Miracle-dz/UniFAR-FTUs huggingface dataset:
Cell Cycle Entry Control in Naïve and Memory CD8+ T Cells

CD8+ T cells play important roles in immunity and immuno-oncology. Upon antigen recognition and co-stimulation, naïve CD8+ T cells escape from dormancy to engage in a complex programme of cellular growth, cell cycle entry and differentiation, resulting in rapid proliferation cycles that has the net effect of producing clonally expanded, antigen-specific cytotoxic T lymphocytes (CTLs). A fraction of activated T cells will re-enter dormancy by differentiating into memory T cells, which have essential roles in adaptive immunity. In this review, we discuss the current understanding of cell cycle entry control in CD8+ T cells and crosstalk between these mechanisms and pathways regulating immunological phenotypes.
Methyltransferase-Deficient Avian Flaviviruses Are Attenuated Due to Suppression of Viral RNA Translation and Induction of a Higher Innate Immunity

The 5’ end of the flavivirus genome contains a type 1 cap structure formed by sequential N-7 and 2’-O methylations by viral methyltransferase (MTase). Cap methylation of flavivirus genome is an essential structural modification to ensure the normal proliferation of the virus. Tembusu virus (TMUV) (genus Flavivirus) is a causative agent of duck egg drop syndrome and has zoonotic potential. Here, we identified the in vitro activity of TMUV MTase and determined the effect of K61-D146-K182-E218 enzymatic tetrad on N-7 and 2’-O methylation. The entire K61-D146-K182-E218 motif is essential for 2’-O MTase activity, whereas N-7 MTase activity requires only D146. To investigate its phenotype, the single point mutation (K61A, D146A, K182A or E218A) was introduced into TMUV replicon (pCMV-Rep-NanoLuc) and TMUV infectious cDNA clone (pACYC-TMUV). K-D-K-E mutations reduced the replication ability of replicon. K61A, K182A and E218A viruses were genetically stable, whereas D146A virus was unstable and reverted to WT virus. Mutant viruses were replication and virulence impaired, showing reduced growth and attenuated cytopathic effects and reduced mortality of duck embryos. Molecular mechanism studies showed that the translation efficiency of mutant viruses was inhibited and a higher host innate immunity was induced. Furthermore, we found that the translation inhibition of MTase-deficient viruses was caused by a defect in N-7 methylation, whereas the absence of 2’-O methylation did not affect viral translation. Taken together, our data validate the debilitating mechanism of MTase-deficient avian flavivirus and reveal an important role for cap-methylation in viral translation, proliferation, and escape from innate immunity.
Thermally Resilient Planar Waveguides in Novel nc-YSZ Transparent Ceramic by fs Laser Pulses

We report on thermally resilient planar waveguides fabricated on nc-YSZ by direct fs-laser inscription in transparent nc-yttria stabilized zirconia (nc-YSZ) polycrystalline ceramic. The waveguides consisted of rectangular sections (4.5 × 2 mm2) on the surface of the sample. Optical characterization at 633 and 810 nm was performed. We estimate a laser-induced refractive index contrast of 10–4. Post-waveguide-fabrication thermal annealing treatments at 750°C for 24 h were carried out to test the resilience of the waveguides and to further reduce the waveguide losses. Both micro-Raman spectroscopy and XPS characterization revealed unmodified lattice and steady chemical features, which are consistent with the waveguide thermal resilience. Our results suggest a promising potential use of nc-YSZ in harsh and high temperature demanding photonic environments.
Optimization of the Return Link Carrier Planning for a Constant Coding and Modulation Satellite Network

