Miracle-dz/UniFAR-FTUs huggingface dataset:
Diverging shifts in spring phenology in response to biodiversity loss in a subtropical forest

QUESTIONS: Despite our increased understanding of how climate change influences plant phenology, it remains poorly understood whether diversity loss could alter phenology as well. Here we investigated the following: (a) do changes in plant diversity affect leaf‐out and flowering dates for woody species; (b) which group of variables are more important in influencing leaf‐out and flowering dates, abiotic variables (soil variables) or biotic variables (plant diversity)? STUDY SITE: A subtropical forest in the Biodiversity–Ecosystem Functioning Experiment of China, located in Jiangxi Province, China. METHODS: Species were planted in various combinations to create plots with varying tree richness: 1, 2, 4, 8, 16 or 24 species. We monitored leaf‐out and flowering dates of eight randomly selected species in 17 plots in 2018. A linear model was used to test whether species diversity was a predictor of leaf‐out/flowering times for each species. We then fit linear mixed‐effects models to assess the combined influence of species diversity, soil Total Carbon and Total Nitrogen on the overall community. RESULTS: In the low‐diversity plots, we found two species leafing out earlier, one leafing out later and four showing no significant difference. Leaf‐out date advanced an average of 0.3 days per species lost. Of all the biotic and abiotic predictor variables, Total Nitrogen was the only one significantly correlated with leaf‐out date. No significant correlation was found between species diversity and flowering date for any of the species. CONCLUSIONS: Our study provides the first empirical evidence concerning the effects of biodiversity loss on plant spring phenology for woody species. Our findings illustrate that fluctuation in plant diversity could alter the timing of leaf‐out and that abiotic variables may be more important than biotic variables in determining leaf‐out dates in subtropical forest. Overall, declining diversity may exacerbate the phenological changes attributed to rising global temperatures.
LincRNA sequences are biased to counteract their translation

Long intergenic non-coding RNAs (lincRNAs) represent a large fraction of transcribed loci in eukaryotic genomes. Although classified as non-coding, most lincRNAs contain putative open reading frames (pORFs), and it is unclear what hinders translation of cytoplasmic lincRNAs. Here, we analysed lincRNA sequences from six eukaryotes, including human and fission yeast, and identified signatures of translational repression. In species under strong selective pressure, i.e. yeast and mostly worm, we detected fewer and shorter pORFs in lincRNAs than in intronic and non-transcribed control regions, and the sequence context around their putative start codons appeared suboptimal for translation initiation. Moreover, trinucleotides (9codons9) in lincRNA pORFs tended to be decoded by tRNAs with fewer gene copies than codons in mRNAs or control regions, likely to impede translation elongation. In order to better understand how in multicellular species varying tRNA and cytoplasmic lincRNA expression levels between cell types affect lincRNA translation regulation, we analysed data from human cell lines. In three out of five cases, we detected signatures of translational repression of cytoplasmic lincRNAs, i.e. a codon usage that corresponded to lower expressed tRNAs than control trinucleotides. Importantly, the degree of codon-tRNA correspondence was in agreement with the ribosome-association strengths of cytoplasmic lincRNAs across cell lines. Together, the codon usage of lincRNA pORFs is biased, and it appears to function to repress ribosome binding. This mechanism is capable of counteracting lincRNA translation in a cell type-specific manner.
A selective PCR-based method for the identification of Phytophthora hibernalis Carne

Preharvest and postharvest brown rot of citrus fruit is responsible for important economic losses thoroughout the world. The disease is commonly caused by several species of Phytophthora. In Spain, citrus brown rot is mainly caused by P. citrophthora, but in the last years outbreaks of the disease in lemon and sweet orange caused by P. hibernalis Carne have been recorded in northwestern citrus-growing areas. In this work, a PCR method has been developed for the diagnostic of P. hibernalis either from isolated mycelia or directly from fruit lesions. One specific primer pair, PHIB1 and PHIB2, was designed from the nucleotide sequences of ITS1 and ITS2 regions. The two primers amplified a 407-bp fragment from the genomic DNA of P. hibernalis that was sequenced (Acc. No. AY827556). Results demonstrated that PCR amplification of ITS regions by primers PHIB1 and PHIB2 followed by DNA sequencing can provide a rapid, selective and reliable identification of P. hibernalis.
An extinct species of Basella: pollen evidence from sediments (~80 ka) in Kerala, India

