Miracle-dz/UniFAR-FTUs huggingface dataset:
Dose-response relationship between the variables of unilateral optogenetic stimulation and transcallosal evoked responses in rat motor cortex

Efficient interhemispheric integration of neural activity between left and right primary motor cortex (M1) is critical for inter-limb motor control. We employed optogenetic stimulation to establish a framework for probing transcallosal M1–M1 interactions in rats. We performed optogenetic stimulation of excitatory neurons in right M1 of male Sprague-Dawley rats. We recorded the transcallosal evoked potential in contralateral left M1 via chronically implanted electrodes. Recordings were performed under anesthesia combination of dexmedetomidine and a low concentration of isoflurane. We systematically varied the stimulation intensity and duration to characterize the relationship between stimulation parameters in right M1 and the characteristics of the evoked intracortical potentials in left M1. Optogenetic stimulation of right M1 consistently evoked a transcallosal response in left M1 with a consistent negative peak (N1) that sometimes was preceded by a smaller positive peak (P1). Higher stimulation intensity or longer stimulation duration gradually increased N1 amplitude and reduced N1 variability across trials. A combination of stimulation intensities of 5–10 mW with stimulus durations of 1–10 ms were generally sufficient to elicit a robust transcallosal response in most animal, with our optic fiber setup. Optogenetically stimulated excitatory neurons in M1 can reliably evoke a transcallosal response in anesthetized rats. Characterizing the relationship between “stimulation dose” and “response magnitude” (i.e., the gain function) of transcallosal M1-to-M1 excitatory connections can be used to optimize the variables of optogenetic stimulation and ensure stimulation efficacy.
Chromosome-scale genome assembly of Camellia sinensis combined with multi-omics provides insights into its responses to infestation with green leafhoppers

The tea plant (Camellia sinensis) is an important economic crop, which is becoming increasingly popular worldwide, and is now planted in more than 50 countries. Tea green leafhopper is one of the major pests in tea plantations, which can significantly reduce the yield and quality of tea during the growth of plant. In this study, we report a genome assembly for DuyunMaojian tea plants using a combination of Oxford Nanopore Technology PromethION™ with high-throughput chromosome conformation capture technology and used multi-omics to study how the tea plant responds to infestation with tea green leafhoppers. The final genome was 3.08 Gb. A total of 2.97 Gb of the genome was mapped to 15 pseudo-chromosomes, and 2.79 Gb of them could confirm the order and direction. The contig N50, scaffold N50 and GC content were 723.7 kb, 207.72 Mb and 38.54%, respectively. There were 2.67 Gb (86.77%) repetitive sequences, 34,896 protein-coding genes, 104 miRNAs, 261 rRNA, 669 tRNA, and 6,502 pseudogenes. A comparative genomics analysis showed that DuyunMaojian was the most closely related to Shuchazao and Yunkang 10, followed by DASZ and tea-oil tree. The multi-omics results indicated that phenylpropanoid biosynthesis, α-linolenic acid metabolism, flavonoid biosynthesis and 50 differentially expressed genes, particularly peroxidase, played important roles in response to infestation with tea green leafhoppers (Empoasca vitis Göthe). This study on the tea tree is highly significant for its role in illustrating the evolution of its genome and discovering how the tea plant responds to infestation with tea green leafhoppers will contribute to a theoretical foundation to breed tea plants resistant to insects that will ultimately result in an increase in the yield and quality of tea.
Identification of amino acid domains of Borrelia burgdorferi P66 that are surface exposed and important for localization, oligomerization, and porin function of the protein

