Miracle-dz/UniFAR-FTUs huggingface dataset:
SINGLe: Accurate detection of single nucleotide polymorphisms using nanopore sequencing in gene libraries

Nanopore sequencing is a powerful single molecule DNA sequencing technology which o ﬀ ers high throughput and long sequence reads. Nevertheless, its high native error rate limits the direct detection of point mutations in individual reads of amplicon libraries, as these mutations are di ﬃ cult to distinguish from the sequencing noise. In this work, we developed SINGLe (SNPs In Nanopore reads of Gene Libraries), a computational method to reduce the noise in nanopore reads of amplicons containing point variations. Our approach uses the fact that all reads are very similar to a wild type sequence, for which we experimentally characterize the position-speci ﬁ c systematic sequencing error pattern. We then use this information to reweight the con ﬁ dence given to nucleotides that do not match the wild type in individual variant reads. We tested this method in a set of variants of KlenTaq, where the true mutation rate was well below the sequencing noise. SINGLe improves between 4 and 9 fold the signal to noise ratio, in comparison to the data returned by the basecaller guppy. Downstream, this approach improves variants clustering and consensus calling. SINGLe is simple to implement and requires only a few thousands reads of the wild type sequence of interest, which can be easily obtained by multiplexing in a single minION run. It does not require any modi ﬁ cation in the experimental protocol, it does not imply a large loss of sequencing throughput, and it can be incorporated down-stream of standard basecalling.
ALUNG October 21/4

Zielinski, Henryk, Ian S. Mudway, Kelly A. Bérubé, Samantha Murphy, Roy Richards, and Frank J. Kelly. Modeling the interactions of particulates with epithelial lining fluid antioxidants. Am. J. Physiol. 277 (Lung Cell. Mol. Physiol. 21): L719–L726, 1999. —Oxidative stress may be a fundamental mode of injury associated with inspired particles. To examine this, we determined the ability of three carbon black particles (CBPs; M120, M880, and R250) and two forms of silicon dioxide, amorphous (Cabosil) and crystalline (DQ12) quartz, to deplete epithelium lining fluid antioxidant defenses. Single and composite antioxidant solutions of uric acid, ascorbic acid (AA), and reduced glutathione (GSH) were examined in the presence of particle concentrations of 150 μg/ml. Uric acid was not depleted by any particle considered. AA was depleted in a near-linear fashion with time by the three different CBPs; however, AA depletion rates varied markedly with CBP type and decreased in the presence of metal chelators. An initially high GSH depletion rate was noted with all CBPs, and this was always accompanied by the appearance of oxidized glutathione. Exposure to Cabosil or DQ12 did not result in the loss of GSH. Together, these data demonstrate that particle type, size, and surface area are all important factors when considering particleantioxidant interactions in the airways.
The Journal of Toxicological Sciences

Prnp knockout mice disrupted PrP-related genes have played an essential role to elucidate the relationship between PrP, a normal host gene product, and PrP, a protease-resistant, infectious PrP; Prnp knockout mice developed by Büeler et al. (1992) were completely protected against scrapie disease when challenged with mouse prions. Furthere, varying expression levels in PrP were revisited along with a varying susceptibility of mouse prions, when mouse Prnp genes were introduced into Prnp mice. How these murine models for human prion-related disease would contribute to the presently ongoing TSE research?
Topic Introduction Imaging Kidney Development

Development of the kidney involves interactions between several cell lineages and complex morphogenetic processes, such as branching of the ureteric bud (UB) to form the collecting duct system and condensation and differentiation of the mesenchymal progenitors to form the nephron epithelia. One of the advantages of the mouse kidney as an experimental system is that it can develop in culture, from the stage of initial branching of the UB (E11.5) for up to a week (although it achieves the size and degree of development of only an E13.5–E14.5 kidney in vivo). The availability of fluorescent proteins (FPs) has provided powerful tools for visualizing the morphogenesis of specific renal structures in organ cultures. Two categories of genetically modified mice that express FPs are useful for visualizing different cell lineages and developmental processes in these organ cultures: (1) transgenic mice that express a fluorescent reporter in the pattern of a specific gene; and (2) Cre reporter mice, which turn on an FP in cells with Cre recombinase activity (and their daughter cells), used in conjunction with cell type-specific Cre transgenic mice. Here, we describe some of the currently available Cre and FP transgenic lines that are useful for the study of kidney development.
Chapter 2 The Diversification of Intra-European Movement

