Miracle-dz/UniFAR-FTUs huggingface dataset:
An Integrative Analysis of Fruit Shape in Capsella rubella and Arabidopsis thaliana

Plant organs develop from a small number of cells into a wide variety of shapes. This development is coordinated by underlying genetic factors that control the organisation and patterning of growth. The Arabidopsis fruit has been studied in detail and genes involved in fruit shape development and organisation have been uncovered. Related species that have divergent fruit forms have not been studied in the same detail and it remains unclear if the mechanisms and genes controlling growth organisation and patterning in fruit are common. Here, I give a general description of fruit shape changes within a time framework for Capsella rubella, which has an elaborate heart-shaped fruit. I used clonal analysis to generate a description of regional growth dynamics within the tissue. Using this data, I generated computational models to explore the coordination of growth and polarity in the Capsella fruit. Based on observations of morphology, growth dynamics and model outputs, Capsella fruit development can be divided into three phases. It is likely that there is a proximodistal polarity field that deforms locally as the fruit grows. Changes in growth rates and orientations parallel and perpendicular to this polarity field during the different phases can account for the morphology and clonal patterns of the Capsella fruit. In addition, I investigated factors important for the development of the heart-shaped fruit of Capsella through forward and reverse genetic approaches. I found FRUITFULL is an important factor for the development of the heart-shape fruit of Capsella but may not be important for the evolutionary differences in fruit shape within the family Simplified versions of the Capsella fruit model accounted for fruit shapes of related species including Arabidopsis. This indicates that the Capsella fruit is a more elaborate form of the evolutionary conserved mechanisms that underlie fruit development in the Brassicaceae.
Age-dependent impairment of disease tolerance is associated with a robust transcriptional response following RNA virus infection in Drosophila

Advanced age in humans is associated with greater susceptibility to and higher mortality rates from infections, including infections with some RNA viruses. The underlying innate immune mechanisms, which represent the first line of defense against pathogens, remain incompletely understood. Drosophila melanogaster is able to mount potent and evolutionarily conserved innate immune defenses against a variety of microorganisms including viruses and serves as an excellent model organism for studying host-pathogen interactions. With its relatively short lifespan, Drosophila also is an organism of choice for aging studies. Despite numerous advantages that this model offers, Drosophila has not been used to its potential to investigate the response of the aged host to viral infection. Here we show that in comparison to younger flies, aged Drosophila succumb more rapidly to infection with the RNA-containing Flock House Virus (FHV) due to an age-dependent defect in disease tolerance. In comparison to younger individuals, we find that older Drosophila mount larger transcriptional responses characterized by differential regulation of more genes and genes regulated to a greater extent. Our results indicate that loss of disease tolerance to FHV with age possibly results from a stronger regulation of genes involved in apoptosis, activation of the Drosophila Immune deficiency (IMD) NF-kB pathway or from downregulation of genes whose products function in mitochondria and mitochondrial respiration. Our work shows that Drosophila can serve as a model to investigate host-virus interactions during aging and sets the stage for future analysis of the age-dependent mechanisms that govern survival and control of virus infections at older age.
An Exploratory Assessment of Epistemic Curiosity in Students at Three Doctor of Pharmacy Programs

