Miracle-dz/UniFAR-FTUs huggingface dataset:
Optical Characterization of Sodium Fluorescein In Vitro and Ex Vivo

Objective The utilization of fluorescein-guided biopsies and resection has been recently discussed as a suitable strategy to improve and expedite operative techniques for the resection of central nervous system (CNS) tumors. However, little is known about the optical properties of sodium fluorescein (NaFl) in human tumor tissue and their potential impact on ex vivo analyses involving fluorescence-based methods. Methods Tumor tissue was obtained from a study cohort of an observational study on the utilization of fluorescein-guided biopsy and resection (n=5). The optical properties of fluorescein-stained tissue were compared to the optical features of the dye in vitro and in control samples consisting of tumor tissue of high-grade glioma patients (n=3) without intravenous (i.v.) application of NaFl. The dye-exposed tumor tissues were used for optical measurements to confirm the detectability of NaFl emission ex vivo. The tissue samples were fixed in 4%PFA, immersed in 30% sucrose, embedded in Tissue-Tek OCT compound, and cut to 10 μm cryosections. Spatially resolved emission spectra from tumor samples were recorded on representative slides with a Confocal Laser Scanning Microscope FV1000 (Olympus GmbH, Hamburg, Germany) upon excitation with λexc = 488 nm. Results Optical measurements of fluorescein in 0.9% sodium chloride (NaCl) under in vitro conditions showed an absorption maximum of λmax abs = 479 nm as detected with spectrophotometer Specord 200 and an emission peak at λmax em = 538 nm recorded with the emCCD detection system of a custom-made microscope-based single particle setup using a 500 nm long-pass filter. Further measurements revealed pH- and concentration-dependent emission spectra of NaFl. Under ex vivo conditions, confocal laser scanning microscopy of fluorescein tumor samples revealed a slight bathochromic shift and a broadening of the emission band. Conclusion Tumor uptake of NaFl leads to changes in the optical properties – a bathochromic shift and broadening of the emission band – possibly caused by the dye’s high pH sensitivity and concentration-dependent reabsorption acting as an inner filter of the dye’s emission, particularly in the short wavelength region of the emission spectrum where absorption and fluorescence overlap. Understanding the ex vivo optical properties of fluorescein is crucial for testing and validating its further applicability as an optical probe for intravital microscopy, immunofluorescence localization studies, and flow cytometry analysis.
How to Induce and Recognize Facial Expression of Emotions by Using Past Emotional Memories: A Multimodal Neuroscientific Algorithm

Emotion expression production and recognition play a decisive and central role in individuals’ life. The consideration and the investigation of emotions result to be especially important allowing to comprehend individuals’ emotional experiences and empathic mechanisms, representing driving knowledge for brain-computer interfaces (BCI), through the implementation of emotional patterns into artificial intelligence tools and computers, and for in-deep comprehension of psychopathology (Balconi et al., 2015a). This article aims to allow the investigation of the neurophysiological correlates and characteristics associated with individuals’ facial expressions production and recognition, considering emotional responses provoked by internal cues based on autobiographic memories, called “self-induced by memories. ” Indeed, as reported by Adolphs (2002), the human brain represents most effectively emotional data through the connection of information between different cerebral areas that allow to state and recognize emotional expressions from different stimuli, as visual or auditory ones. The human brain represents emotional data connecting facial, voice, and movement expressions with individuals’ past experiences. Moreover, the use of different neuroscientific techniques, as positron emission tomography (PET), functional magnetic resonance imaging (fMRI), and magnetoencephalography (MEG), allow observing the involvement of specific cerebral regions in different emotional expressions, providing a map of the emotional brain activation (Balconi and Lucchiari, 2007; Balconi and Pozzoli, 2007; Deak, 2011; Kassam et al., 2013). Specifically, neuroimaging measures are used as input to Affective Computing technologies (Frantzidis et al., 2010). Different studies postulate the existence of discrete emotions, such as happiness, fear, anger, sadness, from which the other emotional states would derive (Ekman, 1999). The theory of discrete emotions has been criticized by the Circumplex Model of Affect (Russell, 1980), that describe and label emotions on the base of two dimensions: valence and arousal. Multimodal information are integrated by the human brain generating an integrated representation of different auditory and visual stimuli (Balconi and Carrera, 2011; Barros and Wermter, 2016).
Impact of Acute Insulin Resistance on Myocardial Blush in Non-Diabetic Patients Undergoing Primary Percutaneous Coronary Intervention

