Miracle-dz/UniFAR-FTUs huggingface dataset:
Methods for Establishing a Renal Cell Carcinoma Tumor Spheroid Model With Immune Infiltration for Immunotherapeutic Studies

Tumor spheroids play an increasingly important role in cancer research. Their ability to recapitulate crucial features of tumor biology that are lost in the classically used 2D models along with their relative simplicity and handiness have made them the most studied 3D tumor model. Their application as a theranostic tool or as a means to study tumor-host interaction is now well-established in various cancers. However, their use in the field of Renal Cell Carcinoma (RCC) remains very limited. The aim of this work is to present methods to implement a basic RCC spheroid model. These methods cover the steps from RCC tumor dissociation to spheroid infiltration by immune cells. We present a protocol for RCC dissociation using Liberase TM and introduce a culture medium containing Epithelial Growth Factor and Hydrocortisone allowing for faster growth of RCC primary cells. We show that the liquid overlay technique allows for the formation of spheroids from cell lines and from primary cultures. We present a method using morphological criteria to select a homogeneous spheroid population based on a Fiji macro. We then show that spheroids can be infiltrated by PBMCs after activation with OKT3 or IL-15. Finally, we provide an example of application by implementing an immune spheroid killing assay allowing observing increased spheroid destruction after treatment with PD-1 inhibitors. Thus the straightforward methods presented here allow for efficient spheroid formation for a simple RCC 3D model that can be standardized and infused with immune cells to study immunotherapies.
Impact of Time-Varying Intensity of Mechanical Ventilation on 28-Day Mortality Depends on Fluid Balance in Patients With Acute Respiratory Distress Syndrome: A Retrospective Cohort Study

Background Recent studies have mainly focused on the association between baseline intensity of mechanical ventilation (driving pressure or mechanical power) and mortality in acute respiratory distress syndrome (ARDS). It is unclear whether the association between the time-varying intensity of mechanical ventilation and mortality is significant and varies according to the fluid balance trajectories. Methods We conducted a secondary analysis based on the NHLBI ARDS Network’s Fluid and Catheter Treatment Trial (FACTT). The primary outcome was 28-day mortality. The group-based trajectory modeling (GBTM) was employed to identify phenotypes based on fluid balance trajectories. Bayesian joint models were used to account for informative censoring due to death during follow-up. Results A total of 1,000 patients with ARDS were included in the analysis. Our study identified two phenotypes of ARDS, and compared patients with Early Negative Fluid Balance (Early NFB) and patients with Persistent-Positive Fluid Balance (Persistent-PFB) accompanied by higher tidal volume, higher static driving pressure, higher mechanical power, and lower PaO2/FiO2, over time during mechanical ventilation. The 28-day mortality was 14.8% in Early NFB and 49.6% in Persistent-PFB (p < 0.001). In the Bayesian joint models, the hazard ratio (HR) of 28-day death for time-varying static driving pressure [HR 1.03 (95% CI 1.01–1.05; p < 0.001)] and mechanical power [HR 1.01 (95% CI 1.002–1.02; p = 0.01)] was significant in patients with Early NFB, but not in patients with Persistent-PFB. Conclusion Time-varying intensity of mechanical ventilation was associated with a 28-day mortality of ARDS in a patient with Early NFB but not in patients with Persistent-PFB.
Human Recombinant Alkaline Phosphatase (Ilofotase Alfa) Protects Against Kidney Ischemia-Reperfusion Injury in Mice and Rats Through Adenosine Receptors

