Miracle-dz/UniFAR-FTUs huggingface dataset:
Taste Quality Representation in the Human Brain

In the mammalian brain, the insula is the primary cortical substrate involved in the perception of taste. Recent imaging studies in rodents have identified a “gustotopic” organization in the insula, whereby distinct insula regions are selectively responsive to one of the five basic tastes. However, numerous studies in monkeys have reported that gustatory cortical neurons are broadly-tuned to multiple tastes, and tastes are not represented in discrete spatial locations. Neuroimaging studies in humans have thus far been unable to discern between these two models, though this may be because of the relatively low spatial resolution used in taste studies to date. In the present study, we examined the spatial representation of taste within the human brain using ultra-high resolution functional magnetic resonance imaging (MRI) at high magnetic field strength (7-tesla). During scanning, male and female participants tasted sweet, salty, sour, and tasteless liquids, delivered via a custom-built MRI-compatible tastant-delivery system. Our univariate analyses revealed that all tastes (vs tasteless) activated primary taste cortex within the bilateral dorsal mid-insula, but no brain region exhibited a consistent preference for any individual taste. However, our multivariate searchlight analyses were able to reliably decode the identity of distinct tastes within those mid-insula regions, as well as brain regions involved in affect and reward, such as the striatum, orbitofrontal cortex, and amygdala. These results suggest that taste quality is not represented topographically, but by a distributed population code, both within primary taste cortex as well as regions involved in processing the hedonic and aversive properties of taste. SIGNIFICANCE STATEMENT The insula is the primary cortical substrate involved in taste perception, yet some question remains as to whether this region represents distinct tastes topographically or via a population code. Using high field (7-tesla), high-resolution functional magnetic resonance imaging in humans, we examined the representation of different tastes delivered during scanning. All tastes activated primary taste cortex within the bilateral mid-insula, but no brain region exhibited any consistent taste preference. However, multivariate analyses reliably decoded taste quality within the bilateral mid-insula as well as the striatum, orbitofrontal cortex, and bilateral amygdala. This suggests that taste quality is represented by a spatial population code within regions involved in sensory and appetitive properties of taste.
Evaluation of fungicides and biocontrol products for the control of Phytophthora root rot of hydrangeas

Abstract Phytophthora root rot is one of the most important diseases in almost all hydrangeas of nursery production. In this study, the efficacy of fungicides and biocontrol products against Phytophthora root rot of hydrangea was assessed in greenhouse and field experiments. Treatments used in field or greenhouse experiments were RootShield PLUS+, MBI110, IT-5103, Grotab, OxiPhos, TerraClean 5.0 + TerraGrow program, Segovis, Pageant Intrinsic, Empress Intrinsic and Subdue Maxx. Pots/plots were inoculated with Phytophthora nicotianae grown on rice grains, sterilised rice grains were used for negative controls. After the trials, plant growth data (total plant weight, root weight, plant height, plant width) were recorded, and roots were assessed for disease severity using a scale of 0–100%. The treatments most effective in reducing Phytophthora root rot severity were Segovis, Empress Intrinsic, Subdue Maxx, TerraClean 5.0 + TerraGrow program in both greenhouse and field experiments. This study will help nursery producers make proper management decisions by using recommended fungicides and biocontrol products of this study in a rotation or alone to manage Phytophthora root rot of hydrangea.
A new method for short-term traffic congestion forecasting based on LSTM

Traffic congestion in metropolitan areas such as shenzhen, has become more and more serious. Over the past decades, many academic and industrial efforts have been made to alleviate this issue. In this paper, we propose a novel approach to predicting short-term traffic congestion. At first, we pre-process the data to get the speed, traffic, lane number of these parameters. Second, we carry out statistical data and create training samples. Third, We establish a hybrid neural network prediction model based on LSTM and substitute the generated samples into training. Finally, we use the model to predict the future congestion situation. The experimental results show that our model achieves good predictive results.
Mechanistic Basis for Control of Early Embryonic Development by a 5’ tRNA Fragment

