Miracle-dz/UniFAR-FTUs huggingface dataset:
Plasmodium vivax Malaria Viewed through the Lens of an Eradicated European Strain

The protozoan Plasmodium vivax is responsible for 42% of all cases of malaria outside Africa. The parasite is currently largely restricted to tropical and subtropical latitudes in Asia, Oceania and the Americas. Though, it was historically present in most of Europe before being finally eradicated during the second half of the 20th century. The lack of genomic information on the extinct European lineage has prevented a clear understanding of historical population structuring and past migrations of P. vivax. We used medical microscope slides prepared in 1944 from malaria-affected patients from the Ebro Delta in Spain, one of the last footholds of malaria in Europe, to generate a genome of a European P. vivax strain. Population genetics and phylogenetic analyses placed this strain basal to a cluster including samples from the Americas. This genome allowed us to calibrate a genomic mutation rate for P. vivax, and to estimate the mean age of the last common ancestor between European and American strains to the 15th century. This date points to an introduction of the parasite during the European colonisation of the Americas. In addition, we found that some known variants for resistance to anti-malarial drugs, including Chloroquine and Sulfadoxine, were already present in this European strain, predating their use. Our results shed light on the evolution of an important human pathogen and illustrate the value of antique medical collections as a resource for retrieving genomic information on pathogens from the past.
Bone stable isotopes indicate a high trophic position for New Zealand’s extinct South Island adzebill (Aptornis defossor) (Gruiformes: Aptornithidae)

The adzebills (Aptornithidae) were an ancient endemic lineage of large flightless Gruiformes that became extinct shortly after Polynesian settlement of New Zealand. The diet and ecology of these enigmatic birds has long been a matter for conjecture, but recent stable isotope analyses of bones of the North Island adzebill (Aptornis otidiformis) have indicated that adzebills may have been predatory. Here, we add to our understanding of adzebill ecology by providing the first stable isotope analyses of South Island adzebill (A. defossor) bones from two Holocene deposits. We interpret the results within frameworks of stable isotope measurements on bones of faunal species with known diets and from the same deposits (thereby mitigating regional effects on isotope values). Our results strongly support the hypothesis that adzebills had a high trophic position. Considered alongside the unique skeletal adaptations of adzebills and the distribution of the species during the Holocene, we suggest that adzebills were most likely terrestrial predators restricted to dry podocarp forests and may have specialised in dismantling rotting logs to obtain invertebrates and/or excavating burrowing animals such as tuatara or the chicks of burrow-nesting birds.
The role of post-Golgi transport pathways and sorting motifs in the plasmodesmal targeting of the movement protein (MP) of Ourmia melon virus (OuMV)

Plants have a highly sophisticated endomembrane system that is targeted by plant viruses for cell-to-cell movement. The movement protein (MP) of Ourmia melon virus (OuMV) is targeted to plasmodesmata (PD) and forms tubules to facilitate cell-to-cell movement. Despite a number of functionally important regions for correct subcellular localization of OuMV MP has been identified, little is known about the pathways OuMV MP hijacks to reach PD. Here, we demonstrate that OuMV MP localizes to the trans-Golgi network (TGN), but not to the multivesicular body/prevacuolar compartment or Golgi, and carries two putative sorting motifs, a tyrosine (Y) and a dileucine (LL) motif, near its N-terminus. Introducing glycine substitutions in these motifs results in loss of OuMV infectivity in Nicotiana benthamiana and Arabidopsis (Arabidopsis thaliana). Live cell imaging of GFP-labeled sorting motif mutants shows that Y motif mutants fail to localize to the TGN, plasma membrane, and PD. Mutations in the LL motif do not impair plasma membrane targeting of MP, but affect its ability to associate with callose deposits at PD. Taken together, these data suggest that both Y and LL motifs are indispensable for targeting of OuMV MP to PD and for efficient systemic infection, but show differences in functionality. This study provides new insights into the role of sorting motifs in intracellular targeting of MPs and vesicle trafficking pathways that plant viruses hijack for cell-to-cell movement.
Long-Term Bioclimatic Modelling the Distribution of the Fire-Bellied Toad, Bombina Bombina (Anura, Bombinatoridae), Under the Influence of Global Climate Change

