cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
EvalAttAI: A Holistic Approach to Evaluating Attribution Maps in Robust and Non-Robust Models
Creators: name: Nielsen, Ian E.
name: Ramachandran, Ravi P.
name: Bouaynaya, Nidhal
name: Fathallah-Shaykh, Hassan M.
name: Rasool, Ghulam
Publisher: name: arXiv
Year: 2023
Subjects: subject: Machine Learning (cs.LG)
subject: Artificial Intelligence (cs.AI)
subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: The expansion of explainable artificial intelligence as a field of research has generated numerous methods of visualizing and understanding the black box of a machine learning model. Attribution maps are generally used to highlight the parts of the input image that influence the model to make a specific decision. On the other hand, the robustness of machine learning models to natural noise and adversarial attacks is also being actively explored. This paper focuses on evaluating methods of attribution mapping to find whether robust neural networks are more explainable. We explore this problem within the application of classification for medical imaging. Explainability research is at an impasse. There are many methods of attribution mapping, but no current consensus on how to evaluate them and determine the ones that are the best. Our experiments on multiple datasets (natural and medical imaging) and various attribution methods reveal that two popular evaluation metrics, Deletion and Insertion, have inherent limitations and yield contradictory results. We propose a new explainability faithfulness metric (called EvalAttAI) that addresses the limitations of prior metrics. Using our novel evaluation, we found that Bayesian deep neural networks using the Variational Density Propagation technique were consistently more explainable when used with the best performing attribution method, the Vanilla Gradient. However, in general, various types of robust neural networks may not be more explainable, despite these models producing more visually plausible attribution maps.
Maskless Generation of Single Silicon Vacancy Arrays in Silicon Carbide by a Focused He+ Ion Beam
Creators: name: He, Zhen-Xuan
name: Li, Qiang
name: Wen, Xiao-Lei
name: Zhou, Ji-Yang
name: Lin, Wu-Xi
name: Hao, Zhi-He
name: Xu, Jin-Shi
name: Li, Chuan-Feng
name: Guo, Guang-Can
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Precise generation of spin defects in solid-state systems is essential for nanostructure fluorescence enhancement. We investigated a method for creating single silicon vacancy defect arrays in silicon carbide using a helium-ion microscope. Maskless and targeted generation can be realized by precisely controlling the focused He+ ion beam with an implantation uncertainty of 60 nm. The generated silicon vacancies were identified by measuring the optically detected magnetic resonance spectrum and room temperature photoluminescence spectrum. We systematically studied the effects of the implantation ion dose on the generated silicon vacancies. After optimization, a conversion yield of ~ 6.95 % and a generation rate for a single silicon vacancy of ~ 35 % were realized. This work paves the way for the integration and engineering of color centers to photonic structures and the application of quantum sensing based on spin defects in silicon carbide.
The Axial Gravitational Ringing of a Spherically Symmetric Black Hole Surrounded by Dark Matter Spike
Creators: name: Zhao, Yuqian
name: Sun, Bing
name: Lin, Kai
name: Cao, Zhoujian
Publisher: name: arXiv
Year: 2023
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: Supermassive black holes at the center of each galaxy may be surrounded by dark matter. Such dark matter admits a spike structure and vanishes at a certain distance from the black hole. This dark matter will impact the spacetime near the black hole and the related ringing gravitational waves can show distinguished features of the black hole without dark matter. In the present work, we focus on the quasi-normal modes of the axial gravitational perturbation who dominate the ringdown process of the perturbed black holes surrounded by dark matter spikes. The relativistic modification results in less impact on QNMs. And the relative ringing frequency difference between the black holes with and without dark matter can be as large as $10^{-2}$. These features can be used in future gravitational wave detection about extremal mass ratio inspiral systems to probe the existence of dark matter around supermassive black holes.
description: 12 pages, 5 figures, 4 tables
title: Generationsübergreifende Mobilitätsbiografien - Dokumentation der Datengrundlage
title: Eine Befragung unter Studierenden, ihren Eltern und Großeltern
titleType: AlternativeTitle
Creators: name: Scheiner, Joachim
name: Sicks, Kathrin
name: Holz-Rau, Christian
Publisher: name: TU Dortmund
Year: 2014
Subjects: subject: 710

description: In den vergangenen Jahren hat sich in der Verkehrsforschung der mobilitätsbiografische Ansatz etabliert. Dieser untersucht die Stabilität und Veränderung des Verkehrshandelns von Personen im Kontext von deren Lebensläufen und den damit assoziierten Schlüsselereignissen, Lern- und Alterungsprozessen. An der Technischen Universität Dortmund wird seit 2007 in jedem Studierendenjahrgang der Raumplanung eine Befragung durchgeführt. Dabei werden wesentliche Elemente der Mobilitätsbiografie der Studierenden sowie ihrer Eltern und Großeltern erfasst. Die Daten erlauben eine Vielzahl von Analysen, etwa Vergleiche zwischen den drei Generationen (Kohorteneffekte), den Einfluss von Eltern auf ihre Kinder (Sozialisationseffekte) oder den Einfluss von Schlüsselereignissen der Haushalts-, Familien-, Erwerbs- und Wohnbiografie (Lebenslaufeffekte) auf das Verkehrshandeln. Die Analysen erfolgen im Rahmen des DFG-Projekts "Mobility Biographies: A Life-Course Approach to Travel Behaviour and Residential Choice". Das vorliegende Arbeitspapier dokumentiert die Datenerhebung, Dateneingabe und Struktur des Datensatzes.
