Chronic heart failure induces early defenestration of liver sinusoidal endothelial cells (LSECs) in mice

AIM

Chronic heart failure (CHF) is often linked to liver malfunction and systemic endothelial dysfunction. However, whether cardio-hepatic interactions in heart failure involve dysfunction of liver sinusoidal endothelial cells (LSECs) is not known. Here we characterize LSECs phenotype in early and end stages of chronic heart failure in a murine model.

METHODS

Right ventricle (RV) function, features of congestive hepatopathy, and the phenotype of primary LSECs were characterized in Tgαq*44 mice, with cardiomyocyte-specific overexpression of the Gαq protein, at the age of 4- and 12-month representative for early and end-stage phases of CHF, respectively.

RESULTS

4- and 12-month-old Tgαq*44 mice displayed progressive impairment of RV function and alterations in hepatic blood flow velocity resulting in hepatic congestion with elevated GGT and bilirubin plasma levels and decreased albumin concentration without gross liver pathology. LSECs isolated from 4- and 12-month-old Tgαq*44 mice displayed significant loss of fenestrae with impaired functional response to cytochalasin B, significant changes in proteome related to cytoskeleton remodeling, and altered vasoprotective function. However, LSECs barrier function and bioenergetics were largely preserved. In 4- and 12-month-old Tgαq*44 mice, LSECs defenestration was associated with prolonged postprandial hypertriglyceridemia and in 12-month-old Tgαq*44 mice with proteomic changes of hepatocytes indicative of altered lipid metabolism.

CONCLUSION

Tgαq*44 mice displayed right-sided HF and altered hepatic blood flow leading to LSECs dysfunction involving defenestration, shift in eicosanoid profile, and proteomic changes. LSECs dysfunction appears as an early and persistent event in CHF, preceding congestive hepatopathy and contributing to alterations in lipoprotein transport and CHF pathophysiology.

FOXP3: A Player of Immunogenetic Architecture in Lung Cancer

The transcription factor forkhead box protein 3 (FOXP3) is considered to be a prominent component of the immune system expressed in regulatory T cells (Tregs). Tregs are immunosuppressive cells that regulate immune homeostasis and self-tolerance. FOXP3 was originally thought to be a Tregs-specific molecule, but recent studies have pinpointed that FOXP3 is expressed in a diversity of benign tumors and carcinomas. The vast majority of the data have shown that FOXP3 is correlated with an unfavorable prognosis, although there are some reports indicating the opposite function of this molecule. Here, we review recent progress in understanding the FOXP3 role in the immunogenetic architecture of lung cancer, which is the leading cause of cancer-related death. We discuss the prognostic significance of tumor FOXP3 expression, tumor-infiltrating FOXP3-lymphocytes, tumor FOXP3 in tumor microenvironments and the potential of FOXP3-targeted therapy.

NAC and Zuotin/Hsp70 chaperone systems coexist at the ribosome tunnel exit in vivo

The area surrounding the tunnel exit of the 60S ribosomal subunit is a hub for proteins involved in maturation and folding of emerging nascent polypeptide chains. How different factors vie for positioning at the tunnel exit in the complex cellular environment is not well understood. We used in vivo site-specific cross-linking to approach this question, focusing on two abundant factors-the nascent chain-associated complex (NAC) and the Hsp70 chaperone system that includes the J-domain protein co-chaperone Zuotin. We found that NAC and Zuotin can cross-link to each other at the ribosome, even when translation initiation is inhibited. Positions yielding NAC-Zuotin cross-links indicate that when both are present the central globular domain of NAC is modestly shifted from the mutually exclusive position observed in cryogenic electron microscopy analysis. Cross-linking results also suggest that, even in NAC's presence, Hsp70 can situate in a manner conducive for productive nascent chain interaction-with the peptide binding site at the tunnel exit and the J-domain of Zuotin appropriately positioned to drive stabilization of nascent chain binding. Overall, our results are consistent with the idea that, in vivo, the NAC and Hsp70 systems can productively position on the ribosome simultaneously.

Higher number of steps is related to lower endogenous progesterone but not estradiol levels in women

OBJECTIVES

Sex steroid hormones are important not only for reproduction but also for many aspects of women's health, including the risk of breast cancer. Physical activity has been shown to influence sex hormone levels in women. This study aimed to investigate a relationship between the average daily number of steps and the sex hormone (estradiol and progesterone) levels in premenopausal women.

MATERIALS AND METHODS

Data were collected from 85 healthy, urban women of reproductive age who performed at least 180 minutes/week of moderate physical activity for two complete menstrual cycles. Physical activity was measured using wrist bands. Estradiol and progesterone concentrations were measured in daily-collected saliva samples in the second menstrual cycle.

RESULTS

There was a significant negative association between the average number of steps taken daily and salivary progesterone levels after adjusting for potential confounding factors (age, BMI). Women who took more than 10,000 steps a day had significantly lower progesterone levels compared to women who took less than 10,000 steps. The association between physical activity and estradiol levels was statistically insignificant.

DISCUSSION

Our results indicate that taking at least 10,000 steps a day reduces progesterone levels, but this intensity of physical activity may not be high enough to affect estradiol levels. Daily step tracking is a valuable element of health promotion, but currently recommended levels of physical activity may not be high enough for healthy premenopausal women to significantly reduce both sex hormone levels and thus their risk of postmenopausal breast cancer.

