Miracle-dz/UniFAR-FTUs huggingface dataset:
Whole-body sorcin invalidation does not cause hypothalamic ER stress nor worsens obesity in C57BL/6 male mice fed a westernized diet

Background Soluble Resistance Related Calcium Binding Protein (sorcin) is a calcium (Ca2+) binding protein which has been shown to play a role in maintaining intracellular endoplasmic reticulum (ER) Ca2+ stores and lowering ER stress. Recently, our lab has demonstrated that sorcin expression was downregulated in the islets of Langerhans of mice fed a high-fat diet or in human islets incubated with the saturated fatty acid palmitate. We also showed that overexpression of sorcin under control of the rat insulin promoter (RIP7) in C57BL/6J mice, or whole body sorcin deletion in 129S1/SvImJ mice, improves or impairs insulin secretion and pancreatic β-cell function respectively. The mechanisms behind this beneficial role of sorcin in the pancreatic β-cell might depend on protection against lipotoxic endoplasmic reticulum (ER) stress through improved ER Ca2+ dynamics and activation of the Activating Transcription Factor 6 (ATF6) branch of the unfolded protein response (UPR). Whether sorcin is also implicated in hypothalamic ER stress during the progression of obesity is unknown. This could potentially contribute to the diminished satiety typically observed in overweight individuals. Aim To investigate a potential role of sorcin in hypothalamic ER stress, leptin resistance, hyperphagia and obesity. Methods Whole-body sorcin null mice, backcrossed onto the C57BL/6J genetic background, were used. Body weight, food intake and EchoMRI body composition were measured in vivo whereas qRT-PCR analysis of sorcin and ER stress markers expression were performed on the arcuate nucleus of the hypothalamus. Leptin signalling through STAT3 phosphorylation was measured by Western blots on sorcin-null HEK293 cells, engineered by CRISPR/Cas9, and transfected with leptin receptor (LepRb). Results Sorcin expression was not influenced in the arcuate nucleus (ARC) of the hypothalamus by diet-induced obesity. Whole-body sorcin ablation did not cause ARC ER stress nor changes in body weight, body composition or food intake in C57BL/6 male mice exposed to a high-fat, high-sugar diet. STAT3 phosphorylation (Y705) in response to leptin was not impaired in sorcin-null HEK293 cells. Conclusion In our model, whole body sorcin ablation did not increase hypothalamic ER stress nor influenced food intake or body weight.
Characterization of p38α signaling networks in cancer cells using quantitative proteomics and phosphoproteomics

p38α (encoded by MAPK14) is a protein kinase that regulates cellular responses to almost all types of environmental and intracellular stresses. Upon activation, p38α phosphorylates many substrates both in the cytoplasm and nucleus, allowing this pathway to regulate a wide variety of cellular processes. While the role of p38α in the stress response has been widely investigated, its implication in cell homeostasis is less understood. To investigate the signaling networks regulated by p38α in normally proliferating cancer cells, we performed quantitative proteomic and phosphoproteomic analyses in breast cancer cells in which this pathway had been either genetically targeted or chemically inhibited. Our study identified with high confidence 35 proteins and 82 phosphoproteins (114 phosphosites) that are modulated by p38α, and highlighted the implication of various protein kinases, including MK2 and mTOR, in the p38α-regulated signaling networks. Moreover, functional analyses revealed an important contribution of p38α to the regulation of cell adhesion, DNA replication and RNA metabolism. Indeed, we provide experimental evidence supporting that p38α negatively regulates cell adhesion, and showed that this p38α function is likely mediated by the modulation of the adaptor protein ArgBP2. Collectively, our results illustrate the complexity of the p38α regulated signaling networks, provide valuable information on p38α-dependent phosphorylation events in cancer cells, and document a mechanism by which p38α can regulate cell adhesion.
A small dynamic leaf-level model predicting photosynthesis in greenhouse tomatoes

