Miracle-dz/UniFAR-FTUs huggingface dataset:
Integrated Bioinformatics Analyses of PIN1, CKX, and Yield-Related Genes Reveals the Molecular Mechanisms for the Difference of Seed Number Per Pod Between Soybean and Cowpea

There is limited advancement on seed number per pod (SNPP) in soybean breeding, resulting in low yield in China. To address this issue, we identified PIN1 and CKX gene families that regulate SNPP in Arabidopsis, analyzed the differences of auxin and cytokinin pathways, and constructed interaction networks on PIN1, CKX, and yield-related genes in soybean and cowpea. First, the relative expression level (REL) of PIN1 and the plasma membrane localization and phosphorylation levels of PIN1 protein were less in soybean than in cowpea, which make auxin transport efficiency lower in soybean, and its two interacted proteins might be involved in serine hydrolysis, so soybean has lower SNPP than cowpea. Then, the CKX gene family, along with its positive regulatory factor ROCK1, had higher REL and less miRNA regulation in soybean flowers than in cowpea ones. These lead to higher cytokinin degradation level, which further reduces the REL of PIN1 and decreases soybean SNPP. We found that VuACX4 had much higher REL than GmACX4, although the two genes essential in embryo development interact with the CKX gene family. Next, a tandem duplication experienced by legumes led to the differentiation of CKX3 into CKX3a and CKX3b, in which CKX3a is a key gene affecting ovule number. Finally, in the yield-related gene networks, three cowpea CBP genes had higher RELs than two soybean CBP genes, low RELs of three soybean-specific IPT genes might lead to a decrease in cytokinin synthesis, and some negative and positive SNPP regulation were found, respectively, in soybean and cowpea. These networks may explain the SNPP difference in the two crops. We deduced that ckx3a or ckx3a ckx6 ckx7 mutants, interfering CYP88A, and over-expressed DELLA increase SNPP in soybean. This study reveals the molecular mechanism for the SNPP difference in the two crops, and provides an important idea for increasing soybean yield.
Hsa_circ_0003204 Knockdown Weakens Ox-LDL-Induced Cell Injury by Regulating miR-188-3p/TRPC6 Axis in Human Carotid Artery Endothelial Cells and THP-1 Cells

Background: Circular RNAs (circRNAs) are involved in atherosclerosis (AS) development. However, the function and mechanism of circRNA hsa_circ_0003204 (circ_0003204) in carotid artery AS remain unclear. Methods: Oxidized low-density lipoprotein (ox-LDL)-treated human carotid artery endothelial cells (HCtAECs) and THP-1 cells were used as cell models of carotid artery AS. Relative levels of circ_0003204, microRNA-188-3p (miR-188-3p), and transient receptor potential canonical channel 6 (TRPC6) were detected by quantitative reverse transcription–polymerase chain reaction or Western blotting. The targeting relationship between circ_0003204 or TRPC6 and miR-188-3p was assessed via dual-luciferase reporter analysis and RNA immunoprecipitation. Cell proliferation was assessed via 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide assay and 5-ethynyl-2′-deoxyuridine (EdU) assay. Cell apoptosis was analyzed via assessing cell caspase-3 activity, apoptosis, and apoptosis-related protein. Inflammatory response was analyzed via analysis of interleukin-1β (IL-1β), IL-6, and tumor necrosis factor-α (TNF-α). Oxidative stress was assessed via determination of reactive oxygen species (ROS), malondialdehyde (MDA), and superoxide dismutase (SOD). Results: Circ_0003204 and TRPC6 levels were elevated, and miR-188-3p expression declined in ox-LDL-treated HCtAECs and THP-1 cells. Circ_0003204 could regulate TRPC6 expression via mediating miR-188-3p. Circ_0003204 silencing weakened ox-LDL-induced viability inhibition and apoptosis in HCtAECs, and inflammatory response and oxidative stress in THP-1 cells via regulating miR-188-3p. MiR-188-3p overexpression attenuated ox-LDL-induced injury in HCtAECs and THP-1 cells by targeting TRPC6. Conclusion: Circ_0003204 knockdown mitigated ox-LDL-induced injury in HCtAECs and THP-1 cells via regulating the miR-188-3p/TRPC6 axis, indicating that circ_0003204 might play an important role in carotid artery AS.
Effect of Trehalose and Sucrose in Post-thaw Quality of Crassostrea angulata Sperm

