Miracle-dz/UniFAR-FTUs huggingface dataset:
Mechanisms of a Cyclobutane-Fused Lactone Hydrolysis in Alkaline and Acidic Conditions

Searching for functional polyesters with stability and degradability is important due to their potential applications in biomedical supplies, biomass fuel, and environmental protection. Recently, a cyclobutane-fused lactone (CBL) polymer was experimentally found to have superior stability and controllable degradability through hydrolysis reactions after activation by mechanical force. In order to provide a theoretical basis for developing new functional degradable polyesters, in this work, we performed a detailed quantum chemical study of the alkaline and acidic hydrolysis of CBL using dispersion-corrected density functional theory (DFT-D3) and mixed implicit/explicit solvent models. Various possible hydrolysis mechanisms were found: BAC2 and BAL2 in the alkaline condition and AAC2, AAL2, and AAL1 in the acidic condition. Our calculations indicated that CBL favors the BAC2 and AAC2 mechanisms in alkaline and acidic conditions, respectively. In addition, we found that incorporating explicit water solvent molecules is highly necessary because of their strong hydrogen-bonding with reactant/intermediate/product molecules.
Fibrin Clot Formation under Oxidative Stress Conditions

During coagulation, the soluble fibrinogen is converted into insoluble fibrin. Fibrinogen is a multifunctional plasma protein, which is essential for hemostasis. Various oxidative posttranslational modifications influence fibrinogen structure as well as interactions between various partners in the coagulation process. The aim was to examine the effects of oxidative stress conditions on fibrin clot formation in arterial atherothrombotic disorders. We studied the changes in in vitro fibrin network formation in three groups of patients—with acute coronary syndrome (ACS), with significant carotid artery stenosis (SCAS), and with acute ischemic stroke (AIS), as well as a control group. The level of oxidative stress marker malondialdehyde measured by LC-MS/MS was higher in SCAS and AIS patients compared with controls. Turbidic methods revealed a higher final optical density and a prolonged lysis time in the clots of these patients. Electron microscopy was used to visualize changes in the in vitro-formed fibrin network. Fibers from patients with AIS were significantly thicker in comparison with control and ACS fibers. The number of fibrin fibers in patients with AIS was significantly lower in comparison with ACS and control groups. Thus, oxidative stress-mediated changes in fibrin clot formation, structure and dissolution may affect the effectiveness of thrombolytic therapy.
Candida Oleophila Proliferated and Accelerated Accumulation of Suberin Poly Phenolic and Lignin at Wound Sites of Potato Tubers

Candida oleophila is a type of biocontrol yeast offering effective postharvest disease control. To the best of our knowledge, the effect of C. oleophila upon the healing of tubers is yet to be studied. The present study addresses the existing knowledge gap by investigating the effect of C. oleophila on wound healing in potato tubers. The results show that C. oleophila colonized and proliferated at the wound sites during the early and intermediate stages of healing. In addition, C. oleophila reduced weight loss of wounded tubers, decreased disease index of inoculated tubers with Fusarium sulphureum, and accelerated accumulation of suberin poly phenolic (SPP) and lignin at wound sites. C. oleophila activated phenylpropanoid metabolism and increased the content of SPP monomers, total phenol, flavonoids, and lignin. Furthermore, the yeast increased H2O2 content as well as peroxidase activity.
Integrative Modelling of Gene Expression and Digital Phenotypes to Describe Senescence in Wheat

Senescence is the final stage of leaf development and is critical for plants’ fitness as nutrient relocation from leaves to reproductive organs takes place. Although senescence is key in nutrient relocation and yield determination in cereal grain production, there is limited understanding of the genetic and molecular mechanisms that control it in major staple crops such as wheat. Senescence is a highly orchestrated continuum of interacting pathways throughout the lifecycle of a plant. Levels of gene expression, morphogenesis, and phenotypic development all play key roles. Yet, most studies focus on a short window immediately after anthesis. This approach clearly leaves out key components controlling the activation, development, and modulation of the senescence pathway before anthesis, as well as during the later developmental stages, during which grain development continues. Here, a computational multiscale modelling approach integrates multi-omics developmental data to attempt to simulate senescence at the molecular and plant level. To recreate the senescence process in wheat, core principles were borrowed from Arabidopsis Thaliana, a more widely researched plant model. The resulted model describes temporal gene regulatory networks and their effect on plant morphology leading to senescence. Digital phenotypes generated from images using a phenomics platform were used to capture the dynamics of plant development. This work provides the basis for the application of computational modelling to advance understanding of the complex biological trait senescence. This supports the development of a predictive framework enabling its prediction in changing or extreme environmental conditions, with a view to targeted selection for optimal lifecycle duration for improving resilience to climate change.
Caries Experience of Adults with Intellectual Disability in the Western Part of Germany

