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Query: "author" (James S. T'ien) .

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1.
General position polynomials
Vesna Iršič, Sandi Klavžar, Gregor Rus, James Tuite, 2024, original scientific article

Abstract: A subset of vertices of a graph $G$ is a general position set if no triple of vertices from the set lie on a common shortest path in $G$. In this paper we introduce the general position polynomial as $\sum_{i \geq 0} a_i x^i$, where $a_i$ is the number of distinct general position sets of $G$ with cardinality $i$. The polynomial is considered for several well-known classes of graphs and graph operations. It is shown that the polynomial is not unimodal in general, not even on trees. On the other hand, several classes of graphs, including Kneser graphs $K(n,2)$, with unimodal general position polynomials are presented.
Keywords: general position set, general position number, general position polynomial, unimodality, trees, Cartesian product of graphs, Kneser graphs
Published in DiRROS: 28.02.2024; Views: 135; Downloads: 93
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2.
Efficacy of trapping protocols for Agrilus jewel beetles : a multi-country assessment
Giacomo Santoiemma, David Williams, Everett G. Booth, Giacomo Cavaletto, James Connell, Gianfranco Curletti, Maarten De Groot, Sarah M. Devine, Abigail Enston, Joseph A. Francese, Eva Groznik, Tine Hauptman, 2024, original scientific article

Abstract: The genus Agrilus is one of the most diverse insect genera worldwide. The larval feeding activity causes extensive damage in both forests and orchards. In addition, more than 30 species have been introduced outside their native range so far, including the emerald ash borer Agrilus planipennis Fairmaire. Thus, the availability of efficient trapping protocols for early detection of Agrilus species at entry points is of utmost importance. In this study we tested whether trapping protocols developed for surveillance of A. planipennis in North America were also effective for other Agrilus species. In particular, through a multi-country assessment we compared the efficacy of detecting Agrilus species on: (i) green glue-coated prism traps vs. green Fluon-coated multi-funnel traps when baited with the green leaf volatile (Z)-3-hexenol or left unbaited; and (ii) green multi-panel traps vs. green multi-panel traps baited with dead adult Agrilus beetles (decoys). A total of 23,481 individuals from 45 Agrilus species were caught. Trap design significantly affected both species richness and abundance of Agrilus species in several of the countries where the trapping experiments were carried out, and green prism traps outperformed green multi-funnel traps in most cases. On the contrary, the addition of a (Z)-3-hexenol lure or dead adult beetle decoys on to traps did not improve trap catches. Our study highlights that reliable trap models to survey Agrilus species are already available, but also that there is the clear need to further investigate chemical ecology of Agrilus species to develop semiochemical lures that can improve detection efficacy.
Keywords: biosecurity, early detection, forest pests, lures, traps, visual stimuli, Agrilus, beetles
Published in DiRROS: 19.01.2024; Views: 223; Downloads: 181
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3.
The effect of duct size, sample size, and fuel composition on concurrent flame spread over large cellulose samples in microgravity
Sandra L. Olson, Gary A. Ruff, Paul V. Ferkul, Jay C. Owens, John Easton, Ya-Ting T. Liao, James S. T'ien, Balazs Toth, Grunde Jomaas, A. Carlos Fernandez-Pello, Guillaume Legros, Augustin Guibaud, Osamu Fujita, Nikolay Smirnov, David L. Urban, 2023, original scientific article

Abstract: Concurrent flame spread data for thermally-thin charring solid fuels are presented from Saffire and BASS experiments performed in habitable spacecraft for three duct sizes, five sample sizes, two materials, and two atmospheres. The flame spread rates and flame lengths were strongly affected by duct size even for the relatively large ducts (> 30 cm tall). A transient excess pyrolysis length (i.e., flame length overshoot) was observed for the cotton fabric that burned away, which indicates that the transient excess pyrolysis length phenomenon is caused by more than just the flame moving into the developing boundary layer thickness as was the case with the SIBAL sample. A burnout time, defined as the pyrolysis length divided by the flame spread rate, normalized the pyrolysis length histories into a single curve with a steady burnout time of 22 s for the SIBAL fabric. The transient excess pyrolysis length is hypothesized to be a post-ignition flame growth transient for the essentially two-dimensional flames where the burnout time becomes very long until the preheat and pyrolysis lengths develop. The three-dimensional flames over narrow samples have lateral thermal expansion and lateral oxygen diffusion which allows them to transition to a steady state length without the transient excess pyrolysis length. Surface temperature profiles, nondimensionalized by the pyrolysis length, indicate that the temperature profiles exhibit the same shape across the pyrolysis zone. A surface energy balance calculation in the preheat region revealed that the heat flux increased rapidly at the pyrolysis front to near the critical heat flux for ignition. An estimate of the acceleration of the inviscid core flow in the duct due to thermal expansion and developing boundary layers on the duct walls and the SIBAL sample surface seems to explain the observed spread rate trends across three duct sizes and multiple sample sizes.
Keywords: concurrent flame spread, microgravity, duct size, sample size, cellulose fabrics
Published in DiRROS: 08.01.2024; Views: 186; Downloads: 38
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4.
Between but not within-species variation in the distribution of fitness effects
Jennifer James, Chedly Kastallya, Katharina Budde, Santiago C. González-Martínez, Pascal Milesi, Tanja Pyhäjärvi, Martin Lascoux, 2023, original scientific article

