Miracle-dz/UniFAR-FTUs huggingface dataset:
Mimicking of Blood Flow Results in a Distinct Functional Phenotype in Human Non-Adherent Classical Monocytes

Simple Summary Monocytes are immune cells of increasing interest as cellular-based therapeutic products in inflammation-related diseases. The underlying mechanism is that isolated monocytes are modified outside the body. After re-injection, monocytes are recruited to the site of inflammation, exerting their therapeutic effect. One current challenge is that isolated monocytes rapidly lose migratory capacity during culture, limiting their therapeutic efficacy. During suspension culture, mimicking blood flow has been shown to preserve the migratory capacity. However, the effects on the inflammatory response and other functional properties have not been studied so far. Hence, the present study investigates the effect of shear flow on cytokine secretion and selected features of human blood-derived classical monocytes. Our results demonstrate that mimicking blood flow resulted in a distinct phenotype with an anti-inflammatory cytokine response and a higher migratory capacity than cultured under static conditions. These features could be particularly relevant for further developing monocyte-based products as unwanted inflammatory signaling at the injection site or peripheral blood circulation will be attenuated. Abstract Ex vivo culture conditions during the manufacturing process impact the therapeutic effect of cell-based products. Mimicking blood flow during ex vivo culture of monocytes has beneficial effects by preserving their migratory ability. However, the effects of shear flow on the inflammatory response have not been studied so far. Hence, the present study investigates the effects of shear flow on both blood-derived naïve and activated monocytes. The activation of monocytes was experimentally induced by granulocyte-macrophage colony-stimulating factor (GM-CSF), which acts as a pro-survival and growth factor on monocytes with a potential role in inflammation. Monocytes were cultured under dynamic (=shear flow) or static conditions while preventing monocytes’ adherence by using cell-repellent surfaces to avoid adhesion-induced differentiation. After cultivation (40 h), cell size, viability, and cytokine secretion were evaluated, and the cells were further applied to functional tests on their migratory capacity, adherence, and metabolic activity. Our results demonstrate that the application of shear flow resulted in a decreased pro-inflammatory signaling concurrent with increased secretion of the anti-inflammatory cytokine IL-10 and increased migratory capacity. These features may improve the efficacy of monocyte-based therapeutic products as both the unwanted inflammatory signaling in blood circulation and the loss of migratory ability will be prevented.
Environment-Dependent Variation in Gut Microbiota of an Oviparous Lizard (Calotes versicolor)

Simple Summary The different gut sections potentially provide different habitats for gut microbiota. We found that Bacteroidetes, Firmicutes, and Proteobacteria were the three primary phyla in gut microbiota of C. versicolor. The relative abundance of dominant phyla Bacteroidetes and Firmicutes exhibited an increasing trend from the small intestine to the large intestine, and there was a higher abundance of genus Bacteroides (Class: Bacteroidia), Coprobacillus and Eubacterium (Class: Erysipelotrichia), Parabacteroides (Family: Porphyromonadaceae) and Ruminococcus (Family: Lachnospiraceae), and Family Odoribacteraceae and Rikenellaceae in the hindgut, and some metabolic pathways were higher in the hindgut. Our results reveal the variations of gut microbiota composition and metabolic pathways in different parts of the lizards’ intestine. Abstract Vertebrates maintain complex symbiotic relationships with microbiota living within their gastrointestinal tracts which reflects the ecological and evolutionary relationship between hosts and their gut microbiota. However, this understanding is limited in lizards and the spatial heterogeneity and co-occurrence patterns of gut microbiota inside the gastrointestinal tracts of a host and variations of microbial community among samples remain poorly understood. To address this issue and provide a guide for gut microbiota sampling from lizards, we investigated the bacteria in three gut locations of the oriental garden lizard (Calotes versicolor) and the data were analyzed for bacterial composition by 16S ribosomal RNA (16S rRNA) gene amplicon sequencing. We found the relative abundance of the dominant phyla exhibited an increasing trend from the small intestine to the large intestine, and phyla Firmicutes, Bacteroidetes and Proteobacteria were the three primary phyla in the gut microbiota of C. versicolor. There were a higher abundance of genus Bacteroides (Class: Bacteroidia), Coprobacillus and Eubacterium (Class: Erysipelotrichia), Parabacteroides (Family: Porphyromonadaceae) and Ruminococcus (Family: Lachnospiraceae), and Family Odoribacteraceae and Rikenellaceae in the sample from the hindgut. The secondary bile acid biosynthesis, glycosaminoglycan degradation, sphingolipid metabolism and lysosome were significantly higher in the hindgut than that in the small intestine. Taken together our results indicate variations of gut microbiota composition and metabolic pathway in different parts of the oriental garden lizard.
EpicPCR 2.0: Technical and Methodological Improvement of a Cutting-Edge Single-Cell Genomic Approach

