Miracle-dz/UniFAR-FTUs huggingface dataset:
Large-Scale Mapping of Axonal Arbors Using High-Density Microelectrode Arrays

Understanding the role of axons in neuronal information processing is a fundamental task in neuroscience. Over the last years, sophisticated patch-clamp investigations have provided unexpected and exciting data on axonal phenomena and functioning, but there is still a need for methods to investigate full axonal arbors at sufficient throughput. Here, we present a new method for the simultaneous mapping of the axonal arbors of a large number of individual neurons, which relies on their extracellular signals that have been recorded with high-density microelectrode arrays (HD-MEAs). The segmentation of axons was performed based on the local correlation of extracellular signals. Comparison of the results with both, ground truth and receiver operator characteristics, shows that the new segmentation method outperforms previously used methods. Using a standard HD-MEA, we mapped the axonal arbors of 68 neurons in <6 h. The fully automated method can be extended to new generations of HD-MEAs with larger data output and is estimated to provide data of axonal arbors of thousands of neurons within recording sessions of a few hours.
Glycan modification of glioblastoma-derived extracellular vesicles enhances receptor-mediated targeting of dendritic cells

ABSTRACT Glioblastoma is the most prevalent and aggressive primary brain tumour for which total tumour lysate-pulsed dendritic cell vaccination is currently under clinical evaluation. Glioblastoma extracellular vesicles (EVs) may represent an enriched cell-free source of tumour-associated (neo-) antigens to pulse dendritic cells (DCs) for the initiation of an anti-tumour immune response. Capture and uptake of EVs by DCs could occur in a receptor-mediated and presumably glycan-dependent way, yet the glycan composition of glioblastoma EVs is unknown. Here, we set out to characterize the glycocalyx composition of glioblastoma EVs by lectin-binding ELISA and comprehensive immunogold transmission electron microscopy (immuno-TEM). The surface glycan profile of human glioblastoma cell line-derived EVs (50–200 nm) was dominated by α-2,3- and α-2,6 linked sialic acid-capped complex N-glycans and bi-antennary N-glycans. Since sialic acids can trigger immune inhibitory sialic acid–binding Ig-like lectin (Siglec) receptors, we screened for Siglec ligands on the EVs. Glioblastoma EVs showed significant binding to Siglec-9, which is highly expressed on DCs. Surprisingly, however, glioblastoma EVs lack glycans that could bind Dendritic Cell-Specific Intercellular adhesion molecule-3-Grabbing Non-integrin (DC-SIGN, CD209), a receptor that mediates uptake and induction of CD4+ and CD8+ T cell activation. Therefore, we explored whether modification of the EV glycan surface could reduce immune inhibitory Siglec binding, while enhancing EV internalization by DCs in a DC-SIGN dependent manner. Desialylation with a pan-sialic acid hydrolase led to reduction of sialic acid expression on EVs. Moreover, insertion of a high-affinity ligand (LewisY) for DC-SIGN resulted in a four-fold increase of uptake by monocyte-derived DCs. In conclusion, we show that the glycocalyx composition of EVs is a key factor of efficient DC targeting and that modification of the EV glycocalyx potentiates EVs as anti-cancer vaccine.
Ligand- and Additive-Free 2-Position-Selective Trifluoromethylation of Heteroarenes Under Ambient Conditions

A highly selective copper-catalyzed trifluoromethylation of indoles is reported with the assistance of a removable directing group. This protocol provides an easy and rapid method to various 2-position-selective trifluoromethylated heteroarenes including indoles, pyrroles, benzofuran, and acetanilide. What is more, the reaction takes place at ambient conditions without any external ligand or additive.
The Transcription Unit Architecture of Streptomyces lividans TK24