description: In recent years the mobility biography approach has been established in transport research. This approach studies the stability and variability in travel behaviour in the context of individuals' life courses and the key events, learning and ageing processes associated with the life course. A questionnaire survey is undertaken among students in spatial planning at Dortmund University of Technology in every study term since 2007. Information is recorded on basic elements of the students' as well as their parents' and grandparents' mobility biographies. The data permit a large variety of analyses, including comparisons between the three generations (cohort effects), the impact of parents on their children (socialisation effects), and the impact of key events in the household, family, employment and residential biography (life course effects) on travel behaviour. In-depth data analysis is undertaken in the DFG-funded project "Mobility Biographies: A Life-Course Approach to Travel Behaviour and Residential Choice". The working paper documents the survey, data entry, and the structure of the data.
description: Arbeitspapiere des Fachgebiets Verkehrswesen und Verkehrsplanung;29
Der Papst über die Verantwortung der katholischen Studenten und Universitätslehrer
Creators: name: Pius XII., Papst
Publisher: name: Herder Korrespondenz
Year: 1970

description: Herder Korrespondenz, Bd. 1 Nr. 3 (1946): Herder Korrespondenz, Band 1, Heft 3
Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production
Creators: name: Andrietta, M. G.S.
name: Pereira, G. A.G.
name: Vidal, R. O.
name: Mieczkowski, P. A.
name: Tavares, F. C.A.
name: Dominska, M.
name: Alcarde, A. R.
name: McCusker, J. H.
name: Netto, O. V.C.
name: Andrietta, S. R.
name: Argueso, J. L.
name: Missawa, S. K.
name: Dietrich, F. S.
name: Gomes, L. H.
name: Carazzolle, M. F.
name: Galzerani, F.
name: Costa, G. G.L.
name: Noronha, M. F.
name: Petes, T. D.
name: Duarte, F. M.
name: Cunha, A. F.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Bioethanol is a biofuel produced mainly from the fermentation of carbohydrates derived from agricultural feedstocks by the yeast Saccharomyces cerevisiae. One of the most widely adopted strains is PE-2, a heterothallic diploid naturally adapted to the sugar cane fermentation process used in Brazil. Here we report the molecular genetic analysis of a PE-2 derived diploid (JAY270), and the complete genome sequence of a haploid derivative (JAY291). The JAY270 genome is highly heterozygous (∼2 SNPs/kb) and has several structural polymorphisms between homologous chromosomes. These chromosomal rearrangements are confined to the peripheral regions of the chromosomes, with breakpoints within repetitive DNA sequences. Despite its complex karyotype, this diploid, when sporulated, had a high frequency of viable spores. Hybrid diploids formed by outcrossing with the laboratory strain S288c also displayed good spore viability. Thus, the rearrangements that exist near the ends of chromosomes do not impair meiosis, as they do not span regions that contain essential genes. This observation is consistent with a model in which the peripheral regions of chromosomes represent plastic domains of the genome that are free to recombine ectopically and experiment with alternative structures. We also explored features of the JAY270 and JAY291 genomes that help explain their high adaptation to industrial environments, exhibiting desirable phenotypes such as high ethanol and cell mass production and high temperature and oxidative stress tolerance. The genomic manipulation of such strains could enable the creation of a new generation of industrial organisms, ideally suited for use as delivery vehicles for future bioenergy technologies.
title: AI4SD Conference Report 2022
Creators: name: Warr, Wendy
Publisher: name: University of Southampton
Year: 2022
Subjects: AI4SD, Conference, Material, Chemicals, Drug Discovery, Artificial Intelligence, Machine Learning, Data Science

description: A report by Wendy A. Warr (wendy@warr.com) on a conference organized by the Artificial Intelligence and Augmented Intelligence for Automated Investigations for Scientific Discovery Network (AI4SD) on March 1-3, 2022 at Chilworth Manor Hotel, Southampton, United Kingdom. The agenda, and details of panelists, speakers and abstracts, and sponsors are available online.
Scalar clouds in charged stringy black hole-mirror system
Creators: name: Li, Ran
name: Zhao, Junkun
name: Wu, Xinghua
name: Zhang, Yanming
Publisher: name: arXiv
Year: 2015
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: It is reported that massive scalar fields can form bound states around Kerr black holes [C. Herdeiro, and E. Radu, Phys. Rev. Lett. 112, 221101 (2014)]. These bound states are called scalar clouds, which have a real frequency $ω=mΩ_H$, where $m$ is the azimuthal index and $Ω_H$ is the horizon angular velocity of Kerr black hole. In this paper, we study scalar clouds in a spherically symmetric background, i.e. charged stringy black holes, with the mirror-like boundary condition. These bound states satisfy the superradiant critical frequency condition $ω=qΦ_H$ for the charged scalar field, where $q$ is the charge of scalar field, and $Φ_H$ is the horizon electrostatic potential. We show that, for the specific set of black hole and scalar field parameters, the clouds are only possible for the specific mirror locations $r_m$. It is shown that the analytical results of mirror location $r_m$ for the clouds are perfectly coincide with the numerical results. We also show that the scalar clouds are also possible when the mirror locations are close to the horizon. At last, we provide an analytical calculation of the specific mirror locations $r_m$ for the scalar clouds in the $qQ\gg 1$ regime.
