Miracle-dz/UniFAR-FTUs huggingface dataset:
Overexpression of Myrothamnus flabellifolia MfWRKY41 confers drought and salinity tolerance by enhancing root system and antioxidation ability in Arabidopsis

Myrothamnus flabellifolia is the only woody resurrection plant discovered so far and could recover from extreme desiccation condition. However, few genes related to its strong drought tolerance have been characterized, and the underlying molecular mechanisms remains mysterious. Members of WRKY transcription factor family are effective in regulating abiotic stress responses or tolerance in various plants. An early dehydration-induced gene encoding a WRKY transcription factor namely MfWRKY41 was isolated from M. flabellifolia, which is homologous to AtWRKY41 of Arabidopsis. It contains a typical WRKY domain and zinc finger motif, and is located in the nucleus. Comparing to wild type, the four transgenic lines overexpressing MfWRKY41 showed better growth performance under drought and salt treatments, and exhibited higher chlorophyll content, lower water loss rate and stomatal aperture and better osmotic adjustment capacity. These results indicated that MfWRKY41 of M. flabellifolia positively regulates drought as well as salinity responses. Interestingly, the root system architecture, including lateral root number and primary root length, of the transgenic lines was enhanced by MfWRKY41 under both normal and stressful conditions, and the antioxidation ability was also significantly improved. Therefore, MfWRKY41 may have potential application values in genetic improvement of plant tolerance to drought and salinity stresses. The molecular mechanism involving in the regulatory roles of MfWRKY41 is worthy being explored in the future.
Prognostic role of elevated VEGF in sepsis: A systematic review and meta-analysis

Background: The incidence and mortality of sepsis are increasing year by year, and there is still a lack of specific biomarkers to predict its prognosis. Prognostic value of vascular endothelial growth factor (VEGF) in predicting the severity and mortality of sepsis has been gradually discovered. Methods: Literature was searched through Embase, PubMed, Web of Science, China National Knowledge Infrastructure(CNKI) and Cochrane Library databases in March 2022. Observational studies, evaluating the impact of VEGF in sepsis outcomes (mortality and severity) are included in this meta-analysis. Risk of bias was assessed with the Newcastle-Ottawa Scale (NOS). Sensitivity and publication bias analyses were also assessed. Meta-regression analysis were performed to identify the potential sources of heterogeneity. Result: A total of 1,574 articles were retrieved from the systematic literature search. We included 20 studies for qualitative and quantitative analysis. Deceased and critically ill patients had higher baseline VEGF levels than survivors and non-severe patients. The pooled sensitivity and specificity for VEGF predicts sepsis mortality were 0.79and 0.76, respectively. the area under the SROC curve was 0.83. Conclusion: High VEGF are associated with poor clinical outcomes for patients diagnosed with sepsis. This study was recorded on PROSPERO, under the registration ID: CRD42022323079.
A Network-Guided Approach to Discover Phytochemical-Based Anticancer Therapy: Targeting MARK4 for Hepatocellular Carcinoma

MAP/microtubule affinity-regulating kinase 4 (MARK4) is associated with various biological functions, including neuronal migration, cell polarity, microtubule dynamics, apoptosis, and cell cycle regulation, specifically in the G1/S checkpoint, cell signaling, and differentiation. It plays a critical role in different types of cancers. Hepatocellular carcinoma (HCC) is the one of the most common forms of liver cancer caused due to mutations, epigenetic aberrations, and altered gene expression patterns. Here, we have applied an integrated network biology approach to see the potential links of MARK4 in HCC, and subsequently identified potential herbal drugs. This work focuses on the naturally-derived compounds from medicinal plants and their properties, making them targets for potential anti-hepatocellular treatments. We further analyzed the HCC mutated genes from the TCGA database by using cBioPortal and mapped out the MARK4 targets among the mutated list. MARK4 and Mimosin, Quercetin, and Resveratrol could potentially interact with critical cancer-associated proteins. A set of the hepatocellular carcinoma altered genes is directly the part of infection, inflammation, immune systems, and cancer pathways. Finally, we conclude that among all these drugs, Gingerol and Fisetin appear to be the highly promising drugs against MARK4-based targets, followed by Quercetin, Resveratrol, and Apigenin.
Early Versus Delayed Enteral Feeding in Predicted Severe Acute Gallstone Pancreatitis: A Retrospective Study

