Miracle-dz/UniFAR-FTUs huggingface dataset:
Selective attention decoding in bimodal cochlear implant users

The growing group of cochlear implant (CI) users includes subjects with preserved acoustic hearing on the opposite side to the CI. The use of both listening sides results in improved speech perception in comparison to listening with one side alone. However, large variability in the measured benefit is observed. It is possible that this variability is associated with the integration of speech across electric and acoustic stimulation modalities. However, there is a lack of established methods to assess speech integration between electric and acoustic stimulation and consequently to adequately program the devices. Moreover, existing methods do not provide information about the underlying physiological mechanisms of this integration or are based on simple stimuli that are difficult to relate to speech integration. Electroencephalography (EEG) to continuous speech is promising as an objective measure of speech perception, however, its application in CIs is challenging because it is influenced by the electrical artifact introduced by these devices. For this reason, the main goal of this work is to investigate a possible electrophysiological measure of speech integration between electric and acoustic stimulation in bimodal CI users. For this purpose, a selective attention decoding paradigm has been designed and validated in bimodal CI users. The current study included behavioral and electrophysiological measures. The behavioral measure consisted of a speech understanding test, where subjects repeated words to a target speaker in the presence of a competing voice listening with the CI side (CIS) only, with the acoustic side (AS) only or with both listening sides (CIS+AS). Electrophysiological measures included cortical auditory evoked potentials (CAEPs) and selective attention decoding through EEG. CAEPs were recorded to broadband stimuli to confirm the feasibility to record cortical responses with CIS only, AS only, and CIS+AS listening modes. In the selective attention decoding paradigm a co-located target and a competing speech stream were presented to the subjects using the three listening modes (CIS only, AS only, and CIS+AS). The main hypothesis of the current study is that selective attention can be decoded in CI users despite the presence of CI electrical artifact. If selective attention decoding improves combining electric and acoustic stimulation with respect to electric stimulation alone, the hypothesis can be confirmed. No significant difference in behavioral speech understanding performance when listening with CIS+AS and AS only was found, mainly due to the ceiling effect observed with these two listening modes. The main finding of the current study is the possibility to decode selective attention in CI users even if continuous artifact is present. Moreover, an amplitude reduction of the forward transfer response function (TRF) of selective attention decoding was observed when listening with CIS+AS compared to AS only. Further studies to validate selective attention decoding as an electrophysiological measure of electric acoustic speech integration are required.
Polystyrene as a vector of heavy metals in hard clam Meretrix lusoria under various salinities

Microplastics and heavy metals are the two main contaminants that are often found in aquatic environments and can lead to major issues for aquatic organisms. Polystyrene (PS) is a type of microplastic that is commonly found in aquatic environments. Hard clams are one of the organisms that are often used as a bioindicator of water pollution, and they can live in a certain salinity range. The objective of this study is to investigate the potential of PS particles as heavy metal vectors in M. lusoria influenced by differences in salinity. The result showed that the highest increase in concentrations of all heavy metals in hard clams was found in those placed at higher salinities. Hard clams that were placed at higher salinity required more water, allowing more PS particles to enter the clams’ bodies. Hard clams placed at salinity 30‰ always gathered significantly more PS particles (p<0.05) than hard clams placed at the other two salinities (20 and 25‰). This is also corroborated by water depletion at a salinity of 30‰, which is significantly higher (p<0.05) than the other two salinities. Our findings indicate that PS particles have the potential as vectors for heavy metal pollutants in hard clams in environments of varying salinity.
Identification of ferroptosis-related genes and predicted overall survival in patients with burns

