Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador

Abstract Characterisation of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic diversity through space and time can reveal trends in virus importation and domestic circulation and permit the exploration of questions regarding the early transmission dynamics. Here, we present a detailed description of SARS-CoV-2 genomic epidemiology in Ecuador, one of the hardest hit countries during the early stages of the coronavirus-19 pandemic. We generated and analysed 160 whole genome sequences sampled from all provinces of Ecuador in 2020. Molecular clock and phylogeographic analysis of these sequences in the context of global SARS-CoV-2 diversity enable us to identify and characterise individual transmission lineages within Ecuador, explore their spatiotemporal distributions, and consider their introduction and domestic circulation. Our results reveal a pattern of multiple international importations across the country, with apparent differences between key provinces. Transmission lineages were mostly introduced before the implementation of non-pharmaceutical interventions, with differential degrees of persistence and national dissemination.
Anticipated effects of abiotic environmental change on intraspecific social interactions

Social interactions are ubiquitous across the animal kingdom. A variety of ecological and evolutionary processes are dependent on social interactions, such as movement, disease spread, information transmission, and density‐dependent reproduction and survival. Social interactions, like any behaviour, are context dependent, varying with environmental conditions. Currently, environments are changing rapidly across multiple dimensions, becoming warmer and more variable, while habitats are increasingly fragmented and contaminated with pollutants. Social interactions are expected to change in response to these stressors and to continue to change into the future. However, a comprehensive understanding of the form and magnitude of the effects of these environmental changes on social interactions is currently lacking. Focusing on four major forms of rapid environmental change currently occurring, we review how these changing environmental gradients are expected to have immediate effects on social interactions such as communication, agonistic behaviours, and group formation, which will thereby induce changes in social organisation including mating systems, dominance hierarchies, and collective behaviour. Our review covers intraspecific variation in social interactions across environments, including studies in both the wild and in laboratory settings, and across a range of taxa. The expected responses of social behaviour to environmental change are diverse, but we identify several general themes. First, very dry, variable, fragmented, or polluted environments are likely to destabilise existing social systems. This occurs as these conditions limit the energy available for complex social interactions and affect dissimilar phenotypes differently. Second, a given environmental change can lead to opposite responses in social behaviour, and the direction of the response often hinges on the natural history of the organism in question. Third, our review highlights the fact that changes in environmental factors are not occurring in isolation: multiple factors are changing simultaneously, which may have antagonistic or synergistic effects, and more work should be done to understand these combined effects. We close by identifying methodological and analytical techniques that might help to study the response of social interactions to changing environments, highlight consistent patterns among taxa, and predict subsequent evolutionary change. We expect that the changes in social interactions that we document here will have consequences for individuals, groups, and for the ecology and evolution of populations, and therefore warrant a central place in the study of animal populations, particularly in an era of rapid environmental change.
Durable Modification of Wood by Benzoylation—Proof of Covalent Bonding by Solution State NMR and DOSY NMR Quick-Test †

A convenient, broadly applicable and durable wood protection was recently published by Kaufmann and Namyslo. This procedure efficiently allows for esterification of wood hydroxyl groups with (1H-benzotriazolyl)-activated functionalized benzoic acids. The result of such wood-modifying reactions is usually monitored by an increase in mass of the wood material (weight percent gain value, WPG) and by infrared spectroscopy (IR). However, diagnostic IR bands suffer from overlap with naturally occurring ester groups, mainly in the hemicellulose part of unmodified wood. In contrast to known NMR spectroscopy approaches that use the non-commonly available solid state techniques, herein we present solution state NMR proof of the covalent attachment of our organic precursors to wood. The finding is based on a time-efficient, non-uniformly sampled (NUS) solution state 1H,13C-HMBC experiment that only needs a tenth of the regular recording time. The appropriate NMR sample of thoroughly dissolved modified wood was prepared by a mild and non-destructive method. The 2D-HMBC shows a specific cross-signal caused by spin–spin coupling over three bonds from the ester carbonyl carbon atom to the α-protons of the esterified wood hydroxyl groups. This specific coupling pathway requires a covalent bonding as a conditio sine qua non. An even more rapid test to monitor the covalent bonding was achieved with an up-to-date diffusion-ordered spectroscopy sequence (Oneshot—DOSY) based on 1H or 19F as the sensitive nucleus. The control experiment in a series of DOSY spectra gave a by far higher D value of (1.22 ± 0.06)∙10−10 m2∙s−1, which is in accordance with fast diffusion of the “free” and thus rapidly moving small precursor molecule provided as its methyl ester. In the case of a covalent attachment to wood, a significantly smaller D value of (0.12 ± 0.01)∙10−10 m2∙s−1 was obtained.
“Does a Good Company Reduce the Unhealthy Behavior of Its Members?”: The Mediating Effect of Organizational Identification and the Moderating Effect of Moral Identity

