cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
The p41 isoform of invariant chain is a chaperone for cathepsin L
Creators: name: Erickson, Ann
name: Driessen, Christoph
name: Bikoff, Elizabeth
name: Lennon-Duménil, Ana Maria
name: Ploegh, Hidde L.
name: Roberts, Rebecca A.
name: Overkleeft, Herman S.
name: Peters, Peter J.
name: Valentijn, Karine
name: Bryant, Paula Wolf
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2001

description: The p41 splice variant of major histocompatibility complex (MHC) class II-associated invariant chain (Ii) contains a 65 aa segment that binds to the active site of cathepsin L (CatL), a lysosomal cysteine protease involved in MHC class II-restricted antigen presentation. This segment is absent from the predominant form of Ii, p31. Here we document the in vivo significance of the p41–CatL interaction. By biochemical means and electron microscopy, we demonstrate that the levels of active CatL are strongly reduced in bone marrow-derived antigen-presenting cells that lack p41. This defect mainly concerns the mature two-chain forms of CatL, which depend on p41 to be expressed at wild-type levels. Indeed, pulse–chase analysis suggests that these mature forms of CatL are degraded by endocytic proteases when p41 is absent. We conclude that p41 is required for activity of CatL by stabilizing the mature forms of the enzyme. This suggests that p41 is not merely an inhibitor of CatL enzymatic activity, but serves as a chaperone to help maintain a pool of mature enzyme in late-endocytic compartments of antigen-presenting cells.
Additional file 1 of A multi-perspective qualitative exploration of the reasons for changes in the physical activity among 10–11-year-old children following the easing of the COVID-19 lockdown in the UK in 2021
Creators: name: Walker, Robert
name: House, Danielle
name: Emm-Collison, Lydia
name: Salway, Ruth
name: Tibbitts, Byron
name: Sansum, Kate
name: Reid, Tom
name: Breheny, Katie
name: Churchward, Sarah
name: Williams, Joanna G.
name: de Vocht, Frank
name: Hollingworth, William
name: Foster, Charlie
name: Jago, Russell
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: FOS: Biological sciences
subject: Science Policy
subject: Sociology
subject: FOS: Sociology
subject: Developmental Biology

description: Additional file 1: Supplementary File. Interview and focus group topic guides.
Parking Behaviour Analysis of Shared E-Bike Users Based on a Real-World Dataset -- A Case Study in Dublin, Ireland
Creators: name: Yan, Sen
name: Liu, Mingming
name: O'Connor, Noel E.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Physics and Society (physics.soc-ph)
subject: FOS: Physical sciences

description: In recent years, an increasing number of shared E-bikes have been rolling out rapidly in our cities. It therefore becomes important to understand new behaviour patterns of the cyclists in using these E-bikes as a foundation for the novel design of shared micromobility services as part of the realisation for next generation intelligent transportation systems. In this paper, we deeply investigate the users' behaviour of shared E-bikes in a case study by using the real-world dataset collected from the shared E-bike company, MOBY, which currently operates in Dublin, Ireland. More specifically, we look into the parking behaviours of users as we know that inappropriate parking of these bikes can not only increase the management costs of the company but also result in other users' inconveniences, especially in situations of battery shortage, which inevitably reduces the overall operational efficacy of these shared E-bikes. Our work has conducted analysis at both bike station and individual level in a fully anonymous and GDPR-Compliant manner, and our results have shown that up to 12.9% of shared E-bike users did not park their bikes properly at the designated stands. Different visualisation tools have been applied to better illustrate our obtained results.
description: The manuscript has been accepted by the IEEE VTC 2022-Spring Conference
The Pleurobranchida Berthella stellata (Risso, 1826) (Mollusca: Gastropoda: Heterobranchia) in the Mediterranean: morphology, biology and molecular analysis of a population in Es Caials (NE Spain)
Creators: name: CÓRDOBA GONZÁLEZ,
name: ENGUÍDANOS,
name: PONTES, Darío Alba Miquel
name: VALDÉS, Ángel
name: BALLESTEROS, Manuel
Publisher: name: Station Biologique de Roscoff (SBR)
Year: 2024

description: Berthella stellata (Risso, 1826), a species of Pleurobranchidae characterized by a Y-shaped white patch on the dorsum, is distributed in the Mediterranean and Eastern Atlantic. In this paper we have compiled records of this species on the Catalonian coast (NE Spain) and studied a permanent population of B. stellata over time in the locality of Es Caials (Costa Brava, NE Spain). Live specimens were collected and photographed and details of their morphology, radula, and jaws, as well as molecular data were studied to compare them with other specimens from different parts of the species distribution range. Our results indicate that despite the color variation, the population of B. stellata from Es Caials shares both morphological and molecular traits with specimens from the Northeast Atlantic and the Mediterranean of Europe, the only regions where the species name B. stellata is applicable, populations from other regions belonging to different species. Also, that this population of this region has been studied over 20 years where we have found that its number of specimens has increased thanks to the stable temperature of the waters of the place and the availability of food.
Supplementary Tables and Figures from A synthesis and meta-analysis of the Fe chemistry of serpentinites and serpentine minerals.
Creators: name: Mayhew, Lisa E.
name: Ellison, Eric T.
Publisher: name: The Royal Society
Year: 2019
Subjects: subject: Geology
subject: FOS: Earth and related environmental sciences
subject: Geochemistry

