Miracle-dz/UniFAR-FTUs huggingface dataset:
Phenotypic and Differential Gene Expression Analyses of Phase Transition in Oedaleus Asiaticus under High-Density Population Stress

Simple Summary Oedaleus asiaticus (Bey-Bienko) is one of the most dominant locust species in grassland and pastoral areas in Inner Mongolia of northern China. It is highly abundant and usually makes up more than half (sometimes even up to 90%) of the local locust community in locust outbreaks. Locust aggregation is a prerequisite for a locust outbreak, requiring phase change from solitary to gregarious individuals. In this study, we used Illumina sequencing technology to screen 3911, 7478, 3142, and 1852 differentially expression genes (DEGs) in Oedaleus asiaticus during phase transition after 1, 3, 5, and 7 days of high-density treatment, respectively, and recorded the transition from green to brown individuals in different stages. The change in expression patterns of JHAMT, JHEH, DIB, HPD, TAT, PAH, DDC, CSP, and TO, which are the key genes of phase transition relevant metabolic pathways, at different stages of the phenotypic transformation suggests their regulatory role in the phenotypic process. This study improves the scientific understanding of phase variation in locusts; the learning can be applied to other insects. Abstract The high-density-dependent phase change from solitary to gregarious individuals in locusts is a typical example of phenotypic plasticity. However, the underlying molecular mechanism is not clear. In this study, first, Oedaleus asiaticus were treated with high-density population stress and then analyzed by Illumina sequencing on days 1, 3, 5, and 7 of the body color change to identify the stage-specific differentially expressed genes (DEGs). The KEGG pathway enrichment analysis of the identified DEGs revealed their role in metabolic pathways. Furthermore, the expression patterns of the nine key DEGs were studied in detail; this showed that the material change in locusts began on the third day of the high-density treatment, with the number of DEGs being the largest, indicating the importance of this period in the phase transition. In addition, the phenotypic change involved several key genes of important regulatory pathways, possibly working in a complex network. Phenotypic plasticity in locusts is multifactorial, involving multilevel material network interactions. This study improves the mechanistic understanding of phenotypic variation in insects at the genetic level.
Independent Associations of Education, Intelligence, and Cognition With Hypertension and the Mediating Effects of Cardiometabolic Risk Factors: A Mendelian Randomization Study

Background: Education, intelligence, and cognition are associated with hypertension, but which one plays the most prominent role in the pathogenesis of hypertension and which modifiable risk factors mediate the causal effects remains unknown. Methods: Using summary statistics of genome-wide association studies of predominantly European ancestry, we conducted 2-sample multivariable Mendelian randomization to estimate the independent effects of education, intelligence, or cognition on hypertension (FinnGen study, 70 651 cases/223 663 controls; UK Biobank, 77 723 cases/330 366 controls) and blood pressure (International Consortium of Blood Pressure, 757 601 participants), and used 2-step Mendelian randomization to evaluate 25 potential mediators of the association and calculate the mediated proportions. Results: Meta-analysis of inverse variance weighted Mendelian randomization results from FinnGen and UK Biobank showed that genetically predicted 1-SD (4.2 years) higher education was associated with 44% (95% CI: 0.40–0.79) decreased hypertension risk and 1.682 mm Hg lower systolic and 0.898 mm Hg lower diastolic blood pressure, independently of intelligence and cognition. While the causal effects of intelligence and cognition on hypertension were not independent of education; 6 out of 25 cardiometabolic risk factors were identified as mediators of the association between education and hypertension, ranked by mediated proportions, including body mass index (mediated proportion: 30.1%), waist-to-hip ratio (22.8%), body fat percentage (14.1%), major depression (7.0%), high-density lipoprotein cholesterol (4.7%), and triglycerides (3.4%). These results were robust to sensitivity analyses. Conclusions: Our findings illustrated the causal, independent impact of education on hypertension and blood pressure and outlined cardiometabolic mediators as priority targets for prevention of hypertension attributable to low education.
Observational determination of the galaxy bias from cosmic variance with a random pointing survey: clustering ofz∼ 2 galaxies from Hubble’s BoRG survey

