cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Large Language Model-Powered Smart Contract Vulnerability Detection: New Perspectives
Creators: name: Hu, Sihao
name: Huang, Tiansheng
name: İlhan, Fatih
name: Tekin, Selim Furkan
name: Liu, Ling
Publisher: name: arXiv
Year: 2023
Subjects: subject: Cryptography and Security (cs.CR)
subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: This paper provides a systematic analysis of the opportunities, challenges, and potential solutions of harnessing Large Language Models (LLMs) such as GPT-4 to dig out vulnerabilities within smart contracts based on our ongoing research. For the task of smart contract vulnerability detection, achieving practical usability hinges on identifying as many true vulnerabilities as possible while minimizing the number of false positives. Nonetheless, our empirical study reveals contradictory yet interesting findings: generating more answers with higher randomness largely boosts the likelihood of producing a correct answer but inevitably leads to a higher number of false positives. To mitigate this tension, we propose an adversarial framework dubbed GPTLens that breaks the conventional one-stage detection into two synergistic stages $-$ generation and discrimination, for progressive detection and refinement, wherein the LLM plays dual roles, i.e., auditor and critic, respectively. The goal of auditor is to yield a broad spectrum of vulnerabilities with the hope of encompassing the correct answer, whereas the goal of critic that evaluates the validity of identified vulnerabilities is to minimize the number of false positives. Experimental results and illustrative examples demonstrate that auditor and critic work together harmoniously to yield pronounced improvements over the conventional one-stage detection. GPTLens is intuitive, strategic, and entirely LLM-driven without relying on specialist expertise in smart contracts, showcasing its methodical generality and potential to detect a broad spectrum of vulnerabilities. Our code is available at: https://github.com/git-disl/GPTLens.
description: 10 pages
Implementation of The South Atlantic Bight Synoptic Offshore Observational Network
Creators: name: Seim, H.E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2000

description: Continuous information on coastal ocean conditions in the South Atlantic Bight (SAB), provided by an interdisciplinary real-time coastal ocean observing network, is now accessible. Many' applications are envisioned. Academic researchers will use the network for targeted research and as a test bed for sensor development. The National Weather Service will use the continuously available meteorological data to predict, more accurately, weather conditions affecting the eastern seaboard of the U.S. Resource managers will be able to manage, more effectively, the use of the SAB coastal waters. The network can also serve as the nucleus of an observing system that will provide in situ observations for a nowcast/ forecast regional coupled ocean/atmosphere model of the SAB.
Dissecting Hydrophobic Hydration and Association
Creators: name: Remsing, Richard C.
name: Weeks, John D.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Soft Condensed Matter (cond-mat.soft)
subject: Chemical Physics (physics.chem-ph)
subject: FOS: Physical sciences

description: We use appropriately defined short ranged reference models of liquid water to clarify the different roles local hydrogen bonding, van der Waals attractions, and long ranged electrostatic interactions play in the solvation and association of apolar solutes in water. While local hydrogen bonding in- teractions dominate hydrophobic effects involving small solutes, longer ranged electrostatic and dis- persion interactions are found to be increasingly important in the description of interfacial structure around large solutes. The hydrogen bond network sets the solute length scale at which a crossover in solvation behavior between these small and large length scale regimes is observed. Unbalanced long ranged forces acting on interfacial water molecules are also important in hydrophobic association, illustrated here by analysis of the association of model methane and buckminsterfullerene solutes.
description: 14 pages
Observation of topologically distinct corner states in "bearded" photonic Kagome lattices
Creators: name: Song, Limin
name: Bongiovanni, Domenico
name: Hu, Zhichan
name: Wang, Ziteng
name: Xia, Shiqi
name: Tang, Liqin
name: Song, Daohong
name: Morandotti, Roberto
name: Chen, Zhigang
Publisher: name: arXiv
Year: 2023
Subjects: subject: Optics (physics.optics)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Kagome lattices represent an archetype of intriguing physics, attracting a great deal of interest in different branches of natural sciences, recently in the context of topological crystalline insulators. Here, we demonstrate two distinct classes of corner states in breathing Kagome lattices (BKLs) with "bearded" edge truncation, unveiling their topological origin. The in-phase corner states are found to exist only in the topologically nontrivial regime, characterized by a nonzero bulk polarization. In contrast, the out-of-phase corner states appear in both topologically trivial and nontrivial regimes, either as bound states in the continuum or as in-gap states depending on the lattice dimerization conditions. Furthermore, the out-of-phase corner states are highly localized, akin to flat-band compact localized states, and they manifest both real- and momentum-space topology. Experimentally, we observe both types of corner states in laser-written photonic bearded-edge BKLs, corroborated by numerical simulations. Our results not only deepen the current understanding of topological corner modes in BKLs, but also provide new insight into their physical origins, which may be applied to other topological BKL platforms beyond optics.
description: 20 pages,4 figures
Additional file 2 of RNA-seq reveals multifaceted gene expression response to Fab production in Escherichia coli fed-batch processes with particular focus on ribosome stalling
Creators: name: Vazulka, Sophie
name: Schiavinato, Matteo
name: Tauer, Christopher
name: Wagenknecht, Martin
name: Cserjan-Puschmann, Monika
name: Striedner, Gerald
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2: Table S1. Differentially expressed genes in B during fed-batch cultivation after 2 h of induction relative to the sample drawn immediately before induction of Fabx expression. Genes also differentially expressed in wild-type BL21(DE3) were excluded. Table S2. Differentially expressed genes in B during fed-batch cultivation after 2 h of induction relative to the sample drawn immediately before induction of FTN2 expression. Genes also differentially expressed in wild-type BL21(DE3) were excluded. Table S3. Differentially expressed genes in B during fed-batch cultivation after 12 h of induction relative to the sample drawn immediately before induction of Fabx expression. Genes also differentially expressed in wild-type BL21(DE3) were excluded. Table S4. Differentially expressed genes in B during fed-batch cultivation after 12 h of induction relative to the sample drawn immediately before induction of FTN2 expression. Genes also differentially expressed in wild-type BL21(DE3) were excluded. Table S5. Differentially expressed genes in H during fed-batch cultivation after 2 h of induction relative to the sample drawn immediately before induction of Fabx expression. Genes also differentially expressed in wild-type HMS174(DE3) were excluded. Table S6. Differentially expressed genes in H during fed-batch cultivation after 2 h of induction relative to the sample drawn immediately before induction of FTN2 expression. Genes also differentially expressed in wild-type HMS174(DE3) were excluded. Table S7. Differentially expressed genes in H during fed-batch cultivation after 12 h of induction relative to the sample drawn immediately before induction of Fabx expression. Genes also differentially expressed in wild-type HMS174(DE3) were excluded. Table S8. Differentially expressed genes in H during fed-batch cultivation after 12 h of induction relative to the sample drawn immediately before induction of FTN2 expression. Genes also differentially expressed in wild-type HMS174(DE3) were excluded.
Neural Shadow Mapping
Creators: name: Datta, Sayantan
name: Nowrouzezahrai, Derek
name: Schied, Christoph
name: Dong, Zhao
Publisher: name: arXiv
Year: 2023
Subjects: subject: Graphics (cs.GR)
subject: FOS: Computer and information sciences

