cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Quantum-like product states constructed from classical networks
Creators: name: Scholes, Gregory D.
name: Amati, Graziano
Publisher: name: arXiv
Year: 2024
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Can complex classical systems be designed to exhibit superpositions of tensor products of basis states, thereby mimicking quantum states? We exhibit a one-to one map between the product basis of quantum states comprising an arbitrary number of qubits and the eigenstates of a construction comprising classical oscillator networks. Specifically, we prove the existence of this map based on Cartesian products of graphs, where the graphs depict the layout of oscillator networks. We show how quantum-like gates can act on the classical networks to allow quantum-like operations in the state space.
COVID-19 vaccination status in Germany: Factors and reasons for not being vaccinated (yet)
Creators: name: Sterl, Sebastian
name: Stelzmann, Daniela
name: Luettschwager, Nils
name: Gerhold, Lars
Publisher: name: Freie Universität Berlin
Year: 2023
Subjects: subject: COVID-19
subject: vaccination status
subject: vaccines
subject: trust
subject: Germany
subject: 600 Technik, Medizin, angewandte Wissenschaften::610 Medizin und Gesundheit::616 Krankheiten

description: Introduction: The COVID-19 pandemic has demonstrated that effective vaccines constitute a central element of successful pandemic control. Although everyone in Germany has had the opportunity to receive a COVID-19 vaccine, some people remain hesitant or refuse to get vaccinated. To address this phenomenon as well as to examine the unvaccinated population more closely, the present study investigates (RQ1) factors explaining the COVID-19 vaccination status (RQ2) trust in different types of COVID-19 vaccines, and (RQ3) people's specific reasons for not getting vaccinated against COVID-19. Methods: We base our findings on a representative survey that we conducted in Germany in December 2021 with 1,310 respondents. Results: In response to the first research question, a logistic regression shows that trust in specific institutions (e.g., medical experts and authorities) is positively related to vaccination status, whereas trust in companies and COVID-19-related social and alternative media consumption decreases the likelihood of being vaccinated. Furthermore (RQ2), while vaccinated people trust mRNA-based vaccines (e.g., BioNTech), most unvaccinated people put greater trust in recently developed protein-based vaccines (e.g., Novavax), albeit on a low level. Finally, our study reveals (RQ3) that the most important reason why people choose not to get vaccinated is that they wish to make their own decisions about their bodies. Conclusion Based on our results, we suggest that a successful vaccination campaign should address COVID-19 risk groups and lower income populations, increase trust in different public institutions and newly developed vaccines in advance, establish a multisectoral approach, and debunk fake news and misinformation. Furthermore, since unvaccinated respondents state that the desire to make their own choices about their body is the main reason why they have not gotten vaccinated against COVID-19, an effective vaccination campaign should emphasize the need for general practitioners who have a closer relationship with their patients who, in turn, trust their doctors.
Effective description of squark interactions
Creators: name: Guasch, Jaume
name: Penaranda, Siannah
name: Sanchez-Florit, Raul
Publisher: name: arXiv
Year: 2008
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We propose an effective description of squark interactions with charginos/neutralinos. We recompute the strong corrections to squark partial decay widths, and compare the full one-loop computation with the effective description. The effective description includes the effective Yukawa couplings, and another logarithmic term which encodes the supersymmetry-breaking. The proposed effective couplings reproduce correctly the radiative-corrected partial decay widths of the squark decays into charginos and neutralinos in all relevant regions of the parameter space.
description: LaTeX, 25 pages, 6 figures, 1 Table. Comments added, typos corrected. Version to be published in JHEP
Universality of the Nf=2 Running Coupling
Creators: name: Murano, K.
name: Aoki, S.
name: Takeda, S.
name: Taniguchi, Y.
Publisher: name: arXiv
Year: 2009
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: FOS: Physical sciences

description: We investigate universality of the Nf=2 running coupling in the Schödinger functional scheme, by calculating the step scaling function in lattice QCD with the renorm alization group (RG) improved gauge action at both weak(u=0.9796) and strong(u=3.3340) couplings, where u=\bar{g}^2_SF with \bar{g}_SF being the running coupling in this scheme. In our main calculations, we use the tree-level value for O(a) improvement coefficients of boundary gauge fields. In addition we employ the 1-loop value for them in order to see how scaling behaviours are affected by them. In the continuum limit, the step scaling function obtained from the RG improved gauge actions agrees with the previous result obtained from the plaquette action within errors at both couplings, though errors of our result are larger. Combined fits using all data with the RG improved action as well as the plaquette action reduce errors in the continuum limit by 2% at the weak coupling and 22% at the strong coupling.
description: 7 pages, 7 figures, talk presented at the XXVI International Symposium on Lattice Field Theory, July 14-19, 2008, Williamsburg, Virginia, USA
Remixing war: An analysis of the reimagination of the Russian–Ukraine war on TikTok
Creators: name: Primig, Florian
name: Szabó, Hanna Dorottya
name: Lacasa, Pilar
Publisher: name: Freie Universität Berlin
Year: 2023
Subjects: subject: social media
subject: TikTok
subject: recontextualisation
subject: remixing
subject: self-representation
subject: affordances
subject: Russia-Ukraine War
subject: qualitative video analysis
subject: 000 Informatik, Informationswissenschaft, allgemeine Werke::070 Publizistische Medien, Journalismus, Verlagswesen::070 Publizistische Medien, Journalismus, Verlagswesen