EpicPCR (Emulsion, Paired Isolation and Concatenation PCR) is a recent single-cell genomic method based on a fusion-PCR allowing us to link a functional sequence of interest to a 16S rRNA gene fragment and use the mass sequencing of the resulting amplicons for taxonomic assignment of the functional sequence-carrying bacteria. Although it is interesting because it presents the highest efficiency for assigning a bacterial host to a marker, epicPCR remains a complex multistage procedure with technical difficulties that may easily impair the approach depth and quality. Here, we described how to adapt epicPCR to new gene targets and environmental matrices while identifying the natural host range of SXT/R391 integrative and conjugative elements in water microbial communities from the Meurthe River (France). We notably show that adding a supplementary PCR step allowed us to increase the amplicon yield and thus the number of reads obtained after sequencing. A comparison of operational taxonomic unit (OTU) identification approaches when using biological and technical replicates demonstrated that, although OTUs can be validated when obtained from three out of three technical replicates, up to now, results obtained from two or three biological replicates give a similar and even a better confidence level in OTU identification, while allowing us to detect poorly represented SXT/R391 hosts in microbial communities.
Evaluation of a brief harm reduction intervention to reduce celebratory drinking among college students

Abstract Objectives: To assess the effectiveness of a harm reduction e-card at increasing protective drinking behaviors and decreasing negative outcomes from consuming alcohol.Participants: Participants were college students who turned 21 years old between January 21 2016 and September 27 2017. A total of 1,064 students completed the posttest: 737 from the experimental group and 327 from the control group.Methods: This study is a randomized controlled trial evaluation. Three days prior to their birthdays, students were randomly selected to receive a harm reduction e-card (experimental group) or not (control group). Three days after their birthdays, all students were sent an electronic posttest survey to the student’s university email address.Results: Students who received the e-card intervention reported employing more protective behaviors than the individuals who did not receive the card. Conclusions: This evaluation concludes that a harm reduction e-card successfully increased the use of protective drinking strategies but did not impact negative outcomes.
Targeting Lipocalin-2 in Inflammatory Breast Cancer Cells with Small Interference RNA and Small Molecule Inhibitors

Inflammatory Breast Cancer (IBC) is an aggressive form of invasive breast cancer, highly metastatic, representing 2–4% of all breast cancer cases in the United States. Despite its rare nature, IBC is responsible for 7–10% of all breast cancer deaths, with a 5-year survival rate of 40%. Thus, targeted and effective therapies against IBC are needed. Here, we proposed Lipocalin-2 (LCN2)—a secreted glycoprotein aberrantly abundant in different cancers—as a plausible target for IBC. In immunoblotting, we observed higher LCN2 protein levels in IBC cells than non-IBC cells, where the LCN2 levels were almost undetectable. We assessed the biological effects of targeting LCN2 in IBC cells with small interference RNAs (siRNAs) and small molecule inhibitors. siRNA-mediated LCN2 silencing in IBC cells significantly reduced cell proliferation, viability, migration, and invasion. Furthermore, LCN2 silencing promoted apoptosis and arrested the cell cycle progression in the G0/G1 to S phase transition. We used in silico analysis with a library of 25,000 compounds to identify potential LCN2 inhibitors, and four out of sixteen selected compounds significantly decreased cell proliferation, cell viability, and the AKT phosphorylation levels in SUM149 cells. Moreover, ectopically expressing LCN2 MCF7 cells, treated with two potential LCN2 inhibitors (ZINC00784494 and ZINC00640089) showed a significant decrease in cell proliferation. Our findings suggest LCN2 as a promising target for IBC treatment using siRNA and small molecule inhibitors.
Mixed methods study evaluating the implementation of the WHO hand hygiene strategy focusing on alcohol based handrub and training among health care workers in Faranah, Guinea

