cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Dynamics of allosteric regulation of the phospholipase C-γ isozymes upon recruitment to membranes
Creators: name: Siraliev-Perez, Edhriz
name: Hoffmann, Reece M
name: Hajicek, Nicole
name: Sondek, John
name: Stariha, Jordan TB
name: Burke, John E
name: Zhang, Qisheng
name: Temple, Brenda RS
name: Jenkins, Meredith L
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2022

description: Numerous receptor tyrosine kinases and immune receptors activate phospholipase C-γ (PLC-γ) isozymes at membranes to control diverse cellular processes including phagocytosis, migration, proliferation, and differentiation. The molecular details of this process are not well understood. Using hydrogen-deuterium exchange mass spectrometry, we show that PLC-γ1 is relatively inert to lipid vesicles that contain its substrate, phosphatidylinositol 4,5-bisphosphate (PIP2), unless first bound to the kinase domain of the fibroblast growth factor receptor (FGFR1). Exchange occurs throughout PLC-γ1 and is exaggerated in PLC-γ1 containing an oncogenic substitution (D1165H) that allosterically activates the lipase. These data support a model whereby initial complex formation shifts the conformational equilibrium of PLC-γ1 to favor activation. This receptor-induced priming of PLC-γ1 also explains the capacity of a kinase-inactive fragment of FGFR1 to modestly enhance the lipase activity of PLC-γ1 operating on lipid vesicles but not a soluble analog of PIP2 and highlights potential cooperativity between receptor engagement and membrane proximity. Priming is expected to be greatly enhanced for receptors embedded in membranes and nearly universal for the myriad of receptors and co-receptors that bind the PLC-γ isozymes.
Impact Study of Numerical Discretization Accuracy on Parameter Reconstructions and Model Parameter Distributions
Creators: name: Plock, Matthias
name: Hammerschmidt, Martin
name: Burger, Sven
name: Schneider, Philipp-Immanuel
name: Schütte, Christof
Publisher: name: arXiv
Year: 2023
Subjects: subject: Computational Physics (physics.comp-ph)
subject: Optics (physics.optics)
subject: Machine Learning (stat.ML)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: In optical nano metrology numerical models are used widely for parameter reconstructions. Using the Bayesian target vector optimization method we fit a finite element numerical model to a Grazing Incidence X-Ray fluorescence data set in order to obtain the geometrical parameters of a nano structured line grating. Gaussian process, stochastic machine learning surrogate models, were trained during the reconstruction and afterwards sampled with a Markov chain Monte Carlo sampler to determine the distribution of the reconstructed model parameters. The numerical discretization parameters of the used finite element model impact the numerical discretization error of the forward model. We investigated the impact of the polynomial order of the finite element ansatz functions on the reconstructed parameters as well as on the model parameter distributions. We showed that such a convergence study allows to determine numerical parameters which allows for efficient and accurate reconstruction results.
description: Submitted to Metrologia Focus Issue on MATHMET 2023 conference
Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing
Creators: name: Mathews, David H
name: Dey, Abhishek
name: Laederach, Alain
name: Mustoe, Anthony M
name: Lackey, Lela
name: Weeks, Kevin M
name: Kumar, Jayashree
name: Waldern, Justin M
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2022

description: Splicing is highly regulated and is modulated by numerous factors. Quantitative predictions for how a mutation will affect precursor mRNA (pre-mRNA) structure and downstream function are particularly challenging. Here, we use a novel chemical probing strategy to visualize endogenous precursor and mature MAPT mRNA structures in cells. We used these data to estimate Boltzmann suboptimal structural ensembles, which were then analyzed to predict consequences of mutations on pre-mRNA structure. Further analysis of recent cryo-EM structures of the spliceosome at different stages of the splicing cycle revealed that the footprint of the Bact complex with pre-mRNA best predicted alternative splicing outcomes for exon 10 inclusion of the alternatively spliced MAPT gene, achieving 74% accuracy. We further developed a β-regression weighting framework that incorporates splice site strength, RNA structure, and exonic/intronic splicing regulatory elements capable of predicting, with 90% accuracy, the effects of 47 known and 6 newly discovered mutations on inclusion of exon 10 of MAPT. This combined experimental and computational framework represents a path forward for accurate prediction of splicing-related disease-causing variants.
One-dimensional scattering of fermions in double Dirac delta potentials
Creators: name: Santamaría-Sanz, Lucía
Publisher: name: arXiv
Year: 2023
Subjects: subject: Quantum Physics (quant-ph)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: The spectrum of bound and scattering states of the one dimensional Dirac Hamiltonian describing fermions distorted by a static background built from two Dirac delta potentials is studied. A distinction will be made between mass-spike and electrostatic Dirac delta-potentials. The second quantisation is then performed to promote the relativistic quantum mechanical problem to a relativistic quantum field theory and study the quantum vacuum interaction energy for fermions confined between opaque plates. The work presented here is a continuation of [Guilarte et al 2019 Front. Phys.7 109].
description: 30 pages, 29 figures
Additional file 5 of Time course of altered DNA methylation evoked by critical illness and by early administration of parenteral nutrition in the paediatric ICU
Creators: name: Verlinden, Ines
name: Güiza, Fabian
name: Derese, Inge
name: Wouters, Pieter J.
name: Joosten, Koen
name: Verbruggen, Sascha C.
name: Berghe, Greet Van Den
name: Vanhorebeek, Ilse
Publisher: name: figshare
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 60506 Virology