Background: Myocardial blush grading is considered to be a novel tool for assessment of coronary microvasculature and myocardial perfusion in patients undergoing coronary angiography and angioplasty, and its reduction identifies patients at high risk. Our study aimed to evaluate the association between acute insulin resistance and myocardial blush in non-diabetic patients with ST-segment elevation myocardial infarction (STEMI). Methods: Two hundred forty non-diabetic patients with STEMI who underwent primary percutaneous coronary intervention were consecutively recruited. The relationship of homeostasis model assessment—estimated insulin resistance (HOMA-IR) to myocardial blush and in-hospital outcome was investigated. Results: Higher HOMA-IR tertile was observed in obese patients, with hyperinsulinemia, had Killip class >1, with higher CPK-MB level and was correlated to impaired myocardial blush after adjusting for the other confounding risk factors. It was also concluded that higher HOMA-IR was independently associated with no/minimal myocardial blush after STEMI. Moreover, it was founded to be an independent predictor of pulmonary edema and impaired left ventricular systolic function. Conclusion: This study revealed that acute insulin resistance was prevalent in non-diabetic patients with STEMI and was an independent predictor for post-infarction myocardial and microvascular injury and poor in-hospital outcome. Trial Registration: The trial was registered at the registry of Clinicaltrials.gov, ClinicalTrials.gov Identifier: NCT04651842, Date of registration: 2nd December 2020 Registry URL, https://clinicaltrials.gov/ct2/show/NCT04385589? cond=Dapagliflozin+in+diabetic+patients&cntry=EG&draw=2&rank=1.
A Nomogram for Predicting Lymphovascular Invasion in Superficial Esophageal Squamous Cell Carcinoma

The lymphovascular invasion (LVI) status facilitates the determination of the optimal therapeutic strategy for superficial esophageal squamous cell carcinoma (SESCC), but in clinical practice, LVI must be confirmed by postoperative pathology. However, studies of the risk factors for LVI in SESCC are limited. Consequently, this study aimed to identify the risk factors for LVI and use these factors to establish a prediction model. The data of 516 patients who underwent radical esophagectomy between January 2007 and September 2019 were retrospectively collected (training set, n=361, January 2007 to May 2015; validation set, n=155, June 2015 to September 2019). In the training set, least absolute shrinkage and selection operator (LASSO) regression and multivariate analyses were utilized to identify predictive factors for LVI in patients with SESCC. A nomogram was then developed using these predictors. The area under the curve (AUC), calibration curve, and decision curve were used to evaluate the efficiency, accuracy, and clinical utility of the model. LASSO regression indicated that the tumor size, depth of invasion, tumor differentiation, lymph node metastasis (LNM), sex, circumferential extension, the presence of multiple lesions, and the resection margin were correlated with LVI. However, multivariate analysis revealed that only the tumor size, depth of invasion, tumor differentiation, and LNM were independent risk factors for LVI. Incorporating these four variables, model 1 achieved an AUC of 0.817 in predicting LVI. Adding circumferential extension to model 1 did not appreciably change the AUC and integrated discrimination improvement, but led to a significant increase in the net reclassification improvement (p=0.011). A final nomogram was constructed by incorporating tumor size, depth of invasion, tumor differentiation, LNM, and circumferential extension and showed good discrimination (training set, AUC=0.833; validation set, AUC=0.819) and good calibration in the training and validation sets. Decision curve analysis demonstrated that the nomogram was clinically useful in both sets. Thus, it is possible to predict the status of LVI using this nomogram scoring system, which can aid the selection of an appropriate treatment plan.
Precocious Metamorphosis of Silkworm Larvae Infected by BmNPV in the Latter Half of the Fifth Instar

