Miracle-dz/UniFAR-FTUs huggingface dataset:
Effectiveness of sexual selection in removing mutations induced with ionizing radiation

Because of the production of males, sexual populations are expected to incur a 50% cost in potential growth rate. However, theory predicts that sexual competition between males can compensate for this cost by decreasing the mutation load of sexual populations. To test this hypothesis, I induced mutations in male bulb mites with ionizing radiation and subjected their progeny (F1) to two selective regimes differing in opportunity for sexual selection. Mutations which were not removed by selection acting on the F1 decreased embryonic viability in the F2. Viability was significantly higher in the treatment in which there was an opportunity for sexual selection than in the treatment in which sexual selection was experimentally eliminated. The results indicate that sexual selection can increase population fitness and, at least partly, compensate for the cost of sex.
Genetic Diversity and Structure of Oryza rufipogon Griff. Populations in the Philippines

Oryza rufipogon Griff. or ‘Rufi’ is the wild progenitor of the cultivated rice, Oryza sativa L. In the Philippines, Rufi was previously known to be found only in Lake Apo, Bukidnon. However, a new population was identified in Lake Napalit in the same province. Based on previous morphological diversity assessment, both populations are unique for at least three characters, i.e., leaf, culm, and awn lengths. Environmental parameters such as rainfall and air temperature also differed between the two lakes. With these, an assessment of Rufi’s genetic diversity at the molecular level is beneficial to further ascertain its usefulness in rice breeding and gain insights on its conservation status. Thus, this study estimated the degree of genetic diversity and determined the population structure of 41 samples of natural Rufi populations in the Philippines using SSR markers. A total of 98 genome wide polymorphic SSR markers were selected to examine the genetic diversity and structure of Rufi populations, along with seven rice cultivars for comparison. Results showed that Philippine Rufi populations have lower genetic diversity compared to cultivated rice accessions and other Rufi populations in Southeast Asia and China. This low genetic diversity suggested that Rufi populations might be in a genetic bottleneck, perhaps due to observed unsustainable farming practices near their habitat and lack of awareness of their importance. A significant population structure and differentiation were determined using the STRUCTURE and phylogenetic analyses. Population differentiation might be due to geographic isolation which prevented gene flow between the two populations and the unique climatic conditions between the two lakes.
Simulations support the interaction of the SARS-CoV-2 spike protein with nicotinic acetylcholine receptors

Changeux et al. recently suggested that the SARS-CoV-2 spike (S) protein may interact with nicotinic acetylcholine receptors (nAChRs). Such interactions may be involved in pathology and infectivity. Here, we use molecular simulations of validated atomically detailed structures of nAChRs, and of the S protein, to investigate this ‘nicotinic hypothesis’. We examine the binding of the Y674-R685 loop of the S protein to three nAChRs, namely the human α4β2 and α7 subtypes and the muscle-like αβγd receptor from Tetronarce californica. Our results indicate that Y674-R685 has affinity for nAChRs and the region responsible for binding contains the PRRA motif, a four-residue insertion not found in other SARS-like coronaviruses. In particular, R682 has a key role in the stabilisation of the complexes as it forms interactions with loops A, B and C in the receptor’s binding pocket. The conformational behaviour of the bound Y674-R685 region is highly dependent on the receptor subtype, adopting extended conformations in the α4β2 and α7 complexes and more compact ones when bound to the muscle-like receptor. In the α4β2 and αβγd complexes, the interaction of Y674-R685 with the receptors forces the loop C region to adopt an open conformation similar to other known nAChR antagonists. In contrast, in the α7 complex, Y674-R685 penetrates deeply into the binding pocket where it forms interactions with the residues lining the aromatic box, namely with TrpB, TyrC1 and TyrC2. Estimates of binding energy suggest that Y674-R685 forms stable complexes with all three nAChR subtypes. Analyses of the simulations of the full-length S protein show that the Y674-R685 region is accessible for binding, and suggest a potential binding orientation of the S protein with nAChRs.
Paracoccidioides Genomes Reflect High Levels of Species Divergence and Little Interspecific Gene Flow

