Miracle-dz/UniFAR-FTUs huggingface dataset:
Generation of Antibody-Drug Conjugate Resistant Models

Simple Summary Antibody-drug conjugates (ADCs) constitute new and effective therapies in cancer. However, resistance is frequently observed in treated patients after a given period of time. That resistance may be present from the beginning of the treatment (primary or de novo resistance) or raise after an initial response to the ADC (secondary resistance). Knowing the causes of those resistances is a necessity in the field as it may help in designing strategies to overcome them. Because of that, it is necessary to develop models that allow the identification of mechanisms of resistance. In this review, we present different approaches that have been used to model ADC resistance in the preclinical setting, and that include the use of established cell lines, patient-derived ex vivo cultures and xenografts primarily or secondarily resistant to the ADC. Abstract In the last 20 years, antibody-drug conjugates (ADCs) have been incorporated into the oncology clinic as treatments for several types of cancer. So far, the Food and Drug Administration (FDA) has approved 11 ADCs and other ADCs are in the late stages of clinical development. Despite the efficacy of this type of drug, the tumors of some patients may result in resistance to ADCs. Due to this, it is essential not only to comprehend resistance mechanisms but also to develop strategies to overcome resistance to ADCs. To reach these goals, the generation and use of preclinical models to study those mechanisms of resistance are critical. Some cells or patient tumors may result in primary resistance to the action of an ADC, even if they express the antigen against which the ADC is directed. Isolated primary tumoral cells, cell lines, or patient explants (patient-derived xenografts) with these characteristics can be used to study primary resistance. The most common method to generate models of secondary resistance is to treat cancer cell lines or tumors with an ADC. Two strategies, either continuous treatment with the ADC or intermittent treatment, have successfully been used to develop those resistance models.
Contrasting Effects of Forest Type and Stand Age on Soil Microbial Activities: An Analysis of Local Scale Variability

Simple Summary The potentially important role of forests in climate change mitigation suggests a strong need for a more detailed understanding of these ecosystems. Besides climatic conditions, diverse forest vegetation creates varied conditions for the activity of soil microorganisms, and particular attention should be focused on a comprehensive study on the influence of different forest types on microbial activities. We conducted an experiment on six different forest soils (two coniferous, two deciduous, and two mixed sites comprising trees of different ages) collected from the same region (Lublin Upland, Poland) to assess the relationship between forest type and seasonal changes in microbial parameters. The annual mean values of the soil microbial indicators suggest that the mature deciduous stand was the most sustainable in microbial activities among the forest soils investigated. The diversity of the forest environment and the multifactorial dependence of the microbiological activity of forest soils necessitates further research in this field, especially using the same soil types. An understanding of forest ecosystem functioning can also be useful for forest management. Abstract Understanding the functioning of different forest ecosystems is important due to their key role in strategies for climate change mitigation, especially through soil C sequestration. In controlled laboratory conditions, we conducted a preliminary study on six different forest soils (two coniferous, two deciduous, and two mixed sites comprising trees of different ages) collected from the same region. The aim was to explore any differences and assess seasonal changes in soil microbial parameters (basal respiration BR, microbial biomass Cmic, metabolic quotient qCO2, dehydrogenase activity DHA, and Cmic:Corg ratio). Indicator- and forest-specific seasonality was assessed. In addition to litter input, soil parameters (pH, nutrient content, texture and moisture) strongly regulated the analyzed microbial indicators. PCA analysis indicated similarity between mature mixed and deciduous forests. Among annual mean values, high Cmic and DHA with simultaneously low qCO2 suggest that the mature deciduous stand was the most sustainable in microbial activities among the investigated forest soils. Research on the interrelationship between soil parameters and forest types with different tree ages needs to be continued and extended to analyze a greater number of forest and soil types.
The Prognostic Value of ADAMTS-13 and von Willebrand Factor in COVID-19 Patients: Prospective Evaluation by Care Setting