In the contemporary business environment where business ethics is critical for organizational performance, the importance of corporate social responsibility (CSR) is increasing. By investigating the mechanism of the effects of CSR on counterproductive work behavior (CWB), the present study suggests that CSR decreases negative employee behavior. Based on social identity theory and context-attitude-behavior framework, this research examines the underlying process and its contingent factor of the association between CSR and CWB. Specifically, this study hypothesizes that CSR decreases CWB by enhancing employees’ organizational identification and that moral identity positively moderates the relationship between CSR and organizational identification. Using three-wave online survey data from 368 employees in Korean firms, this paper tested our hypotheses by conducting moderated mediation analysis with structural equation modeling. The results showed that CSR is negatively related to CWB through organizational identification and that moral identity positively moderates the relationship between CSR and organizational identification. The current study’s findings have crucial theoretical and practical implications in CSR literature.
Pulse train ignition with passively Q-switched laser spark plugs

Leaner burning and downsizing are two concepts pursued by engine developers to reduce fuel consumption and emissions. Both approaches lead to increasing challenges concerning ignition, as these concepts are typically associated with an increase in flow velocity and degree of turbulence as well as raised pressure at the moment of ignition. In this context, the use of miniaturized passively Q-switched laser spark plugs with pulse train ignition is considered as a promising alternative to conventional spark plugs. However, the application of these passively Q-switched laser spark plugs inevitably leads to the question of optimum pulse train parameters. For a better understanding, this study deals with improved flame formation by passively Q-switched laser pulse train ignition under engine-like conditions. The entire ignition process is investigated with a special focus on interactions of consecutive pulses. Therefore, three methods are combined: energy transfer measurements from laser pulse to plasma with high temporal and spatial resolution show the breakdown process depending on different pressures and fluid mixtures. The temperature decrease in the induced plasma is analyzed with measurement strategies for temporal high-resolved plasma spectroscopy especially adapted to passively Q-switched lasers. In combination with high-speed schlieren measurements, the changing local ignition conditions during pulse train ignition are demonstrated. The experiments show how consecutive pulses interact and contribute to the ignition in case of a gas flow. The used prototypes of laser spark plugs are provided by Robert Bosch GmbH.
Preparation and Characterization of Bio-Nanocomposites Film of Chitosan and Montmorillonite Incorporated with Ginger Essential Oil and Its Application in Chilled Beef Preservation

In this study, bio-nanocomposite films containing different proportions of ginger essential oil (GEO), chitosan (Ch), and montmorillonite (MMT) were prepared and characterized, and the antibacterial effect of bio-nanocomposite films on chilled beef was evaluated. Fourier transform infrared analysis showed a series of intense interactions among the components of the bio-nanocomposite films. The infiltration of GEO increased the thickness of the film, reduced the tensile strength of the film, and increased the percentage of breaking elongation and the water vapor permeability. The migration of phenols in the films began to increase exponentially and reached equilibrium at about 48 h. The bio-nanocomposite films (Ch +0.5% GEO group, and Ch + MMT + 0.5% GEO group) effectively delayed the rise of pH, hue angle, and moisture values of chilled beef with time and slowed down the lipid oxidation and the growth of surface microorganisms on chilled beef. Altogether, the prepared biological nanocomposites can be used as promising materials to replace commercial and non-degradable plastic films.
Second-by-second infant and mother emotion regulation and coregulation processes

Abstract Context-appropriate infant physiological functioning may support emotion regulation and mother–infant emotion coregulation. Among a sample of 210 low-income Mexican-origin mothers and their 24-week-old infants, dynamic structural equation modeling (DSEM) was used to examine whether within-infant vagal functioning accounted for between-dyad differences in within-dyad second-by-second emotion regulation and coregulation during free play. Vagal functioning was captured by within-infant mean and variability (standard deviation) of respiratory sinus arrhythmia (RSA) during free play. Infant emotion regulation was quantified as emotional equilibria (within-person mean), volatility (within-person deviation from equilibrium), carryover (how quickly equilibrium is restored following a disturbance), and feedback loops (the extent to which prior affect dampens or amplifies subsequent affect) in positive and negative affect during free play; coregulation was quantified as the influence of one partner's affect on the other's subsequent affect. Among infants with lower RSA variability, positive affect fluctuated around a higher equilibrium, and negative affect fluctuated around a lower equilibrium; these infants exhibited feedback loops where their positive affect dampened their subsequent negative affect. As expected, infants with higher mean RSA exhibited more volatility in positive affect, feedback loops between their positive and negative affect, and stronger mother-driven emotion coregulation. The results highlight differences in simultaneously occurring biological and emotion regulation.
Randomized study of the effects of vitamin D and/or magnesium supplementation on mood, serum levels of BDNF, inflammation, and SIRT1 in obese women with mild to moderate depressive symptoms