Background: In Germany, there is limited evidence on the oral health of adults with intellectual disabilities (AwID). Methods: In 2017/18, dental examinations of AwID and a questionnaire survey of their legal guardians were carried out. The mean D3MFT values were calculated to describe the caries experience. The prevalence of AwID with at least one fissure sealant (FS) was determined and associations between caries experience and various sociodemographic factors (e.g., age, gender, living arrangements) were investigated. Results: The data of 132 AwID (mean age 35.2 years; range 18–69 years) could be included. For all AwIDs the mean D3MFT value was 9.5 (95% CI 8.1–11.0). The mean D3MFT value for the 35–44-year-olds was 10.9 (95% CI 8.4–13.4). All caries-free persons (n = 14) were younger than 45 years. Furthermore, the mean D3MFT value for AwID living with their parents was lower at a statistically significant level than that of AwID in independent living arrangements. Moreover, younger AwIDs (18–34-year-olds) with at least one FS had a statistically significantly lower mean D3MFT value compared to those without any FS (D3MFT: 3.0 vs. 6.7). Conclusions: The dental health of AwID has improved in Germany in recent years, but, on average, AwIDs still have more missing teeth than their peers in the general population. Oral epidemiological studies on AwID should include information on their living arrangements to assess potential associations between sociodemographic factors and oral health.
Optimized Supercritical CO2 Extraction Enhances the Recovery of Valuable Lipophilic Antioxidants and Other Constituents from Dual-Purpose Hop (Humulus lupulus L.) Variety Ella

The article presents the optimization of supercritical CO2 extraction (SFE-CO2) parameters using response surface methodology (RSM) with central composite design (CCD) in order to produce single variety hop (cv. Ella) extracts with high yield and strong in vitro antioxidant properties. Optimized SFE-CO2 (37 MPa, 43 °C, 80 min) yielded 26.3 g/100 g pellets of lipophilic fraction. This extract was rich in biologically active α- and β-bitter acids (522.8 and 345.0 mg/g extract, respectively), and exerted 1481 mg TE/g extract in vitro oxygen radical absorbance capacity (ORAC). Up to ~3-fold higher extraction yield, antioxidant recovery (389.8 mg TE/g pellets) and exhaustive bitter acid extraction (228.4 mg/g pellets) were achieved under the significantly shorter time compared to the commercially used one-stage SFE-CO2 at 10–15 MPa and 40 °C. Total carotenoid and chlorophyll content was negligible, amounting to <0.04% of the total extract mass. Fruity, herbal, spicy and woody odor of extracts could be attributed to the major identified volatiles, namely β-pinene, β-myrcene, β-humulene, α-humulene, α-selinene and methyl-4-decenoate. Rich in valuable bioactive constituents and flavor compounds, cv. Ella hop SFE-CO2 extracts could find multipurpose applications in food, pharmaceutical, nutraceutical and cosmetics industries.
Essential Oil and Major Non-Volatile Secondary Metabolites from the Leaves of Amazonian Piper subscutatum