Background: Endothelial dysfunction, coupled with inflammation, induces thrombo-inflammation. In COVID-19, this process is believed to be associated with clinical severity. Von Willebrand factor (VWF), and a disintegrin and metalloproteinase with thrombospondin motifs 13 (ADAMTS-13), are strong markers of endothelial dysfunction. We evaluated the impact of the VWF/ADAMTS-13 fraction on COVID-19 severity and prognosis. Materials and methods: A cohort study including 74 COVID-19 patients, with 22 admitted to the intensive care unit (ICU) and 52 to the medical ward (MW), was carried out. We also evaluated, in a group of 54 patients who were prospectively observed, whether variations in VWF/ADAMTS-13 correlated with the degree of severity and routine blood parameters. Results: A VWF:RCo/ADAMTS-13 fraction above 6.5 predicted in-hospital mortality in the entire cohort. At admission, a VWF:RCo/ADAMTS-13 fraction above 5.7 predicted admission to the ICU. Furthermore, the VWF:RCo/ADAMTS-13 fraction directly correlated with C-reactive protein (CRP) (Spearman r: 0.51, p < 0.0001) and D-dimer (Spearman r: 0.26, p = 0.03). In the prospective cohort, dynamic changes in VWF:RCo/ADAMTS-13 and the CRP concentration were directly correlated (Spearman r, p = 0.0014). This relationship was significant in both groups (ICU: p = 0.006; MW: p = 0.02). Conclusions: The present findings show that in COVID-19, the VWF/ADAMTS-13 fraction predicts in-hospital mortality. The VWF/ADAMTS-13 fraction may be a helpful tool to monitor COVID-19 patients throughout hospitalization.
Transcriptome Adaptation of the Ovine Mammary Gland to Dietary Supplementation of Extruded Linseed

Simple Summary Milk fatty acid composition and gene expression in the mammary gland were evaluated in dairy ewes supplemented with linseed. The linseed supplementation improves the health and nutrition quality properties of dairy milk, besides affecting the expression of gene networks related to energy balance, RNA binding, circadian rhythm, and nutrient metabolism. This molecular knowledge on the physiology of the mammary gland might provide the basis for more detailed functional studies for future research. Abstract Several dietary strategies were adopted to reduce saturated fatty acids and increase beneficial fatty acids (FA) for human health. Few studies are available about the pathways/genes involved in these processes. Illumina RNA-sequencing was used to investigate changes in the ovine mammary gland transcriptome following supplemental feeding with 20% extruded linseed. Comisana ewes in mid-lactation were fed a control diet for 28 days (control period) followed by supplementation with 20% DM of linseed panel for 28 days (treatment period). Milk production was decreased by 30.46% with linseed supplementation. Moreover, a significant reduction in fat, protein and lactose secretion was also observed. Several unsaturated FAs were increased while short and medium chain saturated FAs were decreased by linseed treatment. Around four thousand (1795 up- and 2133 down-regulated) genes were significantly differentially regulated by linseed supplementation. The main pathways affected by linseed supplementation were those involved in the energy balance of the mammary gland. Principally, the mammary gland of fed linseed sheep showed a reduced abundance of transcripts related to the synthesis of lipids and carbohydrates and oxidative phosphorylation. Our study suggests that the observed decrease in milk saturated FA was correlated to down-regulation of genes in the lipid synthesis and lipid metabolism pathways.
Enhancement of Transgene Expression by Mild Hypothermia Is Promoter Dependent in HEK293 Cells

Mild hypothermia has been widely used to enhance transgene expression and improve the cellular productivity of mammalian cells. This study investigated mild hypothermia-responsive exogenous promoters in human embryonic kidney 293 (HEK293) cells using site-specific integration of various promoter sequences, including CMV, EF1α, SV40, and TK promoters, into the well-known genomic safe harbor site, AAVS1. EGFP expression driven by the CMV promoter increased up to 1.5-fold at 32 °C versus 37 °C under stable expression, while others showed no hypothermic response. Integration of short CMV variants revealed that the CMV-enhancer region is responsible for the positive hypothermic response. CMV-enhancer-specific transcription factors (TFs) were then predicted through in silico analysis and RNA-sequencing analysis, resulting in the selection of one TF, NKX3-1. At 37 °C, overexpression of NKX3-1 in recombinant HEK293 cells expressing EGFP through the CMV promoter (CMV-EGFP) increased EGFP expression up to 1.6-fold, compared with that in CMV-EGFP, the expression level of which was comparable to that of CMV-EGFP at 32 °C. Taken together, this work demonstrates promoter-dependent hypothermia responses in HEK293 cells and emphasizes interactions between endogenous TFs and promoter sequences.
Analysis of EEG Characteristics of Drivers and Driving Safety in Undersea Tunnel