description: Interpretative struggles of global crises are increasingly being reflected on social media networks. TikTok is a relatively new social media platform that has achieved substantial popularity among young people in many parts of the world and is now being used to disseminate and make sense of information about the Russian invasion of Ukraine. Through a user-centered sampling approach, we collected 62 TikTok videos and conducted an in-depth qualitative analysis of them and their uploading profiles to explore how the war was being represented on the platform. Our analysis revealed a strong prevalence of remixing practices among content creators; that is, they recontextualise images, sounds and embodied self-performance within the platform-specific affordances of trends. We found that distant suffering is mediated through the emotive online self-performance of content creators, cuing their audiences toward appropriate emotional responses. Trending sounds situate videos within a singular-motif and context-diverse environment, facilitating what we theorize as affective audio networks.
Additional file 1 of Upregulation of cathepsin L gene under mild cold conditions in young Japanese male adults
Creators: name: Yasukochi, Yoshiki
name: Shin, Sora
name: Wakabayashi, Hitoshi
name: Maeda, Takafumi
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Table S1. The quality of total RNA used in RNA-seq and real-time RT-qPCR analyses.
A Hybrid Multi Objective Particle Swarm Optimization Method to Discover Biclusters in Microarray Data
Creators: name: lashkargir, Mohsen
name: Monadjemi, S. Amirhassan
name: Dastjerdi, Ahmad Baraani
Publisher: name: arXiv
Year: 2009
Subjects: subject: Computational Engineering, Finance, and Science (cs.CE)
subject: Neural and Evolutionary Computing (cs.NE)
subject: FOS: Computer and information sciences

description: In recent years, with the development of microarray technique, discovery of useful knowledge from microarray data has become very important. Biclustering is a very useful data mining technique for discovering genes which have similar behavior. In microarray data, several objectives have to be optimized simultaneously and often these objectives are in conflict with each other. A Multi Objective model is capable of solving such problems. Our method proposes a Hybrid algorithm which is based on the Multi Objective Particle Swarm Optimization for discovering biclusters in gene expression data. In our method, we will consider a low level of overlapping amongst the biclusters and try to cover all elements of the gene expression matrix. Experimental results in the bench mark database show a significant improvement in both overlap among biclusters and coverage of elements in the gene expression matrix.
description: 6 Pages IEEE format, International Journal of Computer Science and Information Security, IJCSIS 2009, ISSN 1947 5500, Impact Factor 0.423, http://sites.google.com/site/ijcsis/
Additional file 2 of Upregulation of cathepsin L gene under mild cold conditions in young Japanese male adults
Creators: name: Yasukochi, Yoshiki
name: Shin, Sora
name: Wakabayashi, Hitoshi
name: Maeda, Takafumi
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2: Fig. S1. Gene expression levels of 13 differentially expressed genes with |LFC| < 1, identified using the DESeq2 program, in each of the study subjects. Normalized counts at the vertical axis represent the estimated expression abundance at the gene level.
Adaptive System Modelling for Active Attenuation of Sound
Creators: name: Wong, Lawrence Yik-Lung .
Publisher: name: London South Bank University
Year: 1992