description: Additional file 5. Summary of ANOVA results comparing DNA methylation levels in patients at different time points during PICU stay versus healthy children. DNA methylation levels of the 147 CpG-sites that were not yet differentially methylated in patients upon PICU admission versus healthy children were compared for patients at day 3, day 5 and day 7 in PICU versus healthy children with the use of ANOVA and application of a false discovery rate of 0.05, with reporting of unadjusted p values.
Cluster and virial expansions for the multi-species Tonks gas
Creators: name: Jansen, Sabine
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mathematical Physics (math-ph)
subject: Combinatorics (math.CO)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: We consider a mixture of non-overlapping rods of different lengths $\ell_k$ moving in $\mathbb{R}$ or $\mathbb{Z}$. Our main result are necessary and sufficient convergence criteria for the expansion of the pressure in terms of the activities $z_k$ and the densities $ρ_k$. This provides an explicit example against which to test known cluster expansion criteria, and illustrates that for non-negative interactions, the virial expansion can converge in a domain much larger than the activity expansion. In addition, we give explicit formulas that generalize the well-known relation between non-overlapping rods and labelled rooted trees. We also prove that for certain choices of the activities, the system can undergo a condensation transition akin to that of the zero-range process. The key tool is a fixed point equation for the pressure.
description: 24 pages in J. Stat. Phys. online 2015
Additional file 7 of Time course of altered DNA methylation evoked by critical illness and by early administration of parenteral nutrition in the paediatric ICU
Creators: name: Verlinden, Ines
name: Güiza, Fabian
name: Derese, Inge
name: Wouters, Pieter J.
name: Joosten, Koen
name: Verbruggen, Sascha C.
name: Berghe, Greet Van Den
name: Vanhorebeek, Ilse
Publisher: name: figshare
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 60506 Virology

description: Additional file 7. Heatmaps of changes in methylation status of all studied CpG-sites of patterns 1–4. Heatmaps summarising the changes in methylation status of the CpG-sites classified to pattern 1, pattern 2, pattern 3 and pattern 4.
(501107) Walter Moody
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
On a structure of random open books and closed braids
Creators: name: Ito, Tetsuya
Publisher: name: arXiv
Year: 2015
Subjects: subject: Geometric Topology (math.GT)
subject: FOS: Mathematics
subject: 57M25, 57M27

description: A result of Malyutin shows that a random walk on the mapping class group gives rise to an element whose fractional Dehn twist coefficient is large or small enough. We show that this leads to several properties of random 3-manifolds and links. For example, random closed braids and open books are hyperbolic.
description: 4 pages, no figure. Theorem 5 is added
Arc building through bimodal magmatism: The Tsukuba Igneous Complex, Japan, and its correlations and connections
Creators: name: Wang, Jing-Yi
name: Santosh, M.
name: Tsunogae, Toshiaki
name: Kim, Sung Won
name: Dong, Yun-Peng
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Physiology
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Sociology
subject: FOS: Sociology
subject: Cancer
subject: Inorganic Chemistry
subject: Science Policy