description: Includes references used in databases and 2 data tables and 6 figures as referenced in the text.
T-loop assembly in vitro involves binding of TRF2 near the 3' telomeric overhang
Creators: name: Griffith, Jack D.
name: Stansel, Rachel M.
name: De Lange, Titia
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2001

description: Mammalian telomeres contain a duplex TTAGGG-repeat tract terminating in a 3′ single-stranded overhang. TRF2 protein has been implicated in remodeling telomeres into duplex lariats, termed t-loops, in vitro and t-loops have been isolated from cells in vivo. To examine the features of the telomeric DNA essential for TRF2-promoted looping, model templates containing a 500 bp double-stranded TTAGGG tract and ending in different single-stranded overhangs were constructed. As assayed by electron microscopy, looped molecules containing most of the telomeric tract are observed with TRF2 at the loop junction. A TTAGGG-3′ overhang of at least six nucleotides is required for loop formation. Termini with 5′ overhangs, blunt ends or 3′ termini with non-telomeric sequences at the junction are deficient in loop formation. Addition of non-telomeric sequences to the distal portion of a 3′ overhang beginning with TTAGGG repeats only modestly diminishes looping. TRF2 preferentially localizes to the junction between the duplex repeats and the single-stranded overhang. Based on these findings we suggest a model for the mechanism by which TRF2 remodels telomeres into t-loops.
A Learning Analytics Tool for Usability Assessment in Moodle Environments
Creators: name: Fenu, Gianni
name: Marras, Mirko
name: Meles, Massimiliano
Publisher: name: Journal of e-Learning and Knowledge Society
Year: 2017

description: The use of analytics technologies is increasingly successful in the e-learning domain. In this paper, we propose a novel model aiming at evaluating usability of interfaces adopted by Learning Management Systems and Massive Open Online Courses platforms based on the comparison between desktop and mobile versions, using specific native indicators. The indicators obtained from log files typically tracked by the e-learning platforms are defined as comparable scores. Then, to put the model into practice, we implemented it into Moodle LMS as a preliminary case study. This contribution promises to reduce both time and cost for quality assessment of user interfaces in the e-learning domain, while ensuring adaptability to different platforms.
description: Journal of e-Learning and Knowledge Society, Vol 13 No 3 (2017): EMEMITALIA Conference 2016
New observation and depth extension of Tethys fimbria Linnaeus, 1767 (Nudibranchia: Tethydidae) from the Sea of Marmara, Turkey
Creators: name: ARTÜZ M, Levent
name: ARTÜZ, O. Bülent
Publisher: name: Station Biologique de Roscoff (SBR)
Year: 2024

description: The dendronotid nudibranch, Tethys fimbria Linnaeus, 1767, which is native to the Mediterranean Sea was caught during beam trawl sampling at a depth of 1175 m in the Sea of Marmara. This species has established populations in the Mediterranean Sea, but has recently been observed off Uçmakdere in the Sea of Marmara, Turkey.
$δ^{44/40}$Ca-$δ^{88/86}$Sr multi-proxy constrains primary origin of Marinoan cap carbonates
Creators: name: Wang, Jiuyuan
name: Jacobson, Andrew D.
name: Sageman, Bradley B.
name: Hurtgen, Matthew T.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: Geophysics (physics.geo-ph)
subject: FOS: Physical sciences

description: The Neoproterozoic Earth experienced at least two global-scale glaciations termed Snowball Earth events. 'Cap carbonates' were widely deposited after the events, but controversy surrounds their origin. Here, we apply the novel $δ^{44/40}$Ca-$δ^{88/86}$Sr multi-proxy to two Marinoan (ca. 635 Ma) cap carbonate sequences from Namibia and show that the rocks archive primary environmental signals deriving from a combination of seawater-glacial meltwater mixing and kinetic isotope effects. In an outer platform section, dolostone $δ^{44/40}$Ca and $δ^{88/86}$Sr values define a line predicted for kinetic mass-dependent isotope fractionation. This dolostone mostly precipitated from meltwater. Moreover, stratigraphically higher samples exhibiting the fastest precipitation rates correlate with elevated 87Sr/86Sr ratios, consistent with long-held expectations that a rapid deglacial weathering pulse forced cap carbonate formation. An inner-platform dolostone shows greater effects from water-mass mixing but still reveals that precipitation rates increased up-section. Overlying limestones show the greatest Ca and Sr contributions from seawater. Amplification of local coastal processes during global ice sheet collapse offers a simple but sufficient proposition to explain the Ca isotope heterogeneity of cap carbonates. Detection of kinetic isotope effects in the rock record provides a basis for developing the $δ^{44/40}$Ca-$δ^{88/86}$Sr multi-proxy as an indicator of saturation state and $p$CO$_2$.
Supplementary Tables and Figures from A synthesis and meta-analysis of the Fe chemistry of serpentinites and serpentine minerals
Creators: name: Mayhew, Lisa E.
name: Ellison, Eric T.
Publisher: name: The Royal Society
Year: 2019
Subjects: subject: Geology
subject: FOS: Earth and related environmental sciences
subject: Geochemistry

