Miracle-dz/UniFAR-FTUs huggingface dataset:
Understanding factors influencing the estimated genetic variance and the distribution of breeding values

This study investigated the main factors influencing the genetic variance and the variance of breeding values (EBV). The first is the variance of genetic values in the base population, and the latter is the variance of genetic values in the population under evaluation. These variances are important as improper variances can lead to systematic bias. The inverse of the genetic relationship matrix (K −1) and the phenotypic variance are the main factors influencing the genetic variance and heritability (h2). These factors and h2 are also the main factors influencing the variance of EBVs. Pedigree- and genomic-based relationship matrices (A and G as K) and phenotypes on 599 wheat lines were used. Also, data were simulated, and a hybrid (genomic-pedigree) relationship matrix (H as K) and phenotypes were used. First, matrix K underwent a transformation (K* = w K + α 11′ + β I), and the responses in the mean and variation of diag(K −1) and offdiag(K −1) elements, and genetic variance in the form of h2 were recorded. Then, the original K was inverted, and matrix K −1 underwent the same transformations as K, and the responses in the h2 estimate and the variance of EBVs in the forms of correlation and regression coefficients with the EBVs estimated based on the original K −1 were recorded. In response to weighting K by w, the estimated genetic variance changed by 1/w. We found that μ(diag(K)) − μ(offdiag(K)) influences the genetic variance. As such, α did not change the genetic variance, and increasing β increased the estimated genetic variance. Weighting K −1 by w was equivalent to weighting K by 1/w. Using the weighted K −1 together with its corresponding h2, EBVs remained unchanged, which shows the importance of using variance components that are compatible with the K −1. Increasing β I added to K −1 increased the estimated genetic variance, and the effect of α 11′ was minor. We found that larger variation of diag(K −1) and higher concentration of offdiag(K −1) around the mean (0) are responsible for lower h2 estimate and variance of EBVs.
Involvement of the cerebellum in migraine

Migraine is a disabling neurological disease characterized by moderate or severe headaches and accompanied by sensory abnormalities, e.g., photophobia, allodynia, and vertigo. It affects approximately 15% of people worldwide. Despite advancements in current migraine therapeutics, mechanisms underlying migraine remain elusive. Within the central nervous system, studies have hinted that the cerebellum may play an important sensory integrative role in migraine. More specifically, the cerebellum has been proposed to modulate pain processing, and imaging studies have revealed cerebellar alterations in migraine patients. This review aims to summarize the clinical and preclinical studies that link the cerebellum to migraine. We will first discuss cerebellar roles in pain modulation, including cerebellar neuronal connections with pain-related brain regions. Next, we will review cerebellar symptoms and cerebellar imaging data in migraine patients. Lastly, we will highlight the possible roles of the neuropeptide calcitonin gene-related peptide (CGRP) in migraine symptoms, including preclinical cerebellar studies in animal models of migraine.
A newly developed strain of Enterococcus faecium isolated from fresh dairy products to be used as a probiotic in lactating Holstein cows

