cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Cost-effectiveness analysis of bimekizumab for the treatment of active psoriatic arthritis in Sweden
Creators: name: Sigurdardottir, Valgerdur
name: Engstrom, Anna
name: Berling, Patric
name: Olofsson, Tor
name: Oldsberg, Linnea
name: Sadler, Susannah
name: Parra, Devian
name: Melis, Lode
name: Willems, Damon
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Medicine
subject: Pharmacology
subject: Biotechnology
subject: Ecology
subject: FOS: Biological sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Science Policy

description: To evaluate the cost-effectiveness of bimekizumab, an inhibitor of IL-17F and IL-17A, against biologic and targeted synthetic disease-modifying antirheumatic drugs (DMARD) for psoriatic arthritis (PsA) from the Swedish healthcare system perspective. A Markov model was developed to simulate the clinical pathway of biologic [b] DMARD-naïve or tumor necrosis factor inhibitor experienced [TNFi-exp] PsA patients over a lifetime horizon. Treatment response was incorporated as achievement of the American College of Rheumatology 50% (ACR50) and Psoriasis Area and Severity Index 75% (PASI75) response, and changes in the Health Assessment Questionnaire-Disability Index (HAQ-DI) score. The efficacy of bimekizumab was obtained from the BE OPTIMAL (bDMARD-naïve) and BE COMPLETE (TNFi-experienced) trials while a network meta-analysis (NMA) informed the efficacy of the comparators. Resource use and drug costs were obtained from published studies and databases of drug retail prices in Sweden. A willingness-to-pay threshold of €50,000 per quality-adjusted life year (QALY) was applied. In bDMARD-naïve patients, bimekizumab achieved greater QALYs (14.08) than with all comparators except infliximab (14.22), dominated guselkumab every 4 and 8 weeks, ixekizumab, secukinumab 300 mg, ustekinumab 45 mg and 90 mg, and was cost-effective against risankizumab, tofacitinib, upadacitinib and TNFis, except adalimumab biosimilar. In TNFi-experienced patients, bimekizumab led to greater QALYs (13.56) than all comparators except certolizumab pegol (13.84), and dominated ixekizumab and secukinumab 300 mg while being cost-effective against all other IL-17A-, IL-23- and JAK inhibitors. An NMA informed the comparative effectiveness estimates. Given gaps in evidence of disease management and indirect costs specific to HAQ-DI scores, and sequential clinical trial evidence in PsA, non-PsA cost data from similar joint conditions were used, and one line of active treatment followed by best supportive care was assumed. Bimekizumab was cost-effective against most available treatments for PsA in Sweden, irrespective of prior TNFi exposure
"Sloppy" nuclear energy density functionals (II): Finite nuclei
Creators: name: Nikšić, Tamara
name: Imbrišak, Marko
name: Vretenar, Dario
Publisher: name: arXiv
Year: 2017
Subjects: subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: A study of parameter sensitivity of nuclear energy density functionals, initiated in the first part of this work \cite{NV.16}, is extended by the inclusion of data on ground-state properties of finite nuclei in the application of the manifold boundary approximation method (MBAM). Density functionals used in self-consistent mean-field calculations, and nuclear structure models based on them, are generally "sloppy" and exhibit an exponential range of sensitivity to parameter variations. Concepts of information geometry are used to identify the presence of effective functionals of lower dimension in parameter space associated with parameter combinations that can be tightly constrained by data. The MBAM is used in an iterative procedure that systematically reduces the complexity and the dimension of parameter space of a sloppy functional, with properties of nuclear matter and data on finite nuclei determining not only the values of model parameters, but also the optimal functional form of the density dependence.
description: Accepted for publication in Physical Review C. arXiv admin note: text overlap with arXiv:1606.08617
Mari nawi ("big canoes"): Aboriginal voyagers in Australia's maritime history, 1788-1855
Creators: name: Smith, Keith Vincent