description: Includes references used in databases and 2 data tables and 6 figures as referenced in the text.
Excesses in the low-mass Higgs-boson search and the W-boson mass measurement
Creators: name: Biekötter, Thomas
name: Heinemeyer, Sven
name: Weiglein, Georg
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The CDF collaboration recently reported a measurement of the $W$-bosos mass, $M_W$, showing a large positive deviation from the Standard Model (SM) prediction. The question arises whether extensions of the SM exist that can accommodate such large values, and what further phenomenological consequences arise from this. A different type of deviation from the SM has been observed experimentally in the searches for light Higgs bosons. CMS has observed two local $\sim 3\,σ$ excesses in the $γγ$ and $τ^+τ^-$ final states for a hypothetical Higgs-boson mass of $\sim 95$ GeV. These two excesses are compatible with the corresponding ATLAS limits. A third excess was observed in the Higgs-boson searches at LEP in the $b \bar b$ final state at the local $\sim 2\,σ$ confidence level at about the same Higgs-boson mass. It was shown recently that the three excesses can be described the the 2HDM extended with a real singlet (N2HDM) of Yukawa type IV, while being in agreement with all other theoretical and experimental constraints. We demonstrate that the parameter space that accomodates the three excesses can also give a large contribution to $M_W$ in agreement with the recent CDF measurement. We discuss further phenomenological consequences of this scenario.
description: 10 pages, 3 figures, v.2: discussion of Z-boson width included, matches published version. arXiv admin note: text overlap with arXiv:2203.13180
Multiple higher-order topological phases with even and odd pairs of zero-energy corner modes in a $C_3$ symmetry broken model
Creators: name: Saha, Sudarshan
name: Nag, Tanay
name: Mandal, Saptarshi
Publisher: name: arXiv
Year: 2022
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: The higher-order corner modes for quantum anomalous Hall insulators in $C_3$ symmetry broken honeycomb lattice have been engineered recently. Here we consider an extended Haldane model in presence of inversion symmetry breaking sub-lattice mass, time-reversal symmetry breaking Zeeman field and spin-orbit coupling interaction where we find that only the quantum spin Hall insulator can host the second-order dipolar phase while the remaining two first-order topological phases do not morph into the latter. Remarkably, four-fold degeneracy of zero-energy dipolar states can be reduced to two-fold under the application (withdrawn) of sub-lattice mass (Zeeman field) term when the spin-orbit coupling is already present. On the other hand, the sub-lattice mass and Zeeman field terms compete with each other to pin down the two mid-gap states at zero-energy in the absence or presence of spin-orbit coupling. Interestingly, the bulk-polarization can topologically characterize the dipolar phase irrespective of the energy of the mid-gap states as long as inversion symmetry is preserved. The effective gap criterion can qualitatively mimic the extent of SOT phase originated by the interplay between finite Zeeman exchange field, sub-lattice mass, and SOC interaction.
description: 7 pages, and 6 figures
Developing Critical Thinking in online search
Creators: name: Petrucco, Corrado
name: Ferranti, Cinzia
Publisher: name: Journal of e-Learning and Knowledge Society
Year: 2017

description: Digital skills especially those related to Information Literacy, are today considered fundamental to the education of students, both at school and at university. Searching and evaluating information found on the Internet is surely an important competency. An effective way to develop this competency is to educate students about the development of critical thinking. The article presents a qualitative-quantitative survey conducted during a course in Educational Technologies within a five year Degree program. The outcomes of the survey reveal some interesting behaviors and perceptions of students when they are faced with the Web search process and the characteristics of their critical thinking processes: some aspects of critical thinking are generally well-supported, but others are acquired only after specific training. Experience shows that if properly motivated by metacognitive reflections and a clear method, students can actually critically evaluate the information presented online, the sources, and the sustainability of the arguments found. positive results also occurred when the evaluation process was done in a collaborative modality.
description: Journal of e-Learning and Knowledge Society, Vol 13 No 3 (2017): EMEMITALIA Conference 2016
Population dynamics of Ruditapes decussatus (Mollusca: Bivalvia) in the Gulf of Gabes, Tunisia
Creators: name: DERBALI, Abdelkarim
name: LOUKIL-BAKLOUTI, Amira
name: ABDMOULEH-KESKES, Fatma
name: DAMMAK-WALHA, Lamia
Publisher: name: Station Biologique de Roscoff (SBR)
Year: 2024

description: Ruditapes decussatus is one of the most abundant bivalve species in the Gulf of Gabes. Its current exploitation status and management are becoming a major concern for the fishing industry in Tunisia. The aim of this study was to ascertain the population structure, growth, mortality and exploitation rate of R. decussatus. Length-frequency data were analyzed for the estimation of population parameters using the FiSATΙΙ software. Asymptotic length (L∞) was found to be 59.95 mm and growth coefficient (K) was 0.70 yr -1. The growth performance index (φ') was 3.40. Total mortality (Z) was estimated by the length-converted catch curve at 2.01 yr-1, fishing mortality (F) at 1.02 yr-1, and natural mortality (M) at 0.99 yr-1. The exploitation rate (E = 0.51 yr-1) indicated that the fishing pressure on the R. decussatus population was relatively high. The condition index was used as a tool to identify optimal and sustainable harvesting periods which correspond to the period between April and June.
Are Computer Adaptive Tests suitable for assessment in MOOCs
Creators: name: Rossano, Veronica
name: Pesare, Enrica
name: Roselli, Teresa
Publisher: name: Journal of e-Learning and Knowledge Society
Year: 2017