To study the influence of the driving environment of an undersea tunnel on driver EEG (electroencephalography) characteristics and driving safety, a real vehicle experiment was performed in the Qingdao Jiaozhou Bay Tunnel. The experimental data of the drivers’ real vehicle experiment were collected using an illuminance meter, EEG instrument, video recorder and other experimental equipment. The undersea tunnel is divided into different areas, and the distribution law of driving environment characteristics, EEG characteristics and vehicle speed characteristics is analyzed. The correlations between the driving environment characteristics, EEG characteristics and vehicle speed characteristics model the variables that pass the correlation test. The driving safety evaluation model of an undersea tunnel is established, and the driving safety in different areas of the undersea tunnel is evaluated. The results show that there are obvious differences in illumination, EEG power change rate, vehicle speed and other variables in different areas of the undersea tunnel. The driving environment characteristics are highly correlated with the β wave power change rate. The driving safety of different areas of the undersea tunnel from high to low is: upslope area, downslope area, exit area and entrance area. The study will provide a theoretical basis for the safe operation of the undersea tunnel.
Combination Treatment with the Vimentin-Targeting Antibody hzVSF and Tenofovir Suppresses Woodchuck Hepatitis Virus Infection in Woodchucks

Current treatment options for patients infected with hepatitis B virus (HBV) are suboptimal, because the approved drugs rarely induce cure due to the persistence of the viral DNA genome in the nucleus of infected hepatocytes, and are associated with either severe side effects (pegylated interferon-alpha) or require life-long administration (nucleos(t)ide analogs). We report here the evaluation of the safety and therapeutic efficacy of a novel, humanized antibody (hzVSF) in the woodchuck model of HBV infection. hzVSF has been shown to act as a viral entry inhibitor, most likely by suppressing vimentin-mediated endocytosis of virions. Targeting the increased vimentin expression on liver cells by hzVSF after infection with HBV or woodchuck hepatitis virus (WHV) was demonstrated initially. Thereafter, hzVSF safety was assessed in eight woodchucks naïve for WHV infection. Antiviral efficacy of hzVSF was evaluated subsequently in 24 chronic WHV carrier woodchucks by monotreatment with three ascending doses and in combination with tenofovir alafenamide fumarate (TAF). Consistent with the proposed blocking of WHV reinfection, intravenous hzVSF administration for 12 weeks resulted in a modest but transient reduction of viral replication and associated liver inflammation. In combination with oral TAF dosing, the antiviral effect of hzVSF was enhanced and sustained in half of the woodchucks with an antibody response to viral proteins. Thus, hzVSF safely but modestly alters chronic WHV infection in woodchucks; however, as a combination partner to TAF, its antiviral efficacy is markedly increased. The results of this preclinical study support future evaluation of this novel anti-HBV drug in patients.
Association Analysis of Polymorphic Variants of the BDNF Gene in Athletes

As BDNF is one of the group of neurotrophins highly influencing the processes happening in the brain, such as the processes of learning and personality creation, we decided to look closer at its genetic variations in association with the personality of a group of athletes and their controls. The study group consisted of 305 volunteers: martial arts athletes (n = 153; mean age = 24.06) and healthy non-athletes as controls (n = 152; mean age = 22.23). Thirty-eight percent of the martial arts group achieved the championship level. Both the martial arts and control subjects were examined using the NEO Five-Factor Personality Inventory (NEO-FFI) and the State-Trait Anxiety Inventory (STAI) scales. The results of the NEO-FFI and STAI inventories were given as sten scores. The conversion of the raw score to the sten scale was performed according to Polish norms for adults. Genomic DNA was extracted from blood leukocytes and then genotyped using a PCR method for the following polymorphisms: BDNF rs10767664 and BDNF rs2030323. We observed statistical significance for both polymorphisms when comparing martial arts athletes with the control group in relation to the conscientiousness and extraversion scales. However, since few extant articles consider this association, our results still require further analysis, probably by considering a larger group.
Species Diversity and Phylogenetic Relationships of Olive Lace Bugs (Hemiptera: Tingidae) Found in South Africa

