cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Additional file 1 of Caudal DMN neurons innervate the spleen and release CART peptide to regulate neuroimmune function
Creators: name: Kobori, Nobuhide
name: Moore, Anthony N.
name: Redell, John B.
name: Dash, Pramod K.
Publisher: name: figshare
Year: 2023
Subjects: subject: Biochemistry
subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Science Policy
subject: Immunology
subject: FOS: Clinical medicine
classificationCode: 111714
subject: Mental Health

description: Additional file 1: Figure S1. CARTp immunoreactivity does not colocalize with the sympathetic marker tyrosine hydroxylase. As sympathetic input into the spleen originates from the celiac ganglia, we examined if CARTp immunoreactivity is present in the celiac ganglia and could have traveled within splenic nerve fascicles to reach the spleen as has been reported for catecholaminergic fibers. A) Representative confocal images of CARTp immunoreactivity in the celiac ganglia. Although bisbenzamide staining revealed a large number of cells, no CARTp-positive cell bodies were detected. B) Drawing of the splenic artery showing the location of the splenic arterial branches. Splenic nerve fascicles travel within the adventitia of the splenic artery, entering the hilum of the spleen proximal to arterial branches. C) Representative image of tyrosine hydroxylaseimmunopositive nerve fascicles traveling within the adventitia of the splenic artery. D) To examine if these nerve fascicles carry CARTp-positive fibers into the spleen, we performed double-label immunohistochemistry for TH and CARTp. Representative images indicating that the nerve fascicles along the splenic artery are TH positive, but not CARTp immunopositive. No specific CARTp or TH immunoreactivities were observed when the primary antibodies were excluded from the staining procedure. Figure S2. The pAAV-TRE-tdTOMATO-WPRE and pAAV-Syn-tTA viruses do not cross synapses to induce tdTomato expression. A) Images of tdTomato and NeuN double-immunostained sections taken from the parabrachial nucleusand paraventricular nucleus, regions known to have monosynaptic connection to the DMN and NTS. tdTomato signal is seen in fibersbut not in the cell bodies of resident neurons. B) tdTomato immunoreactivitywas not detected in either the dorsal root gangliaor nodose ganglion, areas known to supply spleen innervation.
Experimental evidence for the importance of Hund's exchange interaction for the incoherence of the charge carriers in iron-based superconductors
Creators: name: Fink, J.
name: Rienks, E. D. L.
name: Thirupathaiah, S.
name: Nayak, J.
name: van Roekeghem, A.
name: Biermann, S.
name: Wolf, T.
name: Adelmann, P.
name: Jeevan, H. S.
name: Gegenwart, P.
name: Wurmehl, S.
name: Felser, C.
name: Buechner, B.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: Angle-resolved photoemission spectroscopy (ARPES) is used to study the scattering rates of charge carriers from the hole pockets near Gamma in the iron-based high-Tc hole doped superconductors KxBa1-xFe2As2 x=0.4 and KxEu1-xFe2As2 x=0.55$ and the electron doped compound Ba(Fe1-xCox)2As2 x=0.075. The scattering rate for any given band is found to depend linearly on energy, indicating a non-Fermi liquid regime. The scattering rates in the hole-doped compound are considerably larger than those in the electron-doped compounds. In the hole-doped systems the scattering rate of the charge carriers of the inner hole pocket is about three times bigger than the binding energy indicating that the spectral weight is heavily incoherent. The strength of the scattering rates and the difference between electron and hole doped compounds signals the importance of Hund's exchange coupling for correlation effects in these iron-based high-Tc superconductors. The experimental results are in qualitative agreement with theoretical calculations in the framework of combined density functional dynamical mean-field theory.
description: 5 pages; 3 figures
Seroprevalence of Borrelia burgdorferi sensu lato and Anaplasma phagocytophilum Infections in German Horses
Creators: name: Gehlen, Heidrun
name: Inerle, Katharina
name: Bartel, Alexander
name: Stöckle, Sabita Diana
name: Ulrich, Sebastian
name: Briese, Beatrice
name: Straubinger, Reinhard K.
Publisher: name: Freie Universität Berlin
Year: 2023
Subjects: subject: equine Lyme borreliosis
subject: equine granulocytic anaplasmosis
subject: seroprevalence
subject: co-infection
subject: 600 Technik, Medizin, angewandte Wissenschaften::610 Medizin und Gesundheit::616 Krankheiten

