Miracle-dz/UniFAR-FTUs huggingface dataset:
Lysine-based surfactants in nanovesicle formulations: the role of cationic charge position and hydrophobicity in in vitro cytotoxicity and intracellular delivery

Abstract Understanding nanomaterial interactions within cells is of increasing importance for assessing their toxicity and cellular transport. Here, the authors developed nanovesicles containing bioactive cationic lysine-based amphiphiles and assessed whether these cationic compounds increase the likelihood of intracellular delivery and modulate toxicity. Different cytotoxic responses were found among the formulations, depending on surfactant, cell line and endpoint assayed. The induction of mitochondrial dysfunction, oxidative stress and apoptosis were the general mechanisms underlying cytotoxicity. Fluorescence microscopy analysis demonstrated that nanovesicles were internalised by HeLa cells and evidenced that their ability to release endocytosed materials into cell cytoplasm depends on the structural parameters of amphiphiles. The cationic charge position and hydrophobicity of surfactants determine the nanovesicle interactions within the cell and, thus, the resulting toxicity and intracellular behaviour after cell uptake of the nanomaterial. The insights into some toxicity mechanisms of these new nanomaterials contribute in reducing the uncertainty surrounding their potential health hazards.
Single-Cell Sequencing of the Healthy and Diseased Heart Reveals Cytoskeleton-Associated Protein 4 as a New Modulator of Fibroblasts Activation

Background: Genome-wide transcriptome analysis has greatly advanced our understanding of the regulatory networks underlying basic cardiac biology and mechanisms driving disease. However, so far, the resolution of studying gene expression patterns in the adult heart has been limited to the level of extracts from whole tissues. The use of tissue homogenates inherently causes the loss of any information on cellular origin or cell type-specific changes in gene expression. Recent developments in RNA amplification strategies provide a unique opportunity to use small amounts of input RNA for genome-wide sequencing of single cells. Methods: Here, we present a method to obtain high-quality RNA from digested cardiac tissue from adult mice for automated single-cell sequencing of both the healthy and diseased heart. Results: After optimization, we were able to perform single-cell sequencing on adult cardiac tissue under both homeostatic conditions and after ischemic injury. Clustering analysis based on differential gene expression unveiled known and novel markers of all main cardiac cell types. Based on differential gene expression, we could identify multiple subpopulations within a certain cell type. Furthermore, applying single-cell sequencing on both the healthy and injured heart indicated the presence of disease-specific cell subpopulations. As such, we identified cytoskeleton-associated protein 4 as a novel marker for activated fibroblasts that positively correlates with known myofibroblast markers in both mouse and human cardiac tissue. Cytoskeleton-associated protein 4 inhibition in activated fibroblasts treated with transforming growth factor &bgr; triggered a greater increase in the expression of genes related to activated fibroblasts compared with control, suggesting a role of cytoskeleton-associated protein 4 in modulating fibroblast activation in the injured heart. Conclusions: Single-cell sequencing on both the healthy and diseased adult heart allows us to study transcriptomic differences between cardiac cells, as well as cell type-specific changes in gene expression during cardiac disease. This new approach provides a wealth of novel insights into molecular changes that underlie the cellular processes relevant for cardiac biology and pathophysiology. Applying this technology could lead to the discovery of new therapeutic targets relevant for heart disease.
Impact of New Technologies for Middle-Aged and Older Patients: In-Depth Interviews With Type 2 Diabetes Patients Using Continuous Glucose Monitoring

