Miracle-dz/UniFAR-FTUs huggingface dataset:
Uncovering the Role of Metabolism in Oomycete–Host Interactions Using Genome-Scale Metabolic Models

Metabolism is the set of biochemical reactions of an organism that enables it to assimilate nutrients from its environment and to generate building blocks for growth and proliferation. It forms a complex network that is intertwined with the many molecular and cellular processes that take place within cells. Systems biology aims to capture the complexity of cells, organisms, or communities by reconstructing models based on information gathered by high-throughput analyses (omics data) and prior knowledge. One type of model is a genome-scale metabolic model (GEM) that allows studying the distributions of metabolic fluxes, i.e., the “mass-flow” through the network of biochemical reactions. GEMs are nowadays widely applied and have been reconstructed for various microbial pathogens, either in a free-living state or in interaction with their hosts, with the aim to gain insight into mechanisms of pathogenicity. In this review, we first introduce the principles of systems biology and GEMs. We then describe how metabolic modeling can contribute to unraveling microbial pathogenesis and host–pathogen interactions, with a specific focus on oomycete plant pathogens and in particular Phytophthora infestans. Subsequently, we review achievements obtained so far and identify and discuss potential pitfalls of current models. Finally, we propose a workflow for reconstructing high-quality GEMs and elaborate on the resources needed to advance a system biology approach aimed at untangling the intimate interactions between plants and pathogens.
Treating Aggression and Self-destructive Behaviors by Stimulating the Nucleus Accumbens: A Case Series

Self-destructive and aggressive behaviors can have a significant impact on the quality of life of affected individuals and their carrers. While deep brain stimulation (DBS) has been applied to the treatment of self-destructive and aggressive behaviors in isolated cases, clinical data on this treatment modality are still lacking. We therefore assessed responses to treatment with bilateral DBS of the nucleus accumbens in six patients with severe self-destructive and aggressive behaviors. Three patients had Tourette syndrome and three had other underlying predispositions including obsessive compulsive disorder, cerebral palsy, encephalitis, and epilepsy. Patients were followed up for between 2 and 7 years, and patients were assessed using the Modified Overt Aggression Scale (six patients) and the Buss-Perry Aggression Questionnaire (three patients able to complete the questionnaire on their own). DBS reduced self-destructive and aggressive behaviors by 30–100% and by an average of 74.5%. Patients with Tourette syndrome responded better to DBS and improved by 27.3% according to the Buss-Perry Aggression Questionnaire. These results suggest that nuclei accumbens stimulation may be an effective treatment for aggressive and self-destructive behaviors regardless of etiology.
Numerical simulation of lithium granule injection in tokamak edge plasma

To understand how a Li pellet affects the background plasma, the edge plasma code SOLPS combined with a neutral-gas-shield ablation model has been employed to simulate the transport of Li species in the edge plasma during Li pellet injections in a typical EAST H-mode plasma. The simulation results show that a Li pellet 0.5 mm with velocity ∼100 m/s can penetrate the separatrix, and that the electron temperature drops quickly where the pellet passes by while the electron density needs a longer time to respond. The plasma pressure in the pedestal region grows significantly with the pellet size; the pressure gradient changes even more drastically. This work indicates that without accumulative contributions, a pellet 0.7 mm or above in diameter at an injection velocity of 100 m/s is likely to provide a pressure perturbation enough to trigger ELMs in the typical EAST H-mode plasmas used in this work.
Lipid characteristics and tocopherol content of the oils of native avocado cultivars grown in Indonesia