Abstract: New mutations provide the raw material for evolution and adaptation. The distribution of fitness effects (DFE) describes the spectrum of effects of new mutations that can occur along a genome, and is, therefore, of vital interest in evolutionary biology. Recent work has uncovered striking similarities in the DFE between closely related species, prompting us to ask whether there is variation in the DFE among populations of the same species, or among species with different degrees of divergence, that is whether there is variation in the DFE at different levels of evolution. Using exome capture data from six tree species sampled across Europe we characterized the DFE for multiple species, and for each species, multiple populations, and investigated the factors potentially influencing the DFE, such as demography, population divergence, and genetic background. We find statistical support for the presence of variation in the DFE at the species level, even among relatively closely related species. However, we find very little difference at the population level, suggesting that differences in the DFE are primarily driven by deep features of species biology, and those evolutionarily recent events, such as demographic changes and local adaptation, have little impact.
Keywords: DFE, deleterious mutations, population structure, forest trees
Published in DiRROS: 12.12.2023; Views: 271; Downloads: 111
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5.
Integrating geological data in Europe to foster multidisciplinary research
Marc Urvois, Sylvain Grellet, Henning Lorenz, Rainer Haener, Christelle Loiselet, Matthew Harrison, Matija Krivic, Christian Brogaard Pedersen, Marianne B. Wiese, Amelia Baptie, Martin Nayembil, James Trench, Ivor Marsh, Carlo Cipolloni, Chiara d'Ambrogi, Maria Pia Congi, 2022, original scientific article

Abstract: This paper presents novel data discovery and integration, facilitated using borehole logging information with on-demand web services to produce 3D geological structures. This domain interoperability across EPOS was created for the purpose of research, but it is also highly relevant for the response to societal grand challenges such as natural hazards and climate change. European and international interoperability implementation frameworks are well described and used (e.g., INSPIRE, ISO, OGC, and IUGS/CGI). It can be difficult for data providers to deploy web services that support the full semantic data definition (e.g., OGC Complex Feature) to expose several millions of geological entities through web-enabled data portals as required by pan-European projects.
Keywords: EPOS, geological information, borehole, FAIR, linked data
Published in DiRROS: 19.07.2023; Views: 335; Downloads: 114
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6.
7.
Identification of critical transcriptomic signaling pathways in patients with H syndrome and Rosai-Dorfman disease
Samuel Lara-Reyna, James A. Poulter, Elton J.R. Vasconcelos, Mark Kačar, Michael F. McDermott, Reuben Tooze, Rainer Doffinger, Sinisa Savic, 2021, original scientific article

Abstract: Biallelic mutations in SLC29A3 cause histiocytosis-lymphadenopathy plus syndrome, also known as H syndrome (HS). HS is a complex disorder, with ~ 25% of patients developing autoinflammatory complications consisting of unexplained fevers, persistently elevated inflammatory markers, and unusual lymphadenopathies, with infiltrating CD68+, S100+, and CD1a[minus] histiocytes, resembling the immunophenotype found in Rosai-Dorfman disease (RDD). We investigated the transcriptomic profiles of monocytes, non-activated (M0), classically activated (M1), and alternatively activated macrophages (M2) in two patients with HS, one without autoinflammatory (HS1) and one with autoinflammatory complications (HS2). RNA sequencing revealed a dysregulated transcriptomic profile in both HS patients compared to healthy controls (HC). HS2, when compared to HS1, had several differentially expressed genes, including genes associated with lymphocytic-histiocytic predominance (e.g. NINL) and chronic immune activation (e.g. B2M). The transcriptomic and cytokine profiles of HS patients were comparable to patients with SAID with high levels of TNF. SERPINA1 gene expression was found to be upregulated in all patients studied. Moreover, higher levels of IFN[gamma] were found in the serum of both HS patients when compared to HC. Gene ontology (GO) enrichment analysis of the DEGs in HS patients revealed the terms "type I IFN," "IFN[gamma] signaling pathway," and "immune responses" as the top 3 most significant terms for monocytes. Gene expression analysis of lymph node biopsies from sporadic and H syndrome-associated RDD suggests common underlying pathological process. In conclusion, monocytes and macrophages from both HS patients showed transcriptomic profiles similar to SAIDs and also uniquely upregulated IFN[gamma] signature. These findings may help find better therapeutic options for this rare disorder.
Keywords: interferon-gamma, H syndrome, systemic autoinflammatory disease
Published in DiRROS: 08.04.2021; Views: 1157; Downloads: 587
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8.
Sequential afatinib and osimertinib in patients with EGFR mutation-positive non-small-cell lung cancer : final analysis of the GioTag study
Maximilian J Hochmair, Alessandro Morabito, Desiree Hao, Cheng-Ta Yang, Ross A Soo, James C-H Yang, Rasim Gucalp, Balazs Halmos, Angela Märten, Tanja Čufer, 2020, original scientific article