description: There are limited data on Lyme borreliosis (LB), a tick-borne disease caused by the Borrelia burgdorferi sensu lato complex, in horses. Seropositivity is not necessarily associated with clinical disease. Data on seropositivity against Borrelia burgdorferi and Anaplasma phagocytophilum in German horses are sparse. Therefore, serum samples from horses (n = 123) suspected of having Lyme borreliosis and clinically healthy horses (n = 113) from the same stables were tested for specific antibodies against Borrelia burgdorferi sensu lato and Anaplasma phagocytophilum. The samples were screened for antibodies against Borrelia burgdorferi (ELISA and an IgG line immunoblot assay). Furthermore, the samples were examined for antibodies against B. burgdorferi and Anaplasma phagocytophilum with a validated rapid in-house test (SNAP® 4Dx Plus® ELISA). The clinical signs of suspect horses included lameness (n = 36), poor performance (n = 19), and apathy (n = 12). Twenty-three percent (n = 26) of suspect horses and 17% (n = 18) of clinically healthy horses were seropositive for having a Borrelia burgdorferi sensu lato infection (p = 0.371), showing that the detection of specific antibodies against B. burgdorferi alone is not sufficient for a diagnosis of equine LB. Anaplasma phagocytophilum seropositivity and seropositivity against both pathogens was 20%/6% in suspect horses and 16%/2% in the clinically healthy population, showing only minor differences (p = 0.108). Unspecific testing for antibodies against B. burgdorferi without clinical suspicion of Lyme borreliosis is not recommended since the clinical relevance of seropositivity against Borrelia burgdorferi sensu lato remains to be elucidated.
Aggregating quantum repeaters for the quantum internet
Creators: name: Azuma, Koji
name: Kato, Go
Publisher: name: arXiv
Year: 2016
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The quantum internet holds promise for performing quantum communication, such as quantum teleportation and quantum key distribution, freely between any parties all over the globe. For such a quantum internet protocol, a general fundamental upper bound on the performance has been derived [K. Azuma, A. Mizutani, and H.-K. Lo, arXiv:1601.02933]. Here we consider its converse problem. In particular, we present a protocol constructible from any given quantum network, which is based on running quantum repeater schemes in parallel over the network. The performance of this protocol and the upper bound restrict the quantum capacity and the private capacity over the network from both sides. The optimality of the protocol is related to fundamental problems such as additivity questions for quantum channels and questions on the existence of a gap between quantum and private capacities.
description: 5 pages, 2 figures
Challenges in Large Scale Quantum Mechanical Calculations
Creators: name: Ratcliff, Laura E.
name: Mohr, Stephan
name: Huhs, Georg
name: Deutsch, Thierry
name: Masella, Michel
name: Genovese, Luigi
Publisher: name: arXiv
Year: 2016
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: FOS: Physical sciences

description: During the past decades, quantum mechanical methods have undergone an amazing transition from pioneering investigations of experts into a wide range of practical applications, made by a vast community of researchers. First principles calculations of systems containing up to a few hundred atoms have become a standard in many branches of science. The sizes of the systems which can be simulated have increased even further during recent years, and quantum-mechanical calculations of systems up to many thousands of atoms are nowadays possible. This opens up new appealing possibilities, in particular for interdisciplinary work, bridging together communities of different needs and sensibilities. In this review we will present the current status of this topic, and will also give an outlook on the vast multitude of applications, challenges and opportunities stimulated by electronic structure calculations, making this field an important working tool and bringing together researchers of many different domains.
description: accepted for publication by WIREs Computational Molecular Science
Additional file 1 of Vibrio-Sequins - dPCR-traceable DNA standards for quantitative genomics of Vibrio spp
Creators: name: Flütsch, Sabrina
name: Wiestner, Fabian
name: Butticaz, Lisa
name: Moor, Dominik
name: Stölting, Kai N.
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1. Figures S1-S7.
Proceedings Cassting Workshop on Games for the Synthesis of Complex Systems and 3rd International Workshop on Synthesis of Complex Parameters
Creators: name: Brihaye, Thomas
name: Delahaye, Benoît
name: Jezequel, Loïg
name: Markey, Nicolas
name: Srba, Jiří
Publisher: name: arXiv
Year: 2016
Subjects: subject: Software Engineering (cs.SE)
subject: Logic in Computer Science (cs.LO)
subject: FOS: Computer and information sciences

description: This volume contains the joint proceedings of the Workshop on Games for the Synthesis of Complex Systems (CASSTING'16) and of the 3rd International Workshop on Synthesis of Complex Parameters (SynCoP'16). The workshops were held in Eindhoven, The Netherlands, as satellite events of the 19th European Joint Conferences on Theory and Practice of Software (ETAPS'16). Both workshops are closely related in their topics as well as target audience and they shared a joint invited talk given by Giorgio Delzanno.
Additional file 2 of Vibrio-Sequins - dPCR-traceable DNA standards for quantitative genomics of Vibrio spp
Creators: name: Flütsch, Sabrina
name: Wiestner, Fabian
name: Butticaz, Lisa
name: Moor, Dominik
name: Stölting, Kai N.
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2. Table S1. Information on Vibrio-Sequins.
An introduction to the colloidal glass transition
Creators: name: Weeks, Eric R.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: FOS: Physical sciences