Adenosine triphosphate (ATP) released from injured or dying cells is a potent pro-inflammatory “danger” signal. Alkaline phosphatase (AP), an endogenous enzyme that de-phosphorylates extracellular ATP, likely plays an anti-inflammatory role in immune responses. We hypothesized that ilofotase alfa, a human recombinant AP, protects kidneys from ischemia-reperfusion injury (IRI), a model of acute kidney injury (AKI), by metabolizing extracellular ATP to adenosine, which is known to activate adenosine receptors. Ilofotase alfa (iv) with or without ZM241,385 (sc), a selective adenosine A2A receptor (A2AR) antagonist, was administered 1 h before bilateral IRI in WT, A2AR KO (Adora2a–/–) or CD73–/– mice. In additional studies recombinant alkaline phosphatase was given after IRI. In an AKI-on-chronic kidney disease (CKD) ischemic rat model, ilofotase alfa was given after the three instances of IRI and rats were followed for 56 days. Ilofotase alfa in a dose dependent manner decreased IRI in WT mice, an effect prevented by ZM241,385 and partially prevented in Adora2a–/– mice. Enzymatically inactive ilofotase alfa was not protective. Ilofotase alfa rescued CD73–/– mice, which lack a 5′-ectonucleotidase that dephosphorylates AMP to adenosine; ZM241,385 inhibited that protection. In both rats and mice ilofotase alfa ameliorated IRI when administered after injury, thus providing relevance for therapeutic dosing of ilofotase alfa following established AKI. In an AKI-on-CKD ischemic rat model, ilofotase alfa given after the third instance of IRI reduced injury. These results suggest that ilofotase alfa promotes production of adenosine from liberated ATP in injured kidney tissue, thereby amplifying endogenous mechanisms that can reverse tissue injury, in part through A2AR-and non-A2AR-dependent signaling pathways.
Mucosal immunization with an adenoviral vector vaccine confers superior protection against RSV compared to natural immunity

Respiratory syncytial virus (RSV) infections are the leading cause of severe respiratory illness in early infancy. Although the majority of children and adults mount immune responses against RSV, recurrent infections are frequent throughout life. Humoral and cellular responses contribute to an effective immunity but also their localization at respiratory mucosae is increasingly recognized as an important factor. In the present study, we evaluate a mucosal vaccine based on an adenoviral vector encoding for the RSV fusion protein (Ad-F), and we investigate two genetic adjuvant candidates that encode for Interleukin (IL)-1β and IFN-β promoter stimulator I (IPS-1), respectively. While vaccination with Ad-F alone was immunogenic, the inclusion of Ad-IL-1β increased F-specific mucosal immunoglobulin A (IgA) and tissue-resident memory T cells (TRM). Consequently, immunization with Ad-F led to some control of virus replication upon RSV infection, but Ad-F+Ad-IL-1β was the most effective vaccine strategy in limiting viral load and weight loss. Subsequently, we compared the Ad-F+Ad-IL-1β-induced immunity with that provoked by a primary RSV infection. Systemic F-specific antibody responses were higher in immunized than in previously infected mice. However, the primary infection provoked glycoprotein G-specific antibodies as well eventually leading to similar neutralization titers in both groups. In contrast, mucosal antibody levels were low after infection, whereas mucosal immunization raised robust F-specific responses including IgA. Similarly, vaccination generated F-specific TRM more efficiently compared to a primary RSV infection. Although the primary infection resulted in matrix protein 2 (M2)-specific T cells as well, they did not reach levels of F-specific immunity in the vaccinated group. Moreover, the infection-induced T cell response was less biased towards TRM compared to vaccine-induced immunity. Finally, our vaccine candidate provided superior protection against RSV infection compared to a primary infection as indicated by reduced weight loss, virus replication, and tissue damage. In conclusion, our mucosal vaccine candidate Ad-F+Ad-IL-1β elicits stronger mucosal immune responses and a more effective protection against RSV infection than natural immunity generated by a previous infection. Harnessing mucosal immune responses by next-generation vaccines is therefore a promising option to establish effective RSV immunity and thereby tackle a major cause of infant hospitalization.
Impact of Perceived Influence, Virtual Interactivity on Consumer Purchase Intentions Through the Path of Brand Image and Brand Expected Value

Many researchers are currently showing interest in researching consumers who are purchasing the products with the help of new tools, and new kinds of markets are emerging rapidly. M-commerce is a prevalent mode of marketing and is famous among young people of Pakistan. Current research is planned to check the status of consumer purchase intentions (PIs) using perceived influence, virtual interactivity, brand image, and brand expected value among customers who purchase their products with the help of m-commerce. Data was collected from customers who were engaged in buying with the help of m-commerce by using the convenience sampling technique and 227 complete questionnaires were used in final analysis. This research examines the direct impact of perceived influence, virtual interactivity, brand image, and brand expected value on PIs and finds the indirect effect of brand image and brand expected value on the relationships of perceived influence and virtual interactivity with PIs. Results indicate that all the hypotheses of direct relationships are accepted except the hypothesis for the relation of virtual interactivity with consumer PIs. Virtual interactivity has an insignificant positive impact on consumer PIs. Brand expected value has a strong positive effect on consumer PIs among all. The current study proposed four mediational hypotheses. All the proposed mediational hypotheses are accepted.
Measuring and Analysing Marginal Systemic Risk Contribution using CoVaR: A Copula Approach