The conversion of supplemental greenhouse light energy into biomass is not always optimal. Recent trends in global energy prices and discussions on climate change highlight the need to reduce our energy footprint associated with the use of supplemental light in greenhouse crop production. This can be achieved by implementing “smart” lighting regimens which in turn rely on a good understanding of how fluctuating light influences photosynthetic physiology. Here, a simple fit-for-purpose dynamic model is presented. It accurately predicts net leaf photosynthesis under natural fluctuating light. It comprises two ordinary differential equations predicting: 1) the total stomatal conductance to CO2 diffusion and 2) the CO2 concentration inside a leaf. It contains elements of the Farquhar-von Caemmerer-Berry model and the successful incorporation of this model suggests that for tomato (Solanum lycopersicum L.), it is sufficient to assume that Rubisco remains activated despite rapid fluctuations in irradiance. Furthermore, predictions of the net photosynthetic rate under both 400ppm and enriched 800ppm ambient CO2 concentrations indicate a strong correlation between the dynamic rate of photosynthesis and the rate of electron transport. Finally, we are able to indicate whether dynamic photosynthesis is Rubisco or electron transport rate limited. Author summary The cultivation of greenhouse crops under optimised conditions will become increasingly important, with supplemental lighting playing a vital role. However, converting light energy into plant photosynthesis is not always optimal. A potential venue that may lead to the efficient conversion of light energy involves a model-based implementation of “smart” lighting control strategy. This approach does however necessitate a good understanding of how plants harness light energy under natural fluctuating irradiance. Accordingly, as a first step, we have developed a small leaf-level model that predicts dynamic photosynthesis in natural fluctuating light. It may potentially be used in future supplemental light control applications.
Open spaced ridged hydrogel scaffolds containing TiSAMP surface chemistry promotes regeneration and recovery following spinal cord injury

The spinal cord has poor ability to regenerate after injury, which may be due to cell loss, cyst formation, inflammation, and scarring. A promising approach to treat spinal cord injury (SCI) is the use of biomaterials. We have developed a novel hydrogel scaffold fabricated from oligo(poly(ethylene glycol) fumarate) (OPF) as a 0.08 mm thick sheet containing polymer ridges and a cell-attractive surface chemistry on the other side. When the cells are cultured on OPF with the chemical patterning, the cells attach, align, and deposit ECM along the direction of the pattern. Animals implanted with the rolled scaffold sheets had greater hindlimb recovery compared to the multichannel scaffold control, likely due to the greater number of axons growing across. Inflammation, scarring, and ECM deposits were equal across conditions. Overall, the results suggest that the scaffold sheets promote axon outgrowth that can be guided across the scaffold, thereby promoting hindlimb recovery.
The thermoception task: a thermal imaging-based procedure for measuring awareness of changes in peripheral body temperature

Although thermal body signals provide crucial information about the state of an organism, and changes in body temperature may be a sign of affective states (e.g., stress, pain, sexual arousal), research on thermal awareness is limited. Here we developed a task measuring awareness of changes in peripheral body temperature (thermal interoception) and compared it to the classical heartbeat counting task (cardiac interoception). With an infrared lightbulb we delivered stimuli of different temperature intensities to the right hand of 31 healthy participants. Thermal interoceptive accuracy, i.e., the difference between participants’ real and perceived change in hand temperature, showed good inter-individual variability. We found that thermal interoception did not correlate with (and was generally higher than) cardiac interoception, suggesting that different interceptive channels provide separate contributions to awareness of bodily states. Moreover, the results hint at the great salience of thermal signals and the need for thermoregulation in day-to-day life. Finally, thermal interoceptive accuracy was associated with self-reported awareness of body temperature changes, and with the ability to regulate distress by focusing on body sensations. Our task has the potential to significantly increase current knowledge about the role of interoception in cognition and behavior, particularly in social and emotional contexts.
qPCRtools: An R package for qPCR data processing and visualization