Introduction The most frequent adverse health events in healthcare worldwide are healthcare-associated infection. Despite ongoing implementation of the WHO multimodal Hand Hygiene (HH) Improvement Strategy, healthcare-associated infection rate continues to be twofold higher in low- than in high-income countries. This study focused on continued evaluation of HH compliance and knowledge. The mixed method approach, with inclusion of patients and care-givers, provided insight into challenges and facilitators of the WHO HH Improvement Strategy, and highlighted improvement points. Methods An uncontrolled, before-and–after intervention, mixed methods study in Faranah Regional Hospital was conducted from December 2017 to August 2019. The intervention implemented the WHO HH Strategy including HH training for healthcare workers (HCWs), and the relaunch of the local production of alcohol-based handrub (ABHR). A baseline assessment of HH knowledge, perception and compliance of HCWs was done prior to the intervention and compared to two follow-up assessments. The second follow-up assessment was complemented by a qualitative component. Results Overall compliance six months post-intervention was 45.1% and significantly higher than baseline but significantly lower than in first follow-up. Knowledge showed similar patterns of improvement and waning. The perception survey demonstrated high appreciation of the intervention, such as local production of ABHR. HCW’s were concerned about overconsuming of ABHR, however simultaneous quantitative measurements showed that consumption in fact was 36% of the estimated amount needed for sufficient HH compliance. Potential fields for improvement identified by HCWs to enhance sustainability were permanent ABHR availability, having a dedicated person with ownership over continuous simulation HH trainings including simulations to improve technique. Conclusion The study shows that the WHO multimodal HH strategy has a positive effect on HCW compliance and knowledge. Improvement points identified by local staff like sensitization on appropriate ABHR amount per HH action should be considered for sustainable HH improvement.
Factors, Perceptions and Beliefs Associated with Inappropriate Antibiotic Prescribing in German Primary Dental Care: A Qualitative Study

Dentists account for up to 10% of all prescribed antibiotics in primary care, with up to 80% being inappropriate. Targeted approaches to change prescription behavior are scarce. This study aimed at identifying specific barriers and facilitators for prudent antibiotic use in German dentistry by using qualitative methods. Nine in-depth interviews and two focus group discussions with another nine dentists were conducted and analyzed thematically. Dentists described being conflicted by the discordance of available treatment time and the necessity of thorough therapy. Lacking the opportunity of follow-up led to uncertainty. Dentists felt a lack of medical competency concerning prophylaxis for infectious endocarditis. A lack of empowerment to make therapeutic decisions interfered with guideline-conformity. The communication with fellow physicians is conflictual and improvement was wished for. In consequence, dentists felt pressure by potential medico-legal liability. Patients demanding quick and easy pain relief put extra strain on the interviewed dentists. Our hypotheses concord with preliminary data, mainly from the UK, but highlighted specifically medico-legal concerns and interprofessional communication as even greater barriers as described before. Tailored interventional concepts based on our findings may have the potential to lower antibiotic prescriptions in German primary dental care.
Altered Microbial Composition of Drug-Sensitive and Drug-Resistant TB Patients Compared with Healthy Volunteers

Mycobacterium tuberculosis infection has three discernible outcomes: active tuberculosis, latent tuberculosis, or clearance of the bacterium. The outcome of the infection depends on the interaction of the bacterium, the immune system, and the microbiome of the host. The current study uses 16S rRNA sequencing to determine the diversity and composition of the respiratory microbiome of drug-resistant and drug-sensitive tuberculosis patients as well as healthy volunteers. Tuberculosis patients exhibited increased microbial diversity and differentially abundant bacteria than healthy volunteers. Compositional differences were also observed when comparing drug-sensitive or -resistant tuberculosis patients. Finally, we defined and assessed the differences in the core sputum microbiota between tuberculosis patients and healthy volunteers. Our observations collectively suggest that in sputum, Mycobacterium tuberculosis infection is related to altered bacterial diversity and compositional differences of core members of the microbiome, with potential implications for the bacterial pulmonary ecosystem’s stability and function.
Culture-Free Detection of Antibiotic Resistance Markers from Native Patient Samples by Hybridization Capture Sequencing

