Miracle-dz/UniFAR-FTUs huggingface dataset:
GIGANTEA gene expression influence leaf senescence in Populus in two different ways

GIGANTEA (GI) genes have a central role in plant development and influence several processes such as light signaling, circadian rhythm and abiotic stress tolerance. Hybrid aspen T89 (Populus tremula x tremuloides) trees with low GI expression through RNAi have a severely compromised growth. In order to study the effect of reduced GI expression on leaf traits with special emphasis on leaf senescence, we grafted GI-RNAi scions onto wild type (WT) rootstocks and managed to restore scions’ growth. The RNAi line had distorted leaf shape and reduced photosynthesis, probably caused by modulating phloem or stomatal function, increased starch accumulation, higher carbon-to-nitrogen (C/N) ratio and a reduced capacity to withstand moderate light stress. GI-RNAi also induced senescence under long day (LD) and moderate light conditions. Furthermore, the GI-RNAi lines were affected in their capacity to respond to “autumn environmental cues” inducing senescence, a type of leaf senescence with characteristics different from senescence induced directly by stress under LD conditions. Whereas Overexpression of GI delayed senescence. The two different effects on leaf senescence were not affected by the expression of FT (Flowering locus T), were “local” – they followed the genotype of the branch independent on the position in the tree – and trees with modified gene expression grown in the field were affected in a similar way as under controlled conditions. Taken together, GI plays a central role to sense the environmental changes during autumn and determine the appropriate timing for leaf senescence in Populus. One sentence summary Leaf senescence is a complex process that is not well understood, but this paper shows that changing the expression of one gene could influence leaf senescence in Populus trees in two separate ways.
Subepithelial Myofibroblasts Are Critical Regulators of Intestinal Epithelial Restoration

Intestinal epithelial migration is supposed to occur in a passive manner driven by the mitotic pressure exerted either by the cryptal stem cells, under physiological conditions, or the newly formed epithelium, upon damage. However, whether interactions between different neighboring cell types and with the matrix contribute to epithelial movement remain elusive. Here, we developed a novel three-dimensional in vitro intestinal mucosa model of gap closure, that includes both the epithelium and the basement membrane cellular compartments in a spatially relevant manner, to show that intestinal subepithelial myofibroblasts (ISEMFs) play a crucial role in epithelial restoration. ISEMF-derived biochemical cues boost epithelial proliferation and maintain epithelial barrier integrity. While, at the wounded area, ISEMF actively migrate to the epithelial front where they activate and generate ɑ-SMA contractile stress fibers along the direction of the epithelial cells promoting epithelial migration. Furthermore, ISEMF also deposit collagen paths that act as “guide rails” for directing IEC migration. Thus, the mere physical presence of ISEMFs can greatly accelerate restoration in wound healing, which suggests that ISEMFs should be recognized as new potential therapeutic targets.
Widespread occurrence of hybrid internal-terminal exons in human transcriptomes

Alternative RNA processing is a major mechanism for diversifying the human transcriptome. Messenger RNA isoform differences are predominantly driven by alternative first exons, cassette internal exons and alternative last exons. Despite the importance of classifying exons to understand isoform structure, there is a lack of tools to look at isoform-specific exon usage using RNA-sequencing data. We recently observed that alternative transcription start sites often arise near annotated internal exons, creating “hybrid” exons that can be used as both first or internal exons. To investigate the creation of hybrid exons, we built the HIT (Hybrid-Internal-Terminal) exon pipeline that systematically classifies exons depending on their isoform-specific usage. Using a combination of junction reads coverage and probabilistic modeling, the HIT index identified thousands of hybrid first-internal and internal-last exons that were previously misclassified. Hybrid exons are enriched in long genes with at least ten internal exons, have longer flanking introns and strong splice sites. The usage of hybrid exons varies considerably across human tissues, but they are predominantly used in brain, testis and colon cells. Notably, genes involved in RNA splicing have the highest fraction of intra-tissue hybrid exons. Further, we found more than 100,000 inter-tissue hybrid exons that changed from internal to terminal exons across tissues. By developing the first method that can classify exons according to their isoform contexts, our findings demonstrate the existence of hybrid exons, expand the repertoire of tissue-specific terminal exons and uncover unexpected complexities of the human transcriptome.
Seeing beyond the target: Leveraging off-target reads in targeted clinical tumor sequencing to identify prognostic biomarkers