description: Assessment is one of the basic issues in both formal and informal educational contexts. Current online courses are massive and online, thus it is important to find new strategies for improve the effectiveness of evaluation. In MOOCs (Massive Open Online Courses), indeed, there is also the certification of knowledge and skills acquisition that requires more formal and trustworthy methods. Researchers should work to combine pedagogical and technological solutions to guarantee the effectiveness of learning measures. In this context, the Computer Adaptive Testing (CAT) could be useful to better measure the knowledge acquisition using a quiz, as usually happens in MOOCs. These are the premises of this research work that, in order to understand if CAT could be suitable for assessment in MOOCs, proposes a first algorithm to measure the acquired knowledge using a quiz-game. The pilot study attests the appreciation of users.
description: Journal of e-Learning and Knowledge Society, Vol 13 No 3 (2017): EMEMITALIA Conference 2016
Peer assessment to promote Deep Learning and to reduce a Gender Gap in the Traditional Introductory Programming Course
Creators: name: Carbonaro, Antonella
name: Ravaioli, Mirko
Publisher: name: Journal of e-Learning and Knowledge Society
Year: 2017

description: Peer assessment mechanism is becoming increasingly important in different computer programming courses to give students opportunities to learn from each other, to improve the learning experience and to reach efficient learning outcomes. Nevertheless, new methodological approaches developed to help students in computer programming courses have had to deal with a thorough study of the aspects related to the gender difference in this context. The paper presents a web-based system, which improved students' program skills by reviewing peers' source codes and delivering feedback to peers. The purpose was to provide evidence that peer assessment in computer programming has a positive instructive effect. Moreover, we want to investigate if there is a gender gap in the traditional introductory programming course and how can we use peer assessment principles to reduce it.
description: Journal of e-Learning and Knowledge Society, Vol 13 No 3 (2017): EMEMITALIA Conference 2016
Sustainable protective function of sorus tissue during the alternation of generations in Saccharina japonica
Creators: name: ABE, Kenshiro
name: ARIGA, Inori
name: UJI, Toshiki
name: MIZUTA, Hiroyuki
Publisher: name: Station Biologique de Roscoff (SBR)
Year: 2024

description: The processes involved in the life cycling of the brown alga Saccharina japonica were investigated through laboratory culturing experiments. We observed that meiospores were released relatively early from the ripe sorus on the sporophyte. Following the release of free meiospores, there was a partial detachment of the sorus, leading to the release of other reproductive cells. When a small piece of exfoliated sorus tissue was cultured separately, the appearance of gametophytes and then sporophytes occurred later for the free meiospores. These observations suggest that at least two processes are involved in the production of new sporophytes. This phenomenon appears to be an active and regulated reproductive strategy, as these processes were stimulated by the abscisic acid hormone. Additionally, we examined the effects of grazing by sea urchins on the dissemination of reproductive cells. Undigested sorus tissue segments containing sporangia and paraphyses were observed in the digestive tracts, as well as in the faeces released by sea urchins. From these undigested sorus tissue segments, were observed the development of gametophytes and then sporophytes when the faeces were cultured independently. These findings show that herbivores play a role in the dissemination of brown algae reproductive cells and provide evidence for the sustained protective function of sorus tissues, even after detachment from the mother plants and exposure to sea urchin feeding. We discuss the potential importance of these reproductive processes in the persistence and diversity of kelp populations.
Additional file 1 of Digital behaviour change interventions to promote physical activity in overweight and obese adolescents: a systematic review protocol
Creators: name: Kassim, Puteri Shanaz Jahn
name: Muhammad, Noor Azimah
name: Rahman, Nur Faraheen Abdul
name: Sidik, Sherina Mohd
name: Essau, Cecilia A.
name: Shah, Shamsul Azhar
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Science Policy
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 1. PRISMA-P Checklist.
Electronic supplementary material of "Pathogen defence is a potential driver of social evolution in ambrosia beetles".
Creators: name: Nuotclà, Jon A.
name: Biedermann, Peter H. W.
name: Taborsky, Michael
Publisher: name: The Royal Society
Year: 2019
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology
subject: 60801 Animal Behaviour

description: Includes additional detail on laboratory rearing of Xyleborinus saxesenii and techniques used for in situ injection and quantification of pathogens. Figure S1-2 illustrate Aspergillus sp. growing from dead X. saxesenii and the relative cooperative investment by larvae, adult males and females. Tables S1-4 provide detailed information to the outputs of generalised linear mixed models, the origin of the different fungal isolates and an ethogram for the study species X saxesenii
First record of the fried egg jellyfish Phacellophora camtschatica Brandt, 1835 (Cnidaria: Scyphozoa) in mainland Portugal, with notes on occurrences for the Madeira and Azores archipelagos, northeastern Atlantic Ocean
Creators: name: DOS SANTOS, Antonina
name: PIRES, Rita F. T.
name: RIBEIRO, Filipa
name: DIAS, Inês M.
name: SOUSA, Lígia Faria De
name: BARTILOTTI, Cátia
name: FREITAS, Mafalda
Publisher: name: Station Biologique de Roscoff (SBR)
Year: 2024

