Miracle-dz/UniFAR-FTUs huggingface dataset:
Divergent Mechanisms Activating RAS and Small GTPases Through Post-translational Modification

RAS is a founding member of the RAS superfamily of GTPases. These small 21 kDa proteins function as molecular switches to initialize signaling cascades involved in various cellular processes, including gene expression, cell growth, and differentiation. RAS is activated by GTP loading and deactivated upon GTP hydrolysis to GDP. Guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs) accelerate GTP loading and hydrolysis, respectively. These accessory proteins play a fundamental role in regulating activities of RAS superfamily small GTPase via a conserved guanine binding (G)-domain, which consists of five G motifs. The Switch regions lie within or proximal to the G2 and G3 motifs, and undergo dynamic conformational changes between the GDP-bound “OFF” state and GTP-bound “ON” state. They play an important role in the recognition of regulatory factors (GEFs and GAPs) and effectors. The G4 and G5 motifs are the focus of the present work and lie outside Switch regions. These motifs are responsible for the recognition of the guanine moiety in GTP and GDP, and contain residues that undergo post-translational modifications that underlie new mechanisms of RAS regulation. Post-translational modification within the G4 and G5 motifs activates RAS by populating the GTP-bound “ON” state, either through enhancement of intrinsic guanine nucleotide exchange or impairing GAP-mediated down-regulation. Here, we provide a comprehensive review of post-translational modifications in the RAS G4 and G5 motifs, and describe the role of these modifications in RAS activation as well as potential applications for cancer therapy.
Phylogenomics With Hyb-Seq Unravels Korean Hosta Evolution

The genus Hosta (Agavoideae and Asparagaceae) is one of the most popular landscaping and ornamental plants native to temperate East Asia. Their popularity has led to extensive hybridization to develop various cultivars. However, their long history of hybridization, cultivation, and selection has brought about taxonomic confusion in the Hosta species delimitation along with their indistinguishable morphology. Here, we conducted the first broad phylogenetic analyses of Hosta species based on the most comprehensive genomic data set to date. To do so, we captured 246 nuclear gene sequences and plastomes from 55 accessions of Korean Hosta species using the Hyb-Seq method. As a result, this study provides the following novel and significant findings: (1) phylogenetic analyses of the captured sequences retrieved six species of Hosta in South Korea compared to five to eleven species based on the previous studies, (2) their phylogenetic relationships suggested that the large genome size was ancestral and the diversification of Korean Hosta species was accompanied by decreases in genome sizes, (3) comparison between nuclear genes and plastome revealed several introgressive hybridization events between Hosta species, and (4) divergence times estimated here showed that Hosta diverged 35.59 million years ago, while Korean Hosta species rapidly diversified during the late Miocene. Last, we explored whether these genomic data could be used to infer the origin of cultivars. In summary, this study provides the most comprehensive genomic resources to be used in phylogenetic, population, and conservation studies of Hosta, as well as for unraveling the origin of many cultivars.
Measuring Cerebrovascular Reactivity: Sixteen Avoidable Pitfalls

An increase in arterial PCO2 is the most common stressor used to increase cerebral blood flow for assessing cerebral vascular reactivity (CVR). That CO2 is readily obtained, inexpensive, easy to administer, and safe to inhale belies the difficulties in extracting scientifically and clinically relevant information from the resulting flow responses. Over the past two decades, we have studied more than 2,000 individuals, most with cervical and cerebral vascular pathology using CO2 as the vasoactive agent and blood oxygen-level-dependent magnetic resonance imaging signal as the flow surrogate. The ability to deliver different forms of precise hypercapnic stimuli enabled systematic exploration of the blood flow-related signal changes. We learned the effect on CVR of particular aspects of the stimulus such as the arterial partial pressure of oxygen, the baseline PCO2, and the magnitude, rate, and pattern of its change. Similarly, we learned to interpret aspects of the flow response such as its magnitude, and the speed and direction of change. Finally, we were able to test whether the response falls into a normal range. Here, we present a review of our accumulated insight as 16 “lessons learned. ” We hope many of these insights are sufficiently general to apply to a range of types of CO2-based vasoactive stimuli and perfusion metrics used for CVR.
Quantitative Analysis of UV-B Radiation Interception and Bioactive Compound Contents in Kale by Leaf Position According to Growth Progress

