Miracle-dz/UniFAR-FTUs huggingface dataset:
Azolla filiculoides L. as a source of metal-tolerant microorganisms

The metal hyperaccumulator Azolla filiculoides is accompanied by a microbiome potentially supporting plant during exposition to heavy metals. We hypothesized that the microbiome exposition to selected heavy metals will reveal metal tolerant strains. We used Next Generation Sequencing technique to identify possible metal tolerant strains isolated from the metal-treated plant (Pb, Cd, Cr(VI), Ni, Au, Ag). The main dominants were Cyanobacteria and Proteobacteria constituting together more than 97% of all reads. Metal treatment led to changes in the composition of the microbiome and showed significantly higher richness in the Pb-, Cd- and Cr-treated plant in comparison with other (95–105 versus 36–44). In these treatments the share of subdominant Actinobacteria (0.4–0.8%), Firmicutes (0.5–0.9%) and Bacteroidetes (0.2–0.9%) were higher than in non-treated plant (respectively: 0.02, 0.2 and 0.001%) and Ni-, Au- and Ag-treatments (respectively: <0.4%, <0.2% and up to 0.2%). The exception was Au-treatment displaying the abundance 1.86% of Bacteroidetes. In addition, possible metal tolerant genera, namely: Acinetobacter, Asticcacaulis, Anabaena, Bacillus, Brevundimonas, Burkholderia, Dyella, Methyloversatilis, Rhizobium and Staphylococcus, which form the core microbiome, were recognized by combining their abundance in all samples with literature data. Additionally, the presence of known metal tolerant genera was confirmed: Mucilaginibacter, Pseudomonas, Mycobacterium, Corynebacterium, Stenotrophomonas, Clostridium, Micrococcus, Achromobacter, Geobacter, Flavobacterium, Arthrobacter and Delftia. We have evidenced that A. filiculoides possess a microbiome whose representatives belong to metal-resistant species which makes the fern the source of biotechnologically useful microorganisms for remediation processes.
Elements of assisted bodily care: Ethical aspects

Background: Many frail older persons who die in Swedish nursing homes need assisted bodily care. They must surrender their bodies to the authority of assistant nurses, which may affect their autonomy and dignity of identity. While assistant nurses claim to support older persons’ wishes, older persons claim they have to adapt to assistant nurses' routines. The provider–receiver incongruence revealed here warrants investigation. Aim: To describe the elements of assisted bodily care, as performed in a nursing home. Research design: Data were collected through thirty-nine observations of assisted bodily care, analyzed with qualitative content analysis. Participants and research context: Seventeen older persons and twenty-two assistant nurses from a Swedish nursing home. Ethical considerations: The research was conducted in line with the Declaration of Helsinki, further approved by the regional ethics committee. Findings: Findings show that assisted bodily care consists of assistant nurses’ practical work, performed at a high tempo. Assistant nurses still attempt to adapt this work to the older persons’ wishes for self-determination, taking into account their day-to-day state of health. In spite of time pressure and occasional interruptions, there is room for consideration and affection in assisted bodily care. Discussion: Assistant nurses try to promote older persons’ dignity of identity, but sometimes fail, possibly due to lack of time. They nevertheless seem to know the older persons well enough to adapt the assisted bodily care according to their preferences and to support self-determination. This indicates that openness to older persons’ lifeworlds may be more important than the amount of time available. Conclusion: Nursing home contexts might benefit from adopting a person-centered palliative care perspective, highlighting the value of relationships and shared decision-making. If so, older persons and assisted nurses could agree on practices and goals in assisted bodily care beforehand. Such routines may be time-saving and beneficial to all.
Relationship between Cognetia sphagnetorum Vejd. (Oligochaeta, Enchytraeidae) and soil microorganisms : a microcosm experiment

Changes in densities of microorganisms were analysed in Cognetia sphagnetorum Vejd. cultures at normal and low numbers of microorganisms. Different abundance of microorganisms was achieved by using captan and oxytetracycline. During 14 weeks, the following variables were measured: total numbers of bacteria and fungi by plate method, the biomass of microorganisms by PLFA method, content of ions, and activity of acid and alkaline phosphatase and urease. Numbers of enchytraeids increased with numbers of fungi. The presence of animals reduced the activity of soil enzymes and the content of Cl, SO4, Na, Ca, and Mg ions in soil leacheates. An increase in the content of N-NO3 and N-NH4 was not significant.
Endophytic fungi associated with high-altitude Juniperus trees and their antimicrobial activities