The mulberry silkworm (Bombyx mori) is a model organism, and BmNPV is a typical baculovirus. Together, these organisms form a useful model to investigate host–baculovirus interactions. Prothoracic glands (PGs) are also model organs, used to investigate the regulatory effect of synthetic ecdysone on insect growth and development. In this study, day-4 fifth instar silkworm larvae were infected with BmNPV. Wandering silkworms appeared in the infected groups 12 h earlier than in the control groups, and the ecdysone titer in infected larvae was significantly higher than that of the control larvae. We then used RNA sequencing (RNA-seq) to analyze silkworm PGs 48 h after BmNPV infection. We identified 15 differentially expressed genes (DEGs) that were classified as mainly being involved in metabolic processes and pathways. All 15 DEGs were expressed in the PGs, of which Novel01674, BmJing, and BmAryl were specifically expressed in the PGs. The transcripts of BmNGDN, BmTrypsin-1, BmACSS3, and BmJing were significantly increased, and BmPyd3, BmTitin, BmIGc2, Novel01674, and BmAryl were significantly decreased from 24 to 72 h in the PGs after BmNPV infection. The changes in the transcription of these nine genes were generally consistent with the transcriptome data. The upregulation of BmTrypsin-1 and BmACSS3 indicate that these DEGs may be involved in the maturation process in the latter half of the fifth instar of silkworm larvae. These findings further our understanding of silkworm larval development, the interaction between BmNPV infection and the host developmental response, and host–baculovirus interactions in general.
Multiple GPCR Functional Assays Based on Resonance Energy Transfer Sensors

G protein-coupled receptors (GPCRs) represent one of the largest membrane protein families that participate in various physiological and pathological activities. Accumulating structural evidences have revealed how GPCR activation induces conformational changes to accommodate the downstream G protein or β-arrestin. Multiple GPCR functional assays have been developed based on Förster resonance energy transfer (FRET) and bioluminescence resonance energy transfer (BRET) sensors to monitor the conformational changes in GPCRs, GPCR/G proteins, or GPCR/β-arrestin, especially over the past two decades. Here, we will summarize how these sensors have been optimized to increase the sensitivity and compatibility for application in different GPCR classes using various labeling strategies, meanwhile provide multiple solutions in functional assays for high-throughput drug screening.
The Relationship Between Food-Based Pro-inflammatory Diet and Sarcopenia: Findings From a Cross-Sectional Study in Iranian Elderly People

Background: Sarcopenia has rarely been linked to Food-based Inflammatory Potential of the Diet (FIPD) in earlier studies. This study was performed to examine the association of FIPD and sarcopenia and its components. Method: In the cross-sectional research, dietary intakes of 300 randomly-selected elderly adults aged 55 years or older were collected through a validated food frequency questionnaire. We constructed FIPD score based on average consumptions of 28 food items. According to The European Working Group on Sarcopenia definition, sarcopenia and its components such as muscle strength, muscle mass, and gait speed were defined. Result: No significant difference was found between the prevalence of sarcopenia (P = 0.05), low muscle mass (P = 0.27), low handgrip strength (P = 0.72), and lower gait speed (P = 0.14) across tertiles of FIPD score. Moreover, we did not find significant differences among means of handgrip strength (P = 0.65), muscle mass (P = 0.33), and walking speed (P = 0.89) across FIPD categories. However, binary logistic regression analysis indicated a significant positive relationship between FIPD score and odds of sarcopenia; such that subjects in the top vs. those in the bottom FIPD tertile had 155% greater chance of having sarcopenia (OR: 2.55; 95% CI: 1.17–5.55). After controlling for all confounding factors, this association strengthened (OR: 2.67; 95% CI: 1.18–6.01). Conclusion: We found that greater FIPD score, which means a more pro-inflammatory diet, was positively linked with sarcopenia.
Short-Term Outcomes and Predictors of Effectiveness of Tocilizumab in Systemic Juvenile Idiopathic Arthritis: A Prospective Cohort Study

