Miracle-dz/UniFAR-FTUs huggingface dataset:
Using Bayesian Belief Network to Solve Abnormal Symptoms after Vaccination under Modern Information Technology

Rare side effects are weakening confidence in the vaccine. The question is how we interpret the data. Within 15 months after the discovery of the new coronavirus, a variety of effective and safe vaccines against the new coronavirus were available. After receiving the new coronavirus vaccine, some people developed facial paralysis, thigh pain, and even cerebral venous thrombosis. Although these side effects are very rare, and there is a lack of clarity whether there is a causal relationship with the vaccine or not, such news may undermine the confidence of the global vaccine. In order to maintain the confidence of the public, adverse events after vaccination are called ordinary events, and deaths occurring within a few days after vaccination are also interpreted as being caused by their latent diseases. From the following research, the issue of causality divides the vaccinated population into healthy groups and long-term patient groups, and use Bayesian belief network to analyze whether there are symptoms or abnormal events after vaccination as well as the probability distribution of rare illness, death, etc., in order to understand the relationship among each other. Therefore, suspending the administration of COVID vaccine is not a zero-risk option. The reality is that nothing is without risk. Measures to mitigate a risk must be balanced with competitive hazards. Risk seems to be an abstract and vague concept. Risk can be reduced, but it can never be eliminated. The advantage of the Bayesian model is that it is easy to bring the data of various variables into the graph and calculate the posterior data from the known data to strengthen the persuasiveness of vaccination. By using Bayesian Network with PGM Module of Pytorch, the death probability of these two groups can be calculated under abnormal symptoms or without them. The simulation result of death after inoculation is lower than that of normal state without Covid-19 pandemic.
Updating Small Generator Interconnection Procedures for New Market Conditions

Federal and state regulators are faced with the challenge of keeping interconnection procedures updated against a backdrop of evolving technology, new codes and standards, and considerably transformed market conditions. This report is intended to educate policymakers and stakeholders on beneficial reforms that will keep interconnection processes efficient and cost-effective while maintaining a safe and reliable power system.
Research on News Text Classification Based on Hybrid Model

With the rapid development and wide application of information technology and Internet, the amount of various information data is growing explosively. News text information is a more extensive form of text information that people have access to. Using computer to screen and classify these news information effectively can quickly and efficiently obtain valuable information content. With the development of machine learning, text classification has been gradually transferred from manual operation to machine automation. It is a basic step of machine learning to use the classified text information to learn the category features and then classify the unclassified text. Text automatic classification method are many, for the improvement of text automatic classification algorithm, its purpose lies in how to closer to the human way of thinking on the text information classification, the classification results of this can better meet the needs of people for text classification, also convenient and rapid access to valuable information. In this paper, a hybrid model is used to achieve better classification results.
Chinese Weibo Sentiment Classification Method Incorporating Facial Expression Features

The role and value of emoticons in sentiment analysis of Weibo texts is becoming more and more obvious. Research on the sentiment polarity of emoticons can effectively improve the accuracy and effectiveness of sentiment analysis. In this paper, the polarity classification of 84 default common emoticons on the Sina Weibo platform is carried out, an emoji dictionary is constructed, and a Weibo sentiment classification method combining fusion rules and models is proposed. The experimental results show that the sentiment polarity of the text can be judged more accurately when analyzing the sentiment of the Weibo text.
Cold-induced [Ca2+]cyt elevations function to support osmoregulation in marine diatoms

Diatoms are a group of microalgae that are important primary producers in a range of open ocean, freshwater and intertidal environments. The latter can experience significant long- and short-term variability in temperature, from seasonal variations to rapid temperature shifts caused by tidal immersion and emersion. As temperature is a major determinant in the distribution of diatom species, their temperature sensory and response mechanisms likely have important roles in their ecological success. We have examined the mechanisms diatoms use to sense rapid changes in temperature, such as those experienced in the intertidal zone. We find that the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana exhibit a transient cytosolic Ca2+ ([Ca2+]cyt) elevation in response to rapid cooling, similar to those observed in plant and animal cells. However, [Ca2+]cyt elevations were not observed in response to rapid warming. The kinetics and magnitude of cold-induced [Ca2+]cyt elevations correlate with the rate of temperature decrease. We do not find a role for the [Ca2+]cyt elevations in enhancing cold tolerance, but show that cold shock induces a Ca2+-dependent K+ efflux and reduces mortality of P. tricornutum during a simultaneous hypo-osmotic shock. As inter-tidal diatom species may routinely encounter simultaneous cold and hypo-osmotic shocks during tidal cycles, we propose that cold-induced Ca2+ signalling interacts with osmotic signalling pathways to aid in the regulation of cell volume. Our findings provide insight into the nature of temperature perception in diatoms and highlight that cross-talk between signalling pathways may play an important role in their cellular responses to multiple simultaneous stressors.
Cardiac ventricular myosin and slow skeletal myosin exhibit dissimilar chemo-mechanical properties despite the same myosin heavy chain isoform

