cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Non-Homogeneous Haze Removal via Artificial Scene Prior and Bidimensional Graph Reasoning
Creators: name: Wei, Haoran
name: Wu, Qingbo
name: Li, Hui
name: Ngan, King Ngi
name: Li, Hongliang
name: Meng, Fanman
name: Xu, Linfeng
Publisher: name: arXiv
Year: 2021
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: Due to the lack of natural scene and haze prior information, it is greatly challenging to completely remove the haze from a single image without distorting its visual content. Fortunately, the real-world haze usually presents non-homogeneous distribution, which provides us with many valuable clues in partial well-preserved regions. In this paper, we propose a Non-Homogeneous Haze Removal Network (NHRN) via artificial scene prior and bidimensional graph reasoning. Firstly, we employ the gamma correction iteratively to simulate artificial multiple shots under different exposure conditions, whose haze degrees are different and enrich the underlying scene prior. Secondly, beyond utilizing the local neighboring relationship, we build a bidimensional graph reasoning module to conduct non-local filtering in the spatial and channel dimensions of feature maps, which models their long-range dependency and propagates the natural scene prior between the well-preserved nodes and the nodes contaminated by haze. To the best of our knowledge, this is the first exploration to remove non-homogeneous haze via the graph reasoning based framework. We evaluate our method on different benchmark datasets. The results demonstrate that our method achieves superior performance over many state-of-the-art algorithms for both the single image dehazing and hazy image understanding tasks. The source code of the proposed NHRN is available on https://github.com/whrws/NHRNet.
Responsiveness of genes to long-range transcriptional regulation
Creators: name: Georgieva, Radina
Publisher: name: Imperial College London
Year: 2022

description: Developmental genes are highly regulated at the level of transcription and exhibit complex spatial and temporal expression patterns. Key developmental loci are frequently spanned by clusters of conserved non-coding elements (CNEs), referred to as genomic regulatory blocks (GRBs), that have been subject to extreme levels of purifying selection during metazoan evolution. CNEs have been shown to function as long-range enhancers, activating transcription of their developmental target genes over vast genomic distances and bypassing more proximally located unresponsive genes (bystanders). Despite their role in the establishment of cell identity during development, many of these long-range regulatory landscapes remain poorly characterised. In this thesis, I develop a computational method for the genome-wide identification of regulatory enhancer-promoter associations in human and mouse, based on co-variation of enhancer and promoter transcriptional activity across a comprehensive set of tissues and cell types, in combination with chromatin contact data. Using this method, I demonstrate that previously predicted GRB target genes are amongst the genes with the highest level of enhancer responsiveness in the genome, and are frequently associated with extremely long-range enhancers. Remarkably, the activity of some previously predicted bystanders is also weakly but significantly associated with enhancer activity, challenging the notion that the promoters of bystanders are unresponsive to enhancers. Next, I systematically annotate human genes with elevated enhancer responsiveness and identify more than 600 putative target genes, associated with the regulation of a wide range of developmental processes, from pattern specification to axonogenesis, as well as with disease. The analysis performed in this thesis has facilitated the identification of hundreds of previously uncharacterised enhancer-responsive genes and their long-range regulatory landscapes, allowing the study of their unique properties.
The EGFR Is Required for Proper Innervation to the Skin
Creators: name: Evenson, Jackie E.
name: Lee, Tang-Cheng
name: Maklad, Adel
name: Bichsel, Kyle J.
name: Threadgill, David W.
name: Hansen, Laura A.
name: Nicolai, Jodi R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: EGFR family members are essential for proper peripheral nervous system development. A role for EGFR itself in peripheral nervous system development in vivo, however, has not been reported. We investigated whether EGFR is required for cutaneous innervation using Egfr null and skin-targeted Egfr mutant mice. Neuronal markers; including PGP9.5, GAP-43, acetylated tubulin, and neurofilaments; revealed that Egfr null dorsal skin was hyperinnervated with a disorganized pattern of innervation. In addition, receptor subtypes such as lanceolate endings were disorganized and immature. To determine whether the hyperinnervation phenotype resulted from a target-derived effect of loss of EGFR, mice lacking EGFR expression in the cutaneous epithelium were examined. These mice retained other aspects of the cutaneous Egfr null phenotype but exhibited normal innervation. The sensory deficits in Egfr null dorsal skin were not associated with any abnormality in the morphology or density of dorsal root ganglion (DRG) neurons or Schwann cells. However, explant and dissociated cell cultures of DRG revealed more extensive branching in Egfr null cultures. These data demonstrate that EGFR is required for proper cutaneous innervation during development and suggest that it limits axonal outgrowth and branching in a DRG-autonomous manner.
On polynomial collocation for Cauchy singular integral equations with fixed singularities
Creators: name: Junghanns, Peter
name: Rathsfeld, Andreas
Publisher: name: Weierstrass Institute
Year: 2000
Subjects: subject: Cauchy singular integral equation
subject: Mellin kernel
subject: polynomial collocation
subject: stability
subject: convergence
subject: 45L10
subject: 65R20