Clinical tumor sequencing is rapidly becoming a standard component of clinical care, providing essential information for selecting amongst treatment options and providing prognostic value. Here we develop a robust and scalable software platform (SBT: Seeing Beyond the Target) that mines discarded components of clinical sequences to produce estimates of a rich set of omics features including rDNA and mtDNA copy number, microbial species abundance, and T and B cell receptor sequences. We validate the accuracy of SBT via comparison to multimodal data from the TCGA and apply SBT to a tumor panel cohort of 2,920 lung adenocarcinomas to identify associations of clinical value. We replicated known associations of somatic events in TP53 with changes in rDNA (p=0.012); as well as diversity of BCR and TCR repertoires with the biopsy site (p=2.5×10−6, p<10−20). We observed striking differences in EGFR mutant lung cancers versus wild-type, including higher rDNA copy number and lower immune repertoire diversity. Integrating clinical outcomes, we identified significant prognostic associations with overall survival, including SBT estimates of 5S rDNA (p=1.9×10−4, hazard ratio = 1.22) and TCR diversity (p=2.7×10−3, hazard ratio=1.77). Both novel survival associations replicated in 1,302 breast carcinoma and 1,651 colorectal cancer tumors. We anticipate that feature estimates derived by SBT will yield novel biomarker hypotheses and open research opportunities in existing and emerging clinical tumor sequencing cohorts.
Extraction and Characterization of Pectin from Peels of Lemon (Citrus limon), Grape Fruit (Citrus paradisi) and Sweet Orange (Citrus sinensis)

This research study aimed at comparing the characteristics of three different pectins and to see which one is more suitable for industrial applications. Pectin, which is a family of complex polysaccharides that contains 1, 4- linked x and β galactosyluronic acid residues was extracted using alcohol precipitation method from peels of lemon, grape and sweet orange after which it was characterized using both qualitative and quantitative analysis to determine and compare the color equivalent weight methoxyl content, each content solubility in cold and hot alkali, pH as well as sugar and organic acid. The result showed that the colors of the pectin from these 3 sources were the same i.e., Brown they were all soluble in hot and cold alkali and water, the moisture content, the methoxyl content and the ash were all higher in the pectin extracted from peels of sweet orange with 95.25, 5.79 and 35%, respectively. However, the equivalent weight of the pectin extracted from peels of grape was higher with 793.6 mg/mol. The overall results showed that the pectin from these sources were suitable for industrial use.
Metabolomic and Lipidomic Approaches to Evaluate the Effects of Eucommia ulmoides Leaves on Milk Quality and Biochemical Properties