Metalla-Carbaporphyrinoids Consisting of an Acyclic N-Confused Tetrapyrrole Analogue Served as Stable Near-Infrared-II Dyes

We present herein the synthesis of novel pseudo-metalla-carbaporphyrinoid species (1M: M=Pd and Pt) achieved through the inner coordination of palladium(II) and platinum(II) with an acyclic N-confused tetrapyrrin analogue. Despite their tetrapyrrole frameworks being small, akin to well-known porphyrins, these species exhibit an unusually narrow HOMO-LUMO gap, resulting in an unprecedentedly low-energy absorption in the second near-infrared (NIR-II) region. Density functional theory (DFT) calculations revealed unique dπ-pπ-conjugated electronic structures involving the metal dπ-ligand pπ hybridized molecular orbitals of 1M. Magnetic circular dichroism (MCD) spectroscopy confirmed distinct electronic structures. Remarkably, the complexes feature an open-metal coordination site in the peripheral NN dipyrrin site, forming hetero-metal complexes (1Pd-BF2 and 1Pt-BF2) through boron difluoride complexation. The resulting hetero metalla-carbaporphyrinoid species displayed further redshifted NIR-II absorption, highly efficient photothermal conversion efficiencies (η; 62-65 %), and exceptional photostability. Despite the challenges associated with the theoretical and experimental assessment of dπ-pπ-conjugated metalla-aromaticity in relatively larger (more than 18π electrons) polycyclic ring systems, these organometallic planar tetrapyrrole systems could serve as potential molecular platforms for aromaticity-relevant NIR-II dyes.

Conditioning and pseudoconditioning differently change intrinsic excitability of inhibitory interneurons in the neocortex

Many studies indicate a broad role of various classes of GABAergic interneurons in the processes related to learning. However, little is known about how the learning process affects intrinsic excitability of specific classes of interneurons in the neocortex. To determine this, we employed a simple model of conditional learning in mice where vibrissae stimulation was used as a conditioned stimulus and a tail shock as an unconditioned one. In vitro whole-cell patch-clamp recordings showed an increase in intrinsic excitability of low-threshold spiking somatostatin-expressing interneurons (SST-INs) in layer 4 (L4) of the somatosensory (barrel) cortex after the conditioning paradigm. In contrast, pseudoconditioning reduced intrinsic excitability of SST-LTS, parvalbumin-expressing interneurons (PV-INs), and vasoactive intestinal polypeptide-expressing interneurons (VIP-INs) with accommodating pattern in L4 of the barrel cortex. In general, increased intrinsic excitability was accompanied by narrowing of action potentials (APs), whereas decreased intrinsic excitability coincided with AP broadening. Altogether, these results show that both conditioning and pseudoconditioning lead to plastic changes in intrinsic excitability of GABAergic interneurons in a cell-specific manner. In this way, changes in intrinsic excitability can be perceived as a common mechanism of learning-induced plasticity in the GABAergic system.

Physiological arousal underlies preferential access to visual awareness of fear-conditioned (and possibly disgust-conditioned) stimuli

Fear and disgust have been associated with opposite influences on visual processing, even though both constitute negative emotions that motivate avoidance behavior and entail increased arousal. In the current study, we hypothesized that (a) homeostatic relevance modulates early stages of visual processing, (b) through widespread physiological responses, and that (c) the direction of these modulations depends on whether an emotion calls for immediate regulatory behavior or not. Specifically, we expected that increased arousal should facilitate the detection of fear-related stimuli, and inhibit the detection of disgust-related stimuli. These hypotheses were tested in two preregistered experiments (data collected in 2022, total N = 120, ethnically homogeneous Polish sample). Using a novel, response bias-free version of the breaking continuous flash suppression paradigm, we examined localization and discrimination of fear- and disgust-conditioned stimuli at individually determined perceptual thresholds. Our first hypothesis was confirmed: fear-conditioned stimuli were detected and discriminated better than neutral stimuli, and the magnitude of conditioning-related perceptual preference was related to arousal during conditioning acquisition. In contrast with our second hypothesis, perceptual access to disgust-conditioned stimuli was not diminished. Exploratory analyses suggest that discrimination of disgust-conditioned stimuli was also enhanced, although these effects appeared weaker than those evoked by fear conditioning. The current study strengthens previous evidence for facilitated perception of threatening objects and shows for the first time that stimuli evoking disgust might also gain preferential access to awareness. The results imply that homeostatically relevant stimuli are prioritized by the visual system and that this preference is grounded in the underlying arousal levels. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

The number of nuclei in compacted embryos, assessed by optical coherence microscopy, is a non-invasive and robust marker of mouse embryo quality