description: Active Noise Cancellation (ANC) is the process of using a secondary sound source to cancel an undesired primary sound. Using a system modelling approach, the parameters representing both the process model and the disturbance model are obtained for the overall ANC configuration. The acoustical elements in these two models are thoroughly investigated, including analysis based on a novel transfer function technique. Parametric system identification methods are developed to estimate the process and disturbance models. After verification by computer simulations, these algorithms are implemented in a practical set-up both in real and non-real time. The controller, which regulates the process generating the secondary sound, is thoroughly investigated using feedforward and feedback design. Adaptive processing is also incorporated to accommodate the time-varying nature of the overall system. Extensive computer simulation verifies the ANC controller design for both broadband and periodic sound. Finally, a digital signal processing (DSP) environment is developed, incorporating both high-level software and DSP hardware. From this set-up, a real-time adaptive noise controller is successfully implemented giving significant noise attenuation. There is an attenuation up to 25dB for periodic sound, while for broad-band sound, an attenuation up to 10dB can be achieved. This work, which has blended together acoustic modelling, adaptive control and design of a DSP environment, proposes one solution to the ANC problem.
The Variation of the Galaxy Luminosity Function with Group Properties
Creators: name: Robotham, Aaron
name: Phillipps, Steve
name: de Propris, Roberto
Publisher: name: arXiv
Year: 2010
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We explore the shape of the galaxy luminosity function (LF) in groups of different mass by creating composite LFs over large numbers of groups. Following previous work using total group luminosity as the mass indicator, here we split our groups by multiplicity and by estimated virial (group halo) mass, and consider red (passive) and blue (star forming) galaxies separately. In addition we utilise two different group catalogues (2PIGG and Yang et al.) in order to ascertain the impact of the specific grouping algorithm and further investigate the environmental effects via variations in the LF with position in groups. Our main results are that LFs show a steepening faint end for early type galaxies as a function of group mass/ multiplicity, with a much suppressed trend (evident only in high mass groups) for late type galaxies. Variations between LFs as a function of group mass are robust irrespective of which grouping catalogue is used, and broadly speaking what method for determining group `mass' is used. We find in particular that there is a significant deficit of low-mass passive galaxies in low multiplicity groups, as seen in high redshift clusters. Further to this, the variation in the LF appears to only occur in the central regions of systems, and in fact seems to be most strongly dependent on the position in the group relative to the virial radius. Finally, distance-rank magnitude relations were considered. Only the Yang groups demonstrated any evidence of a correlation between a galaxy's position relative to the brightest group member and its luminosity. 2PIGG possessed no such gradient, the conclusion being the FOF algorithm suppresses the signal for weak luminosity--position trends and the Yang grouping algorithm naturally enhances it.
description: 20 pages, 29 figures, accepted for submission to MNRAS
Reentrant spin glass state in Mn doped Ni2MnSn shape memory alloy
Creators: name: Chatterjee, S.
name: Giri, S.
name: De, S. K.
name: Majumdar, S.
Publisher: name: arXiv
Year: 2008
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: The ground state properties of the ferromagnetic shape memory alloy of nominal composition Ni2Mn1.36Sn0.64 have been studied by dc magnetization and ac susceptibility measurements. Like few other Ni-Mn based alloys, this sample exhibits exchange bias phenomenon. The observed exchange bias pinning was found to originate right from the temperature where a step-like anomaly is present in the zero-field-cooled magnetization data. The ac susceptibility study indicates the onset of spin glass freezing near this step-like anomaly with clear frequency shift. The sample can be identified as a reentrant spin glass with both ferromagnetic and glassy phases coexisting together at low temperature at least in the field-cooled state. The result provides us an comprehensive view to identify the magnetic character of various Ni-Mn-based shape memory alloys with competing magnetic interactions.
description: 5 figures
Additional file 3 of Upregulation of cathepsin L gene under mild cold conditions in young Japanese male adults
Creators: name: Yasukochi, Yoshiki
name: Shin, Sora
name: Wakabayashi, Hitoshi
name: Maeda, Takafumi
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 3: Fig. S2. Relative quantification levels of CTSL measured using real-time RT-qPCR and the comparative Ct method. The bold black bars represent median values. The vertical axis represents the mean relative quantification of CTSL transcripts.
The Kasteleyn transition in three dimensions: spin ice in a [100] field
Creators: name: Jaubert, Ludovic D. C.
name: Chalker, J. T.
name: Holdsworth, P. C. W.
name: Moessner, R.
Publisher: name: arXiv
Year: 2009
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We discuss the nearest neighbour spin ice model in the presence of a magnetic field placed along the cubic [100] direction. As recently shown in Phys. Rev. Lett. 100, 067207, 2008, the symmetry sustaining ordering transition observed at low temperature is a three dimensional Kasteleyn transition. We confirm this with numerical data using a non-local algorithm that conserves the topological constraints at low temperature and from analytic calculations from a Bethe lattice of corner sharing tetrahedra . We present a thermodynamic description of the Kasteleyn transition and discuss the relevance of our results to recent neutron scattering experiments on spin ice materials.
ShapG: new feature importance method based on the Shapley value
Creators: name: Zhao, Chi
name: Liu, Jing
name: Parilina, Elena
Publisher: name: arXiv
Year: 2024
Subjects: subject: Artificial Intelligence (cs.AI)
subject: Computer Science and Game Theory (cs.GT)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences
subject: 68T01, 68T20