Paracoccidioides is the causal agent of a systemic mycosis in Latin America. Most of the inference of the evolutionary history of Paracoccidioides has used only a few molecular markers. ABSTRACT The fungus Paracoccidioides is a prevalent human pathogen endemic to South America. The genus is composed of five species. In this report, we use 37 whole-genome sequences to study the allocation of genetic variation in Paracoccidioides. We tested three genome-wide predictions of advanced speciation, namely, that all species should be reciprocally monophyletic, that species pairs should be highly differentiated along the whole genome, and that there should be low rates of interspecific gene exchange. We find support for these three hypotheses. Species pairs with older divergences show no evidence of gene exchange, while more recently diverged species pairs show evidence of modest rates of introgression. Our results indicate that as divergence progresses, species boundaries become less porous among Paracoccidioides species. Our results suggest that species in Paracoccidioides are at different stages along the divergence continuum. IMPORTANCE Paracoccidioides is the causal agent of a systemic mycosis in Latin America. Most of the inference of the evolutionary history of Paracoccidioides has used only a few molecular markers. In this report, we evaluate the extent of genome divergence among Paracoccidioides species and study the possibility of interspecific gene exchange. We find that all species are highly differentiated. We also find that the amount of gene flow between species is low and in some cases is even completely absent in spite of geographic overlap. Our study constitutes a systematic effort to identify species boundaries in fungal pathogens and to determine the extent of gene exchange among fungal species.
Weakening Dust Storm Intensity in Arid Central Asia Due to Global Warming Over the Past 160 Years

Dust storms occur frequently in arid central Asia (ACA) and greatly influence the regional ecology/environment, human health, and security, as well as the global climate. To date, neither the patterns nor the underlying mechanisms of dust storms in ACA are fully understood, partly due to the lack of long-term historical records. Here, we reconstruct a dust storm history of the past ∼160 years in northwest China, based on high-resolution sedimentary proxies retrieved from Lake Karakul (located in the core zone of ACA). We find that changes in the sedimentary coarse fraction (grain size > 64 μm) in Lake Karakul are correlated with both historical and modern observed dust storms. The reconstructed dust storm intensity shows a decreasing trend since AD 1850s, with three high occurrence intervals at AD 1870s–1910s, AD 1930s–1940s, and AD 1960s–1980s. We contend that changes in temperature and wind speed could have dominated the frequency and intensity of dust storms in northwest China during the record periods: temperature controls the wind speed and then the dust storm frequency/intensity; lower temperature corresponding to higher wind speed, and higher dust storm frequency/intensity, and vice versa. The observed anthropogenic global warming could have led to a decrease in atmospheric temperature gradients and decline in wind speed and then decreasing dust storm frequency/intensity. Providing this stands, less and weaker dust storms are expected under a continuously anthropogenic warming scenario.
Gender Differences Are Encoded Differently in the Structure and Function of the Human Brain Revealed by Multimodal MRI

Despite widely reported gender differences in both brain structure and brain function, very few studies have examined the relationship between the structural differences and the functional differences between genders. Here, different imaging measures including both structural [i.e., gray matter volume (GMV)] and functional [i.e., regional homogeneity (ReHo) and functional connectivity (FC)] measures were employed to detect the gender differences in the human brain based on univariate and multivariate approaches with a sample of 290 healthy adults (155 females). The univariate analyses revealed that gender differences were detected in both structural (i.e., GMV) and functional (ReHo or FC) imaging measures, mainly manifested as greater values in females than in males in regions of the frontal, parietal, occipital lobes and cerebellum. Importantly, there was little overlap between the differences detected in GMV and those detected in ReHo and FC, and their differences between genders were not correlated with each other. The multivariate pattern analyses revealed that each of these measures had discriminative power to successfully distinguish between genders (classification accuracy: 94.3%, 90.73%, and 83.89% for GMV, ReHo, and FC, respectively) and their combination further improved the classification performance (96.6%). Our results suggest that gender differences are encoded in both brain structure and brain function, but in different manners. The finding of different and complementary information contained in structural and functional differences between genders highlights the complex relationship between brain structure and function, which may underlie the complex nature of gender differences in behavior.
Safety and Efficacy of Chest Physiotherapy in Patients With COVID-19: A Critical Review

