cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Spontaneous Appearance of Low-dimensional Magnetic Electron System on Semiconductor Nanostructures
Creators: name: Sawada, Keisuke
name: Iwata, Jun-Ichi
name: Oshiyama, Atsushi
Publisher: name: arXiv
Year: 2015
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We find that spin-polarized ground states emerge in nanofacets which are self-organized on SiC (0001) surfaces. Our large-scale density-functional calculations reveal that the nanofacet formed by bunching of single bilayer steps generates peculiar carbon dangling bond states localized at but extended along step edges. The flat-band characteristics of those C states cause either ferromagnetic or anti-ferromagnetic chains on covalent semiconductors.
Responding to the Call
Creators: name: David, Kor
name: David, Kor
Publisher: name: Unknown
Year: 2022
Subjects: subject: Agricultural and Food Policy
subject: Nigeria
subject: Policy
subject: Economics
subject: Agriculture

description: While on the field, we were given in-depth information and knowledge about soils by our lead. The team was divided into two groups to facilitate coverage of the farmer fields in the selected LGAs.
ALMA [OIII] 88um Emitters. Signpost of Early Stellar Buildup and Reionization in the Universe.
Creators: name: Carrera, Rafael Navarro
Publisher: name: Zenodo
Year: 2022
Subjects: Epoch of Reioniztion, Extragalactic Astronomy, Galaxies, High Redshift

description: During the or EoR (400 Myr to 1 Gyr after the beginning of the universe) matter stopped being neutral. The causes and origin of this phenomenon are not yet fully understood. New information of galaxies in the EoR such as their physical properties, age of stellar population and emission fraction of ionizing photons will allow us to further deepen our knowledge of this objects. GO1 JWST approved proposal #1840 (Álvarez-Márquez+21) will shed light on the epoch of reionization by means of studying a sample of high redshift, [OIII] 88 μm emitting galaxies previously detected with radio interferometer ALMA (Atacama Large Millimetric Array) in order to understand how their light can ionise atoms. In this work we study whether structure of stellar and ISM galactic components can be recovered and if star formation history can be estimated from SED fitting using JWST NIRCam photometric + NIRSPec spectroscopic data.
REC: Fast sparse regression-based multicategory classification
Creators: name: Lu, X.
name: Zhang, C.
name: Singh, D.
name: Prins, J.F.
name: Zhu, Z.
name: Liu, Y.
name: Jones, C.
name: Liu, J.
name: Hu, Y.
Publisher: name: International Press of Boston, Inc.
Year: 2017

description: Recent advance in technology enables researchers to gather and store enormous data sets with ultra high dimensionality. In bioinformatics, microarray and next generation sequencing technologies can produce data with tens of thousands of predictors of biomarkers. On the other hand, the corresponding sample sizes are often limited. For classification problems, to predict new observations with high accuracy, and to better understand the effect of predictors on classification, it is desirable, and often necessary, to train the classifier with variable selection. In the literature, sparse regularized classification techniques have been popular due to the ability of simultaneous classification and variable selection. Despite its success, such a sparse penalized method may have low computational speed, when the dimension of the problem is ultra high. To overcome this challenge, we propose a new sparse REgression based multicategory Classifier (REC). Our method uses a simplex to represent different categories of the classification problem. A major advantage of REC is that the optimization can be decoupled into smaller independent sparse penalized regression problems, and hence solved by using parallel computing. Consequently, REC enjoys an extraordinarily fast computational speed. Moreover, REC is able to provide class conditional probability estimation. Simulated examples and applications on microarray and next generation sequencing data suggest that REC is very competitive when compared to several existing methods.
Measuring large optical reflection matrices of turbid media
Creators: name: Yu, Hyeonseung
name: Park, Jung-Hoon
name: Park, YongKeun
Publisher: name: arXiv
Year: 2015
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We report the measurement of a large optical reflection matrix (RM) of a highly disordered medium. Incident optical fields onto a turbid sample are controlled by a spatial light modulator, and the corresponding fields reflected from the sample are measured using full-field Michelson interferometry. The number of modes in the measured RM is set to exceed the number of resolvable modes in the scattering media. We successfully study the subtle intrinsic correlations in the RM which agrees with the theoretical prediction by random-matrix theory when the effect of the limited numerical aperture on the eigenvalue distribution of the RM is taken into account. The possibility of the enhanced delivery of incident energy into scattering media is also examined from the eigenvalue distribution which promises efficient light therapeutic applications.
Current Site-specific management guidelines and schedules for the 9 PROFOUND forest sites of the regional forest sector in ISIMIP
Creators: name: Reyer, Christopher P.O.; Schelhaas, Mart-Jan; Mäkelä, Annikki; Peltoniemi, Mikko; Gutsch, Martin; Mahnken, Mats; Loustau, Denis; Martel, Simon; Merganičová, Katarína; Meesenburg, Henning; Rötzer, Thomas; Heym, Michael; Collalti, Alessio; D'Andrea, Ettore; Matteucci, Giorgio; Ibrom, Andreas; Kvist Johannsen, Vivian
Publisher: name: Zenodo
Year: 2023
Subjects: FORMASAM
ISIMIP
PROFOUND

