cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
On the universality of anomalous scaling exponents of structure functions in turbulent flows
Creators: name: Saw, E-W.
name: Debue, P.
name: Kuzzay, D.
name: Daviaud, F.
name: Dubrulle, B.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Chaotic Dynamics (nlin.CD)
subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences

description: All previous experiments in open turbulent flows (e.g. downstream of grids, jet and atmospheric boundary layer) have produced quantitatively consistent values for the scaling exponents of velocity structure functions. The only measurement in closed turbulent flow (von Kármán swirling flow) using Taylor-hypothesis, however, produced scaling exponents that are significantly smaller, suggesting that the universality of these exponents are broken with respect to change of large scale geometry of the flow. Here, we report measurements of longitudinal structure functions of velocity in a von Kármán setup without the use of Taylor-hypothesis. The measurements are made using Stereo Particle Image Velocimetry at 4 different ranges of spatial scales, in order to observe a combined inertial subrange spanning roughly one and a half order of magnitude. We found scaling exponents (up to 9th order) that are consistent with values from open turbulent flows, suggesting that they might be in fact universal.
description: Under review in J. Fluid Mech
MOESM1 of Expression of the Hippo transducer TAZ in association with WNT pathway mutations impacts survival outcomes in advanced gastric cancer patients treated with first-line chemotherapy
Creators: name: Melucci, Elisa
name: Casini, Beatrice
name: Ronchetti, Livia
name: Pizzuti, Laura
name: Sperati, Francesca
name: Pallocca, Matteo
name: Nicola, Francesca De
name: Goeman, Frauke
name: Gallo, Enzo
name: Amoreo, Carla
name: Sergi, Domenico
name: Terrenato, Irene
name: Vici, Patrizia
name: Lauro, Luigi Di
name: Diodoro, Maria
name: Pescarmona, Edoardo
name: Barba, Maddalena
name: Mazzotta, Marco
name: Mottolese, Marcella
name: Fanciulli, Maurizio
name: Ciliberto, Gennaro
name: Maria, Ruggero De
name: Buglioni, Simonetta
name: Maugeri-SaccĂ, Marcello
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1. First-line chemotherapy regimens and schedules (NÂ =Â 86).
Evidence for a Time Lag in Solar Modulation of Galactic Cosmic Rays
Creators: name: Tomassetti, Nicola
name: Orcinha, Miguel
name: Barao, Fernando
name: Bertucci, Bruna
Publisher: name: arXiv
Year: 2017
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Space Physics (physics.space-ph)
subject: FOS: Physical sciences

description: The solar modulation effect of cosmic rays in the heliosphere is an energy-, time-, and particle-dependent phenomenon which arises from a combination of basic particle transport processes such as diffusion, convection, adiabatic cooling, and drift motion. Making use of a large collection of time-resolved cosmic-ray data from recent space missions, we construct a simple predictive model of solar modulation which depends on direct solar-physics inputs: the number of solar sunspots and the tilt angle of the heliospheric current sheet. Under this framework, we present calculations of cosmic-ray proton spectra, positron/electron and antiproton/proton ratios and their time dependence in connection with the evolving solar activity. We report evidence for a time-lag $Δ{T}=8.1\pm\,1.2$ months, between solar activity data and cosmic-ray flux measurements in space, which reflects the dynamics of the formation of the modulation region. This result enables us to forecast the cosmic-ray flux near Earth well in advance by monitoring solar activity
description: Published as gold open access in ApJ Letters
Additional file 9: of Sequence analysis of European maize inbred line F2 provides new insights into molecular and chromosomal characteristics of presence/absence variants
Creators: name: Darracq, Aude
name: Vitte, Clémentine
name: Nicolas, Stéphane
name: Duarte, Jorge
name: Jean-Philippe Pichon
name: Mary-Huard, Tristan
name: Chevalier, Céline
name: Bérard, Aurélie
name: Marie-Christine Le Paslier
name: Rogowsky, Peter
name: Charcosset, Alain
name: Joets, Johann
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Sociology
subject: FOS: Sociology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Classification of PAVs with mapped short-reads count (see Methods). (PDF 224 kb)
Diversity in gatekeeping positions: lessons learnt and guidelines
Creators: name: Niebel, Viktoria
Publisher: name: Zenodo
Year: 2024
Subjects: gender
gender equality
GEP
intersectionality
co-design
gender pay gap
diversity
gatekeeping positions
HEIs

description: Thisdeliverable "Diversity in gatekeeping positions: lessons learnt and guidelines" was prepared and accomplished for the Deliverable D6.2 of the RESET project (this project has received funding from the European Union's Horizon 2020 framework for Research and Innovationunder GA 101006560). The material of these deliverable reflects only the authors' view and the Commission is not responsible for any use that may be made of the information it contains. This deliverable may be subject to final acceptance by the European Commission.

 

 

This report “Diversity in gatekeeping positions: lessons learnt and guidelines" (D6.2) is submitted by RUB as part of Work Package 6 – Act upon governance and upgrade existing excellence policy towards greater inclusiveness.

