cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Deformations Within Moving Kinetochores Reveal Different Sites of Active and Passive Force Generation
Creators: name: Salmon, E. D.
name: Mitchison, T. J.
name: Dumont, S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Kinetochores mediate chromosome segregation at mitosis. They are thought to contain both active, force-producing and passive, frictional interfaces with microtubules whose relative locations have been unclear. We inferred mechanical deformation within single kinetochores during metaphase oscillations by measuring average separations between fluorescently labeled kinetochore subunits in living cells undergoing mitosis. Inter-subunit distances were shorter in kinetochores moving toward poles than those moving away. Inter-subunit separation decreased abruptly when kinetochores switched to poleward movement, and decreased further when pulling force increased, suggesting that active force generation during poleward movement compresses kinetochores. The data revealed an active force -generating interface within kinetochores, and a separate passive frictional interface located at least 20 nm away poleward. Together, these interfaces allow persistent attachment with intermittent active force generation.
Evolution of an MCM Complex in Flies That Promotes Meiotic Crossovers by Blocking BLM Helicase
Creators: name: Jones, C. D.
name: Kohl, K. P.
name: Sekelsky, J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Generation of meiotic crossovers in many eukaryotes requires the elimination of anti-crossover activities by using the Msh4-Msh5 heterodimer to block helicases. Msh4 and Msh5 have been lost from the flies
Extrachromosomal MicroDNAs and Chromosomal Microdeletions in Normal Tissues
Creators: name: Layer, R.
name: Shibata, Y.
name: Willcox, S.
name: Kumar, P.
name: Gagan, J. R.
name: Griffith, J. D.
name: Dutta, A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: We have identified tens of thousands of short extrachromosomal circular DNAs (microDNA) in mouse tissues as well as mouse and human cell lines. These microDNAs are 200–400 bp long, derived from unique non-repetitive sequence and are enriched in the 5' untranslated regions of genes, exons and CpG islands. Chromosomal loci that are enriched sources of microDNA in adult brain are somatically mosaic for micro-deletions that appear to arise from the excision of microDNAs. Germline microdeletions identified by the "Thousand Genomes" project may also arise from the excision of microDNAs in the germline lineage. We have thus identified a new DNA entity in mammalian cells and provide evidence that their generation leaves behind deletions in different genomic loci.
Generation of a Synthetic Memory Trace
Creators: name: Baumgaertel, K.
name: Hwang, S. Y.
name: Garner, A. R.
name: Kentros, C.
name: Rowland, D. C.
name: Mayford, M.
name: Roth, B. L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: We investigated the effect of activating a competing, artificially generated, neural representation on encoding of contextual fear memory. We used a cfos based transgenic approach to introduce the hM3Dq DREADD receptor into neurons based on their natural activity patterns. Neural activity can then be specifically and inducibly increased in the hM3Dq expressing neurons by an exogenous ligand. When an ensemble of neurons for one context (ctxA) was artificially activated during conditioning in a distinct context (ctxB), animals formed a hybrid memory representation. Reactivation of the artificially stimulated network within the conditioning context was required for retrieval of the memory. The memory was specific for the spatial pattern of neurons artificially activated during learning while similar stimulation impaired recall when not part of the initial conditioning.
TALEs from a spring -- superelasticity of Tal effector protein structures
Creators: name: Flechsig, Holger
Publisher: name: arXiv
Year: 2014
Subjects: subject: Biomolecules (q-bio.BM)
subject: Soft Condensed Matter (cond-mat.soft)
subject: Biological Physics (physics.bio-ph)
subject: FOS: Biological sciences
subject: FOS: Physical sciences

description: A simple force-probe setup is employed to study the mechanical properties of transcription activator-like effector (TALE) proteins in computer experiments. It is shown that their spring-like arrangement benefits superelastic behaviour which is manifested by large-scale global conformational changes along the helical axis, thus linking structure and dynamics in TALE proteins. As evidenced from the measured force-extension curves the dHax3 and PthXo1 TALEs behave like linear springs, obeying Hooke's law, for moderate global structural changes. For larger deformations, however, the proteins exhibit nonlinearities and the structures become stiffer the more they are stretched. Flexibility is not homogeneously distributed over TALE structure, but instead soft spots which correspond to the RVD loop residues and present key agents in the transmission of conformational motions are identified.
description: 6 pages, 4 figures
Intestinal Inflammation Targets Cancer-Inducing Activity of the Microbiota
Creators: name: Jobin, C.
name: Perez-Chanona, E.
name: Abujamel, T.
name: Fodor, A. A.
name: Keku, T. O.
name: Uronis, J. M.
name: Dogan, B.
name: Campbell, B. J.
name: Arthur, J. C.
name: Hansen, J. J.
name: Simpson, K. W.
name: Tomkovich, S.
name: Muhlbauer, M.
name: Rhodes, J. M.
name: Rogers, A. B.
name: Stintzi, A.
name: Fan, T.-J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Inflammation alters host physiology to promote cancer, as seen in colitis-associated colorectal cancer (CRC). Here we identify the intestinal microbiota as a target of inflammation that impacts the progression of CRC. High-throughput sequencing revealed that inflammation modifies gut microbial composition in colitis-susceptible interleukin-10-deficient (Il10−/−) mice. Monocolonization with the commensal Escherichia coli NC101 promoted invasive carcinoma in azoxymethane (AOM)-treated Il10−/− mice. Deletion of the polyketide synthase (pks) genotoxic island from E. coli NC101 decreased tumor multiplicity and invasion in AOM/Il10−/− mice, without altering intestinal inflammation. Mucosa-associated pks+ E. coli were found in a significantly high percentage of inflammatory bowel disease (IBD) and CRC patients. This suggests that in mice, colitis can promote tumorigenesis by altering microbial composition and inducing the expansion of microorganisms with genotoxic capabilities.
Colouring Dresden – Mit einer offenen Citizen-Science-Plattform Gebäudewissen kartieren, erforschen und vermitteln und dabei Baukultur und klimagerechte Architektur in Dresden unterstützen
Creators: name: Hecht, Robert
name: Danke, Tabea
name: Rieche, Theodor
Publisher: name: Zenodo
Year: 2023
Subjects: DFNS 2023
Colouring Dresden
Colouring Cities
CCRP
Citizen Science
Open Citizen Science
Gebäudewissen
Baukultur
klimagerechte Architektur
Klimaanpassung
zirkuläres Bauen
Typologie
Gebäudemerkmal
Umweltrisiken