description: We present a neural extension of basic shadow mapping for fast, high quality hard and soft shadows. We compare favorably to fast pre-filtering shadow mapping, all while producing visual results on par with ray traced hard and soft shadows. We show that combining memory bandwidth-aware architecture specialization and careful temporal-window training leads to a fast, compact and easy-to-train neural shadowing method. Our technique is memory bandwidth conscious, eliminates the need for post-process temporal anti-aliasing or denoising, and supports scenes with dynamic view, emitters and geometry while remaining robust to unseen objects.
description: Project Page: https://sayan1an.github.io/neuralShadowMapping.html
Measurement of the Transition Form Factor in $ϕ\to π^0 e^+ e^-$ with the KLOE detector
Creators: name: Mascolo, Matteo
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Experiment (hep-ex)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: By studying the invariant-mass distribution of the $e^+e^-$ in conversion decays, it is possible to learn more about mesons structure and underlying quark dynamics. At KLOE, the study of the $ϕ\to π^0 e^+e^-$ process is currently going to be finalized. At present, about 9000 events have been selected from a data sample of 1.7 fb$^{-1}$ from 2004/2005 data taking campaign. A very good agreement between data and Monte Carlo distributions has been achieved for all interesting kinematical variables. A preliminary invariant-mass spectrum of $e^{+}e^{-}$ is presented.
description: 6 pages, 2 figures
Emerging Trends in the Conduction and Application of Research Skills Among College of Education Lectures in Akwa Ibom and Cross River State of Nigeria.
Creators: name: Ojini, R.A.
name: Udosen, E.J.
name: Ulayi, Agnes
Publisher: name: figshare
Year: 2023
Subjects: classificationCode: 390201
subject: Education policy

description: The purpose of this study was to find out the influence of research trends on application of research skills among College of Education lecturers in Akwa Ibom and Cross River States. The population of the study was 921 lecturers in three colleges of education. The independent variables were individual to collaborative research and school to conference training for research. The dependents variable was application of research skills (sub-divided into problem identification skill, research question/hypothesis formulation skill, literature review skill, sampling skill, and instrumentation skill, use of statistical tool skill and overall application of research skill.). Ex-post facto design was used, while stratified sampling technique was deployed to select 550 lecturers in three colleges of education. Data was collected using research trends and application of Research Skills Questionnaire (RCBARTSQ). Two hypotheses were tested at .05 alpha level using One Way Analysis of Variance (ANOVA) and Fisher's Least significant difference t-test where appropriate. The result revealed that individual to collaborative research significantly influenced lecturers' application of research skills while school to conference training for research does not. From the result, it was concluded that lecturers' trends from individual to collaborative research enhance application of research skills. It was therefore recommended among others that the Federal Government should consider collaborative research publication as criteria for promotion and professional advancement as well as extend conference training to cover not less than two days per conference.
Landscapes of care : youth perspectives on gentrification and desired geographies in Austin, Texas
Creators: name: Martin Benitez, Paulina Gabrielle
Publisher: name: The University of Texas at Austin
Year: 2023
Subjects: Gentrification
Policing
Youth
Countermapping