Gravitational clustering broadens the count-in-cells distribution of galaxies for surveys along uncorrelated (well-separated) lines of sight beyond Poisson noise. A number of methods have proposed to measure this excess "cosmic" variance to constrain the galaxy bias (i.e. the strength of clustering) independently of the two-point correlation function. Here we present an observational application of these methods using data from 141 uncorrelated fields (~700 arcmin$^2$ total) from Hubble's Brightest of Reionizing Galaxies (BoRG) survey. We use BoRG's broad-band imaging in optical and near infrared to identify N~1000 photometric candidates at z~2 through a combination of colour selection and photometric redshift determination, building a magnitude-limited sample with $m_{AB}\leq24.5$ in F160W. We detect a clear excess in the variance of the galaxy number counts distribution compared to Poisson expectations, from which we estimate a galaxy bias $b \approx 3.63 \pm 0.57$. When divided by SED-fit classification into ~400 early-type and ~600 late-type candidates, we estimate biases of $b_{early} \approx 4.06 \pm 0.67$ and $b_{late} \approx 2.98 \pm 0.98$ respectively. These estimates are consistent with previous measurements of the bias from the two-point correlation function, and demonstrate that with $N\gtrsim100$ sight-lines, each containing $N\gtrsim5$ objects, the counts-in-cell analysis provides a robust measurement of the bias. This implies that the method can be applied effectively to determine clustering properties (and characteristic dark-matter halo masses) of z~6-9 galaxies from a pure-parallel James Webb Space Telescope survey similar in design to Hubble's BoRG survey.
Trajectories of child growth, child development, and home child‐rearing quality during the Covid pandemic in rural Nepal

Abstract Background Children, especially disadvantaged children in poor countries, were expected to be among the “biggest victims” of the Covid pandemic. Economic burdens, decreased nutritious foods, reduced medical care, school closures, and ill‐health or death of family members were predicted to increase child undernutrition and developmental delays, and diminish home child‐rearing quality. Methods A planned nutrition intervention could not be implemented due to Covid restrictions. However, three surveys (pre‐Covid [December 2019], July 2021, and September 2021) in 280 Nepali households (309 parent‐dyads, 368 children, 6–66 months old) collected demographics, child anthropometry and development (Ages and Stages Questionnaire‐3 [ASQ‐3]), and home child‐rearing quality (caregiver engagement, learning resources, adult supervision [UNICEF's Multiple Indicator Cluster Survey]). Mixed‐effect regression models adjusted for household (wealth, maternal education) and child factors (age, gender) and survey round. Results Height, mid‐upper‐arm circumference, and head circumference measurements improved over time. The total ASQ‐3 score did not change: Communication scores increased while fine motor and personal‐social scores declined. Girls' growth and development worsened more than boys. Caregiver engagement (especially mothers') generally declined, but learning resource availability increased. More children were left unsupervised at Round 2 than Round 1 or 3. Conclusions In this sample, some aspects of child growth, development, and home child‐rearing quality improved while others declined. Better understanding of these changes in child well‐being and the family environment during the pandemic could provide insight on how to protect children during future crises.
Morphology and Phylogeny of Pestalotiopsis (Sporocadaceae, Amphisphaeriales) from Fagaceae Leaves in China

