Miracle-dz/UniFAR-FTUs huggingface dataset:
Episodic evolution of a eukaryotic NADK repertoire of ancient provenance

NAD kinase (NADK) is the sole enzyme that phosphorylates nicotinamide adenine dinucleotide (NAD+/NADH) into NADP+/NADPH, which provides the chemical reducing power in anabolic (biosynthetic) pathways. While prokaryotes typically encode a single NADK, eukaryotes encode multiple NADKs. How these different NADK genes are all related to each other and those of prokaryotes is not known. Here we conduct phylogenetic analysis of NADK genes and identify major clade-defining patterns of NADK evolution. First, almost all eukaryotic NADK genes belong to one of two ancient eukaryotic sister clades corresponding to cytosolic (“cyto”) and mitochondrial (“mito”) clades. Secondly, we find that the cyto-clade NADK gene is duplicated in connection with loss of the mito-clade NADK gene in several eukaryotic clades or with acquisition of plastids in Archaeplastida. Thirdly, we find that horizontal gene transfers from proteobacteria have replaced mitochondrial NADK genes in only a few rare cases. Last, we find that the eukaryotic cyto and mito paralogs are unrelated to independent duplications that occurred in sporulating bacteria, once in mycelial Actinobacteria and once in aerobic endospore-forming Firmicutes. Altogether these findings show that the eukaryotic NADK gene repertoire is ancient and evolves episodically with major evolutionary transitions. Author Summary Metabolic enzymes are central to all living organisms and key to understanding the evolution of life on Earth. One important component of all metabolic pathways is the participation of chemically-reducing cofactors such as the redox system of NAD+ and NADH molecules. All living cells also possess a system for shifting their intracellular pool of NAD+ and NADH into NADP+ and NADPH via phosphorylation by the NAD kinase (NADK). Phosphorylation by NADK allows cells to regulate the use of their main chemical redox system for anabolic growth and the synthesis of basic cellular components. In our study we provide the first comprehensive analysis of the NAD kinase family. We find that eukaryotes possess two ancient NADK gene families of unknown provenance and also find unrelated bacterial families that also possess dual NADK genes. We also find that while NADK evolution has been mostly stable through the eons, this family has evolved substantially in association with the evolution of specific clades of organisms. Altogether these results provide a metabolic picture of the tree of life and its evolution.
Vernacular Heritage as a Response to Climate: Lessons for Future Climate Resilience from Rize, Turkey

Vernacular heritage is undergoing rapid changes caused by the effects of the changing climate, such as loss of lands, biodiversity, building materials, integrity, traditional knowledge, and maladaptation. However, little is known about the causes of deterioration in vernacular heritage sites under changing climate and landscape conditions from a user perspective. This paper provides insights into the perceptions of local people on climate change and how it has changed the landscape in the Fındıklı district of Rize in the Eastern Black Sea area of Turkey. The study proposed analyzing vernacular architecture as a heritage category for localizing the management of climate change impacts using field survey, on-site observations, and unstructured interviews with local people. The results of the shared concerns regarding the changing climate and landscapes from a local perspective evoke the use of narratives as a tool for local authorities to include local communities in building resilience of cultural heritage to climate change.
A hybrid deep clustering approach for robust cell type profiling using single-cell RNA-seq data

Single-cell RNA sequencing (scRNA-seq) is a recent technology that enables fine-grained discovery of cellular subtypes and specific cell states. Analysis of scRNA-seq data routinely involves machine learning methods, such as feature learning, clustering, and classification, to assist in uncovering novel information from scRNA-seq data. However, current methods are not well suited to deal with the substantial amount of noise that is created by the experiments or the variation that occurs due to differences in the cells of the same type. To address this, we developed a new hybrid approach, deep unsupervised single-cell clustering (DUSC), which integrates feature generation based on a deep learning architecture by using a new technique to estimate the number of latent features, with a model-based clustering algorithm, to find a compact and informative representation of the single-cell transcriptomic data generating robust clusters. We also include a technique to estimate an efficient number of latent features in the deep learning model. Our method outperforms both classical and state-of-the-art feature learning and clustering methods, approaching the accuracy of supervised learning. We applied DUSC to a single-cell transcriptomics data set obtained from a triple-negative breast cancer tumor to identify potential cancer subclones accentuated by copy-number variation and investigate the role of clonal heterogeneity. Our method is freely available to the community and will hopefully facilitate our understanding of the cellular atlas of living organisms as well as provide the means to improve patient diagnostics and treatment.
Geolocation Solver of IoT Devices for Active and Assisted Living