description: 6 pages, 7 figures. Analytical Study of clouds in $qQ\gg 1$ regime is added
Spectral multipliers for the Kohn Laplacian on forms on the sphere in $\mathbb{C}^n$
Creators: name: Casarino, Valentina
name: Cowling, Michael G.
name: Martini, Alessio
name: Sikora, Adam
Publisher: name: arXiv
Year: 2015
Subjects: subject: Analysis of PDEs (math.AP)
subject: Functional Analysis (math.FA)
subject: FOS: Mathematics
subject: 42B15, 43A85 (Primary), 32V20 (Secondary)

description: The unit sphere $\mathbb{S}$ in $\mathbb{C}^n$ is equipped with the tangential Cauchy-Riemann complex and the associated Laplacian $\Box_b$. We prove a Hörmander spectral multiplier theorem for $\Box_b$ with critical index $n-1/2$, that is, half the topological dimension of $\mathbb{S}$. Our proof is mainly based on representation theory and on a detailed analysis of the spaces of differential forms on $\mathbb{S}$.
description: 28 pages
Mouse population-guided resequencing reveals that variants in CD44 contribute to acetaminophen-induced liver injury in humans
Creators: name: Paigen, K.
name: Harris, S. C.
name: Sackler, R. S.
name: Ross, P. K.
name: Tennant, R.
name: Stylianou, I. M.
name: Boorman, G. A.
name: Su, S.
name: Rusyn, I.
name: Harris, C.
name: Threadgill, D. W.
name: Contractor, T.
name: Wiltshire, T.
name: Watkins, P. B.
name: Bogue, M.
name: Smith, P. C.
name: Harbourt, D. E.
name: Russo, M. W.
name: Harrill, A. H.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Interindividual variability in response to chemicals and drugs is a common regulatory concern. It is assumed that xenobiotic-induced adverse reactions have a strong genetic basis, but many mechanism-based investigations have not been successful in identifying susceptible individuals. While recent advances in pharmacogenetics of adverse drug reactions show promise, the small size of the populations susceptible to important adverse events limits the utility of whole-genome association studies conducted entirely in humans. We present a strategy to identify genetic polymorphisms that may underlie susceptibility to adverse drug reactions. First, in a cohort of healthy adults who received the maximum recommended dose of acetaminophen (4 g/d × 7 d), we confirm that about one third of subjects develop elevations in serum alanine aminotransferase, indicative of liver injury. To identify the genetic basis for this susceptibility, a panel of 36 inbred mouse strains was used to model genetic diversity. Mice were treated with 300 mg/kg or a range of additional acetaminophen doses, and the extent of liver injury was quantified. We then employed whole-genome association analysis and targeted sequencing to determine that polymorphisms in Ly86, Cd44, Cd59a, and Capn8 correlate strongly with liver injury and demonstrated that dose-curves vary with background. Finally, we demonstrated that variation in the orthologous human gene, CD44, is associated with susceptibility to acetaminophen in two independent cohorts. Our results indicate a role for CD44 in modulation of susceptibility to acetaminophen hepatotoxicity. These studies demonstrate that a diverse mouse population can be used to understand and predict adverse toxicity in heterogeneous human populations through guided resequencing.
mCPT at SemEval-2023 Task 3: Multilingual Label-Aware Contrastive Pre-Training of Transformers for Few- and Zero-shot Framing Detection
Creators: name: Reiter-Haas, Markus
name: Ertl, Alexander
name: Innerebner, Kevin
name: Lex, Elisabeth
Publisher: name: arXiv
Year: 2023
Subjects: subject: Computation and Language (cs.CL)
subject: Artificial Intelligence (cs.AI)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences
subject: I.2.7; I.7; J.7

description: This paper presents the winning system for the zero-shot Spanish framing detection task, which also achieves competitive places in eight additional languages. The challenge of the framing detection task lies in identifying a set of 14 frames when only a few or zero samples are available, i.e., a multilingual multi-label few- or zero-shot setting. Our developed solution employs a pre-training procedure based on multilingual Transformers using a label-aware contrastive loss function. In addition to describing the system, we perform an embedding space analysis and ablation study to demonstrate how our pre-training procedure supports framing detection to advance computational framing analysis.
description: Presented at SemEval'23
Broad chromosomal domains of histone modification patterns in C. elegans
Creators: name: Takasaki, T.
name: Kimura, H.
name: Liu, X. S.
name: Ercan, S.
name: Kolasinska-Zwierz, P.
name: Ikegami, K.
name: Taing, S.
name: Egelhofer, T. A.
name: Liu, T.
name: Lieb, J. D.
name: Latorre, I.
name: Jensen, M.
name: Vielle, A.
name: Shin, H.
name: Strome, S.
name: Rosenbaum, H.
name: Rechtsteiner, A.
name: Desai, A.
name: Cheung, M.-S.
name: Iniguez, A. L.
