Miracle-dz/UniFAR-FTUs huggingface dataset:
PPA_A_204111 1199..1211

Department of Pharmacy, Sint Maartenskliniek, Nijmegen, the Netherlands; Department of Rheumatology, Sint Maartenskliniek, Nijmegen, the Netherlands; Nivel (Netherlands Institute for Health Services Research), Utrecht, the Netherlands; Care and Public Health Research Institute (CAPHRI), Maastricht University, Maastricht, the Netherlands; Department of Internal Medicine, Division of Rheumatology, Maastricht University Medical Centre+, Maastricht, the Netherlands; Department of Rheumatology, Reade, Amsterdam, the Netherlands; Department of Rheumatology, Erasmus Medical Centre, Rotterdam, the Netherlands; Department of Rheumatology and Clinical Immunology, Medisch Spectrum Twente, Enschede, the Netherlands; Department of Psychology, Health and Technology, Arthritis Center Twente, University of Twente, Enschede, the Netherlands; Department of Rheumatology, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Pharmacy, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Clinical Pharmacy and Toxicology, Maastricht University Medical Centre+, Maastricht, the Netherlands; Department of PharmacoTherapy, Epidemiology & Economics (PTEE), Groningen Research Institute of Pharmacy, Faculty of Mathematics and Natural Sciences, University of Groningen, Groningen, the Netherlands Background: Although patients have different treatment preferences, these individual
Assessment of deep learning algorithms for 3D instance segmentation of confocal image datasets

Segmenting three dimensional microscopy images is essential for understanding phenomena like morphogenesis, cell division, cellular growth and genetic expression patterns. Recently, deep learning (DL) pipelines have been developed which claim to provide high accuracy segmentation of cellular images and are increasingly considered as the state-of-the-art for image segmentation problems. However, it remains difficult to define their relative performance as the concurrent diversity and lack of uniform evaluation strategies makes it difficult to know how their results compare. In this paper, we first made an inventory of the available DL methods for 3D segmentation. We next implemented and quantitatively compared a number of representative DL pipelines, alongside a highly efficient non-DL method named MARS. The DL methods were trained on a common dataset of 3D cellular confocal microscopy images. Their segmentation accuracies were also tested in the presence of different image artifacts. A new method for segmentation quality evaluation was adopted which isolates segmentation errors due to under/over segmentation. This is complemented with new visualization strategies that make interactive exploration of segmentation quality possible. Our analysis shows that the DL pipelines have very different levels of accuracy. Two of them show high performance, and offer clear advantages in terms of adaptability to new data.
Strong formulations for network design problems with connectivity requirements

The network design problem with connectivity requirements (NDC) includes as special cases a wide variety of celebrated combinatorial optimization problems including the minimum spanning tree, Steiner tree, and survivable network design problems. We develop strong formulations for two versions of the edge‐connectivity NDC problem: unitary problems requiring connected network designs, and nonunitary problems permitting nonconnected networks as solutions. We (1) present a new directed formulation for the unitary NDC problem that is stronger than a natural undirected formulation; (2) project out two classes of valid inequalities—partition inequalities, and combinatorial design inequalities—that generalize known classes of valid inequalities for the Steiner tree problem to the unitary NDC problem; and (3) show how to strengthen and direct nonunitary problems. Our results provide a unifying framework for strengthening formulations for NDC problems, and demonstrate the power of flow‐based formulations for network design problems with connectivity requirements. © 2005 Wiley Periodicals, Inc. NETWORKS, Vol. 45(2), 61–79 2005
mirna-101-5p inhibits the growth and aggressiveness of nsclc cells through targeting cXcl6