Background: Systemic Juvenile Idiopathic Arthritis (sJIA) is a unique category of juvenile arthritis in which interleukin 6 plays a major pathogenic role. This study aimed to describe the therapeutic short-term outcomes among patients with sJIA starting tocilizumab (TCZ) therapy and to identify possible predictors of treatment response. Methods: We conducted a prospective observational study including 65 patients with sJIA meeting ILAR classification criteria with active disease despite conventional therapy that were treated by TCZ between August 2019 and October 2020 as the first-line biological therapy. Clinical and serological parameters were recorded at baseline and after 1 year of TCZ therapy. Results: After 1 year, 25% of the patients achieved minimal disease activity and 35% achieved clinically inactive disease. A significant reduction of the 10-joint juvenile arthritis disease activity score and acute phase reactants was also observed. Patients with younger age (≤7 years), shorter disease duration (≤3 years), lower disease activity, and higher serum ferritin and systemic manifestations showed more favorable results. Conclusion: Patients with sJIA showed favorable disease outcomes with TCZ treatment for 1 year, especially if the drugs were administered earlier in the disease course and in younger patients with a more pronounced inflammatory status. Our results may help to define the profile of patients with sJIA who are more likely to benefit from IL-6 blockade.
Telemonitored Human Circadian Temperature Dynamics During Daily Routine

Background Circadian rhythms in body temperature coordinate peripheral molecular clocks, hence they could potentially predict optimal treatment timing (chronotherapy) in individual patients. Circadian parameters in chest surface body temperature (Chesttemp) were recorded remotely and in real time through the use of wearable sensors. Methods The dynamics of circadian oscillations in Chesttemp and core body temperature (Coretemp) and their moderation by sex and age were analysed in 38 men and 50 women, aged 21–78 years. In two studies (ST1 and ST2), Chesttemp was measured every minute and teletransmitted using a BLE-connected sensor for 3.6–28.3 days. Additionally, in ST2, Coretemp was recorded per minute in 33 age- and sex-stratified subjects using electronic ingestible pills with radio-frequency transmissions. Circadian parameters were computed using spectral analysis and cosinor modelling. The temporal relations between Chesttemp and Coretemp cosinor parameters were summarised with principal component (PC) analysis. The effect of sex and age was analysed through multivariate regression. Results Using spectral analysis, a dominant period of 24- or 12-h was identified in 93.2% of the Chesttemp and in 100% of the Coretemp time series. The circadian parameters varied largely between-subjects both for Chesttemp (ranges: mesors, 33.2–36.6°C; amplitudes, 0.2–2.5°C; acrophases, 14:05–7:40), and Coretemp (mesors, 36.6–37.5°C; amplitudes, 0.2–0.7°C; bathyphases, 23:50–6:50). Higher PC loadings mainly corresponded to (i) large Chesttemp amplitudes, and phase advance of both temperature rhythms for the first PC (PC1, 27.2% of variance var.), (ii) high mesors in both temperature rhythms for PC2 (22.4% var.), and (iii) large Coretemp amplitudes for PC3 (12.9% var.). Chesttemp and Coretemp mesors and PC2 loadings decreased in females, while remaining quite stable in males as a function of age. In contrast, Coretemp amplitude and PC3 loadings increased with age in females, but decreased in males. Finally, older subjects, both female and male, displayed a reduction in ultradian variabilities, and an increase in both Chesttemp circadian amplitude and PC1 loadings. Interpretation The dynamics relations between Chesttemp and Coretemp rhythms were largely moderated by age and sex, with results suggesting that treatment timing could be most critical for therapeutic index in women and in order people.
Tracing Evolution Through Protein Structures: Nature Captured in a Few Thousand Folds

This article is dedicated to the memory of Cyrus Chothia, who was a leading light in the world of protein structure evolution. His elegant analyses of protein families and their mechanisms of structural and functional evolution provided important evolutionary and biological insights and firmly established the value of structural perspectives. He was a mentor and supervisor to many other leading scientists who continued his quest to characterise structure and function space. He was also a generous and supportive colleague to those applying different approaches. In this article we review some of his accomplishments and the history of protein structure classifications, particularly SCOP and CATH. We also highlight some of the evolutionary insights these two classifications have brought. Finally, we discuss how the expansion and integration of protein sequence data into these structural families helps reveal the dark matter of function space and can inform the emergence of novel functions in Metazoa. Since we cover 25 years of structural classification, it has not been feasible to review all structure based evolutionary studies and hence we focus mainly on those undertaken by the SCOP and CATH groups and their collaborators.
The Effects of Sex-Type, the Sex of the Avatar, and Salience of the Sex of the Avatar on Emotional Valence and Arousal

