Miracle-dz/UniFAR-FTUs huggingface dataset:
Health, Lifestyle, and Psycho-Social Determinants of Poor Sleep Quality During the Early Phase of the COVID-19 Pandemic: A Focus on UK Older Adults Deemed Clinically Extremely Vulnerable

Background: Several studies have assessed the impact of COVID-19-related lockdowns on sleep quality across global populations. However, no study to date has specifically assessed at-risk populations, particularly those at highest risk of complications from coronavirus infection deemed “clinically-extremely-vulnerable-(COVID-19CEV)” (as defined by Public Health England). Methods: In this cross-sectional study, we surveyed 5,558 adults aged ≥50 years (of whom 523 met criteria for COVID-19CEV) during the first pandemic wave that resulted in a nationwide-lockdown (April–June 2020) with assessments of sleep quality (an adapted sleep scale that captured multiple sleep indices before and during the lockdown), health/medical, lifestyle, psychosocial and socio-demographic factors. We examined associations between these variables and sleep quality; and explored interactions of COVID-19CEV status with significant predictors of poor sleep, to identify potential moderating factors. Results: Thirty-seven percent of participants reported poor sleep quality which was associated with younger age, female sex and multimorbidity. Significant associations with poor sleep included health/medical factors: COVID-19CEV status, higher BMI, arthritis, pulmonary disease, and mental health disorders; and the following lifestyle and psychosocial factors: living alone, higher alcohol consumption, an unhealthy diet and higher depressive and anxiety symptoms. Moderators of the negative relationship between COVID-19CEV status and good sleep quality were marital status, loneliness, anxiety and diet. Within this subgroup, less anxious and less lonely males, as well as females with healthier diets, reported better sleep. Conclusions: Sleep quality in older adults was compromised during the sudden unprecedented nation-wide lockdown due to distinct modifiable factors. An important contribution of our study is the assessment of a “clinically-extremely-vulnerable” population and the sex differences identified within this group. Male and female older adults deemed COVID-19CEV may benefit from targeted mental health and dietary interventions, respectively. This work extends the available evidence on the notable impact of lack of social interactions during the COVID-19 pandemic on sleep, and provides recommendations toward areas for future work, including research into vulnerability factors impacting sleep disruption and COVID-19-related complications. Study results may inform tailored interventions targeted at modifiable risk factors to promote optimal sleep; additionally, providing empirical data to support health policy development in this area.
Mixed Infant Feeding Is Not Associated With Increased Risk of Decelerated Growth Among WIC-Participating Children in Southern California

Background: The Special Supplemental Nutrition Program for Women, Infants, and Children (WIC) provides nutrition assistance to half of infants born in the United States. The nationally representative WIC Infants and Toddler Feeding Practices Study-2 (ITFPS-2) reported a caloric deficit at 7 months among infants receiving WIC mixed feeding packages, suggesting these infants may be at risk for growth deceleration/faltering. Methods: Longitudinal administrative data collected prospectively from WIC participants in Southern California between 2010 and 2019 were used (n = 16,255). Infant lengths and weights were used to calculate weight-for-length (WLZ), weight-for-age (WAZ) and length-for-age (LAZ) z-scores at different time points. Growth deceleration/faltering was determined at 9, 12, 18, and 24 months by the change in z-score from the last measurement taken ≤ 6 months of age. Infant feeding was categorized by the food package (breastfeeding, mixed feeding, and formula feeding) infants received from WIC at 7 months. Poisson regression models were used to evaluate the association between WIC infant package at 7 months and deceleration/faltering at 9, 12, 18, and 24 months. Results: The proportion of infants displaying decelerated/faltering growth was low for all infant food package groups. Receiving the WIC mixed feeding package at 7 months of age was not associated with WLZ, WAZ, and LAZ deceleration/faltering growth. Conclusions: Growth deceleration/faltering rates were very low among WIC participating children in Southern California, highlighting the critical role of nutrition assistance in supporting adequate growth in early childhood.
Plasma Lipidomics Identifies Unique Lipid Signatures and Potential Biomarkers for Patients With Aortic Dissection