Sperm cryopreservation can be a helpful tool in reproductive management and preservation of biodiversity. However, the freezing methodologies lead to some damage in structure and function of cells that may compromise post-thaw sperm activity. Cryoprotectant supplementation with sugars proved to be a successful strategy to reduce cryodamage in sperm of several species, once allowing to stabilize the plasma membrane constituents. Therefore, this study intends to understand the effects of sugars in the plasma membrane, DNA integrity, and oxidative response during Portuguese oyster sperm cryopreservation. Three cryoprotectants solutions with an initial concentration of 20% dimethyl sulfoxide (DMSO) and 20% DMSO complemented with 0.9 M trehalose or sucrose in artificial seawater were employed. Sperm samples of mature males were individually collected and diluted 1:10 (v/v) in artificial seawater followed by addition of cryoprotectants [1:1 (v/v)]. Thereafter, sperm was loaded into 0.5 ml straws, maintained at 4°C for 10 min, frozen in a programmable biofreezer at −6°C/min from 0 to −70°C, and stored in liquid nitrogen. Samples were thawed in a 37°C bath for 10 s. Several techniques were performed to evaluate post-thaw quality. Sperm motility and DNA integrity were analyzed by using computer-assisted sperm analysis (CASA) software and comet assay. Flow cytometry was employed to determine membrane and acrosome integrity and to detect intracellular reactive oxygen species (ROS) and apoptosis activity. Lipid peroxidation was determined by malondialdehyde (MDA) detection by using spectrophotometry. Sperm antioxidant capacity was evaluated through glutathione peroxidase, glutathione reductase, and superoxide dismutase. Motility was not affected by the extenders containing sugars; these compounds did not reduce the DNA damage. However, both the trehalose and sucrose protected plasma membrane of cells by increasing cell viability and significantly reducing MDA content. The same finding was observed for the ROS, where live cells registered significantly lower levels of ROS in samples cryopreserved with sugars. The activity of antioxidant enzymes was higher in treatments supplemented with sugars, although not significant. In conclusion, the addition of sugars seems to play an important role in protecting the Crassostrea angulata sperm membrane during cryopreservation, showing potential to improve the post-thaw sperm quality and protect the cells from cryoinjuries.
The Impact of Mismatch Repair Status on Prognosis of Patients With Gastric Cancer: A Multicenter Analysis

Background The clinical role of deficient DNA mismatch repair (dMMR)/microsatellite instability-high (MSI-H) in gastric cancer (GC) is still controversial. We aimed to analyze the relationship between dMMR/MSI-H and clinicopathological features along with survival. Methods Patients who were diagnosed with GC at the three big cancer centers in China from 2015 to 2020 were evaluated retrospectively. MMR/MSI status was assessed using immunohistochemistry/PCR. Clinical and pathological data were collected from the medical record system. Results A total of 196 patients with dMMR/MSI-H status were enrolled for analysis. The prevalence of MSI-H/dMMR in GC was 6.6%. Another 694 proficient MMR (pMMR) GC patients were enrolled for comparison. Compared with pMMR patients, dMMR/MSI-H patients were associated with older age, female predominance, distal location in the stomach, earlier TNM stage, intestinal subtype, better differentiation, and more negative HER2 status. The median overall survival (OS) of the dMMR/MSI-H group was better than that of the pMMR/microsatellite stability (MSS) group (not reached vs. 53.9 months, p = 0.014). Adjuvant chemotherapy had no impact in both disease-free survival (DFS) and OS of dMMR/MSI-H patients (p = 0.135 and 0.818, respectively). dMMR/MSI-H patients had poorer response and progression-free survival (PFS) of first-line chemotherapy, though they were statistically significant (p = 0.361 and 0.124, respectively). Conclusions dMMR/MSI-H GC patients have specific clinicopathological characteristics and better prognosis than pMMR patients.
Dual-Focused Transformational Leadership, Teachers’ Satisfaction of the Need for Relatedness, and the Mediating Role of Social Support