description: Colloids are suspensions of small solid particles in a liquid, and exhibit glassy behavior when the particle concentration is high. In these samples, the particles are roughly analogous to individual molecules in a traditional glass. This model system has been used to study the glass transition since the 1980's. In this Viewpoint we summarize some of the intriguing behaviors of the glass transition in colloids, and discuss open questions.
description: Review article which is more concise than Hunter & Weeks, Rep. Prog. Phys. 2012
Recent results for the proton spin decomposition from lattice QCD
Creators: name: Alexandrou, Constantia
name: Constantinou, Martha
name: Hadjiyiannakou, Kyriakos
name: Kallidonis, Christos
name: Koutsou, Giannis
name: Jansen, Karl
name: Panagopoulos, Haralambos
name: Steffens, Fernanda
name: Vaquero, Alejandro
name: Wiese, Christian
Publisher: name: arXiv
Year: 2016
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The exact decomposition of the proton spin has been a much debated topic, on the experimental as well as the theoretical side. In this talk we would like to report on recent non-perturbative results and ongoing efforts to explore the proton spin from lattice QCD. We present results for the relevant generalized form factors from gauge field ensembles that feature a physical value of the pion mass. These generalized form factors can be used to determine the total spin and angular momentum carried by the quarks. In addition we present first results for our ongoing effort to compute the angular momentum of the gluons in the proton.
description: 6 pages, 2 figures, 2 tables, talk given at the XXIV International Workshop on Deep-Inelastic Scattering and Related Subjects, 11-15 April 2016, DESY Hamburg, Germany
Recovering Architectural Variability of a Family of Product Variants
Creators: name: Shatnawi, Anas
name: Seriai, Abdelhak
name: Sahraoui, Houari
Publisher: name: arXiv
Year: 2016
Subjects: subject: Software Engineering (cs.SE)
subject: FOS: Computer and information sciences

description: A Software Product Line (SPL) aims at applying a pre-planned systematic reuse of large-grained software artifacts to increase the software productivity and reduce the development cost. The idea of SPL is to analyze the business domain of a family of products to identify the common and the variable parts between the products. However, it is common for companies to develop, in an ad-hoc manner (e.g. clone and own), a set of products that share common functionalities and differ in terms of others. Thus, many recent research contributions are proposed to re-engineer existing product variants to a SPL. Nevertheless, these contributions are mostly focused on managing the variability at the requirement level. Very few contributions address the variability at the architectural level despite its major importance. Starting from this observation, we propose, in this paper, an approach to reverse engineer the architecture of a set of product variants. Our goal is to identify the variability and dependencies among architectural-element variants at the architectural level. Our work relies on Formal Concept Analysis (FCA) to analyze the variability. To validate the proposed approach, we experimented on two families of open-source product variants; Mobile Media and Health Watcher. The results show that our approach is able to identify the architectural variability and the dependencies.
Gastruloid-derived primordial germ cell-like cells develop dynamically within integrated tissues.
Creators: name: Cooke, Christopher B
name: Barrington, Christopher
name: Baillie-Benson, Peter
name: Nichols, Jennifer
name: Moris, Naomi
Publisher: name: The Francis Crick Institute
Year: 2023
Subjects: classificationCode: Tumour Biology
subject: Tumour Biology
classificationCode: Stem Cells
subject: Stem Cells
classificationCode: Chemical Biology & High Throughput
subject: Chemical Biology & High Throughput
classificationCode: Gene Expression
subject: Gene Expression
classificationCode: Genetics & Genomics
subject: Genetics & Genomics
classificationCode: Developmental Biology
subject: Developmental Biology
classificationCode: Computational & Systems Biology
subject: Computational & Systems Biology
classificationCode: Genome Integrity & Repair
subject: Genome Integrity & Repair
classificationCode: Human Biology & Physiology
subject: Human Biology & Physiology
classificationCode: Synthetic Biology
subject: Synthetic Biology

description: Primordial Germ Cells (PGCs) are the early embryonic precursors of gametes - sperm and egg cells. PGC-like cells (PGCLCs) can currently be derived in vitro from pluripotent cells exposed to signalling cocktails and aggregated into large embryonic bodies, but these do not recapitulate the native embryonic environment during PGC formation. Here we show that mouse gastruloids, a three-dimensional in vitro model of gastrulation, contain a population of Gastruloid-derived PGC-like cells (Gld-PGCLCs) that resemble early PGCs in vivo. Importantly, the conserved organisation of mouse gastruloids leads to coordinated spatial and temporal localisation of Gld-PGCLCs relative to surrounding somatic cells, even in the absence of specific exogenous PGC-specific signalling or extraembryonic tissues. In gastruloids, self-organised interactions between cells and tissues, including the endodermal epithelium, enables the specification and subsequent maturation of a pool of Gld-PGCLCs. As such, mouse gastruloids represent a new source of PGCLCs in vitro and, due to their inherent co-development, serve as a novel model to study the dynamics of PGC development within integrated tissue environments.
Additional file 3 of Vibrio-Sequins - dPCR-traceable DNA standards for quantitative genomics of Vibrio spp
Creators: name: Flütsch, Sabrina
name: Wiestner, Fabian
name: Butticaz, Lisa
name: Moor, Dominik
name: Stölting, Kai N.
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 3. Table S2. Oligonucleotides and probes used in this study.
On the wellposedness of the KdV equation on the space of pseudomeasures
Creators: name: Kappeler, Thomas
name: Molnar, Jan
Publisher: name: arXiv
Year: 2016
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics
subject: 37K10 (primary) 35Q53, 35D05 (secondary)