This paper is devoted to the quantification and analysis of marginal risk contribution of a given single financial institution i to the risk of a financial system s. Our work expands on the CoVaR concept proposed by Adrian and Brunnermeier as a tool for the measurement of marginal systemic risk contribution. We first give a mathematical definition of CoVaR_{\alpha}^{s|L^i=l}. Our definition improves the CoVaR concept by expressing CoVaR_{\alpha}^{s|L^i=l} as a function of a state l and of a given probability level \alpha relative to i and s respectively. Based on Copula theory we connect CoVaR_{\alpha}^{s|L^i=l} to the partial derivatives of Copula through their probabilistic interpretation and definitions (Conditional Probability). Using this we provide a closed formula for the calculation of CoVaR_{\alpha}^{s|L^i=l} for a large class of (marginal) distributions and dependence structures (linear and non-linear). Our formula allows a better analysis of systemic risk using CoVaR in the sense that it allows to define CoVaR_{\alpha}^{s|L^i=l} depending on the marginal distributions of the losses of i and s respectively and the copula between L^i and L^s. We discuss the implications of this in the context of the quantification and analysis of systemic risk contributions. %some mathematical This makes possible the For example we will analyse the marginal effects of L^i, L^s and C of the risk contribution of i.
Induction of heartwood formation in young Indian sandalwood (Santalum album L.) by gas elicitors

Induction of heartwood formation in 6-year-old Indian sandalwood (Santalum album L.) trees by treatment with carbon dioxide, ethylene, nitrogen, and wounding was investigated. All treatments induced fragrant heartwood formation upward and downward from the drill hole. The amount of heartwood formed above and below the drill hole depended on the treatment in the order nitrogen>carbon dioxide>ethylene>wounding, whereas the radial extension proportion was, in order, nitrogen>carbon dioxide>ethylene=wounding. Based on the chemical analysis (GC–MS) and evaluation of the essential oil quality and heartwood properties, heartwood induced by carbon dioxide showed the maximum similarities to naturally formed heartwood, which included the same color, similar chemical composition, reasonable oil content, and quality essential oil, whereas ethylene, nitrogen, and wounding treatment showed fewer similarities to natural heartwood. The results suggest that carbon dioxide is a promising candidate gas elicitor for inducing heartwood formation in young S. album.
Limitation of multiparticle correlations for studying the event-by-event distribution of harmonic flow in heavy-ion collisions

The sensitivity of flow harmonics from cumulants on the event-by-event flow distribution $p(v_n)$ is investigated using a simple central moment expansion approach. For narrow distribution whose width is much smaller than the mean $\sigma_n\ll $, the difference between the first three higher-order cumulant estimates $v_n\{4\}$, $v_n\{6\}$ and $v_n\{8\}$ are not very sensitive to the shape of $p(v_n)$. For broad distribution $\sigma_n\gtrsim $, the higher-order cumulant estimates differ from each other but may change sign and become ill-defined. This sign change arises from the choice of $p(v_n)$, without the need to invoke non-flow effects. Direct extraction of $p(v_n)$ via a data-driven unfolding method is a more preferred approach for flow distribution measurement.
Mutational Profile and Potential Molecular Therapeutic Targets of Pheochromocytoma

Purpose Pheochromocytoma/paraganglioma (PCC/PGL; collectively known as PPGL) can be driven by germline and somatic mutations in susceptibility genes. We aimed to investigate the mutation profile and clinical features of pathogenic genes in highly genetically heterogeneous PPGL and to preliminary explore molecular therapeutic targets in PPGL. Methods We established a panel of 260 genes, including susceptibility genes of PPGL and other important tumorigenic genes to sequence 107 PPGL tissues. Results Overall, 608 genomic mutations were identified in 107 PPGL tissues. Almost 57% of PPGL tissue samples exhibited pathogenic mutations, and the most frequently mutated gene was SDHB (15/107, 14%). SDHB and HRAS were the most commonly mutated genes in germline-mutated PPGL (25/107, 23%) and nongermline-mutated PPGL (36/107, 34%), respectively. In addition, novel pathogenic mutations were detected in sporadic PPGL. PPGL with mutations in the hypoxia pathway had an earlier onset and higher norepinephrine level than those in the kinase pathway. Receptor tyrosine kinase (RTK; 22%, 24/107), mitogen-activated protein kinase (MAPK; 14%, 15/107), and tyrosine kinase (TK; 2%, 2/107) pathways were the most frequently mutated pathways in PPGL. Conclusion Our results provided the genetic mutation profile in PPGL tissues. Genetic mutations in PPGL were mainly concentrated in the RTK, TK, and MAPK pathways, suggesting potential molecular therapeutic targets for PPGL.
Dynamics of Viral Infection and Evolution of SARS-CoV-2 Variants in the Calabria Area of Southern Italy