description: Besonders in Städten wie Dresden, die verschiedene Baustile im Stadtbild vereinen, braucht es innovative Lösungen, um den Gebäudebestand klimagerecht und unter Achtung der Baukultur nachhaltig zu entwickeln. Zu den Maßnahmen gehören u. a. die energetische Bestandssanierung, Klimaanpassungsmaßnahmen in Bezug auf Hitze, Starkregen oder Hochwasser sowie der Ausbau der erneuerbaren Energien. Dazu braucht es Daten und Informationen über den Gebäudebestand, die jedoch oft nicht vorliegen oder nutzbar sind. Colouring Dresden erprobt als Citizen-Science-Projekt Konzepte, wie Wissenslücken über den Gebäudebestand gefüllt werden können. Citizen Scientists tragen Gebäudeinformation, wie Gebäudealter, Materialität oder Geschossigkeit in eine Karte ein. Die Gebäude nehmen durch die eingetragene Information einen spezifischen Farbwert der Legende an. Die gewonnenen Erkenntnisse sind relevant für Hochwasser- und Hitzemodellierungen und helfen somit die Widerstandsfähigkeit (Resilienz) gegenüber Klimarisikoereignissen zu bewerten. Weiteres Ziel stellt der Aufbau eines ko-kreativen Netzwerks aus Akteur*innen dar, welche die Colouring Dresden-Plattform inhaltlich und technisch weiterentwickelt und eine Implementierung in andere Themenfelder und Städte ermöglicht. Parallel wird Wissen über die Themen Baukultur und klimagerechte Architektur in Citizen-Science- Aktionen vermittelt. Hierbei entsteht ein Mehrwert für die Gesellschaft, die Wissenschaft und alle Beteiligten durch Sensibilisierung, Motivation und Teilhabe an einer Transformation. Das Projekt trägt demnach dazu bei, nachhaltige Maßnahmen zu entwickeln, um den Gebäudebestand in Dresden klimaresilienter zu gestalten.
Additional file 2 of Neuroinflammation regulates the balance between hippocampal neuron death and neurogenesis in an ex vivo model of thiamine deficiency
Creators: name: Cassiano, Larissa M. G.
name: Oliveira, Marina S.
name: Pioline, Jeanne
name: Salim, Anna C. M.
name: Coimbra, Roney S.
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Physiology
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 110309 Infectious Diseases

description: Additional file 2. Differentially expressed genes in OHCs cultured for 9 days in TD compared to the controls. List of genes with increased or reduced expression in OHCs in response to 9 days of TD, found in contrast analysis with DESeq2 software. Genes with Fold Change greater than 1.5 and adjusted P value lower than 0.01 were considered as differentially expressed. UNIPROT identifiers, protein names and gene symbols were obtained with DAVID web-software using Ensembl identifiers.
Proposal on Model Based Current Overshoot Suppression of Receiver Side Coil in Drone Wireless Power Transfer System
Creators: name: Fujimoto, Kota
name: Hamada, Takumi
name: Fujimoto, Hiroshi
Publisher: name: arXiv
Year: 2023
Subjects: subject: Systems and Control (eess.SY)
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: This paper proposes a model-based control method in the wireless power transfer (WPT) system by operating a semi-bridgeless active rectifier (SBAR) to suppress the secondary coil current overshoot. By damping the current overshoot, it is possible to reduce the rectifier's rated current and decrease the rectifier's size, which is beneficial for the lightweight-oriented system such as drones. In the control method, an inverse of the plant model is used to calculate the reference input to the system. The current overshoot is reduced by operating the SBAR under the duty ratio calculated from the model. To confirm the performance of the proposed method, the simulation and the experiment using the WPT prototype are conducted. The experimental results show that the proposed method can suppress the secondary coil current overshoot. The results suggest it is possible to realize the lighter secondary system by applying the proposed method.
description: This paper was presented at IEEE 2022 Wireless Power Week (WPW)
Additional file 4 of Atheroprone fluid shear stress-regulated ALK1-Endoglin-SMAD signaling originates from early endosomes
Creators: name: Mendez, Paul-Lennard
name: Obendorf, Leon
name: Jatzlau, Jerome
name: Burdzinski, Wiktor
name: Reichenbach, Maria
name: Nageswaran, Vanasa
name: Haghikia, Arash
name: Stangl, Verena
name: Hiepen, Christian
name: Knaus, Petra
Publisher: name: figshare
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Physiology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 4. Uncropped Western Blot images.
Additional file 3 of Neuroinflammation regulates the balance between hippocampal neuron death and neurogenesis in an ex vivo model of thiamine deficiency
Creators: name: Cassiano, Larissa M. G.
name: Oliveira, Marina S.
name: Pioline, Jeanne
name: Salim, Anna C. M.
name: Coimbra, Roney S.
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Physiology
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 110309 Infectious Diseases

