Miracle-dz/UniFAR-FTUs huggingface dataset:
Application of high-resolution processing in seismic data based on an improved synchrosqueezing transform

This study proposes a high-resolution processing technique for seismic data based on the improved synchrosqueezing transform (SST). The SST rearranges the complex spectrum of the wavelet transform along the frequency axis. However, the energy is not concentrated in the position with the faster frequency change rate. To overcome these problems, the proposed method first transformed the seismic signal into an analytical one via Hilbert transformation and then determined the phase correction value (x0(t)) before and after the transformation. This was achieved using the instantaneous frequency attribute (ω(t)) of the analytical signal and a specific frequency (ω0) selected as the dominant frequency of the input data to adjust the change rate of the signal frequency before the SST falls close to zero, which can improve the time–frequency resolution after compression transformation. The essence of this method only adjusts the phase of the signal before and after transformation, without affecting the inverse expression of the SST. The one- and two-dimensional model data results show that the proposed method can better identify the time–frequency distribution characteristics of seismic signals and improve their resolution and the focusing effect in the time–frequency domain. The proposed method shows good prospects for application in gas reservoir detection and identification.
Rapid and simple analysis of short and long sequencing reads using DuesselporeTM

Transcriptome analysis experiments enable researchers to gain extensive insights into the molecular mechanisms underlying cell physiology and disease. Oxford Nanopore Technologies (ONT) has recently been developed as a fast, miniaturized, portable, and cost-effective alternative to next-generation sequencing (NGS). However, RNA-Seq data analysis software that exploits ONT portability and allows scientists to easily analyze ONT data everywhere without bioinformatics expertise is not widely available. We developed DuesselporeTM, an easy-to-follow deep sequencing workflow that runs as a local webserver and allows the analysis of ONT data everywhere without requiring additional bioinformatics tools or internet connection. DuesselporeTM output includes differentially expressed genes and further downstream analyses, such as variance heatmap, disease and gene ontology plots, gene concept network plots, and exports customized pathways for different cellular processes. We validated DuesselporeTM by analyzing the transcriptomic changes induced by PCB126, a dioxin-like PCB, and a potent aryl hydrocarbon receptor (AhR) agonist in human HaCaT keratinocytes, a well-characterized model system. DuesselporeTM was specifically developed to analyze ONT data, but we also implemented NGS data analysis. DuesselporeTM is compatible with Linux, Microsoft, and Mac operating systems and allows convenient, reliable, and cost-effective analysis of ONT and NGS data.
Regulation of plant biotic interactions and abiotic stress responses by inositol polyphosphates

Inositol pyrophosphates (PP-InsPs), derivatives of inositol hexakisphosphate (phytic acid, InsP6) or lower inositol polyphosphates, are energy-rich signaling molecules that have critical regulatory functions in eukaryotes. In plants, the biosynthesis and the cellular targets of these messengers are not fully understood. This is because, in part, plants do not possess canonical InsP6 kinases and are able to synthesize PP-InsP isomers that appear to be absent in yeast or mammalian cells. This review will shed light on recent discoveries in the biosynthesis of these enigmatic messengers and on how they regulate important physiological processes in response to abiotic and biotic stresses in plants.
Exploration of beta-arrestin isoform signaling pathways in delta opioid receptor agonist-induced convulsions

