gebhart/patrepeval huggingface dataset:
Comparison of Prokaryotic and Eukaryotic Communities in Soil Samples with and without Tomato Bacterial Wilt Collected from Different Fields (2017)

Biocontrol agents (BCA) effectively suppress soil-borne disease symptoms using natural antagonistic prokaryotes or eukaryotes. The main issue associated with the application of BCA is that disease reduction effects are unstable under different field conditions. In order to identify potentially effective BCA among several fields, we compared prokaryotic and eukaryotic communities in soil with and without tomato bacterial wilt from three different fields, each of which had the same field management and similar soil characteristics. Soil samples were collected from three fields and two depths because bacterial wilt pathogens were present in soil at a depth greater than 40 cm. We classified soil samples based on the presence or absence of the bacterial phcA gene, a key gene for bacterial wilt pathogenicity and tomato disease symptoms. Pyrosequencing of the prokaryotic 16S rRNA gene and eukaryotic internal transcribed spacer region sequences showed that the diversity and richness of the communities mostly did not correlate with disease symptoms. Prokaryotic and eukaryotic community structures were affected more by regional differences than the appearance of disease. Several prokaryotes and eukaryotes were more abundant in soil that lacked disease symptoms, and eight prokaryotes and one eukaryote of this group were commonly detected among the three fields. Some of these taxa were not previously found in disease-suppressive soil. Our results suggest that several prokaryotes and eukaryotes control plant disease symptoms.
Coordinate regulation of the human TAP1 and LMP2 genes from a shared bidirectional promoter (2020)

Recently, four genes (TAP1, TAP2, LMP2, LMP7) involved or potentially involved in the processing and transport of major histocompatibility complex class I-associated antigen to the endoplasmic reticulum have been identified. We now report the initial characterization of the bidirectional promoter for the human transporter associated with antigen processing 1 (TAP1) and low molecular mass polypeptide 2 (LMP2) genes. These genes are divergently transcribed from a central promoter region of only 593 bp. Functional analysis using a bidirectional reporter system demonstrates the minimal 593-bp promoter is sufficient for concurrent expression in both directions. There is no TATA box homology at either end but there is a prevalence of GC boxes. Transcription is initiated at multiple sites for each gene without any of the TAP1 transcripts overlapping with the LMP2 transcripts. The region proximal to the TAP1 gene is required for maximal basal level expression of not only TAP1 but also LMP2. Furthermore, this region is necessary for tumor necrosis factor alpha (TNF-alpha) induction of both genes. Site-specific mutations of an NF-kappa B element in the TAP1 proximal region blocked induction by TNF-alpha in both the TAP1 and LMP2 directions. An adjacent GC box was required for basal expression of both genes as well as augmenting the TNF-alpha induction of the distal LMP2 gene. In vivo genomic foot-printing of this region revealed strong protein/DNA interactions at the NF-kappa B and GC box consensus sequences. In vitro binding studies confirmed the capacity of the NF- kappa B site to bind p50/p65 and p52/p65 heterodimers and of the GC box to bind Sp1. Thus, the promoter elements proximal to the TAP1 gene play a significant role in regulating basal and induced expression of both TAP1 and LMP2. The findings presented in this report clearly link LMP2 expression with TAP1 expression and provide additional suggestive evidence linking LMP2 to class I antigen presentation.
Expression level and differential JAK2-V617F–binding of the adaptor protein Lnk regulates JAK2-mediated signals in myeloproliferative neoplasms (2010)

Activating mutations in signaling molecules, such as JAK2-V617F, have been associated with myeloproliferative neoplasms (MPNs). Mice lacking the inhibitory adaptor protein Lnk display deregulation of thrombopoietin/thrombopoietin receptor signaling pathways and exhibit similar myeloproliferative characteristics to those found in MPN patients, suggesting a role for Lnk in the molecular pathogenesis of these diseases. Here, we showed that LNK levels are up-regulated and correlate with an increase in the JAK2-V617F mutant allele burden in MPN patients. Using megakaryocytic cells, we demonstrated that Lnk expression is regulated by the TPO-signaling pathway, thus indicating an important negative control loop in these cells. Analysis of platelets derived from MPN patients and megakaryocytic cell lines showed that Lnk can interact with JAK2-WT and V617F through its SH2 domain, but also through an unrevealed JAK2-binding site within its N-terminal region. In addition, the presence of the V617F mutation causes a tighter association with Lnk. Finally, we found that the expression level of the Lnk protein can modulate JAK2-V617F-dependent cell proliferation and that its different domains contribute to the inhibition of multilineage and megakaryocytic progenitor cell growth in vitro. Together, our results indicate that changes in Lnk expression and JAK2-V617F-binding regulate JAK2-mediated signals in MPNs.
Generation of 6.3 ps optical pulses at a 10 GHzrepetition rate using apackaged electroabsorption modulator and dispersion compensatingfibre (1994)