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: The English ships that came into Port Jackson in 1788 changed the lives of the Indigenous People forever. Theirs was a canoe culture and saltwater, as much as the land, was their natural habitat. The alien invaders dispossessed them of their land and brought the smallpox virus that, within two years, killed more than half the original population. -- Driven by the will to survive, many among the surviving Aborigines proved to be resilient. In an unexpected way, the English ships would enable them to adapt to the new reality and to make the transition from bark canoes to ocean-going ships. -- This thesis charts the life experiences of those who remade their lives and played a significant role in Australia's early maritime history, actively assisting the colonists to explore and settle their own country. -- The study focus is on Indigenous People who sailed through Port Jackson in the period 1788-1855. It brings to the foreground men and women whose contribution has never been properly acknowledged, adding the names of some 65 Aboriginal voyagers from Port Jackson, Botany Bay and the Hawkesbury and Shoalhaven rivers to our shared history. -- They would become boatmen, sailors, sealers, whalers and pilots, guides, go-betweens and trackers, valued for their skills and knowledge. Their assistance and cooperation contributed to the fledgling colonial economy. In later years some were officially created 'chiefs' and given land grants, fishing boats and gorgets. -- They were present at critical events as they followed the expanding geography of exploration and the establishment of settlements like Newcastle, Hobart and Melbourne. -- Some, like Bennelong and Bungaree, are famous, but the majority are unknown. -- This work is the result of three years of research, following a paper trail of scattered primary documents: ship's musters, logs, official journals and despatches, petitions, shipping arrival and departures records, shipping news and Claims and Demand notices. It draws on oral, linguistic, pictorial, anthropological and genealogical evidence. -- Fresh research has clarified some historical facts and corrected some longstanding errors.
Enhanced Structural Stability and Photo Responsiveness of CH3NH3SnI3 Perovskite via Pressure-Induced Amorphization and Recrystallization
Creators: name: Lü, Xujie
name: Wang, Yonggang
name: Stoumpos, Constantinos C.
name: Hu, Qingyang
name: Guo, Xiaofeng
name: Chen, Haijie
name: Yang, Liuxiang
name: Smith, Jesse S.
name: Yang, Wenge
name: Zhao, Yusheng
name: Xu, Hongwu
name: Kanatzidis, Mercouri G.
name: Jia, Quanxi
Publisher: name: arXiv
Year: 2016
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: An organic-inorganic halide perovskite of CH3NH3SnI3 with significantly improved structural stability is obtained via pressure-induced amorphization and recrystallization. In situ high-pressure resistance measurements reveal an increased electrical conductivity by 300% in the pressure-treated perovskite. Photocurrent measurements also reveal a substantial enhancement in visible-light responsiveness. The mechanism underlying the enhanced properties is demonstrated to be associated with the improved structural stability.
Semi-local Exchange Energy Functional For Two-Dimensional Quantum Systems: A Step Beyond Generalized Gradient Approximations
Creators: name: Jana, Subrata
name: Samal, Prasanjit
Publisher: name: arXiv
Year: 2017
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Semi-local density functionals for the exchange-correlation energy of electrons are extensively used as it produce realistic and accurate results for finite and extended systems. The choice of techniques play crucial role in constructing such functionals of improved accuracy and efficiency. An accurate and efficient semi-local exchange energy functional in two dimensions is constructed by making use of the corresponding hole based on the density matrix expansion. The exchange hole involved is localized under the generalized coordinate transformation and satisfies all the relevant constraints. Comprehensive testing and excellent performance of the functional is demonstrated versus exact exchange results. The functional also achieves remarkable accuracy by substantially reducing the errors present in the local and non-empirical density functionals proposed so far for two dimensional systems. The underlying principles involved in the functional construction are physically appealing and practically useful for developing range separated and non-local functionals in two dimensions.
description: 6 pages, 3 figures
Additional file 6: Figure S6. of Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel sequencing
Creators: name: MacConaill, Laura
name: Burns, Robert
name: Anwesha Nag
name: Coleman, Haley
name: Slevin, Michael
name: Giorda, Kristina
name: Light, Madelyn
name: Lai, Kevin
name: Jarosz, Mirna
name: McNeill, Matthew
name: Ducar, Matthew
name: Meyerson, Matthew
name: Thorner, Aaron
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Science Policy
subject: Hematology