In this study, we report on the results of SARS-CoV-2 surveillance performed in an area of Southern Italy for 12 months (from March 2021 to February 2022). To this study, we have sequenced RNA from 609 isolates. We have identified circulating VOCs by Sanger sequencing of the S gene and defined their genotypes by whole-genome NGS sequencing of 157 representative isolates. Our results indicated that B.1 and Alpha were the only circulating lineages in Calabria in March 2021; while Alpha remained the most common variant between April 2021 and May 2021 (90 and 73%, respectively), we observed a concomitant decrease in B.1 cases and appearance of Gamma cases (6 and 21%, respectively); C.36. 3 and Delta appeared in June 2021 (6 and 3%, respectively); Delta became dominant in July 2021 while Alpha continued to reduce (46 and 48%, respectively). In August 2021, Delta became the only circulating variant until the end of December 2021. As of January 2022, Omicron emerged and took over Delta (72 and 28%, respectively). No patient carrying Beta, Iota, Mu, or Eta variants was identified in this survey. Among the genomes identified in this study, some were distributed all over Europe (B1_S477N, Alpha_L5F, Delta_T95, Delta_G181V, and Delta_A222V), some were distributed in the majority of Italian regions (B1_S477N, B1_Q675H, Delta_T95I and Delta_A222V), and some were present mainly in Calabria (B1_S477N_T29I, B1_S477N_T29I_E484Q, Alpha_A67S, Alpha_A701S, and Alpha_T724I). Prediction analysis of the effects of mutations on the immune response (i.e., binding to class I MHC and/or recognition of T cells) indicated that T29I in B.1 variant; A701S in Alpha variant; and T19R in Delta variant were predicted to impair binding to class I MHC whereas the mutations A67S identified in Alpha; E484K identified in Gamma; and E156G and ΔF157/R158 identified in Delta were predicted to impair recognition by T cells. In conclusion, we report on the results of SARS-CoV-2 surveillance in Regione Calabria in the period between March 2021 and February 2022, identified variants that were enriched mainly in Calabria, and predicted the effects of identified mutations on host immune response.
Multiple latent variables but functionally dependent output mappings underlying the recognition of own- and other-race faces for Chinese individuals: Evidence from state-trace analysis

To explore the number of latent variables underlying recognition of own- and other-race faces for Chinese observers, we conducted a study-recognition task where orientation, stimuli type, and duration were manipulated in the study phase and applied state trace analysis as a statistic method. Results showed that each state trace plot on each pair of stimuli types matched a single monotonic curve when stimuli type was set to state factor, but separate curves between face and non-face showed up when the state factor was orientation. The results implied that at least two latent variables affected recognition performance in the inversion paradigm. Besides, the unidimensional structure between own- and other-race faces regardless of the state factor suggested that Chinese participants used the same recognition mechanism for unfamiliar own- and other-race faces in the inversion paradigm.
Perceived corporate social responsibility and pro-environmental behaviour: Insights from business schools of Peshawar, Pakistan