P66, a bifunctional integral outer membrane protein, is necessary for Borrelia burgdorferi to establish initial infection and to disseminate in mice. The integrin binding function of P66 facilitates extravasation and dissemination, but the role of its porin function during murine infection has not been investigated. A limitation to studying P66 porin function during mammalian infection has been the lack of structural information for P66. In this study, we experimentally characterized specific domains of P66 with regard to structure and function. First, we aligned the amino acid sequences of P66 from Lyme disease-causing Borrelia and relapsing fever-causing Borrelia to identify conserved and unique domains between these disease-causing clades. Then, we examined whether specific domains of P66 are exposed on the surface of the bacteria by introducing c-Myc epitope tags into each domain of interest. The c-Myc epitope tag inserted C-terminally to E33 (highly conserved domain), to T187 (integrin binding region domain and a non-conserved domain), and to E334 (non-conserved domain) were all detected on the surface of Borrelia burgdorferi. The c-Myc epitope tag inserted C-terminally to E33 and D303 in conserved domains disrupted P66 oligomerization and porin function. In a murine model of infection, the E33 and D303 mutants exhibited decreased infectivity and dissemination. Taken together, these results suggest the importance of these conserved domains, and potentially P66 porin function, in vivo.
Not useful to inform teaching practice? Student teachers hold skeptical beliefs about evidence from education science

A goal of teacher education is to promote evidence-based teaching. Teacher beliefs are assumed to act as facilitators or barriers to evidence-based thinking and practices. In three sub-studies with a total of N = 346 German student teachers, the extent of student teachers’ beliefs about education science and their consequences and sources were investigated. First, the results of questionnaire data indicated that student teachers held skeptical beliefs about education science: On average, they perceived education science as less complex than their subject disciplines and as less important for successful teaching than their subject didactics. Additionally, they endorsed myths about learning and teaching. Second, the more skeptical the student teachers’ beliefs, the lower their engagement in education science courses within teacher education. Third, hypotheses about potential sources of these skeptical beliefs were experimentally tested as starting points for changing beliefs. The results showed that the “soft” research methods typical of education science and a general tendency to perceive research findings as trivial (hindsight bias) might contribute to this devaluation. Furthermore, students studying the natural sciences and students with little experience with education science held more skeptical beliefs.
Using theoretical frameworks to analyze democratic student–teacher engagement and autonomous learning for academic achievement in Zimbabwe

Positive student–teacher engagement that fosters independent and supported learning is the fulcrum for academic success. This paper investigates stakeholder opinions on the intrinsic importance of a democratic student–teacher relationship and autonomous learning in mediating students’ academic progress in Zimbabwean secondary schools. This case study’s qualitative data was gathered through interviews and focus groups. We used Foucault’s theory of power relations and the self-determination theory of motivation to frame our findings. The 40 participants from two secondary schools were general teachers (n = 12), guidance and counseling teachers (n = 2), educational psychologists (n = 2), and form 5 students (n = 24), selected through purposive sampling techniques. The data were analyzed using the thematic content analysis approach. Findings revealed participants’ perceptions that democratic student–teacher relationships and autonomous learning opportunities may serve as a panacea to enhance students’ participation, motivation, and overall academic performance. The study recommends in-service training to teachers regarding policies, directives, and public acts that inform and educate on how student–teacher relationships may be enhanced to foster autonomous learning. Future longitudinal studies could investigate the long-term effects of positive student–teacher engagement and teacher-supported autonomous learning on student academic achievement.
Observations of ion upflow and 630.0 nm emission during pulsating aurora

In this study, we report observations made by filtered (557.7 and 630.0 nm) All-Sky Imagers located at Poker Flat, Alaska alongside Poker Flat Incoherent Scatter Radar data for an event observed on 5 February 2017. Together, the data indicate ion upflow in the vicinity of pulsating aurora. Additionally, the data show a strong 630.0 nm (red-line) auroral emission. Observations of pulsating aurora are typically reported at 557.7 and 427.8 nm, as these wavelengths are more sensitive to high-energy (∼ tens of keV) electron precipitation. In contrast, 630.0 nm emission is generated preferentially by low-energy soft electron precipitation (∼ hundreds of eV), and is less commonly observed. The All-Sky Imager data discussed here are unusual in that they suggest regions of enhanced soft electron precipitation in conjunction with enhanced ambipolar electric fields, which are a known factor contributing to ion outflow.
Cuproptosis depicts tumor microenvironment phenotypes and predicts precision immunotherapy and prognosis in bladder carcinoma