Background Continuous glucose monitoring (CGM) uses subcutaneous sensors and records the average interstitial sensor current every 5 min in the recorder; data are subsequently exported to a computer 4 to 7 days later when calibration with self-measured blood glucose is made retrospectively. How middle-aged and older patients perceive the added technology intervention is not clear. Objective The study aimed to understand the factors associated with the adoption of new technology in diabetes care, to understand the feelings and behaviors while using it, and to determine the changes in attitudes and behavior after completing the use of the new technology at the 3-month follow-up. Methods Middle-aged and older type 2 diabetes patients who had received professional continuous glucose monitoring (iPro 2 [Medtronic]) were invited for semistructured in-depth interviews on the day of the CGM sensor removal and at 3 months after CGM-based counseling. A phenomenography approach was used to analyze the interview data. Results A total of 20 type 2 diabetes patients (aged 53 to 72 years, 13 males and 7 females, 4 to 40 years duration of diabetes, mean glycated hemoglobin 8.54% [SD 0.71%]) completed 2 sections of semistructured in-depth interviews. Physician guidance and participant motivation toward problem solving were found to be factors associated with adoption of the device. Participants indicated that technology can be a reminder, a supervisor, and a visualizer of blood glucose, all of which are helpful for disease management. However, CGM is somewhat inconvenient, and some participants also reported that the provision of this new technology might be a hint of disease progression. There was a higher percentage of women compared with men who reported that CGM can be a reminder or a supervisor to help them with diet control. Conclusions Physician guidance and participants’ degree of motivation are keys to adopting new technology in the case of middle-aged and older adults. Although the CGM sensor may cause inconvenience to patients on their limited body movement when wearing the device, it is helpful for diet control and is an effective behavioral modification tool that offers support, especially in the case of women.
Shiunko and Chuoko, topical Kampo medicines, inhibit the expression of gehA encoding the extracellular lipase in Cutibacterium acnes

Antimicrobial agents have been used for eradication of Cutibacterium (formerly Propionibacterium) acnes that is an exacerbation factor of the skin disease acne vulgaris. However, the use of antibiotics is associated with an increased risk of promoting the emergence of resistant bacteria and leading to skin dysbiosis. Traditional Japanese Kampo medicines, such as Keigairengyoto, are used to treat acne. However, there is incomplete understanding regarding their functional mechanism in treatment of acne. In this study, we examined the antimicrobial and anti‐lipase activity of the Kampo medicines used empirically for acne treatment. Three oral medicines, Keigairengyoto, Seijoboufuto and Jumihaidokuto, were found to inhibit the growth of C. acnes and decrease the lipase activity. Especially, Keigairengyoto caused remarkable decrease of bacterial lipase activity. Furthermore, topical medicines such as Shiunko and Chuoko significantly decreased the lipase activity in a dose‐dependent manner, without inhibiting C. acnes growth. The topical medicines were found to inhibit the expression of gehA, which codes for extracellular lipase. Our results indicate that Shiunko and Chuoko have potential as effective acne therapeutic agents, especially because they do not promote the emergence of antimicrobial‐resistant bacteria and skin dysbiosis.
Indigoid dyes by group E monooxygenases: mechanism and biocatalysis

Abstract Since ancient times, people have been attracted by dyes and they were a symbol of power. Some of the oldest dyes are indigo and its derivative Tyrian purple, which were extracted from plants and snails, respectively. These ‘indigoid dyes’ were and still are used for coloration of textiles and as a food additive. Traditional Chinese medicine also knows indigoid dyes as pharmacologically active compounds and several studies support their effects. Further, they are interesting for future technologies like organic electronics. In these cases, especially the indigo derivatives are of interest but unfortunately hardly accessible by chemical synthesis. In recent decades, more and more enzymes have been discovered that are able to produce these indigoid dyes and therefore have gained attention from the scientific community. In this study, group E monooxygenases (styrene monooxygenase and indole monooxygenase) were used for the selective oxygenation of indole (derivatives). It was possible for the first time to show that the product of the enzymatic reaction is an epoxide. Further, we synthesized and extracted indigoid dyes and could show that there is only minor by-product formation (e.g. indirubin or isoindigo). Thus, group E monooxygenase can be an alternative biocatalyst for the biosynthesis of indigoid dyes.
Biphasic mechanosensitivity of T cell receptor-mediated spreading of lymphocytes