The δ-opioid receptor (δOR) has been considered as a therapeutic target in multiple neurological and neuropsychiatric disorders particularly as δOR agonists are deemed safer alternatives relative to the more abuse-liable µ-opioid receptor drugs. Clinical development of δOR agonists, however, has been challenging in part due to the seizure-inducing effects of certain δOR agonists. Especially agonists that resemble the δOR-selective agonist SNC80 have well-established convulsive activity. Close inspection suggests that many of those seizurogenic δOR agonists efficaciously recruit β-arrestin, yet surprisingly, SNC80 displays enhanced seizure activity in β-arrestin 1 knockout mice. This finding led us to hypothesize that perhaps β-arrestin 1 is protective against, whereas β-arrestin 2 is detrimental for δOR-agonist-induced seizures. To investigate our hypothesis, we characterized three different δOR agonists (SNC80, ADL5859, ARM390) in cellular assays and in vivo in wild-type and β-arrestin 1 and β-arrestin 2 knockout mice for seizure activity. We also investigated downstream kinases associated with β-arrestin-dependent signal transduction. We discovered that δOR agonist-induced seizure activity strongly and positively correlates with β-arrestin 2 efficacy for the agonist, but that indirect inhibition of ERK activation using the MEK inhibitor SL327 did not inhibit seizure potency and duration. Inhibition of the PI3K/AKT/mTOR signaling with honokiol but not PQR530, attenuated SNC80 seizure duration in β-arrestin 1 knockout, but honokiol did not reduce SNC80-induced seizures in wild-type mice. Ultimately, our results indicate that β-arrestin 2 is correlated with δOR agonist-induced seizure intensity, but that global β-arrestin 1 knockout mice are a poor model system to investigate their mechanism of action.
A minimally manipulated preservation and virus inactivation method for amnion/chorion

Allogeneic amnion tissues have been widely used in tissue repair and regeneration, especially a remarkable trend of clinical uses in chronic wound repair. The virus inactivation procedures are necessary and required to be verified for the clinical use and approval of biological products. Cobalt-60 (Co-60) or electron-beam (e-beam) is the common procedure for virus and bacterial reduction, but the excessive dose of irradiation was reported to be harmful to biological products. Herein, we present a riboflavin (RB)-ultraviolet light (UV) method for virus inactivation of amnion and chorion tissues. We used the standard in vitro limiting dilution assay to test the viral reduction capacity of the RB-UV method on amnion or chorion tissues loaded with four types of model viruses. We found RB-UV was a very effective procedure for inactivating viruses of amnion and chorion tissues, which could be used as a complementary method to Co-60 irradiation. In addition, we also screened the washing solutions and drying methods for the retention of growth factors.
The relations between mental well-being and burnout in medical staff during the COVID-19 pandemic: A network analysis

Background Although poor mental well-being (MW) has been documented among individuals experiencing burnout during the coronavirus-19 (COVID-19) pandemic, little is known about the complex interrelationship between different components of MW and burnout. This study investigates this relationship among medical staff during the COVID-19 pandemic through network analysis. Methods A total of 420 medical staff were recruited for this study. Components of MW were measured by the 14-item Warwick-Edinburgh Mental Well-being Scale (WEMWBS), and components of burnout were measured by a 15-item Maslach Burnout Inventory-General Survey (MBI-GS) Questionnaire. Network structure was constructed via network analysis. Bridge variables were identified via the bridge centrality index. Results The edges across two communities (i.e., MW community and burnout community) are almost negative, such as edge MW2 (“Useful”) – B14 (“Worthwhile”) and edge MW1 (“Optimistic about future”) – B13 (“Happy”). The edges within each community are nearly positive. In the MW community, components MW1 (“Optimistic about future”) and MW6 (“Dealing with problems”) have the lowest bridge centrality. And in the community of burnout, components B13 (“Happy”) and B14 (“Worthwhile”) have the lowest bridge expected influence. Conclusion We present the first study to apply the network approach to model the potential pathways between distinct components of MW and burnout. Our findings suggest that promoting optimistic attitudes and problem-solving skills may help reduce burnout among medical staff during the pandemic.
Plenoptic camera based on a liquid crystal microlens array

A type of liquid crystal microlens array (LCMLA) with tunable focal length by the voltage signals applied between its top and bottom electrodes, is fabricated and then the common optical focusing characteristics are tested. The relationship between the focal length and the applied voltage signals is given. The LCMLA is integrated with an image sensor and further coupled with a main lens so as to construct a plenoptic camera. Several raw images at different voltage signals applied are acquired and contrasted through the LCMLA-based plenoptic camera constructed by us. Our experiments demonstrate that through utilizing a LCMLA in a plenoptic camera, the focused zone of the LCMLA-based plenoptic camera can be shifted effectively only by changing the voltage signals loaded between the electrodes of the LCMLA, which is equivalent to the extension of the depth of field.
Consumer attitudes toward bacteriophage applications to pet food