Sinusoidal modulation of an MQW InGaAsP/InGaAsP EA modulator at a 10 GHz repetition rate was used to generate optical pulses of width as low as 7 ps. Pulses were linearly compressed using 400 m of dispersion compensating fibre and approximately transform limited pulses of 6.3 ps width were measured.
THE CHEMISTRY OF o-TERPHENYL. III. SULFONIC ACIDS (1949)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTHE CHEMISTRY OF o-TERPHENYL. III. SULFONIC ACIDSC. F. H. ALLEN and D. M. BURNESSCite this: J. Org. Chem. 1949, 14, 1, 163–168Publication Date (Print):January 1, 1949Publication History Published online1 May 2002Published inissue 1 January 1949https://pubs.acs.org/doi/10.1021/jo01153a023https://doi.org/10.1021/jo01153a023research-articleACS PublicationsRequest reuse permissionsArticle Views168Altmetric-Citations7LEARN 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-Alertsclose Get e-Alerts
Abstract 964: Inhibiting glycolysis with an LDHA inhibitor: A new solution to an old problem (2014)

Abstract Tumors exhibit altered metabolic profiles compared to normal, non-transformed tissues. In the presence of oxygen, most differentiated cells convert glucose to ATP by oxidative phosphorylation (OX-PHOS), whereas tumor cells consume glucose and convert it to lactate, a phenomenon known as “aerobic glycolysis” or the “Warburg effect”. There is increased interest in targeting glycolysis as a therapeutic strategy in oncology, and one of the key enzymes in this pathway is lactate dehydrogenase (LDH), which catalyzes the conversion of pyruvate to lactate in the last step of glycolysis. A small molecule LDHA inhibitor that was identified by high throughput screening was optimized to generate GNE-140, which has a biochemical EC50 of 0.005 μM and inhibits MiaPaCa-2 pancreatic cell proliferation with an EC50 of 0.25 μM. We show that inhibition of LDHA reduces carbon flux from pyruvate to lactate, impairs glycolysis, and leads to global effects in cell metabolism. Cells cease proliferation within 24 hours of LDHA inhibition, yet only undergo cell death following sustained pathway inhibition. Finally, we show that pancreatic cell lines that are resistant to LDHA inhibition can be re-sensitized to LDHA inhibition by inhibiting OX-PHOS. In conclusion, we describe a potent cell active LDHA inhibitor that modulates glycolysis, induces cell death, and that can be used to help evaluate the importance of LDHA in tumor growth. Citation Format: Thomas O'Brien, Hans Purkey, Anna Hitz, Dave Peterson, Aaron Boudreau, Christopher Delnagro, Mandy Kwong, Rebecca Hong, Min Gao, Jodi Pang, Alex Vanderbilt, Simon Williams, Laurent Salphati, Deepak Sampath, Georgia Hatzivassiliou, Marie Evangelista. Inhibiting glycolysis with an LDHA inhibitor: A new solution to an old problem. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 964. doi:10.1158/1538-7445.AM2014-964
Optimizing the MPEG-4 encoder-advanced diamond zonal search (2002)

Motion estimation (ME) is an important part of the MPEG-4 encoder, due to its significant impact on the bitrate and the output quality of the encoded sequence. Unfortunately this feature occupies a significant part of the encoding time especially when using the straightforward full search (FS) algorithm. The diamond search (DS) was recently accepted as a fast motion estimation algorithm for the MPEG-4 VM. In this paper we propose a new algorithm named advanced diamond zonal search (ADZS), which is significantly faster than DS (in terms of number of checking points and total encoding time) and gives similar, if not better, quality (in terms of PSNR) of the output sequence. This is more obvious in the high bit rate cases. Our experiments verify the superiority of the proposed algorithm.
Design of a Smart Device with Fuzzy Multi-criteria Group Decision Making System for The Elderly (2021)