Background Though immune checkpoint inhibitors (ICIs) exhibit durable efficacy in bladder carcinomas (BLCAs), there are still a large portion of patients insensitive to ICIs treatment. Methods We systematically evaluated the cuproptosis patterns in BLCA patients based on 46 cuproptosis related genes and correlated these cuproptosis patterns with tumor microenvironment (TME) phenotypes and immunotherapy efficacies. Then, for individual patient’s evaluation, we constructed a cuproptosis risk score (CRS) for prognosis and a cuproptosis signature for precise TME phenotypes and immunotherapy efficacies predicting. Results Two distinct cuproptosis patterns were generated. These two patterns were consistent with inflamed and noninflamed TME phenotypes and had potential role for predicting immunotherapy efficacies. We constructed a CRS for predicting individual patient’s prognosis with high accuracy in TCGA-BLCA. Importantly, this CRS could be well validated in external cohorts including GSE32894 and GSE13507. Then, we developed a cuproptosis signature and found it was significantly negative correlated with tumor-infiltrating lymphocytes (TILs) both in TCGA-BLCA and Xiangya cohorts. Moreover, we revealed that patients in the high cuproptosis signature group represented a noninflamed TME phenotype on the single cell level. As expected, patients in the high cuproptosis signature group showed less sensitive to immunotherapy. Finally, we found that the high and low cuproptosis signature groups were consistent with luminal and basal subtypes of BLCA respectively, which validated the role of signature in TME in terms of molecular subtypes. Conclusions Cuproptosis patterns depict different TME phenotypes in BLCA. Our CRS and cuproptosis signature have potential role for predicting prognosis and immunotherapy efficacy, which might guide precise medicine.
External walking environment differentially affects muscle synergies in children with cerebral palsy and typical development

Despite external environmental changes in walking, such as manipulating gait speed, previous studies have shown that the underlying muscle synergy structures (synergy weights or vectors) rarely vary. The purpose of this study is to examine if external environmental changes to the walking task influence muscle synergies in children with cerebral palsy (CP) and/or typical development (TD). To identify muscle synergies, we extracted muscle synergies from eight children with CP and eight age-matched TD in three treadmill walking conditions, e.g., baseline (adjusted to individual comfortable walking speed), variable speed (VS), or restricted foot width (RW). Then, we grouped similar muscle synergies using k-mean clustering and discriminant analyses from all datasets of individual synergy structures. Proportion tests exhibited six clusters of muscle synergies predominantly arising from children with CP and four clusters from children with TD. Also, the proportion of muscle synergies was significantly different in four of the CP-preferred clusters across conditions. Specifically, the proportion of the baseline condition was significantly different from VS and RW conditions in one and two clusters, respectively. The proportion was significantly different between VS and RW conditions in four clusters. Cadence and step lengths differed across conditions but not groups which makes the group differences in proportion even more notable. In contrast, step width, while significantly lower in CP, did not differ across conditions. Our findings demonstrate that muscle synergies in children with CP are more sensitive to changes in the external walking environment than in typically developing children.
Observation of hole Peregrine soliton in a multicomponent plasma with critical density of negative ions

The evolution of hole Peregrine soliton (appearing as a deep trough between two crests) from ion‐acoustic perturbations excited in a multicomponent plasma with critical density of negative ions has been observed. The observed soliton is described by the rational solution of the cubic nonlinear Schrödinger equation, which can appear as an isolated high peak or a deep hole depending on the phase of the underlying carrier wave relative to the envelope. The measured amplitude of the hole Peregrine soliton (depth from crest to trough) is found to be more than twice the background wave height. The experimental observations are compared with the theoretical results obtained from the solution of the cubic nonlinear Schrödinger equation. The frequency spectrum of the Peregrine soliton is analyzed and found to be triangular in shape.
Lectures on elliptic curves