This study used a two-part questionnaire to investigate consumer knowledge and attitudes toward bacteriophage applications in pet food, pet food safety, and environmental sustainability. Part 1 included questions about pet food safety, sustainability, and knowledge and attitudes toward bacteriophages. Next, participants reviewed educational materials about each, and Part 2 assessed if this increased knowledge of, or changed attitudes toward, bacteriophage application. Participants (n = 80), were recruited through Amazon Mechanical Turk (MT) (n = 45) and Social Media (SM) (n = 35). Mean responses in Part 1 and Part 2 were compared by paired t-tests, and mean responses between MT and SM were compared by t-tests. Participants reported pet food safety was important to them (combined proportion strongly agree or agree, mean ± SD) (75/80, 94%, MT 4.66 ± 0.60, SM 4.71 ± 0.95) and were most concerned with raw pet food safety (51/80, 64%, MT 3.88 ± 0.80, SM 3.17 ± 1.40). Participants rated environmental sustainability as important (61/80, 76%, MT 3.86 ± 0.94, SM 3.97 ± 0.66); however, it was not a strong driver of pet food purchasing (26/80, 33%, MT 3.31 ± 1.25, SM 2.82 ± 0.82). Overall, data showed an increase in knowledge of bacteriophages following a review of educational material. However, in the SM group, no statistically significant difference was observed in the comfort eating food with bacteriophage additives (SM Part 1 3.37 ± 1.05, SM Part 2 3.48 ± 1.12, p = 0.279), whereas the MT group did show an increase (MT Part 1 3.57 ± 1.01, MT Part 2 4.08 ± 0.92, p < 0.001). In the SM group, no statistically significant difference was observed in comfort feeding their pet food with bacteriophage additives (SM Part 1 3.40 ± 1.03, SM Part 2 3.45 ± 1.14, p = 0.571), whereas the MT group did show an increase (MT Part 1 3.57 ± 0.98, MT Part 2 4.31 ± 0.84, p < 0.001). The strongest objections related to safety concerns (20/53, 38%, MT 2.83 ± 0.96, SM 3.27 ± 0.84). These results demonstrate that despite increasing knowledge, there is still hesitancy among some consumers toward bacteriophage applications in pet food.
Host induced gene silencing of Magnaporthe oryzae by targeting pathogenicity and development genes to control rice blast disease

Rice blast disease caused by the hemi-biotrophic fungus Magnaporthe oryzae is the most destructive disease of rice world-wide. Traditional disease resistance strategies for the control of rice blast disease have not proved durable. HIGS (host induced gene silencing) is being developed as an alternative strategy. Six genes (CRZ1, PMC1, MAGB, LHS1, CYP51A, CYP51B) that play important roles in pathogenicity and development of M. oryzae were chosen for HIGS. HIGS vectors were transformed into rice calli through Agrobacterium-mediated transformation and T0, T1 and T2 generations of transgenic rice plants were generated. Except for PMC1 and LHS1, HIGS transgenic rice plants challenged with M. oryzae showed significantly reduced disease compared with non-silenced control plants. Following infection with M. oryzae of HIGS transgenic plants, expression levels of target genes were reduced as demonstrated by Quantitative RT-PCR. In addition, treating M. oryzae with small RNA derived from the target genes inhibited fungal growth. These findings suggest RNA silencing signals can be transferred from host to an invasive fungus and that HIGS has potential to generate resistant rice against M. oryzae.
Physiological and transcriptional responses to heat stress and functional analyses of PsHSPs in tree peony (Paeonia suffruticosa)