Objective. To determine the level of epistemic curiosity in a sample of student pharmacists from three Doctor of Pharmacy (PharmD) programs as well as any differences in epistemic curiosity levels that exist between programs and with regard to professional year. Methods. Litman’s Epistemic Curiosity Scale (ECS) was administered to student pharmacists at three different PharmD programs. Descriptive statistics were calculated, and overall mean ECS scores as well as mean scores on epistemic curiosity motivated by intellectual interest (I-type) and informational deprivation (D-type) were compared among student pharmacists at the three institutions using analysis of variance. Reliability analyses were also performed on the data. Results. A total of 569 out of 1143 eligible students responded to the survey, for an overall response rate of 49.8%. The mean overall ECS score was 27.6 (SD=4.9). Mean I-type epistemic curiosity was 14.9 (SD=2.8) overall, but was statistically different among the schools. Mean D-type epistemic curiosity was 12.7 (SD=3.2) overall, but was statistically similar among the programs. Overall, the data demonstrated good internal consistency, with a Cronbach’s alpha of . 81. Conclusion. This study was the first to characterize epistemic curiosity in student pharmacists and included data from multiple years and multiple programs. Future analyses should investigate associations between epistemic curiosity and other factors of interest to help elucidate how better understanding epistemic curiosity or enhancing it in student pharmacists may help facilitate student success.
Characterization and expression QTL analysis of TaABI4, a pre-harvest sprouting related gene in wheat

Pre-harvest sprouting (PHS) induced by the decline of seed dormancy causes a severe reduction in crop yield and flour quality. In this study, we isolated and characterized TaABI4, an ABA-responsive transcription factor that participates in regulating seed germination in wheat. Sequence analysis revealed that TaABI4 has three homologues, located on chromosomes 1A/1B/1D. TaABI4 contains a conserved AP2 domain, and AP2-associated, LRP, and potential PEST motifs. Putative cis-acting regulatory elements (CE1-like box, W-box, ABRE elements, and RY-elements) were identified in the TaABI4 promoter region that showed high conservation in 17 wheat cultivars and wheat-related species. Expression profiling of TaABI4 indicated that it is a seed-specific gene accumulating during the middle stages of seed development. Transcript accumulation of TaABI4 in wheat cultivar Chuanmai 32 (CM32, PHS susceptible) was 5.07-fold and 1.39-fold higher than that in synthetic hexaploidy wheat SHW-L1 (PHS resistant) at 15DPA and 20DPA, respectively. Six expression quantitative trait loci (eQTL) of TaABI4 on chromosome 2A, 2D, 3B, and 4A were characterized based on the accumulated transcripts of TaABI4 in SHW-L1 and CM32 derived recombinant inbred lines. These QTLs explained from 10.7% to 46.1% of the trait variation with 4.53~10.59 of LOD scores, which contain genes that may affect the expression of TaABI4.
Comparative Evolutionary Patterns of Burkholderia cenocepacia and B. multivorans During Chronic Co-infection of a Cystic Fibrosis Patient Lung

During chronic respiratory infections of cystic fibrosis (CF) patients, bacteria adaptively evolve in response to the nutritional and immune environment as well as influence other infecting microbes. The present study was designed to gain insights into the genetic mechanisms underlying adaptation and diversification by the two most prevalent pathogenic species of the Burkholderia cepacia complex (Bcc), B. cenocepacia and B. multivorans. Herein, we study the evolution of both of these species during coinfection of a CF patient for 4.4 years using genome sequences of 9 B. multivorans and 11 B. cenocepacia. This co-infection spanned at least 3 years following initial infection by B. multivorans and ultimately ended in the patient’s death by cepacia syndrome. Both species acquired several mutations with accumulation rates of 2.08 (B. cenocepacia) and 2.27 (B. multivorans) SNPs/year. Many of the mutated genes are associated with oxidative stress response, transition metal metabolism, defense mechanisms against antibiotics, and other metabolic alterations consistent with the idea that positive selection might be driven by the action of the host immune system, antibiotic therapy and low oxygen and iron concentrations. Two orthologous genes shared by B. cenocepacia and B. multivorans were found to be under strong selection and accumulated mutations associated with lineage diversification. One gene encodes a nucleotide sugar dehydratase involved in lipopolysaccharide O-antigen (OAg) biosynthesis (wbiI). The other gene encodes a putative two-component regulatory sensor kinase protein required to sense and adapt to oxidative- and heavy metal- inducing stresses. This study contributes to understanding of shared and species-specific evolutionary patterns of B. cenocepacia and B. multivorans evolving in the same CF lung environment.
Framework for Quantification of the Dynamics of Root Colonization by Pseudomonas fluorescens Isolate SBW25