Fuzzy Multi-criteria Group Decision-Making Systems (FMCGDMS) allow complex decision making comprising of more than one domain of knowledge for specific problems. This paper proposes the design of a prototype intelligent device named SmartPiant that will allow the monitoring of routine activities of the elderly who live independently or spend much of their time alone, through measurable variables represented by sensors and actuators. Sensors and actuators are connected to an embedded system (Raspberry Pi), which internally contains the fuzzy multi-criteria system for making complex decisions regarding the performance of the elderly in activities related to three objectives. The objectives covered are: well-being, which encourages older people to have physical and virtual interaction with family or friends, and perform mind exercises through a mobile application; health which focuses on reminding older adults to consume their medications on time using an alarm and maintain physical activity and security which determines if the older adult is in a risky situation based on input from a panic button and issues an alert. The system's actuators will emit a stimulus specific to each critical objective based on assessing performance using a colour coded scheme. The system is evaluated on specific use case scenarios.
Turbo1500: Core-Based Design for Test and Diagnosis (2009)

Tool support is crucial in widespread adoption of a standard. This article describes a set of tools and associated flow for DFT insertion and test generation based on IEEE Std 1500.
Pellet-fueled I-mode plasmas in ASDEX Upgrade (2023)

Abstract This letter reports on the efforts carried out at the ASDEX Upgrade tokamak to integrate I-mode plasmas with pellet fueling and to increase the I-mode Greenwald fraction <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:msub> <mml:mi>f</mml:mi> <mml:mrow> <mml:mrow> <mml:mi mathvariant="normal">G</mml:mi> <mml:mi mathvariant="normal">W</mml:mi> </mml:mrow> </mml:mrow> </mml:msub> </mml:math> , two important requirements for any DEMO operational scenario. For the first time, stationary I-mode plasmas have been achieved with pellet fueling and the core Greenwald fraction has been increased up to 0.8. Larger <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:msub> <mml:mi>f</mml:mi> <mml:mrow> <mml:mrow> <mml:mi mathvariant="normal">G</mml:mi> <mml:mi mathvariant="normal">W</mml:mi> </mml:mrow> </mml:mrow> </mml:msub> </mml:math> were not achieved due to technical constraints rather than to a physics-based limit. Pellet-fueled I-mode plasmas exhibit enhanced core and edge density, while core and edge temperature are reduced. Nonetheless, edge normalized gradients remain I-mode-like, namely shallow for the density and steep for the temperature. The I-mode energy confinement time is found to obey two distinct density dependencies: for <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:msub> <mml:mi>f</mml:mi> <mml:mrow> <mml:mrow> <mml:mi mathvariant="normal">G</mml:mi> <mml:mi mathvariant="normal">W</mml:mi> </mml:mrow> </mml:mrow> </mml:msub> <mml:mo>&lt;</mml:mo> <mml:mn>0.4</mml:mn> </mml:math> it rises with increasing <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:msub> <mml:mi>f</mml:mi> <mml:mrow> <mml:mrow> <mml:mi mathvariant="normal">G</mml:mi> <mml:mi mathvariant="normal">W</mml:mi> </mml:mrow> </mml:mrow> </mml:msub> </mml:math> , while for <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:msub> <mml:mi>f</mml:mi> <mml:mrow> <mml:mrow> <mml:mi mathvariant="normal">G</mml:mi> <mml:mi mathvariant="normal">W</mml:mi> </mml:mrow> </mml:mrow> </mml:msub> <mml:mo>&gt;</mml:mo> <mml:mn>0.4</mml:mn> </mml:math> the energy confinement time plateaus with increasing <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:msub> <mml:mi>f</mml:mi> <mml:mrow> <mml:mrow> <mml:mi mathvariant="normal">G</mml:mi> <mml:mi mathvariant="normal">W</mml:mi> </mml:mrow> </mml:mrow> </mml:msub> </mml:math> , or even decreases with <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:msub> <mml:mi>f</mml:mi> <mml:mrow> <mml:mrow> <mml:mi mathvariant="normal">G</mml:mi> <mml:mi mathvariant="normal">W</mml:mi> </mml:mrow> </mml:mrow> </mml:msub> </mml:math> for the pellet-fueled plasmas. Similarities with Ohmic and L-mode energy confinement time dependency on density are discussed.
Role of Detergents in Conformational Exchange of a G Protein-coupled Receptor (2012)

