Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Characterization of VAR2 among IBV Infected poultry in Lebanon

Background: IBV is very important disease affecting mainly the respiratory tract of chickens. In Lebanon; there is a few data concerning the IBV among poultry flocks. Objectives: The aim of the present study is to detect the molecular characterize IBV in samples collected from Lebanese flocks geographically distributed in 7 Governorates. Methods: Blood sera, tracheal swabs and tissue organs were collected from 60 poultry flocks from different ages, different type of raising which were housed in different Governorates in Lebanon including, broilers, layer hens of breeders, backyard chickens and ducks for serosurveillance and molecular characterization. Also; sequence analysis of the same IBV-positive samples. Results: flocks had shown high discrepancy of CV% values with regard to ELISA results against IB virus. Out of 60 flocks tested; 12 were positive to the presence of IBV by rt-RT-PCR despite the fact that the detected flocks had a history of previous IBV vaccination except for backyard chickens and ducks. Sequence analysis for three IBV detected viruses had shown 99% similarity with VAR2 serotype present in Egypt. Conclusion: VAR2-IBV is circulating among chickens demonstrating mortalities which affect poultry industry in Lebanon.
GIS-modeling of the Range Shifts of the Sub-fossil and Extant European Pond Turtle (Emys orbicularis) in Eastern Europe in Holocene

The study of the dynamics of the European pond turtle’s Emys orbicularis range and distribution as an indicator of climate change in the past, present, and future is most relevant in connection with the protected status of this species in Europe. Based on our original finds, 25 archaeological sites yielding 1623 remains of 1504 individuals of subfossil pond turtles, current marginal distribution in Latvia, Ukraine, Russia, and literature data, we analyzed 437 records of Holocene turtles and 2847 current records of pond turtles. We identified areas that could serve as refugia for E. orbicularis, as a result of GIS modeling, while using 19 bioclimatic variables from the Worldclim and PaleoClim data bases. The data obtained confirm current hypotheses regarding the origin of more than 10 mtDNA lineages of E. orbicularis and the existence of multiple glacial refugia, and considerable Holocene home range dynamics.
Cover Crops Impacts on Louisiana Corn Production and Soil Properties

Conventionally managed, continuous monoculture row-crop production has depleted the soil of nutrients, organic matter, and overall productivity. This has increased the need for external inputs, specifically N, to meet crop demand. Despite the growing interest in conservation practices, including minimal tillage and cover crops, little work has been reported in the Mid-South region. Cereal rye (Secale cereal L.), forage radish (Raphanus sativus var. longipinnatus L.), berseem clover (Trifolium alexandrinum L.), crimson clover (Trifolium incarnatum L), winter pea (Pisium sativum L), hairy vetch (Vicia villosa Roth), and a cereal rye–forage radish mix were seeded in discrete blocks in October 2014, 2015, and 2016 along with a non-cover fallow. Each block was divided into 16 sub-plots to which one of four N fertilizer rates (0, 235, 268, and 302 kg N ha-1) were applied. Corn (Zea mays L.) grain yields increased with additions of N fertilizer; however, no difference was observed between the three fertilizer rates in 2 of 3 yr. Cover crops aided in the uptake and recycling of inorganic N, potentially reducing losses and providing N for subsequent cash crops. Following legume cover crops, corn grain yields were maximized with the addition of 235 kg N ha-1. Inclusion of grass and brassicas with no additional N input reduced corn grain yield, which remained lower than yield measured following legumes up to the 302 kg N ha-1 rate. Secondary benefits of cover crops included increased soil C (36%) and N (22%), and N cycling over a 2-yr period.
Catoptria luctiferella (Hübner, 1813) (Lepidoptera: Pyralidae: Crambinae)’nın Türkiye için Yeni Kaydı

Turkiye'nin guneyindeki Hatay ilinde bulunan Pyralidae faunasinin belirlenmesi calismanin amacini olusturmaktadir. Catoptria luctiferella’nin onemli taksonomik ozellikleri tanimlanmistir. Bu calisma ile Catoptria luctiferella Turkiye'den ilk kez bildirilmistir
Conformational Dynamics of Nonenveloped Circovirus Capsid to the Host Cell Receptor

