Session-based Recommendation with Graph Neural Networks

The problem of session-based recommendation aims to predict user actions based on anonymous sessions. Previous methods model a session as a sequence and estimate user representations besides item representations to make recommendations. Though achieved promising results, they are insufficient to obtain accurate user vectors in sessions and neglect complex transitions of items. To obtain accurate item embedding and take complex transitions of items into account, we propose a novel method, i.e. Session-based Recommendation with Graph Neural Networks, SR-GNN for brevity. In the proposed method, session sequences are modeled as graph-structured data. Based on the session graph, GNN can capture complex transitions of items, which are difficult to be revealed by previous conventional sequential methods. Each session is then represented as the composition of the global preference and the current interest of that session using an attention network. Extensive experiments conducted on two real datasets show that SR-GNN evidently outperforms the state-of-the-art session-based recommendation methods consistently.Comment: 9 pages, 4 figures, accepted by AAAI Conference on Artificial Intelligence (AAAI-19

Molecular characterization and function analysis of the vitellogenin receptor from the cotton bollworm, Helicoverpa armigera (Hubner) (Lepidoptera, Noctuidae)

Developing oocytes accumulate plentiful yolk protein during oogenesis through receptor-mediated endocytosis. The vitellogenin receptor (VgR), belonging to the low-density lipoprotein receptor (LDLR) family, regulates the absorption of yolk protein. In this work, the full-length vitellogenin receptor (HaVgR) in the cotton bollworm Helicoverpa armigera was identified, encoding a 1817 residue protein. Sequence alignment revealed that the sequence of HaVgR contained all of the conservative structural motifs of LDLR family members, and phylogenetic analysis indicated that HaVgR had a high identity among Lepidoptera and was distinct from that of other insects. Consistent with other insects, HaVgR was specifically expressed in ovarian tissue. The developmental expression pattern showed that HaVgR was first transcribed in the newly metamorphosed female adults, reached a peak in 2-day-old adults and then declined. Western blot analysis also revealed an ovarian-specific and developing expression pattern, which was consistent with the HaVgR mRNA transcription. Moreover, RNAi-mediated HaVgR knockdown strongly reduced the VgR expression in both the mRNA and protein levels, which inhibited the yolk protein deposition in the ovaries, led to the dramatic accumulation of vitellogenin and the up-regulation of HaVg expression in hemolymph, and eventually resulted in a declined fecundity. Together, all of these findings demonstrate that HaVgR is a specific receptor in uptake and transportation of yolk protein for the maturation of oocytes and that it plays a critical role in female reproduction

Diel Patterns of Variable Fluorescence and Carbon Fixation of Picocyanobacteria Prochlorococcus-Dominated Phytoplankton in the South China Sea Basin

The various photosynthetic apparatus and light utilization strategies of phytoplankton are among the critical factors that regulate the distribution of phytoplankton and primary productivity in the ocean. Active chlorophyll fluorescence has been a powerful technique for assessing the nutritional status of phytoplankton by studying the dynamics of photosynthesis. Further studies of the energetic stoichiometry between light absorption and carbon fixation have enhanced understanding of the ways phytoplankton adapt to their niches. To explore the ecophysiology of a Prochlorococcus-dominated phytoplankton assemblage, we conducted studies of the diel patterns of variable fluorescence and carbon fixation by phytoplankton in the oligotrophic South China Sea (SCS) basin in June 2017. We found that phytoplankton photosynthetic performance at stations SEATS and SS1 were characterized by a nocturnal decrease, dawn maximum, and midday decrease of the maximum quantum yield of PSII (Fv(′)/Fm(′), which has been denoted as both Fv/Fm and Fv′/Fm′) in the nutrient-depleted surface layer. That these diel patterns of Fv(′)/Fm(′) were similar to those in the tropical Pacific Ocean suggests macro-nutrient and potentially micro-nutrient stress. However, the fact that variations were larger in the central basin than at the basin's edge implied variability in the degree of nutrient limitation in the basin. The estimated molar ratio of gross O2 production to net production of carbon (GOP:NPC) of 4.9:1 was similar to ratios reported across the world's oceans. The narrow range of the GOP:NPC ratios is consistent with the assumption that there is a common strategy for photosynthetic energy allocation by phytoplankton. That photo-inactivated photosystems or nonphotochemical quenching rather than GOP accounted for most of the radiation absorbed by phytoplankton explains why the maximum quantum yield of carbon fixation was rather low in the oligotrophic SCS