Background: The purpose of this study is to explore the potential biological roles of miR-101-5p in the progression of non-small-cell lung carcinoma (NSCLC). Methods: The levels of miR-101-5p and chemokine (C-X-C motif) ligand 6 (CXCL6) in NSCLC tissues and cells were detected using the quantitative real-time PCR (qRT-PCR) assay. Proliferation, colony formation, migration and invasion assays were conducted using miR-101-5p-transfected NSCLC cells in vitro. The expression of CXCL6 was measured using immunofluorescence assay. Xenograft model and lung metastasis model were constructed to further reveal the precise roles of miR-101-5p in the lung metastasis and growth of NSCLC cells in vivo. Results: miR-101-5p was underregulated in NSCLC tissues when compared with that in the normal controls. The levels of miR-101-5p were lower in NSCLC cells (H1975, A549, HCC827 and H1650) than in non-tumorigenic human bronchial epithelial cells (BEAS-2B). Overregulation of miR-101-5p restrained the aggressiveness phenotypes of NSCLC cells in vitro. Furthermore, overregulation of miR-101-5p reduced the tumor growth and pulmonary metastasis of NSCLC cells in vivo. CXCL6 was the target gene of miR-101-5p in NSCLC. The mRNA levels of CXCL6 were negatively associated with the levels of miR-101-5p in NSCLC tissues. Finally, the rescue experiments suggested that the inhibitory role of miR-101-5p was mediated by regulating the expression of CXCL6 in NSCLC. Conclusion: These findings indicated that overregulation of miR-101-5p restrained the progression of NSCLC cells by targeting CXCL6 and might function as a potential therapeutic target for NSCLC.
Cryptography and Network Security

This book includes the following chapters : Introduction; Mathematics of Cryptography; Traditional Symmetric-Key Ciphers; Mathematics of Cryptography; Introduction to Modern Symmetric-Key Ciphers; Data Encryption Standard (DES); Advanced Encryption Standard (AES); Encipherment Using Modern Symmetric-Key Ciphers; Mathematics of Cryptography; Asymmetric-Key Cryptography; Message Integrity and Message Authentication; Cryptographic Hash Functions; Digital Signature; Entity Authentication; Key Management; Security at the Application Layer: PGP and S/MIME; Security at the Transport Layer: SSL and TLS; and Security at the Network Layer: IPSec.
Improving Web accessibility through an enhanced open-source browser &

V. L. Hanson J. P. Brezin S. Crayne S. Keates R. Kjeldsen J. T. Richards C. Swart S. Trewin The accessibilityWorks project provides software enhancements to the Mozillae Web browser and allows users to control their browsing environment. Although Web accessibility standards specify markup that must be incorporated for Web pages to be accessible, these standards do not ensure a good experience for all Web users. This paper discusses user controls that facilitate a number of adaptations that can greatly increase the usability of Web pages for a diverse population of users. In addition to transformations that change page presentation, innovations are discussed that enable mouse and keyboard input correction as well as vision-based control for users unable to use their hands for computer input.
IR-06-006 Coevolution of Slow-fast Populations : Evolutionary Sliding , Evolutionary Pseudo-equilibria , and Complex Red Queen Dynamics

2 Introduction . 3 Coevolutionary dynamics of slow-fast populations: general results . 4 A model of predator-prey eco-evolutionary dynamics. 6 Results and discussion. 8 Concluding comments . 12 References . 14 Figure captions . 18 Figures . 19 Electronic Appendix . 1 COEVOLUTION OF SLOW-FAST POPULATIONS: EVOLUTIONARY SLIDING, EVOLUTIONARY PSEUDO-EQUILIBRIA, AND COMPLEX RED QUEEN DYNAMICS F. Dercole, R. Ferrière, A. Gragnani, S. Rinaldi DEI, Politecnico di Milano Via Ponzio 34/5, 20133 Milano, Italy Ph: +39 02 2399 3484; Fax: +39 02 2399 3412 fabio.dercole@polimi.it Mathematical Eco-Evolutionary Theory (MEET) Group Laboratoire d’Ecologie, Ecole Normale Supérieure, Paris, France Department of Ecology and Evolutionary Biology University of Arizona, Tucson AZ, USA Adaptive Dynamics Network IIASA, Laxenburg, Austria IEIIT, CNR, Politecnico di Milano, Milano, Italy To whom correspondence should be addressed Running title: Coevolution of slow-fast populations
Communicating uncertainties in sea surface temperature

￼￼￼￼￼A project on sea surface temperature is generating new climate data records from satellite observations. The data are independent of in situ observations and are harmonious across satellite sensors to maximize stability and have realistic, context-sensitive uncertainty estimates at all spatial and temporal scales. ￼￼The project, part of the European Space Agency Climate Change Initiative ￼￼(SST CCI), now seeks to establish a useful method for communicating uncertainty in sea surface temperatures. This goal was the impetus for a workshop held in November 2014 in Exeter in the United Kingdom, summarised in this article.
Handbook of Vascular Biometrics

