Miracle-dz/UniFAR-FTUs huggingface dataset:
Advances, challenges and opportunities of phylogenetic and social network analysis using COVID-19 data

Coronavirus disease 2019 (COVID-19) has attracted research interests from all fields. Phylogenetic and social network analyses based on connectivity between either COVID-19 patients or geographic regions and similarity between syndrome coronavirus 2 (SARS-CoV-2) sequences provide unique angles to answer public health and pharmaco-biological questions such as relationships between various SARS-CoV-2 mutants, the transmission pathways in a community and the effectiveness of prevention policies. This paper serves as a systematic review of current phylogenetic and social network analyses with applications in COVID-19 research. Challenges in current phylogenetic network analysis on SARS-CoV-2 such as unreliable inferences, sampling bias and batch effects are discussed as well as potential solutions. Social network analysis combined with epidemiology models helps to identify key transmission characteristics and measure the effectiveness of prevention and control strategies. Finally, future new directions of network analysis motivated by COVID-19 data are summarized.
Trunk and lower extremity long-axis rotation exercise improves forward single leg jump landing neuromuscular control

ABSTRACT Background Anterior cruciate ligament (ACL) injuries often involve sudden single leg loading with directional changes. Trunk and lower extremity (LE) load transfer and muscle power are directly coupled during these movements. The effect of trunk and LE long-axis rotation training on forward single leg drop jump landing and stabilization (FSLDJLS) was studied. Methods Using block randomization (gender), 36 (18 men, 18 women) subjects were assigned to experimental (nine, 20 min exercise sessions) and control groups with equal subject number. Ground reaction force (1000 Hz), kinematic (60 Hz) and LE EMG (1000 Hz) data were synchronously collected. Statistical analysis compared pre- and post-test neuromuscular control mean change differences (MCD), and hip flexion-LE peak EMG % maximum volitional isometric contraction (%MVIC) (expressed as decimal equivalents), mean change difference (MCD) relationships. Results The experimental group had greater landing knee flexion (3.5 ± 3.6° vs. −0.4 ± 3.3°, p = .002) MCD, greater dynamic LE stiffness after landing (0.09 ± 0.14 vs. −0.11 ± 0.14, p = .001) MCD, and increased gluteus maximus (GMAX) (0.20 ± 0.39%MVIC vs. −0.23 ± 0.46%MVIC, p = .006) and gluteus medius (GMED) EMG amplitude (0.22 ± 0.31 vs. −0.07 ± 0.36%MVIC, p = .018) MCD. This group also had decreased GMAX (−166.5 ± 403.6 ms vs. 89.3 ± 196 ms, p = .025), GMED (−75.9 ± 126.8 ms vs. 131.2 ± 207.1 ms, p = .002) and vastus lateralis (−109.1 ± 365 ms vs. 205.5 vs. 510 ms, p = .04) activation duration MCD. More experimental group subjects had increased landing knee flexion MCD (15/18 vs. 8/18, p = .015), increased dynamic LE stiffness MCD (15/18 vs. 2/18, p < .0001) and increased GMAX (15/18 vs. 7/18, p = .006) and GMED (17/18 vs. 10/18, p = .007) EMG amplitude MCD, and reduced GMAX (12/18 vs. 6/18, p = .046), GMED (11/18 vs. 5/18, p = .044), rectus femoris (12/18 vs. 6/18, p = .046), and vastus lateralis (13/18 vs. 7/18, p = .044) EMG activation duration MCD. Only the experimental group displayed significant relationships between landing and peak hip flexion and peak LE EMG amplitude MCD. Conclusion Increased dynamic LE stiffness, increased hip muscle EMG amplitude and decreased hip and knee muscle activation duration MCD in the experimental group suggests improved LE neuromuscular control.
Similar inflammatory response and conduit artery vascular function between sexes following induced inflammation

What is the central question of this study? Are there sex differences in vascular function following induced inflammation when oestrogen is typically similar between sexes? What is the main finding and its importance? The present study suggests no sex differences in conduit artery vascular responses to acutely induced inflammation during the low‐oestrogen phase of the menstrual cycle in premenopausal women. However, women exhibit lower microvascular function than men. Overall, the results underpin the role of oestrogen in previously observed sex differences and the importance of reporting the phase in the hormonal cycle when women are studied.
O papel do extrato de Rhodiola rosea e Chlorella na modulação de cicatrizes queloideanas = The role of Rhodiola rosea extract and Chlorella in the modulation of keloid scars