Fungal endophytes were isolated from twigs of Juniperus procera (Cupressaceae) collected from Taif region (Saudi Arabia). Twenty-six different taxa were recovered. The overall foliar colonization rate was 36%. A total of 144 isolates were obtained and identified into six distinct operational taxonomic units based on the sequencing of the internal transcribed spacer regions of the rRNA gene. The most prevalent fungi were Aspergillus fumigatus, Penicillium oxalicum, Preussia sp. , Peyronellaea eucalyptica, Peyronellaea sancta and Alternaria tenuissima. A total of 144 isolates were tested for antibacterial and antifungal activities against Staphylococcus aureus, Klebsiella pneumoniae, Candida albicans and Fusarium solani in which 52 isolates showed antimicrobial activity against at least one of the tested microbes. Aspergillus fumigatus (7 isolates), Hypocrea lutea (4), Penicillium oxalicum (10) and Preussia sp. (5) presented the strongest antimicrobial activity. This study confirmed the variation of different isolates of the same species in terms of antibacterial activity. Also, it indicated that the endophytic fungi of Juniperus procera plants should be another potential source of bioactive antimicrobial agents.
Microbiota and Human Reproduction: The Case of Female Infertility

During the last decade, the availability of next-generation sequencing-based approaches has revealed the presence of microbial communities in almost all the human body, including the reproductive tract. As for other body sites, this resident microbiota has been involved in the maintenance of a healthy status. As a consequence, alterations due to internal or external factors may lead to microbial dysbiosis and to the development of pathologies. Female reproductive microbiota has also been suggested to affect infertility, and it may play a key role in the success of assisted reproductive technologies, such as embryo implantation and pregnancy care. While the vaginal microbiota is well described, the uterine microbiota is underexplored. This could be due to technical issues, as the uterus is a low biomass environment. Here, we review the state of the art regarding the role of the female reproductive system microbiota in women’s health and human reproduction, highlighting its contribution to infertility.
Normal and Maladaptive Personality Traits as Predictors of Motives for Social Media Use and Its Effects on Well-Being

This study aimed to identify the motives for social media sites use in the general population and determine what personality traits (normal and maladaptive) predict different motives for social media sites use. Another objective was to analyze which motives for SMSs use are related to well-being. The sample consisted of 420 subjects (211 men, 209 women), mean age 40.29 years (SD = 14.93). Data were gathered using the Big Five Inventory, the Personality Inventory for DSM-5-Brief Form -Adult, the Mental Health Continuum-Short Form, and a scale designed ad hoc to evaluate the motives for social media sites use. The results showed that the most frequent motives were Personal relationship maintenance/Search for information, Pastime/Exhibitionism, and Search for companionship. In addition, it was found that normal and, especially, maladaptive personality traits increased the explained variance for the three motives for social media sites use, beyond age and gender. Predictors of relationship initiation and pastime/exhibitionism motives were related to more negative features (e.g., antagonism and disinhibition) than predictors of personal relationship maintenance/search for information. Finally, personal relationship maintenance/search for information was positively related to all the components of well-being, while the other motives for social media sites use were negatively associated with well-being.
Genetic diversity of Bradyrhizobium japonicum field population revealed by RAPD fingerprinting

RAPD fingerprinting was used for strain identification and the assessment of genetic diversity within a field population of Bradyrhizobium japonicum. Total genomic DNAs from 13 field isolates and two inoculant strains were amplified using six different 10‐mer primers. Different and informative band patterns were obtained for all strains analysed. Cluster analysis unexpectedly revealed that none of the field isolates was identical to inoculant strains which were regularly used for soybean inoculation. Among field isolates two highly divergent groups were determined. The results indicate that RAPD is a very discriminative and efficient method for differentiating and studying genetic diversity of B. japonicum strains.
Liraglutide Ameliorates Lipotoxicity-Induced Oxidative Stress by Activating the NRF2 Pathway in HepG2 Cells