description: In this paper we consider a polynomial collocation method for the numerical solution of Cauchy singular integral equations with fixed singularities over the interval, where the fixed singularities are supposed to be of Mellin convolution type. For the stability and convergence of this method in weighted L2 spaces, we derive necessary and sufficient conditions.
The Thomsen-Friedenreich Antigen-Binding Lectin Jacalin Interacts with Desmoglein-1 and Abrogates the Pathogenicity of Pemphigus Foliaceus Autoantibodies In Vivo
Creators: name: Park, Moonhee
name: Hilario-Vargas, Julio
name: Zhao, Minglang
name: Li, Ning
name: McInnes, David M.
name: Prisayanh, Phillip S.
name: Diaz, Luis A.
name: Liu, Zhi
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Pemphigus foliaceus (PF) is an autoimmune skin blistering disease mediated by pathogenic autoantibodies against the desmosomal core glycoprotein desmoglein 1 (Dsg1). This study demonstrated that the O-glycan-specific plant lectin jacalin binds Dsg1 and inhibits the interaction of Dsg1/PF IgG. N-glycosylation is not involved in the interaction of Dsg1/jacalin or Dsg1/PF IgG. Subcutaneous injection of jacalin into neonatal mice drastically reduced PF IgG deposition at the epidermal cell surface and blocked PF IgG-induced skin blisters, both clinically and histologically. Interestingly, another plant lectin peanut agglutinin (PNA), which shares the same carbohydrate specificity toward the O-linked carbohydrate structure known as Thomsen-Friedenreich antigen (TF antigen, Galβ1-3GalNAcα-O-Ser/Thr), also bound Dsg1 and blocked the skin blistering. In contrast, the plant lectin vicia villosa-B4 (VVL-B4), which shares the carbohydrate specificity toward the O-linked monosaccharide known as Thomsennouveau antigen (Tn antigen, GalNAc-α1-O-Ser/Thr) did not bind Dsg1 and did not show a protective effect against the disease induced by the autoantibodies. Collectively, these results suggest that the binding of jacalin to O-linked TF carbohydrate motifs on Dsg1 impairs the Dsg1/PF autoantibody interactions and abrogates its pathogenicity in vivo. TF-specific binding ligands may have a potential therapeutic value for PF.
A carrier relaxation bottleneck probed in single InGaAs quantum dots using integrated superconducting single photon detectors
Creators: name: Reithmaier, G.
name: Flassig, F.
name: Hasch, P.
name: Lichtmannecker, S.
name: Müller, K.
name: Vuckovic, J.
name: Gross, R.
name: Kaniber, M.
name: Finley, J. J.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Using integrated superconducting single photon detectors we probe ultra-slow exciton capture and relaxation dynamics in single self-assembled InGaAs quantum dots embedded in a GaAs ridge waveguide. Time-resolved luminescence measurements performed with on- and off-chip detection reveal a continuous decrease in the carrier relaxation time from 1.22 $\pm$ 0.07 ns to 0.10 $\pm$ 0.07 ns upon increasing the number of non-resonantly injected carriers. By comparing off-chip time-resolved spectroscopy with spectrally integrated on-chip measurements we identify the observed dynamics in the rise time ($τ_r$) as arising from a relaxation bottleneck at low excitation levels. From the comparison with the temporal dynamics of the single exciton transition with the on-chip emission signal, we conclude that the relaxation bottleneck is circumvented by the presence of charge carriers occupying states in the bulk material and the two-dimensional wetting layer continuum. A characteristic -2/3 power law dependence of the rise time is observed suggesting Auger-type scattering between carriers trapped in the quantum dot and the two-dimensional wetting layer continuum which circumvents the phonon relaxation bottleneck.
Extractive Summarization of Call Transcripts
Creators: name: Biswas, Pratik K.
name: Iakubovich, Aleksandr
Publisher: name: arXiv
Year: 2021
Subjects: subject: Computation and Language (cs.CL)
subject: FOS: Computer and information sciences

description: Text summarization is the process of extracting the most important information from the text and presenting it concisely in fewer sentences. Call transcript is a text that involves textual description of a phone conversation between a customer (caller) and agent(s) (customer representatives). This paper presents an indigenously developed method that combines topic modeling and sentence selection with punctuation restoration in condensing ill-punctuated or un-punctuated call transcripts to produce summaries that are more readable. Extensive testing, evaluation and comparisons have demonstrated the efficacy of this summarizer for call transcript summarization.
description: Journal paper
Oxford University Press Archives, Oxford
Creators: name: Giltaij, Jacob
Publisher: name: Zenodo
Year: 2018
Subjects: Fritz Schulz
Fritz Pringsheim