Corporate Social Responsibility (CSR) and environmental sustainability have become urgent concerns for contemporary businesses. This study focuses on the interplay between corporate social responsibility perceptions and pro-environmental behaviour (PEB) in response to experts’ call for research on the micro-foundations of corporate social responsibility. In addition, it reveals the mechanism underpinning how perceived CSR shapes pro-environmental behaviour in an understudied developing context. Empirically, a qualitative multiple-case research design is utilised by selecting three business schools from Peshawar, Pakistan. Fourteen semi-structured interviews were conducted with senior management and faculty to collect data. Besides primary data, a qualitative documentary review is used to enhance the research. Data analysis is done through the thematic network technique. Plantation, cleanliness, waste reduction, and energy conservation are the environmental aspects of CSR as regarded by employees. In addition, perceived CSR shapes pro-environmental behaviour via environmental knowledge and awareness, eco-civic sense, environmental values, personality traits, religious perspective, and perceived organisational support for the environment. This study provides original additions to the CSR literature by suggesting eco-civic sensibility and religious perspective as new CSR drivers for pro-environmental conduct. Incorporating stakeholder salience into the context of the present study also advances CSR research. The findings are also valuable for management to make the CSR agenda of business schools more strategic, comprehensive, and centred on the priorities of salient stakeholders.
Decoding Neuropathic Pain: Can We Predict Fluctuations of Propagation Speed in Stimulated Peripheral Nerve?

To understand neural encoding of neuropathic pain, evoked and resting activity of peripheral human C-fibers are studied via microneurography experiments. Before different spiking patterns can be analyzed, spike sorting is necessary to distinguish the activity of particular fibers of a recorded bundle. Due to single-electrode measurements and high noise contamination, standard methods based on spike shapes are insufficient and need to be enhanced with additional information. Such information can be derived from the activity-dependent slowing of the fiber propagation speed, which in turn can be assessed by introducing continuous “background” 0.125–0.25 Hz electrical stimulation and recording the corresponding responses from the fibers. Each fiber's speed propagation remains almost constant in the absence of spontaneous firing or additional stimulation. This way, the responses to the “background stimulation” can be sorted by fiber. In this article, we model the changes in the propagation speed resulting from the history of fiber activity with polynomial regression. This is done to assess the feasibility of using the developed models to enhance the spike shape-based sorting. In addition to human microneurography data, we use animal in-vitro recordings with a similar stimulation protocol as higher signal-to-noise ratio data example for the models.
Comprehensive Analysis of the Immunogenomics of Triple-Negative Breast Cancer Brain Metastases From LCCC1419

Background Triple negative breast cancer (TNBC) is an aggressive variant of breast cancer that lacks the expression of estrogen and progesterone receptors (ER and PR) and HER2. Nearly 50% of patients with advanced TNBC will develop brain metastases (BrM), commonly with progressive extracranial disease. Immunotherapy has shown promise in the treatment of advanced TNBC; however, the immune contexture of BrM remains largely unknown. We conducted a comprehensive analysis of TNBC BrM and matched primary tumors to characterize the genomic and immune landscape of TNBC BrM to inform the development of immunotherapy strategies in this aggressive disease. Methods Whole-exome sequencing (WES) and RNA sequencing were conducted on formalin-fixed, paraffin-embedded samples of BrM and primary tumors of patients with clinical TNBC (n = 25, n = 9 matched pairs) from the LCCC1419 biobank at UNC—Chapel Hill. Matched blood was analyzed by DNA sequencing as a comparison for tumor WES for the identification of somatic variants. A comprehensive genomics assessment, including mutational and copy number alteration analyses, neoantigen prediction, and transcriptomic analysis of the tumor immune microenvironment were performed. Results Primary and BrM tissues were confirmed as TNBC (23/25 primaries, 16/17 BrM) by immunohistochemistry and of the basal intrinsic subtype (13/15 primaries and 16/19 BrM) by PAM50. Compared to primary tumors, BrM demonstrated a higher tumor mutational burden. TP53 was the most frequently mutated gene and was altered in 50% of the samples. Neoantigen prediction showed elevated cancer testis antigen- and endogenous retrovirus-derived MHC class I-binding peptides in both primary tumors and BrM and predicted that single-nucleotide variant (SNV)-derived peptides were significantly higher in BrM. BrM demonstrated a reduced immune gene signature expression, although a signature associated with fibroblast-associated wound healing was elevated in BrM. Metrics of T and B cell receptor diversity were also reduced in BrM. Conclusions BrM harbored higher mutational burden and SNV-derived neoantigen expression along with reduced immune gene signature expression relative to primary TNBC. Immune signatures correlated with improved survival, including T cell signatures. Further research will expand these findings to other breast cancer subtypes in the same biobank. Exploration of immunomodulatory approaches including vaccine applications and immune checkpoint inhibition to enhance anti-tumor immunity in TNBC BrM is warranted.