Introduction Burns are a common trauma associated with considerable mortality and morbidity. Although a lot is known regarding burns' pathogenesis, the involvement of ferroptosis is uncertain. Here, we aimed to explore vital ferroptosis-related genes and molecules in burns, through bioinformatics analysis, to uncover new effective therapeutic targets. Methods The FerrDb database was used to acquire ferroptosis-related genes and GSE19743 was downloaded from Gene Expression Omnibus (GEO), a dataset with analysis of control and burned individuals. Hub genes were selected with Cytoscape software, and Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted. Cox proportional hazard function and Kaplan-Meier survival analyses were implemented to screen prognosis-related genes. Additionally, the miRWalk database was used to acquire the miRNAs relevant to our hub genes function and analyzed for enrichment. Result We identified 64 differentially expressed genes and through the intersection with ferroptosis-related genes, 10 were selected as hub genes. GO analysis revealed that the hub genes' most enriched activities were response to oxidative stress, pyridine-containing compound metabolic processes, and reactive oxygen species metabolic processes. KEGG pathways' analysis showed that these overlapped genes were enriched in several pathways, namely, in VEGF signaling. Furthermore, the molecular miRNA functions significantly enriched were signal transduction and cell communication, namely, the biological pathways of the glypican pathway and the ErbB receptor signaling network. SLC40A1 and GPT2 genes were found to be associated with overall survival, suggesting an important role in burn prognosis. Discussion This study may improve our understanding of the underlying burn mechanisms and provide a new direction for the prevention of poor outcomes, advances in burns treatment, and drug development.
Electrophysiological biomarkers and age characterize phenotypic heterogeneity among individuals with major depressive disorder

Introduction: Despite the high need for effective treatments for major depressive disorder (MDD), the development of novel medicines is hampered by clinical, genetic and biological heterogeneity, unclear links between symptoms and neural dysfunction, and tenuous biomarkers for clinical trial contexts of use. Methods: In this study, we examined the International Study to Predict Optimized Treatment in Depression (iSPOT-D) clinical trial database for new relationships between auditory event-related potential (ERP) responses, demographic features, and clinical symptoms and behavior, to inform strategies for biomarker-driven patient stratification that could be used to optimize future clinical trial design and drug development strategy in MDD. Results: We replicate findings from previous analyses of the classic auditory oddball task in the iSPOT-D sample showing smaller than typical N1 and P300 response amplitudes and longer P300 latencies for target and standard stimuli in patients with MDD, suggesting altered bottom-up sensory and top-down attentional processes. We further demonstrate that age is an important contributor to clinical group differences, affecting both topographic distribution of the clinically informative ERP responses and the types of the stimuli sensitive to group differences. In addition, the observed brain-behavior associations indicate that levels of anxiety and stress are major contributing factors to atypical sensory and attentional processing among patients with MDD, particularly in the older subgroups. Discussion: Our novel findings support the possibility of accelerated cognitive aging in patients with MDD and identify the frontal P300 latency as an additional candidate biomarker of MDD. These results from a large, well-phenotyped sample support the view that heterogeneity of the clinical population with MDD can be systematically characterized based on age and neural biomarkers of sensory and attentional processing, informing patient stratification strategies in the design of clinical trials.
Temporal prediction error triggers amygdala-dependent memory updating in appetitive operant conditioning in rats

Reinforcement learning theories postulate that prediction error, i.e., a discrepancy between the actual and expected outcomes, drives reconsolidation and new learning, inducing an updating of the initial memory. Pavlovian studies have shown that prediction error detection is a fundamental mechanism in triggering amygdala-dependent memory updating, where the temporal relationship between stimuli plays a critical role. However, in contrast to the well-established findings in aversive situations (e.g., fear conditioning), only few studies exist on prediction error in appetitive operant conditioning, and even less with regard to the role of temporal parameters. To explore if temporal prediction error in an appetitive operant paradigm could generate an updating and consequent reconsolidation and/or new learning of temporal association, we ran four experiments in adult male rats. Experiment 1 verified whether an unexpected delay in the time of reward’s availability (i.e., a negative temporal prediction error) in a single session produces an updating in long-term memory of temporal expectancy in an appetitive operant conditioning. Experiment 2 showed that negative prediction errors, either due to the temporal change or through reward omission, increased in the basolateral amygdala nucleus (BLA) the activation of a protein that is critical for memory formation. Experiment 3 revealed that the presence of a protein synthesis inhibitor (anisomycin) in the BLA during the session when the reward was delayed (Error session) affected the temporal updating. Finally, Experiment 4 showed that anisomycin, when infused immediately after the Error session, interfered with the long-term memory of the temporal updating. Together, our study demonstrated an involvement of BLA after a change in temporal and reward contingencies, and in the resulting updating in long-term memory in appetitive operant conditioning.
Changing features of the Northern Hemisphere 500-hPa circumpolar vortex

