cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Efficiently identifying genome-wide changes with next-generation sequencing data
Creators: name: Huang, Weichun
name: Vincent Jordan, Nicole
name: Johnson, Gary L.
name: Abell, Amy N.
name: Li, Leping
name: Umbach, David M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: We propose a new and effective statistical framework for identifying genome-wide differential changes in epigenetic marks with ChIP-seq data or gene expression with mRNA-seq data, and we develop a new software tool EpiCenter that can efficiently perform data analysis. The key features of our framework are: (i) providing multiple normalization methods to achieve appropriate normalization under different scenarios, (ii) using a sequence of three statistical tests to eliminate background regions and to account for different sources of variation and (iii) allowing adjustment for multiple testing to control false discovery rate (FDR) or family-wise type I error. Our software EpiCenter can perform multiple analytic tasks including: (i) identifying genome-wide epigenetic changes or differentially expressed genes, (ii) finding transcription factor binding sites and (iii) converting multiple-sample sequencing data into a single read-count data matrix. By simulation, we show that our framework achieves a low FDR consistently over a broad range of read coverage and biological variation. Through two real examples, we demonstrate the effectiveness of our framework and the usages of our tool. In particular, we show that our novel and robust ‘parsimony’ normalization method is superior to the widely-used ‘tagRatio’ method. Our software EpiCenter is freely available to the public.
Linear Streptomyces plasmids form superhelical circles through interactions between their terminal proteins
Creators: name: Huang, Chih Hung
name: Tsai, Hsiu Hui
name: Tessmer, Ingrid
name: Chen, Carton W.
name: Erie, Dorothy A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Linear chromosomes and linear plasmids of Streptomyces possess covalently bound terminal proteins (TPs) at the 5′ ends of their telomeres. These TPs are proposed to act as primers for DNA synthesis that patches the single-stranded gaps at the 3′ ends during replication. Most (‘archetypal’) Streptomyces TPs (designated Tpg) are highly conserved in size and sequence. In addition, there are a number of atypical TPs with heterologous sequences and sizes, one of which is Tpc that caps SCP1 plasmid of Streptomyces coelicolor. Interactions between the TPs on the linear Streptomyces replicons have been suggested by electrophoretic behaviors of TP-capped DNA and circular genetic maps of Streptomyces chromosomes. Using chemical cross-linking, we demonstrated intramolecular and intermolecular interactions in vivo between Tpgs, between Tpcs and between Tpg and Tpc. Interactions between the chromosomal and plasmid telomeres were also detected in vivo. The intramolecular telomere interactions produced negative superhelicity in the linear DNA, which was relaxed by topoisomerase I. Such intramolecular association between the TPs poses a post-replicational complication in the formation of a pseudo-dimeric structure that requires resolution by exchanging TPs or DNA.
Cusp Summations and Cusp Relations of Simple Quad Lenses
Creators: name: Chu, Zhe
name: Li, G. L.
name: Lin, W. P.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We review five often used quad lens models, each of which has analytical solutions and can produce four images at most. Each lens model has two parameters, including one that describes the intensity of non-dimensional mass density, and the other one that describes the deviation from the circular lens. In our recent work, we have found that the cusp and the fold summations are not equal to 0, when a point source infinitely approaches a cusp or a fold from inner side of the caustic. Based on the magnification invariant theory, which states that the sum of signed magnifications of the total images of a given source is a constant, we calculate the cusp summations for the five lens models. We find that the cusp summations are always larger than 0 for source on the major cusps, while can be larger or smaller than 0 for source on the minor cusps. We also find that if these lenses tend to the circular lens, the major and minor cusp summations will have infinite values, and with positive and negative signs respectively. The cusp summations do not change significantly if the sources are slightly deviated from the cusps. In addition, through the magnification invariants, we also derive the analytical signed cusp relations on the axes for three lens models. We find that both on the major and the minor axes the larger the lenses deviated from the circular lens, the larger the signed cusp relations. The major cusp relations are usually larger than the absolute minor cusp relations, but for some lens models with very large deviation from circular lens, the minor cusp relations can be larger than the major cusp relations.
description: 8 pages, 4 figures, accepted for publication in MNRAS
Die Bedeutung der Sprache für Kinder mit Migrationshintergrund
Darstellung von Wissensbeständen zum Thema Erste Hilfe im sachunterrichtlichen Kontext
Creators: name: Zeybek, Durdane
Publisher: name: Universität Kassel
Year: 2022
Subjects: subject: Mehrsprachigkeit
subject: Migrationshintergrund
subject: Sachunterricht
subject: Gesundheitserziehung
subject: Lernstandsbezogene Fallanalyse
subject: 300
subject: 370
subject: Mehrsprachigkeit
subject: Migrationshintergrund
subject: Sachunterricht
subject: Gesundheitserziehung
subject: Erste Hilfe
subject: Deutschland

description: Zugleich: Dissertation, Universität Kassel, 2021
Additional file 1 of Identifying barriers and facilitators to successful implementation of computerized clinical decision support systems in hospitals: a NASSS framework-informed scoping review
Creators: name: Abell, Bridget
name: Naicker, Sundresan
name: Rodwell, David
name: Donovan, Thomasina
name: Tariq, Amina
name: Baysari, Melissa
name: Blythe, Robin
name: Parsons, Rex
name: McPhail, Steven M.
Publisher: name: figshare
Year: 2023
Subjects: subject: Information Systems
subject: FOS: Computer and information sciences

