Miracle-dz/UniFAR-FTUs huggingface dataset:
A redox-active switch in fructosamine-3-kinases expands the regulatory repertoire of the protein kinase superfamily

Evolutionarily conserved cysteine residues mediate the sensitivity of the metabolic kinase FN3K to shifts in redox status. Kinase regulation conserved under stress Oxidative stress is necessary for normal cellular function and tissue physiology but can also be pathological, and its effects are mediated in part through functional modification of various proteins. Shrestha et al. and Byrne et al. found that the oxidation of kinases at active site–adjacent cysteine residues, which were conserved across the eukaryotic kinome, regulated cell metabolism and mitosis. Shrestha et al. found that conserved cysteine residues within the diabetes-associated metabolic kinase FN3K acted as a toggle switch upon oxidation, promoting its functional oligomerization and consequently altering cellular redox status. Byrne et al. found that oxidation of mitotic kinases in human cells and yeast suppressed kinase catalytic activity and, in yeast, impaired cellular division. Exploring the effect of chronic oxidative stress on kinase function and how that may be spatiotemporally regulated may enable the development of new targeted therapeutics. Aberrant regulation of metabolic kinases by altered redox homeostasis substantially contributes to aging and various diseases, such as diabetes. We found that the catalytic activity of a conserved family of fructosamine-3-kinases (FN3Ks), which are evolutionarily related to eukaryotic protein kinases, is regulated by redox-sensitive cysteine residues in the kinase domain. The crystal structure of the FN3K homolog from Arabidopsis thaliana revealed that it forms an unexpected strand-exchange dimer in which the ATP-binding P-loop and adjoining β strands are swapped between two chains in the dimer. This dimeric configuration is characterized by strained interchain disulfide bonds that stabilize the P-loop in an extended conformation. Mutational analysis and solution studies confirmed that the strained disulfides function as redox “switches” to reversibly regulate the activity and dimerization of FN3K. Human FN3K, which contains an equivalent P-loop Cys, was also redox sensitive, whereas ancestral bacterial FN3K homologs, which lack a P-loop Cys, were not. Furthermore, CRISPR-mediated knockout of FN3K in human liver cancer cells altered the abundance of redox metabolites, including an increase in glutathione. We propose that redox regulation evolved in FN3K homologs in response to changing cellular redox conditions. Our findings provide insights into the origin and evolution of redox regulation in the protein kinase superfamily and may open new avenues for targeting human FN3K in diabetic complications.
Fractal analysis of concurrently prepared latex rubber casts of the bronchial and vascular systems of the human lung

Fractal geometry (FG) is a branch of mathematics that instructively characterizes structural complexity. Branched structures are ubiquitous in both the physical and the biological realms. Fractility has therefore been termed nature's design. The fractal properties of the bronchial (airway) system, the pulmonary artery and the pulmonary vein of the human lung generates large respiratory surface area that is crammed in the lung. Also, it permits the inhaled air to intimately approximate the pulmonary capillary blood across a very thin blood–gas barrier through which gas exchange to occur by diffusion. Here, the bronchial (airway) and vascular systems were simultaneously cast with latex rubber. After corrosion, the bronchial and vascular system casts were physically separated and cleared to expose the branches. The morphogenetic (Weibel's) ordering method was used to categorize the branches on which the diameters and the lengths, as well as the angles of bifurcation, were measured. The fractal dimensions (DF) were determined by plotting the total branch measurements against the mean branch diameters on double logarithmic coordinates (axes). The diameter-determined DF values were 2.714 for the bronchial system, 2.882 for the pulmonary artery and 2.334 for the pulmonary vein while the respective values from lengths were 3.098, 3.916 and 4.041. The diameters yielded DF values that were consistent with the properties of fractal structures (i.e. self-similarity and space-filling). The data obtained here compellingly suggest that the design of the bronchial system, the pulmonary artery and the pulmonary vein of the human lung functionally comply with the Hess–Murray law or ‘the principle of minimum work’.
Grand Challenges for Catalytic Remediation in Environmental and Energy Applications Toward a Cleaner and Sustainable Future