The tropospheric circumpolar vortex (CPV), an important signature of processes steering the general atmospheric circulation, surrounds each pole and is linked to the surface weather conditions. The CPV can be characterized by its area and circularity ratio (Rc), which both vary temporally. This research advances previous work identifying the daily 500-hPa Northern Hemispheric CPV (NHCPV) area, Rc, and temporal trends in its centroid by examining linear trends and periodic cycles in NHCPV area and Rc (1979–2017). Results suggest that NHCPV area has increased linearly over time. However, a more representative signal of the planetary warming may be the temporally weakening gradient which has blurred NHCPV distinctiveness—perhaps a new indicator of Arctic amplification. Rc displays opposing trends in subperiods and an insignificant overall trend. Distinct annual and semiannual cycles exist for area and Rc over all subperiods. These features of NHCPV change over time may impact surface weather/climate.
The involvement of the primo vascular system in local enteritis and its modification by electroacupuncture

Introduction The primo vascular system (PVS), an intensive network structure, has been claimed to be representative of the acupuncture meridian. Here, we explored the role of the PVS in local enteritis and its modification by acupuncture. Methods Chronic cecitis in rabbits was induced by 2,4,6-trinitro-benzene-sulfonic acid (TNBS). The PVS on the cecum was visualized with trypan blue staining, and collected with the help of microsurgical forceps under an optical stereomicroscope. Results The increased primo vessels (PVs) and primo nodes (PNs) of the PVS on the surface of the cecum were induced by local inflammation, which was positively correlated with the inflammatory cells in the cecal mucosa. Tandem mass tag (TMT) based proteomic analysis revealed that 110 differentiated proteins of the PVS existed between TNBS-treated and control rabbits; 65 proteins were upregulated, while 45 proteins were downregulated. These proteins were mainly enriched in inflammation- and immunity-related processes, such as inflammatory cell proliferation, antigen presentation, and cell adhesion in the proliferated PVS (data are available via ProteomeXchange with the identifiers PXD034280). Importantly, TNBS-induced cecitis, the proliferated PVS and inflammation response-related proteins (CD40, CD45, HLA-DRA1, LAMP1, JAGN1 and FGL1) in the PVS were alleviated or reversed by repetitive electroacupuncture (EA) stimulations. Conclusion These results suggest that the proliferated PVS and its active inclusions were related to the inflammatory process, which was modified by EA. Our study provides a new avenue for further exploration of the mechanism by which EA exerts anti-inflammatory effects.
Nitrogen assimilation and photorespiration become more efficient under chloride nutrition as a beneficial macronutrient