— Latest enhancements in IoT devices and in communication technologies, has brought new ideas that are capable of providing advanced sensing of the surrounding environment. On the other hand, average life expectancy has grown, resulting in a considerable increase in the number of elderly people. Consequently, there is a constant search for new solutions, to support an Active and Assisted Living (AAL) of these people. This paper aims to propose a solution to help in knowing the location of IoT devices that could be helping these people. The proposed solution takes into consideration the risk factors of the target persons, at any given time and as well as the technical constraints of the device, such as available power and communications. Thus, a proﬁle -based decision is taken autonomously either by the device or its integrated system to ensure the use of the best geolocation technology in each situation.
Maritime Transport VIII

In the past decade a strong commitment in terms of environmental protection and sustainable development in port sector is noted. In order to achieve and maintain the environmental performance of port it is necessary to establish guidelines and priorities. This paper presents status and priorities which are marked within the European port sector through ESPO`s Ecoports environmental reports for the period 2013-2018. The change of environmental priorities in the port sector over the years has been noticed and therefore potential reasons for priority changes are addressed in this paper. The general aim of set priorities is to provide information about the high priority environmental issues and thus set the framework for guidance and initiatives that influence the environmental performance of the port. The analysis indicates that most of European ports actively work to protect the environment and thus guarantee sustainable development. From 2016 to 2018 the top 3 priorities have been the same (air quality, noise and energy efficiency), while air quality has remained the number one priority of the European ports since 2013. It is interesting to highlight that climate change priority which has been introduced in 2017 has been rapidly climbing the ranks and went up by 3 places in 2018.
Reconfigurable Photonic Microwave Mixer With Mixing Spurs Suppressed and Dispersion Immune for Radio-Over-Fiber System

In this article, a reconfigurable mixer based on only one dual-polarization quadrature phase shift -keying modulator (DP-QPSKM) is proposed and comprehensively demonstrated for a radio-over-fiber (RoF) system. By changing the detection unit and adjusting the dc voltages, the single-ended, double-balanced, image (IM)-free, mixing spurs suppressed, and dispersion-immune mixing can be implemented. Experimental results show that the ~60-dB IM rejection ratio and the spur suppression ratio are achieved. Moreover, the dispersion-induced power fading is successfully compensated by the dc voltage adjustment. The spurious-free dynamic range (SFDR) is about 100.56 dB.Hz2/3. Only one optical path is required without extra optical filters or phase-related devices, which makes the structure concise and stable. This structure would be more compact to meet the potential of integration if a dispersion medium with smaller size is available.
A Literature Review of Studies into the Prevalence and Frequency of Men’s Pornography Use

Abstract This review aims to provide information on the prevalence and frequency of adult males’ pornography use. It appears, the majority (> 80%) of adult men have accessed pornography at some point, and in the past year (40–70%). Around half of younger men (25 or under) are weekly consumers. Pornography use tapers-off with age. Relatively few (<10%) younger men have accessed violent pornography in the past year. The Internet is the primary method of access. Pornography use is associated with masturbation; use during partnered sex is less common. Differences in consumption rates between heterosexual and gay and bisexual men are discussed.
Energy-Efficient Autonomous Navigation of Solar-Powered UAVs for Surveillance of Mobile Ground Targets in Urban Environments

In this paper, we consider the navigation of a group of solar-powered unmanned aerial vehicles (UAVs) for periodical monitoring of a set of mobile ground targets in urban environments. We consider the scenario where the number of targets is larger than that of the UAVs, and the targets spread in the environment, so that the UAVs need to carry out a periodical surveillance. The existence of tall buildings in urban environments brings new challenges to the periodical surveillance mission. They may not only block the Line-of-Sight (LoS) between a UAV and a target, but also create some shadow region, so that the surveillance may become invalid, and the UAV may not be able to harvest energy from the sun. The periodical surveillance problem is formulated as an optimization problem to minimize the target revisit time while accounting for the impact of the urban environment. A nearest neighbour based navigation method is proposed to guide the movements of the UAVs. Moreover, we adopt a partitioning scheme to group targets for the purpose of narrowing UAVs’ moving space, which further reduces the target revisit time. The effectiveness of the proposed method is verified via computer simulations.
Flavone Synthase II (CYP93B) of Antarctic Plant Colobanthus quitensis (Kunth) Bartl.

