Miracle-dz/UniFAR-FTUs huggingface dataset:
Lexical representation explains cortical entrainment during speech perception

Results from a recent neuroimaging study on spoken sentence comprehension have been interpreted as evidence for cortical entrainment to hierarchical syntactic structure. We present a simple computational model that predicts the power spectra from this study, even though the model's linguistic knowledge is restricted to the lexical level, and word-level representations are not combined into higher-level units (phrases or sentences). Hence, the cortical entrainment results can also be explained from the lexical properties of the stimuli, without recourse to hierarchical syntax.
Experimental infection of bumblebees with honeybee-associated viruses: no direct fitness costs but potential future threats to novel wild bee hosts

Pathogen spillover represents an important cause of biodiversity decline. For wild bee species such as bumblebees, many of which are in decline, correlational data point towards viral spillover from managed honeybees as a potential cause. Yet, impacts of these viruses on wild bees are rarely evaluated. Here, in a series of highly controlled laboratory infection assays with well-characterized viral inocula, we show that three viral types isolated from honeybees (deformed wing virus genotype A, deformed wing virus genotype B and black queen cell virus) readily replicate within hosts of the bumblebee Bombus terrestris. Impacts of these honeybee-derived viruses - either injected or fed - on the mortality of B. terrestris workers were, however, negligible and probably dependent on host condition. Our results highlight the potential threat of viral spillover from honeybees to novel wild bee species, though they also underscore the importance of additional studies on this and other wild bee species under field-realistic conditions to evaluate whether pathogen spillover has a negative impact on wild bee individuals and population fitness.
Combined eDNA and Acoustic Analysis Reflects Diel Vertical Migration of Mixed Consortia in the Gulf of Mexico

Oceanic diel vertical migration (DVM) constitutes the daily movement of various mesopelagic organisms migrating vertically from depth to feed in shallower waters and return to deeper water during the day. Accurate classification of taxa that participate in DVM remains non-trivial, and there can be discrepancies between methods. DEEPEND consortium (www.deependconsortium.org) scientists have been characterizing the diversity and trophic structure of pelagic communities in the northern Gulf of Mexico (nGoM). Profiling has included scientific echosounders to provide accurate and quantitative estimates of organismal density and timing as well as quantitative net sampling of micronekton. The use of environmental DNA (eDNA) can detect uncultured microbial taxa and the remnants that larger organisms leave behind in the environment. eDNA offers the potential to increase understanding of the DVM and the organisms that participate. Here we used real-time shipboard echosounder data to direct the sampling of eDNA in seawater at various time-points during the ascending and descending DVM. This approach allowed the observation of shifts in eDNA profiles concurrent with the movement of organisms in the DVM as measured by acoustic sensors. Seawater eDNA was sequenced using a high-throughput metabarcoding approach. Additionally, fine-scale acoustic data using an autonomous multifrequency echosounder was collected simultaneously with the eDNA samples and changes in organism density in the water column were compared with changes in eDNA profiles. Our results show distinct shifts in eukaryotic taxa such as copepods, cnidarians, and tunicates, over short timeframes during the DVM. These shifts in eDNA track changes in the depth of sound scattering layers (SSLs) of organisms and the density of organisms around the CTD during eDNA sampling. Dominant taxa in eDNA samples were mostly smaller organisms that may be below the size limit for acoustic detection, while taxa such as teleost fish were much less abundant in eDNA data compared to acoustic data. Overall, these data suggest that eDNA, may be a powerful new tool for understanding the dynamics and composition of the DVM, yet challenges remain to reconcile differences among sampling methodologies.
Traditional Use of Medicinal Plants in South-Eastern Serbia (Pčinja District): Ethnopharmacological Investigation on the Current Status and Comparison With Half a Century Old Data