UV-B (280–315 nm) radiation has been used as an effective tool to improve bioactive compound contents in controlled environments, such as plant factories. However, plant structure changes with growth progress induce different positional distributions of UV-B radiation interception, which cause difficulty in accurately evaluating the effects of UV-B on biosynthesis of bioactive compounds. The objective of this study was to quantitatively analyze the positional distributions of UV-B radiation interception and bioactive compound contents of kales (Brassica oleracea L. var. acephala) with growth progress and their relationships. Short-term moderate UV-B levels did not affect the plant growth and photosynthetic parameters. Spatial UV-B radiation interception was analyzed quantitatively by using 3D-scanned plant models and ray-tracing simulations. As growth progressed, the differences in absorbed UV-B energy between leaf positions were more pronounced. The concentrations of total phenolic compound (TPC) and total flavonoid compound (TFC) were higher with more cumulative absorbed UV-B energy. The cumulative UV energy yields for TFC were highest for the upper leaves of the older plants, while those for TPC were highest in the middle leaves of the younger plants. Despite the same UV-B levels, the UV-B radiation interception and UV-B susceptibility in the plants varied with leaf position and growth stage, which induced the different biosynthesis of TFC and TPC. This attempt to quantify the relationship between UV-B radiation interception and bioactive compound contents will contribute to the estimation and production of bioactive compounds in plant factories.
Emotion and Psychophysiological Responses During Emotion–Eliciting Film Clips in an Eating Disorders Sample

Background: Greater vulnerability to negative emotions appears associated with the development and maintenance of eating disorders (EDs). A systematic review of psychophysiological studies using emotion-eliciting film clips reveals that there are no studies examining the effect of standardized validated film clips on psychophysiological response across a range of EDs. Methods: Using standardized validated film clips without ED-specific content, the present study examined self-reported emotions and psychophysiological responses of women with Binge-Eating Disorder (BED; n = 57), Anorexia Nervosa (AN; n = 16), Bulimia Nervosa (BN; n = 34), and Healthy Controls (HCs; n = 26) at Baseline, during Neutral, Sad, Happy, and Fear-inducing film clips, and at Recovery. Results: Throughout the protocol, the ED groups reported significantly greater sadness and anxiety than HCs. Additionally, the AN group reported more fear, the BED group more frustration, and the BED and BN groups more tension than HCs. Compared to HCs, the BED group reported stronger urges to binge throughout the protocol, whereas BN group reported stronger urges to binge relative to the HC group only at Baseline and Recovery. The BN and BED groups experienced decreased urges to binge during all film clips compared to Baseline. Respiratory Sinus Arrhythmia levels were significantly lower in the BED group compared to HCs and the BN group throughout the protocol. Discussion: Standardized validated film clips can be used to elicit expected self-reported emotion and skin conductance responses in ED groups, although individuals with EDs compared HCs report greater negative emotions. Interestingly, film clips appeared to reduce urges to binge in binge-eating groups.
Long-Term Pollen Monitoring in the Benelux: Evaluation of Allergenic Pollen Levels and Temporal Variations of Pollen Seasons

Airborne pollen is a major cause of allergic rhinitis, affecting between 10 and 30% of the population in Belgium, the Netherlands, and Luxembourg (Benelux). Allergenic pollen is produced by wind pollinating plants and released in relatively low to massive amounts. Current climate changes, in combination with increasing urbanization, are likely to affect the presence of airborne allergenic pollen with respect to exposure intensity, timing as well as duration. Detailed analysis of long-term temporal trends at supranational scale may provide more comprehensive insight into these phenomena. To this end, the Spearman correlation was used to statistically compare the temporal trends in airborne pollen concentration monitored at the aerobiological stations which gathered the longest time-series (30–44 years) in the Benelux with a focus on the allergenic pollen taxa: Alnus, Corylus, Betula, Fraxinus, Quercus, Platanus, Poaceae, and Artemisia. Most arboreal species showed an overall trend toward an increase in the annual pollen integral and peak values and an overall trend toward an earlier start and end of the pollen season, which for Betula resulted in a significant decrease in season length. For the herbaceous species (Poaceae and Artemisia), the annual pollen integral and peak values showed a decreasing trend. The season timing of Poaceae showed a trend toward earlier starts and longer seasons in all locations. In all, these results show that temporal variations in pollen levels almost always follow a common trend in the Benelux, suggesting a similar force of climate change-driven factors, especially for Betula where a clear positive correlation was found between changes in temperature and pollen release over time. However, some trends were more local-specific indicating the influence of other environmental factors, e.g., the increasing urbanization in the surroundings of these monitoring locations. The dynamics in the observed trends can impact allergic patients by increasing the severity of symptoms, upsetting the habit of timing of the season, complicating diagnosis due to overlapping pollen seasons and the emergence of new symptoms due allergens that were weak at first.
Two and Three-Dimensional Echocardiography in Primary Mitral Regurgitation: Practical Hints to Optimize the Surgical Planning