description: With wide application of Artificial Intelligence (AI), it has become particularly important to make decisions of AI systems explainable and transparent. In this paper, we proposed a new Explainable Artificial Intelligence (XAI) method called ShapG (Explanations based on Shapley value for Graphs) for measuring feature importance. ShapG is a model-agnostic global explanation method. At the first stage, it defines an undirected graph based on the dataset, where nodes represent features and edges are added based on calculation of correlation coefficients between features. At the second stage, it calculates an approximated Shapley value by sampling the data taking into account this graph structure. The sampling approach of ShapG allows to calculate the importance of features efficiently, i.e. to reduce computational complexity. Comparison of ShapG with other existing XAI methods shows that it provides more accurate explanations for two examined datasets. We also compared other XAI methods developed based on cooperative game theory with ShapG in running time, and the results show that ShapG exhibits obvious advantages in its running time, which further proves efficiency of ShapG. In addition, extensive experiments demonstrate a wide range of applicability of the ShapG method for explaining complex models. We find ShapG an important tool in improving explainability and transparency of AI systems and believe it can be widely used in various fields.
description: This paper has been published in the journal "Engineering Applications of Artificial Intelligence"
Generalization of navigation memory in honeybees
Creators: name: Bullinger, Eric
name: Greggers, Uwe
name: Menzel, Randolf
Publisher: name: Freie Universität Berlin
Year: 2023
Subjects: subject: landmark learning
subject: orientation flight
subject: observational learning
subject: matching landmarks
subject: random search
subject: elongated ground structures
subject: 500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::570 Biowissenschaften; Biologie

description: Flying insects like the honeybee learn multiple features of the environment for efficient navigation. Here we introduce a novel paradigm in the natural habitat, and ask whether the memory of such features is generalized to novel test conditions. Foraging bees from colonies located in 5 different home areas were tested in a common area for their search flights. The home areas differed in the arrangements of rising natural objects or their lack, and in the existence or lack of elongated ground structures. The test area resembled partly or not at all the layout of landmarks in the respective home areas. In particular, the test area lacked rising objects. The search flights were tracked with harmonic radar and quantified by multiples procedures, extracting their differences on an individual basis. Random search as the only guide for searching was excluded by two model calculations. The frequencies of directions of flight sectors differed from both model calculations and between the home areas in a graded fashion. Densities of search flight fixes were used to create heat maps and classified by a partial least squares regression analysis. Classification was performed with a support vector machine in order to account for optimal hyperplanes. A rank order of well separated clusters was found that partly resemble the graded differences between the ground structures of the home areas and the test area. The guiding effect of elongated ground structures was quantified with respect to the sequence, angle and distance from these ground structures. We conclude that foragers generalize their specific landscape memory in a graded way to the landscape features in the test area, and argue that both the existence and absences of landmarks are taken into account. The conclusion is discussed in the context of the learning and generalization process in an insect, the honeybee, with an emphasis on exploratory learning in the context of navigation.
Dark blue-green: Cave-inhabiting cyanobacteria as a model for astrobiology
Creators: name: Jung, Patrick
name: Harion, Felix
name: Wu, Shujie
name: Nürnberg, Dennis J.
name: Bellamoli, Francesco
name: Guillen, Antonio
name: Leira, Manuel
name: Lakatos, Michael
Publisher: name: Freie Universität Berlin
Year: 2023
Subjects: subject: emerse photobioreactor
subject: polyhydroxybutyrate
subject: biofilm bioreactor
subject: far-red photosynthesis
subject: calcification
subject: 500 Naturwissenschaften und Mathematik::520 Astronomie::520 Astronomie und zugeordnete Wissenschaften

description: Subterranean environments on Earth serve as an analog for the study of microbes on other planets, which has become an active area of research. Although it might sound contradictory that photosynthetic cyanobacteria thrive in extreme low light environments, they are frequent inhabitants of caves on Earth. Throughout the phylum these cyanobacteria have developed unique adaptations that cannot only be used for biotechnological processes but also have implications for astrobiology. They can, for example, both accommodate for the low light conditions by producing specific pigments that allow photosynthesis in near-infrared (IR) radiation/far-red light, and they can synthesize bioplastic compounds and calcium carbonate sheaths which represent valuable resources during human colonization of other planets or rock bodies. This article will highlight the potential benefits of cave-inhabiting cyanobacteria and will present a suitable bioreactor technique for the utilization of these special microbes during future space missions.
Genomic insight into Campylobacter jejuni isolated from commercial turkey flocks in Germany using whole-genome sequencing analysis
Creators: name: El-Adawy, Hosny
name: Hotzel, Helmut
name: García-Soto, Silvia
name: Tomaso, Herbert
name: Hafez, Hafez M.
name: Schwarz, Stefan
name: Neubauer, Heinrich
name: Linde, Jörg
Publisher: name: Freie Universität Berlin
Year: 2023
Subjects: subject: Campylobacter jejuni
subject: turkeys
subject: genetic diversity
subject: WGS
subject: MLST
subject: resistome
subject: virulome
subject: 600 Technik, Medizin, angewandte Wissenschaften::630 Landwirtschaft::630 Landwirtschaft und verwandte Bereiche