Circovirus, comprising one capsid protein, is the smallest nonenveloped virus and induces lymphopenia. Circovirus can be used to explore the cell adhesion mechanism of nonenveloped viruses. We developed a single-molecule fluorescence resonance energy transfer (smFRET) assay to directly visualize the capsid’s conformational feature. The capsid underwent reversible dynamic transformation between three conformations. The cell surface receptor heparan sulfate (HS) altered the dynamic equilibrium of the capsid to the high-FRET state, revealing the HS binding region. Neutralizing antibodies restricted capsid transition to a low-FRET state, masking the HS binding domain. The lack of positively charged amino acids in the HS binding site reduced cell surface affinity and attenuated virus infectivity via conformational changes. These intrinsic characteristics of the capsid suggested that conformational dynamics is critical for the structural changes occurring upon cell surface receptor binding, supporting a dynamics-based mechanism of receptor binding. Importance Viral proteins were commom working as ligand to interacte with cell surface glycosaminoglycan receptors to achieve the virus attachment, during which the conformational dynamics of the protein ligand are also vital for the binding properties. In this study, PCV2 capsid and heparin sulfate were used to study the protein conformational dynamics of nonenveloped and icosahedral circovirus capsid during triggering to cell surface receptor. we demonstrated the PCV2 capsid could acts as a dynamic machine, spontaneously adopting multiple conformations with reversible interconversion and intrinsic conformational features could be regulated by glycosaminoglycan receptors and neutralizing antibodies. These increased our understanding of the mechanism by which nonenveloped virus attach to cells.
Composition and Stability of the Oxidative Phosphorylation System in the Halophile Plant Cakile maritima

Mitochondria play a central role in the energy metabolism of plants. At the same time, they provide energy for plant stress responses. We here report a first view on the mitochondrial Oxidative Phosphorylation (OXPHOS) system of the halophile (salt tolerant) plant Cakile maritima. Mitochondria were purified from suspension cultures of C. maritima and for comparison of Arabidopsis thaliana, a closely related glycophyte (salt sensitive) plant. Mitochondria were treated with digitonin and solubilized protein complexes were analyzed by 2D Blue native/SDS polyacrylamide gel electrophoresis. The OXPHOS systems of the two compared plants exhibit some distinct differences. C. maritima mitochondria include a very abundant respiratory supercomplex composed of monomeric complex I and dimeric complex III. At the same time the complexes II and IV are of reduced abundance. The stability of the OXPHOS complexes was investigated by combined salt and temperature treatments of isolated mitochondria. ATP synthase (complex V) is of increased stability in C. maritima. Also, the I + III2 supercomplex is present in high abundance during stress treatments. These results give insights into the mitochondrial contribution to the plant salt stress response.
Chaos-based CAZAC scheme for secure transmission in OFDM-PON

To effectively resist malicious eavesdropping and performance deterioration, a novel chaos-based secure transmission scheme is proposed to enhance the physical layer security and reduce peak-to-average power ratio (PAPR) in orthogonal frequency division multiplexing passive optical network (OFDM-PON). By the randomly extracting operation of common CAZAC values, the specially-designed constant amplitude zero autocorrelation (CAZAC) is created for system encryption and PAPR reduction enhancing the transmission security. This method is verified in ~10-Gb/s encrypted OFDM-PON with 20-km fiber transmission. Results show that, compared to common OFDM-PON, our scheme achieves ~3-dB PAPR reduction and ~1-dB receiver sensitivity improvement.
Genome sequence of the cluster root forming white lupin