In this paper, we propose an approach to optimize the frequency plan and associated bandwidth allocation in the return link of a broadband satellite network, by exploring several design techniques for carrier allocation plans. Since bandwidth is a limited resource in satellite telecommunications, the minimization of bandwidth usage is a core issue that satellite communication service providers must solve, in particular for networks using a constant coding and modulation plan, which lacks the flexibility found in newer satellite communication products and can be subject to hardware constraints. This problematic led us to raise the following question: how can the long term bandwidth requirement of the network be minimized, given a set of ground terminals, of Modulations and Codings, and of discrete bandwidths. In this document we formally define the long-term carrier allocation problem and analyze current practical solutions. We subsequently investigate two other potential solutions, found to be more bandwidth-efficient: one based on heuristics and another based on integer linear programming. Finally, we look at the impact of several parameters on the performance of those three methods. Overall we observed marginal reductions in bandwidth, however significant gains were reached for networks with small return links with low committed information rate, a case in which some constant coding and modulation networks could fall. We concluded that those networks could benefit from our methods and see a significant reduction in bandwidth, and subsequently operational costs, at low implementation costs.
Potential Value of TNF-α (–376 G/A) Polymorphism and Cystatin C (CysC) in the Diagnosis of Sepsis Associated Acute Kidney Injury (S-AK I) and Prediction of Mortality in Critically Ill patients

Sepsis Associated Kidney Injury represents a major health concern as it is frequently associated with increased risk of mortality and morbidity. We aimed to evaluate the potential value of TNF-α (−376 G/A) and cystatin C in the diagnosis of S-AKI and prediction of mortality in critically ill patients. This study included 200 critically ill patients and 200 healthy controls. Patients were categorized into 116 with acute septic shock and 84 with sepsis, from which 142 (71%) developed S-AKI. Genotyping of TNF-α (−376 G/A) was performed by RT-PCR and serum CysC was assessed by Enzyme Linked Immunosorbent Assay. Our results showed a highly significant difference in the genotype frequencies of TNF-α (−376 G/A) SNP between S-AKI and non-AKI patients (p < 0.001). Additionally, sCysC levels were significantly higher in the S-AKI group (p = 0.011). The combination of both sCysC and TNF-α (−376 G/A) together had a better diagnostic ability for S-AKI than sCysC alone (AUC = 0.610, 0.838, respectively). Both GA and AA genotypes were independent predictors of S-AKI (p= < 0.001, p = 0.002 respectively). Additionally, sCysC was significantly associated with the risk of S-AKI development (Odds Ratio = 1.111). Both genotypes and sCysC were significant predictors of non-survival (p < 0.001), suggesting their potential role in the diagnosis of S-AKI and prediction of mortality.
Which Comes First in Sports Vision Training: The Software or the Hardware Update? Utility of Electrophysiological Measures in Monitoring Specialized Visual Training in Youth Athletes

In the present study we combined popular methods of sports vision training (SVT) with traditional oculomotor protocols of Optometric Vision Therapy (OVT) and electrophysiological indexes of EEG and VEP activity to monitor training progress and changes in performance of youth ice hockey players without the history of concussion. We hypothesized that administration of OVT protocols before SVT training may result in larger performance improvements compared to the reverse order due to the initial strengthening of visual hardware capable of handling greater demands during training of visuomotor integration and information processing skills (visual software). In a cross-over design 53 youth ice hockey players (ages 13–18) were randomly assigned to one of the two training groups. Group one (hardware-software group) completed 5 weeks of oculomotor training first followed by 5 weeks of software training. For group 2 (software-hardware) the order of procedures were reversed. After 10 weeks of training both groups significantly improved their performance on all but one measure of the Nike/Senaptec Sensory station measures. Additionally, the software-hardware training order resulted in significantly lower frontal theta-to-gamma amplitude ratios on the Nike/Senaptec test of Near-Far Quickness as well as in faster P100 latencies. Both training orders also resulted in significant decreases in post-treatment P100 amplitude to transient VEP stimuli as well as decreased theta-gamma ratios for perception span, Go/No-Go and Hand Reaction time. The observed changes in the electrophysiological indexes in the present study are thought to reflect greater efficiency in visual information processing and cognitive resource allocation following 10 weeks of visual training. There is also some evidence of the greater effectiveness of the software-hardware training order possibly due to the improved preparedness of the oculomotor system in the youth athletes for administration of targeted protocols of the Optometric Vision Therapy.
Matrix Metalloproteinase 2 Is Associated With Secondary Caries Independent From the Restorative Material