description: Additional file 3. Functional enrichment analysis of the 89 differentially expressed genes using the Database for Annotation, Visualization and Integrated Discovery (DAVID) software. Considered only molecules and/or relationships where (species = Rattus norvegicus). Predictions with P value lower than 0.05 in Fisher’s test were considered statistically significant.
Illustrating SUSY breaking effects on various inflation mechanisms
Creators: name: Abe, Hiroyuki
name: Aoki, Shuntaro
name: Hasegawa, Fuminori
name: Yamada, Yusuke
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We consider the supersymmetry breaking effects on typical inflation models with different types of Kähler potential. The critical size of supersymmetry-breaking scale, above which the flatness of the inflaton potential is spoiled, drastically changes model by model. We present the universal description of such effects in terms of a field-dependent scaling factor by which gravity-mediated supersymmetry breaking terms are suppressed or enhanced, based on the conformal supergravity framework. Such a description would be useful when we estimate them in constructing supersymmetric models of particle cosmology.
description: 20pages, 3 figures, v2: a reference added, v3: Appendix B added
Additional file 4 of Neuroinflammation regulates the balance between hippocampal neuron death and neurogenesis in an ex vivo model of thiamine deficiency
Creators: name: Cassiano, Larissa M. G.
name: Oliveira, Marina S.
name: Pioline, Jeanne
name: Salim, Anna C. M.
name: Coimbra, Roney S.
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Physiology
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 110309 Infectious Diseases

description: Additional file 4. Functional enrichment analysis of the 89 differentially expressed genes using the Ingenuity Pathway Analysis (IPA) software. Considered only molecules and/or relationships where (species = Rat) AND (confidence = experimentally observed or highly predicted) AND (tissues/ cell lineage = Hippocampus OR all CNS cell lines OR UNSPECIFIED CNS lines). Predictions with P value lower than 0.05 in Fisher’s test were considered statistically significant.
Performance OptimizationTactics for Blockchain: A Systematic Literature Review
Creators: name: Lv, Weilong
Publisher: name: figshare
Year: 2025
Subjects: classificationCode: 461206
subject: Software architecture
classificationCode: 460605
subject: Distributed systems and algorithms
classificationCode: 460602
subject: Concurrent/parallel systems and technologies

description: The files contain the appendix of the paper Performance Optimization Tactics for Blockchain: A Systematic Literature Review. They include supplementary materials that provide additional details on the reviewed studies, methodologies, and data used in the analysis.
Misaligned Protoplanetary Disks in a Young Binary System
Creators: name: Jensen, Eric L. N.
name: Akeson, Rachel
Publisher: name: arXiv
Year: 2014
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: Many extrasolar planets follow orbits that differ from the nearly coplanar and circular orbits found in our solar system; orbits may be eccentric or inclined with respect to the host star's equator, and the population of giant planets orbiting close to their host stars suggests significant orbital migration. There is currently no consensus on what produces such orbits. Theoretical explanations often invoke interactions with a binary companion star on an orbit that is inclined relative to the planet's orbital plane. Such mechanisms require significant mutual inclinations between planetary and binary star orbital planes. The protoplanetary disks in a few young binaries are misaligned, but these measurements are sensitive only to a small portion of the inner disk, and the three-dimensional misalignment of the bulk of the planet-forming disk mass has hitherto not been determined. Here we report that the protoplanetary disks in the young binary system HK Tau are misaligned by 60°-68°, so one or both disks are significantly inclined to the binary orbital plane. Our results demonstrate that the necessary conditions exist for misalignment-driven mechanisms to modify planetary orbits, and that these conditions are present at the time of planet formation, apparently due to the binary formation process.
description: Published in Nature, July 31 2014. 18 pages. This version has slight differences from the final published version. Final version is available at http://www.nature.com/nature/journal/v511/n7511/full/nature13521.html
Novel representation of the general Heun's functions. Back to the beginning
Creators: name: Fiziev, Plamen P.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Classical Analysis and ODEs (math.CA)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Mathematics
subject: FOS: Physical sciences
subject: 34A25, 34B30, 11B37