ABSTRACT Objectives This study aimed to evaluate the effects of vitamin D and/or magnesium supplementation on mood, serum levels of BDNF, inflammation, and SIRT1 in obese women with mild to moderate depressive symptoms. Methods In this trial, the 108 obese women with mild to moderate depressive symptoms were randomly allocated into 4 groups: (1) co- supplementation group (n = 27): receiving a 50000 IU vitamin D soft gel weekly + a 250- mg magnesium tablet daily; (2) vitamin D group (n = 27): receiving a 50000 IU vitamin D soft gel weekly + a magnesium placebo daily; (3) magnesium group (n = 27): receiving a vitamin D placebo weekly + a 250- mg magnesium tablet daily; (4) control group (n = 27): receiving a vitamin D placebo weekly + a magnesium placebo daily, for 8 weeks. Before and after the intervention, anthropometric indices, depressive symptoms, serum levels of BDNF, 25(OH)-D, inflammation, and SIRT1, were measured. Results At the end of the study, ANCOVA demonstrated significant differences between the 4 groups in 25(OH)-D, magnesium, TNF-α, IL-6, and BDNF levels. But, we found no significant differences in terms of hs-CRP and SIRT1 levels. A significant reduction in depression score was observed in 3 intervention groups and also in control group. No significant differences in BDI-II score were shown among the 4 groups at the end of the intervention. Conclusion Vitamin D plus magnesium supplementation in obese women with mild to moderate depressive symptoms has beneficial influences on mood, serum levels of BDNF, inflammation, and SIRT1.
Predictors of Changes in Cognitive Function in Older Korean Adults: The 2006–2018 Korean Longitudinal Study of Aging

Cognitive decline with normal aging varies widely among individuals. This study aimed to investigate predictors of longitudinal changes in cognitive function in community-dwelling Korean adults aged 65 years and older. Data from 727 older adults who participated in the Korean Longitudinal Study of Aging (KLoSA) survey from 2006 (baseline) until 2018 (seventh wave) were used. Cognitive performance was assessed with the Korean Mini-Mental State Examination. The participants were retrospectively classified into normal cognition, mild cognitive impairment, and moderate/severe cognitive impairment. Education, income, religion, living area, alcohol intake, smoking, physical activity, handgrip strength, functional dependency, depression, comorbidity, medications, fall experience, and unintentional weight loss were included as covariates. A linear mixed regression analysis showed that a steeper decline in cognitive function over time was significantly associated with parameters of poor socio-economic status, health conditions, and unhealthy behaviors. Individuals with mild cognitive impairment or moderate/severe cognitive impairment were likely to have steeper cognitive declines compared with individuals with normal cognition. The current findings of the study showed that age-related cognitive decline was multifactorial in older Korean adults.
Risk Factors of 30-Day All-Cause Mortality in Patients with Carbapenem-Resistant Klebsiella pneumoniae Bloodstream Infection

An optimal antimicrobial regimen for the treatment of patients with carbapenem-resistant Klebsiella pneumoniae (CRKP) bloodstream infection (BSI) is currently unavailable. This study aimed to identify the appropriate antibiotics and the risk factors of all-cause mortality for CRKP BSI patients. This retrospective cohort study included the hospitalized patients with CRKP BSI. Primary outcome was 30-day all-cause mortality. Cox regression analysis was used to evaluate the risk factors of 30-day mortality. A total of 89 patients were included with a 30-day mortality of 52.1%. A total of 52 (58.4%) patients were treated with appropriate antimicrobial regimens and 58 (65.2%) isolates carried blaKPC-2 genes. Microbiologic eradication within 7 days (adjusted hazard ratio [HR] = 0.09, p < 0.001), platelet count (per 1 × 104/mm3, adjusted HR = 0.95, p = 0.002), and Pitt bacteremia scores (adjusted HR = 1.40, p < 0.001) were independently associated with 30-day all-cause mortality. No effective antimicrobial regimens were identified. In conclusion, risk factors of 30-day mortality in patients with CRKP BSI included microbiologic eradication > 7 days, lower platelet count, and a higher Pitt bacteremia score. These findings render a new insight into the clinical landscape of CRKP BSI.
Snapshots of a Non-Canonical RdRP in Action