The myosin II motors are ATP-powered, force-generating machines driving cardiac and muscle contraction. Myosin II heavy chain isoform-beta (β-MyHC) is primarily expressed in the ventricular myocardium and slow-twitch muscle fibers, such as in M. soleus. M. soleus-derived myosin II (SolM-II) is often used as an alternative to the ventricular β-cardiac myosin (βM-II); however, the direct assessment of detailed biochemical and mechanical features of the native myosins is limited. By employing the optical trapping method, we examined the mechanochemical properties of the native myosins isolated from rabbit heart ventricle and M. soleus muscles at the single-molecule level. Contrary to previous reports, the purified motors from the two tissue sources, despite the same MyHC isoform, displayed distinct motile and ATPase kinetic properties. βM-II was ∼threefold faster in the actin filament-gliding assay than SolM-II. The maximum acto-myosin (AM) detachment rate derived in single-molecule assays was ∼threefold higher in βM-II. The stroke size for both myosins was comparable. The stiffness of the ‘AM rigor’ cross-bridge was also similar for both the motor forms. The stiffness of βM-II was found to be determined by the nucleotide state of the actin-bound myosin. Our analysis revealed distinct kinetic differences, i.e., a higher AM detachment rate for the βM-II, corresponding to the ADP release rates from the cross-bridge, thus elucidating the observed differences in the motility driven by βM-II and SolM-II. These studies have important implications for the future choice of tissue sources to gain insights into cardiomyopathies
Optimized high-throughput screening of non-coding variants identified from genome-wide association studies

The vast majority of disease-associated single nucleotide polymorphisms identified from genome-wide association study (GWAS) are localized in non-coding regions. A significant fraction of these variants impact transcription factors binding to enhancer elements and alter gene expression. To functionally interrogate the activity of such variants we developed snpSTARRseq, a high-throughput experimental method that can interrogate the functional impact of hundreds to thousands of non-coding variants on enhancer activity. snpSTARRseq dramatically improves signal-to-noise by utilizing a novel sequencing and bioinformatic approach that increases both insert size and number of variants tested per loci. Using this strategy, we interrogated 70 of 140 known prostate cancer (PCa) risk-associated loci and demonstrated that 26 (37%) of them harbor 36 SNPs that significantly altered enhancer activity. Combining these results with chromosomal looping data we could identify interacting genes and provide a mechanism of action for 20 PCa GWAS risk regions. When benchmarked to orthogonal methods, snpSTARRseq showed a strong correlation with in vivo experimental allelic-imbalance studies whereas there was no correlation with predictive in silico approaches. Overall, snpSTARRseq provides an integrated experimental and computational framework to functionally test non-coding genetic variants.
Variation in cytonuclear expression accommodation among allopolyploid plants

Cytonuclear coevolution is a common feature among plants, which coordinates gene expression and protein products between the nucleus and organelles. Consequently, lineage-specific differences may result in incompatibilities between the nucleus and cytoplasm in hybrid taxa. Allopolyploidy is also a common phenomenon in plant evolution. The hybrid nature of allopolyploids may result in cytonuclear incompatibilities, but the massive nuclear redundancy created during polyploidy affords additional avenues for resolving cytonuclear conflict (i.e., cytonuclear accommodation). Here we evaluate expression changes in organelle-targeted nuclear genes for six allopolyploid lineages that represent four genera (i.e., Arabidopsis, Arachis, Chenopodium, and Gossypium) and encompass a range in polyploid ages. Because incompatibilities between the nucleus and cytoplasm could potentially result in biases toward the maternal homoeolog and/or maternal expression level, we evaluate patterns of homoeolog usage, expression bias, and expression level dominance in cytonuclear genes relative to the background of non-cytonuclear expression changes and to the diploid parents. Although we find subsets of cytonuclear genes in most lineages that match our expectations of maternal preference, these observations are not consistent among either allopolyploids or categories of organelle-targeted genes. Our results indicate that cytonuclear expression accommodation may be a subtle and/or variable phenomenon that does not capture the full range of mechanisms by which allopolyploid plants resolve nuclear-cytoplasmic incompatibilities.
Single-cell transcriptome profiles of Drosophila fruitless-expressing neurons from both sexes