description: Forest management guidelines for forest simulation models for 9 forest sites of the regional forest sector in ISIMIP
description: Developed in the FORMASAM project. EFI Network Fund "Forest Management Scenarios for Adaptation and Mitigation" (FORMASAM) Intersectoral Impact Model Intercomparison Project (ISIMIP)
description: {"references": ["Reyer et al. 2020, https://doi.org/10.5194/essd-12-1295-2020"]}
Preschoolers optimize the timing of conversational turns - Addendum 06.09.22
Creators: name: Gambi, Chiara
name: Rabagliati, Hugh
name: Lindsay, Laura
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Psychology
subject: FOS: Psychology
subject: Social and Behavioral Sciences

description: This registration records changes to Lindsay, Gambi, & Rabagliati (2019), https://osf.io/ypc6k following attempts at reproducing the original results by a group of independent coders. Details of their attempts can be found here: https://psyarxiv.com/729qt/ and here: https://osf.io/xzke7/ (Article 104).
Extragenic suppressor mutations in ΔripA disrupt stability and function of LpxA
Creators: name: Lovullo, E.D.
name: Dotson, G.D.
name: Kawula, T.H.
name: Collins, E.J.
name: Miller, C.N.
name: Brunton, J.C.
name: Jenkins, R.J.
name: Romanchuk, A.
name: Steele, S.P.
name: Jones, C.D.
name: Taft-Benz, S.A.
Publisher: name: BioMed Central Ltd.
Year: 2015

description: Background: Francisella tularensis is a Gram-negative bacterium that infects hundreds of species including humans, and has evolved to grow efficiently within a plethora of cell types. RipA is a conserved membrane protein of F. tularensis, which is required for growth inside host cells. As a means to determine RipA function we isolated and mapped independent extragenic suppressor mutants in ΔripA that restored growth in host cells. Each suppressor mutation mapped to one of two essential genes, lpxA or glmU, which are involved in lipid A synthesis. We repaired the suppressor mutation in lpxA (S102, LpxA T36N) and the mutation in glmU (S103, GlmU E57D), and demonstrated that each mutation was responsible for the suppressor phenotype in their respective strains. We hypothesize that the mutation in S102 altered the stability of LpxA, which can provide a clue to RipA function. LpxA is an UDP-N-acetylglucosamine acyltransferase that catalyzes the transfer of an acyl chain from acyl carrier protein (ACP) to UDP-N-acetylglucosamine (UDP-GlcNAc) to begin lipid A synthesis. Results: LpxA was more abundant in the presence of RipA. Induced expression of lpxA in the ΔripA strain stopped bacterial division. The LpxA T36N S102 protein was less stable and therefore less abundant than wild type LpxA protein. Conclusion: These data suggest RipA functions to modulate lipid A synthesis in F. tularensis as a way to adapt to the host cell environment by interacting with LpxA.
Searching for a second occultation in EPIC 204376071
Creators: name: Alonso, Roi
name: Deeg, Hans J.
name: Rappaport, Saul
Publisher: name: Zenodo
Year: 2022

description: EPIC 204376071 is an young (~10 Myr) M star (estimated mass ~0.16 M☉, and radius 0.63 R☉), probable member of the Upper Sco association, that exhibited a 80% drop in flux lasting one day, in the course of one campaign of the K2 mission (Rappaport et al. 2019). Different scenarios have been proposed to explain this feature, some of them requiring a periodic behaviour of these events. With only one event observed, it becomes challenging to obtain further observations to investigate further the origin of the abrupt flux drops, and start confirming/rejecting possible scenarios. We have obtained new photometric observations, and analysed archival photometry, with the goal to identify additional flux drops on this star, and get the ephemeris, should these events be periodic.
description: {"references": ["2019MNRAS.485.2681R"]}
title: A Post-Quantum Secure Subscription Concealed Identifier for 6G
Creators: name: Ulitzsch, Vincent Quentin
name: Park, Shinjo
name: Marzougui, Soundes
name: Seifert, Jean-Pierre
Publisher: name: ACM
Year: 2022
Subjects: subject: 000 Informatik, Informationswissenschaft, allgemeine Werke::000 Informatik, Wissen, Systeme::000 Informatik, Informationswissenschaft, allgemeine Werke
subject: Key Encapsulation Mechanism
subject: post-quantum cryptography
subject: SUCI
subject: SUPI
subject: 5G
subject: 6G

description: 5G saw the introduction of an encrypted user identifier, the Subscriber Concealed Identifier (SUCI), to provide confidentiality of the subscriber's whereabouts and identities. The SUCI protects the new generation of cellular networks against tracking devices, so-called IMSI-catchers, which have undermined users' confidentiality ever since the inception of cellular networks. However, the potential advent of large-scale quantum computers in the near future threatens to compromise the confidentiality provided by the SUCI yet again. The security of the public-key cryptography that underpins the SUCI relies on the hardness of the discrete logarithm problem. Using Shor's algorithm, a quantum adversary could break the SUCI's cryptography and once more gain the capability to track and identify users. Advancements in quantum computing are unpredictable, and a breakthrough might be only a decade away. Given the slow nature of standards and their implementation, it is thus necessary to already integrate now quantum-resistant cryptography into the current and also next-generation (6G) cellular networks. To contribute to this development, we propose a post-quantum secure scheme for the SUCI calculation, \textttKEMSUCI. To this end, we first analyze the weak points in the current SUCI calculation scheme when considering quantum attacks. We then describe an alternative SUCI calculation scheme based on post-quantum secure key-encapsulation mechanisms (KEMs). Our proposed scheme can use any of the KEMs submitted to the NIST call for standardization of post-quantum secure cryptography (PQC) schemes. For the usage in \textttKEMSUCI, the KEM should provide efficient execution on a SIM card and induce little network communication overhead. We evaluate all of the NIST PQC finalists under these aspects and identify Kyber and Saber as the best fit. Instantiated with these KEMs, \textttKEMSUCI can be integrated into 5G and 6G. Compared to the existing SUPI protection schemes, \textttKEMSUCI exhibits faster execution speed and only little communication overhead.
Draft genome sequences of a phylogenetically diverse suite of Pseudomonas syringae strains from multiple source populations
Creators: name: Sands, D.C.
name: Baltrus, D.A.
name: Yourstone, S.
name: Lind, A.
name: Dangl, J.L.
name: Morris, C.E.
name: Jones, C.D.
name: Guilbaud, C.
Publisher: name: American Society for Microbiology
Year: 2014