Abstract Although glucagon-like peptide-1 (GLP-1) analogue has been reported to suppress oxidative stress in non-alcoholic fatty liver disease (NAFLD), an effective therapeutic agent for NAFLD is currently unavailable. Therefore, in this study, we aimed to investigate the protective effects of the GLP-1 analogue liraglutide against lipotoxicity-induced oxidative stress in HepG2 cells and to elucidate the underlying mechanisms. HepG2 cells were cultured for 48 hours and treated with a free fatty acid (FFA) mixture: FFA mixture and liraglutide or FFA mixture, liraglutide, and exendin (9–39). Lipid accumulation was examined by oil red O staining. Oxidative stress was assessed by measuring the levels of intracellular reactive oxygen species using 2′,7′-dichlorofluorescein diacetate and thiobarbituric acid-reactive substances, whereas antioxidant capacity was assessed by measuring the activity of superoxide dismutase and catalase. Expression of the nuclear factor erythroid-2-related factor 2 (NRF2) gene and the genes encoding antioxidant enzymes was analyzed using quantitative RT-PCR. Cellular and nuclear NRF2 expression levels were assessed using immunofluorescence cell staining and western blotting. Liraglutide treatment reduced high fat-induced lipid formation and the levels of oxidative stress markers and increased antioxidant enzyme activity in HepG2 cells. Liraglutide treatment increased the mRNA expression of NRF2 target genes, induced NRF2 nuclear translocation, and increased nuclear NRF2 levels without altering NRF2 mRNA expression. Collectively, these results indicate that liraglutide exhibits a protective effect against lipotoxicity-induced oxidative stress, possibly via modulation of NRF2 and expression of antioxidant enzymes in liver cells.
Timing of entry of Streptococcus uberis into the mammary gland of the dairy cow

Abstract Streptococcus uberis do not colonise the teat canal and appear to invade the mammary gland of the dairy cow by direct entry though the canal. When they enter the mammary gland, and the early resulting processes, are unclear. Experimental infusions of the lactating mammary gland have been made to determine outcomes of infection, mastitis and disease. Infusion of 500 cfu bacteria was made immediately after milking (8 and 16 h intermilking interval) and 1, 4 or 12 h prior to milking. A mastitis resulted from all infusions, probably in response to the skim milk carrier. Infusions post milking resulted in clinical mastitis in more than half of the quarters, whereas infusion 1 h premilking created no clinical mastitis. Infusion 4 or 12 h pre milking resulted in the most severe reactions, with all quarters developing moderate to severe clinical mastitis. This was more rapid with the 4 h pre milking group. The results demonstrate that the initial inflammatory response caused by an invasion of the mammary gland is not necessarily protective against establishment of a pathogen, and that especially the response to invasion in the intermilking interval is often insufficient to prevent infection and/or disease.
Can the Implicit Association Test Serve as a Valid Measure of Automatic Cognition? A Response to Schimmack (2021)

Much of human thought, feeling, and behavior unfolds automatically. Indirect measures of cognition capture such processes by observing responding under corresponding conditions (e.g., lack of intention or control). The Implicit Association Test (IAT) is one such measure. The IAT indexes the strength of association between categories such as “planes” and “trains” and attributes such as “fast” and “slow” by comparing response latencies across two sorting tasks (planes–fast/trains–slow vs. trains–fast/planes–slow). Relying on a reanalysis of multitrait–multimethod (MTMM) studies, Schimmack (this issue, p. 396) argues that the IAT and direct measures of cognition, for example, Likert scales, can serve as indicators of the same latent construct, thereby purportedly undermining the validity of the IAT as a measure of individual differences in automatic cognition. Here we note the compatibility of Schimmack’s empirical findings with a range of existing theoretical perspectives and the importance of considering evidence beyond MTMM approaches to establishing construct validity. Depending on the nature of the study, different standards of validity may apply to each use of the IAT; however, the evidence presented by Schimmack is easily reconcilable with the potential of the IAT to serve as a valid measure of automatic processes in human cognition, including in individual-difference contexts.
The impact of an integrated depression and HIV treatment program on mental health and HIV care outcomes among people newly initiating antiretroviral therapy in Malawi