Chloride (Cl−) and nitrate ( NO 3 − ) are closely related anions involved in plant growth. Their similar physical and chemical properties make them to interact in cellular processes like electrical balance and osmoregulation. Since both anions share transport mechanisms, Cl− has been considered to antagonize NO 3 − uptake and accumulation in plants. However, we have recently demonstrated that Cl− provided at beneficial macronutrient levels improves nitrogen (N) use efficiency (NUE). Biochemical mechanisms by which beneficial Cl− nutrition improves NUE in plants are poorly understood. First, we determined that Cl− nutrition at beneficial macronutrient levels did not impair the NO 3 − uptake efficiency, maintaining similar NO 3 − content in the root and in the xylem sap. Second, leaf NO 3 − content was significantly reduced by the treatment of 6 mM Cl− in parallel with an increase in NO 3 − utilization and NUE. To verify whether Cl− nutrition reduces leaf NO 3 − accumulation by inducing its assimilation, we analysed the content of N forms and the activity of different enzymes and genes involved in N metabolism. Chloride supply increased transcript accumulation and activity of most enzymes involved in NO 3 − assimilation into amino acids, along with a greater accumulation of organic N (mostly proteins). A reduced glycine/serine ratio and a greater ammonium accumulation pointed to a higher activity of the photorespiration pathway in leaves of Cl−-treated plants. Chloride, in turn, promoted higher transcript levels of genes encoding enzymes of the photorespiration pathway. Accordingly, microscopy observations suggested strong interactions between different cellular organelles involved in photorespiration. Therefore, in this work we demonstrate for the first time that the greater NO 3 − utilization and NUE induced by beneficial Cl− nutrition is mainly due to the stimulation of NO 3 − assimilation and photorespiration, possibly favouring the production of ammonia, reductants and intermediates that optimize C-N re-utilization and plant growth. This work demonstrates new Cl− functions and remarks on its relevance as a potential tool to manipulate NUE in plants.
Data-driven approach to integrating genomic and behavioral preclinical traumatic brain injury research

Understanding recovery from TBI is complex, involving multiple systems and modalities. The current study applied modern data science tools to manage this complexity and harmonize large-scale data to understand relationships between gene expression and behavioral outcomes in a preclinical model of chronic TBI (cTBI). Data collected by the Moody Project for Translational TBI Research included rats with no injury (naïve animals with similar amounts of anesthetic exposure to TBI and sham-injured animals), sham injury, or lateral fluid percussion TBI, followed by recovery periods up to 12 months. Behavioral measures included locomotor coordination (beam balance neuroscore) and memory and cognition assessments (Morris water maze: MWM) at multiple timepoints. Gene arrays were performed using hippocampal and cortical samples to probe 45,610 genes. To reduce the high dimensionality of molecular and behavioral domains and uncover gene–behavior associations, we performed non-linear principal components analyses (NL-PCA), which de-noised the data. Genomic NL-PCA unveiled three interpretable eigengene components (PC2, PC3, and PC4). Ingenuity pathway analysis (IPA) identified the PCs as an integrated stress response (PC2; EIF2-mTOR, corticotropin signaling, etc.), inflammatory factor translation (PC3; PI3K-p70S6K signaling), and neurite growth inhibition (PC4; Rho pathways). Behavioral PCA revealed three principal components reflecting the contribution of MWM overall speed and distance, neuroscore/beam walk, and MWM platform measures. Integrating the genomic and behavioral domains, we then performed a ‘meta-PCA’ on individual PC scores for each rat from genomic and behavioral PCAs. This meta-PCA uncovered three unique multimodal PCs, characterized by robust associations between inflammatory/stress response and neuroscore/beam walk performance (meta-PC1), stress response and MWM performance (meta-PC2), and stress response and neuroscore/beam walk performance (meta-PC3). Multivariate analysis of variance (MANOVA) on genomic–behavioral meta-PC scores tested separately on cortex and hippocampal samples revealed the main effects of TBI and recovery time. These findings are a proof of concept for the integration of disparate data domains for translational knowledge discovery, harnessing the full syndromic space of TBI.
Adding of apatinib and camrelizumab to overcome de novo trastuzumab resistance of HER2-positive gastric cancer: A case report and literature review

Background: Studies confirmed that trastuzumab plus fluorouracil-based chemotherapy improves the survival to more than 1 year in human with human epidermal growth factor receptor-2 (HER2)-positive advanced gastric cancer. However, there are still a small proportion of patients who do not benefit from trastuzumab treatment. Case summary: Here, we described a case report of de novo trastuzumab resistance in HER2-positive gastric cancer. Concomitant cyclin-E1 (CCNE1) and HER2 amplification are associated with de novo trastuzumab resistance. Genomic analysis demonstrated CCNE1 amplification and TP53 mutation in a HER2-positive gastric cancer patient. This patient achieved significant survival benefit and good safety when the patient received triple regimens consisting of trastuzumab, apatinib, and camrelizumab. Conclusion: Trastuzumab plus camrelizumab plus apatinib has the potential efficacy in HER2-positive gastric cancer patients who were previously treated with trastuzumab plus chemotherapy. This may lead to a new solution to trastuzumab resistance.
Gut microbiota signatures in tissues of the colorectal polyp and normal colorectal mucosa, and faeces