Abstract: Aim: Final overall survival (OS) and time on treatment analysis of patients with EGFR mutation-positive non-small-cell lung cancer (NSCLC) who received sequential afatinib and osimertinib. Patients & methods: Patients (n = 203) had T790M-positive disease following first-line afatinib and started osimertinib treatment >/=10 months before data entry. Primary outcome was time on treatment; OS analysis was exploratory. Results: Median time on treatment with afatinib and osimertinib was 27.7 months (90% CI: 26.7-29.9). Median OS was 37.6 months (90% CI: 35.5-41.3); median OS was 41.6 and 44.8 months in Del19-positive patients and Asian patients, respectively. Conclusion: In real-world clinical practice, sequential afatinib and osimertinib was associated with encouraging outcomes in patients with EGFR mutation-positive NSCLC, especially in Del19-positive patients and Asian patients.
Keywords: non-small cell lung carcinoma -- therapy, drug therapy, afatinib, osimertinib, GioTag study
Published in DiRROS: 18.11.2020; Views: 1473; Downloads: 1239
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9.
Sequential treatment with afatinib and osimertinib in patients with EGFR mutation-positive non-small-cell lung cancer : an observational study
Maximilian J Hochmair, Alessandro Morabito, Desiree Hao, Cheng-Ta Yang, Ross A Soo, James C-H Yang, Rasim Gucalp, Balazs Halmos, Lara Wang, Amanda Golembesky, Angela Märten, Tanja Čufer, 2018, original scientific article

Abstract: Aim: To assess outcomes in patients with EGFR mutation-positive (Del19, L858R) non-small-cell lung cancer receiving sequential afatinib and osimertinib in a real-world clinical setting. Materials & methods: In this retrospective, observational, multicenter study, patients (n = 204) had T790M-positive disease following first-line afatinib and started osimertinib treatment [>/=]10 months prior to data entry. Primary outcome was time on treatment. Results: Overall median time on treatment was 27.6 months (90% CI: 25.9-31.3), 30.3 months (90% CI: 27.6-44.5) in Del19-positive patients and 46.7 months (90% CI: 26.8-not reached) in Asians. The 2-year overall survival was 78.9%. Conclusion: In real-world clinical practice, sequential afatinib and osimertinib facilitates prolonged, chemotherapy-free treatment in patients with T790M acquired resistance, and is a potentially attractive strategy, especially for Del19-positive tumors.
Keywords: lung neoplasms -- therapy, non-small-cell lung cancer, afatinib, osimertinib, epidermal growth factor receptor, EGFR, observational study
Published in DiRROS: 09.11.2020; Views: 1488; Downloads: 914
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10.
Sequential afatinib and osimertinib in patients with EGFR mutation-positive non-small-cell lung cancer : updated analysis of the observational GioTag study
Maximilian J Hochmair, Alessandro Morabito, Desiree Hao, Cheng-Ta Yang, Ross A Soo, James C-H Yang, Rasim Gucalp, Balazs Halmos, Lara Wang, Angela Märten, Tanja Čufer, 2019, original scientific article

Abstract: Aims: Overall survival (OS) and updated time to treatment failure (TTF) analysis of patients with EGFR mutation-positive (Del19, L858R) non-small-cell lung cancer who received sequential afatinib/osimertinib in the real-world GioTag study. Patients & methods: Patients had T790M-positive disease following first-line afatinib and received osimertinib treatment (n = 203). Primary outcome was TTF. The OS analysis was exploratory. Results: Median OS was 41.3 months (90% CI: 36.8-46.3) overall and 45.7 months (90% CI: 45.3-51.5) in patients with Del19-positive tumors (n = 149); 2-year survival was 80 and 82%, respectively. Updated median TTF with afatinib and osimertinib was 28.1 months (90% CI: 26.8-30.3). Conclusion: Sequential afatinib/osimertinib was associated with encouraging OS/TTF in patients with EGFR T790M-positive non-small-cell lung cancer, especially in patients with Del19-positive tumors.
Keywords: non-small cell lung carcinoma - therapy, drug therapy, afatinib, osimertinib, GioTag study
Published in DiRROS: 11.09.2020; Views: 1420; Downloads: 1032
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