cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Laser-generated plasmas in length scales relevant for thin film growth and processing: simulation and experiment
Creators: name: Harris, Sumner B.
name: Paiste, Jacob H.
name: Holdsworth, Tharon J.
name: Arslanbekov, Robert R.
name: Camata, Renato P.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Applied Physics (physics.app-ph)
subject: Plasma Physics (physics.plasm-ph)
subject: FOS: Physical sciences

description: In pulsed laser deposition, thin film growth is mediated by a laser-generated plasma, whose properties are critical for controlling the film microstructure. The advent of 2D materials has renewed the interest in how this ablation plasma can be used to manipulate the growth and processing of atomically thin systems. For such purpose, a quantitative understanding of the density, charge state, and kinetic energy of plasma constituents is needed at the location where they contribute to materials processes. Here we study laser-induced plasmas over expansion distances of several centimeters from the ablation target, which is the relevant length scale for materials growth and modification. The study is enabled by a fast implementation of a laser ablation/plasma expansion model using an adaptive Cartesian mesh solver. Simulation outcomes for KrF excimer laser ablation of Cu are compared with Langmuir probe and optical emission spectroscopy measurements. Simulation predictions for the plasma-shielding threshold, the ionization state of species in the plasma, and the kinetic energy of ions, are in good correspondence with experimental data. For laser fluences of 1-4 J/cm$^2$, the plume is dominated by Cu$^0$, with small concentrations of Cu$^{+}$ and electrons at the expansion front. Higher laser fluences (e.g., 7 J/cm$^2$) lead to a Cu$^{+}$-rich plasma, with a fully ionized leading edge where Cu$^{2+}$ is the dominant species. In both regimes, simulations indicate the presence of a low-density, high-temperature plasma expansion front with a high degree of ionization that may play a significant role in doping, annealing, and kinetically-driven phase transformations in 2D materials.
Universal continuous-variable quantum computation: Requirement of optical nonlinearity for photon counting
Creators: name: Bartlett, Stephen D.
name: Sanders, Barry C.
Publisher: name: arXiv
Year: 2001
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Although universal continuous-variable quantum computation cannot be achieved via linear optics (including squeezing), homodyne detection and feed-forward, inclusion of ideal photon counting measurements overcomes this obstacle. These measurements are sometimes described by arrays of beam splitters to distribute the photons across several modes. We show that such a scheme cannot be used to implement ideal photon counting and that such measurements necessarily involve nonlinear evolution. However, this requirement of nonlinearity can be moved "off-line," thereby permitting universal continuous-variable quantum computation with linear optics.
description: 6 pages, no figures, replaced with published version
Additional file 1: of Prevalence of pathogenic/likely pathogenic variants in the 24 cancer genes of the ACMG Secondary Findings v2.0 list in a large cancer cohort and ethnicity-matched controls
Creators: name: Kim, Jung
name: Luo, Wen
name: Wang, Mingyi
name: Wegman-Ostrosky, Talia
name: Frone, Megan
name: Johnston, Jennifer
name: Nickerson, Michael
name: Rotunno, Melissa
name: Li, Shengchao
name: Achatz, Maria
name: Brodie, Seth
name: Dean, Michael
name: Andrade, Kelvin
name: Fortes, Fernanda
name: Gianferante, Matthew
name: Khincha, Payal
name: McMaster, Mary
name: McReynolds, Lisa
name: Pemov, Alexander
name: Pinheiro, Maisa
name: Santiago, Karina
name: Alter, Blanche
name: Caporaso, Neil
name: Gadalla, Shahinaz
name: Goldin, Lynn
name: Greene, Mark
name: Loud, Jennifer
name: Yang, Xiaohong
name: Freedman, Neal
name: Gapstur, Susan
name: Gaudet, Mia
name: Calista, Donato
name: Ghiorzo, Paola
name: Fargnoli, Maria
name: Nagore, Eduardo
name: Peris, Ketty
name: Puig, Susana
name: Landi, Maria
name: Hicks, Belynda
name: Zhu, Bin
name: Liu, Jia
name: Sampson, Joshua
name: Chanock, Stephen
name: Mirabello, Lisa
name: Morton, Lindsay
name: Biesecker, Leslie
name: Tucker, Margaret
name: Savage, Sharon
name: Goldstein, Alisa
name: Stewart, Douglas
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Mathematical Sciences not elsewhere classified
subject: Developmental Biology
subject: Marine Biology
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Supplemental Methods. Detailed methods on DNA preparation, hybridization, exome sequencing, variant calling, use of ethnicity-informative variation, quality control, and capture region matching. (PDF 233 kb)
How the Mechanical Properties and Thickness of Glass Affect TPaD Performance
Creators: name: Xu, Heng
name: Peshkin, Michael A.
name: Colgate, J. Edward
Publisher: name: arXiv
Year: 2019
Subjects: subject: Human-Computer Interaction (cs.HC)
subject: Robotics (cs.RO)
subject: FOS: Computer and information sciences