Primary mitral regurgitation (MR) is the second most common valvular disease, characterized by a high burden in terms of quality of life, morbidity, and mortality. Surgical treatment is considered the best therapeutic strategy for patients with severe MR, especially if they are symptomatic. However, pre-operative echocardiographic evaluation is an essential step not only for surgical candidate selection but also to avoid post-operative complications. Therefore, a strong collaboration between cardiologists and cardiac surgeons is fundamental in this setting. A meticulous pre-operative echocardiographic exam, both with transthoracic or transesophageal echocardiography, followed by a precise report containing anatomical information and parameters should always be performed to optimize surgical planning. Moreover, intraoperative transesophageal evaluation is often required by cardiac surgeons as it may offer additive important information with different hemodynamic conditions. Three-dimensional echocardiography has recently gained higher consideration and availability for the evaluation of MR, providing more insights into mitral valve geometry and MR mechanism. This review paper aims to realize a practical overview on the main use of basic and advanced echocardiography in MR surgical planning and to provide a precise checklist with reference parameters to follow when performing pre-operative echocardiographic exam, in order to aid cardiologists to provide a complete echocardiographic evaluation for MR operation planning from clinical and surgical point-of-view.
The Effect of Radiation on the Gut Bacteriome of Aedes albopictus

The sterile insect technique (SIT) has been developed as a component of area-wide integrated pest management approaches to control the populations of Aedes albopictus, a mosquito vector capable of transmission of dengue, Zika and chikungunya viruses. One of the key factors for the success of SIT is the requirement of high biological quality sterile males, which upon their release would be able to compete with wild males for matings with wild females in the field. In insects, gut bacteriome have played a catalytic role during evolution significantly affecting several aspects of their biology and ecology. Given the importance of gut-associated bacterial species for the overall ecological fitness and biological quality of their hosts, it is of interest to understand the effects of radiation on the gut-associated bacteriome of Ae. albopictus. In this study, the effect of radiation on the composition and density levels of the gut-associated bacterial species at the pupal stage as well as at 1- and 4-day-old males and females was studied using 16S rRNA gene-based next generation sequencing (NGS) and quantitative PCR (qPCR) approaches. Age, diet, sex, and radiation were shown to affect the gut-associated bacterial communities, with age having the highest impact triggering significant changes on bacterial diversity and clustering among pupae, 1- and 4-day-old adult samples. qPCR analysis revealed that the relative density levels of Aeromonas are higher in male samples compared to all other samples and that the irradiation triggers an increase in the density levels of both Aeromonas and Elizabethkingia in the mosquito gut at specific stages. Our results suggest that Aeromonas could potentially be used as probiotics to enhance protandry and sex separation in support of SIT applications against Ae. albopictus, while the functional role of Elizabethkingia in respect to oxidative stress and damage in irradiated mosquitoes needs further investigation.
Biocomputational Architecture Based on Particle Physics

Domestic greywater produced via household chores has a major contribution to environmental pollution and is also the best-untapped energy source. Since the past decade, in the different fields, enormous efforts have been made to reach the bio-energy from bio-waste. These efforts consist of a wide range of thermochemical, bio-chemical, and microbial fuel cells; etc. however, all these efforts are in their infancy. They have high cost and are efficient on a large-scale; furthermore, these efforts used a non-intelligent process that has led to lack of development in this type of review. This ongoing research presents the smart design process that leads to hybrid energy via the intersection of computation, wastewater, and microorganisms and aims to introduce the novel bio-computational machine based on particle Physics. Therefore, we will investigate the mixture of the microbial fuel cells, specifically “Spirulina” micro-algae, and household chores greywater. In the computational framework, we propose high-precise fluid simulation with the advantage of particle position and dynamic physics for the conversion of the mixture of “Spirulina medium,” and household chore greywater makes energy control possible through flow, and management of the type of solution mix, by transferring data from the modules to the digital environment. Finally, these datasets simulate behavior based on the physical properties of each particle. The procedure works in a parametric computer-aided design (CAD) environment and through Grasshopper within Rhinoceros Software by syncing bio-computational machine to the digital environment. The solenoid valve and fluid flow controller applied between the nutritious tank and energy conversion tank measure nutritional consumption and sends it to the digital environment numerically with an Arduino-Uno board kit. These batch numerical signals are stored in our local database then are combined with the particle physics engine and simulate the material behavior; also, they provide the ability to control our bio-computational machine digitally.
Influence of Loss Aversion and Income Effect on Consumer Food Choice for Food Safety and Quality Labels