Simple Summary Olive lace bugs feed on wild and cultivated Olea europaea, causing a negative impact on plant vitality and development. These insects are known to affect olive orchards in South Africa, the country where most of the olive and olive products on the continent are produced. However, the diversity of species of these pests is not clear. Morphological analysis and DNA barcoding showed the presence of Cysteochila lineata, Plerochila australis, Neoplerochila paliatseasi and Neoplerochila sp. Further analyses of genetic divergence and phylogenetic clustering in 30 species in 18 genera of Tingidae using new and publicly available DNA barcodes showed that the majority of sequences deposited on BOLD Systems were correctly assigned to species. The complete mitochondrial genomes of the four species found in South Africa were sequenced to assess their phylogenetic position within Tingidae. The four olive lace bugs formed one cluster of species, and the genus Cysteochila was not monophyletic as C. lineata grouped with the other three olive lace bugs but C. chiniana was placed in a different cluster. This result suggests that lace bug species that feed on olive trees may have a common ancestor and calls for further research on potential adaptations to O. europaea. Abstract Olive lace bugs (Hemiptera: Tingidae) are small sap-sucking insects that feed on wild and cultivated Olea europaea. The diversity of olive lace bug species in South Africa, the most important olive producer on the continent, has been incompletely surveyed. Adult specimens were collected in the Western Cape province for morphological and DNA-based species identification, and sequencing of complete mitogenomes. Cysteochila lineata, Plerochila australis, Neoplerochila paliatseasi and Neoplerochila sp. were found at 12 sites. Intra- and interspecific genetic divergences and phylogenetic clustering in 30 species in 18 genera of Tingidae using new and publicly available DNA barcodes showed high levels of congruity between taxonomic and genetic data. The phylogenetic position of the four species found in South Africa was inferred using new and available mitogenomes of Tingidae. Notably, olive lace bugs formed a cluster of closely related species. However, Cysteochila was non-monophyletic as C. lineata was recovered as a sister species to P. australis whereas Cysteochila chiniana, the other representative of the genus, was grouped with Trachypeplus jacobsoni and Tingis cardui in a different cluster. This result suggests that feeding on O. europaea may have a common origin in Tingidae and warrants future research on potential evolutionary adaptations of olive lace bugs to this plant host.
The Synergistic Effect of Time of Exposure, Distance and No Use of Personal Protective Equipment in the Determination of SARS-CoV-2 Infection: Results of a Contact Tracing Follow-Up Study in Healthcare Workers

The aim of this study is to assess the effect of contact time, contact distance and the use of personal protective equipment on the determination of SARS-CoV-2 infection in healthcare workers (HCWs). This study consists of an analysis of data gathered for safety reasons at the Sapienza Teaching Hospital Policlinico Umberto I in Rome through the surveillance system that was put into place after the worsening of the COVID-19 pandemic. The studied subjects consist of HCWs who were put under health surveillance, i.e., all employees who were in contact with subjects who were confirmed to have tested positive for SARS-CoV-2. The HCWs under surveillance were monitored for a period encompassing ten days after the date of contact, during which they undertook nasopharyngeal swab tests analysed through RT-PCR (RealStar® SARS-CoV-2 Altona Diagnostic–Germany). Descriptive and univariate analyses have been undertaken, considering the following as risk factors: (a) no personal protective equipment use (PPE); (b) Distance < 1 m between the positive and contact persons; (c) contact time > 15′. Finally, a Cox regression and an analysis of the level of synergism between factors, as specified by Rothman, were carried out. We analysed data from 1273 HCWs. Of these HCWs, 799 (62.8%) were females, with a sample average age of 47.8 years. Thirty-nine (3.1%) tested positive during surveillance. The overall incidence rate was 0.4 per 100 person-days. Time elapsed from the last exposure and a positive RT-PCR result ranged from 2 to 17 days (mean = 7, median = 6 days). In the univariate analysis, a distance <1 m and a contact time > 15′ proved to be risk factors for the SARS-CoV-2 infection, with a hazard ratio (HR) of 2.62 (95% CI: 1.11–6.19) and 3.59 (95% IC: 1.57–8.21), respectively. The synergism analysis found the highest synergism between the “no PPE use” x “Contact time”. The synergy index S remains strongly positive also in the analysis of the factors “no PPE use” x “Distance” and “Time of contact” x “Distance”. This study confirms the absolute need to implement safety protocols during the pandemic and to use the correct PPE within health facilities in order to prevent SARS-CoV-2 infection. The analysis shows that among the factors considered (contact time and distance, no use of PPE), there is a strong synergistic effect.
Transcriptome and Methylome Analysis Reveal Complex Cross-Talks between Thyroid Hormone and Glucocorticoid Signaling at Xenopus Metamorphosis