The essential oil and the major non-volatile secondary metabolites from the leaves of Piper subscutatum (Miq.) C. DC. (Family Piperaceae), collected in the Ecuadorian Amazon, were analyzed for the first time in the present study. The essential oil was submitted to chemical and enantioselective analyses by GC-MS and GC-FID. (E)-β-caryophyllene (25.3–25.2%), β-chamigrene (10.3–7.8%), (E)-nerolidol (8.1–7.7%), β-selinene (7.2–7.7%), δ-cadinene (2.7–3.9%), bicyclogermacrene (3.7–2.4%), and β-pinene (2.6–3.4%) were the major components. The enantioselective analysis, carried out on a β-cyclodextrin-based column, showed four scalemic mixtures in which (1R,5R)-(+)-α-pinene, (1S,5S)-(−)-β-pinene, (S)-(−)-limonene, and (1R,2S,6S,7S,8S)-(−)-α-copaene were the major enantiomers, with enantiomeric excesses of 28.8%, 77.8%, 18.4%, and 6.0%, respectively. The study was complemented with the chemical analysis of the organic fraction dissolved in the hydrolate, whose major components were 6-methyl-5-hepten-2-one (63.7–64.4%) and linalool (6.5–6.0%). Concerning the non-volatile fraction, five lignans were the major components. (–)-Beilshminol B, (–)-grandisin, (–)-3′,4′-methylenedioxy-3,4,5-trimethoxy-7,7′-epoxylignan, (–)-3′,4′-methylenedioxy-3,4,5,5′-tetramethoxy-7,7′-epoxylignan, and (–)-3,4,3′,4′-dimethylenedioxy-5,5′-dimethoxy-7,7′-epoxylignan were identified by means of NMR spectroscopy, mass spectrometry and X-ray crystallography. The absolute configuration 7S,8S,7′S,8′S was tentatively assigned to all of them.
Comparative Transcriptome Analysis Reveals Sex-Based Differences during the Development of the Adult Parasitic Wasp Cotesia vestalis (Hymenoptera: Braconidae)

The endoparasitic wasp Cotesia vestalis is an important biological agent for controlling the population of Plutella xylostella, a major pest of cruciferous crops worldwide. Though the genome of C. vestalis has recently been reported, molecular mechanisms associated with sexual development have not been comprehensively studied. Here, we combined PacBio Iso-Seq and Illumina RNA-Seq to perform genome-wide profiling of pharate adult and adult development of male and female C. vestalis. Taking advantage of Iso-Seq full-length reads, we identified 14,466 novel transcripts as well as 8770 lncRNAs, with many lncRNAs showing a sex- and stage-specific expression pattern. The differentially expressed gene (DEG) analyses showed 2125 stage-specific and 326 sex-specific expressed genes. We also found that 4819 genes showed 11,856 alternative splicing events through combining the Iso-Seq and RNA-Seq data. The results of comparative analyses showed that most genes were alternatively spliced across developmental stages, and alternative splicing (AS) events were more prevalent in females than in males. Furthermore, we identified six sex-determining genes in this parasitic wasp and verified their sex-specific alternative splicing profiles. Specifically, the characterization of feminizer and doublesex splicing between male and female implies a conserved regulation mechanism of sexual development in parasitic wasps.
Lipid-Based Nanostructures for the Delivery of Natural Antimicrobials

Encapsulation can be a suitable strategy to protect natural antimicrobial substances against some harsh conditions of processing and storage and to provide efficient formulations for antimicrobial delivery. Lipid-based nanostructures, including liposomes, solid lipid nanoparticles (SLNs), and nanostructured lipid nanocarriers (NLCs), are valuable systems for the delivery and controlled release of natural antimicrobial substances. These nanostructures have been used as carriers for bacteriocins and other antimicrobial peptides, antimicrobial enzymes, essential oils, and antimicrobial phytochemicals. Most studies are conducted with liposomes, although the potential of SLNs and NLCs as antimicrobial nanocarriers is not yet fully established. Some studies reveal that lipid-based formulations can be used for co-encapsulation of natural antimicrobials, improving their potential to control microbial pathogens.
The Role of Autophagy in Varicella Zoster Virus Infection

Autophagy is an evolutionary conserved cellular process serving to degrade cytosolic organelles or foreign material to maintain cellular homeostasis. Autophagy has also emerged as an important process involved in complex interactions with viral pathogens during infection. It has become apparent that autophagy may have either proviral or antiviral roles, depending on the cellular context and the specific virus. While evidence supports an antiviral role of autophagy during certain herpesvirus infections, numerous examples illustrate how herpesviruses may also evade autophagy pathways or even utilize this process to their own advantage. Here, we review the literature on varicella zoster virus (VZV) and autophagy and describe the mechanisms by which VZV may stimulate autophagy pathways and utilize these to promote cell survival or to support viral egress from cells. We also discuss recent evidence supporting an overall antiviral role of autophagy, particularly in relation to viral infection in neurons. Collectively, these studies suggest complex and sometimes opposing effects of autophagy in the context of VZV infection. Much remains to be understood concerning these virus–host interactions and the impact of autophagy on infections caused by VZV.
Integrative Taxonomic, Ecological and Genotyping Study of Charophyte Populations from the Egyptian Western-Desert Oases and Sinai Peninsula

