Miracle-dz/UniFAR-FTUs huggingface dataset:
Zircon of Triassic Age in the Stuttgart Formation (Schilfsandstein)—Witness of Tephra Fallout in the Central European Basin and New Constraints on the Mid-Carnian Episode

The Carnian Stuttgart-Formation (Schilfsandstein) of the Central European Basin contains relics of Triassic volcanic detritus in form of euhedral zircon grains and authigenic analcime. Multiple LA-ICP-MS spot analyses of single zircon crystals from an outcrop near Heilbronn (SW Germany) yielded weighted average 206Pb/238U ages between 250 and 230 Ma, providing evidence for tephra fallout in the southern part of the Central European Basin related to Olenekian, Anisian–Ladinian and Carnian volcanic activity. The tephra was probably transported by monsoonal circulations from volcanic centres of the NW Tethys to the Central European Basin. The four youngest zircon crystals gave a weighted average 206Pb/238U age of 231.1 ± 1.6 Ma (10 analyses), which is interpreted to date syn-depositional tephra fallout into the fluvial Lower Schilfsandstein Member of the Stuttgart Formation. This new maximum depositional age provides the first evidence that deposition of the Stuttgart Formation, which represents the type-example of the mid-Carnian episode, a global episode of enhanced flux of siliciclastic detritus and related environmental perturbations, occurred during the Tuvalian 2 substage at ca. 231 Ma, about 3 million years later than suggested by previous correlations. Zircon grains with weighted average 206Pb/238U ages of 236.0 ± 1.2 Ma (n = 17) and 238.6 ± 1.5 Ma (n = 6) and 206Pb/238U ages between 241 ± 6 and 250 ± 3 Ma point to the presence of tephra in early Carnian to Olenekian strata of the Keuper to Buntsandstein Groups. Traces of these reworked tephra were incorporated into the Stuttgart Formation due to fluvial erosion in the southern Central European Basin and at its margins.
The Role of Leadership in Public Sector Innovation: A Systematic Review and Meta-Analysis of the Management of COVID-19 in Asian Countries

Strong leadership in public sector innovation can empower governments to address community challenges in new ways in light of the challenges posed by the global coronavirus pandemic. Coronavirus management policy, pandemic responses, needs, and options are reflected in various Asian countries in respective published literature, but a summarized synthesis is not available. Using a systematic review approach (PRISMA), this study has analyzed the role of leadership in public sector innovation in COVID-19 management and synthesized 23 articles from 23 different Asian countries. In the light of available data, public sector innovation (PSI) and the role played by the leadership of each country' have been found to be largely inter-dependent. The current review provides a cross-section of the ongoing nature of the pandemic, as management responses and trend data in the countries are still emerging or evolving. Additionally, our study contributes a current state report regarding the barriers facing the leadership of Asian countries in mitigating the global pandemic through PSI. Our study found that a strong political leadership presence combined with a technocratic approach and a highly-skilled public sector workforce, could lead to more tremendous success in managing the outbreak. Furthermore, religious leadership was also found to have a potentially significant role in COVID-19 management strategies.
Application of Sparse Representation in Bioinformatics

Inspired by L1-norm minimization methods, such as basis pursuit, compressed sensing, and Lasso feature selection, in recent years, sparse representation shows up as a novel and potent data processing method and displays powerful superiority. Researchers have not only extended the sparse representation of a signal to image presentation, but also applied the sparsity of vectors to that of matrices. Moreover, sparse representation has been applied to pattern recognition with good results. Because of its multiple advantages, such as insensitivity to noise, strong robustness, less sensitivity to selected features, and no “overfitting” phenomenon, the application of sparse representation in bioinformatics should be studied further. This article reviews the development of sparse representation, and explains its applications in bioinformatics, namely the use of low-rank representation matrices to identify and study cancer molecules, low-rank sparse representations to analyze and process gene expression profiles, and an introduction to related cancers and gene expression profile database.
Integration of Transcriptome and Methylome Analyses Provides Insight Into the Pathway of Floral Scent Biosynthesis in Prunus mume