The present global pandemic of COVID-19 has brought the whole world to a standstill, causing morbidity, death, and changes in personal roles. The more common causes of morbidity and death in these patients include pneumonia and respiratory failure, which cause the patients to require artificial ventilation and other techniques that can improve respiratory function. One of these techniques is chest physiotherapy, and this has been shown to improve gas exchange, reverse pathological progression, and reduce or avoid the need for artificial ventilation when it is provided very early in other respiratory conditions. For patients with COVID-19, there is limited evidence on its effect, especially in the acute stage and in patients on ventilators. In contrast, in patients after discharge, chest physiotherapy in the form of respiratory muscle training, cough exercise, diaphragmatic training, stretching exercise, and home exercise have resulted in improved FEV1 (L), FVC (L), FEV1/FVC%, diffusing lung capacity for carbon monoxide (DLCO%), endurance, and quality of life, and a reduction in anxiety and depression symptoms. However, there are still controversies on whether chest physiotherapy can disperse aerosols and accelerate the rate of spread of the infection, especially since COVID-19 is highly contagious. While some authors believe it is possible, others believe the aerosol generated by chest physiotherapy is not within respirable range. Therefore, measures such as the use of surgical masks, tele-rehabilitation, and self-management tools can be used to limit cross-infection.
Soak systems of an Irish raised bog : a multidisiciplinary study of their origin, ecology, conservation and restoration

Soak systemen (systemen met een laagveenvegetatie omgeven door ombrotroof veen), kortweg soaks, zijn zeldzame elementen in hoogvenen die bijdragen aan de heterogeniteit van deze ecosystemen. Ze worden beschouwd als belangrijke elementen in het hoogveen die behouden en hersteld dienen te worden. Teneinde meer inzicht te krijgen in soak systemen, hebben wij historisch, biogeochemisch en ecologisch onderzoek verricht aan twee soaks in Clara bog
The Impact of Entrepreneurial Passion on Psychology and Behavior of Entrepreneurs

In order to study the influence of entrepreneurial passion on entrepreneurs’ psychology and behavior, based on the theory of self-efficacy, a model of relationship between entrepreneurial passion and entrepreneurs’ psychology and behavior was constructed, relevant hypotheses were proposed, and the promotion mechanism of entrepreneurial passion on entrepreneurial behavior and enterprise performance was analyzed. A survey of 300 entrepreneurs from Hangzhou, Wenzhou, Jiaxing, Shaoxing, and Huzhou was conducted to verify the reliability of the questionnaire through statistical description and analysis. Then exploratory factor analysis and confirmatory factor analysis (CFA) were conducted to test the correlation between variables. Finally, the structural equation was simulated to verify the correctness of the proposed hypothesis and model. The results show that the designed questionnaire has good reliability [the correction item total correlation coefficients (CITC) of all scales are greater than 0.3, values of Cronbach’s α are higher than 0.6], the validity (all inventory accumulation explanation degree are higher than 50%) and the fitting (χ2/df values of all scales are less than 3, comparative fitness index (CFI), goodness of fitness index (GFI), and incremental fitness index (IFI) are greater than 0.9, root-mean-square error of approximation (RMSEA) value is less than 0.08). The direct effect of harmonious passion on entrepreneurial persistence and enterprise performance is not significant, while the direct effect of compulsive passion on entrepreneurial persistence and enterprise performance is significant. Harmonious passion (P < 0.001) and compulsive passion (P < 0.01) are significantly correlated with entrepreneurial self-efficacy, and self-efficacy plays a mediating role between entrepreneurial passion and entrepreneur psychology and behavior (P < 0.05), and the hypothesis proposed is basically valid. Therefore, entrepreneurial passion can positively guide the entrepreneurial persistence of entrepreneurs, and at the same time promote the performance of enterprises by stimulating the positive emotions of entrepreneurs. In addition, entrepreneurs can enhance their entrepreneurial role identity, maintain a positive attitude, stimulate creativity, and innovation, to enhance their sense of energy efficiency. The government can also promote successful business cases to build an inclusive and innovative social environment and stimulate the entrepreneurial passion of entrepreneurs. This study reveals the relationship between entrepreneurial passion, self-efficacy, and entrepreneur psychology and behavior, and extends the application of entrepreneurial passion in the field of entrepreneurship.
Prominent Receptors of Liver Sinusoidal Endothelial Cells in Liver Homeostasis and Disease