Basic psychological need satisfaction is essential for the wellbeing of teachers and motivation at work. Transformational leadership contributes to the development and maintenance of a respectful, constructive atmosphere, a supportive working climate, and has been suggested to be a crucial factor for the satisfaction of the need for relatedness of employees. Transformational leadership is also considered as an ideal leadership style in the school setting, but most studies did not distinguish between individual and team effects of this leadership behavior. In the present study, we applied the dual-focused model of transformational leadership and focused on social processes to address the question of whether individual- and group-focused transformational leadership behavior contribute differently to satisfaction of the need for relatedness of teachers. Based on longitudinal data with three measurement points across one school year of N = 1,217 teachers, results of structural equational models supported the notion of the dual effects of transformational leadership: Individual-focused transformational leadership was directly positively related to change in satisfaction of the need for relatedness of teachers. The relationship between group-focused transformational leadership and change in satisfaction of the need for relatedness was mediated by received social support from team members. These findings emphasize the importance of school leadership behavior of principals for satisfaction of the need for relatedness of teachers. The satisfaction of the need for relatedness is, therefore, not only satisfied through the direct interaction between the school principal and the individual teacher but also through interactions of the school principal with the whole team. Our results confirm that school principals should focus their leadership behavior both on individual need satisfaction of teachers as well as on team development.
Chromosome-Scale Genome Assembly for Chinese Sour Jujube and Insights Into Its Genome Evolution and Domestication Signature

Sour or wild jujube fruits and dried seeds are popular food all over the world. In this study, we reported a high-quality genome assembly of sour jujube (Ziziphus jujuba Mill. var. spinosa), with a size of 406 Mbp and scaffold N50 of 30.3 Mbp, which experienced only γ hexaploidization event, without recent genome duplication. Population structure analysis identified four jujube subgroups (two domesticated ones, i.e., D1 in West China and D2 in East/SouthEast China, semi-wild, and wild), which underwent an evolutionary history of a significant decline of effective population size during the Last Glacial Period. The respective selection signatures of three subgroups were discovered, such as strong peaks on chromosomes #3 in D1, #1 in D2, and #4 in wild. Genes under the most significant selection on chromosomes #4 in wild were confirmed to be involved in fruit variations among jujube accessions, in transcriptomic analysis. Our study offered novel insights into the jujube population structure and domestication and provided valuable genomic resources for jujube improvement in stress response and fruit flavor in the future.
Prevalence of Overweight and Obesity in People With Severe Mental Illness: Systematic Review and Meta-Analysis