description: This thesis is the culmination of collaborative work centering youth in Austin and their lived experiences of gentrification and policing in the city, in addition to their imaginaries for what an Austin that cares about its residents could look, feel, and be like. Youth participants (ages 16-18) from the Caminos program at the Emma S. Barrientos Mexican American Cultural Center in Austin were interviewed, participated in arts and counter-mapping methods, and co-analysis for the purpose of better understanding these experiences. While the project began with a focus on the mental health impacts of gentrification for Austin youth and the application of a social determinants of health framework for planning, the project evolved to encompass the racialized nature of policing in Austin, its impacts on youth access to and use of public space, and its impacts on youth experiences in school settings. Overall, the study holds implications for the need to deeply consider abolitionist theory and practice; ethics of care; and youth-centered initiatives in the planning field.
Extended Kalman Filter State Estimation for Autonomous Competition Robots
Creators: name: Kou, Ethan
name: Haggenmiller, Acshi
Publisher: name: arXiv
Year: 2023
Subjects: subject: Systems and Control (eess.SY)
subject: Robotics (cs.RO)
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: FOS: Computer and information sciences

description: Autonomous mobile robot competitions judge based on a robot's ability to quickly and accurately navigate the game field. This means accurate localization is crucial for creating an autonomous competition robot. Two common localization methods are odometry and computer vision landmark detection. Odometry provides frequent velocity measurements, while landmark detection provides infrequent position measurements. The state can also be predicted with a physics model. These three types of localization can be "fused" to create a more accurate state estimate using an Extended Kalman Filter (EKF). The EKF is a nonlinear full-state estimator that approximates the state estimate with the lowest covariance error when given the sensor measurements, the model prediction, and their variances. In this paper, we demonstrate the effectiveness of the EKF by implementing it on a 4-wheel mecanum-drive robot simulation. The position and velocity accuracy of fusing together various combinations of these three data sources are compared. We also discuss the assumptions and limitations of an EKF.
Optimized multi-site local orbitals in the large-scale DFT program CONQUEST
Creators: name: Nakata, Ayako
name: Bowler, David R.
name: Miyazaki, Tsuyoshi
Publisher: name: arXiv
Year: 2015
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Chemical Physics (physics.chem-ph)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences

description: We introduce numerical optimization of multi-site support functions in the linear-scaling DFT code CONQUEST. Multi-site support functions, which are linear combinations of pseudo-atomic orbitals on a target atom and those neighbours within a cutoff, have been recently proposed to reduce the number of support functions to the minimal basis while keeping the accuracy of a large basis [J. Chem. Theory Comput., 2014, 10, 4813]. The coefficients were determined by using the local filter diagonalization (LFD) method [Phys. Rev. B, 2009, 80, 205104]. We analyse the effect of numerical optimization of the coefficients produced by the LFD method. Tests on crystalline silicon, a benzene molecule and hydrated DNA systems show that the optimization improves the accuracy of the multi-site support functions with small cutoffs. It is also confirmed that the optimization guarantees the variational energy minimizations with multi-site support functions.
description: 25 pages, 3 figures, submitted to Phys. Chem. Chem. Phys
A Mixed Stirring Mechanism for Debris Discs with Giant and Dwarf Planetary Perturbations
Creators: name: Muñoz-Gutiérrez, Marco A.
name: Marshall, Jonathan P.
name: Peimbert, Antonio
Publisher: name: arXiv
Year: 2023
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: Debris discs consist of belts of bodies ranging in size from dust grains to planetesimals; these belts are visible markers of planetary systems around other stars that can reveal the influence of extrasolar planets through their shape and structure. Two key stirring mechanisms -- self-stirring by planetesimals and secular perturbation by an external giant planet -- have been identified to explain the dynamics of planetesimal belts; their relative importance has been studied independently, but are yet to be considered in combination. In this work we perform a suite of 286 N-body simulations exploring the evolution of debris discs over 1~Gyr, combining the gravitational perturbations of both dwarf planets embedded in the discs, and an interior giant planet. Our systems were somewhat modeled after the architecture of the outer Solar system: a Solar mass star, a single massive giant planet at 30~au ($M_{\rm GP} =$ 10 to 316~$\mathrm{M}_{\oplus}$), and a debris disc formed by 100 massive dwarf planets and 1000 massless particles ($M_{\rm DD} =$ 3.16 to 31.6~$\mathrm{M}_{\oplus}$). We present the evolution of both the disc and the giant planet after 1~Gyr. The time evolution of the average eccentricity and inclination of the disc is strongly dependent on the giant planet mass as well as on the remaining disc mass. We also found that efficient stirring is achieved even with small disc masses. In general, we find that a mixed mechanism is more efficient in the stirring of cold debris discs than either mechanism acting in isolation.
description: Accepted for publication in MNRAS. 11 pages, 6 figures (4 animated). Animated figures can be found at https://figshare.com/projects/Mixed_Stirring_of_Debris_Discs/136118
Dimensions of Community Inclusion in Research: Using Evaluation to Improve Community Engagement Across the Research Design-to-Dissemination Continuum
Creators: name: Dave, Gaurav
name: Smith, Jeffrey
name: Lucas, Valerie A.
name: Osinuga, Abisola
name: Kuhn, Marlena K.
name: Hayes, Barrie E.
name: Carr, Tara
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2022

description: Background
Rapid Diagnostics for Underserved Populations (RADx-UP) is a multisite grant with a coordinating center funded by the National Institutes of Health to increase COVID-19 testing access. RADx-UP includes over 125 research projects working with underserved communities across the United States, its territories, and Tribal Nations. Program evaluation includes tracking and analyzing RADx-UP peer-reviewed publications across multiple community inclusion dimensions to (1) assess contributions to community engagement knowledge base and (2) strengthen community partner inclusion throughout the research design-to-dissemination continuum across the consortium.