Keloid scars are defined as the end product of a chronic inflammatory process that culminates in tissue overgrowth and hardening as a result of excessive collagen deposition. Studies in the literature show that cytokines and growth factors increase the metabolic activity of fibroblasts, thus activating intracellular signaling pathways leading to exacerbated production of extracellular matrix components and consequent formation of these keloid scars. In spite of the large number of treatments available, the results have been inconsistent and unsuccessful. In this context, the search for alternative therapies has aroused the interest of the pharmaceutical and cosmetic industries. In this study, we evaluate the in vitro and ex vivo modulating ability of the alga Chlorella in the intracellular mechanisms of the inflammatory response in the skin, aiming to prevent or minimize the clinical manifestations of keloids scars. Previous results from our laboratory have demonstrated the adaptogenic ability of this alga, which encouraged such investigation. Our results showed that Chlorella modulates immunological and fibroproliferative parameters involved in keloid formation. This activity demonstrated by the alga might be considered an important tool in the attempt to restore the normal cellular metabolic activity, thus contributing to the reduction in the appearance of keloids.
Drought-related cholera outbreaks in Africa and the implications for climate change: a narrative review

ABSTRACT Africa has historically seen several periods of prolonged and extreme droughts across the continent, causing food insecurity, exacerbating social inequity and frequent mortality. A known consequence of droughts and their associated risk factors are infectious disease outbreaks, which are worsened by malnutrition, poor access to water, sanitation and hygiene and population displacement. Cholera is a potential causative agent of such outbreaks. Africa has the highest global cholera burden, several drought-prone regions and high levels of inequity. Despite this, research on cholera and drought in Africa is lacking. Here, we review available research on drought-related cholera outbreaks in Africa and identify a variety of potential mechanisms through which these outbreaks occurred, including poor access to water, marginalization of refugees and nomadic populations, expansion of informal urban settlements and demographic risks. Future climate change may alter precipitation, temperature and drought patterns, resulting in more extremes, although these changes are likely to be spatially heterogeneous. Despite high uncertainty in future drought projections, increases in drought frequency and/or durations have the potential to alter these related outbreaks into the future, potentially increasing cholera burden in the absence of countermeasures (e.g. improved sanitation infrastructure). To enable effective planning for a potentially more drought-prone Africa, inequity must be addressed, research on the health implications of drought should be enhanced, and better drought diplomacy is required to improve drought resilience under climate change.
SMYD1 alleviates septic myocardial injury by inhibiting endoplasmic reticulum stress.

Sepsis-induced cardiomyopathy (SIC) is a major complication of sepsis. SET and MYND domain containing 1 (SMYD1) has central importance in heart development, and its role in SIC has not been identified. Herein, we found that the expression of SMYD1 was downregulated in myocardial tissues of SIC patients (from GEO database: GSE79962) and lipopolysaccharide (LPS)-induced SIC rats, and LPS-induced H9c2 cardiomyocytes. We used LPS-stimulated H9c2 cells that mimic sepsis in vitro to explore the function of SMYD1 in SIC. MTT assay, LDH and CK-MB release assay, flow cytometry, and ELISA assay showed that SMYD1 overexpression enhanced cell viability, alleviated cell injury, impeded apoptosis, and reduced the level of pro-inflammatory factors and NF-κB activation under the condition of LPS stimulation. Moreover, SMYD1 exerted protective effect on H9c2 cells stimulated with LPS through relieving endoplasmic reticulum (ER) stress. In conclusion, overexpression of SMYD1 alleviates cardiac injury through relieving ER stress during sepsis.
Unpacking characteristics of spirituality through the lens of persons of colour living with serious illness: The need for nurse-based education to increase understanding of the spiritual dimension in healthcare.