description: One well-known class of surface haptic devices that we have called TPaDs (Tactile Pattern Displays) uses ultrasonic transverse vibrations of a touch surface to modulate fingertip friction. This paper addresses the power consumption of glass TPaDs, which is an important consideration in the context of mobile touchscreens. In particular, based on existing ultrasonic friction reduction models, we consider how the mechanical properties (density and Young's modulus) and thickness of commonly-used glass formulations affect TPaD performance, namely the relation between its friction reduction ability and its real power consumption. Experiments performed with eight types of TPaDs and an electromechanical model for the fingertip-TPaD system indicate: 1) TPaD performance decreases as glass thickness increases; 2) TPaD performance increases as the Young's modulus and density of glass decrease; 3) real power consumption of a TPaD decreases as the contact force increases. Proper applications of these results can lead to significant increases in TPaD performance.
description: IEEE Transactions on Haptics
Forming stars on a viscous timescale: the key to exponential stellar profiles in disk galaxies?
Creators: name: Slyz, A.
name: Devriendt, J.
name: Silk, J.
name: Burkert, A.
Publisher: name: arXiv
Year: 2001
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We argue for implementing star formation on a viscous timescale in hydrodynamical simulations of disk galaxy formation and evolution. Modelling two-dimensional isolated disk galaxies with the Bhatnagar-Gross-Krook (BGK) hydrocode, we verify the analytic claim of various authors that if the characteristic timescale for star formation is equal to the viscous timescale in disks, the resulting stellar profile is exponential on several scale lengths whatever the initial gas and dark matter profile. This casts new light on both numerical and semi-analytical disk formation simulations which either (a) commence star formation in an already exponential gaseous disk, (b) begin a disk simulation with conditions known to lead to an exponential, i.e. the collapse of a spherically symmetric nearly uniform sphere of gas in solid body rotation under the assumption of specific angular momentum conservation, or (c) in simulations performed in a hierarchical context, tune their feedback processes to delay disk formation until the dark matter halos are slowly evolving and without much substructure so that the gas has the chance to collapse under conditions known to give exponentials. In such models, star formation follows a Schmidt-like law, which for lack of a suitable timescale, resorts to an efficiency parameter. With star formation prescribed on a viscous timescale however, we find gas and star fractions after $\sim$ 12 Gyr that are consistent with observations without having to invoke any ``fudge factor'' for star formation. Our results strongly suggest that despite our gap in understanding the exact link between star formation and viscosity, the viscous timescale is indeed the natural timescale for star formation.
description: 18 pages, 12 figures, submitted to MNRAS
Analogy Based Valuation of Commodity Options
Creators: name: Siddiqi, Hammad
name: Siddiqi, Hammad
Publisher: name: Unknown
Year: 2015
Subjects: subject: Financial Economics
subject: Implied Volatility Smile
subject: Implied Volatility Skew
subject: Reverse Skew
subject: Forward Skew
subject: Analogy Making
subject: Commodity Call Option
subject: Commodity Futures Contract

description: Typically, three types of implied volatility smiles are seen in commodity options: the reverse skew, the smile, and the forward skew. I put forward an economic explanation for all three types of implied volatility smiles based on the idea that a commodity call option is valued in analogy with its underlying futures contract, where the underlying futures price follows geometric Brownian motion. Closed form solutions for commodity calls and puts exist in the presence of transaction costs. Analogy based jump diffusion model is also developed. The smiles are steeper with jump diffusion when compared with smiles with geometric Brownian motion.
Additional file 1 of "Strong Teeth": an early-phase study to assess the feasibility of an oral health intervention delivered by dental teams to parents of young children
Creators: name: Giles, Erin
name: K. A. Gray-Burrows
name: A. Bhatti
name: L. Rutter
name: J. Purdy
name: T. Zoltie
name: S. Pavitt
name: Z. Marshman
name: R. West
name: P. F. Day
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Additional file 1. “Strong Teeth” Self-Report Questionnaire.
Path-Sensitive Atomic Commit: Local Coordination Avoidance for Distributed Transactions
Creators: name: Soethout, Tim
name: van der Storm, Tijs
name: Vinju, Jurgen
Publisher: name: arXiv
Year: 2019
Subjects: subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: Programming Languages (cs.PL)
subject: Software Engineering (cs.SE)
subject: FOS: Computer and information sciences

description: Context: Concurrent objects with asynchronous messaging are an increasingly popular way to structure highly available, high performance, large-scale software systems. To ensure data-consistency and support synchronization between objects such systems often use distributed transactions with Two-Phase Locking (2PL) for concurrency control and Two-Phase commit (2PC) as atomic commitment protocol. Inquiry In highly available, high-throughput systems, such as large banking infrastructure, however, 2PL becomes a bottleneck when objects are highly contended, when an object is queuing a lot of messages because of locking. Approach: In this paper we introduce Path-Sensitive Atomic Commit (PSAC) to address this situation. We start from message handlers (or methods), which are decorated with pre- and post-conditions, describing their guards and effect. Knowledge: This allows the PSAC lock mechanism to check whether the effect of two incoming messages at the same time are independent, and to avoid locking if this is the case. As a result, more messages are directly accepted or rejected, and higher overall throughput is obtained. Grounding: We have implemented PSAC for a state machine-based DSL called Rebel, on top of a runtime based on the Akka actor framework. Our performance evaluation shows that PSAC exhibits the same scalability and latency characteristics as standard 2PL/2PC, and obtains up to 1.8 times median higher throughput in congested scenarios. Importance: We believe PSAC is a step towards enabling organizations to build scalable distributed applications, even if their consistency requirements are not embarrassingly parallel.
Flexibility in the Market for International Carbon Credits and Price Dynamics. Difference with European Allowances
Creators: name: Gavard, Claire
name: Kirat, Djamel
name: Gavard, Claire
name: Kirat, Djamel
Publisher: name: Unknown
Year: 2015
Subjects: subject: Environmental Economics and Policy
subject: Resource /Energy Economics and Policy
subject: European Allowances International Credits
subject: Emissions Trading
subject: Power Sector
subject: Time Series Analysis