The role of flavonoids in plant-environmental stress has many biotechnological applications, in this way Antarctic plants have an important potential for molecular farming. However, the concentration and exploitation of resource are highly restricted, for this reason the use of enzymatic machinery of the Antarctic plants have importance for in vitro flavonoid production for different biotechnological applications. Despite their potential applications, key enzymes for flavonoid biosynthesis are poorly studied in non-model plants. In this work, we studied the flavonoid key enzyme, flavone synthase II (FNS II) in C. quitensis. The results show a cooperative kinetic model for NADPH and naringenin. The temperature and pH stability assays show optimal temperature between 20-30 °C, with an operative range from 2 to 37 °C, pH stability shows an optimum of 7.0 to 8.0, with operative range from 3.0 to 8.0, demonstrating a big thermal and pH-stability, an interesting characteristic to in vitro production of flavones.
Antifungal Activity of Lactic Acid Bacteria Isolated from Peanuts, Gari, and Orange Fruit Juice against Food Aflatoxigenic Molds

ABSTRACT This study aims to evaluate the antifungal activity of lactic acid bacteria (LAB) from some Cameroonian food commodities against mycotoxigenic and spoilage molds. Following LAB isolation, the antifungal activity of the isolates was assessed. The organic acids were quantified using high-performance liquid chromatography and the ability of the LAB to reduce mold biomass and aflatoxin production was evaluated. The LAB were identified and the biopreservative potential of strain LO3 was evaluated on tomato paste. Nine percent of the strains isolated showed broad antifungal activity. The activity was due to the effect of organic acids comprising lactic, acetic, 4-hydroxy-3-phenyllactic and 3-phenyllactic acids. Lactobacillus plantarum LO3 exhibiting the highest and broadest antifungal activity was selected and showed the capacity to inhibit fungal growth and aflatoxin production in vitro. Moreover, this strain and its cell-free supernatant showed the ability to prevent aflatoxigenic mold growth in tomato paste without altering its physico-chemical and organoleptic properties.
Dynamic Evaluation Strategies for Multiple Aircrafts Formation Using Collision and Matching Probabilities

Configuration evaluation is a key technology to be considered in the design of multiple aircrafts formation (MAF) configurations with high dynamic properties in engineering applications. This paper deduces the relationship between relative velocity, dynamic safety distance and dynamic adjacent distance of formation members, then divides the formation states into collision-state and matching-state. Meanwhile, probability models are constructed based on the binary normal distribution of relative distance and relative velocity. Moreover, configuration evaluation strategies are studied by quantitatively analyzing the denseness and the basic capabilities according to the MAF collision-state probability and the MAF matching-state probability, respectively. The scale of MAF is grouped into 5 levels, and previous lattice-type structures are extended into four degrees by taking the relative velocities into account to instruct the configuration design under complex task conditions. Finally, hardware-in-loop (HIL) simulation and outfield flight test results are presented to verify the feasibility of these evaluation strategies.
Channel Sounding and Ray Tracing for Intrawagon Scenario at mmWave and Sub-mmWave Bands

In order to realize the vision of “smart rail mobility,” a seamless high-data rate wireless connectivity with up to dozens of gigahertz bandwidth will be required. This forms a strong motivation for exploring the underutilized millimeter wave (mmWave) and sub-mmWave bands. In this article, the wireless channel in one “smart rail mobility” scenario—the intrawagon scenario—is characterized through ultrawideband (UWB) channel sounding and ray tracing (RT) at mmWave and sub-mmWave bands. To begin with, a series of horizontal directional scan-sounding measurements are performed inside a real high-speed train wagon at 60 and 300 GHz frequency bands with a bandwidth of 8 GHz. Correspondingly, the channel characteristics such as Rician $K$ -factor, root-mean-square (rms) delay spread (DS), azimuth spread of arrival, and azimuth spread of departure are extracted and analyzed. Based on the measurements, a self-developed RT simulator is validated through the reconstruction of the three-dimensional wagon model and the calibration of the electromagnetic (EM) properties of the main materials. This gives the chance to physically interpret the measurement results and characterize the intrawagon mmWave and sub-mmWave channels more comprehensively through extensive RT simulations.
On the modelling of interface roughness scattering in AlGaN/GaN heterostructures

AlGaN/GaN heterostructures are attractive for high-power radiofrequency applications due to the wide bandgap of GaN and the high values of spontaneous and piezoelectric polarisation in such material systems, which lead to high breakdown voltages and high 2D carrier concentrations. It is of particular interest to accurately model the 2DEG mobilities in these structures, as different scattering mechanisms can limit the total mobility at different temperatures and carrier concentrations. In this paper, we present a semi-classical modelling framework for low-field mobility in AlGaN/GaN heterostructures, focussing especially on the impact of interface roughness (IFR) scattering on the low-temperature mobility. The framework is validated by comparing calculated mobility values with experimental data, and different ways of modelling the IFR scattering are investigated. A non-linear IFR scattering model is used to obtain the best match to measured data for different Al-contents in the AlGaN layer in case of a low potential barrier at the heterointerface, while the temperature dependence of mobility with a high potential barrier in an AlGaN/AlN/GaN system is best matched with IFR models where the squared scattering matrix elements depend linearly on the roughness power spectrum.
A Semi-Automatic Dispenser for Solid and Liquid Food in Aquatic Facilities

