Engineering REST-Specific Synthetic PUF Proteins to Control Neuronal Gene Expression: A Combined Experimental and Computational Study

Regulation of gene transcription is an essential mechanism for differentiation and adaptation of organisms. A key actor in this regulation process is the repressor element 1 (RE1)-silencing transcription factor (REST), a transcriptional repressor that controls more than 2000 putative target genes, most of which are neuron-specific. With the purpose of modulating REST expression, we exploited synthetic, ad hoc designed, RNA binding proteins (RBPs) able to specifically target and dock to REST mRNA. Among the various families of RBPs, we focused on the Pumilio and FBF (PUF) proteins, present in all eukaryotic organisms and controlling a variety of cellular functions. Here, a combined experimental and computational approach was used to design and test 8- and 16-repeat PUF proteins specific for REST mRNA. We explored the conformational properties and atomic features of the PUF-RNA recognition code by Molecular Dynamics simulations. Biochemical assays revealed that the 8- and 16-repeat PUF-based variants specifically bind the endogenous REST mRNA without affecting its translational regulation. The data also indicate a key role of stacking residues in determining the binding specificity. The newly characterized REST-specific PUF-based constructs act as excellent RNA-binding modules and represent a versatile and functional platform to specifically target REST mRNA and modulate its endogenous expression

Deep learning-based pixel-wise lesion segmentation on oral squamous cell carcinoma images

Oral squamous cell carcinoma is the most common oral cancer. In this paper, we present a performance analysis of four different deep learning-based pixel-wise methods for lesion segmentation on oral carcinoma images. Two diverse image datasets, one for training and another one for testing, are used to generate and evaluate the models used for segmenting the images, thus allowing to assess the generalization capability of the considered deep network architectures. An important contribution of this work is the creation of the Oral Cancer Annotated (ORCA) dataset, containing ground-truth data derived from the well-known Cancer Genome Atlas (TCGA) dataset

Sleep Macrostructure and NREM Sleep Instability Analysis in Pediatric Developmental Coordination Disorder

Developmental Coordination Disorder (DCD) is considered to be abnormal motor skills learning, identified by clumsiness, slowness, and/or motor inaccuracy impairing the daily-life activities in all ages of life, in the absence of sensory, cognitive, or neurological deficits impairment. The present research focuses on studying DCD sleep structure and Cyclic Alternating Pattern (CAP) parameters with a full overnight polysomnography and to study the putative correlations between sleep architecture and CAP parameters with motor coordination skills. The study was a cross-sectional design involving 42 children (26M/16F; mean age 10.12 ± 1.98) selected as a DCD group compared with 79 children (49M/30F; mean age 9.94 ± 2.84) identified as typical (no-DCD) for motor ability and sleep macrostructural parameters according to the MABC-2 and polysomnographic (PSG) evaluations. The two groups (DCD and non-DCD) were similar for age (p = 0.715) and gender (p = 0.854). More significant differences in sleep architecture and CAP parameters were found between two groups and significant correlations were identified between sleep parameters and motor coordination skills in the study population. In conclusion, our data show relevant abnormalities in sleep structure of DCD children and suggest a role for rapid components of A phases on motor coordination development

Impact of the 2014 American Academy of Pediatrics recommendation and of the resulting limited financial coverage by the Italian Medicines Agency for palivizumab prophylaxis on the RSV-associated hospitalizations in preterm infants during the 2016-2017 epidemic season: a systematic review of seven Italian reports