description: We study a novel type of solutions of the general Heun's equation, based on its symmetric form. We derive the symmetry group of this equation which is a proper extension of the Mobius group. The new series solution treat simultaneously and on an equal footing all singular points.
description: 5 pages, tex file, no figures, Proceedings of the International Conference DAYS on DIFFRACTION 2014
Triggering a Cell Shape Change by Exploiting Preexisting Actomyosin Contractions
Creators: name: McClellan, Joseph H.
name: Roh-Johnson, Minna
name: Tulu, U. Serdar
name: Betzig, Eric
name: Goldstein, Bob
name: Gao, Liang
name: Werts, Adam D.
name: Shemer, Gidi
name: Kiehart, Daniel P.
name: Higgins, Christopher D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Apical constriction changes cell shapes, driving critical morphogenetic events including gastrulation in diverse organisms and neural tube closure in vertebrates. Apical constriction is thought to be triggered by contraction of apical actomyosin networks. We found that apical actomyosin contractions began before cell shape changes in both C. elegans and Drosophila. In C. elegans, actomyosin networks were initially dynamic, contracting and generating cortical tension without significant shrinking of apical surfaces. Apical cell-cell contact zones and actomyosin only later moved increasingly in concert, with no detectable change in actomyosin dynamics or cortical tension. Thus, apical constriction appears to be triggered not by a change in cortical tension but by dynamic linking of apical cell-cell contact zones to an already contractile apical cortex.
title: Attentional Processing of Visual Stimuli: What Makes a Face a Face?
Creators: name: Chapman, Samuel L.
Publisher: name: Old Dominion University
publisherIdentifier: https://ror.org/04zjtrb98
publisherIdentifierScheme: ROR
Year: 1995

description: Reaction time (RT) and accuracy have been used to investigate the manner in which humans process visual stimuli for many years. Some researchers have found evidence of serial processing (e.g., Sternberg, 1969a) while others have shown that some visual stimuli are processed in parallel (e.g., Neisser, 1963). There have been very few studies investigating the processing of schematic faces with respect to RT and accuracy. The present study investigates the mechanisms associated with the recognition of schematic faces with respect to RT and accuracy.

Forty-two Old Dominion University students were shown a target face for ten seconds and were then shown a series of display sets varying on 4, 5, or 6 features. The display set contained either 4, 6, 8, or 10 faces, and half of the trials were conditions where the target face was in the display set and half of the trails did not contain the target face. It was hypothesized that subjects would show serial search strategies for increases in set size, parallel strategies if the faces were ecologically valid, and learning effects over blocks of trials.

Two ANOVAs were performed on the data. First, 3 levels of features x 4 levels of display set size x 2 levels of trials x 2 levels of display set type x 2 levels of block were analyzed with the respect to the dependent measures RT and accuracy. For RT, 4 main effects and 8 interactions were found to be significant. For accuracy, 2 main effects and 4 interactions were found to be significant. Second, 2 levels of display set type x 3 levels of minimal difference (DMIN), a variable reflecting the closest non-match to the target face, were analyzed with respect to RT and accuracy. For both RT and accuracy, the main effect for DMIN and the interaction was found to be significant.

The results supported the serial processing and learning effects hypotheses. Although there was an indication that parallel processing might have occurred, a RT-accuracy trade-off negated the support for the parallel processing hypothesis.

Future research could include investigations into the salience of features, an increase in the ecological validity of the faces, and variations in the presentation of stimuli.
Additional file 5 of Neuroinflammation regulates the balance between hippocampal neuron death and neurogenesis in an ex vivo model of thiamine deficiency
Creators: name: Cassiano, Larissa M. G.
name: Oliveira, Marina S.
name: Pioline, Jeanne
name: Salim, Anna C. M.
name: Coimbra, Roney S.
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Physiology
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 110309 Infectious Diseases

description: Additional file 5. Pearson’s correlation coefficients between the expression level (mRNA) of selected genes altered by TD after 4, 7 and 9 days in OHCs. Correlations with P value lower than 0.05 were considered statistically significant.
Volatile analyses from Field evidence for the role of plant volatiles induced by caterpillar oral secretion in prey localization by predatory social wasps
Creators: name: Grof-Tisza, Patrick
name: Turlings, Ted
name: Bustos-Segura, Carlos
name: Benrey, Betty
Publisher: name: The Royal Society
Year: 2024
Subjects: classificationCode: 310399
subject: Ecology not elsewhere classified

description: Full list of found volatiles
Using public archives of high resolution spectrographs
Creators: name: Casamiquela, Laia
Publisher: name: Zenodo
Year: 2023