ABSTRACT The oils obtained from three Indonesian avocado (Persea americana) cultivars namely Merah bundar, Ijo bundar and Ijo panjang, were compared to the oils obtained from imported Fuerte and Shepard avocado varieties in terms of lipid characteristics and tocopherol content. The oils of all avocado varieties existed in a semisolid form, except that of the Fuerte variety. Free fatty acids and peroxide levels in the oils obtained from locally grown avocado were lower than the levels in the oils obtained from imported avocados, implying that local avocado oils have a better oxidative stability. Interestingly, the tocopherol (alpha, beta, gamma and delta) content of local avocado oils was also much higher than that of imported avocado oils. Meanwhile, differences in the FTIR spectrum of avocado oils were found at frequencies of 1034 and 968 cm−1. There were also some differences in the fatty acid and triacylglycerol composition of avocado oils. Due to these differences, the physicochemical characteristics and the solidification and thermal profiles of the oils obtained from local avocado cultivars were completely different from those of the imported avocado varieties (Fuerte and Shepard).
Effect of Calcium and Manganese Supplementation on Heat Resistance of Spores of Bacillus Species Associated With Food Poisoning, Spoilage, and Fermentation

Bacterial spores often survive thermal processing used in the food industry, while heat treatment leads not only to a decrease in the nutritional and organoleptic properties of foods, but also to a delay in fermentation of fermented foods. Selective reduction of undesirable spores without such impediments is an ongoing challenge for food scientists. Thus, increased knowledge of the spore-forming bacteria is required to control them. In this study, the heat resistance results (D100°C) of the spores of four Bacillus species were determined and compared to previous literature, and found that B. cereus has significantly lower heat resistance than the other Bacillus species, B. coagulans, B. subtilis, and B. licheniformis. Using the spores of these strains, this study also evaluated the effects of single and combined supplementation of calcium (0.00–2.00 mM) and manganese (0.00–0.50 mM) on heat resistance (D100°C). The results revealed that the spores of B. licheniformis and B. cereus displayed the smallest heat resistance when sporulated on media rich in calcium. Conversely, B. coagulans spores and B. subtilis spores exhibited the greatest heat resistance when sporulated under calcium-rich conditions. The opposite results (stronger heat resistance for B. licheniformis spores and B. cereus spores, and smaller heat resistance for B. coagulans spores and B. subtilis spores) were obtained when the spores were formed on media poor in the minerals (particularly calcium). Based on the results, the Bacillus species were divided into two groups: B. licheniformis and B. cereus; and B. coagulans and B. subtilis. The study provides valuable insight to selectively reduce spores of undesirable Bacillus species in the food industry.
Multi-Domain Touchscreen-Based Cognitive Assessment of C57BL/6J Female Mice Shows Whole-Body Exposure to 56Fe Particle Space Radiation in Maturity Improves Discrimination Learning Yet Impairs Stimulus-Response Rule-Based Habit Learning

Astronauts during interplanetary missions will be exposed to galactic cosmic radiation, including charged particles like 56Fe. Most preclinical studies with mature, “astronaut-aged” rodents suggest space radiation diminishes performance in classical hippocampal- and prefrontal cortex-dependent tasks. However, a rodent cognitive touchscreen battery unexpectedly revealed 56Fe radiation improves the performance of C57BL/6J male mice in a hippocampal-dependent task (discrimination learning) without changing performance in a striatal-dependent task (rule-based learning). As there are conflicting results on whether the female rodent brain is preferentially injured by or resistant to charged particle exposure, and as the proportion of female vs. male astronauts is increasing, further study on how charged particles influence the touchscreen cognitive performance of female mice is warranted. We hypothesized that, similar to mature male mice, mature female C57BL/6J mice exposed to fractionated whole-body 56Fe irradiation (3 × 6.7cGy 56Fe over 5 days, 600 MeV/n) would improve performance vs. Sham conditions in touchscreen tasks relevant to hippocampal and prefrontal cortical function [e.g., location discrimination reversal (LDR) and extinction, respectively]. In LDR, 56Fe female mice more accurately discriminated two discrete conditioned stimuli relative to Sham mice, suggesting improved hippocampal function. However, 56Fe and Sham female mice acquired a new simple stimulus-response behavior and extinguished this acquired behavior at similar rates, suggesting similar prefrontal cortical function. Based on prior work on multiple memory systems, we next tested whether improved hippocampal-dependent function (discrimination learning) came at the expense of striatal stimulus-response rule-based habit learning (visuomotor conditional learning). Interestingly, 56Fe female mice took more days to reach criteria in this striatal-dependent rule-based test relative to Sham mice. Together, our data support the idea of competition between memory systems, as an 56Fe-induced decrease in striatal-based learning is associated with enhanced hippocampal-based learning. These data emphasize the power of using a touchscreen-based battery to advance our understanding of the effects of space radiation on mission critical cognitive function in females, and underscore the importance of preclinical space radiation risk studies measuring multiple cognitive processes, thereby preventing NASA’s risk assessments from being based on a single cognitive domain.
Left Ventricular Longitudinal Dyssynchrony by CMR Feature Tracking Is Related to Adverse Prognosis in Advanced Arrhythmogenic Cardiomyopathy