Optical coherence microscopy (OCM) visualizes nuclei in live, unlabeled cells. As most cells are uninucleated, the number of nuclei in embryos may serve as a proxy of the cell number, providing important information on developmental status of the embryo. Importantly, no other non-invasive method currently allows for the cell number count in compacted embryos. We addressed the question of whether OCM, by providing the number of nuclei in compacted mouse embryos, may help evaluate embryo quality. We subjected compacted embryonic Day 3 (E3.0: 72 h after onset of insemination) mouse embryos to OCM scanning and correlated nuclei number and developmental potential. Implantation was assessed using an outgrowth assay (in vitro model meant to reflect embryonic ability to implant in vivo). Embryos with more cells at E3.0 (>18 cells) were more likely to reach the blastocyst stage by E4.0 and E5.0 (P ≪ 0.001) and initiate hatching by E5.0 (P < 0.05) than those with fewer cells (<12 cells). Moreover, the number of cells at E3.0 strongly correlated with the total number of cells in E4.0 and E5.0 embryos (ρ = 0.71, P ≪ 0.001 and ρ = 0.61, P ≪ 0.001, respectively), also when only E4.0 and E5.0 blastocysts were considered (ρ = 0.58, P ≪ 0.001 and ρ = 0.56, P ≪ 0.001, respectively). Additionally, we observed a strong correlation between the number of cells at E3.0 and the number of trophectoderm cells in E4.0 and E5.0 blastocysts (ρ = 0.59, P ≪ 0.001 and ρ = 0.57, P ≪ 0.001, respectively). Importantly, embryos that had more cells at E3.0 (>18 cells) were also more likely to implant in vitro than their counterparts with fewer cells (<12 cells; P ≪ 0.001). Finally, we tested the safety of OCM imaging, demonstrating that OCM scanning affected neither the amount of reactive oxygen species nor mitochondrial activity in the embryos. OCM also did not hinder their preimplantation development, ability to implant in vitro, or to develop to term after transfer to recipient females. Our data indicate that OCM imaging provides important information on embryo quality. As the method seems to be safe for embryos, it could be a valuable addition to the current repertoire of embryo evaluation methods. However, our study was conducted only on mouse embryos, so the proposed protocol would require optimization in order to be applied in other species.

Oxygen is an essential gasotransmitter directly sensed via protein gasoreceptors

The current restrictive criteria for gasotransmitters exclude oxygen (O2) as a gasotransmitter in vertebrates. In this manuscript, I propose a revision of gasotransmitter criteria to include O2 per se as a signaling molecule and 'essential gasotransmitter' for vertebrates. This revision would enable us to search for protein-based O2-binding sensors (gasoreceptors) in all cells in the brain or other tissues rather than specialized tissues such as the carotid body or gills. If microorganisms have protein-based O2-binding sensors or gasoreceptors such as DosP or FixL or FNR with diverse signaling domains, then eukaryotic cells must also have O2-binding sensors or gasoreceptors. Just as there are protein-based receptor(s) for nitric oxide (GUCY1A, GUCY1B, CLOCK, NR1D2) in cells of diverse tissues, it is reasonable to consider that there are protein-based receptors for O2 in cells of diverse tissues as well. In mammals, O2 must be acting as a gasotransmitter or gaseous signaling molecule via protein-based gasoreceptors such as androglobin that very likely mediate acute sensing of O2. Accepting O2 as an essential gasotransmitter will enable us to search for gasoreceptors not only for O2 but also for other nonessential gasotransmitters such as hydrogen sulfide, ammonia, methane, and ethylene. It will also allow us to investigate the role of environment-derived metal ions in acute gas (or solute) sensing within and between organisms. Finally, accepting O2 per se as a signaling molecule acting via gasoreceptors will open up the field of gasocrinology.

Multiomics-Based Feature Extraction and Selection for the Prediction of Lung Cancer Survival

Lung cancer is a global health challenge, hindered by delayed diagnosis and the disease's complex molecular landscape. Accurate patient survival prediction is critical, motivating the exploration of various -omics datasets using machine learning methods. Leveraging multi-omics data, this study seeks to enhance the accuracy of survival prediction by proposing new feature extraction techniques combined with unbiased feature selection. Two lung adenocarcinoma multi-omics datasets, originating from the TCGA and CPTAC-3 projects, were employed for this purpose, emphasizing gene expression, methylation, and mutations as the most relevant data sources that provide features for the survival prediction models. Additionally, gene set aggregation was shown to be the most effective feature extraction method for mutation and copy number variation data. Using the TCGA dataset, we identified 32 molecular features that allowed the construction of a 2-year survival prediction model with an AUC of 0.839. The selected features were additionally tested on an independent CPTAC-3 dataset, achieving an AUC of 0.815 in nested cross-validation, which confirmed the robustness of the identified features.

Noncentrosymmetric Triangular Magnet CaMnTeO6: Strong Quantum Fluctuations and Role of s0 versus s2 Electronic States in Competing Exchange Interactions

Noncentrosymmetric triangular magnets offer a unique platform for realizing strong quantum fluctuations. However, designing these quantum materials remains an open challenge attributable to a knowledge gap in the tunability of competing exchange interactions at the atomic level. Here, a new noncentrosymmetric triangular S = 3/2 magnet CaMnTeO6 is created based on careful chemical and physical considerations. The model material displays competing magnetic interactions and features nonlinear optical responses with the capability of generating coherent photons. The incommensurate magnetic ground state of CaMnTeO6 with an unusually large spin rotation angle of 127°(1) indicates that the anisotropic interlayer exchange is strong and competing with the isotropic interlayer Heisenberg interaction. The moment of 1.39(1) µB, extracted from low-temperature heat capacity and neutron diffraction measurements, is only 46% of the expected value of the static moment 3 µB. This reduction indicates the presence of strong quantum fluctuations in the half-integer spin S = 3/2 CaMnTeO6 magnet, which is rare. By comparing the spin-polarized band structure, chemical bonding, and physical properties of AMnTeO6 (A = Ca, Sr, Pb), how quantum-chemical interpretation can illuminate insights into the fundamentals of magnetic exchange interactions, providing a powerful tool for modulating spin dynamics with atomically precise control is demonstrated.