Eucommia ulmoides leaves (EUL) contain a variety of natural bioactive compounds including chlorogenic acid, geniposide acid, and aucubin. These bioactive chemicals improve immune function and regulate lipid metabolism. The aim of this study was to investigate the effects of EUL on the biochemical properties of milk. Twenty Holstein dairy cows were randomly allocated to two groups fed a control (CTR, diet without EUL, n = 10) or EUL (diet containing 3% EUL, dry matter, n = 10) diet for 55 d. At the end of the experimental period (d 55), milk samples were collected and analyzed to determine their composition. Though levels of milk fat, protein, lactose, and total milk solids were similar between the groups, small molecules, metabolites, lipids, and cytokines differed. Compared with the CTR group, the EUL group had an improved cluster of differentiation (CD)4/CD8 ratio (P < 0.05) and lower interleukin (IL)-8 and IL-6 content (P < 0.05). Metabolomics analysis identified 14 metabolites including 7Z, 10Z, 13Z, 16Z, 19Z-docosapentaenoic acid (FC = 3.129), adrenic acid (FC = 2.830), and eicosapentaenoic acid (FC=1.685) as having significantly increased in the EUL group (P < 0.05) while 11 metabolites, including indole-2-carboxylic acid (FC = 0.636), cholic acid (FC = 0.430), and creatine (FC = 0.784) had significantly decreased (P < 0.05). Based on a constructed metabolome map, linoleic acid metabolism had the highest impact value for EUL. A total of 21 lipid classes and 1,094 lipid species were detected in the milk by lipidomic analysis, among which 40 differed significantly between the CTR and EUL groups. The present findings showed that the EUL altered milk composition. Correlation analysis showed that 7Z, 10Z, 13Z, 16Z, 19Z-docosapentaenoic acid, adrenic acid, and eicosapentaenoic acid levels were negatively correlated with those of the inflammatory factors IL-6 and IL-8 (P < 0.05), indicating that EUL improved milk quality by reducing inflammatory factors and increasing the CD4/CD8 ratio. Overall, our data demonstrate that EUL had positive effects on milk antioxidant parameters, immune indices, and micro-composition metabolism, thereby improving milk quality.
Frontal EEG-Based Multi-Level Attention States Recognition Using Dynamical Complexity and Extreme Gradient Boosting

Measuring and identifying the specific level of sustained attention during continuous tasks is essential in many applications, especially for avoiding the terrible consequences caused by reduced attention of people with special tasks. To this end, we recorded EEG signals from 42 subjects during the performance of a sustained attention task and obtained resting state and three levels of attentional states using the calibrated response time. EEG-based dynamical complexity features and Extreme Gradient Boosting (XGBoost) classifier were proposed as the classification model, Complexity-XGBoost, to distinguish multi-level attention states with improved accuracy. The maximum average accuracy of Complexity-XGBoost were 81.39 ± 1.47% for four attention levels, 80.42 ± 0.84% for three attention levels, and 95.36 ± 2.31% for two attention levels in 5-fold cross-validation. The proposed method is compared with other models of traditional EEG features and different classification algorithms, the results confirmed the effectiveness of the proposed method. We also found that the frontal EEG dynamical complexity measures were related to the changing process of response during sustained attention task. The proposed dynamical complexity approach could be helpful to recognize attention status during important tasks to improve safety and efficiency, and be useful for further brain-computer interaction research in clinical research or daily practice, such as the cognitive assessment or neural feedback treatment of individuals with attention deficit hyperactivity disorders, Alzheimer’s disease, and other diseases which affect the sustained attention function.
Feeling for the Other With Ease: Prospective Actors Show High Levels of Emotion Recognition and Report Above Average Empathic Concern, but Do Not Experience Strong Distress

Differences in empathic abilities between acting, dance, and psychology students were explored, in addition to the appropriateness of existing empathy measures in the context of these cohorts. Students (N = 176) across Higher Education Institutions in the United Kingdom and Europe were included in the online survey analysis, consisting of the Reading the Mind in the Eyes (RME) test, the Interpersonal Reactivity Index (IRI), the Empathy Quotient (EQ), and the E-drawing test (EDT), each measuring particular facets of empathy. Based on existing evidence and our understanding of the discipline practices, we predicted that acting students would perform the best at identifying people’s emotional expressions but might lack other cognitive or affective empathy skills, particularly those related to emotional reactions. This cohort thus provides an opportunity to evaluate different empathy measures. While actors showed significantly higher RME scores than dancers, the difference between actors and psychologists was marginal. Moreover, actors’ scores did not differ significantly on other empathy measures, such as their concern for others’ emotional wellbeing or fantasy, both measured by IRI subscales. Psychology students scored highest in the IRI perspective taking subscale and the data supported anecdotal evidence that psychologists were more concerned for others’ emotional wellbeing than dancers or actors. Dancers seemed the least concerned with others’ perspectives and emotional states, which we explained through a somatosensory ‘inward’ focus required by their art form. Nevertheless, compared to the general population, our groups reported higher empathic abilities on all IRI subscales except for personal distress. Altogether, our study shows that the RME, the IRI, and the EDT vary in their susceptibility to different facets of empathic abilities in acting, dance, and psychology students whereas the EQ does not. Emotions can be expressed and perceived through language, facial expressions, or behavior. As many empathy tests focus on one type of signal they might miss other strategies. Where empathy tests are applied to individuals that have a predominance to read or respond to others in a particular way, as we showed through these three disciplines, they might not capture these empathic strategies. We thus propose that empathy tests must evolve by means of integrating varied forms of communication.
The Role of Intermittent Fasting in Parkinson's Disease

