gebhart/patrepeval huggingface dataset:
Iron-oxo aggregates. Crystal structures and solution characterization of 2-hydroxy-1,3-xylylenediaminetetraacetic acid complexes (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIron-oxo aggregates. Crystal structures and solution characterization of 2-hydroxy-1,3-xylylenediaminetetraacetic acid complexesBruce P. Murch, Fontaine C. Bradley, Paul D. Boyle, Vasilios Papaefthymiou, and Lawrence Que Jr.Cite this: J. Am. Chem. Soc. 1987, 109, 26, 7993–8003Publication Date (Print):December 1, 1987Publication History Published online1 May 2002Published inissue 1 December 1987https://pubs.acs.org/doi/10.1021/ja00260a009https://doi.org/10.1021/ja00260a009research-articleACS PublicationsRequest reuse permissionsArticle Views597Altmetric-Citations84LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Transcriptional regulation of plant sugar transporter genes by beneficial rhizobacteria (2021)

In their natural environment, plants live in close interaction with complex populations of microorganisms, including rhizobacteria species commonly referred to as ‘Plant Growth Promoting Rhizobacteria’ (PGPR). A growing body of evidence demonstrates the importance of sugar transport in plant pathogen resistance and in plant-microorganism mutualistic symbioses. Using an in vitro experimental system, including the model plant species Arabidopsis thaliana, two PGPR strains (Pseudomonas simiae PICF7 and Burkholderia phytofirmans PsJN) and a non-PGPR strain (Escherichia coli), we conducted a comprehensive set of phenotypic and gene expression analyses to explore the role and regulation of sugar transporter genes in plant-PGPR interactions. In physical contact with the seedling roots, or solely via the emission of bacterial volatile compounds, the two PGPR strains tested improved the growth and development of the Arabidopsis seedlings and altered the expression of several plant sugar transporter genes. Our results also revealed both conserved and strain-specific transcriptional regulation mechanisms.
Inhibition of CTLA-4 Function by the Regulatory Subunit of Serine/Threonine Phosphatase 2A (2002)

The catalytic subunit of the serine/threonine phosphatase 2A (PP2A) can interact with the cytoplasmic tail of CTLA-4. However, the molecular basis and the biological significance of this interaction are unknown. In this study, we report that the regulatory subunit of PP2A (PP2AA) also interacts with the cytoplasmic tail of CTLA-4. Interestingly, TCR ligation induces tyrosine phosphorylation of PP2AA and its dissociation from CTLA-4 when coligated. The association between PP2AA and CTLA-4 involves a conserved three-lysine motif in the juxtamembrane portion of the cytoplasmic tail of CTLA-4. Mutations of these lysine residues prevent the binding of PP2AA and enhance the inhibition of IL-2 gene transcription by CTLA-4, indicating that PP2A represses CTLA-4 function. Our data imply that the lysine-rich motif in CTLA-4 may be used to identify small molecules that block its binding to PP2A and act as agonists for CTLA-4 function.
Occurrence of tumor antigen pRL1a specific CD8 T cells in spleen cells from syngeneic BALB/c, semiallogeneic (BALB/c x C57BL/6)F1 and allogeneic C57BL/6 mice (2002)

We investigated the generation of CD8 cytotoxic T-lymphocytes (CTL) that recognized a dominant pRL1a peptide bound to H-2L(d) molecule on RL male 1 leukemia in spleen cells from RL male 1-bearing syngeneic BALB/c, semiallogeneic CB6F1 and allogeneic B6 mice by repetitive in vitro stimulation with RL male 1 tumor. CD8 T cells in cultures were also analyzed by H-2L(d)/pRL1a tetramer staining. We showed that pRL1a-specific CTL were more efficiently generated in spleen cells from RL male 1-bearing high responder CB6F1 mice than in low responder BALB/c mice, and this correlated well with the occurrence of H-2L(d)/pRL1a tetramer binding CD8 T cells. Furthermore, we showed that in spleen cells from RL male 1-bearing allogeneic B6 mice, H-2L(d)/pRL1a complex specific CD8 T cells were present at a significant frequency. H-2L(d)/pRL1a recognizing B6 CTL but not BALB/c or CB6F1 CTL gradually lost CD8 expression on their surface by multiplication of in vitro stimulation.
A stereospeifically<sup>18</sup>O-labelled deoxydinucleoside phosphate block for incorporation into an oligonucleotide (1983)