This article presents and discusses several hot topics and current trends for Catalytic Remediation in processes of significant environmental and energy importance. These topics seem to have the potentiality to guide future endeavors and synergistic interactions of several scientific disciplines, not limited to the chemists' and chemical engineers' communities, toward a common goal of great importance that is “Toward a cleaner (green) and sustainable future. ” Under this context, the following main topics and grand challenges are addressed here: (i) Further in-depth understanding and fine-tuning surface chemistry, catalytic activity, promotion, and stability, (ii) Current Advances and future perspectives in catalytic remediation of mobile and stationary sources' emissions (elimination of NOx, N2O, VOCs, CO, soot, etc.)–“Emissions Control Catalysis,” (iii) Clean energy production related catalytic reactions – H2 production and purification, (iv) Catalytic CO2 hydrogenation (CO2 utilization/recycling), (v) Photo-electro-Catalysis: Managing the effects of co-existence and mixtures of multiple pollutants in realistic conditions; understanding the interfacial reaction mechanism between reactants and photocatalysts; selectivity enhancement and intermediates/byproducts inhibition; development of catalysts with abundant and stable electrochemical active sites; precise identification of the time-resolved reaction information at the interface. Several sub-topics between them are also highlighted.
Contrasting evolutionary responses in two co-distributed species of Galaxias (Pisces, Galaxiidae) in a river from the glaciated range in Southern Chile

Life-history traits are among the most important factors affecting population abundance and genetic diversity of species. Here, we analysed the genetic patterns of two Galaxias species with different life-history traits to investigate how these biological differences impacted their evolution in the Valdivia River basin, Southern Chile. We analysed mitochondrial DNA (mtDNA) sequences from 225 individuals of Galaxias maculatus and 136 of G. platei to compare patterns of genetic diversity, structure and demographic growth across the basin. Galaxias maculatus presented higher genetic diversity and higher genetic structure than G. platei. Demographic analyses showed G. maculatus kept a higher population size over time, with a signal of demographic expansion in the last 250 kyr. Whereas Galaxias platei, exhibited lower, but constant population size over time. Furthermore, haplotype networks revealed higher lineage diversity in G. maculatus with a tendency to occupy different areas of the basin. Coalescent simulations ruled out that genetic differences between species could be explained by stochastic processes (genetic drift), suggesting species-specific biological differences as responsible for the observed genetic differences. We discuss how differences in life-history traits and past glaciations interact to shape the evolutionary history of the two Galaxias species.
Predictors of Health-Related Quality of Life and Influencing Factors for COVID-19 Patients, a Follow-Up at One Month

Objective To survey the health-related quality of life (HRQoL) and its influencing factors among patients with COVID-19 in their first medical follow up. Methods All patients diagnosed with COVID-19 were discharged from 12 hospitals in Wenzhou, Zhejiang from Jan 17, 2020 to Mar 20, 2020. Prospectively collected and analyzed data included demographics, clinical symptoms, comorbidity, and chest CT imaging features at the first follow up, 1 month after discharge. All patients underwent the HRQoL evaluation with the Chinese version of Short-Form 36-item questionnaire (SF-36) as well as a general condition questionnaire. Factors associated with SF-36 were constructed using linear regression. Predictors of impaired physical component summary (PCS) and a mental component summary (MCS) were identified by logistic regression. Results SF-36 demonstrated a significant difference in HRQoL in patients with COVID-19, except in physical function (PF), when compared to the general Chinese population (p<0.05). The multiple linear regressions demonstrated that age was negatively associated with PF, role physical (RP), but positively associated with vitality (VT) (p<0.05). PF, bodily pain (BP), and role-emotional (RE) were negatively associated with the female sex (p<0.05). For mental health, the clinical subtypes were significant associated factors (p < 0.05). Length of stay (LOS) was strongly negatively associated with RE and RP, and positively associated with VT (p< 0.05). Logistical regression revealed that non-obese overweight (OR 3.71) and obesity (OR 3.94) were risk factors for a low PCS and female sex (OR 2.22) was a risk factor for a low MCS. Conclusions Health-related quality of life was poor among COVID-19 patients at the 1 month follow-up. Patients suffered from significant physical and psychological impairment. Therefore, prospective monitoring of individuals exposed to SARS-CoV-2 is needed in order to fully understand the long-term impact of COVID-19, as well as to inform prompt and efficient interventions to alleviate suffering.
U Recurrent Neural Network for Polyphonic Sound Event Detection and Localization

