cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Developing communities of commensal bacteria to enhance immune defences to infection
Creators: name: Larkinson, Max Louis Yeung
Publisher: name: Imperial College London
Year: 2023

description: The microbiota is the collective term referring to the diverse range of microorganisms which colonise the human body and other forms of higher life. This complex and dynamic community contains trillions of bacteria and other microbes; it has evolved alongside the host and inhabits all environmentally exposed surfaces within the body. As a result, the microbiota plays a critical role in host health and disease. In particular, the microbiota has been shown to be invaluable for a normal functioning immune system, with disruption to the microbiota resulting in increased susceptibility to pathogenic infection, as well as a multitude of inflammatory or autoimmune diseases. Microbiota-mediated regulation of the innate immune system is facilitated through the production of pattern recognition receptor (PRR) ligands and short-chain fatty acids (SCFAs). While both mechanisms of immune regulation are well-studied independently, the combine effect of these two pathways is far less well understood, despite occurring constantly during homeostasis. In this thesis, we show that the effect of PRR ligands and SCFAs on macrophages in isolation is distinct compared to their combined effect. We demonstrate that SCFAs modulate cytokine production induced by PRR activation, resulting from co-stimulation of macrophages with a wide range of commensal bacteria and different SCFAs. These SCFAs elicit either a pro- or anti-inflammatory effect depending on the sequential order of treatments. We also show that stimulation of PRRs by certain commensal bacteria is able to rescue macrophages from the cytotoxic concentrations of SCFAs, found within the host. Finally, using a Clostridium difficile infection (CDI) mouse model, we demonstrate that a combination of SCFA treatment and commensal bacteria inoculation, significantly reduces C. difficile load and increases expression of the antimicrobial peptide Reg3γ, in comparison to each treatment in isolation. The work outlined in this thesis provides a foundation for novel microbiome-based therapeutics, which can harness the combined potential of both PRR- and SCFA-mediated immune regulation, to enhance immune defences to infection.
Methods and materials for "An inverse relation between expressiveness and grammatical integration"
Creators: name: Dingemanse, Mark
name: Akita, Kimi
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: corpus linguistics
subject: data
subject: ideophones
subject: Japanese
subject: R
subject: Rmarkdown

description: Data and scripts underlying a paper on expressiveness and grammatical integration, by Mark Dingemanse and Kimi Akita (Journal of Linguistics, 2016). Download and view analysis.html for readable R code and figures, or check analysis.Rmd for the source. The data is in ExpInt.txt (CSV) and ExpInt.Rdata (R). If you find this to be of use, please cite the paper: Dingemanse, Mark and Kimi Akita. (2016) An inverse relation between expressiveness and grammatical integration: on the morphosyntactic typology of ideophones, with special reference to Japanese. Journal of Linguistics.
Non-Markovian Dynamics in Chiral Quantum Networks with Spins and Photons
Creators: name: Ramos, Tomás
name: Vermersch, Benoît
name: Hauke, Philipp
name: Pichler, Hannes
name: Zoller, Peter
Publisher: name: arXiv
Year: 2016
Subjects: subject: Quantum Physics (quant-ph)
subject: Atomic Physics (physics.atom-ph)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We study the dynamics of chiral quantum networks consisting of nodes coupled by unidirectional or asymmetric bidirectional quantum channels. In contrast to familiar photonic networks where driven two-level atoms exchange photons via 1D photonic nanostructures, we propose and study a setup where interactions between the atoms are mediated by spin excitations (magnons) in 1D $XX$ spin chains representing spin waveguides. While Markovian quantum network theory eliminates quantum channels as structureless reservoirs in a Born-Markov approximation to obtain a master equation for the nodes, we are interested in non-Markovian dynamics. This arises from the nonlinear character of the dispersion with band-edge effects, and from finite spin propagation velocities leading to time delays in interactions. To account for the non-Markovian dynamics we treat the quantum degrees of freedom of the nodes and connecting channels as a composite spin system with the surrounding of the quantum network as a Markovian bath, allowing for an efficient solution with time-dependent density matrix renormalization group techniques. We illustrate our approach showing non-Markovian effects in the driven-dissipative formation of quantum dimers, and we present examples for quantum information protocols involving quantum state transfer with engineered elements as basic building blocks of quantum spintronic circuits.
description: updated version
Convolution of Picard-Fuchs equations
Creators: name: Movasati, Hossein
name: Reiter, Stefan
Publisher: name: arXiv
Year: 2016
Subjects: subject: Algebraic Geometry (math.AG)
subject: Mathematical Physics (math-ph)
subject: Classical Analysis and ODEs (math.CA)
subject: Complex Variables (math.CV)
subject: FOS: Mathematics
subject: FOS: Physical sciences

description: We determine explicit generators for a cohomology group constructed from a solution of a fuchsian linear differential equation and describe its relation with cohomology groups with coefficients in a local system. In the parameterized case, this yields into an algorithm which computes new fuchsian differential equations from those depending on multi-parameters. This generalizes the classical convolution of solutions of fuchsian differential equations.
description: 17 pages
High Performance Li-Air Battery Using Different Gaseous Species
Creators: name: Jaradat, Ahmad
Publisher: name: University of Illinois at Chicago
Year: 2023