The G protein-coupled β(2)-adrenoreceptor (β(2)AR) signals through the heterotrimeric G proteins G(s) and G(i) and β-arrestin. As such, the energy landscape of β(2)AR-excited state conformers is expected to be complex. Upon tagging Cys-265 of β(2)AR with a trifluoromethyl probe, (19)F NMR was used to assess conformations and possible equilibria between states. Here, we report key differences in β(2)AR conformational dynamics associated with the detergents used to stabilize the receptor. In dodecyl maltoside (DDM) micelles, the spectra are well represented by a single Lorentzian line that shifts progressively downfield with activation by appropriate ligand. The results are consistent with interconversion between two or more states on a time scale faster than the greatest difference in ligand-dependent chemical shift (i.e. >100 Hz). Given that high detergent off-rates of DDM monomers may facilitate conformational exchange between functional states of β(2)AR, we utilized the recently developed maltose-neopentyl glycol (MNG-3) diacyl detergent. In MNG-3 micelles, spectra indicated at least three distinct states, the relative populations of which depended on ligand, whereas no ligand-dependent shifts were observed, consistent with the slow exchange limit. Thus, detergent has a profound effect on the equilibrium kinetics between functional states. MNG-3, which has a critical micelle concentration in the nanomolar regime, exhibits an off-rate that is 4 orders of magnitude lower than that of DDM. High detergent off-rates are more likely to facilitate conformational exchange between distinct functional states associated with the G protein-coupled receptor.
Multicolor fluorescence images and fluorescence ratio images of green apples at harvest and during storage (2012)

With a multicolor fluorescence imaging system the fluorescence images of freshly harvested light-green apples were measured in the four major fluorescence bands of green plant tissue, i.e., the fluorescence bands F440 (blue), F520 (green), F690 (red), and F740 (far-red). By a pixel-to-pixel division of the fluorescence images we also determined the fluorescence ratio images blue/green (F440/F520), blue/red (F440/F690), and blue/far-red (F440/F740), as well as the chlorophyll fluorescence ratio red/far-red (F690/F740). In addition, the changes of fluorescence yield in the four fluorescence bands and of the fluorescence ratios were studied during the storage and ripening of Braeburn apples during 2,3, and 6 months at standard conditions of 4 °C and 90% relative humidity. The blue and green fluorescence bands increased during storage and ripening, whereas the far-red band continuously declined with decreasing chlorophyll content. In contrast, the intensity of the red chlorophyll fluorescence band F690 slight...
An Effective New Intestinal Anastomosis Method (2016)

BACKGROUND This study aimed to establish an easy, safe, and cost-saving intestinal anastomotic method. MATERIAL AND METHODS Between January 2014 and February 2016, a total of 150 patients with gastric cancer who underwent surgery in the Department of General Surgery of Xuzhou Medical University Affiliated Hospital were divided into 2 groups: the treatment group (80) using new hand-sewn anastomoses, and the control group (70) using stapled anastomoses. Briefly, a new hand-sewn anastomosis of continuous suture without inversion was performed, with the first layer encompassing the entire layer of the intestinal wall. The edge was about 5 mm, and the stitch spacing was about 6 mm. Continuous suturing was performed only in the seromuscular layer of intestinal wall for the second layer, with the same edge and stitch spacing as the first layer. All 70 patients in the control group underwent intestinal stapled anastomoses. Surgical anastomotic time and cost, postoperative anastomotic bleeding, leakage, and stricture were recorded and analyzed. RESULTS The surgical anastomotic time using the new method was relatively short compared with the control group (8±1.6 min vs. 9±2.8 min), and the cost of anastomosis using the new method was significantly lower compared to the control group ($30±6.8 vs. $1000±106.2). The new method exhibited lower anastomotic bleeding (0/80 vs. 2/70) and anastomotic leakage (0/80 vs. 1/70), but similar anastomotic stricture (0/80 vs. 0/70). CONCLUSIONS Our results suggest the new hand-sewn intestinal anastomosis is a safe, easy-to-learn, cost-saving, and time-saving method that also avoids some of the drawbacks of the stapled anastomoses.
Molecular cloning and expression of a novel glycolipid sulfotransferase in Mycobacterium tuberculosis The GenBank/EMBL/DDBJ accession number for the sequence (gene Rv1373) reported in this paper is Z81011. (2002)