Abstract The article describes the potential distribution area of B. bombina and fi gure out the signifi cant climatic factors of the species at a home range scale. Th is species is listed on Appendix II of the Bern Convention and on Annexes II and IV of the EU Natural Habitats Directive. It is protected by national legislation in many countries, occurs in many protected areas, and is listed in many national and sub-national Red Data books and lists. We collected the occurrence records and a set of climatic variables including 19 factors from 10’ resolution historical (summarizing annual trends, seasonality and extreme conditions during 1961-1990) and projected data (2050) available at the CliMond database. As a result, under climate predictions for 2050 there may be a substantial north and north-west shift of optimal habitat. Under such a scenario B. bombina populations may suff er mostly in the east and south of Ukraine. Under the modelled scenario the species representation in protected areas throughout the home range should be considered, but especially in Ukraine.
Interbull validation test for genomic evaluations

Genomic evaluations (GEBV) can be validated by comparing GEBVs of bulls in the youngest age classes to the daughter yield deviations (DYD) that the bulls will receive later. The GEBV are calculated from truncated data where the last four years of phenotypic data are removed. The test consists of weighted linear regression of DYD on GEBV. The intercept, regression coefficient and the coefficient of determination R are interpreted to represent average bias, prediction bias, and the validation accuracy, respectively.
Passive Control for Bilinear Stochastic Systems with Bounded Control

Abstract This paper investigates the problem of passive control for a class of bilinear stochastic systems. It assumes that the multiple dimensional control is bounded. Based on storage function method, passivity condition for the bilinear stochastic systems is presented by introducing a bounded nonlinear feedback controller. Moreover, input and output strict stochastic passivity, the relationship between output strict stochastic passivity and stochastic L 2 gain from input to output, and stochastic KYP (Kalman-Yakubovich-Popov) property for bilinear stochastic systems have been considered. A numerical example is provided to show the effectiveness of the method.
Mushroom science in Cuba: towards new opportunities for developing functional foods/nutraceuticals.

Mushroom science in Cuba allows the valorization of agricultural by-products into functional foods/nutraceuticals for human consumption to address objectives of sustainability and biotechnological development. Much research work done in Cuban eastern region has been performed on the Pleurotus genus, whose cultivation has increased greatly during the last few decades. Pleurotus species, like many edible and medicinal mushrooms, are a good source of immunomodulators and “host defense potentiators” (HDPs). In this context, dietetic supplements with a high therapeutic potential acting on the immune system and formulated from refined or partially refined mushroom extracts, or from dried mycelia/fruiting bodies biomass are referred as “mushroom immunoceuticals”. The present study examined the synergy exerted by the structural diversity of biomolecules found in Pleurotus crude extracts and powders on immune responses of both immunocompetent and immunodeficient Balb/c mice. Pleurotus derived-products could potentiate the host defense mechanisms in vivo and should be promising for further pharmacological studies. The effects on cell immunity are especially valuable in the prophylaxis of tumors, immunodeficiencies and as co-adjuvant in chemotherapy. The results also demonstrate that not only mushrooms but also their mycelia may be a good candidate for nutraceuticals production. Through this immunological “window” we are assisting to a revolution in mushroom science characterized by the diversity of compounds found in mushrooms and on the other hand, by the possibilities given by the abundance of specific molecular targets. An extended knowledge of the immuno-enhancing activity of Pleurotus nutraceuticals would be useful in understanding their potential applications for immunonutrition and immunotherapy.
Classification of Small Flat Oysters of Ostrea stentina Species Complex and a New Species Ostrea neostentina sp. nov. (Bivalvia: Ostreidae)