name: Dernburg, A. F.
name: Ahringer, J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Chromatin immunoprecipitation identifies specific interactions between genomic DNA and proteins, advancing our understanding of gene-level and chromosome-level regulation. Based on chromatin immunoprecipitation experiments using validated antibodies, we define the genome-wide distributions of 19 histone modifications, one histone variant, and eight chromatin-associated proteins in Caenorhabditis elegans embryos and L3 larvae. Cluster analysis identified five groups of chromatin marks with shared features: Two groups correlate with gene repression, two with gene activation, and one with the X chromosome. The X chromosome displays numerous unique properties, including enrichment of monomethylated H4K20 and H3K27, which correlate with the different repressive mechanisms that operate in somatic tissues and germ cells, respectively. The data also revealed striking differences in chromatin composition between the autosomes and between chromosome arms and centers. Chromosomes I and III are globally enriched for marks of active genes, consistent with containing more highly expressed genes, compared to chromosomes II, IV, and especially V. Consistent with the absence of cytological heterochromatin and the holocentric nature of C. elegans chromosomes, markers of heterochromatin such as H3K9 methylation are not concentrated at a single region on each chromosome. Instead, H3K9 methylation is enriched on chromosome arms, coincident with zones of elevated meiotic recombination. Active genes in chromosome arms and centers have very similar histone mark distributions, suggesting that active domains in the arms are interspersed with heterochromatin-like structure. These data, which confirm and extend previous studies, allow for in-depth analysis of the organization and deployment of the C. elegans genome during development.
MPEC 2023-R12 : 2023 QD8
Creators: name: Minor Planet Center Staff
Publisher: name: The Minor Planet Center
Year: 2023
Subjects: subject: Small Solar System bodies
valueUri: http://astrothesaurus.org/uat/1469
subject: 2023 QD8

description: The Minor Planet Electronic Circulars contain information on unusual minor planets, routine data on comets and natural satellites, and occasional editorial announcements.  They are published on behalf of Division F of the International Astronomical Union by the Minor Planet Center, Smithsonian Astrophysical Observatory, Cambridge, MA 02138, U.S.A.
General algorithm for non-relativistic diffeomorphism invariance
Creators: name: Banerjee, Rabin
name: Mitra, Arpita
name: Mukherjee, Pradip
Publisher: name: arXiv
Year: 2015
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: An algorithmic approach towards the formulation of non-relativistic diffeomorphism invariance has been developed which involves both matter and gauge fields. A step by step procedure has been provided which can accommodate all types of (abelian) gauge interaction. The algorithm is applied to the problem of a two dimensional electron moving under an external field and also under the Chern-Simons dynamics.
description: 30 pages, no figure, Section 4 has been modified, New section 5 has been introduced, to appear in Physical Review D
Thermodynamical versus logical irreversibility: a concrete objection to Landauer's principle
Creators: name: Lairez, D.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Classical Physics (physics.class-ph)
subject: FOS: Physical sciences

description: Landauer's principle states that the logical irreversibility of an operation, such as erasing one bit, whatever its physical implementation, necessarily implies its thermodynamical irreversibility. In this paper, a very simple counterexample of physical implementation (that uses a two-to-one relation between logic and thermodynamic states) is given that allows to erase one bit in a thermodynamical quasistatic manner (i.e. that may tend to be reversible if slowed down enough).
Development and implementation of machine learning models for dynamic risk prediction models in health care applications (2023)
Creators: name: Heidi Søgaard Christensen, Charles Vesteghem
Publisher: name: Zenodo
Year: 2023

description: Traditional risk prediction generates a risk estimate at a defined timepoint in a patient’s disease trajectory,
 for example the risk of death within 30 days following a surgical procedure.
 In contrast, dynamic risk prediction enables prediction of risk at any time point.
 This allows to continuously monitor a patient’s risk profile and forms the basis for intervention if the predicted risk increases.
 In this course, we will explore methodological and technical solutions, as well as corresponding challenges,
 for developing and implementing such solutions in health care. The course includes the following topics: 1) Data management: This part of the course considers the challenges of preparing heterogenous longitudinal health data for prediction.
 We will cover the various steps involved in this process, including data formatting, feature engineering, and splitting strategies for model validation.
 This will include discussion about how to handle irregularly sampled health data, data leakage, class imbalance, temporal robustness, normalization,
 and other potential biases. 2) Modelling: In this part of the course, participants will be led through the process of building such models.
 We will introduce both basic and more advanced dynamic machine learning prediction algorithms, such as gradient tree boosting, random forest,
 and LSTM and discuss issues related to performance metrics and hyperparameter optimization, for example Bayesian optimization. 3) Implementation: In the last part of the course, we will consider the challenges associated with the implementation of predictive tools in the clinic.
 This includes technical aspects about hosting, user interface, and access to live data, including an introduction to the FHIR standard.
 Regulatory and organizational issues will also be discussed.
 During the project the participants will get hands on experience covering realistic scenarios related to the subjects discussed.
 This will include data management of representative data sets, training models and hands on introduction to the FHIR set-up.