Liver sinusoidal endothelial cells (LSECs) are the most abundant non-parenchymal cells lining the sinusoidal capillaries of the hepatic system. LSECs are characterized with numerous fenestrae and lack basement membrane as well as a diaphragm. These unique morphological characteristics of LSECs makes them the most permeable endothelial cells of the mammalian vasculature and aid in regulating flow of macromolecules and small lipid-based structures between sinusoidal blood and parenchymal cells. LSECs have a very high endocytic capacity aided by scavenger receptors (SR), such as SR-A, SR-B (SR-B1 and CD-36), SR-E (Lox-1 and mannose receptors), and SR-H (Stabilins). Other high-affinity receptors for mediating endocytosis include the FcγRIIb, which assist in the antibody-mediated removal of immune complexes. Complemented with intense lysosomal activity, LSECs play a vital role in the uptake and degradation of many blood borne waste macromolecules and small (<280 nm) colloids. Currently, seven Toll-like receptors have been investigated in LSECs, which are involved in the recognition and clearance of pathogen-associated molecular pattern (PAMPs) as well as damage associated molecular pattern (DAMP). Along with other SRs, LSECs play an essential role in maintaining lipid homeostasis with the low-density lipoprotein receptor-related protein-1 (LRP-1), in juxtaposition with hepatocytes. LSECs co-express two surface lectins called L-Specific Intercellular adhesion molecule-3 Grabbing Non-integrin Receptor (L-SIGN) and liver sinusoidal endothelial cell lectin (LSECtin). LSECs also express several adhesion molecules which are involved in the recruitment of leukocytes at the site of inflammation. Here, we review these cell surface receptors as well as other components expressed by LSECs and their functions in the maintenance of liver homeostasis. We further discuss receptor expression and activity and dysregulation associated with the initiation and progression of many liver diseases, such as hepatocellular carcinoma, liver fibrosis, and cirrhosis, alcoholic and non-alcoholic fatty liver diseases and pseudocapillarization with aging.
Mesenchymal Stromal Cell Uses for Acute Kidney Injury—Current Available Data and Future Perspectives: A Mini-Review

There is growing evidence concerning the potential use of mesenchymal stromal cells (MSCs) for different tissue injuries. Initially, the intended physiological use of MSCs was due to their ability to differentiate and replace damaged cells. However, MSCs have multiple effects, including being able to significantly modulate immunological responses. MSCs are currently being tested for neurodegenerative diseases, graft vs. host disease, kidney injury, and other chronic unremitting tissue damage. Using MSCs in acute tissue damage is only now being studied. Acute kidney injury (AKI) is a common cause of morbidity and mortality. After the primary insult, overactivation of the immune system culminates in additional secondary potentially permanent kidney damage. MSCs have the potential to ameliorate the secondary damage, and recent studies have shed important light on their mechanisms of action. This article summarizes the basics of MSCs therapy, the newly discovered mechanisms of action, and their potential application in the setting of AKI.
Identification of Alzheimer's EEG With a WVG Network-Based Fuzzy Learning Approach

A novel analytical framework combined fuzzy learning and complex network approaches is proposed for the identification of Alzheimer's disease (AD) with multichannel scalp-recorded electroencephalograph (EEG) signals. Weighted visibility graph (WVG) algorithm is first applied to transform each channel EEG into network and its topological parameters were further extracted. Statistical analysis indicates that AD and normal subjects show significant difference in the structure of WVG network and thus can be used to identify Alzheimer's disease. Taking network parameters as input features, a Takagi-Sugeno-Kang (TSK) fuzzy model is established to identify AD's EEG signal. Three feature sets—single parameter from multi-networks, multi-parameters from single network, and multi-parameters from multi-networks—are considered as input vectors. The number and order of input features in each set is optimized with various feature selection methods. Classification results demonstrate the ability of network-based TSK fuzzy classifiers and the feasibility of three input feature sets. The highest accuracy that can be achieved is 95.28% for single parameter from four networks, 93.41% for three parameters from single network. In particular, multi-parameters from the multi-networks set obtained the best result. The highest accuracy, 97.12%, is achieved with five features selected from four networks. The combination of network and fuzzy learning can highly improve the efficiency of AD's EEG identification.
Mutations in the TolC Periplasmic Domain Affect Substrate Specificity of the AcrAB-TolC Pump

