greenhouse simulations revealed the persistence of genetically modified (gm) yeasts when these were used as fertilizers, as vintners do with yeast lees after the fermentation process. Furthermore, the persistence of engineered yeast was also monitored in fermentations, after bottling, and after biological treatment of winery waste water. It turned out that engineered wine yeast strains behave like non-engineered wine yeasts. They also persist in the winery interior and installations as well as becoming part of the yeast flora on grape vines in a vineyard with annual fluctuations in the composition of the yeast populations.
Image processing of particle detection for asbestos qualitative analysis support method -particle counting by using color variance of background (2008)

In this paper, we propose the technique classifying background area automatically by calculating the color variance in the RGB space of the picture. By this technique, the background classification robust to change of the background brightness and the background color was enabled. Moreover, we show the effectiveness of this technique by performing particle detection and verifying the result of counting. We aim at development of the particle detector which performs particle counting automatically about the ldquodispersion staining methodrdquo which is one of the processes of asbestos analysis. We used the pictures taken by phase contrast microscopy used for a ldquodispersion staining methodrdquo.
Drug discovery and development scheme for liver-targeting bridged nucleic acid antisense oligonucleotides (2021)

Antisense oligonucleotides (ASOs) containing bridged nucleic acids (BNAs) have been proven to be very powerful. However, ensuring a reliable discovery and translational development scheme for this class of ASOs with wider therapeutic windows remains a fundamental challenge. We here demonstrate the robustness of our scheme in the context of the selection of ASOs having two different BNA chemistries (2,'4'-BNA/locked nucleic acid [LNA] and amido-bridged nucleic acid [AmNA]) targeting human proprotein convertase subtilisin/kexin type 9 (PCSK9). The scheme features a two-step process, including (1) a unique and sensitive <i>in vitro</i> screening approach, called Ca<sup>2+</sup> enrichment of medium (CEM) transfection, and (2) a ligand-targeted drug delivery approach to better reach target tissues, averting unintended accumulation of ASOs. Using CEM screening, we identified a candidate ASO that shows >70% cholesterol-lowering action in monkeys. An <i>N</i>-acetylgalactosamine (GalNAc) ligand then was appended to the candidate ASO to further broaden the therapeutic margin by altering the molecule's pharmacokinetics. The GalNAc conjugate, HsPCSK9-1811-LNA, was found to be at least ten times more potent in non-human primates (compared with the unconjugated counterpart), with reduced nephrotoxicity in rats. Overall, we successfully showed that our drug development scheme is better suited for selecting clinically relevant BNA-based ASOs, especially for the treatment of liver-associated diseases.
Circuit theoretical aspects of optical communication links (2015)

Three topics are addressed: Optimum frequency allocation for optical communication channels, a lumped element microwave filter with high side steepness, and a mixer with infinite third order intercept point.
Persistent Organic Pollutants and the Association with Thyroid Hormone Homeostasis in Placenta (2019)

PDS 74: Pregnancy outcomes, Exhibition Hall (PDS), Ground floor, August 26, 2019, 1:30 PM - 3:00 PM Background: Prenatal exposure to persistent organic pollutants (POPs) can interfere with thyroid hormone (TH) homeostasis, resulting in disorders in fetal and postnatal development [1]. Here we aim to develop a method for TH determination in placenta and examine the associations of THs with POPs. Methods: Liquid chromatography with quadrupole time-of-flight mass spectrometry (LC-Q-TOF-MS) method was developed for the quantification of thyroxine (T4), 3,3’,5-triiodothyronine (T3), and 3,3’,5’-triiodothyronine (rT3), 3,3’-diiodo-L-thyronine (T2), 3,5-diiodo-L-thyronine (rT2), 3-iodo-L-thyronine (T1) and 3-iodothyronamine (T1AM) in placenta [2]. Fifty-eight placenta samples were collected from a Danish birth cohort study. The levels of THs and a wide variety of POPs, including polybrominated diphenyl ethers (PBDEs), polychlorinated biphenyls (PCBs), polychlorinated dibenzo-p-dioxins/furans (PCDD/Fs), organotin chemicals (OTCs), organochlorine pesticides (OCPs) were measured. The associations between placental THs and various POPs were analyzed using multiple linear regression [3]. Results: The LC-Q-TOF-MS method developed here showed high sensitivity and selectivity. T4, T3, rT3, and T2 were measured in human placenta. Five PBDEs, 35 PCBs, 14 PCDD/Fs, 3 OTCs, 25 OCPs were also quantified. Some significant associations were observed here: a) T4 was inversely associated with BDEs 99, 100, ΣPBDE, and 2378-TCDD, and positively associated with 1234678-HpCDF; b) T3 was positively associated with 2378-TCDF and 12378-PeCDF; c) rT3 was positively associated with PCB 81, 12378-PeCDF and 234678-HxCDF, and inversely associated with tributyltin (TBT), ΣOTC, and methoxychlor (MOC). Conclusion: This study shows that POP exposures were associated with TH levels in placenta, which leads to the concerns of environmental exposure on the proper development of the fetus and children. The method here allows a comprehensive evaluation of TH homeostasis in research of environmental exposures. References: [1] P.D. Noyes, et al. Environ Sci Technol, 47 (2013) 10012-10021. [2] Z.M. Li, et al. J Chromatogr A 1534 (2017) 85-92. [3] Z.M. Li, et al. Endocrinology 159 (2018) 3473-3481.
Convolutional Random Walk Networks for Semantic Image Segmentation (2016)

Most current semantic segmentation methods rely on fully convolutional networks (FCNs). However, their use of large receptive fields and many pooling layers cause low spatial resolution inside the deep layers. This leads to predictions with poor localization around the boundaries. Prior work has attempted to address this issue by post-processing predictions with CRFs or MRFs. But such models often fail to capture semantic relationships between objects, which causes spatially disjoint predictions. To overcome these problems, recent methods integrated CRFs or MRFs into an FCN framework. The downside of these new models is that they have much higher complexity than traditional FCNs, which renders training and testing more challenging. In this work we introduce a simple, yet effective Convolutional Random Walk Network (RWN) that addresses the issues of poor boundary localization and spatially fragmented predictions with very little increase in model complexity. Our proposed RWN jointly optimizes the objectives of pixelwise affinity and semantic segmentation. It combines these two objectives via a novel random walk layer that enforces consistent spatial grouping in the deep layers of the network. Our RWN is implemented using standard convolution and matrix multiplication. This allows an easy integration into existing FCN frameworks and it enables end-to-end training of the whole network via standard back-propagation. Our implementation of RWN requires just $131$ additional parameters compared to the traditional FCNs, and yet it consistently produces an improvement over the FCNs on semantic segmentation and scene labeling.