Colonization of the root surface, or rhizoplane, is one of the first steps for soil-borne bacteria to become established in the plant microbiome. However, the relative contributions of processes, such as bacterial attachment and proliferation is not well characterized, and this limits our ability to comprehend the complex dynamics of microbial communities in the rhizosphere. The work presented here addresses this knowledge gap. A model system was developed to acquire quantitative data on the colonization process of lettuce (Lactuca sativa L. cultivar. All Year Round) roots by Pseudomonas fluorescens isolate SBW25. A theoretical framework is proposed to calculate attachment rate and quantify the relative contribution of bacterial attachment to colonization. This allows the assessment of attachment rates on the root surface beyond the short time period during which it can be quantified experimentally. All techniques proposed are generic and similar analyses could be applied to study various combinations of plants and bacteria, or to assess competition between species. In the future this could allow for selection of microbial traits that improve early colonization and maintenance of targeted isolates in cropping systems, with potential applications for the development of biological fertilizers.
Strong ‘functional’ divergence of tropical reef fish assemblages along the global diversity gradient

Coral reefs are experiencing declines due to climate change and local human impacts. While at local scale biodiversity loss induces shifts in community structure, previous biogeographical analyses recorded consistent taxonomic structure of fish communities across global coral reefs. This suggest that regional communities represent a random subset of the global species and traits pool, whatever their species richness. Using distributional data on 3,586 fish species and latest advances in species distribution models we show that the global distribution of reef fishes is influenced by two major traits (body size and diet) and produces a strong divergence in the trait structure of assemblages across the biodiversity gradient. This divergence is best explained by the isolation of reefs during past unfavorable climatic conditions and highlights the risk of a global community re-organization if the ongoing climate-induced reef fragmentation is not halted.
EFFECT OF PHOSPHORUS LEVELS ON GROWTH AND YIELD OF FENUGREEK (TRIGONELLA FOENUM GRAECUM L.) GROWN UNDER DIFFERENT SPATIAL ARRANGEMENTS

Effect of different phosphorus levels (0, 30, 45, 60 kg P2O5 ha) and spatial arrangement of 1.8 × 6 m, 2.4 × 6 m and 3 × 6 m for row spacing 30, 40, and 50 cm, respectively on growth and yield of fenugreek was investigated at Research Area, University college of Agriculture, Bahauddin Zakariya University Multan, during 2003-2004. Spatial arrangement only affected fenugreek plant population per unit area. Interaction effect of phosphorus and spatial arrangement was non-significant on growth and yield of fenugreek. Phosphorus application improved the performance of fenugreek plants for number of seeds plant, 1000 seed weight, biological yield, seed yield and harvest index of fenugreek. Number of branches and pods per plant remained unaffected by phosphorus application. Significant increased seed yield of fenugreek (1358.29 kg ha) was obtained for the crop raised with 60 kg P2O5 ha but was statistically at par with 45 kg P2O5 ha (1326.47 kg ha). It is concluded that optimum dose of phosphorus for fenugreek crop is 45 kg P2O5 ha. It is also suggested that further research should be done on planting geometry of fenugreek under different environmental conditions.
Wearing Face Masks Strongly Confuses Counterparts in Reading Emotions

Wearing face masks is one of the essential means to prevent the transmission of certain respiratory diseases such as coronavirus disease 2019 (COVID-19). Although acceptance of such masks is increasing in the Western hemisphere, many people feel that social interaction is affected by wearing a mask. In the present experiment, we tested the impact of face masks on the readability of emotions. The participants (N = 41, calculated by an a priori power test; random sample; healthy persons of different ages, 18–87 years) assessed the emotional expressions displayed by 12 different faces. Each face was randomly presented with six different expressions (angry, disgusted, fearful, happy, neutral, and sad) while being fully visible or partly covered by a face mask. Lower accuracy and lower confidence in one’s own assessment of the displayed emotions indicate that emotional reading was strongly irritated by the presence of a mask. We further detected specific confusion patterns, mostly pronounced in the case of misinterpreting disgusted faces as being angry plus assessing many other emotions (e.g., happy, sad, and angry) as neutral. We discuss compensatory actions that can keep social interaction effective (e.g., body language, gesture, and verbal communication), even when relevant visual information is crucially reduced.
Amyotrophic Lateral Sclerosis: A Neurodegenerative Motor Neuron Disease With Ocular Involvement