The objective of this study was to investigate the effects of avatar sex, salience of avatar sex, and player sex-type on less conscious embodied emotional arousal and valence vs. consciously perceived emotional arousal and valence elicited by a gaming experience. The experiment conducted a 2 avatar sex (female × male) × 2 salience of avatar sex (high × low) × 2 player sex-type (sex-typed × non-sex-typed) mixed model factorial design. Participants were randomly assigned to one of two gameplay conditions (high-salience male and female avatar or low-salience male and female avatar) and then played two 15-min sessions of a video game—one session playing the game as a male avatar and one session playing the game as a female avatar. The order in which participants played as either a male or female avatar was randomized. Psychophysiological indicators of arousal (skin conductance) and valence (facial electromyography) were recorded during gameplay. Self-report measures of arousal and valence were obtained immediately after each 15-min session of gameplay. Data analysis tested hypotheses concerning the effects of avatar sex, salience of avatar sex, and player sex-type separately on real-time embodied variation in arousal and valence as revealed through physiological indicators and conscious perception of arousal and valence obtained through self-report measures.
Organic Compost to Improve Contaminated Soil Quality and Plant Fertility

Abstract The use of stabilization techniques for the recovery of trace element–contaminated soils has steadily increased in the last decades. A short-term pot experiment was carried out under semifield conditions using two organic amendments (biosolid compost and “alperujo” compost) and two plant species (Medicago polymorpha and Poa annua). The effect of amendments and plant species on chemical properties (pH, total organic carbon, water soluble carbon, N-Kjeldhal, available K, and available P) and on enzyme activities (dehydrogenase, urease, &bgr;-glucosidase, and acid phosphatase) of two trace element–contaminated soils with different pH values (6.32 and 3.23) was studied. No significant effects of amendment addition and plant rhizosphere were found in the neutral contaminated soil. However, in the acid soil, noticeable effects due to organic amendment addition, especially biosolid compost, were found. Indeed, the most remarkable effects were the increase in soil pH and improvement of soil conditions for the establishment of the vegetation. Moreover, a marked decrease in trace element availability and an increase in the nutritional status of plants due to the improvement of soil fertility were observed in the acid soil. Both plants tested could be acceptable candidates for phytostabilization techniques. The application of amendments is crucial in acidic contaminated soils, whereas in neutral contaminated soils, this application should be evaluated in economic terms.
The Good and the Bad: Ecological Interaction Measurements Between the Urinary Microbiota and Uropathogens

The human body harbors numerous populations of microorganisms in various ecological niches. Some of these microbial niches, such as the human gut and the respiratory system, are well studied. One system that has been understudied is the urinary tract, primarily because it has been considered sterile in the absence of infection. Thanks to modern sequencing and enhanced culture techniques, it is now known that a urinary microbiota exists. The implication is that these species live as communities in the urinary tract, forming microbial ecosystems. However, the interactions between species in such an ecosystem remains unknown. Various studies in different parts of the human body have highlighted the ability of the pre-existing microbiota to alter the course of infection by impacting the pathogenicity of bacteria either directly or indirectly. For the urinary tract, the effect of the resident microbiota on uropathogens and the phenotypic microbial interactions is largely unknown. No studies have yet measured the response of uropathogens to the resident urinary bacteria. In this study, we investigate the interactions between uropathogens, isolated from elderly individuals suffering from UTIs, and bacteria isolated from the urinary tract of asymptomatic individuals using growth measurements in conditioned media. We observed that bacteria isolated from individuals with UTI-like symptoms and bacteria isolated from asymptomatic individuals can affect each other’s growth; for example, bacteria isolated from symptomatic individuals affect the growth of bacteria isolated from asymptomatic individuals more negatively than vice versa. Additionally, we show that Gram-positive bacteria alter the growth characteristics differently compared to Gram-negative bacteria. Our results are an early step in elucidating the role of microbial interactions in urinary microbial ecosystems that harbor both uropathogens and pre-existing microbiota.