description: Here, we report the draft genome sequences for 7 phylogenetically diverse isolates of Pseudomonas syringae, obtained from numerous environmental sources and geographically proximate crop species. Overall, these sequences provide a wealth of information about the differences (or lack thereof) between isolates from disease outbreaks and those from other sources.
Note on uncertainty relations in doubly special relativity and rainbow gravity
Creators: name: Son, Edwin J.
name: Kim, Wontae
Publisher: name: arXiv
Year: 2015
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We present commutation relations depending on the rainbow functions which are slightly different from the well-known results. However, the advantage of these new commutation relations are compatible with the calculation of the Hawking temperature in the rainbow Schwarzschild black hole.
description: 7 pages
Tribological properties of carbon-reinforced epoxy composites - A review
Creators: name: SAHIN, Yusuf
Publisher: name: Metallurgy and Materials Science Research Institute Chulalongkorn University
Year: 2020
Subjects: Polymeric composites
Tribology
Wear mechanism
Coefficient of Friction
Process optimization
TM and RSM

description: Journal of Metals Materials and Minerals, 30, 2, 1-21
Searching for a second occultation in EPIC 204376071
Creators: name: Alonso, Roi
name: Deeg, Hans J.
name: Rappaport, Saul
Publisher: name: Zenodo
Year: 2022

description: EPIC 204376071 is a young (~10 Myr) M star (estimated mass ~0.16 M☉, and radius 0.63 R☉), probable member of the Upper Sco association, that exhibited an 80% drop in flux lasting one day, in the course of one campaign of the K2 mission (Rappaport et al. 2019). Different scenarios have been proposed to explain this feature, some of them requiring a periodic behaviour of these events. With only one event observed, it becomes challenging to obtain further observations to investigate further the origin of the abrupt flux drops, and start confirming/rejecting possible scenarios. We have obtained new photometric observations, and analysed archival photometry, with the goal to identify additional flux drops on this star, and get the ephemeris, should these events be periodic.
description: {"references": ["2019MNRAS.485.2681R"]}
String diagrams for traced and compact categories are oriented 1-cobordisms
Creators: name: Spivak, David I.
name: Schultz, Patrick
name: Rupel, Dylan
Publisher: name: arXiv
Year: 2015
Subjects: subject: Category Theory (math.CT)
subject: FOS: Mathematics
subject: 18D10, 18D50, 18D05

description: We give an alternate conception of string diagrams as labeled 1-dimensional oriented cobordisms, the operad of which we denote by Cob/O, where O is the set of string labels. The axioms of traced (symmetric monoidal) categories are fully encoded by Cob/O in the sense that there is an equivalence between (Cob/O)-algebras, for varying O, and traced categories with varying object set. The same holds for compact (closed) categories, the difference being in terms of variance in O. As a consequence of our main theorem, we give a characterization of the 2-category of traced categories solely in terms of those of monoidal and compact categories, without any reference to the usual structures or axioms of traced categories. In an appendix we offer a complete proof of the well-known relationship between the 2-category of monoidal categories with strong monoidal functors and the 2-category of monoidal categories whose object set is free with strict functors; similarly for traced and compact categories.
description: 53 pages; small reorganization and clarifications from v2
O'ZBEKISTONDA ISLOMIY MOLIYA TIZIMINI QO'LLASH IMKONIYATLARI
Creators: name: Nizomxonov, Elbekxon
Publisher: name: Zenodo
Year: 2024

description: Ushbu maqolada islomiy moliya tushunchasi, uning oddiy moliya tizimidan farqlari va afzalliklari bayon qilingan. Dunyo islomiy moliya bozori holati, unda islom banklarining tutgan o‘rni tahlil qilingan. Xalqaro tajribalar o‘rganilib, aholining moliyaviy xizmatlardan foydalanish muammolari ko‘rsatilgan va ularni bartaraf etish yo‘nalishlari taklif etilgan.
Genetic testing reveals some mislabeling but general compliance with a ban on herbivorous fish harvesting in Belize
Creators: name: Mcfield, M.D.
name: Bruno, J.F.
name: Castillo, K.D.
name: Jones, C.D.
name: Cox, C.E.
name: Wares, J.P.
Publisher: name: Wiley-Blackwell
Year: 2013

description: Overfishing of herbivorous fishes is one of the primary causes of Caribbean coral reef decline. In Belize, herbivorous fishes comprised 28% of the catch from 2005 to 2008. In 2009, the Belize Fisheries Department implemented a national ban on herbivorous fish harvesting to mitigate high-macroalgal cover on much of the Belize Barrier Reef. However, compliance with this approach has not been evaluated. We assessed the proportion of herbivorous fish in local markets by genetically identifying fish fillets sold in five major towns in Belize from 2009 to 2011. We found that 5-7% of 111 fillets were identified as herbivorous fish and 32-51% were mislabeled. A 5-7% proportion of parrotfish in local markets suggests some ongoing parrotfish harvesting. However, our results suggest that the ban has reduced herbivorous fish harvesting and has the potential to help facilitate the restoration of coral reef ecosystems.
Detection of Industrial Compounds via Atmospheric Chemical Reaction Network Topology
Creators: name: Fisher, Tessa
Publisher: name: Zenodo
Year: 2022