description: In the first project, I developed an air-breathing sheet-type flexible Li-O2 battery operating under different conditions (oxygen, dry air, and ambient air). The flexible battery showed an excellent performance (370 cycles in pure oxygen, 250 cycles in dry air and 240 cycles in ambient air) under a high current density of 1 A/g. It was uncovered that there is an excellent synergy between different components of the battery including electrolyte/redox mediator, cathode catalyst and Fomblin-based protection layer suppressing H2O permeation into the battery cell. The battery operating in ambient air exhibited a superior performance including high charge/discharge curves stability, excellent rate capability and a deep-discharge capacity as high as 56 Ah/g before and after bending. The obtained results open a new direction in utilizing Li-O2 batteries in flexible and wearable electronics. In the second project, I developed a high performance Li-CO2 battery chemistry based on a novel combination of a mid-entropy cathode catalyst of (NbTa)0.5BiS3 and an electrolyte combination of ZnI2, lithium bis(trifluoromethanesulfonyl)imide (LiTFSI), dimethyl sulfoxide (DMSO) and ionic liquid (IL) of 1-Ethyl-3-methylimidazolium tetrafluoroborate (EMIM-BF4) with the volumetric ratio of 9:1. The battery is capable to operate under high rates (0.3, 0.5 mA/cm2) and high capacities of 0.2, 0.3 and 0.5 mAh/cm2 (corresponding to 2000, 3000, and 5000 mAh/g, respectively). The achieved capacities and current rates are by far the highest values to be reported in the literature for this type of battery. In the third project, I have developed Li-CO2 battery with novel cathode catalyst of Sb0.67Bi1.33Te3 that showed an excellent performance, up to 220 cycles at high current density of 1 mA/cm2, with capacity of 0.2 mA/cm2, far exceeding values reported in the literature for Li-CO2 battery. These results demonstrate the role of Chalcogenide (Te) and the optimized volume of ionic liquid in improving the battery performance and showed the crucial role of catalyst (Sb0.67Bi1.33Te3) in stabilizing the charge potential with high CO2ER capability.
Development and application of deep learning and spatial statistics within 3D bone marrow imaging
Creators: name: Adams, George
Publisher: name: Imperial College London
Year: 2022

description: The bone marrow is a highly specialised organ, responsible for the formation of blood cells. Despite 50 years of research, the spatial organisation of the bone marrow remains an area full of controversy and contradiction. One reason for this is that imaging of bone marrow tissue is notoriously difficult. Secondly, efficient methodologies to fully extract and analyse large datasets remain the Achilles heels of imaging-based research. In this thesis I present a pipeline for generating 3D bone marrow images followed by the large-scale data extraction and spatial statistical analysis of the resulting data. Using these techniques, in the context of 3D imaging, I am able to identify and classify the location of hundreds of thousands of cells within various bone marrow samples. I then introduce a series of statistical techniques tailored to work with spatial data, resulting in a 3D statistical map of the tissue from which multi-cellular interactions can be clearly understood. As an illustration of the power of this new approach, I apply this pipeline to diseased samples of bone marrow with a particular focus on leukaemia and its interactions with CD8+ T cells. In so doing I show that this novel pipeline can be used to unravel complex multi-cellular interactions and assist researchers in understanding the processes taking place within the bone marrow.
Atom-Field Entanglement in Cavity QED: Nonlinearity and Saturation
Creators: name: Rogers, Robert
name: Cummings, Nick
name: Pedrotti, Leno
name: Rice, Perry
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We investigate the degree of entanglement between an atom and a driven cavity mode, in the presence of dissipation. Previous work has shown that in the limit of weak driving fields, the steady state entanglement is proportional to the square of the driving intensity. This quadratic dependence is due to the generation of entanglement by the creation of pairs of photons/excitations. In this work we investigate the entanglement between an atom and a cavity in the presence of multiple photons. Nonlinearity of the atomic response is needed to generate entanglement, but as that nonlinearity saturates the entanglement vanishes. We posit that this is due to spontaneous emission, which puts the atom in the ground state and the atom-field state into a direct product state. An intermediate value of the driving field, near the field that saturates the atomic response, optimizes the atom-field entanglement. In a parameter regime for which multiphoton resonances occur, we find that entanglement recurs at those resonances. \cite{Shamailov-10} In this regime, we find that the entanglement decreases with increaing photon number. We also investigate, in the bimodal regime of Alsing et. al.\cite{Alsing-91-DressedState} \cite{Alsing-92-DSS}\cite{Carm-15-X}, the entanglement as a function of atom and/or cavity detuning. Here we find that there is evidence of a phase transition in the entanglement, which occurs at $2ε/g \geq 1$.
description: 16 pages, 9 figures
Improving the accuracy of black carbon measurements for air quality and climate change
Creators: name: Ciupek, Krzysztof
Publisher: name: Imperial College London
Year: 2023