Parkinson disease (PD) is the second most common neurodegenerative disease, affecting ∼2% of the population over age 70. Disease prevalence increases with age and, given the aging population, may triple in the next few years (1). The neurodegenerative mechanism leading to PD is still not completely elucidated. Alpha-synuclein may drive the neurodegenerative process of PD. When aggregated in neurons as intracellular Lewy bodies, it constitutes the pathologic hallmark of PD (2). On the other hand, mitochondrial dysfunction, oxidative stress, and selective neuronal loss each contribute to PD pathology (3). Unfortunately, there remains no disease-modifying treatment in PD despite multiple trials of promising preclinical targets. Supplements and dietary interventions have been periodically considered as possible therapeutic approaches to impact disease progression and severity in related neurodegenerative disorders (3). One such intervention is intermittent fasting (IF). This viewpoint seeks to describe the putative pathophysiologic relationships amongmitochondria, alpha-synuclein and PD risk genes and to provide a background for the rationale or the use of IF and similar mitochondrial-targeting therapies in PD. Finally, we propose an outline for determining the efficacy of an IF intervention in PD.
Effect of Temperature and Selection for Growth on Intracellular Lipid Accumulation and Adipogenic Gene Expression in Turkey Pectoralis Major Muscle Satellite Cells

As multipotential stem cells, satellite cells (SCs) have the potential to express adipogenic genes resulting in lipid synthesis with thermal stress. The present study determined the effect of temperature on intracellular lipid synthesis and adipogenic gene expression in SCs isolated from the pectoralis major (p. major) muscle of 7-day-old fast-growing modern commercial (NC) turkeys compared to SCs from unselected slower-growing turkeys [Randombred Control Line 2 (RBC2)]. Since proliferating and differentiating SCs have different responses to thermal stress, three incubation strategies were used: (1) SCs proliferated at the control temperature of 38°C and differentiated at 43° or 33°C; (2) SCs proliferated at 43° or 33°C and differentiated at 38°C; or (3) SCs both proliferated and differentiated at 43°, 38°, or 33°C. During proliferation, lipid accumulation increased at 43°C and decreased at 33°C with the NC line showing greater variation than the RBC2 line. During proliferation at 43°C, peroxisome proliferator-activated receptor-γ (PPARγ) and neuropeptide-Y (NPY) expression was reduced to a greater extent in the NC line than the RBC2 line. At 33°C, expression of PPARγ, NPY, and CCAAT/enhancer-binding protein-β (C/EBPβ) was upregulated, but only in the RBC2 line. During differentiation, both lines showed greater changes in lipid accumulation and in C/EBPβ and NPY expression if the thermal challenge was initiated during proliferation. These data suggest that adipogenic gene expression is more responsive to thermal challenge in proliferating SCs than in differentiating SCs, and that growth-selection has increased temperature sensitivity of SCs, which may significantly affect breast muscle structure and composition.
Neural Oscillation During Mental Imagery in Sport: An Olympic Sailor Case Study

The purpose of the current study was to examine the cortical correlates of imagery depending on instructional modality (guided vs. self-produced) using various sports-related scripts. According to the expert-performance approach, we took an idiosyncratic perspective analyzing the mental imagery of an experienced two-time Olympic athlete to verify whether different instructional modalities of imagery (i.e., guided vs. self-produced) and different scripts (e.g., training or competition environment) could differently involve brain activity. The subject listened to each previously recorded script taken from two existing questionnaires concerning imagery ability in sport and then was asked to imagine the scene for a minute. During the task, brain waves were monitored using EEG (32-channel g. Nautilus). Our findings indicate that guided imagery might induce higher high alpha and SMR (usually associated with selective attention), whereas self-produced imagery might facilitate higher low alpha (associated with global resting state and relaxation). Results are discussed in light of the neural efficiency hypothesis as a marker of optimal performance and transient hypofrontality as a marker of flow state. Practical mental training recommendations are presented.
Signatures of B Cell Receptor Repertoire Following Pneumocystis Infection