The objective of this study was to determine the ability of an isolated strain (EGY_NRC1) or commercial (NCIMB 11181) Enterococcus faecium as a probiotic for lactating cows. Two experiments were conducted: In Experiment 1, the effects of three levels (1, 2, and 3 g/kg diet, DM basis) of isolated and commercial E. faecium on in vitro ruminal fermentation kinetics, gas, methane (CH4) and nutrient degradability were determined. In Experiment 2, thirty multiparous Holstein cows (633 ± 25.4 kg body weight) with 7 days in milk, were randomly assigned to 3 treatments in a completely randomized design in a 60-day experiment. Cows were fed without any additives (control treatment) or supplemented with 2 g/kg feed daily of E. faecium EGY_NRC1 (contain 1.1 × 109 CFU/g) or commercial E. faecium NCIMB 11181 (contain 2 × 1012 CFU/g). Diets were prepared to meet cow's nutrient requirements according to NRC recommendations. Probiotic doses were based on the in vitro Experiment 1. Feed intake, digestibility, blood parameters and lactation performance were evaluated. In Experiment 1, the isolated E. faecium linearly and quadratically increased (P < 0.001) in vitro total gas production (TGP), the degradability of dry matter (dDM) and organic matter (dOM) while decreased (P < 0.05) methane (CH4) percent of TGP, NH3CH4 production, and pH. The commercial E. faecium increased TGP and decreased (P < 0.01) CH4 production, pH and increased the dDM and dOM, short chain fatty acids and ruminal NH3-N concentration. In Experiment 2, the isolated E. faecium increased (P < 0.01) total tract digestibility of DM, neutral and acid detergent fiber, daily milk production and feed efficiency compared to the control treatment without affecting feed intake and milk composition. Moreover, the isolated E. faecium increased (P < 0.05) the proportion of C18:1 trans-9, C18:2 cis-9-12 and C18:2 trans-10 cis-12. Both isolated and commercial E. faecium improved (P < 0.01) organic matter, crude protein and nonstructural carbohydrates digestibility, increased serum glucose (P = 0.002) and decreased serum cholesterol (P = 0.002). Additionally, both E. faecium strains decreased C23:0 (P = 0.005) in milk. In conclusion, the use of E. faecium (isolated and commercial) at 2 g/kg DM of feed improved feed efficiency and production performance, with superior effects on animal performance from isolated E. faecium compared to the commercial one.
Corrigendum to “Games With Imperfectly Observable Actions in Continuous Time”

Sannikov (2007) investigated properties of perfect public equilibria in continuous-time repeated games. This note points out that the proof of Lemma 6, required for the proof of the main theorem (Theorem 2), contains an error in computing a Hessian matrix. A correct proof of Lemma 6 is provided using an additional innocuous assumption and a generalized version of Lemma 5. Copyright 2010 The Econometric Society.
The effect of narcotics on ferroptosis-related molecular mechanisms and signalling pathways

Ferroptosis is a novel programmed cell death form characterized by iron-mediated reactive oxygen species-induced lipid peroxidation and subsequent cell damage that is distinct from apoptosis, necroptosis, pyroptosis, and autophagy. Most studies on ferroptosis are based on its function and mechanism, but there have been relatively few studies on the effects of drugs, especially anaesthetics, on ferroptosis. Therefore, we summarized the recent literature on the effects of anaesthetics on ferroptosis to understand the underlying mechanism. In particular, we focused on the targets of various anaesthetics in different mechanisms of ferroptosis and the effects of ferroptosis induction or inhibition by narcotics on various diseases. The aims of this review are to provide a relatively reasonable drug regimen for clinicians, to explore potential ferroptosis protection drugs and targets, to reduce perioperative complications and to improve the postoperative performance of patients, especially those who are critically ill.
The hidden financial catastrophe of chronic kidney disease under universal coverage and Thai “Peritoneal Dialysis First Policy”

Objective Universal health coverage can decrease the magnitude of the individual patient's financial burden of chronic kidney disease (CKD), but the residual financial hardship from the patients' perspective has not been well-studied in low and middle-income countries (LMICs). This study aimed to evaluate the residual financial burden in patients with CKD stage 3 to dialysis in the “PD First Policy” under Universal Coverage Scheme (UCS) in Thailand. Methods This multicenter nationwide cross-sectional study in Thailand enrolled 1,224 patients with pre-dialysis CKD, hemodialysis (HD), and peritoneal dialysis (PD) covered by UCS and other health schemes for employees and civil servants. We interviewed patients to estimate the proportion with catastrophic health expenditure (CHE) and medical impoverishment. The risk factors associated with CHE were analyzed by multivariable logistic regression. Results Under UCS, the total out-of-pocket expenditure in HD was over two times higher than PD and nearly six times higher than CKD stages 3–4. HD suffered significantly more CHE and medical impoverishment than PD and pre-dialysis CKD [CHE: 8.5, 9.3, 19.5, 50.0% (p < 0.001) and medical impoverishment: 8.0, 3.1, 11.5, 31.6% (p < 0.001) for CKD Stages 3–4, Stage 5, PD, and HD, respectively]. In the poorest quintile of UCS, medical impoverishment was present in all HD and two-thirds of PD patients. Travel cost was the main driver of CHE in HD. In UCS, the adjusted risk of CHE increased in PD and HD (OR: 3.5 and 16.3, respectively) compared to CKD stage 3. Conclusions Despite universal coverage, the residual financial burden remained high in patients with kidney failure. CHE was considerably lower in PD than HD, although the rates remained alarmingly high in the poor. The “PD First' program” could serve as a model for other LMICs. However, strategies to minimize financial distress should be further developed, especially for the poor.
Predictive value of the presence of Prevotella and the ratio of Porphyromonas gingivalis to Prevotella in saliva for esophageal squamous cell carcinoma