Background Depression is highly prevalent among patients newly starting antiretroviral treatment (ART) in Malawi and many other countries. Untreated depression at ART initiation can disrupt the HIV care continuum. Effective approaches for depression screening and treatment exist for low-resource settings, but they are rarely applied. Identifying effective implementation strategies are critical. Methods A pilot program integrated depression screening and treatment into routine HIV care using existing staff at two public health clinics in Malawi in two phases; a screening-only “control” phase and an active “intervention” phase. During the intervention phase, providers prescribed antidepressants or referred patients for Friendship Bench problem-solving therapy. We evaluated the program’s impact on retention in HIV care, viral suppression, and depression remission at 6 months using tabular comparisons and log-binomial models to estimate adjusted risk ratios and mean differences among the intervention group relative to the control group. Results Nearly all consenting participants were screened for depression appropriately and 25% had mild to severe depressive symptoms. During the intervention phase, 86% of participants with mild depressive symptoms started Friendship Bench therapy and 96% of participants with moderate to severe depressive symptoms started antidepressants. Few participants in the intervention group received consistent depression treatment over their first 6 months in care. In the adjusted main analysis, program exposure did not demonstrably affect most HIV or mental health outcomes, though the probability of currently being on ART at 6 months was significantly lower among the intervention group than the control group [RR 0.6(95%CI: 0.4–0.9)]. Conclusions While it is feasible to integrate depression screening and treatment initiation into ART initiation, providing ongoing depression treatment over time is challenging. Similar implementation science studies focused on maintaining depression management will be increasingly important as we strive to understand and test the best ways to implement evidence-based depression treatment within HIV care.
Rapid impact of β‐amyloid on Paxillin in a neural cell line

β‐amyloid1‐42 (Aβ) is a naturally occuring peptide whose accumulation in the brain is putatively coupled to Alzheimer's disease pathogenesis. Deleterious effects of Aβ on neurons have been linked to the inappropriate activation of signaling pathways within the cell (reviewed in Yankner, 1996), including tyrosine phosphorylation of focal adhesion kinase (FAK) (Zhang et al., 1994, 1996a,b). Here we have investigated the effects of Aβ on paxillin in a neural cell line. Paxillin, a substrate for FAK, is thought to act as a signal “integrator,” functioning to link other proteins into multi‐molecular signaling complexes (reviewed in Turner, 1994). Treatment of the rat central nervous system B103 cell line with aggregates of Aβ was found to induce the tyrosine phosphorylation of paxillin within 30 min, nearly 24 hr prior to significant cell death. Particularly striking was a subsequent “mobilization” of paxillin to the cytoskeleton in Aβ‐treated cells. The amount of paxillin associated with the cytoskeleton in Aβ‐treated cells was increased 10‐fold over controls. The Aβ‐induced paxillin accumulation could be visualized immunocytochemically, with an increase in number and size of paxillin‐labeled focal contacts upon treatment with Aβ. This effect was specific, in that vinculin, another focal contact protein, was unaffected by Aβ. Disruption of f‐actin, which inhibits both Aβ‐induced neurotoxicity (Furukawa and Mattson, 1995) and focal contact signaling in B103 cells (Zhang et al., 1996b) was found to block the cytoskeletal paxillin accumulation. The rapid tyrosine phosphorylation and cytoskeletal mobilization of paxillin links Aβ to the activation of focal contact signaling events that may influence neuronal cytoskeletal architecture, gene expression, synaptic plasticity and cell viability. J. Neurosci. Res. 50:979–989, 1997. © 1997 Wiley‐Liss, Inc.
Short-axis versus long-axis approach in ultrasound-guided central venous cannulation: an updated systematic review and meta-analysis

: short-axis long-axis ultrasound-guided central venous cannulation. Methods Electronic bibliographic databases including PubMed, Cochrane Library, Science Direct, and Web of Science were searched for randomized controlled trials comparing ultrasound-guided central venous cannulation via the LAX and SAX approaches published during the period from January, 2011 to October, 2017. We extracted the data from the eligible studies and assessed the first-attempt success rate, overall puncture success rate and complication rate of the two approaches. The relative risk (RR) with the 95% CI was calculated using a fixed or random effects model. Results Seven randomized controlled trials were included for meta-analysis. The results showed that the first-attempt success rate was significantly higher in the SAX group than in the LAX group (RR=1.27, 95% CI : 1.11-1.46; P =0.0005, I 2 =49%), but the overall puncture success rate did not differ significantly between the two approaches (RR=1.04, 95% CI : 0.97-1.10; P =0.27, I 2 =84%). The incidence of accidental arterial puncture with the SAX approach was significantly lower than that with the LAX approach (RR=1.04; 95% CI : 1.01-1.08; P =0.01, I 2 =30%). Conclusion Ultrasound-guided central venous cannulation via the SAX approach, as compared with the LAX approach,canincreasefirst-attemptsuccessrateandreducetheincidenceofaccidentalarterialpuncture.
Seroprevalence of three paramyxoviruses; Hendra virus, Tioman virus, Cedar virus and a rhabdovirus, Australian bat lyssavirus, in a range expanding fruit bat, the Grey-headed flying fox (Pteropus poliocephalus)