description: Additional file 1. Refinement of search strategy.
DigiTala's questionnaire for upper-secondary language teachers on oral language skills
Creators: name: von Zansen, Anna
Publisher: name: Zenodo
Year: 2023
Subjects: DigiTala
upper-secondary language teachers
teacher beliefs
questionnaire
survey
oral language assessment
oral language skills

description: The teacher questionnaire was conducted by the DigiTala project in the beginning of the year 2023. The questionnaire included follow-up items that have been used by the research team earlier and enable. The teachers got contacted through different mailing lists but a link to the questionnaire was also distributed through social media. In total 129 teachers answered the questionnaire. The questionnaire consisted of 5 sections: the first concerned teachers' background information, in the second section the teachers were asked about their oral language assessment practices, in the third section teachers responded to items dealing with the future of oral language assessment, in the fourth section teachers were asked about the Digitala Moodle plugin while the last section concerned teachers' needs for further training. We thank the colleagues and teachers involved in testing and developing the questionnaire for their insightful comments
Cluster Density Matrix Embedding Theory for Quantum Spin Systems
Creators: name: Fan, Zhuo
name: Jie, Quanlin
Publisher: name: arXiv
Year: 2015
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We applied cluster density matrix embedding theory, with some modifications, to a spin lattice system. The reduced density matrix of the impurity cluster is embedded in the bath states, which are a set of block-product states. The ground state of the impurity model is formulated using a variational wave function. We tested this theory in a two-dimensional (2-D) spin-1/2 J1-J2 model for a square lattice. The ground-state energy (GSE) and the location of the phase boundaries agree well with the most accurate previous results obtained using the quantum Monte Carlo and coupled cluster methods. Moreover, this cluster density matrix embedding theory is cost-effective and convenient for calculating the von Neumann entropy, which is related to the quantum phase transition.
description: 24 pages, 5figs, accepted by Phys. Rev. B
Supplements S1 to S7 from Biotic predictors complement models of bat and bird responses to climate and tree diversity in European forests.
Creators: name: Barbaro, Luc
name: Allan, Eric
name: Ampoorter, Evy
name: Castagneyrol, Bastien
name: Yohan Charbonnier
name: Wandeler, Hans De
name: Kerbiriou, Christian
name: Milligan, Harriet T.
name: Vialatte, Aude
name: Carnol, Monique
name: Deconchat, Marc
name: Pallieter De Smedt
name: Jactel, Hervé
name: Koricheva, Julia
name: Viol, Isabelle Le
name: Muys, Bart
name: Scherer-Lorenzen, Michael
name: Verheyen, Kris
name: Plas, Fons Van Der
Publisher: name: The Royal Society
Year: 2019
Subjects: subject: Ecology
subject: FOS: Biological sciences

description: S1 Location map; S2 rarefaction curves; S3 bat and bird trait tables; S4 bat STIs; S5 bat SSIs; S6 null models for FDiv; S7 additional sampling methods
The American War in Afghanistan Concluded Precisely as it had begun, but the Outcome was War Crime
Creators: name: Ibrahimy, Habibullah
Publisher: name: figshare
Year: 2023
Subjects: Conflict of laws (incl. private international law)
International finance
International and development communication
Public international law
International humanitarian and human rights law
International and comparative law not elsewhere classified
International criminal law

description: War crimes are described as acts that gravely violate the Geneva Conventions, Additional Protocol I, and Additional Protocol II, as well as the rules and conventions of war established by the Hague Conventions of 1899 and 1907. Although the occupying power should be bound by several provisions of the 1949 Fourth Geneva Convention as long as "such Power exercises the functions of government in such territory," the protection of civilians and prisoners of war during military occupation is extended for a year after the end of hostilities, even in the case where there is no armed resistance. This article includes a concise overview of incidents where war crimes are alleged to have taken place, including the summary execution of enemy combatants who have been captured, abuse of detainees during interrogation, the use of torture, violence against civilians and non-combatants, and the needless destruction of civilian property.
Additional file 2 of Identifying barriers and facilitators to successful implementation of computerized clinical decision support systems in hospitals: a NASSS framework-informed scoping review
Creators: name: Abell, Bridget
name: Naicker, Sundresan
name: Rodwell, David
name: Donovan, Thomasina
name: Tariq, Amina
name: Baysari, Melissa
name: Blythe, Robin
name: Parsons, Rex
name: McPhail, Steven M.
Publisher: name: figshare
Year: 2023
Subjects: subject: Information Systems
subject: FOS: Computer and information sciences