Small flat oysters of the genus Ostrea were collected from China, Japan, and the United States for identification and phylogenetic analysis. Fragments of mitochondrial cytochrome oxidase subunit I and 16S rRNA genes were sequenced in 57 specimens. Shell morphology and phylogenetic analyses identified four closely related groups in the Ostrea stentina/equestris/ aupouria species complex, supporting recent and ongoing speciation. Groups 1 and 2 are both O. equestris (Say, 1834), representing two divergent populations from the Asian Pacific and the Americas, respectively. Groups 3 and 4 are two separate species independent of O. equestris. Group 4 is O. stentina occurring in northern Spain, Portugal, Morocco, and northern Tunisia. Group 3 is a new species Ostrea neostentina sp. nov. found in southeastern Spain, eastern Tunisia, Hong Kong, and Japan. The occurrence of O. equestris in both Atlantic and Pacific oceans, from Argentina, Columbia, the United States, Gulf of California, Japan, and China to New Zealand, is unusual and highlights wide connectivity of Ostrea species as part of the marine ecosystem. This study provides the first record of O. equestris and O. neostentina sp. nov. along the southern coast of China and adds to the understanding of the diversity, global distribution, and evolution of Ostrea species.
Calcium looping with inherent energy storage for decarbonisation of coal-fired power plant

Implementation of carbon capture and storage, nuclear power stations and wide utilisation of renewable energy sources have been identified as capable of reducing around 42% of the energy sector’s cumulative CO2 emissions between 2009 and 2050. In scenarios assuming high shares of renewable energy sources in the energy portfolio, energy storage technologies and the remaining power generating assets would be required to flexibly balance energy supply and demand. With nuclear power plants operating at base load, this task would be handled by flexible fossil fuel power plants with CO2 capture. However, mature CO2 capture systems were shown to impose high efficiency penalties (8–12.5% points) and are better suited for base-load operation. An emerging calcium looping process, which has also been considered for energy storage, has been found to offer lower efficiency penalties (5–8% points). This study presents a concept of the calcium looping process with inherent energy storage for decarbonisation of the coal-fired power plant. Analysis has revealed that the possible routes for energy storage in this process include CaO/CaCO3 solids storage, CaO/Ca(OH)2 solids storage and cryogenic O2 storage systems. Comparison of the CaO/CaCO3 storage and cryogenic O2 storage systems revealed that implementation of the latter would result in higher turndown of the entire system and would offer higher energy density. Also, the hydration reaction was found to improve the energy density of the CaO/CaCO3 energy storage system by 57.4%, from 307.2 kWth h m−3 to 483.6 kWth h m−3. Economic evaluation of the proposed concepts revealed that application of the cryogenic O2 storage system in the calcium looping CO2 capture process has the potential to increase the profitability of the integrated system, even over the reference coal-fired power plant without CO2 capture.
Simulating and assessing boson sampling experiments with phase-space representations

The search for new, application-specific quantum computers designed to outperform any classical computer is driven by the ending of Moore's law and the quantum advantages potentially obtainable. Photonic networks are promising examples, with experimental demonstrations and potential for obtaining a quantum computer to solve problems believed classically impossible. This introduces a challenge: how does one design or understand such photonic networks? We develop novel complex phase-space software for simulating these photonic networks, and apply this to boson sampling experiments. Our techniques give sampling errors orders of magnitude lower than experimental measurements of correlations, for the same number of samples. We show that these techniques remove systematic errors in previous algorithms for estimating correlations, with order of magnitude improvements in errors in some cases. In addition to that, we obtain a scalable channel-combination strategy for assessment of boson sampling devices.
A case of ‘mistaken identity’: structurally similar ligand inhibits Thymidylate Kinase causing reversible filamentation of E. coli

Understanding genotype-phenotype relationship is a central problem in modern biology. Here we report that several destabilizing mutations in E. coli Dihydrofolate Reductase (DHFR) enzyme result in pronounced yet reversible filamentation of bacterial cells. We find that drop in DHFR activity in the mutants results in massive metabolic shifts leading to significant excess of dUMP and dCTP in the pyrimidine biosynthesis pathway. Both deoxyribonucleotides inhibit downstream essential enzyme Thymidylate Kinase (Tmk) which phosphorylates dTMP, eventually leading to almost complete loss of the DNA building block dTTP. Severe imbalance in deoxyribonucleotide levels ultimately leads to DNA damage, SOS response and filamentation. Supplementation of dTMP in the medium competitively alleviates Tmk inhibition and rescues filamentation, thereby illustrating a classic case of enzyme inhibition by structural mimic of its cognate ligand. Overall, this study highlights the complex interconnected nature of the metabolic network, and the fundamental role of folate metabolism in shaping the cell.
Micropropagación de Guadua angustifolia Kunth a partir de explantes nodales