Streptomyces lividans is an attractive host for production of heterologous proteins and secondary metabolites of other Streptomyces species. To fully harness the industrial potential of S. lividans, understanding its metabolism and genetic regulatory elements is essential. This study aimed to determine its transcription unit (TU) architecture and elucidate its diverse regulatory elements, including promoters, ribosome binding sites, 5′-untranslated regions, and transcription terminators. Total 1,978 transcription start sites and 1,640 transcript 3′-end positions were identified, which were integrated to determine 1,300 TUs, consistent with transcriptomic profiles. The conserved promoter sequences were found as 5′-TANNNT and 5′-TGAC, representing the −10 and −35 elements, respectively. Analysis of transcript 3′-end positions revealed the presence of distinctive terminator sequences and the RNA stem structure responsible for the determination of the 3′-boundary of a transcript. Functionally related genes are likely to be regulated simultaneously by using similar promoters and being transcribed as a poly-cistronic TU. Poly-cistronic TUs were further processed or alternatively transcribed into multiple TUs to fine-regulate individual genes in response to environmental conditions. The TU information and regulatory elements identified will serve as invaluable resources for understanding the complex regulatory mechanisms of S. lividans and to elevate its industrial potential.
Forest Stands in Phyllitido-Aceretum Community Occurring on Limestone Rocks and Shelves – Comparison of their Structure in Strictly Protected and Managed Forests

ABSTRACT The aim of the study was to determine the structure of forest stands in rare Phyllitido-Aceretum communities, which grow in extremely harsh conditions – steep limestone slopes and rock shelves. Permanent research plots were established in five well-developed patches of Phyllitido-Aceretum communities from Kraków-Częstochowa Upland (Poland). Two of the plots were located in strictly protected areas of the Ojców National Park, whereas another three were established in the managed forests of Olkusz Forest District. The species composition of the forest stands was determined, including all dead and live trees and their diameters at breast height were measured. Moreover, the horizontal coordinates of each tree were measured to determine the spatial pattern of the trees. Ripley's L function was used for the spatial pattern analysis. The research showed that the patches of Phyllitido-Aceretum communities are characterized by rich species composition of tree layers; nine species were found. There was no significant difference in the species composition between the living and dead trees and the shares of particular species were similar. The density and share of live trees in the phytocoenoses located within the strict protection zone were significantly lower than in managed forests. On the contrary, the same parameters when calculated for dead trees were significantly higher in phytocoenoses located in protected zones than in managed forests. The spatial distribution of the trees in all the analysed plots (except one) displayed a clumped pattern, which is observed in various spatial scales and reflects the habitat mosaics and life strategies of species typical for Phyllitido-Aceretum community.
Evaluation of the Nasopharyngeal Microbiota in Beef Cattle Transported to a Feedlot, With a Focus on Lactic Acid-Producing Bacteria

The nasopharyngeal (NP) microbiota is important in defining respiratory health in feedlot cattle, with certain NP commensals potentially protecting against bovine respiratory disease (BRD) pathogens. In the present study, we evaluated longitudinal changes in the NP microbiota with a focus on lactic acid-producing bacteria (LAB) and their linkage with BRD-associated bacteria in steers (n = 13) that were first transported to an auction market, and then to a feedlot. Deep nasopharyngeal swabs were collected at the farm before transportation to the auction market (day 0), at feedlot placement (day 2), and 5 (day 7) and 12 (day 14) days after feedlot placement. Swabs were processed for the assessment of the NP microbiota using 16S rRNA gene sequencing, and for the detection of Mannheimia haemolytica, Pasteurella multocida, and Histophilus somni by culturing. Possible associations among the top 15 most relatively abundant bacterial genera were predicted using a stepwise-selected generalized linear mixed model. Correlations between LAB and BRD-associated Pasteurellaceae families were also assessed. In addition, antimicrobial activity of selected LAB isolates against M. haemolytica was evaluated in vitro. A noticeable shift was observed in the NP microbial community structure, and in the relative abundance of LAB families as a result of auction market exposure, transport and feedlot placement. Varying degrees of positive or negative associations between the 15 most relatively abundant genera were observed. Many of the LAB families were inversely correlated with the BRD-associated Pasteurellaceae family as the cattle were transported to the auction market and then to the feedlot. Nearly all steers were culture-negative for M. haemolytica and H. somni, and P. multocida became less prevalent after feedlot placement. Isolates from the Lactobacillaceae, Streptococcaceae, and Enterococcaceae families inhibited the growth of M. haemolytica. The results of this study indicated that the NP microbiota became more diverse with an increase in microbial richness following transport to an auction market and feedlot. This study provides evidence of potential cooperation and exclusion taking place in the respiratory microbial community of cattle which may be useful for developing microbial-based strategies to mitigate BRD.
Association of Social Jetlag With Sleep Quality and Autonomic Cardiac Control During Sleep in Young Healthy Men