Phytoplankton photophysiology across tropical eddies: Deconvolving nutrient, light, and community signals

Fast repetition rate fluorometry (FRRf) based on active chlorophyll fluorescence is a powerful, noninvasive tool for studying phytoplankton physiological status at high spatial and temporal resolution. The South China Sea (SCS) is one of the largest tropical–subtropical marginal seas in the world, which plays an important role in modulating regional carbon budget and climate. In this study, underway in situ FRRf measurements were carried out throughout the outer continental shelf of the northern SCS, the basin of the northern SCS, the cyclonic eddy influenced domain in the western SCS, and the basin of the southeastern SCS. Pronounced diurnal variability of FRRf-derived parameters were observed, characterized by a large midday depression and slight nocturnal depression of the maximum quantum yield of photosystem II ( F v /F m ) and a slight increase in the functional absorption cross-section of photosystem II photochemistry (σ PSII ) at noon. F v /F m at the surface was typically as low as 0.1–0.3 and exhibited higher values (~0.4) where internal waves occurred. The cyclonic eddy increased F v /F m slightly, implying that it had a limited impact on surface phytoplankton photophysiology. With proper interpretation, FRRf has been a powerful tool to assess the physiological status of phytoplankton in the sea and to correlate that to ocean dynamics in an unprecedented fine scale

Picoeukaryotic Diversity And Activity in the Northwestern Pacific Ocean Based on rDNA and rRNA High-Throughput Sequencing

Picoeukaryotes play an important role in the biogenic element cycle and energy flow in oligotrophic ecosystems. However, their biodiversity and activity are poorly studied in open ocean systems, such as the northwestern Pacific Ocean, which is characterized by a complex hydrological setting. Here, we investigated the diversity and activity of picoeukaryotes in the northwestern Pacific Ocean using high-throughput sequencing targeting the V9 region of 18S rDNA and rRNA. Our results showed that the DNA picoeukaryotic communities were mainly represented by Mamiellophyceae, MAST, MALV-II, Spirotrichea, Prymnesiophyceae, and MALV-I (69.33% of the total DNA reads), and the RNA communities were dominated by Spirotrichea, Mamiellophyceae, MAST, Pelagophyceae, and MALV-II (67.46% of the total RNA reads). The number of operational taxonomic units (OTUs) was significantly affected by temperature and salinity, and was decreased with the increasing nutrient concentration both in the DNA and RNA surveys. Significant differences were observed in the community composition between DNA-based and RNA-based molecular approaches, and these differences were mainly attributed to Mamiellophyceae, Spirotrichea, and Pelagophyceae. The RNA: DNA ratio was used as a proxy for relative metabolic activity of the individual OTUs. We found that the relative metabolic activities of Mamiellophyceae, Spirotrichea, and Pelagophyceae species in the northwestern Pacific Ocean were highly affected by the nutrient concentration, i.e., the NO3 + NO2 and SiO3 concentration. Overall, our study shed light on picoeukaryotic diversity and distribution in the northwestern Pacific Ocean and revealed the correlation between the diversity, relative metabolic activities of marine picoeukaryotes, and the environmental factors

The protective mechanism of Dehydromiltirone in diabetic kidney disease is revealed through network pharmacology and experimental validation

Background:Salvia miltiorrhiza (SM) is an effective traditional Chinese medicine for treating DKD, but the exact mechanism is elusive. In this study, we aimed to investigate and confirm the method underlying the action of the active components of SM in the treatment of DKD.Methods: Renal tissue transcriptomics and network pharmacology of DKD patients was performed to identify the active components of SM and the disease targets of DKD. Next, the point of convergence among these three groups was studied. Potential candidate genes were identified and analyzed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The component-target networks were modelled and visualized with Cytoscape. In addition, docking studies were performed to validate our potential target predictions. Lastly, in vitro and in vivo experiments were performed to understand the role of Dehydromiltirone (DHT), the active component of SM, in the phenotypic switching of mesangial cells.Results: Transcriptomics of DKD patients’ renal tissues screened 4,864 differentially expressed genes. Eighty-nine active components of SM and 161 common targets were found. Functional enrichment analysis indicated that 161 genes were enriched in apoptosis, the PI3K-AKT signaling pathway, and the AGE-RAGE signaling pathway in diabetes complications. Molecular docking and molecular dynamic simulations show that DHT can bind to functional PIK3CA pockets, thereby becoming a possible inhibitor of PIK3CA. In vitro study demonstrated that DHT reduced the expression of phenotypic switching markers α-SMA, Col-I, and FN in HMCs by downregulating the over-activation of the PI3K-AKT signaling pathway through the inhibition of PIK3CA. Furthermore, the DKD mouse model confirmed that DHT could reduce proteinuria and improve glomerular hypertrophy in vivo.Conclusion: DHT was identified as the key active component of SM, and its therapeutic effect on DKD was achieved by inhibiting the phenotypic switching of mesangial cells via the PIK3CA signaling pathway

