Miracle-dz/UniFAR-FTUs huggingface dataset:
No-Reference Video Quality Assessment Using Natural Spatiotemporal Scene Statistics

Robust spatiotemporal representations of natural videos have several applications including quality assessment, action recognition, object tracking etc. In this paper, we propose a video representation that is based on a parameterized statistical model for the spatiotemporal statistics of mean subtracted and contrast normalized (MSCN) coefficients of natural videos. Specifically, we propose an asymmetric generalized Gaussian distribution (AGGD) to model the statistics of MSCN coefficients of natural videos and their spatiotemporal Gabor bandpass filtered outputs. We then demonstrate that the AGGD model parameters serve as good representative features for distortion discrimination. Based on this observation, we propose a supervised learning approach using support vector regression (SVR) to address the no-reference video quality assessment (NRVQA) problem. The performance of the proposed algorithm is evaluated on publicly available video quality assessment (VQA) datasets with both traditional and in-capture/authentic distortions. We show that the proposed algorithm delivers competitive performance on traditional (synthetic) distortions and acceptable performance on authentic distortions. The code for our algorithm will be released at https://www.iith. ac.in/lfovia/downloads.html.
Oncological genetic counseling (OGC) for high-risk hereditary cancer: what can hospital anxiety and depression scale (HADs) tell us?

PURPOSE This study aimed to verify whether and how anxiety and depression symptoms are associated both to socio-demographic and clinical variables (age, civil status, type of cancer diagnosed, time elapsed between cancer diagnosis and Oncologic Genetic Counseling/OGC, number of relatives affected by cancer) and to psychological features (presence/absence of previous psychological suffering), subjective cancer risk perception, psychological attitude approaching/OGC) in a sample of Caucasian patients accessing OGC. METHODS 201 participants (193 female and 8 male) accessing OGC in the Istituto di Ricovero e Cura Carattere Scientifico (IRCCS) Giovanni Paolo II in Bari completed the Hospital Depression and Anxiety Scale (HADs) that was analyzed as global scoring, anxiety (HAD-A) and depression subscale (HAD-D). RESULTS In our sample, higher HADs, HAD-A and HAD-D scorings were associated in different ways to both socio-demographic information (age: p value 0.019), clinical and medical features (personal history of cancer: HAD-D p value 0.02; months elapsed between diagnosis and OGC, HAD-A p value 0.004 and HADs p value 0.008) and psychological dimensions (approaching genetic counseling: anxiety p value 0.06; fear p value 0.02; duty p value 0.04). CONCLUSION This study showed that during the process of oncological genetic counseling the importance of taking into consideration not only medical variables but also cognitive and emotional aspects from both the individual and family spheres, in order to assure adequate care of the patient.
Aggressive morphologic variants of mantle cell lymphoma characterized with high genomic instability showing frequent chromothripsis, CDKN2A/B loss, and TP53 mutations: A multi‐institutional study

Aggressive morphologic variants of mantle cell lymphoma (MCL), including blastoid and pleomorphic (B/P‐MCL), are rare and associated with poor clinical outcomes. The genomic landscape of these variants remains incompletely explored. In this multi‐institutional study, we describe recurrent mutations and novel genomic copy number alterations (CNAs) in B/P‐MCL, using next generation sequencing and SNP‐array. Chromothripsis, a recently described phenomenon of massive chromosomal rearrangements, was identified in eight of 13 (62%) B/P MCL cases, and a high degree of genomic complexity with frequent copy number gains and losses was also seen. In contrast, a comparative cohort of nine cases of conventional MCL (C‐MCL) showed no chromothripsis and less complexity. Twelve of 13 (92%) B/P‐MCL cases showed loss of CDKN2A/B (6 biallelic and 6 monoallelic losses); while only one C‐MCL showed monoallelic CDKN2A/B loss. In B/P‐MCL, TP53 was the most commonly mutated gene, with mutations present in eight cases (62%), six of which showed concurrent loss of chromosome 17p. Of the eight cases with chromothripsis, six (85%) harbored TP53 mutations. Other recurrent mutations in B/P‐MCL included ATM (7, 53%), CCND1 (5, 38%), NOTCH1 (2, 18%), NOTCH2, and BIRC3 (each in 3, 23%). Here, we describe high genomic instability associated with chromothripsis and a high frequency of CDKN2A/B and TP53 alterations in the aggressive variants of MCL. The nonrandom chromothripsis events observed in B/P‐MCL may be an indicator of clinically aggressive MCL. In addition, frequent CDKN2A deletion and high genomic instability may provide potential targets for alternative treatment.
Structure of the RNA-dependent RNA polymerase from COVID-19 virus