In biological research, qPCR is a technique that is frequently used to measure gene expression levels. The calculation of gene amplification efficiency is a critical step in the processing of qPCR data since it helps to decide which method to employ to compute gene expression levels. Here, we introduce the R package qPCRtools, which enables users to analyze the efficiency of gene amplification. Additionally, this software can determine gene expression levels using one of three approaches: the conventional curve-based method, the 2−ΔΔCt method, and the SATQPCR method. The qPCRtools package produces a table with the statistical data of each method as well as a figure with a box or bar plot illustrating the results. The R package qPCRtools is freely available at CRAN (https://CRAN.R-project.org/package=qPCRtools) or GitHub (https://github.com/lixiang117423/qPCRtools/tree/main/CRAN/qPCRtools).
Reinventing talent management: How to maximize performance in higher education

Talent management is considered a new organizational priority in managing people that both academicians and practitioners discuss. The purpose of this research was to examine the role of talent management (TM), knowledge management (KM), university transformation (UT), and academic climate (AC) in increasing the performance of private higher education institutions (PHEIs). This research applied a quantitative approach by collecting data from 382 lecturers who worked at various private universities in Indonesia. Online questionnaires were used to collect the data using a stratified random sampling method. Then these data were analyzed using Structural Equation Modeling–Partial Least Square. The findings indicated that systematic application of talent management and knowledge management, university transformation, and academic climate in PHEIs improves organizational performance. Developing a plan to transform their talent and the business process is the key to emphasizing its importance in shaping the character and quality of PHEIs. The practical implication, PHEIs must offer a conducive academic climate for talented lecturers. The study offers a value-add to the resource-based view theory, managing talent and knowledge as essential resources for organizational transformation to maximize organizational performance.
Urinary proteome analysis of acute kidney injury in post-cardiac surgery patients using enrichment materials with high-resolution mass spectrometry

Background: Cardiac surgery-associated acute kidney injury (CSA-AKI) may increase the mortality and incidence rates of chronic kidney disease in critically ill patients. This study aimed to investigate the underlying correlations between urinary proteomic changes and CSA-AKI. Methods: Nontargeted proteomics was performed using nano liquid chromatography coupled with Orbitrap Exploris mass spectrometry (MS) on urinary samples preoperatively and postoperatively collected from patients with CSA-AKI. Gemini C18 silica microspheres were used to separate and enrich trypsin-hydrolysed peptides under basic mobile phase conditions. Differential analysis was conducted to screen out urinary differential expressed proteins (DEPs) among patients with CSA-AKI for bioinformatics. Kyoto Encyclopedia of Genes and Genomes (KEGG) database analysis was adopted to identify the altered signal pathways associated with CSA-AKI. Results: Approximately 2000 urinary proteins were identified and quantified through data-independent acquisition MS, and 324 DEPs associated with AKI were screened by univariate statistics. According to KEGG enrichment analysis, the signal pathway of protein processing in the endoplasmic reticulum was enriched as the most up-regulated DEPs, and cell adhesion molecules were enriched as the most down-regulated DEPs. In protein–protein interaction analysis, the three hub targets in the up-regulated DEPs were α-1-antitrypsin, β-2-microglobulin and angiotensinogen, and the three key down-regulated DEPs were growth arrest-specific protein 6, matrix metalloproteinase-9 and urokinase-type plasminogen activator. Conclusion: Urinary protein disorder was observed in CSA-AKI due to ischaemia and reperfusion. The application of Gemini C18 silica microspheres can improve the protein identification rate to obtain highly valuable resources for the urinary DEPs of AKI. This work provides valuable knowledge about urinary proteome biomarkers and essential resources for further research on AKI.
Combined transcriptomic and proteomic analysis reveals multiple pathways involved in self-pollen tube development and the potential roles of FviYABBY1 in self-incompatibility in Fragaria viridis