Balkan Peninsula is one of the most important biodiversity centers in Europe. Despite that, the usage of plant species in the traditional medicine of some Balkan regions remained largely unexplored in the past. This study aimed to collect and document data on the traditional use of medicinal plants in Pčinja district in South-Eastern Serbia, which is among the least developed regions in Serbia. Also, comparison with data collected by Dr. Jovan Tucakov, in a book called Herbal therapy was conducted. The survey was carried out using semi-structured interviews and 113 informants were interviewed. Quantitative ethnobotany factors were calculated, allowing us discussing the results. The informants reported data on 86 medicinal plants belonging to 43 families in Pčinja district. Lamiaceae, Asteraceae, and Rosaceae were the dominant locally used families. The species with the highest number of use reports were Mentha piperita, Matricaria chamomilla, and Hypericum perforatum. Gastrointestinal ailments, respiratory problems and skin diseases were the most frequently reported indications. Usually, the administration was primarily oral followed by topical applications. Leaves were dominantly exploited plant parts and the most frequent preparation form was infusion. Medicinal plants in Pčinja district are mainly used as a mode of primary health care for treating minor health issues. After comparing our results with the ones collected half a century ago by Dr. Jovan Tucakov we can conclude that plant species mentioned in our investigation previously had a much wider spectrum of application.
Gut Microbiome and Metabolome Were Altered and Strongly Associated With Platelet Count in Adult Patients With Primary Immune Thrombocytopenia

Gut microbiota has been implicated in the pathogenesis of many autoimmune diseases. This is still an area of active research given that the role of gut microbiota on the primary immune thrombocytopenia (ITP) remains unclear. In this study, fecal samples of 30 untreated adult primary ITP patients and 29 healthy controls (HCs) were used to investigate the gut microbial community and metabolite profiles. Our results show that fecal bacteria such as Blautia, Streptococcus, and Lactobacillus are enriched, whereas bacteria such as Bacteroides are depleted in ITP patients. Notably, fecal metabolites such as fatty acyls and glycerophospholipids are enriched and strongly correlate with discrepant gut microbiota. Furthermore, combinations of Weissella and Streptococcus anginosus, or Cer (t18:0/16:0), Cer (d18:1/17:0), and 13-hydroxyoctadecanoic acid could provide good diagnostic markers for ITP. Moreover, a strong negative correlation was found between platelet count and altered gut microbiota such as S. anginosus and gut metabolites such as Cer (t18:0/16:0) in ITP. In conclusion, dysbiosis of both gut microbiota and metabolome develops in ITP patients compared to HCs. Several ITP-altered gut bacteria and metabolites can be diagnostic biomarkers for ITP, and are highly correlated with platelet count, suggesting that they may also play a role in ITP pathogenesis.
ApoB48 as an Efficient Regulator of Intestinal Lipid Transport

Fatty meals induce intestinal secretion of chylomicrons (CMs) containing apolipoprotein (Apo) B48. These CMs travel via the lymphatic system before entering the circulation. ApoB48 is produced after post-transcriptional RNA modification by Apobec-1 editing enzyme, exclusively in the small intestine of humans and most other mammals. In contrast, in the liver where Apobec-1 editing enzyme is not expressed (except in rats and mice), the unedited transcript encodes a larger protein, ApoB100, which is used in the formation of very low-density lipoproteins (VLDL) to transport liver-synthesized fat to peripheral tissues. Apobec-1 knockout (KO) mice lack the ability to perform ApoB RNA editing, and thus, express ApoB100 in the intestine. These mice, maintained on either a chow diet or high fat diet, have body weight gain and food intake comparable to their wildtype (WT) counterparts on the respective diet; however, they secrete larger triglyceride (TG)-rich lipoprotein particles and at a slower rate than the WT mice. Using a lymph fistula model, we demonstrated that Apobec-1 KO mice also produced fewer CMs and exhibited reduced lymphatic transport of TG in response to duodenal infusion of TG at a moderate dose; in contrast, the Apobec-1 KO and WT mice had similar lymphatic transport of TG when they received a high dose of TG. Thus, the smaller, energy-saving ApoB48 appears to play a superior role in comparison with ApoB100 in the control of intestinal lipid transport in response to dietary lipid intake, at least at low to moderate lipid levels.
TMEM16F Aggravates Neuronal Loss by Mediating Microglial Phagocytosis of Neurons in a Rat Experimental Cerebral Ischemia and Reperfusion Model