description: Subduction zones are the gateways of large-scale material and energy exchange. The SW Japan region is one of the important regions to understand ongoing convergent margin processes with continuous island arc magmatism. Here we investigate the bimodal magmatic suites from the Tsukuba area in Japan based on petrology, geochemistry and zircon U-Pb-Hf isotopes. Magmatic rocks in the Tsukuba area comprise two compositionally different groups: 1) a mafic group comprising Hbl-gabbros of ~66 Ma and 2) a felsic group represented by two pulses of granitoids at ~66 Ma and ~78 Ma, respectively. All these rocks display calc-alkaline affinity and negative Nb, and Ta anomalies, with a bimodal classification represented by a significant silica gap between the mafic and felsic members. The Hbl-gabbro witnessed plagioclase and amphibole fractionation as evidenced by the humped REE pattern and positive Eu and Sr anomalies. Zircon grains from the Hbl-gabbros show ƐHf (t) values in the range of −7.7 to −4.0 with a peak at −6.4, indicating an enriched mantle source modified by slab-derived fluids. The petrological and geochemical characteristics of Hbl-gabbros are similar to those in the magmatic suite of SW Japan, suggesting that Cretaceous arc magmatism in Tsukuba is an extension of the coeval magmatic belt in SW Japan. Two pulses of granitoids identified in this study are similar in composition and are both classified as I-type granite. The relative uniform high SiO2 (70–75%) and large variation of Hf isotope (−21.0 to −4.0) indicates the granitoids formed by lower crustal melting. The Hf model ages (2479–1392 Ma) of granitoids are significantly older than those of coeval granitoids in SW Japan which show Nd model ages at 1435–748 Ma. This indicates that the arc magmatism in the Tsukuba area involved older lower crust linked to a possible micro-continent derived from the Southern Korean Peninsula.
Non-Linear Interference Challenging Topological Protection of Chiral Edge States
Creators: name: Michen, Benjamin
name: Budich, Jan Carl
Publisher: name: arXiv
Year: 2023
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: Optics (physics.optics)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We report on a non-linear scattering effect that challenges the notion of topological protection for wave packets propagating in chiral edge modes. Specifically, in a Floquet topological system close to resonant driving and with a non-linear potential, we demonstrate how a wave packet propagating in a chiral edge mode may be irreversibly deflected by scattering off a localized wave-packet, or pass the collision region virtually unaffected in an approximately linear fashion. An experimentally accessible knob to tune between those two scenarios is provided by the relative phase between the involved wave-packets. This genuinely non-linear interference phenomenon is in stark contrast to linear scattering off a static impurity, which cannot destroy a topological edge state. Besides corroborating our findings with numerically exact simulations, we propose two physical platforms where our predictions may be verified with state of the art experimental techniques: First, a coupled waveguide setting where non-linearity has been engineered via an intensity-dependent optical index. Second, a Bose-Einstein condensate of cold atoms in an optical Honeycomb lattice governed by a non-linear Gross-Pitaevskii equation that effectively accounts for many-body interactions.
Additional file 6 of Time course of altered DNA methylation evoked by critical illness and by early administration of parenteral nutrition in the paediatric ICU
Creators: name: Verlinden, Ines
name: Güiza, Fabian
name: Derese, Inge
name: Wouters, Pieter J.
name: Joosten, Koen
name: Verbruggen, Sascha C.
name: Berghe, Greet Van Den
name: Vanhorebeek, Ilse
Publisher: name: figshare
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 60506 Virology

description: Additional file 6. Evolution of DNA methylation over time of pattern 1–4 in individual critically ill patients. Detailed time profiles are shown for ten patients of representative CpG-sites classified to pattern 1, pattern 2, pattern 3, and pattern 4.
Hot Ammonia around Young O-type Stars. II. JVLA imaging of highly-excited metastable ammonia masers in W51-North
Creators: name: Goddi, Ciriaco
name: Henkel, Christian
name: Zhang, Qizhou
name: Zapata, Luis
name: Wilson, Thomas L.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We have used the JVLA at the 1 cm band to map five highly-excited metastable inversion transitions of ammonia, (J,K)=(6,6), (7,7), (9,9), (10,10), and (13,13), in W51 IRS2 with ~0.2 angular resolution. We present detections of both thermal (extended) ammonia emission in the five inversion lines, with rotational states ranging in energy from about 400 to 1700 K, and point-like ammonia maser emission in the (6,6), (7,7), and (9,9) lines. The thermal ammonia emits around a velocity of 60 km/s, near the cloud's systemic velocity, is elongated in the east-west direction across 4" and is confined by the HII regions W51d, W51d1, and W51d2. The ammonia masers are observed in the eastern tip of the dense clump traced by thermal ammonia, offset by 0.65" to the East from its emission peak, and have a peak velocity at ~47.5 km/s. No maser components are detected near the systemic velocity. The ammonia masers are separated by 0.65" (3500 AU) from the (rare) vibrationally-excited SiO masers, excited by the deeply-embedded YSO W51-North. This excludes that the two maser species are excited by the same object. Interestingly, the ammonia masers originate at the same sky position as a peak in a submm line of SO2 imaged with the SMA, tracing a face-on circumstellar disk/ring around W51-North. In addition, the thermal emission from the most highly excited ammonia lines, (10,10) and (13,13), shows two main condensations, the dominant one towards W51-North with the SiO/H2O masers, and a weaker peak at the ammonia maser position. We propose a scenario where the ring seen in SO2 emission is a circumbinary disk surrounding (at least) two high-mass YSOs, W51-North (exciting the SiO masers) and a nearby companion (exciting the ammonia masers), separated by 3500 AU. This finding indicates a physical connection (in a binary) between the two rare SiO and ammonia maser species.
description: 11 pages, 7 figures, accepted by Astronomy & Astrophysics
title: Characterization and Pharmacological Modulation of Ion Transport Mechanisms Involved in the Innate Defence of Human Airway Epithelium
Creators: name: Genovese, Michele
Publisher: name: The Open University
Year: 2024