Introduction 1. Curves of genus: introduction 2. p-adic numbers 3. The local-global principle for conics 4. Geometry of numbers 5. Local-global principle: conclusion of proof 6. Cubic curves 7. Non-singular cubics: the group law 8. Elliptic curves: canonical form 9. Degenerate laws 10. Reduction 11. The p-adic case 12. Global torsion 13. Finite basis theorem: strategy and comments 14. A 2-isogeny 15. The weak finite basis theorem 16. Remedial mathematics: resultants 17. Heights: finite basis theorem 18. Local-global for genus principle 19. Elements of Galois cohomology 20. Construction of the jacobian 21. Some abstract nonsense 22. Principle homogeneous spaces and Galois cohomology 23. The Tate-Shafarevich group 24. The endomorphism ring 25. Points over finite fields 26. Factorizing using elliptic curves Formulary Further reading Index.
Short-term responses of Spinach (Spinacia oleracea L.) to the individual and combinatorial effects of Nitrogen, Phosphorus and Potassium and silicon in the soil contaminated by boron

While of lesser prevalence than boron (B) deficient soils, B-rich soils are important to study as they can cause B toxicity in the field and subsequently decrease crop yields in different regions of the world. We have conducted the present study to examine the role of the individual or combined application of silicon (Si) and NPK fertilizer in B-stressed spinach plants (Spinacia oleracea L.). S. oleracea seedlings were subjected to different NPK fertilizers, namely, low NPK (30 kg ha–2) and normal NPK (60 kg ha–2)], which were also supplemented by Si (3 mmol L–1), for varying levels of B in the soil i.e., 0, 250, and 500 mg kg–1. Our results illustrated that the increasing levels of B in the soil caused a substantial decrease in the plant height, number of leaves, number of stems, leaf area, plant fresh weight, plant dry weight, chlorophyll a, chlorophyll b, total chlorophyll, carotenoid content, net photosynthesis, stomatal conductance, transpiration rate, magnesium content in the roots, magnesium contents in the shoots, phosphorus content in the roots, phosphorus content in the leaves in the shoots, iron content in the roots, iron content in the shoots, calcium content in the roots, and calcium content in the shoots. However, B toxicity in the soil increased the concentration of malondialdehyde, hydrogen peroxide, and electrolyte leakage which were also manifested by the increasing activities of enzymatic [superoxidase dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX)], and non-enzymatic antioxidants (phenolic, flavonoid, ascorbic acid, and anthocyanin content). B toxicity in the soil further increased the concentration of organic acids in the roots such as oxalic acid, malic acid, formic acid, citric acid, acetic acid, and fumaric acid. The addition of Si and fertilizer levels in the soil significantly alleviated B toxicity effects on S. oleracea by improving photosynthetic capacity and ultimately plant growth. The increased activity of antioxidant enzymes in Si and NPK-treated plants seems to play a role in capturing stress-induced reactive oxygen species, as was evident from the lower levels of oxidative stress indicators, organic acid exudation, and B concentration in the roots and shoots of Si and NPK-treated plants. Research findings, therefore, suggested that the Si and NPK application can ameliorate B toxicity in S. oleracea seedlings and result in improved plant growth and composition under metal stress as depicted by the balanced exudation of organic acids.
ZAR1: Guardian of plant kinases

A key facet of innate immunity in plants entails the recognition of pathogen “effector” virulence proteins by host Nucleotide-Binding Leucine-Rich Repeat Receptors (NLRs). Among characterized NLRs, the broadly conserved ZAR1 NLR is particularly remarkable due to its capacity to recognize at least six distinct families of effectors from at least two bacterial genera. This expanded recognition spectrum is conferred through interactions between ZAR1 and a dynamic network of two families of Receptor-Like Cytoplasmic Kinases (RLCKs): ZED1-Related Kinases (ZRKs) and PBS1-Like Kinases (PBLs). In this review, we survey the history of functional studies on ZAR1, with an emphasis on how the ZAR1-RLCK network functions to trap diverse effectors. We discuss 1) the dynamics of the ZAR1-associated RLCK network; 2) the specificity between ZRKs and PBLs; and 3) the specificity between effectors and the RLCK network. We posit that the shared protein fold of kinases and the switch-like properties of their interactions make them ideal effector sensors, enabling ZAR1 to act as a broad spectrum guardian of host kinases.
Saponins from Panax notoginseng ameliorate steroid resistance in lupus nephritis through regulating lymphocyte-derived exosomes in mice