description: Abstract: With spectral analysis of terrestrial exoplanets approaching on the near horizon, new tools are required to analyze the characteristics of these atmospheres. One approach is measuring the topology of the topology of the atmospheric chemical reaction network. Building on previous works using network topology to understand atmospheric disequilibria (Fisher et al 2022) and the interface between biospheres and atmospheres (Walker et al 2021), we propose modeling Earth-like atmospheres with and without the presence of industrial compounds. In particular, we will examine how atmospheric network topology is affected by the introduction of CFCs. This investigation may help identify spectral signatures that indicate the presence of CFCs indirectly and that are more easily detectable.
Μανουήλ Β΄ Παλαιολόγος, Διάλογος Ηθικός ή Περί Γάμου. Μορφή και Θέματα
Creators: name: Παπαγιαννάκη, Άννα Δημητρίου
Publisher: name: Aristotle University of Thessaloniki
Year: 2023
Subjects: Βυζάντιο
Γάμος
Πολιτική
Byzantium
Marriage
Politics

description: Το πρότυπο του φιλόσοφου-βασιλέα που ενσαρκώνει ο επιφανής, κοσμικός άρχοντας και φωτισμένος θεολόγος, Μανουήλ Β’ Παλαιολόγος, έχει σφραγίσει ανεξίτηλα την ταραγμένη περίοδο του Ύστερου Βυζαντίου, εποχή προϊούσας κατάρρευσης και αποδυνάμωσης της άλλοτε κραταιάς αυτοκρατορίας. Η εργασία στόχο έχει να διερευνήσει τη μορφή, το γραμματειακό είδος του εν λόγω έργου, που ομοιάζει με ρητορικό αγώνα διττών λόγων, μέσω επιχειρηματολογίας κι αντιλογιών, καθώς και να εντοπίσει κοινωνικοπολιτικά ζητήματα της εποχής που διατρέχουν το κείμενο, μέσα από τις αντικρουόμενες απόψεις των συνομιλητών, του Μανουήλ Β΄ και της μητέρας του Ελένης Καντακουζηνής. Ειδικότερα θα μελετηθεί η χειρόγραφη παράδοση που διέσωσε το έργο αυτό, δηλαδή ο κώδικας Vindobonensis Philologicus gr. 98, 15ου αι, που ανήκει στο Βησσαρίωνα και ο Parisinus gr. 3041, 15ου αι., κώδικας για τον οποίο υποστηρίχθηκε από μεγάλο αριθμό μελετητών η θεωρία ότι στο εν λόγω έργο έγινε σχολαστική επαναπροσέγγιση του κειμένου από τον ίδιο τον συγγραφέα. Ακόμη, θα παρουσιαστούν οι εκδόσεις του έργου, τα περιστατικά συγγραφής του ( αφορμή, χρόνος και τόπος σύνταξής του) και τα θέματα που πραγματεύεται.
description: The ideal of the philosopher-king embodied by the illustrious secular ruler and enlightened theologian Manuel II Palaeologos haw indelibly sealed it turbulent period of Late Byzantium, a time of progressive collapse and weakening of the once mighty empire. The work aims to investigate the form, the clerical genre of the work in question, which resembles rhetorical struggle of double standards, through argumentation and counterarguments, as well as identify socio-political issues of the period that run through the text, through the conflicting views of the interlocutors, Manuel II and his mother, Eleni Kantakouzini. In particular, the handwritten tradition that saved this work will be studied, that is the codex Vindobonensis Philologicus gr. 3041, 15th century, which belongs in Bessarion and Parisinus gr. 3041, 15th century, code for which supported by a large number of scholars the theory that in said work the text was meticulously revised by the author himself. Furthermore, the editions of the work, the incidents of its writing (occasion, time and place of its writing) and the topics it deals with.
title: The Weekend: Time, Space and Everyday Life in Manchester and Salford
Creators: name: Ebrey, Jill
Publisher: name: Goldsmiths, University of London
Year: 2006