Certain patients, despite receiving proper treatment, still show higher failure rates of restorative dental treatments. The aim of this work was to test if MMP2 and MMP3 alleles are overrepresented in individuals with secondary caries. A total of 1,089 individuals from the University of Pittsburgh School of Dental Medicine Dental Registry and DNA Repository project were selected for this study. From this total, 341 individuals were selected for having a record of secondary caries in any type of restoration and were matched with 748 individuals by sex, age, ethnicity, and restorative work in the same teeth that did not fail. Genomic DNA extracted from saliva was used to obtain genotypes in five markers of MMP2 and MMP3 using TaqMan chemistry and end-point analysis. Chi-square was used to test if differences in allele and genotype distributions were statistically different at an alpha of 0.05. The less common allele and homozygote genotype of MMP2 rs9923304 were less commonly found among individuals with secondary caries. The less common allele of MMP2 rs2287074 was also less frequent among individuals with secondary caries. These results provide statistical evidence for the role of MMP2 in failure of restorations due to secondary caries. We can conclude that MMP2 variation impacts the risk of having secondary caries, independent of the restorative material.
PUCHI Regulates Giant Cell Morphology During Root-Knot Nematode Infection in Arabidopsis thaliana

Parasitic root-knot nematodes transform the host’s vascular cells into permanent feeding giant cells (GCs) to withdraw nutrients from the host plants. GCs are multinucleated metabolically active cells with distinctive cell wall structures; however, the genetic regulation of GC formation is largely unknown. In this study, the functions of the Arabidopsis thaliana transcription factor PUCHI during GC development were investigated. PUCHI expression was shown to be induced in early developing galls, suggesting the importance of the PUCHI gene in gall formation. Despite the puchi mutant not differing significantly from the wild type in nematode invasion and reproduction rates, puchi GC cell walls appeared to be thicker and lobate when compared to the wild type, while the cell membrane sometimes formed invaginations. In three-dimensional (3D) reconstructions of puchi GCs, they appeared to be more irregularly shaped than those in the wild type, with noticeable cell-surface protrusions and folds. Interestingly, the loss-of-function mutant of 3-KETOACYL-COA SYNTHASE 1 showed GC morphology and cell wall defects similar to those of the puchi mutant, suggesting that PUCHI may regulate GC development via very long chain fatty acid synthesis.
A Scoring System for Assessing the Risk of Malignant Partially Cystic Thyroid Nodules Based on Ultrasound Features

Objective To assess the ultrasound (US) features of partially cystic thyroid nodules (PCTNs) and to establish a scoring system to further improve the diagnostic accuracy. Methods A total of 262 consecutive nodules from September 2017 to March 2020 were included in a primary cohort to construct a scoring system. Moreover, 83 consecutive nodules were enrolled as an validation cohort from May 2018 to August 2020. All nodules were determined to be benign or malignant according to the pathological results after surgery or ultrasound-guided fine-needle aspiration (US-FNA). The US images and demographic characteristics of the patients were analyzed. The ultrasound features of PCTNs were extracted from primary cohort by two experienced radiologists. The features extracted were used to develop a scoring system using logistic regression analysis. Receiver operating characteristic (ROC) curves were applied to evaluate the diagnostic efficacy of the scoring system in both the primary cohort and validation cohort. In addition, the radiologists evaluated the benign and malignant PCTNs of the validation cohort according to the ACR TI-RADS guidelines and clinical experience, and the accuracy of their diagnosis were compared with that of the scoring system. Results Based on the eight features of PCTNs, the scoring system showed good differentiation and reproducibility in both cohorts. The scoring system was based on eight features of PCTNs and showed good performance. The area under the curve (AUC) was 0.876 (95% CI, 0.830 - 0.913) in the primary cohort and 0.829(95% CI, 0.730 - 0.903) in the validation cohort. The optimal cutoff value of the scoring system for the diagnosis of malignant PCTNs was 4 points, with a good sensitivity of 71.05% and specificity of 87.63%. The scoring system (AUC=0.829) was superior to radiologists (AUC= 0.736) in diagnosing PCTNs and is a promising method for clinical application. Conclusions The scoring system described herein is a convenient and clinically valuable method that can diagnose PCTNs with relatively high accuracy. The use of this method to diagnose PCTNs, which have been previously underestimated, will allow PCTNs to receive reasonable attention, and assist radiologist to confidently diagnose the benignity or malignancy.
The Role of English as a Foreign Language Teachers’ and Learners’ Emotions and Language Achievement and Success