DNA methylation is a common epigenetic modification involved in regulating many biological processes. However, the epigenetic mechanisms involved in the formation of floral scent have rarely been reported within a famous traditional ornamental plant Prunus mume emitting pleasant fragrance in China. By combining whole-genome bisulfite sequencing and RNA-seq, we determined the global change in DNA methylation and expression levels of genes involved in the biosynthesis of floral scent in four different flowering stages of P. mume. During flowering, the methylation status in the “CHH” sequence context (with H representing A, T, or C) in the promoter regions of genes showed the most significant change. Enrichment analysis showed that the differentially methylated genes (DMGs) were widely involved in eight pathways known to be related to floral scent biosynthesis. As the key biosynthesis pathway of the dominant volatile fragrance of P. mume, the phenylpropane biosynthesis pathway contained the most differentially expressed genes (DEGs) and DMGs. We detected 97 DMGs participated in the most biosynthetic steps of the phenylpropane biosynthesis pathway. Furthermore, among the previously identified genes encoding key enzymes in the biosynthesis of the floral scent of P. mume, 47 candidate genes showed an expression pattern matching the release of floral fragrances and 22 of them were differentially methylated during flowering. Some of these DMGs may or have already been proven to play an important role in biosynthesis of the key floral scent components of P. mume, such as PmCFAT1a/1c, PmBEAT36/37, PmPAL2, PmPAAS3, PmBAR8/9/10, and PmCNL1/3/5/6/14/17/20. In conclusion, our results for the first time revealed that DNA methylation is widely involved in the biosynthesis of floral scent and may play critical roles in regulating the floral scent biosynthesis of P. mume. This study provided insights into floral scent metabolism for molecular breeding.
ESBL Producing Escherichia coli in Faecal Sludge Treatment Plants: An Invisible Threat to Public Health in Rohingya Camps, Cox's Bazar, Bangladesh

Introduction: Human faecal sludge contains diverse harmful microorganisms, making it hazardous to the environment and public health if it is discharged untreated. Faecal sludge is one of the major sources of E. coli that can produce extended-spectrum β-lactamases (ESBLs). Objective: This study aimed to investigate the prevalence and molecular characterization of ESBL-producing E. coli in faecal sludge samples collected from faecal sludge treatment plants (FSTPs) in Rohingya camps, Bangladesh. Methods: ESBL producing E. coli were screened by cultural as well as molecular methods and further characterized for their major ESBL genes, plasmid profiles, pathotypes, antibiotic resistance patterns, conjugation ability, and genetic similarity. Results: Of 296 isolates, 180 were phenotypically positive for ESBL. All the isolates, except one, contained at least one ESBL gene that was tested (blaCTX−M−1, blaCTX−M−2, blaCTX−M−8, blaCTX−M−9, blaCTX−M−15, blaCTX−M−25, blaTEM, and blaSHV). From plasmid profiling, it was observed that plasmids of 1–211 MDa were found in 84% (151/180) of the isolates. Besides, 13% (24/180) of the isolates possessed diarrhoeagenic virulence genes. From the remaining isolates, around 51% (79/156) harbored at least one virulence gene that is associated with the extraintestinal pathogenicity of E. coli. Moreover, 4% (3/156) of the isolates were detected to be potential extraintestinal pathogenic E. coli (ExPEC) strains. Additionally, all the diarrhoeagenic and ExPEC strains showed resistance to three or more antibiotic groups which indicate their multidrug-resistant potential. ERIC-PCR differentiated these pathogenic isolates into seven clusters. In addition to this, 16 out of 35 tested isolates transferred plasmids of 32–112 MDa to E. coli J53 recipient strain. Conclusion: The present study implies that the faecal sludge samples examined here could be a potential origin for spreading MDR pathogenic ESBL-producing E. coli. The exposure of Rohingya individuals, living in overcrowded camps, to these organisms poses a severe threat to their health.
Unraveling the Complexity to Observe Associations Between Welfare Indicators and Hair Cortisol Concentration in Dairy Calves