Se evaluó el efecto de diferentes estrategias de desinfección, así como de varias concentraciones de la citoquinina 6-bencilamino purina (BAP) en el medio de cultivo, sobre el establecimiento y desarrollo in vitro de explantes nodales de Guadua angustifolia Kunth. Se observó que la utilización de explantes de plantas cultivadas en invernadero y la desinfección secuencial con un detergente alcalino, una mezcla de Benomyl y Agrimycin, seguidos de hipoclorito de sodio (1.5%), permitió reducir la contaminación externa en los explantes. Además, la incorporación en el medio de cultivo de un agente biocida, desarrollado para ser utilizado en cultivo in vitro de plantas (Plant Preservative Mixture®), a una concentración de 2 ml/l, redujo el desarrollo de organismos contaminantes localizados en el interior de los explantes. De las concentraciones de BAP evaluadas, la mayor brotación de yemas axilares se observó con 3 mg/l. Las yemas brotadas crecieron rápidamente, con la consiguiente formación de un eje con varias hojas. El sucesivo subcultivó de estos ejes, cada tres semanas en el mismo medio, permitió la formación de nuevos ejes laterales, así como de raíces. Al cabo de 6 subcultivos, se observó la formación de macollas compuestas por 8-12 ejes. La división posterior de estas macollas en grupos de 5-6, ejes permitió la multiplicación de estas plantas.
Microsatellite assessment of walrus ( Odobenus rosmarus rosmarus ) stocks in Canada

Walruses in Canada are currently subdivided into seven stocks based on summering areas; Western Jones Sound (WJS), Baffin Bay (BB), Penny Strait-Lancaster Sound (PS-LS), North Foxe Basin (N-FB), Central Foxe Basin (C-FB), Hudson Bay Davis Strait (HB-DS) and Southern and Eastern Hudson Bay (SE-HB). In this study, walrus were sampled from six of the seven stocks (SE-HB samples were not available) and genotyped at 10 microsatellite loci. All stocks were genetically diverse (average heterozygosity of 0.58) with no evidence of inbreeding (average F IS of 0.03). We detected significant genetic differentiation among the stocks and a pattern of genetic spatial autocorrelation that suggests a moderate effect of geographic distance on gene flow among stocks. Bayesian clustering suggested the six recognized stocks were elements of two larger genetic clusters - a northern Arctic population (containing BB, WJS, and PS-LS stocks) and a central Arctic population (containing C-FB, N-FB, and HB-DS stocks). These populations are moderately differentiated ( F ST = 0.07), but based on evidence of contemporary movement from assignment tests, are not completely isolated. There was support for maintaining the WJS stock and a combined BB+PS-LS stock, although the latter conclusion is based on a small sample size. Similarly, there was some evidence suggesting separation of the Foxe Basin stocks from the HB-DS but not the N-FB from the C-FB stock. However, given that there are morphological and chemical differences between N-FB and C-FB stocks, there is currently insufficient evidence to support a revision of the current stock designations.
An Economic Analysis of the Systematic Use of Mapping Systems during Catheter Ablation Procedures: Single Center Experience

Introduction In this study we estimated the cost-effectiveness of adopting 3D Nonfluoroscopic Mapping Systems (NMSs) for catheter ablation (CA). Methods This study includes patients who underwent supraventricular tachycardia (SVT) CA and atrial fibrillation (AF) CA from 2007 to 2016. A comparison was conducted between a reference year (2007) and the respective years for the two types of procedure in which the maximum optimization of patients' exposure using NMSs was obtained. We compared the data of all SVT CA performed solely using fluoroscopy in 2007 (Group I) and all SVT CA procedures performed using fluoroscopy together with an NMS in 2011 (Group II). There was also an important comparison made between AF CA procedures performed in 2007 (Group III) and AF CA in 2012 (Group IV), where patients' treatment in both years included the use of an NMS but where the software and hardware versions of the NMS were different. Two cost-effectiveness analyses were carried out. The first method was based on the alpha value (AV): the AV is a monetary reference value of avoided unit of exposure and is expressed as $/mansievert. The second one was based on the value of a statistical life (VSL): the VSL does not represent the cost value of a person's life, but the amount that a community would be willing to pay to reduce the risk of a person's death. The costs estimated from these two methods were compared to the real additional cost of using an NMS during that type of procedure in our EP Lab. Results The use of NMS reduced the effective dose of about 2.3 mSv for SVT and 23.8 mSv for AF CA procedures. The use of NMS, applying directly AV or VSL values, was not cost-effective for SVT CA for the most countries, whereas the use of an NMS during an AF CA seemed to be cost-effective for most of them. Conclusions In our analysis the cost-effectiveness of the systematic use of NMSs strongly depended on the AV and VSL values considered. Nonetheless, the approach seemed to be cost-effective only during AF CA procedures.
Second Culture and Second Nature: Fact, post-Fact, and the Social Construction of Scientific Objects