Present-day information available on the charophyte macroalgae in Egypt, including their phylogenetic affinities, remains largely incomplete. In this study, nine charophyte populations were collected from different aquatic biotopes across the Egyptian Western-Desert Oases and Sinai Peninsula. All populations were investigated using an integrative polyphasic approach including phylogenetic analyses inferred from the chloroplast-encoded gene (rbcL) and the internal transcribed spacer (ITS1) regions, in parallel with morphotaxonomic assignment, ultrastructure of the oospore walls, and autecology. The specimens identified belonged to the genera Chara, Nitella, and Tolypella, with predominance of the first genus to which five species were assigned though they presented some interesting aberrant taxonomic features: C. aspera, C. contraria, C. globata, C. tomentosa, and C. vulgaris. Based on our integrative study, the globally rare species C. globata was reported for the second time for the whole African continent. The genus Nitella was only represented by N. flagellifera, and based on the available literature, it is a new record for North Africa. Noteworthy, an interesting Tolypella sp. , morphologically very similar to T. glomerata, was collected and characterized and finally designated with the working name ‘Tolypella sp. PBA–1704 from a desert, freshwater wetland’, mainly based on its concatenated rbcL+ITS1 phylogenetic position. This study not only improved our understanding on the diversity, biogeography and autecological preferences of charophytes in Egypt, but it also broadened our knowledge on this vulnerable algal group in North Africa, emphasizing the need of more in-depth research work in the future, particularly in the less–impacted desert habitats.
Peptide Triazole Thiol Irreversibly Inactivates Metastable HIV-1 Env by Accessing Conformational Triggers Intrinsic to Virus–Cell Entry

KR13, a peptide triazole thiol previously established to inhibit HIV-1 infection and cause virus lysis, was evaluated by flow cytometry against JRFL Env-presenting cells to characterize induced Env and membrane transformations leading to irreversible inactivation. Transiently transfected HEK293T cells were preloaded with calcein dye, treated with KR13 or its thiol-blocked analogue KR13b, fixed, and stained for gp120 (35O22), MPER (10E8), 6-helix-bundle (NC-1), immunodominant loop (50-69), and fusion peptide (VRC34.01). KR13 induced dose-dependent transformations of Env and membrane characterized by transient poration, MPER exposure, and 6-helix-bundle formation (analogous to native fusion events), but also reduced immunodominant loop and fusion peptide exposure. Using a fusion peptide mutant (V504E), we found that KR13 transformation does not require functional fusion peptide for poration. In contrast, simultaneous treatment with fusion inhibitor T20 alongside KR13 prevented membrane poration and MPER exposure, showing that these events require 6-helix-bundle formation. Based on these results, we formulated a model for PTT-induced Env transformation portraying how, in the absence of CD4/co-receptor signaling, PTT may provide alternate means of perturbing the metastable Env-membrane complex, and inducing fusion-like transformation. In turn, the results show that such transformations are intrinsic to Env and can be diverted for irreversible inactivation of the protein complex.
A Multi-Rheology Design Method of Sheeting Polymer Extrusion Dies Based on Flow Network and the Winter–Fritz Design Equation