It is preserved that one of the noteworthy influential subjects of success and achievement is emotions, and enhancing emotions is dominant in promoting the language learning of students in the classroom. Although emotions are an integral part of the practices of both educators and students, their function has been sidelined due to the emphasis on intellectual instead of emotional scopes of foreign language learning. Therefore, the present theoretical review tries to refocus on the role of emotions of teachers and learners and their effects on language success and achievement. Successively, the effectiveness of verdicts for educators, students, syllabus designers, and future researchers are deliberated.
Extracellular Vesicle Proteins and MicroRNAs Are Linked to Chronic Post-Traumatic Stress Disorder Symptoms in Service Members and Veterans With Mild Traumatic Brain Injury

Symptoms of post-traumatic stress disorder (PTSD) are common in military populations, and frequently associated with a history of combat-related mild traumatic brain injury (mTBI). In this study, we examined relationships between severity of PTSD symptoms and levels of extracellular vesicle (EV) proteins and miRNAs measured in the peripheral blood in a cohort of military service members and Veterans (SMs/Vs) with chronic mTBI(s). Participants (n = 144) were divided into groups according to mTBI history and severity of PTSD symptoms on the PTSD Checklist for DSM-5 (PCL-5). We analyzed EV levels of 798 miRNAs (miRNAs) as well as EV and plasma levels of neurofilament light chain (NfL), Tau, Amyloid beta (Aβ) 42, Aβ40, interleukin (IL)-10, IL-6, tumor necrosis factor-alpha (TNFα), and vascular endothelial growth factor (VEGF). We observed that EV levels of neurofilament light chain (NfL) were elevated in participants with more severe PTSD symptoms (PCL-5 ≥ 38) and positive mTBI history, when compared to TBI negative controls (p = 0.024) and mTBI participants with less severe PTSD symptoms (p = 0.006). Levels of EV NfL, plasma NfL, and hsa-miR-139–5p were linked to PCL-5 scores in regression models. Our results suggest that levels of NfL, a marker of axonal damage, are associated with PTSD symptom severity in participants with remote mTBI. Specific miRNAs previously linked to neurodegenerative and inflammatory processes, and glucocorticoid receptor signaling pathways, among others, were also associated with the severity of PTSD symptoms. Our findings provide insights into possible signaling pathways linked to the development of persistent PTSD symptoms after TBI and biological mechanisms underlying susceptibility to PTSD.
Beyond the Binary: Sexual and Reproductive Health Considerations for Transgender and Gender Expansive Adolescents

Awareness and visibility of transgender individuals have grown exponentially. However, conceptualizing sexual and reproductive health (SRH) as “women's” or “men's” health services further marginalizes transgender and gender-expansive (TGE) youth. Multiple reviews and commentaries have been published on the topic of SRH care for adults under the umbrella term of sexual and gender minorities, all with a call to action for more inclusive care and the need for more clinical research involving TGE individuals, and notably, TGE youth. Results from adult TGE studies are often translated to describe adolescent models. However, models specific to adolescent TGE populations are needed to understand their unique SRH needs. This review will describe the current literature relating to SRH needs of TGE youth and adults, highlighting key areas with significant disparities in need of further research. This comprehensive summary will also provide recommendations for clinicians and researchers with the goal of improving SRH care and obtaining wider representation in both clinical settings and research directed toward TGE youth.
Autonomic Function in Parkinson's Disease Subjects Across Repeated Short-Term Dry Immersion: Evidence From Linear and Non-linear HRV Parameters