Ancestral environmental conditions can instruct offspring development, although the mechanism(s) underlying such transgenerational epigenetic inheritance is unclear. In murine models focused on paternal dietary effects, we and others have identified tRNA fragments (tRFs) in mature sperm as potential carriers of epigenetic information. In our search for molecular targets of specific tRFs, we observed that altering the level of 5’-tRF Glycine-GCC (tRF-GG) in mouse embryonic stem cells (mESCs) and preimplantation embryos modulates the expression of the endogenous retrovirus MERV-L and genes regulated by MERV-L. Intriguingly, transient derepression of MERV-L is associated with totipotency of two-cell stage embryos and a subset of two-cell-like mESCs. Here, I reveal the mechanistic basis for tRF-GG regulation of MERV-L. I show that tRF-GG supports the production of numerous small nuclear RNAs associated with the Cajal body, in mouse and human embryonic stem cells. In particular, tRF-GG modulates the levels of U7 snRNA to ensure an adequate supply of histone proteins. This in turn safeguards heterochromatin-mediated transcriptional repression of MERV-L elements. Importantly, tRF-GG effects on histone mRNA levels, activity of a histone 3’UTR reporter, and expression of MERV-L associated transcripts can all be suppressed by appropriate manipulation of U7 RNA levels. I also show that hnRNPF and H bind directly to tRF-GG, and display a stark overlap of in vivo functions to tRF-GG. Together, this data uncovers a conserved mechanism for a 5’ tRNA fragment in the fine-
Widespread arginine phosphorylation in human cells - a novel protein PTM revealed by mass spectrometry

Arginine phosphorylation (pArg) is recently discovered as a ubiquitous protein N- phosphorylation in bacteria. However, its prevalence and roles in mammalian cells remain largely unknown due to the lack of established workflow and the inherent lability of the phosphoramidate (P-N) bond. Emerging evidence suggests that N-phosphorylation may extensively exist in eukaryotes and play crucial roles. We report an experimental phosphoproteomic workflow, which for the first time allowed to reveal the widespread occurrence of pArg in human cells by mass spectrometry. By virtue of this approach, we identified 152 high-confidence pArg sit]es derived from 118 proteins. Remarkably, the discovered phosphorylation motif and gene ontology of pArg hint a possible cellular function of arginine phosphorylation by regulating the favorability of propeptide convertase substrate. The generated extensive data set should enable a better understanding of the biological functions of eukaryotic pArg in the future.
Dissecting complex phenotypes via multiple transcriptome-based GWAS

Genome-Wide Association Study (GWAS) have been widely used to detect the QTLs based on Linkage Disequilibrium (LD) relationships between SNPs and QTLs. However, in conventional GWAS both false positive and false negative results cause serious concerns. In this research, we developed three different transcriptome-based GWAS approaches which are complementary to conventional SNP-based GWAS. The ability to identify trait-associated genes in these three different methods are supported by cross-validation, transposon knockout mutants, and the analysis of a gene regulatory networks. In summary, we provide novel methods of detecting trait associated loci to further understand the complex gene regulatory systems which will benefit plants, animals, and disease treatment development in the future.
Multiple Changes Underlie Allelic Divergence of CUP2 Between Saccharomyces Species

Under the model of micromutationism, phenotypic divergence between species is caused by accumulation of many small-effect changes. While mapping the causal changes to single nucleotide resolution could be difficult for diverged species, genetic dissection via chimeric constructs allows us to evaluate whether a large-effect gene is composed of many small-effect nucleotide changes. In a previously described non-complementation screen, we found an allele difference of CUP2, a copper-binding transcription factor, underlies divergence in copper resistance between Saccharomyces cerevisiae and S. uvarum. Here, we tested whether the allele effect of CUP2 was caused by multiple nucleotide changes. By analyzing chimeric constructs containing four separate regions in the CUP2 gene, including its distal promoter, proximal promoter, DNA binding domain and transcriptional activation domain, we found that all four regions of the S. cerevisiae allele conferred copper resistance, with the proximal promoter showing the largest effect, and that both additive and epistatic effects are likely involved. These findings support a model of multiple changes underlying evolution and suggest an important role of both protein coding and cis-regulatory changes in evolution.
RNAPosers: Machine Learning Classifiers For RNA-Ligand Poses

Determining the 3-dimensional (3D) structures of ribonucleic acid (RNA)-small molecule complexes is critical to understanding molecular recognition in RNA. Computer docking can, in principle, be used to predict the 3D structure of RNA-small molecule complexes. Unfortunately, retrospective analysis has shown that the scoring functions that are typically used to rank poses tend to misclassify non-native poses as native, and vice versa. This misclassification of non-native poses severely limits the utility of computer docking in the context pose prediction, as well as in virtual screening. Here, we use machine learning to train a set of pose classifiers that estimate the relative “nativeness” of a set of RNA-ligand poses. At the heart of our approach is the use of a pose “fingerprint” that is a composite of a set of atomic fingerprints, which individually encode the local “RNA environment” around ligand atoms. We found that by ranking poses based on the classification scores from our machine learning classifiers, we were able to recover native-like poses better than when we ranked poses based on their docking scores. With a leave-one-out training and testing approach, we found that one of our classifiers could recover poses that were within 2.5 Å of the native poses in ∼80% of the 88 cases we examined, and similarly, on a separate validation set, we could recover such poses in ∼70% of the cases. Our set of classifiers, which we refer to as RNAPosers, should find utility as a tool to aid in RNA-ligand pose prediction and so we make RNAPosers open to the academic community via https://github.com/atfrank/RNAPosers.
Combining ability effects for yield traits in rice (Oryza sativa L.) under sodic soil