The polyphonic sound event detection and localization (SELD) system indicates the temporal onset and offset time of sound events to be detected and tracks the spatial location of the acoustic source. It involves two processes, the sound event detection (SED) and the estimation of the direction of arrival (DOA). However, previous models only extract features by simply stacking convolutional layers, thus leading to two problems, one is that the network is difficult to deepen and the expressive capability of the model is limited, another problem is that they utilize only highlevel features, and lack a feature description of the low-level texture features of the sound signal. In this paper, a novel model called U recurrent neural network (URNN) is proposed to alleviate those problems, it combines the low-level and high-level features in the model without significantly increasing computation costs, and exploits the identity layer to make the network deeper. The proposed method is evaluated on the Detection and Classification of Acoustic Scenes and Events (DCASE) 2019 Task 3 dataset [1], which covers distinct overlapping sound events collected from different environments. Experimental results show that the proposed URNN significantly reduce the SELD error by 16.2% compared to the baseline model SELDnet [2] and 2.5% compared to the improved convolutional recurrent neural network (CRNN).
Gut instincts: vitamin D/vitamin D receptor and microbiome in neurodevelopment disorders

The gut microbiome regulates a relationship with the brain known as the gut–microbiota–brain (GMB) axis. This interaction is influenced by immune cells, microbial metabolites and neurotransmitters. Recent findings show gut dysbiosis is prevalent in autism spectrum disorder (ASD) as well as attention deficit hyperactivity disorder (ADHD). There are previously established negative correlations among vitamin D, vitamin D receptor (VDR) levels and severity of ASD as well as ADHD. Both vitamin D and VDR are known to regulate homeostasis in the brain and the intestinal microbiome. This review summarizes the growing relationship between vitamin D/VDR signalling and the GMB axis in ASD and ADHD. We focus on current publications and summarize the progress of GMB in neurodevelopmental disorders, describe effects and mechanisms of vitamin D/VDR in regulating the microbiome and synoptically highlight the potential applications of targeting vitamin D/VDR signalling in neurodevelopment disorders.
Integration Between Cerebral Hemispheres Contributes to Defense Mechanisms

Defense mechanisms are mental functions which facilitate coping when real or imagined events challenge personal wishes, needs, and feelings. Whether defense mechanisms have a specific neural basis is unknown. The present research tested the hypothesis that interhemispheric integration plays a critical role in defense mechanism development, by studying a unique sample of patients born without the corpus callosum (agenesis of the corpus callosum; AgCC). Adults with AgCC (N = 27) and matched healthy volunteers (N = 30) were compared on defense mechanism use across increasing levels of developmental maturity (denial, least; projection, intermediate; identification, most). Narratives generated in response to Thematic Apperception Test images were scored according to the Defense Mechanism Manual. Greater use of denial and less identification was found in persons with AgCC, compared to healthy comparisons. This difference emerged after age 18 when full maturation of defenses among healthy individuals was expected. The findings provide clinically important characterization of social and emotional processing in persons with AgCC. More broadly, the results support the hypothesis that functional integration across the hemispheres is important for the development of defense mechanisms.
NEK7 Coordinates Rapid Neuroinflammation After Subarachnoid Hemorrhage in Mice