description: Campylobacter (C.) jejuni is a zoonotic bacterium of public health significance. The present investigation was designed to assess the epidemiology and genetic heterogeneity of C. jejuni recovered from commercial turkey farms in Germany using whole-genome sequencing. The Illumina MiSeq® technology was used to sequence 66 C. jejuni isolates obtained between 2010 and 2011 from commercial meat turkey flocks located in ten German federal states. Phenotypic antimicrobial resistance was determined. Phylogeny, resistome, plasmidome and virulome profiles were analyzed using whole-genome sequencing data. Genetic resistance markers were identified with bioinformatics tools (AMRFinder, ResFinder, NCBI and ABRicate) and compared with the phenotypic antimicrobial resistance. The isolates were assigned to 28 different sequence types and 11 clonal complexes. The average pairwise single nucleotide-polymorphisms distance of 14,585 SNPs (range: 0–26,540 SNPs) revealed a high genetic distinction between the isolates. Thirteen virulence-associated genes were identified in C. jejuni isolates. Most of the isolates harbored the genes flaA (83.3%) and flaB (78.8%). The wlaN gene associated with the Guillain–Barré syndrome was detected in nine (13.6%) isolates. The genes for resistance to ampicillin (blaOXA), tetracycline [tet(O)], neomycin [aph(3')-IIIa], streptomycin (aadE) and streptothricin (sat4) were detected in isolated C. jejuni using WGS. A gene cluster comprising the genes sat4, aph(3′)-IIIa and aadE was present in six isolates. The single point mutation T86I in the housekeeping gene gyrA conferring resistance to quinolones was retrieved in 93.6% of phenotypically fluoroquinolone-resistant isolates. Five phenotypically erythromycin-susceptible isolates carried the mutation A103V in the gene for the ribosomal protein L22 inferring macrolide resistance. An assortment of 13 β-lactam resistance genes (blaOXA variants) was detected in 58 C. jejuni isolates. Out of 66 sequenced isolates, 28 (42.4%) carried plasmid-borne contigs. Six isolates harbored a pTet-like plasmid-borne contig which carries the tet(O) gene. This study emphasized the potential of whole-genome sequencing to ameliorate the routine surveillance of C. jejuni. Whole-genome sequencing can predict antimicrobial resistance with a high degree of accuracy. However, resistance gene databases need curation and updates to revoke inaccuracy when using WGS-based analysis pipelines for AMR detection.
Manifestations of topological effects in graphene
Creators: name: Pachos, Jiannis K.
Publisher: name: arXiv
Year: 2008
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
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: Graphene is a monoatomic layer of graphite with Carbon atoms arranged in a two dimensional honeycomb lattice configuration. It has been known for more than sixty years that the electronic structure of graphene can be modelled by two-dimensional massless relativistic fermions. This property gives rise to numerous applications, both in applied sciences and in theoretical physics. Electronic circuits made out of graphene could take advantage of its high electron mobility that is witnessed even at room temperature. In the theoretical domain the Dirac-like behavior of graphene can simulate high energy effects, such as the relativistic Klein paradox. Even more surprisingly, topological effects can be encoded in graphene such as the generation of vortices, charge fractionalization and the emergence of anyons. The impact of the topological effects on graphene's electronic properties can be elegantly described by the Atiyah-Singer index theorem. Here we present a pedagogical encounter of this theorem and review its various applications to graphene. A direct consequence of the index theorem is charge fractionalization that is usually known from the fractional quantum Hall effect. The charge fractionalization gives rise to the exciting possibility of realizing graphene based anyons that unlike bosons or fermions exhibit fractional statistics. Besides being of theoretical interest, anyons are a strong candidate for performing error free quantum information processing.
description: 20 pages, 15 figures, invited article, to appear in Contemporary Physics
Stabilizing All Kahler Moduli in Type IIB Orientifolds
Creators: name: Bobkov, Konstantin
name: Braun, Volker
name: Kumar, Piyush
name: Raby, Stuart
Publisher: name: arXiv
Year: 2010
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We describe a simple and robust mechanism that stabilizes all Kahler moduli in Type IIB orientifold compactifications. This is shown to be possible with just one non-perturbative contribution to the superpotential coming from either a D3-instanton or D7-branes wrapped on an ample divisor. This moduli-stabilization mechanism is similar to and motivated by the one used in the fluxless G_2 compactifications of M-theory. After explaining the general idea, explicit examples of Calabi-Yau orientifolds with one and three Kahler moduli are worked out. We find that the stabilized volumes of all two- and four-cycles as well as the volume of the Calabi-Yau manifold are controlled by a single parameter, namely, the volume of the ample divisor. This feature would dramatically constrain any realistic models of particle physics embedded into such compactifications. Broad consequences for phenomenology are discussed, in particular the dynamical solution to the strong CP-problem within the framework.
description: RevTeX, 24 pages, 2 tables, 1 figure.
Discovery of HPV-associated genomic alterations in cervical cancer
Creators: name: Porter, Vanessa Lynn
Publisher: name: University of British Columbia
Year: 2024