Fully protected diastereoisomers of deoxyguanylyl (3' leads to 5') deoxyadenosine stereospecifically labelled on phosphorus with oxygen-18 have been synthesized by oxidation of phosphite triester intermediates in the presence of 18O-labelled water. The diastereoisomers have been chromatographically separated and their absolute configuration at phosphorus determined. (Rp)-[18O]deoxyguanylyl (3' leads to 5')deoxyadenosine has been prepared by complete deprotection of the parent diastereoisomer of the Sp configuration. Methylation of the former compound permits assignment of the absolute configurations of the methyl esters of N1-methyldeoxyguanylyl (3' leads to 5') N1-methyldeoxyadenosine.
A High Dose of Dietary Berberine Improves Gut Wall Morphology, Despite an Expansion of <i>Enterobacteriaceae</i> and a Reduction in Beneficial Microbiota in Broiler Chickens (2023)

Phytogenic products are embraced as alternatives to antimicrobials, and some are known to mitigate intestinal inflammation and ensure optimal gut health and performance in broiler chickens. Dietary inclusion of berberine, a benzylisoquinoline alkaloid found in plants, is believed to exert gut health-promoting effects through modulation of the gut microbiota; however, there are only a few studies investigating its effects in chickens. The aim of this study was to investigate the interplay between dietary supplementation of a high concentration of berberine, the gastrointestinal microbiota, and histomorphological parameters in the gut. Berberine was shown to increase villus length and decrease crypt depth and CD3<sup>+</sup> T-lymphocyte infiltration in the gut tissue of chickens at different ages. Berberine affected the diversity of the gut microbiota from the jejunum to the colon, both at a compositional and functional level, with larger effects observed in the large intestine. A high concentration of berberine enriched members of the <i>Enterobacteriaceae</i> family and depleted members of the <i>Ruminococcaceae</i>, <i>Lachnospiraceae</i>, and <i>Peptostreptococcaceae</i> families, as well as tended to reduce butyrate production in the cecum. <i>In vivo</i> results were confirmed by <i>in vitro</i> growth experiments, where increasing concentrations of berberine inhibited the growth of several butyrate-producing strains while not affecting that of <i>Enterobacteriaceae</i> strains. Positive correlations were found between berberine levels in plasma and villus length or villus-to-crypt ratio in the jejunum. Our study showed that berberine supplementation at a high concentration improves chicken gut morphology toward decreased inflammation, which is likely not mediated by the induced gut microbiota shifts. <b>IMPORTANCE</b> Dietary additives are widely used to reduce intestinal inflammation and enteritis, a growing problem in the broiler industry. Berberine, with anti-inflammatory, antioxidant, and antimicrobial activity, would be an interesting feed additive in this regard. This study investigates for the first time the impact of berberine supplementation on the chicken gastrointestinal microbiota, as a potential mechanism to improve gut health, together with histological effects in the small intestine. This study identified a dose-effect of berberine on the gut microbiota, indicating the importance of finding an optimal dose to be used as a dietary additive.
Time-domain electromagnetic plane waves in static and dynamic conducting media. II (1995)

For pt.I see ibid., vol.36, no.3, p.221 (1994). The electromagnetic field inside a lossy half-space for the case of a transient electromagnetic plane wave impinging on the half-space from free space is derived. The losses in the half-space are modeled by assuming either a static (J=/spl sigma/E) or a dynamic (/spl tauspl part/Jspl part/t+J=/spl sigmasub 0/E) conducting medium. Solutions are derived directly from the first order system of partial differential equations, i.e. the Maxwell equations. Plots for the total fields at the half-space boundary are given and expressions for the fields anywhere inside the half-space based on these boundary fields are given. Asymptotic formulae for late and early times are derived for the case of a step function as well as a square pulse plane wave.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Statistical Considerations in Designing Tests of Mine Detection Systems: 1 - Measures Related to the Probability of Detection (1998)

One of the primary metrics used to gauge the performance of mine detection systems is PD, the probability of detecting an actual mine that is encountered by the sensor. In this report statistical issues and techniques that are relevant to the estimation of PD are discussed. Appropriate methods are presented for summarizing the performance of a single detection system, for comparing different systems, and for determining the sample size (number of target mines) required for a desired degree of precision. References are provided to pertinent sources within the extensive literature on statistical estimation and experimental design. A companion report addresses the estimation of detection system false alarm rates.
Campylobacter upsaliensis gastroenteritis in childhood (1999)

C. upsaliensis is a rare cause of gastroenteritis in young children and, compared with C. jejuni infection, is associated with significantly lower rates of fever, acute diarrhea and rectal bleeding.
Relationship Among Peripheral Leukocyte Counts, Etiologic Agents and Clinical Manifestations in Acute Otitis Media (2004)

Significantly higher leukocyte counts and ANCs were found in pneumococcal AOM than in AOM caused by H. influenzae or in culture-negative AOM. A significant decrease in leukocyte counts was found during antibiotic therapy for AOM, regardless of etiology and bacteriologic outcome. Isolation of S. pneumoniae and fever were each significantly associated with increased peripheral leukocyte and ANCs.
Synthetic Peptides Analogue to Enamel Proteins Promote Osteogenic Differentiation of MC3T3-E1 and Mesenchymal Stem Cells (2011)