Aortic dissection (AD) is a catastrophic cardiovascular emergency with a poor prognosis, and little preceding symptoms. Abnormal lipid metabolism is closely related to the pathogenesis of AD. However, comprehensive lipid alterations related to AD pathogenesis remain unclear. Moreover, there is an urgent need for new or better biomarkers for improved risk assessment and surveillance of AD. Therefore, an untargeted lipidomic approach based on ultra-high-performance liquid chromatograph-mass spectrometry was employed to unveil plasma lipidomic alterations and potential biomarkers for AD patients in this study. We found that 278 of 439 identified lipid species were significantly altered in AD patients (n = 35) compared to normal controls (n = 32). Notably, most lipid species, including fatty acids, acylcarnitines, cholesteryl ester, ceramides, hexosylceramides, sphingomyelins, lysophosphatidylcholines, lysophosphatidylethanolamines, phosphatidylcholines, phosphatidylinositols, diacylglycerols, and triacylglycerols with total acyl chain carbon number ≥54 and/or total double bond number ≥4 were decreased, whereas phosphatidylethanolamines and triacylglycerols with total double bond number <4 accumulated in AD patients. Besides, the length and unsaturation of acyl chains in triacylglycerols and unsaturation of 1-acyl chain in phosphatidylethanolamines were decreased in AD patients. Moreover, lysophosphatidylcholines were the lipids with the largest alterations, at the center of correlation networks of lipid alterations, and had excellent performances in identifying AD patients. The area under the curve of 1.0 and accuracy rate of 100% could be easily obtained by lysophosphatidylcholine (20:0/0:0) or its combination with lysophosphatidylcholine (17:0/0:0) or lysophosphatidylcholine (20:1/0:0). This study provides novel and comprehensive plasma lipidomic signatures of AD patients, identifies lysophosphatidylcholines as excellent potential biomarkers, and would be beneficial to the pathogenetic study, risk assessment and timely diagnosis and treatment of AD.
An Stomatin, Prohibitin, Flotillin, and HflK/C-Domain Protein Required to Link the Phage-Shock Protein to the Membrane in Bacillus subtilis

Membrane surveillance and repair is of utmost importance to maintain cellular integrity and allow cellular life. Several systems detect cell envelope stress caused by antimicrobial compounds and abiotic stresses such as solvents, pH-changes and temperature in bacteria. Proteins containing an Stomatin, Prohibitin, Flotillin, and HflK/C (SPFH)-domain, including bacterial flotillins have been shown to be involved in membrane protection and membrane fluidity regulation. Here, we characterize a bacterial SPFH-domain protein, YdjI that is part of a stress induced complex in Bacillus subtilis. We show that YdjI is required to localize the ESCRT-III homolog PspA to the membrane with the help of two membrane integral proteins, YdjG/H. In contrast to classical flotillins, YdjI resides in fluid membrane regions and does not enrich in detergent resistant membrane fractions. However, similarly to FloA and FloT from B. subtilis, deletion of YdjI decreases membrane fluidity. Our data reveal a hardwired connection between phage shock response and SPFH proteins.
DeepBhvTracking: A Novel Behavior Tracking Method for Laboratory Animals Based on Deep Learning

Behavioral measurement and evaluation are broadly used to understand brain functions in neuroscience, especially for investigations of movement disorders, social deficits, and mental diseases. Numerous commercial software and open-source programs have been developed for tracking the movement of laboratory animals, allowing animal behavior to be analyzed digitally. In vivo optical imaging and electrophysiological recording in freely behaving animals are now widely used to understand neural functions in circuits. However, it is always a challenge to accurately track the movement of an animal under certain complex conditions due to uneven environment illumination, variations in animal models, and interference from recording devices and experimenters. To overcome these challenges, we have developed a strategy to track the movement of an animal by combining a deep learning technique, the You Only Look Once (YOLO) algorithm, with a background subtraction algorithm, a method we label DeepBhvTracking. In our method, we first train the detector using manually labeled images and a pretrained deep-learning neural network combined with YOLO, then generate bounding boxes of the targets using the trained detector, and finally track the center of the targets by calculating their centroid in the bounding box using background subtraction. Using DeepBhvTracking, the movement of animals can be tracked accurately in complex environments and can be used in different behavior paradigms and for different animal models. Therefore, DeepBhvTracking can be broadly used in studies of neuroscience, medicine, and machine learning algorithms.
Type I Interferons Are Involved in the Intracellular Growth Control of Mycobacterium abscessus by Mediating NOD2-Induced Production of Nitric Oxide in Macrophages