Background Imbalance of oral salivary microbiota has been linked to the pathogenesis of a variety of systemic diseases, and oral bacterial species have been shown to be useful biomarkers for systemic diseases.This study aimed to characterize the alterations of oral microbiota in patients with esophageal squamous cell carcinoma (ESCC) and to evaluate the diagnostic performance of oral microbial biomarkers for ESCC. Methods The relative abundance of flora in saliva samples was analyzed by 16S rDNA sequencing, and differences in the species present in samples from ESCC patients and healthy controls (HCs) were identified by analyzing species diversity and performing LEfSe analysis. Receiver operating characteristic (ROC) curve analysis was applied to evaluate the diagnostic performance of the characteristic bacteria individually and in combination. Results Differences in bacterial diversity indexes were observed for the saliva of ESCC patients versus HCs (P<0.05), but principal coordinate analysis did not detect a significant difference in the composition of oral microbiota between ESCC patients and HCs (P>0.05). LEfSe analysis showed that Leptotrichia, Porphyromonas (Pg), Streptococcus, Rothia, Lactobacillus and Peptostreptococcus were more abundant in ESCC patient saliva than in HC saliva, whereas Haemophilus, Alloprevotella (All), Prevotella_7, Prevotella (Pre), Prevotella_6, Pasteurellaceae and Pasteurellales were significantly less abundant in ESCC patient saliva (P<0.05). From ROC curve analysis, Pg could detect ESCC with an area under the ROC curve (AUC) of 0.599, sensitivity of 62.2%, and specificity of 70%, whereas the ratio of Pg/Pre had an AUC of 0.791, sensitivity of 93.3%, and specificity of 62.3%. Moreover, the combination of the Pg/Pre and Pg/All ratios showed further improved diagnostic performance for ESCC (AUC=0.826) and even good sensitivity and specificity for the diagnosis of early ESCC (68.2% and 86%, respectively; AUC=0.786). Conclusion This study shows that Pg in saliva can be used as a characteristic marker of ESCC, and the ratios of Pg/Pre and Pg/All offered significantly improved diagnostic performance, especially for early ESCC.
Protostellar disc formation enabled by removal of small dust grains

It has been shown that a realistic level of magnetization of dense molecular cloud cores can suppress the formation of a rotationally supported disk (RSD) through catastrophic magnetic braking in the axisymmetric ideal MHD limit. In this study, we present conditions for the formation of RSDs through non-ideal MHD effects computed self-consistently from an equilibrium chemical network. We find that removing from the standard MRN distribution the large population of very small grains (VSGs) of ~10 $\AA$ to few 100 $\AA$ that dominate the coupling of the bulk neutral matter to the magnetic field increases the ambipolar diffusivity by ~1--2 orders of magnitude at densities below 10$^{10}$ cm$^{-3}$. The enhanced ambipolar diffusion (AD) in the envelope reduces the amount of magnetic flux dragged by the collapse into the circumstellar disk-forming region. Therefore, magnetic braking is weakened and more angular momentum can be retained. With continuous high angular momentum inflow, RSDs of tens of AU are able to form, survive, and even grow in size, depending on other parameters including cosmic-ray ionization rate, magnetic field strength, and rotation speed. Some disks become self-gravitating and evolve into rings in our 2D (axisymmetric) simulations, which have the potential to fragment into (close) multiple systems in 3D. We conclude that disk formation in magnetized cores is highly sensitive to chemistry, especially to grain sizes. A moderate grain coagulation/growth to remove the large population of VSGs, either in the prestellar phase or during free-fall collapse, can greatly promote AD and help formation of tens of AU RSDs.
Peripheral absolute eosinophil count identifies the risk of serious immune-related adverse events in non-small cell lung cancer