The COVID-19 RNA-synthesizing machine Many in the scientific community have mobilized to understand the virus that is causing the global coronavirus disease 2019 (COVID-19) pandemic. Gao et al. focused on a complex that plays a key role in the replication and transcription cycle of the virus. They used cryo–electron microscopy to determine a 2.9-angstrom-resolution structure of the RNA-dependent RNA polymerase nsp12, which catalyzes the synthesis of viral RNA, in complex with two cofactors, nsp7 and nsp8. nsp12 is a target for nucleotide analog antiviral inhibitors such as remdesivir, and the structure may provide a basis for designing new antiviral therapeutics. Science, this issue p. 779 The structure of the COVID-19 virus polymerase essential for viral replication provides a basis for the design of new antiviral drugs. A novel coronavirus [severe acute respiratory syndrome–coronavirus 2 (SARS-CoV-2)] outbreak has caused a global coronavirus disease 2019 (COVID-19) pandemic, resulting in tens of thousands of infections and thousands of deaths worldwide. The RNA-dependent RNA polymerase [(RdRp), also named nsp12] is the central component of coronaviral replication and transcription machinery, and it appears to be a primary target for the antiviral drug remdesivir. We report the cryo–electron microscopy structure of COVID-19 virus full-length nsp12 in complex with cofactors nsp7 and nsp8 at 2.9-angstrom resolution. In addition to the conserved architecture of the polymerase core of the viral polymerase family, nsp12 possesses a newly identified β-hairpin domain at its N terminus. A comparative analysis model shows how remdesivir binds to this polymerase. The structure provides a basis for the design of new antiviral therapeutics that target viral RdRp.
Summarizing societal guidelines regarding bronchoscopy during the COVID‐19 pandemic

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for pandemic coronavirus disease 2019 (COVID-19), is predominantly transmitted via large droplets and fomites. However, healthcare workers (HCW) participating in aerosol-generating procedures such as bronchoscopy, endotracheal intubation, upper gastrointestinal endoscopy, otolaryngological procedures involving the upper airway and tracheotomy are also at risk for aerosoltransmitted infection. Given the well-documented asymptomatic SARS-CoV-2 infection with viral shedding, infectious aerosol might also be generated from asymptomatic patients as community prevalence rises. Several bronchology societies have issued guidelines regarding bronchoscopy during the COVID-19 pandemic. However, none are comprehensive and significant uncertainty remains regarding in whom to perform bronchoscopy and how to perform it safely in this rapidly changing clinical environment. No data specific to bronchoscopy in COVID-19 are yet available, so most recommendations are expert opinion derived from observations made during prior respiratory viral outbreaks including SARS, Middle East respiratory syndrome (MERS) and influenza. Tables 1 and 2 summarize existing guidelines regarding bronchoscopy in patients not suspected of harbouring SARS-CoV-2 and in those known or suspected to be suffering from COVID-19, respectively. All societies reviewed recommend postponing elective procedures and limiting
Mesenchymal and MAPK Expression Signatures Associate with Telomerase Promoter Mutations in Multiple Cancers