description: We analyze the price dynamics of European allowances and international carbon credits in the second phase of the European carbon market. We develop and use a model combining fundamental drivers associated with the demand for quotas by installations and risk-return considerations related to the financial nature of carbon permits. We estimate it with autoregressive conditional heteroskedasticity models. Although carbon permits present some characteristics of financial assets, we find that an increased volatility is not associated with an increased return. The price of allowances and credits are explained by similar factors. However, whereas the corresponding returns present comparable dynamics, the long-term relationships between the price of these two types of permits and their drivers differ significantly. While the price of allowances is demand-driven, we suggest the existence of a supply-side effect for credits, and explain it by the flexibility in the related market. The impact of the European economic activity is less visible on credits than on allowances. The price elasticity of allowances with regards to the coal and gas prices is negative in time periods of low economic activity while it is positive in the rest of the time. We suggest an explanation for this dynamics difference.
Additional file 1 of Preoperative anxiety and its association with patients’ desire for support - an observational study in adults
Creators: name: Salzmann, Stefan
name: Rienmüller, Stephen
name: Kampmann, Stefan
name: Euteneuer, Frank
name: Rüsch, Dirk
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Additional file 1: German version of the Amsterdam Preoperative Anxiety and Information Scale (APAIS), (Part 4 of the questionnaire). Description: Wording of the validated German translation [11] of the English version of the APAIS published by Moerman and colleagues [9].
Caryocolum amaurella
Creators: name: Junnilainen, Jari
name: Karsholt, Ole
name: Nupponen, Kari
name: Kaitila, Jari-Pekka
name: Nupponen, Timo
name: Olschwang, Vladimir
Publisher: name: Zenodo
Year: 2010
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Lepidoptera
Gelechiidae
Caryocolum
Caryocolum amaurella

description: Caryocolum amaurella (M. Hering, 1924)
Arkaim 23.VII.1998; Moskovo 10.VII.1997, 11.VII.1998, 16.VII.2007. A total of 5 exx.
 Distribution. C and N Europe to the Ural Mountains. Outside Europe in Turkey.
 Remarks. This species is new to Russia.
description: Published as part of Junnilainen, Jari, Karsholt, Ole, Nupponen, Kari, Kaitila, Jari-Pekka, Nupponen, Timo & Olschwang, Vladimir, 2010, The gelechiid fauna of the southern Ural Mountains, part II: list of recorded species with taxonomic notes (Lepidoptera: Gelechiidae) 2367, pp. 1-68 in Zootaxa 2367 (1) on page 53, DOI: 10.11646/zootaxa.2367.1.1, http://zenodo.org/record/10093655
The white dwarf cooling sequence in the old open cluster NGC 188
Creators: name: Andreuzzi, Gloria
name: Richer, Harvey B.
name: Limongi, Marco
name: Bolte, Michael
Publisher: name: arXiv
Year: 2002
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We develop the white dwarf luminosity function (LF) of the old open cluster NGC 188 in order to determine a lower limit to the age of the cluster by using the faint end of the cooling sequence. To produce an extensive sequence of the cooling white dwarfs we imaged four contiguous HST-WFPC2 fields in the center of the cluster in the F555W and F814W filters. After imposing selection criteria on the detected objects we found a white dwarf cooling sequence (down to V ~26.5) including 28 candidate white dwarfs in the cluster. The exposures are not deep enough to reach the end of this sequence, but the results of our analysis allow us to establish a lower limit to the age of the cluster independently of the isochrone fit to the cluster turnoff. The most ancient white dwarfs found are ~4 Gyr old, an age that is set solely by the photometric limit of our data. Classical methods provide an estimate of \~7 Gyr (Sarajedini et al., 1999).
description: 6 pages, 5 figures, accepted on Astronomy and Astrophysics
Towards justifying computer algebra algorithms in Isabelle/HOL
Creators: name: Li, Wenda
Publisher: name: Apollo - University of Cambridge Repository
Year: 2019
Subjects: formal verification
theorem proving
Isabelle/HOL
computer algebra
cylindrical algebraic decomposition