The literature on free movement among the 28 member states of the European Union (EU) divides along two main themes. The first set of studies analyses the nature and type of intra-European movement. Here, the central focus tends to be one of the main migration flows within Europe – namely, the movement of Central and Eastern Europeans (CEE) who are mostly citizens of the EU (Black et al. 2010). In migration studies, this freedom of movement within the EU is increasingly articulated in terms of ‘East’ to ‘West’ migration. Many studies show how this migration pattern within Western Europe is expanding beyond the seasonal and circular forms of labour migration that initially characterized CEE migration, to one characterized by more permanence (e.g., Recchi 2008; Favell 2008; Eade et al. 2006; Düvell and Vogel 2006; Engbersen et al. 2011, 2013; Castro-Martin and Cortina 2015). To illustrate, Engbersen et al. (2011; Engbersen et al. 2013) contend that along the two axes of attachment to country of origin and destination, there are now four categories of intra-European movement: (1) bi-national; (2) circular; (3) settlement and; (4) “footloose”. This typology captures the fact that some migrants preserve transnational ties that attach them to their region of origin as well as their host countries while others remain permanently in receiving societies, later reuniting with family members or establishing new families in the receiving country (ibid.). Others still may continue their expedition to other parts of Europe or may rather end up “footloose”, experiencing problems accessing the labour market in the receiving country as their ties with the home country fade (ibid.). Studies also show that different types of migration are related to different stages of migration, moving from an initial stage of temporary work abroad, through transnational commuting to permanent
A consumer­focused value­based analysis

and how smart marketing should be applied; and also to identify and define the inter-channel and intra-channel level interactions and synergies that will add the greatest value across their marketing system. The framework however, though smart-retailing-focused is still generic and only provides the ‘ingredients’ and ‘recipe principles’ for the design of a smart retailing marketing strategy of individual businesses. Its practical application therefore, to individual business, inevitably requires refinement and adaptation according to the specific characteristics, environmental contexts and strategic orientations of individual business.
Diagnostics for Monitoring-based Commissioning *

Synopsis This paper presents a case for application of automated monitoring, analysis and diagnostic tools for monitoring-based commissioning. Selected examples are presented in which such tools have been used successfully to support commissioning activities in southwestern Canada and the U.S. Pacific Northwest. The first example involves use of spreadsheet-based tools to automatically generate diagnostic plots that are visually examined for specific features that reveal operational problems in space conditioning systems of large commercial buildings. The findings then guide re-tuning actions to increase building energy efficiency. This is followed by application of a tool for continuous monitoring of whole-building energy use to automatically track energy savings resulting from a utility commissioning program. This tool also provides a means by which to detect degradation of savings and performance to guide monitoring-based commissioning actions. The potential use of automated diagnostic tools for chillers and packaged air conditioners is then described for continually commissioning these units. The paper concludes with a discussion of the impacts of this approach on commissioning, including potential time savings, associated cost savings, and improvements in the quality of commissioning.
Temperature dependent load partitioning and slip mode transition in a eutectic AlCoCrFeNi<inf>2.1</inf> high entropy alloy