In a substantial fraction of cancers TERT promoter (TERTp) mutations drive expression of the catalytic subunit of telomerase, contributing to their proliferative immortality. We conducted a pan-cancer analysis of cell lines and find a TERTp mutation expression signature dominated by epithelial-to-mesenchymal transition and MAPK signaling. These data indicate that TERTp mutants are likely to generate distinctive tumor microenvironments and intercellular interactions. Analysis of high-throughput screening tests of 546 small molecules on cell line growth indicated that TERTp mutants displayed heightened sensitivity to specific drugs, including RAS pathway inhibitors, and we found that inhibition of MEK1 and 2, key RAS/MAPK pathway effectors, inhibited TERT mRNA expression. Consistent with an enrichment of mesenchymal states in TERTp mutants, cell lines and some patient tumors displayed low expression of the central adherens junction protein E-cadherin, and we provide evidence that its expression in these cells is regulated by MEK1/2. Several mesenchymal transcription factors displayed elevated expression in TERTp mutants including ZEB1 and 2, TWIST1 and 2, and SNAI1. Of note, the developmental transcription factor SNAI2/SLUG was conspicuously elevated in a significant majority of TERTp-mutant cell lines, and knock-down experiments suggest that it promotes TERT expression. Implications: Cancers harboring TERT promoter mutations are often more lethal, but the basis for this higher mortality remains unknown. Our study identifies that TERTp mutants, as a class, associate with a distinct gene and protein expression signature likely to impact their biological and clinical behavior and provide new directions for investigating treatment approaches for these cancers.
A VTA to Basal Amygdala Dopamine Projection Contributes to Signal Salient Somatosensory Events during Fear Learning

The amygdala is a brain area critical for the formation of fear memories. However, the nature of the teaching signal(s) that drive plasticity in the amygdala are still under debate. Here, we use optogenetic methods to investigate the contribution of ventral tegmental area (VTA) dopamine neurons to auditory-cued fear learning in male mice. The amygdala is a brain area critical for the formation of fear memories. However, the nature of the teaching signal(s) that drive plasticity in the amygdala are still under debate. Here, we use optogenetic methods to investigate the contribution of ventral tegmental area (VTA) dopamine neurons to auditory-cued fear learning in male mice. Using anterograde and retrograde labeling, we found that a sparse and relatively evenly distributed population of VTA neurons projects to the basal amygdala (BA). In vivo optrode recordings in behaving mice showed that many VTA neurons, among them putative dopamine neurons, are excited by footshocks, and acquire a response to auditory stimuli during fear learning. Combined cfos imaging and retrograde labeling in dopamine transporter (DAT) Cre mice revealed that a large majority of BA projectors (>95%) are dopamine neurons, and that BA projectors become activated by the tone-footshock pairing of fear learning protocols. Finally, silencing VTA dopamine neurons, or their axon terminals in the BA during the footshock, reduced the strength of fear memory as tested 1 d later, whereas silencing the VTA-central amygdala (CeA) projection had no effect. Thus, VTA dopamine neurons projecting to the BA contribute to fear memory formation, by coding for the saliency of the footshock event and by signaling such events to the basal amygdala. SIGNIFICANCE STATEMENT Powerful mechanisms of fear learning have evolved in animals and humans to enable survival. During fear conditioning, a sensory cue, such as a tone (the conditioned stimulus), comes to predict an innately aversive stimulus, such as a mild footshock (the unconditioned stimulus). A brain representation of the unconditioned stimulus must act as a teaching signal to instruct plasticity of the conditioned stimulus representation in fear-related brain areas. Here we show that dopamine neurons in the VTA that project to the basal amygdala contribute to such a teaching signal for plasticity, thereby facilitating the formation of fear memories. Knowledge about the role of dopamine in aversively motivated plasticity might allow further insights into maladaptive plasticities that underlie anxiety and post-traumatic stress disorders in humans.
Effect of adalimumab on the expression profile of mRNA, and protein associated with JAK/STAT signaling pathway in fibroblast exposed to lipopolysaccharide

The aim of this study was to assess the effect of adalimumab on the expression level of mRNA and protein TNF‐α, IFN‐γ, IL‐17, IL12A, IL12B, and IL23A in the culture of normal human fibroblasts, in which the LPS inflammation process was induced. The NHDF culture was exposed to the effect of LPS in the concentrations of 1, 2, and 10 μg/mL for 2, 8, and 24 hour periods, and then adalimumab was added at the concentration of 8 μg/mL, it was then incubated for 2, 8, and 24 hour. Cells unexposed to LPS and adalimumab constituted the control. The microarray expression techniques, RTqPCR, and ELISA assay were used. Irrespectively of the concentration of LPS used and the incubation time of it with cells overexpression of the analyzed genes is present, with increasing factor concentration used to induce inflammation and incubation time with it, expression of the assessed genes was greater. In turn, adding the anti‐TNF drug to the culture caused the silencing of the expression of the mRNAs and proteins. It was confirmed that LPS and adalimumab above all affect the expression of genes and proteins dependent on the interaction of IL‐12 with receptors, which are TNF‐α and IFN‐γ, and to a lesser extent also modulate IL‐17.
Influence of Demographic and Lifestyle Variables on Plasma Magnesium Concentrations and Their Associations with Cardiovascular Risk Factors in a Mediterranean Population