description: Additional file 2. Visual summary of synthesis and analysis process and mapping to key results and figures.
Regulation of nucleotide excision repair activity by transcriptional and post-transcriptional control of the XPA protein
Creators: name: Kang, Tae Hong
name: Reardon, Joyce T.
name: Sancar, Aziz
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: The XPA (Xeroderma pigmentosum A) protein is one of the six core factors of the human nucleotide excision repair system. In this study we show that XPA is a rate-limiting factor in all human cell lines tested, including a normal human fibroblast cell line. The level of XPA is controlled at the transcriptional level by the molecular circadian clock and at the post-translational level by a HECT domain family E3 ubiquitin ligase called HERC2. Stabilization of XPA by downregulation of HERC2 moderately enhances excision repair activity. Conversely, downregulation of XPA by siRNA reduces excision repair activity in proportion to the level of XPA. Ubiquitination and proteolysis of XPA are inhibited by DNA damage that promotes tight association of the protein with chromatin and its dissociation from the HERC2 E3 ligase. Finally, in agreement with a recent report, we find that XPA is post-translationally modified by acetylation. However, contrary to the previous claim, we find that in mouse liver only a small fraction of XPA is acetylated and that downregulation of SIRT1 deacetylase in two human cell lines does not affect the overall repair rate. Collectively, the data reveal that XPA is a limiting factor in excision repair and that its level is coordinately regulated by the circadian clock, the ubiquitin–proteasome system and DNA damage.
A Capstone Project Submitted to the School of Graduate Studies of Addis Ababa University in Partial Fulfillment of the Requirements for the Degree Masters of Hospital and Health Care Administration
Creators: name: NEBAT TOFFIK
Publisher: name: Zenodo
Year: 2018

description: Introduction: Patient satisfaction is a primary means of measuring the effectiveness of healthcare delivery. Patients

have Explicit desires for quality services when they visit health institutions. The care in the OPD is believed to

indicate thequality of services of a hospital and is reflected by patients' satisfaction with the services being provided.

Hence, this Study aimed to determine the level and determinants of patient satisfaction with outpatient department of

St Paul’s Hospital millennium medical collage A.A, Ethiopia

Problem Statement: --in St Paul’s Hospital Millennium medical college, out patient satisfaction score is below the

standard which is56% at pre-assessment period but the standard is above 80%.

Objective: -To improve out patient satisfaction of St Paul’s Hospital millennium medical collage from baseline of

56%in February 2018GC to 75%in June 2018 GC this 75% is decided after different literatures reviewed and also

because of shortage of time and cost
Accessing phonon polaritons in hyperbolic crystals by ARPES
Creators: name: Tomadin, Andrea
name: Principi, Alessandro
name: Song, Justin C. W.
name: Levitov, Leonid S.
name: Polini, Marco
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Recently studied hyperbolic materials host unique phonon-polariton (PP) modes. The ultra-short wavelengths of these modes, which can be much smaller than those of conventional exciton-polaritons, are of high interest for extreme sub-diffraction nanophotonics schemes. Polar hyperbolic materials such as hexagonal boron nitride can be used to realize strong long-range coupling between PP modes and extraneous charge degrees of freedom. The latter, in turn, can be used to control and probe PP modes. Of special interest is coupling between PP modes and plasmons in an adjacent graphene sheet, which opens the door to accessing PP modes by angle-resolved photoemission spectroscopy (ARPES). A rich structure in the graphene ARPES spectrum due to PP modes is predicted, providing a new probe of PP modes and their coupling to graphene plasmons.
Tup1 stabilizes promoter nucleosome positioning and occupancy at transcriptionally plastic genes
Creators: name: Mieczkowski, Piotr A.
name: Rizzo, Jason M.
name: Buck, Michael J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Despite technical advances, the future of chromatin mapping studies requires an ability to draw accurate comparisons between different chromatin states to enhance our understanding of genome biology. In this study, we used matched chromatin preparations to enable specific and accurate comparisons of Saccharomyces cerevisiae chromatin structures in the presence and absence of the co-repressor protein Tup1. Analysis of wild-type and tup1 Δ chromatin data sets revealed unique organizational themes relating to the function of Tup1. Regulatory regions bound by Tup1 assumed a distinct chromatin architecture composed of a wide nucleosome-depleted region, low occupancy/poorly positioned promoter nucleosomes, a larger number and wider distribution of transcription factor-binding sites and downstream genes with enhanced transcription plasticity. Regions of Tup1-dependent chromatin structure were defined for the first time across the entire yeast genome and are shown to strongly overlap with activity of the chromatin remodeler Isw2. Additionally, Tup1-dependent chromatin structures are shown to relate to distinct biological processes and transcriptional states of regulated genes, including Tup1 stabilization of Minus 1 and Minus 2 promoter nucleosomes at actively repressed genes. Together these results help to enhance our mechanistic understanding of Tup1 regulation of chromatin structure and gene expression.
Two-dimensional discrete topology optimization and comparison of mathematical problem formulations
Creators: name: Panagiotopoulos, Vasilios
Publisher: name: Zenodo
Year: 2022