Eutectic high entropy alloys are gaining increasing attention due to their excellent castability and combination of strength and ductility in the as-cast state. However, the detailed behavior of the nano-scale lamellar microstructure during deformation, and in particular the interaction between the phases, is not well understood. Here we use in-situ neutron diffraction during tensile testing over a wide temperature range (77–673 K) to obtain new insights into the temperature dependent mechanical interactions between and within phases during initial plastic deformation of an AlCoCrFeNi 2 . 1 eutectic high entropy alloy. The load was transferred from the L1 2 to the B2 phase during the yielding process, and the changing load distribution within the L1 2 phase with increasing temperature strongly suggests that ⟨ 110 ⟩ { 001 } cube slip is activated at room temperature and above. This points towards alloying design for delayed octahedral-to-cube slip transition as a possible strategy for increasing the high temperature strength of material.
ZERO-COST COLLAR STRATEGY FOR CHILEAN EXPORTERS: BLACK-SCHOLES VALUATION VS MONTE CARLO SIMULATIONS, ESTRATEGIA COLLAR COSTO CERO PARA EXPORTADORES CHILENOS. VALUACION DE BLACK-SCHOLES VS SIMULACIONES DE MONTECARLO

Monte Carlo Simulation (MCS) is an important technique used in finance to value European options in general and hedging strategies of exchange rate risk in particular. However, Hull (2012) indicates that this technique demands much computing time to achieve a high level of precision. In spite of the above, this article shows that the standard errors associated with MCS can be significantly reduced by increasing the number of random walks. Additionally, it is shown that the valuation of zero-cost collar strategy followed by a Chilean exporter, who seeks monthly coverage against foreign exchange risk, converges at the same price either using the Black-Scholes model or MCS when the number of random walks increases through simulations. Finally, the effectiveness of zero-cost collar strategy is evaluated. This strategy shows clear economic benefits associated of being implemented in periods of appreciation of the Chilean peso against the U.S. dollar.
Harmonic Modulation of Proton MR Precessional Phase by Pulsatile Motion : 307 Origin of Spinal CSF Flow Phenomena

The effects of pulsatile motion on MR imaging of spinal CSF were quantitatively evaluated with a spine phantom that simulated spinal CSF pulsation. Two fundamental interdependent pulsation flow phenomena were observed: variable reductions in signal intensity of pulsatile CSF (signal loss) and spatial mismapping of this signal beyond the confines of the subarachnoid space (phase-shift images). Phase-shift images were observed as multiple regions of signal intensity conforming morphologically to the subarachnoid space but displaced symmetrically from it along the phase-encoding axis, either added to or subtracted from stationary signal intensity. Both CSF pulsation flow phenomena occurred secondary to harmonic modulation of proton precessional phase (temporal phase shift) by the unique pulsatile motion of spinal CSF when the repetition time was not an integral multiple of the pulsation period. Each flow phenomenon was analyzed with the spine phantom independently to control individual imaging and physiologic parameters including imaging plane, repetition time, echo time, slice thickness, number of echoes, number of excitations, CSF pulsation amplitude, and CSF pulsation period. In the axial plane, signal loss was present on both firstand secondecho images and was more pronounced with larger pulsation amplitudes and smaller slice thicknesses. A quantitative relationship between these two parameters allowed the prediction of CSF pulsation amplitude when the slice thickness was known and the CSF signal intensity was measured. In the sagittal plane, signal loss was present on first-echo images, was more pronounced with larger pulsation amplitudes, and underwent incomplete even-echo rephasing on second-echo images. Phase-shift images were influenced by the relationship between repetition time and CSF pulsation period. They were partly eliminated on sagittal but not on axial second-echo images because of incomplete even-echo rephasing. Both signal loss and phase-shift images were completely eliminated with CSF gating or pseudogating, indicating the rationale for gating during clinical spinal MR. The clinical significance of these findings is that awareness of the existence of spinal CSF pulsation flow phenomena avoids diagnostiC confusion, whereas understanding their etiology provides a rational approach, such as CSF gating, to eliminate them.
Cost of water use: A driver of future investments into water-efficient thermal power plants?