description: Schematic of the experiment used to measure adapter contamination and multiplexed capture index hopping. Replicate libraries were prepared using 16 unique dual-matched UMI adapters and enriched with the IDT xGen AML Cancer Panel in pools of 1, 4, 8, and 16. Each multiplexing experiment was sequenced on separate Illumina NextSeq runs. (PDF 819 kb)
Quantifying the Total Effect of Edge Interventions in Discrete Multistate Networks
Creators: name: Murrugarra, David
name: Dimitrova, Elena
Publisher: name: arXiv
Year: 2019
Subjects: subject: Molecular Networks (q-bio.MN)
subject: FOS: Biological sciences

description: Developing efficient computational methods to assess the impact of external interventions on the dynamics of a network model is an important problem in systems biology. This paper focuses on quantifying the global changes that result from the application of an intervention to produce a desired effect, which we define as the total effect of the intervention. The type of mathematical models that we will consider are discrete dynamical systems which include the widely used Boolean networks and their generalizations. The potential interventions can be represented by a set of nodes and edges that can be manipulated to produce a desired effect on the system. We use a class of regulatory rules called nested canalizing functions that frequently appear in published models and were inspired by the concept of canalization in evolutionary biology. In this paper, we provide a polynomial normal form based on the canalizing properties of regulatory functions. Using this polynomial normal form, we give a set of formulas for counting the maximum number of transitions that will change in the state space upon an edge deletion in the wiring diagram. These formulas rely on the canalizing structure of the target function since the number of changed transitions depends on the canalizing layer that includes the input to be deleted. We also present computations on random networks to compare the exact number of changes with the upper bounds provided by our formulas. Finally, we provide statistics on the sharpness of these upper bounds in random networks.
description: 10 pages, 8 figures
Charity and the letters of Barsanuphius and John of Gaza
Creators: name: Choi, Hyung Guen
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: This dissertation examines the Letters of Barsanuphius and John in order to analyse their view of charity (giving gifts, welcoming strangers and caring for the sick), as well as the relationship between the Gazan advisors, wealth and benefactors. First of all, we investigate the Gazan holy men's attitude towards giving gifts to the poor. They primarily advise their lay interlocutors to get involved in giving gifts by mentioning the spiritual rewards available. However, they do impose some limitations on monastic giving; they suggest only mature monks participate in such giving in order to protect the younger monastic disciples from distractions that might interrupt their ascetic lives. Episcopal leaders are also expected to protect their congregations from outside officials, performing their role as guides and protectors. With regard to entertaining strangers, the respected Gazan elders place a great deal of emphasis on hospitality within the scope of one's own personal ability. Furthermore, they recommend different levels of hospitality in proportion to the status of recipients, as well as charity with discernment. They suggest that their interlocutors do what they can to help the destitute, taking into consideration their physical, material and psychological needs. However, just as with the giving of charity, the main focus of John and Barsanuphius is not the poor themselves, but rather the care of their own lay and monastic followers. The last charitable activity which we investigate in this thesis is caring for the sick. Both Barsanuphius and John generally encourage their lay patients to seek cures for their illnesses with contemporary medical care and practices. However, they do take a somewhat ambivalent attitude towards monastic patients. While they permit some sick monks to use vii medical facilities and nursing care to cure their illnesses, they also encourage others to endure bodily suffering in order to obtain spiritual profit.Overall, Barsanuphius and John require their lay and monastic disciples to perform charity in different ways. While they do consider the beneficiaries, their spiritual direction is basically concentrated on the benefactors, in particular, their spiritual and ascetic wellbeing. This spiritual direction is related to their self-understanding as spiritual fathers, meditators and intercessors as well as defenders.
General Finnish DMP guidance
Creators: name: Tuuli-Project
Publisher: name: Zenodo
Year: 2018

description: National guidance and questions that assist with data management planning have been updated in 28.11.2018. A group of experts co-operated in writing the guidance. The members of the group came from Finnish universities, research institutions and The Academy of Finland. The work was coordinated by Tuuli office, which is funded (2015-2018) by Ministry in Education and Culture. The questions and guidance have been modified based on user feedback to make them more explicit and easier to understand. The questions and guidance will be updated annually in the future as well. As the expertise of the users increases it would be useful that the structure of the guidance stays the same. From 2019 the Finnish national guidance follows the Core Requirements for Data management Plans launched by Science Europe. (1)  The guidance is in English, Finnish and Swedish. The guidance has been composed in the national Tuuli-project. https://wiki.helsinki.fi/x/g5w6Cg References (1) Science Europe, (2018) Practical Guide to the International Alignment of Research Data Managemen, https://www.scienceeurope.org/wp-content/uploads/2018/12/SE_RDM_Practical_Guide_Final.pdf
Improving RNA secondary structure prediction via state inference with deep recurrent neural networks
Creators: name: Willmott, Devin
name: Murrugarra, David
name: Ye, Qiang
Publisher: name: arXiv
Year: 2019
Subjects: subject: Biomolecules (q-bio.BM)
subject: FOS: Biological sciences
subject: 92

description: The problem of determining which nucleotides of an RNA sequence are paired or unpaired in the secondary structure of an RNA, which we call RNA state inference, can be studied by different machine learning techniques. Successful state inference of RNA sequences can be used to generate auxiliary information for data-directed RNA secondary structure prediction. Bidirectional long short-term memory (LSTM) neural networks have emerged as a powerful tool that can model global nonlinear sequence dependencies and have achieved state-of-the-art performances on many different classification problems. This paper presents a practical approach to RNA secondary structure inference centered around a deep learning method for state inference. State predictions from a deep bidirectional LSTM are used to generate synthetic SHAPE data that can be incorporated into RNA secondary structure prediction via the Nearest Neighbor Thermodynamic Model (NNTM). This method produces predicted secondary structures for a diverse test set of 16S ribosomal RNA that are, on average, 25 percentage points more accurate than undirected MFE structures. These improvements range from several percentage points for some sequences to nearly 50 percentage points for others. Accuracy is highly dependent on the success of our state inference method, and investigating the global features of our state predictions reveals that accuracy of both our state inference and structure inference methods are highly dependent on the similarity of the sequence to the dataset. This paper presents a deep learning state inference tool, trained and tested on 16S ribosomal RNA. Converting these state predictions into synthetic SHAPE data with which to direct NNTM can result in large improvements in secondary structure prediction accuracy, as shown on a test set of 16S rRNA.
description: 15 pages, 3 figures, and 5 tables
Cost-effectiveness of NT-proBNP-supported screening of chronic heart failure in patients with or without type 2 diabetes in Austria and Switzerland
Creators: name: Walter, Evelyn
name: Arrigo, Mattia
name: Allerstorfer, Sigrid
name: Marty, Petra
name: Hülsmann, Martin
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Cancer
subject: Mental Health
subject: Hematology