Transkripte von Gruppendiskussionen im Rahmen der Evaluation von Path2Integrity
Creators: name: Niesel, Dennis
name: Wilder, Nicolaus
Publisher: name: Zenodo
Year: 2023
Subjects: Path2Integrity, Group Discussions, Transcripts

description: The transcripts compiled in this document were produced as part of the evaluation of the EU Horizon2020 project Path2Integrity (https://www.path2integrity.eu). They are part of a larger mixed methods evaluation whose quantitative data have also been published on Zenodo (https://zenodo.org/communities/path2integrity). For the qualitative part of the study, group discussions were conducted, transcribed and then analysed using the documentary method.
description: {"references": ["Przyborski, A. & Wohlrab-Sahr, M. (2014): Qualitative Sozialforschung. Ein Arbeitsbuch. M\u00fcnchen: Oldenbourg Wissenschaftsverlag GmbH."]}
Metals Production Requirements for Rapid Photovoltaics Deployment
Creators: name: Kavlak, Goksin
name: McNerney, James
name: Jaffe, Robert L.
name: Trancik, Jessika E.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Physics and Society (physics.soc-ph)
subject: FOS: Physical sciences

description: If global photovoltaics (PV) deployment grows rapidly, the required input materials need to be supplied at an increasing rate. In this paper, we quantify the effect of PV deployment levels on the scale of metals production. For example, we find that if cadmium telluride {copper indium gallium diselenide} PV accounts for more than 3% {10%} of electricity generation by 2030, the required growth rates for the production of indium and tellurium would exceed historically-observed production growth rates for a large set of metals. In contrast, even if crystalline silicon PV supplies all electricity in 2030, the required silicon production growth rate would fall within the historical range. More generally, this paper highlights possible constraints to the rate of scaling up metals production for some PV technologies, and outlines an approach to assessing projected metals growth requirements against an ensemble of past growth rates from across the metals production sector. The framework developed in this paper may be useful for evaluating the scalability of a wide range of materials and devices, to inform technology development in the laboratory, as well as public and private research investment.
Der Papst über die Grundlagen eines wahren Friedens (Auszüge aus den Weihnachtsbotschaften 1941 und 1942)
Creators: name: Pius XII., Papst
Publisher: name: Herder Korrespondenz
Year: 1970

description: Herder Korrespondenz, Bd. 1 Nr. 3 (1946): Herder Korrespondenz, Band 1, Heft 3
Collaborative Cross mice and their power to map host susceptibility to Aspergillus fumigatus infection
Creators: name: Tayem, Hanna
name: Pardo-Manuel de Villena, Fernando
name: Goodstadt, Leo
name: Mott, Richard
name: Yalcin, Binnaz
name: Cleak, James
name: Durrant, Caroline
name: Iraqi, Fuad A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: The Collaborative Cross (CC) is a genetic reference panel of recombinant inbred lines of mice, designed for the dissection of complex traits and gene networks. Each line is independently descended from eight genetically diverse founder strains such that the genomes of the CC lines, once fully inbred, are fine-grained homozygous mosaics of the founder haplotypes. We present an analysis of 120 CC lines, from a cohort of the CC bred at Tel Aviv University in collaboration with the University of Oxford, which at the time of this study were between the sixth and 12th generations of inbreeding and substantially homozygous at 170,000 SNPs. We show how CC genomes decompose into mosaics, and we identify loci that carry a deficiency or excess of a founder, many being deficient for the wild-derived strains WSB/EiJ and PWK/PhJ. We phenotyped 371 mice from 66 CC lines for a susceptibility to Aspergillus fumigatus infection. The survival time after infection varied significantly between CC lines. Quantitative trait locus (QTL) mapping identified genome-wide significant QTLs on chromosomes 2, 3, 8, 10 (two QTLs), 15, and 18. Simulations show that QTL mapping resolution (the median distance between the QTL peak and true location) varied between 0.47 and 1.18 Mb. Most of the QTLs involved contrasts between wild-derived founder strains and therefore would not segregate between classical inbred strains. Use of variation data from the genomes of the CC founder strains refined these QTLs further and suggested several candidate genes. These results support the use of the CC for dissecting complex traits.
Absence of topological protection of the interface states in $\mathbb{Z}_2$ photonic crystals
Creators: name: Xu, Shupeng
name: Wang, Yuhui
name: Agarwal, Ritesh
Publisher: name: arXiv
Year: 2023
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: Inspired from electronic systems, topological photonics aims to engineer new optical devices with robust properties. In many cases, the ideas from topological phases protected by internal symmetries in fermionic systems are extended to those protected by crystalline symmetries. One such popular photonic crystal model was proposed by Wu and Hu in 2015 for realizing a bosonic $\mathbb{Z}_2$ topological crystalline insulator with robust topological edge states, which led to intense theoretical and experimental studies. However, rigorous relationship between the bulk topology and edge properties for this model, which is central to evaluating its advantage over traditional photonic designs, has never been established. In this work we revisit the expanded and shrunken honeycomb lattice structures proposed by Wu and Hu by using topological quantum chemistry tools and show that they are topologically trivial in the sense that symmetric, localized Wannier functions can be constructed. We show that the $\mathbb{Z}$ and $\mathbb{Z}_2$ type classification of the Wu-Hu model are equivalent to the $C_2T$ protected Euler class and the second Stiefel-Whitney class respectively, with the latter characterizing the full valence bands of Wu-Hu model indicating only a higher order topological insulator (HOTI) phase. We show that the Wu-Hu interface states can be gapped by a uniform topology preserving $C_6$ and $T$ symmetric perturbation, which demonstrates the trivial nature of the interface. Our results reveals that topology is not a necessary condition for the reported helical edge states in many photonics systems and opens new possibilities for interface engineering that may not be constrained to require topological designs.