Several studies have shown that a low magnesium (Mg) intake in the diet is associated with greater cardiovascular risk and greater risk of diabetes. However, the results are not consistent in all populations. To minimize the biases derived from diet measurement, more objective biomarkers of magnesium status have been proposed. Although there is still no ideal biomarker for Mg, several studies have shown that plasma Mg concentrations could be a relatively acceptable biomarker for cardiovascular risk assessment. However, further studies are required to better characterize this marker in different populations. Our aim was to analyze the association between plasma Mg concentrations (measured through inductively coupled plasma mass spectrometry (ICP-MS)) methods, and cardiovascular risk factors in individuals from a general Mediterranean population (aged 18–80 years). The influence of demographic and lifestyle variables, including adherence to the Mediterranean diet, on plasma Mg concentrations was analyzed. The mean Mg level of the population studied was 0.77 ± 0.08 mmol/L, the prevalence of hypomagnesemia (<0.70 mmol/L) being 18.6%. We did not find any statistically significant differences between plasma Mg concentrations and sex, age, tobacco smoking and total adherence to the Mediterranean diet (p > 0.05). We found a statistically significant association between plasma Mg concentrations and the prevalence of type-2 diabetes (0.77 ± 0.08 mmol/L in non-diabetics versus 0.73 ± 0.13 mmol/L in diabetics; p = 0.009). Despite the low prevalence of type-2 diabetes in this population (11.24% in subjects with hypomagnesemia versus 3.91%, in normomagnesemia; p = 0.005), hypomagnesemia was associated with greater odds of being diabetic in comparison with normomagnesemia (OR = 3.36; p = 0.016, even after adjustment for sex, age, obesity, and medications). On the other hand, no statistically significant association of plasma Mg concentrations with obesity, hypertension, fasting triglycerides, HDL-cholesterol or uric acid was found. However, in contrast to what was initially expected, a statistically significant association was found between plasma Mg concentrations (basically in the highest quartile) and greater total cholesterol (p < 0.05) and LDL-cholesterol concentrations (p < 0.05). In conclusion, our results contribute to increasing the evidence gathered by numerous studies on the inverse association between hypomagnesemia and type-2 diabetes, as well as to the observation, previously reported in some studies, of a direct association with hypercholesterolemia. This paradoxical link should be deeply investigated in further studies.
Consumers Associate High-Quality (Fine) Wines with Complexity, Persistence, and Unpleasant Emotional Responses

The conventional method for the sensory evaluation of wine is based on visual, olfactory and gustatory perceptions described by a domain-specific language. This is a complex task, requiring extensive training, which is not feasible from a consumer perspective. The objective of this study was to apply a wine tasting sheet, including sensory and emotional responses, to simplify the recognition of fine white wines by consumers. First, a panel of 15 semi-trained judges evaluated eight sensory attributes through Optimized Descriptive Profile (ODP) methodology. Then, a group of 104 consumers evaluated five white wines with different sensory characteristics using an improved emotional wine tasting sheet. The emotions and sensations most frequently associated with white wines were obtained through the Check-All-That-Apply (CATA) approach. The eight sensory attributes were significant (p-value < 0.05) in the distinction of wines by the ODP. Likewise, the distinction of the wines also provided significant differences in all the emotional and sensory attributes (p-value < 0.05). The different wine styles could be distinguished by Principal Component Analysis (PCA) using the semi-trained judges or the consumer responses. The highest score in the “global evaluation” was given to two young, fruity wines characterized by high aromatic “initial impression”. The two fine wines, including a 2004 Burgundy Pouilly-Fuissé, were the lowest rated in “initial impression” and “global evaluation”, although they were considered by the consumers among the most complex and persistent. These wines were also most frequently associated with unpleasant emotions by the CATA test. The recognition of these fine wine attributes and their incongruity with emotional responses can be used in a rapid way by professionals to explain the different wine styles to consumers.
Comparative Genomics of Two New HF1-like Haloviruses