RNA viruses typically encode their own RNA-dependent RNA polymerase (RdRP) to ensure genome replication and transcription. The closed “right hand” architecture of RdRPs encircles seven conserved structural motifs (A to G) that regulate the polymerization activity. The four palm motifs, arranged in the sequential order A to D, are common to all known template dependent polynucleotide polymerases, with motifs A and C containing the catalytic aspartic acid residues. Exceptions to this design have been reported in members of the Permutotetraviridae and Birnaviridae families of positive single stranded (+ss) and double-stranded (ds) RNA viruses, respectively. In these enzymes, motif C is located upstream of motif A, displaying a permuted C–A–B–D connectivity. Here we study the details of the replication elongation process in the non-canonical RdRP of the Thosea asigna virus (TaV), an insect virus from the Permutatetraviridae family. We report the X-ray structures of three replicative complexes of the TaV polymerase obtained with an RNA template-primer in the absence and in the presence of incoming rNTPs. The structures captured different replication events and allowed to define the critical interactions involved in: (i) the positioning of the acceptor base of the template strand, (ii) the positioning of the 3’-OH group of the primer nucleotide during RNA replication and (iii) the recognition and positioning of the incoming nucleotide. Structural comparisons unveiled a closure of the active site on the RNA template-primer binding, before rNTP entry. This conformational rearrangement that also includes the repositioning of the motif A aspartate for the catalytic reaction to take place is maintained on rNTP and metal ion binding and after nucleotide incorporation, before translocation.
Environment-Sensitive Fluorescence of 7-Nitrobenz-2-oxa-1,3-diazol-4-yl (NBD)-Labeled Ligands for Serotonin Receptors

Serotonin is a neurotransmitter that plays a crucial role in the regulation of several behavioral and cognitive functions by binding to a number of different serotonin receptors present on the cell surface. We report here the synthesis and characterization of several novel fluorescent analogs of serotonin in which the fluorescent NBD (7-nitrobenz-2-oxa-1,3-diazol-4-yl) group is covalently attached to serotonin. The fluorescent ligands compete with the serotonin1A receptor specific radiolabeled agonist for binding to the receptor. Interestingly, these fluorescent ligands display a high environmental sensitivity of their fluorescence. Importantly, the human serotonin1A receptor stably expressed in CHO-K1 cells could be specifically labeled with one of the fluorescent ligands with minimal nonspecific labeling. Interestingly, we show by spectral imaging that the NBD-labeled ligand exhibits a red edge excitation shift (REES) of 29 nm when bound to the receptor, implying that it is localized in a restricted microenvironment. Taken together, our results show that NBD-labeled serotonin analogs offer an attractive fluorescent approach for elucidating the molecular environment of the serotonin binding site in serotonin receptors. In view of the multiple roles played by the serotonergic systems in the central and peripheral nervous systems, these fluorescent ligands would be useful in future studies involving serotonin receptors.
Assessing the need for on-campus medication abortion at California Community Colleges

Abstract Objective: No studies have assessed the need for abortion access at California Community Colleges (CCCs), despite recent research and legislative attention toward on-campus medication abortion access at California’s public universities, and the fact that CCCs enroll more than twice the number of students per year as the public universities. Methods: A demographic analysis compares student populations at California’s public universities and CCCs using publicly-available data. Monthly demand for medication abortion among CCC students is estimated based on campus enrollment data, and age-, method- and state-adjusted abortion rates. Results: There is demographic similarity amongst these student populations with respect to gender and age makeup, supporting the use of methods created to estimate abortion demand in California public university students in this study. It is estimated that in total, CCC students seek 865 − 1,109 medication abortions each month. Conclusions: There is a clear need for medication abortion access at CCCs.
Distilling innovative US autism care programs that address widely perceived unmet patient and family needs

Current mainstream care for autistic individuals is fragmented, narrow, and poorly individualized. To better describe cutting-edge autism care, we searched for care programs in the United States that had been collaboratively designed with patients and families and that carry the highest potential to improve the quality of life of autistic individuals and their families. Using a modified Delphi method, we gathered input via conversations and surveys from 55 autistic adults, family members, practicing clinicians, and autism specialized researchers. As a result, 90 innovative autism care programs were nominated. We distilled these nominations to 15 programs across the United States by applying researcher-selected criteria, such as providing services actively and having data on program effectiveness. Then, we recruited 10 experts to rate the novelty, clinical benefits to individuals, clinical benefits to family caregivers, care costs for autistic individuals, societal costs, adaptability, and feasibility of the 15 programs. Common features of the 15 programs include care coordination and integration, care delivery, payment, and providing care in underserved clinical areas. Lay abstract Currently, the quality of care for autistic individuals is not good. Many care services for autistic individuals are not well coordinated, nor are they tailored. We wanted to find out a better model for autism care and believed that the autism community knows where these programs are. So, we had conversations with and surveyed 55 autistic adults, family members, clinicians, and researchers. They shared 90 innovative autism care programs that had been collaboratively designed with patients and families and that are likely to improve the quality of life of autistic individuals and their families. We then narrowed down the 90 nominated programs to 15 programs across the United States by applying researcher-selected criteria, such as providing services actively and having data on program effectiveness. We compiled a list of these innovative, quality autism care programs.