description: As verification efforts using interactive theorem proving grow, we are in need of certified algorithms in computer algebra to tackle problems over the real numbers. This is important because uncertified procedures can drastically increase the size of the trust base and under- mine the overall confidence established by interactive theorem provers, which usually rely on a small kernel to ensure the soundness of derived results. This thesis describes an ongoing effort using the Isabelle theorem prover to certify the cylindrical algebraic decomposition (CAD) algorithm, which has been widely implemented to solve non-linear problems in various engineering and mathematical fields. Because of the sophistication of this algorithm, people are in doubt of the correctness of its implementation when deploying it to safety-critical verification projects, and such doubts motivate this thesis. In particular, this thesis proposes a library of real algebraic numbers, whose distinguishing features include a modular architecture and a sign determination algorithm requiring only rational arithmetic. With this library, an Isabelle tactic based on univariate CAD has been built in a certificate-based way: external, untrusted code delivers solutions in the form of certificates that are checked within Isabelle. To lay the foundation for the multivariate case, I have formalised various analytical results including Cauchy’s residue theorem and the bivariate case of the projection theorem of CAD. During this process, I have also built a tactic to evaluate winding numbers through Cauchy indices and verified procedures to count complex roots in some domains. The formalisation effort in this thesis can be considered as the first step towards a certified computer algebra system inside a theorem prover, so that various engineering projections and mathematical calculations can be carried out in a high-confidence framework.
Efficient algebraic solution for a time-dependent quantum harmonic oscillator
Creators: name: Tibaduiza, D. M.
name: Pires, L. B.
name: Szilard, D.
name: Rego, A. L. C.
name: Zarro, C. A. D.
name: Farina, C.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Using operator ordering techniques based on BCH-like relations of the su(1,1) Lie algebra and a time-splitting approach,we present an alternative method of solving the dynamics of a time-dependent quantum harmonic oscillator for any initial state. We find an iterative analytical solution given by simple recurrence relations that are very well suited for numerical calculations. We use our solution to reproduce and analyse some results from literature in order to prove the usefulness of the method and, based on these references, we discuss efficiency in squeezing, when comparing the parametric resonance modulation and the Janszky-Adam scheme.
description: 15 pages, 5 figures
PDAC single cell datasets integration and annotation for deconvolution
Creators: name: Lamothe, Lucie
name: Blum, Yuna
name: Kermezli, Yasmina
name: Richard, Magali
Publisher: name: Zenodo
Year: 2025
Subjects: subject: Pancreas
subject: Cancer
subject: Single-Cell Analysis
subject: Deconvolution
subject: Annotation

description: Poster for Bigre Days - Grenoble Feb 2025

Accuracy of bulk deconvolution algorithms to infer tumor composition is currently limited. A promissing approach consist of using single-cell referenced profiles for deconvolution. 

Here we present our work strategy to contribute to the creation of new robust single-cell reference profiles.
The Anglo-Dutch Imperial Meridian in the Indian Ocean World, 1795-1820
Creators: name: Wilson, James David
Publisher: name: Apollo - University of Cambridge Repository
Year: 2019
Subjects: Indian Ocean
British Empire
Dutch Empire
Global History
Nineteenth Century

description: What happened when the Dutch and British empires overlapped across the Indian Ocean in the late eighteenth century? Histories of these empires generally focus on their early modern rivalry through patterns of war and trade that subsided after Britain’s invasion of Dutch colonies during the French Revolutionary and Napoleonic Wars (1792-1815). Instead, this thesis unearths the relationship between Britain’s capture of three Dutch Indian Ocean colonies – Ceylon, Java, and the Cape Colony – and the rise of the modern state-building enterprises of the British empire. It traces a collection of Anglo-Dutch epistemic exchanges initiated in littoral spaces amid occupation, comprised of political ideas, such as liberalism and autocracy; policies of settlement and work; and cultural information tied to gender and status. These exchanges generated epistemic interdependencies between British and Dutch colonists, establishing new and intrusive ruling practices that shaped British governance while recycling models of colonialism and revolutionary change from the Dutch empire. I chart this history through contingent life histories describing people who travelled between the Cape, Java, and Ceylon. These include a Dutch teacher, whose involvement in republicanism and anti-slavery reveals that Dutch liberalism was used by Britain’s despots to extend their powers. I follow Chinese migrants who show how engagements between Chinese and British and Dutch colonists determined British policies of landholding and labour. I trace Dutch and British ruling elites who reveal that officials created migration regulations tied to Dutch notions of status. This is the period of C.A. Bayly’s ‘imperial meridian’, which describes the British empire’s transformation into garrison states in the Indian Ocean in answer to a global age of revolutions. Conversely, this thesis maps the rise of Britain’s empire over an Anglo-Dutch faultline linking the early modern and modern eras, revolutionary and counter-revolutionary practices, and the connections and conflicts of an Indian Ocean world.
description: Funded by grants from the Cambridge Home and EU Scholarship Scheme; Prince Consort Fund; Smuts Memorial Fund; and Cambridge History Faculty.
Caryocolum petryi
Creators: name: Junnilainen, Jari
name: Karsholt, Ole
name: Nupponen, Kari
name: Kaitila, Jari-Pekka
name: Nupponen, Timo
name: Olschwang, Vladimir
Publisher: name: Zenodo
Year: 2010
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Lepidoptera
Gelechiidae
Caryocolum
Caryocolum petryi