B cells play vital roles in host defense against Pneumocystis infection. However, the features of the B cell receptor (BCR) repertoire in disease progression remain unclear. Here, we integrated single-cell RNA sequencing and single-cell BCR sequencing of immune cells from mouse lungs in an uninfected state and 1–4 weeks post-infection in order to illustrate the dynamic nature of B cell responses during Pneumocystis infection. We identified continuously increased plasma cells and an elevated ratio of (IgA + IgG) to (IgD + IgM) after infection. Moreover, Pneumocystis infection was associated with an increasing naïve B subset characterized by elevated expression of the transcription factor ATF3. The proportion of clonal expanded cells progressively increased, while BCR diversity decreased. Plasma cells exhibited higher levels of somatic hypermutation than naïve B cells. Biased usage of V(D)J genes was observed, and the usage frequency of IGHV9-3 rose. Overall, these results present a detailed atlas of B cell transcriptional changes and BCR repertoire features in the context of Pneumocystis infection, which provides valuable information for finding diagnostic biomarkers and developing potential immunotherapeutic targets.
Genome-Wide Variants Associated With Longitudinal Survival Outcomes Among Individuals With Coronary Artery Disease

Objective Coronary artery disease (CAD) is an age-associated condition that greatly increases the risk of mortality. The purpose of this study was to identify gene variants associated with all-cause mortality among individuals with clinically phenotyped CAD using a genome-wide screening approach. Approach and Results We performed discovery (n = 1,099), replication (n = 404), and meta-analyses (N = 1,503) for association of genomic variants with survival outcome using secondary data from White participants with CAD from two GWAS sub-studies of the Duke Catheterization Genetics Biorepository. We modeled time from catheterization to death or last follow-up (median 7.1 years, max 12 years) using Cox multivariable regression analysis. Target statistical screening thresholds were p × 10–8 for the discovery phase and Bonferroni-calculated p-values for the replication (p < 5.3 × 10–4) and meta-analysis (p < 1.6 × 10–3) phases. Genome-wide analysis of 785,945 autosomal SNPs revealed two SNPs (rs13007553 and rs587936) that had the same direction of effect across all three phases of the analysis, with suggestive p-value association in discovery and replication and significant meta-analysis association in models adjusted for clinical covariates. The rs13007553 SNP variant, LINC01250, which resides between MYTIL and EIPR1, conferred increased risk for all-cause mortality even after controlling for clinical covariates [HR 1.47, 95% CI 1.17–1.86, p(adj) = 1.07 × 10–3 (discovery), p(adj) = 0.03 (replication), p(adj) = 9.53 × 10–5 (meta-analysis)]. MYT1L is involved in neuronal differentiation. TSSC1 is involved in endosomal recycling and is implicated in breast cancer. The rs587936 variant annotated to DAB2IP was associated with increased survival time [HR 0.65, 95% CI 0.51–0.83, p(adj) = 4.79 × 10–4 (discovery), p(adj) = 0.02 (replication), p(adj) = 2.25 × 10–5 (meta-analysis)]. DAB2IP is a ras/GAP tumor suppressor gene which is highly expressed in vascular tissue. DAB2IP has multiple lines of evidence for protection against atherosclerosis. Conclusion Replicated findings identified two candidate genes for further study regarding association with survival in high-risk CAD patients: novel loci LINC01250 (rs13007553) and biologically relevant candidate DAB2IP (rs587936). These candidates did not overlap with validated longevity candidate genes. Future research could further define the role of common variants in survival outcomes for people with CAD and, ultimately, improve longitudinal outcomes for these patients.