description: Heart failure (HF) is a clinical syndrome with a global burden. Signs and symptoms of HF are nonspecific and often shared with other conditions. The N-terminal prohormone of brain natriuretic peptide (NT-proBNP) serves as a useful biomarker for the diagnosis of HF not only in patients with acute symptoms but also in outpatients with an ambiguous clinical presentation. The aim of the analysis is to evaluate the cost-effectiveness of implementing NT-proBNP in the diagnostic algorithm in patients with/without type 2 diabetes mellitus (T2DM), compared with a diagnosis based primarily on clinical signs or symptoms from the perspective of the Austrian and Swiss healthcare system. A time-discrete Markov model was developed to simulate the effect/improvement (lifetime-costs, quality-adjusted life-years [QALYs], and life-years [LYs]) due to an NT-proBNP screening in undetected HF patients. Undetected HF patients are included in the model according to a distribution of New York Heart Association (NYHA) classes. The model considers disease progression by transition of NYHA classes. Undetected patients may remain undetected or be detected with the help of NT-proBNP or symptoms. Patients with known HF exhibit a slower disease progression. The probability of dying is influenced by the respective NYHA class. Direct costs (2021 € or CHF) were derived from published sources. QALYs, LYs, and costs were discounted (3% p.a.). In the per-patient analysis (at age 60 over lifetime), the incremental cost–utility ratio (ICUR)/QALY of NT-proBNP vs. no screening was €3,042 for HF patients in Austria. Considering the total cohort of undetected HF patients (n = 9,377) with the corresponding age structure over a lifetime, the ICUR increases to €4,356. In Switzerland, the per-patient results show an ICUR of CHF 897. Considering the total cohort of undetected HF patients (n = 6,826) the ICUR amounts to CHF 4,513. If indirect costs are considered, NT-proBNP screening becomes the dominant strategy in both countries. Overall, the analysis concludes that screening with NT-proBNP is a highly cost-effective or cost-saving diagnostic option for patients with HF, and a sensitivity analysis confirmed these findings.
Localized dark solitons and vortices in defocusing media with spatially inhomogeneous nonlinearity
Creators: name: Zeng, Jianhua
name: Malomed, Boris A.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Pattern Formation and Solitons (nlin.PS)
subject: Optics (physics.optics)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Recent studies have demonstrated that defocusing cubic nonlinearity with local strength growing from the center to the periphery faster than $r^{D}$, in space of dimension $D$ with radial coordinate $r$, supports a vast variety of robust bright solitons. In the framework of the same model, but with a weaker spatial-growth rate, $\sim r^{α}$ with $α\leq D$, we here test the possibility to create stable\textit{\ localized continuous waves} (LCWs) in one- and two-dimensional (1D and 2D) geometries, \textit{% localized dark solitons} (LDSs) in 1D, and \textit{localized dark vortices} (LDVs) in 2D, which are all realized as loosely confined states with a divergent norm. Asymptotic tails of the solutions, which determine the divergence of the norm, are constructed in a universal analytical form by means of the Thomas-Fermi approximation (TFA). Global approximations for the LCWs, LDSs, and LDVs are constructed on the basis of interpolations between analytical approximations available far from (TFA) and close to the center. In particular, the interpolations for the 1D LDS, as well as for the 2D LDVs, are based on a \textquotedblleft deformed-tanh" expression, which is suggested by the usual 1D dark-soliton solution. In addition to the 1D fundamental LDSs with the single notch, and 2D vortices with $S=1$, higher-order LDSs with multiple notches are found too, as well as double LDVs, with $S=2$. Stability regions for the modes under the consideration are identified by means of systematic simulations, the LCWs being completely stable in 1D and 2D, as they are ground states in the corresponding settings. Basic evolution scenarios are identified for those vortices which are unstable. The settings considered in this work may be implemented in nonlinear optics and in Bose-Einstein condensates.
description: 9 pages,9 figures,Physical Review E, in press
Synchronicity phenomenon in cluster patterns
Creators: name: Nakanishi, Tomoki
Publisher: name: arXiv
Year: 2019
Subjects: subject: Rings and Algebras (math.RA)
subject: FOS: Mathematics