description: Phacellophora camtschatica, a cosmopolitan species, occurring mostly in cold and temperate waters, was recorded for the first time in mainland Portugal in 2020. The occurrence was confirmed through photographs of the sighting registered by the citizen science program GelAvista, which was created to fill the gap on the knowledge about jellyfish in Portugal. Additional sightings were received for the Madeira and Azores archipelagos in 2019 and 2020 to 2021, respectively. Considering the information published for the species to date, these occurrences are discussed, adding to the existing knowledge on the distribution of the species for the north eastern Atlantic Ocean. The study also highlights the importance and usefulness of citizen science programs for increasing knowledge and monitoring of marine organisms.
The Milky Way and Andromeda galaxies in a constrained hydrodynamical simulation: morphological evolution
Creators: name: Scannapieco, Cecilia
name: Creasey, Peter
name: Nuza, Sebastian E.
name: Yepes, Gustavo
name: Gottloeber, Stefan
name: Steinmetz, Matthias
Publisher: name: arXiv
Year: 2015
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We study the two main constituent galaxies of a constrained simulation of the Local Group as candidates for the Milky Way (MW) and Andromeda (M31). We focus on the formation of the stellar discs and its relation to the formation of the group as a rich system with two massive galaxies, and investigate the effects of mergers and accretion as drivers of morphological transformations. We use a state-of-the-art hydrodynamical code which includes star formation, feedback and chemical enrichment to carry out our study. We run two simulations, where we include or neglect the effects of radiation pressure from stars, to investigate the impact of this process on the morphologies and star formation rates of the simulated galaxies. We find that the simulated M31 and MW have different formation histories, even though both inhabit, at z=0, the same environment. These differences directly translate into and explain variations in their star formation rates, in-situ fractions and final morphologies. The M31 candidate has an active merger history, as a result of which its stellar disc is unable to survive unaffected until the present time. In contrast, the MW candidate has a smoother history with no major mergers at late times, and forms a disc that grows steadily; at z=0 the simulated MW has an extended, rotationally-supported disc which is dominant over the bulge. Our two feedback implementations predict similar evolution of the galaxies and their discs, although some variations are detected, the most important of which is the formation time of the discs: in the model with weaker/stronger feedback the discs form earlier/later. In summary, by comparing the formation histories of the two galaxies, we conclude that the particular merger/accretion history of a galaxy rather than its environment at the LG-scales is the main driver of the formation and subsequent growth or destruction of galaxy discs.
description: 12 pages, 7 figures, accepted for publication in A&A
t-loops at trypanosome telomeres
Creators: name: Cross, George A.M.
name: Griffith, Jack D.
name: De Lange, Titia
name: Muñoz-Jordán, Jorge L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2001

description: Mammalian telomeres form large duplex loops (t-loops) that may sequester chromosome ends by invasion of the 3′ TTAGGG overhang into the duplex TTAGGG repeat array. Here we document t-loops in Trypanosoma brucei, a kinetoplastid protozoan with abundant telomeres due to the presence of many minichromosomes. These telomeres contained 10–20 kb duplex TTAGGG repeats and a 3′ TTAGGG overhang. Electron microscopy of psoralen/UV cross-linked DNA revealed t-loops in enriched telomeric restriction fragments and at the ends of isolated minichromosomes. In mammals, t-loops are large (up to 25 kb), often comprising most of the telomere. Despite similar telomere lengths, trypanosome t-loops were much smaller (∼1 kb), indicating that t-loop sizes are regulated. Coating of non-cross-linked minichromosomes with Escherichia coli single-strand binding protein (SSB) often revealed 3′ overhangs at both telomeres and several cross-linked minichromosomes had t-loops at both ends. These results suggest that t-loops and their prerequisite 3′ tails can be formed on the products of both leading and lagging strand synthesis. We conclude that t-loops are a conserved feature of eukaryotic telomeres.
A crystallographic view of interactions between Dbs and Cdc42: PH domain-assisted guanine nucleotide exchange
Creators: name: Campbell, Sharon L.
name: Siderovski, David P.
name: Worthylake, David K.
name: Sondek, John
name: Snyder, Jason T.
name: Rossman, Kent L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: Dbl-related oncoproteins are guanine nucleotide exchange factors (GEFs) specific for Rho guanosine triphosphatases (GTPases) and invariably possess tandem Dbl (DH) and pleckstrin homology (PH) domains. While it is known that the DH domain is the principal catalytic subunit, recent biochemical data indicate that for some Dbl-family proteins, such as Dbs and Trio, PH domains may cooperate with their associated DH domains in promoting guanine nucleotide exchange of Rho GTPases. In order to gain an understanding of the involvement of these PH domains in guanine nucleotide exchange, we have determined the crystal structure of a DH/PH fragment from Dbs in complex with Cdc42. The complex features the PH domain in a unique conformation distinct from the PH domains in the related structures of Sos1 and Tiam1·Rac1. Consequently, the Dbs PH domain participates with the DH domain in binding Cdc42, primarily through a set of interactions involving switch 2 of the GTPase. Comparative sequence analysis suggests that a subset of Dbl-family proteins will utilize their PH domains similarly to Dbs.
Electronic supplementary material of "Pathogen defence is a potential driver of social evolution in ambrosia beetles"
Creators: name: Nuotclà, Jon A.
name: Biedermann, Peter H. W.
name: Taborsky, Michael
Publisher: name: The Royal Society
Year: 2019
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology
subject: 60801 Animal Behaviour