The increasing incidence of antimicrobial resistance (AMR) is a major global challenge. Routine techniques for molecular AMR marker detection are largely based on low-plex PCR and detect dozens to hundreds of AMR markers. To allow for comprehensive and sensitive profiling of AMR markers, we developed a capture-based next generation sequencing (NGS) workflow featuring a novel AMR marker panel based on the curated AMR database ARESdb. Our primary objective was to compare the sensitivity of target enrichment-based AMR marker detection to metagenomics sequencing. Therefore, we determined the limit of detection (LOD) in synovial fluid and urine samples across four key pathogens. We further demonstrated proof-of-concept for AMR marker profiling from septic samples using a selection of urine samples with confirmed monoinfection. The results showed that the capture-based workflow is more sensitive and requires lower sequencing depth compared with metagenomics sequencing, allowing for comprehensive AMR marker detection with an LOD of 1000 CFU/mL. Combining the ARESdb AMR panel with 16S rRNA gene sequencing allowed for the culture-free detection of bacterial taxa and AMR markers directly from septic patient samples at an average sensitivity of 99%. Summarizing, the newly developed ARESdb AMR panel may serve as a valuable tool for comprehensive and sensitive AMR marker detection.
GRP78 Overexpression Triggers PINK1-IP3R-Mediated Neuroprotective Mitophagy

An experimental model of spinal root avulsion (RA) is useful to study causal molecular programs that drive retrograde neurodegeneration after neuron-target disconnection. This neurodegenerative process shares common characteristics with neuronal disease-related processes such as the presence of endoplasmic reticulum (ER) stress and autophagy flux blockage. We previously found that the overexpression of GRP78 promoted motoneuronal neuroprotection after RA. After that, we aimed to unravel the underlying mechanism by carrying out a comparative unbiased proteomic analysis and pharmacological and genetic interventions. Unexpectedly, mitochondrial factors turned out to be most altered when GRP78 was overexpressed, and the abundance of engulfed mitochondria, a hallmark of mitophagy, was also observed by electronic microscopy in RA-injured motoneurons after GRP78 overexpression. In addition, GRP78 overexpression increased LC3-mitochondria tagging, promoted PINK1 translocation, mitophagy induction, and recovered mitochondrial function in ER-stressed cells. Lastly, we found that GRP78-promoted pro-survival mitophagy was mediated by PINK1 and IP3R in our in vitro model of motoneuronal death. This data indicates a novel relationship between the GRP78 chaperone and mitophagy, opening novel therapeutical options for drug design to achieve neuroprotection.
Effects of hypoxia on DNA hydroxymethylase Tet methylcytosine dioxygenase 2 in a KG-1 human acute myeloid leukemia cell line and its mechanism

Hypoxia is involved in the epigenetic modification of leukemia. As an important DNA hydroxymethylase and a tumor suppressor gene, the expression regulating mechanism of Tet methylcytosine dioxygenase 2 (TET2) remains unclear. The aim of the present study was to explore whether hypoxia and hypoxia-inducible factor 1α (HIF-1α) regulate TET2 gene expression and its demethylation function in acute myeloid leukemia (AML). The human AML cell line KG-1 was used in the present study. The results demonstrated that hypoxia could increase proliferation, enhance metabolism and inhibit apoptosis in KG-1 cells, as detected by the cell counting kit-8 assay, lactate dehydrogenase assay and Annexin V-FITC/propidium iodide staining, respectively. Hypoxia reduced the genome methylation status in KG-1 cells detected using 5-methylcytosine and 5-hydroxymethylcytosine detection kits. In addition, HIF-1α overexpression increased TET2 expression, 5-hmC level and cyclin-dependent kinase inhibitor 2B [p15(INK4B)] gene demethylation compared with the HIF-1α non-overexpression group in KG-1 cells detected by reverse transcription-quantitative PCR, western blotting, 5-hydroxymethylcytosine detection kits and methylation-specific PCR, respectively. The inhibition of HIF-1α by inhibitor YC-1 reduced demethylation in KG-1 cells by decreasing TET2 expression. It was also revealed that HIF-1α could enhance TET2 transcriptional activity by binding to the hypoxia response element of the TET2 gene promoter region using chromatin immunoprecipitation and luciferase reporter gene assays. TET2 may be a potential target gene regulated by HIF-1α. Hypoxia was demonstrated to regulate the expression of TET2 by HIF-1α, which in turn affected the methylation and expression of downstream target genes and served a role in the occurrence and progression of leukemia. In the present study, the association between hypoxia metabolism and epigenetic regulation in AML was investigated and the findings provided a new idea and experimental basis for the diagnosis and treatment of hematologic malignancies.
The Role of Lung Ultrasound in the Management of the Critically Ill Neonate—A Narrative Review and Practical Guide