Tree peony (Paeonia suffruticosa) is a traditional Chinese flower that is not resistant to high temperatures, and the frequent sunburn during summer limits its normal growth. The lack of understanding of the molecular mechanisms in tree peony has greatly restricted the improvement of novel heat-tolerant varieties. Therefore, we treated tree peony cultivar “Yuhong” (P. suffruticosa “Yuhong”) at normal (25°C) and high temperatures (40°C) and sequenced the transcriptomes, to investigate the molecular responsive mechanisms to heat stress. By comparing the transcriptomes, a total of 7,673 differentially expressed genes (DEGs) were detected comprising 4,220 upregulated and 3,453 downregulated genes. Functional annotation showed that the DEGs were mainly related to the metabolic process, cells and binding, carbon metabolism, and endoplasmic reticulum protein processing. qRT-PCR revealed that three sHSP genes (PsHSP17.8, PsHSP21, and PsHSP27.4) were upregulated in the response of tree peony to heat stress. Tissue quantification of the transgenic lines (Arabidopsis thaliana) showed that all three genes were most highly expressed in the leaves. The survival rates of transgenic lines (PsHSP17.8, PsHSP21, and PsHSP27.4) restored to normal growth after high-temperature treatment were 43, 36, and 31%, respectively. In addition, the activity of superoxide dismutase, accumulation of free proline, and chlorophyll level was higher than those of the wild-type lines, while the malondialdehyde content and conductivity were lower, and the membrane lipid peroxidation reaction of the wild-type plant was more intense. Our research found several processes and pathways related to heat resistance in tree peony including metabolic process, single-organism process, phenylpropane biosynthesis pathway, and endoplasmic reticulum protein synthesis pathway. PsHSP17.8, PsHSP21, and PsHSP27.4 improved heat tolerance by increasing SOD activity and proline content. These findings can provide genetic resources for understanding the heat-resistance response of tree peony and benefit future germplasm innovation.
The reward and punishment responsivity and motivation questionnaire (RPRM-Q): A stimulus-independent self-report measure of reward and punishment sensitivity that differentiates between responsivity and motivation

Reward and punishment sensitivity seem important traits in understanding behavior in general and psychopathology in particular. Though the definitions used for reward and punishment sensitivity differentiate between responsivity and motivation, the measures thus far used to assess these constructs do not. Further, specificity of the type of reward (e.g., drugs) and punishment (e.g., spiders) in questionnaires might result in measurement bias especially when examining the relationship with psychopathology. Therefore, we developed a stimulus-independent multidimensional questionnaire of reward and punishment sensitivity that differentiates between responsivity and motivation. This study addresses the psychometric qualities of this newly developed reward and punishment responsivity and motivation questionnaire (RPRM-Q). On the basis of exploratory ordinal factor analysis (N = 273) that was used to examine the quality of the initial pool of 39 items, the number of items was reduced to 18. Confirmatory ordinal factor analysis on the remaining items in an independent sample (N = 328) supported a 18-item four-factor model, and showed acceptable to good internal reliability. The relationship between the subscales of the RPRM-Q and often used questionnaires was examined in the combined sample (N = 601), which showed some first support for the ability of the new questionnaire to differentiate between responsivity and motivation to approach/avoid. The findings indicate that the RPRM-Q might be a helpful instrument to further test the relevance of punishment and reward sensitivity in psychopathology.
Synergistic effect of co-culture rhizosphere Streptomyces: A promising strategy to enhance antimicrobial activity and plant growth-promoting function

Rhizosphere Streptomyces is one of the important types of rhizosphere microorganisms that plays an important role in promoting plant growth and controlling plant diseases to maintain agricultural ecosystem balance and green ecological agriculture development as beneficial bacteria. Microbial co-culture simulates the complex biocommunity in nature, which has more advantages than the monoculture with a synergistic effect. As the key signal mediums of microorganisms, plants, and their interactions, microbial metabolites are of great significance in revealing their functional mechanism. In this study, two potential plant growth-promoting rhizobacteria, Streptomyces albireticuli MDJK11, and Streptomyces alboflavus MDJK44, were selected to explore the effects of co-culture and monoculture on plant growth promotion and disease prevention, and the metabolic material basis was analyzed by metabonomics. Results showed that Streptomyces MDJK11, MDJK44 monoculture, and co-culture condition all showed good growth promoting and antimicrobial effects. Moreover, as compared to the monoculture, the co-culture showed the advantage of a synergistic enhancement effect. LC-MS-based metabonomics analysis showed the metabolic material bases of Streptomyces for plant growth promotion and disease prevention were mainly plant hormone and antibiotics and the co-culture condition could significantly stimulate the production of plant hormone promoters and macrolide, cyclic peptide, and aminoglycoside antibiotics. The study proved that the co-cultures of S. albireticuli MDJK11 and S. alboflavus MDJK44 have great potential in crop growth promotion and disease prevention.
Viewpoint of operating room nurses about factors associated with the occupational burnout: A qualitative study