description: Human papillomavirus (HPV) is the necessary driver of cervical cancer, a disease that largely affects females from underdeveloped nations and is prevalent among HIV-positive individuals. Altered regulation of the viral genome and HPV-driven genomic instability of the host genome are both implicated in transforming HPV infection into cancer. The regulation of viral genes often changes when the HPV genome becomes integrated into the host genome, which is seen in about 70% of cervical tumours. In addition, different high-risk HPV types have distinct disease characteristics, which has been underappreciated when studying HPV-driven molecular changes. To study HPV-driven molecular differences in cervical cancers, I analysed 118 tumours from Ugandan patients, of whom 72 were HIV-positive, using whole genome, whole transcriptome, and targeted epigenome sequencing. I detected HPV clade-specific differences in DNA methylation, promoter- and enhancer-associated histone marks, gene expression, and patient survival. The observed changes in epigenetic landscapes and the activation of cell invasion pathways may contribute to the reduced survival among patients infected with clade A7 HPV types. To resolve the dysregulation associated with HPV integration, I analysed 63 cervical cancer genomes using long-read sequencing. I identified six categories of integration events based on HPV-human genomic structures. Of all HPV integrants, defined as two HPV-human breakpoints bridged by an HPV sequence, 24% contained variable copies of HPV between the breakpoints, a phenomenon I termed heterologous integration. Analysis of DNA methylation within and in proximity to the HPV genome at individual integration events revealed relationships between methylation status of the integrant and its orientation and structure. Dysregulation of the human epigenome and neighbouring gene expression in cis with the HPV-integrated allele was observed over megabase-ranges of the genome. By elucidating the HPV clade-associated tumour landscapes and integration-associated structural, epigenetic, and allele-specific impacts, I provide insight into the key oncogenic mechanisms of HPV in cervical cancer.
Soliton solutions of nonlinear Schroedinger equation on simple networks
Creators: name: Sobirov, Z.
name: Matrasulov, D.
name: Sabirov, K.
name: Sawada, S.
name: Nakamura, K.
Publisher: name: arXiv
Year: 2009
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: FOS: Physical sciences

description: We show soliton solutions of nonlinear Schroedinger equation on simple networks consisting of vertices and bonds, where the strength of cubic nonlinearity is different from bond to bond. We concentrate on reflectionless propagation of Zakharov-Shabat's solitons through a branched chain, namely, a primary star graph consisting of three semi-infinite bonds connected at a vertex. The conservation of the norm and the global current elucidates: (1) the solution on each bond is a part of the universal soliton solution on a simple 1-dimensional (1-d) chain but multiplied by the inverse of square root of bond-dependent nonlinearity; (2) nonlinearities at individual bonds around each vertex must satisfy a sum rule. Under these conditions, all other conservation rules for a simple 1-d chain have proved to hold for multi-soliton solutions on graphs. The argument is extended to other graphs, i.e., general star graphs, tree graphs, loop graphs and their combinations. Numerical evidence is also given on the reflectionless propagation of a soliton through a branched chain.
description: 18 pages, 11 pages
Additional file 4 of Upregulation of cathepsin L gene under mild cold conditions in young Japanese male adults
Creators: name: Yasukochi, Yoshiki
name: Shin, Sora
name: Wakabayashi, Hitoshi
name: Maeda, Takafumi
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 4: Fig. S3. Hierarchical tree of GO terms in the biological process category. Significantly overrepresented GO terms (FDR < 0.05) are shown in red characters.
Molecular dynamics study of hcp/fcc nucleation and growth in bcc iron driven by uniaxial strain
Creators: name: Wang, Baotian
name: Shao, Jianli
name: Zhang, Guangcai
name: Li, Weidong
name: Zhang, Ping
Publisher: name: arXiv
Year: 2009
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Molecular dynamics simulations are performed to investigate the structural phase transition in body-centered cubic (bcc) single crystal iron under high strain rate loading. We study the nucleation and growth of the hexagonal-close-packed (hcp) and face-centered-cubic (fcc) phases, and their crystal orientation dependence. Results reveal that the transition pressures are less dependent on the crystal orientations ($\mathtt{\sim}$14 GPa for loading along [001], [011], and [111] directions). However, the pressure interval of mixed phase for [011] loading is much shorter than loading along other orientations. And the temperature increased amplitude for [001] loading is evidently lower than other orientations. The hcp/fcc nucleation process is presented by the topological medium-range-order analysis. For loading along [001] direction, we find that the hcp structure occurs firstly and grows into laminar morphology in the (011)$_{\text{bcc}}$ planes with a little fcc atoms as intermediate structure. For loading along [011] and [111] directions, both the hcp and fcc structures nucleation and growth along the \{110\}$_{\text{bcc}}$ planes are observed, whose morphology is also discussed.
description: 6 pages, 8 figures
Late-bound code generation
Creators: name: Taylor, Matthew Robert
Publisher: name: Imperial College London
Year: 2022