Few genomes of the HF1-group of viruses are currently available, and further examples would enhance the understanding of their evolution, improve their gene annotation, and assist in understanding gene function and regulation. Two novel HF1-group haloviruses, Serpecor1 and Hardycor2, were recovered from widely separated hypersaline lakes in Australia. Both are myoviruses with linear dsDNA genomes and infect the haloarchaeon Halorubrum coriense. Both genomes possess long, terminal direct repeat (TDR) sequences (320 bp for Serpecor1 and 306 bp for Hardycor2). The Serpecor1 genome is 74,196 bp in length, 57.0% G+C, and has 126 annotated coding sequences (CDS). Hardycor2 has a genome of 77,342 bp, 55.6% G+C, and 125 annotated CDS. They show high nucleotide sequence similarity to each other (78%) and with HF1 (>75%), and carry similar intergenic repeat (IR) sequences to those originally described in HF1 and HF2. Hardycor2 carries a DNA methyltransferase gene in the same genomic neighborhood as the methyltransferase genes of HF1, HF2 and HRTV-5, but is in the opposite orientation, and the inferred proteins are only distantly related. Comparative genomics allowed us to identify the candidate genes mediating cell attachment. The genomes of Serpecor1 and Hardycor2 encode numerous small proteins carrying one or more CxxC motifs, a signature feature of zinc-finger domain proteins that are known to participate in diverse biomolecular interactions.
Interactions among Odorants, Phenolic Compounds, and Oral Components and Their Effects on Wine Aroma Volatility

To determine the impact of oral physiology on the volatility of typical wine aroma compounds, mixtures of a synthetic wine with oral components (centrifuged human saliva (HS), artificial saliva with mucin (AS), and buccal epithelial cells (BC)) were prepared. Each wine type was independently spiked with four relevant wine odorants (guaiacol, β-phenyl ethanol, ethyl hexanoate, and β-ionone). Additionally, the impact of four types of phenolic compounds (gallic acid, catechin, grape seed extract, and a red wine extract) on aroma volatility in the HS, AS, and BC wines was also assessed. Static headspace was measured at equilibrium by solid phase microextraction–GC/MS analysis. Results showed a significant impact of oral components on the volatility of the four tested odorants. Independently of the type of aroma compound, aroma volatility was in general, higher in wines with BC. Moreover, while guaiacol and ethyl hexanoate volatility was significantly lower in wines with HS compared to wines with AS, β-ionone showed the opposite behavior, which might be related to metabolism and retention of mucin, respectively. Phenolic compounds also showed a different effect on aroma volatility depending on the type of compound and wine. Gallic acid had little effect on polar compounds but it enhanced the volatility of the most hydrophobic ones (ethyl hexanoate and β-ionone). In general, flavonoid type polyphenols significantly reduced the volatility of both polar (guaiacol and β-phenyl ethanol) and hydrophobic compounds (β-ionone in HS and BC wines), but through different mechanisms (e.g., π–π interactions and hydrophobic binding for polar and apolar odorants respectively). On the contrary, flavonoids enhanced the volatility of ethyl hexanoate, which might be due to the inhibition exerted on some salivary enzymes (e.g., carboxyl esterase) involved in the metabolism of this odorant molecule.
Is It All about the Price? An Analysis of the Purchase Intention for Organic Food in a Discount Setting by Means of Structural Equation Modeling

In recent years, discount grocery retailers have expanded their global reach and added to their traditional no-frills offerings to also cater to hedonic consumer needs. In addition to a larger product assortment and a more pleasant shopping experience, they now sell organic food, which commands a price premium compared to non-organic alternatives. To understand organic food in a discount setting, this study sets out to examine the factors that influence discount grocery shoppers’ purchase intention for organic food. To study this relationship, this paper tests several factors in a structural equation model, finding a positive relationship between hedonic shopping values, environmental concern, as well as health consciousness and the purchase intention for organic food. In our model, based on a US consumer survey (n = 394), price consciousness exhibited a direct and negative relationship with the purchase intention for organic food. Furthermore, this study found that that the impact of environmental concern, health consciousness, and hedonic shopping value is greater on the purchase intention of organic food than that of price consciousness, even in this discount setting. This study concludes by discussing these results and attempting to outline potential areas for future research, as well as managerial implications.