Drosophila melanogaster reproductive behaviors are orchestrated by fruitless neurons. We performed single-cell RNA-sequencing on fru P1 pupal neurons. Uniform Manifold Approximation and Projection (UMAP) clustering generates an atlas containing 113 clusters. While the male and female neurons overlap in UMAP space, more than half the UMAP clusters have sex-differences in neuron number, and nearly all clusters display sex-differential expression. Based on an examination of enriched marker genes, we annotate clusters as circadian clock neurons, mushroom body Kenyon cell neurons, neurotransmitter- and/or neuropeptide-producing, and those that express doublesex. Enriched marker gene analyses also shows that genes that encode members of the immunoglobulin superfamily of cell adhesion molecules, transcription factors, neuropeptides, neuropeptide receptors, and Wnts have unique patterns of enriched expression across the clusters. In vivo spatial gene-expression links to the UMAP clusters are provided. A functional analysis of fru P1 circadian neurons shows they have dimorphic roles in sleep/activity and period length. Given that most clusters are comprised of male and female neurons indicates that the sexes have fru P1 neurons with common gene expression programs. Sex-specific expression is overlaid on this program, to build the potential for vastly different sex-specific behaviors.
Field and experimental data together with computational models reveal how cleaner fish adjust decisions in a biological market

While it is generally straightforward to quantify individual performance in cognitive experiments, identifying the underlying cognitive processes remains a major challenge. Often, different mechanistic underpinnings yield similar performances, and Lloyd Morgan’s cannon warrants acceptance of the simpler explanation. Alternatively, when the different mechanisms interact with environmental conditions, variation in performance across environments might allow to statistically infer the mechanism responsible. We illustrate this point by fitting computational models to experimental data on performance by wild-caught cleaner fish Labroides dimidiatus in an ephemeral reward task, as well as cleaner and client fish densities from the locations of capture. Using Bayesian statistics to fit the model parameters to performance data revealed that cleaner fish most likely estimate future consequences of an action, while it appears unlikely that the removal of the ephemeral reward acts as psychological punishment (negative reinforcement). Incorporating future consequences also yields performances that can be considered the result of locally optimal decision-rules, in contrast to the negative reinforcement mechanism. We argue that the combination of computational models with data is a powerful tool to infer the mechanistic underpinnings of cognitive performance. Author summary Performance in behavioural experiments is often used to assess the cognitive abilities of animals. However, animals can get to the same outcome in alternative ways. Thus, the outcome of the experiments does not tell us how animals achieve their performance. In order to overcome this limitation, we used a set of computational models, which provide predictions on how alternative cognitive mechanisms perform in the face of varying environmental conditions, and compare their predictions to performance data from individuals that experienced different conditions throughout their life. Our study system is the cleaner fish Labroides dimidiatus, a coral reef fish that feeds off ectoparasites and dead tissue from the skin of other reef fishes. Cleaner fish often have to choose among alternative clients seeking their cleaning service, and the optimal choice is often hard to achieve. Our performance experiments mimic the natural choices the cleaner fish make. The combination of experiments and computational models points to cleaner fish abilities to account for the future effect of their choices by estimating the long term expected value of those choices. Estimating long term value is a mechanism involved in human foresight.
Cohesin erases genomic-proximity biases to drive stochastic Protocadherin expression for proper neural wiring

Clustered Protocadherin (Pcdh) proteins act as cell-surface recognition barcodes for neural circuit formation. Neurites expressing the same barcode repel each other, but this mechanism is deployed in two different ways. For instance, convergence of olfactory sensory neuron (OSN) projections requires stochastic expression of distinct Pcdh isoforms in individual cells, while tiling of neural arbors of serotonergic neurons (5-HTs) requires expression of the same isoform, Pcdhαc2. Despite their essential role, however, the molecular mechanisms of cell-type specific Pcdh barcoding remain a mystery. Here, we uncover a new role of cohesin: that of regulating distance-independent enhancer-promoter interactions to enable random Pcdh isoform choice via DNA loop extrusion in OSNs. Remarkably, this step mediates DNA demethylation of Pcdh promoters and their CTCF binding sites, thus directing CTCF to the chosen promoter. In contrast, the uniform pattern of Pcdh expression in 5-HTs is achieved through conventional cohesin-independent, distance-dependent enhancer/promoter interactions, that favor choice of the nearest isoform. Thus, cell-type specific cohesin deployment converts a distance-dependent and deterministic regulatory logic into a distance-independent and stochastic one. We propose that this mechanism provides an elegant strategy to achieve distinct patterns of Pcdh expression that generate wiring instructions to meet the connectivity requirements of different neural classes.
Structure of the human RAD17–RFC clamp loader and 9–1–1 checkpoint clamp bound to a dsDNA–ssDNA junction