D6.2 embarks on an exploration of gender dynamics within gatekeeping, leadership, and decisionmaking realms, with a focus on higher education institutions (HEIs). It sets out to provide valuable insights into these domains. The concepts of gatekeeping and micropolitics within HEIs are explored, setting the thematic stage for the report (Chapter 2). The report builds on the examination and analysis of RESET’s GEPs 1.0 goals and measures, and of the results of Co-Designing workshops engaging women in decision-making positions (Chapter 3). Drawing from the insights gleaned in Chapter 3, Chapter 4 expounds upon key lessons learned. These lessons emphasise the "fix the institutions" approach by highlighting the significance of implementing quotas, illustrated through the cascade model, and advocating for gender competency in the selection and performance of leadership roles.In Chapter 5 comprehensive guidelines are presented. These guidelines encompass eight areas of intervention designed to fortify diversity within gatekeeping positions, offering practical strategies to foster gender equity and diversity in gatekeeping positions
Selective extraction of antimicrobial agents from Jodina rhombifolia by supercritical fluid carbon dioxide: phytochemical profile
Creators: name: Marín, Edith M.
name: Reyes, María G.
name: Audisio, Marcela C.
name: Zacur, José L.
name: Uriburu, María L.
name: Nicotra, Viviana E.
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biochemistry
subject: Biotechnology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Plant Biology
subject: FOS: Biological sciences

description: The goals of this study were to determine the phytochemical profile of Jodina rhombifolia and to evaluate the ability of supercritical fluids (ScFCO2) to selectively extract the metabolites responsible for the bioactivity. This species has simple aromatic compounds and lignan monomers, as well as glycerides containing epoxidized saturated fatty acids. Regarding the extraction by ScFCO2, the extracts showed a higher antimicrobial activity against human pathogenic strains, with respect to the ethanolic extracts obtained from plant residues after extraction by ScFCO2. Furthermore, the bioactive compounds were concentrated in just 1% P/P of the weight of the dry plant material. Extraction by ScFCO2 was carried out under different conditions of pressure and temperature, with the best results being obtained at 30 °C and 30 MPa. The results obtained demonstrate the advantages of ScFCO2 extractions over classical solvent extractions, in terms of improved safety and the ability to selectively extract the compounds of interest.
Transition of EMRIs through resonance: corrections to higher order in the on-resonance flux modification
Creators: name: Mihaylov, Deyan P.
name: Gair, Jonathan
Publisher: name: arXiv
Year: 2017
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: Extreme mass ratio in-spirals (EMRIs) are candidate events for gravitational wave detection in the millihertz range (by detectors like LISA and eLISA). These events involve a stellar-mass black hole, or a similar compact object, descending in the gravitational field of a supermassive black hole, eventually merging with it. Properties of the in-spiralling trajectory away from resonance are well known and have been studied extensively, however little is known about the behaviour of these binary systems at resonance, when the radial and lateral frequencies of the orbit become commensurate. We describe the two existing models, the instantaneous frequency approach used by Gair, Bender, and Yunes, and the standard two timescales approach implemented by Flanagan and Hinderer. In both cases, the exact treatment depends on the modelling of the gravitational self-force, which is currently not available. We extend the results in Gair, Bender and Yunes to higher order in the on-resonance flux modification, and argue that the instantaneous frequency approach is also a valid treatment of the resonance problem. The non-linear differential equations which arise in treating resonances are interesting from a mathematical view point. We present our algorithm for perturbative solutions and the results to third order in the infinitesimal parameter, and discuss the scope of this approach.
description: 72 pages, 39 figures, 1 table. Presented at the poster session of the American Physical Society April Meeting 2017
Additional file 8: Figure S7. of Sequence analysis of European maize inbred line F2 provides new insights into molecular and chromosomal characteristics of presence/absence variants
Creators: name: Darracq, Aude
name: Vitte, Clémentine
name: Nicolas, Stéphane
name: Duarte, Jorge
name: Jean-Philippe Pichon
name: Mary-Huard, Tristan
name: Chevalier, Céline
name: Bérard, Aurélie
name: Marie-Christine Le Paslier
name: Rogowsky, Peter
name: Charcosset, Alain
name: Joets, Johann
Publisher: name: figshare
Year: 2018
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Sociology
subject: FOS: Sociology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Example of PAVs genotyping using resequencing data. Classification of PAVs in inbred line EP1 based on information from 20X sequencing depth. Each dot represents one PAV. Green and red dots correspond to PAVs that are confidently classified as present and absent, respectively (80% of all PAVs). Black dots correspond to unclassified PAVs (20% of all PAVs). (PDF 279 kb)
title: ADCO, Cartulaire général de Cîteaux, dit de Jean de Cirey, (XVe siècle), tome VI, Cart. 190 (11 H 75), 316 folios, f. 0143v
Creators: name: de la Côte d'Or, Archives départementales
name: Archives Départementales De La Côte-D'Or
name: Petot, Frédérique
name: Projet CBMA
name: CG21/F.PETOT/2012
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2020
Subjects: subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris
subject: Corpus Burgundiae Medii Aevi
subject: Chartes de la Bourgogne du Moyen Âge
subject: cartulaire