Using levels of the stress hormone cortisol as an indicator for welfare is a common, but debated practice. In this observational study, hair cortisol concentration (HCC) of samples from 196 dairy calves from 7 to 302 days of age collected from 12 Swedish farms was determined using a commercially available ELISA. An assessment of animal welfare, assessed using animal-based indicators, was performed on the day of sampling. First, methodological factors with the potential to impact HCC and the effect of age were analyzed using generalized additive models. This revealed a significant peak in hair cortisol in young calves (around 50 days of age) and an association between fecal contamination of hair samples and the level of cortisol extracted. Second, associations between welfare indicators and HCC were explored using cluster analysis and regularized regression. The results show a complex pattern, possibly related to different coping styles of the calves, and indicators of poor welfare were associated with both increased and decreased hair cortisol levels. High cortisol levels were associated with potential indicators of competition, while low cortisol levels were associated with the signs of poor health or a poor environment. When running the regularized regression analysis without the contaminated hair samples and with the contaminated samples (including a contamination score), the results did not change, indicating that it may be possible to use a contamination score to correct for contamination.
The Complete Chloroplast Genome Sequences of Eight Fagopyrum Species: Insights Into Genome Evolution and Phylogenetic Relationships

Buckwheat (Fagopyrum genus, Polygonaceae), is an annual or perennial, herbaceous or semi-shrub dicotyledonous plant. There are mainly three cultivated buckwheat species, common buckwheat (Fagopyrum esculentum) is widely cultivated in Asia, Europe, and America, while Tartary buckwheat (F. tataricum) and F. cymosum (also known as F. dibotrys) are mainly cultivated in China. The genus Fagopyrum is taxonomically confusing due to the complex phenotypes of different Fagopyrum species. In this study, the chloroplast (cp) genomes of three Fagopyrum species, F. longistylum, F. leptopodum, F. urophyllum, were sequenced, and five published cp genomes of Fagopyrum were retrieved for comparative analyses. We determined the sequence differentiation, repeated sequences of the cp genomes, and the phylogeny of Fagopyrum species. The eight cp genomes ranged, gene number, gene order, and GC content were presented. Most of variations of Fagopyrum species cp genomes existed in the LSC and SSC regions. Among eight Fagopyrum chloroplast genomes, six variable regions (ndhF-rpl32, trnS-trnG, trnC, trnE-trnT, psbD, and trnV) were detected as promising DNA barcodes. In addition, a total of 66 different SSR (simple sequence repeats) types were found in the eight Fagopyrum species, ranging from 8 to 16 bp. Interestingly, many SSRs showed significant differences especially in some photosystem genes, which provided valuable information for understanding the differences in light adaptation among different Fagopyrum species. Genus Fagopyrum has shown a typical branch that is distinguished from the Rumex, Rheum, and Reynoutria, which supports the unique taxonomic status in Fagopyrum among the Polygonaceae. In addition, phylogenetic analysis based on the cp genomes strongly supported the division of eight Fagopyrum species into two independent evolutionary directions, suggesting that the separation of cymosum group and urophyllum group may be earlier than the flower type differentiation in Fagopyrum plants. The results of the chloroplast-based phylogenetic tree were further supported by the matK and Internal Transcribed Spacer (ITS) sequences of 17 Fagopyrum species, which may help to further anchor the taxonomic status of other members in the urophyllum group in Fagopyrum. This study provides valuable information and high-quality cp genomes for identifying species and evolutionary analysis for future Fagopyrum research.
INL reconstruction of A/D converters via parametric spectral estimation

The work presented in this paper builds on previous research done by the authors detailing a novel procedure for obtaining a very fast measurement of the integral nonlinearity of an ADC. The core of the method is the parametric spectral estimation of the ADC output; the static characteristic is subsequently reconstructed as a sum of Chebyshev polynomials, in accordance with a previously developed procedure. The method allows one to test an ADC with sinusoids of any reasonable amplitude (even a slight overdrive is allowed), frequency (no synchronization is needed) and phase (which is digitally compensated). This approach is less accurate than the histogram test but incomparably faster (about 8000 samples are sufficient regardless of the ADC resolution).
Towards Effective Patient Simulators