description: Includes additional detail on laboratory rearing of Xyleborinus saxesenii and techniques used for in situ injection and quantification of pathogens. Figure S1-2 illustrate Aspergillus sp. growing from dead X. saxesenii and the relative cooperative investment by larvae, adult males and females. Tables S1-4 provide detailed information to the outputs of generalised linear mixed models, the origin of the different fungal isolates and an ethogram for the study species X saxesenii
Search for Higgs boson decays to a Z boson and a photon in proton-proton collisions at $\sqrt{s}$ = 13 TeV
Creators: name: CMS Collaboration
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: Results are presented from a search for the Higgs boson decay H $\to$ Z$γ$, where Z $\to$ $\ell^+\ell^-$ with $\ell$ = e or $μ$. The search is performed using a sample of proton-proton (pp) collision data at a center-of-mass energy of 13 TeV, recorded by the CMS experiment at the LHC, corresponding to an integrated luminosity of 138 fb$^{-1}$. Events are assigned to mutually exclusive categories, which exploit differences in both event topology and kinematics of distinct Higgs production mechanisms to enhance signal sensitivity. The signal strength $μ$, defined as the product of the cross section and the branching fraction [$σ($pp $\to$ H$)\mathcal{B}($H $\to$ Z$γ)$] relative to the standard model prediction, is extracted from a simultaneous fit to the $\ell^+\ell^-γ$ invariant mass distributions in all categories and is found to be $μ$ = 2.4 $\pm$ 0.9 for a Higgs boson mass of 125.38 GeV. The statistical significance of the observed excess of events is 2.7 standard deviations. This measurement corresponds to $σ($pp $\to$ H$)\mathcal{B}($H $\to$ Z$γ)$ = 0.21 $\pm$ 0.08 pb. The observed (expected) upper limit at 95% confidence level on $μ$ is 4.1 (1.8). The ratio of branching fractions $\mathcal{B}($H $\to$ Z$γ) / \mathcal{B}($H $\to$ $γγ)$ is measured to be 1.5 $^{+0.7}_{-0.6}$, which agrees with the standard model prediction of 0.69 $\pm$ 0.04 at the 1.5 standard deviation level.
description: Replaced with the published version. Added the journal reference and the DOI. All the figures and tables can be found at http://cms-results.web.cern.ch/cms-results/public-results/publications/HIG-19-014 (CMS Public Pages)
CHIP activates HSF1 and confers protection against apoptosis and cellular stress
Creators: name: Xu, Wanping
name: Dai, Qian
name: Wu, Yaxu
name: McDonough, Holly
name: Li, Hui Hua
name: Whaley, Ryan A.
name: Neckers, Len
name: Cyr, Douglas
name: Zhang, Chunlian
name: Patterson, Cam
name: Godfrey, Virginia
name: Madamanchi, Nageswara
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2003

description: Induction of molecular chaperones is the characteristic protective response to environmental stress, and is regulated by a transcriptional program that depends on heat shock factor 1 (HSF1), which is normally under negative regulatory control by molecular chaperones Hsp70 and Hsp90. In metazoan species, the chaperone system also provides protection against apoptosis. We demonstrate that the dual function co-chaperone/ubiquitin ligase CHIP (C-terminus of Hsp70-interacting protein) regulates activation of the stress-chaperone response through induced trimerization and transcriptional activation of HSF1, and is required for protection against stress-induced apoptosis in murine fibroblasts. The consequences of this function are demonstrated by the phenotype of mice lacking CHIP, which develop normally but are temperature-sensitive and develop apoptosis in multiple organs after environmental challenge. CHIP exerts a central and unique role in tuning the response to stress at multiple levels by regulation of protein quality control and transcriptional activation of stress response signaling.
Spatio-temporal distribution of the calanoid copepod genus Centropages in relation to environmental factors in the southern Adriatic Sea (NE Mediterranean)
Creators: name: VUKANIĆ, Vera
name: MALOVIĆ, Miodrag
name: VUKANIĆ, Dušan
name: MILOSAVLJEVIĆ, Nataša
Publisher: name: Station Biologique de Roscoff (SBR)
Year: 2024