AIMS AND OBJECTIVES To examine the characteristics of spirituality as expressed by persons of colour living with serious illness. BACKGROUND Spiritual, Religious and Existential Care, as specified in the National Consensus Project (NCP) Guidelines, is a core domain of palliative nursing. DESIGN OF THE STUDY A constructionist approach to narrative analysis was used for this study and reported in accordance with the COREQ guideline. METHODS In-depth narrative interviews were conducted with 20 participants. These participants included persons of colour living with serious illness who were admitted to an acute-care hospital. Through a deductive coding approach, a codebook was created based on a broad definition of spirituality including: religion, self, family, community, nature and art/music/literature. RESULTS The major themes expressed were religion, self and family. Subthemes of religion included increased faith, support of the church community and God's intervention in patients' lives. Subthemes of self included increased self-worth, self-awareness of one's place in the world and individualised transition to new meaning in life. Subthemes of family included family adding meaning and purpose to their lives, family as an important source of strength and support, wanting to regain their health to go back to caring for their families, and believing that their illness had brought their family closer together. CONCLUSION The thematic analysis revealed a broader existential aspect of what brought value, meaning and purpose into their lives, despite their progressive physical illness. More research is needed to understand spiritual, religious or existential needs of persons of colour living with serious illness and how nurses can best support these needs. By understanding the components of spirituality, nurses can learn to recognise the signs of spiritual distress. This awareness also helps to know when a spiritual specialist is needed-either the patient's own spiritual guide(s) or the hospital chaplain. Nurses can also use spiritual assessment tools when performing a general assessment on the patient. RELEVANCE TO CLINICAL PRACTICE By understanding the components of spirituality, nurses can learn to recognise the signs of spiritual distress. This awareness also helps to know when a spiritual specialist is needed-either the patient's own spiritual guide(s) or the hospital chaplain. Nurses can also use spiritual assessment tools when performing a general assessment on the patient.
Analyzing the scaffold diversity of cyclin‐dependent kinase inhibitors and revisiting the clinical and preclinical pipeline

Kinases have gained an important place in the list of vital therapeutic targets because of their overwhelming clinical success in the last two decades. Among various clinically validated kinases, the cyclin‐dependent kinases (CDK) are one of the extensively studied drug targets for clinical development. Food and Drug Administration has approved three CDK inhibitors for therapeutic use, and at least 27 inhibitors are under active clinical development. In the last decade, research and development in this area took a rapid pace, and thus the analysis of scaffold diversity is essential for future drug design. Available reviews lack the systematic study and discussion on the scaffold diversity of CDK inhibitors. Herein we have reviewed and critically analyzed the chemical diversity present in the preclinical and clinical pipeline of CDK inhibitors. Our analysis has shown that although several scaffolds represent CDK inhibitors, only the amino‐pyrimidine is a well‐represented scaffold. The three‐nitrogen framework of amino‐pyrimidine is a fundamental hinge‐binding unit. Further, we have discussed the selectivity aspects among CDKs, the clinical trial dose‐limiting toxicities, and highlighted the most advanced clinical candidates. We also discuss the changing paradigm towards selective inhibitors and an overview of ATP‐binding pockets of all druggable CDKs. We carefully analyzed the clinical pipeline to unravel the candidates that are currently under active clinical development. In addition to the plenty of dual CDK4/6 inhibitors, there are many selective CDK7, CDK9, and CDK8/19 inhibitors in the clinical pipeline.
Synthesis of novel pyrroles and fused pyrroles as antifungal and antibacterial agents

Abstract Pyrroles and its fused forms possess antimicrobial activities, they can easily interact with biomolecules of living systems. A series of substituted pyrroles, and its fused pyrimidines and triazines forms have been synthesised, all newly synthesised compound structures were confirmed by spectroscopic analysis. Generally, the compounds inhibited growth of some important human pathogens, the best effect was given by: 2a, 3c, 4d on Gram-positive bacteria and was higher on yeast (C. albicans), by 5c on Gram-negative bacteria and by 5a then 3c on filamentous fungi (A. fumigatus and F. oxysporum). Such results present good antibacterial and antifungal potential candidates to help overcome the global problem of antibiotic resistance and opportunistic infections outbreak. Compound 3c gave the best anti-phytopathogenic effect at a 50-fold lower concentration than Kocide 2000, introducing a safe commercial candidate for agricultural use. The effect of the compounds on DNA was monitored to detect the mode of action.
Long-Known Music Exposure Effects on Brain Imaging and Cognition in Early-Stage Cognitive Decline: A Pilot Study.