description: Caryocolum petryi (O. Hofmann, 1899)
Miass 26.VI.1997 (1♂); Verbljushka 10.IX.1998 (1♀). Genitalia slide H. Hendriksen 3996.
 Distribution. Scattered records from the Pyrenées, the Alps, Germany, Hungary and in northern Europe (Sweden, Finland, Latvia, Lithuania) to the Ural Mountains. Outside of Europe in Mongolia (Huemer 1989) and Siberia (Tuva).
 Remarks. This species in new to the European part of Russia.
description: Published as part of Junnilainen, Jari, Karsholt, Ole, Nupponen, Kari, Kaitila, Jari-Pekka, Nupponen, Timo & Olschwang, Vladimir, 2010, The gelechiid fauna of the southern Ural Mountains, part II: list of recorded species with taxonomic notes (Lepidoptera: Gelechiidae) 2367, pp. 1-68 in Zootaxa 2367 (1) on page 53, DOI: 10.11646/zootaxa.2367.1.1, http://zenodo.org/record/10093655
Additional file 2 of Preoperative anxiety and its association with patients’ desire for support - an observational study in adults
Creators: name: Salzmann, Stefan
name: Rienmüller, Stephen
name: Kampmann, Stefan
name: Euteneuer, Frank
name: Rüsch, Dirk
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Additional file 2: English version of the Amsterdam Preoperative Anxiety and Information Scale (APAIS). Wording of the English version of the APAIS published by Moerman and colleagues [9]. Items have to be rated by participants on a 1 (not at all) to 5 (extremely) Likert scale.
Quantifying expression variability in single-cell RNA sequencing data
Creators: name: Eling, Nils
Publisher: name: Apollo - University of Cambridge Repository
Year: 2019
Subjects: single-cell RNA sequencing
transcriptional noise
Bayesian statistics
spermatogenesis
immune system
ageing
T cells
regression

description: Transcriptional noise is an intrinsic feature of cell populations and plays a driving role in mammalian development, tissue homoeostasis and immune function. While expression heterogeneity, a phenotypic readout of transcriptional noise, has been broadly studied in prokaryotic model systems or by profiling individual genes, few whole-transcriptome studies in mammalian systems have been reported. The development of single-cell RNA sequencing technologies introduced powerful tools to investigate transcriptional differences between individual cells, therefore allowing the in-depth characterisation of expression variability. In this thesis, I computationally analysed single-cell RNA sequencing data to understand transcriptional variability and expanded a statistical model to avoid confounding effects when quantifying such variability. First, I profiled individual transcriptomes of CD4$^+$ T cells, identifying a global decrease in transcriptional variability upon immune activation. By extending this analysis across two sub-species of mice, I identified an evolutionarily conserved set of immune response genes for which transcriptional variability increases during ageing. I used a Bayesian modelling framework to quantify mean expression and transcriptional variability but due to a strong confounding effect between these two parameters, variability analysis was restricted to genes that are similarly expressed across the tested conditions. To address this problem, I extended the computational framework allowing the parallel assessment of changes in mean expression and variability. Within this Bayesian framework, I introduced a joint prior linking mean expression and variability parameters, which allowed a residual over-dispersion to be measured for each gene. This measure allowed me to statistically assess changes in variability even for genes with differences in mean expression between conditions. Finally, I applied the model to identify temporal changes in variability over the time-course of spermatogenesis. This unidirectional differentiation process involves several complex steps before mature sperm form from spermatogonial stem cells. When profiling changes in variability across this developmental time-course, peaks in variability are caused by rapid changes in gene expression along the differentiation trajectory. This thesis provides a deeper understanding of technical and biological factors that drive transcriptional variability and offers a basis for future research to characterise its role in health and disease.
description: Funding was provided via the EMBL international PhD programme
National Forest Programmes in Scandinavian Political Culture
Creators: name: Ollonqvist, Pekka
name: Hanninen, Harri
name: Ollonqvist, Pekka
name: Hanninen, Harri
Publisher: name: Unknown
Year: 2004
Subjects: subject: Environmental Economics and Policy
subject: Land Economics/Use
subject: corporatism
subject: forest policy programmes
subject: political culture.

description: National forest programme (NFP) as a new forest policy tool, was launched in the Rio Summit in 1992. It emphasizes participation, delegation and inter-sectoral coordination. The adaptation of these principles in the forest policy in Finland, Norway and Sweden are discussed in this paper. The stage of the NFP process in each of them is very different in spite of the common structural features in the political culture. Separate policy actions related to the identification of sustainable forest management were arranged in Finland (forest specific environmental program in 1994) and in Norway (Living Forests Program in 1998) whereas in Sweden a specific process has not been identifiable prior to Environmental Code 1999 and Quality Criteria. The compulsory process towards regional forest programs in Finland promoted delegation and regional participation. No NFP-specific revisions in delegation has been named in Norway or Sweden. The Finnish government had as incentive to start a participatory political process towards NFP in order to maintain and even increase public subsidies to timber management investments, whereas Norway and Sweden had already abandoned such subsidies.
Number of loops of size h in growing scale-free networks
Creators: name: Bianconi, Ginestra
name: Capocci, Andrea
Publisher: name: arXiv
Year: 2002
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: FOS: Physical sciences

description: The hierarchical structure of scale-free networks has been investigated focusing on the scaling of the number $N_h(t)$ of loops of size h as a function of the system size. In particular we have found the analytic expression for the scaling of $N_h(t)$ in the Barabási-Albert (BA) scale-free network. We have performed numerical simulations on the scaling law for $N_h(t)$ in the BA network and in other growing scale free networks, such as the bosonic network (BN) and the aging nodes (AN) network. We show that in the bosonic network and in the aging node network the phase transitions in the topology of the network are accompained by a change in the scaling of the number of loops with the system size.
description: 4 pages, 3 figures
Additional file 8 of Gut dysbiosis promotes prostate cancer progression and docetaxel resistance via activating NF-κB-IL6-STAT3 axis
Creators: name: Zhong, Weibo
name: Wu, Kaihui
name: Long, Zining
name: Zhou, Xumin
name: Zhong, Chuanfan
name: Wang, Shuo
name: Lai, Houhua
name: Guo, Yufei
name: Lv, Daojun
name: Lu, Jianming
name: Mao, Xiangming
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Ecology
subject: Science Policy
subject: Biological Sciences not elsewhere classified
subject: Cancer