Innovative Green Alginate-Cellulose Composite for Light Lanthanides: Experimental Design and Comprehensive Studies on Kinetics, Equilibrium, Thermodynamics, and Reusability

Nowadays, there is a great interest in efficient adsorbent development due to the recent demand for lanthanides, which are widely used in high-tech technology. Alginates, owing to their natural occurrence, gel formation capability, and safety, could be promising feasible adsorbents for lanthanide removal. This study proposes the alginate-cellulose composite as an ecological, sustainable adsorbent for light lanthanide sorption. The structure, morphology, qualitative and quantitative compositions, average diameter, and pHpzc of the composite were discussed in great detail. Using the batch approach, sorption trials were performed to evaluate the metal sorption performance. The maximum lanthanide accumulation was attained at pH 5.0 and a dosage of 0.05 g. The uptake kinetics are successfully explained by the Ho and McKay model, whereas the equilibrium data is best represented by the Langmuir equation. The presence of Cl-, NO3 -, SO4 2-, Ni(II), and Co(II) did not have any impact on the adsorption capacity. In turn, the presence of Fe(III) ions led to a 15 % reduction in the adsorption. The lanthanide ions were eluted from the adsorbent following the treatment with 0.1 M HNO3. The adsorbent retained over 95 % of its initial adsorption capacity after 6 series of sorption/desorption studies.

Oligodendrocyte progenitor cells' fate after neonatal asphyxia-Puzzling implications for the development of hypoxic-ischemic encephalopathy

Premature birth or complications during labor can cause temporary disruption of cerebral blood flow, often followed by long-term disturbances in brain development called hypoxic-ischemic (HI) encephalopathy. Diffuse damage to the white matter is the most frequently detected pathology in this condition. We hypothesized that oligodendrocyte progenitor cell (OPC) differentiation disturbed by mild neonatal asphyxia may affect the viability, maturation, and physiological functioning of oligodendrocytes. To address this issue, we studied the effect of temporal HI in the in vivo model in P7 rats with magnetic resonance imaging (MRI), microscopy techniques and biochemical analyses. Moreover, we recreated the injury in vitro performing the procedure of oxygen-glucose deprivation on rat neonatal OPCs to determine its effect on cell viability, proliferation, and differentiation. In the in vivo model, MRI evaluation revealed changes in the volume of different brain regions, as well as changes in the directional diffusivity of water in brain tissue that may suggest pathological changes to myelinated neuronal fibers. Hypomyelination was observed in the cortex, striatum, and CA3 region of the hippocampus. Severe changes to myelin ultrastructure were observed, including delamination of myelin sheets. Interestingly, shortly after the injury, an increase in oligodendrocyte proliferation was observed, followed by an overproduction of myelin proteins 4 weeks after HI. Results verified with the in vitro model indicate, that in the first days after damage, OPCs do not show reduced viability, intensively proliferate, and overexpress myelin proteins and oligodendrocyte-specific transcription factors. In conclusion, despite the increase in oligodendrocyte proliferation and myelin protein expression after HI, the production of functional myelin sheaths in brain tissue is impaired. Presented study provides a detailed description of oligodendrocyte pathophysiology developed in an effect of HI injury, resulting in an altered CNS myelination. The described models may serve as useful tools for searching and testing effective of effective myelination-supporting therapies for HI injuries.

Dental caries in living and extinct strepsirrhines with insights into diet

Dental caries is one of the most common diseases afflicting modern humans and occurs in both living and extinct non-human primates, as well as other mammalian species. Compared to other primates, less is known about the etiology or frequency of caries among the Strepsirrhini. Given the link between caries and diet, caries frequency may be informative about the dietary ecology of a given animal. Understanding rates of caries in wild populations is also critical to assessing dental health in captive populations. Here, we examine caries frequency in a sample of 36 extant strepsirrhine species (n = 316 individuals) using odontological collections of wild-, non-captive animals housed at the American Museum of Natural History by counting the number of specimens characterized by the disease. Additionally, in the context of studying caries lesions in strepsirrhines, case studies were also conducted to test if similar lesions were found in their fossil relatives. In particular, two fossil strepsirrhine species were analyzed: the earliest Late Eocene Karanisia clarki, and the subfossil lemur Megaladapis madagascariensis. Our results suggest that caries affects 13.92% of the extant individuals we examined. The frugivorous and folivorous taxa were characterized by the highest overall frequency of caries, whereas the insectivores, gummivores, and omnivores had much lower caries frequencies. Our results suggest that caries may be common among wild populations of strepsirrhines, and in fact is more prevalent than in many catarrhines and platyrrhines. These findings have important implications for understanding caries, diet, and health in living and fossil taxa.