description: STO is a mathematical form finding problem formulation, that the last years matured, from an academic subject to an applied sciences’ practical design tool. So far, STO is implemented in real-world applications of the automotive, aerospace and other fields of the mechanical engineering industry. Its contribution to the AEC industry is limited to applications that rely only on the conceptual design process. The main scope of this research is to establish some mathematical STO formulations for supporting the design phases of large-scale civil engineering structural systems from the conceptual design phase to the final one. The interpretation and constructability of the final layout of the STO procedure, is a specific issue that is considered throughout this research. The generation of structural systems composed of discrete members is also an aim of the presented study.
Chromatin architectures at fission yeast transcriptional promoters and replication origins
Creators: name: Huberman, Joel A.
name: Buck, Michael J.
name: Givens, Robert M.
name: Rizzo, Jason M.
name: Mieczkowski, Piotr A.
name: Lai, William K.M.
name: Bard, Jonathan E.
name: Leatherwood, Janet
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: We have used micrococcal nuclease (MNase) digestion followed by deep sequencing in order to obtain a higher resolution map than previously available of nucleosome positions in the fission yeast, Schizosaccharomyces pombe. Our data confirm an unusually short average nucleosome repeat length, ∼152 bp, in fission yeast and that transcriptional start sites (TSSs) are associated with nucleosome-depleted regions (NDRs), ordered nucleosome arrays downstream and less regularly spaced upstream nucleosomes. In addition, we found enrichments for associated function in four of eight groups of genes clustered according to chromatin configurations near TSSs. At replication origins, our data revealed asymmetric localization of pre-replication complex (pre-RC) proteins within large NDRs—a feature that is conserved in fission and budding yeast and is therefore likely to be conserved in other eukaryotic organisms.
Supplements S1 to S6 from Biotic predictors complement models of bat and bird responses to climate and tree diversity in European forests
Creators: name: Barbaro, Luc
name: Allan, Eric
name: Ampoorter, Evy
name: Castagneyrol, Bastien
name: Yohan Charbonnier
name: Wandeler, Hans De
name: Kerbiriou, Christian
name: Milligan, Harriet T.
name: Vialatte, Aude
name: Carnol, Monique
name: Deconchat, Marc
name: Pallieter De Smedt
name: Jactel, Hervé
name: Koricheva, Julia
name: Viol, Isabelle Le
name: Muys, Bart
name: Scherer-Lorenzen, Michael
name: Verheyen, Kris
name: Plas, Fons Van Der
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Ecology
subject: FOS: Biological sciences

description: S1 rarefaction curves; S2 bat and bird trait tables; S3 bat STIs; S4 bat SSIs; S5 null models for FDiv; S6 additional sampling methods
Determinants of mRNA recognition and translation regulation by Lin28
Creators: name: Ma, Wei
name: Xu, Jie
name: Huang, Yingqun
name: Newman, Martin A.
name: Hammond, Scott M.
name: Qiao, Chong
name: Lei, Xin Xiang
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Lin28 is critical for stem cell maintenance and is also associated with advanced human malignancies. Our recent genome-wide studies mark Lin28 as a master post-transcriptional regulator of a subset of messenger RNAs important for cell growth and metabolism. However, the molecular basis underpinning the selective mRNA target regulation is unclear. Here, we provide evidence that Lin28 recognizes a unique motif in multiple target mRNAs, characterized by a small but critical ‘A’ bulge flanked by two G:C base pairs embedded in a complex secondary structure. This motif mediates Lin28-dependent stimulation of translation. As Lin28 is also known to inhibit the biogenesis of a cohort of miRNAs including let-7, we propose that Lin28 binding to different RNA types (precursor miRNAs versus mRNAs) may facilitate recruitment of different co-factors, leading to distinct regulatory outcomes. Our findings uncover a putative yet unexpected motif that may constitute a mechanistic base for the multitude of functions regulated by Lin28 in both stem cells and cancer cells.
The VIMOS Public Extragalactic Redshift Survey (VIPERS). Hierarchical scaling and biasing
Creators: name: Cappi, A.
name: Marulli, F.
name: Bel, J.
name: Cucciati, O.
name: Branchini, E.
name: de la Torre, S.
name: Moscardini, L.
name: Bolzonella, M.
name: Guzzo, L.
name: Abbas, U.
name: Adami, C.
name: Arnouts, S.