description: The central issue is an analysis of the social construction and significance of the weekend. This is examined in the contexts of both historical and contemporary Manchester and Salford. The analysis uses theories of spatiality and temporality within everyday life, examining the extent to which the weekend can be considered both different to, and part of, everyday life. It considers whether the weekend can still (or could ever) be considered a more autonomous `time space' or if `flexible' working patterns will undermine it. In that these micro processes of everyday life are where the macro economic policies are enacted, this study has wider political implications. Two main methods are employed. Primary and secondary historical source materials used to understand aspects of both the development of the weekend and the way in which it has been practised in Manchester and Salford. The contemporary weekend is addressed through two pieces of fieldwork; one with people holding allotments in south Manchester and the other with supermarket workers in Salford. These consist of interviews with individuals which were recorded, transcribed and manually coded to develop themes. The analysis indicates that the weekend remains an important and pervasive institution. However, for some social groups, notably those working in the retail sector, the weekend is being eroded. There is increasingly a divide between workers like these, who are expected to work at weekends, and those who have weekends `off as a matter of course. Key areas of the analysis include marking the boundary between the week and the weekend, what people do, who they see and where they go; in short, an assessment of how the everyday spatialities and temporalities of interviewees construct their weekends. As well as contributing to our understanding of the hitherto relatively unexplored institution of the weekend itself, this thesis adds to our understanding of the temporal and spatial construction of our social world and the constraints under which this process operates.
Herschel spectroscopic observations of the compact obscured nucleus in Zw 049.057
Creators: name: Falstad, N.
name: González-Alfonso, E.
name: Aalto, S.
name: van der Werf, P. P.
name: Fischer, J.
name: Veilleux, S.
name: Meléndez, M.
name: Farrah, D.
name: Smith, H. A.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: Context. The LIRG Zw 049.057 contains a compact obscured nucleus where a considerable amount of the galaxy's luminosity is generated. This nucleus contains a dusty environment that is rich in molecular gas. One approach to probing this kind of environment and to revealing what is hidden behind the dust is to study the rotational lines of molecules that couple well with the IR radiation emitted by the dust. Methods. We observed Zw 049.057 with PACS and SPIRE onboard the Herschel Space Observatory in rotational lines of H2O, H218O, OH, 18OH, and [O I]. We modeled the unresolved core of the galaxy using a spherically symmetric radiative transfer code. Results. We present the full SPIRE FTS spectrum of Zw 049.057, along with relevant spectral scans in the PACS range. We find that a minimum of two different components (nuclear and extended) are required in order to account for the rich molecular line spectrum. The nuclear component has a radius of 10-30 pc, a very high infrared surface brightness (1e14 Lsun/kpc2), warm dust (Td > 100 K), and a very large H2 column density (NH2 = 1e24-1e25 cm-2). The modeling also indicates high nuclear H2O (5e-6) and OH (4e-6) abundances relative to H2 as well as a low 16O/18O-ratio of 50-100. We also find a prominent infall signature in the [O I] line. We tentatively detect a 500 km/s outflow in the H2O 313->202 line. Conclusions. The high surface brightness of the core indicates the presence of either a buried active galactic nucleus or a very dense nuclear starburst.nThe H2O abundance is comparable to that of other compact (ultra-)luminous infrared galaxies such as NGC 4418 and Arp 220 - and also to hot cores in the Milky Way. The enhancement of 18O is a possible indicator that the nucleus of Zw 049.057 is in a similar evolutionary stage as the nuclei of Arp 220 - and more advanced than NGC 4418.
description: 14 pages, 10 figures, Accepted for publication in Astronomy and Astrophysics
The Linear KdV Equation with an Interface
Creators: name: Deconinck, Bernard
name: Sheils, Natalie E.
name: Smith, David A.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics

description: The interface problem for the linear Korteweg-de Vries (KdV) equation in one-dimensional piecewise homogeneous domains is examined by constructing an explicit solution in each domain. The location of the interface is known and a number of compatibility conditions at the boundary are imposed. We provide an explicit characterization of sufficient interface conditions for the construction of a solution using Fokas's Unified Transform Method. The problem and the method considered here extend that of earlier papers to problems with more than two spatial derivatives.
description: 23 pages, 8 figures
Dynamic evolution of pathogenicity revealed by sequencing and comparative genomics of 19 pseudomonas syringae isolates
Creators: name: Nishimura, M.T.
name: Baltrus, D.A.
name: Chang, J.H.
name: Grant, S.R.
name: Mukhtar, M.S.
name: Romanchuk, A.
name: Roach, J.
name: Cherkis, K.
name: Dangl, J.L.
name: Jones, C.D.
Publisher: name: Public Library of Science
Year: 2011

description: Closely related pathogens may differ dramatically in host range, but the molecular, genetic, and evolutionary basis for these differences remains unclear. In many Gram- negative bacteria, including the phytopathogen Pseudomonas syringae, type III effectors (TTEs) are essential for pathogenicity, instrumental in structuring host range, and exhibit wide diversity between strains. To capture the dynamic nature of virulence gene repertoires across P. syringae, we screened 11 diverse strains for novel TTE families and coupled this nearly saturating screen with the sequencing and assembly of 14 phylogenetically diverse isolates from a broad collection of diseased host plants. TTE repertoires vary dramatically in size and content across all P. syringae clades; surprisingly few TTEs are conserved and present in all strains. Those that are likely provide basal requirements for pathogenicity. We demonstrate that functional divergence within one conserved locus, hopM1, leads to dramatic differences in pathogenicity, and we demonstrate that phylogenetics-informed mutagenesis can be used to identify functionally critical residues of TTEs. The dynamism of the TTE repertoire is mirrored by diversity in pathways affecting the synthesis of secreted phytotoxins, highlighting the likely role of both types of virulence factors in determination of host range. We used these 14 draft genome sequences, plus five additional genome sequences previously reported, to identify the core genome for P. syringae and we compared this core to that of two closely related non-pathogenic pseudomonad species. These data revealed the recent acquisition of a 1 Mb megaplasmid by a sub-clade of cucumber pathogens. This megaplasmid encodes a type IV secretion system and a diverse set of unknown proteins, which dramatically increases both the genomic content of these strains and the pan-genome of the species.
title: Benjamin Cooke (1734-93), Composer and Academician:Science, Ancient Authority and the Advancement of English Music
Creators: name: Eggington, Timothy John
Publisher: name: Goldsmiths, University of London
Year: 2008