description: The airway epithelium plays a protective role against microbial pathogens delivered by inhaled air. We used cultured bronchial epithelia, differentiated in vitro under air-liquid interface condition, to study the defence mechanisms of the airway epithelium against pathogens, with a particular focus on those regulated by intracellular Ca2+. As a first step, we investigated the response to inflammatory stimuli, in particular IL-4 and IL-17/TNF-α,which both elicited profound changes in transepithelial ion transport mechanisms but with some important differences. IL-4 strongly increased the expression and function of the Ca2+-activated Cl- channel TMEM16A, and decreased the Na+ absorption mediated by ENaC. In contrast, the IL-17/TNF-α treatment had no effect on TMEM16A and markedly increased ENaC function. This condition could promote dehydration of the airway surface, and impairment of mucociliary clearance, particularly in patients affected by cystic fibrosis (CF) which suffer from defective function of CFTR, a second type of Cl- channel.
We thought that potentiators of TMEM16A-mediated Cl- secretion could be useful to improve airway surface hydration and hence mucociliary clearance, in particular under inflammatory conditions associated with IL-17/TNF-α and in CF patients. To find TMEM16A potentiators, we screened a large (11,300 compounds) library with a functional assay. We found three active molecules, ARN7149, ARN4550, and ARN11391. Analysis of mechanism of action of these compounds indicate they act upstream TMEM16A. In particular, ARN7149 is a potentiator of the purinergic P2RY2 receptor, whereas ARN11391 is a potentiator of the inositol triphosphate receptor ITPR1. Interestingly, ARN7149 and ARN4550 also caused inhibition of ENaC, probably by causing breakdown of PIP2, a known regulator of ENaC function. Combined effects on TMEM16A (potentiation) and ENaC (inhibition) could have beneficial effects on mucociliary clearance.We also evaluated the specificity of known pharmacological inhibitors of TMEM16A, in particular niclosamide, which has been used to assign physiological roles to TMEM16A. Surprisingly, most compounds, except Ani9, showed an indirect mechanism of action involving alteration of mechanisms that control intracellular Ca2+ mobilization. Therefore, conclusions based on many TMEM16A inhibitors need to be reconsidered.
Finally, we investigated the role of TRPV4, a Ca2+ channel that acts as a sensor of mechanical and chemical stimuli. It has been shown that TRPV4 activation enhances the beating of cilia in the airway epithelium. We found that TRPV4 has an additional role in innate defence mechanisms. Indeed, stimulation of TRPV4-dependent Ca2+ influx resulted in H2O2 release, a potential bactericidal molecule.
title: Ein stabiles 2-Aza-pentalen
Creators: name: Hafner, Klaus
name: Schmidt, Frank
Publisher: name: Wiley
Year: 2023

description: Nach der Synthese einfacher carbocyclischer Pentalene[¹] sind deren Aza-Analoga von besonderem Interesse, da ihre Eigenschaften in starkem Maße von der Stellung der Stickstoffatome abhängen dürften.
Additional file 8 of Time course of altered DNA methylation evoked by critical illness and by early administration of parenteral nutrition in the paediatric ICU
Creators: name: Verlinden, Ines
name: Güiza, Fabian
name: Derese, Inge
name: Wouters, Pieter J.
name: Joosten, Koen
name: Verbruggen, Sascha C.
name: Berghe, Greet Van Den
name: Vanhorebeek, Ilse
Publisher: name: figshare
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 60506 Virology