name: Bottini, D.
name: Coupon, J.
name: Davidzon, I.
name: De Lucia, G.
name: Fritz, A.
name: Franzetti, P.
name: Fumana, M.
name: Garilli, B.
name: Granett, B. R.
name: Ilbert, O.
name: Iovino, A.
name: Krywult, J.
name: Brun, V. Le
name: Fèvre, O. Le
name: Maccagni, D.
name: Małek, K.
name: McCracken, H. J.
name: Paioro, L.
name: Polletta, M.
name: Pollo, A.
name: Scodeggio, M.
name: Tasca, L. A. . M.
name: Tojeiro, R.
name: Vergani, D.
name: Zanichelli, A.
name: Burden, A.
name: Di Porto, C.
name: Marchetti, A.
name: Marinoni, C.
name: Mellier, Y.
name: Nichol, R. C.
name: Peacock, J. A.
name: Percival, W. J.
name: Phleps, S.
name: Schimd, C.
name: Schlagenhaufer, H.
name: Wolk, M.
name: Zamorani, G.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We investigate the higher-order correlation properties of the VIMOS Public Extragalactic Redshift Survey (VIPERS) to test the hierarchical scaling hypothesis at z~1 and the dependence on galaxy luminosity, stellar mass, and redshift. We also aim to assess deviations from the linearity of galaxy bias independently from a previously performed analysis of our survey (Di Porto et al. 2014). We have measured the count probability distribution function in cells of radii 3 < R < 10 Mpc/h, deriving $σ_{8g}$, the volume-averaged two-,three-,and four-point correlation functions and the normalized skewness $S_{3g}$ and kurtosis $S_{4g}$ for volume-limited subsamples covering the ranges $-19.5 \le M_B(z=1.1)-5log(h) \le -21.0$, $9.0 < log(M*/M_{\odot} h^{-2}) \le 11.0$, $0.5 \le z < 1.1$. We have thus performed the first measurement of high-order correlations at z~1 in a spectroscopic redshift survey. Our main results are the following. 1) The hierarchical scaling holds throughout the whole range of scale and z. 2) We do not find a significant dependence of $S_{3g}$ on luminosity (below z=0.9 $S_{3g}$ decreases with luminosity but only at 1σ-level). 3) We do not detect a significant dependence of $S_{3g}$ and $S_{4g}$ on scale, except beyond z~0.9, where the dependence can be explained as a consequence of sample variance. 4) We do not detect an evolution of $S_{3g}$ and $S_{4g}$ with z. 5) The linear bias factor $b=σ_{8g}/σ_{8m}$ increases with z, in agreement with previous results. 6) We quantify deviations from the linear bias by means of the Taylor expansion parameter $b_2$. Our results are compatible with a null non-linear bias term, but taking into account other available data we argue that there is evidence for a small non-linear bias term.
description: 20 pages, 14 figures, accepted for publication in Astronomy and Astrophysics
Targeted silencing of the oncogenic transcription factor SOX2 in breast cancer
Creators: name: Rots, Marianne G.
name: Stolzenburg, Sabine
name: Qian, Haili
name: Strahl, Brian D.
name: Yuan, Xinni
name: Blancafort, Pilar
name: Rivenbark, Ashley G.
name: Beltran, Adriana S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: The transcription factor (TF) SOX2 is essential for the maintenance of pluripotency and self-renewal in embryonic stem cells. In addition to its normal stem cell function, SOX2 over-expression is associated with cancer development. The ability to selectively target this and other oncogenic TFs in cells, however, remains a significant challenge due to the ‘undruggable’ characteristics of these molecules. Here, we employ a zinc finger (ZF)-based artificial TF (ATF) approach to selectively suppress SOX2 gene expression in cancer cells. We engineered four different proteins each composed of 6ZF arrays designed to bind 18 bp sites in the SOX2 promoter and enhancer region, which controls SOX2 methylation. The 6ZF domains were linked to the Kruppel Associated Box (SKD) repressor domain. Three engineered proteins were able to bind their endogenous target sites and effectively suppress SOX2 expression (up to 95% repression efficiencies) in breast cancer cells. Targeted down-regulation of SOX2 expression resulted in decreased tumor cell proliferation and colony formation in these cells. Furthermore, induced expression of an ATF in a mouse model inhibited breast cancer cell growth. Collectively, these findings demonstrate the effectiveness and therapeutic potential of engineered ATFs to mediate potent and long-lasting down-regulation of oncogenic TF expression in cancer cells.
Bibliothèque du Service historique de la Défense - Une réinformatisation utile à la transition bibliographique : reformater ses données et intégrer le Sudoc
Creators: name: Bourdilleau, Théo
Publisher: name: Zenodo
Year: 2023
Subjects: Transition Bibliographique
Unimarc
Réinformatisation en bibliothèque