BACKGROUND Repeated exposure to long-known music has been shown to have a beneficial effect on cognitive performance in patients with AD. However, the brain mechanisms underlying improvement in cognitive performance are not yet clear. OBJECTIVE In this pilot study we propose to examine the effect of repeated long-known music exposure on imaging indices and corresponding changes in cognitive function in patients with early-stage cognitive decline. METHODS Participants with early-stage cognitive decline were assigned to three weeks of daily long-known music listening, lasting one hour in duration. A cognitive battery was administered, and brain activity was measured before and after intervention. Paired-measures tests evaluated the longitudinal changes in brain structure, function, and cognition associated with the intervention. RESULTS Fourteen participants completed the music-based intervention, including 6 musicians and 8 non-musicians. Post-baseline there was a reduction in brain activity in key nodes of a music-related network, including the bilateral basal ganglia and right inferior frontal gyrus, and declines in fronto-temporal functional connectivity and radial diffusivity of dorsal white matter. Musician status also significantly modified longitudinal changes in functional and structural brain measures. There was also a significant improvement in the memory subdomain of the Montreal Cognitive Assessment. CONCLUSION These preliminary results suggest that neuroplastic mechanisms may mediate improvements in cognitive functioning associated with exposure to long-known music listening and that these mechanisms may be different in musicians compared to non-musicians.
Bizarreness and Typicality Effects of Color on Object Recognition Memory

The bizarreness effect on object recognition is a strong phenomenon, but its influence has been inconsistent for bizarre object color. In this study, we manipulated three factors in separate experiments to determine whether a color bizarreness effect on object recognition memory would occur and, if not, why. Participants first saw (i.e., learned) object pictures that were either bizarrely or typically colored; they then completed a recognition memory test. In three experiments, we then manipulated (a) degree of color bizarreness (Experiment 1), (b) the orientation task (Experiment 2), and (c) additional demands for object identification (Experiment 3). In Experiment 1, we provided 49 undergraduate participants with object pictures whose colors were typical, moderately atypical, or bizarre and found no color bizarreness effect on recognition memory even for extremely bizarre colors. In Experiment 2, we manipulated the orientation task in that 28 young adult participants expressed their preferences for the pictures on a three-point scale while another 28 participants judged how natural the pictures were. Each orientation task group better recognized typically-colored rather than bizarrely-colored objects (typicality effect). In Experiment 3, we asked 27 young adults to identify the objects during the learning phase to ensure that they paid attention to the objects’ bizarre colors; recognition memory was then unaffected by either color bizarreness or typicality. Thus, despite a general bizarreness effect in recognition memory, bizarre colors are less likely to influence object recognition memory.
Degradation of antimicrobial resistance genes within stockpiled beef cattle feedlot manure

Abstract Degradation of antimicrobial resistance genes (ARG) in manure from beef cattle administered (kg−1 feed) 44 mg of chlortetracycline (CTC), 44 mg of chlortetracycline plus sulfamethazine (CTCSMZ), 11 mg of tylosin (TYL), or no antimicrobials (Control) was examined. Manure was stockpiled and quantitative PCR (qPCR) was used to assess tetracycline [tet(C), (L), (M), (W)], erythromycin [erm(A), (B), (F), (X)], and sulfamethazine [sul(1), (2)] ARG and 16S rDNA. After 102 d, copies of all ARG decreased by 0.3 to 1.5 log10 copies (g dry matter)−1. Temperature in the interior of piles averaged ≥ 55 °C for 10 d, except for CTCSMZ, but did not reach 55 °C at pile exteriors. Compared to Control, CTCSMZ increased (P < 0.05) tet(C), tet(M), tet(W), sul(1), and sul(2) in stockpiled manure. Copies of 16S rDNA remained higher (P < 0.05) in CTCSMZ than Control for the first 26 d. Levels of most ARG did not differ between the interior and exterior of stockpiles. Our results suggest that stockpiled manure would still introduce ARG to land upon manure application, but at levels lower than if manure was applied fresh.
Comparative effects of on‐pump versus off‐pump coronary artery bypass grafting surgery on serum cytokine and chemokine levels