description: Additional file 8. Identification of CpG-sites differentially methylated in patients upon PICU admission as compared with healthy children. DNA methylation levels of patients upon PICU admission were compared with those of healthy children with the use of ANOVA and application of a false discovery rate of 0.05. Unadjusted p values for the 12 CpG-sites already differentially methylated in patients upon PICU admission versus healthy controls are shown.
Diffusion of intruders in granular suspensions: Enskog theory and random walk interpretation
Creators: name: González, Rubén Gómez
name: Abad, Enrique
name: Yuste, Santos Bravo
name: Garzó, Vicente
Publisher: name: arXiv
Year: 2023
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: The Enskog kinetic theory is applied to compute the mean square displacement of intruders immersed in a granular gas of smooth inelastic hard spheres (grains). Both species (intruders and grains) are surrounded by an interstitial molecular gas (background) that plays the role of a thermal bath. The influence of the latter on the motion of intruders and grains is modeled via a standard viscous drag force supplemented by a stochastic Langevin-like force proportional to the background temperature. We solve the corresponding Enskog--Lorentz kinetic equation by means of the Chapman--Enskog expansion truncated to first order in the gradient of the intruder number density. The integral equation for the diffusion coefficient is solved by considering the first two Sonine approximations. To test these results, we also compute the diffusion coefficient from the numerical solution of the inelastic Enskog equation by means of the direct simulation Monte Carlo method. We find that the first Sonine approximation generally agrees well with the simulation results, although significant discrepancies arise when the intruders become lighter than the grains. Such discrepancies are largely mitigated by the use of the second-Sonine approximation, in excellent agreement with computer simulations even for moderately strong inelasticities and/or dissimilar mass and diameter ratios. We invoke a random walk picture of the intruders' motion to shed light on the physics underlying the intricate dependence of the diffusion coefficient on the main system parameters. This approach, recently employed to study the case of an intruder immersed in a granular gas, also proves useful in the present case of a granular suspension. Finally, we discuss the applicability of our model to real systems in the self-diffusion case. We conclude that collisional effects may strongly impact the diffusion coefficient of the grains.
description: 24 pages, 16 figures; to be published in Physical Review E
Exploring competing density order in the ionic Hubbard model with ultracold fermions
Creators: name: Messer, Michael
name: Desbuquois, Rémi
name: Uehlinger, Thomas
name: Jotzu, Gregor
name: Huber, Sebastian
name: Greif, Daniel
name: Esslinger, Tilman
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: Materials Science (cond-mat.mtrl-sci)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We realize and study the ionic Hubbard model using an interacting two-component gas of fermionic atoms loaded into an optical lattice. The bipartite lattice has honeycomb geometry with a staggered energy-offset that explicitly breaks the inversion symmetry. Distinct density-ordered phases are identified using noise correlation measurements of the atomic momentum distribution. For weak interactions the geometry induces a charge density wave. For strong repulsive interactions we detect a strong suppression of doubly occupied sites, as expected for a Mott insulating state, and the externally broken inversion symmetry is not visible anymore in the density distribution. The local density distributions in different configurations are characterized by measuring the number of doubly occupied lattice sites as a function of interaction and energy-offset. We further probe the excitations of the system using direction dependent modulation spectroscopy and discover a complex spectrum, which we compare with a theoretical model.
description: 5+3 pages
DMPs as part of local organisation, for FAIRness and policy compliance
Creators: name: Jimena, Linares
name: Tschink, Daniel
Publisher: name: Zenodo
Year: 2023
Subjects: WinterSchool2022
NFDI4Biodiversity
Training&Education

description: The first step in the data life cycle involves planning. A data management plan (DMP) is a document that facilitates this. As formal documents, DMPs favor local organizations and guarantee FAIRness and policy compliance.
(501103) Walter Gower
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Bulk universality of sparse random matrices
Creators: name: Huang, Jiaoyang
name: Landon, Benjamin
name: Yau, Horng-Tzer
Publisher: name: arXiv
Year: 2015
Subjects: subject: Probability (math.PR)
subject: Mathematical Physics (math-ph)
subject: FOS: Mathematics
subject: FOS: Physical sciences

description: We consider the adjacency matrix of the ensemble of Erdős-Rényi random graphs which consists of graphs on $N$ vertices in which each edge occurs independently with probability $p$. We prove that in the regime $pN \gg 1$ these matrices exhibit bulk universality in the sense that both the averaged $n$-point correlation functions and distribution of a single eigenvalue gap coincide with those of the GOE. Our methods extend to a class of random matrices which includes sparse ensembles whose entries have different variances.
description: 20 pages
Aerosol Transport Modeling: The Key Link Between Lung Infections of Individuals and Populations
Creators: name: Jiang, Yi
name: Borojeni, Azadeh A.T.
name: Darquenne, Chantal
name: Colebank, Mitchel J.
name: Madas, Balázs G.
name: Forest, M. Gregory
name: Tawhai, Merryn
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2022