Efficient photocatalytic nitrogen fixation from air under sunlight via iron-doped WO$_3$
Creators: name: Shen, Yuanfang
name: Shou, Jingxuan
name: Chen, Liangchen
name: Han, Weihang
name: Zhang, Luping
name: Chen, Yutong
name: Tu, Xuewei
name: Zhang, Shangfu
name: Sun, Qiang
name: Chang, Yurong
name: Zheng, Hui
Publisher: name: arXiv
Year: 2022
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Soft Condensed Matter (cond-mat.soft)
subject: Chemical Physics (physics.chem-ph)
subject: FOS: Physical sciences

description: Photocatalytic nitrogen fixation from air directly under sunlight can contribute significantly to carbon neutralization. It is an ideal pathway to replace the industrial Haber Bosch process in future. A Fe-doped layered WO$_3$ photocatalyst containing oxygen vacancies was developed which can fix nitrogen from air directly under sunlight at atmospheric pressure. The iron doping enhances the transport efficiency of photogenerated electrons. The photocatalytic efficiency is around 4 times higher than that of pure WO$_3$. The optimum nitrogen fixation conditions were examined by orthogonal experiments and its nitrogen fixation performance could reach up to 477 $μ\text{g} \cdot \text{g}_{\text{cat}}^{-1} \cdot \text{h}^{-1}$ under sunlight. In addition, the process of nitrogen fixation was detected by situ infrared, which confirmed the reliability of nitrogen fixation. Also, modelling on the interactions between light and the photocatalyst was carried out to study the distribution of surface charge and validate the light absorption of the photocatalyst. This work provides a simple and cheap strategy for photocatalytic nitrogen fixation from air under mild conditions.
Conductance asymmetry in proximitized magnetic topological insulator junctions with Majorana modes
Creators: name: Di Miceli, Daniele
name: Zsurka, Eduárd
name: Legendre, Julian
name: Moors, Kristof
name: Schmidt, Thomas
name: Serra, Llorenç
Publisher: name: arXiv
Year: 2023
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We theoretically discuss electronic transport via Majorana states in magnetic topological insulator-superconductor junctions with an asymmetric split of the applied bias voltage. We study normal-superconductor-normal (NSN) junctions made of narrow (wire-like) or wide (film-like) magnetic topological insulator slabs with a central proximitized superconducting sector. The occurrence of charge non-conserving Andreev processes entails a nonzero conductance related to an electric current flowing to ground from the proximitized sector of the NSN junction. We show that topologically-protected Majorana modes require an antisymmetry of this conductance with respect to the point of equally split bias voltage across the junction.
Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration
Creators: name: Blobel, G. A.
name: Chiaromonte, F.
name: Morrissey, C.
name: Drautz, D.
name: Song, L.
name: Ernst, J.
name: Furey, T. S.
name: Cheng, Y.
name: Dorman, C. M.
name: Keller, C. A.
name: Chen, K.-B.
name: Miller, W.
name: Kellis, M.
name: Zhang, Y.
name: Schuster, S. C.
name: Shibata, Y.
name: Kumar, S. A.
name: Mishra, T.
name: Giardine, B.
name: Weiss, M. J.
name: Crawford, G. E.
name: Hardison, R. C.
name: Pimkin, M.
name: Taylor, J.
name: Wu, W.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Interplays among lineage-specific nuclear proteins, chromatin modifying enzymes, and the basal transcription machinery govern cellular differentiation, but their dynamics of action and coordination with transcriptional control are not fully understood. Alterations in chromatin structure appear to establish a permissive state for gene activation at some loci, but they play an integral role in activation at other loci. To determine the predominant roles of chromatin states and factor occupancy in directing gene regulation during differentiation, we mapped chromatin accessibility, histone modifications, and nuclear factor occupancy genome-wide during mouse erythroid differentiation dependent on the master regulatory transcription factor GATA1. Notably, despite extensive changes in gene expression, the chromatin state profiles (proportions of a gene in a chromatin state dominated by activating or repressive histone modifications) and accessibility remain largely unchanged during GATA1-induced erythroid differentiation. In contrast, gene induction and repression are strongly associated with changes in patterns of transcription factor occupancy. Our results indicate that during erythroid differentiation, the broad features of chromatin states are established at the stage of lineage commitment, largely independently of GATA1. These determine permissiveness for expression, with subsequent induction or repression mediated by distinctive combinations of transcription factors.
Local Invariants Vanishing on Stationary Horizons: A Diagnostic for Locating Black Holes
Creators: name: Page, Don N.
name: Shoom, Andrey A.