description: It has been known that several objects such as cluster variables, coefficients, seeds, and $Y$-seeds in different cluster patterns with common exchange matrices share the same periodicity under mutations. We call it synchronicity phenomenon in cluster patterns. In this expository note we explain the mechanism of synchronicity based on several fundamental results on cluster algebra theory such as separation formulas, sign-coherence, Laurent positivity, duality, and detropicalization obtained by several authors. We also show that all synchronicity properties studied in this paper are naturally extended to cluster patterns of generalized cluster algebras, up to the Laurent positivity conjecture.
description: v1: 21pages; v2: 22 pages, references added, minor changes, v3: 23 pages, Sec. 4.1, 5.1, 5.2 revised, Sec.5.6 added, +minor changes, v4: 39 pages, major revision, Part II for generalized cluster algebras added
The complete sequence of chloroplast genome of Baeckea frutescens Linaeus 1753 (Myrtoideae), a traditional folk medicinal plant
Creators: name: Ling, Chengcheng
name: Zhang, Menglei
name: Ma, Wenwen
name: Liu, Menyu
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Plant Biology

description: Baeckea frutescens Linaeus 1753, as a traditional folk medicine in South East Asia, possesses sesquiterpenes, phloroglucinols, chromones, and essential oil, and is utilized for traditional Chinese medicinal purposes. The genetic diversity of the plant must be better understood, considering its significance. The complete chloroplast (cp) genome of B. frutescens was sequenced and assembled by using Illumina paired-end data, marking a significant advancement toward comprehending its genetic composition. The complete cp genome is 158,939 bp in length and contains 128 genes, consisting of 83 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. Phylogenetic analyses indicated that B. frutescens and other the 13 were clustered to the family of Myrtaceae. These findings are crucial for the conservation and utilization of this important plant species. Additionally, they underscore the potential for future research on the evolution and preservation of B. frutescens, which could be advantageous in pharmaceutical applications.
Menger curvatures and $C^{1,α}$ rectifiability of measures
Creators: name: Ghinassi, Silvia
name: Goering, Max
Publisher: name: arXiv
Year: 2019
Subjects: subject: Metric Geometry (math.MG)
subject: Classical Analysis and ODEs (math.CA)
subject: FOS: Mathematics
subject: 28A75, 28A12

description: We further develop the relationship between $β$-numbers and discrete curvatures to provide a new proof that under weak density assumptions, finiteness of the pointwise discrete curvature $\operatorname{curv}^α_{μ;2}(x,r)$ at $μ$- a.e. $x \in \mathbb{R}^{m}$ implies that $μ$ is $C^{1,α}$ $n$-rectifiable.
description: To appear in Archiv der Mathematik
Additional file 1: Table S1. of Gene-trait matching across the Bifidobacterium longum pan-genome reveals considerable diversity in carbohydrate catabolism among human infant strains
Creators: name: Arboleya, Silvia
name: Bottacini, Francesca
name: OâConnell-Motherway, Mary
name: C. Ryan
name: R. Ross
name: Sinderen, Douwe Van
name: Stanton, Catherine
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 60506 Virology

description: Bifidobacterium longum genomes publicly available used for different analysis along the study. Table S2. EC annotation numbers of the in silico glycosyl hydrolases predicted. Table S3. Carbohydrates used for in vitro assays. (DOC 152Â kb)
Tomogram-based comparison of geostatistical models: Application to the MAcro-Dispersion Experiment (MADE) site
Creators: name: Linde, N.
name: Lochbühler, T.
name: Dogan, M.
name: Van Dam, R. L.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Geophysics (physics.geo-ph)
subject: FOS: Physical sciences

description: We propose a new framework to compare alternative geostatistical descriptions of a given site. Multiple realizations of each of the considered geostatistical models and their corresponding tomograms (based on inversion of noise-contaminated simulated data) are used as a multivariate training image. The training image is scanned with a direct sampling algorithm to obtain conditional realizations of hydraulic conductivity that are not only in agreement with the geostatistical model, but also honor the spatially varying resolution of the site-specific tomogram. Model comparison is based on the quality of the simulated geophysical data from the ensemble of conditional realizations. The tomogram in this study is obtained by inversion of cross-hole ground-penetrating radar (GPR) first-arrival travel time data acquired at the MAcro-Dispersion Experiment (MADE) site in Mississippi (USA). Various heterogeneity descriptions ranging from multi-Gaussian fields to fields with complex multiple-point statistics inferred from outcrops are considered. Under the assumption that the relationship between porosity and hydraulic conductivity inferred from local measurements is valid, we find that conditioned multi-Gaussian realizations and derivatives thereof can explain the crosshole geophysical data. A training image based on an aquifer analog from Germany was found to be in better agreement with the geophysical data than the one based on the local outcrop, which appears to under-represent high hydraulic conductivity zones. These findings are only based on the information content in a single resolution-limited tomogram and extending the analysis to tracer or higher resolution surface GPR data might lead to different conclusions (e.g., that discrete facies boundaries are necessary).
Eigenvalues and dynamical degrees of self-maps on abelian varieties
Creators: name: Hu, Fei
Publisher: name: arXiv
Year: 2019
Subjects: subject: Algebraic Geometry (math.AG)
subject: Dynamical Systems (math.DS)
subject: FOS: Mathematics
subject: 14G17, 14K05, 16K20