Lupus nephritis (LN) is the most common and severe type of organ damage and an important primary disease in end-stage renal failure in patients with systemic lupus erythematosus (SLE). Clinical guidelines recommend steroid treatment, but steroid resistance has become a major factor leading to treatment failure and affecting prognosis. Our previous study demonstrated that Saponins from Panax Notoginseng (Panax ginseng saponins, PNS) could reverse steroid resistance of lymphocytes by downregulating P-glycoprotein (P-gp) expression and provide renal protection in LN mice, but the mechanism by which lymphocytes transmit these related messages to renal lamina propria cells is not clear. Therefore, we further elucidated this mechanism through holistic experiments. In this study, low-dose methylprednisolone (0.8 mg/kg/day, MP) was used to induce a steroid-resistant lupus nephritis (SR-LN) mouse model in weeks one to four, and a therapeutic steroid dosage (MP 12 mg/kg/day) or a combined PNS (PNS 100 mg/kg/day) treatment was administered from week five to eight. Lymphocyte-derived exosomes (Lyme-Exos) were isolated from the spleens of mice and injected into untreated homozygous LN mice for 14 days via the tail vein. At the end of the experiment, the efficacy and mechanism of action of different groups of Lyme-Exos on LN mice were observed. The results revealed that exogenously injected Lyme-Exos were effectively taken up by the kidney and affected the progression of kidney disease. Steroid-resistant lymphocyte-derived exosomes intervented with PNS significantly downregulated the levels of silent information regulator-related enzyme 1 (Sirt1), multidrug resistance gene 1 (MDR1), and P-gp in the renal cortex and glomerular endothelial cells (GECs); reduced serum autoantibody [antinuclear antibody (ANA) and anti-double-stranded DNA (dsDNA)] levels and inflammatory markers (WBC, PCR, and PCT); improved renal function; and attenuated urinary microalbumin excretion. Additionally, renal histopathological damage (HE staining) and fibrosis (Masson staining) were improved, and immune complex (IgG) deposition and membrane attack complex (C5b-9) production were significantly reduced; the gene levels of inflammatory factors (INF-γ, MCP-1, IL-8, IL-17, vWF, VCAM-1, IL-1β, IL-6, PTX3) in the renal cortex were downregulated. Taken together, this study showed that PNS may alleviate steroid resistance in GEC by interfering with steroid-resistant Lyme-Exos to ameliorate LN progression, which will likely provide insights into developing a new LN treatment. Graphical Abstract
Evolution of research trends in artificial intelligence for breast cancer diagnosis and prognosis over the past two decades: A bibliometric analysis

Objective In recent years, among the available tools, the concurrent application of Artificial Intelligence (AI) has improved the diagnostic performance of breast cancer screening. In this context, the present study intends to provide a comprehensive overview of the evolution of AI for breast cancer diagnosis and prognosis research using bibliometric analysis. Methodology Therefore, in the present study, relevant peer-reviewed research articles published from 2000 to 2021 were downloaded from the Scopus and Web of Science (WOS) databases and later quantitatively analyzed and visualized using Bibliometrix (R package). Finally, open challenges areas were identified for future research work. Results The present study revealed that the number of literature studies published in AI for breast cancer detection and survival prediction has increased from 12 to 546 between the years 2000 to 2021. The United States of America (USA), the Republic of China, and India are the most productive publication-wise in this field. Furthermore, the USA leads in terms of the total citations; however, hungry and Holland take the lead positions in average citations per year. Wang J is the most productive author, and Zhan J is the most relevant author in this field. Stanford University in the USA is the most relevant affiliation by the number of published articles. The top 10 most relevant sources are Q1 journals with PLOS ONE and computer in Biology and Medicine are the leading journals in this field. The most trending topics related to our study, transfer learning and deep learning, were identified. Conclusion The present findings provide insight and research directions for policymakers and academic researchers for future collaboration and research in AI for breast cancer patients.