Background: Most work in endocrinology focus on the action of a single hormone, and very little on the cross-talks between two hormones. Here we characterize the nature of interactions between thyroid hormone and glucocorticoid signaling during Xenopus tropicalis metamorphosis. Methods: We used functional genomics to derive genome wide profiles of methylated DNA and measured changes of gene expression after hormonal treatments of a highly responsive tissue, tailfin. Clustering classified the data into four types of biological responses, and biological networks were modeled by system biology. Results: We found that gene expression is mostly regulated by either T3 or CORT, or their additive effect when they both regulate the same genes. A small but non-negligible fraction of genes (12%) displayed non-trivial regulations indicative of complex interactions between the signaling pathways. Strikingly, DNA methylation changes display the opposite and are dominated by cross-talks. Conclusion: Cross-talks between thyroid hormones and glucocorticoids are more complex than initially envisioned and are not limited to the simple addition of their individual effects, a statement that can be summarized with the pseudo-equation: TH ∙ GC > TH + GC. DNA methylation changes are highly dynamic and buffered from genome expression.
Novel Contact Lenses Embedded with Drug-Loaded Zwitterionic Nanogels for Extended Ophthalmic Drug Delivery

Therapeutic ophthalmic contact lenses with prolonged drug release and improved bioavailability have been developed to circumvent tedious eye drop instillation. In this work, zwitterionic nanogels based on poly(sulfobetaine methacrylate) (PSBMA) were easily fabricated by one-step reflux-precipitation polymerization, with the advantages of being surfactant-free and morphology controlled. Then, the ophthalmic drug levofloxacin (LEV) was encapsulated into the nanogels. A set of contact lenses with varied nanogel-loading content was fabricated by the cast molding method, with the drug-loaded nanogels dispersed in pre-monomer solutions composed of 2-hydroxyethyl methacrylate (HEMA) and N-vinyl-2-pyrrolidone (NVP). The structure, surface morphology, water contact angle (WCA), equilibrium water content (EWC), transmittance, and mechanical properties of the contact lenses were subsequently investigated, and in vitro drug release and biocompatibility were further evaluated. As a result, the optimized contact lens with nanogel-loading content of 8 wt% could sustainably deliver LEV for ten days, with critical lens properties within the range of recommended values for commercial contact lenses. Moreover, cell viability assays revealed that the prepared contact lenses were cytocompatible, suggesting their significant potential as an alternative to traditional eye drops or ointment formulations for long-term oculopathy treatment.
Metformin Triggers Apoptosis and Induction of the G0/G1 Switch 2 Gene in Macrophages

Metformin is a widely used antidiabetic drug for the treatment of type 2 diabetes and has been recently demonstrated to possess anti-inflammatory properties via AMPK-mediated modulation of M2 macrophage activation. However, the anti-inflammatory mechanisms of metformin on inflammatory macrophages are still not fully elucidated. In this study, we found that metformin induced apoptosis in macrophages. In particular, metformin induced apoptosis of M1 macrophages, based on M1 marker genes in apoptotic macrophages. Next, we comprehensively screened metformin-responsive genes in macrophages by RNA-seq and focused on the extrinsic apoptotic signaling pathway. The G0/G1 switch 2 gene (G0S2) was robustly up-regulated by metformin in macrophages. Overexpression of G0S2 significantly induced apoptosis of macrophages in a dose-dependent manner and blunted the function of the crucial anti-apoptotic gene Bcl-2, which was significantly reduced by metformin. These findings show that metformin promoted apoptosis of macrophages, especially M1 macrophages, via G0S2 induction and provides a novel anti-inflammatory mechanism of metformin through induction of macrophage apoptosis.