description: As organist of Westminster Abbey and conductor of the Academy of Ancient Music for most of the second half of the eighteenth century, Benjamin Cooke constitutes an important yet now forgotten figure. Extant Cooke manuscripts preserved in the Cooke Collection at the Royal College of Music represent an extensive though hitherto little examined source through which this study is made possible. In Cooke's compositions, musical tastes and theoretical writings may be perceived an all encompassing philosophy according to which not only the materials of music but even elements of musical style are seen to be governed by a priori principles. In this approach may be observed a philosophy consistent with wider eighteenth-century thinking, according to which antiquity and science were viewed as a source of universal and immutable truth. Chapters 1 and 2 of this thesis set out the intellectual background to Cooke's theoretical writings and assess the significance of his unpublished treatise Musical Conjectures. Here we see how Cooke used his learning to resolve musical issues of his day (such as tuning) and to hone critical tools for the assessment of music. Chapter 3 provides a survey of the Cooke Collection. Here Cooke's editing of early music reveals an aspiration to map the musical past in order to establish terms of reference for the present, knowledge which impinged upon his own composing. Chapters 4 and 5 survey a representative sample of Cooke's compositions, culminating with an in-depth examination of two defining works, The Morning Hymn and Collins's Ode. Although these reveal a pronounced debt to music of the previous 200 years, they also exhibit a profound sense of innovation and creativity in style and language. In this we find an aspiration to advance music in a manner consistent with later eighteenth-century imperatives for simplicity, whilst retaining the gravitas and substance inherent in earlier styles.
Associations between cannabis dispensary density and cannabis use behaviors and related harms: a systematic review protocol
Creators: name: Dr. Pamela Trangenstein
name: Emily Jones
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2020

description: This systematic review protocol details planned actions of our review team. Document includes purpose, research question(s), inclusion and exclusion criteria, and planned methods for searching the literature, data extraction, and quality assessment.
A note on optimal sampling strategy for structural variant detection using optical mapping
Creators: name: Jones, C.D.
name: Li, W.
name: Hannig, J.
Publisher: name: Taylor and Francis Inc.
Year: 2020

description: Structural variants compose the majority of human genetic variation, but are difficult to accurately assess using current genomic sequencing technologies. Optical mapping technologies, which measure the size of chromosomal fragments between labeled markers, offer an alternative approach. As these technologies mature toward becoming clinical tools, there is a need to develop an approach for determining the optimal strategy for sampling biological material in order to detect a structural variant at some threshold. Here we develop an optimization approach using a simple, yet realistic, model of the genomic mapping process using a hypergeometric distribution and probabilistic concentration inequalities. Our approach is both computationally and analytically tractable and includes a novel approach to getting tail bounds of hypergeometric distribution. We show that if a genomic mapping technology can sample most of the chromosomal fragments within a sample, comparatively little biological material is needed to detect a variant at high confidence.
Antenna-coupled silicon-organic hybrid integrated photonic crystal modulator for broadband electromagnetic wave detection
Creators: name: Zhang, Xingyu
name: Hosseini, Amir
name: Subbaraman, Harish
name: Wang, Shiyi
name: Zhan, Qiwen
name: Luo, Jingdong
name: Jen, Alex K. -Y.
name: Chung, Chi-jui
name: Yan, Hai
name: Pan, Zeyu
name: Nelson, Robert L.
name: Lee, Charles Y. -C.
name: Chen, Ray T.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: In this work, we design, fabricate and characterize a compact, broadband and highly sensitive integrated photonic electromagnetic field sensor based on a silicon-organic hybrid modulator driven by a bowtie antenna. The large electro-optic (EO) coefficient of organic polymer, the slow-light effects in the silicon slot photonic crystal waveguide (PCW), and the broadband field enhancement provided by the bowtie antenna, are all combined to enhance the interaction of microwaves and optical waves, enabling a high EO modulation efficiency and thus a high sensitivity. The modulator is experimentally demonstrated with a record-high effective in-device EO modulation efficiency of r33=1230pm/V. Modulation response up to 40GHz is measured, with a 3-dB bandwidth of 11GHz. The slot PCW has an interaction length of 300um, and the bowtie antenna has an area smaller than 1cm2. The bowtie antenna in the device is experimentally demonstrated to have a broadband characteristics with a central resonance frequency of 10GHz, as well as a large beam width which enables the detection of electromagnetic waves from a large range of incident angles. The sensor is experimentally demonstrated with a minimum detectable electromagnetic power density of 8.4mW/m2 at 8.4GHz, corresponding to a minimum detectable electric field of 2.5V/m and an ultra-high sensitivity of 0.000027V/m Hz^-1/2 ever demonstrated. To the best of our knowledge, this is the first silicon-organic hybrid device and also the first PCW device used for the photonic detection of electromagnetic waves. Finally, we propose some future work, including a Teraherz wave sensor based on antenna-coupled electro-optic polymer filled plasmonic slot waveguide, as well as a fully packaged and tailgated device.
description: 20 pages, 16 figures
A note on the Erdös-Faber-Lovász Conjecture: quasigroups and complete digraphs
Creators: name: Araujo-Pardo, Gabriela
name: Rubio-Montiel, Christian
name: Vazquez-Avila, Adrian
Publisher: name: arXiv
Year: 2015
Subjects: subject: Combinatorics (math.CO)
subject: FOS: Mathematics
subject: 05C20

