Miracle-dz/UniFAR-FTUs huggingface dataset:
Changes in the Ultrastructure of Candida albicans Treated with Cationic Peptides

Candida albicans is becoming increasingly harmful for humans, which determines the need for new effective antifungal preparations. Currently, when testing antifungals, various morphological methods are used, among which transmission electron microscopy (TEM) is not the leading one. In this work, we used TEM to study the submicroscopic changes in C. albicans cells induced by cationic peptides R9F2 and (KFF)3K. Studies were performed on C. albicans-34 strain from the Collection of EMTC of ICBFM SB RAS in logarithmic phase. R9F2 and (KFF)3K showed an antifungal effect (MIC 10 and 20 μM) and suppressed fungal hyphal growth. Semithin and ultrathin sections of fungal suspensions incubated with 10 μM of peptides were studied at regular intervals from 15 min to 24 h. The first target of both peptides was plasmalemma, and its “alignment” was the only common morphological manifestation of their effect. Other changes in the plasmalemma and alteration of the vacuole and cell wall ultrastructure distinctly differed in cells treated with R9F2 and (KFF)3K peptides. In general, our work has shown pronounced differences of the temporal and morphologic characteristics of the effect of peptides, evidently related to their physicochemical properties. The benefit of TEM studies of ultrathin sections for understanding the mechanisms of action of antifungal drugs is shown.
The effect of gold and silver nanoparticles, chitosan and their combinations on bacterial biofilms of food-borne pathogens

Abstract The antimicrobial activity of gold and silver nanoparticles (AuNPs, AgNPs), chitosan (CS) and their combinations was established by determining the minimum inhibitory concentration for planktonic (MICPC80) and biofilm growth (MICBC80), for biofilm formation (MICBF80), metabolic activity (MICBM80) and reduction (MICBR80), and for the metabolic activity of preformed biofilm (MICMPB80). Biofilms were quantified in microtitre plates by crystal violet staining and metabolic activity was evaluated by the MTT assay. Chitosan effectively suppressed biofilm formation (0.31–5 mg ml−1) in all the tested strains, except Salmonella enterica Infantis (0.16–2.5 mg ml−1) where CS and its combination with AgNPs induced biofilm formation. Nanoparticles inhibited biofilm growth only when the highest concentrations were used. Even though AuNPs, AgNPs and CS were not able to remove biofilm mass, they reduced its metabolic activity by at least 80%. The combinations of nanoparticles with CS did not show any significant positive synergistic effect on the tested target properties.
"It should not be that difficult to manage a condition that is so frequent": A qualitative study on hospital nurses' experience of delirium guidelines.

AIMS AND OBJECTIVES To explore hospital nurses' experiences of enablers and barriers to apply the recommendations of a hospital delirium guideline, focusing on identification and non-pharmacological prevention and treatment. BACKGROUND Nurses' application of delirium guidelines is important as they have a pivotal role in identifying, preventing and managing delirium. Research is sparse concerning barriers and enablers to nurses´ application of guideline recommendations on non-pharmacological prevention and treatment of delirium. DESIGN Qualitative design using focus group and individual interviews. METHODS Twenty-three nurses, nurse supervisors and senior staff nurses from four departments in a Danish 530-bed university hospital participated in the study. The interview guide was based on the Theoretical Domains Framework. Data was analyzed using inductive content analysis. The COREQ checklist was used preparing the manuscript. RESULTS The analysis identified four main categories concerning barriers and enablers to applying the recommendations of a delirium guideline; factors relating to employing the guideline, the individual nurse, collaboration, and the context. Lack of identification of delirium and lack of preventive actions were prominent, with inter-related barriers such as lack of knowledge, lack of meaningfulness, lack of priority, lack of resources and working conditions, causing frustration and discouragement in the nurses. CONCLUSIONS The study identified a wide range of barriers and enablers experienced by hospital nurses to the application of a delirium guideline, showing the complexity of delirium care and applying guidelines. RELEVANCE TO CLINICAL PRACTICE Improving the identification, prevention and treatment for patients with delirium requires a determined and focused effort from all stakeholders, both clinicians, leaders and policy makers. Nurses, nurse leaders and educators must be aware of the barriers and enablers related to knowledge, attitudes and cooperation. Managers and policymakers must be aware of the organizational factors related to priority and working conditions.
Factors Disrupting Melatonin Secretion Rhythms During Critical Illness