Publisher: name: arXiv
Year: 2015
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: Inspired by the example of Abdelqader and Lake for the Kerr metric, we construct local scalar polynomial curvature invariants that vanish on the horizon of any stationary black hole: the squared norms of the wedge products of n linearly independent gradients of scalar polynomial curvature invariants, where n is the local cohomogeneity of the spacetime.
description: 5 pages, LaTeX, additional material added, retitled at the suggestion of the Physical Review Letters editor when accepting the paper
Nitrification inhibitors reduce N2O emissions induced by application of biogas digestate to oilseed rape
Creators: name: Kesenheimer, Katharina
name: Augustin, Jürgen
name: Hegewald, Hannes
name: Köbke, Sarah
name: Dittert, Klaus
name: Räbiger, Thomas
name: Quiñones, Teresa Suárez
name: Prochnow, Annette
name: Hartung, Jens
name: Fuß, Roland
name: Stichnothe, Heinz
name: Flessa, Heinz
name: Ruser, Reiner
Publisher: name: Humboldt-Universität zu Berlin
Year: 2021
Subjects: subject: GHG reduction
subject: N-fertilization
subject: Winter oilseed rape
subject: Nitrification inhibition
subject: Yield-related emission
subject: Biodiesel
subject: 550 Geowissenschaften
subject: 620 Ingenieurwissenschaften und zugeordnete Tätigkeiten

description: Winter oilseed rape (WOSR) is the major oil crop cultivated in Europe and the most important feedstock for biodiesel. Up to 90% of the greenhouse gas (GHG) emissions from biodiesel production can occur during oilseed rape cultivation. Therefore, mitigation strategies are required and need to focus on direct nitrous oxide (N2O) emission as one of the largest GHG contributors in biodiesel production. Earlier studies show that nitrification inhibitors (NIs) can reduce N2O emissions derived from N-fertilization. Since information on the effect of biogas digestates with or without NIs on N2O emissions from WOSR fields is scarce, the aim of this study was to evaluate their effects on N2O emissions, mineral N dynamics, and oil yield in WOSR production fertilized with digestate. The study was conducted at five sites across Germany over three years resulting in 15 full site-years data sets. Across all sites and years, N2O emission from WOSR fertilized with biogas digestate (180 kg NH4+-N ha−1yr−1) ranged between 0.2 and 3.5 kg N2O–N ha−1 yr−1. Due to the reduction of the nitrate concentrations following digestate application, application of NI significantly reduced annual N2O emission by 36%. Our results demonstrate that NI can be an effective measure for reducing N2O emissions from digestate application, but its effectiveness depends on soil and weather conditions, and ultimately on the site-specific potential for N2O production and release. There was no effect of NI application on grain and oil yield.
Searching for dark matter subhalos in the Fermi-LAT catalog with Bayesian neural networks
Creators: name: Butter, Anja
name: Krämer, Michael
name: Manconi, Silvia
name: Nippel, Kathrin
Publisher: name: arXiv
Year: 2023
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: About a third of the $γ$-ray sources detected by the Fermi Large Area Telescope (Fermi-LAT) remain unidentified, and some of these could be exotic objects such as dark matter subhalos. We present a search for these sources using Bayesian neural network classification methods applied to the latest 4FGL-DR3 Fermi-LAT catalog. We first simulate the $γ$-ray properties of dark matter subhalos using models from N-body simulations and semi-analytical approaches to the subhalo distribution. We then assess the detectability of this sample in the 4FGL-DR3 catalog using the Fermi-LAT analysis tools. We train our Bayesian neural network to identify candidate dark matter subhalos among the unidentified sources in the 4FGL-DR3 catalog. Our results allow us to derive conservative bounds on the dark matter annihilation cross section by excluding unidentified sources classified as astrophysical-like by our networks. We estimate the number of candidate dark matter subhalos for different dark matter masses and provide a publicly available list for further investigation. Our bounds on the dark matter annihilation cross section are comparable to previous results and become particularly competitive at high dark matter masses.
description: 32 pages, 14 figures, Few comments and references added; typo corrected in figure caption
Ethical and practical challenges of sharing data from genome-wide association studies: The eMERGE Consortium experience
Creators: name: Li, R.
name: Fullerton, S. M.
name: Waudby, C.
name: Smith, M. E.
name: Wolf, W. A.
name: McCarty, C. A.
name: Clayton, E. W.
name: McGuire, A. L.
name: Ramos, E.
name: Koenig, B. A.
name: Dressler, L. G.
name: Basford, M.
name: Somkin, C. P.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: In 2007, the National Human Genome Research Institute (NHGRI) established the Electronic MEdical Records and GEnomics (eMERGE) Consortium (www.gwas.net) to develop, disseminate, and apply approaches to research that combine DNA biorepositories with electronic medical record (EMR) systems for large-scale, high-throughput genetic research. One of the major ethical and administrative challenges for the eMERGE Consortium has been complying with existing data-sharing policies. This paper discusses the challenges of sharing genomic data linked to health information in the electronic medical record (EMR) and explores the issues as they relate to sharing both within a large consortium and in compliance with the National Institutes of Health (NIH) data-sharing policy. We use the eMERGE Consortium experience to explore data-sharing challenges from the perspective of multiple stakeholders (i.e., research participants, investigators, and research institutions), provide recommendations for researchers and institutions, and call for clearer guidance from the NIH regarding ethical implementation of its data-sharing policy.