Methods
We identify RADx-UP publications through monthly grant number searches in PubMed and Scopus and quarterly PI surveys. Through April 2022, 76 publications have been identified and analyzed as part of ongoing evaluation through 2024. We analyze publications quarterly to (1) thematically code, (2) extract community engagement strategies, and (3) examine patterns of academic-community collaborations among co-authorship networks.

Results
A key emergent theme from content analysis was collaborative partnerships; effective community engagement strategies identified included social media, community-collaborative partnerships, and community stakeholder meetings. Collaboration analyses of publications indicated that 11% included community-based coauthor(s), and 37% included a community stakeholder acknowledgement. Evaluation findings were shared via interactive dashboards on the RADx-UP website, which project teams report allow for contextualization of findings.

Conclusion
We developed an evaluation approach for tracking and analyzing community engagement across the research design-to-dissemination continuum. Findings support RADx-UP consortium efforts to increase community inclusion in research by augmenting training and support. Program evaluators can adapt our approach to foster research equity and inclusion.
Polarimetric Reverberation Mapping in Medium-Band Filters
Creators: name: Shablovinskaya, Elena
name: Popović, Luka Č.
name: Uklein, Roman
name: Malygin, Eugene
name: Ilić, Dragana
name: Ciroi, Stefano
name: Oparin, Dmitry
name: Crepaldi, Luca
name: Slavcheva-Mihova, Lyuba
name: Mihov, Boyko
name: Nikolov, Yanko
Publisher: name: arXiv
Year: 2023
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: Earlier, we suggested the "reload" concept of the polarimetric reverberation mapping of active galactic nuclei (AGN), proposed for the first time more than 10 years ago. We have successfully tested this approach of reverberation mapping of the broad emission line on the galaxy Mrk 6. It was shown that such an idea allows one to look at the AGN central parsec structure literally in a new light. However, the method originally assumed the use of spectropolarimetric observations, expensive in terms of telescope time, and implemented on rare large telescopes. Currently, we propose an adaptation of the polarimetric reverberation mapping of broad lines in medium-band filters following the idea of the photometric reverberation mapping, when filters are selected so that their bandwidth is oriented to the broad line and the surrounding continuum near. In this paper, we present the progress status of such monitoring conducted jointly at the Special astrophysical observatory and Asiago Cima Ekar observatory (OAPd/INAF) with support from Rozhen National Astronomical Observatory (NAO), some first results for the most frequently observed AGNs Mrk 335, Mrk 509, and Mrk 817, and the discussion of the future perspectives of the campaign.
description: Published in Universe
Robustness of chimera states for coupled FitzHugh-Nagumo oscillators
Creators: name: Omelchenko, Iryna
name: Provata, Astero
name: Hizanidis, Johanne
name: Schoell, Eckehard
name: Hoevel, Philipp
Publisher: name: arXiv
Year: 2014
Subjects: subject: Adaptation and Self-Organizing Systems (nlin.AO)
subject: Chaotic Dynamics (nlin.CD)
subject: FOS: Physical sciences

description: Chimera states are complex spatio-temporal patterns that consist of coexisting domains of spatially coherent and incoherent dynamics. This counterintuitive phenomenon was first observed in systems of identical oscillators with symmetric coupling topology. Can one overcome these limitations? To address this question, we discuss the robustness of chimera states in networks of FitzHugh-Nagumo oscillators. Considering networks of inhomogeneous elements with regular coupling topology, and networks of identical elements with irregular coupling topologies, we demonstrate that chimera states are robust with respect to these perturbations, and analyze their properties as the inhomogeneities increase. We find that modifications of coupling topologies cause qualitative changes of chimera states: additional random links induce a shift of the stability regions in the system parameter plane, gaps in the connectivity matrix result in a change of the multiplicity of incoherent regions of the chimera state, and hierarchical geometry in the connectivity matrix induces nested coherent and incoherent regions.
Sustainable Energy Transition in the Philippines: Balancing Renewables, Land Use, and Biodiversity
Creators: name: Voskanyan Marine
Publisher: name: Zenodo
Year: 2023
Subjects: CLEW