Aims 1) To determine the pooled prevalence of overweight and obesity in people with severe mental illness (SMI), overall and by type of SMI, geographical region, and year of data collection; and 2) to assess the likelihood of overweight and obesity, in people with SMI compared with the general population. Methods PubMed, Medline, EMBASE, and PsycINFO databases were searched to identify observational studies assessing the prevalence of obesity in adults with SMI. Screening, data extraction and risk of bias assessments were performed independently by two co-authors. Random effect estimates for the pooled prevalence of overweight and obesity and the pooled odds of obesity in people with SMI compared with the general population were calculated. Subgroup analyses were conducted for types of SMI, setting, antipsychotic medication, region of the world, country income classification, date of data collection and sex. We assessed publication bias and performed a series of sensitivity analyses, excluding studies with high risk of bias, with low sample size and those not reporting obesity according to WHO classification. Result 120 studies from 43 countries were included, the majority were from high income countries. The pooled prevalence of obesity in people with SMI was 25.9% (95% C.I. = 23.3-29.1) and the combined pooled prevalence of overweight and obesity was 60.1% (95% C.I. = 55.8-63.1). Sub-Saharan Africa (13.0%, 95%C.I. = 6.7-25.1) and South Asia (17.7%, 95%C.I. = 10.5-28.5) had the lowest prevalence of obesity whilst North Africa and the Middle East (35.8%, 95%C.I. = 23.8-44.8) reported the highest prevalence. People with SMI were 3.04 more likely (95% C.I. = 2.42-3.82) to have obesity than the general population, but there was no difference in the prevalence of overweight. Women with schizophrenia were 1.44 (95% C.I. = 1.25-1.67) times more likely than men with schizophrenia to live with obesity; however, no gender differences were found among those with bipolar disorder. Conclusion People with SMI have a markedly high prevalence and higher odds of obesity than the general population. This may contribute to the very high prevalence of physical health conditions and mortality in this group. People with SMI around the world would likely benefit from interventions to reduce and prevent obesity.
Political Communication Patterns of Young Adults in Germany

While the political communication and participation activities of young adults are changing, this is often not adequately captured by research due to a too narrow conceptualization of the phenomenon. Our approach conceptualizes political communication as activities comprising the reception of political content, interpersonal communication regarding political issues and political participation. We incorporated both analog and digital media, as well as different forms of political participation, to reflect the complex reality of political communication activities of young adults in the digital age. On the basis of a sample from 2013, we investigated the patterns of political communication of young adults (ages 18–33 years). This age group represents the first generation to have grown up under the ubiquitous influence of the internet and other modern information technologies. In addition, we examined factors influencing the formation of different political communication patterns of this generation. Results of cluster analyses demonstrated that young adults should not be seen as a homogeneous group. Rather, we found six communication types. Interestingly, no online-only type of political communication was revealed, By applying multinomial logistic regression analysis, we were able to demonstrate that socio-demographic variables, individual resources and cognitive involvement in politics influence the likelihood of belonging to more active political communication types. The present study investigated various information and communication opportunities of young adults, and is rare in terms of the richness of data provided. Our conceptual innovative approach enables a better understanding of young adults’ complex political communication patterns. Moreover, our approach encourages follow-up research, as our results provide a valuable starting point for intergenerational comparisons regarding changes in political engagement among young adults in Germany, as well as for cross-country analysis regarding different generations of young adults.
PaleoView3D: FROM SPECIMEN TO ONLINE DIGITAL MODEL

Recent technological advancements in 3D data acquisition and the ability to digitize museum collections have revolutionized the way one can access and visualize paleontological specimens. Instruments like high-resolution CT scanners and 3D laser scanners have simplified the digitization process, paving the way for 3D online museums. The goals of this study were two-fold. First, to automate, standardize, and document the laser scanning/modeling technique used to generate models for one such database, PaleoView3D. Second, using PaleoView3D as a test case, to illustrate the necessity for other websites to include detailed error studies, modeling protocols, and associated metadata to facilitate the comparative use of online morphological data. Automation and standardization were achieved by coating specimens with ammonium chloride, constructing a nine-specimen multiscan platform, and implementing an autosurfacing macro which combined reduced modeling time by 60%. An extensive error study was performed to test the accuracy of this technique using controls of known dimensions. The process was highly accurate in all three dimensions with percent errors of: 1D = 0.4%; 2D = 0.05%; 3D = 1.74%. Because many of the specimens digitized were casts, a molding/casting error study was also performed. First and second generation casts (i.e., a “cast of a cast”) deviated from the original specimen a maximum of ± 0.074 mm and, as expected, variation increased slightly with subsequent generations. By standardizing and documenting the methodology and accuracy of this technique, researchers can make an informed decision concerning how to utilize models from PaleoView3D.
Posttraumatic Stress Symptoms Among Chinese College Students During the COVID-19 Pandemic: A Longitudinal Study