description: Nowadays there is a huge amount of valuable observing material available in public archives of high-resolution spectrographs. The community can benefit from the re-analysis of these spectra to obtain precise parametrisation and chemical compositions of stars, in particular by combining multiple observations of the same star.
 However, to ensure consistency, there is an important work of homogenisation of the spectra coming from different observational configurations or even different instruments. Common calibration and validation samples are also required.
 In this talk, I will present my latest works, where I have combined thousands of spectra from 1- different instruments to study a sample of open cluster stars and the Gaia FGK Benchmark stars. I will show which science we can do from such systematic queries to public spectral archives, strategies to homogenise the analysis, and how to evaluate the precision and accuracy.
A Guanosine-Centric Mechanism for RNA Chaperone Function
Creators: name: Gorelick, R. J.
name: Lickwar, C. R.
name: Bower, B. D.
name: Lieb, J. D.
name: Znosko, B. M.
name: Grohman, J. K.
name: Weeks, K. M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: RNA chaperones are ubiquitous, heterogeneous proteins essential for RNA structural biogenesis and function. We investigated the mechanism of chaperone-mediated RNA folding by following the time-resolved dimerization of the packaging domain of a retroviral RNA at nucleotide resolution. In the absence of the nucleocapsid (NC) chaperone, dimerization proceeded via multiple, slow-folding intermediates. In the presence of NC, dimerization occurred rapidly via a single structural intermediate. The RNA binding domain of hnRNP A1 protein (UP1), a structurally unrelated chaperone, also accelerated dimerization. Both chaperones interacted primarily with guanosine residues. Replacing guanosine with more weakly pairing inosine yielded an RNA that folded rapidly without a facilitating chaperone. These results show RNA chaperones can simplify RNA folding landscapes by weakening intramolecular interactions involving guanosine and explain many RNA chaperone activities.
Detachment of semiflexible polymer chains from a substrate - a Molecular Dynamics investigation
Creators: name: Paturej, J.
name: Erbas, A.
name: Milchev, A.
name: Rostiashvili, V. G.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: Using Molecular Dynamics simulations, we study the force-induced detachment of a coarse-grained model polymer chain from an adhesive substrate. One of the chain ends is thereby pulled at constant speed off the attractive substrate and the resulting saw-tooth profile of the measured mean force $< f >$ vs height $D$ of the end-segment over the plane is analyzed for a broad variety of parameters. It is shown that the observed characteristic oscillations in the $< f >$-$D$ profile depend on the bending and not on the torsional stiffness of the detached chains. Allowing for the presence of hydrodynamic interactions (HI) in a setup with explicit solvent and DPD-thermostat, rather than the case of Langevin thermostat, one finds that HI have little effect on the $< f >$-$D$ profile. Also the change of substrate affinity with respect to the solvent from solvophilic to solvophobic is found to play negligible role in the desorption process. In contrast, a changing ratio $ε_s^A / ε_s^B$ of the binding energies of $A$- and $B$-segments in the detachment of an $AB$-copolymer from adhesive surface strongly changes the $< f >$-$D$ profile whereby the $B$-spikes vanish when $ε_s^A / ε_s^B < 0.15$. Eventually, performing an atomistic simulation of a (bio)-polymer {\it polyglycine}, we demonstrate that the simulation results, derived from our coarse-grained model, comply favorably with those from the all-atom simulation.
description: Latex, 12 pages, 8 figures, to appear in JCP
Early evolution of the extraordinary Nova Del 2013 (V339 Del)
Creators: name: Skopal, A.
name: Drechsel, H.
name: Tarasova, T. N.
name: Kato, T.
name: Fujii, M.
name: Teyssier, F.
name: Garde, O.
name: Guarro, J.
name: Edlin, J.
name: Buil, C.
name: Antao, D.
name: Terry, J. N.
name: Lemoult, T.
name: Charbonnel, S.
name: Bohlsen, T.
name: Favaro, A.
name: Graham, K.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We determine the temporal evolution of the luminosity L(WD), radius R(WD) and effective temperature Teff of the white dwarf (WD) pseudophotosphere of V339 Del from its discovery to around day 40. Another main objective was studying the ionization structure of the ejecta. These aims were achieved by modelling the optical/near-IR spectral energy distribution (SED) using low-resolution spectroscopy (3500 - 9200 A), UBVRcIc and JHKLM photometry. During the fireball stage (Aug. 14.8 - 19.9, 2013), Teff was in the range of 6000 - 12000 K, R(WD) was expanding non-uniformly in time from around 66 to around 300 (d/3 kpc) R(Sun), and L(WD) was super-Eddington, but not constant. After the fireball stage, a large emission measure of 1.0-2.0E+62 (d/3 kpc)**2 cm**(-3) constrained the lower limit of L(WD) to be well above the super-Eddington value. The evolution of the H-alpha line and mainly the transient emergence of the Raman-scattered O VI 1032 A line suggested a biconical ionization structure of the ejecta with a disk-like H I region persisting around the WD until its total ionization, around day 40. It is evident that the nova was not evolving according to the current theoretical prediction. The unusual non-spherically symmetric ejecta of nova V339 Del and its extreme physical conditions and evolution during and after the fireball stage represent interesting new challenges for the theoretical modelling of the nova phenomenon.
description: 14 pages, 9 figures, 3 tables, accepted for Astronomy and Astrophysics
Video from Field evidence for the role of plant volatiles induced by caterpillar oral secretion in prey localization by predatory social wasps
Creators: name: Grof-Tisza, Patrick
name: Turlings, Ted
name: Bustos-Segura, Carlos
name: Benrey, Betty
Publisher: name: The Royal Society
Year: 2024
Subjects: classificationCode: 310399
subject: Ecology not elsewhere classified