The present study was conducted to analyze the combining ability for yield and its contributing traits in rice (Oryza sativa L.). Rice, being a staple food for more than 70 per cent of national population is the source of livelihood for 120-150 million rural households. The major objective of a plant breeder is to create genetic variability upto maximum extent possible in the existing germplasm because the genetic variability and combining ability estimates provide the basis for selection of suitable genotypes in any breeding programme. The combining ability effects, which are supposed to be manifestation of nonadditive components of genetic variance, are valuable for discrimination of superior crosses for their genetic worth as breeding materials. The estimates of combining ability of 39 crosses for 12 characters were analyzed during the experiment. Six crosses, NDRK 2011-18 x Gujarat 70, CSR 36 x CSR 43, Sarjoo 52 x Pusa Sugandha 4, NDRK 2011-19 x Pusa Sugandha 4, NDRK 2011-17 x CSR 43 and Sarjoo 52 x CSR 43 showed significant and positive combining ability effects for grain yield per plant as well as some other yield components. In general, the crosses showing significant and desirable combining ability effects were associated with better per se performance for the respective traits.
Deep Mutational Scanning Comprehensively Maps How Zika Envelope Protein Mutations Affect Viral Growth and Antibody Escape

Zika virus has recently been shown to be associated with severe birth defects. The virus’s E protein mediates its ability to infect cells and is also the primary target of the antibodies that are elicited by natural infection and vaccines that are being developed against the virus. Therefore, determining the effects of mutations to this protein is important for understanding its function, its susceptibility to vaccine-mediated immunity, and its potential for future evolution. We completely mapped how amino acid mutations to the E protein affected the virus’s ability to grow in cells in the laboratory and escape from several antibodies. The resulting maps relate changes in the E protein’s sequence to changes in viral function and therefore provide a valuable complement to existing maps of the physical structure of the protein. ABSTRACT Functional constraints on viral proteins are often assessed by examining sequence conservation among natural strains, but this approach is relatively ineffective for Zika virus because all known sequences are highly similar. Here, we take an alternative approach to map functional constraints on Zika virus’s envelope (E) protein by using deep mutational scanning to measure how all amino acid mutations to the E protein affect viral growth in cell culture. The resulting sequence-function map is consistent with existing knowledge about E protein structure and function but also provides insight into mutation-level constraints in many regions of the protein that have not been well characterized in prior functional work. In addition, we extend our approach to completely map how mutations affect viral neutralization by two monoclonal antibodies, thereby precisely defining their functional epitopes. Overall, our study provides a valuable resource for understanding the effects of mutations to this important viral protein and also offers a roadmap for future work to map functional and antigenic selection to Zika virus at high resolution. IMPORTANCE Zika virus has recently been shown to be associated with severe birth defects. The virus’s E protein mediates its ability to infect cells and is also the primary target of the antibodies that are elicited by natural infection and vaccines that are being developed against the virus. Therefore, determining the effects of mutations to this protein is important for understanding its function, its susceptibility to vaccine-mediated immunity, and its potential for future evolution. We completely mapped how amino acid mutations to the E protein affected the virus’s ability to grow in cells in the laboratory and escape from several antibodies. The resulting maps relate changes in the E protein’s sequence to changes in viral function and therefore provide a valuable complement to existing maps of the physical structure of the protein.
Microbial extracellular polysaccharide production and aggregate stability controlled by Switchgrass (Panicum virgatum) root biomass and soil water potential

Deep-rooting perennial grasses are promising feedstock for biofuel production, especially in marginal soils lacking organic material, nutrients, and/or that experience significant water stress. Perennial grass roots can alter surrounding soil conditions and influence microbial activities, particularly the production of extracellular polymeric substances composed primarily of extracellular polysaccharides (EPS). These polymers can alleviate cellular moisture and nutrient stress, and enhance soil characteristics through improved water retention and aggregate stability, the latter of which may in turn enhance carbon persistence. In this study we used a 13CO2 tracer greenhouse experiment to examine the effect of switchgrass cultivation on the production and origin of EPS in a marginal soil with five fertilization/water treatments (control, +N, +NP, +P, low water). Soils with both added nitrogen and phosphorus had the highest root biomass, EPS and percentage of water-stable soil aggregates. Multiple linear regression analyses revealed root biomass was the most important determinant for soil EPS production, potentially by controlling carbon supply and diurnal changes in soil water potential. Path analysis highlighted the role of soil water potential were and EPS on with water-stable soil aggregates, indicating that EPS concentration and soil aggregation have similar drivers in this soil. High mannose content confirmed the microbial origin of EPS. 13CO2 labeling indicated that 0.18% of newly fixed plant carbon was incorporated into EPS. Analysis of field samples suggests that EPS is significantly enhanced under long-term switchgrass cultivation. Our results demonstrate that switchgrass cultivation can promote microbial production of EPS, providing a mechanism to enhance sustainability of marginal soils.
Synthesis of a Wheat/Maize Hybrid CENH3 Gene, the Genetic Transformation of Wheat, Its Chromosomal Localization and Effects on Chromosome Behaviors in Wheat/Maize Somatic Hybrids