Pestalotiopsis is a common fungal genus inhabiting plant tissues as endophytes, pathogens, and saprophytes. Fagaceae is a plant family including many important tree species, such as Castanea mollissima and Quercus spp. In this study, diseased leaves of Fagaceae in China were investigated, and 16 Pestalotiopsis species were identified based on morphology and phylogeny of combined loci of internal transcribed spacers (ITS), the translation elongation factor 1-α (tef1), and the beta-tubulin (tub2) genes. ABSTRACT Fagaceae is a family of flowering plants widely distributed in the Northern Hemisphere, including deciduous and evergreen trees and shrubs. Species of Pestalotiopsis are well-known agents of leaf spot diseases, but targeted sampling on Fagaceae is still missing. To determine the diversity of Pestalotiopsis species associated with Fagaceae leaf spot in China, investigations were conducted in the main areas of Fagaceae distribution from 2016 to 2021. Diseased leaf tissues were collected, and fungal isolates were obtained from leaf spots. In the present study, 43 isolates of Pestalotiopsis were studied based on combined morphology and phylogeny. As a result, 10 new species were identified, viz., Pestalotiopsis anhuiensis, P. castanopsidis, P. changjiangensis, P. cyclobalanopsidis, P. foliicola, P. guangxiensis, P. guizhouensis, P. lithocarpi, P. shaanxiensis, and P. silvicola, and six new host records were recognized. IMPORTANCE Pestalotiopsis is a common fungal genus inhabiting plant tissues as endophytes, pathogens, and saprophytes. Fagaceae is a plant family including many important tree species, such as Castanea mollissima and Quercus spp. In this study, diseased leaves of Fagaceae in China were investigated, and 16 Pestalotiopsis species were identified based on morphology and phylogeny of combined loci of internal transcribed spacers (ITS), the translation elongation factor 1-α (tef1), and the beta-tubulin (tub2) genes. Among these, 10 new species were found, and six new host records were revealed. Our study significantly updates the taxonomy of Pestalotiopsis and enhances our understanding of leaf diseases of Fagaceae hosts.
Can air purification improve sleep quality? A 2‐week randomised‐controlled crossover pilot study in healthy adults

Insufficient quantity and quality of sleep is a public health concern that can be addressed by interventions for improving sleep outcomes. Environmental factors such as poor air quality are a potential target for intervention, particularly in light of associations between air pollution and worse sleep. The aim of this pilot study was to investigate the effects of using an air purifier on sleep outcomes and mood in 30 healthy adults. There were two conditions: (i) air purifier with a high‐efficiency particulate air filter; (ii) air purifier with a placebo filter. Participants undertook both conditions, each over 2 weeks with a 2‐week washout, following a counterbalanced, double‐blind design. Daily sleep outcomes were measured with actigraphy watches and sleep diaries, whilst daily mood was assessed with the Positive and Negative Affect Schedule. The Insomnia Severity Index, the Pittsburgh Sleep Quality Index, and symptoms of anxiety and depression were measured pre‐ and post‐. The purifier filter was associated with increased total sleep time for an average of 12 min per night, and increased total time in bed for an average of 19 min per night relative to the placebo. There were several sleep and mood outcomes for which no changes were observed, and time awake after sleep onset was higher for the purifier filter. Air quality was better during the high‐efficiency particulate air filter condition. These findings offer positive indications that environmental interventions that improve air quality can have benefits for sleep outcomes in healthy populations who are not exhibiting clinical sleep disturbances.
Antimicrobial and antioxidant properties and quantitative screening of phytochemicals of Fraxinus excelsior L. and Eschscholtzia californica Cham. mother tinctures

Abstract The antioxidant and antimicrobial activities of Fraxinus excelsior L. and Eschscholtzia californica Cham. mother tinctures against a range of foodborne bacteria were investigated to determine the major components and to analyse the action spectrum and antimicrobial effectiveness of the extracts. Results demonstrated a significant antioxidant activity of Fraxinus excelsior L. and a lower activity of Eschscholtzia californica Cham. and a good chemical phenolic composition with the highest content of flavonoids. The Fraxinus excelsior L. and Eschscholtzia californica Cham. mother tinctures demonstrated a middle-high antimicrobial activity against, respectively, 66.67% and 43.33% of all tested bacteria. The inhibitory activity showed a moderate effect on the growth of the sensitive strains in presence of extracts minimum inhibitory concentration. The synergistic actions of bioactive compounds detected in the extracts might be on the basis of antioxidant and biological activities observed and should be used in pharmaceutical, food preservation, alternative medicine and natural therapies fields. Graphical Abstract
VSGs Expressed during Natural T. b. gambiense Infection Exhibit Extensive Sequence Divergence and a Subspecies-Specific Bias towards Type B N-Terminal Domains