Food safety and food quality are two closely related aspects of the food management system. The difference between the two is that one keeps consumers safe while the other keeps consumers satisfied. This study examined the differences in how consumers value food safety and food quality with a focus on the influence of loss aversion on one’s psychological level and of income effect on one’s socio-demographic level. Our findings indicate that loss aversion and income effect significantly influence the way consumers value food safety vs. quality labels when considering potential health risks and food price. High risk-averse and low-income consumers with strong loss aversion and a weak income effect show a higher demand for food safety labels as a way to ensure easy access to safety indications. Low risk-averse and high-income consumers with weak loss aversion and a strong income effect show a higher demand for food quality labels because they hope to gain more health benefits from high-quality food at good prices. This study provides insights that will assist public authorities and food industry in balancing food safety control and food quality improvement in order to meet the heterogeneous market demand changing alongside the transition of China’s food consumption and production.
Maternal High-Fat Diet Exposure During Gestation and Lactation Affects Intestinal Development in Suckling Rats

Maternal health and diet influence metabolic status and play a crucial role in the development of metabolic function in offspring and their susceptibility to metabolic diseases in adulthood. The pathogenesis of various metabolic disorders is often associated with impairment in intestinal structure and function. Thus, the aim of the current study was to determine the effects of maternal exposure to a high fat diet (HFD), during gestation and lactation, on small intestinal growth and maturation in rat pups at 21 days old. Female, Wistar Han rats were fed either a breeding diet (BD) or high fat diet (HFD), from mating until the 21st day of lactation. Maternal HFD exposure increased body weight, BMI and adiposity. Compared to the maternal BD, HFD exposure influenced small intestine histomorphometry in a segment-dependent manner, changed the activity of brush border enzymes and had an impact on intestinal contractility via changes in cholinergic signaling. Moreover, offspring from the maternal HFD group had upregulated mRNA expression of cyclooxygenase (COX)-2, which plays a role in the inflammatory process. These results suggest that maternal HFD exposure, during gestation and lactation, programs the intestinal development of the offspring in a direction toward obesity as observed changes are also commonly reported in models of diet-induced obesity. The results also highlight the importance of maternal diet preferences in the process of developmental programming of metabolic diseases.
The Clinical Characteristics of ARDS in Children With Hematological Neoplasms

In order to explore the clinical characteristics of pediatric patients admitted to the pediatric intensive care unit (PICU) who suffered from hematological neoplasms complicated with acute respiratory distress syndrome (ARDS), we retrospectively analyzed 45 ARDS children with hematological neoplasms who were admitted to the PICU of Shanghai Children's Medical Center from January 1, 2014, to December 31, 2020. The 45 children were divided into a survival group and a non-survival group, a pulmonary ARDS group and an exogenous pulmonary ARDS group, and an agranulocytosis group and a non-agranulocytosis group, for statistical analysis. The main clinical manifestations were fever, cough, progressive dyspnea, and hypoxemia; 55.6% (25/45) of the children had multiple organ dysfunction syndrome (MODS). The overall mortality rate was 55.6% (25/45). The vasoactive inotropic score (VIS), pediatric critical illness scoring (PCIS), average fluid volume in the first 3 days and the first 7 days, and the incidence of MODS in the non-survival group were all significantly higher than those in the survival group (P < 0.05). However, total length of mechanical ventilation and length of hospital stay and PICU days in the non-survival group were significantly lower than those in the survival group (P < 0.05). The PCIS (OR = 0.832, P = 0.004) and the average fluid volume in the first 3 days (OR = 1.092, P = 0.025) were independent risk factors for predicting death. Children with exogenous pulmonary ARDS were more likely to have MODS than pulmonary ARDS (P < 0.05). The mean values of VIS, C-reactive protein (CRP), and procalcitonin (PCT) in children with exogenous pulmonary ARDS were also higher (P < 0.05). After multivariate analysis, PCT was independently related to exogenous pulmonary ARDS. The total length of hospital stay, peak inspiratory pressure (PIP), VIS, CRP, and PCT in the agranulocytosis group were significantly higher than those in the non-agranulocytosis group (P < 0.05). Last, CRP and PIP were independently related to agranulocytosis. In conclusion, children with hematological neoplasms complicated with ARDS had a high overall mortality and poor prognosis. Children complicated with MODS, positive fluid balance, and high VIS and PCIS scores were positively correlated with mortality. In particular, PCIS score and average fluid volume in the first 3 days were independent risk factors for predicting death. Children with exogenous pulmonary ARDS and children with agranulocytosis were in a severely infected status and more critically ill.