description: The CLEWS (Climate, Land, Energy, and Water Systems) analysis in the Philippines identifies the current energy mix, fossil fuel dependency, renewable energy potential, land use implications, environmental impact, and provides policy recommendations for achieving sustainable energy goals.
Additional file 2 of Metagenomic characterization of a novel non-ammonia-oxidizing Thaumarchaeota from hadal sediment
Creators: name: Zhang, Ru-Yi
name: Wang, Yan-Ren
name: Liu, Ru-Long
name: Rhee, Sung-Keun
name: Zhao, Guo-Ping
name: Quan, Zhe-Xue
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2: Figure S1. Metagenomic reads based on community constitution. Thaumarchaeota (equivalent to GTDB-Tk classification Thermoproteota) was found to be the dominant archaea in the sediment samples collected from nine different depths in the Mariana Challenger Deep. The numbers of metagenome-assembled genomes (MAGs) in each phylum are shown in brackets. MT1 to MT9 mean samples were collected from different depths: MT1, 0–2 cm; MT2, 2–3 cm; MT3, 3–4 cm; MT4, 4–5 cm; MT5, 5–6 cm; MT6, 6–7 cm; MT7; 7–8 cm; MT8, 8–9 cm; and MT9, 9–10 cm. Figure S2. Contig composition-independent profile of the assembled metagenome from Challenger Deep sediments. Circles represent contigs in the assembled metagenome of the MT1 sample, scaled by the square root of their length. Only contigs ≥ 5 kbp are shown. Circles are colored according to the taxonomy annotation by GTDB-Tk. Figure S3. Average nucleotide identity (ANI) of Group-3.unk Thaumarchaeota. MT1_thaum1 and MT7_thaum2 are metagenome-assembled genomes (MAGs) from this study. MT1_thaum1 and MT7_thaum2 have high similarity to Candidatus_Nitrosopumilus_sp_MTA1, which was binned from Mariana Trench water samples obtained at a depth of 8000 m in a previous study (1). MT1_thaum1 and other four related MAGs reconstructed from public metagenomic datasets in Group-3.unk showed high ANI value (> 0.82) with intra-group comparison but low ANI value (< 0.73) with MAGs of other groups. Figure S4. Occupation ratio of organic metabolism-related archaeal Clusters of Orthologous Genes (arCOGs) categories of sub-groups of Thaumarchaeota. Ammonia-oxidizing archaea (AOA) have the lowest ratio of organic metabolism COGs; however, other groups have equivalent numbers of organic metabolism-related COGs, which indicate a heterotroph habitat. Group-3.a has lower organic metabolism-related COGs than other non-AOA sub-groups and Aigarchaeota. Wilcoxon test, NS P>0.05, * 0.01
Reaction times and reaction asynchrony results from Communication and action predictability: two complementary strategies for successful cooperation
Creators: name: Woźniak, Mateusz
name: Knoblich, Guenther
Publisher: name: The Royal Society
Year: 2022
Subjects: subject: 170299 Cognitive Science not elsewhere classified
subject: FOS: Psychology
subject: 179999 Psychology and Cognitive Sciences not elsewhere classified

description: Reaction times and reaction asynchrony results
A Putative Lipoprotein Mediates Cell-Cell Contact for Type VI Secretion System-Dependent Killing of Specific Competitors
Creators: name: Speare, L.
name: Septer, A.N.
name: Woo, M.
name: Dunn, A.K.
Publisher: name: American Society for Microbiology
Year: 2022

description: Interbacterial competition is prevalent in host-associated microbiota, where it can shape community structure and function, impacting host health in both positive and negative ways. However, the factors that permit bacteria to discriminate among their various neighbors for targeted elimination of competitors remain elusive. We identified a putative lipoprotein (TasL) in Vibrio species that mediates cell-cell attachment with a subset of target strains, allowing inhibitors to target specific competitors for elimination. Here, we describe this putative lipoprotein, which is associated with the broadly distributed type VI secretion system (T6SS), by studying symbiotic Vibrio fischeri, which uses the T6SS to compete for colonization sites in their squid host. We demonstrate that TasL allows V. fischeri cells to restrict T6SS-dependent killing to certain genotypes by selectively integrating competitor cells into aggregates while excluding other cell types. TasL is also required for T6SS-dependent competition within juvenile squid, indicating that the adhesion factor is active in the host. Because TasL homologs are found in other host-associated bacterial species, this newly described cell-cell attachment mechanism has the potential to impact microbiome structure within diverse hosts.
Activation of the type VI secretion system in the squid symbiont vibrio fischeri requires the transcriptional regulator tasr and the structural proteins TssM and TssA
Creators: name: Smith, S.
name: Septer, A.N.
name: Garikipati, A.
name: Salvato, F.
name: Kleiner, M.
Publisher: name: American Society for Microbiology
Year: 2021