description: Archival notes from the Oxford University Press Archives, Oxford. Schulz CP ED 000129: Files from the OUP archives regarding OUP and the works of Schulz written for the Press, the Oxford History of Legal Science in particular. Schulz CP GE 000344: Files from the OUP archives regarding OUP and the Rockefeller Foundation, New York. Schulz CP GE 000345: Files from the OUP archives regarding OUP and the Rockefeller Foundation, New York. Schulz PB ED 010382: Files from the OUP archives regarding OUP and the works of Schulz written for the Press, particularly the Manual of Roman law/Classical Roman law. Schulz PB ED 010383: Files from the OUP archives regarding OUP and the works of Schulz written for the Press, particularly the History of Roman legal science. Schulz PB ED 010384: Files from the OUP archives regarding OUP and the works of Schulz written for the Press, particularly the Principles of Roman law.
Exciton Footprint of Self-assembled AlGaAs Quantum Dots in Core-Shell Nanowires
Creators: name: Fontana, Yannik
name: Corfdir, Pierre
name: Van Hattem, Barbara
name: Russo-Averchi, Eleonora
name: Heiss, Martin
name: Sonderegger, Samuel
name: Magen, Cesar
name: Arbiol, Jordi
name: Phillips, Richard T.
name: Morral, Anna Fontcuberta i
Publisher: name: arXiv
Year: 2014
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Quantum-dot-in-nanowire systems constitute building blocks for advanced photonics and sensing applications. The electronic symmetry of the emitters impacts their function capabilities. Here, we study the fine structure of gallium-rich quantum dots nested in the shell of GaAs-AlGaAs core-shell nanowires. We used optical spectroscopy to resolve the splitting resulting from the exchange terms and extract the main parameters of the emitters. Our results indicate that the quantum dots can host neutral as well as charges excitonic complexes and that the excitons exhibit a slightly elongated footprint, with the main axis tilted with respect to the growth axis. GaAs-AlGaAs emitters in a nanowire are particularly promising for overcoming the limitations set by strain in other systems, with the benefit of being integrated in a versatile photonic structure.
Improved management of issue dependencies in issue trackers of large collaborative projects
Creators: name: Raatikainen, Mikko
name: Motger, Quim
name: Lüders, Clara Marie
name: Franch, Xavier
name: Myllyaho, Lalli
name: Kettunen, Elina
name: Marco, Jordi
name: Tiihonen, Juha
name: Halonen, Mikko
name: Männistö, Tomi
Publisher: name: arXiv
Year: 2021
Subjects: subject: Software Engineering (cs.SE)
subject: FOS: Computer and information sciences
subject: D.2.1

description: Issue trackers, such as Jira, have become the prevalent collaborative tools in software engineering for managing issues, such as requirements, development tasks, and software bugs. However, issue trackers inherently focus on the lifecycle of single issues, although issues have and express dependencies on other issues that constitute issue dependency networks in large complex collaborative projects. The objective of this study is to develop supportive solutions for the improved management of dependent issues in an issue tracker. This study follows the Design Science methodology, consisting of eliciting drawbacks and constructing and evaluating a solution and system. The study was carried out in the context of The Qt Company's Jira, which exemplifies an actively used, almost two-decade-old issue tracker with over 100,000 issues. The drawbacks capture how users operate with issue trackers to handle issue information in large, collaborative, and long-lived projects. The basis of the solution is to keep issues and dependencies as separate objects and automatically construct an issue graph. Dependency detections complement the issue graph by proposing missing dependencies, while consistency checks and diagnoses identify conflicting issue priorities and release assignments. Jira's plugin and service-based system architecture realize the functional and quality concerns of the system implementation. We show how to adopt the intelligent supporting techniques of an issue tracker in a complex use context and a large data-set. The solution considers an integrated and holistic system view, practical applicability and utility, and the practical characteristics of issue data, such as inherent incompleteness.
description: Accepted for publication in IEEE Transactions on Software Engineering. Published online 05 October 2022. 21 pages, 3 figures, 8 tables
IgG Autoantibody Response against Keratinocyte Cadherins in Endemic Pemphigus Foliaceus (Fogo Selvagem)
Creators: name: Culton, Donna A.
name: James, Kirk
name: Rivitti, Evandro A.
name: Hans-Filho, Gunter
name: Diaz, Luis A.
name: Qaqish, Bahjat F.
name: Flores, Gustavo
name: Aoki, Valeria
name: Maldonado, Mike
name: Prisayanh, Phillip
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: It is well established that autoantibodies against desmoglein 3 and desmoglein 1 are relevant in the pathogenesis of pemphigus vulgaris and pemphigus foliaceus, including its endemic form, Fogo Selvagem (FS). Isolated reports have shown that in certain patients with these diseases, autoantibodies against other desmosomal cadherins and E-cadherin may also be present. The goal of this investigation was to determine if FS patients and normal individuals living in endemic areas possess autoantibodies against other desmosomal cadherins and E-cadherin. Testing a large number of FS and endemic control sera by ELISA we find a consistent and specific autoantibody response against desmoglein 1 and other keratinocyte cadherins in these individuals, which is quite different from US controls. Overall, the highest correlations among the autoantibody responses tested are in the endemic controls, followed by FS patients, and lowest in the US controls. These findings suggest that multiple, perhaps cross reactive, keratinocyte cadherins are recognized by FS patients and endemic controls.
title: Intraspecific differences of seed longevity between ragweed populations in Hungary
Creators: name: Kazinczi, Gabriella
name: Kerepesi, Ildikó
Publisher: name: Julius Kühn-Institut
Year: 2016