Background The optimal timing of enteral nutrition (EN) initiation in predicted severe acute gallstone pancreatitis (SAGP) and its influence on disease outcomes are not well known. Methods We conducted a retrospective study of patients with predicted SAGP treated with endoscopic retrograde cholangiopancreatography and EN. The patients were classified into two groups according to the timing of EN initiation after admission: within 48 h, and more than 48 h. The primary outcome was in-hospital mortality. The secondary outcomes were length of hospital stay, need for intensive care admission, need for surgical intervention, improvements in blood test results after 7-10 days of EN, incidence of pancreatic necrosis and infection, and hospital care costs. The microbiological profiles of infectious complications were also evaluated. Results Of the 98 patients, 31 and 67 started EN within 48 h, and more than 48 h after admission, respectively. Early EN was associated with a decrease in in-hospital mortality (0 vs. 11.9%; p=0.045), length of hospital stay (median:18 vs. 27 days; p=0.001), need for intensive care admission (3.2% vs. 20.9%; p=0.032), and hospital care costs (median:9,289 vs. 13,518 US$; p=0.007), compared to delayed EN. Moreover, early EN for 7-10 days had more beneficial effects on blood test results than delayed EN, including total protein (p=0.03) and CRP (p=0.006) levels. However, the need for surgical intervention and incidence of pancreatic necrosis did not differ between the two groups. In our study, Gram-negative bacteria were the main responsible pathogens (50.5%). Infection with multidrug-resistant organisms (MDRO) was found in 19.4% of the patients. The most common MDRO was MDR Enterococcus faecium. Early EN was not superior in reducing incidence of infected pancreatic necrosis, bacteremia, polymicrobial infection, or MDROs. Conclusions In patients with predicted SAGP, early EN is associated with a decrease in in-hospital mortality, length of hospital stay, need of intensive care admission, and hospital care costs, compared to delayed EN. There are no significant benefits of early EN in reducing the rate of infection-related complications. Further studies with larger sample sizes are warranted.
Nutrient Inputs Alleviate Negative Effects of Early and Subsequent Flooding on Growth of Polygonum hydropiper With the Aid of Adventitious Roots

Riparian plants are exposed to harmful stress induced by flooding, which is often accompanied by eutrophication in the Three Gorges Reservoir Region. The phenomenon is mainly caused by domestic sewage discharges, slow water flow, and agricultural fertilizer pollution. Simulating abiotic stress, such as flooding at the initial period, can act as a signal and induce positive responses of plants to subsequent severe stress. In addition, eutrophication supplies nutrients, provides a favorable environment in the early stages of plant, and facilitates good performance in later development. However, whether early flooding (with or without eutrophication) acts as positive cue or as stress on plants at different developmental stages remains unclear. To address this question, seeds of Polygonum hydropiper were collected from low and high elevations in the hydro-fluctuation belt of the Three Gorges Reservoir Region. Plants germinated from these seeds were subjected to shallower and shorter early flooding treatments with or without eutrophication. Subsequently, plants were subjected to deeper and longer flooding treatments with or without eutrophication. Early flooding and eutrophic flooding significantly induced generation of adventitious roots, suggesting morphological adaptation to flooding. Although early flooding and eutrophic flooding treatments did not increase plant biomass in subsequent treatments compared with control, stem length, length and width of the 1st fully expanded leaf, and biomass of plants in the early eutrophic treatment were higher than these of the early flooding treatment plants. These results suggest a negative lag-effect of early flooding, and also indicate that nutrient inputs can alleviate such effects. Similarly, subsequent eutrophic flooding also enhanced plant growth compared with subsequent flooding, showing significantly higher values of leaf traits and adventitious root number. Plants originated from low elevation had significantly higher functional leaf length and stem biomass compared with those from high elevation. These results suggest that nutrient inputs can alleviate negative effects of early and subsequent flooding on growth of P. hydropiper with the generation of adventitious roots.
The application of an instrument for non-destructive measurements of soil temperature and resistance profiles at a high Arctic field site

Abstract. An easily constructed and installed instrument for measuring colocated soil temperature and resistance profiles is described. Minimum disturbance to the soil structure is achieved. The system indicates the melting front of permafrost at a high Arctic field site and shows the effect and extent of summer rainfall events upon the soil water profile. The system is capable of long-term recording of soil moisture profiles at a frequency commensurate with eddy correlation measurements of the surface fluxes of water vapour and carbon dioxide; it thus provides the information necessary for understanding the processes involved in the soil-atmosphere exchange of water and carbon dioxide.
TRAPS mutations in Tnfrsf1a decrease the responsiveness to TNFα via reduced cell surface expression of TNFR1