Supplemental Digital Content is available in the text. Objectives: The circadian system modulates many important physiologic processes, synchronizing tissue-specific functions throughout the body. We sought to characterize acute alterations of circadian rhythms in critically ill patients and to evaluate associations between brain dysfunction, systemic multiple organ dysfunction, environmental stimuli that entrain the circadian rhythm (zeitgebers), rest-activity rhythms, and the central circadian rhythm-controlled melatonin secretion profile. Design: Prospective study observing a cohort for 24–48 hours beginning within the first day of ICU admission. Setting: Multiple specialized ICUs within an academic medical center. Patients: Patients presenting from the community with acute onset of either intracerebral hemorrhage as a representative neurologic critical illness or sepsis as a representative systemic critical illness. Healthy control patients were studied in using modified constant routine in a clinical research unit. Interventions: None. Measurements and Main Results: Light, feeding, activity, medications, and other treatment exposures were evaluated along with validated measures of encephalopathy (Glasgow Coma Scale), multiple organ system function (Sequential Organ Failure Assessment score), and circadian rhythms (profiles of serum melatonin and its urinary metabolite 6-sulphatoxymelatonin). We studied 112 critically ill patients, including 53 with sepsis and 59 with intracerebral hemorrhage. Environmental exposures were abnormal, including light (dim), nutritional intake (reduced or absent and mistimed), and arousal stimuli (increased and mistimed). Melatonin amplitude and acrophase timing were generally preserved in awake patients but dampened and delayed with increasing encephalopathy severity. Melatonin hypersecretion was observed in patients exposed to catecholamine vasopressor infusions, but unaffected by sedatives. Change in vasopressor exposure was the only factor associated with changes in melatonin rhythms between days 1 and 2. Conclusions: Encephalopathy severity and adrenergic agonist medication exposure were the primary factors contributing to abnormal melatonin rhythms. Improvements in encephalopathy and medical stabilization did not rapidly normalize rhythms. Urinary 6-sulphatoxymelatonin is not a reliable measure of the central circadian rhythm in critically ill patients.
Astragalus polysaccharides attenuate pulmonary fibrosis by inhibiting the epithelial-mesenchymal transition and NF-κB pathway activation

Astragalus polysaccharides (APS), the active ingredients isolated from the plant Astragalus, have been reported to have numerous biological activities, including anti-inflammatory and antitumor activities. However, the effect of APS on pulmonary fibrosis (PF) remains unknown. The present study aimed to evaluate the protective effect of APS against PF and to explore its underlying mechanisms by using in vivo and in vitro models. A mouse in vivo model of bleomycin-induced PF and an in vitro model of transforming growth factor β1 (TGF-β1)-stimulated human lung epithelial A549 cells were established. Histopathologic examination and collagen deposition were investigated by hematoxylin and eosin staining and Masson staining, and by detecting the hydroxyproline content. The expression of related genes was analyzed by western blotting, reverse transcription-quantitative (RT-q) PCR, immunofluorescence and immunohistochemistry. The results from the in vivo mouse model demonstrated that treatment with APS could ameliorate collagen deposition and reduce fibrotic area and hydroxyproline content in the matrix. Furthermore, APS significantly inhibited the epithelial-mesenchymal transition (EMT), as evidenced by an increased level of E-cadherin and a decreased expression of vimentin and alpha smooth muscle actin. Furthermore, APS treatment significantly decreased TGF-β1-induced EMT and NF-κB pathway activation in vitro. The results from the present study provided new insights on PF regression via the anti-fibrotic effects of APS.
Severe Plastid Genome Size Reduction in a Mycoheterotrophic Orchid, Danxiaorchis singchiana, Reveals Heavy Gene Loss and Gene Relocations