Regulation of biomineralization processes are mediated by extracellular matrix proteins that often exhibit proline-rich regions. Advanced bioinformatic methods were used to design the structure of artificial peptides (P1, P2, P3) based on proline-rich domains of extracellular proteins. Their effect on osteoblast differentiation and in vitro biomineralization was tested on MC3T3-E1 and human umbilical cord mesenchymal stem cells (hUCMSCs) and compared to the commercially available enamel matrix derivative (EMD). MC3T3-E1 and hUCMSCs treated with the synthetic peptides showed a decreased cytotoxicity after 24-48 h of treatment compared to control. MC373-E1 cells treated with EMD showed lower expression of osteoblast markers genes than cells treated with P2, except for collagen type I. In hUCMSCs, OC gene expression was higher in P2-treated cells compared to those treated with EMD or control. ALP activity was markedly increased in MC3T3-E1 cells incubated with P2 compared to other treatments. Similar results were observed in hUCMSCs. Further, P2 increased calcium deposition rate compared to EMD or control either in MC3T3-E1 or hUCMSCs. The observed effects of proline-rich peptides hold potential for both clinical applications and as a research tool in further investigations of the molecular basis of induced osteogenic cell differentiation.
Supplementary Tables S5 and S6 from A Novel RAF Kinase Inhibitor with DFG-Out–Binding Mode: High Efficacy in BRAF-Mutant Tumor Xenograft Models in the Absence of Normal Tissue Hyperproliferation (2023)

&lt;p&gt;Analysis of mouse tissues and exploratory toxicological assessment in rats revealed a favorable rodent safety profile for BI 882370.&lt;/p&gt;
Data prefetching for software DSMs (1998)

In this paper we propose and evaluate the Adaptive++ technique, a novel runtime-only data prefetching strategy for software-based distributed shared-memory systems (software DSMs). Adaptive++ improves the performance of regular parallel applications running on software DSMs by using the past history of memory access faults to adapt between repeated-phase and repeated-stride prefetching modes. Adaptive++ does not issue prefetches during periods when the application is not exhibiting one of these two types of behavior and is thus behaving irregularly. Through detailed execution-driven simulations of several applications, we show that our prefetching technique is very successful at reducing the data access overheads of regular applications running on the TreadMarks software DSM. Adaptive++ also reduces the overhead of applications that are not strictly regular but that exhibit periods of regularity. In terms of overall performance, our results show that Adaptive++ can provide speedup improvements as significant as 34% on 16 processors. A direct comparison against two runtime-only prefetching techniques proposed thus far shows that Adaptive++ is consistently competitive in terms of performance, while being able to optimize a larger set of applications. Our main conclusion is that Adaptive++ should definitely be considered by software DSM designers as an effective way of tolerating the overhead of remote data accesses.
Additive Manufacturing of Recycled Composites (2022)

Abstract An additive remanufacturing process for mechanically recycled glass fibers and thermally recycled carbon fibers was developed. The main purpose was to demonstrate the feasibility of an additive remanufacturing process starting from recycled glass and carbon fibers to obtain a new photo- and thermally-curable composite. 3D printable and UV-curable inks were developed and characterized for new ad-hoc UV-assisted 3D printing apparatus. Rheological behavior was investigated and optimized considering the 3D printing process, the recyclate content, and the level of dispersion in the matrix. Some requirements for the new formulations were defined. Moreover, new printing apparatuses were designed and modified to improve the remanufacturing process. Different models and geometries were defined with different printable ink formulations to test material mechanical properties and overall process quality on the final pieces. To sum up, 3D printable inks with different percentages of recycled glass fiber and carbon fiber reinforced polymers were successfully 3D printed.
Bit-Interleaved Time-Space Codes for Fading Channels (2000)

Bit-interleaved coded modulation (BICM) is known to provide a robust solution to the coding prob- lem for wireless channels, as it provides at the same time a large Hamming distance and a large (albeit nonoptimum) Euclidean distance. As BICM splits the code design into the selection of the encoder and the selection of a modula- tion scheme, the design task is simpler than with standard space-time codes. In this paper we investigate the performance of BICM over a multiple-antenna channel by evaluating its information-theoretic limits. Further, we provide some design guidelines and we check our results via some simulations.
ChemInform Abstract: Regio‐ and Chemoselective Multiple Functionalization of Chloropyrazine Derivatives. Application to the Synthesis of Coelenterazine. (2009)

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 of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
A Method for Fast, High-Precision Characterization of Synthetic Biology Devices (2012)