Cerebral ischemia is a severe, acute condition, normally caused by cerebrovascular disease, and results in high rates of disability, and death. Phagoptosis is a newly recognized form of cell death caused by phagocytosis of viable cells, and has been reported to contribute to neuronal loss in brain tissue after ischemic stroke. Previous data indicated that exposure of phosphatidylserine to viable neurons could induce microglial phagocytosis of such neurons. Phosphatidylserine can be reversibly exposed to viable cells as a result of a calcium-activated phospholipid scramblase named TMEM16F. TMEM16F-mediated phospholipid scrambling on platelet membranes is critical for hemostasis and thrombosis, which plays an important role in Scott syndrome and has been confirmed by much research. However, few studies have investigated the association between TMEM16F and phagocytosis in ischemic stroke. In this study, a middle-cerebral-artery occlusion/reperfusion (MCAO/R) model was used in adult male Sprague-Dawley rats in vivo, and cultured neurons were exposed to oxygen-glucose deprivation/reoxygenation (OGD/R) to simulate cerebral ischemia-reperfusion (I/R) injury in vitro. We found that the protein level of TMEM16F was significantly increased at 12 h after I-R injury both in vivo and in vitro, and reversible phosphatidylserine exposure was confirmed in neurons undergoing I/R injury in vitro. Additionally, we constructed a LV-TMEM16F-RNAi transfection system to suppress the expression of TMEM16F during and after cerebral ischemia. As a result, TMEM16F knockdown alleviated motor function injury and decreased the microglial phagocytosis of viable neurons in the penumbra through inhibiting the “eat-me” signal phosphatidylserine. Our data indicate that reducing neuronal phosphatidylserine-exposure via deficiency of TMEM16F blocks phagocytosis of neurons and rescues stressed-but-still-viable neurons in the penumbra, which may contribute to reducing infarct volume and improving functional recovering.
Functional Characterization of Begging Calls in Thin-Billed Prions Pachyptila belcheri Chicks

Abstract. Chicks beg to solicit food and care from their parents. Previous studies of nocturnally feeding Thin-billed Prions (Pachyptila belcheri) showed that chicks convey information about their condition to their parents by means of begging calls. However, those studies used tape-recorders with a limited recording duration, which precluded the recording of complete nights, so only the first begging sessions per night were analysed. Here we present data on begging call intensities and the acoustic parameters of begging elements obtained using digital voice recorders, which enabled complete nights to be recorded. Chicks used from one to five begging sessions per night. We found that the parameters of the first calling sessions did not reflect body condition, whereas the duration of begging sessions and the number of begging calls over the whole night was correlated with the chicks' body condition and the sizes of the meals delivered by the parents. The acoustic parameters of begging call elements were not correlated with body condition. Chicks did not change call frequencies according to their state of nutrition. All call parameters, including the acoustic parameters of chick begging calls, were highly chick-specific. We further tested for age effects and found strong correlations between call features and the age of chicks. The results of the present study show that some begging parameters, e.g. the duration of begging sessions and the number of begging calls over the whole night, are connected with condition, while others, such as acoustic parameters, are linked with individual chick recognition.
Growth, physiological and transcriptomic analysis of the perennial ryegrass Lolium perenne in response to saline stress