Background Occupational burnout is a mental health problem that among nurses may lead not only to physical and psychological complications, but also to a decrease in the quality of patient care. Considering the stressful nature of surgery, operating room nurses may be at a greater risk. Therefore, the present study aimed to identifying factors associated with the occupational burnout from the perspective of operating room nurses. Materials and methods This qualitative study was conducted in Iran in 2021 using conventional content analysis. Sampling was performed using purposeful sampling method with maximum variation. In order to collect data, individual, semi-structured interviews were performed with 18 operating room nurses. Interviews continued until data saturation. Data were recorded, transcribed and analyzed using steps proposed by Graneheim and Lundman. Data management was performed using MAXQDA-2020 software. Four criteria provided by Guba and Lincoln were used to improve the study’s trustworthiness and rigor. Results A main theme, 4 categories and 15 subcategories were extracted from the data. The main theme is “gradual burnout due to job tension” and categories and subcategories include organizational factors (manager incompetence, organizational indifference, ambiguity in organizational role, organizational inconsistency), interpersonal factors (surgeon aggression, surgeon authoritarianism, surgeon failure to manage stress, unprofessional behavior of nurses), Occupational nature factors (psychological factors and occupational hazards) as well as individual factors (occupational attitude, unprofessional behavior, emotional involvement, demographic factors, physical factors). Conclusion Numerous factors associated with burnout in operating room nurses, which may put the personnel under more pressure. According to these factors, nursing managers and operating room nurses can consider effective strategies to prevent or coping with burnout.
Altered pattern analysis and identification of subjective cognitive decline based on morphological brain network

Subjective cognitive decline (SCD) is considered the first stage of Alzheimer’s disease (AD). Accurate diagnosis and the exploration of the pathological mechanism of SCD are extremely valuable for targeted AD prevention. However, there is little knowledge of the specific altered morphological network patterns in SCD individuals. In this present study, 36 SCD cases and 34 paired-matched normal controls (NCs) were recruited. The Jensen-Shannon distance-based similarity (JSS) method was implemented to construct and derive the attributes of multiple brain connectomes (i.e., morphological brain connections and global and nodal graph metrics) of individual morphological brain networks. A t-test was used to discriminate between the selected nodal graph metrics, while the leave-one-out cross-validation (LOOCV) was used to obtain consensus connections. Comparisons were performed to explore the altered patterns of connectome features. Further, the multiple kernel support vector machine (MK-SVM) was used for combining brain connectomes and differentiating SCD from NCs. We showed that the consensus connections and nodal graph metrics with the most discriminative ability were mostly found in the frontal, limbic, and parietal lobes, corresponding to the default mode network (DMN) and frontoparietal task control (FTC) network. Altered pattern analysis demonstrated that SCD cases had a tendency for modularity and local efficiency enhancement. Additionally, using the MK-SVM to combine the features of multiple brain connectomes was associated with optimal classification performance [area under the curve (AUC): 0.9510, sensitivity: 97.22%, specificity: 85.29%, and accuracy: 91.43%]. Therefore, our study highlighted the combination of multiple connectome attributes based on morphological brain networks and offered a valuable method for distinguishing SCD individuals from NCs. Moreover, the altered patterns of multidimensional connectome attributes provided a promising insight into the neuroimaging mechanism and early intervention in SCD subjects.