Novel insights into RAGE signaling pathways during the progression of amyotrophic lateral sclerosis in RAGE-deficient SOD1 G93A mice

Amyotrophic lateral sclerosis (ALS) is neurodegenerative disease characterized by a progressive loss of motor neurons resulting in paralysis and muscle atrophy. One of the most prospective hypothesis on the ALS pathogenesis suggests that excessive inflammation and advanced glycation end-products (AGEs) accumulation play a crucial role in the development of ALS in patients and SOD1 G93A mice. Hence, we may speculate that RAGE, receptor for advanced glycation end-products and its proinflammatory ligands such as: HMGB1, S100B and CML contribute to ALS pathogenesis. The aim of our studies was to decipher the role of RAGE as well as provide insight into RAGE signaling pathways during the progression of ALS in SOD1 G93A and RAGE-deficient SOD1 G93A mice. In our study, we observed alternations in molecular pattern of proinflammatory RAGE ligands during progression of disease in RAGE KO SOD1 G93A mice compared to SOD1 G93A mice. Moreover, we observed that the amount of beta actin (ACTB) as well as Glial fibrillary acidic protein (GFAP) was elevated in SOD1 G93A mice when compared to mice with deletion of RAGE. These data contributes to our understanding of implications of RAGE and its ligands in pathogenesis of ALS and highlight potential targeted therapeutic interventions at the early stage of this devastating disease. Moreover, inhibition of the molecular cross-talk between RAGE and its proinflammatory ligands may abolish neuroinflammation, gliosis and motor neuron damage in SOD1 G93A mice. Hence, we hypothesize that attenuated interaction of RAGE with its proinflammatory ligands may improve well-being and health status during ALS in SOD1 G93A mice. Therefore, we emphasize that the inhibition of RAGE signaling pathway may be a therapeutic target for neurodegenerative diseases.

The use of LA-ICP-MS as an auxiliary tool to assess the pulmonary toxicity of molybdenum(IV) sulfide (MoS2) nano- and microparticles

OBJECTIVES

Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) has considerable applicative potential for both qualitative and quantitative analyses of elemental spatial distribution and concentration. It provides high resolutions at pg-level detection limits. These qualities make it very useful for analyzing biological samples. The present study responds to the growing demand for adequate analytical methods which would allow to assess the distribution of nanostructured molybdenum(IV) disulfide (MoS2) in organs. It was also motivated by an apparent lack of literature on the biological effects of MoS2 in living organisms. The study was aimed at using LA-ICP-MS for comparing micro- and nanosized MoS2 ditribution in selected rat tissue samples (lung, liver, brain and spleen tissues) after the intratracheal instillation (7 administrations) of MoS2 nano- and microparticles vs. controls.

MATERIAL AND METHODS

The experimental study, approved by the Ethics Committee for Animal Experiments was performed using albino Wistar rats. This was performed at 2-week intervals at a dose of 5 mg/kg b.w., followed by an analysis after 90 days of exposure. The MoS2 levels in control tissues were determined with the laser ablation system at optimized operating conditions. The parameter optimization process for the LA system was conducted using The National Institute of Standards and Technology (NIST) glass standard reference materials.

RESULTS

Instrument parameters were optimized. The study found that molybdenum (Mo) levels in the lungs of microparticle-exposed rats were higher compared to nanoparticle-exposed rats. The opposite results were found for liver and spleen tissues. Brain Mo concentrations were below the detection limit.

CONCLUSIONS

The LA-ICP-MS technique may be used as an important tool for visualizing the distribution of Mo on the surface of soft samples through quantitative and qualitative elemental mapping. Int J Occup Med Environ Health. 2024;37(1):18-33.

imputomics: web server and R package for missing values imputation in metabolomics data

MOTIVATION

Missing values are commonly observed in metabolomics data from mass spectrometry. Imputing them is crucial because it assures data completeness, increases the statistical power of analyses, prevents inaccurate results, and improves the quality of exploratory analysis, statistical modeling, and machine learning. Numerous Missing Value Imputation Algorithms (MVIAs) employ heuristics or statistical models to replace missing information with estimates. In the context of metabolomics data, we identified 52 MVIAs implemented across 70 R functions. Nevertheless, the usage of those 52 established methods poses challenges due to package dependency issues, lack of documentation, and their instability.

RESULTS

Our R package, 'imputomics', provides a convenient wrapper around 41 (plus random imputation as a baseline model) out of 52 MVIAs in the form of a command-line tool and a web application. In addition, we propose a novel functionality for selecting MVIAs recommended for metabolomics data with the best performance or execution time.

AVAILABILITY AND IMPLEMENTATION

'imputomics' is freely available as an R package (github.com/BioGenies/imputomics) and a Shiny web application (biogenies.info/imputomics-ws). The documentation is available at biogenies.info/imputomics.

Fabrication of alginate-based hydrogel microparticle via ruthenium-catalyzed photocrosslinking

In this study, we developed an alginate-based microparticle production process via sodium ruthenium(II) tris-bipyridyl dication (Ru)/ammonium persulfate (SPS)-mediated visible light crosslinking system using a microfluidic device. Microparticles were prepared by crosslinking phenolic-substituted alginate (AlgPh) and incorporated gelatin (GelPh) in an aqueous solution containing SPS, which flowed into an ambient immiscible liquid paraffin-containing Ru using coaxial double orifice microfluidic device. The hydrogel microparticles appeared with the desired geometries and dimensions under optimal conditions. The concentration of AlgPh and light intensity were the most critical parameters for harvesting spherical microparticles with homogeneous size distribution. The physical properties of the prepared AlgPh microparticles were characterized and compared with Alg-Ca microparticles. Cell viability and proliferation preserved on AlgPh/GelPh hydrogel surfaces. Also, encapsulated cells in microparticles were also viable and proliferated well over 13 days after encapsulation. In brief, the results proved the feasibility of fabricating AlgPh vehicles via Ru/SPS-mediated system and visible light irradiation as a simple and efficient three-dimensional platform, which are applicable for various tissue engineering and cell delivery purposes.