description: Spatial and temporal variability of Copepoda was studied at four stations in the Bay of Boka Kotorska and five stations in the open waters of the South Adriatic Sea in 2008. The research area included three sectors differing in geographical and hydrological conditions: The Bay of Boka Kotorska, the estuary of the Bojana river (both with the typical neritic Copepod fauna), and offshore waters of South Adriatic Sea (with the pelagic species). Four species from the genus Centropages Kröyer, 1849 were registered: C. typicus Kröyer, 1849, C. kröyeri Giesbrecht, 1893, C. violaceus (Claus, 1863) and C. ponticus Karavaev, 1895. Only one of the species, C. typicus, was encountered at all nine stations. By examining the seasonal distribution and abundance of specimens, as well as the ecological properties of the researched area, we observed particular behavioural pattern in distribution and abundance of certain species that had not been described previously. The conclusion is that the seasonal differences in the horizontal distribution are associated with the dynamics of the hydrographic conditions of the South Adriatic Sea. Significant relationships have been reported between C. kröyeri abundance and the temperature and dissolved oxygen concentration, and C. typicus abundance and pH factor.
Bubble Universes With Different Gravitational Constants
Creators: name: Takamizu, Yu-ichi
name: Maeda, Kei-ichi
Publisher: name: arXiv
Year: 2015
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We argue a scenario motivated by the context of string landscape, where our universe is produced by a new vacuum bubble embedded in an old bubble and these bubble universes have not only different cosmological constants, but also their own different gravitational constants. We study these effects on the primordial curvature perturbations. In order to construct a model of varying gravitational constants, we use the Jordan-Brans-Dicke (JBD) theory where different expectation values of scalar fields produce difference of constants. In this system, we investigate the nucleation of bubble universe and dynamics of the wall separating two spacetimes. In particular, the primordial curvature perturbation on superhorizon scales can be affected by the wall trajectory as the boundary effect. We show the effect of gravitational constant in the exterior bubble universe can provide a peak like a bump feature at a large scale in a modulation of power spectrum.
description: 15 pages, 6 figures
Supplemental text and figures from Social influence and interaction bias can drive emergent behavioural specialization and modular social networks across systems.
Creators: name: Tokita, Christopher K.
name: Tarnita, Corina E.
Publisher: name: The Royal Society
Year: 2020
Subjects: subject: 60114 Systems Biology
subject: FOS: Biological sciences
subject: 60199 Biochemistry and Cell Biology not elsewhere classified
subject: 69999 Biological Sciences not elsewhere classified
subject: Computational Biology

description: This file contains additional analytical calculations showing how group size and interaction bias can influence self-organized behavioural specialization. Additionally, supplemental figures are included here.
Integrative Taxonomy of Hermundura annandalei Fauvel, (Phyllodocida: Pilargidae) from Sundarbans estuarine system, India
Creators: name: BHAUMIK, Snigdha
name: MANDAL, Sumit
Publisher: name: Station Biologique de Roscoff (SBR)
Year: 2024

description: The polychaete Hermundura annandalei was first described as Talehsapia annandalei based on two specimens collected in Taleh-Sap, Thailand. Due to taxonomic controversies, genus Hermundura underwent several re-descriptions and revisions before being established as a senior synonym of Talehsapia, Parandalia and Loandalia. The pilargid polychaete species, Hermundura annandalei Fauvel, 1932 is reported from the intertidal habitats of river Matla in the Sundarbans estuarine system. The species has been identified based on integrative taxonomic approach using morphological examination and supported by Cytochrome Oxidase Subunit I (mtCOI) gene. For the first time the mtCOI region of H. annandalei is sequenced and the nucleotide variation is compared with its congeners. The inter-specific distances between the sequenced H. annandalei and other Hermundura species mined from the BOLD database ranged from 15.73%-16.11%. Neighbor-Joining and Maximum Likelihood dendrograms with 1000 bootstrap replications were constructed for H. annandalei selecting twelve mtCOI sequences from NCBI and BOLD databases. The present report might be a stepping stone to building a comprehensive DNA barcode database of polychaete species from the largest mangrove ecosystem of the world: The Sunderbans.
Holographic dark energy from minimal supergravity
Creators: name: Landim, Ricardo C. G.
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We embed models of holographic dark energy coupled to dark matter in minimal supergravity plus matter, with one chiral superfield. We analyze two cases. The first one has the Hubble radius as the infrared cutoff and the interaction between the two fluids is proportional to the energy density of the dark energy. The second case has the future event horizon as infrared cutoff while the interaction is proportional to the energy density of both components of the dark sector.
description: 7 pages, typos corrected, accepted for publication in IJMPD
Supplemental text and figures from Social influence and interaction bias can drive emergent behavioural specialization and modular social networks across systems
Creators: name: Tokita, Christopher K.
name: Tarnita, Corina E.
Publisher: name: The Royal Society
Year: 2019
Subjects: subject: 60114 Systems Biology
subject: FOS: Biological sciences
subject: 60199 Biochemistry and Cell Biology not elsewhere classified
subject: 69999 Biological Sciences not elsewhere classified
subject: Computational Biology

description: This file contains additional analytical calculations showing how group size and interaction bias can influence self-organized behavioural specialization. Additionally, supplemental figures are included here.
Cytosolic HSP90 associates with and modulates the Arabidopsis RPM1 disease resistance protein
Creators: name: Krishna, Priti
name: Tornero, Pablo
name: Dangl, Jeffery L.
name: Hubert, David A.
name: Shirasu, Ken
name: Takahashi, Akira
name: Belkhadir, Youssef
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2003