A longitudinal assessment of the prevalence of posttraumatic stress symptoms (PTSS) and risk factors is indispensable for further prevention and/or treatment. The longitudinal web-based survey enrolled 1,164 college students in China. Measured at two time points (February and August 2020), PTSS, demographic information, adverse childhood experiences (ACEs), resilience and self-compassion information were collected to explicate the prevalence and predictors of PTSS concurrently and over time. Results showed that although PTSS generally declined throughout the 6 months after the outbreak of COVID-19, the prevalence remained relatively high. Resilience and self-compassion negatively predicted PTSS concurrently and longitudinally. While subjective family socioeconomic status (SES) and ACEs at Wave 1 did not predict PTSS under COVID-19 at Wave 1, but both significantly predicted PTSS at Wave 2. Findings implicate potential targets for detecting and intervening on symptoms of trauma in this vulnerable population.
Effect of Mydriasis-Caused Intraocular Pressure Changes on Corneal Biomechanical Metrics

Purpose: To evaluate the dependence of biomechanical metrics on intraocular pressure (IOP). Methods: 233 refractive surgery patients were included in this study—all were examined 3 times with the Corvis ST before and after dilation, and the differences (∆) in the main device parameters were assessed. The data collected included the biomechanically corrected IOP (bIOP), the central corneal thickness (CCT), and six dynamic corneal response (DCR) parameters, namely DA, DARatio2mm, IIR, SP-A1, CBI, and SSI. Participants were divided into three groups according to the changes in patients’ bIOP after mydriasis. Results: Intra-operator repeatability was generally high in most of the DCR parameters obtained before and after dilation. The mean changes in bIOP and CCT after dilation were −0.12 ± 1.36 mmHg and 1.95 ± 5.23 μm, respectively. Only ∆DARatio2mm, ∆IIR, and ∆CBI exhibited a statistically significant correlation with ∆CCT (p < 0.05). The changes in all DCR parameters, especially ∆DA and ∆SP-A1 were also correlated with ∆bIOP (p < 0.01)—a 1-mmHg change in bIOP was associated, on average, with 5.612 and −0.037 units of change in SP-A1 and DA, respectively. In contrast, the weakest correlation with ∆bIOP was exhibited by ∆SSI. Conclusion: Most corneal DCR parameters, provided by the Corvis ST, were correlated with IOP, and more weakly with CCT. Changes experienced in CCT and IOP should therefore be considered in studies on corneal biomechanics and how it is affected by disease progression and surgical or medical procedures.
Colon Cancer-Related Genes Identification and Function Study Based on Single-Cell Multi-Omics Integration

Transcriptomes and DNA methylation of colon cancer at the single-cell level are used to identify marker genes and improve diagnoses and therapies. Seven colon cancer subtypes are recognized based on the single-cell RNA sequence, and the differentially expressed genes regulated by dysregulated methylation are identified as marker genes for different types of colon cancer. Compared with normal colon cells, marker genes of different types show very obvious specificity, especially upregulated genes in tumors. Functional enrichment analysis for marker genes indicates a possible relation between colon cancer and nervous system disease, moreover, the weak immune system is verified in colon cancer. The heightened expression of markers and the reduction of methylation in colon cancer promote tumor development in an extensive mechanism so that there is no biological process that can be enriched in different types.
Spread-spectrum code and carrier synchronization errors caused by multipath and interference

The influence of multipath propagation and spread-spectrum interference on code and carrier synchronization is investigated. Both coherent and noncoherent delay lock loops (DLLs) are considered, with arbitrary early-late spacings up to one chip time. The coherent DLL is shown to have a major advantage; for a relatively high fading bandwidth, it has negligible tracking errors, while a noncoherent DLL always has a certain bias error. The results are particularly interesting for spread-spectrum positioning systems like Global Positioning System (GPS) and GLONASS. >