Danxiaorchis singchiana (Orchidaceae) is a leafless mycoheterotrophic orchid in the subfamily Epidendroideae. We sequenced the complete plastome of D. singchiana. The plastome has a reduced size of 87,931 bp, which includes a pair of inverted repeat (IR) regions of 13,762 bp each that are separated by a large single copy (LSC) region of 42,575 bp and a small single copy (SSC) region of 17,831 bp. When compared to its sister taxa, Cremastra appendiculata and Corallorhiza striata var. involuta, D. singchiana showed an inverted gene block in the LSC and SSC regions. A total of 61 genes were predicted, including 21 tRNA, 4 rRNA, and 36 protein-coding genes. While most of the housekeeping genes were still intact and seem to be protein-coding, only four photosynthesis-related genes appeared presumably intact. The majority of the presumably intact protein-coding genes seem to have undergone purifying selection (dN/dS < 1), and only the psaC gene was positively selected (dN/dS > 1) when compared to that in Cr. appendiculata. Phylogenetic analysis of 26 complete plastome sequences from 24 species of the tribe Epidendreae had revealed that D. singchiana diverged after Cr. appendiculata and is sister to the genus Corallorhiza with strong bootstrap support (100%).
Targeting the Tumor Microenvironment with Fluorescence-Activatable Bispecific Endoglin/Fibroblast Activation Protein Targeting Liposomes

Liposomes are biocompatible nanocarriers with promising features for targeted delivery of contrast agents and drugs into the tumor microenvironment, for imaging and therapy purposes. Liposome-based simultaneous targeting of tumor associated fibroblast and the vasculature is promising, but the heterogeneity of tumors entails a thorough validation of suitable markers for targeted delivery. Thus, we elucidated the potential of bispecific liposomes targeting the fibroblast activation protein (FAP) on tumor stromal fibroblasts, together with endoglin which is overexpressed on tumor neovascular cells and some neoplastic cells. Fluorescence-quenched liposomes were prepared by hydrating a lipid film with a high concentration of the self-quenching near-infrared fluorescent dye, DY-676-COOH, to enable fluorescence detection exclusively upon liposomal degradation and subsequent activation. A non-quenched green fluorescent phospholipid was embedded in the liposomal surface to fluorescence-track intact liposomes. FAP- and murine endoglin-specific single chain antibody fragments were coupled to the liposomal surface, and the liposomal potentials validated in tumor cells and mice models. The bispecific liposomes revealed strong fluorescence quenching, activatability, and selectivity for target cells and delivered the encapsulated dye selectively into tumor vessels and tumor associated fibroblasts in xenografted mice models and enabled their fluorescence imaging. Furthermore, detection of swollen lymph nodes during intra-operative simulations was possible. Thus, the bispecific liposomes have potentials for targeted delivery into the tumor microenvironment and for image-guided surgery.
Temporal Dynamics of Treatment Receipt in a Text Message Intervention for Physical Activity: Single-Group, Within-Person Trial