Habitat-mediated global change is driving shifts in species’ distributions which can alter the spatial risks associated with emerging zoonotic pathogens. Many emerging infectious pathogens are transmitted by highly mobile species, including bats, which can act as spill-over hosts for pathogenic viruses. Over three years, we investigated the seroepidemiology of paramyxoviruses and Australian bat lyssavirus in a range-expanding fruit bat, the Grey-headed flying fox (Pteropus poliocephalus), in a new camp in Adelaide, South Australia. Over six, biannual, sampling sessions, we quantified median florescent intensity (MFI) antibody levels for four viruses for a total of 297 individual bats using a multiplex Luminex binding assay. Where appropriate, florescence thresholds were determined using finite mixture modelling to classify bats’ serological status. Overall, apparent seroprevalence of antibodies directed at Hendra, Cedar and Tioman virus antigens was 43.2%, 26.6% and 95.7%, respectively. We used hurdle models to explore correlates of seropositivity and antibody levels when seropositive. Increased body condition was significantly associated with Hendra seropositivity (Odds ratio = 3.67; p = 0.002) and Hendra virus levels were significantly higher in pregnant females (p = 0.002). While most bats were seropositive for Tioman virus, antibody levels for this virus were significantly higher in adults (p < 0.001). Unexpectedly, all sera were negative for Australian bat lyssavirus. Temporal variation in antibody levels suggests that antibodies to Hendra virus and Tioman virus may wax and wane on a seasonal basis. These findings suggest a common exposure to Hendra virus and other paramyxoviruses in this flying fox camp in South Australia.
Real‐World Outcomes Associated With Methotrexate, Sulfasalazine, and Hydroxychloroquine Triple Therapy Versus Tumor Necrosis Factor Inhibitor/Methotrexate Combination Therapy in Patients With Rheumatoid Arthritis

Though randomized controlled trials have demonstrated relatively comparable clinical outcomes with triple therapy (methotrexate [MTX], sulfasalazine [SSZ], and hydroxychloroquine [HCQ]) compared to combination therapy (tumor necrosis factor inhibitor [TNFi] and MTX), real‐world experiences comparing these strategies have not been well studied.
Identification and Comparative Analysis of Long Non-Coding RNA in the Skeletal Muscle of Two Dezhou Donkey Strains

Long non-coding RNA (lncRNA) has been extensively studied in many livestock. However, compared with other livestock breeds, there is less research regarding donkey lncRNA function. It has been reported that lncRNA plays an important role in the timing control of development, aging, and death of livestock. Therefore, the study of donkey skeletal muscle lncRNA is of great significance for exploring donkey meat production performance. In this study, RNA-Seq was used to perform high-throughput sequencing of skeletal muscle (longissimus dorsi and gluteus) of two Dezhou donkey strains (SanFen and WuTou). The differentially expressed lncRNAs were screened between different strains and tissues. Then candidate genes for conjoint analysis were screened based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Finally, the accuracy of the sequencing data was verified by real-time quantitative polymerase chain reaction (RT-qPCR). Herein, we identified 3869 novel lncRNAs and 73 differentially expressed lncRNAs. Through the comparison between groups, the specific expression of lncRNAs were found in different strains and muscle tissues. Importantly, we constructed the lncRNA-miRNA-mRNA interaction network and found three important candidate lncRNAs (MSTRG.9787.1, MSTRG.3144.1, and MSTRG.9886.1) and four candidate genes (ACTN1, CDON, FMOD, and BMPR1B). Analysis of the KEGG pathway indicates that the TGF-β signaling pathway plays a pivotal role in the growth and development of skeletal muscle in Dezhou donkey strains.