description: Cartulaire général de Cîteaux, dit de Jean de Cirey, (XVe siècle), tome VI, Archives départementales de la Côte-d'Or, Cart. 190 (11 H 75), 316 folios, f. 0143v, Numérisation en mode image.
description: Relation: http://www.cbma-project.eu/
description: Bibliographic citation: Cartulaire général de Cîteaux, dit de Jean de Cirey, (XVe siècle), tome VI, Archives départementales de la Côte-d'Or, Cart. 190 (11 H 75), 316 folios, f. 0143v, in Projet CBMA - Corpus Burgundiae Medii Aevi [Ressource en ligne], https:// manuscrits.cbma-project.eu/
description: Provenance: abbaye de Cîteaux
description: Provenance: http://www.wikidata.org/entity/Q843261
description: Provenance: https://www.geonames.org/3024876
description: Provenance: http://www.idref.fr/030974844/id
description: Provenance: https://catalogue.bnf.fr/ark:/12148/cb12228351v
The Development and Validation of a Medicines Optimisation Tool for Use in Adults With Severe Mental Illness (OPTIMISE)
Creators: name: Carolan, Aoife
Publisher: name: Royal College of Surgeons in Ireland
Year: 2022
Subjects: subject: 110319 Psychiatry (incl. Psychotherapy)
subject: FOS: Clinical medicine

description: Background and Objectives: The life expectancy of people with Severe Mental Illness (SMI) is considerably shorter than those without SMI. Multimorbidity and poorer physical health outcomes contribute significantly to health inequality.. Screening tools could offer an opportunity to assist clinicians in decision making and optimising medicines to protect the physical health of people with SMI. When applied in the clinical setting, screening tools such as STOPP/START and STOPPFrail result in improvements in prescribing and patient outcomes. We aimed to design a medicines optimisation tool (OPTIMISE) to assist optimising medicines and protect the physical health of adults with SMI.
Methods: The OPTIMISE was drafted with reference to the literature, and the Delphi consensus technique used to develop and validate the contents. A 17 member panel of experts from the UK and Ireland completed 2 rounds of Delphi, rating their level of agreement to 83 prescribing indicators using a 5-point Likert scale. Indicators with a median value of 1 or 2 and 75th centile value of ≤2 were accepted for inclusion. Interrater reliability was assessed among 4 healthcare professionals across 20 datasets and the chance corrected level of agreement (kappa) was calculated.
Results: Consensus was achieved after 2 rounds of Delphi validation for the inclusion of 63 prescribing indicators in the final OPTIMISE tool. When interrater reliability of OPTIMISE was assessed between physicians and pharmacists, kappa was 0.75, indicating a substantial level of agreement which is comparable to other medicines optimisation tools. Average time to complete the tool was 9 minutes.
Conclusion: OPTIMISE is a 63 indicator medicines optimisation tool, validated using Delphi methodology, to assist decision making among healthcare professionals treating people with SMI. The tool has the potential to enhance medicines optimisation, and ensure that primary and secondary preventative medicines are considered when clinically indicated. Further validation of this tool is needed, including application of the tool to a larger cohort and in diverse clinical settings. Wider application of OPTIMISE would provide an opportunity to improve prescribing quality, prevent avoidable adverse effects and improve physical health outcomes.
title: Ανάλυση Λογιστικών-Χρηματοοικονομικών Καταστάσεων
Creators: name: Apostolou, Apostolos
Publisher: name: Kallipos, Open Academic Editions
Year: 2016
Subjects: ΛΟΓΙΣΤΙΚΗ
ΑΝΑΛΥΣΗ
ΛΟΓΙΣΤΙΚΕΣ-ΧΡΗΜΑΤΟΟΙΚΟΝΟ0ΜΙΚΕΣ ΚΑΤΑΣΤΑΣΕΙΣ
Accounting
Analysis
Financial Statements

description: To βιβλίο αναμένεται να αξιοποιηθεί

σε μαθήματα που περιέχονται στη βάση του ΕΥΔΟΞΟΥ σε ΑΕΙ και ΤΕΙ ,( εκτος του Τμηματος Δημ.Διοίκησης του Παντείου Πανεπιστημίου όπου διδάσκει ο συγγραφέας) καθόσον ο τίτλος διαφορετική ονομασία ,όπως λ.χ ΑΝΑΛΥΣΗ ΙΣΟΛΟΓΙΣΜΩΝ,ΑΝΑΛΥΣΗ ΛΟΓΙΣΤΙΚΩΝ ΚΑΤΑΣΤΑΣΕΩΝ ΑΠΟΤΕΛΕΙ ΒΑΣΙΚΌ ΜΆΘΗΜΑ σε όλα τα Τμήματα Οικονομικών Επιστημών , Διοίκησης Ε πιχειρήσεων ,Λογιστικής & Χρηματοοικονομικής ,και γενικότερα Τμήματα Οικονομικής κατεύθυνσης ΤΕΙ (Υγέιας,Τουριστικά κ.λ.π.),ίσως και στο Διοίκησης Επιχειρήσεων του ΕΑΠ.