Background Mobile technology has increased the reach of health behavior interventions but raised new challenges in assessing the fidelity of treatment receipt. Fidelity can be compromised if participant fatigue or burden reduces engagement, leading to missed or delayed treatments for just-in-time interventions. Objective This study aimed to investigate the temporal dynamics of text message receipt confirmations. Methods Community-dwelling adults (N=10) were sent five text messages daily for 4 months (5598 messages sent in total), with a financial incentive to confirm receipt of 75% or more messages. Results Overall, the message receipt confirmation rate was very high (5504/5598, 98.32%) and timely (eg, two-thirds of confirmations within 2 min). Confirmation times were slightly slower on weekends (vs weekdays) and as a function of the cumulative time in the study. Neither time of message delivery nor message content was associated with message confirmation latencies. Conclusions Participants receiving financial incentives to confirm text message receipt exhibit extremely high and fast confirmation rates, although receipt confirmations were somewhat less timely on weekends (vs weekdays) and later in the intervention. The social calendar and treatment fatigue should be considered when planning text message–based interventions, especially if treatments are intended for a just-in-time delivery that requires extended engagement and precise timing.
ErCas12a CRISPR-MAD7 for Model Generation in Human Cells, Mice, and Rats

MAD7 is an engineered class 2 type V-A CRISPR-Cas (Cas12a/Cpf1) system isolated from Eubacterium rectale. Analogous to Cas9, it is an RNA-guided nuclease with demonstrated gene editing activity in Escherichia coli and yeast cells. Here, we report that MAD7 is capable of generating indels and fluorescent gene tagging of endogenous genes in human HCT116 and U2OS cancer cell lines, respectively. In addition, MAD7 is highly proficient in generating indels, small DNA insertions (23 bases), and larger integrations ranging from 1 to 14 kb in size in mouse and rat embryos, resulting in live-born transgenic animals. Due to the different protospacer adjacent motif requirement, small-guide RNA, and highly efficient targeted gene disruption and insertions, MAD7 can expand the CRISPR toolbox for genome enginnering across different systems and model organisms.
Pharmacological treatment of depression: A systematic review comparing clinical practice guideline recommendations

Depression affects over 300 million individuals worldwide and is responsible for most of the 800,000 annual suicides. Clinical practice guidelines (CPGs) for treatment of depression, founded on scientific evidence, are essential to improve patient care. However, economic and sociocultural factors may influence CPG elaboration, potentially leading to divergences in their recommendations. Consequently, we analyzed pharmacological recommendations for the treatment of depression from the most relevant CPGs. We included four CPGs with scores ≥ 80% for Domain 3 (rigor of development) on the Appraisal of Guidelines for Research and Evaluation and two other commonly used CPGs. The recommendations, their strengths, and the level of evidence were extracted from each CPG by two independent researchers and grouped as follows: (1) general recommendations for the pharmacological treatment for depression (suicide risk, acute treatment, continuation and maintenance phases, and treatment discontinuation); (2) treatment of non-responsive or partially responsive patients; and (3) treatment for subtypes of depression (chronic, psychotic, catatonic, melancholic, seasonal, somatic, mixed, and atypical). Only 50% of CPGs included recommendations for the risk of suicide associated with pharmacotherapy. All CPGs included serotonin selective reuptake inhibitors (SSRIs) as first-line treatment; however, one CPG also included agomelatine, milnacipran, and mianserin as first-line alternatives. Recommendations for depression subtypes (catatonic, atypical, melancholic) were included in three CPGs. The strength of recommendation and level of evidence clearly differed among CPGs, especially regarding treatment augmentation strategies. We conclude that, although CPGs converged in some recommendations (e.g., SSRIs as first-line treatment), they diverged in cardinal topics including the absence of recommendations regarding the risk of suicide associated with pharmacotherapy. Consequently, the recommendations listed in a specific CPG should be followed with caution.
Variability in engagement and progress in efficacious integrated collaborative care for primary care patients with obesity and depression: Within-treatment analysis in the RAINBOW trial