description: Additional file 8. Sequencing data for fecal samples of both PCa patients and mice.
Hamiltonian regularisation of shallow water equations with uneven bottom
Creators: name: Clamond, Didier
name: Dutykh, Denys
name: Mitsotakis, Dimitrios
Publisher: name: arXiv
Year: 2019
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: Numerical Analysis (math.NA)
subject: Exactly Solvable and Integrable Systems (nlin.SI)
subject: Atmospheric and Oceanic Physics (physics.ao-ph)
subject: FOS: Physical sciences
subject: FOS: Mathematics
subject: 74J15 (primary), 74S10, 74J30 (secondary)

description: The regularisation of nonlinear hyperbolic conservation laws has been a problem of great importance for achieving uniqueness of weak solutions and also for accurate numerical simulations. In a recent work, the first two authors proposed a so-called Hamiltonian regularisation for nonlinear shallow water and isentropic Euler equations. The characteristic property of this method is that the regularisation of solutions is achieved without adding any artificial dissipation or ispersion. The regularised system possesses a Hamiltonian structure and, thus, formally preserves the corresponding energy functional. In the present article we generalise this approach to shallow water waves over general, possibly time-dependent, bottoms. The proposed system is solved numerically with continuous Galerkin method and its solutions are compared with the analogous solutions of the classical shallow water and dispersive Serre-Green-Naghdi equations. The numerical results confirm the absence of dispersive and dissipative effects in presence of bathymetry variations.
description: 11 pages, 4 figures, 1 table, 26 references, 1 appendix. Other author's papers can be downloaded at http://www.denys-dutykh.com/
Supplemental anayses & results from Phase synchronization varies systematically with linguistic structure composition
Creators: name: Brennan, Jonathan R.
name: Martin, Andrea E.
Publisher: name: The Royal Society
Year: 2019
Subjects: subject: Neuroscience
subject: 170299 Cognitive Science not elsewhere classified
subject: FOS: Psychology

description: Computation in neuronal assemblies is putatively reflected in the excitatory and inhibitory cycles of activation distributed throughout the brain. In speech and language processing, coordination of these cycles resulting in phase synchronization has been argued to reflect the integration of information on different timescales (e.g. segmenting acoustics signals to phonemic and syllabic representations; (Giraud and Poeppel 2012 Nat. Neurosci. 15, 511. (doi:10.1038/nn.3063)). A natural extension of this claim is that phase synchronization functions similarly to support the inference of more abstract higher-level linguistic structures (Martin 2016 Front. Psychol. 7, 120; Martin and Doumas 2017 PLoS Biol. 15, e2000663. (doi:10.1371/journal.pbio.2000663); Martin and Doumas. 2019 Curr. Opin. Behav. Sci. 29, 77–83. (doi:10.1016/j.cobeha.2019.04.008)). Hale et al. (Hale et al. 2018 Finding syntax in human encephalography with beam search. (http://arxiv.org/abs/1806.04127) showed that syntactically driven parsing decisions predict EEG responses in the time domain; here we ask whether phase synchronization in the form of either inter-trial phrase coherence or cross-frequency coupling (CFC) between high-frequency (i.e. gamma) bursts and lower-frequency carrier signals (i.e. delta, theta), changes as the linguistic structures of compositional meaning (viz., bracket completions, as denoted by the onset of words that complete phrases) accrue. We use a naturalistic story-listening EEG dataset from Hale et al. to assess the relationship between linguistic structure and phase alignment. We observe increased phase synchronization as a function of phrase counts in the delta, theta, and gamma bands, especially for function words. A more complex pattern emerged for CFC as phrase count changed, possibly related to the lack of a one-to-one mapping between ‘size’ of linguistic structure and frequency band—an assumption that is tacit in recent frameworks. These results emphasize the important role that phase synchronization, desynchronization, and thus, inhibition, play in the construction of compositional meaning by distributed neural networks in the brain.This article is part of the theme issue ‘Towards mechanistic models of meaning composition’.
Are Quantum Computing Models Realistic?
Creators: name: Kak, Subhash
Publisher: name: arXiv
Year: 2001
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The commonly used circuit model of quantum computing leaves out the problems of imprecision in the initial state preparation, particle statistics (indistinguishability of particles belonging to the same quantum state), and error correction (current techniques cannot correct all small errors). The initial state in the circuit model computation is obtained by applying potentially imprecise Hadamard gate operations whereas useful quantum computation requires a state with no uncertainty. We review some limitations of the circuit model and speculate on the question if a hierarchy of quantum-type computing models exists.
description: 9 pages with corrections
title: Self-assembling behaviour of the peptide hormone PYY3-36 and its lipidated conjugates for future applications in controlling satiety levels
Creators: name: Burholt, Samuel
Publisher: name: University of Reading
Year: 2021