description: Let $X$ be a smooth projective variety over an algebraically closed field, and $f\colon X\to X$ a surjective self-morphism of $X$. The $i$-th cohomological dynamical degree $χ_i(f)$ is defined as the spectral radius of the pullback $f^{*}$ on the étale cohomology group $H^i_{\textrm{ét}}(X, \mathbf{Q}_\ell)$ and the $k$-th numerical dynamical degree $λ_k(f)$ as the spectral radius of the pullback $f^{*}$ on the vector space $\mathsf{N}^k(X)_{\mathbf{R}}$ of real algebraic cycles of codimension $k$ on $X$ modulo numerical equivalence. Truong conjectured that $χ_{2k}(f) = λ_k(f)$ for all $0 \le k \le \dim X$ as a generalization of Weil's Riemann hypothesis. We prove this conjecture in the case of abelian varieties. In the course of the proof we also obtain a new parity result on the eigenvalues of self-maps of abelian varieties in prime characteristic, which is of independent interest.
description: Minor revision, accepted by J. Algebraic Geom., comments welcome!
Returning to Ararat and home at last: Western Armenian diasporan discourse on return to 'Eastern' Armenia
Creators: name: Karamanian, Armen
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: Centuries of division under foreign rule led to the physical and linguistic separation of the Armenian nation into an eastern and western portion. The Armenian Genocide represented the final chapter in this division as the two components diverged further apart; the eastern component becoming an independent, then Soviet Armenia, and the western component constituting Eastern Turkey as its Armenian inhabitants were exterminated and deported, with those surviving forming the diaspora. Armenia's independence in 1991 presented its mostly Western Armenian diaspora with an opportunity to return to a homeland. However, upon return, diasporans were confronted wit h a contrasting eastern narrative of 'Armenianness', unlike the Western Armenian and hybrid identities they possessed . Thirty Western Armenian returnees were interviewed in Armenia, with each returnee's journey of homecoming analysed using discourse theory to discover the presence of power during interactions between returnees and locals, and to determine the returnees' ability to alter discourse away from a dominant E astern Armenian narrative. Experiences show that returnees, unlike many of their generational predecessors, accept the Republic of Armenia as their homeland, relegating Western Armenia to symbolic history. As returnees adjust to life in Armenia , they switch their speech to Eastern Armenian as a sign of acceptance and integration. However, their past Western Armenian and diasporan identities are maintained, adding to the hybridity of their identity as a blended Spyurkahayastan t si (diaspora + Armenian of Armenia). 1 The process of homecoming for returnees is a negotiation of their past identity and the dominant E astern Armenian narrative of the homeland. This negotiation results in an acceptance of the linguistic component of the homeland's narrative, a recognition of the dominant E astern Armenian culture, and a hybridisation of their cultural identity. Armenia remains ill - prepared to welcome the diversity of the Armenian narrative presented by returnees, which in turn presents a challenge to attracting future returnees who require reasons other than patriotism to relocate to Armenia. Nevertheless, Armenia provides a home for returnees in the land not west, but east of Ararat.
Health state utility estimation of Mycobacterium avium complex pulmonary disease using a time trade-off approach
Creators: name: Murata, Tatsunori
name: Morimoto, Kozo
name: Matsuyama, Fujio
name: Yamada, Mayumi
name: Feliciano, Joseph
name: Hassan, Mariam
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Medicine
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Cancer
subject: Science Policy