The use of constructionism by climate change deniers and ‘9-11 truthers’ to support ‘post-fact’ arguments in recent political and social debates has created controversy within science studies. Here, I seek to re-evaluate what constructionists actually say about facts in science. Through revisiting Gaston Bachelard – a key influence on scientific constructionism – I argue that science can penetrate to the ‘noumenal core’ of the phenomena it studies because it constructs them. This, however, need not imply that facts can be whatever we want them to be.
Analysis of profit efficiency among rice processors in Ekiti and Ebonyi states, Nigeria

The decision by a firm manager to produce or not must be properly harnessed in order to bring about profitability, efficiency and re-investment. Profit efficiency examines the profitability of a firm in relation to other firms in the same industry. This study examines the profit efficiency of rice processors in Ekiti and Ebonyi states in Nigeria. With the use of multistage random sampling technique, a total of 200 rice processors were sampled for the study. Two Local Government Areas (LGAs) from each state were randomly selected. Twenty-five processors were selected from each of four processing sites/centres per LGA. The study utilized the Data Envelopment Analysis (DEA) to estimate the profit efficiency of processors in the study area. The result showed that Ekiti state processors had a profit efficiency of 88 percent, while those in Ebonyi state had 79 percent. In Ekiti state, processors were least profit efficient in transportation (14%), hiring of operating space (10%) and payment for duties and taxes (28%). In Ebonyi state, processors were least profit efficient in communication (13%), rice paddy (21%), maintenance and repairs (21%), transportation (28%) and fuel (35%). It is recommended that more attention be paid to input supply and subsidy to alleviate the cost incurred and thus attract maximum profit. Provision of good motor-able roads to paddy-source and processing centres will also contribute to the reduction of transportation cost.
Intrinsic elasticity of nucleosomes is encoded by histone variants and calibrated by their binding partners

Significance Nucleosomes are the base units that organize eukaryotic genomes. Besides the canonical histone, histone variants create unique local chromatin domains that fine-tune transcription, replication, DNA damage repair, and faithful chromosome segregation. We developed computational and single-molecule nanoindentation tools to determine mechanical properties of histone variant nucleosomes. We found that the CENP-A nucleosome variant is more elastic than the canonical H3 nucleosome but becomes stiffer when bound to its partner CENP-C. In addition, CENP-C induces cross-array clustering, creating a chromatin state that is less accessible. These data suggest that innate material properties of nucleosomes can influence the ultimate chromatin state, and thereby influence biological outcomes. Histone variants fine-tune transcription, replication, DNA damage repair, and faithful chromosome segregation. Whether and how nucleosome variants encode unique mechanical properties to their cognate chromatin structures remains elusive. Here, using in silico and in vitro nanoindentation methods, extending to in vivo dissections, we report that histone variant nucleosomes are intrinsically more elastic than their canonical counterparts. Furthermore, binding proteins, which discriminate between histone variant nucleosomes, suppress this innate elasticity and also compact chromatin. Interestingly, when we overexpress the binding proteins in vivo, we also observe increased compaction of chromatin enriched for histone variant nucleosomes, correlating with diminished access. Taken together, these data suggest a plausible link between innate mechanical properties possessed by histone variant nucleosomes, the adaptability of chromatin states in vivo, and the epigenetic plasticity of the underlying locus.