Social jetlag (SJL), the difference in sleep timing between work and free days is a consequence of the discrepancy between the individual’s circadian rhythm and the social clock. SJL is considered a chronic stress factor and has been linked to various health problems. In this field study, we examined for the first time the association between SJL and cardiac regulation during sleep. 33 healthy young men aged 20–26 years participated in the study. The median SJL was used as a cut-off value to assign the participants into two groups with either lower or higher SJL. As a marker of autonomic control we analyzed heart rate variability (HRV) and addressed intra-individual differences between workdays and free days. In subjects with higher SJL, pNN50, an indicator of vagal activity was lower in the first 3 h of sleep on workday as compared to free day (day × sleep block × group, p = 0.015), indicating a more adaptable regulation on free days, when subjects slept according to their own preference. However, in subjects with lower SJL, no HRV differences were found between the two nights. SJL showed correlation with the free day-workday differences of both pNN50 and another vagal index, RMSSD in the first 2 h of sleep (p = 0.023 and 0.047, respectively). In subjects with higher SJL, a different HF power on workdays and free days (p = 0.031) also indicated that a shift in sleep timing is accompanied by an altered parasympathetic activity in the first few hours of sleep. Furthermore, subjective sleep quality on workdays was negatively associated with SJL (p = 0.02), and subjects with higher SJL reported worse sleep quality on workday than on free day (p = 0.027). Taken together, our data call attention on the potential effect of SJL on sleep quality and vagal activity during sleep.
Pediatric Type II Tibial Spine Fractures: Addressing the Treatment Controversy With a Mixed-Effects Model

Background: Tibial spine fractures, although relatively rare, account for a substantial proportion of pediatric knee injuries with effusions and can have significant complications. Meyers and McKeever type II fractures are displaced anteriorly with an intact posterior hinge. Whether this subtype of pediatric tibial spine fracture should be treated operatively or nonoperatively remains controversial. Surgical delay is associated with an increased risk of arthrofibrosis; thus, prompt treatment decision making is imperative. Purpose: To assess for variability among pediatric orthopaedic surgeons when treating pediatric type II tibial spine fractures. Study Design: Cross-sectional study. Methods: A discrete choice experiment was conducted to determine the patient and injury attributes that influence the management choice. A convenience sample of 20 pediatric orthopaedic surgeons reviewed 40 case vignettes, including physis-blinded radiographs displaying displaced fractures and a description of the patient’s sex, age, mechanism of injury, and predominant sport. Surgeons were asked whether they would treat the fracture operatively or nonoperatively. A mixed-effects model was then used to determine the patient attributes most likely to influence the surgeon’s decision, as well as surgeon training background, years in practice, and risk-taking behavior. Results: The majority of respondents selected operative treatment for 85% of the presented cases. The degree of fracture displacement was the only attribute significantly associated with treatment choice (P < .001). Surgeons were 28% more likely to treat the fracture operatively with each additional millimeter of displacement of fracture fragment. Over 64% of surgeons chose to treat operatively when the fracture fragment was displaced by ≥3.5 mm. Significant variation in surgeon’s propensity for operative treatment of this fracture was observed (P = .01). Surgeon training, years in practice, and risk-taking scores were not associated with the respondent’s preference for surgical treatment. Conclusion: There was substantial variation among pediatric orthopaedic surgeons when treating type II tibial spine fractures. The decision to operate was based on the degree of fracture displacement. Identifying current treatment preferences among surgeons given different patient factors can highlight current variation in practice patterns and direct efforts toward promoting the most optimal treatment strategies for controversial type II tibial spine fractures.
Mucosal-Pull Induction of Lung-Resident Memory CD8 T Cells in Parenteral TB Vaccine-Primed Hosts Requires Cognate Antigens and CD4 T Cells