description: A decomposition of a simple graph $G$ is a pair $(G,P)$ where $P$ is a set of subgraphs of $G$, which partitions the edges of $G$ in the sense that every edge of $G$ belongs to exactly one subgraph in $P$. If the elements of $P$ are induced subgraphs then the decomposition is denoted by $[G,P]$. A $k$-$P$-coloring of a decomposition $(G,P)$ is a surjective function that assigns to the edges of $G$ a color from a $k$-set of colors, such that all edges of $H\in P$ have the same color, and, if $H_1,H_2\in P$ with $V(H_1)\cap V(H_2)\neq\emptyset$ then $E(H_1)$ and $E(H_2)$ have different colors. The \emph{chromatic index} $χ'((G,P))$ of a decomposition $(G,P)$ is the smallest number $k$ for which there exists a $k$-$P$-coloring of $(G,P)$. The well-known Erdös-Faber-Lovász Conjecture states that any decomposition $[K_n,P]$ satisfies $χ'([K_n,P])\leq n$. We use quasigroups and complete digraphs to give a new family of decompositions that satisfy the conjecture.
description: 4 pages, 1 figure
Unbound motion of massive particles in the Schwarzschild metric: Analytical description in case of strong deflection
Creators: name: Tsupko, Oleg Yu.
Publisher: name: arXiv
Year: 2015
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: Deflection angles of massive test particles moving along an unbound trajectory in the Schwarzschild metric are considered for the case of large deflection. We analytically consider the strong deflection limit, which is opposite to the commonly applied small deflection approximation and corresponds to the situation when a massive particle moves from infinity, makes several revolutions around a central object and goes to infinity. For this purpose we rewrite an integral expression for the deflection angle as an explicit function of the parameters determining the trajectory and expand it. Remarkably, in the limiting case of strong deflection, we succeed in deriving for the first time the analytical formulas for deflection angles as explicit functions of parameters at infinity. In particular, we show that in this case the deflection angle can be calculated as an explicit function of the impact parameter and velocity at infinity beyond the usual assumption of small deflection.
description: See also our previous paper arXiv:1305.7032
Virus expression detection reveals RNA-sequencing contamination in TCGA
Creators: name: Jones, C.
name: Mose, L.E.
name: Selitsky, S.R.
name: Parker, J.S.
name: Marron, D.
name: Hoadley, K.A.
name: Hollern, D.
name: Dittmer, D.P.
name: Perou, C.M.
Publisher: name: BioMed Central Ltd.
Year: 2020

description: Background: Contamination of reagents and cross contamination across samples is a long-recognized issue in molecular biology laboratories. While often innocuous, contamination can lead to inaccurate results. Cantalupo et al., for example, found HeLa-derived human papillomavirus 18 (H-HPV18) in several of The Cancer Genome Atlas (TCGA) RNA-sequencing samples. This work motivated us to assess a greater number of samples and determine the origin of possible contaminations using viral sequences. To detect viruses with high specificity, we developed the publicly available workflow, VirDetect, that detects virus and laboratory vector sequences in RNA-seq samples. We applied VirDetect to 9143 RNA-seq samples sequenced at one TCGA sequencing center (28/33 cancer types) over 5 years. Results: We confirmed that H-HPV18 was present in many samples and determined that viral transcripts from H-HPV18 significantly co-occurred with those from xenotropic mouse leukemia virus-related virus (XMRV). Using laboratory metadata and viral transcription, we determined that the likely contaminant was a pool of cell lines known as the "common reference", which was sequenced alongside TCGA RNA-seq samples as a control to monitor quality across technology transitions (i.e. microarray to GAII to HiSeq), and to link RNA-seq to previous generation microarrays that standardly used the "common reference". One of the cell lines in the pool was a laboratory isolate of MCF-7, which we discovered was infected with XMRV; another constituent of the pool was likely HeLa cells. Conclusions: Altogether, this indicates a multi-step contamination process. First, MCF-7 was infected with an XMRV. Second, this infected cell line was added to a pool of cell lines, which contained HeLa. Finally, RNA from this pool of cell lines contaminated several TCGA tumor samples most-likely during library construction. Thus, these human tumors with H-HPV or XMRV reads were likely not infected with H-HPV 18 or XMRV.
Rhythmanalysis of Street Food Vending: Spatiality, Temporality and Embodiment
Creators: name: Erciyas, Fatos Ozkan
Publisher: name: University of Leicester
Year: 2023
Subjects: Uncategorized

description: Since the 2008 financial crisis, there has been an increased interest in street vending in developed countries. The councils in many UK cities have encouraged street vending activities and viewed them as a welcome addition to the cities’ diverse retailscapes and consumptionscapes. This thesis explores how street markets are co-produced and negotiated between different stakeholders, how the market rhythms of street food vending are interspersed with the daily rhythms of these stakeholders, and how street vending (re)produces capitalist rhythms between marketplace actors. Chatzidakis and McEachern (2013) call for more socio-relational discussions of space by repositioning ‘space’ at the forefront of the discussions in marketing and consumer research scholarship. Despite an advent of research that centralises spatiality, only a few studies consider the temporal and embodied dimensions of space. To fill this gap, this thesis aims to analyse marketplace relations and practices by considering the tripartite concepts of spatiality, temporality and embodiment in the street food vending context. Drawing on the work of Henri Lefebvre, this thesis contributes to the scholarship of space in marketing by advancing discussions pertaining to marketplace relations. Rhythmanalysis informs the theoretical framework and methodology of the thesis, which involve an immersive ethnography of the everyday relations that pervade street food vending in over 100 days of observations within 16 months. In addition, I conducted over 50 in-depth and in-situ interviews with stakeholders. This thesis demonstrates how a holistic approach to temporality, spatiality and embodiment in marketing theory can further the understanding of marketplace relations and finds that a rhythmic approach to understanding time and space is warranted to transcend the entrenched dualistic thinking (of time-space) in marketing scholarship. This study finds that street markets are constituted by polyrhythmic rhythms and the consumption of street food is corporeally fuelled by cyclical rhythms as well as linear rhythms.
A P53-Independent DNA Damage Response Suppresses Oncogenic Proliferation and Genome Instability
Creators: name: Parker, J.S.
name: Rashid, N.U.
name: Reis-Filho, J.S.
name: Petrini, J.H.J.
name: Kumar, R.J.
name: Mose, L.E.
name: Wen, Y.H.
name: Gupta, G.P.
name: Powell, S.N.
name: Simpson, D.A.
name: Fagan-Solis, K.D.
name: Martelotto, L.G.
name: Ho, A.Y.
Publisher: name: Elsevier B.V.
Year: 2020