description: The recent COVID-19 pandemic has propelled the field of aerosol science to the forefront, particularly the central role of virus-laden respiratory droplets and aerosols. The pandemic has also highlighted the critical need, and value for, an information bridge between epidemiological models (that inform policymakers to develop public health responses) and within-host models (that inform the public and health care providers how individuals develop respiratory infections). Here, we review existing data and models of generation of respiratory droplets and aerosols, their exhalation and inhalation, and the fate of infectious droplet transport and deposition throughout the respiratory tract. We then articulate how aerosol transport modeling can serve as a bridge between and guide calibration of within-host and epidemiological models, forming a comprehensive tool to formulate and test hypotheses about respiratory tract exposure and infection within and between individuals.
(501104) Merfyn [Harman] Williams
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Appendix 1: Commensurating Abend's incommensurables
Creators: name: Rasmussen, Erik Børve
name: Johannessen, Lars Emil Fagernes
Publisher: name: Zenodo
Year: 2023
Subjects: subject: Sociology
subject: FOS: Sociology
subject: Theory
subject: Theorizing
subject: Gabriel Abend

description: This is the appendix to our article "Theorizing theory: invitation to a broader conversation about ‘theory’ in sociology", to be published in the journal Sociology Compass.
Physiologically Informed Bayesian Analysis of ASL fMRI Data
Creators: name: Frau-Pascual, Aina
name: Vincent, Thomas
name: Sloboda, Jennifer
name: CIUCIU, Philippe
name: Forbes, Florence
Publisher: name: arXiv
Year: 2015
Subjects: subject: Applications (stat.AP)
subject: Neurons and Cognition (q-bio.NC)
subject: FOS: Computer and information sciences
subject: FOS: Biological sciences

description: Arterial Spin Labelling (ASL) functional Magnetic Resonance Imaging (fMRI) data provides a quantitative measure of blood perfusion, that can be correlated to neuronal activation. In contrast to BOLD measure, it is a direct measure of cerebral blood flow. However, ASL data has a lower SNR and resolution so that the recovery of the perfusion response of interest suffers from the contamination by a stronger hemodynamic component in the ASL signal. In this work we consider a model of both hemodynamic and perfusion components within the ASL signal. A physiological link between these two components is analyzed and used for a more accurate estimation of the perfusion response function in particular in the usual ASL low SNR conditions.
(501105) Mary Brown
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Quantum channel decomposition with pre- and post-selection
Creators: name: Nagai, Ryo
name: Kanno, Shu
name: Sato, Yuki
name: Yamamoto, Naoki
Publisher: name: arXiv
Year: 2023
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The quantum channel decomposition techniques, which contain the so-called probabilistic error cancellation and gate/wire cutting, are powerful approach for simulating a hard-to-implement (or an ideal) unitary operation by concurrently executing relatively easy-to-implement (or noisy) quantum channels. However, such virtual simulation necessitates an exponentially large number of decompositions, thereby significantly limiting their practical applicability. This paper proposes a channel decomposition method for target unitaries that have their input and output conditioned on specific quantum states, namely unitaries with pre- and post-selection. Specifically, we explicitly determine the requisite number of decomposing channels, which could be significantly smaller than the selection-free scenario. Furthermore, we elucidate the structure of the resulting decomposed unitary. We demonstrate an application of this approach to the quantum linear solver algorithm, highlighting the efficacy of the proposed method.
description: published version, 11 pages, 5 figures
Rußrindenkrankheit an Ahorn (Cryptostroma corticale); Waldschutzinfo Nr. 10 / 2018
Creators: name: Langer, Gitta Jutta
name: Bußkamp, Johanna
name: Rohde, Martin
Publisher: name: Zenodo
Year: 2018
Subjects: Rußrindenkrankheit; Cryptostroma corticale; sooty bark disease; Acer pseudoplatanus

description: As a result of the dry summer of 2018, there was an increased incidence of sooty bark disease in the member states of the NW-FVA, especially in Hesse and Saxony-Anhalt. The disease is caused by the invasive fungus Cryptostroma corticale, which is native to North America.The fungus is spread by spores (conidia) in the air. In Germany, sooty bark disease occurs mainly on sycamore maple (Acer pseudoplatanus), less frequently on Acer platanoides and Acer campestre. The fungus affects both forest and park trees.
Development of the InTelligence And Machine LEarning (TAME) Toolkit for Introductory Data Science, Chemical-Biological Analyses, Predictive Modeling, and Database Mining for Environmental Health Research
Creators: name: Ring, Caroline
name: Jaspers, Ilona
name: Koval, Lauren E.
name: Rider, Cynthia V.
name: Fry, Rebecca C.
name: Boyles, Rebecca
name: Reif, David M.
name: Rager, Julia E.
name: Patlewicz, Grace
name: Ward-Caviness, Cavin
name: Roell, Kyle
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2022