Background: The only pharmacologic prophylaxis against respiratory syncytial virus (RSV) infection in preterm infants is the humanized monoclonal antibody palivizumab. After the 2014 modification of the American Academy of Pediatrics (AAP) recommendations, the Italian Medicines Agency (AIFA) limited the financial coverage for palivizumab prescriptions to otherwise healthy preterm infants with < 29 weeks of gestational age (wGA) aged < 12 months at the beginning of the 2016-2017 RSV season. However, due to the effect on disease severity and hospitalizations following this limitation, shown by several Italian clinical studies, in November 2017 AIFA reinstated the financial coverage for these infants. In this systematic review, we critically summarize the data that show the importance of palivizumab prophylaxis. Methods: Data from six Italian pediatric institutes and the Italian Network of Pediatric Intensive Care Units (TIPNet) were retrieved from the literature and considered. The epidemiologic information for infants 29-36 wGA, aged < 12 months and admitted for viral-induced acute lower respiratory tract infection were retrospectively reviewed. RSV-associated hospitalizations were compared between the season with running limitation, i.e. 2016-2017, versus 2 seasons before (2014-2015 and 2015-2016) and one season after (2017-2018) the AIFA limitation. Results: During the 2016-2017 RSV epidemic season, when the AIFA limited the financial coverage of palivizumab prophylaxis based on the 2014 AAP recommendation, the study reports on a higher incidences of RSV bronchiolitis and greater respiratory function impairment. During this season, we also found an increase in hospitalizations and admissions to the Pediatric Intensive Care Units and longer hospital stays, incurring higher healthcare costs. During the 2016-2017 epidemic season, an overall increase in the number of RSV bronchiolitis cases was also observed in infants born full term, suggesting that the decreased prophylaxis in preterm infants may have caused a wider infection diffusion in groups of infants not considered to be at risk. Conclusions: The Italian results support the use of palivizumab prophylaxis for otherwise healthy preterm (29-36 wGA) infants aged < 6 months at the beginning of the RSV season

Squeezed-state quantum key distribution upon imperfect reconciliation

We address the security of continuous-variable quantum key distribution with squeezed states upon realistic conditions of noisy and lossy environment and limited reconciliation efficiency. Considering the generalized preparation scheme and clearly distinguishing between classical and quantum resources, we investigate the effect of finite squeezing on the tolerance of the protocol to untrusted channel noise. For a long-distance strongly attenuating channel and the consequent low reconciliation efficiency, we show that feasible limited squeezing is surprisingly sufficient to provide the security of Gaussian quantum key distribution in the presence of untrusted noise. We explain the effect by behaviour of the Holevo quantity, which describes the information leakage, and is effectively minimized by the squeezed states.Comment: 14 pages, 7 figure

Physical activity, ketogenic diet, and epilepsy: A mini-review

One-third of patients with epilepsy do not respond to antiepileptic drugs and may seek complementary and alternative treatment modalities. Dietary therapies, such as the ketogenic diet (KD), the modified Atkins diet, as well as the medium-chain triglyceride and the low glycaemic index diets, have been successfully implemented with some forms of epilepsy and are growing in utilization. The KD is a high-fat, low-protein, low-carbohydrate diet that has been used for various conditions for over a century. Insights into the mechanism of action of these diets may provide more targeted interventions for patients with epilepsy. Knowledge of these mechanisms is growing and includes neuroprotective effects on oxidative stress, neuroinflammation, potassium channels in the brain, and mitochondrial function. In this review, we explain the role of physical exercise and the ketogenic diet on epilepsy

Real-time full bandwidth measurement of spectral noise in supercontinuum generation

The ability to measure real-time fluctuations of ultrashort pulses propagating in optical fiber has provided significant insights into fundamental dynamical effects such as modulation instability and the formation of frequency-shifting rogue wave solitons. We report here a detailed study of real-time fluctuations across the full bandwidth of a fiber supercontinuum which directly reveals the significant variation in measured noise statistics across the spectrum, and which allows us to study correlations between widely separated spectral components. For two different propagation distances corresponding to the onset phase of spectral broadening and the fully-developed supercontinuum, we measure real time noise across the supercontinuum bandwidth, and we quantify the supercontinuum noise using statistical higher-order moments and a frequency-dependent intensity correlation map. We identify correlated spectral regions within the supercontinuum associated with simultaneous sideband generation, as well as signatures of pump depletion and soliton-like pump dynamics. Experimental results are in excellent agreement with simulations

Nocturnal obstructive respiratory events severity is associated with low parental quality