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease that causes degeneration of the lower and upper motor neurons and is the most prevalent motor neuron disease. This disease is characterized by muscle weakness, stiffness, and hyperreflexia. Patients survive for a short period from the onset of the disease. Most cases are sporadic, with only 10% of the cases being genetic. Many genes are now known to be involved in familial ALS cases, including some of the sporadic cases. It has also been observed that, in addition to genetic factors, there are numerous molecular mechanisms involved in these pathologies, such as excitotoxicity, mitochondrial disorders, alterations in axonal transport, oxidative stress, accumulation of misfolded proteins, and neuroinflammation. This pathology affects the motor neurons, the spinal cord, the cerebellum, and the brain, but recently, it has been shown that it also affects the visual system. This impact occurs not only at the level of the oculomotor system but also at the retinal level, which is why the retina is being proposed as a possible biomarker of this pathology. The current review discusses the main aspects mentioned above related to ALS, such as the main genes involved, the most important molecular mechanisms that affect this pathology, its ocular involvement, and the possible usefulness of the retina as a biomarker.
Probiotics in Medicine: A Long Debate

During the last years probiotics gained the attention of clinicians for their use in the prevention and treatment of multiple diseases. Probiotics main mechanisms of action include enhanced mucosal barrier function, direct antagonism with pathogens, inhibition of bacterial adherence and invasion capacity in the intestinal epithelium, boosting of the immune system and regulation of the central nervous system. It is accepted that there is a mutual communication between the gut microbiota and the liver, the so-called “microbiota-gut-liver axis” as well as a reciprocal communication between the intestinal microbiota and the central nervous system through the “microbiota-gut-brain axis. ” Moreover, recently the “gut-lung axis” in bacterial and viral infections is considerably discussed for bacterial and viral infections, as the intestinal microbiota amplifies the alveolar macrophage activity having a protective role in the host defense against pneumonia. The importance of the normal human intestinal microbiota is recognized in the preservation of health. Disease states such as, infections, autoimmune conditions, allergy and other may occur when the intestinal balance is disturbed. Probiotics seem to be a promising approach to prevent and even reduce the symptoms of such clinical states as an adjuvant therapy by preserving the balance of the normal intestinal microbiota and improving the immune system. The present review states globally all different disorders in which probiotics can be given. To date, Stronger data in favor of their clinical use are provided in the prevention of gastrointestinal disorders, antibiotic-associated diarrhea, allergy and respiratory infections. We hereby discuss the role of probiotics in the reduction of the respiratory infection symptoms and we focus on the possibility to use them as an adjuvant to the therapeutic approach of the pandemic COVID-19. Nevertheless, it is accepted by the scientific community that more clinical studies should be undertaken in large samples of diseased populations so that the assessment of their therapeutic potential provide us with strong evidence for their efficacy and safety in clinical use.
Stress, Anxiety, and Change in Alcohol Use During the COVID-19 Pandemic: Findings Among Adult Twin Pairs