description: Bacteria have evolved diverse strategies to compete for a niche, including the type VI secretion system (T6SS), a contact-dependent killing mechanism. T6SSs are common in bacterial pathogens, commensals, and beneficial symbionts, where they affect the diversity and spatial structure of host-associated microbial communities. Although T6SS gene clusters are often located on genomic islands (GIs), which may be transferred as a unit, the regulatory strategies that promote gene expression once the T6SS genes are transferred into a new cell are not known. We used the squid symbiont Vibrio fischeri to identify essential regulatory factors that control expression of a strain-specific T6SS encoded on a GI. We found that a transcriptional reporter for this T6SS is active only in strains that contain the T6SS-encoding GI, suggesting the GI encodes at least one essential regulator. A transposon screen identified seven mutants that could not activate the reporter. These mutations mapped exclusively to three genes on the T6SS-containing GI that encode two essential structural proteins (a TssA-like protein and TssM) and a transcriptional regulator (TasR). Using T6SS reporters, reverse transcription-PCR (RT-PCR), competition assays, and differential proteomics, we found that all three genes are required for expression of many T6SS components, except for the TssA-like protein and TssM, which are constitutively expressed. Based on these findings, we propose a model whereby T6SS expression requires conserved structural proteins, in addition to the essential regulator TasR, and this ability to self-regulate may be a strategy to activate T6SS expression upon transfer of T6SS-encoding elements into a new bacterial host. IMPORTANCE Interbacterial weapons like the T6SS are often located on mobile genetic elements, and their expression is highly regulated. We found that two conserved structural proteins are required for T6SS expression in Vibrio fischeri. These structural proteins also contain predicted GTPase and GTP binding domains, suggesting their role in promoting T6SS expression may involve sensing the energetic state of the cell. Such a mechanism would provide a direct link between T6SS activation and cellular energy levels, providing a “checkpoint” to ensure the cell has sufficient energy to build such a costly weapon. Because these regulatory factors are encoded within the T6SS gene cluster, they are predicted to move with the genetic element to activate T6SS expression in a new host cell.
Environmental viscosity modulates interbacterial killing during habitat transition
Creators: name: Kleiner, M.
name: Salvato, F.
name: Smith, S.
name: Septer, A.N.
name: Speare, L.
Publisher: name: American Society for Microbiology
Year: 2020

description: Symbiotic bacteria use diverse strategies to compete for host colonization sites. However, little is known about the environmental cues that modulate interbacterial competition as they transition between free-living and host-associated lifestyles. We used the mutualistic relationship between Eupyrmna scolopes squid and Vibrio fischeri bacteria to investigate how intraspecific competition is regulated as symbionts move from the seawater to a host-like environment. We recently reported that V. fischeri uses a type VI secretion system (T6SS) for intraspecific competition during host colonization. Here, we investigated how environmental viscosity impacts T6SS-mediated competition by using a liquid hydrogel medium that mimics the viscous host environment. Our data demonstrate that although the T6SS is functionally inactive when cells are grown under low-viscosity liquid conditions similar to those found in seawater, exposure to a host-like high-viscosity hydrogel enhances T6SS expression and sheath formation, activates T6SS-mediated killing in as little as 30 min, and promotes the coaggregation of competing genotypes. Finally, the use of mass spectrometry-based proteomics revealed insights into how cells may prepare for T6SS competition during this habitat transition. These findings, which establish the use of a new hydrogel culture condition for studying T6SS interactions, indicate that V. fischeri rapidly responds to the physical environment to activate the competitive mechanisms used during host colonization. IMPORTANCE Bacteria often engage in interference competition to gain access to an ecological niche, such as a host. However, little is known about how the physical environment experienced by free-living or host-associated bacteria influences such competition. We used the bioluminescent squid symbiont Vibrio fischeri to study how environmental viscosity impacts bacterial competition. Our results suggest that upon transition from a planktonic environment to a host-like environment, V. fischeri cells activate their type VI secretion system, a contact-dependent interbacterial nanoweapon, to eliminate natural competitors. This work shows that competitor cells form aggregates under host-like conditions, thereby facilitating the contact required for killing, and reveals how V. fischeri regulates a key competitive mechanism in response to the physical environment.
Peculiar symmetry structure of some known discrete nonautonomous equations
Creators: name: Garifullin, Rustem N.
name: Habibullin, Ismagil T.
name: Yamilov, Ravil I.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Exactly Solvable and Integrable Systems (nlin.SI)
subject: FOS: Physical sciences

description: We study the generalized symmetry structure of three known discrete nonautonomous equations. One of them is the semidiscrete dressing chain of Shabat. Two others are completely discrete equations defined on the square lattice. The first one is a discrete analogue of the dressing chain introduced by Levi and Yamilov. The second one is a nonautonomous generalization of the potential discrete KdV equation or, in other words, the H1 equation of the well-known Adler-Bobenko-Suris list. We demonstrate that these equations have generalized symmetries in both directions if and only if their coefficients, depending on the discrete variables, are periodic. The order of the simplest generalized symmetry in at least one direction depends on the period and may be arbitrarily high. We substantiate this picture by some theorems in the case of small periods. In case of an arbitrarily large period, we show that it is possible to construct two hierarchies of generalized symmetries and conservation laws. The same picture should take place in case of any nonautonomous equation of the Adler-Bobenko-Suris list.
description: 25 pages, submitted to J Phys A
CL2QCD - Lattice QCD based on OpenCL
Creators: name: Philipsen, Owe
name: Pinke, Christopher
name: Sciarra, Alessandro
name: Bach, Matthias
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: FOS: Physical sciences