Human African trypanosomiasis is a neglected tropical disease primarily caused by the extracellular parasite Trypanosoma brucei gambiense. To avoid elimination by the host, these parasites repeatedly replace their variant surface glycoprotein (VSG) coat. ABSTRACT Trypanosoma brucei gambiense is the primary causative agent of human African trypanosomiasis (HAT), a vector-borne disease endemic to West and Central Africa. The extracellular parasite evades antibody recognition within the host bloodstream by altering its variant surface glycoprotein (VSG) coat through a process of antigenic variation. The serological tests that are widely used to screen for HAT use VSG as one of the target antigens. However, the VSGs expressed during human infection have not been characterized. Here, we use VSG sequencing (VSG-seq) to analyze the VSGs expressed in the blood of patients infected with T. b. gambiense and compared them to VSG expression in Trypanosoma brucei rhodesiense infections in humans as well as Trypanosoma brucei brucei infections in mice. The 44 VSGs expressed during T. b. gambiense infection revealed a striking bias toward expression of type B N termini (82% of detected VSGs). This bias is specific to T. b. gambiense, which is unique among T. brucei subspecies in its chronic clinical presentation and anthroponotic nature. The expressed T. b. gambiense VSGs also share very little similarity to sequences from 36 T. b. gambiense whole-genome sequencing data sets, particularly in areas of the VSG protein exposed to host antibodies, suggesting the antigen repertoire is under strong selective pressure to diversify. Overall, this work demonstrates new features of antigenic variation in T. brucei gambiense and highlights the importance of understanding VSG repertoires in nature. IMPORTANCE Human African trypanosomiasis is a neglected tropical disease primarily caused by the extracellular parasite Trypanosoma brucei gambiense. To avoid elimination by the host, these parasites repeatedly replace their variant surface glycoprotein (VSG) coat. Despite the important role of VSGs in prolonging infection, VSG expression during human infections is poorly understood. A better understanding of natural VSG gene expression dynamics can clarify the mechanisms that T. brucei uses to alter its VSG coat. We analyzed the expressed VSGs detected in the blood of patients with trypanosomiasis. Our findings indicate that there are features of antigenic variation unique to human-infective T. brucei subspecies and that natural VSG repertoires may vary more than previously expected.
Improving Infinium MethylationEPIC data processing: re-annotation of enhancers and long noncoding RNA genes and benchmarking of normalization methods

ABSTRACT Illumina Infinium DNA Methylation (5mC) arrays are a popular technology for low-cost, high-throughput, genome-scale measurement of 5mC distribution, especially in cancer and other complex diseases. After the success of its HumanMethylation450 array (450k), Illumina released the MethylationEPIC array (850k) featuring increased coverage of enhancers. Despite the widespread use of 850k, analysis of the corresponding data remains suboptimal: it still relies mostly on Illumina’s default annotation, which underestimates enhancerss and long noncoding RNAs. Results: We have thus developed an approach, based on the ENCODE and LNCipedia databases, which greatly improves upon Illumina’s default annotation of enhancers and long noncoding transcripts. We compared the re-annotated 850k with both 450k and reduced-representation bisulphite sequencing (RRBS), another high-throughput 5mC profiling technology. We found 850k to cover at least three times as many enhancers and long noncoding RNAs as either 450k or RRBS. We further investigated the reproducibility of the three technologies, applying various normalization methods to the 850k data. Most of these methods reduced variability to a level below that of RRBS data. We then used 850k with our new annotation and normalization to profile 5mC changes in breast cancer biopsies. 850k highlighted aberrant enhancer methylation as the predominant feature, in agreement with previous reports. Our study provides an updated processing approach for 850k data, based on refined probe annotation and normalization, allowing for improved analysis of methylation at enhancers and long noncoding RNA genes. Our findings will help to further advance understanding of the DNA methylome in health and disease.
Additive interaction between dietary inflammatory index and some key risk factors of multiple sclerosis: a population-based incident case–control study