Mycobacterium abscessus (MAB) is one of the rapidly growing, multidrug-resistant non-tuberculous mycobacteria (NTM) causing various diseases including pulmonary disorder. Although it has been known that type I interferons (IFNs) contribute to host defense against bacterial infections, the role of type I IFNs against MAB infection is still unclear. In the present study, we show that rIFN-β treatment reduced the intracellular growth of MAB in macrophages. Deficiency of IFN-α/β receptor (IFNAR) led to the reduction of nitric oxide (NO) production in MAB-infected macrophages. Consistently, rIFN-β treatment enhanced the expression of iNOS gene and protein, and NO production in response to MAB. We also found that NO is essential for the intracellular growth control of MAB within macrophages in an inhibitor assay using iNOS-deficient cells. In addition, pretreatment of rIFN-β before MAB infection in mice increased production of NO in the lungs at day 1 after infection and promoted the bacterial clearance at day 5. However, when alveolar macrophages were depleted by treatment of clodronate liposome, rIFN-β did not promote the bacterial clearance in the lungs. Moreover, we found that a cytosolic receptor nucleotide-binding oligomerization domain 2 (NOD2) is required for MAB-induced TANK binding kinase 1 (TBK1) phosphorylation and IFN-β gene expression in macrophages. Finally, increase in the bacterial loads caused by reduction of NO levels was reversed by rIFN-β treatment in the lungs of NOD2-deficient mice. Collectively, our findings suggest that type I IFNs act as an intermediator of NOD2-induced NO production in macrophages and thus contribute to host defense against MAB infection.
Molecular Epidemiology of Extraintestinal Pathogenic Escherichia coli Causing Hemorrhagic Pneumonia in Mink in Northern China

The molecular epidemiology and biological characteristics of Escherichia coli associated with hemorrhagic pneumonia (HP) mink from five Chinese Provinces were determined. From 2017 to 2019, 85 E. coli strains were identified from 115 lung samples of mink suffering from HP. These samples were subjected to serotyping, antimicrobial susceptibility, detection of virulence genes, phylogenetic grouping, whole-genome sequencing, drug resistant gene, multilocus sequence typing (MLST) and biofilm-forming assays. E. coli strains were divided into 18 serotypes. Thirty-nine E. coli strains belonged to the O11 serotype. Eighty-five E. coli strains were classified into seven phylogenetic groups: E (45.9%, 39/85), A (27.1%, 23/85), B1 (14.1%, 12/85), B2 (3.7%, 3/85), D (3.7%, 3/85), F (2.4%, 2/85) and clade I (1.2%, 1/85). MLST showed that the main sequence types (STs) were ST457 (27/66), All E. coli strains had ≥4 virulence genes. The prevalence of virulence was 98.8% for yijp and fimC, 96.5% for iucD, 95.3% for ompA, 91.8% for cnf-Ⅰ, 89.4% for mat, 82.3% for hlyF, and 81.2% for ibeB. The prevalence of virulence genes iss, cva/cvi, aatA, ibeA, vat, hlyF, and STa was 3.5–57.6%. All E. coli strains were sensitive to sulfamethoxazole, but high resistance was shown to tetracycline (76.5%), chloramphenicol (71.8%), ciprofloxacin (63.5%) and florfenicol (52.9%), resistance to other antibiotics was 35.3–16.5%. The types and ratios of drug-resistance genes were tet(A), strA, strB, sul2, oqxA, blaTEM-1B, floR, and catA1 had the highest frequency from 34%-65%, which were consistent with our drug resistance phenotype tetracycline, florfenicol, quinolones, chloramphenicol, the bla-NDM-I and mcr-I were presented in ST457 strains. Out of 85 E. coli strains, six (7.1%) possessed a strong ability, 12 (14.1%) possessed a moderate ability, and 64 (75.3%) showed a weak ability to form biofilm. Our data will aid understanding of the epidemiological background and provide a clinical basis for HP treatment in mink caused by E. coli.
Flood-Rings Production Modulated by River Regulation in Eastern Boreal Canada