description: Black carbon (BC) and elemental carbon (EC) are widely used parameters to quantify carbonaceous particles in ambient air. They are important for climate modelling, source apportionment of air pollutants and formulating and evaluating air quality policy. This thesis investigates both practical and fundamental aspects of these measurements. UK air monitoring network data over the period 2014 2019 showed that BC concentrations from Aethalometer instruments decreased at all sites (-12.5% y^-1 at the traffic site), whereas the EC concentrations changed less, and increased at the rural site. Despite these differences, the trends in the mass absorption cross section (MAC) parameter of the particles decreased at all sites with rates from -5.5% y^-1 to -10.1% y^-1. Interpretation of these results is difficult, because any changes in the properties of the aerosol particles will affect measurements of BC and EC in different ways, so that separating real changes from method artefacts is challenging. Instrumental upgrades within the unstandardised method for BC could lead to uncertainty in long term trends, impacting policy evaluation. Comparison campaigns in London showed that the results from different models of collocated Aethalometer (AE22 and AE33) had consistent differences of up to 40%; most likely due to inappropriate internal correction factors. This highlights the need to calibrate Aethalometers with defined synthetic aerosols. A facility for generating synthetic aerosols containing different particle types was developed and characterised at the National Physical Laboratory (NPL). This facility demonstrated the ability to generate uncoated soot particles and oxidised, coated soot particles (similar to “fresh” and “aged” soot in the atmosphere) in a consistent and controllable way. Differences in BC concentrations measured by the AE22 and AE33 Aethalometer in field tests were reproduced in the new test facility at NPL. Data analysis from field and laboratory experiments are presented and discussed, together with suggestions for future work.
Globally stable microresonator Turing pattern formation for coherent high-power THz radiation on-chip
Creators: name: Huang, Shu-Wei
name: Yang, Jinghui
name: Yang, Shang-Hua
name: Yu, Mingbin
name: Kwong, Dim-Lee
name: Zelevinsky, Tanya
name: Jarrahi, Mona
name: Wong, Chee Wei
Publisher: name: arXiv
Year: 2016
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: In nonlinear microresonators driven by continuous-wave (cw) lasers, Turing patterns have been studied in the formalism of Lugiato-Lefever equation with emphasis on its high coherence and exceptional robustness against perturbations. Destabilization of Turing pattern and transition to spatio-temporal chaos, however, limits the available energy carried in the Turing rolls and prevents further harvest of their high coherence and robustness to noise. Here we report a novel scheme to circumvent such destabilization, by incorporating the effect of local mode hybridizations, and attain globally stable Turing pattern formation in chip-scale nonlinear oscillators, achieving a record high power conversion efficiency of 45% and an elevated peak-to-valley contrast of 100. The stationary Turing pattern is discretely tunable across 430 GHz on a THz carrier, with a fractional frequency sideband non-uniformity measured at 7.3x10^-14. We demonstrate the simultaneous microwave and optical coherence of the Turing rolls at different evolution stages through ultrafast optical correlation techniques. The free running Turing roll coherence, 9 kHz in 200 ms and 160 kHz in 20 minutes, is transferred onto a plasmonic photomixer for one of the highest power THz coherent generation at room-temperature, with 1.1% optical-to-THz power conversion. Its long-term stability can be further improved by more than two orders of magnitude, reaching an Allan deviation of 6x10^-10 at 100 s, with a simple computer-aided slow feedback control. The demonstrated on-chip coherent high-power Turing-THz system is promising to find applications in astrophysics, medical imaging, and wireless communications.
Berry Fermi Liquid Theory
Creators: name: Chen, Jing-Yuan
name: Son, Dam Thanh
Publisher: name: arXiv
Year: 2016
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We develop an extension of the Landau Fermi liquid theory to systems of interacting fermions with non-trivial Berry curvature. We propose a kinetic equation and a constitutive relation for the electromagnetic current that together encode the linear response of such systems to external electromagnetic perturbations, to leading and next-to-leading orders in the expansion over the frequency and wave number of the perturbations. We analyze the Feynman diagrams in a large class of interacting quantum field theories and show that, after summing up all orders in perturbation theory, the current-current correlator exactly matches with the result obtained from the kinetic theory.
description: v2: typos fixed, v3: some issues clarified, typos fixed, v4: an error fixed; 46 pages
Nonconservation of lepton current and asymmetry of relic neutrinos
Creators: name: Dvornikov, Maxim
name: Semikoz, Victor B.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The neutrino asymmetry in the early universe plasma, $n_ν- n_{\bar ν}$, is calculated both before and after the electroweak phase transition (EWPT). The leptogenesis before EWPT within the standard model is well known to be driven by the abelian anomaly in a massless hypercharge field. The generation of the neutrino asymmetry in the Higgs phase after EWPT, in its turn, has not been considered previously because of the absence of any quantum anomaly in an external electromagnetic field for such electroneutral particles as neutrino, unlike the Adler anomaly for charged left and right polarized massless electrons in the same electromagnetic field. Using the neutrino Boltzmann equation, modified by the Berry curvature term in the momentum space, we establish the violation of the macroscopic neutrino current in plasma after EWPT and exactly reproduce the nonconservation of the lepton current in the symmetric phase before EWPT arising in quantum field theory due to the non-zero lepton hypercharge and corresponding triangle anomaly in an external hypercharge field. In the last case the violation of the lepton current is derived through the kinetic approach without the computation of the corresponding Feynman diagrams. Then the new kinetic equation is applied for the calculation of the neutrino asymmetry accounting for the the Berry curvature and the electroweak interaction with background fermions in the Higgs phase, including the stage after the neutrino decoupling at the absence of neutrino collisions in plasma. This asymmetry is found to be rather small to be observed. Thus, a difference of the relic neutrino and antineutrino densities, if exists, should be acquired mainly in the symmetric phase before EWPT.
description: 14 pages in pdfLaTeX, 1 eps figure; paper was significantly revised, title was changed, Sec. 2 was added, Secs. 3 and 4.1 were revised, version to be published in JETP
The Mittag-Leffler Fitting of the Phillips Curve
Creators: name: Skovranek, Tomas
Publisher: name: arXiv
Year: 2016
Subjects: subject: General Economics (econ.GN)
subject: FOS: Economics and business