Significance The ability of a T cell to explore environmental mechanical cues, through bonds formed by its special receptors called T cell receptors (TCRs), is crucial for the first steps of immune recognition. Here we show that the response of T cells, quantified in terms of their spreading behavior, is biphasic with substrate stiffness when mediated through TCRs. However, when the ligands of the T cell integrins are additionally involved, the cellular response becomes monotonic. Based on a mesoscale model, this ligand-specific response can be attributed to differences in force sensitivity and effective stiffness of the link formed between the ligand/receptor pairs and the actin cytoskeleton. This may provide a general mechanism for immune cells to discriminate mechanosensitive bonds. Mechanosensing by T cells through the T cell receptor (TCR) is at the heart of immune recognition. While the mechanobiology of the TCR at the molecular level is increasingly well documented, its link to cell-scale response is poorly understood. Here we explore T cell spreading response as a function of substrate rigidity and show that remarkably, depending on the surface receptors stimulated, the cellular response may be either biphasic or monotonous. When adhering solely via the TCR complex, T cells respond to environmental stiffness in an unusual fashion, attaining maximal spreading on an optimal substrate stiffness comparable to that of professional antigen-presenting cells. However, in the presence of additional ligands for the integrin LFA-1, this biphasic response is abrogated and the cell spreading increases monotonously with stiffness up to a saturation value. This ligand-specific mechanosensing is effected through an actin-polymerization–dependent mechanism. We construct a mesoscale semianalytical model based on force-dependent bond rupture and show that cell-scale biphasic or monotonous behavior emerges from molecular parameters. As the substrate stiffness is increased, there is a competition between increasing effective stiffness of the bonds, which leads to increased cell spreading and increasing bond breakage, which leads to decreased spreading. We hypothesize that the link between actin and the receptors (TCR or LFA-1), rather than the ligand/receptor linkage, is the site of this mechanosensing.
Histologic transformation to small-cell lung cancer following gefitinib and radiotherapy in a patient with pulmonary adenocarcinoma

Introduction: Targeted therapies against epidermal growth factor receptor (EGFR) have revolutionized the treatment of a subset of lung adenocarcinomas that have EGFR-activating mutations; however, all patients treated with EGFR tyrosine kinase inhibitors (TKIs) ultimately develop resistance. Histologic transformation of EGFR-mutant adenocarcinoma to small cell lung cancer (SCLC) is a resistance mechanism rarely reported in the literature. Case presentation: We describe the case of a woman with metastatic lung cancer adenocarcinoma with mutated EGFR with an initial response to gefitinib and radiation therapy, who progressed after 18 months due to the development of a resistance mechanism. The new biopsy performed after progression highlighted histologic transformation to SCLC, while maintaining the original EGFR mutation. Conclusions: To better identify patients who progress after TKIs and radiation therapy, it is important to perform tumor rebiopsy and collect data to study mechanisms of acquired EGFR TKI resistance.
Biomarker discordance between primary breast cancer and bone or bone marrow metastases

BACKGROUND Discordance in biomarker expression between primary and metastatic tumor sites has been reported in several studies; yet, few have examined this feature in bone lesions. METHODS We retrospectively enrolled patients with breast cancer metastasis to the bone or bone marrow, excluding cases where samples from both the primary and metastatic lesions were not available. Expression patterns of the estrogen receptor (ER), progesterone receptor (PgR), human epidermal growth factor receptor 2 (HER2) and Ki67 were compared in primary tumors and bone or bone marrow lesions. RESULTS Forty-six patients with a median age of 52 years (range, 34-72 years) were included in the study. Discordant rates of ER, PgR and HER2 were 20%, 46% and 0%, respectively. Physicians usually determined treatment options considering the results of biomarker re-evaluation. It is unlikely that biomarker discordance was related to prior treatment. CONCLUSIONS Biomarker discordance in bone or bone marrow lesions is common in patients with breast cancer. An accurate and thorough analysis of biomarkers and metastatic tumor properties is important for clinical decision-making.
Association Between the Activity Space Exposure to Parks in Childhood and Adolescence and Cognitive Aging in Later Life