description: Julius-Kühn-Archiv, Nr. 455 (2016): HALT Ambrosia - final project report and general publication of project findings
TALABALARNING DIGITAL KOMPETENSIYALARINI  ANIQLASH YUZASIDAN PEDAGOGIK TAJRIBA-SINOV ISHLARINING MAZMUNI
Creators: name: Sheraliyev, Odiljon
Publisher: name: Zenodo
Year: 2023

description: Ushbu maqolada talabalar digital kompetensiyani aniqlash yuzasidan pedagogik tajriba-sinov ishlarining mazmuni, tajriba-sinov ishlarining statistik tahlili  keltirilgan.
Achieving Fairness with a Simple Ridge Penalty
Creators: name: Scutari, Marco
name: Panero, Francesca
name: Proissl, Manuel
Publisher: name: arXiv
Year: 2021
Subjects: subject: Machine Learning (cs.LG)
subject: Methodology (stat.ME)
subject: FOS: Computer and information sciences

description: In this paper we present a general framework for estimating regression models subject to a user-defined level of fairness. We enforce fairness as a model selection step in which we choose the value of a ridge penalty to control the effect of sensitive attributes. We then estimate the parameters of the model conditional on the chosen penalty value. Our proposal is mathematically simple, with a solution that is partly in closed form, and produces estimates of the regression coefficients that are intuitive to interpret as a function of the level of fairness. Furthermore, it is easily extended to generalised linear models, kernelised regression models and other penalties; and it can accommodate multiple definitions of fairness. We compare our approach with the regression model from Komiyama et al. (2018), which implements a provably-optimal linear regression model; and with the fair models from Zafar et al. (2019). We evaluate these approaches empirically on six different data sets, and we find that our proposal provides better goodness of fit and better predictive accuracy for the same level of fairness. In addition, we highlight a source of bias in the original experimental evaluation in Komiyama et al. (2018).
description: 16 pages, 9 figures
Cross-interactive residual smoothing for global and block Lanczos-type solvers for linear systems with multiple right-hand sides
Creators: name: Aihara, Kensuke
name: Imakura, Akira
name: Morikuni, Keiichi
Publisher: name: arXiv
Year: 2021
Subjects: subject: Numerical Analysis (math.NA)
subject: FOS: Mathematics
subject: 65F10, 65F45

description: Global and block Krylov subspace methods are efficient iterative solvers for large sparse linear systems with multiple right-hand sides. However, global or block Lanczos-type solvers often exhibit large oscillations in the residual norms and may have a large residual gap relating to the loss of attainable accuracy of the approximations. Conventional residual smoothing schemes suppress these oscillations but cannot improve the attainable accuracy, whereas a recent residual smoothing scheme enables the improvement of the attainable accuracy for single right-hand side Lanczos-type solvers. The underlying concept of this scheme is that the primary and smoothed sequences of the approximations and residuals influence one another, thereby avoiding the severe propagation of rounding errors. In the present study, we extend this cross-interactive residual smoothing to the case of solving linear systems with multiple right-hand sides. The resulting smoothed methods can reduce the residual gap with a low additional cost compared to their original counterparts. We demonstrate the effectiveness of the proposed approach through rounding error analysis and numerical experiments.
description: 21 pages, 5 figures
Chloroquine Promotes Apoptosis in Melanoma Cells by Inhibiting BH3 Domain–Mediated PUMA Degradation
Creators: name: Androphy, Elliot J.
name: Sun, Yang
name: Lakhter, Alexander J.
name: Naidu, Samisubbu R.
name: Kaufmann, William K.
name: Travers, Jeffrey B.
name: Sahu, Ravi P.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: The BH3-only protein PUMA counters Bcl-2 family anti-apoptotic proteins and promotes apoptosis. Although PUMA is a key regulator of apoptosis, the post-transcriptional mechanisms that control PUMA protein stability are not understood. We show that a lysosome-independent activity of chloroquine prevents degradation of PUMA protein, promotes apoptosis and reduces the growth of melanoma xenografts in mice. Compared to wild–type PUMA, a BH3 domain deleted PUMA protein showed impaired decay in melanoma cells. Fusion of the BH3 domain to a heterologous protein led to its rapid turnover that was inhibited by chloroquine. While both chloroquine and inhibitors of lysosomal proteases stalled autophagy, only choroquine stabilized PUMA protein and promoted apoptosis. Our results reveal a lysosomal protease independent activity of chloroquine that selectively promotes apoptosis in melanoma cells.
Universitätsarchiv, Karl-Franzens-Universität, Graz
Creators: name: Giltaij, Jacob
Publisher: name: Zenodo
Year: 2018
Subjects: Paul Koschaker