description: In this paper, a mathematical model based on the one-parameter Mittag-Leffler function is proposed to be used for the first time to describe the relation between unemployment rate and inflation rate, also known as the Phillips curve. The Phillips curve is in the literature often represented by an exponential-like shape. On the other hand, Phillips in his fundamental paper used a power function in the model definition. Considering that the ordinary as well as generalised Mittag-Leffler function behaves between a purely exponential function and a power function it is natural to implement it in the definition of the model used to describe the relation between the data representing the Phillips curve. For the modelling purposes the data of two different European economies, France and Switzerland, were used and an "out-of-sample" forecast was done to compare the performance of the Mittag-Leffler model to the performance of the power-type and exponential-type model. The results demonstrate that the ability of the Mittag-Leffler function to fit data that manifest signs of stretched exponentials, oscillations or even damped oscillations can be of use when describing economic relations and phenomenons, such as the Phillips curve.
description: 20 pages, 4 figures, 3 tables, 7 numbered equations
Predicting Age at Menarche from Changes in Linear Growth vs. Body Fat
Creators: name: Martin, Melanie
name: Valeggia, Claudia
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Anthropology
subject: FOS: Sociology
subject: anthropometry
subject: Biological Anthropology
subject: Evolutionary Medicine
subject: Fat threshold hypothesis
subject: Life History Theory
subject: Menarche
subject: Puberty
subject: Public Health
subject: Skeletal maturation hypothesis

description: Pubertal onset and progression vary widely across human populations, though the causes of this variation are debated. Both skeletal growth and adiposity exhibit rapid growth during adolescence that is mediated by energy availability, and both have been proposed to moderate pubertal development. We argue that reproductive maturation should be more attuned to skeletal growth than adiposity, as the former is a better indicator of long-term nutritional conditions during childhood than is adiposity, and is correlated with pelvic growth. We will test the relative strength of changes in height vs. anthropometric markers of body fat in predicting age at menarche using data collected from Qom females in 2011-2015. The project overview, data files, and description of hypotheses, pre-processing steps, and data analysis protocol are included with this registration.
Fiber Optics Smart Strucures For Non-Destructive Applications
Creators: name: ISLAM, MD. NADIMUL
Publisher: name: figshare
Year: 2022
Subjects: Networking and communications
Theory of computation not elsewhere classified
Distributed computing and systems software not elsewhere classified

description: Optical fiber sensors are becoming increasingly famous and are well accepted for structural sensing and monitoring in variety of fields at the same time they are developing fast. For non-destructive testing applications optical fiber sensors are best devices because of their unique properties like small size, light weight and importantly dielectric glass construction that render them immune to electrical noise and EM interference which you cannot find in conventional electronic sensing system that use electronic components. In this particular paper we study how fiber operates using various principles, different sensors types followed by advantages and applications of optical fiber sensors for NDT (non- destructive testing) like structural sensing and monitoring in civil engineering, aerospace oil and gas and the most recent that includes monitoring of natural landscapes that extend over area such as earthquake fault lines and volcanicmotionvolcanicmotion.
Designing Kitaev spin liquids in metal-organic frameworks
Creators: name: Yamada, Masahiko G.
name: Fujita, Hiroyuki
name: Oshikawa, Masaki
Publisher: name: arXiv
Year: 2016
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Materials Science (cond-mat.mtrl-sci)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Kitaev's honeycomb lattice spin model is a remarkable exactly solvable model, which has a particular type of spin liquid (Kitaev spin liquid) as the ground state. Although its possible realization in iridates and $α$-RuCl$_3$ has been vigorously discussed recently, these materials have substantial non-Kitaev direct exchange interactions and do not have a spin liquid ground state. We propose metal-organic frameworks (MOFs) with Ru$^{3+}$ (or Os$^{3+}$) forming the honeycomb lattice as promising candidates for a more ideal realization of Kitaev-type spin models where the direct exchange interaction is strongly suppressed. The great flexibility of MOFs allows generalization to other three-dimensional lattices, for potential realization of a variety of spin liquids such as a Weyl spin liquid.
description: 6+11 pages, 2+7 figures, 0+1 table; the final submitted version to appear in PRL
On the Planar Split Thickness of Graphs
Creators: name: Eppstein, David
name: Kindermann, Philipp
name: Kobourov, Stephen
name: Liotta, Giuseppe
name: Lubiw, Anna
name: Maignan, Aude
name: Mondal, Debajyoti
name: Vosoughpour, Hamideh
name: Whitesides, Sue
name: Wismath, Stephen
Publisher: name: arXiv
Year: 2015
Subjects: subject: Combinatorics (math.CO)
subject: FOS: Mathematics