Trichodesmium around Australia: A view from space

Responsible for half of the ocean's nitrogen input through nitrogen fixation, the saltwater cyanobacterium Trichodesmium is ubiquitous in global tropical and subtropical oceans but particularly abundant around Australia. However, although the earliest report goes back to the 18th century, the knowledge of where and when large quantities of Trichodesmium can be found around Australia is still incomplete. Based on satellite imagery and deep learning, we quantified relative abundance of Trichodesmium around Australia for the period of 2012–2021. Surface aggregations of Trichodesmium were found almost everywhere except the southern coast, with a cumulative footprint exceeding 4.6 million km2. Strong seasonality was found, with peak months between September and November. The spatial distributions and seasonality were found to correlate well with water temperature, iron-rich dust from Australian desert, and black carbon aerosols from frequent bushfires. With the projected ocean warming in the coming century, Trichodesmium may expand further south, making the cumulative footprint even larger

Responses of marine phytoplankton communities to environmental changes : new insights from a niche classification scheme

Predicting changes of phytoplankton communities in response to global warming is one of the challenges of ecological forecasting. One of the constraints is the paucity of general principles applicable to community ecology. Based on a synecological analysis of a decadal-scale database, we created a niche habitat classification scheme relating nine phytoplankton groups to fifteen statistically refined realized niches comprised of three niche dimensions: temperature, irradiance, and nitrate concentrations. The niche scheme assigned the nine phytoplankton groups to three types of niches: a cold type, a warm type, and a type associated with high irradiance and high nitrate concentrations. The fact that phytoplankton groups in cold niches were governed by irradiance and those in warm niches by nitrate is consistent with general ecological theories, but the fact that diatoms were the only dominant group in high-irradiance, high-nitrate niches challenges the idea based on autecological studies that diatoms are generally better adapted to low-irradiance, high-nutrient conditions. When combined with an irradiance model, the niche scheme revealed that photoinhibition of Prochlorococcus, which is predicted from autecological studies, is a function of temperature. We used the niche scheme to predict the responses of phytoplankton communities to environmental changes due to seawater warming and eutrophication. The results of the study suggest that a synecological analysis of large databases from field studies facilitates identification of general principles of community ecology that can be used to forecast responses of biological communities to environmental changes

Responses of marine phytoplankton communities to environmental changes: New insights from a niche classification scheme.

Predicting changes of phytoplankton communities in response to global warming is one of the challenges of ecological forecasting. One of the constraints is the paucity of general principles applicable to community ecology. Based on a synecological analysis of a decadal-scale database, we created a niche habitat classification scheme relating nine phytoplankton groups to fifteen statistically refined realized niches comprised of three niche dimensions: temperature, irradiance, and nitrate concentrations. The niche scheme assigned the nine phytoplankton groups to three types of niches: a cold type, a warm type, and a type associated with high irradiance and high nitrate concentrations. The fact that phytoplankton groups in cold niches were governed by irradiance and those in warm niches by nitrate is consistent with general ecological theories, but the fact that diatoms were the only dominant group in high-irradiance, high-nitrate niches challenges the idea based on autecological studies that diatoms are generally better adapted to low-irradiance, high-nutrient conditions. When combined with an irradiance model, the niche scheme revealed that photoinhibition of Prochlorococcus, which is predicted from autecological studies, is a function of temperature. We used the niche scheme to predict the responses of phytoplankton communities to environmental changes due to seawater warming and eutrophication. The results of the study suggest that a synecological analysis of large databases from field studies facilitates identification of general principles of community ecology that can be used to forecast responses of biological communities to environmental changes