description: Research in environmental health is becoming increasingly reliant upon data science and computational methods that can more efficiently extract information from complex datasets. Data science and computational methods can be leveraged to better identify relationships between exposures to stressors in the environment and human disease outcomes, representing critical information needed to protect and improve global public health. Still, there remains a critical gap surrounding the training of researchers on these in silico methods. We aimed to address this gap by developing the inTelligence And Machine lEarning (TAME) Toolkit, promoting trainee-driven data generation, management, and analysis methods to “TAME” data in environmental health studies. Training modules were developed to provide applications-driven examples of data organization and analysis methods that can be used to address environmental health questions. Target audiences for these modules include students, post-baccalaureate and post-doctorate trainees, and professionals that are interested in expanding their skillset to include recent advances in data analysis methods relevant to environmental health, toxicology, exposure science, epidemiology, and bioinformatics/cheminformatics. Modules were developed by study coauthors using annotated script and were organized into three chapters within a GitHub Bookdown site. The first chapter of modules focuses on introductory data science, which includes the following topics: setting up R/RStudio and coding in the R environment; data organization basics; finding and visualizing data trends; high-dimensional data visualizations; and Findability, Accessibility, Interoperability, and Reusability (FAIR) data management practices. The second chapter of modules incorporates chemical-biological analyses and predictive modeling, spanning the following methods: dose-response modeling; machine learning and predictive modeling; mixtures analyses; -omics analyses; toxicokinetic modeling; and read-across toxicity predictions. The last chapter of modules was organized to provide examples on environmental health database mining and integration, including chemical exposure, health outcome, and environmental justice indicators. Training modules and associated data are publicly available online (https://uncsrp.github.io/Data-Analysis-Training-Modules/). Together, this resource provides unique opportunities to obtain introductory-level training on current data analysis methods applicable to 21st century science and environmental health.
Editorial: Next Generation User-Adaptive Wearable Robots
Creators: name: Sharma, Nitin
name: Bulea, Thomas C.
name: Su, Hao
name: Sikdar, Siddhartha
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2022

description: Wearable robots, including powered exoskeletons and robotic prostheses, have created new possibilities for mobility augmentation and restoration among individuals with a variety of movement disorders, including spinal cord injury, stroke, amputation, and other neurological conditions (Esquenazi et al., 2017; Rodríguez-Fernández et al., 2021). Exoskeleton technology has progressed to create utility for unimpaired individuals by supporting load carriage, reducing joint loading or improving metabolic efficiency (Sawicki et al., 2020). Despite this progress, exoskeleton deployment in real-world, community environments remains limited. While there are multiple barriers to ubiquitous exoskeleton use, a key lynchpin is development of robust control systems that adapt to user intent, support the variety of mobility tasks that may be encountered, and account for variation in the user’s voluntary effort across such tasks.
Soft-metric based channel decoding for photon counting receivers
Creators: name: Mondin, Marina
name: Daneshgaran, Fred
name: Bari, Inam
name: Delgado, Maria Teresa
name: Olivares, Stefano
name: Paris, Matteo G. A.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We address photon-number-assisted, polarization- based, binary communication systems equipped with photon counting receivers. In these channels information is encoded in the value of polarization phase-shift but the carrier has and additional degree of freedom, i.e. its photon distribution, which may be exploited to implement binary input-multiple output (BIMO) channels also in the presence of a phase-diffusion noise affecting the polarization. Here we analyze the performances of these channels, which approach capacity by means of iteratively decoded error correcting codes. In this paper we use soft-metric- based low density parity check (LDPC) codes for this purpose. In order to take full advantage of all the information available at the output of a photon counting receiver, soft information is generated in the form of log-likelihood ratios, leading to improved frame error rate (FER) and bit error rate (BER) compared to binary symmetric channels (BSC). We evaluate the classical capacity of the considered BIMO channel and show the potential gains that may be provided by photon counting detectors in realistic implementations.
description: 8 pages, 8 figures, to appear on the IEEE Journal of Selected Topics in Quantum Electronics
Supportive Care and Symptom Management for Patients With Immunoglobulin Light Chain (AL) Amyloidosis
Creators: name: Byku, Mirnela
name: Traub, Rebecca E.
name: Tuchman, Sascha A.
name: Hladik, Gerald A.
name: Jensen, Christopher E.
name: Jain, Koyal
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2022