description: In this paper we prove a wellposedness result of the KdV equation on the space of periodic pseudo-measures, also referred to as the Fourier Lebesgue space $\mathscr{F}\ell^{\infty}(\mathbb{T},\mathbb{R})$, where $\mathscr{F}\ell^{\infty}(\mathbb{T},\mathbb{R})$ is endowed with the weak* topology. Actually, it holds on any weighted Fourier Lebesgue space $\mathscr{F}\ell^{s,\infty}(\mathbb{T},\mathbb{R})$ with $-1/2 < s \le 0$ and improves on a wellposedness result of Bourgain for small Borel measures as initial data. A key ingredient of the proof is a characterization for a distribution $q$ in the Sobolev space $H^{-1}(\mathbb{T},\mathbb{R})$ to be in $\mathscr{F}\ell^{\infty}(\mathbb{T},\mathbb{R})$ in terms of asymptotic behavior of spectral quantities of the Hill operator $-\partial_{x}^{2} + q$. In addition, wellposedness results for the KdV equation on the Wiener algebra are proved.
description: 45 pages. arXiv admin note: text overlap with arXiv:1502.05857
Empirical investigation of global wildfire drivers and development of a new flammability parametrisation for the INFERNO fire model
Creators: name: Kuhn-Regnier, Alexander Horst Ferdinand
Publisher: name: Imperial College London
Year: 2022

description: Wildfires have a significant impact on the Earth’s vegetation, atmospheric composition, and climate. There is also growing evidence that fire behaviour has already been altered in response to climate change. Given the anticipated increase in climate conditions conducive to wildfires in many regions of the world, there is an urgent need to advance our understanding of the drivers of wildfires and improve their representation in global Earth system models. Recognising and predicting such responses to climate change and the associated feedbacks is one of the key challenges of the field, and integrated vegetation–fire models have the potential to accomplish this goal. However, the relationship between wildfire activity and past vegetation productivity is still unclear. It has been hypothesised that this strongly contributes to the poor performance of state-of-the-art fire models in representing observed vegetation–fire relationships. Thus, this thesis examines the role of seasonal and long-term vegetation dynamics (and fuel accumulation dynamics) that are of fundamental importance for global wildfires due to their impact on fuel availability during the fire season. In addition to instantaneous climatic conditions, the seasonality of antecedent vegetation and climate conditions controlling fuel build-up and fuel drying was found to be important for the prediction of burnt area in an empirical analysis of wildfire drivers. These were then used to modify the vegetation parametrisation of the INFERNO fire model. By using sigmoidal relationships to explicitly consider antecedent vegetation and climate conditions, global performance was improved. Finally, the new model was evaluated using sensitivity analyses, demonstrating the overarching importance of dryness and temperature while also disentangling the different impacts model parameters have on the magnitude and phase performance of the new parametrisation.
Real-space post-processing correction of thermal drift and piezoelectric actuator nonlinearities in scanning tunneling microscope images
Creators: name: Yothers, Mitchell P.
name: Browder, Aaron E.
name: Bumm, Lloyd A.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Instrumentation and Detectors (physics.ins-det)
subject: FOS: Physical sciences