Lung ultrasound makes use of artifacts generated by the ratio of air and fluid in the lung. Recently, an enormous increase of research regarding lung ultrasound emerged, especially in intensive care units. The use of lung ultrasound on the neonatal intensive care unit enables the clinician to gain knowledge about the respiratory condition of the patients, make quick decisions, and reduces exposure to ionizing radiation. In this narrative review, the possibilities of lung ultrasound for the stabilization and resuscitation of the neonate using the ABCDE algorithm will be discussed.
Multistage Mechanical Activation of Multilayer Carbon Nanotubes in Creation of Electric Heaters with Self-Regulating Temperature

The article deals with research related to the issues of nanomodification of elastomers as a basis of electric heaters with self-regulating temperature. The effect of multistage mechanical activation of multilayer carbon nanotubes (MCNTs) with graphite on the uniformity of the temperature field distribution on the surface of nanomodified organosilicon elastomer has been studied. The influence of the stages of mechanical action on the parameters of MCNTs is revealed. It has been ascertained that for the MCNTs/graphite bulk material, which has passed the stage of mechanical activation in the vortex layer apparatus, a more uniform distribution of the temperature field and an increase in temperature to 57.1 °C at the supply voltage of 100 V are typical. The distribution of the temperature field in the centrifugal paddle mixer “WF-20B” for mixing MCNTs with graphite has been investigated. It has been found that there is also a thermal effect in addition to the mechanical action on the MCNTs in the paddle mixer “WF-20B”. The thermal effect is associated with the transfer of the mechanical energy of friction of the binary mixture MCNTs/graphite on the paddle and the walls of the vessel. The multiplicity of the starting current Ip to the nominal In (Ip/In) is 5 for the first sample, 7.5 for the second sample, and 10 for the third sample at the supply voltage of 100 V. The effect of reducing the starting current and stabilizing the temperature indicates the presence of self-regulation, which is expressed in maintaining a certain level of temperature.
Anti-Inflammatory Effects of Endogenously Released Adenosine in Synovial Cells of Osteoarthritis and Rheumatoid Arthritis Patients

Exogenous adenosine and its metabolite inosine exert anti-inflammatory effects in synoviocytes of osteoarthritis (OA) and rheumatoid arthritis (RA) patients. We analyzed whether these cells are able to synthesize adenosine/inosine and which adenosine receptors (ARs) contribute to anti-inflammatory effects. The functionality of synthesizing enzymes and ARs was tested using agonists/antagonists. Both OA and RA cells expressed CD39 (converts ATP to AMP), CD73 (converts AMP to adenosine), ADA (converts adenosine to inosine), ENT1/2 (adenosine transporters), all AR subtypes (A1, A2A, A2B and A3) and synthesized predominantly adenosine. The CD73 inhibitor AMPCP significantly increased IL-6 and decreased IL-10 in both cell types, while TNF only increased in RA cells. The ADA inhibitor DAA significantly reduced IL-6 and induced IL-10 in both OA and RA cells. The A2AAR agonist CGS 21680 significantly inhibited IL-6 and induced TNF and IL-10 only in RA, while the A2BAR agonist BAY 60-6583 had the same effect in both OA and RA. Taken together, OA and RA synoviocytes express the complete enzymatic machinery to synthesize adenosine/inosine; however, mainly adenosine is responsible for the anti- (IL-6 and IL-10) or pro-inflammatory (TNF) effects mediated by A2A- and A2BAR. Stimulating CD39/CD73 with simultaneous ADA blockage in addition to TNF inhibition might represent a promising therapeutic strategy.