Επίσης μπορεί να αξιοποιηθεί και σε προπτυχιακά και μεταπτυχιακά τμήματα ,ειδικά για διδασκαλία-απλή κατανόηση βασικών εννοιών προς σπουδαστές που προέρχονται απο μη οικονομικές Σχολές ( καθόσον το 2ο Κεφάλαιο του βιβλίου με τίτλο ΧΡΗΜΑΤΟΟΙΚΟΝΟΜΙΚΕΣ ΚΑΤΑΣΤΑΣΕΙΣ ΕΛΛΗΝΙΚΩΝ ΕΠΙΧΕΙΡΗΣΕΩΝ ΚΑΙ ΣΤΟΙΧΕΙΑ ΛΟΓΙΣΤΙΚΗΣ ΠΡΑΚΤΙΚΗΣ καλύπτει ,όπως θα αναφερθεί στο σχετικό πεδίο,ικανοποιητικά το υπόψη θέμα ).

Επίσης μπορεί να αξιοποιηθεί και απο στελέχη επιχειρήσεων ένεκα της φύσεως του μαθήματος

Συνολικά διδάσκοντες ,φοιτητές,σπουδαστές ,στελέχη επιχειρήσεων ,μπορουν να βρούν υλικό για κατανόηση θεμάτων που σχετίζονται με θέματα όπως :
 χρηματοοικονομικη αναλυση λογιστικων καταστασεων, χρηματοοικονομικες καταστασεις ελληνικων επιχειρησεων και στοιχεια λογιστικης πρακτικης,αριθμοδεικτες ,πηγες-χρησεις κεφαλαιων –κατάσταση ταμειακων ροων ,ανάλυση της αποδοσης του μανατζμεντ,αποτιμηση επιχειρησεων & εκτιμηση αξιας μετοχων
Finite determinacy of matrices and ideals
Creators: name: Greuel, Gert-Martin
name: Pham, Thuy Huong
Publisher: name: arXiv
Year: 2017
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: 14B05, 15B07, 13A50, 13F25

description: The main aim of this paper is to characterize ideals I in the power series ring R=K[[x1,...,xs]] that are finitely determined up to contact equivalence by proving that this is the case if and only if I is an isolated complete intersection singularity, provided dim(R/I) > 0 and K is an infinite field (of arbitrary characteristic). Here two ideals I and J are contact equivalent if the local K-algebras R/I and R/J are isomorphic. If I is minimally generated by a1,...,am, we call I finitely contact determined if it is contact equivalent to any ideal J that can be generated by b1,...,bm with ai - bi in ^k for some integer k. We give also computable and semicontinuous determinacy bounds. The above result is proved by considering left-right equivalence on the ring M of m x n matrices A with entries in R and we show that the Fitting ideals of a finitely determined matrix in M have maximal height, a result of independent interest. The case of ideals is treated by considering 1-column matrices. Fitting ideals together with a special construction are used to prove the characterization of finite determinacy for ideals in R. Some results of this paper are known in characteristic 0, but they need new (and more sophisticated) arguments in positive characteristic partly because the tangent space to the orbit of the left-right group cannot be described in the classical way. In addition we point out several other oddities, including the concept of specialization for power series, where the classical approach (due to Krull) does not work anymore. We include some open problems and a conjecture.
description: References updated, clearer formulation of some statements. To appear in Journal of Algebra
Efficient Yet Deep Convolutional Neural Networks for Semantic Segmentation
Creators: name: Kamran, Sharif Amit
name: Sabbir, Ali Shihab
Publisher: name: arXiv
Year: 2017
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: Semantic Segmentation using deep convolutional neural network pose more complex challenge for any GPU intensive task. As it has to compute million of parameters, it results to huge memory consumption. Moreover, extracting finer features and conducting supervised training tends to increase the complexity. With the introduction of Fully Convolutional Neural Network, which uses finer strides and utilizes deconvolutional layers for upsampling, it has been a go to for any image segmentation task. In this paper, we propose two segmentation architecture which not only needs one-third the parameters to compute but also gives better accuracy than the similar architectures. The model weights were transferred from the popular neural net like VGG19 and VGG16 which were trained on Imagenet classification data-set. Then we transform all the fully connected layers to convolutional layers and use dilated convolution for decreasing the parameters. Lastly, we add finer strides and attach four skip architectures which are element-wise summed with the deconvolutional layers in steps. We train and test on different sparse and fine data-sets like Pascal VOC2012, Pascal-Context and NYUDv2 and show how better our model performs in this tasks. On the other hand our model has a faster inference time and consumes less memory for training and testing on NVIDIA Pascal GPUs, making it more efficient and less memory consuming architecture for pixel-wise segmentation.
description: 8 pages
Zebrafish reveal new roles for Fam83f in hatching and the DNA damage-mediated autophagic response.
Creators: name: Jones, Rebecca A
name: Cooper, Fay
name: Kelly, Gavin
name: Barry, David
name: Renshaw, Matthew J
name: Sapkota, Gopal
name: Smith, James C
Publisher: name: The Francis Crick Institute
Year: 2024
Subjects: classificationCode: Tumour Biology
subject: Tumour Biology
classificationCode: Stem Cells
subject: Stem Cells
classificationCode: Signalling & Oncogenes
subject: Signalling & Oncogenes
classificationCode: Chemical Biology & High Throughput
subject: Chemical Biology & High Throughput
classificationCode: Gene Expression
subject: Gene Expression
classificationCode: Genetics & Genomics
subject: Genetics & Genomics
classificationCode: Developmental Biology
subject: Developmental Biology
classificationCode: Computational & Systems Biology
subject: Computational & Systems Biology
classificationCode: Genome Integrity & Repair
subject: Genome Integrity & Repair
classificationCode: Model organisms
subject: Model organisms
classificationCode: Imaging
subject: Imaging