description: Immunoglobulin light chain (AL) amyloidosis is a disorder of clonal plasma cells characterized by deposition of amyloid fibrils in a variety of tissues, leading to end-organ injury. Renal or cardiac involvement is most common, though any organ outside the central nervous system can develop amyloid deposition, and symptomatic presentations may consequently vary. The variability and subtlety of initial clinical presentations may contribute to delayed diagnoses, and organ involvement is often quite advanced and symptomatic by the time a diagnosis is established. Additionally, while organ function can improve with plasma-cell-directed therapy, such improvement lags behind hematologic response. Consequently, highly effective supportive care, including symptom management, is essential to improve quality of life and to maximize both tolerance of therapy and likelihood of survival. Considering the systemic nature of the disease, close collaboration between clinicians is essential for effective management.
Analytic evaluation of non-adiabatic couplings within the complex absorbing potential equation-of-motion coupled-cluster method
Creators: name: Chatterjee, Koushik
name: Koczor-Benda, Zsuzsanna
name: Feng, Xintian
name: Krylov, Anna I.
name: Jagau, Thomas-C.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We present the theory for the evaluation of non-adiabatic couplings (NACs) involving resonance states within the complex absorbing potential equation-of-motion coupled-cluster (CAP-EOM-CC) framework implemented within the singles and doubles approximation. Resonance states are embedded in the continuum and undergo rapid decay through autodetachment. In addition, nuclear motions can facilitate transitions between different resonances and between resonances and bound states. These non-adiabatic transitions affect the chemical fate of resonances and have distinct spectroscopic signatures. The NAC vector is a central quantity needed to model such effects. In the CAP-EOM-CC framework, resonance states are treated on the same footing as bound states. Using the example of fumaronitrile, which supports a bound radical anion and several anionic resonances, we analyze the non-adiabatic coupling between bound states and pseudocontinuum states, between bound states and resonances and between two resonances. We find that the NAC between a bound state and a resonance is nearly independent of the CAP strength and thus straightforward to evaluate whereas the NAC between two resonance states or between a bound state and a pseudocontinuum state is more difficult to evaluate.
MTG8 interacts with LHX6 to specify cortical interneuron subtype identity.
Creators: name: Asgarian, Zeinab
name: Oliveira, Marcio Guiomar
name: Stryjewska, Agata
name: Maragkos, Ioannis
name: Rubin, Anna Noren
name: Magno, Lorenza
name: Pachnis, Vassilis
name: Ghorbani, Mohammadmersad
name: Hiebert, Scott Wayne
name: Denaxa, Myrto
name: Kessaris, Nicoletta
Publisher: name: The Francis Crick Institute
Year: 2022
Subjects: subject: Neurosciences
subject: FOS: Clinical medicine
subject: Model organisms
subject: Genetics & Genomics
subject: Developmental Biology
subject: Stem Cells

description: Cortical interneurons originating in the embryonic medial ganglionic eminence (MGE) diverge into a range of different subtypes found in the adult mouse cerebral cortex. The mechanisms underlying this divergence and the timing when subtype identity is set up remain unclear. We identify the highly conserved transcriptional co-factor MTG8 as being pivotal in the development of a large subset of MGE cortical interneurons that co-expresses Somatostatin (SST) and Neuropeptide Y (NPY). MTG8 interacts with the pan-MGE transcription factor LHX6 and together the two factors are sufficient to promote expression of critical cortical interneuron subtype identity genes. The SST-NPY cortical interneuron fate is initiated early, well before interneurons migrate into the cortex, demonstrating an early onset specification program. Our findings suggest that transcriptional co-factors and modifiers of generic lineage specification programs may hold the key to the emergence of cortical interneuron heterogeneity from the embryonic telencephalic germinal zones.
(501101) William Edward G. Westheuser
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Duality between amplitude and derivative coupled particle detectors in the limit of large energy gaps
Creators: name: Perche, T. Rick
name: Zambianco, Matheus H.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Quantum Physics (quant-ph)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We present a duality between a particle detector model coupled to the amplitude of a scalar field and coupled to the field's derivative in the limit of large energy gaps. We show that the results of the models can be mapped to each other in a one-to-one fashion modulo a rescaling by the detector's gap. Our analysis is valid for arbitrary scalar fields in curved spacetimes, and requires minimal assumptions regarding the detectors. The duality also applies to the case where more than one detector is coupled to the field. This shows that many examples of entanglement harvesting with amplitude coupled UDW detectors give exactly the same result as derivative coupled detectors that interact with the field in the same region of spacetime.
description: 9 pages, 3 figures + appendix