description: To obtain appropriate health state utility values for cost-effectiveness analyses of new Mycobacterium avium complex pulmonary disease (MAC-PD) treatments. The impact of MAC-PD severity and symptoms on quality of life (QoL) also were quantified. A questionnaire describing four health states, MAC-positive severe, MAC-positive moderate, MAC-positive mild, and MAC-negative, was developed based on St. George’s Respiratory Questionnaire (SGRQ) Symptom and Activity scores from the CONVERT trial. The time trade-off (TTO) method with ping-pong titration procedure was used to estimate health state utilities. Regression analyses assessed the impacts of covariates. Of 319 Japanese adults (49.8% female, mean age 44.8 years), mean (95% CI) health state utility scores (MAC-positive severe, MAC-positive moderate, MAC-positive mild, and MAC-negative) were 0.252 (0.194–0.310), 0.535 (0.488–0.582), 0.816 (0.793–0.839), and 0.881 (0.866–0.896), respectively. MAC-negative state utility scores were significantly higher than MAC-positive severe (mean difference [95% CI], 0.629 [0.574–0.684]), MAC-positive moderate (0.346 [0.304–0.389]), and MAC-positive mild (0.065 [0.048–0.082]) scores (p < .001 each). Most participants would trade survival duration to avoid MAC-positive states (97.5% to avoid MAC-positive severe; 88.7% MAC-positive moderate; 61.4% MAC-positive mild). Regression analyses to investigate the impact of background characteristics showed similar utility differences between health states when not adjusted for covariates. Some participant demographics differed from the general population; however, this did not impact utility differences among health states as regression analyses adjusting for demographics did not affect these differences. Similar investigations are needed among patients with MAC-PD and in other countries. This study evaluating the impact of MAC-PD on utilities using the TTO method demonstrates that differences in utilities are dependent on the severity of respiratory symptoms and their impacts on daily activities and QoL. These results could contribute to a better quantification of the value of MAC-PD treatments and improve assessments of cost-effectiveness.
ALERT: Accurate Learning for Energy and Timeliness
Creators: name: Wan, Chengcheng
name: Santriaji, Muhammad
name: Rogers, Eri
name: Hoffmann, Henry
name: Maire, Michael
name: Lu, Shan
Publisher: name: arXiv
Year: 2019
Subjects: subject: Performance (cs.PF)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: An increasing number of software applications incorporate runtime Deep Neural Networks (DNNs) to process sensor data and return inference results to humans. Effective deployment of DNNs in these interactive scenarios requires meeting latency and accuracy constraints while minimizing energy, a problem exacerbated by common system dynamics. Prior approaches handle dynamics through either (1) system-oblivious DNN adaptation, which adjusts DNN latency/accuracy tradeoffs, or (2) application-oblivious system adaptation, which adjusts resources to change latency/energy tradeoffs. In contrast, this paper improves on the state-of-the-art by coordinating application- and system-level adaptation. ALERT, our runtime scheduler, uses a probabilistic model to detect environmental volatility and then simultaneously select both a DNN and a system resource configuration to meet latency, accuracy, and energy constraints. We evaluate ALERT on CPU and GPU platforms for image and speech tasks in dynamic environments. ALERT's holistic approach achieves more than 13% energy reduction, and 27% error reduction over prior approaches that adapt solely at the application or system level. Furthermore, ALERT incurs only 3% more energy consumption and 2% higher DNN-inference error than an oracle scheme with perfect application and system knowledge.
The complete mitochondrial genome and phylogenetic analysis for Rhabdophis chiwen (squamata: colubridae)
Creators: name: Chen, Jingyun
name: Luo, Jingxue
name: Wang, Ji
name: Song, Huina
name: Duan, Mingwen
name: Zhu, Guang-Xiang
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Science Policy

description: Rhabdophis chiwen is currently found so far in Sichuan Province, China, where it predominantly feeds on earthworms and firefly larvae. In this study, we sequenced and analyzed the mitochondrial genome of R. chiwen, which measured 17,646 bp in length and encompassed 37 genes along with two control regions. The base composition revealed percentages of 33.20% A, 25.94% T, 13.27% G, and 27.59% C. Phylogenetic analyses indicate that R. chiwen belongs to the family Colubridae and forms a sister branch with R. tigrinus. This study successfully obtained the first complete mitochondrial genome of R. chiwen, offering crucial genetic data for its evolutionary history and conservation.
The Laplace transform of the integrated Volterra Wishart process
Creators: name: Jaber, Eduardo Abi
Publisher: name: arXiv
Year: 2019
Subjects: subject: Probability (math.PR)
subject: Computational Finance (q-fin.CP)
subject: FOS: Mathematics
subject: FOS: Economics and business

description: We establish an explicit expression for the conditional Laplace transform of the integrated Volterra Wishart process in terms of a certain resolvent of the covariance function. The core ingredient is the derivation of the conditional Laplace transform of general Gaussian processes in terms of Fredholm's determinant and resolvent. Furthermore , we link the characteristic exponents to a system of non-standard infinite dimensional matrix Riccati equations. This leads to a second representation of the Laplace transform for a special case of convolution kernel. In practice, we show that both representations can be approximated by either closed form solutions of conventional Wishart distributions or finite dimensional matrix Riccati equations stemming from conventional linear-quadratic models. This allows fast pricing in a variety of highly flexible models, ranging from bond pricing in quadratic short rate models with rich autocorrelation structures, long range dependence and possible default risk, to pricing basket options with covariance risk in multivariate rough volatility models.
Generalized Matrix polynomials of Tree Laplacians indexed by Symmetric functions and the GTS poset
Creators: name: Nagar, Mukesh Kumar
name: Sivasubramanian, Sivaramakrishnan
Publisher: name: arXiv
Year: 2019
Subjects: subject: Combinatorics (math.CO)
subject: FOS: Mathematics
subject: 05C05, 06A06, 15A15