description: Obesity is a global healthissue with nations struggling to deal with itstreatmentand economic impacts. Modified peptide hormones have already been shown to be effective at improving the treatment of other chronic conditions such as lymphoma or anaemia. However, peptide hormones, especially those targeted in treating obesity, are known to suffer from short drug lifetimes and thus requiring frequent administration. For the drug to take effect over a longer period requires a gel matrix-based drug carrier or a modification to the peptide itself. This thesis looks at how to use peptide modifications to potentially improve the delivery methods and efficacy of drugs used to control satiety levels. Anovel lipopeptide, based on Peptide Tyrosine-Tyrosine (PYY3-36), was characterised by using circular dichroism spectroscopy (CD), small angle X-ray scattering, critical aggregation concentration experiments, and cryo-TEM. Studies were completed to investigate the secondary structures and the self-assembly processes over a range of physiological pHs and temperatures. While native PYY3-36failedto form gels, PYY lipopeptides formed into gels with elongated fibre-like structures with a secondary structural change from α-helical to β-sheet. Gels formed from natural peptides and water offer the potential for a highly biocompatible gel with a slow release profile. Using the same analytical techniques, the thesis goes on to investigate co-aggregation of PYY3-36with β-cyclodextrin to establish if this common low-cost drug carrier can be used as an alternative delivery method. The results showed that β-cyclodextrin did show aggregation around the twisted sheet structure of the self-assembled PYY3-36butdidnot show co-assembly or encapsulation, rendering it ineffective as a delivery mechanism. Lipidated PYY3-36was mixed with lipopolysaccharide (LPS), providing some insight into how lipidated PYY3-36 could interact with amphiphilic molecules such as bacteria endotoxins. The results show that LPS do co-assemble with lipidated PYY3-36,however, unexpectedly the lipidated PYY3-36 elongated fibre structure remains largely unchanged following the co-assembly. The implications of this observation warrant further analysis. Ultimately, the findings of this thesis could be applied to the development of drug formulations for other conditions, such as lymphoma or anaemia, which would benefit from the lipidation of large peptides that enable slow release mechanisms. Additionally, the results within this thesis add knowledge to the fundamental research of self-assembly and clarifies the effects of lipidation on larger peptides that allow gelation to occur.
Caryocolum repentis Huemer & Luquet 1992
Creators: name: Junnilainen, Jari
name: Karsholt, Ole
name: Nupponen, Kari
name: Kaitila, Jari-Pekka
name: Nupponen, Timo
name: Olschwang, Vladimir
Publisher: name: Zenodo
Year: 2010
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Lepidoptera
Gelechiidae
Caryocolum
Caryocolum repentis

description: Caryocolum repentis Huemer & Luquet, 1992
Arkaim 09.VII.1997 (1♂).
 Distribution. C Europe (the Alps), Spain, Russia (S Ural).
 Remarks. This species is new to Russia.
description: Published as part of Junnilainen, Jari, Karsholt, Ole, Nupponen, Kari, Kaitila, Jari-Pekka, Nupponen, Timo & Olschwang, Vladimir, 2010, The gelechiid fauna of the southern Ural Mountains, part II: list of recorded species with taxonomic notes (Lepidoptera: Gelechiidae) 2367, pp. 1-68 in Zootaxa 2367 (1) on page 53, DOI: 10.11646/zootaxa.2367.1.1, http://zenodo.org/record/10093655
Cosmological constraints from the redshift dependence of the Alcock-Paczynski effect: Possibility of estimateing the non-linear systematics using fast simulations
Creators: name: Ma, Qinglin
name: Guo, Yiqing
name: Li, Xiao-Dong
name: Wang, Xin
name: Miao, Haitao
name: Li, Zhigang
name: Sabiu, Cristiano G.
name: Park, Hyunbae
Publisher: name: arXiv
Year: 2019
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: The tomographic AP method is so far the best method in separating the Alcock-Paczynski (AP) signal from the redshift space distortion (RSD) effects and deriving powerful constraints on cosmological parameters using the $\lesssim40h^{-1}\ \rm Mpc$ clustering region. To guarantee that the method can be easily applied to the future large scale structure (LSS) surveys, we study the possibility of estimating the systematics of the method using fast simulation method. The major contribution of the systematics comes from the non-zero redshift evolution of the RSD effects, which is quantified by $\hatξ_{Δs}(μ,z)$ in our analysis, and estimated using the BigMultidark exact N-body simulation and approximate COLA simulation samples. We find about 5\%/10\% evolution when comparing the $\hatξ_{Δs}(μ,z)$ measured as $z=0.5$/$z=1$ to the measurements at $z=0$. We checked the inaccuracy in the 2pCFs computed using COLA, and find it 5-10 times smaller than the intrinsic systematics of the tomographic AP method, indicating that using COLA to estimate the systematics is good enough. Finally, we test the effect of halo bias, and find $\lesssim$1.5\% change in $\hatξ_{Δs}$ when varying the halo mass within the range of $2\times 10^{12}$ to $10^{14}$ $M_{\odot}$. We will perform more studies to achieve an accurate and efficient estimation of the systematics in redshift range of $z=0-1.5$.
description: 13 pages, 6 figures. Accepted to ApJ
The Use of Social Network Tools in Iran and the Impact of Improper Communication and Trancparency of Informatio Security and Privacy
Creators: name: Shaghaghi, Arash
name: Bigham, Bahram Sadeghi
Publisher: name: figshare
Year: 2021
Subjects: subject: 10299 Applied Mathematics not elsewhere classified
subject: FOS: Mathematics
subject: Applied Computer Science
subject: Theoretical Computer Science