description: We have developed a real-space method to correct distortion due to thermal drift and piezoelectric actuator nonlinearities on scanning tunneling microscope images using Matlab. The method uses the known structures typically present in high-resolution atomic and molecularly-resolved images as an internal standard. Each image feature (atom or molecule) is first identified in the image. The locations of each feature's nearest neighbors (NNs) are used to measure the local distortion at that location. The local distortion map across the image is simultaneously fit to our distortion model, which includes thermal drift in addition to piezoelectric actuator hysteresis and creep. The image coordinates of the features and image pixels are corrected using an inverse transform from the distortion model. We call this technique the thermal-drift, hysteresis, and creep transform (DHCT). Performing the correction in real space allows defects, domain boundaries, and step edges to be excluded with a spatial mask. Additional real-space image analyses are now possible with these corrected images. Using graphite(0001) as model system, we show lattice fitting to the corrected image, averaged unit cell images, and symmetry-averaged unit cell images. Statistical analysis of the distribution of the image features around their best-fit lattice sites measures the aggregate noise in the image, which can be expressed as feature confidence ellipsoids.
description: 38 pages, 15 figures
Additional file 4 of Vibrio-Sequins - dPCR-traceable DNA standards for quantitative genomics of Vibrio spp
Creators: name: Flütsch, Sabrina
name: Wiestner, Fabian
name: Butticaz, Lisa
name: Moor, Dominik
name: Stölting, Kai N.
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 4. Table S3. Sample information.
On the Host Galaxy of GRB 150101B and the Associated Active Galactic Nucleus
Creators: name: Xie, Chen
name: Fang, Taotao
name: Wang, Junfeng
name: Liu, Tong
name: Jiang, Xiaochuan
Publisher: name: arXiv
Year: 2016
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We present a multi-wavelength analysis of the host galaxy of short-duration gamma-ray burst (GRB) 150101B. Follow-up optical and X-ray observations suggested that the host galaxy, 2MASX J12320498-1056010, likely harbors a low-luminosity active galactic nuclei (AGN). Our modeling of the spectral energy distribution (SED) has confirmed the nature of the AGN, making it the first reported GRB host that contains an AGN. We have also found the host galaxy is a massive elliptical galaxy with stellar population of $\sim 5.7\ Gyr$, one of the oldest among the short-duration GRB hosts. Our analysis suggests that the host galaxy can be classified as an X-ray bright, optically normal galaxy (XBONG), and the central AGN is likely dominated by a radiatively inefficient accretion flow (RIAF). Our work explores interesting connection that may exist between GRB and AGN activities of the host galaxy, which can help understand the host environment of the GRB events and the roles of AGN feedback.
description: 5 pages, 2 figures, accepted for publication in ApJL
Surface state decoherence in loop quantum gravity, a first toy model
Creators: name: Feller, Alexandre
name: Livine, Etera R.
Publisher: name: arXiv
Year: 2016
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: The quantum-to-classical transition through decoherence is a major facet of the semi-classical analysis of quantum models that are supposed to admit a classical regime, as quantum gravity should be. A particular problem of interest is the decoherence of black hole horizons and holographic screens induced by the bulk-boundary coupling with interior degrees of freedom. Here in this paper we present a first toy-model, in the context of loop quantum gravity, for the dynamics of a surface geometry as an open quantum system at fixed total area. We discuss the resulting decoherence and recoherence and compare the exact density matrix evolution to the commonly used master equation approximation {\it à la} Lindblad underlining its merits and limitations. The prospect of this study is to have a clearer understanding of the boundary decoherence of black hole horizons seen by outside observers.
description: 21 pages
Probing domain walls in cylindrical magnetic nanowires with electron holography
Creators: name: Staňo, Michal
name: Jamet, Ségolène
name: Toussaint, Jean-Christophe
name: Bochmann, Sebastian
name: Bachmann, Julien
name: Masseboeuf, Aurélien
name: Gatel, Christophe
name: Fruchart, Olivier
Publisher: name: arXiv
Year: 2016
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We probe magnetic domain walls in cylindrical soft magnetic nanowires using electron holography. We detail the modelling of expected contrast for both transverse and Bloch point domain walls and provide comparison with experimental observations performed on NiCo nanowires, involving also both magnetic and electrostatic contribution to the electron holography map. This allows the fast determination of the domain wall type without the need for uneasy and time-consuming experimental removal of the electrostatic contribution. Finally, we describe and implement a new efficient algorithm for calculating the magnetic contrast.
description: 3 pages, 2 figures
Additional file 8 of Vibrio-Sequins - dPCR-traceable DNA standards for quantitative genomics of Vibrio spp
Creators: name: Flütsch, Sabrina
name: Wiestner, Fabian
name: Butticaz, Lisa
name: Moor, Dominik
name: Stölting, Kai N.
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 8. Information on amplicon location.
Phases of Attractive Fermi Gases in Synthetic Dimensions
Creators: name: Ghosh, Sudeep Kumar
name: Greschner, Sebastian
name: Yadav, Umesh K.
name: Mishra, Tapan
name: Rizzi, Matteo
name: Shenoy, Vijay B.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: FOS: Physical sciences

description: A novel way to produce quantum Hall ribbons in a cold atomic system is to use M hyperfine states of atoms in a 1D optical lattice to mimic an additional "synthetic dimension". A notable aspect here is that the SU(M) symmetric interaction between atoms manifests as "infinite ranged" along the synthetic dimension. We study the many body physics of fermions with attractive interactions in this system. We use a combination of analytical field theoretic and numerical density matrix renormalization group (DMRG) methods to reveal the rich ground state phase diagram of the system, including novel phases such as squished baryon fluids. Remarkably, changing the parameters entails unusual crossovers and transitions, e. g., we show that increasing the magnetic field (that produces the Hall effect) may convert a "ferrometallic" state at low fields to a "squished baryon superfluid" (with algebraic pairing correlations) at high fields. We also show that this system provides a unique opportunity to study quantum phase separation in a multiflavor ultracold fermionic system.
description: 6 pages, 4 figures and supplementary material (11 pages)
Characterising Mer and Axl receptor tyrosine kinase expression and transcriptomic profiling of myeloid cells in hepatocellular carcinoma
Creators: name: Mukherjee, Sujit
Publisher: name: Imperial College London
Year: 2022