description: We present the Lattice QCD application CL2QCD, which is based on OpenCL and can be utilized to run on Graphic Processing Units as well as on common CPUs. We focus on implementation details as well as performance results of selected features. CL2QCD has been successfully applied in LQCD studies at finite temperature and density and is available at http://code.compeng.uni-frankfurt.de/projects/clhmc .
description: 10 pages, 5 figures; posters presented at the 32nd International Symposium on Lattice Field Theory (23-28 June 2014, Columbia University New York, NY, USA)
Additional file 1 of Sex and gender correlates of sexually polymorphic cognition
Creators: name: Cartier, Louis
name: Guérin, Mina
name: Saulnier, Fanny
name: Cotocea, Ioana
name: Mohammedi, Amine
name: Moussaoui, Fadila
name: Kheloui, Sarah
name: Juster, Robert-Paul
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Physiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Science Policy
subject: Mental Health

description: Additional file 1. Table S1: Correlation matrix of cognitive task performances for participants. Table S2: Regression table of Digit Span performances according to all five sex*gender factors and covariates. Table S3: Regression table of Five-Point Test performances according to all five sex*gender factors and covariates.
Scalable synthesis and characterization of multilayer $γ$-graphyne, new carbon crystals with a small direct bandgap
Creators: name: Desyatkin, Victor G.
name: Martin, William B.
name: Aliev, Ali E.
name: Chapman, Nathaniel E.
name: Fonseca, Alexandre F.
name: Galvão, Douglas S.
name: Miller, E. Roy
name: Stone, Kevin H.
name: Wang, Zhong
name: Zakhidov, Dante
name: Limpoco, F. Ted
name: Almahdali, Sarah R.
name: Parker, Shane M.
name: Baughman, Ray H.
name: Rodionov, Valentin O.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: $γ$-Graphyne is the most symmetric sp2/sp1 allotrope of carbon, which can be viewed as graphene uniformly expanded through insertion of two-carbon acetylenic units between all the aromatic rings. To date, synthesis of bulk $γ$-graphyne has remained a challenge. We here report the synthesis of multilayer $γ$-graphyne through crystallization-assisted irreversible cross-coupling polymerization. Comprehensive characterization of this new carbon phase is described, including synchrotron X-ray diffraction, electron diffraction, lateral force microscopy, Raman and infrared spectroscopy, and cyclic voltammetry. Experiments indicate that $γ$-graphyne is a 0.48 eV bandgap semiconductor, with a hexagonal a-axis spacing of 6.88 Å and an interlayer spacing of 3.48 Å, which is consistent with theoretical predictions. The observed crystal structure has an aperiodic sheet stacking. The material is thermally stable up to 240 $^\circ$C but undergoes a transformation at higher temperatures. While conventional 2D polymerizations and reticular chemistry rely on error correction through reversibility, we demonstrate that a periodic covalent lattice can be synthesized under purely kinetic control. The reported methodology is scalable and inspires extension to other allotropes of the graphyne family.
description: Additional supporting information files are available at https://pubs.acs.org/doi/10.1021/jacs.2c06583
The first "water fountain" collimated outflow in a planetary nebula
Creators: name: Gomez, J. F.
name: Suarez, O.
name: Bendjoya, Ph.
name: Rizzo, J. R.
name: Miranda, L. F.
name: Green, J. A.
name: Uscanga, L.
name: Garcia-Garcia, E.
name: Lagadec, E.
name: Guerrero, M. A.
name: Ramos-Larios, G.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: "Water fountains" (WFs) are evolved objects showing high-velocity, collimated jets traced by water maser emission. Most of them are in the post-Asymptotic Giant Branch and they may represent one of the first manifestations of collimated mass loss in evolved stars. We present water maser, carbon monoxide, and mid-infrared spectroscopic data (obtained with the Australia Telescope Compact Array, Herschel Space Observatory, and the Very Large Telescope, respectively) toward IRAS 15103--5754, a possible planetary nebula (PN) with WF characteristics. Carbon monoxide observations show that IRAS 15103-5754 is an evolved object, while the mid-IR spectrum displays unambiguous [NeII] emission, indicating that photoionization has started and thus, its nature as a PN is confirmed. Water maser spectra show several components spreading over a large velocity range ~75 km/s and tracing a collimated jet. This indicates that the object is a WF, the first WF known that has already entered the PN phase. However, the spatial and kinematical distribution of the maser emission in this object are significantly different from those in other WFs. Moreover, the velocity distribution of the maser emission shows a "Hubble-like" flow (higher velocities at larger distances from the central star), consistent with a short-lived, explosive mass-loss event. This velocity pattern is not seen in other WFs (presumably in earlier evolutionary stages). We therefore suggest that we are witnessing a fundamental change of mass-loss processes in WFs, with water masers being pumped by steady jets in post-AGB stars, but tracing explosive/ballistic events as the object enters the PN phase.
description: To be published in The Astrophysical Journal. 7 pages, 4 figures
A Novel Framework for Handling Sparse Data in Traffic Forecast
Creators: name: Zygouras, Nikolaos
name: Gunopulos, Dimitrios
Publisher: name: arXiv
Year: 2023
Subjects: subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: The ever increasing amount of GPS-equipped vehicles provides in real-time valuable traffic information for the roads traversed by the moving vehicles. In this way, a set of sparse and time evolving traffic reports is generated for each road. These time series are a valuable asset in order to forecast the future traffic condition. In this paper we present a deep learning framework that encodes the sparse recent traffic information and forecasts the future traffic condition. Our framework consists of a recurrent part and a decoder. The recurrent part employs an attention mechanism that encodes the traffic reports that are available at a particular time window. The decoder is responsible to forecast the future traffic condition.
HTTE: A Hybrid Technique For Travel Time Estimation In Sparse Data Environments
Creators: name: Zygouras, Nikolaos
name: Panagiotou, Nikolaos
name: Li, Yang
name: Gunopulos, Dimitrios
name: Guibas, Leonidas
Publisher: name: arXiv
Year: 2023
Subjects: subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: Travel time estimation is a critical task, useful to many urban applications at the individual citizen and the stakeholder level. This paper presents a novel hybrid algorithm for travel time estimation that leverages historical and sparse real-time trajectory data. Given a path and a departure time we estimate the travel time taking into account the historical information, the real-time trajectory data and the correlations among different road segments. We detect similar road segments using historical trajectories, and use a latent representation to model the similarities. Our experimental evaluation demonstrates the effectiveness of our approach.
description: Proceedings of the 27th ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems. 2019
Magnetization reversal assisted by half antivortex states in nanostructured circular cobalt disks
Creators: name: Lara, Antonio
name: Dobrovolskiy, Oleksandr V.
name: Prieto, José L.
name: Huth, Michael
name: Aliev, Farkhad G.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: The half antivortex, a fundamental topological structure which determines magnetization reversal of submicron magnetic devices with domain walls, has been suggested also to play a crucial role in spin torque induced vortex core reversal in circular disks. Here we report on magnetization reversal in circular disks with nanoholes through consecutive metastable states with half antivortices. In-plane anisotropic magnetoresistance and broadband susceptibility measurements accompanied by micromagnetic simulations reveal that cobalt disks with two and three linearly arranged nanoholes directed at 45 and 135 degrees with respect to the external magnetic field show reproducible step-like changes in the anisotropic magnetoresistance and magnetic permeability due to transitions between different intermediate states mediated by vortices and half antivortices confined to the dot nanoholes and edges, respectively. Our findings are relevant for the development of multi-hole based spintronic and magnetic memory devices.
Draft genome sequences of type VI secretion system-encoding vibrio fischeri strains FQ-A001 and ES401
Creators: name: Mandel, M.J.
name: Miyashiro, T.
name: Bultman, K.M.
name: Septer, A.N.
name: Cecere, A.G.
Publisher: name: American Society for Microbiology
Year: 2019