description: Motivated by applications in graph drawing and information visualization, we examine the planar split thickness of a graph, that is, the smallest $k$ such that the graph is $k$-splittable into a planar graph. A $k$-split operation substitutes a vertex $v$ by at most $k$ new vertices such that each neighbor of $v$ is connected to at least one of the new vertices. We first examine the planar split thickness of complete graphs, complete bipartite graphs, multipartite graphs, bounded degree graphs, and genus-1 graphs. We then prove that it is NP-hard to recognize graphs that are $2$-splittable into a planar graph, and show that one can approximate the planar split thickness of a graph within a constant factor. If the treewidth is bounded, then we can even verify $k$-splittability in linear time, for a constant $k$.
Extreme robustness of scaling in sample space reducing processes explains Zipf's law in diffusion on directed networks
Creators: name: Corominas-Murtra, Bernat
name: Hanel, Rudolf
name: Thurner, Stefan
Publisher: name: arXiv
Year: 2016
Subjects: subject: Physics and Society (physics.soc-ph)
subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: FOS: Physical sciences

description: It has been shown recently that a specific class of path-dependent stochastic processes, which reduce their sample space as they unfold, lead to exact scaling laws in frequency and rank distributions. Such Sample Space Reducing processes (SSRP) offer an alternative new mechanism to understand the emergence of scaling in countless processes. The corresponding power law exponents were shown to be related to noise levels in the process. Here we show that the emergence of scaling is not limited to the simplest SSRPs, but holds for a huge domain of stochastic processes that are characterized by non-uniform prior distributions. We demonstrate mathematically that in the absence of noise the scaling exponents converge to $-1$ (Zipf's law) for almost all prior distributions. As a consequence it becomes possible to fully understand targeted diffusion on weighted directed networks and its associated scaling laws law in node visit distributions. The presence of cycles can be properly interpreted as playing the same role as noise in SSRPs and, accordingly, determine the scaling exponents. The result that Zipf's law emerges as a generic feature of diffusion on networks, regardless of its details, and that the exponent of visiting times is related to the amount of cycles in a network could be relevant for a series of applications in traffic-, transport- and supply chain management.
description: 11 pages, 5 figures
Assessment of Molecular Detection Tests for 'Candidatus Liberibacter' Species in Citrus: Test Performance Study and Proficiency Test Results
Creators: name: Raaymakers, Tom M.
name: Warbroek, Tim
name: van Doorn, Bo J.A.
name: Volkers, Rita J.M.
name: Blom, Nathalie I.
name: Bergsma-Vlami, Maria
Publisher: name: Zenodo
Year: 2023
Subjects: Plant Health
Plant pest diagnostics
Huanglongbing
Citrus greening disease

description: Huanglongbing (HLB), also known as Citrus greening disease, is a lethal disease of Citrus caused by three obligate biotrophic bacteria: 'Candidatus Liberibacter africanus' (CaLaf), 'Candidatus Liberibacter americanus' (CaLam), and 'Candidatus Liberibacter asiaticus' (CaLas). These quarantine pests are considered priority pests by the European Union (EU) due to their potential economic, environmental, and social impact. Several molecular tests have been developed for the detection of HLB-associated bacteria in citrus plants. In 2020, an international test performance study (TPS) conducted by the Netherlands Institute for Vectors, Invasive plants and Plant health (NIVIP) evaluated three promising molecular tests for the detection of 'Candidatus Liberibacter' species. Subsequently, we organized a proficiency test (PT) for the molecular detection of HLB-associated bacteria. This PT was mandatory for the EU national reference laboratories (NRLs). The NRLs made use of one or more of the detection tests assessed in the TPS.
description: {"references": ["Hocquellet et al., (1999). Mol. Cell. Probes 13:373-379.", "Li et al., (2006). J. Microbiol. Methods 66:104-115.", "Quintana-Gonz\u00e1lez de Chaves et al., (2023). Sci. Rep. 13:3338.", "Teixeira et al., (2005). Mol. Cell. Probes 19:173-179.", "PM 7/121 (2) (2021). EPPO Bul. 51:267-282."]}
Stapled Peptides as Novel Chemical Probes for the Treatment of Castration-Resistant Prostate Cancer
Creators: name: Siddiqui, Zamia
Publisher: name: University of Illinois at Chicago
Year: 2023

description: A major unmet medical need in prostate cancer therapy is developing new treatments for castration-resistant prostate cancer (CRPC), an advanced form of prostate cancer associated with poor prognosis and reduced survival. The five-year survival rate for men with distant metastatic prostate cancer is 30%, compared to 100% survival in men with localized prostate cancer. The progression of prostate cancer is driven by the androgen receptor (AR) which consists of three domains [DNA-binding domain (DBD), ligand-binding domain (LBD), transactivation domain (NTD)] and a hinge region. A rapidly emerging mechanism of resistance in CRPC is the development of constitutively active AR splice variants that lack the LBD. This study seeks to diminish AR signaling by targeting the NTD using stapled peptides that inhibit SRC-1, a coactivator of the AR. AR transactivation is controlled mainly by the AF-1 region in the NTD. Solution NMR studies from our collaborators and previously published literature has shown that the Tau1 region in the AR AF-1 interacts with SRC-1. Our hypothesis is that stapled peptides mimicking AR Tau1 will disrupt the interaction between AF-1 and SRC-1. Our research presents the design and synthesis of hydrocarbon stapled peptides and diversity-oriented peptides using solid phase peptide synthesis. We used computational chemistry to improve the design of these peptides by creating a homology model that was used for sequence recovery and alanine scanning experiments. Future studies will characterize the stapled peptides, with the use of our recently developed proteolytic assays, to study their susceptibility to enzymatic degradation, and circular dichroism, to investigate their helicity. Diminished AR signaling through this approach may lead to novel AR-directed therapy for CRPC.
Letter from W.T. Nollaline to William Elliot Griffis, April 11, 1894
Creators: name: Nollaline, W. T.
Publisher: name: No Publisher Supplied
Year: 1894