In this paper we give an overview of the field of patient simulators and provide qualitative and quantitative comparison of different modeling and simulation approaches. Simulators can be used to train human caregivers but also to develop and optimize algorithms for clinical decision support applications and test and validate interventions. In this paper we introduce three novel patient simulators with different levels of representational accuracy: HeartPole, a simplistic transparent rule-based system, GraphSim, a graph-based model trained on intensive care data, and Auto-ALS—an adjusted version of an educational software package used for training junior healthcare professionals. We provide a qualitative and quantitative comparison of the previously existing as well as proposed simulators.
An Adverse Outcome Pathway for Decreased Lung Function Focusing on Mechanisms of Impaired Mucociliary Clearance Following Inhalation Exposure

Adverse outcome pathways (AOPs) help to organize available mechanistic information related to an adverse outcome into key events (KEs) spanning all organizational levels of a biological system(s). AOPs, therefore, aid in the biological understanding of a particular pathogenesis and also help with linking exposures to eventual toxic effects. In the regulatory context, knowledge of disease mechanisms can help design testing strategies using in vitro methods that can measure or predict KEs relevant to the biological effect of interest. The AOP described here evaluates the major processes known to be involved in regulating efficient mucociliary clearance (MCC) following exposures causing oxidative stress. MCC is a key aspect of the innate immune defense against airborne pathogens and inhaled chemicals and is governed by the concerted action of its functional components, the cilia and airway surface liquid (ASL). The AOP network described here consists of sequences of KEs that culminate in the modulation of ciliary beat frequency and ASL height as well as mucus viscosity and hence, impairment of MCC, which in turn leads to decreased lung function.
Study on LVRT Decoupling Dual Synchronous Current Controller

Under three-phase grid asymmetric fault conditions, use traditional PI controller of PV inverters to inject symmetric current positive sequence into the grid, ignoring the impact of the negative sequence current on LVRT, thus traditional PI controller does not apply to three-phase grid asymmetric faults. The paper proposes the decoupling dual synchronous current controller to reject positive, negative sequence current into the grid simultaneously and adopt positive and negative sequence flexible control to determine the active current reference and reactive current reference, avoiding the various drawbacks such as power control, totally positive sequence control bringing. Experiment verify the science and feasibility that decoupling dual synchronous current controller applies to asymmetric faults riding-through.
Shedding Structured Light on Molecular Immunity: The Past, Present and Future of Immune Cell Super Resolution Microscopy

In the two decades since the invention of laser-based super resolution microscopy this family of technologies has revolutionised the way life is viewed and understood. Its unparalleled resolution, speed, and accessibility makes super resolution imaging particularly useful in examining the highly complex and dynamic immune system. Here we introduce the super resolution technologies and studies that have already fundamentally changed our understanding of a number of central immunological processes and highlight other immunological puzzles only addressable in super resolution.
Preservation of Fluorescence Signal and Imaging Optimization for Integrated Light and Electron Microscopy

Life science research often needs to define where molecules are located within the complex environment of a cell or tissue. Genetically encoded fluorescent proteins and or fluorescence affinity-labeling are the go-to methods. Although recent fluorescent microscopy methods can provide localization of fluorescent molecules with relatively high resolution, an ultrastructural context is missing. This is solved by imaging a region of interest with correlative light and electron microscopy (CLEM). We have adopted a protocol that preserves both genetically-encoded and antibody-derived fluorescent signals in resin-embedded cell and tissue samples and provides high-resolution electron microscopy imaging of the same thin section. This method is particularly suitable for dedicated CLEM instruments that combine fluorescence and electron microscopy optics. In addition, we optimized scanning EM imaging parameters for samples of varying thicknesses. These protocols will enable rapid acquisition of CLEM information from samples and can be adapted for three-dimensional EM.
Preparation of ZnO/Brucite Functional Composite Powder by the Mechanochemical Method