In the polymer sheet processing industry, the primary objective when designing a coat-hanger die is to achieve a uniform velocity distribution at the exit of the extrusion die outlet. This velocity distribution depends on the internal flow channels of the die, rheological parameters and extrusion process conditions. As a result, coat-hanger dies are often designed for each polymer based on its individual rheological data and other conditions. A multi-rheology method based on a flow network model and the Winter–Fritz equation is proposed and implemented for the calculation, design and optimization of flat sheeting polymer extrusion dies. This method provides a fast and accurate algorithm to obtain die design geometries with constant wall-shear rates and optimal outlet velocity distributions. The geometric design when complemented and validated with fluid flow simulations could be applied for multi-rheological fluid models such as the power-law, Carreau–Yasuda and Cross. This method is applied to sheet dies with both circular- and rectangular-shaped manifolds for several rheological fluids. The designed geometrical parameters are obtained, and the associated fluid simulations are performed to demonstrate its favorable applicability without being limited to only the power-law rheology. The two such designed dies exhibit 32.9 and 21.5 percent improvement in flow uniformity compared to the previous methods for dies with circular and rectangular manifolds, respectively.
Genotoxicity and Gene Expression in the Rat Lung Tissue following Instillation and Inhalation of Different Variants of Amorphous Silica Nanomaterials (aSiO2 NM)

Several reports on amorphous silica nanomaterial (aSiO2 NM) toxicity have been questioning their safety. Herein, we investigated the in vivo pulmonary toxicity of four variants of aSiO2 NM: SiO2_15_Unmod, SiO2_15_Amino, SiO2_7 and SiO2_40. We focused on alterations in lung DNA and protein integrity, and gene expression following single intratracheal instillation in rats. Additionally, a short-term inhalation study (STIS) was carried out for SiO2_7, using TiO2_NM105 as a benchmark NM. In the instillation study, a significant but slight increase in oxidative DNA damage in rats exposed to the highest instilled dose (0.36 mg/rat) of SiO2_15_Amino was observed in the recovery (R) group. Exposure to SiO2_7 or SiO2_40 markedly increased oxidative DNA lesions in rat lung cells of the exposure (E) group at every tested dose. This damage seems to be repaired, since no changes compared to controls were observed in the R groups. In STIS, a significant increase in DNA strand breaks of the lung cells exposed to 0.5 mg/m3 of SiO2_7 or 50 mg/m3 of TiO2_NM105 was observed in both groups. The detected gene expression changes suggest that oxidative stress and/or inflammation pathways are likely implicated in the induction of (oxidative) DNA damage. Overall, all tested aSiO2 NM were not associated with marked in vivo toxicity following instillation or STIS. The genotoxicity findings for SiO2_7 from instillation and STIS are concordant; however, changes in STIS animals were more permanent/difficult to revert.
Exercise Ventilatory Inefficiency in Post-COVID-19 Syndrome: Insights from a Prospective Evaluation

Introduction: Coronavirus disease 2019 (COVID-19) is a systemic disease characterized by a disproportionate inflammatory response in the acute phase. This study sought to identify clinical sequelae and their potential mechanism. Methods: We conducted a prospective single-center study (NCT04689490) of previously hospitalized COVID-19 patients with and without dyspnea during mid-term follow-up. An outpatient group was also evaluated. They underwent serial testing with a cardiopulmonary exercise test (CPET), transthoracic echocardiogram, pulmonary lung test, six-minute walking test, serum biomarker analysis, and quality of life questionaries. Results: Patients with dyspnea (n = 41, 58.6%), compared with asymptomatic patients (n = 29, 41.4%), had a higher proportion of females (73.2 vs. 51.7%; p = 0.065) with comparable age and prevalence of cardiovascular risk factors. There were no significant differences in the transthoracic echocardiogram and pulmonary function test. Patients who complained of persistent dyspnea had a significant decline in predicted peak VO2 consumption (77.8 (64–92.5) vs. 99 (88–105); p < 0.00; p < 0.001), total distance in the six-minute walking test (535 (467–600) vs. 611 (550–650) meters; p = 0.001), and quality of life (KCCQ-23 60.1 ± 18.6 vs. 82.8 ± 11.3; p < 0.001). Additionally, abnormalities in CPET were suggestive of an impaired ventilatory efficiency (VE/VCO2 slope 32 (28.1–37.4) vs. 29.4 (26.9–31.4); p = 0.022) and high PETCO2 (34.5 (32–39) vs. 38 (36–40); p = 0.025). Interpretation: In this study, >50% of COVID-19 survivors present a symptomatic functional impairment irrespective of age or prior hospitalization. Our findings suggest a potential ventilation/perfusion mismatch or hyperventilation syndrome.