Salinization of soil is a global environmental concern. To bioremediate or use saline-alkali lands, most studies focused on screening of halophytes and breeding of saline-tolerant non-halophyte vegetables. Seldom studies investigated effects of salinity on general landscape plants, which are important for landscape construction in urban areas. In the present study, effects of salinity on seed germination and seedling growth of the perennial ryegrass Lolium perenne were investigated. The final seed germination rate was not affected at salinity up to 6.4‰. Partial seedlings wilted in all saline treatments and the mortality of L. perenne was positively correlated with salinity. Treatments with salinity equal to or lower than 1.6‰ did not affect length and dry weight of shoot and root. These results suggested that L. perenne could be sowed and then grow well in low-salinity areas. To explore the underlying physiological mechanisms, contents of photosynthetic pigments and antioxidant indices were determined. The results showed that contents of chlorophyll a, b and carotenoid significantly decreased in all saline treatments, in comparison to the control. Similarly, activities of superoxide dismutase and peroxidase decreased and contents of glutathione and malondialdehyde increased in saline treatments. Additionally, transcriptome analysis identified 792 differentially expressed genes (DEGs) in L. perenne shoots between 6.4‰ saline treatment and the control. Compared with the control, genes in relation to iron transportation and amino acid metabolism were downregulated, but genes participating in energy metabolism were upregulated. These changes would inhibit toxicity of ion accumulation and provide more energy for plants to resist saline stress.
Integrative Bioinformatics Approaches to Screen Potential Prognostic Immune-Related Genes and Drugs in the Cervical Cancer Microenvironment

In developing countries, cervical cancer is still the major cause of cancer-related death among women. To better understand the correlation between tumor microenvironment (TME) and prognosis of cervical cancer, we screened 1367 differentially expressed genes (DEGs) of cervical cancer samples in The Cancer Genome Atlas (TCGA) database using Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data (ESTIMATE) algorithm-derived immune scores. Then, we extracted 401 tumor immune microenvironment (TIME)-related DEGs that related to patients’ survival outcomes. Protein-protein interaction (PPI) network and functional enrichment analysis revealed that the prognostic genes mainly participated in myeloid leukocyte activation, adaptive immune response regulation, and receptor signaling pathways. A total of 79 key prognostic DEGs were obtained through PPI network. A TF-lncRNA-miRNA-mRNA regulatory network was constructed to explore the potential regulatory mechanism. 4 genes (CCR7, PD-1, ZAP70, and CD28) were validated in another independent cohort of cervical cancer from the Gene Expression Omnibus (GEO) database. Finally, potential drugs for key prognostics DEGs were predicted using DrugBank. In conclusion, we obtained a list of potential prognostic TIME-related genes and potential predicted drugs by integrative bioinformatics approaches. A comprehensive understanding of prognostic genes within the TIME may provide new strategies for cervical cancer treatment.
Phytochemical screening on four edible legumes ( Vigna subterranean, Glycine max, Arachis hypogea, and Vigna uniguiculata ) found in eastern Nigeria

The results of the phytochemical screening carried out on the seeds of Vigna subterranea (Bambara groundnut), Glycine max (Soya beans), Arachis hypogea (Groundnut) and Vigna uniguiculata (Black eyed peas) showed the presence of useful phytonutrients. The results showed that V. subterranea contained the highest percentage of alkaloids (0.41%) while A. hypogea showed the lowest yield of alkaloid (0.25%). V. uniguiculata had the highest saponin content with (0.44%) while A. hypogea with the lowest (0.25%). The highest yield of flavonoids was found in V. uniguiculata with 0.33% while the lowest yield was obtained in A. hypogea with 0.18%. The highest phenols yield were obtained from V. subterranea with 0.36% while G. max showed the lowest with 0.26%. The percentage of tannins was highest in V. uniguiculata but lowest in A. hypogea . The results of the phytochemical screening on the four species of legumes were discussed in relations to their usefulness to mankind.
Empathy Mediates the Relationship Between Motivations After Transgression and Forgiveness

Previous studies found the associations between motivations after transgression and forgiveness in adults. However, less is known about the relationship between transgression-related motivations and forgiveness among adolescents and the potential mediating role of empathy. These questions were investigated among 445 Chinese adolescents using the Tendency to Forgive Scale, the Transgression-Related Interpersonal Motivations Inventory, and the Interpersonal Reactivity Index. The results found a negative relationship between avoidance and revenge motivation and forgiveness tendency and a positive association between benevolent motivation and forgiveness tendency. In addition, the study also revealed a partial mediating role of empathy regarding the effect of the transgression-related motivations on forgiveness tendency. These findings suggested that empathy plays a vital role in the relationship between transgression-related motivations and forgiveness among adolescents.
Aurora A regulation by reversible cysteine oxidation reveals evolutionarily conserved redox control of Ser/Thr protein kinase activity