Objectives: Left ventricular (LV) involvement has been associated with unfavorable prognosis in arrhythmogenic cardiomyopathy (ACM). We aim to evaluate LV mechanics by cardiovascular magnetic resonance-feature tracking (CMR-FT) in ACM patients with right ventricular (RV) dysfunction. Methods: We retrospectively recruited ACM patients diagnosed according to the revised Task Force Criteria (rTFC) from January 2015 to July 2017. All patients underwent CMR examinations and collections of clinical, electrocardiographic data. The strain and dyssynchrony parameters of LV and RV were analyzed. These patients were followed, and primary study outcome was defined as a composite of cardiovascular events (arrhythmic events and heart transplantation), secondary study outcome included arrhythmic events. Results: Eighty-nine ACM patients (40.40 ± 13.98 years, 67.42% male) were included. LV and RV ejection fractions were 49.12 ± 12.02% and 22.28 ± 10.11%, respectively. During a median (IQR) follow-up for 18.20 (11.60-30.04) months, 30 patients experienced cardiovascular events which included 22 patients who experienced arrhythmic events. Patients with cardiovascular events had impaired LV global longitudinal strain (−10.82 ± 2.77 vs. −12.61 ± 3.18%, p = 0.010), impaired LV global circumferential strain (−11.81 ± 2.40 vs. −13.04 ± 2.83%, p = 0.044), and greater LV longitudinal dyssynchrony (LVLD) (80.98 ± 30.98 vs. 64.23 ± 25.51 ms, p = 0.012) than those without. After adjusting for age, sex, and other confounding factors, LVLD ≥89.15 ms was an independent risk factor for cardiovascular events (HR: 4.50, 95% CI: 1.94 to 10.42; p = 0.001) and for arrhythmic events (HR: 4.79, 95% CI: 1.74 to 13.20; p = 0.003). Conclusions: LVLD by CMR-FT was an independent risk factor for cardiovascular and arrhythmic events in ACM patients in advanced stage, which could provide prognostic value for this subtype.
On the Species Delimitation of the Maddenia Group of Prunus (Rosaceae): Evidence From Plastome and Nuclear Sequences and Morphology

The recognition, identification, and differentiation of closely related plant species present significant and notorious challenges to taxonomists. The Maddenia group of Prunus, which comprises four to seven species, is an example of a group in which species delimitation and phylogenetic reconstruction have been difficult, due to the lack of clear morphological distinctions, limited sampling, and low informativeness of molecular evidence. Thus, the precise number of species in the group and the relationships among them remain unclear. Here, we used genome skimming to generate the DNA sequence data for 22 samples, including 17 Maddenia individuals and five outgroups in Amygdaloideae of Rosaceae, from which we assembled the plastome and 446 single-copy nuclear (SCN) genes for each sample. The phylogenetic relationships of the Maddenia group were then reconstructed using both concatenated and coalescent-based methods. We also identified eight highly variable regions and detected simple sequence repeats (SSRs) and repeat sequences in the Maddenia species plastomes. The phylogenetic analysis based on the complete plastomes strongly supported three main subclades in the Maddenia group of Prunus, while five subclades were recognized based on the nuclear tree. The phylogenetic network analysis detected six hybridization events. Integrating the nuclear and morphological evidence, we proposed to recognize five species within the Maddenia group, i.e., Prunus fujianensis, P. himalayana, P. gongshanensis, P. hypoleuca, and P. hypoxantha. Within this group, the first three species are well-supported, while the gene flow occurring throughout the Maddenia group seems to be especially frequent between P. hypoleuca and P. hypoxantha, eroding the barrier between them. The phylogenetic trees based on eight concatenated hypervariable regions had a similar topology with the complete plastomes, showing their potential as molecular markers and effective barcodes for further phylogeographic studies on Maddenia.
Clinical Implication of Caloric and Video Head Impulse Tests for Patients With Enlarged Vestibular Aqueduct Presenting With Vertigo