Based on a global and comprehensive empirical study, this paper analyses the regional impact of water use economics on the decision to invest in new thermal power projects. Investments today are primarily determined by water availability and regulations, and less by the financial implications of water use. The paper aims to help design effective policies and decision-making tools to support long-term investments in water use improvement solutions. It concludes by arguing that there is a need for a new investment decision model which captures the total value of water solutions, rather than focusing only on direct cost variations between different technological options. © 2015 The Authors. Published by Elsevier B.V. Peer-review under responsibility of Stockholm International Water Institute.
February 2020 Imaging of 99 mTc-DMSA and 18 F-FDG in humans using a Si / CdTe Compton camera

The Compton camera can simultaneously acquire images of multiple isotopes injected in a body; therefore, it has the potential to introduce a new subfield in the field of biomedical imaging applications. The objective of this study is to assess the ability of a prototype semiconductorbased silicon/cadmium telluride (Si/CdTe) Compton camera to simultaneously image the distributions of technetium (99mTc)-dimercaptosuccinic acid (DMSA) (141 keV emission) and 18F-fluorodeoxyglucose (FDG) (511 keV emission) injected into a human volunteer. 99mTc-DMSA and 18F-FDG were injected intravenously into a 25-year-old male volunteer. The distributions of 99mTc-DMSA and 18F-FDG were simultaneously made visible by setting a specified energy window for each radioisotope. The images of these radiopharmaceuticals acquired using the prototype Compton camera were superimposed onto computed tomography images for reference. The reconstructed image showed that 99mTc-DMSA had accumulated in both kidneys, which is consistent with the well-known diagnostic distribution determined by clinical imaging via singlephoton emission computed tomography. In the 18F-FDG image, there is broad distribution around the liver and kidneys, which was expected based on routine clinical positron emission tomography imaging. The current study demonstrated for the first time that the Si/CdTe Compton camera was capable of simultaneously imaging the distributions of two radiopharmaceuticals, 99mTc-DMSA and 18F-FDG, in a human body. These results suggest that the Si/CdTe Compton camera has the potential to become a novel modality for nuclear medical diagnoses enabling multi-probe simultaneous tracking. LETTER 2020 Original content from this work may be used under the terms of the Creative Commons Attribution 3.0 licence. Any further distribution of this work must maintain attribution to the author(s) and the title of the work, journal citation and DOI. RECEIVED
Prolactin Receptors in Mammary Carcinoma Cells 1

Three types of experimental mammary carcinomas, the 7 , 12-dimethylbenzanthracene-induced and R3230AC carci nomas in the rat and the C3HBA carcinoma ofthe mouse, were assayed for prolactin receptor activity. The prolactin â€ ̃25I-bindingactivities of particles derived from the 7, 12dimethylbenzanthracene-induced and R3230AC carcino mas exhibited the properties of high affinity (Kd = 7.1 x l0@'Cand 6.0 x l0'C M, respectively), low capacity, satura bility at levels for physiological saturation, and hormonal specificity. However, two other hormones, placental lacto gen and growth hormone, exhibited significant competitive displacement of bound prolactin-'251 in proportion to their known lactogenic activities. The specific prolactin-125 I-bind ing activities of these carcinoma cells were found to reside in the plasma membrane and were inactivated by treatment with trypsin or by heating. These properties ofthe prolactin â€ ̃251-bindingactivities of these carcinomas are identical to those of the prolactin receptor of the mammary alveolar cells of rats and mice. Quantitative assays of receptor activities in these carcino mas revealed three individual patterns. The 7, 12-dimethyl benzanthracene-induced carcinoma, which is known to be characteristically dependent upon prolactin for growth, exhibited a range of specific activities which varied between 30 and 80% of the lactational mammary gland. The R3230AC carcinoma, which has been shown to be prolactin responsive for milk protein synthesis but not for growth, had a tissue concentration of prolactin receptor activity that was approximately 15% of that of lactational mammary gland. The C3HBA carcinoma, a relatively autonomous tumor, had no detectable prolactin receptor activity. The results provide evidence for the existence of prolactin receptors in certain mammary carcinoma cells and suggest that the degreeof prolactin dependenceof suchcarcinomas may be characterized by the relative numbers of prolactin receptors present.
Spring Microservices