We present a novel, low-footprint and low-cost semi-automatic system for delivering solid and liquid food to zebrafish, and more generally to aquatic animals raised in racks of tanks. It is composed of a portable main module equipped with a contactless reader that adjusts the quantity to deliver for each tank, and either a solid food module or a liquid food module. Solid food comprises virtually any kind of dry powder or grains below two millimeters in diameter, and, for liquid-mediated food, brine shrimps (Artemia salina) and rotifers (Rotifera) have been successfully tested. Real-world testing, feedback and validation have been performed in a zebrafish facility for several months. In comparison with manual feeding this system mitigates the appearance of musculoskeletal disorders among regularly-feeding staff, and let operators observe the animals’ behavior instead of being focused on quantities to deliver. We also tested the accuracy of both humans and our dispenser and found that the semi-automatic system is much more reliable, with respectively 7-fold and 84-fold drops in standard deviation for solid and liquid food.
Wine with a Bouquet of Biodiversity: Assessing Agricultural Adoption of Conservation Practices in Chile

Summary Promoting conservation practices in agriculture to protect biodiversity of rare Mediterranean ecosystems is nowhere more critical than in Chile, where less than 2% of the Mediterranean region is formally protected. We used the theory of planned behaviour to assess what influences Chilean winegrowers’ conservation behaviour and tested whether a sustainability programme was effective. We compared winegrowers involved in the programme with a comparison group, using semi-structured interviews at 23 wineries to determine predictors of conservation practice adoption at vineyards. The intervention group had higher levels of conservation behaviour than the comparison group and practised integrated pest management and exotic species control more frequently. Managers’ views on conservation practices as doing ‘what is right’ with regards to nature and the environment were evident in both groups. However, programme winegrowers recognized more cultural benefits of nature and reported a broader spectrum of organizational and community stakeholder influence. Economic resources were perceived as a major barrier, as well as the lack of data connecting biodiversity conservation with wine quality and production. This study demonstrates the multidimensional nature of winegrowers’ motivations and barriers for adopting conservation practices, which is critical to addressing the significant challenges facing biodiversity conservation and the promotion of sustainable agricultural systems.
New Outbreaks of Verticillium Wilt on Hop in Oregon Caused by Nonlethal Verticillium albo-atrum

In 2006 and 2007, outbreaks of Verticillium wilt on hop were detected on two farms in Oregon. Some Verticillium pathogens cause minor damage to hop but others can kill susceptible cultivars: strains of lethal V. albo-atrum are not known to occur in Oregon. Studies were conducted to determine the identity of the Verticillium species associated with these outbreaks and their virulence to hop to devise an appropriate response to the outbreaks. Isolates were recovered from wilted plants, and identified as V. albo-atrum based on morphological characters and ITS region sequence. Pathogenicity assays conducted on a set of differential cultivars indicated all isolates had a low to intermediate level of virulence. Inspection and mapping of all symptomatic and dead plants in a hop yard on an affected farm indicated that 29.3% and 19.7% of plants had symptoms of Verticillium wilt in 2006 and 2007, respectively. However, the number of dead or missing plants did not increase from 2006 to 2007 (0.26% in both years). There was a clear directionality to the pattern of symptomatic plants among rows running north-south vs. east-west in 2006, although directionality was less pronounced in 2007. These findings indicate that the recent outbreaks of V. albo-atrum on hop in Oregon were caused by nonlethal strains, which has key implications for devising management strategies on the affected farms.
Impact of post-harvest storage and freezing of palm fruits on the extraction yield and quality of African crude palm oil extracted in the laboratory

In the frame of African artisanal small-scale extraction of palm oil, the effects of post-harvest storage time and freezing of palm fruits on the extraction yield and quality of crude palm oil (CPO) were studied at laboratory scale using a process mimicking artisanal extraction. The extraction yield and free fatty acid (FFA) content of CPO increased with the length of fruit storage time at room temperature and freezing. FFA, total fatty acid and triacylglycerol profiles indicated a lack of specificity of the lipases at work. During post-harvest storage, the carotenoid content of CPO decreased slightly, tocopherols and tocotrienols (tocols) remained steady, while lipid oxidation remained at a very low level. For frozen fruits, carotene and tocol contents decreased sharply as a function of storage time, thought remaining quite high, but decreasing amounts of secondary oxidation products were detected. The FFA content and lipid oxidation level were highly correlated, indicating a pro-oxidant effect of FFAs. To conclude, three days of storage prior to artisanal extraction seemed the best trade-off between extraction yield and CPO quality. Combined storage at room temperature and freezing of palm fruits led to a large range of FFA contents in CPO. Optimization of the FFA contents of artisanal CPOs in line with local consumer’s demand calls for an assessment of their functional properties and sensory perception of foods formulated with CPOs.