The exposure to green space in early life may support better cognitive aging in later life. However, this exposure is usually measured using the residential location alone. This disregards the exposure to green spaces in places frequented during daily activities (i.e., the ‘activity space’). Overlooking the multiple locations visited by an individual over the course of a day is likely to result in poor estimation of the environmental exposure and therefore exacerbates the contextual uncertainty. A child’s activity space is influenced by factors including age, sex, and the parental perception of the neighborhood. This paper develops indices of park availability based on individuals’ activity spaces (home, school, and the optimal route to school). These measures are used to examine whether park availability in childhood is related to cognitive change much later in life. Multi-level linear models, including random effects for schools, were used to test the association between park availability during childhood and adolescence and cognitive aging (age 70 to 76) in the Lothian Birth Cohort 1936 participants (N = 281). To test for the effect modification, these models were stratified by sex and road traffic accident (RTA) density. Park availability during adolescence was associated with better cognitive aging at a concurrently low RTA density (β = 0.98, 95% CI: 0.36 to 1.60), but not when the RTA density was higher (β = 0.22, 95% CI: −0.07 to 0.51). Green space exposure during early life may be important for optimal cognitive aging; this should be evidenced using activity space-based measures within a life-course perspective.
Pard3 suppresses glioma invasion by regulating RhoA through atypical protein kinase C/NF‐κB signaling

Partitioning defective protein 3 (Pard3) has been reported to inhibit the progression of numerous human cancer cell types. However, the role of Pard3 in glioma progression remains unclear. In this study, the expression of Pard3 was measured in human gliomas of different grades by both quantitative polymerase chain reaction and Western blotting. The effect of Pard3 on glioma progression was tested using cell counting kit‐8 assays, EdU assays, colony formation assays, cell migration, and invasion assays and tumor xenografts. The effect of Pard3 on Ras homolog family member A (RhoA) protein levels, subcellular localization, and transcriptional activity was measured by immunoblotting and immunofluorescence. Our results indicate that Pard3 functions as a tumor suppressor in gliomas and that the loss of Pard3 protein is strongly associated with a higher grade and poorer outcome. Pard3 overexpression inhibits glioma progression by upregulating RhoA protein levels. However, the level of GTP‐RhoA protein remained unchanged. Further evidence demonstrates that Pard3 regulates RhoA protein levels, subcellular localization and transcriptional activity by activating atypical protein kinase C/NF‐κB signaling. Mouse modeling experiments show that Pard3 overexpression inhibits glioma cell growth in vivo. Taken together, these findings identify RhoA as a novel target of Pard3 in gliomas and substantiate a novel regulatory role for Pard3 in glioma progression. This study reveals that Pard3 plays an inhibitory role in gliomas by regulating RhoA, which reveals a potential benefit for Pard3 activators in the prevention and therapy of gliomas.
Effects of Dissolved Organic Carbon on Copper Toxicity to Embryos of Mytilus galloprovincialis as Measured by Diffusive Gradient in Thin Films

Diffusive gradient in thin films (DGT) potentially better quantifies bioavailable copper (Cu) in seawater. Laboratory exposure of DGTs and Mytilus galloprovincialis embryos at varying concentrations of dissolved organic carbon and Cu were performed to resolve the degree to which mimicry of toxicity buffering occurs in passive sampler quantification. The results provide preliminary median effect concentrations (EC50s) ranging from 4.8 to 11.5 µg/L as CDGT Cu over the span of 0.896 to 8.36 mg/L DOC. Environ Toxicol Chem 2019;00:1‐6. Published 2019 Wiley Periodicals, Inc. on behalf of SETAC. This article is a US government work and, as such, is in the public domain in the United States of America.
Development and validation of an open source Monte Carlo dosimetry model for wide‐beam CT scanners using Fluka