description: Expresses satisfaction with the growing rate of missions (missionaries). Informs Griffis that the total has risen to 250 (after only 100 in the first 10 years), and expects the number to double this year.
Pre-Service Teachers’ Perceived Value of General Pedagogical Knowledge for Practice: Relations with Epistemic Beliefs and Source Beliefs
Creators: name: Schneider, Jürgen
name: Merk, Samuel
name: Syring, Marcus
name: Rosman, Tom
name: Rueß, Julia
Publisher: name: Open Science Framework
Year: 2022

description: This repository contains the preregistration and the data concerning the manuscript "Pre-Service Teachers’ Perceived Value of General Pedagogical Knowledge for Practice: Relations with Epistemic Beliefs and Source Beliefs"
Extrasolar planets as a probe of modified gravity
Creators: name: Santos, Marcelo Vargas dos
name: Mota, David F.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We propose a new method to test modified gravity theories, taking advantage of the available data on extrasolar planets. We computed the deviations from the Kepler third law and use that to constrain gravity theories beyond General Relativity. We investigate gravity models which incorporate three screening mechanisms: the Chameleon, the Symmetron and the Vainshtein. We find that data from exoplanets orbits are very sensitive to the screening mechanisms putting strong constraints in the parameter space for the Chameleon models and the Symmetron, complementary and competitive to other methods, like interferometers and solar system. With the constraints on Vainshtein we are able to work beyond the hypothesis that the crossover scale is of the same order of magnitude than the Hubble radius $r_c \sim H_0^{-1}$, which makes the screening work automatically, testing how strong this hypothesis is and the viability of other scales.
description: 7 pages, 5 figures, Published in Physics Letters B
A Cultural Probe Kit on Social Cohesion: Activity book and Diary
Creators: name: Pescarin, Sofia
name: Bonanno, Vanessa
Publisher: name: Zenodo
Year: 2022
Subjects: Digital Heritage
Social Cohesion
Multimodal Design
Interactive Media
Cultural Probe Kit

description: This booklet has been used to explore the complexity of Social Cohesion concept, providing it in its paper version to groups of potential users of interactive media applications in the field of Cultural Heritage. It has been also used by designers to explore cultural behaviours and needs of their audience, in the creation of digital applications. It includes an Activity Book (with 8 activities) and a Diary.
On the de Rham homology and cohomology of a complete local ring in equicharacteristic zero
Creators: name: Switala, Nicholas
Publisher: name: arXiv
Year: 2016
Subjects: subject: Commutative Algebra (math.AC)
subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: Primary 13D45, 14F40

description: Let $A$ be a complete local ring with a coefficient field $k$ of characteristic zero, and let $Y$ be its spectrum. The de Rham homology and cohomology of $Y$ have been defined by R. Hartshorne using a choice of surjection $R \rightarrow A$ where $R$ is a complete regular local $k$-algebra: the resulting objects are independent of the chosen surjection. We prove that the Hodge-de Rham spectral sequences abutting to the de Rham homology and cohomology of $Y$, beginning with their $E_2$-terms, are independent of the chosen surjection (up to a degree shift in the homology case) and consist of finite-dimensional $k$-spaces. These $E_2$-terms therefore provide invariants of $A$ analogous to the Lyubeznik numbers. As part of our proofs we develop a theory of Matlis duality in relation to $\mathcal{D}$-modules that is of independent interest. Some of the highlights of this theory are that if $R$ is a complete regular local ring containing $k$ and $\mathcal{D}$ is the ring of $k$-linear differential operators on $R$, then the Matlis dual $D(M)$ of any left $\mathcal{D}$-module $M$ can again be given a structure of left $\mathcal{D}$-module, and if $M$ is a holonomic $\mathcal{D}$-module, then the de Rham cohomology spaces of $D(M)$ are $k$-dual to those of $M$.
description: 62 pages
Stellenwert der Bildfusion von Positronenemissionstomographie und Computertomographie bei onkologischen Erkrankungen des Pankreas
Creators: name: Niehues, Stefan Markus
Publisher: name: Humboldt-Universität zu Berlin, Medizinische Fakultät - Universitätsklinikum Charité
Year: 2002
Subjects: subject: Computertomographie
subject: Bildfusion
subject: Positronenemissionstomographie
subject: Pankreaskarzinom
subject: Image fusion
subject: CT
subject: PET
subject: Pancreatic carcinoma
subject: 610 Medizin
subject: 33 Medizin
subject: XH 7500