description: The FAM83 (Family with sequence similarity 83) family is highly conserved in vertebrates, but little is known of the functions of these proteins beyond their association with oncogenesis. Of the family, FAM83F is of particular interest because it is the only membrane-targeted FAM83 protein. When overexpressed, FAM83F activates the canonical Wnt signalling pathway and binds to and stabilizes p53; it therefore interacts with two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development, and here we report the generation of fam83f knock-out (KO) zebrafish, which we have used to study the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the hatching gland of developing zebrafish embryos, and that fam83f KO embryos hatch earlier than their wild-type (WT) counterparts, despite developing at a comparable rate. We also demonstrate that fam83f KO embryos are more sensitive to ionizing radiation than WT embryos-an unexpected finding, bearing in mind the previously reported ability of FAM83F to stabilize p53. Transcriptomic analysis shows that loss of fam83f leads to downregulation of phosphatidylinositol-3-phosphate (PI(3)P) binding proteins and impairment of cellular degradation pathways, particularly autophagy, a crucial component of the DNA damage response. Finally, we show that Fam83f protein is itself targeted to the lysosome when overexpressed in HEK293T cells, and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated suggest that Fam83f plays an important role in autophagic/lysosomal processes, resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo.
Additional file 7: Figure S6. of Sequence analysis of European maize inbred line F2 provides new insights into molecular and chromosomal characteristics of presence/absence variants
Creators: name: Darracq, Aude
name: Vitte, Clémentine
name: Nicolas, Stéphane
name: Duarte, Jorge
name: Jean-Philippe Pichon
name: Mary-Huard, Tristan
name: Chevalier, Céline
name: Bérard, Aurélie
name: Marie-Christine Le Paslier
name: Rogowsky, Peter
name: Charcosset, Alain
name: Joets, Johann
Publisher: name: figshare
Year: 2018
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: Sociology
subject: FOS: Sociology
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Bioinformatics workflow of pan-genome sequence building. All steps are described in details in the method section. (PDF 702 kb)
SARS-CoV-2 main protease and papain-like protease inhibition by abietane-type diterpenes isolated from the branches of Glyptostrobus pensilis using molecular docking studies
Creators: name: Phong, Nguyen Viet
name: Trang, Nguyen Minh
name: Quyen, Cao Thao
name: Le Tuan Anh, Hoang
name: Le Ba Vinh
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Molecular Biology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified
subject: Cancer