Centromere-specific histone H3 (CENH3) replaces the canonical histone H3 in nucleosomes of functional centromeres, and plays important roles in faithful chromosome segregation during cell division. CENH3 is also important in the recognition of alien centromeres and determines the accommodation or elimination of alien chromosomes in interspecific or intergenic hybridization. In this study, a maize full length CENH3 with a yellow fluorescent protein (YFP) tag at C-terminus (ZmCENH3-YFP) and a synthetic hybrid wmCENH3 with the N-terminus from wheat CENH3 and the histone fold domain (HFD) from maize tagged with a red fluorescent protein (RFP) at the C-terminus (wmCENH3-RFP) were transformed to wheat by biolistics transformation. Transgenic wheat plants with both ZmCNEH3-YFP and wmCENH3-RFP genes were identified by PCR. The expression of ZmCENH3-YFP was not observed, while the expression of wmCENH3-RFP could be detected by RT-PCR, direct fluorescence microscopy, and immunostaining with anti-RFP antibody. The expressed wmCENH3-RFP was localized to nuclei as dotted patterns, indicating its targeting to wheat centromeres. Somatic hybridization was performed between wmCENH3-RFP transgenic wheat and transgenic maize that expressed a ZmCENH3-YFP gene to investigate chromosome behaviors in somatic hybrids. Cytological and FISH analyses of somatic hybrid cells showed the formation of micronuclei and lagging chromatin in both somatic hybridizations with or without the wmCENH3-RFP transgene, indicating that ectopically expressed wmCENH3 could not overcome chromosome elimination in wheat/maize somatic hybrids. Immunostaining of wmCENH3-RFP and ZmCENH3-YFP in early stage somatic hybrid cells indicated that both wmCENH3-RFP and ZmCENH3-YFP proteins were expressed, but their binding patterns changed from the commonly observed dotted patterns to diffused ones, suggesting that the inactivation of CENH3 might be a factor for chromosome elimination in wheat/maize somatic hybridization.
Fatal Case of Lassa Fever, Bangolo District, Côte d’Ivoire, 2015

Lassa fever has not been reported in Côte d’Ivoire. We performed a retrospective analysis of human serum samples collected in Côte d’Ivoire in the dry seasons (January–April) during 2015–2018. We identified a fatal human case of Lassa fever in the Bangolo District of western Côte d’Ivoire during 2015.
The use of pituitary adenylate cyclase-activating polypeptide in the pre-maturation system improves in vitro developmental competence from small follicles of porcine oocytes

Objective We investigated how pituitary adenylate cyclase-activating polypeptide (PACAP) affects embryonic development during pre-in vitro maturation (pre-IVM) using porcine oocytes isolated from small follicles. Methods We divided the follicles into the experimental groups by size (SF, small follicles; MF, medium follicles) and treated with and without PACAP and cultured for 18 hours (Pre-SF[−]PACAP; without PACAP, Pre-SF[+]PACAP; with PACAP) before undergoing IVM. The gene expression related to extracellular matrix formation (amphiregulin, epiregulin, and hyaluronan synthase 2 [HAS2]) and apoptosis (Bcl-2-associated X [BAX], B-cell lymphoma 2, and cysteine-aspartic acid protease 3) was investigated after maturation. The impact on developmental competence was assessed by the cleavage and blastocyst rate and total cell number of blastocysts in embryos generated from parthenogenesis (PA) and in vitro fertilization (IVF). Results Cleavage rates in the Pre-SF(+)PACAP after PA were significantly higher than SF and Pre-SF(−)PACAP (p<0.05). The cleavage rates between MF and Pre- SF(+)PACAP groups yielded no notable differences after IVF. Pre-SF(+)PACAP displayed the higher rate of blastocyst formation and greater total cell number than SF and Pre-SF(−)PACAP (p<0.05). Cumulus cells showed significant upregulation of HAS2 mRNA in the Pre-SF(+)PACAP compared to the SF (p<0.05). In comparison to other groups, the Pre-SF(+)PACAP group displayed a downregulation in mRNA expression of BAX in matured oocytes (p<0.05). Conclusion The PACAP treatment during pre-IVM improved the developmental potential of porcine oocytes derived from SF by regulating cumulus expansion and apoptosis of oocytes.