This open access handbook provides the first comprehensive overview of biometrics exploiting the shape of human blood vessels for biometric recognition, i.e. vascular biometrics, including finger vein recognition, hand/palm vein recognition, retina recognition, and sclera recognition. After an introductory chapter summarizing the state of the art in and availability of commercial systems and open datasets/open source software, individual chapters focus on specific aspects of one of the biometric modalities, including questions of usability, security, and privacy. The book features contributions from both academia and major industrial manufacturers.
A logic for SDSI's linked local name spaces: preliminary version

M. Abadi (1998) has introduced a logic to explicate the meaning of local names in SDSI, the simple distributed security infrastructure proposed by Rivest and Lampson. Abadi's logic does not correspond precisely to SDSI, however, it draws conclusions about local names that do not follow from SDSI's name resolution algorithm. Moreover its semantics is somewhat unintuitive. This paper presents the logic of local name containment, which does not suffer from these deficiencies. It has a clear semantics and provides a tight characterization of SDSI name resolution. The semantics is shown to be closely related to that of logic programs, leading to an approach to the efficient implementation of queries concerning local names. A complete axiomatization of the logic is also provided.
Tackling gaps in developing life-changing treatments for dementia

47 Since the G8 Dementia Summit in 2013, a number of initiatives have been established with the aim 48 of facilitating the discovery of a disease-modifying treatment for dementia by 2025. This report is a 49 summary of the findings and recommendations of a meeting titled ‘Tackling gaps in developing life - 50 changing treatments for dementia’, hosted by Alzheimer’s Research U K in May 2018. The aim of the 51 meeting was to identify, review and highlight the areas in dementia research that are not currently 52 being addressed by existing initiatives. It reflects the views of leading experts in the field of 53 neurodegeneration research challenged with developing a strategic action plan to address these 54 gaps and make recommendations on how to achieve the G8 Dementia Summit goals. The plan calls 55 for significant advances in: (1) translating newly identified genetic risk factors into a better 56 understanding of the impacted biological processes; (2) enhanced understanding of selective 57 neuronal resilience to inform novel drug targets; (3) facilitating robust and reproducible drug target 58 validation; (4) appropriate and evidence-based selection of appropriate subjects for proof-of- 59 concept clinical trials; (5) improving approaches to assess drug-target engagement in humans; and 60 (6) innovative approaches to conducting clinical trials if we are able to detect disease 10-15 years 61 earlier than we currently do today. 62
Genetic diversity of teak populations in native regions and plantations in Myanmar detected by microsatellite markers

Teak (Tectona grandis L.f) has been regarded as one of the world’s most precious tropical tree species because it provides premium timber with a number of very desirable properties including high durability, strength and workability; resistance to fungi, termites and weathering; and a beautiful grain and color (PANDEY and BROWN, 2000; KAOSA-ARD, 2003). Its natural distribution is limited to a discontinuous range in South and Southeast Asia from the Indian subcontinent to Myanmar, Thailand and Laos (KHANDURI et al., 2008). Natural populations of teak in its native countries have decreased through over-exploitation, illegal cutting and other factors such as the transformation of land-use systems, so that logging from natural forests was banned in the late 1980s in India, Thailand and Laos but not in Myanmar (PANDEY and BROWN, 2000). Teak is now a threatened species and conservation effort is urgently needed to safeguard the genetic resources of teak from degraded natural teak forests. Genetic diversity and genetic variation are key component of the stability of forest resources (RAJORA et al., 2000). It is therefore important to evaluate the genetic diversity and genetic divergence of natural populations in native countries to facilitate conservation efforts aimed at maintaining species’ genetic resources. Genetic studies on teak populations in its native countries of India, Thailand and Laos have been conducted using plant materials derived from international provenance trials established in the early 1970s (KEIDING et al., 1986; KJAER et al., 1995), and from natural forests and plantations. Previous population genetic studies have used various DNA markers such as allozymes (KERTADIKARA and PRAT, 1995; KJAER and SEIGISMUND, 1996), sequence characterized amplified regions (SCAR) (ISODA et al., 2000), random amplified polymorphic DNA (RAPD) (WATANABE et al., 2004), amplified fragment length polymorphisms (AFLP) (SHRESTHA et al., 2005), inter simple sequence repeats (ISSR) (NARAYANAN et al., 2007), and simple sequence repeats (SSR) (FOFANA et al., 2008, 2009; MINN et al., 2014). SSRs are arguably the most informative of these marker types due to their hyper-polymorphic nature and codominance (POWELL, 1996). Genetic diversity of teak populations in native regions and plantations in Myanmar detected by microsatellite markers
Etude du comportement magnétique et spectral de l'effet Faraday dans des oxydes métalliques dopés par des nanoparticules magnétiques de ferrite de cobalt