Abstract The genus Basella belongs to family Basellaceae and is comprised of five species. Out of these, Basella alba is pantropical in distribution, B. paniculata is endemic to south-eastern Africa and the other three species viz. B. excavata, B. leandriana and B. madagascariensis are endemic to Madagascar. The palynological study of an organic layer buried ~80 ka in Chaganacherry, Kerala revealed a rich diversity of rainforest pollen and estuarine/marine palynomorphs indicating warm and humid climate coupled with sea level high stand. The Basella pollen recorded from this sediment shows intermediate characters of two extant Basella species. While it resembles B. paniculata in being pantocolpate (20), it shows affinity with B. alba in sexine characters. The recovered pollen was therefore, ascertained to be a new species, named here as B. keralensis sp. nov. The age correlation of the studied sediment was carried out by fingerprinting (Rare Earth Elements) of Youngest Toba Tuff (YTT) (glass shards) which spread in the atmosphere through a volcanic eruption in Sumatra ~74 ka and also with marine palynomorph markers correlating the interglacial Marine Isotopic Stage 5a (~80 ka). It is inferred that earlier, the genus Basella comprised of six species out of which Basella keralensis sp. nov. became extinct and until now neither the fossil record nor the extant form of this is known in records from any part of the World.
Time Series Analysis of Transatlantic Market Interactions: Evidence from Crude Oil and Gasoline Prices

This paper investigates the interactions of spot markets for crude oil and regular gasoline in a transatlantic context. A cointegrated vector autoregressive (VAR) system is estimated using weekly time series data for spot prices of representative crude oil and regular gasoline in Europe and the US. The cointegrated VAR analysis shows that the US crude oil plays the role of long-run price leadership, influencing the price determination of the other commodities in the VAR system. Cointegrating vectors are then normalized and restricted so that the underlying long-run market interactions may be interpreted in terms of causal chains. Finally, a parsimonious equilibrium correction system is estimated in order to reveal the short-run market interactions.
ON THE NATURE OF THE HERBIG B[e] STAR BINARY SYSTEM V921 SCORPII: DISCOVERY OF A CLOSE COMPANION AND RELATION TO THE LARGE-SCALE BIPOLAR NEBULA

Belonging to the group of B[e] stars, V921 Scorpii is associated with a strong infrared excess and permitted and forbidden line emission, indicating the presence of low- and high-density circumstellar gas and dust. Many aspects of V921 Sco and other B[e] stars still remain mysterious, including their evolutionary state and the physical conditions resulting in the class-defining characteristics. In this Letter, we employ Very Large Telescope Interferometer/AMBER spectro-interferometry in order to reconstruct high-resolution (λ/2B = 0.″0013) model-independent interferometric images for three wavelength bands around 1.65, 2.0, and 2.3 μm. In our images, we discover a close (25.0 ± 0.8 mas, corresponding to ∼29 ± 0.9 AU at 1.15 kpc) companion around V921 Sco. Between two epochs in 2008 and 2009, we measure orbital motion of ∼7°, implying an orbital period of ∼35 years (for a circular orbit). Around the primary star, we detect a disk-like structure with indications for a radial temperature gradient. The polar axis of this AU-scale disk is aligned with the arcminute-scale bipolar nebula in which V921 Sco is embedded. Using Magellan/IMACS imaging, we detect multi-layered arc-shaped substructure in the nebula, suggesting episodic outflow activity from the system with a period of ∼25 years, roughly matching the estimated orbital period of the companion. Our study supports the hypothesis that the B[e] phenomenon is related to dynamical interaction in a close binary system.
Emotional design and its contributions to digital educational technology in health and nursing : integrative review