Sulfated trehalose glycolipids are among the most characteristic cell wall molecules of virulent strains of Mycobacterium tuberculosis. They comprise a family of trehalose-2-sulfate esters with an array of acyl fatty acids at various positions of the trehalose moiety. Although their structure has been well characterized, most of the enzymes involved in their biosynthesis, such as sulfotransferases, are unknown. It is demonstrated here by metabolic labelling with 35S abundant incorporation into sulfolipids of M. tuberculosis strains, in comparison to Mycobacterium avium, Mycobacterium bovis BCG and Mycobacterium smegmatis. The most abundant sulfolipid, sulfolipid I, is present in virulent strains H37Rv and Erdman, but absent in attenuated H37Ra. Sulfotransferase assays with the donor substrate 3'-phosphoadenosine-5'-[35S]phosphosulfonate and whole cell lysates of H37Ra resulted in the synthesis of four major sulfolipids (I, II, IV and VI). A search for sulfotransferase gene sequences in M. tuberculosis yielded gene Rv1373, a 981 bp gene slightly homologous (24% identity) to eukaryotic aryl-sulfotransferases. Rv1373 was cloned by PCR and expressed as a 39 kDa recombinant his-tagged protein. The recombinant M. tuberculosis aryl-sulfotransferase exhibited activity towards the cerebroside glycolipids glucosyl- and galactosylceramide. No activity was detected with sulfatide (3'-sulfated galactosylceramide), suggesting that sulfation of galactosylceramide may occur at C-3 of the galactose. Treatment of sulfated products with ceramide glycanase resulted in the release of 35S-labelled material showing that sulfation was at the saccharide moiety (galactose or glucose) of the ceramide. Assays with the M. tuberculosis aryl-sulfotransferase and total H37Ra glycolipids showed one major product corresponding to sulfolipid IV. These results demonstrate that Rv1373 encodes a novel glycolipid sulfotransferase with activity towards typical ceramide glycolipids and mycobacterial trehalose glycolipids.
Ligands containing alternating 2,6-linked pyridine and 2,5-linked thiophene units 1 (1998)

A variety of linear assemblies of alternating pyridine (2,6-linked) [P] and thiophene (2,5-linked) [T] units have been generated with up to seven units and their macrocyclisation investigated. The optimal methods involved the palladium(>0>) catalysed reaction of thienyl Grignard reagents with bromopyridines. In this way were made TPT, TPTPT, TPTPTPT, BrPTPBr and various XCH2PTPTPCH2X derivatives (X = H, Br, OH, OR and SBu-t). Alternative routes whereby pyridine units were 2,6-linked by CH2SCH2 units, with the intention of converting the bridge groups into thiophenes by a Hinsberg reaction, were also studied. The latter products {(HOCH2[P]CH2)2S and (HOCH2[P]CH2SCH2)2[P]} proved to be highly effective ligands for transition metals, especially divalent ones such as Co2+, Ni2+ and Zn2+. No macrocyclisations were effective.
Structure and closure of connexin gap junction channels (2014)

Connexin gap junctions comprise assembled channels penetrating two plasma membranes for which gating regulation is associated with a variety of factors, including voltage, pH, Ca(2+), and phosphorylation. Functional studies have established that various parts of the connexin peptides are related to channel closure and electrophysiology studies have provided several working models for channel gating. The corresponding structural models supporting these findings, however, are not sufficient because only small numbers of closed connexin structures have been reported. To fully understand the gating mechanisms, the channels should be visualized in both the open and closed states. Electron crystallography and X-ray crystallography studies recently revealed three-dimensional structures of connexin channels in a couple of states in which the main difference is the conformation of the N-terminal domain, which have helped to clarify the structure in regard to channel closure. Here the closure models for connexin gap junction channels inferred from structural and functional studies are described in the context of each domain of the connexin protein associated with gating modulation.