White lupin (Lupinus albus L.) is a legume that produces seeds recognized for their high protein content and good nutritional value (lowest glycemic index of all grains, high dietary fiber content, and zero gluten or starch)1–5. White lupin can form nitrogen-fixing nodules but has lost the ability to form mycorrhizal symbiosis with fungi6. Nevertheless, its root system is well adapted to poor soils: it produces cluster roots, constituted of dozens of determinate lateral roots that improve soil exploration and phosphate remobilization7. As phosphate is a limited resource that comes from rock reserves8, the production of cluster roots is a trait of interest to improve fertilizers efficiency. Using long reads sequencing technologies, we provide a high-quality genome sequence of a modern variety of white lupin (2n=50, 451 Mb), as well as de novo assemblies of a landrace and a wild relative. We describe how domestication impacted soil exploration capacity through the early establishment of lateral and cluster roots. We identify the APETALA2 transcription factor LaPUCHI-1, homolog of the Arabidopsis morphogenesis coordinator9, as a potential regulator of this trait. Our high-quality genome and companion genomic and transcriptomic resources enable the development of modern breeding strategies to increase and stabilize yield and to develop new varieties with reduced allergenic properties (caused by conglutins10), which would favor the deployment of this promising culture.
Societal attention toward extinction threats

Public attention and interest in the fate of endangered species is a crucial prerequisite for effective conservation programs. Societal awareness and values will largely determine whether conservation initiatives receive necessary support and lead to adequate policy change. Using text data mining, we assessed general public attention toward climate change and biological invasions, which represent two key threats for endangered amphibian, reptile, bird and mammal species in three European countries (France, Germany and the United Kingdom). Our analysis revealed that public attention patterns differed among species groups and countries but was globally higher for climate change than for biological invasions. Both threats received better recognition in threatened than in non-threatened species, as well as in native species than in species from other countries and regions. The relative level of attention toward the two threats corresponded well with the listing of the threats and their severity within the IUCN Red List. We conclude that more efficient communication regarding the threat from biological invasions should be developed, and that conservation practitioners should take advantage of the existing attention toward the threat of climate change.
Wildlife and Livelihoods in the Cardamom Mountains, Cambodia

This study provides a preliminary assessment of the use of wild meat and fish by rural communities in the Northern Cardamoms, Cambodia. We used a case-study approach in three villages, to identify key characteristics and drivers of wildlife use, with a view to informing the design of future larger-scale investigations of wild meat and fish use in the Cardamoms. Interviews with 41 households, conducted from August - October 2013, were used to investigate the main livelihood activities of each household, including hunting and fishing activity, key hunting techniques and hunted and consumed species. Group discussions with households and hunters were used to determine the relative importance of hunting and fishing as a livelihood activity and food source. We found that over 80% of interviewed households hunted, and similarly over 90% fished. Hunters employed a range of techniques, and caught at least 38 different mammal, bird and reptile species. However, our results suggest that arable farming is the backbone of livelihoods in these villages, providing the bulk of household incomes, and that most households are hunting to prevent crop-raiding, or opportunistically, rather than to supply the commercial trade. While households expressed a preference for wild meat, bought domestic meats and fish were eaten more frequently. A potentially lucrative commercial trade with high profits per animal exists but catches are unpredictable, and hunting is dangerous. However, as many species populations are already heavily depleted, even low hunting offtakes could have significant impacts on vulnerable species. Previous research suggests that commercial hunting which targets larger-bodied and high-value species for the international wildlife trade is mainly conducted by professional hunting groups, external to local communities. The importance of agricultural trade to local communities suggests that ‘wildlife-friendly farming’ initiatives may help to both secure a fair and reliable price for village agricultural products, while promoting conservation of biodiversity in the Cardamoms mountains. However, due to the likely larger impacts of commercial hunting groups, declines in biodiversity are likely to continue without stricter enforcement of wildlife trade laws in Cambodia’s towns and cities, and the reduction of demand for wildlife products in consumer countries.
Drifting codes within a stable coding scheme for working memory

Working memory (WM) is important to maintain information over short time periods to provide some stability in a constantly changing environment. However, brain activity is inherently dynamic, raising a challenge for maintaining stable mental states. To investigate the relationship between WM stability and neural dynamics, we used electroencephalography to measure the neural response to impulse stimuli during a WM delay. Multivariate pattern analysis revealed representations were both stable and dynamic: there was a clear difference in neural states between time-specific impulse responses, reflecting dynamic changes, yet the coding scheme for memorized orientations was stable. This suggests that a stable subcomponent in WM enables stable maintenance within a dynamic system. A stable coding scheme simplifies readout for WM-guided behaviour, whereas the low-dimensional dynamic component could provide additional temporal information. Despite having a stable subspace, WM is clearly not perfect – memory performance still degrades over time. Indeed, we find that even within the stable coding scheme, memories drift during maintenance. When averaged across trials, such drift contributes to the width of the error distribution.
PsyMuKB: A De Novo Variant Knowledge Base Integrating Transcriptional and Translational Information to Identify Isoform-specific Mutations in Developmental Disorders