Tissue-resident memory T cells (TRM) are critical to host defense at mucosal tissue sites. However, the parenteral route of immunization as the most commonly used immunization route in practice is not effective in inducing mucosal TRM cells particularly in the lung. While various respiratory mucosal (RM)-pull strategies are exploited to mobilize parenteral vaccine-primed T cells into the lung, whether such RM-pull strategies can all or differentially induce Ag-specific TRM cells in the lung remains unclear. Here, we have addressed this issue by using a parenteral TB vaccine-primed and RM-pull model. We show that both Ag-independent and Ag-dependent RM-pull strategies are able to mobilize Ag-specific CD8 T cells into the lung. However, only the RM-pull strategy with cognate antigens can induce robust Ag-specific CD8 TRM cells in the lung. We also show that the cognate Ag-based RM-pull strategy is the most effective in inducing TRM cells when carried out during the memory phase, as opposed to the effector phase, of T cell responses to parenteral prime vaccination. We further find that cognate Ag-induced CD4 T cells play an important role in the development of CD8 TRM cells in the lung. Our study holds implications in developing effective vaccine strategies against respiratory pathogens.
Caribbean Near-Shore Coral Reef Benthic Community Response to Changes on Sedimentation Dynamics and Environmental Conditions

Coral reefs are facing unprecedented global, regional and local threats that continue to degrade near-shore habitats. Water quality degradation due to unsustainable development practices at coastal watersheds is one of the greatest stressors across multiple spatial scales. The goal of this study was to assess near-shore coral reef benthic community spatio-temporal response to sedimentation patterns, weather, and oceanographic dynamics at Bahia Tamarindo and Punta Soldado in Culebra Island, Puerto Rico. Benthic data were collected across a distance gradient from the shore through high-resolution images at marked belt transects. Environmental data were assessed and contrasted with benthic assemblages using multivariate correlations and multiple linear regression. Coral colony abundance and coral recruit assemblages showed significant variation among seasons, sites and distance zones (PERMANOVA, p<0.01). Species diversity (H’n) increased at both study sites with distance from shore and the most conspicuous coral recruit species were stress-tolerant Porites astreoides, P. porites, and Siderastrea radians. Difference in coral abundance and coral recruits per site had a strong significant negative relationship with sediment characteristics and depth (p<0.05). Near-shore coral reef benthic community structure was significantly different between sites and distance zones from shore, with depth having an important role shaping reef zonation. Changes in benthic community structure were associated with local sediment distribution patterns emerging from human alteration of coastal watersheds and natural events that cause terrigenous sediment deposition and sand resuspension across the reef. Coral cover was significantly lower at zones more exposed to recurrent sedimentation stress (p<0.01). It was also correlated with sediment texture (p=0.006) and terrigenous sediment deposition (p=0.016). Scleractinian coral cover had an inverse relationship with gorgonian and macroalgae cover. In a short-term period, a pattern of increased dominance of encrusting calcareous algae Ramicrusta textilis and invasive sponge Dictyonella funicularis were documented. Changing land use and increased frequency of extreme weather events, as a consequence of global patterns of climate change, may play an important role shaping near-shore coral reefs benthic communities and could threaten the resilience of coastal regions. Therefore, collaborative and trans-disciplinary ecosystem-based management efforts are urgently needed to effectively reduce land-based stressors and foster near-shore coral reef recovery.
Effect of heat treatment and addition of 4-META to silane on microtensile bond strength of IPS e.max CAD ceramic to resin cement