Isotope effects accompanying δ2 H, δ18 O and δ17 O analyses of aqueous saline solutions using cavity ring-down laser spectroscopy

RATIONALE

The presence of substantial amounts of dissolved salts creates serious difficulties in isotope analyses of water samples using conventional isotope ratio mass spectrometry. Although nowadays laser-based instruments are increasingly used for this purpose, a comprehensive assessment of isotope effects associated with direct analyses of aqueous saline solutions using this technology is lacking.

METHODS

Here we report the results of laboratory experiments aimed at quantifying isotope effects associated with direct, δ2 H, δ18 O and δ17 O analyses of single-salt solutions and double-salt mixtures prepared with a water of known isotopic composition. Three single-salt solutions (NaCl, CaCl2 and MgSO4 ) and two double-salt mixtures (NaCl + CaCl2 and NaCl + MgSO4 ) were prepared and investigated for a wide range of molalities. The triple-isotope composition of the prepared solutions was analysed with the aid of a Picarro L2140-i Cavity Ring-Down Spectroscopy analyser.

RESULTS

The NaCl and CaCl2 solutions revealed small negative salt effects, independent of molality and comparable with measurement uncertainty. The MgCl2 solution showed the highest salt effects, reaching saturated solution ca. +2.7‰ (2 H), -3.5‰ (18 O) and -1.7‰ (17 O). Salt effects for the double-salt mixtures generally mirrored the effects observed for the single-salt solutions. The observed salt effects are discussed in the context of processes occurring during the injection of the salt solutions into the vaporizer unit of the CRDS analyser.

CONCLUSIONS

The presented study has demonstrated feasibility of direct, triple-isotope analyses of aqueous salt solutions using a Picarro L2140-i CRDS analyser for a broad range of salinities up to saturated conditions. Large uncertainties of 17 O-excess determinations for solutions forming hydrated salts preclude the use of this parameter for interpretation purposes.

TNF-α protects from exacerbated myocarditis and cardiac death by suppressing expansion of activated heart-reactive CD4+ T cells

AIMS

Tumour necrosis factor α (TNF-α) represents a classical pro-inflammatory cytokine, and its increased levels positively correlate with the severity of many cardiovascular diseases. Surprisingly, some heart failure patients receiving high doses of anti-TNF-α antibodies showed serious health worsening. This work aimed to examine the role of TNF-α signalling on the development and progression of myocarditis and heart-specific autoimmunity.

METHODS AND RESULTS

Mice with genetic deletion of TNF-α (Tnf+/- and Tnf-/-) and littermate controls (Tnf+/+) were used to study myocarditis in the inducible and the transgenic T cell receptor (TCRM) models. Tnf+/- and Tnf-/- mice immunized with α-myosin heavy chain peptide (αMyHC) showed reduced myocarditis incidence, but the susceptible animals developed extensive inflammation in the heart. In the TCRM model, defective TNF-α production was associated with increased mortality at a young age due to cardiomyopathy and cardiac fibrosis. We could confirm that TNF-α as well as the secretome of antigen-activated heart-reactive effector CD4+ T (Teff) cells effectively activated the adhesive properties of cardiac microvascular endothelial cells (cMVECs). Our data suggested that TNF-α produced by endothelial in addition to Teff cells promoted leucocyte adhesion to activated cMVECs. Analysis of CD4+ T lymphocytes from both models of myocarditis showed a strongly increased fraction of Teff cells in hearts, spleens, and in the blood of Tnf+/- and Tnf-/- mice. Indeed, antigen-activated Tnf-/- Teff cells showed prolonged long-term survival and TNF-α cytokine-induced cell death of heart-reactive Teff.

CONCLUSION

TNF-α signalling promotes myocarditis development by activating cardiac endothelial cells. However, in the case of established disease, TNF-α protects from exacerbating cardiac inflammation by inducing activation-induced cell death of heart-reactive Teff. These data might explain the lack of success of standard anti-TNF-α therapy in heart failure patients and open perspectives for T cell-targeted approaches.

Dysregulated iron homeostasis in dystrophin-deficient cardiomyocytes: correction by gene editing and pharmacological treatment

AIMS

Duchenne muscular dystrophy (DMD)-associated cardiomyopathy is a serious life-threatening complication, the mechanisms of which have not been fully established, and therefore no effective treatment is currently available. The purpose of the study was to identify new molecular signatures of the cardiomyopathy development in DMD.