description: Using various chromatographic methods, five abietane-type diterpenes were isolated from the branches of Glyptostrobus pensilis for the first time. The chemical structures of the isolates were identified by modern spectroscopic techniques, including 1H and 13C nuclear magnetic resonance spectroscopy and by comparison with the literature. In addition, the binding potential of the isolated compounds to replicase protein, SARS-CoV-2 main protease and papain-like protease, were examined using molecular docking studies. In silico results suggested that G. pensilis as well as abietane-types diterpenes are potential candidates for the prevention and treatment of SARS-CoV-2.
Decoupling of Magnetic Fields in Collapsing Protostellar Envelopes and Disk Formation and Fragmentation
Creators: name: Zhao, Bo
name: Caselli, Paola
name: Li, Zhi-Yun
name: Krasnopolsky, Ruben
Publisher: name: arXiv
Year: 2017
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Efficient magnetic braking is a formidable obstacle to the formation of rotationally supported disks (RSDs) around protostars in magnetized dense cores. We have previously shown, through 2D (axisymmetric) non-ideal MHD simulations, that removing very small grains (VSGs: ~10 Å$~$to few 100 Å) can greatly enhance ambipolar diffusion and enable the formation of RSDs. Here we extend the simulations of disk formation enabled by VSG removal to 3D. We find that the key to this scenario of disk formation is that the drift velocity of the magnetic field almost cancels out the infall velocity of the neutrals in the $10^2$-$10^3$ AU-scale "pseudo-disk" where the field lines are most severely pinched and most of protostellar envelope mass infall occurs. As a result, the bulk neutral envelope matter can collapse without dragging much magnetic flux into the disk-forming region, which lowers the magnetic braking efficiency. We find that the initial disks enabled by VSG removal tend to be Toomre-unstable, which leads to the formation of prominent spiral structures that function as centrifugal barriers. The piling-up of infall material near the centrifugal barrier often produces dense fragments of tens of Jupiter masses, especially in cores that are not too strongly magnetized. Some fragments accrete onto the central stellar object, producing bursts in mass accretion rate. Others are longer lived, although whether they can survive long-term to produce multiple systems remains to be ascertained. Our results highlight the importance of dust grain evolution in determining the formation and properties of protostellar disks and potentially multiple systems.
description: 22 pages, 22 figures. Accepted by MNRAS
Antibacterial, anti-biofilm, and anti-adhesive activities of melittin, a honeybee venom-derived peptide, against quinolone-resistant uropathogenic Escherichia coli (UPEC)
Creators: name: Lima, William Gustavo
name: Filho, Francisco Leandro Batista
name: Lima, Iasmin Pinheiro
name: Simião, Daniela Carolina
name: Brito, Júlio César Moreira
name: da Cruz Nizer, Waleska Stephanie
name: Cardoso, Valbert Nascimento
name: Fernandes, Simone Odília Antunes
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biochemistry
subject: Space Science
subject: Microbiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Cancer
subject: Hematology
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Here, we demonstrated the in vitro and in vivo antibacterial and anti-biofilm activities of melittin, a peptide derived from honeybee venom, against uropathogenic Escherichia coli (UPEC) resistant to quinolones. The minimum inhibitory concentration (MIC) of melittin varied from 0.5 to 8 μM. The bactericidal effect was considered rapid and potent (ranging from 3.0 to 6.0 h after incubation) against a quinolone-resistant and Extended Spectrum Beta-lactamase (ESBL)-producing UPEC strain. Prior exposure to melittin did not reduce the MIC of the quinolones tested, but it decreased the MIC of ceftizoxime by 8-fold due to its ability to form pores in the membrane. Furthermore, melittin disrupted mature biofilms (39.58% at 32 μM) and inhibited the adhesion of this uropathogen to the surfaces of urethral catheter. These results show that melittin is a promising molecule that can be incorporated into invasive urethral medical devices to prevent urinary infections caused by multidrug-resistant UPECs.
Extensive deep neural networks for transferring small scale learning to large scale systems
Creators: name: Mills, Kyle
name: Ryczko, Kevin
name: Luchak, Iryna
name: Domurad, Adam
name: Beeler, Chris
name: Tamblyn, Isaac
Publisher: name: arXiv
Year: 2017
Subjects: subject: Computational Physics (physics.comp-ph)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We present a physically-motivated topology of a deep neural network that can efficiently infer extensive parameters (such as energy, entropy, or number of particles) of arbitrarily large systems, doing so with O(N) scaling. We use a form of domain decomposition for training and inference, where each sub-domain (tile) is comprised of a non-overlapping focus region surrounded by an overlapping context region. The size of these regions is motivated by the physical interaction length scales of the problem. We demonstrate the application of EDNNs to three physical systems: the Ising model and two hexagonal/graphene-like datasets. In the latter, an EDNN was able to make total energy predictions of a 60 atoms system, with comparable accuracy to density functional theory (DFT), in 57 milliseconds. Additionally EDNNs are well suited for massively parallel evaluation, as no communication is necessary during neural network evaluation. We demonstrate that EDNNs can be used to make an energy prediction of a two-dimensional 35.2 million atom system, over 1 square micrometer of material, at an accuracy comparable to DFT, in under 25 minutes. Such a system exists on a length scale visible with optical microscopy and larger than some living organisms.
description: EDNN training code and tutorials available at http://kylemills.net/ednn, porous graphene dataset available for download at https://doi.org/10.4224/c8sc04578j.data
Additional file 6: Figure S5. of Sequence analysis of European maize inbred line F2 provides new insights into molecular and chromosomal characteristics of presence/absence variants
Creators: name: Darracq, Aude
name: Vitte, Clémentine
name: Nicolas, Stéphane
name: Duarte, Jorge
name: Jean-Philippe Pichon
name: Mary-Huard, Tristan
name: Chevalier, Céline
name: Bérard, Aurélie
name: Marie-Christine Le Paslier
name: Rogowsky, Peter
name: Charcosset, Alain
name: Joets, Johann
Publisher: name: figshare
Year: 2018
Subjects: subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: Sociology
subject: FOS: Sociology
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: 60506 Virology
subject: Computational Biology