Background Immune-related adverse events (irAEs) have drawn a lot of attention lately as a result of the predominance of immunotherapy in advanced non-small cell lung cancer (NSCLC). However, the clinical evidence for irAEs in real life is limited. In this paper, the occurrence of irAEs in Chinese NSCLC patients was examined, and possible risk factors for the emergence of severe irAEs were discovered. Methods Our retrospective investigation assessed the occurrence of adverse events (AEs) and prognosis of 213 patients who received immunotherapy for NSCLC. Using univariate and multivariate logistic regression models, the association between clinicopathological traits and the incidence of severe irAEs was investigated. To assess the prognostic impact of irAEs, survival data was analyzed. Results Among the 213 NSCLC patients, 122 (57.3%) had irAEs of any grade, and 38 (17.8%) had high-grade (grade 3-5) AEs. Baseline peripheral absolute eosinophil count (AEC) (HR 6.58, 95% CI: 1.5-28.8, P=0.012) was found to be an independent predictor of high-grade irAEs by multivariate analysis. The survival analysis revealed that patients with severe irAEs had worse OS (15.7 vs. 20.8 months, 95% CI: 11.6-19.8 vs. 16.0-25.5, P=0.026). Conclusion According to our findings, the peripheral absolute eosinophil count (AEC) is a reliable indicator of severe irAEs in NSCLC. Serious irAEs that occur in patients often reflect poor prognoses. In the future, high-grade irAEs should receive more attention.
Drivers of water quality in Afromontane-savanna rivers

Although several studies have investigated the relationships between water quality in rivers and the types of land use within their catchments, many aspects of these relationships remain unclear in Afromontane-savanna rivers, especially the interactions between catchment land use, seasonality and stream size. Afromontane-savanna catchments present a unique situation where headwater regions and lowlands have experienced more dramatic land cover change, but mid-elevation regions remained rather natural. We examined the influence of seasonality, catchment land use and stream size, including their interactions, on water physico-chemistry, nutrients and major ions in the Afromontane-savanna Mara River in Kenya, using data collected from 2010 to 2018 at >150 sampling sites in the Kenyan part of the river. We developed generalized linear mixed models (GLMMs) to explore the influence of seasonality (dry and wet seasons), land use (forest, mixed, agriculture and grasslands), stream size (stream orders 1–7), and their interactions on river water quality. Water quality variables included physico-chemical measures (pH, dissolved oxygen [DO] concentration, temperature, electrical conductivity, total dissolved solids [TDS], turbidity, total suspended solids [TSS] and particulate organic matter [POM]), nutrients ( N H 4 + , N O 3 − , total dissolved nitrogen [TDN], total nitrogen [TN], soluble reactive phosphorus [SRP], total phosphorus [TP] and dissolved organic carbon), and major ions (Cl−, F−, S O 4 2 − , Na+, K+, Ca2+, Mg2+, Fe2+, H C O 3 − and Si). There were clear differences in average values of most water quality variables among land uses with sites in savanna grasslands having high levels of major ions, ammonium and P, while agricultural sites had higher dissolved fraction of N (except ammonium). Stream order was a poor predictor of water quality, and most parameters did not display any relationship (either linear or non-linear) with stream size. Our results can be used to efficiently enhance water quality by developing strategies for stream restoration and management based on the predomination type of land use in the catchments.
The symptoms of postpartum depression observed by family members: A pilot study

Postpartum Depression (PPD) is a burden on women's mental health after delivery, predominantly occurring in the 1st year. PPD poses a threat to the mother's life and affects the quality of childcare. Early detection by family members of depressive symptoms is critical. This study aimed to examine the role of family members in reporting depressive symptoms of PPD among new mothers. A cross-sectional study was conducted, where 56 family members were asked to report depressive symptoms observed in new mothers. At the same time, the new mothers were also screened for PPD using the Edinburgh Postpartum Depression Scale (EPDS). Binary logistic regression was performed. Depressive symptoms of new mothers reported by family members, including emotional and behavioral disturbance, being under stress, high anxiety, isolation, changing lifestyle, and inability to take care of their children, were found as predictors of PPD.
Sex-based metabolic and microbiota differences in roots and rhizosphere soils of dioecious papaya (Carica papaya L.)