description: Ce retour d'expérience de la réinformatisation menée à la bibliothèque du Service historique de la Défense a été présenté à l'occasion de la séquence "l'actualité transition bibliographique dans mon établissement" lors de la réunion plénière du 24 janvier 2023. Deux aspects y sont principalement abordés : le travail de reformatage des données du Marc21 à l'Unimarc et l'accompagnement ainsi que la formation des équipes en lien avec l'application de nouvelles normes de la transition bibliographique et l'intégration du Sudoc.
Additional file 1 of Post COVID-19 condition and health-related quality of life: a longitudinal cohort study in the Belgian adult population
Creators: name: Smith, Pierre
name: De Pauw, Robby
name: Van Cauteren, Dieter
name: Demarest, Stefaan
name: Drieskens, Sabine
name: Cornelissen, Laura
name: Devleesschauwer, Brecht
name: De Ridder, Karin
name: Charafeddine, Rana
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: Science Policy
classificationCode: 111714
subject: Mental Health

description: Additional file 1.
The Drosophila 7SK snRNP and the essential role of dHEXIM in development
Creators: name: Saunders, Abbie
name: Rogers, Jason T.
name: Sedore, Stanley C.
name: Brogie, John E.
name: Rajendra, T. K.
name: Lis, John T.
name: Nguyen, Duy
name: Matera, A. Greg
name: Price, David H.
name: Uguen, Patricia
name: Krueger, Brian J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Regulation of the positive transcription elongation factor, P-TEFb, plays a major role in controlling mammalian transcription and this is accomplished in part by controlled release of P-TEFb from the 7SK snRNP that sequesters the kinase in an inactive state. We demonstrate here that a similar P-TEFb control system exists in Drosophila. We show that an RNA previously suggested to be a 7SK homolog is, in fact, associated with P-TEFb, through the action of a homolog of the human HEXIM1/2 proteins (dHEXIM). In addition, a Drosophila La related protein (now called dLARP7) is shown to be the functional homolog of human LARP7. The Drosophila 7SK snRNP (d7SK snRNP) responded to treatment of cells with P-TEFb inhibitors and to nuclease treatment of cell lysates by releasing P-TEFb. Supporting a critical role for the d7SK snRNP in Drosophila development, dLARP7 and dHEXIM were found to be ubiquitously expressed throughout embryos and tissues at all stages. Importantly, knockdown of dHEXIM was embryonic lethal, and reduction of dHEXIM in specific tissues led to serious developmental defects. Our results suggest that regulation of P-TEFb by the d7SK snRNP is essential for the growth and differentiation of tissues required during Drosophila development.
An equal area law for holographic entanglement entropy of the AdS-RN black hole
Creators: name: Nguyen, Phuc H.
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: The Anti-de Sitter-Reissner-Nordstrom (AdS-RN) black hole in the canonical ensemble undergoes a phase transition similar to the liquid-gas phase transition, i.e. the isocharges on the entropy-temperature plane develop an unstable branch when the charge is smaller than a critical value. It was later discovered that the isocharges on the entanglement entropy-temperature plane also exhibit the same van der Waals-like structure, for spherical entangling regions. In this paper, we present numerical results which sharpen this similarity between entanglement entropy and black hole entropy, by showing that both of these entropies obey Maxwell's equal area law to an accuracy of around 1 %. Moreover, we checked this for a wide range of size of the spherical entangling region, and the equal area law holds independently of the size. We also checked the equal area law for AdS-RN in 4 and 5 dimensions, so the conclusion is not specific to a particular dimension. Finally, we repeated the same procedure for a similar, van der Waals-like transition of the dyonic black hole in AdS in a mixed ensemble (fixed electric potential and fixed magnetic charge), and showed that the equal area law is not valid in this case. Thus the equal area law for entanglement entropy seems to be specific to the AdS-RN background.
description: 17 pages, multiple figures. v4: matches published version
On fractional Laplacians -- 3
Creators: name: Musina, Roberta
name: Nazarov, Alexander I.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics
subject: 47A63, 35A23

description: We investigate the role of the noncompact group of dilations in $\mathbb R^n$ on the difference of the quadratic forms associated to the fractional Dirichlet and Navier Laplacians. Then we apply our results to study the Brezis--Nirenberg effect in two families of noncompact boundary value problems involving the Navier-Laplacian.
description: 13 pages
Main analysis and additional results from Toxins or medicines? Phytoplankton diets mediate host and parasite fitness in a freshwater system.
Creators: name: Sánchez, Kristel F.
name: Huntley, Naomi
name: Duffy, Meghan A.
name: Hunter, Mark D.
Publisher: name: The Royal Society
Year: 2019
Subjects: subject: Ecology
subject: FOS: Biological sciences

description: This file contains all the analysis done for the study and additional figures of the main results. It also contains results on resistance not provided on the main manuscript. This file also contains a table with general information on the phytoplankton strains used in our study
A non-catalytic role of DNA polymerase η in recruiting Rad18 and promoting PCNA monoubiquitination at stalled replication forks
Creators: name: Tateishi, Satoshi
name: Durando, Michael
name: Vaziri, Cyrus
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Trans-lesion DNA synthesis (TLS) is a DNA damage-tolerance mechanism that uses low-fidelity DNA polymerases to replicate damaged DNA. The inherited cancer-propensity syndrome xeroderma pigmentosum variant (XPV) results from error-prone TLS of UV-damaged DNA. TLS is initiated when the Rad6/Rad18 complex monoubiquitinates proliferating cell nuclear antigen (PCNA), but the basis for recruitment of Rad18 to PCNA is not completely understood. Here, we show that Rad18 is targeted to PCNA by DNA polymerase eta (Polη), the XPV gene product that is mutated in XPV patients. The C-terminal domain of Polη binds to both Rad18 and PCNA and promotes PCNA monoubiquitination, a function unique to Polη among Y-family TLS polymerases and dissociable from its catalytic activity. Importantly, XPV cells expressing full-length catalytically-inactive Polη exhibit increased recruitment of other error-prone TLS polymerases (Polκ and Polι) after UV irradiation. These results define a novel non-catalytic role for Polη in promoting PCNA monoubiquitination and provide a new potential mechanism for mutagenesis and genome instability in XPV individuals.
The Temporal Constitution of Democracies
Creators: name: Schäfer, Andreas
name: Merkel, Wolfgang
Publisher: name: Humboldt-Universität zu Berlin
Year: 2021
Subjects: subject: time requirements
subject: cycles
subject: horizons
subject: collective memory
subject: acceleration
subject: crisis
subject: vulnerability
subject: stability
subject: legitimacy
subject: states of emergency
subject: 320 Politikwissenschaft (Politik und Regierung)