Introduction The RAINBOW randomized clinical trial validated the efficacy of an integrated collaborative care intervention for obesity and depression in primary care, although the effect was modest. To inform intervention optimization, this study investigated within-treatment variability in participant engagement and progress. Methods Data were collected in 2014–2017 and analyzed post hoc in 2018. Cluster analysis evaluated patterns of change in weekly self-monitored weight from week 6 up to week 52 and depression scores on the Patient Health Questionnaire-9 (PHQ-9) from up to 15 individual sessions during the 12-month intervention. Chi-square tests and ANOVA compared weight loss and depression outcomes objectively measured by blinded assessors to validate differences among categories of treatment engagement and progress defined based on cluster analysis results. Results Among 204 intervention participants (50.9 [SD, 12.2] years, 71% female, 72% non-Hispanic White, BMI 36.7 [6.9], PHQ-9 14.1 [3.2]), 31% (n = 63) had poor engagement, on average completing self-monitored weight in <3 of 46 weeks and <5 of 15 sessions. Among them, 50 (79%) discontinued the intervention by session 6 (week 8). Engaged participants (n = 141; 69%) self-monitored weight for 11–22 weeks, attended almost all 15 sessions, but showed variable treatment progress based on patterns of change in self-monitored weight and PHQ-9 scores over 12 months. Three patterns of weight change (%) represented minimal weight loss (n = 50, linear β1 = -0.06, quadratic β2 = 0.001), moderate weight loss (n = 61, β1 = -0.28, β2 = 0.002), and substantial weight loss (n = 12, β1 = -0.53, β2 = 0.005). Three patterns of change in PHQ-9 scores represented moderate depression without treatment progress (n = 40, intercept β0 = 11.05, β1 = -0.11, β2 = 0.002), moderate depression with treatment progress (n = 20, β0 = 12.90, β1 = -0.42, β2 = 0.006), and milder depression with treatment progress (n = 81, β0 = 7.41, β1 = -0.23, β2 = 0.003). The patterns diverged within 6–8 weeks and persisted throughout the intervention. Objectively measured weight loss and depression outcomes were significantly worse among participants with poor engagement or poor progress on either weight or PHQ-9 than those showing progress on both. Conclusions Participants demonstrating poor engagement or poor progress could be identified early during the intervention and were more likely to fail treatment at the end of the intervention. This insight could inform individualized and timely optimization to enhance treatment efficacy. Trial registration ClinicalTrials.gov# NCT02246413.
The linker domain of the SNARE protein SNAP25 acts as a flexible molecular spacer that ensures efficient S-acylation

S-Acylation of the SNARE protein SNAP25 (synaptosome-associated protein of 25 kDa) is mediated by a subset of Golgi zinc finger DHHC-type palmitoyltransferase (zDHHC) enzymes, particularly zDHHC17. The ankyrin repeat domain of zDHHC17 interacts with a short linear motif known as the zDHHC ankyrin repeat–binding motif (zDABM) in SNAP25 (112VVASQP117), which is downstream of its S-acylated, cysteine-rich domain (85CGLCVCPC92). Here, we investigated the importance of a flexible linker region (amino acids 93–111, referred to hereafter as the “mini-linker” region) that separates the zDABM and S-acylated cysteines in SNAP25. Shortening the mini-linker did not affect the SNAP25–zDHHC17 interaction but blocked S-acylation. Insertion of additional flexible glycine-serine repeats had no effect on S-acylation, but extended and rigid alanine-proline repeats perturbed it. A SNAP25 mutant in which the mini-linker region was substituted with a flexible glycine-serine linker of the same length underwent efficient S-acylation. Furthermore, this mutant displayed the same intracellular localization as WT SNAP25, indicating that the amino acid composition of the mini-linker is not important for SNAP25 localization. Using the results of previous peptide array experiments, we generated a SNAP25 mutant predicted to have a higher-affinity zDABM. This mutant interacted with zDHHC17 more strongly but was S-acylated with reduced efficiency in HEK293T cells, implying that a lower-affinity interaction of the SNAP25 zDABM with zDHHC17 is optimal for S-acylation efficiency. These results show that amino acids 93–111 in SNAP25 act as a flexible molecular spacer that ensures efficient coupling of the SNAP25–zDHHC17 interaction and S-acylation of SNAP25.