Dioecious plant species have a high genetic variation that is important for coping with or adapting to environmental stress through natural selection. Intensive studies have reported dimorphism morphism in morphology, physiology, as well as biotic and abiotic stress responses in dioecious plants. Here, we demonstrated the dimorphism of metabolic profile and the preference of some microorganisms in the roots and rhizosphere soils of male and female papaya. The metabolic composition of roots were significantly different between the males and females. Some sex hormones occurred in the differential metabolites in roots and rhizosphere soils. For example, testosterone was up-regulated in male papaya roots and rhizosphere soils, whereas norgestrel was up-regulated in the female papaya roots, indicating a possible balance in papaya roots to control the sexual differentiation. Plant hormones such as BRs, JAs, SA and GAs were also detected among the differential metabolites in the roots and rhizosphere soils of dioecious papaya. In addition, some metabolites that have medicinal values, such as ecliptasaponin A, crocin, berberine and sapindoside A were also expressed differentially between the two sexes. Numerous differential metabolites from the papaya roots were secreted in the soil, resulting in the differences in microbial community structure in the roots and rhizosphere soils. Some nitrogen-fixing bacteria such as Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Brevundimonas and Microvirga were enriched in the male papaya roots or rhizosphere soils. While Candidatus Solibacter and Tumebacillus, which utilize organic matters, were enriched in the roots or rhizosphere soils of the female papaya. Some differences in the fungi abundance were also observed in both male and female papaya roots. These findings uncovered the effect of sex types on the metabolic and microbiota differences in roots and rhizosphere soils in papaya and will lead to investigations of underlining genomic and molecular mechanisms.
Exciton dynamics in conjugated polymer systems

Exciton dynamics in π-conjugated polymers systems encompass multiple time and length scales. Ultrafast femtosecond processes are intrachain and involve a quantum mechanical correlation of the exciton and nuclear degrees of freedom. In contrast, post-picosecond processes involve the incoherent Förster transfer of excitons between polymer chains. Exciton dynamics is also strongly determined by the spatial and temporal disorder that is ubiquitous in conjugated polymers. Since excitons are delocalized over hundreds of atoms, a theoretical understanding of these processes is only realistically possible by employing suitably parametrized coarse-grained exciton-phonon models. Moreover, to correctly account for ultrafast processes, the exciton and phonon modes must be treated on the same quantum mechanical basis and the Ehrenfest approximation must be abandoned. This further implies that sophisticated numerical techniques must be employed to solve these models. This review describes our current theoretical understanding of exciton dynamics in conjugated polymer systems. We begin by describing the energetic and spatial distribution of excitons in disordered polymer systems, and define the crucial concept of a “chromophore” in conjugated polymers. We also discuss the role of exciton-nuclear coupling, emphasizing the distinction between “fast” and “slow” nuclear degrees of freedom in determining “self-trapping” and “self-localization” of exciton-polarons. Next, we discuss ultrafast intrachain exciton decoherence caused by exciton-phonon entanglement, which leads to fluorescence depolarization on the timescale of 10-fs. Interactions of the polymer with its environment causes the stochastic relaxation and localization of high-energy delocalized excitons onto chromophores. The coupling of excitons with torsional modes also leads to various dynamical processes. On sub-ps timescales it causes exciton-polaron formation (i.e., exciton localization and local polymer planarization). Conversely, on post-ps timescales stochastic torsional fluctuations cause exciton-polaron diffusion along the polymer chain and at higher temperatures to transient exciton delocalization via extended exciton states. We next describe a first-principles, Förster-type model of interchain exciton transfer and diffusion in the condensed phase, whose starting point is a realistic description of the donor and acceptor chromophores. Finally, we discuss condensed phase transient exciton delocalization in highly-ordered nanofibers. We survey experimental results and explain how they can be understood in terms of our theoretical description of exciton dynamics coupled to information on polymer multiscale structures. The review also contains a brief critique of computational methods to simulate exciton dynamics.