Objective: Despite of the large prevalence of obstructive sleep apnea syndrome (OSAS) in pediatric age, numerous aspects of its impact on day life and on parental quality are still poor studied and considered in the clinical management. The study evaluated the stress levels and copying styles in a large sample of mother of children with OSAS. Method: 374 mothers of children affected by OSAS (mOSAS) were compared with a group of mothers of 421 neurotypical healthy children (mTDC) for stress perceived stress levels and for coping strategies. Subjects were recruited from Italian Regions in Sicily, Campania, Calabria and Umbria. Results: Among both groups mOSAS and mTDC no differences were reported for children age (p=0.340), children gender (p=0.956), similarly for age of mothers (p=0.188). Discussion: The perceived stress assessment in mOSAS showed higher rate of all parental stress scores of PSI-SF: Parental Distress domain (p<0.001), Difficult Child subscale (p<0.001), Parent-Child Dysfunctional Interaction domain (p<0.001) and Total Stress subscale score (p <0.001) than mTDC. Regarding the CISS evaluation, mOSAS reported higher scores in emotion-oriented (p<0.001) and avoidance-oriented (p <0.001) scales, while low task-oriented coping style scale score was reported (p<0.001) than mTDC. Pearson’s correlation analysis showed significant values for AHI, ODI and mdes SpO2 for each scale of PSI-SF questionnaire, particularly relevant for P-CDI (p<0.001), DC (p<0.001) and Stress Tot (p<0.001). Conclusion: Pediatric OSAS tends to cause maternal high stress levels than controls, with a significant correlation between respiratory parameters and all PSI-SF scores. Moreover, mothers of affected children showed significantly differences in emotion-oriented and avoidance-oriented coping tasks. The present study suggested the importance of evaluation for caregivers of children affected by OSAS

Deficits in mitochondrial TCA cycle and OXPHOS precede rod photoreceptor degeneration during chronic HIF activation

Background: Major retinal degenerative diseases, including age-related macular degeneration, diabetic retinopathy and retinal detachment, are associated with a local decrease in oxygen availability causing the formation of hypoxic areas affecting the photoreceptor (PR) cells. Here, we addressed the underlying pathological mechanisms of PR degeneration by focusing on energy metabolism during chronic activation of hypoxia-inducible factors (HIFs) in rod PR. Methods: We used two-photon laser scanning microscopy (TPLSM) of genetically encoded biosensors delivered by adeno-associated viruses (AAV) to determine lactate and glucose dynamics in PR and inner retinal cells. Retinal layer-specific proteomics, in situ enzymatic assays and immunofluorescence studies were used to analyse mitochondrial metabolism in rod PRs during chronic HIF activation. Results: PRs exhibited remarkably higher glycolytic flux through the hexokinases than neurons of the inner retina. Chronic HIF activation in rods did not cause overt change in glucose dynamics but an increase in lactate production nonetheless. Furthermore, dysregulation of the oxidative phosphorylation pathway (OXPHOS) and tricarboxylic acid (TCA) cycle in rods with an activated hypoxic response decelerated cellular anabolism causing shortening of rod photoreceptor outer segments (OS) before onset of cell degeneration. Interestingly, rods with deficient OXPHOS but an intact TCA cycle did not exhibit these early signs of anabolic dysregulation and showed a slower course of degeneration. Conclusion: Together, these data indicate an exceeding high glycolytic flux in rods and highlight the importance of mitochondrial metabolism and especially of the TCA cycle for PR survival in conditions of increased HIF activity

Regenerative memory in time-delayed neuromorphic photonic resonators

We investigate a photonic regenerative memory based upon a neuromorphic oscillator with a delayed self-feedback (autaptic) connection. We disclose the existence of a unique temporal response characteristic of localized structures enabling an ideal support for bits in an optical buffer memory for storage and reshaping of data information. We link our experimental implementation, based upon a nanoscale nonlinear resonant tunneling diode driving a laser, to the paradigm of neuronal activity, the FitzHugh-Nagumo model with delayed feedback. This proof-of-concept photonic regenerative memory might constitute a building block for a new class of neuron-inspired photonic memories that can handle high bit-rate optical signals