description: Video link of caterpillar predation by predatory wasps
Extreme neutron stars from Extended Theories of Gravity
Creators: name: Astashenok, Artyom V.
name: Capozziello, Salvatore
name: Odintsov, Sergei D.
Publisher: name: arXiv
Year: 2014
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We discuss neutron stars with strong magnetic mean fields in the framework of Extended Theories of Gravity. In particular, we take into account models derived from $f(R)$ and $f(\cal G)$ extensions of General Relativity where functions of the Ricci curvature invariant $R$ and the Gauss-Bonnet invariant ${\cal G}$ are respectively considered. Dense matter in magnetic mean field, generated by magnetic properties of particles, is described by assuming a model with three meson fields and baryons octet. As result, the considerable increasing of maximal mass of neutron stars can be achieved by cubic corrections in $f(R)$ gravity. In principle, massive stars with $M> 4 M_{\odot}$ can be obtained. On the other hand, stable stars with high strangeness fraction (with central densities $ρ_{c}\sim 1.5-2.0$ GeV/fm$^{3}$) are possible considering quadratic corrections of $f(\cal {G})$ gravity. The magnetic field strength in the star center is of order $6-8\times 10^{18}$ G. In general, we can say that other branches of massive neutron stars are possible considering the extra pressure contributions coming from gravity extensions. Such a feature can constitute both a probe for alternative theories and a way out to address anomalous self-gravitating compact systems.
description: 12 pages, 2 figures, to be published in JCAP
C57BL/6N Mutation in Cytoplasmic FMRP interacting protein 2 Regulates Cocaine Response
Creators: name: Yoo, S.-H.
name: Kourrich, S.
name: Kumar, V.
name: Huang, H. C.
name: Churchill, G.
name: Kim, K.
name: Joseph, C.
name: Bonci, A.
name: Takahashi, J. S.
name: Vitaterna, M. H.
name: Pardo-Manuel de Villena, F.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: The inbred mouse C57BL/6J is the reference strain for genome sequence and for most behavioral and physiological phenotypes. However the International Knockout Mouse Consortium uses an embryonic stem cell line derived from a related C57BL/6N substrain. We found that C57BL/6N has lower acute and sensitized response to cocaine and methamphetamine. We mapped a single causative locus and identified a non-synonymous mutation of serine to phenylalanine (S968F) in Cytoplasmic FMR interacting protein 2 (Cyfip2) as the causative variant. The S968F mutation destabilizes CYFIP2 and deletion of the C57BL/6N mutant allele leads to acute and sensitized cocaine response phenotypes. We propose CYFIP2 is a key regulator of cocaine response in mammals and present a framework to utilize mouse substrains to discover novel genes and alleles regulating behavior.
Indications of M-dwarf Deficits in the Halo and Thick Disk of the Galaxy
Creators: name: Konishi, Mihoko
name: Shibai, Hiroshi
name: Sumi, Takahiro
name: Fukagawa, Misato
name: Matsuo, Taro
name: Samland, Matthias S.
name: Yamamoto, Kodai
name: Sudo, Jun
name: Itoh, Yoichi
name: Arimoto, Nobuo
name: Kajisawa, Masaru
name: Abe, Lyu
name: Brandner, Wolfgang
name: Brandt, Timothy D.
name: Carson, Joseph
name: Currie, Thayne
name: Egner, Sebastian E.
name: Feldt, Markus
name: Goto, Miwa
name: Grady, Carol A.
name: Guyon, Olivier
name: Hashimoto, Jun
name: Hayano, Yutaka
name: Hayashi, Masahiko
name: Hayashi, Saeko S.
name: Henning, Thomas
name: Hodapp, Klaus W.
name: Ishii, Miki
name: Iye, Masanori
name: Janson, Markus
name: Kandori, Ryo
name: Knapp, Gillian R.
name: Kudo, Tomoyuki
name: Kusakabe, Nobuhiko
name: Kuzuhara, Masayuki
name: Kwon, Jungmi
name: McElwain, Michael W.
name: Miyama, Shoken
name: Morino, Jun-Ichi
name: Moro-Martín, Amaya
name: Nishimura, Tetsuo
name: Pyo, Tae-Soo
name: Serabyn, Eugene
name: Suenaga, Takuya
name: Suto, Hiroshi
name: Suzuki, Ryuji
name: Takahashi, Yasuhiro H.
name: Takami, Hideki
name: Takato, Naruhisa
name: Terada, Hiroshi
name: Thalmann, Christian
name: Tomono, Daigo
name: Turner, Edwin L.
name: Usuda, Tomonori
name: Watanabe, Makoto
name: Wisniewski, John P.
name: Yamada, Toru
name: Tamura, Motohide
Publisher: name: arXiv
Year: 2014
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We compared the number of faint stars detected in deep survey fields with the current stellar distribution model of the Galaxy and found that the detected number in the H band is significantly smaller than the predicted number. This indicates that M-dwarfs, the major component, are fewer in the halo and the thick disk. We used archived data of several surveys in both the north and south field of GOODS (Great Observatories Origins Deep Survey), MODS in GOODS-N, and ERS and CANDELS in GOODS-S. The number density of M-dwarfs in the halo has to be 20+/-13% relative to that in the solar vicinity, in order for the detected number of stars fainter than 20.5 mag in the H band to match with the predicted value from the model. In the thick disk, the number density of M-dwarfs must be reduced (52+/-13%) or the scale height must be decreased (~600 pc). Alternatively, overall fractions of the halo and thick disks can be significantly reduced to achieve the same effect, because our sample mainly consists of faint M-dwarfs. Our results imply that the M-dwarf population in regions distant from the Galactic plane is significantly smaller than previously thought. We then discussed the implications this has on the suitability of the model predictions for the prediction of non-companion faint stars in direct imaging extrasolar planet surveys by using the best-fit number densities.
description: 22 pages, 9 figures, accepted for Publications of the Astronomical Society of Japan
X-ray absorption spectroscopy study of the electronic and magnetic proximity effects in YBa$_2$Cu$_3$O$_{7}$/La$_{2/3}$Ca$_{1/3}$MnO$_3$ and La$_{2-x}$Sr$_x$CuO$_4$/La$_{2/3}$Ca$_{1/3}$MnO$_3$ multilayers
Creators: name: Uribe-Laverde, M. A.
name: Das, S.
name: Sen, K.
name: Marozau, I.
name: Perret, E.
name: Alberca, A.
name: Heidler, J.
name: Piamonteze, C.
name: Merz, M.
name: Nagel, P.
name: Schuppler, S.
name: Munzar, D.
name: Bernhard, C.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: With x-ray absorption spectroscopy we investigated the orbital reconstruction and the induced ferromagnetic moment of the interfacial Cu atoms in YBa$_2$Cu$_3$O$_{7}$/La$_{2/3}$Ca$_{1/3}$MnO$_3$ (YBCO/LCMO) and La$_{2-x}$Sr$_{x}$CuO$_4$/La$_{2/3}$Ca$_{1/3}$MnO$_3$ (LSCO/LCMO) multilayers. We demonstrate that these electronic and magnetic proximity effects are coupled and are common to these cuprate/manganite multilayers. Moreover, we show that they are closely linked to a specific interface termination with a direct Cu-O-Mn bond. We furthermore show that the intrinsic hole doping of the cuprate layers and the local strain due to the lattice mismatch between the cuprate and manganite layers are not of primary importance. These findings underline the central role of the covalent bonding at the cuprate/manganite interface in defining the spin-electronic properties.
description: 8 pages, 4 figures
Classical trajectories in polar-asymmetric laser fields: Synchronous THz and XUV emission
Creators: name: Gragossian, Aram
name: Seletskiy, Denis V.
name: Sheik-Bahae, Mansoor
Publisher: name: arXiv
Year: 2014
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: Synchronous extreme ultraviolet (XUV) and single-cycle terahertz (THz) bursts are generated in argon plasma induced by intense two-color femtosecond laser pulses. Correlations between the intensity of the even and odd high-harmonics and the THz radiation are found by studying the phase-delay between the excitation pulses at 800 and 400 nm as well as the degree of polar asymmetry in the incident electric field. Experiments in both the weak- and strong- polar asymmetric regimes show remarkable agreement with a simple analytical model based on classical electron trajectories in an arbitrary synthetic electric field.
description: 6 pages, 4 figures
title: Summary of an ICPPR Non-Apis workshop – Subgroup higher tier (bumble bees and solitary bees) with recommendations for a semi-field experimental design
Creators: name: Knaebe, Silvio
name: Alscher, Annika
name: Classen, Christian
name: Exeler, Nina
name: Franke, Lea
name: Fricke, Julian
name: Frommberger, Malte
name: Sorli Guerola, Juan
name: Hecht-Rost, Sabine
name: Kimmel, Stefan
name: Klein, Olaf
name: Lückmann, Johannes
name: Molitor, Claire
name: Peters, Britta
name: Schneider, Christof
Publisher: name: Julius Kühn-Institut
Year: 2018