The catalytic activity of multiple Ser/Thr kinases is regulated through a conserved Cys-based redox mechanism. Kinase regulation conserved under stress Oxidative stress is necessary for normal cellular function and tissue physiology but can also be pathological, and its effects are mediated in part through functional modification of various proteins. Shrestha et al. and Byrne et al. found that the oxidation of kinases at active site-adjacent cysteine residues, which were conserved across the eukaryotic kinome, regulated cell metabolism and mitosis. Shrestha et al. found that conserved cysteine residues within the diabetes-associated metabolic kinase FN3K acted as a toggle switch upon oxidation, promoting its functional oligomerization and consequently altering cellular redox status. Byrne et al. found that oxidation of mitotic kinases in human cells and yeast suppressed kinase catalytic activity and, in yeast, impaired cellular division. Exploring the effect of chronic oxidative stress on kinase function and how that may be spatiotemporally regulated may enable the development of new targeted therapeutics. Reactive oxygen species (ROS) are physiological mediators of cellular signaling and play potentially damaging roles in human diseases. In this study, we found that the catalytic activity of the Ser/Thr kinase Aurora A was inhibited by the oxidation of a conserved cysteine residue (Cys290) that lies adjacent to Thr288, a critical phosphorylation site in the activation segment. Cys is present at the equivalent position in ~100 human Ser/Thr kinases, a residue that we found was important not only for the activity of human Aurora A but also for that of fission yeast MAPK-activated kinase (Srk1) and PKA (Pka1). Moreover, the presence of this conserved Cys predicted biochemical redox sensitivity among a cohort of human CAMK, AGC, and AGC-like kinases. Thus, we predict that redox modulation of the conserved Cys290 of Aurora A may be an underappreciated regulatory mechanism that is widespread in eukaryotic Ser/Thr kinases. Given the key biological roles of these enzymes, these findings have implications for understanding physiological and pathological responses to ROS and highlight the importance of protein kinase regulation through multivalent modification of the activation segment.
Mining Significant Microblogs for Misinformation Identification: An Attention-based Approach

With the rapid growth of social media, massive misinformation is also spreading widely on social media, such as microblog, and bring negative effects to human life. Nowadays, automatic misinformation identification has drawn attention from academic and industrial communities. For an event on social media usually consists of multiple microblogs, current methods are mainly based on global statistical features. However, information on social media is full of noisy and outliers, which should be alleviated. Moreover, most of microblogs about an event have little contribution to the identification of misinformation, where useful information can be easily overwhelmed by useless information. Thus, it is important to mine significant microblogs for a reliable misinformation identification method. In this paper, we propose an Attention-based approach for Identification of Misinformation (AIM). Based on the attention mechanism, AIM can select microblogs with largest attention values for misinformation identification. The attention mechanism in AIM contains two parts: content attention and dynamic attention. Content attention is calculated based textual features of each microblog. Dynamic attention is related to the time interval between the posting time of a microblog and the beginning of the event. To evaluate AIM, we conduct a series of experiments on the Weibo dataset and the Twitter dataset, and the experimental results show that the proposed AIM model outperforms the state-of-the-art methods.
LiDAR-Stereo: Dense Depth Estimation from Sparse LiDAR and Stereo Images

Obtaining accurate depth information is vital for real world 3D perception, and a combination of different sensors is frequently used for better performance. In this paper, we propose an approach for high-precision depth estimation by jointly utilizing information acquired from stereo cameras and LiDAR sensors. More specifically, we design novel convolutional neural network (CNN) architecture with two novel units: monocular completion unit and stereo fusion unit, and the complementary properties of sparse LiDAR and dense stereo images are fully explored in a boosting manner. Extensive experiments on both synthetic and real datasets have shown that the proposed approach achieves significant improvements over state-of-the-art techniques in terms of both subjective and objective evaluations.