Coronary artery bypass grafting (CABG) surgery with two methods (on‐pump or off‐pump) can be used to rescue individuals with severe coronary artery disease (CAD). Each method might cause an inflammatory response, which can lead to some complications. The aim of this study was to compare the changes in serum concentrations of IFN‐γ, tumor necrosis factor (TNF)‐α, interleukin (IL)‐1α, IL‐1β, IL‐2, IL‐4, IL‐6, IL‐8, IL‐10, VEGF, MCP‐1, and epidermal growth factor between the two CABG surgery methods. Forty‐eight patients (22 = on‐pump, 26 = off‐pump) who underwent on‐pump or off‐pump CABG surgery were enrolled in this study. Serum cytokines levels were measured in two blood samples, the first sample was taken from each patient in the morning of the day of surgery after a 12‐hr fasting and the second sample on the first postoperative day at 24‐hr after surgery. In baseline, comparisons between the two groups of on‐pump/off‐pump surgery did not show any significant difference in demographic data, anthropometric parameters, lipid profile indices, and high‐sensitivity C‐reactive protein levels (p > .05). There was a significant difference between the serum levels of IL‐4, IL‐6, IL‐10, vascular endothelial growth factor (VEGF), IFN‐γ, and MCP‐1 in patients with on‐pump surgery and a significant increase in serum IL‐6 (p < .001), IL8 (p < .05), VEGF (p < .001), and IFN‐γ (p < .01) levels in patients with off‐pump surgery in post‐operation stage compared to pre‐operation. Cardiopulmonary pump in patients under CABG surgery can activate systemic inflammation and the changes of serum cytokines levels in off‐pump CABG were lower compared with on‐pump CABG.
Constrained Choice: Children's and Adults' Attribution of Choice to a Humanoid Robot

Young children, like adults, understand that human agents can flexibly choose different actions in different contexts, and they evaluate these agents based on such choices. However, little is known about children's tendencies to attribute the capacity to choose to robots, despite increased contact with robotic agents. In this paper, we compare 5- to 7-year-old children's and adults' attributions of free choice to a robot and to a human child by using a series of tasks measuring agency attribution, action prediction, and choice attribution. In morally neutral scenarios, children ascribed similar levels of free choice to the robot and the human, while adults were more likely to ascribe free choice to the human. For morally relevant scenarios, however, both age groups considered the robot's actions to be more constrained than the human's actions. These findings demonstrate that children and adults hold a nuanced understanding of free choice that is sensitive to both the agent type and constraints within a given scenario.
Cross-national validation of the social media disorder scale: findings from adolescents from 44 countries

Background and aims There is currently no cross-national validation of a scale that measures problematic social media use (SMU). The present study investigated and compared the psychometric properties of the social media disorder (SMD) scale among young adolescents from different countries. Design Validation study. Setting and participants Data came from 222 532 adolescents from 44 countries participating in the health behaviour in school-aged children (HBSC) survey (2017/2018). The HBSC survey was conducted in the European region and Canada. Participants were on average aged 13.54 years (standard deviation = 1.63) and 51.24% were girls. Measurement Problematic SMU was measured using the nine-item SMD scale with dichotomous response options. Findings Confirmatory factor analyses (CFA) showed good model fit for a one-factor model across all countries (minimum comparative fit index (CFI) and Tucker–Lewis index (TLI) = 0.963 and 0.951, maximum root mean square error of approximation (RMSEA) and standardized root mean square residual (SRMR) = 0.057 and 0.060), confirming structural validity. The internal consistency of the items was adequate in all countries (minimum alpha = 0.840), indicating that the scale provides reliable scores. Multi-group CFA showed that the factor structure was measurement invariant across countries (ΔCFI = -0.010, ΔRMSEA = 0.003), suggesting that adolescents’ level of problematic SMU can be reliably compared cross-nationally. In all countries, gender and socio-economic invariance was established, and age invariance was found in 43 of 44 countries. In line with prior research, in almost all countries, problematic SMU related to poorer mental wellbeing (range βSTDY = 0.193–0.924, P < 0.05) and higher intensity of online communication (range βSTDY = 0.163–0.635, P < 0.05), confirming appropriate criterion validity. Conclusions The social media disorder scale appears to be suitable for measuring and comparing problematic social media use among young adolescents across many national contexts.