Ce travail de these est consacre a l’etude des proprietes magneto-optiques de nanoparticules (NP) magnetiques de ferrite de cobalt (CoFe2O4) sous forme liquide et lorsqu’elles sont bloquees dans une matrice de silice produite par voie sol-gel. Cette derniere dispersion constitue un materiau composite a activite magneto-optique obtenu par un procede basse temperature qui le rend totalement compatible avec les technologies d’integration. A plus long terme, ce materiau pourra contribuer a l’integration de composants non-reciproques. L’objectif de ce travail est d’une part l’identification du type de NP qui maximise la rotation Faraday et le facteur de merite (rapport de la rotation Faraday a l’absorption) dans le but d’ameliorer la qualite magneto-optique du materiau composite. Et d’autre part, il s’agit d’ameliorer la comprehension des phenomenes physiques lies aux effets magneto-optiques de ces nanoparticules et le lien avec leurs caracteristiques physiques. L’etude est menee sur des NP magnetiques synthetisees et dispersees en phase aqueuse au laboratoire PHENIX (UMR CNRS 8234). Les mesures optiques et magneto-optiques realisees au laboratoire Hubert Curien (UMR CNRS 5516) ont ete completees par des mesures magnetiques XMCD au synchrotron SOLEIL. L’etude des differentes nanoparticules magnetiques a revele que l’utilisation d’une petite taille de NP permet de multiplier par deux le facteur de merite du materiau pour une longueur d’onde de 1,5 µm, soit une division par deux des pertes pour les composants magneto-optiques vises. L’analyse du comportement spectral de l’effet Faraday illustre l’influence de la distribution cationique des ions Co2+ et Fe3+ dans la structure cristalline. Couplee aux mesures XMCD, l’analyse montre le besoin d’une localisation de l’ion Co2+ en site tetraedrique dans la structure spinelle pour maximiser l’effet Faraday a 1,5µm, et obtenir une anisotropie uniaxe qui permette une pre-orientation aisee des NP lors de la gelification
High Temperature Superconductors

One of the pioneers who introduced superconductivity of metal solids was Kamerlingh Onnes (1911). Researchers always struggled to make observations towards superconductivity at high temperatures for achieving goals of evaluating normal room temperature superconductors. The physical properties are based entirely on the behavior of conventional and metal superconductors as a result of high-temperature superconductors. Various synthetic approaches are employed to fabricate high-temperature superconductors, but solid-state thermochemical process which involves mixing, calcinating, and sintering is the easiest approach. Emerging novel high-temperature superconductors mainly engaged with technological applications such as power transmission, Bio-magnetism, and Tokamaks high magnetic field. Finally, in this chapter, we will discuss a brief outlook, future prospects, and finished with possible science fiction and some opportunities with high-temperature superconductors.
Edinburgh Research Explorer Interaction of COP1 and UVR8 regulates UV-B-induced photomorphogenesis and stress acclimation in Arabidopsis