Context: In the use of digital technology educational, besides of the functionality and usability, the emotional aspects for human satisfaction gains importance. Objectives: To identify the contributions of the emotional design in educational technology for health and nursing. Methodology: Integrative review through the LILACS, MEDLINE, PsycINFO and IndexPsi databases, from 2001 to 2011, searching publications on design, emotion, educational technology, health and nursing. Protocol review and thematic categorization were performed. Results: Five primary studies were considered from the inclusion and exclusion criteria, in which 40% of them were classified as very good and 60% good, according the agree and ability to respond to the main question, but most have low level of evidence. Qualitative meta-synthesis of the raised the design of technology helps in motivating student and learning feedback, allows interaction between students and learning facilitators and enhances the link between theory and practice. Conclusion: Although important and promising, the analysis and discussion of emotional design in educational technology is still incipient in health and nursing, with research gaps.
Social buffering of stress in a group-living fish

Living in groups affords individuals many benefits, including the opportunity to reduce stress. In mammals, such ‘social buffering’ of stress is mediated by affiliative relationships and production of the neuropeptide oxytocin, but whether these mechanisms facilitate social buffering across vertebrates remains an open question. Therefore, we evaluated whether the social environment influenced the behavioural and physiological recovery from an acute stressor in a group-living cichlid, Neolamprologus pulcher. Individual fish that recovered with their social group displayed lower cortisol levels than individuals that recovered alone. This social buffering of the stress response was associated with a tendency towards lower transcript abundance of arginine vasotocin and isotocin in the preoptic area of the brain, suggesting reduced neural activation of the stress axis. Individuals that recovered with their social group quickly resumed normal behaviour but received fewer affiliative acts following the stressor. Further experiments revealed similar cortisol levels between individuals that recovered in visual contact with their own social group and those in visual contact with a novel but non-aggressive social group. Collectively, our results suggest that affiliation and familiarity per se do not mediate social buffering in this group-living cichlid, and the behavioural and physiological mechanisms responsible for social buffering may vary across vertebrates.
The cryptic regulation of diversity by functionally complementary large tropical forest herbivores

Tropical forests hold some of the world's most diverse communities of plants. Many populations of large‐bodied herbivores are threatened in these systems, yet their ecological functions and contribution towards the maintenance of high levels of plant diversity are poorly known. The impact of these herbivores on plant communities through antagonistic seed and seedling predation has received much attention, whilst their relevance as seed dispersal agents has been largely overlooked in experimental studies. Here, we tested how two key and functionally distinct large generalist mammalian herbivore species (the tapir Tapirus terrestris – a solitary browser and generalist seed disperser, and the white‐lipped peccary Tayassu pecari – a group‐living generalist seed/seedling predator) affect spatiotemporal patterns of diversity of seedling communities in tropical forests. We conducted a long‐term multi‐region landscape‐scale exclusion experiment across four regions of the Atlantic forest of Brazil, representing a functional gradient of defaunation where these species were either present and absent in isolation and in combination. Our results indicate that mammalian herbivores have a substantial role in regulating beta diversity in space and time. Seedling recruitment was strongly limited by the presence of the seed/seedling predator species (the peccary), but the presence of the browser and seed disperser (the tapir) had null net effects. Alpha diversity of seedlings at the community level did not respond to large herbivore exclusion at any region, whereas beta diversity decreased only where both herbivores were simultaneously excluded. Surprisingly, the synergic positive effect of both herbivore types on beta diversity was linked to increased evenness amongst dominant plant species, and a simultaneous decrease in alpha diversity of rare species. Synthesis. Together, these results challenge the common perception that large tropical forest herbivores maintain tropical forest diversity through antagonistic interactions, suggesting instead a synergistic effect of antagonistic predation and mutualistic seed dispersal on regional compositional diversity and local community assembly. We suggest that the defaunation of large‐bodied herbivores with complementary functions strongly affects the structure and dynamics of plant communities through cryptic mechanisms that remain largely unexplored.
Long-Term Potentiation Induces Extrasynaptic Exocytosis of Glun2A-containing NMDA Receptors that is Mainly Controlled by SNAP23