description: Die Detektion des Pankreaskarzinoms oder die Unterscheidung zwischen einem Karzinom und einer chronischen Pankreatitis bleibt ein diagnostisches Problem. Jedes bisher eingesetzte bildgebende Verfahren hat seine Vor- und Nachteile. Die Bildfusion macht sich die verschiedenen Stärken und Schwächen der einzelnen Bildgebungen zum Vorteil und kombiniert diese mit dem Ziel, die Stärken zu addieren und die Schwächen zu reduzieren. In dieser Arbeit werden Bilder der CT und der Positronenemissionstomographie miteinander kombiniert, um sowohl eine hohe anatomische Auflösung zu erreichen als auch auf Stoffwechseleigenschaften des Gewebes zurückgreifen zu können. Die Auswertung ergab, dass die Bildfusion hinsichtlich der Karzinomdetektion der CT und der PET überlegen ist. Auch für Umgebungsinfiltration, Lymphknotenbefall und Fernmetastasen ergab die Auswertung bessere Ergebnisse als für die jeweiligen Einzelmodalitäten. Die Bildfusion kann die Akkuratheit der verschiedenen Untersuchungen verbessern und ohne technisch großen Aufwand wie auch ohne weitere Patientenbelastung um wertvolle Information ergänzen. Damit stellt die Bildfusion eine wertvolle Methode zur Erkennung und Visualisierung vor allem kleiner und schwer zu lokalisierender Neoplasien dar. Ebenfalls bietet sie eine genaue Möglichkeit zur Biopsie- und Bestrahlungsplanung.
description: The differentiation between pancreatic carcinoma and inflammatory pancreatic diseases remains a diagnostic problem. Every imaging method available has its own lack of information. Image-fusion uses the strength and the disadvantage of each imaging method. Trough the combination of the images advantages are combined whereas the disadvantages are reduced. In this study images of CT and PET were fused to archive a high anatomic resolution and the information about tissue metabolism. The evaluation showed the superiority of fused images in comparison to the single modalities regarding the detection of lesions, the infiltration of surrounding tissue and lymph nodes as well as detection of distant metastases. Image fusion improves accuracy of CT and PET without huge technical effort or patient-strain while providing useful accessory information. For this reason image-fusion presents a valuable method for detection and visualisation of particularly small lesions in early tumor stage. Furthermore it offers administrable information for biopsy and radiation-planning.
Some geometrical properties of the Oscillator group
Creators: name: Aryanejad, Yadollah
Publisher: name: arXiv
Year: 2016
Subjects: subject: Differential Geometry (math.DG)
subject: FOS: Mathematics

description: We consider the oscillator group equipped with a bi-invariant Lorentzian metric, and then some geometrical properties of this group i.e. homogeneous Ricci solitons and harmonicity properties of invariant vector fields are obtained. We also determine all vector fields which are critical points for the energy functional restricted to vector fields. Vector fields defining harmonic maps are also determined, and the energy of critical points is explicitly calculated.
description: arXiv admin note: substantial text overlap with arXiv:1412.6336, arXiv:1410.7626
Gushel-Mukai varieties: linear spaces and periods
Creators: name: Debarre, Olivier
name: Kuznetsov, Alexander
Publisher: name: arXiv
Year: 2016
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: 14J45, 14J35, 14J40, 14M15

description: Beauville and Donagi proved in 1985 that the primitive middle cohomology of a smooth complex cubic fourfold and the primitive second cohomology of its variety of lines, a smooth hyperkähler fourfold, are isomorphic as polarized integral Hodge structures. We prove analogous statements for smooth complex Gushel-Mukai varieties of dimension 4 (resp. 6), i.e., smooth dimensionally transverse intersections of the cone over the Grassmannian Gr(2,5), a quadric, and two hyperplanes (resp. of the cone over Gr(2,5) and a quadric). The associated hyperkähler fourfold is in both cases a smooth double cover of a hypersurface in ${\bf P}^5$ called an EPW sextic.
description: 44 pages. Lemma 2.1 slightly expanded. Lemma 2.2, Lemma 3.3 (a Lefschetz-type result for cyclic coverings proved by Cornalba), and Lemma 3.7 are new. Other minor corrections
Introduction to the HBM NeuroAI course 2023: artificial neural networks as models of the brain in cognitive neuroscience
Creators: name: Bellec, Pierre
name: Isil Bilgin
Publisher: name: Zenodo
Year: 2023
Subjects: neuroimaging, brain models, AI, brain encoding, brain decoding