description: Background: TAM receptor tyrosine kinases attenuate pro-inflammatory signalling in myeloid cells and maintain tissue homeostasis through apoptotic cell clearance (efferocytosis). Two members of the TAM-RTK family, MerTK and Axl, are overexpressed in human cancers; MerTK+ macrophages display a regulatory phenotype (M2c) similar to tumour associated macrophages (TAMs). MerTK+ and Axl+ macrophages contribute to immune paresis in liver disease. Little is known about MerTK and Axl expressing myeloid cells in HCC. In this thesis I characterise their expression and phenotype in circulating and tissue-resident myeloid cells, explore drivers for their expansion and function in vitro and utilise transcriptomics to interrogate wider TAM phenotype in human HCC. Methods: Tissue and blood were collected from patients undergoing surgery or awaiting treatment for HCC. TAM-RTK expressing myeloid cells were identified using immunohistochemistry. Flow cytometry of isolated immune cell populations was utilised to understand their abundance and phenotype; in vitro conditioning and co-culture experiments were devised to recapitulate the tumour microenvironment, identify potential drivers for MerTK and Axl expression and assay their function. Serum and tissue homogenates were analysed for levels of TAM-RTK ligands. Transcriptomic analysis of tumour and liver derived myeloid cells was undertaken. Results: MerTK+ macrophages are evident within inflammatory infiltrates in HCC. There is modest expansion of myeloid cells expressing MerTK and Axl in the tumour microenvironment, however gene expression is not upregulated and neither are downstream signalling cascades. In vitro conditioning does stimulate Axl but not MerTK expression and promotes immune-regulatory cytokine production. TAMs exhibit a ‘post-phagocytic’ phenotype with upregulation of C1Q, scavenger receptor Stabilin-1 and APOE. Conclusions: TAM-RTK signalling is not activated within the tumour microenvironment. Transcriptomic analysis has identified an immune regulatory post-phagocytic and efferocytotic phenotype; further work is needed to evaluate the significance of this in the tumour biology of HCC, if it is not mediated through MerTK and Axl signalling.
Combined effects of Sr substitution and pressure on the ground states in CaFe$_2$As$_2$
Creators: name: Knöner, S.
name: Gati, E.
name: Köhler, S.
name: Wolf, B.
name: Tutsch, U.
name: Ran, S.
name: Torikachvili, M. S.
name: Bud'ko, S. L.
name: Canfield, P. C.
name: Lang, M.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: We present a detailed study of the combined effects of Sr substitution and hydrostatic pressure on the ground-state properties of CaFe$_2$As$_2$. Measurements of the electrical resistance and magnetic susceptibility, both at ambient and finite pressure $P$ $\leq$ 2$\,$GPa, were performed on Ca$_{1-x}$Sr$_x$Fe$_2$As$_2$ single crystals grown out of Sn flux. We find that upon Sr substitution the ranges of stability of both the structural-magnetic transition and the transition into the non-magnetic collapsed tetragonal phase are shifted to higher pressure levels with the latter moving at a higher rate. This suggests the possibility of separating the two phase lines, which intersect already at elevated temperatures for $x$ = 0 and low Sr concentration levels. For $x$ = 0.177 we find strong evidence that both phases remain separated down to lowest temperature and that a zero-resistance state emerges in this intermediate pressure window. This observation indicates that Sr-substitution combined with hydrostatic pressure provides another route for stabilizing superconductivity in CaFe$_2$As$_2$. Our results are consistent with the notion that (i) preserving the fluctuations associated with the structural-magnetic transition to low temperatures is vital for superconductivity to form in this material and that (ii) the non-magnetic collapsed tetragonal phase is detrimental for superconductivity.
description: 11 pages, 10 figures
Meiosis in Plasmodium: how does it work?
Creators: name: Guttery, David S
name: Zeeshan, Mohammad
name: Holder, Anthony A
name: Tromer, Eelco C
name: Tewari, Rita
Publisher: name: The Francis Crick Institute
Year: 2023
Subjects: classificationCode: Biochemistry & Proteomics
subject: Biochemistry & Proteomics
classificationCode: Cell Biology
subject: Cell Biology
classificationCode: Model organisms
subject: Model organisms
classificationCode: Infectious Disease
subject: Infectious Disease

description: Meiosis is sexual cell division, a process in eukaryotes whereby haploid gametes are produced. Compared to canonical model eukaryotes, meiosis in apicomplexan parasites appears to diverge from the process with respect to the molecular mechanisms involved; the biology of Plasmodium meiosis, and its regulation by means of post-translational modification, are largely unexplored. Here, we discuss the impact of technological advances in cell biology, evolutionary bioinformatics, and genome-wide functional studies on our understanding of meiosis in the Apicomplexa. These parasites, including Plasmodium falciparum, Toxoplasma gondii, and Eimeria spp., have significant socioeconomic impact on human and animal health. Understanding this key stage during the parasite's life cycle may well reveal attractive targets for therapeutic intervention.
Additional file 1 of Regenerative potential of multinucleated cells: bone marrow adiponectin-positive multinucleated cells take the lead
Creators: name: Moein, Shiva
name: Ahmadbeigi, Naser
name: Adibi, Rezvan
name: Kamali, Sara
name: Moradzadeh, Kobra
name: Nematollahi, Pardis
name: Nardi, Nance Beyer
name: Gheisari, Yousof
Publisher: name: figshare
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Physiology
subject: FOS: Biological sciences
classificationCode: 59999
subject: Environmental Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
classificationCode: 69999
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Hematology
subject: Computational Biology

description: Additional file 1. Table S1: Histopathology scoring of irradiated mice BM sections.
Formation of plasma around a small meteoroid: 2. Implications for radar head echo
Creators: name: Dimant, Y. S.
name: Oppenheim, M. M.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: FOS: Physical sciences