In this experiment, ZnO/brucite composite powder was prepared through the mechanochemical method; further, the properties, particle morphology, and structure of the composite powder were characterized. The results show that mechanical grinding action can promote the production of a large number of surface ions with unsaturated coordination number on the surface of brucite and ZnO particles, thereby promoting hydroxylation of the particle surfaces. The addition of NaOH to the composite system can also aid the further activation of the surface of the brucite and ZnO particles and the formation of more associated hydroxyl groups. Finally, a core–shell composite powder is formed with weak forces such as hydrogen bonds and van der Waals forces as the connecting bonds.
Thoracic Aorta Diameter Calculation by Artificial Intelligence Can Predict the Degree of Arterial Stiffness

Background: Arterial aging is characterized by decreased vascular function, caused by arterial stiffness (AS), and vascular morphological changes, caused by arterial dilatation. We analyzed the relationship of pre-AS and AS, as assessed by cardio ankle vascular index (CAVI), with arterial diameters (AD) at nine levels, from the aortic sinus to the abdominal aorta, as measured by artificial intelligence (AI) on non-enhanced chest computed tomography (CT) images. Methods: Overall, 801 patients who underwent both chest CT scan and arterial elasticity test were enrolled. Nine horizontal diameters of the thoracic aorta (from the aortic sinuses of Valsalva to the abdominal aorta at the celiac axis origin) were measured by AI using CT. Patients were divided into non-AS (mean value of the left and right CAVIs [M.CAVI] < 8), pre-AS (8 ≤ M.CAVI < 9), and AS (M.CAVI ≥ 9) groups. We compared AD differences among groups, analyzed the correlation of age, ADs, and M.CAVI or the mean pressure-independent CAVI (M.CAVI0), Furthermore, we evaluated the risk predictors and the diagnostic value of the nine ADs for pre-AS and AS. Results: The AD at mid descending aorta (MD) correlated strongest with CAVI (r = 0.46, p < 0.001) or M.CAVI0 (r = 0.42, p < 0.001). M.CAVI was most affected by the MD AD and by age. An increase in the MD AD independently predicted the occurrence of pre-AS or AS. For MD AD, every 4.37 mm increase caused a 14% increase in the pre-AS and AS risk and a 13% increase in the AS risk. With a cut-off value of 26.95 mm for the MD AD, the area under the curve (AUC) for identifying the risk of AS was 0.743. With a cut-off value of 25.15 mm, the AUC for identifying the risk of the stage after the prophase of AS is 0.739. Conclusions: Aging is associated with an increase in AD and a decrease in arterial elasticity. An increase in AD, particularly at the MD level is an independent predictor of AS development.
Prevalence, Pattern and Predictors for Dyslipidemia of Chinese Women With Polycystic Ovary Syndrome

Objective: To investigate the prevalence, pattern and risk predictors for dyslipidemia among Chinese women with polycystic ovary syndrome (PCOS). Study Design and Methods: A total of 1,000 women diagnosed as PCOS by modified Rotterdam criteria were enrolled in 27 hospitals across China in a randomized controlled trial. Anthropometric, metabolic parameters, sex hormone, and lipid levels were measured at the baseline visit. Dyslipidemia was defined according to total cholesterol (TC), low density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), and triglycerides (TG) level. Independent t-test and logistic regression were used to identify predictors for dyslipidemia. Area under the receiver operating characteristic curve (AUC) was calculated. Results: A total of 41.3% of the women had dyslipidemia, and the prevalence of abnormal TC, LDL-C, HDL-C, and TG were 8.6, 9.1, 26.9, and 17.5%, respectively. Logistic regression found that age, waist circumference, insulin, follicle-stimulating hormone, and sex hormone-binding globulin were independent predictors for dyslipidemia. When combining these predictors, the AUC was 0.744. The cut-off points were age >28.5 years, waist circumference >86.5 cm, insulin >96.0 pmol/L, follicle-stimulating hormone <5.6 mIU/mL, and sex hormone-binding hormone <31.0 nmol/L, respectively. Conclusion: Dyslipidemia was common in Chinese women with PCOS, and low HDL-C level was the predominant lipid abnormality. Age, waist circumference, follicle-stimulating hormone, insulin and sex hormone-binding globulin were predictive for dyslipidemia among Chinese women with PCOS.