METHODS AND RESULTS

For modelling of DMD-associated cardiomyopathy, we prepared three pairs of isogenic control and dystrophin-deficient human induced pluripotent stem cell (hiPSC) lines. Two isogenic hiPSC lines were obtained by CRISPR/Cas9-mediated deletion of DMD exon 50 in unaffected cells generated from healthy donor and then differentiated into cardiomyocytes (hiPSC-CM). The latter were subjected to global transcriptomic and proteomic analyses followed by more in-depth investigation of selected pathway and pharmacological modulation of observed defects. Proteomic analysis indicated a decrease in the level of mitoNEET protein in dystrophin-deficient hiPSC-CM, suggesting alteration in iron metabolism. Further experiments demonstrated increased labile iron pool both in the cytoplasm and mitochondria, a decrease in ferroportin level and an increase in both ferritin and transferrin receptor in DMD hiPSC-CM. Importantly, CRISPR/Cas9-mediated correction of the mutation in the patient-derived hiPSC reversed the observed changes in iron metabolism and restored normal iron levels in cardiomyocytes. Moreover, treatment of DMD hiPSC-CM with deferoxamine (DFO, iron chelator) or pioglitazone (mitoNEET stabilizing compound) decreased the level of reactive oxygen species in DMD hiPSC-CM.

CONCLUSION

To our knowledge, this study demonstrated for the first time impaired iron metabolism in human DMD cardiomyocytes, and potential reversal of this effect by correction of DMD mutation or pharmacological treatment. This implies that iron overload-regulating compounds may serve as novel therapeutic agents in DMD-associated cardiomyopathy.

A Combination of β-Aescin and Newly Synthesized Alkylamidobetaines as Modern Components Eradicating the Biofilms of Multidrug-Resistant Clinical Strains of Candida glabrata

The current trend in microbiological research aimed at limiting the development of biofilms of multidrug-resistant microorganisms is increasingly towards the search for possible synergistic effects between various compounds. This work presents a combination of a naturally occurring compound, β-aescin, newly synthesized alkylamidobetaines (AABs) with a general structure-CnTMDAB, and antifungal drugs. The research we conducted consists of several stages. The first stage concerns determining biological activity (antifungal) against selected multidrug-resistant strains of Candida glabrata (C. glabrata) with the highest ability to form biofilms. The second stage of this study determined the activity of β-aescin combinations with antifungal compounds and alkylamidobetaines. In the next stage of this study, the ability to eradicate a biofilm on the polystyrene surface of the combination of β-aescin with alkylamidobetaines was examined. It has been shown that the combination of β-aescin and alkylamidobetaine can firmly remove biofilms and reduce their viability. The last stage of this research was to determine the safety regarding the cytotoxicity of both β-aescin and alkylamidobetaines. Previous studies on the fibroblast cell line have shown that C9 alkylamidobetaine can be safely used as a component of anti-biofilm compounds. This research increases the level of knowledge about the practical possibilities of using anti-biofilm compounds in combined therapies against C. glabrata.

Comparison of the Antibacterial Activity of Selected Deep Eutectic Solvents (DESs) and Deep Eutectic Solvents Comprising Organic Acids (OA-DESs) Toward Gram-Positive and Gram-Negative Species

Deep eutectic solvents (DESs) have been intensively investigated in recent years for their antibacterial properties, with DESs that comprise organic acids (OA-DESs) showing promising antibacterial action. However a majority of the reports focused only on a limited number strains and techniques, which is not enough to determine the antibacterial potential of a substance. To bridge this gap, the antibacterial activity of classical DESs and OA-DESs is assessed on twelve Gram-negative and Gram-positive bacteria strains, with some of them exhibiting specific resistance toward antibiotics. The investigated formulations of OA-DESs comprise glycolic, malic, malonic, and oxalic acids as representatives of this group. Using a range of microbiological assays as well as physicochemical characterization methods, a major difference of the effectiveness between the two groups is demonstrated, with OA-DESs exhibiting, as expected, greater antibacterial effectiveness than classical DESs. Most interestingly, slight differences in the minimum inhibitory and bactericidal concentration values as well as time-kill kinetics profiles are observed between Gram-positive and Gram-negative strains. Transmission electron microscopy analysis reveals the effect of the treatment of the bacteria with the representatives of both groups of DESs, which allows us to better understand the possible mechanism-of-action of these novel materials.

Understanding the joint evolution of dispersal and host specialisation using phytophagous arthropods as a model group

Theory generally predicts that host specialisation and dispersal should evolve jointly. Indeed, many models predict that specialists should be poor dispersers to avoid landing on unsuitable hosts while generalists will have high dispersal abilities. Phytophagous arthropods are an excellent group to test this prediction, given extensive variation in their host range and dispersal abilities. Here, we explore the degree to which the empirical literature on this group is in accordance with theoretical predictions. We first briefly outline the theoretical reasons to expect such a correlation. We then report empirical studies that measured both dispersal and the degree of specialisation in phytophagous arthropods. We find a correlation between dispersal and levels of specialisation in some studies, but with wide variation in this result. We then review theoretical attributes of species and environment that may blur this correlation, namely environmental grain, temporal heterogeneity, habitat selection, genetic architecture, and coevolution between plants and herbivores. We argue that theoretical models fail to account for important aspects, such as phenotypic plasticity and the impact of selective forces stemming from other biotic interactions, on both dispersal and specialisation. Next, we review empirical caveats in the study of this interplay. We find that studies use different measures of both dispersal and specialisation, hampering comparisons. Moreover, several studies do not provide independent measures of these two traits. Finally, variation in these traits may occur at scales that are not being considered. We conclude that this correlation is likely not to be expected from large-scale comparative analyses as it is highly context dependent and should not be considered in isolation from the factors that modulate it, such as environmental scale and heterogeneity, intrinsic traits or biotic interactions. A stronger crosstalk between theoretical and empirical studies is needed to understand better the prevalence and basis of the correlation between dispersal and specialisation.