description: Archival notes from Universitätsarchiv, Karl-Franzens-Universität zu Graz, Graz. Universitätsarchiv Graz, Phil. WS 1897/1898. Universitätsarchiv Graz, Phil. SS 1898. Universitätsarchiv Graz, Jur WS 1898/1899. Universitätsarchiv Graz, Jur SS 1899. Universitätsarchiv Graz, Jur WS 1899/1900. Universitätsarchiv Graz, Jur SS 1900. Universitätsarchiv Graz, Jur WS 1900/1901. Universitätsarchiv Graz, Jur SS 1901. Universitätsarchiv Graz, Jur WS 1901/1902. Universitätsarchiv Graz, Jur ex 1904/1905.
Mucosal Pemphigus Vulgaris Anti-Dsg3 IgG Is Pathogenic to the Oral Mucosa of Humanized Dsg3 Mice
Creators: name: Roberts, James C.
name: Culton, Donna A.
name: Li, Ning
name: Diaz, Luis A.
name: Park, Moonhee
name: Liu, Zhi
name: McCray, Suzanne K.
name: Anhalt, Grant J.
name: Cowley, Dale O.
name: Zedek, Daniel C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: There are two major clinical subsets of pemphigus vulgaris (PV), mucosal PV (mPV) and mucocutaneous PV (mcPV). The mPV subset exhibits anti-human desmoglein (Dsg) 3 autoantibodies that fail to recognize murine Dsg3; thus, passive transfer experiments of mPV IgG into WT mice have been unsuccessful at inducing disease. We therefore generated a fully humanized Dsg3 (hDSG3) murine model utilizing a human Dsg3 transgenic animal crossed to the murine Dsg3 knockout line. Expression of hDsg3 in the mucosa rescues the murine Dsg3 knockout phenotype. Well characterized mPV sera bind mucosal epithelia from the hDsg3 mice, but not mucosal tissues from WT mice by as detected by indirect immunofluorescence. The majority of mPV sera preferentially recognize hDsg3 compared to mDsg3 by immunoprecipitation as well. Passive transfer of mPV IgG into adult hDsg3 mice, but not WT mice, induces suprabasilar acantholysis in mucosal tissues, thus confirming pathogenicity of mPV anti-hDsg3 IgG in vivo. Human anti-hDsg3 antibodies are detected in perilesional mucosa as well as in sera of recipient mice by immunofluorescence. These findings suggest that the Dsg3 epitopes targeted by pathogenic mPV IgG are human specific. This hDsg3 mouse model will be invaluable in studying the clinical transition from mPV to mcPV.
Universitätsarchiv, Friedrich-Wilhelms-Universität, Bonn
Creators: name: Giltaij, Jacob
Publisher: name: Zenodo
Year: 2018
Subjects: Fritz Schulz
Paul Koschaker

description: Archival notes from Universitätsarchiv, Friedrich-Wilhelms-Universität Bonn. Lehrauftragtes Koschaker, Paul 4413: Personal data and documents on the visiting professorship of Paul Koschaker. Personalakte Prof. Dr. Koschaker, Paul 4413 PA: Documents regarding the visiting professorship of Paul Koschaker. Personalakte Schulz, Fritz 9234: Personal acts of Schulz present at the archive of the Friedrich-Wilhelms-Universität Bonn.
Optimality conditions for robust nonsmooth multiobjective optimization problems in Asplund spaces
Creators: name: Saadati, Maryam
name: Oveisiha, Morteza
Publisher: name: arXiv
Year: 2021
Subjects: subject: Optimization and Control (math.OC)
subject: FOS: Mathematics

description: We employ a fuzzy optimality condition for the Frechet subdifferential and some advanced techniques of variational analysis such as formulae for the subdifferentials of an infinite family of nonsmooth functions and the coderivative scalarization to investigate robust optimality condition and robust duality for a nonsmooth/nonconvex multiobjective optimization problem dealing with uncertain constraints in arbitrary Asplund spaces. We establish necessary optimality conditions for weakly and properly robust efficient solutions of the problem in terms of the Mordukhovich subdifferentials of the related functions. Further, sufficient conditions for weakly and properly robust efficient solutions as well as for robust efficient solutions of the problem are provided by presenting new concepts of generalized convexity. Finally we formulate a Mond-Weir-type robust dual problem to the reference problem, and examine weak, strong, and converse duality relations between them under the pseudo convexity assumptions.
The Circadian Clock Controls Sunburn Apoptosis and Erythema in Mouse Skin
Creators: name: Ye, Rui
name: Kemp, Michael G.
name: Sancar, Aziz
name: Gaddameedhi, Shobhan
name: Selby, Christopher P.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Epidemiological studies of humans and experimental studies with mouse models suggest that sunburn resulting from exposure to excessive UV light and damage to DNA confers an increased risk for melanoma and non-melanoma skin cancer. Previous reports have shown that both nucleotide excision repair, which is the sole pathway in humans for removing UV photoproducts, and DNA replication, are regulated by the circadian clock in mouse skin. Furthermore, the timing of UV exposure during the circadian cycle has been shown to affect skin carcinogenesis in mice. Because sunburn and skin cancer are causally related, we investigated UV-induced sunburn apoptosis and erythema in mouse skin as a function of circadian time. Interestingly, we observed that sunburn apoptosis, inflammatory cytokine induction, and erythema were maximal following an acute early morning exposure to UV and minimal following an afternoon exposure. Early morning exposure to UV also produced maximal activation of Atr-mediated DNA damage checkpoint signaling including activation of the tumor suppressor p53, which is known to control the process of sunburn apoptosis. To our knowledge these data provide the first evidence that the circadian clock plays an important role in the erythemal response in UV-irradiated skin. The early morning is when DNA repair is at a minimum, thus the acute responses likely are associated with unrepaired DNA damage. The prior report that mice are more susceptible to skin cancer induction following chronic irradiation in the AM, when p53 levels are maximally induced, is discussed in terms of the mutational inactivation of p53 during chronic irradiation.
Genetic effects of tissue-specific enhancers in schizophrenia and hypertrophic cardiomyopathy
Creators: name: Osimo, Emanuele Felice
Publisher: name: Imperial College London
Year: 2023