Tumor necrosis factor (TNF) receptor-associated periodic syndrome (TRAPS) is an autoinflammatory periodic fever syndrome associated with heterozygous mutations in TNFRSF1A, which encodes TNF receptor type I (TNFR1). Although possible proinflammatory mechanisms have been proposed, most previous studies were performed using in vitro overexpression models, which could lead to undesirable inflammatory responses due to artificial overexpression. It is crucial to reproduce heterozygous mutations at physiological expression levels; however, such studies remain limited. In this study, we generated TRAPS mutant mice and analyzed their phenotypes. Three Tnfrsf1a mutant strains were generated by introducing T79M, G87V, or T90I mutation. T79M is a known mutation responsible for TRAPS, whereas G87V is a TRAPS mutation that we have reported, and T90I is a variant of unknown significance. Using these murine models, we investigated whether TRAPS mutations could affect the inflammatory responses in vivo and in vitro. We found that none of the mutant mice exhibited detectable inflammatory phenotypes under standard housing conditions for 1 year. Interestingly, TRAPS mutant (T79M and G87V) mice had reduced mortality rates after the administration of lipopolysaccharide (LPS) and D-galactosamine, which induce TNFα-dependent lethal hepatitis. Moreover, TRAPS mutations strongly suppressed the development of TNFα-mediated arthritis when crossed with human TNFα transgenic mice. In in vitro primary bone marrow-derived macrophage cultures, the T79M and G87V mutations attenuated the inflammatory responses to TNFα compared with the wild-type, whereas these mutations did not alter the responsiveness of these cells to LPS. The T90I mutant macrophages behaved similarly to wild type in response to LPS and TNFα. The TNFR1 levels were increased in whole-cell lysates of TRAPS mutant macrophages, whereas the cell surface expression of TNFR1 was significantly decreased in TRAPS mutant macrophages. Taken together, TRAPS mutations did not augment the inflammatory responses to TNFα and LPS; instead, they suppressed the response to TNFα via decreased cell surface expression of TNFR1. The stimulation of lymphotoxin-α, adenosine triphosphate, and norepinephrine in primary macrophages or various stimuli in murine splenocytes did not induce detectable inflammatory responses. In conclusion, TRAPS mutations suppressed responsiveness to TNFα, and TRAPS-associated inflammation is likely induced by unconfirmed disease-specific proinflammatory factors.
Effects of Psychological Discomfort on Social Networking Site (SNS) Usage Intensity During COVID-19

To cope with the COVID-19 pandemic, many countries are implementing social measures. Social distancing, working from home, and non-face-to-face lectures have led to major changes in people's activities. Since face-to-face classes are restricted, students in higher education become to feel psychological and cognitive discomforts such as isolation and risk perception. The purpose of this study is to explore the effects of psychological discomforts on the social network site (SNS) usage intensity of University students. Using structural equation modeling (SEM), this study applied SmartPLS 3.3. 9 to analyze 271 valid samples. The results show that the affective risk perception significantly affects social distancing attitude. Cognitive risk perception is positively related to social distancing intention. In addition, cabin fever syndrome influences SNS usage intensity, affective risk perception, and cognitive risk perception. In conclusion, psychological discomfort partially affects the intensity of SNS use. Therefore, the government should set policies by reflecting citizens' mental difficulties and SNS activities together. Moreover, companies are needed to carefully consider the risk of the sense of isolation when marketing to SNS users.
The impact of a group based, remotely delivered weight loss intervention in women with polycystic ovary syndrome on ovulation, quality of life and body composition

Background Obesity and visceral adiposity are associated with anovulation. The most common cause of anovulatory infertility in women of reproductive age is polycystic ovary syndrome (PCOS). We conducted this formative study to examine the effects of a remotely delivered, group-based lifestyle program for women with overweight/obesity and PCOS on ovulation, PCOS related quality of life (PCOSQ) and body composition. Methods Women with anovulatory infertility caused by PCOS (N = 12) were enrolled in a 6-month high-intensity weight management intervention. Participants were asked to attend 45 min., group behavioral lifestyle sessions, delivered remotely by a registered dietitian weekly across the 6-mo. study and comply with a reduced energy diet, increased physical activity (225 min/wk.), and self-monitoring of weight, physical activity and diet. Diets consisted of five portion-controlled meals (three shakes + two entrees), at least five servings of fruits/vegetables, and ad libitum non-caloric beverages daily. Wilcoxon signed-rank tests were used to assess changes in outcomes across the intervention. Results Twelve women received the weight loss intervention (mean age = 32.7 ± 4.2 yrs., BMI = 36.8 ± 4.5 kg/m2, 92% college educated), and 8 completed the intervention. Eight (67%) women reported ovulating during the intervention with an average time to ovulation of 57 ± 45 days. Women lost an average of 3.85 ± 5.94 kg (p = 0.02), decreased their BMI (−1.61 ± 1.09 kg/m2; p = 0.04), and waist circumference (−4.54 ± 3.03 cm; p = 0.04) over the 6-mo. intervention. Additionally, self-reported menstrual problems measured by PCOSQ significantly improved over the study (p = 0.03). Conclusion A multicomponent group-based, remotely delivered, lifestyle intervention delivered remotely is a feasible and potentially scalable option to achieve clinically relevant (>3%) weight loss in women with PCOS. Clinical trial registration www.clinicaltrials. gov, identifier: NCT03677362.
New MS lesion segmentation with deep residual attention gate U-Net utilizing 2D slices of 3D MR images