De novo variants (DNVs) are one of the most significant contributors to severe early-onset genetic disorders such as autism spectrum disorder, intellectual disability, and other developmental and neuropsychiatric (DNP) disorders. Currently, a plethora of DNVs have being identified through the use of next-generation sequencing and much effort has been made to understand their impact at the gene level; however, there has been little exploration of the impact at the isoform level. The brain contains a high level of alternative splicing and regulation, and exhibits a more divergent splicing program than other tissues; therefore, it is crucial to explore variants at the transcriptional regulation level to better interpret the mechanisms underlying DNP disorders. To facilitate better usage and improve the isoform-level interpretation of variants, we developed the PsyMuKB (NeuroPsychiatric Mutation Knowledge Base), a knowledge base containing a comprehensive, carefully curated list of DNVs with transcriptional and translational annotations to enable identification of isoform-specific mutations. PsyMuKB allows a flexible search of genes or variants and provides both table-based descriptions and associated visualizations, such as expression, transcript genomic structures, protein interactions, and the mutation sites mapped on the protein structures. It also provides an easy-to-use web interface, allowing users to rapidly visualize the locations and characteristics of mutations and the expression patterns of the impacted genes and isoforms. PsyMuKB thus constitutes a valuable resource for identifying tissue-specific de novo mutations for further functional studies of related disorders. PsyMuKB is freely accessible at http://psymukb.net.
Integrating Sentinel-2 Imagery with AquaCrop for Dynamic Assessment of Tomato Water Requirements in Southern Italy

A research study was conducted in an open field tomato crop in order to: (i) Evaluate the capability of Sentinel-2 imagery to assess tomato canopy growth and its crop water requirements; and (ii) explore the possibility to predict crop water requirements by assimilating the canopy cover estimated by Sentinel-2 imagery into AquaCrop model. The pilot area was in Campania, a region in the south west of Italy, characterized by a typical Mediterranean climate, where field campaigns were conducted in seasons 2017 and 2018 on processing tomato. Crop water use and irrigation requirement were estimated by means of three different methods: (i) The AquaCrop model; (ii) an irrigation advisory service based on Sentinel-2 imagery known as IRRISAT and (iii) assimilating the canopy cover estimated by Sentinel-2 imagery into AquaCrop model Sentinel-2 imagery proved to be effective for monitoring canopy growth and for predicting irrigation water requirements during mid-season stage of the crop, when the canopy is fully developed. Conversely, the integration of the Sentinel-2 imagery with a crop growth model can contribute to improve the irrigation water requirement predictions in the early and development stage of the crop, when the soil evaporation is not negligible with respect to the total evapotranspiration.
Plenasium xiei sp. nov. from the Cretaceous of Northeast China: Additional evidence for the longevity of osmundaceous ferns