description: Let $T$ be a tree on $n$ vertices with $q$-Laplacian $L_T^q$ and Laplacian matrix $L_T$. Let $GTS_n$ be the generalized tree shift poset on the set of unlabelled trees on $n$ vertices. Inequalities are known between coefficients of the immanantal polynomial of $L_T$ (and $L_T^q$) as we go up the poset $GTS_n$. Using the Frobenius characteristic, this can be thought as a result involving the schur symmetric function $s_λ$. In this paper, we use an arbitrary symmetric function to define a {\it generalized matrix function} of an $n \times n$ matrix. When the symmetric function is the monomial and the forgotten symmetric function, we generalize such inequalities among coefficients of the generalized matrix polynomial of $L_T^q$ as we go up the $GTS_n$ poset.
description: 11 pages
Additional file 5: Figure S5. of Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel sequencing
Creators: name: MacConaill, Laura
name: Burns, Robert
name: Anwesha Nag
name: Coleman, Haley
name: Slevin, Michael
name: Giorda, Kristina
name: Light, Madelyn
name: Lai, Kevin
name: Jarosz, Mirna
name: McNeill, Matthew
name: Ducar, Matthew
name: Meyerson, Matthew
name: Thorner, Aaron
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified

description: Level of cross-talk using unique, dual-matched indexed adapters on Illumina HiSeq 2500. The 96-well plate layout represents the adapter plate. A total of 35 adapters were synthesized. Thirty-four samples consisting of PDX (n = 4), tissue samples (n = 20), and cancer cell lines (n = 10) underwent library construction using IDT-synthesized unique, dual-matched indexed adapters (green). Libraries were pooled, hybrid captured using a custom bait set, and then sequenced on a single lane of an Illumina HiSeq 2500 flow cell. Numbers in each well represent the number of fragments that passed standard Illumina filters and demultiplexed using only perfect sequence matches on all TS-96 indices. (PDF 184 kb)
The impact of presentation rate on the effectiveness of subtitles in learning
Creators: name: Alsharif, Ahmed
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: Subtitling has received increasing scholarly attention in audiovisual translation studies. Most of the existing literature has been centred on the benefits of subtitling for learners, but not on how subtitles are presented (e.g. subtitle presentation speed, layout, etc.). The impact of the presentation rate or appearance of subtitles on learners has therefore not been explored sufficiently. Some well-explored topics in subtitling research include language learning, film comprehension and cognitive load (cf., Danan, 2004; d'Ydewalle et al., 1991; Garza, 1991; Kruger, Hefer, & Matthew, 2013; Paas et al., 2004). However, little research has been conducted to investigate the impact of presentation rate on learning, comprehension or cognitive load. Given the increasing use of subtitles in education, an investigation into this aspect has significant theoretical and applied implications, particularly at a time when technological advances have made it possible to create verbatim subtitles relatively cheap to produce. The experiment in this study has two levels (English as a foreign language, and English as first or second language) and four conditions, namely a control condition without subtitles, and three experimental conditions in which the subtitle speed has been manipulated: 1) verbatim (an average of about 17 CPS); 2) standard (an average of 15 CPS; 3) and edited (an average of 12.5 CPS). A total of 172 students form King Khalid University (Saudi Arabia) and Macquarie University (Australia) participated in this experiment. Participants were assigned to four groups: (1) a group of 42 participants watching the verbatim video; (2) a group of 40 participants watching the edited video; a group of 53 participants watching the standard video; and (4) a control group of 37 participants watching the video without subtitles. Participants were assigned randomly to the four groups. After inviting students, those who accepted to participate were asked to watch a 6-minute history video and then fill out three questionnaires: a biographical questionnaire; a cognitive load questionnaire, adopted from Brünken et al. (2003); and a comprehension test which was used as an indicator of performance. This experiment study has found that all subtitle conditions were beneficial when compared to the unsubtitled video in the case of the Arabic group. Particularly, edited subtitles had a significant impact on the results obtained for the Arabic group. In terms of English speakers, however, edited subtitles increased CL and also resulted in lower comprehension, indicating that those subtitles were not useful for this particular group. All English speakers outperformed Arabic speakers under all conditions, particularly in the unsubtitled condition where the difference was significant -- abstract.
Adversarial Example Generation using Evolutionary Multi-objective Optimization
Creators: name: Suzuki, Takahiro
name: Takeshita, Shingo
name: Ono, Satoshi
Publisher: name: arXiv
Year: 2020
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Cryptography and Security (cs.CR)
subject: Machine Learning (cs.LG)
subject: Neural and Evolutionary Computing (cs.NE)
subject: Machine Learning (stat.ML)
subject: FOS: Computer and information sciences

description: This paper proposes Evolutionary Multi-objective Optimization (EMO)-based Adversarial Example (AE) design method that performs under black-box setting. Previous gradient-based methods produce AEs by changing all pixels of a target image, while previous EC-based method changes small number of pixels to produce AEs. Thanks to EMO's property of population based-search, the proposed method produces various types of AEs involving ones locating between AEs generated by the previous two approaches, which helps to know the characteristics of a target model or to know unknown attack patterns. Experimental results showed the potential of the proposed method, e.g., it can generate robust AEs and, with the aid of DCT-based perturbation pattern generation, AEs for high resolution images.