In northeastern boreal Canada, the long-term perspective on spring flooding is hampered by the absence of long gage records. Changes in the tree-ring anatomy of periodically flooded trees have allowed the reconstruction of historical floods in unregulated hydrological systems. In regulated rivers, the study of flood rings could recover past flood history, assuming that the effects of hydrological regulation on their production can be understood. This study analyzes the effect of regulation on the flood-ring occurrence (visual intensity and relative frequency) and on ring widths in Fraxinus nigra trees growing at five sites distributed along the Driftwood River floodplain. Driftwood River was regulated by a dam in 1917 that was replaced at the same location in 1953. Ring width revealed little, to no evidence, of the impact of river regulation, in contrast to the flood rings. Prior to 1917, high relative frequencies of well-defined flood rings were recorded during known flood years, as indicated by significant correlations with reconstructed spring discharge of the nearby Harricana River. After the construction and the replacement of the dam, relative frequencies of flood rings and their intensities gradually decreased. Flood-ring relative frequencies after 1917, and particularly after 1953, were mostly composed of weakly defined (less distinct) flood rings with some corresponding to known flood years and others likely reflecting dam management. The strength of the correlations with the instrumental Harricana River discharge also gradually decrease starting after 1917. Compared with upper floodplain trees, shoreline trees at each site recorded flood rings less frequently following the construction of the first but especially of the second dam, indicating that water level regulation limited flooding in the floodplains. Compared with the downstream site to the dam, the upstream ones recorded significantly more flood rings in the postdam period, reemphasizing the importance of considering the position of the site along with the river continuum and site conditions in relation to flood exposure. The results demonstrated that sampling trees in multiple riparian stands and along with various hydrological contexts at a far distance of the dams could help disentangle the flooding signal from the dam management signal.
Differences in Self-Directed Learning: Middle-School Students’ Autonomous Outdoor Studying

The use of self-directed learning (SDL) is an increasingly widespread trend in schools, although its core—the student’s attentional capability for multi-level processing—to construct relevant concepts and at the same time to keep in mind the needed sub-items, while also directing one’s own learning, has not been thoroughly investigated. We examined autonomous learning outdoors in small groups with 122 school students aged 14–16 years (the period that, through the developmental peculiarities of puberty, causes variety in cognitive skills). To detect whether individual characteristics reflect in students’ SDL progress, we measured participants’ pre-knowledge, their problem-solving strategies, and post-knowledge. We also asked about their prior SDL experience. The results showed 1) relations between one’s pre-and post-knowledge levels; 2) the impact of gender in the SDL efficacy; 3) the difficulty to memorize in the course of complex tasks while learning on one’s own. Our work gives insight into the SDL-specific heightened cognitive demand: school students’ cognitive obstacles in heavy load conditions and their prolonged maturation of executive functions—especially in adolescence as this age group passes its normal biological spurts of the human developmental path—which may differ individually.
“Stay at Home”: The Effects of the COVID-19 Lockdown on Household Food Waste in Colombia