TolC and the other members of the outer membrane factor (OMF) family are outer membrane proteins forming trimeric channels that serve as a conduit for most actively effluxed substrates in Gram-negative bacteria by providing a key component in a multitude of tripartite efflux-pumps. Current models of tripartite pump assembly ascribe substrate selection to the inner-membrane transporter and periplasmic-adapter protein (PAP) assembly, suggesting that TolC is a passive, non-selective channel. While the membrane-embedded portion of the protein adopts a porin-like fold, the periplasmic domain of TolC presents a unique “alpha-barrel” architecture. This alpha-barrel consists of pseudo-continuous α-helices forming curved coiled-coils, whose tips form α-helical hairpins, relaxation of which results in a transition of TolC from a closed to an open-aperture state allowing effective efflux of substrates through its channel. Here, we analyzed the effects of site-directed mutations targeting the alpha-barrel of TolC, of the principal tripartite efflux-pump Escherichia coli AcrAB-TolC, on the activity and specificity of efflux. Live-cell functional assays with these TolC mutants revealed that positions both at the periplasmic tip of, and partway up the TolC coiled-coil alpha-barrel domain are involved in determining the functionality of the complex. We report that mutations affecting the electrostatic properties of the channel, particularly the D371V mutation, significantly impact growth even in the absence of antibiotics, causing hyper-susceptibility to all tested efflux-substrates. These results suggest that inhibition of TolC functionality is less well-tolerated than deletion of tolC, and such inhibition may have an antibacterial effect. Significantly and unexpectedly, we identified antibiotic-specific phenotypes associated with novel TolC mutations, suggesting that substrate specificity may not be determined solely by the transporter protein or the PAP, but may reside at least partially with the TolC-channel. Furthermore, some of the effects of mutations are difficult to reconcile with the currently prevalent tip-to-tip model of PAP-TolC interaction due to their location higher-up on the TolC alpha-barrel relative to the proposed PAP-docking sites. Taken together our results suggest a possible new role for TolC in vetting of efflux substrates, alongside its established role in tripartite complex assembly.
Loss of the Major Phosphatidylserine or Phosphatidylethanolamine Flippases Differentially Affect Phagocytosis

The lipids phosphatidylserine (PtdSer) and phosphatidylethanolamine (PtdEth) are normally asymmetrically localized to the cytosolic face of membrane bilayers, but can both be externalized during diverse biological processes, including cell division, cell fusion, and cell death. Externalized lipids in the plasma membrane are recognized by lipid-binding proteins to regulate the clearance of cell corpses and other cell debris. However, it is unclear whether PtdSer and PtdEth contribute in similar or distinct ways to these processes. We discovered that disruption of the lipid flippases that maintain PtdSer or PtdEth asymmetry in the plasma membrane have opposite effects on phagocytosis in Caenorhabditis elegans embryos. Constitutive PtdSer externalization caused by disruption of the major PtdSer flippase TAT-1 led to increased phagocytosis of cell debris, sometimes leading to two cells engulfing the same debris. In contrast, PtdEth externalization caused by depletion of the major PtdEth flippase TAT-5 or its activator PAD-1 disrupted phagocytosis. These data suggest that PtdSer and PtdEth externalization have opposite effects on phagocytosis. Furthermore, externalizing PtdEth is associated with increased extracellular vesicle release, and we present evidence that the extent of extracellular vesicle accumulation correlates with the extent of phagocytic defects. Thus, a general loss of lipid asymmetry can have opposing impacts through different lipid subtypes simultaneously exerting disparate effects.