description: The specific institutionalization of time is a major defining element of democracies and a vulnerable condition of their stability and legitimacy. The first part of the chapter covers the regular temporal routines of democratic systems. In the synchronic dimension, it considers the time requirements of democratic practices and examines the timed relationship between different levels and actors of the democratic system. In the diachronic dimension, the chapter asks for the time horizons that temporal constitutions of democracies create for political actors—related to future expectations and to past experiences. The second part of the chapter turns to time challenges democracies face today. First, it addresses the issue of social acceleration that goes along with potential vulnerabilities and adaptabilities of democratic systems. Second, the chapter discusses problems created by situations of crisis in states of emergency and in democratic transitions. Based on that, the chapter draws some conclusions for future research.
The electron in three-dimensional momentum space
Creators: name: Bacchetta, Alessandro
name: Mantovani, Luca
name: Pasquini, Barbara
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We study the electron as a system composed by an electron and a photon, using lowest order perturbation theory. We derive the leading-twist transverse-momentum-dependent distribution functions for both the electron and photon in the dressed electron, thereby offering a three-dimensional description of the dressed electron in momentum space. To obtain the distribution functions, we apply both the formalism of light-front wave function overlap representation and the diagrammatic approach. We perform the calculations both in light-cone gauge and Feynman gauge, and we present a detailed discussion of the role of the Wilson lines to obtain gauge-independent results. We provide numerical results and plots for many of the computed distributions.
description: 25 pages, 14 figures
Formation of Rotational Discontinuities in Compressive three-dimensional MHD Turbulence
Creators: name: Yang, Liping
name: Zhang, Lei
name: He, Jiansen
name: Tu, Chuanyi
name: Wang, Linghua
name: Marsch, Eckart
name: Wang, Xin
name: Zhang, Shaohua
name: Feng, Xueshang
Publisher: name: arXiv
Year: 2015
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Space Physics (physics.space-ph)
subject: FOS: Physical sciences

description: Measurements of solar wind turbulence reveal the ubiquity of discontinuities. In this study, we investigate how the discontinuities, especially rotational discontinuities (RDs), are formed in magnetohydrodynamic (MHD) turbulence. In a simulation of the decaying compressive three-dimensional (3-D) MHD turbulence with an imposed uniform background magnetic field, we detect RDs with sharp field rotations and little variations of magnetic field intensity as well as mass density. At the same time, in the de Hoffman-Teller (HT) frame, the plasma velocity is nearly in agreement with the Alfvén speed, and is field-aligned on both sides of the discontinuity. We take one of the identified RDs to analyze in details its 3-D structure and temporal evolution. By checking the magnetic field and plasma parameters, we find that the identified RD evolves from the steepening of the Alfvén wave with moderate amplitude, and that steepening is caused by the nonuniformity of the Alfvén speed in the ambient turbulence.
description: Five figures enclosed. Submitted to Astrophys. J., Under referring
Additional file 1 of Potential of Y. lipolytica epoxide hydrolase for efficient production of enantiopure (R)-1,2-octanediol
Creators: name: Godase, Vijaya P.
name: Kumar, V. Ravi
name: Kumar, Ameeta Ravi
Publisher: name: figshare
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Biotechnology
classificationCode: 39999
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Developmental Biology
subject: Marine Biology
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Hematology