Background: Subarachnoid hemorrhage (SAH) is a devastating disease which leads to high morbidity and mortality. Recent studies have indicated that, never in mitosis gene A-related expressed kinase 7 (NEK7), is involved in NLRP3 (NLR family, pyrin domain containing 3) associated inflammation, which may result in subsequent cellular and vascular damage. The aim of this study was to investigate whether NEK7 is involved in the pathophysiology of subarachnoid hemorrhage. Methods: 455 adult male C57B6J mice, weighing 22 to 30 g, were used to investigate the time course of NEK7 expression in the ipsilateral cortex after SAH, and to investigate the intrinsic function and mechanism of NEK7. A vascular puncture model was used to create the mouse SAH model, and intracerebroventricular injection was used to deliver NEK7 recombinant protein, NEK7 small interfering RNA, nigericin, and MCC950. Neurological score, brain water content, Evans blue extravasation, immunofluorescence, and western blot were evaluated for neurological outcome, neuronal apoptosis, blood-brain barrier damage, microglia accumulation, and the mechanism of NEK7 and NLRP3 activation. Results: Our results exhibited that intrinsic NEK7 was elevated after SAH in the cortex of the left/ipsilateral hemisphere and was colocalized with microglia, endothelial cells, neuron, astrocyte, and oligodendrocyte, and highly expressed in microglia and endothelial cells after SAH. NEK7 recombinant protein aggravated neurological deficits, brain edema, neuronal apoptosis, BBB permeability, microglial accumulation, and activated caspase-1 and IL-1β maturation, while NEK7 small interfering RNA injection reversed those effects. Nigericin administration enhanced ASC oligomerization, caspase-1 and IL-1β maturation without increasing the protein level of NLRP3, and ASC oligomerization and caspase-1 IL-1β maturation reduced when combined with NEK7 knockdown or MCC950 delivery. We found the level of NEK7 expression increased after SAH and could activate the downstream NLRP3 pathway to induce caspase-1, IL-1β expression and then increased the BBB opening, microglia accumulation and neuronal apoptosis after SAH. Conclusions: This study demonstrated for the first time that NEK7 mediated the harmful effects of neuronal apoptosis and BBB disruption after SAH, which may potentially be mediated by the NEK7/NLRP3 signal. NEK7 served as a co-component for NLRP3 inflammasome activation after SAH. NEK7 may be a promising target on the management of SAH patients.
Changes in DNA 5-Hydroxymethylcytosine Levels and the Underlying Mechanism in Non-functioning Pituitary Adenomas

Epigenetic factors have been proven to contribute to pituitary adenoma formation. 5-hydroxymethylcytosine (5hmC), which is catalyzed by ten-eleven translocation 2 (TET2), is related to DNA demethylation. In order to explore the pathogenesis of non-functioning pituitary adenomas (NFPAs), we detected genomic 5hmC levels in 57 NFPAs and 5 normal pituitary glands, and TET2 expression, distribution and TET2 alteration. Genomic 5hmC levels in NFPAs were significantly lower than those in normal pituitary glands (0.38‰ (0.24‰, 0.61‰) vs. 2.47‰ (1.56‰, 2.83‰), P < 0.0001). There was positive correlation of 5hmC levels with TET2 total and nuclear expression in NFPAs (r = 0.461, P = 0.018; r = 0.458, P = 0.019). Genomic 5hmC levels in NFPAs with TET2 p.P29R were significantly lower than those in wild type NFPAs (0.33 ± 0.18‰ vs. 0.51 ± 0.25‰, P = 0.021). We found genomic 5hmC loss in human NFPAs for the first time. Genomic 5hmC levels may be affected by TET2 expression, subcellular localization and TET2 mutation.
Can Camp Get You Into a Better Secondary School? A Field Experiment of Targeted Instruction in Kenya

Abstract Access to quality secondary schooling can be life changing for students in developing contexts. In Kenya, entrance to such schools was historically determined by performance on a high-stakes exam. Understandably then, preparation for this exam is a priority for families and educators. To increase the share of students entering these schools, some educational providers offer targeted instruction for students they believe have a chance of securing a spot. We use a randomized control trial to evaluate the impact of these “symposia” programs—week-long, sleep-away camps where eighth-grade students receive a burst of academic instruction from teachers who are selected based on merit. While similar models have been tested in the United States, less is known about this type of intervention in developing settings. We find these programs were not particularly effective for the average nominated student relative to a typical week of school. However, we find large, positive effects among students attending schools from which few students are nominated for symposia. We provide suggestive evidence that this was because students from low-representation schools had fewer pre-camp practice test resources outside of school. The results have implications for program design and the growing literature on the effectiveness of appropriately targeted individualized instruction.
Rice Biofortification With Zinc and Selenium: A Transcriptomic Approach to Understand Mineral Accumulation in Flag Leaves