description: Size distribution of B73 and F2-specific sequences. All PAVs exhibit similar size distribution except F2 unanchored PAVs, which are more numerous and include larger sequences. (PDF 28 kb)
The Red Sea marine sponge Spongia irregularis: metabolomic profiling and cytotoxic potential supported by in silico studies
Creators: name: Abdelaleem, Enas Reda
name: Samy, Mamdouh Nabil
name: Ahmed, Safwat A.
name: Aboulmagd, Asmaa M.
name: Alhadrami, Albaraa Hani
name: Rateb, Mostafa E.
name: Abdelmohsen, Usama Ramadan
name: Desoukey, Samar Yehia
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biochemistry
subject: Space Science
subject: Pharmacology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: The current study discusses the chemical composition of the marine sponge Spongia irregularis using LC-HRESIMS. The metabolomic profiling resulted in the annotation of 17 metabolites of different chemical classes. Additionally, evaluation of the cytotoxic activities of the total extract and different fractions were carried out against three different cell lines where the n-butanol fraction exhibited the highest cytotoxic effects against HepG-2, MCF-7 and CACO-2 cell lines with IC50 values of 9.6 ± 0.02, 4.3 ± 0.10 and 5.6 ± 0.03 µg/mL, respectively. Also, the study was supported by docking study of the identified compounds for binding affinity to MSK1.
The Effect of Thermal Velocities on Structure Formation in N-body Simulations of Warm Dark Matter
Creators: name: Leo, Matteo
name: Baugh, Carlton M.
name: Li, Baojiu
name: Pascoli, Silvia
Publisher: name: arXiv
Year: 2017
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We investigate the impact of thermal velocities in N-body simulations of structure formation in warm dark matter models. Adopting the commonly used approach of adding thermal velocities, randomly selected from a Fermi-Dirac distribution, to the gravitationally-induced velocities of the simulation particles, we compare the matter and velocity power spectra measured from CDM and WDM simulations, in the latter case with and without thermal velocities. This prescription for adding thermal velocities introduces numerical noise into the initial conditions, which influences structure formation. At early times, the noise affects dramatically the power spectra measured from simulations with thermal velocities, with deviations of the order of $\sim \mathcal{O}(10)$ (in the matter power spectra) and of the order of $\sim \mathcal{O}(10^2)$ (in the velocity power spectra) compared to those extracted from simulations without thermal velocities. At late times, these effects are less pronounced with deviations of less than a few percent. Increasing the resolution of the N-body simulation shifts these discrepancies to higher wavenumbers. We also find that spurious haloes start to appear in simulations which include thermal velocities at a mass that is $\sim$3 times larger than in simulations without thermal velocities.
description: 31 pages, 31 figures, LaTeX. Minor changes, references added. Matches the version published on JCAP
Additional file 8 of Postoperative circulating tumor DNA as markers of recurrence risk in stages II to III colorectal cancer
Creators: name: Chen, Gong
name: Peng, Junjie
name: Xiao, Qian
name: Wu, Hao-Xiang
name: Wu, Xiaojun
name: Wang, Fulong
name: Li, Liren
name: Ding, Peirong
name: Zhao, Qi
name: Li, Yaqi
name: Wang, Da
name: Shao, Yang
name: Bao, Hua
name: Pan, Zhizhong
name: Ding, Ke-Feng
name: Cai, Sanjun
name: Wang, Feng
name: Xu, Rui-Hua
Publisher: name: figshare
Year: 2021
Subjects: Medicine
Cell Biology
Molecular Biology
Biological Sciences not elsewhere classified
Mathematical Sciences not elsewhere classified
Cancer

description: Additional file 8: Figure S2. Preoperative examination of CEA and ctDNA in 240 evaluable patients stratified by pathological stage. (Nine patients with no CEA information available pre-operation).
Additional file 9: Table S6. of Adaptive genomic evolution of opsins reveals that early mammals flourished in nocturnal environments
Creators: name: Borges, Rui
name: Johnson, Warren
name: OâBrien, Stephen
name: CidĂĄlia Gomes
name: Heesy, Christopher
name: Antunes, Agostinho
Publisher: name: figshare
Year: 2018
Subjects: subject: Space Science
subject: Medicine
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 20199 Astronomical and Space Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Sociology
subject: FOS: Sociology

description: Saturation analysis. The presence of saturation in base substitution for each of the opsin gene alignment was tested by comparing half of the expected theoretical saturation index when assuming full saturation (Iss.c, critical value) with the observed saturation index (Iss). The absence of substitution saturation is verified when Iss is lower than Iss.c for a significant p-value. (PDF 107Â kb)
title: ADCO, Cartulaire général de Cîteaux, dit de Jean de Cirey, (XVe siècle), tome V, Cart. 189 (11 H 74), 316 folios, f. 0212r
Creators: name: de la Côte d'Or, Archives départementales
name: Archives Départementales De La Côte-D'Or
name: Petot, Frédérique
name: Projet CBMA
name: CG21/F.PETOT/2012
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2020
Subjects: subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris
subject: Corpus Burgundiae Medii Aevi
subject: Chartes de la Bourgogne du Moyen Âge
subject: cartulaire

description: Cartulaire général de Cîteaux, dit de Jean de Cirey, (XVe siècle), tome V, Archives départementales de la Côte-d'Or, Cart. 189 (11 H 74), 316 folios, f. 0212r, Numérisation en mode image.
description: Relation: http://www.cbma-project.eu/
description: Bibliographic citation: Cartulaire général de Cîteaux, dit de Jean de Cirey, (XVe siècle), tome V, Archives départementales de la Côte-d'Or, Cart. 189 (11 H 74), 316 folios, f. 0212r, in Projet CBMA - Corpus Burgundiae Medii Aevi [Ressource en ligne], https:// manuscrits.cbma-project.eu/
description: Provenance: abbaye de Cîteaux
description: Provenance: http://www.wikidata.org/entity/Q843261
description: Provenance: https://www.geonames.org/3024876
description: Provenance: http://www.idref.fr/030974844/id
description: Provenance: https://catalogue.bnf.fr/ark:/12148/cb12228351v
A quantum Szilard engine without heat from a thermal reservoir
Creators: name: Mohammady, M. Hamed
name: Anders, Janet
Publisher: name: arXiv
Year: 2017
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We study a quantum Szilard engine that is not powered by heat drawn from a thermal reservoir, but rather by projective measurements. The engine is constituted of a system $\mathcal{S}$, a weight $\mathcal{W}$, and a Maxwell demon $\mathcal{D}$, and extracts work via measurement-assisted feedback control. By imposing natural constraints on the measurement and feedback processes, such as energy conservation and leaving the memory of the demon intact, we show that while the engine can function without heat from a thermal reservoir, it must give up at least one of the following features that are satisfied by a standard Szilard engine: (i) repeatability of measurements; (ii) invariant weight entropy; or (iii) positive work extraction for all measurement outcomes. This result is shown to be a consequence of the Wigner-Araki-Yanase (WAY) theorem, which imposes restrictions on the observables that can be measured under additive conservation laws. This observation is a first-step towards developing "second-law-like" relations for measurement-assisted feedback control beyond thermality.
Additional file 9: Figure S9. of Systematic comparison of small RNA library preparation protocols for next-generation sequencing
Creators: name: Cloelia Dard-Dascot
name: Naquin, Delphine
name: D’Aubenton-Carafa, Yves
name: Alix, Karine
name: Thermes, Claude
name: Dijk, Erwin Van
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Sociology
subject: FOS: Sociology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Numbers of known human piRNAs identified. We determined the numbers of known piRNAs identified with the various protocols. For each protocol, one million of reads were trimmed and the 19–24 nt inserts were used for mapping to human piRNAs in piRBase (see Methods for details). Shown are the mean values of at least two independent experiments with standard deviations represented by error bars. (PDF 1.01 mb)
Enhanced antibacterial, antioxidant and anticancer activity of caffeic acid by simple acid-base complexation with spermine/spermidine
Creators: name: Mude, Hemanjali
name: Balapure, Aniket
name: Thakur, Anindita
name: Ganesan, Ramakrishnan
name: Dutta, Jayati Ray
Publisher: name: Taylor & Francis
Year: 2022
Subjects: Biophysics
Biochemistry
Neuroscience
Pharmacology
Biotechnology
Environmental Sciences not elsewhere classified
Chemical Sciences not elsewhere classified
Cancer