Engineering biological systems with predictable behavior is a founda-tional goal of synthetic biology. To accomplish this, it is important to accurately characterize the behavior of biological devices. Prior charac-terization efforts, however, have generally not yielded enough high-quality information to enable compositional design. In the TASBE (A Tool-Chain to Accelerate Synthetic Biological Engineering) project we have developed a new characterization technique capable of producing such data. This document describes the techniques we have developed, along with exam-ples of their application, so that the techniques can be accurately used by others.
Virtual I/O caching (2011)

A leading cause of reduced or unpredictable application performance in distributed systems is contention at the storage layer, where resources are multiplexed among many concurrent data intensive workloads. We target the shared storage cache, used to alleviate disk I/O bottlenecks, and propose a new caching paradigm to both improve performance and reduce memory requirements for HPC storage systems.
Phosphorylation of SDT repeats in the MDC1 N terminus triggers retention of NBS1 at the DNA damage–modified chromatin (2008)

DNA double-strand breaks (DSBs) trigger accumulation of the MRE11-RAD50-Nijmegen breakage syndrome 1 (NBS1 [MRN]) complex, whose retention on the DSB-flanking chromatin facilitates survival. Chromatin retention of MRN requires the MDC1 adaptor protein, but the mechanism behind the MRN-MDC1 interaction is unknown. We show that the NBS1 subunit of MRN interacts with the MDC1 N terminus enriched in Ser-Asp-Thr (SDT) repeats. This interaction was constitutive and mediated by binding between the phosphorylated SDT repeats of MDC1 and the phosphate-binding forkhead-associated domain of NBS1. Phosphorylation of the SDT repeats by casein kinase 2 (CK2) was sufficient to trigger MDC1-NBS1 interaction in vitro, and MDC1 associated with CK2 activity in cells. Inhibition of CK2 reduced SDT phosphorylation in vivo, and disruption of the SDT-associated phosphoacceptor sites prevented the retention of NBS1 at DSBs. Together, these data suggest that phosphorylation of the SDT repeats in the MDC1 N terminus functions to recruit NBS1 and, thereby, increases the local concentration of MRN at the sites of chromosomal breakage.
SETDB1 prevents TET2-dependent activation of IAP retroelements in naïve embryonic stem cells (2018)

Our results demonstrate a novel and unexpected role for SETDB1 in protecting IAPs from TET2-dependent histone arginine demethylation.
A mechanistic investigation of the three-component radical photoinitiator system Eosin Y spirit soluble,N-methyldiethanolamine, and diphenyliodonium chloride (2001)

Photo-DSC and in situ, time-resolved, laser-induced, steady-state fluorescence spectroscopy were used to study the initiation mechanism of the three-component system: Eosin Y spirit soluble (EYss), N-methyldiethanolamine, and diphenyliodonium chloride. Kinetic studies based on photo-DSC revealed that the fastest polymerization occurred when all three components were present (the next fastest was with the dye/amine pair, and the slowest was with the dye/iodonium pair). However, the laser-induced fluorescence experiments showed that the pairwise reaction between the eosin and iodonium bleaches the dye much more rapidly than does the reaction between the eosin and amine. We concluded that although a direct eosin/amine reaction can produce active radicals in the three-component system, this reaction is largely overshadowed by the eosin/iodonium reaction, which does not produce active radicals as effectively. We proposed that the amine reduces the oxidized dye radical formed in the eosin/iodonium reaction back to its original state as well as the simultaneous production of an active initiating amine-based radical. Because of the difference in the pairwise reaction rates for eosin/amine and eosin/iodonium, it is likely that this regeneration reaction was the primary source of active radicals in the three-component eosin/amine/iodonium system. © 2001 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 39: 715–723, 2001
Extracellular Vesicles of Mesenchymal Stromal Cells Can be Taken up by Microglial Cells and Partially Prevent The Stimulation Induced by β-Amyloid (2021)

Abstract Mesenchymal stromal/stem cells (MSCs) have great capacity for immune regulation. MSCs provide protective paracrine effects, which are partially exerted by extracellular vesicles (EVs). It has been reported that MSCs-derived EVs (MSC-EVs) contain soluble factors, such as cytokines, chemokines, growth factors and even microRNAs, which confer them similar anti-inflammatory and regenerative effects to MSCs. Moreover, MSCs modulate microglia activation through a dual mechanism of action that relies both on cell contact and secreted factors. Microglia cells are the central nervous system immune cells and the main mediators of the inflammation leading to neurodegenerative disorders. Here, we investigated whether MSC-EVs affect the activation of microglia cells by β-amyloid aggregates. We show that the presence of MSC-EVs can prevent the upregulation of pro-inflammatory mediators such as tumor necrosis factor (TNF)-α and nitric oxide (NO). Both are up-regulated in neurodegenerative diseases representing chronic inflammation, as in Alzheimer’s disease. We demonstrate that MSC-EVs are internalized by the microglia cells. Further, our study supports the use of MSC-EVs as a promising therapeutic tool to treat neuroinflammatory diseases.