Background: Silane promotes bonding between ceramic and resin cement. Silane function could be improved by heat treatment and adding 4-Methacryloxyethyl trimellitate anhydride (4-META). The aim of this study was to assess the effect of heat treatment and adding 4-META to silanes on the microtensile bond strength of IPS e.max CAD ceramic and resin cement. Materials and Methods: In this in vitro study, 32 IPS e.max CAD blocks (6 mm × 6 mm × 4 mm) were randomly divided into 8 groups of 4. The ceramic surfaces were etched by 10% hydrofluoric (HF) for 20 s, and Clearfil Ceramic Primer Plus, Clearfil Porcelain Bond Activator (CPA) +4-META, CPA + Clearfil SE Bond (CPA + SE), and Bis-Silane with and without Oven drying at 100°C for 5 min were applied on the ceramic surfaces as silanes, and then, the ceramics were bonded to composite disks by dual-cured resin cements. Ultimately, a total of 120 sticks ( 1 mm × 1 mm × 8 mm) were subjected to microtensile bond strength test (15 sticks from each group) and the failure types were assessed by stereomicroscope at 40x. Data were analyzed by two-sided analysis of variance test and Student's t-test the P values were considered to be < 0.05. Results: The Bis Silane group (two bottles) showed maximum bond strength (P = 0.009). Heat treatment significantly reduced the bond strength in Bis Silane (P = 0.0001); but, in other groups, it did not show significant effect on the bond strength. Adding 4-META to CPA did not significantly affect the microtensile bond strength of IPS e.max CAD ceramic to resin cement, and there was no difference in mode of failure between groups. Conclusion: The effect of silane type was significant on the microtensile bond strength of the ceramic to resin cement. The effect of 4-META on the bond strength was not significant. The interaction between silane type and heat treatment on the bond strength of ceramic to resin cement was also significant.
Relationship between dysfunctional beliefs and stress coping methods in drug-addicted patients: A sample of Turkey

Background: Dysfunctional beliefs are believed to have an effect on substance abuse. Drug-addicted individuals experience difficulties with coping in stressful situations and therefore, start reusing these drugs. Aim: This study was conducted to determine the relationship between dysfunctional beliefs and stress coping methods in drug-addicted patients. Materials and Methods: The population of this descriptive and cross-sectional research study comprised 51 patients who were admitted to the Alcohol and Drug Addiction Treatment Center of a state hospital, diagnosed with drug addiction, and consented to participate in our study. The data were collected by using the Sociodemographic Information Form, the Dysfunctional Attitude Scale (DAS), and the Coping Assessment Questionnaire (COPE). The data obtained were evaluated by percentage, correlation, one-way analysis of variance, Mann–Whitney U-test, and Kruskal–Wallis test. Results: The average COPE score of the drug-addicted patients was found to be 171.60 ± 23.35. The average DAS score of the drug-addicted patients was determined to be 161.66 ± 36.94. A statistically significant difference was found between the DAS and COPE scores of the patients (P < 0.05). Conclusions: It can be concluded that these patients have dysfunctional beliefs and exhibit emotion-focused coping attitudes. More comparative studies investigating the dysfunctional beliefs of alcohol- and drug-addicted people and coping methods should be conducted.
Remineralization potential of dentifrice containing nanohydroxyapatite on artificial carious lesions of enamel: A comparative in vitro study

Background: A carious lesion is the accumulation of numerous episodes of demineralization and remineralization, rather than a unidirectional demineralization process. Tooth destruction can be arrested or reversed by the frequent delivery of fluoride or calcium/phosphorous ions to the tooth surface. Nanohydroxyapatite particle-containing dentifrices are the newer generation of products which claim to remineralize enamel lesions effectively. The aim of this study was to evaluate and compare the remineralization ability of dentifrices containing nanohydroxyapatite, NovaMin, and amine fluoride on artificial enamel caries. Materials and Methods: In this in vitro study, extracted sound premolars were placed in a demineralizing solution to produce deep artificial carious lesions. The teeth were then sectioned longitudinally and divided into three groups (n = 16 in each group): Group A (nanohydroxyapatite), Group B (NovaMin), and Group C (fluoride). The sections were then subjected to pH cycling for 7 days. Polarized light microscopy was utilized to record the depth of the lesions before and after treatment with the selected dentifrices. Changes in the mean lesion depth were statistically analyzed by one-way ANOVA and t-test. The level of significance was assessed at P < 0.05. Results: The lesion depth decreased significantly by 10.56% in Group A, 6.73% in Group B, and 9.58% in Group C (paired t-test, P < 0.001). When comparisons were made across the groups, no statistical significance was found between the Groups A, B, and C (ANOVA test, P > 0.05). Conclusion: All three dentifrices were found to be effective in remineralizing artificial carious lesions. Nanohydroxyapatite dentifrice produced significantly better results compared to fluoride- and NovaMin-containing dentifrices, instigating for its use in the management of early carious lesions.