description: This paper calculates the spatial distribution of the plasma responsible for radar head echoes by applying the kinetic theory developed in the companion paper (Dimant and Oppenheim, arXiv:1608.08524). This results in a set of analytic expressions for the plasma density as a function of distance from the meteoroid. It shows that, at distances less than a collisional mean-free-path from the meteoroid surface, the plasma density drops in proportion to $1/R$ where $R$ is the distance from the meteoroid center; and, at distances much longer than the mean-free-path behind the meteoroid, the density diminishes at a rate proportional to $1/R^{2}$. The results of this paper should be used for modeling and analysis of radar head echoes.
description: 18 pages, 4 figures
Determining the vibrations between sensor and sample in SQUID microscopy
Creators: name: Schiessl, Daniel
name: Kirtley, John R.
name: Paulius, Lisa
name: Rosenberg, Aaron J.
name: Palmstrom, Johanna C.
name: Ullah, Rahim R.
name: Holland, Connor M.
name: Jung, Y. -K. -K.
name: Ketchen, Mark B.
name: Gibson,, Gerald W.
name: Moler, Kathryn A.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Vibrations can cause noise in scanning probe microscopies. Relative vibrations between the scanning sensor and the sample are important but can be more difficult to determine than absolute vibrations or vibrations relative to the laboratory. We measure the noise spectral density in a scanning SQUID microscope as a function of position near a localized source of magnetic field, and show that we can determine the spectra of all three components of the relative sensor-sample vibrations. This method is a powerful tool for diagnosing vibrational noise in scanning microscopies.
description: 4 pages, 3 figures
ADVANCED CANINE HEALTH MANAGEMENT: NAVIGATING THE PATH TO RECOVERY IN GENERALIZED DEMODICOSIS TREATMENT FOR GERMAN SHEPHERDS
Creators: name: Aisha, Khan
Publisher: name: CARSON JOURNAL
Year: 2024
Subjects: Canine Demodicosis, red mange, follicular mange, Demodex spp, localized demodicosis

description: Canine Demodicosis, commonly known as red mange or follicular mange, is a challenging ectoparasitic refractory skin disease affecting dogs. It stems from the excessive proliferation of Demodex spp mites within hair follicles and occasionally sebaceous glands, precipitating dermatological disturbances. This review delves into the intricate facets of Canine Demodicosis, exploring its causes, manifestations, and impact on affected canines. The disease manifests when these mites colonize hair follicles and sebaceous glands, leading to a spectrum of presentations from localized to generalized demodicosis. The latter is characterized by pronounced dermatological alterations encompassing erythema, alopecia, follicular hyperkeratosis, pustules, and crusts across the body. The condition is often further complicated by secondary pyoderma, exacerbating its severity [5]. In severe instances, generalized demodicosis poses a potentially life-threatening risk, emphasizing the need for early recognition and intervention. Intriguingly, Demodex mites are not exclusive to afflicted dogs, with a prevalence of 5.4% even among ostensibly healthy canines [2]. This highlights the complex interplay between mite presence and disease development. The canine demodicosis landscape is sculpted by three key Demodex species: Demodex canis, the most prevalent; Demodex injai, characterized by a robust physique; and Demodex cornei, distinguished by a shorter stature, approximately half that of D. canis. All three species engender disease in canines, adding nuance to the disease's etiology. A deeper comprehension of Canine Demodicosis hinges on grasping the life cycle of D. canis, which encompasses four stages: a fusiform egg, a six-legged larva, an eight-legged nymph, and an eight-legged adult. This intricate progression likely unfolds over a span of 20-35 days, significantly influencing disease dynamics. This review synthesizes a comprehensive perspective on Canine Demodicosis, fostering awareness of its multifaceted aspects
Additional file 2 of Regenerative potential of multinucleated cells: bone marrow adiponectin-positive multinucleated cells take the lead
Creators: name: Moein, Shiva
name: Ahmadbeigi, Naser
name: Adibi, Rezvan
name: Kamali, Sara
name: Moradzadeh, Kobra
name: Nematollahi, Pardis
name: Nardi, Nance Beyer
name: Gheisari, Yousof
Publisher: name: figshare
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Physiology
subject: FOS: Biological sciences
classificationCode: 59999
subject: Environmental Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
classificationCode: 69999
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Hematology
subject: Computational Biology

description: Additional file 2. Table S2: List of primers.
Deep learning for accelerated magnetic resonance imaging
Creators: name: Seegoolam, Krishna Gavindrajee
Publisher: name: Imperial College London
Year: 2022