description: Julius-Kühn-Archiv, Nr. 462 (2018): Hazards of pesticides to bees 13th International Symposium of the ICP-PR Bee Protection Group 18. - 20. October 2017, València (Spain) - Proceedings -
Supplementary materials for Lukito et al (2024) Effects of fMRI neurofeedback of right inferior frontal cortex on inhibitory brain activation in children with ADHD. Philos. Trans. R. Soc. B
Creators: name: Lukito, Steve Daniel
name: Lam, Sheut-Ling
name: Criaud, Marion
name: Westwood, Sam
name: Kowalczyk, Olivia
name: Curran, Sarah
name: Barrett, Nadia
name: Abbott, Christopher
name: Liang, Holan
name: Simonoff, Emily
name: Barker, Gareth
name: Giampietro, Vincent
name: Rubia, Katya
Publisher: name: The Royal Society
Year: 2024
Subjects: classificationCode: 320999
subject: Neurosciences not elsewhere classified

description: Lukito Stop fMRI NF PHILTRANSB_R2_FINAL_supplementary.docx
Characterization of classical Gaussian processes using quantum probes
Creators: name: Benedetti, Claudia
name: Paris, Matteo G. A.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We address the use of a single qubit as a quantum probe to characterize the properties of classical noise. In particular, we focus on the characterization of classical noise arising from the interaction with a stochastic field described by Gaussian processes. The tools of quantum estimation theory allow us to find the optimal state preparation for the probe, the optimal interaction time with the external noise, and the optimal measurement to effectively extract information on the noise parameter. We also perform a set of simulated experiments to assess the performances of maximum likelihood estimator, showing that the asymptotic regime, where the estimator is unbiased and efficient, is approximately achieved after few thousands repeated measurements on the probe system.
description: 7 pages, 4 figures, to appear in Phys. Lett. A
Charles Sanders Peirce and Coimbra
Creators: name: Junqueira, Robert Martins
Publisher: name: Zenodo
Year: 2020