NMDA receptors (NMDAR) are key players in the initiation of synaptic plasticity that underlies learning and memory. Long-term potentiation (LTP) of synapses require an increased calcium current via NMDA channels to trigger modifications in postsynaptic density (PSD). It is generally believed that the amount of NMDARs on the postsynaptic surface remains stationary, whereas their subunit composition is dynamically fluctuated during this plasticity process. However, the molecular machinery underlying this subunit-specific regulation remains largely elusive. Here, by detecting the time-lapse changes of surface GluN2A and GluN2B subunit levels using biochemical approaches, surface immunostaining, live-imaging and super-resolution microscopy, we uncovered a transient increase of surface GluN2A-type NMDARs shortly after the induction of chemical long term potentiation (cLTP). These augmented sub-diffraction-limited GluN2A clusters predominantly exist in extrasynaptic domains. We also showed that the spine-enriched SNARE associated protein SNAP-23, and to a minor extent its homologue SNAP-25, control both the basal and regulated surface level of GluN2A receptors. Using a total internal reflection fluorescence microscopy (TIRFM) based live-imaging assay, we resolved and analyzed individual exocytic events of NMDARs in live neurons and found that cLTP raised the frequency of NMDAR exocytosis at extrasynaptic regions, without altering the duration or the package size of these events. Our study thereby provides direct evidence that synaptic plasticity controls the postsynaptic exocytosis machinery, which induces the insertion of more GluN2A receptors into the extrasynaptic area. Significance Statement Memory formation involves the long-term modification of synapses, which is called synaptic plasticity. In the postsynaptic density (PSD) of excited neurons, this modification process occurs on a minute timescale, initiated by the opening of NMDARs that trigger downstream cascades to fix the potentiation (LTP) at specific synapses for longer timescales. Here, using a novel live-imaging assay we resolved the dynamic delivery of NMDARs to the cell surface, and found that only the insertion frequency, not the duration of individual insertion or number of GluN2A subunits each of these NMDAR vesicles contains, was altered during the synaptic potentiation process. We also identified SNAP-23 as the key molecule mediating this activity dependent NMDAR surface delivery. This study provides a novel mechanism of how NMDARs are regulated in the short window to initiate the long-lasting synaptic modifications.
Antibody Engineering and Therapeutics

The 24th Antibody Engineering & Therapeutics meeting brought together a broad range of participants who were updated on the latest advances in antibody research and development. Organized by IBC Life Sciences, the gathering is the annual meeting of The Antibody Society, which serves as the scientific sponsor. Preconference workshops on 3D modeling and delineation of clonal lineages were featured, and the conference included sessions on a wide variety of topics relevant to researchers, including systems biology; antibody deep sequencing and repertoires; the effects of antibody gene variation and usage on antibody response; directed evolution; knowledge-based design; antibodies in a complex environment; polyreactive antibodies and polyspecificity; the interface between antibody therapy and cellular immunity in cancer; antibodies in cardiometabolic medicine; antibody pharmacokinetics, distribution and off-target toxicity; optimizing antibody formats for immunotherapy; polyclonals, oligoclonals and bispecifics; antibody discovery platforms; and antibody-drug conjugates.
Lower methionine/cystine ratio in low‐protein diet improves animal reproductive performance by modulating methionine cycle