description: Medical imaging has aided the biggest advance in the medical domain in the last century. Whilst X-ray, CT, PET and ultrasound are a form of imaging that can be useful in particular scenarios, they each have disadvantages in cost, image quality, ease-of-use and ionising radiation. MRI is a slow imaging protocol which contributes to its high cost to run. However, MRI is a very versatile imaging protocol allowing images of varying contrast to be easily generated whilst not requiring the use of ionising radiation. If MRI can be made to be more efficient and smart, the effective cost of running MRI may be more affordable and accessible. The focus of this thesis is decreasing the acquisition time involved in MRI whilst maintaining the quality of the generated images and thus diagnosis. In particular, we focus on data-driven deep learning approaches that aid in the image reconstruction process and streamline the diagnostic process. We focus on three particular aspects of MR acquisition. Firstly, we investigate the use of motion estimation in the cine reconstruction process. Motion allows us to combine an abundance of imaging data in a learnt reconstruction model allowing acquisitions to be sped up by up to 50 times in extreme scenarios. Secondly, we investigate the possibility of using under-acquired MR data to generate smart diagnoses in the form of automated text reports. In particular, we investigate the possibility of skipping the imaging reconstruction phase altogether at inference time and instead, directly seek to generate radiological text reports for diffusion-weighted brain images in an effort to streamline the diagnostic process. Finally, we investigate the use of probabilistic modelling for MRI reconstruction without the use of fully-acquired data. In particular, we note that acquiring fully-acquired reference images in MRI can be difficult and nonetheless may still contain undesired artefacts that lead to degradation of the dataset and thus the training process. In this chapter, we investigate the possibility of performing reconstruction without fully-acquired references and furthermore discuss the possibility of generating higher quality outputs than that of the fully-acquired references.
Additional file 3 of Regenerative potential of multinucleated cells: bone marrow adiponectin-positive multinucleated cells take the lead
Creators: name: Moein, Shiva
name: Ahmadbeigi, Naser
name: Adibi, Rezvan
name: Kamali, Sara
name: Moradzadeh, Kobra
name: Nematollahi, Pardis
name: Nardi, Nance Beyer
name: Gheisari, Yousof
Publisher: name: figshare
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Physiology
subject: FOS: Biological sciences
classificationCode: 59999
subject: Environmental Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
classificationCode: 69999
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Hematology
subject: Computational Biology

description: Additional file 3. Fig. S1: The frequency of polyploid cells in normal BM. A. A representative graph for cytofluorometric DNA content analysis of BM. B. The frequency of different BM populations is quantified based on three independent experiments.
Relativistic Energy Analysis Of Five Dimensional q-Deformed Radial Rosen-Morse Potential Combined With q-Deformed Trigonometric Scarf Non-Central Potential Using Asymptotic Iteration Method (AIM)
Creators: name: Pramono, Subur
name: Suparmi, A
name: Cari, Cari
Publisher: name: arXiv
Year: 2016
Subjects: subject: Quantum Physics (quant-ph)
subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences
subject: 83E15

description: In this work, we study the exact solution of Dirac equation in the hyper-spherical coordinate under influence of separable q-Deformed quantum potentials. The q-deformed hyperbolic Rosen-Morse potential is perturbed by q-deformed non-central trigonometric Scarf potentials, where whole of them can be solved by using Asymptotic Iteration Method (AIM). This work is limited to spin symmetry case. The relativistic energy equation and orbital quantum number equation lD-1 have been obtained using Asymptotic Iteration Method. The upper radial wave function equations and angular wave function equations are also obtained by using this method. The relativistic energy levels are numerically calculated using Mat Lab, the increase of radial quantum number n causes the increase of bound state relativistic energy level both in dimension D = 5 and D = 3. The bound state relativistic energy level decreases with increasing of both deformation parameter q and orbital quantum number nl.
description: 11 pages, 1 figure
Episodic Model For Star Formation History and Chemical Abundances in Giant and Dwarf Galaxies
Creators: name: Debsarma, Suma
name: Chattopadhyay, Tanuka
name: Das, Sukanta
name: Pfenniger, Daniel
Publisher: name: arXiv
Year: 2016
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences
subject: 37N

description: In search for a synthetic understanding, a scenario for the evolution of the star formation rate and the chemical abundances in galaxies is proposed, combining gas infall from galactic halos, outflow of gas by supernova explosions, and an oscillatory star formation process. The oscillatory star formation model is a consequence of the modelling of the fractional masses changes of the hot, warm and cold components of the interstellar medium. The observed periods of oscillation vary in the range $(0.1-3.0)\times10^{7}$\,yr depending on various parameters existing from giant to dwarf galaxies. The evolution of metallicity varies in giant and dwarf galaxies and depends on the outflow process. Observed abundances in dwarf galaxies can be reproduced under fast outflow together with slow evaporation of cold gases into hot gas whereas slow outflow and fast evaporation is preferred for giant galaxies. The variation of metallicities in dwarf galaxies supports the fact that low rate of SNII production in dwarf galaxies is responsible for variation in metallicity in dwarf galaxies of similar masses as suggested by various authors.
description: Accepted in MNRAS 2016
Tunable two-dimensional electron gas at the surface of thermoelectric material In$_4$Se$_3$
Creators: name: Fukutani, K.
name: Sato, T.
name: Galiy, P. V.
name: Sugawara, K.
name: Takahashi, T.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Materials Science (cond-mat.mtrl-sci)
subject: Quantum Gases (cond-mat.quant-gas)
subject: FOS: Physical sciences

description: We report the discovery of two-dimensional electron gas (2DEG) at the surface of thermoelectric material In$_4$Se$_3$ by angle-resolved photoemission spectroscopy. The observed 2DEG exhibits a nearly isotropic band dispersion with a considerably small effective mass of m* = 0.16 m_0, and its carrier density shows a significant temperature dependence, leading to unconventional metal-semiconductor transition at the surface. The observed wide-range thermal tunability of 2DEG in In$_4$Se$_3$ gives rise to additional degrees of freedom to better control the surface carriers of semiconductors.