Medicinal plants with anti-SARS-CoV activity repurposing for treatment of COVID-19 infection : a systematic review and meta-analysis.
Creators: name: Ebenezer, Oluwakemi
name: Bodede, Olusola
name: Awolade, Paul
name: Jordaan, Maryam A.
name: Ogunsakin, Ropo E.
name: Shapi, Michael
Publisher: name: Mangosuthu University of Technology (MUT)
Year: 2023
Subjects: Medicinal and biomolecular chemistry not elsewhere classified

description: The novel SARS-CoV-2 (severe acute respiratory syndrome coronavirus) has emerged as a significant threat to public health with startling drawbacks in all sectors globally. This study investigates the practicality of some medicinal plants for SARS-CoV-2 therapy using a systematic review and meta-analysis of their reported SARS-CoV-1 inhibitory potencies. Relevant data were systematically gathered from three databases, viz., Web of Science, PubMed and Scopus. The information obtained included botanical information, extraction method and extracts concentrations, as well as the proposed mechanisms. Fourteen articles describing 30 different plants met our eligibility criteria. Random effects model and subgroup analysis were applied to investigate heterogeneity. According to subgroup analysis, the sub?stantial heterogeneity of the estimated mean based on the IC50 values reporting the most potent anti-SARS-CoV 3C- -like protease (3CLpro) inhibitors (10.07 %, p < 0.0001), was significantly higher compared to the most active anti?SARS-CoV papain-like protease (PLpro) inhibitors (6.12 %, p < 0.0001). More importantly, the literature analysis revealed that fruit extracts of Rheum palmatum L. and the compound cryptotanshinone isolated from the root of Salvia miltiorrhiza (IC50 = 0.8 ± 0.2 mmol L–1) were excellent candidates for anti- -SARS-CoV targeting PLpro. Meanwhile, iguesterin (IC50 = 2.6 ± 0.6 mmol L–1) isolated from the bark of Tripterygium regelii emerged as the most excellent candidate for anti-SARS- -CoV targeting 3CLpro. The present systematic review and meta-analysis provide valuable and comprehensive infor?mation about potential medicinal plants for SARS-CoV-2 inhibition. The chemotypes identified herein can be adopted as a starting point for developing new drugs to contain the novel virus.
A Short Introduction to Reionization Physics
Creators: name: Choudhury, Tirthankar Roy
Publisher: name: arXiv
Year: 2022
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: The epoch of reionization probes the state of our universe when the very first stars formed and ionized the hydrogen atoms in the surrounding medium. Since the epoch has not yet been probed observationally, it is often called the "final frontier" of observational cosmology. This final frontier is attracting a lot of attention because of the availability of a large number of telescopes in a wide variety of wavebands. This review article summarizes some of the concepts required to understand the interesting physics of reionization and how to analyze the high-redshift universe using related observations.
description: Review article published in a special issue of General Relativity and Gravitation in memory of Professor T. Padmanabhan
Kac-Moody symmetries in one-dimensional bosonic systems
Creators: name: Tang, Wei
name: Haegeman, Jutho
Publisher: name: arXiv
Year: 2023
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: High Energy Physics - Theory (hep-th)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: In conformal field theories, when the conformal symmetry is enhanced by a global Lie group symmetry, the original Virasoro algebra can be extended to Kac-Moody algebra. In this paper, we extend the lattice construction of the Kac-Moody generators introduced in Wang et al., [Phys. Rev. B. 106, 115111 (2022)] to continuous systems and apply it to one-dimensional continuous boson systems. We justify this microscopic construction of Kac-Moody generators in two ways. First, through phenomenological bosonization, we express the microscopic construction in terms of the boson operators in the bosonization context, which can be related to the Kac-Moody generators in conformal field theories. Second, we study the behavior of the Kac-Moody generators in the integrable Lieb-Liniger model, and reveal its underlying particle-hole excitation picture through Bethe ansatz solutions. Finally, we test the computation of the Kac-Moody generator in the continuous matrix product state simulations, paving the way for more challenging non-integrable systems.
description: 15 pages, 7 figures; published version
The Cosmic Battery in Astrophysical Accretion Disks
Creators: name: Contopoulos, Ioannis
name: Nathanail, Antonios
name: Katsanikas, Matthaios
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: The aberrated radiation pressure at the inner edge of the accretion disk around an astrophysical black hole imparts a relative azimuthal velocity on the electrons with respect to the ions which gives rise to a ring electric current that generates large scale poloidal magnetic field loops. This is the Cosmic Battery established by Contopoulos and Kazanas in 1998. In the present work we perform realistic numerical simulations of this important astrophysical mechanism in advection-dominated accretion flows-ADAF. We confirm the original prediction that the inner parts of the loops are continuously advected toward the central black hole and contribute to the growth of the large scale magnetic field, whereas the outer parts of the loops are continuously diffusing outward through the turbulent accretion flow. This process of inward advection of the axial field and outward diffusion of the return field proceeds all the way to equipartition, thus generating astrophysically significant magnetic fields on astrophysically relevant timescales. We confirm that there exists a critical value of the magnetic Prandtl number between unity and 10 in the outer disk above which the Cosmic Battery mechanism is suppressed.
description: 11 pages, 5 figures, acceped for publication in the Astrophysical Journal