Build scalable microservices with Spring, Docker, and MesosAbout This BookLearn how to efficiently build and implement microservices in Spring, and how to use Docker and Mesos to push the boundaries of what you thought possible Examine a number of real-world use cases and hands-on code examples. Distribute your microservices in a completely new way Who This Book Is ForIf you are a Spring developers and want to build cloud-ready, internet-scale applications to meet modern business demands, then this book is for you Developers will understand how to build simple Restful services and organically grow them to truly enterprise grade microservices ecosystems. What You Will LearnGet to know the microservices development lifecycle processSee how to implement microservices governance Familiarize yourself with the microservices architecture and its benefits Use Spring Boot to develop microservices Find out how to avoid common pitfalls when developing microservicesBe introduced to end-to-end microservices written in Spring Framework and Spring Boot In Detail The Spring Framework is an application framework and inversion of the control container for the Java platform. The framework's core features can be used by any Java application, but there are extensions to build web applications on top of the Java EE platform. This book will help you implement the microservice architecture in Spring Framework, Spring Boot, and Spring Cloud. Written to the latest specifications of Spring, you'll be able to build modern, Internet-scale Java applications in no time. We would start off with the guidelines to implement responsive microservices at scale. We will then deep dive into Spring Boot, Spring Cloud, Docker, Mesos, and Marathon. Next you will understand how Spring Boot is used to deploy autonomous services, server-less by removing the need to have a heavy-weight application server. Later you will learn how to go further by deploying your microservices to Docker and manage it with Mesos. By the end of the book, you'll will gain more clarity on how to implement microservices using Spring Framework and use them in Internet-scale deployments through real-world examples. Style and approach The book follows a step by step approach on how to develop microservices using Spring Framework, Spring Boot, and a set of Spring Cloud components that will help you scale your applications.
Title Fabrication of CsPbBr3 Thick Films by Using a Mist Deposition Method for Highly Sensitive X-ray Detection

X-ray imaging is an important technique used for medical imaging and non-destructive inspection of industrial products. Highly sensitive X-ray detectors which enable X-ray imaging at low dose rate are required to reduce the risk of cancer. Recently, metal halide perovskite materials have demonstrated excellent X-ray detection performance including high sensitivity due to their high absorption coefficient, high carrier mobility, and long carrier lifetime. However, there are few studies on perovskite thick films with large area which is essential for the application to X-ray imaging devices. In this study, a polymer is employed as a buffer layer to avoid a film exfoliation, which makes it difficult to fabricate perovskite thick films, and a 110-μm-thick CsPbBr3 film is successfully obtained using a scalable solution method. In addition, an X-ray detector based on the CsPbBr3 thick film is fabricated and achieves a high sensitivity of 11,840 μC Gyair–1 cm–2. This sensitivity is about 600 times higher than that of currently commercial a-Se X-ray detectors.
Financial Performance Evaluation of Food and Drink Index Using Fuzzy MCDM Approach

Performance evaluation presents a very complex field involving different criteria and contradicted information. Though, there is an insisting need to a reliable and consistent approach where the application procedures are not complicated. In this study, a fuzzy Multi Criteria Decision Making (MCDM) approach is developed to evaluate the financial performance of companies listed in food and drink index of Istanbul Stock Exchange. Financial ratios were identified to create a base for financial performance evaluation in the areas of: profitability, efficiency, growth, liquidity, leverage and market ratios. Weight coefficients were obtained by the objective method of Fuzzy Shannon’s Entropy (FSE). Evaluation and ranking were made on the base of the new method of Fuzzy Evaluation Based on Distance from Average Solution (FEDAS). In order to test the reliability of the approach a scenario analysis is conducted based on CRITIC weighting method. Comparison with other MCDM methods and spearman correlation are conducted to test validity of the proposed approach. The proposed approach is reliable and provides the most suitable result comparing with other MCDM methods.