Fragaria viridis exhibits S-RNase-based gametophytic self-incompatibility, in which S-RNase is the major factor inhibiting pollen tube growth. However, the pathways involved in and the immediate causes of the inhibition of pollen tube growth remain unknown. Here, interactive RNA sequencing and proteome analysis revealed changes in the transcriptomic and proteomic profiles of F. viridis styles harvested at 0 and 24 h after self-pollination. A total of 2,181 differentially expressed genes and 200 differentially abundant proteins were identified during the pollen development stage of self-pollination. Differentially expressed genes and differentially abundant proteins associated with self-incompatible pollination were further mined, and multiple pathways were found to be involved. Interestingly, the expression pattern of the transcription factor FviYABBY1, which is linked to polar growth, differed from those of other genes within the same family. Specifically, FviYABBY1 expression was extremely high in pollen, and its expression trend in self-pollinated styles was consistent with that of S-RNase. Furthermore, FviYABBY1 interacted with S-RNase in a non-S haplotype way. Therefore, FviYABBY1 affects the expression of polar growth-related genes in self-pollen tubes and is positively regulated by S-RNase.
Immune-related gene signature associates with immune landscape and predicts prognosis accurately in patients with Wilms tumour

Wilms tumour (WT) is the most common kidney malignancy in children. Chemoresistance is the leading cause of tumour recurrence and poses a substantial therapeutic challenge. Increasing evidence has underscored the role of the tumour immune microenvironment (TIM) in cancers and the potential for immunotherapy to improve prognosis. There remain no reliable molecular markers for reflecting the immune landscape and predicting patient survival in WT. Here, we examine differences in gene expression by high-throughput RNA sequencing, focused on differentially expressed immune-related genes (IRGs) based on the ImmPort database. Via univariate Cox regression analysis and Lasso-penalized Cox regression analysis, IRGs were screened out to establish an immune signature. Kaplan-Meier curves, time-related ROC analysis, univariate and multivariate Cox regression studies, and nomograms were used to evaluate the accuracy and prognostic significance of this signature. Furthermore, we found that the immune signature could reflect the immune status and the immune cell infiltration character played in the tumour microenvironment (TME) and showed significant association with immune checkpoint molecules, suggesting that the poor outcome may be partially explained by its immunosuppressive TME. Remarkably, TIDE, a computational method to model tumour immune evasion mechanisms, showed that this signature holds great potential for predicting immunotherapy responses in the TARGET-wt cohort. To decipher the underlying mechanism, GSEA was applied to explore enriched pathways and biological processes associated with immunophenotyping and Connectivity map (CMap) along with DeSigN analysis for drug exploration. Finally, four candidate immune genes were selected, and their expression levels in WT cell lines were monitored via qRT-PCR. Meanwhile, we validated the function of a critical gene, NRP2. Taken together, we established a novel immune signature that may serve as an effective prognostic signature and predictive biomarker for immunotherapy response in WT patients. This study may give light on therapeutic strategies for WT patients from an immunological viewpoint.
First observation of paired microseismic signals during solution salt mining

To monitor the status of cavern roof instability induced by solution salt mining, we deployed a surface microseismic monitoring system for Dongxing salt mine, Dingyuan county, China. The microseismic monitoring system consists of 11 three-component geophones installed in shallow holes of 5 m deep. From 7-month continuous monitoring data, we have detected a novel type of signal that consists of two events. The first event has a long duration (>15 s) and generally has higher frequencies at the beginning. The 2nd event has a shorter duration of ∼3 s with lower frequencies. The two events are separated by ∼30–90 s in time. From May 2017 to November 2017, there are a total of 88 distinct paired signals with two events in sequence. We propose the first event corresponds to a series of fracturing processes on the cavern roof, and microseismic signals associated with different fractures are mixed and overlapped to produce a mixed signal with a longer duration. Due to a series of fracturing processes, some zones of cavern roof become instable and some rock debris may fall from the roof and collide on the cavern floor. This collision can produce a short duration signal, which corresponds to the 2nd event of the paired signal. The further analysis of polarities of the first arrivals for the 2nd event further proves its collision origin. The time interval between two events is related to the time for the falling rock debris through the brine, which is controlled by the cavern height and various physical properties of the rock debris and brine. Through the detailed analysis of paired signals, we can have a better understanding of the cavity development status for solution salt mining.
Retinal organoids and microfluidic chip-based approaches to explore the retinitis pigmentosa with USH2A mutations