The RAD9-RAD1-HUS1 (9-1-1) clamp forms one half of the DNA damage checkpoint system that signals the presence of substantial regions of single-stranded DNA arising from replication fork collapse or resection of DNA double strand breaks. Loaded at the 5’-recessed end of a dsDNA-ssDNA junction by the RAD17-RFC clamp loader complex, the phosphorylated C-terminal tail of the RAD9 subunit of 9-1-1 engages with the mediator scaffold TOPBP1 which in turn activates the ATR kinase, localised through the interaction of its constitutive partner ATRIP with RPA-coated ssDNA. Using cryogenic electron microscopy (cryoEM) we have determined the structure of a complex of the human RAD17-RFC clamp loader bound to human 9-1-1, engaged with a dsDNA-ssDNA junction. The structure answers the key questions of how RAD17 confers specificity for 9-1-1 over PCNA, and how the clamp loader specifically recognises the recessed 5’ DNA end and fixes the orientation of 9-1-1 on the ssDNA.
Allosteric Inhibitors of Zika Virus NS2B-NS3 Protease Targeting Protease in “Super-Open” Conformation

Zika virus (ZIKV) is a member of the Flaviviridae family and is considered a major health threat causing cases of microcephaly in newborns and Guillain-Barré syndrome in adults. Here we targeted a transient deep and hydrophobic pocket of the super-open conformation of ZIKV NS2B-NS3 protease to overcome the limitations of the orthosteric inhibitors. After virtual docking screening of approximately 7 million compounds against the novel allosteric site we selected the top seven candidates and tested them in an enzymatic assay. Six out of seven top candidates selected by the docking screen inhibited ZIKV NS2B-NS3 protease proteolytic activity at low micromolar concentrations, as well as suppressing viral replication. These six compounds, targeting the selected protease pocket conserved in ZIKV as well as several other Flaviviruses, have opened an opportunity for a new kind of drug candidate that might be useful to treat several flaviviral infections.
Autonomous Robot for Measuring Room Impulse Responses

Far-ﬁeld speech recognition for e.g. home automation or smart assistants has to cope with moving speakers in reverberant environments. Simulating stationary or even moving speakers in realistic environments enables to make speech processing technology more robust. This paper introduces an autonomous robot for recording a database of Room Impulse Responses (RIRs) at a high spatial resolution. This supports the creation of realistic simulation environments. These RIRs can be exploited to generate multi-channel speech mixtures of static or moving speakers for various applications.
Brain Functional Connectivity in de novo Parkinson's Disease Patients Based on Clinical EEG

In Parkinson's disease (PD), cortical–subcortical interplay plays a relevant role in affecting clinical performance. Functional MRI sequences described changes in functional connectivity at different stages of disease. Scarce are, instead, the investigations examining brain connectivity in patients with PD at early stages of disease. For this aim, here we analyzed the differences in functional connectivity between de novo, never treated, PD patients and healthy controls. The analyses were based upon custom-written scripts on the Matlab platform, combined with high-level functions of Fieldtrip, Brainstorm, and Brain Connectivity toolboxes. First, we proceeded to the spectral analysis of the EEG data in the five frequency bands (δ-θ-α-β-γ). Second, we calculated functional connectivity matrices based on both coherency (COH) and imaginary part of coherency (iCOH), in the δ-θ-α-β-γ frequency bands. Then, four network measures (density, transitivity, global efficiency, and assortativity) were computed in identified connectivity matrices. Finally, we compared the spectral density, functional connectivity matrices, and network measured between healthy controls and de novo PD patients through two-samples T-test. A total of 21 de novo PD patients and 20 healthy subjects were studied. No differences were observed in spectral analysis between the two groups, with the exception of the γ band where a significant increase in power density was found in PD patients. A reduced connectivity in the main EEG frequency bands (α-β frequency bands) was observed in PD patients compared to controls, while a hyperconnectivity was found in PD patients in γ band. Among the network measures, a reduced assortativity coefficient was found in de novo PD patients in α frequency band. Our results show the occurrence of early EEG functional connectivity alterations from the initial stages of PD. From this point of view, connectivity analysis may ease a better understanding of the complexity of PD physiopathology.
Understanding the Adaptive Mechanisms of Plants to Enhance Phosphorus Use Efficiency on Podzolic Soils in Boreal Agroecosystems

Being a macronutrient, phosphorus (P) is the backbone to complete the growth cycle of plants. However, because of low mobility and high fixation, P becomes the least available nutrient in podzolic soils; hence, enhancing phosphorus use efficiency (PUE) can play an important role in different cropping systems/crop production practices to meet ever-increasing demands in food, fiber, and fuel. Additionally, the rapidly decreasing mineral phosphate rocks/stocks forced to explore alternative resources and methods to enhance PUE either through improved seed P reserves and their remobilization, P acquisition efficiency (PAE), or plant's internal P utilization efficiency (IPUE) or both for sustainable P management strategies. The objective of this review article is to explore and document important domains to enhance PUE in crop plants grown on Podzol in a boreal agroecosystem. We have discussed P availabilities in podzolic soils, root architecture and morphology, root exudates, phosphate transporters and their role in P uptake, different contributors to enhance PAE and IPUE, and strategies to improve plant PUE in crops grown on podzolic soils deficient in P and acidic in nature.