description: Caffeic acid (CA) is a naturally occurring plant-derived polyphenol possessing diverse biological properties. However, the poor water-solubility of CA restricts its widespread applications. On the other hand, biogenic amines such as spermine and spermidine are natural constituents in eukaryotes. In this work, we present water-soluble complexes of CA with spermine and spermidine by exploiting the acid-base interaction. Four different compositions have been prepared by varying the CA to amine ratios, whose chemical structures have been probed in detail using Fourier-transform infrared spectroscopy (FT-IR) and nuclear magnetic resonance (NMR) studies that have revealed the acid-base interaction between the constituent precursors. The obtained acid-base complexes at their native pH values have shown enhanced antibacterial and antioxidant activities than pristine CA. Further, the CA-polyamine complexes have shown high anticancer performances in the concentration range that is compatible with the normal cell lines.
A space-time tradeoff for implementing a function with master equation dynamics
Creators: name: Wolpert, David H.
name: Kolchinsky, Artemy
name: Owen, Jeremy A.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Emerging Technologies (cs.ET)
subject: Biological Physics (physics.bio-ph)
subject: Quantitative Methods (q-bio.QM)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences
subject: FOS: Biological sciences

description: Master equations are commonly used to model the dynamics of physical systems, including systems that implement single-valued functions like a computer's update step. However, many such functions cannot be implemented by any master equation, even approximately, which raises the question of how they can occur in the real world. Here we show how any function over some "visible" states can be implemented with master equation dynamics--if the dynamics exploits additional, "hidden" states at intermediate times. We also show that any master equation implementing a function can be decomposed into a sequence of "hidden" timesteps, demarcated by changes in what state-to-state transitions have nonzero probability. In many real-world situations there is a cost both for more hidden states and for more hidden timesteps. Accordingly, we derive a "space-time" tradeoff between the number of hidden states and the number of hidden timesteps needed to implement any given function.
description: 17 pages, 2 figures
10β-Hydroxyestra-1,4-diene-3,17-dione as potential antiproliferative agent: in vitro biological evaluation and in silico studies
Creators: name: Canário, Catarina
name: Matias, Mariana
name: de Brito, Vanessa
name: Cruz-Vicente, Pedro
name: Soeiro, Pedro
name: Santos, Adriana O.
name: Falcão, Amílcar
name: Silvestre, Samuel
name: Alves, Gilberto
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Cancer

description: 10β-Hydroxyestra-1,4-diene-3,17-dione (HEDD) is a natural product described as having neuroprotective activity. However, the cytotoxic properties of this quinol are barely studied. Thus, the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay was performed in six cell lines (MCF-7, T47-D, LNCaP, HepaRG, Caco-2 and NHDF). Additionally, an in vitro estrogenicity assay and a cell viability analysis together with in silico molecular docking studies were carried out in order to understand the potential mechanism of cytotoxicity. Computational predictions of its pharmacokinetic and toxicity properties were also performed. Surprisingly, HEDD displayed marked cytotoxic activity, particularly against hormone-dependent cancer cells and the flow cytometry analysis revealed that HEDD markedly reduced the viability of hepatic cancer cells. Molecular docking studies suggested a high affinity towards the estrogen receptor α and 17β-hydroxysteroid dehydrogenase type 1. Moreover, it was predicted that HEDD may have good oral bioavailability and a low maximum tolerated dose in humans.
Additional file 1: of The perceived impact of family physicians on the district health system in South Africa: a cross-sectional survey
Creators: name: Pressentin, Klaus Von
name: Mash, Robert
name: Baldwin-Ragaven, Laurel
name: Botha, Roelf
name: Indiran Govender
name: Steinberg, Wilhelm
name: Esterhuizen, Tonya
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: Science Policy

description: Full list of HREC approvals and PHRC/DRC permissions (DOCX 16Â kb)