Background Colorectal polyps are the most common precursors of colorectal cancer (CRC). The close relationship has been observed between colorectal polyps and gut microbiota. However, gut microbiota signatures among sampling sites in patients with colorectal polyps and healthy adults remain elusive. Aims To learn about gut microbiota signatures in tissues of the colorectal polyp and normal colorectal mucosa, and faeces. Methods We performed 16S rRNA gene sequencing and bioinformatic analysis for the microbiota in the normal colorectal mucosa, the colorectal polyps and faeces of adults with colorectal polyps (n = 24) and in faeces and normal mucosa of healthy adults (n = 16) in this preliminary trial. Results The Ace and Chao indexes were higher in the normal colorectal mucosa and polyp tissues compared to faecal samples (P < 0.05). The composition of microbiota based on PCoA and ANOSIM analysis showed the significant differences only between faeces and tissues of the normal mucosa and polyp (P < 0.05). Based on the LEfSe analysis, the abundances of Bacteroides, Prevotella-2 and Agathobacter were higher, whereas the abundances of Haemophilus, Escherichia_Shigella, Fusobacterium and Streptococcus were lower in faeces both in patients with colorectal polyp and healthy individuals, compared with those in the normal mucosa in two groups or polyp tissues. In healthy individuals, the abundance of Fusobacterium was significantly higher in the normal colorectal mucosa than in faeces. Moreover, there was no significant difference in the abundance of Fusobacterium between the normal colorectal mucosa and polyps in patients with colorectal polyps, but it was significantly higher in the mucosa and polyps than in faeces. Remarkably, the abundance of Fusobacterium in the normal colorectal mucosa was significantly higher in healthy individuals than in the polyp group. Conclusions The microbial structure in faeces differs from that in tissues of polyp and normal mucusa. Additionally, Fusobacterium may be a normal colonizer in colonic mucosa, and an abnormal increase of Fusobacterium detected in faeces may be related with the injury of the colorectal mucosa. The difference of the faecal microbiota and mucosal microbiota should be carefully considered in studies on gut microbiota in patients with colorectal lesions.
Outlier analyses and genome-wide association study identify glgC and ERD6-like 4 as candidate genes for foliar water-soluble carbohydrate accumulation in Trifolium repens

Increasing water-soluble carbohydrate (WSC) content in white clover is important for improving nutritional quality and reducing environmental impacts from pastoral agriculture. Elucidation of genes responsible for foliar WSC variation would enhance genetic improvement by enabling molecular breeding approaches. The aim of the present study was to identify single nucleotide polymorphisms (SNPs) associated with variation in foliar WSC in white clover. A set of 935 white clover individuals, randomly sampled from five breeding pools selectively bred for divergent (low or high) WSC content, were assessed with 14,743 genotyping-by-sequencing SNPs, using three outlier detection methods: PCAdapt, BayeScan and KGD-FST. These analyses identified 33 SNPs as discriminating between high and low WSC populations and putatively under selection. One SNP was located in the intron of ERD6-like 4, a gene coding for a sugar transporter located on the vacuole membrane. A genome-wide association study using a subset of 605 white clover individuals and 5,757 SNPs, identified a further 12 SNPs, one of which was associated with a starch biosynthesis gene, glucose-1-phosphate adenylyltransferase, glgC. Our results provide insight into genomic regions underlying WSC accumulation in white clover, identify candidate genomic regions for further functional validation studies, and reveal valuable information for marker-assisted or genomic selection in white clover.