Household food waste represents one of the main challenges for sustainable development as this directly affects the economy of food consumers, the loss of natural resources and generates additional greenhouse gas emissions. The COVID-19 pandemic and its mitigation strategies caused one of the most serious economic crises in recent decades and could become the worst economic crisis that Latin America has had in its history. The objective of this study is to analyze changes in food waste behavior during the COVID-19 lockdown in Colombia in 2020, applying the Theory of Planned Behavior (TPB). For this purpose, we conducted a survey with 581 Colombian food consumers, which examined the influence of intentions to not waste food, subjective norms, some situational predictors, questions related to the COVID-19 pandemic, and the control of perceived behavior on food waste. The results suggest that the TPB can predict the intention to not waste food and, through it, the actual household food waste behavior, considering the lockdown in Colombia as an external shock. We observe that regarding the intention to not waste food, the most relevant variables are attitudes, subjective norms, control of the perceived behavior, and concerns regarding the Covid-19 pandemic. These variables increase the probability on average by a 0.8 Odds Ratio that the intention not to waste food increases, too. Regarding food waste behavior, whether it is considered ordinal or nominal, we see that the most relevant variables are intention, financial attitudes, and control of perceived behavior, doubling the probability that food waste behavior will improve. Based on the results, we provide recommendations for interested stakeholders that can help in the design of instruments for household food waste reduction.
Anthocyanins: From Mechanisms of Regulation in Plants to Health Benefits in Foods

Anthocyanins represent the major red, purple, and blue pigments in many flowers, fruits, vegetables, and cereals. They are also recognized as important health-promoting components in the human diet with protective effects against many chronic diseases, including cardiovascular diseases, obesity, and cancer. Anthocyanin biosynthesis has been studied extensively, and both biosynthetic and key regulatory genes have been isolated in many plant species. Here, we will provide an overview of recent progress in understanding the anthocyanin biosynthetic pathway in plants, focusing on the transcription factors controlling activation or repression of anthocyanin accumulation in cereals and fruits of different plant species, with special emphasis on the differences in molecular mechanisms between monocot and dicot plants. Recently, new insight into the transcriptional regulation of the anthocyanin biosynthesis, including positive and negative feedback control as well as epigenetic and post-translational regulation of MYB-bHLH-WD40 complexes, has been gained. We will consider how knowledge of regulatory mechanisms has helped to produce anthocyanin-enriched foods through conventional breeding and metabolic engineering. Additionally, we will briefly discuss the biological activities of anthocyanins as components of the human diet and recent findings demonstrating the important health benefits of anthocyanin-rich foods against chronic diseases.
Unraveling Aβ-Mediated Multi-Pathway Calcium Dynamics in Astrocytes: Implications for Alzheimer’s Disease Treatment From Simulations

The accumulation of amyloid β peptide (Aβ) in the brain is hypothesized to be the major factor driving Alzheimer’s disease (AD) pathogenesis. Mounting evidence suggests that astrocytes are the primary target of Aβ neurotoxicity. Aβ is known to interfere with multiple calcium fluxes, thus disrupting the calcium homeostasis regulation of astrocytes, which are likely to produce calcium oscillations. Ca2+ dyshomeostasis has been observed to precede the appearance of clinical symptoms of AD; however, it is experimentally very difficult to investigate the interactions of many mechanisms. Given that Ca2+ disruption is ubiquitously involved in AD progression, it is likely that focusing on Ca2+ dysregulation may serve as a potential therapeutic approach to preventing or treating AD, while current hypotheses concerning AD have so far failed to yield curable therapies. For this purpose, we derive and investigate a concise mathematical model for Aβ-mediated multi-pathway astrocytic intracellular Ca2+ dynamics. This model accounts for how Aβ affects various fluxes contributions through voltage-gated calcium channels, Aβ-formed channels and ryanodine receptors. Bifurcation analysis of Aβ level, which reflected the corresponding progression of the disease, revealed that Aβ significantly induced the increasing [Ca2+]i and frequency of calcium oscillations. The influence of inositol 1,4,5-trisphosphate production (IP3) is also investigated in the presence of Aβ as well as the impact of changes in resting membrane potential. In turn, the Ca2+ flux can be considerably changed by exerting specific interventions, such as ion channel blockers or receptor antagonists. By doing so, a “combination therapy” targeting multiple pathways simultaneously has finally been demonstrated to be more effective. This study helps to better understand the effect of Aβ, and our findings provide new insight into the treatment of AD.