description: The type VI secretion system (T6SS) facilitates lethal competition between bacteria through direct contact. Comparative genomics has facilitated the study of these systems in Vibrio fischeri, which colonizes the squid host Euprymna scolopes. Here, we report the draft genome sequences of two lethal V. fischeri strains that encode the T6SS, FQ-A001 and ES401.
New Transient ULX Candidate in NGC 4254: Evidence of Circumbinary Disk?
Creators: name: Allak, Sinan
Publisher: name: arXiv
Year: 2023
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: This paper presents the identification of a new transient ULX candidate (ULX-3) with reaching a peak luminosity of ~ 4e39 erg/s in NGC 4254 by using archival Chandra, Swift X-Ray Telescope (Swift/XRT), Hubble Space Telescope (HST), and James Webb Space Telescope (JWST) observations. From precise astrometric calculations, unique optical, near-infrared (NIR) and mid-infrared (mid-IR) counterparts were found. The spectral energy distribution (SED) and color-magnitude diagrams (CMDs) of counterparts of the new ULX candidate were plotted to constrain the nature of the possible donor star. Evidence of a circumbinary disk was found from its SED with two blackbody temperatures of 1000 and 200 K. Moreover, according to the X-ray hardness ratios, ULX-3 exhibits very hard to very soft transitions as seen in some high-mass X-ray binaries (HMXBs) with Be-star donors Moreover, ULX-3 varies by more than two orders of magnitude in the 0.3-10 keV energy band as seen in typical transient ULXs.
description: ACCEPTED for publication in MNRAS
РЕГИСТРАТОР МАГНИТНОЙ АКТИВНОСТИ модель IDL-09. Техническое описание и инструкция по эксплуатации. Троицк: ИЗМИРАН, 2006. - 19 с.
Creators: name: Любимов В.В.
Publisher: name: Zenodo
Year: 2006
Subjects: Магнитное поле, феррозондовые магнитометры, магнитные измерения, компонентные магнитометры, магнитные возмущения, магнитные бури

description: Регистратор магнитной активности (РМА) IDL-09, является высокочувствительным компонентным магнитометром, предназначенным для измерения в реальном времени, регистрации, хранения, анализа и представления данных измерений вариаций D-составляющей вектора магнитной индукции (ВМИ) поля Земли или вариаций одной из составляющих ВМИ: Н, Z, Х, Y, а также для исследования полей, создаваемых искусственными источниками, для систем, служащих для привязки и ориентации объектов по магнитному полю и для специальных целей. РМА автоматически отслеживает текущие магнитные возмущения путем расчета и визуализации в реальном времени индекса магнитной активности, для оповещения о зафиксированном возмущении предусмотрен встроенный звуковой сигнализатор.