description: Most human conditions develop in genetically susceptible individuals from the interaction with environmental risk factors. These complex disorders result from the summation of effects from multiple genetic risk loci. Genome-wide association studies (GWASes) measure the association of single nucleotide polymorphisms (SNPs) with traits or conditions, and allow the creation of individualised polygenic risk scores. However, these explain only a small portion of a condition’s genetic heritability. Further, there is evidence that schizophrenia GWAS signals are enriched within genomic regulatory blocks, which are clusters of conserved non-coding elements that span key developmental loci and function as long-range enhancers activating transcription of target developmental genes. This suggests that enhancer-based annotations might be useful to refine polygenic signals for schizophrenia. In this work, I aimed to increase the amount of variance explained by PRS for schizophrenia, and a comparison condition hypertrophic cardiomyopathy, using tissue-specific regulatory enhancer-promoter annotations. To do so, I developed neural- and cardiac-specific enhancer lists, which I tested for enrichment, respectively, in schizophrenia and hypertrophic cardiomyopathy (HCM) heritability. I found that neural-specific enhancers are highly enriched in schizophrenia heritability -- especially when overlapping genomic regulatory blocks. Then I created partitioned polygenic risk scores for enhancer-based and non-enhancer-based SNPs, where enhancer-based SNPs are prioritised. I further compared the amount of adjusted heritability for both conditions explained by original GWAS vs partitioned polygenic risk scores, and found up to a 6.5% increase in the Coefficient of Determination for schizophrenia, and similar amounts for HCM -- however, this was not statistically significant. The increasing trend was specific for brain-expressed enhancers in schizophrenia, while it was widespread for HCM. Finally, I considered whether neural-specific enhancer-based partitions might be better modelled in GWAS using nonadditive effects, however my results were inconclusive due to small sample sizes.
Legislative & Prenormative actions
Creators: name: Duran, Maria Vera
Publisher: name: Zenodo
Year: 2023

description: This deliverable (D7.7), prepared within the WP7: “Pre-normative studies, dissemination,
 communication, and exploitation”, offers a panoramic description of the legislative context as
 well as the standardization landscape for multilayer plastic films.
 The first section (PART A) of this deliverable addresses the EU directives and National plans in
 particular in France, Spain, the Netherlands and Finland, having impacts on multilayer films
 circularity, from their design to their end-of-life management and recycling. This includes offer
 and demand, business models, regulation through tax, EU & National drivers, etc...
 The report covers legislative texts which are not legally binding (i.e. Communications and
 Recommendations), as well as those that are (i.e. Directives and Regulations).
 A second section (PART B) collects information on the standardization landscape and needs for
 updated or new standards to achieve circularity of multilayer films, supported by the CIMPA
 partners involved in technical standardisation committees. As a result, this deliverable includes
 a list of standards and technical bodies, with recommendations on actions about them.
 CIMPA project is focused on multilayer films from food and agricultural applications, thus, the
 legislation on the packaging and agriculture plastic sector are analyzed in this document.
 However, being the packaging sector the largest plastic end-use market, and due to the growing
 generation of packaging waste, more policy, legislation, and standardization initiatives are
 found for the packaging than agriculture sector.
 This document will be reviewed and updated including the developments of legislative actions
 and standards. A final report on legislative and pre-normative actions, with recommendations
 for legislative revisions and updated or new standards will be produced by M35.
Density matrix formulation of dynamical systems
Creators: name: Das, Swetamber
name: Green, Jason R.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Chaotic Dynamics (nlin.CD)
subject: FOS: Physical sciences