description: Each time a function or method is invoked during the execution of a program, a stream of instructions is issued to some underlying hardware platform. But exactly what underlying hardware, and which instructions, is usually left implicit. However in certain situations it becomes important to control these decisions. For example, particular problems can only be solved in real-time when scheduled on specialised accelerators, such as graphics coprocessors or computing clusters. We introduce a novel operator for hygienically reifying the behaviour of a runtime function instance as a syntactic fragment, in a language which may in general differ from the source function definition. Translation and optimisation are performed by recursively invoked, dynamically dispatched code generators. Side-effecting operations are permitted, and their ordering is preserved. We compare our operator with other techniques for pragmatic control, observing that: the use of our operator supports lifting arbitrary mutable objects, and neither requires rewriting sections of the source program in a multi-level language, nor interferes with the interface to individual software components. Due to its lack of interference at the abstraction level at which software is composed, we believe that our approach poses a significantly lower barrier to practical adoption than current methods. The practical efficacy of our operator is demonstrated by using it to offload the user interface rendering of a smartphone application to an FPGA coprocessor, including both statically and procedurally defined user interface components. The generated pipeline is an application-specific, statically scheduled processor-per-primitive rendering pipeline, suitable for place-and-route style optimisation. To demonstrate the compatibility of our operator with existing languages, we show how it may be defined within the Python programming language. We introduce a transformation for weakening mutable to immutable named bindings, termed let-weakening, to solve the problem of propagating information pertaining to named variables between modular code generating units.
Calculation of fission observables through event-by-event simulation
Creators: name: Randrup, J.
name: Vogt, R.
Publisher: name: arXiv
Year: 2009
Subjects: subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: The increased interest in more exclusive fission observables has demanded more detailed models. We present here a new computational model, FREYA, that aims to meet this need by producing large samples of complete fission events from which any observable of interest can then be extracted consistently, including arbitrary correlations. The various model assumptions are described and the potential utility of the model is illustrated by means of several novel correlation observables.
description: 11 pages, 12 eps figures
Additional file 1 of Efficacy and safety of iruplinalkib (WX-0593) in ALK-positive crizotinib-resistant advanced non-small cell lung cancer patients: a single-arm, multicenter phase II study (INTELLECT)
Creators: name: Shi, Yuankai
name: Chen, Jianhua
name: Zhang, Helong
name: Zhang, Zhihong
name: Zhang, Yiping
name: Wang, Zhehai
name: Zhang, Shucai
name: Zhao, Jian
name: Liu, Chunling
name: Wang, Xiuwen
name: Zhao, Yanqiu
name: Hu, Changlu
name: Yang, Lei
name: Hao, Xuezhi
name: Wang, Lin
name: Liu, Yunpeng
name: Yu, Yan
name: Zhao, Jun
name: Wang, Mengzhao
name: Zhang, Liangming
name: Sun, Sanyuan
name: Hu, Yanping
name: Gu, Kangsheng
name: Hang, Xiaosheng
name: Shan, Jinlu
name: Zhang, Yu
name: Tan, Bangxian
name: Yang, Weihua
name: Yang, Runxiang
name: Si, Meimei
name: Geng, Huaize
name: Li, Hui
name: Kang, Xiaoyan
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Biotechnology
subject: Environmental Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Science Policy
subject: Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1: Table S1. Summary of comorbidities in ≥ 5% patients in FAS. Table S2. Investigator-assessed efficacy of iruplinalkib in FAS. Figure S1. Waterfall plots of the subgroup BOR of target lesions by IRC in FAS. Figure S2. Waterfall plot of BOR by investigator in FAS. Figure S3. Swimmer plot of iruplinalkib exposure and response by investigator in FAS. Figure S4. Minimum plasma iruplinalkib concentration at each time point in the pharmacokinetics analysis set.
Phase-space analysis of interacting phantom cosmology
Creators: name: Chen, Xi-ming
name: Gong, Yungui
name: Saridakis, Emmanuel N.
Publisher: name: arXiv
Year: 2008
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We perform a detailed phase-space analysis of various phantom cosmological models, where the dark energy sector interacts with the dark matter one. We examine whether there exist late-time scaling attractors, corresponding to an accelerating universe and possessing dark energy and dark matter densities of the same order. We find that all the examined models, although accepting stable late-time accelerated solutions, cannot alleviate the coincidence problem, unless one imposes a form of fine-tuning in the model parameters. It seems that interacting phantom cosmology cannot fulfill the basic requirement that led to its construction.
description: 6 figures, use revtex, v2: minor corrections, references added, accepted for publication in JCAP
Research and development for the data, trigger and control card in preparation for Hi-Lumi lhc
Creators: name: Monk, David
Publisher: name: Imperial College London
Year: 2022