Background: Advances in synthetic biology will require spatio-temporal regulation of biological processes in heterologous host cells. We develop a light-switchable, two-hybrid interaction in yeast, based upon the Arabidopsis proteins PHYTOCHROME A and FAR-RED ELONGATED HYPOCOTYL 1-LIKE. Light input to this regulatory module allows dynamic control of a light-emitting LUCIFERASE reporter gene, which we detect by real-time imaging of yeast colonies on solid media. Results: The reversible activation of the phytochrome by red light, and its inactivation by far-red light, is retained. We use this quantitative readout to construct a mathematical model that matches the system's behaviour and predicts the molecular targets for future manipulation. Conclusion: Our model, methods and materials together constitute a novel system for a eukaryotic host with the potential to convert a dynamic pattern of light input into a predictable gene expression response. This system could be applied for the regulation of genetic networks both known and synthetic.
A micromechanics-inspired constitutive model for shape-memory alloys

This paper presents a three-dimensional constitutive model for shape-memory alloys that generalizes the one-dimensional model presented earlier (Sadjadpour and Bhattacharya 2007 Smart Mater. Struct. 16 S51–62). These models build on recent micromechanical studies of the underlying microstructure of shape-memory alloys, and a key idea is that of an effective transformation strain of the martensitic microstructure. This paper explains the thermodynamic setting of the model, demonstrates it through examples involving proportional and non-proportional loading, and shows that the model can be fitted to incorporate the effect of texture in polycrystalline shape-memory alloys.
A multi-centre evaluation of eleven clinically feasible brain PET / MRI attenuation correction techniques using a large cohort of patients

Claes N. Ladefoged, Ian Law, Udunna Anazodo, Keith St. Lawrence, David Izquierdo-Garcia, Ciprian Catana, Ninon Burgos, M. Jorge Cardoso, Sebastien Ourselin, Brian Hutton, Inés Mérida, Nicolas Costes, Alexander Hammers, Didier Benoit, Søren Holm, Meher Juttukonda, Hongyu An, Jorge Cabello, Mathias Lukas, Stephan Nekolla, Sibylle Ziegler, Matthias Fenchel, Bjoern Jakoby, Michael E. Casey, Tammie Benzinger, Liselotte Højgaard, Adam E. Hansen, Flemming L. Andersen
Text Mining for Biology and Biomedicine

Text mining is defined by Hearst (1999) as the automatic discovery of new, previously unknown, information from unstructured textual data. This is often seen as comprising of three major tasks: information retrieval (gathering relevant documents), information extraction (extracting information of interest from these documents), and data mining (discovering new associations among the extracted pieces of information). Most researchers in the natural language processing (NLP) community are familiar with work on information extraction and its subtasks such as noun phrase chunking, named entity recognition, and anaphora resolution, typically applied to newswire articles. The explosive growth of biomedical literature has prompted increasing interest in applying such techniques to biomedical text in order to address the information overload faced by domain experts. This is reflected by the proliferation of articles reviewing this work (Reviews 2006), which typically appear in bioinformatics journals and target experts in biosciences as their primary audience. Text Mining for Biology and Biomedicine provides an overview of the fundamental approaches to biomedical NLP in more depth than is typically offered in a review article. The book consists of an introductory chapter written by the editors and nine chapters that each discuss a different subarea of biomedical NLP. Each chapter is authored by researcher(s) with significant contributions to the overviewed subarea. In the introductory chapter, Sophia Ananiadou and John McNaught adhere to the definition of text mining by Hearst (p. 1), although their interpretation lays more emphasis on the unstructured nature of the input textual data than on the potential novelty of the output information. Those “interested in organizing, searching, discovering, or communicating biological knowledge” (p. 2) are the targeted readers of the book. The book aims to provide them with an “extensive summarization and discussion of the research literature in text mining and reported systems, geared towards informing and educating rather than oriented towards other text mining experts” (p. 3). Information retrieval is placed outside the scope of the book, which focuses on performing familiar tasks such as named entity recognition (NER) and information extraction (IE) on biomedical text, but also extensively discusses problems that are less studied in general NLP but are of particular importance in this area, such as the exploitation of domain-specific knowledge sources, the construction of terminologies, how to deal with abbreviations, and so on. An outline of the main aims and challenges in biomedical NLP is followed by an overview of how these issues are discussed in each chapter. Chapter 2, “Levels of natural language processing for text mining” by Udo Hahn and Joachim Wermter, first explains how each level of linguistic analysis (i.e., morphology, syntax, and semantics) is associated with distinct NLP components. Then a reference architecture for text mining that combines these components with each other