description: Charles S. Peirce, “one of America’s greatest and most original thinkers” (Gaines 2018), was born in Cambridge, MA, in 1839. Peirce began his studies at college in 1855 and graduated in 1859, when he started to work for the U. S. Coast and Geodetic Survey, where his assignments included measuring the intensity of the earth’s gravitational field using swinging pendulums, often designed by him. In 1863, Peirce obtained a bachelor of science degree in chemistry. In 1873, Peirce was nominated member of Washington’s Philosophical Society, and in 1877, he was elected to be a member of the National Academy of Sciences. In 1879, Peirce began teaching Logic at Johns Hopkins University, a second job he kept until 1884. Meanwhile, in 1880, Peirce was elected a member of the London Mathematical Society. During this period (79-84), when Peirce occupied his only academic position, he had various students who happened to make a name for themselves, such as Christine Ladd-Franklin, Thorstein Veblen and John Dewey. After Peirce lost the Johns Hopkins job, he was left with his job – which came to an end in 1891 – at the U. S. Coast and Geodetic Survey, plus the twofold task of composing entries for the Century Dictionary and writing book reviews for the Nation. Inter alia, Peirce, who never finished a book, was a philosopher, an inventor, experimental psychologist, historian of science and expert in mathematics, astronomy, chemistry, cartography, and metaphysics, whose writings – which extend over around six decades, from the late 1850s until his death in 1914, in Milford, PA – amount to over ninety-thousand pages: about twelve-thousand published plus eighty-thousand manuscripts. After Peirce’s death, his unpublished manuscripts were bought by the Department of Philosophy at Harvard University. Anyhow, Peirce published on a vast collection of topics, and this material got spread among various publication media.
Enumeration of idempotents in diagram semigroups and algebras
Creators: name: Dolinka, Igor
name: East, James
name: Evangelou, Athanasios
name: FitzGerald, Des
name: Ham, Nicholas
name: Hyde, James
name: Loughlin, Nicholas
Publisher: name: arXiv
Year: 2014
Subjects: subject: Group Theory (math.GR)
subject: Combinatorics (math.CO)
subject: Representation Theory (math.RT)
subject: FOS: Mathematics
subject: 20M20, 20M10, 20M17, 05E15, 05A18

description: We give a characterisation of the idempotents of the partition monoid, and use this to enumerate the idempotents in the finite partition, Brauer and partial Brauer monoids, giving several formulae and recursions for the number of idempotents in each monoid as well as various $\mathscr R$-, $\mathscr L$- and $\mathscr D$-classes. We also apply our results to determine the number of idempotent basis elements in the finite dimensional partition, Brauer and partial Brauer algebras.
description: Small changes to intro and references. To appear in Journal of Combinatorial Theory, Series A. 26 pages, 4 figures, 10 tables
Additional file 1 of Introducing oxygen transfer rate measurements as a novel method for time-resolved cytotoxicity assessment in shake flasks
Creators: name: Ihling, Nina
name: Munkler, Lara Pauline
name: Paul, Richard
name: Lang, Dietmar
name: Büchs, Jochen
Publisher: name: figshare
Year: 2022
Subjects: subject: Biochemistry
subject: Space Science
subject: Physiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Cancer

description: Additional file 1. Additional Data, Additional Table S1, Additional Figures S1–S7.
Cancer Pharmacogenomics: Early Promise, But Concerted Effort Needed
Creators: name: McLeod, H. L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: The past decade has brought together substantial advances in human genome analysis and a maturation of understanding of tumor biology. While there is much progress still to be had, there are now several prominent examples in which tumor-associated somatic mutations have been used to identify cellular signaling pathways in tumors. This in turn has led to the development of targeted therapies, with somatic mutations serving as genomic predictors of tumor response and providing new leads for drug development. There is also a realization that germline DNA variants can help optimize cancer drug dosing and predict the susceptibility of patients to the adverse side effects of these drugs; knowledge that ultimately can be used to improve the benefit:risk ratio of cancer treatment for individual patients.
Local Kondo temperatures in atomic chains
Creators: name: Agundez, Ricardo
name: Salfi, Joe
name: Rogge, Sven
name: Blaauboer, Miriam
Publisher: name: arXiv
Year: 2014
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We study the effect of disorder in strongly interacting small atomic chains. Using the Kotliar- Ruckenstein slave-boson approach we diagonalize the Hamiltonian via scattering matrix theory. We numerically solve the Kondo transmission and the slave-boson parameters that allow us to calculate the Kondo temperature. We demonstrate that in the weak disorder regime, disorder in the energy levels of the dopants induces a non-screened disorder in the Kondo couplings of the atoms. We show that disorder increases the Kondo temperature of a perfect chain. We find that this disorder in the couplings comes from a local distribution of Kondo temperatures along the chain. We propose two experimental setups where the impact of local Kondo temperatures can be observed.
Supplementry figures 1_2_3_4_5_6 from Moesin contributes to heat shock gene response through direct binding the Med15 subunit of the Mediator complex in the nucleus
Creators: name: Kristó, Ildikó
name: Kovács, Zoltán
name: Szabó, Anikó
name: Borkúti, Péter
name: Gráf, Alexandra
name: Sánta, Ádám Tamás
name: Pettkó-Szandtner, Aladár
name: Ábrahám, Edit
name: Honti, Viktor
name: Lipinszki, Zoltan
name: Vilmos, Péter
Publisher: name: The Royal Society
Year: 2024
Subjects: classificationCode: 310199
subject: Biochemistry and cell biology not elsewhere classified

description: Control immunostainings to visualize correct protein expression and localization.