description: The Mre11-Rad50-Nbs1 complex is a DNA double-strand break sensor that mediates a tumor-suppressive DNA damage response (DDR) in cells undergoing oncogenic stress, yet the mechanisms underlying this effect are poorly understood. Using a genetically inducible primary mammary epithelial cell model, we demonstrate that Mre11 suppresses proliferation and DNA damage induced by diverse oncogenic drivers through a p53-independent mechanism. Breast tumorigenesis models engineered to express a hypomorphic Mre11 allele exhibit increased levels of oncogene-induced DNA damage, R-loop accumulation, and chromosomal instability with a characteristic copy number loss phenotype. Mre11 complex dysfunction is identified in a subset of human triple-negative breast cancers and is associated with increased sensitivity to DNA-damaging therapy and inhibitors of ataxia telangiectasia and Rad3 related (ATR) and poly (ADP-ribose) polymerase (PARP). Thus, deficiencies in the Mre11-dependent DDR drive proliferation and genome instability patterns in p53-deficient breast cancers and represent an opportunity for therapeutic exploitation.
Science Communication Webinar Series: Talking to the Media Presentation
Creators: name: Grist, Hannah
name: Paterson, Euan
Publisher: name: Zenodo
Year: 2020

description: Blue-Action coordinated a series of webinars on climate science communication in 2020. These were aimed at early-career researchers, but anyone who wishes to engage people with their research at any stage will find them valuable. This webinar was delivered on 19th June 2020 by Euan Paterson, who is the Communications and Media Officer at the Scottish Association for Marine Science. Euan is trained in journalism, and spent over a decade working in print media, before moving to work at the Institute. He brought his years of experience on both sides of the relationship to the webinar, sharing some insights and ideas on how to engage with the media. These are the slides for Euan's presentation. To see the recording of the webinar, please visit: https://doi.org/10.5281/zenodo.3906360
NFDI4Cat Newsletter Issue #3 - October 2022
Creators: name: Espinoza, Sara
name: Mikley, Tina
Publisher: name: Zenodo
Year: 2022
Subjects: catalysis
Digitalisation
NFDI

description: This is the third issue of the NFDI4Cat newsletter. The NFDI4Cat newsletter is a short compilation about our project results. A short and concise overview that keeps you up to date with our work. You can subscribe to it here!
Tight Junction Protein Claudin-7 Is Essential for Intestinal Epithelial Stem Cell Self-Renewal and Differentiation
Creators: name: Parker, J.
name: Yang, J.
name: Lu, Q.
name: Sabu, S.
name: Benderman, L.J.
name: Chen, Y.-H.
name: Ding, L.
name: Xing, T.
Publisher: name: Elsevier Inc
Year: 2020

description: Background & Aims: Claudin-7 (Cldn7) is a tight junction (TJ) membrane protein located at the apical TJ and basolateral side of intestinal epithelial cells. Deletion of Cldn7 by gene targeting leads to the inflammatory bowel disease–like phenotype in mice, which includes weight loss, diarrhea, mucosa ulceration, and severe intestinal epithelial damage. In this study, we test our hypothesis that Cldn7 plays a critical role in regulating intestinal crypt stem cell functions. Methods: Gene expression microarray, quantitative reverse-transcription polymerase chain reaction, in situ hybridization, histologic examinations, immunoblotting, 3-dimensional organoid culture, and various treatments to rescue Cldn7-deficient organoid defects were conducted using global Cldn7 knockout mice and inducible, conditional Cldn7 knockout mice. Results: Gene deletion of Cldn7 in intestines showed significant alteration of expression profiles with striking down-regulation of intestinal crypt stem cell markers such as Olfm4, dislocated proliferative cells, and disrupted epithelial cell differentiation. In addition, the isolated Cldn7-deficient crypts where the stem cells reside were either unable to survive at all or formed defective spheroids, highlighting the functional impairment of crypt stem cells in the absence of Cldn7. Remarkably, the Cldn7-expressing organoids with buddings underwent rapid cell degeneration within days after turning off Cldn7 expression in the culture. We identified that activation of Wnt/β-catenin signaling rescued the organoid defects caused by Cldn7 deletion. Conclusions: In this study, we show that Cldn7 is indispensable in controlling Wnt/β-catenin signaling–dependent intestinal epithelial stem cell survival, self-renewal, and cell differentiation. This study could open a door to study roles of TJ proteins in stem cell regulations in other tissues and organs.