Abstract Background As the extend of low‐protein diets in many countries including China, more researches of amino acid nutrition (AA) have been carried out. But the ideal AA pattern, especially the reasonable proportion of amino acids such as the desired methionine (Met): cystine (Cys) ratios are not yet clear. Objectives In this article, the experiments of low‐protein diet with varying ratios of Met:Cys (low ratio of 1:3, medium ratio of 1:1, and high ratio of 3:1) were conducted to investigate the effect on mice growth and reproductive performance. Results The result indicated that the lower Met:Cys ratio improves reproductive performance in male mice, but the growth performance were no change in all groups. Meanwhile, the abnormality rate of sperm increased as the ratio of methionine and cystine increased. Quantitative analysis showed that the low Met:Cys ratio has obviously decreased the expression of Bax protein and the concentrations of testosterone in male serum, but Prm2, Pgk2, Bcl‐2, Bak1, and AR gene were made no difference. Furthermore, different Met:Cys ratios have significant effects on the modulated methionine cycle by increasing the expressions of MAT2B, GNMT, and BHMT in low Met:Cys ratio. On the other hand, it was also found that there were increases in GSH‐Px enzyme activities and decreases in MDA levels in male serum. Conclusions Overall, the present study showed that a dietary lower Met:Cys ratio in a low‐protein diet had a positive influence on the reproductive performance of male animal through obviously improving sperm quality and antioxidant capacity, and inhibiting apoptosis. And the study provided new pieces of evidence to re‐evaluate the role of precise sulfur amino acid nutrition in a low‐protein diet.
COMBINED PROFILING IN ASPEN A SYSTEMS BIOLOGY APPROACH

This thesis presents efficient systems biology modelling strategies for integrating complex multi-platform datasets in order to increase our understanding of stress biology, wood formation and secondary cell wall formation in Populus trees and connected responses to perturbations in organisms, particularly aspen. It is based on studies reported in four appended papers, designated Papers I-IV. Paper I describes an enhanced framework for investigating and understanding multilevel oxidative stress responses and their influence on phenotypic variation in transgenic hipI-superoxide dismutase Populus plants. Paper II presents a modelling strategy based on a combination of Principal Component Analysis (PCA), Orthogonal Projections to Latent Structures (OPLS), and an enhanced stepwise linear modelling approach. This strategy revealed major transitions in the proteomes along the wood developmental series in Populus tremula (aspen) pinpointing, for example, the location of the cambial cell divisions leading to phloem and xylem cells, and the location of the secondary cell wall formation zone. A pairwise multivariate OPLS approach was applied in the study described in Paper III to analyse proteome dynamics during tension wood formation of Populus trees. Pairwise comparisons of four corresponding phases/tissue types in normal and tension wood formation allowed identification of several processes that were strongly enhanced and/or unique during tension wood formation. These multidisciplinary approaches together with a recently developed formulation of the OnPLS method was used in Paper IV to analyse a set of transgenic Populus trees carrying an RNAi construct for the Populus secretory carrier-associated membrane protein3 (PttSCAMP3) gene. Multilevel analysis of datasets from nine platforms (RNA sequencing, proteomic, metabolomic and wood chemical analyses) revealed a critical function for PttSCAMP proteins in wood formation and elucidated the underlying molecular mechanism. The systems biology approach presented in this thesis provides novel types of tools for elucidating stress responses and wood formation in Populus trees. Exploitation of very recent advances in multivariate methods such as OnPLS allowed the simultaneous combination of transcriptomic, proteomic and metabolomic data, as well as identification of differences and connections between the data sets, which would not have been possible using standard statistical methods.
Evaluating the potential of a large-scale polysemy network as a model of plausible semantic shifts

We present a very large network of crosslinguistic polysemies, and compare the notion of semantic relatedness it encodes to the catalogue of semantic shifts maintained by the Russian Academy of Sciences. We separately evaluate all types of semantic shifts featured in the catalogue, including shifts occurring during semantic evolution, during borrowing, and during morphological derivation. The comparison shows that over one third of the attested semantic shifts take place between close neighbors in the network. This can be considered strong evidence for the usefulness of polysemy networks in modelling most types of lexical change, making them a valuable resource e.g. for semantic reconstruction or future automatization of cognate detection. We also show that the semantic shifts which occur during morphological derivation form a divergent class, and might need to be modelled separately.