description: Physical systems that dissipate, mix and develop turbulence also irreversibly transport statistical density. In statistical physics, laws for these processes have a mathematical form and tractability that depends on whether the description is classical or quantum mechanical. Here, we establish a theory for density transport in any classical dynamical system that is analogous to the density matrix formulation of quantum mechanics. Defining states in terms of a classical density matrix leads to generalizations of Liouville's theorem and Liouville's equation, establishing an alternative computationally-tractable basis for nonequilibrium statistical mechanics. The formalism is complete with classical commutators and anti-commutators that embed measures of local instability and chaos and are directly related to Poisson brackets when the dynamics are Hamiltonian. It also recovers the traditional Liouville equation and the Liouville theorem by imposing trace preservation or Hamiltonian dynamics. Applying to systems that are driven, transient, dissipative, regular, and chaotic, this formalism has the potential for broad applications.
description: Section "Case studies": damped Harmonic oscillator discussion expanded, a new plot added in appendix F
Flaws in the U.S. Food and Drug Administration's Rationale for Supporting the Development and Approval of BiDil as a Treatment for Heart Failure Only in Black Patients
Creators: name: Ellison, George T. H.
name: Kahn, Jonathan D.
name: Kaufman, Jay S.
name: Martin, Paul A.
name: Head, Rosemary F.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: The U.S. Food and Drug Administration's (FDA) rationale for supporting the development and approval of BiDil (a combination of hydralazine hydrochloride and isosorbide dinitrate; H-I) for heart failure specifically in black patients was based on under-powered, post hoc subgroup analyses of two relatively old trials (V-HeFT I and II), which were further complicated by substantial covariate imbalances between racial groups. Indeed, the only statistically significant difference observed between black and white patients was found without any adjustment for potential confounders in samples that were unlikely to have been adequately randomized. Meanwhile, because the accepted baseline therapy for heart failure has substantially improved since these trials took place, their results cannot be combined with data from the more recent trial (A-HeFT) amongst black patients alone. There is therefore little scientific evidence to support the approval of BiDil only for use in black patients, and the FDA's rationale fails to consider the ethical consequences of recognizing racial categories as valid markers of innate biological difference, and permitting the development of group-specific therapies that are subject to commercial incentives rather than scientific evidence or therapeutic imperatives. This paper reviews the limitations in the scientific evidence used to support the approval of BiDil only for use in black patients; calls for further analysis of the V-HeFT I and II data which might clarify whether responses to H-I vary by race; and evaluates the consequences of commercial incentives to develop racialized medicines. We recommend that the FDA revise the procedures they use to examine applications for race-based therapies to ensure that these are based on robust scientific claims and do not undermine the aims of the 1992 Revitalization Act.
A Trade Secret Model for Genomic Biobanking
Creators: name: Cadigan, R. Jean
name: Mitchell, Robert
name: Davis, Arlene M.
name: Dobson, Allison W.
name: Gladden, Ryan Q.
name: Conley, John M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Genomic biobanks present ethical challenges that are qualitatively unique and quantitatively unprecedented. Many critics have questioned whether the current system of informed consent can be meaningfully applied to genomic biobanking. Proposals for reform have come from many directions, but have tended to involve incremental change in current informed consent practice. This paper reports on our efforts to seek new ideas and approaches from those whom informed consent is designed to protect: research subjects. Our model emerged from semi-structured interviews with healthy volunteers who had been recruited to join either of two biobanks (some joined, some did not), and whom we encouraged to explain their concerns and how they understood the relationship between specimen contributors and biobanks. These subjects spoke about their DNA and the information it contains in ways that were strikingly evocative of the legal concept of the trade secret. They then described the terms and conditions under which they might let others study their DNA, and there was a compelling analogy to the commonplace practice of trade secret licensing. We propose a novel biobanking model based on this trade secret concept, and argue that it would be a practical, legal, and ethical improvement on the status quo.
What Research Ethics Should Learn from Genomics and Society Research: Lessons from the ELSI Congress of 2011
Creators: name: Kuczynski, Kristine
name: King, Nancy M. P.
name: Henderson, Gail E.
name: Michie, Marsha
name: Juengst, Eric T.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Research on the ethical, legal, and social implications (ELSI) of human genomics has devoted significant attention to the research ethics issues that arise from genomic science as it moves through the translational process. Given the prominence of these issues in today's debates over the state of research ethics overall, these studies are well positioned to contribute important data, contextual considerations, and policy arguments to the wider research ethics community's deliberations, and ultimately to develop a research ethics that can help guide biomedicine's future. In this essay, we illustrate this thesis through an analytic summary of the research presented at the 2011 ELSI Congress, an international meeting of genomics and society researchers. We identify three pivotal factors currently shaping genomic research, its clinical translation, and its societal implications: (1) the increasingly blurred boundary between research and treatment; (2) uncertainty — that is, the indefinite, indeterminate, and incomplete nature of much genomic information and the challenges that arise from making meaning and use of it; and (3) the role of negotiations between multiple scientific and non-scientific stakeholders in setting the priorities for and direction of biomedical research, as it is increasingly conducted “in the public square.”
Analysis of relative dispersion of two particles by Lagrangian stochastic models and DNS methods
Creators: name: Kurbanmuradov, Orazgeldi
name: Orszag, Steven A.
name: Sabelfeld, Karl K.
name: Yeung, P. K.
Publisher: name: Weierstrass Institute
Year: 2000
Subjects: subject: Turbulent flows
subject: Lagrangian trajectories
subject: separation vector
subject: DNS method
subject: 65C05
subject: 76N20

description: Comparisons of the Q1D against the known Lagrangian stochastic well-mixed quadratic form models and the moments approximation models are presented. In the case of modestly large Reynolds numbers turbulence (Re λ ⋍ 240) the comparison of the Q1D model with the DNS data is made. Being in a qualitatively agreemnet with the DNS data, the Q1D model predicts higher rate of separation. Realizability of Q1D model extracted from the transport equation with a quadratic form of the conditional acceleration is shown.
Efficiency in colonoscopy
Creators: name: Ahmad, Ahmir
Publisher: name: Imperial College London
Year: 2022