description: When the Large Hadron Collider (LHC) increases its luminosity by an order of magnitude in the coming decade, the experiments that sit upon it must also be upgraded to continue to their physics performance in the increasingly demanding environment. To achieve this, the Compact Muon Solenoid (CMS) experiment will make use of tracking information in the Level-1 trigger for the first time, meaning that track reconstruction must be achieved in less than 4 μs in an all-FPGA architecture. MUonE is an experiment aiming to make an accurate measurement of the the hadronic contribution to the anomalous magnetic moment of the muon. It will achieve this by making use of similar apparatus to that designed for CMS and benefit from the research and development efforts there. This thesis presents both development and testing work for the readout chain from tracker module to back-end processing card, as well as the results and analysis of a beam test used to validate this chain for both CMS and the MUonE experiment.
Deep learning quantum Monte Carlo for solids
Creators: name: Qian, Yubing
name: Li, Xiang
name: Li, Zhe
name: Ren, Weiluo
name: Chen, Ji
Publisher: name: arXiv
Year: 2024
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences

description: Deep learning has deeply changed the paradigms of many research fields. At the heart of chemical and physical sciences is the accurate ab initio calculation of many-body wavefunction, which has become one of the most notable examples to demonstrate the power of deep learning in science. In particular, the introduction of deep learning into quantum Monte Carlo (QMC) has significantly advanced the frontier of ab initio calculation, offering a universal tool to solve the electronic structure of materials and molecules. Deep learning QMC architectures were initial designed and tested on small molecules, focusing on comparisons with other state-of-the-art ab initio methods. Methodological developments, including extensions to real solids and periodic models, have been rapidly progressing and reported applications are fast expanding. This review covers the theoretical foundation of deep learning QMC for solids, the neural network wavefunction ansatz, and various of other methodological developments. Applications on computing energy, electron density, electric polarization, force and stress of real solids are also reviewed. The methods have also been extended to other periodic systems and finite temperature calculations. The review highlights the potentials and existing challenges of deep learning QMC in materials chemistry and condensed matter physics.
Material Limitations on the Detection Limit in Refractometry
Creators: name: Skafte-Pedersen, Peder
name: Nunes, Pedro S.
name: Xiao, Sanshui
name: Mortensen, Niels Asger
Publisher: name: arXiv
Year: 2009
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We discuss the detection limit for refractometric sensors relying on high-Q optical cavities and show that the ultimate classical detection limit is given by min{Dn} > eta with n+i*eta being the complex refractive index of the material under refractometric investigation. Taking finite Q factors and filling fractions into account, the detection limit declines. As an example we discuss the fundamental limits of silicon-based high-Q resonators, such as photonic crystal resonators, for sensing in a bio-liquid environment, such as a water buffer. In the transparency window of silicon the detection limit becomes almost independent on the filling fraction, while in the visible, the detection limit depends strongly on the filling fraction because silicon absorbs strongly.
description: Published in Special Issue "Laser Spectroscopy and Sensing", Edited by Prof. M.W. Sigrist
Additional file 1 of A SISCAPA-based approach for detection of SARS-CoV-2 viral antigens from clinical samples
Creators: name: Mangalaparthi, Kiran K.
name: Chavan, Sandip
name: Madugundu, Anil K.
name: Renuse, Santosh
name: Vanderboom, Patrick M.
name: Maus, Anthony D.
name: Kemp, Jennifer
name: Kipp, Benjamin R.
name: Grebe, Stefan K.
name: Singh, Ravinder J.
name: Pandey, Akhilesh
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Additional file 1: Figure S1. Figure showing the correlation of peak areas across the entire range of synthetic peptide amounts spiked in phosphate buffered saline followed by enrichment and targeted analysis.
Ladder operators and coherent states for continuous spectra
Creators: name: Geloun, Joseph Ben
name: Klauder, John R.
Publisher: name: arXiv
Year: 2009
Subjects: subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: The notion of ladder operators is introduced for systems with continuous spectra. We identify two different kinds of annihilation operators allowing the definition of coherent states as modified "eigenvectors" of these operators. Axioms of Gazeau-Klauder are maintained throughout the construction.
description: Typos corrected
Supplementary of Learning with Instance-Dependent Noisy Labels by Anchor Hallucination and Hard Sample Label Correction
Creators: Po-Hsuan Huang
Chia-Ching Lin
Chih-Fan Hsu
Ming-Ching Chang
Wei-Chao Chen
Publisher: name: IEEE Signal Processing Society
Year: 2024

description: Supplementary of Learning with Instance-Dependent Noisy Labels by Anchor Hallucination and Hard Sample Label Correction