The novel coronavirus (COVID-19) has impacted the lives of people worldwide since being declared a pandemic on March 11, 2020. Social restrictions aimed at flattening the curve may be associated with an increase in stress and anxiety, which may increase the use of alcohol as a coping mechanism. The objective of this study was to examine if stress and anxiety were associated with changes in alcohol use in a sample of adult twins. Twins allowed us to control for genetic and shared environmental factors that would confound the alcohol - mental health relationship. Twins (N = 3,971; 909 same-sex pairs) from the Washington State Twin Registry (WSTR) completed an online survey examining several health-related behaviors and outcomes and their self-reported changes due to COVID-19. About 14% of the respondents reported an increase in alcohol use. We found an association between both stress and anxiety and increased alcohol use, where twins with higher levels of stress and anxiety were more likely to report an increase in alcohol consumption. The associations were small and confounded by between-family factors and demographic characteristics. However, there was no significant difference in stress or anxiety levels between non-drinkers and those who reported no change in alcohol use. Our findings suggest that individuals’ mental health may be associated with changes in alcohol use during the COVID-19 pandemic.
High Altitude Is Beneficial for Antioxidant Components and Sweetness Accumulation of Rabbiteye Blueberry

To better understand the effect of growing location on the phytochemical compounds and sensory properties of blueberry (Vaccinium spp.), here we investigated rabbiteye blueberry ‘Brightwell’ (Vaccinium ashei cv. ‘Brightwell’) grown in 10 locations of China. Significant differences in terms of total soluble solids, titratable acidity, flavonoids, phenols, as well as proanthocyanidins and anthocyanins, were found in the fruits (berries) of blueberry plants among the different sampled locations. Furthermore, their sensory properties, which evaluated by the electronic tongue method, also significantly differed among the 10 locations. The content of flavonoids, phenols, proanthocyanidins, and anthocyanins all had significant correlations with sensory properties, except that of aftertaste-astringency. A key finding to emerge was that blueberry plants grown at high altitude locations harbored a high content of total soluble solids, flavonoids, phenols, proanthocyanidins, and anthocyanins along with high scores for the sweetness. These results suggested cultivating blueberry at high altitude can produce fruit that not only possess pronounced beneficial health effects but also good taste.
Reduction of T Lymphoma Cells and Immunological Invigoration in a Patient Concurrently Affected by Melanoma and Sezary Syndrome Treated With Nivolumab

Despite the recent availability of several new drugs in hemato-oncology, T-cell lymphomas are still incurable and PD-1 blockade could represent a therapeutic chance for selected patients affected by these malignancies, although further studies are required to understand the biological effects of anti-PD-1 mAbs on neoplastic T-cells and to identify biomarkers for predicting and/or monitoring patients’ response to therapy. Sezary Syndrome (SS) represents a rare and aggressive variant of cutaneous T cell lymphoma (CTCL) with a life expectancy of less than 5 years, characterized by the co-presence of neoplastic lymphocytes mainly in the blood, lymph nodes and skin. In this study we analyzed longitudinal blood samples and lesional skin biopsies of a patient concurrently affected by SS and melanoma who underwent 22 nivolumab administrations. In blood, we observed a progressive reduction of SS cell number and a raise in the percentage of normal CD4+ and CD8+ T cells and NK cells over total leukocytes. Eight weeks from the start of nivolumab, these immune cell subsets showed an increase of Ki67 proliferation index that positively correlated with their PD-1 expression. Conversely, SS cells displayed a strong reduction of Ki67 positivity despite their high PD-1 expression. On skin biopsies we observed a marked reduction of SS cells which were no more detectable at the end of therapy. We also found an increase in the percentage of normal CD4+ T cells with a concomitant decrease of that of CD8+ and CD4+ CD8+ T cells, two cell subsets that, however, acquired a cytotoxic phenotype. In summary, our study demonstrated that nivolumab marked reduced SS tumor burden and invigorated immune responses in our patient. Our data also suggest, for the first time, that Ki67 expression in circulating neoplastic and immune cell subsets, as well as an enrichment in T cells with a cytotoxic phenotype in lesional skin could be valuable markers to assess early on treatment SS patients’ response to PD-1 blockade, a therapeutic strategy under clinical investigation in CTCL (ClinicalTrials.gov NCT03385226, NCT04118868).