description: The Arabidopsis protein RPM1 activates disease resistance in response to Pseudomonas syringae proteins targeted to the inside of the host cell via the bacterial type III delivery system. We demonstrate that specific mutations in the ATP-binding domain of a single Arabidopsis cytosolic HSP90 isoform compromise RPM1 function. These mutations do not affect the function of related disease resistance proteins. RPM1 associates with HSP90 in plant cells. The Arabidopsis proteins RAR1 and SGT1 are required for the action of many R proteins, and display some structural similarity to HSP90 co-chaperones. Each associates with HSP90 in plant cells. Our data suggest that (i) RPM1 is an HSP90 client protein; and (ii) RAR1 and SGT1 may function independently as HSP90 cofactors. Dynamic interactions among these proteins can regulate RPM1 stability and function, perhaps similarly to the formation and regulation of animal steroid receptor complexes.
Arak Inequalities for Concentration Functions and the Littlewood-Offord Problem
Creators: name: Eliseeva, Yulia S.
name: Götze, Friedrich
name: Zaitsev, Andrei Yu.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Probability (math.PR)
subject: FOS: Mathematics
subject: Primary 60F05, secondary 60E15, 60G50

description: Let $X,X_1,\ldots,X_n$ be independent identically distributed random variables. In this paper we study the behavior of concentration functions of weighted sums $\sum_{k=1}^{n}a_k X_k$ with respect to the arithmetic structure of coefficients $a_k$ in the context of the Littlewood--Offord problem. Concentration results of this type received renewed interest in connection with distributions of singular values of random matrices. Recently, Tao and Vu proposed an Inverse Principle in the Littlewood-Offord problem. We discuss the relations between the Inverse Principle of Tao and Vu as well as that of Nguyen and Vu and a similar principle formulated for sums of arbitrary independent random variables in the work of Arak from the 1980's.
description: 21 pages
The M-dwarfs in Multiples (MinMs) survey - I. Stellar multiplicity among low-mass stars within 15 pc
Creators: name: Ward-Duong, K.
name: Patience, J.
name: De Rosa, R. J.
name: Bulger, J.
name: Rajan, A.
name: Goodwin, S. P.
name: Parker, Richard J.
name: McCarthy, D. W.
name: Kulesa, C.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We present a large-scale, volume-limited companion survey of 245 late-K to mid-M (K7-M6) dwarfs within 15 pc. Infrared adaptive optics (AO) data were analysed from the Very Large Telescope, Subaru Telescope, Canada-France-Hawaii Telescope, and MMT Observatory to detect close companions to the sample from $\sim$1 au to 100 au, while digitised wide-field archival plates were searched for wide companions from $\sim$100 au to 10,000 au. With sensitivity to the bottom of the main sequence over a separation range of 3 au to 10,000 au, multiple AO and wide-field epochs allow us to confirm candidates with common proper motions, minimize background contamination, and enable a measurement of comprehensive binary statistics. We detected 65 co-moving stellar companions and find a companion star fraction of $23.5 \pm 3.2$ per cent over the 3 au to 10,000 au separation range. The companion separation distribution is observed to rise to a higher frequency at smaller separations, peaking at closer separations than measured for more massive primaries. The mass ratio distribution across the $q = 0.2 - 1.0$ range is flat, similar to that of multiple systems with solar-type primaries. The characterisation of binary and multiple star frequency for low-mass field stars can provide crucial comparisons with star forming environments and hold implications for the frequency and evolutionary histories of their associated disks and planets.
description: Accepted for publication in the Monthly Notices of the Royal Astronomical Society, 2015 February 20. 34 pages and 21 figures, with 7 tables presented here in their entirety. All tables and the full set of figures in the Appendix to appear in the electronic version of the journal
The consistency, the composition and the causality of the asynchronous flows
Creators: name: Vlad, Serban E.
Publisher: name: arXiv
Year: 2015
Subjects: subject: General Mathematics (math.GM)
subject: FOS: Mathematics
subject: 94C10

description: Let $Φ:\{0,1\}^{n}\longrightarrow\{0,1\}^{n}$. The asynchronous flows are (discrete time and real time) functions that result by iterating the coordinates $Φ_{i}$ independently on each other. The purpose of the paper is that of showing that the asynchronous flows fulfill the properties of consistency, composition and causality that define the dynamical systems. The origin of the problem consists in modelling the asynchronous circuits from the digital electrical engineering.
description: 9 pages, 2 figures
Optimal flat functions in Carleman-Roumieu ultraholomorphic classes in sectors
Creators: name: Jiménez-Garrido, Javier
name: Miguel-Cantero, Ignacio
name: Sanz, Javier
name: Schindl, Gerhard
Publisher: name: arXiv
Year: 2022
Subjects: subject: Complex Variables (math.CV)
subject: Functional Analysis (math.FA)
subject: FOS: Mathematics
subject: Primary 47A57, secondary 44A10, 46E10

description: We construct optimal flat functions in Carleman-Roumieu ultraholomorphic classes associated to general strongly nonquasianalytic weight sequences, and defined on sectors of suitably restricted opening. A general procedure is presented in order to obtain linear continuous extension operators, right inverses of the Borel map, for the case of regular weight sequences in the sense of Dyn'kin. Finally, we discuss some examples (including the well-known $q$-Gevrey case) where such optimal flat functions can be obtained in a more explicit way.
description: 29 pages. Important improvements, mainly in Section 3: a simplified concept of optimal flat function is introduced, and their general construction is provided for strongly non-quasianalytic weight sequences and in narrow enough sectors