Retinitis pigmentosa (RP) is a leading cause of vision impairment and blindness worldwide, with limited medical treatment options. USH2A mutations are one of the most common causes of non-syndromic RP. In this study, we developed retinal organoids (ROs) and retinal pigment epithelium (RPE) cells from induced pluripotent stem cells (iPSCs) of RP patient to establish a sustainable in vitro RP disease model. RT-qPCR, western blot, and immunofluorescent staining assessments showed that USH2A mutations induced apoptosis of iPSCs and ROs, and deficiency of the extracellular matrix (ECM) components. Transcriptomics and proteomics findings suggested that abnormal ECM-receptor interactions could result in apoptosis of ROs with USH2A mutations via the PI3K-Akt pathway. To optimize the culture conditions of ROs, we fabricated a microfluidic chip to co-culture the ROs with RPE cells. Our results showed that this perfusion system could efficiently improve the survival rate of ROs. Further, ECM components such as laminin and collagen IV of ROs in the RP group were upregulated compared with those maintained in static culture. These findings illustrate the potential of microfluidic chip combined with ROs technology in disease modelling for RP.
PANoptosis-based molecular clustering and prognostic signature predicts patient survival and immune landscape in colon cancer

PANoptosis is a newly-discovered cell death pathway that involves crosstalk and co-ordination between pyroptosis, apoptosis, and necroptosis processes. However, the roles of PANoptosis-related genes (PRGs) in prognosis and immune landscape of colon cancer remain widely unknown. Here, we performed a bioinformatics analysis of expression data of nineteen PRGs identified from previous studies and clinical data of colon cancer patients obtained from TCGA and GEO databases. Colon cancer cases were divided into two PRG clusters, and prognosis-related differentially expressed genes (PRDEGs) were identified. The patient data were then separated into two corresponding distinct gene clusters, and the relationship between the risk score, patient prognosis, and immune landscape was analyzed. The identified PRGs and gene clusters correlated with patient survival and immune system and cancer-related biological processes and pathways. A prognosis signature based on seven genes was identified, and patients were divided into high-risk and low-risk groups based on the calculated risk score. A nomogram model for prediction of patient survival was also developed based on the risk score and other clinical features. Accordingly, the high-risk group showed worse prognosis, and the risk score was related to immune cell abundance, cancer stem cell (CSC) index, checkpoint expression, and response to immunotherapy and chemotherapeutic drugs. Results of quantitative real-time polymerase chain reaction (qRT-PCR) showed that LGR5 and VSIG4 were differentially expressed between normal and colon cancer samples. In conclusion, we demonstrated the potential of PANoptosis-based molecular clustering and prognostic signatures for prediction of patient survival and tumor microenvironment (TME) in colon cancer. Our findings may improve our understanding of the role of PANoptosis in colon cancer, and enable the development of more effective treatment strategies.
Effect of familiarity and recollection during constrained retrieval on incidental encoding for new “foil” information

Behavioral studies have demonstrated differences in the effect of constrained retrieval of semantic vs. non-semantic information on the encoding of foils. However, the impact of recognition on foils between semantic and non-semantic trials remains unclear. This study thus examines the roles of recognition—familiarity and recollection—in constrained retrieval for foils. We applied the event-related brain potentials (ERPs) data of new/old effects to elucidate the neural mechanisms underlying the “foil effect. ” Participants encoded semantic and non-semantic tasks (Phase 1), were tested in a blocked memory task with new words presented as foils (Phase 2), and performed a surprise recognition task involving foils and completely new words (Phase 3). Behavioral results showed better recognition performance regarding reaction times and accuracy by hit and correct reject for semantic vs. non-semantic trials in Phase 2. Conversely, inferior recognition performance in reaction times and accuracy by hit and correct reject was noted for semantic vs. non-semantic foils in Phase 3. ERP results showed more positive Frontal N400 (FN400) for hit in non-semantic trials, more positive late positive component (LPC) for correct rejects in semantic trials in Phase 2, and more positive LPC for hits in both semantic and non-semantic trials only in Phase 3. Through dual-processing theory, we prove that different task types in constrained retrieval depend on different retrieval processes. Particularly, familiarity may be applied more often in non-semantic trials, and recollection in semantic trials. The difference in processes between semantic and non-semantic trials during constrained retrieval affects incidental encoding of foils.