description: The Use of Social Network Tools in Iran and the Impact of Improper Communication and Trancparency of Informatio Security and Privacy
TIL O'RGANISHDAGI PSIXOLOGIK OMILLAR
Creators: name: Ramazonova, F.A.
name: G'ulomjonova, D.F.
Publisher: name: Zenodo
Year: 2025

description: Ushbu maqolada til o'rganishga ta'sir qiluvchi psixologik omillar, jumladan, motivatsiya, xavotir, kognitiv rivojlanish, o'ziga bo'lgan ishonch va ijtimoiy omillar ahamiyati tahlil qilingan. Til o'rganish nafaqat so'zlar va grammatik qoidalarni o'rganish jarayoni, balki bu jarayon insonning psixologik holati, his-tuyg'ulari, e'tibori va motivatsiyasi bilan chambarchas bog'liqdir. Motivatsiya, ichki va tashqi motivatsiya, o'quvchilarning til o'rganishga bo'lgan qiziqish va ishtiyoqini saqlashda muhim rol o'ynaydi. Xavotir esa o'quvchilarni tilni erkin ishlatishdan tortinib, til o'rganish jarayonini sekinlashtirishi mumkin. Piaget va Vygotsky kabi mutaxassislarning kognitiv rivojlanish nazariyalari, o'quvchilarning intellektual qobiliyatlari til o'rganish muvaffaqiyatiga qanday ta'sir qilishini tushuntiradi[1]. Shuningdek, o'ziga bo'lgan ishonch til o'rganishda muhim omil sifatida ajralib turadi, bu o'quvchilarga qiyinchiliklarni yengib o'tishga va o'rganish jarayonida faol ishtirok etishga yordam beradi. Maqola, psixologik omillarni tushunishning o'quvchilarning til o'rganishidagi muvaffaqiyatini oshirish va samarali ta'lim strategiyalarini ishlab chiqishda qanday yordam berishini ta'kidlaydi.

[1]  Gardner, R. C., & Lambert, W. E. (1972). Attitudes and Motivation in Second-Language Learning. Rowley, MA: Newbury House.
Odd- and even-denominator fractional quantum Hall states in monolayer WSe$_2$
Creators: name: Shi, Qianhui
name: Shih, En-Min
name: Gustafsson, Martin V.
name: Rhodes, Daniel A.
name: Kim, Bumho
name: Watanabe, Kenji
name: Taniguchi, Takashi
name: Papić, Zlatko
name: Hone, James
name: Dean, Cory R.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Monolayer (ML) semiconducting transition-metal dichalcogenides (TMDs) represent a unique class of two-dimensional (2D) electron systems. Their atomically thin structure -- just like graphene -- facilitates gate-tunability, while the sizable band gap and strong spin-orbit coupling hold promise for properties beyond graphene. Measurements under large magnetic fields have revealed an unusual LL structure, distinct from other 2D electron systems. However, owing to limited sample quality and poor electrical contact, probing the lowest Landau levels (LLs) has been challenging, and observation of electron correlations within the fractionally filled LLs regime has not been possible. Here, through bulk electronic compressibility measurements, we investigate the LL structure of ML WSe$_2$ in the extreme quantum limit, and observe fractional quantum Hall (FQH) states in the lowest three LLs. The odd-denominator FQH sequences demonstrate a systematic evolution with the LL orbital index, which has not been observed in any other system but is consistent with generic theoretical expectations. In addition, we observe an even-denominator state in the second LL that is expected to host non-Abelian statistics. Our results suggest that the 2D semiconductors can provide an experimental platform that closely resembles idealized theoretical models in the quantum Hall regime.
description: typos in v1 corrected
Infrared Space Observatories: How to Mitigate Zodiacal Dust Intereference
Creators: name: Gurfil, P.
name: Kasdin, J.
name: Arrell, R.
name: Seager, S.
name: Nissanke, S. M.
Publisher: name: arXiv
Year: 2001
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: (Abridged) Out-of-the-ecliptic trajectories that are beneficial to space observatories such as the Terrestrial Planet Finder and other potential mid-IR missions are introduced. These novel trajectories result in significantly reduced background noise from the zodiacal dust radiation and therefore allow a reduction in telescope collecting area and hence cost. Two types of optimal trajectories that are energetically feasible were derived using genetic algorithms. These are highly inclined non-Keplerian heliocentric orbits. The first optimal trajectory can use existing launch technology and the zodiacal brightness for this trajectory is reduced by at least 50% for 60% of the mission lifetime. The second optimal trajectory requires planned improvement in launch technology but it renders a zodiacal cloud brightness reduction by at least 70% for 82% of the mission lifetime. Heliocentric orbits at 5 AU have been discussed because the zodiacal dust concentration is extremely low there and the energy requirements to reach these trajectories are low if gravitational assists can be used. Unfortunately such orbits are impractical because of high cost, power source constraints (inability to use solar cells), communication delays, and a long travel time before data return. Additionally, the energy requirements to reach our low and high energy optimal trajectories are respectively half as much and equivalent to a direct trip to 5AU with no planetary gravitational assists.
description: submitted to ApJ, 24 pages incl. 12 figures