Multiple sclerosis (MS) is an autoimmune disease that causes lesions in the central nervous system of humans due to demyelinating axons. Magnetic resonance imaging (MRI) is widely used for monitoring and measuring MS lesions. Automated methods for MS lesion segmentation have usually been performed on individual MRI scans. Recently, tracking lesion activity for quantifying and monitoring MS disease progression, especially detecting new lesions, has become an important biomarker. In this study, a unique pipeline with a deep neural network that combines U-Net, attention gate, and residual learning is proposed to perform better new MS lesion segmentation using baseline and follow-up 3D FLAIR MR images. The proposed network has a similar architecture to U-Net and is formed from residual units which facilitate the training of deep networks. Networks with fewer parameters are designed with better performance through the skip connections of U-Net and residual units, which facilitate information propagation without degradation. Attention gates also learn to focus on salient features of the target structures of various sizes and shapes. The MSSEG-2 dataset was used for training and testing the proposed pipeline, and the results were compared with those of other proposed pipelines of the challenge and experts who participated in the same challenge. According to the results over the testing set, the lesion-wise F1 and dice scores were obtained as a mean of 48 and 44.30%. For the no-lesion cases, the number of tested and volume of tested lesions were obtained as a mean of 0.148 and 1.488, respectively. The proposed pipeline outperformed 22 proposed pipelines and ranked 8th in the challenge.
The influence of firm’s feedbacks on user-generated content’s linguistic style matching–An explanation based on communication accommodation theory

In virtual brand communities, users and firms continuously use different or similar linguistic styles to communicate with each other. Existing literature has demonstrated that the linguistic style matching (LSM) between the coming users’ posts [user-generated content (UGC)] and existing firms’ content will influence users’ behavior, like promoting users to release more posts. However, little research has been conducted to analyze how firms’ feedbacking behaviors influence LSM. To fill the gap, this paper uses Python to measure the LSM between 69,463 posts from 9,777 users and existing firms’ generated content in the MIUI community and examines the impact of firms’ feedbacks on this LSM. The results show that the firms’ feedbacks frequency increased the LSM, but the firms’ feedbacks text length decreased the LSM. In addition, users’ textual sentiment and the published text length moderate the impact of firms’ feedbacks (e.g., frequency, text length) on LSM. Specifically, the users’ textual sentiment valence increases the positive effect of firms’ feedbacks frequency and weakens the negative effect of firms’ feedbacks text length on LSM. The users’ produced content text length reduced the positive effect of firms’ feedbacks frequency and offset the negative effect of the firms’ feedbacks text length on LSM. Further, the effects above are significant for the relatively active users but not for the inactive ones. Based on communication accommodation theory, this paper investigates the impact of firms’ feedbacks frequency and text length on subsequent users’ posting behaviors, providing an essential reference for guiding firms’ virtual brand community management.
microTrait: A Toolset for a Trait-Based Representation of Microbial Genomes

Remote sensing approaches have revolutionized the study of macroorganisms, allowing theories of population and community ecology to be tested across increasingly larger scales without much compromise in resolution of biological complexity. In microbial ecology, our remote window into the ecology of microorganisms is through the lens of genome sequencing. For microbial organisms, recent evidence from genomes recovered from metagenomic samples corroborate a highly complex view of their metabolic diversity and other associated traits which map into high physiological complexity. Regardless, during the first decades of this omics era, microbial ecological research has primarily focused on taxa and functional genes as ecological units, favoring breadth of coverage over resolution of biological complexity manifested as physiological diversity. Recently, the rate at which provisional draft genomes are generated has increased substantially, giving new insights into ecological processes and interactions. From a genotype perspective, the wide availability of genome-centric data requires new data synthesis approaches that place organismal genomes center stage in the study of environmental roles and functional performance. Extraction of ecologically relevant traits from microbial genomes will be essential to the future of microbial ecological research. Here, we present microTrait, a computational pipeline that infers and distills ecologically relevant traits from microbial genome sequences. microTrait maps a genome sequence into a trait space, including discrete and continuous traits, as well as simple and composite. Traits are inferred from genes and pathways representing energetic, resource acquisition, and stress tolerance mechanisms, while genome-wide signatures are used to infer composite, or life history, traits of microorganisms. This approach is extensible to any microbial habitat, although we provide initial examples of this approach with reference to soil microbiomes.