ABSTRACT Background Recently, dietary inflammatory index (DII) has been introduced as a significant risk factor for MS. We examined the interaction between dietary inflammatory index and some formerly demonstrated key risk factors of multiple sclerosis (MS). Material and Methods We conducted a population-based incident case–control study of 547 MS cases and 1057 controls. Multiplicative and additive interaction were assessed using interaction term in the logistic regression model and synergy index (SI), respectively. Results Additive interaction was detected between DII and drug abuse (SI = 2.58; 95% CI: 1.14–5.82), gender (SI = 2.00; 95% CI: 1.39–2.87) and history of depression (SI = 1.68; 95% CI: 1.04–2.72) on the risk scale. The risk of MS in drug abusers with DII ≥ 0 was 10.4-times higher than that in non-drug abusers with DII < 0 (OR = 10.4, 95% CI: 5.12–21.02, P < 0.001). We also found that women with DII ≥ 0 had a 9.2 times larger risk compared with the men with DII < 0(OR = 9.2, 95% CI: 6.3–13.5, P < 0.001). Similarly, the risk of MS was remarkably higher in those with a history of depression and DII >0 (OR = 7.6, 95% CI: 5.1–11.5, P < 0.001). There was no evidence of multiplicative interaction between DII and the other risk factors of MS on the risk scale. Conclusions We identified additive interaction between DII and drug abuse, gender and history of depression on MS. Further studies are needed to understand the underlying mechanisms of these detected interactions.
Spectral properties of a hybrid-qubit model based on a two-dimensional quantum dot

The design and study of hybrid qubits is driven by their ability to get along the best of charge qubits and of spin qubits, {\em i.e.} the speed of operation of the former and the very slow decoherence rates of the latter ones. There are several proposals to implement hybrid qubits, this works focuses on the spectral properties of an one-electron hybrid qubit. By design, the information would be stored in the electronic spin and the switching between the qubit basis states would be achieved using an external ac electric field. The electron is confined in a two-dimensional quantum dot, whose confining potential is given by a quartic potential, features that are typical of GaAS quantum dots. Besides the confining potential that characterizes the quantum dot there are two static magnetic fields applied to the system, one is a large constant Zeeman field and the other one has a constant gradient. We study the spectral properties of the model Hamiltonian, a Scr\"odinger-Pauli Hamiltonian with realistic parameters, using the Ritz method. In particular, we look for regions of the parameter space where the lowest eigenenergies and their eigenfunctions allow to define a qubit which is stable under perturbations to the design parameters. We put special attention to the constraints that the design imposes over the magnetic fields, the tuning of the energy gap between the qubit states and the expectation value of the spin operator where the information would be stored.
Solar diameter with 2012 Venus transit

The role of Venus and Mercury transits is crucial to know the past history of the solar diameter. Through the W parameter, the logarithmic derivative of the radius with respect to the luminosity, the past values of the solar luminosity can be recovered. The black drop phenomenon affects the evaluation of the instants of internal and external contacts between the planetary disk and the solar limb. With these observed instants compared with the ephemerides the value of the solar diameter is recovered. The black drop and seeing effects are overcome with two fitting circles, to Venus and to the Sun, drawn in the undistorted part of the image. The corrections of ephemerides due to the atmospheric refraction will also be taken into account. The forthcoming transit of Venus will allow an accuracy on the diameter of the Sun better than 0.01 arcsec, with good images of the ingress and of the egress taken each second. Chinese solar observatories are in the optimal conditions to obtain valuable data for the measurement of the solar diameter with the Venus transit of 5/6 June 2012 with an unprecedented accuracy, and with absolute calibration given by the ephemerides.