description: Global trends, including demographic changes, are significantly increasing the demand and cost of healthcare. Endoscopy services are no exception and, even before the Covid-19 pandemic, significant pressure resulted in many units failing to meet cancer wait targets. The need to improve efficiency has never been greater and particularly so for colonoscopy which significantly reduces morbidity and mortality from colorectal cancer. Today, advances in colonoscope technologies and emergence of artificial intelligence offer the potential for improved colonoscopy practice. The aim of this thesis is to explore how efficiency in colonoscopy can be enhanced throughout the patient pathway. Five major studies were performed evaluating bowel preparation (CLEANSE), polyp detection (AI-DETECT), optical diagnosis (DISCARD3), insertion technique (WAVE) and post-colonoscopy colorectal cancer (AI-DETECT). CLEANSE is an evaluation of a novel low-volume same-day bowel preparation regime (Plenvu) and showed this offers a more efficient bowel cleansing option than standard regimens. AI-DETECT is a randomised study evaluating a computer-aided detection (CADe) system (GI Genius) and showed a borderline significant improvement in polyp detection is achieved amongst high performing endoscopists. DISCARD3 is a major evaluation of optical diagnosis with a “resect and discard” strategy exploring the learning curve, quality assurance process, causes of error and economic impact. This study shows such a strategy is feasible and safe and could potentially be implemented with a quality assurance process in place within the English Bowel Cancer Screening Progamme (BCSP). WAVE is a randomised study evaluating colonoscopy insertion technique. This showed a ‘hybrid’ insertion technique is more efficient than a water-exchange colonoscopy technique. REFLECT is a retrospective evaluation of post-colonoscopy colorectal cancer cases identified at national level and showed after local root cause analysis a significant proportion were in fact detected cancers. These studies provide valuable insights that we hope will ultimately lead to more efficient colonoscopy whilst maintaining quality and enhancing patient care.
Clinical Integration of Next Generation Sequencing: Coverage and Reimbursement Challenges
Creators: name: Deverka, Patricia A.
name: Dreyfus, Jennifer C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Public and private payers face complex decisions regarding whether, when, and how to cover and reimburse for next generation sequencing (NGS)-based tests. Yet a predictable reimbursement pathway is critical both for patient access and incentives to provide the market with better clinical evidence. While preliminary data suggests that payers will use similar evidentiary standards as those used to evaluate established molecular diagnostic tests, the volume and complexity of information generated by NGS raises a host of additional considerations for payers that are specific to this technology.
Good enough practices in data management and how to translate these in data management plans (DMPs)
Creators: name: Milotic, Tanja
Publisher: name: Zenodo
Year: 2018
Subjects: research data management
biodiversity data
freshwater biodiversity
data archaeology
SAFRED

description: This document provides some generic guidelines for the preparation of a data management plan (DMP) and gives guidance for research data management (RDM). These guidelines have been drafted as an output of the Belgian SAFRED project. The goal of the Belspo funded BRAIN project SAFRED (Saving Freshwater Biodiversity Research Data) was to achieve systematic recovery and publication of data generated in freshwater research. SAFRED ran from the end of 2015 until september 2018 and was collaborative project between KULeuven, UGent, ULg, INBO, UNamur, BBPf, BOKU and RBINSto publish Belgian freshwater biodiversity data. The mobilised data were published online at GBIF with the assistance of the Belgian Biodiversity Platform and the Freshwater Information Platform. As many of the problems of retrieving old research data could have been avoided by good data management, these guidelines for research data management and DMP writing have been written in order to avoid similar problems in future projects and to stimulate project partners to improve their day-to-day data management practices. As the purpose of this project was to recover freshwater biodiversity data, examples are given for biodiversity data, but most of the guidelines are easily applicable for other fields of research as well.
Asteroseismic stellar activity relations
Creators: name: Bonanno, A.
name: Corsaro, E.
name: Karoff, C.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: In asteroseismology an important diagnostic of the evolutionary status of a star is the small frequency separation which is sensitive to the gradient of the mean molecular weight in the stellar interior. It is thus interesting to discuss the classical age-activity relations in terms of this quantity. Moreover, as the photospheric magnetic field tends to suppress the amplitudes of acoustic oscillations, it is important to quantify the importance of this effect by considering various activity indicators. We propose a new class of age-activity relations that connects the Mt. Wilson $S$ index and the average scatter in the light curve with the small frequency separation and the amplitude of the p-mode oscillations. We used a Bayesian inference to compute the posterior probability of various empirical laws for a sample of 19 solar-like active stars observed by the Kepler telescope. We demonstrate the presence of a clear correlation between the Mt. Wilson $S$ index and the relative age of the stars as indicated by the small frequency separation, as well as an anti-correlation between the $S$ index and the oscillation amplitudes. We argue that the average activity level of the stars shows a stronger correlation with the small frequency separation than with the absolute age that is often considered in the literature. The phenomenological laws discovered in this paper have the potential to become new important diagnostics to link stellar evolution theory with the dynamics of global magnetic fields. In particular we argue that the relation between the Mt. Wilson $S$ index and the oscillation amplitudes is in good agreement with the findings of direct numerical simulations of magneto-convection.
description: 5 pages, 4 figures, 2 tables. Accepted for publication in A&A