description: Supplementary Material 1
BlackOPs: increasing confidence in variant detection through mappability filtering
Creators: name: Cabanski, Christopher R.
name: Neil Hayes, D.
name: Prins, Jan F.
name: Perou, Charles M.
name: Soloway, Matthew
name: Wilkerson, Matthew D.
name: Parker, Joel S.
name: Liu, Jinze
name: Marron, J. S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Identifying variants using high-throughput sequencing data is currently a challenge because true biological variants can be indistinguishable from technical artifacts. One source of technical artifact results from incorrectly aligning experimentally observed sequences to their true genomic origin (‘mismapping’) and inferring differences in mismapped sequences to be true variants. We developed BlackOPs, an open-source tool that simulates experimental RNA-seq and DNA whole exome sequences derived from the reference genome, aligns these sequences by custom parameters, detects variants and outputs a blacklist of positions and alleles caused by mismapping. Blacklists contain thousands of artifact variants that are indistinguishable from true variants and, for a given sample, are expected to be almost completely false positives. We show that these blacklist positions are specific to the alignment algorithm and read length used, and BlackOPs allows users to generate a blacklist specific to their experimental setup. We queried the dbSNP and COSMIC variant databases and found numerous variants indistinguishable from mapping errors. We demonstrate how filtering against blacklist positions reduces the number of potential false variants using an RNA-seq glioblastoma cell line data set. In summary, accounting for mapping-caused variants tuned to experimental setups reduces false positives and, therefore, improves genome characterization by high-throughput sequencing.
Observation of S = 1/2 quasi-one-dimensional magnetic and magneto-dielectric behavior in a cubic SrCuTe2O6
Creators: name: Koteswararao, B.
name: Panda, S. K.
name: Kumar, R.
name: Yoo, Kyongjun
name: Mahajan, A. V.
name: Dasgupta, I.
name: Chen, B. H.
name: Kim, Kee Hoon
name: Chou, F. C.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We investigate magnetic, thermal, and dielectric properties of SrCuTe2O6, which is isostructural to PbCuTe2O6, a recently found, Cu-based 3D frustrated magnet with a corner sharing triangular spin network having dominant first and second nearest neighbor (nn) couplings [B. Koteswararao, et al. Phys. Rev. B 90, 035141 (2014)]. Although SrCuTe2O6 has a structurally similar spin network, but the magnetic data exhibit the characteristic features of a typical quasi -one-dimensional magnet, which mainly resulted from the magnetically dominant third nn coupling, uniform chains. The magnetic properties of this system are studied via magnetization (M), heat capacity (Cp), dielectric constant, measurements along with ab-initio band structure calculations. Magnetic susceptibility chi(T) data show a broad maximum at 32 K and the system orders at low temperatures TN1=5.5 K and TN2=4.5 K, respectively. The analysis of chi(T) data gives an intra-chain coupling, J3/kB, to be about - 42 K with non-negligible frustrated inter-chain couplings (J1/kB and J2/kB). The hopping parameters obtained from LDA band structure calculations also suggest the presence of coupled uniform chains. The observation of simultaneous anomalies in dielectric constant at TN1 and TN2 suggests the presence of magneto-dielectric effect in SrCuTe2O6. A magnetic phase diagram is also built based on M, C p, and dielectric constant results.
description: 16 pages, 9 figures
Cell cycle stage-specific roles of Rad18 in tolerance and repair of oxidative DNA damage
Creators: name: Yang, Yang
name: Sproul, Chris
name: Durando, Michael
name: Oh, Sehyun
name: Hendrickson, Eric A.
name: Greenwalt, Alicia M.
name: Vaziri, Cyrus
name: Kaufmann, William
name: Smith-Roe, Stephanie L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: The E3 ubiquitin ligase Rad18 mediates tolerance of replication fork-stalling bulky DNA lesions, but whether Rad18 mediates tolerance of bulky DNA lesions acquired outside S-phase is unclear. Using synchronized cultures of primary human cells, we defined cell cycle stage-specific contributions of Rad18 to genome maintenance in response to ultraviolet C (UVC) and H2O2-induced DNA damage. UVC and H2O2 treatments both induced Rad18-mediated proliferating cell nuclear antigen mono-ubiquitination during G0, G1 and S-phase. Rad18 was important for repressing H2O2-induced (but not ultraviolet-induced) double strand break (DSB) accumulation and ATM S1981 phosphorylation only during G1, indicating a specific role for Rad18 in processing of oxidative DNA lesions outside S-phase. However, H2O2-induced DSB formation in Rad18-depleted G1 cells was not associated with increased genotoxin sensitivity, indicating that back-up DSB repair mechanisms compensate for Rad18 deficiency. Indeed, in DNA LigIV-deficient cells Rad18-depletion conferred H2O2-sensitivity, demonstrating functional redundancy between Rad18 and non-homologous end joining for tolerance of oxidative DNA damage acquired during G1. In contrast with G1-synchronized cultures, S-phase cells were H2O2-sensitive following Rad18-depletion. We conclude that although Rad18 pathway activation by oxidative lesions is not restricted to S-phase, Rad18-mediated trans-lesion synthesis by Polη is dispensable for damage-tolerance in G1 (because of back-up non-homologous end joining-mediated DSB repair), yet Rad18 is necessary for damage tolerance during S-phase.
Details of ssDNA annealing revealed by an HSV-1 ICP8–ssDNA binary complex
Creators: name: Makhov, Alexander M.
name: Ludtke, Steven J.
name: Griffith, Jack D.
name: Tolun, Gökhan
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Infected cell protein 8 (ICP8) from herpes simplex virus 1 was first identified as a single-strand (ss) DNA-binding protein. It is essential for, and abundant during, viral replication. Studies in vitro have shown that ICP8 stimulates model replication reactions, catalyzes annealing of complementary ssDNAs and, in combination with UL12 exonuclease, will catalyze ssDNA annealing homologous recombination. DNA annealing and strand transfer occurs within large oligomeric filaments of ssDNA-bound ICP8. We present the first 3D reconstruction of a novel ICP8–ssDNA complex, which seems to be the basic unit of the DNA annealing machine. The reconstructed volume consists of two nonameric rings containing ssDNA stacked on top of each other, corresponding to a molecular weight of 2.3 MDa. Fitting of the ICP8 crystal structure suggests a mechanism for the annealing reaction catalyzed by ICP8, which is most likely a general mechanism for protein-driven DNA annealing.
title: Maladie d’Alzheimer : soulager les symptômes comportementaux et psychologiques de la démence, un bienfait pour la qualité de vie
title: Maladie d’Alzheimer : soulager les symptômes comportementaux et psychologiques de la démence, un bienfait pour la qualité de vie
titleType: AlternativeTitle
Creators: name: Anderes, Lauriane
name: Sivaguru, Cajatthiry
Publisher: name: Unknown
Year: 0
Subjects: subject: Alzheimer

description: Avec le vieillissement de la population en Suisse, les cas de démences accompagnant de Symptômes Comportementaux et Psychologiques de la Démence (SCPD) sont en croissance exponentielle. En effet, plus la population est âgée, plus la prévalence de développer une maladie de type Alzheimer augmente. La prise en soin de ces pathologies est complexe. Des traitements médicamenteux sont utilisés pour soulager les patients présentant des SCPD. Cependant, les effets secondaires sont importants. C’est la raison pour laquelle la mise en place d’interventions infirmières s’avère nécessaire dans le but de soulager les SCPD et d’améliorer la qualité de vie des résidents.
Main analysis and additional results from Toxins or medicines? Phytoplankton diets mediate host and parasite fitness in a freshwater system
Creators: name: Sánchez, Kristel F.
name: Huntley, Naomi
name: Duffy, Meghan A.
name: Hunter, Mark D.
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Ecology
subject: FOS: Biological sciences

description: This file contains all the analysis done for the study and additional figures of the main results. It also contains results on resistance not provided on the main manuscript. This file also contains a table with general information on the phytoplankton strains used in our study