Several studies have shown that “dry” immersion appears as a promising method of rehabilitation for Parkinson's disease. Still, little is known about the cardiovascular reaction in “dry” immersion (DI), especially in Parkinson's disease (PD). Therefore, this study was aimed to evaluate the effect of repeated 45-min DI sessions on autonomic function in subjects with PD. The study group consisted of 20 subjects with PD [13 men, seven women, aged 51–66 years old, Hoehn & Yahr (H&Y) staged 1–3] were enrolled in the study according to inclusion and non-inclusion criteria. The DI program was comprised of seven 45-min DI sessions, applied within 25–30 days. Blood pressure (BP), heart rate (HR), and electrocardiogram (ECG) in the standard lead II were recorded at 1st, 4th, and 7th DI, before, on the 15, 30, and 40th min of DI session. Autonomic function was assessed with analysis of heart rate variability (HRV) using Kubios Standard version 2 software. Linear (time- and frequency-domain) and non-linear (correlation dimension, entropies, DFA1 and DFA2, percent of determinism, and recurrence) were computed. At baseline condition, time- and frequency-domain HRV parameters showed low variability of HR, which indicates reduced autonomic neurogenic control of HR. Throughout the DI session, systolic and diastolic BP has decreased by 5–7 mm Hg (p < 0.001), and time- and frequency-domain parameters of HRV have significantly increased, what can be regarded as compensatory mechanisms of hemodynamics during DI. The structure of the regulatory input to the heart seen by HRV was characterized by low complexity and reduced autonomic neurogenic control of HR. Across the program of DI sessions, the hypotensive effect was documented, but no notable modification of the HRV-parameters was found. The absence of long-term modification of the studied parameters can be attributed both to deconditioning environmental effect of DI and limited adaptation of the organism due to neurodegeneration in PD. That should be taken into consideration when planning rehabilitation measures in subjects of older age and chronic somatic diseases with modeled microgravity.
Circular RNA Circ-0002570 Accelerates Cancer Progression by Regulating VCAN via MiR-587 in Gastric Cancer

Background Circular RNAs (circRNAs) are closely associated with the occurrences and progress of gastric cancer (GC). We aimed to delve into the function and pathological mechanism of Circular RNA-0002570 (circ-0002570) in GC progression. Methods CircRNAs differentially expressed in GC were screened using bioinformatics technology. The expression of circ-0002570 was detected in GC specimens and cells via qRT-PCR, and the prognostic values of circ-0002570 were determined. The functional roles of circ-0002570 on proliferation, migration, and invasion in GC cells were explored in vitro and in vivo. Interaction of circ-0002570, miR-587, and VCAN was confirmed by dual-luciferase reporter assays, Western blotting, and rescue experiments. Results Circ-0002570 expression was distinctly increased in GC tissues compared to adjacent normal specimens, and GC patients with higher circ-0002570 expressions displayed a short survival. Functionally, knockdown of circ-0002570 resulted in the inhibition of cell proliferation, migration, and invasion, and suppressed tumor growth in vivo. Mechanistically, miR-587 was sponged by circ-0002570. VCAN expression in NSCLC was directly inhibited by miR-587. Overexpression of circ-0002570 prevented VCAN from miR-587-mediated degradation and thus facilitated GC progression. Conclusion The circ-0002570-miR-587-VCAN regulatory pathway promoted the progression of GC. Our findings provided potential new targets for the diagnosis and therapy of GC.
A Living Income for Cocoa Producers in Côte d'Ivoire and Ghana?

It is often claimed that cocoa producers are poor, but the extent of their poverty is rarely defined. We analyzed six data sets derived from household questionnaires of 385–88,896 cocoa producers in Côte d'Ivoire and Ghana. Across all data sets, many households (30–58%) earn a gross income below the World Bank extreme poverty line and the majority (73–90%) do not earn a Living Income. Households with less income per person per day generally achieve lower cocoa yields, consist of more household members, have a smaller land size available, and rely more on cocoa income than households with higher incomes. When comparing the effects of increasing prices and yields on gross income, yield increases lead to larger benefits especially for the poorest households. Doubling the cocoa price would leave 15–25% of households with a gross income below the extreme poverty line and 53–65% below the Living Income benchmark. At yields of 600 kg/ha, against current yields around 300 kg/ha, these percentages are reduced to 7–11 and 48–62%, respectively, while at yields of 1,500 kg/ha only 1–2% of households remain below the extreme poverty line and 13–20% below the Living Income benchmark. If we assume that the production costs of achieving a yield of 1,500 kg/ha are 30% of revenue, still only 2–4% of households earn a net income below the extreme poverty line and 25–32% below the Living Income benchmark. Whilst sustainable intensification of cocoa production is undoubtedly a strong approach to increase cocoa yields and farmer incomes, achieving this does not come without pitfalls. The poorer households face multiple barriers to invest in cocoa production. A better understanding of cocoa producing households and the resources available to them, as well as the opportunity for alternative income generation, is required to tailor options to increase their income. The utility and interpretability of future household surveys would be drastically improved if definitions and variables addressed were approached in a standardized way.