Background: By examining the clinical features and results of video head impulse test (vHIT) and caloric tests in patients with enlarged vestibular aqueduct (EVA) presenting with vertigo, we aimed to investigate the function of angular vestibulo-ocular reflex (VOR) and its clinical implications. Methods: Nine patients with EVA manifesting with vertigo were enrolled. The medical history, audiological examination, imaging, and the results of the caloric test and the vHIT were analyzed. Results: Of the nine patients with EVA (eight bilateral and one unilateral case), five were pediatric cases. All 17 ears exhibited sensorineural hearing loss (SNHL). Enlarged vestibular aqueduct patients can present with recurrent (seven cases) or single (two cases) vertigo attack, trauma-induced (two cases), or spontaneous (seven cases) vertigo. Diminished caloric responses were observed in 77.8% (7/9) of the patients (four cases unilaterally and three bilaterally), while unilateral abnormal vHIT results in 11.1% (1/9) patients. Abnormal caloric and normal horizontal vHIT responses were found in 66.7% (6/9) of EVA patients. Conclusions: Vestibular manifestations in EVA are diverse. Enlarged vestibular aqueduct patients with vertigo can present with a reduced caloric response and normal horizontal vHIT, and this pattern of angular VOR impairment was also found in other hydropic ear diseases.
Children’s Motivation to Learn at Home During the COVID-19 Pandemic: Insights From Indian Parents

The COVID-19 pandemic has forced millions children worldwide to learn at home. Recent reports showed that this had a negative impact on children’s motivation to learn. The current study investigated what factors were associated with a child’s motivation during the pandemic and how parents motivated their children to learn at home. A total of 1,041 parents from India filled out a close-ended survey to help shed light on the issues. The results confirmed that children in India were significantly less motivated to learn during (vs before) the pandemic and revealed that a child’s motivation to learn at home was associated with multiple factors, such as household income, parents’ employment status, child’s academic achievement, and parent’s enjoyment in homeschooling. In contrast, the availability and usage of various technological resources bore no relation to a child’s motivation. Finally, the current data showed that Indian parents most frequently used TV time, words of encouragement, and play/game time as motivators; the least popular motivators were money, new toys, and physical punishment. Exploratory analyses showed that a child’s motivation to learn tended to be lower when parents used more physical punishment to “motivate” their children. These findings were discussed in relation to public/education policies.
Microbiota–Gut–Brain Axis and Epilepsy: A Review on Mechanisms and Potential Therapeutics

The gut–brain axis refers to the bidirectional communication between the gut and brain, and regulates intestinal homeostasis and the central nervous system via neural networks and neuroendocrine, immune, and inflammatory pathways. The development of sequencing technology has evidenced the key regulatory role of the gut microbiota in several neurological disorders, including Parkinson’s disease, Alzheimer’s disease, and multiple sclerosis. Epilepsy is a complex disease with multiple risk factors that affect more than 50 million people worldwide; nearly 30% of patients with epilepsy cannot be controlled with drugs. Interestingly, patients with inflammatory bowel disease are more susceptible to epilepsy, and a ketogenic diet is an effective treatment for patients with intractable epilepsy. Based on these clinical facts, the role of the microbiome and the gut–brain axis in epilepsy cannot be ignored. In this review, we discuss the relationship between the gut microbiota and epilepsy, summarize the possible pathogenic mechanisms of epilepsy from the perspective of the microbiota gut–brain axis, and discuss novel therapies targeting the gut microbiota. A better understanding of the role of the microbiota in the gut–brain axis, especially the intestinal one, would help investigate the mechanism, diagnosis, prognosis evaluation, and treatment of intractable epilepsy.
Music in Quarantine: Connections Between Changes in Lifestyle, Psychological States, and Musical Behaviors During COVID-19 Pandemic