description: This is a short introduction to a one-day course on neuroAI models for cognitive neuroscience. A detailed description of the course can be found on the following website: https://neuroai-educational.github.io The topics covered in the course are as follows: Technical construction of the brain models: An introduction of fundamental concepts applicability of AI in the neuroscience research; Brain decoding and encoding: Identifying cognitive states based on brain activity (brain decoding); and predicting brain activity based on the activity of an artificial neural network (brain encoding); Multimodal overview of NeuroAI: Implementation of AI in various sensory modality processing including vision, auditory, language. Ethics and future of NeuroAI: Ethical concerns and potential future directions in the field.
The Triton Charge Radius to Next-to-next-to-leading order in Pionless Effective Field Theory
Creators: name: Vanasse, Jared
Publisher: name: arXiv
Year: 2015
Subjects: subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: The triton point charge radius is calculated to next-to-next-to-leading order (NNLO) in pionless effective field theory ($\mathrm{EFT}(\not{\!π})$), yielding a prediction of $1.14\pm0.19$ fm (leading order), $1.59\pm0.08$ fm (next-to leading order), and $1.62\pm0.03$ fm (NNLO) in agreement with the current experimental extraction of $1.5978\pm0.040$ fm [Angeli and Marinova, At. Data Nucl. Data Tables 99, 69 (2013)]. The error at NNLO is due to cutoff variation ($\sim$ 1%) within a reasonable range of calculated cutoffs and from a $\mathrm{EFT}(\not{\!π})$ error estimate ($\sim$ 1.5%). In addition new techniques are introduced to add perturbative corrections to bound and scattering state calculations for short range effective field theories, but with a focus on their use in $\mathrm{EFT}(\not{\!π})$
description: v1: 41 pages, 21 figures; v2: 47 pages, 19 figures; v3: 51 pages 19 figures
Charge-multiplicity and collision-energy dependence of $p_t$ spectra from $p$-$p$ collisions at the relativistic heavy-ion collider and large hadron collider
Creators: name: Trainor, Thomas A.
Publisher: name: arXiv
Year: 2016
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: A two-component (soft + hard) model (TCM) of hadron production in yields and spectra derived from the charge-multiplicity dependence of 200 GeV p-p collisions at the relativistic heavy ion collider (RHIC) is extended to describe p-p spectrum data from the large hadron collider (LHC) up to 13 TeV. The LHC data include spectrum ratios that provide only partial information on the TCM. The LHC ratio method is applied to well-understood 200 GeV spectrum data to derive an algebraic link between spectrum ratios and the full TCM. Some aspects of the form of the hard component on transverse momentum are found to be $n_{ch}$ dependent. LHC spectrum ratios are then analyzed to obtain $n_{ch}$ and collision-energy (over three orders of magnitude) dependence of isolated soft and hard TCM spectrum components. The energy dependence of the spectrum soft component is a new result suggesting a relation to Gribov diffusion. The spectrum hard component varies simply and smoothly with $n_{ch}$ suggesting bias of the underlying jet spectrum and linearly with QCD parameter $\log(s/s_0)$, its properties consistent with minimum-bias reconstructed-jet spectrum measurements.
description: 24 pages, 22 figures
Holographic entanglement chemistry
Creators: name: Caceres, Elena
name: Nguyen, Phuc H.
name: Pedraza, Juan F.
Publisher: name: arXiv
Year: 2016
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We use the Iyer-Wald formalism to derive an extended first law of entanglement that includes variations in the cosmological constant, Newton's constant and --in the case of higher-derivative theories-- all the additional couplings of the theory. In Einstein gravity, where the number of degrees of freedom $N^2$ of the dual field theory is a function of $Λ$ and $G$, our approach allows us to vary $N$ keeping the field theory scale fixed or to vary the field theory scale keeping $N$ fixed. We also derive an extended first law of entanglement for Gauss-Bonnet and Lovelock gravity and show that in these cases all the extra variations reorganize nicely in terms of the central charges of the theory. Finally, we comment on the implications for renormalization group flows and c-theorems in higher dimensions.
description: 38 pages, typos corrected, version published in Phys. Rev. D
On the Remodeling Conjecture for Toric Calabi-Yau 3-Orbifolds
Creators: name: Fang, Bohan
name: Liu, Chiu-Chu Melissa
name: Zong, Zhengyu
Publisher: name: arXiv
Year: 2016
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: 14N35 (Primary), 14J33 (Secondary)

description: The Remodeling Conjecture proposed by Bouchard-Klemm-Mariño-Pasquetti (BKMP) [arXiv:0709.1453, arXiv:0807.0597] relates the A-model open and closed topological string amplitudes (the all genus open and closed Gromov-Witten invariants) of a semi-projective toric Calabi-Yau 3-manifold/3-orbifold to the Eynard-Orantin invariants of its mirror curve. It is an all genus open-closed mirror symmetry for toric Calabi-Yau 3-manifolds/3-orbifolds. In this paper, we present a proof of the BKMP Remodeling Conjecture for all genus open-closed orbifold Gromov-Witten invariants of an arbitrary semi-projective toric Calabi-Yau 3-orbifold relative to an outer framed Aganagic-Vafa Lagrangian brane. We also prove the conjecture in the closed string sector at all genera.
description: 85 pages, 4 figures; final version
Orbital-selective Mott phases of a one-dimensional three-orbital Hubbard model studied using computational techniques
Creators: name: Liu, Guangkun
name: Kaushal, Nitin
name: Li, Shaozhi
name: Bishop, Christopher B.
name: Wang, Yan
name: Johnston, Steve
name: Alvarez, Gonzalo
name: Moreo, Adriana
name: Dagotto, Elbio
Publisher: name: arXiv
Year: 2016
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: A recently introduced one-dimensional three-orbital Hubbard model displays orbital-selective Mott phases with exotic spin arrangements such as spin block states [J. Rincón {\em et al.}, Phys. Rev. Lett. \textbf{112}, 106405 (2014)]. In this publication we show that the Constrained-Path Quantum Monte Carlo (CPQMC) technique can accurately reproduce the phase diagram of this multiorbital one-dimensional model, paving the way to future CPQMC studies in systems with more challenging geometries, such as ladders and planes. The success of this approach relies on using the Hartree-Fock technique to prepare the trial states needed in CPQMC. We also study a simplified version of the model where the pair-hopping term is neglected and the Hund coupling is restricted to its Ising component. The corresponding phase diagrams are shown to be only mildly affected by the absence of these technically difficult-to-implement terms. This is confirmed by additional Density Matrix Renormalization Group and Determinant Quantum Monte Carlo calculations carried out for the same simplified model, with the latter displaying only mild Fermion sign problems. We conclude that these methods are able to capture quantitatively the rich physics of the several orbital-selective Mott phases (OSMP) displayed by this model, thus enabling computational studies of the OSMP regime in higher dimensions, beyond static or dynamic mean field approximations.
description: 13 pages, 14 figures