Human malnutrition due to micronutrient deficiencies, particularly with regards to Zinc (Zn) and Selenium (Se), affects millions of people around the world, and the enrichment of staple foods through biofortification has been successfully used to fight hidden hunger. Rice (Oryza sativa L.) is one of the staple foods most consumed in countries with high levels of malnutrition. However, it is poor in micronutrients, which are often removed during grain processing. In this study, we have analyzed the transcriptome of rice flag leaves biofortified with Zn (900 g ha–1), Se (500 g ha–1), and Zn-Se. Flag leaves play an important role in plant photosynthesis and provide sources of metal remobilization for developing grains. A total of 3170 differentially expressed genes (DEGs) were identified. The expression patterns and gene ontology of DEGs varied among the three sets of biofortified plants and were limited to specific metabolic pathways related to micronutrient mobilization and to the specific functions of Zn (i.e., its enzymatic co-factor/coenzyme function in the biosynthesis of nitrogenous compounds, carboxylic acids, organic acids, and amino acids) and Se (vitamin biosynthesis and ion homeostasis). The success of this approach should be followed in future studies to understand how landraces and other cultivars respond to biofortification.
Anisakis simplex products impair intestinal epithelial barrier function and occludin and zonula occludens-1 localisation in differentiated Caco-2 cells

Background Anisakis spp. are nematode parasites found in a wide range of marine organisms. Human beings may accidentally become infected, showing the symptoms of anisakiasis and allergic responses. There has been evidence of increased intestinal permeability in A. simplex–sensitized subjects and that specific IgE titres increase in some allergic patients when fishery products are re-introduced into their diet. The aims of this work were to study the effect of A. simplex crude extract on the intestinal integrity and permeability by using Caco-2 cell monolayer. To analyse the capacity of Ani s 4 allergen to cross the epithelial barrier. Methodology/Principal findings Cellular bioenergetics, transepithelial electrical resistance, viability, permeability, reactive oxygen species generation and immunofluorescent staining of tight junction proteins were analysed. A. simplex crude extract compromises the Caco-2 cell monolayer integrity in a dose-dependent manner. This effect is detected at 1 hour of culture and integrity is recovered after 24 hours of culture. The epithelial barrier disruption is accompanied by an increase in paracellular permeability and reactive oxygen species production and by a delocalization of occludin and zonula occludens-1. Finally, Ani s 4, a thermostable and resistant to digestion allergen with cystatin activity, is able to cross the epithelial barrier in Caco-2 monolayer and reach a cumulative mean percentage of 22.7% of total concentration in the basolateral side after 24 hours of culture. Conclusions/Significance Our results demonstrate that A. simplex induces an early and reversible alteration of integrity and permeability of Caco-2 cell monolayer and that an underlying mechanism of this effect would involve the oxidative stress and disruption of epithelial tight junctions. Additionally, it has been shown that Ani s 4 allergen is able to cross the epithelial barrier. These findings could explain the increased intestinal permeability observed in Anisakis-sensitized patients, the changes over time in IgE sensitization to A. simplex allergens, and the specific IgE persistence in Anisakis allergy.
The Impact of Sugar-Sweetened Beverage Consumption on the Liver: A Proteomics-Based Analysis

Cardiometabolic complications such as the metabolic syndrome and Type 2 Diabetes Mellitus (T2DM) are major causes of global morbidity and mortality. As sugar-sweetened beverages (SSBs) are implicated in this process, this study aimed to obtain greater mechanistic insights. Male Wistar rats (~200 g) were gavaged with a local SSB every day for a period of six months while the control group was gavaged with an iso-volumetric amount of water. Experimental dosages were calculated according to the surface area-to-volume ratio and were equivalent to 125 mL/day (in human terms). A proteomic analysis was performed on isolated liver samples and thereafter, markers of endoplasmic reticulum (ER) stress, antioxidant/oxidant capacity, calcium regulation, and mitochondrial functionality were assessed. These data show that SSB consumption resulted in (a) the induction of mild hepatic ER stress; (b) altered hepatic mitochondrial dynamics; and (c) perturbed calcium handling across mitochondria-associated ER membranes. Despite significant changes in markers of ER stress, the antioxidant response and calcium handling (proteomics data), the liver is able to initiate adaptive responses to counteract such stressors. However, the mitochondrial data showed increased fission and decreased fusion that may put the organism at risk for developing insulin resistance and T2DM in the longer term.