Music is not only the art of organized sound but also a compound of social interaction among people, built upon social and environmental foundations. Since the beginning of the COVID-19 outbreak, containment measures such as shelter-in-place, lockdown, social distancing, and self-quarantine have severely impacted the foundation of human society, resulting in a drastic change in our everyday experience. In this paper, the relationships between musical behavior, lifestyle, and psychological states during the shelter-in-place period of the COVID-19 pandemic are investigated. An online survey on musical experience, lifestyle changes, stress level, musical behaviors, media usage, and environmental sound perception was conducted. The survey was conducted in early June 2020. Responses from 620 people in 24 countries were collected, with the large proportion of the responses coming from the U.S. (55.5%) and India (21.4%). Structural equation modeling (SEM) analysis revealed causal relationships between lifestyle, stress, and music behaviors. Elements such as stress-level change, work risk, and staying home contribute to changes in musical experiences, such as moderating emotion with music, feeling emotional with music, and being more attentive to music. Stress-level change was correlated with work risk and income change, and people who started living with others due to the outbreak, especially with their children, indicated less change in stress level. People with more stress-level change tended to use music more purposefully for their mental well-being, such as to moderate emotions, to influence mood, and to relax. In addition, people with more stress-level change tend to be more annoyed by neighbors' noise. Housing type was not directly associated with annoyance; however, attention to environmental sounds decreased when the housing type was smaller. Attention to environmental and musical sounds and the emotional responses to them are highly inter-correlated. Multi-group SEM based on musicians showed that the causal relationship structure for professional musicians differs from that of less-experienced musicians. For professional musicians, staying at home was the only component that caused all musical behavior changes; stress did not cause musical behavior changes. Regarding Internet use, listening to music via YouTube and streaming was preferred over TV and radio, especially among less-experienced musicians, while participation in the online music community was preferred by more advanced musicians. This work suggests that social, environmental, and personal factors and limitations influence the changes in our musical behavior, perception of sonic experience, and emotional recognition, and that people actively accommodated the unusual pandemic situations using music and Internet technologies.
Impact of Synchronous and Asynchronous Settings of Online Teaching and Learning in Higher Education on Students’ Learning Experience During COVID-19

The sudden impact of the COVID-19 pandemic challenged universities to provide students with online teaching and learning settings that were both immediately applicable and supportive of quality learning. This resulted in a broad variety of synchronous and asynchronous online settings of teaching and learning. While some courses balanced both kinds, others offered either predominantly synchronous or asynchronous teaching and learning. In a survey study with students (N=3,056) and teachers (N=396) from a large German university, we explored whether a predominance of synchronous or asynchronous teaching and learning settings in higher education was associated with certain student experiences and outcomes. Additionally, we examined how well these two types of teaching and learning settings support students’ basic psychological needs for autonomy, competence, and relatedness proposed by self-determination theory (SDT). Data were collected after the first online semester due to the COVID-19 pandemic. The results imply that from the students’ perspective, the teaching methods involved in the two settings of teaching and learning differ with regard to their potential to support social interaction and to support basic psychological needs as proposed by SDT. Students who studied mostly in synchronous settings reported more peer-centered activities such as feedback in comparison to students in mostly asynchronous settings. In contrast, teachers perceived fewer differences between teaching methods in synchronous and asynchronous settings, especially regarding feedback activities. Further, students in mostly synchronous settings reported greater support of their basic psychological needs for competence support and relatedness as well as a greater overall satisfaction with the online term compared to students in mostly asynchronous settings. Across all students, greater fulfillment of psychological needs and higher technology acceptance coincided with outcomes that are more favorable. Implications for the post-pandemic classroom are drawn.