A new species of the Osmundaceae, Plenasium xiei sp. nov., is herein described from the Cretaceous of Northeast China. The specimens examined here represent the earliest unequivocal record of the extant genus Plenasium in Eurasia based on fossil rhizomes. The rhizome consists of a central stem with a mantle of petiole bases and adventitious roots. The stem contains an ectophloic‐dictyoxylic siphonostele and a two‐layered cortex. The C‐shaped leaf trace bears two protoxylem bundles at the point of separation from the stele. The pith is heterogeneous. The parenchymatous inner cortex is thinner than the sclerenchymatous outer cortex. Lobed sclerenchyma bands occur at the adaxial sides of the stem xylem strands, in the concavity of the leaf trace, and along the adaxial side of the vascular bundles of the petiole base. In distal petiole portions, the sclerenchyma band splits into several groups in the transverse view. Sclerenchyma rings are heterogeneous with an abaxial sclerenchymatous arc of thick‐walled fibers. Numerous sclerenchyma strands of thick‐walled fibers appear in the petiolar inner cortex and the stipular wing. These fossils provide unambiguous evidence for the existence of subgenus Plenasium of modern Plenasium by at least the Late Cretaceous, demonstrating the longevity of this extant subgenus. Altogether the leaf and rhizome fossil records of Plenasium indicate that this genus was widely distributed across North America and Eurasia from the Early Cretaceous to the Early Cenozoic, followed by a range restriction to Eurasia in the Late Cenozoic. Extant Plenasium species are only known from East and Southeast Asia.
Template Switching Mediates Contractions of a Repetitive Coding Region in S. cerevisiae

The C-terminal domain (CTD) is an essential domain of the largest subunit of RNA polymerase II, Rpb1p, and is composed of 26 tandem repeats of a seven-amino acid sequence, YSPTSPS. Despite being an essential domain within an essential gene, we have previously demonstrated that the CTD coding region is genetically unstable. Furthermore, yeast with a truncated or mutated CTD sequence are capable of promoting spontaneous genetic expansion or contraction of this coding region to improve fitness. We investigated the mechanism by which the CTD contracts using a tet-off reporter system for RPB1 to monitor genetic instability within the CTD coding region. We report that contractions require the post-replication repair factor Rad5p but, unlike expansions, not the homologous recombination factors Rad51p and Rad52p. Sequence analysis of contraction events reveals that deleted regions are flanked by microhomologies. We also find that G-quadruplex forming sequences predicted by the QGRS Mapper are enriched on the noncoding strand of the CTD compared to the body of RPB1. Formation of G-quadruplexes in the CTD coding region could block the replication fork, necessitating post-replication repair by template switching. We propose that contractions of the CTD result when microhomologies misalign during Rad5p-dependent template switching via fork reversal.
Iron concentrations in the in vitro cultivation of native Brazilian orchid Schomburgkia crispa

In vitro cultivation is a highly important biotechnological method widely used for the production of orchid seedlings, but it is necessary to study the suitability of the nutrients used in different kinds of formulation, as the nutritional requirement varies according to the species. The objective was to evaluate different concentrations of iron in the in vitro cultivation of Schomburgkia crispa Lindl seedlings. Seedlings were obtained from seeds germinated in vitro. Modified MS culture medium was used with half of the macronutrient concentration. The micronutrients were added according to the original formulation, except for the iron which was added from a stock solution of FeEDTA (FeSO4.7H2O: 5.6 g L-1 and EDTA: 7.48 g L-1) at 0.0; 2.5; 5.0; 7.5; 10.0 and 12.5mL L-1. At 200 days after seedling transplantation, shoot height, root length, number of leaves, shoot number, leaf length, leaf width, aerial and root dry mass, chlorophyll a, b and carotenoids content were evaluated. A completely randomized design was used, with six treatments and ten replicates of five seedlings. Regression analysis was performed at 5% of significance. The increase in iron concentration caused a reduction in root length and an increase in the number of leaves and shoots. The concentration of 4.13 mL L-1 of FeEDTA was the one that provided the best in vitro growth of S. crispa plants. High concentrations of iron caused a reduction of initial development, but stimulated an increase in the number of shoots.
Micarea fennica, a new lignicolous lichen species from Finland

A new species Micarea fennica is described based on phenotypic and molecular features. The species is characterized by a pale olive green, bright green or greyish green minutely granular thallus composed of goniocysts, and stalked pycnidia that are dark grey to dark brown with Sedifolia-grey pigment in the wall structures (K+ violet, C+ violet), 0.2–0.5(–1) mm tall and covered by a thin white tomentum. The species produces micareic acid. Micarea fennica is similar to M. hedlundii and M. botryoides, but differs by having a paler granular thallus, stalked dark grey to dark brown pycnidia covered by a thin white tomentum and the production of micareic acid. The new species occupies soft lignum of late decay stages and is probably rare.