Abstract Purpose Development and validation of an open source Fluka‐based Monte Carlo source model for diagnostic patient dose calculations. Methods A framework to simulate a computed tomography (CT) scanner using Fluka Monte Carlo particle transport code was developed. The General Electric (GE) Revolution scanner with the large body filter and 120 kV tube potential was characterized using measurements. The model was validated on benchmark CT test problems and on dose measurements in computed tomography dose index (CTDI) and anthropomorphic phantoms. Axial and helical operation modes with provision for tube current modulation (TCM) were implemented. The particle simulations in Fluka were accelerated by executing them on a high‐performance computing cluster. Results The simulation results agreed to better than an average of 4% of the reference simulation results from the AAPM Report 195 test scenarios, namely: better than 2% for both test problems in case 4 using the PMMA phantom, and better than 5% of the reference result for 14 of 17 organs in case 5, and within 10% for the three remaining organs. The Fluka simulation results agreed to better than 2% of the air kerma measured in‐air at isocenter of the GE Revolution scanner. The simulated air kerma in the center of the CTDI phantom overestimated the measurement by 7.5% and a correction factor was introduced to account for this. The simulated mean absorbed doses for a chest scan of the pediatric anthropomorphic phantom was completed in ~9 min and agreed to within the 95% CI for bone, soft tissue, and lung measurements made using MOSFET detectors for fixed current axial and helical scans as well as helical scan with TCM. Conclusion A Fluka‐based Monte Carlo simulation model of axial and helical acquisition techniques using a wide‐beam collimation CT scanner demonstrated good agreement between measured and simulated results for both fixed current and TCM in complex and simple geometries. Code and dataset will be made available at https://github.com/chezhia/FLUKA_CT.
The atypical RhoU/Wrch1 Rho GTPase controls cell proliferation and apoptosis in the gut epithelium

The mammalian gut epithelium displays among the highest rates of self‐renewal, with a turnover time of less than 5 days. Renewal involves concerted proliferation at the bottom of the crypt, migration and differentiation along the crypt‐villus axis and anoïkis/shedding in the luminal epithelium. Renewal is controlled by interplay between signalling pathways, among which canonical and non‐canonical Wnt signals play prominent roles. Overall 92% of colon tumours show increased canonical Wnt signalling resulting from mutations, established as major driver steps towards carcinogenesis.
High‐Performance Materials for 3D Printing in Chemical Synthesis Applications

3D printing has emerged as an enabling technology for miniaturization. High‐precision printing techniques such as stereolithography are capable of printing microreactors and lab‐on‐a‐chip devices for efficient parallelization of biological and biochemical reactions under reduced uptake of reactants. In the world of chemistry, however, up until now, miniaturization has played a minor role. The chemical and thermal stability of regular 3D printing resins is insufficient for sustaining the harsh conditions of chemical reactions. Novel material formulations that produce highly stable 3D‐printed chips are highly sought for bringing chemistry up‐to‐date on the development of miniaturization. In this work, a brief review of recent developments in highly stable materials for 3D printing is given. This work focuses on three highly stable 3D‐printable material systems: transparent silicate glasses, ceramics, and fluorinated polymers. It is further demonstrated that 3D printing is also a versatile technique for surface structuring of polymers to enhance their wetting performance. Such micro/nanostructuring is key to selectively wetting surface patterns that are versatile for chemical arrays and droplet synthesis.
DNA Replication Through Strand Displacement During Lagging Strand DNA Synthesis in Saccharomyces cerevisiae

This review discusses a set of experimental results that support the existence of extended strand displacement events during budding yeast lagging strand DNA synthesis. Starting from introducing the mechanisms and factors involved in leading and lagging strand DNA synthesis and some aspects of the architecture of the eukaryotic replisome, we discuss studies on bacterial, bacteriophage and viral DNA polymerases with potent strand displacement activities. We describe proposed pathways of Okazaki fragment processing via short and long flaps, with a focus on experimental results obtained in Saccharomyces cerevisiae that suggest the existence of frequent and extended strand displacement events during eukaryotic lagging strand DNA synthesis, and comment on their implications for genome integrity.