A cross talk between microbial metabolites and host immunity: Its relevance for allergic diseases

BACKGROUND

Allergic diseases, including respiratory and food allergies, as well as allergic skin conditions have surged in prevalence in recent decades. In allergic diseases, the gut microbiome is dysbiotic, with reduced diversity of beneficial bacteria and increased abundance of potential pathogens. Research findings suggest that the microbiome, which is highly influenced by environmental and dietary factors, plays a central role in the development, progression, and severity of allergic diseases. The microbiome generates metabolites, which can regulate many of the host's cellular metabolic processes and host immune responses.

AIMS AND METHODS

Our goal is to provide a narrative and comprehensive literature review of the mechanisms through which microbial metabolites regulate host immune function and immune metabolism both in homeostasis and in the context of allergic diseases.

RESULTS AND DISCUSSION

We describe key microbial metabolites such as short-chain fatty acids, amino acids, bile acids and polyamines, elucidating their mechanisms of action, cellular targets and their roles in regulating metabolism within innate and adaptive immune cells. Furthermore, we characterize the role of bacterial metabolites in the pathogenesis of allergic diseases including allergic asthma, atopic dermatitis and food allergy.

CONCLUSION

Future research efforts should focus on investigating the physiological functions of microbiota-derived metabolites to help develop new diagnostic and therapeutic interventions for allergic diseases.

The peaks and valleys of narcissism: The factor structure of narcissistic states and their relations to trait measures

Although interindividual differences in narcissism are well studied, little is known about assessing narcissism at the within-person level. To fill this research gap, we investigated whether the narcissism construct is represented in the same way at the between- and within-person levels. We analyzed four established narcissism measures across multiple studies. In each of the studies, participants completed narcissism measures in ecological momentary assessment or daily diary studies. Equivalent construct representation across between- and within-person narcissism (i.e., cross-level measurement invariance) was found. State narcissism measures showed convergent validities for the trait narcissism scales. Moreover, we also found that antagonistic narcissism was most strongly related to within-person variability in narcissism. Our investigation sheds new light on the structure and assessment of narcissism on the within-person level by providing a comprehensive examination of its measurement. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Iron uptake pathway of Escherichia coli as an entry route for peptide nucleic acids conjugated with a siderophore mimic

Bacteria secrete various iron-chelators (siderophores), which scavenge Fe3+ from the environment, bind it with high affinity, and retrieve it inside the cell. After the Fe3+ uptake, bacteria extract the soluble iron(II) from the siderophore. Ferric siderophores are transported inside the cell via the TonB-dependent receptor system. Importantly, siderophore uptake paths have been also used by sideromycins, natural antibiotics. Our goal is to hijack the transport system for hydroxamate-type siderophores to deliver peptide nucleic acid oligomers into Escherichia coli cells. As siderophore mimics we designed and synthesized linear and cyclic Nδ-acetyl-Nδ-hydroxy-l-ornithine based peptides. Using circular dichroism spectroscopy, we found that iron(III) is coordinated by the linear trimer with hydroxamate groups but not by the cyclic peptide. The internal flexibility of the linear siderophore oxygen atoms and their interactions with Fe3+ were confirmed by all-atom molecular dynamics simulations. Using flow cytometry we found that the designed hydroxamate trimer transports PNA oligomers inside the E. coli cells. Growth recovery assays on various E. coli mutants suggest the pathway of this transport through the FhuE outer-membrane receptor, which is responsible for the uptake of the natural iron chelator, ferric-coprogen. This pathway also involves the FhuD periplasmic binding protein. Docking of the siderophores to the FhuE and FhuD receptor structures showed that binding of the hydroxamate trimer is energetically favorable corroborating the experimentally suggested uptake path. Therefore, this siderophore mimic, as well as its conjugate with PNA, is most probably internalized through the hydroxamate pathway.

Biochemical Approach to Poly(Lactide)-Copper Composite-Impact on Blood Coagulation Processes

The paper presents the investigation of the biological properties of Poly(Lactide)-Copper composite material obtained by sputter deposition of copper onto Poly(lactide) melt-blown nonwoven fabrics. The functionalized composite material was subjected to microbial activity tests against colonies of Gram-positive (Staphylococcus aureus), Gram-negative (Escherichia coli, Pseudomonas aeruginosa) bacteria, Chaetomium globosum and Candida albicans fungal mold species and biochemical-hematological tests including the evaluation of the Activated Partial Thromboplastin Time, Prothrombin Time, Thrombin Time and electron microscopy fibrin network imaging. The substantial antimicrobial and antifungal activities of the Poly(Lactide)-Copper composite suggests potential applications as an antibacterial/antifungal material. The unmodified Poly(Lactide) fabric showed accelerated human blood plasma clotting in the intrinsic pathway, while copper plating abolished this effect. Unmodified PLA itself could be used for the preparation of wound dressing materials, accelerating coagulation in the case of hemorrhages, and its modifications with the use of various metals might be applied as new customized materials where blood coagulation process could be well controlled, yielding additional anti-pathogen effects.

WEIRD-Confucian comparisons: Ongoing cultural biases in psychology's evidence base and some recommendations for improving global representation

The realization that most behavioral science research focuses on cultures labeled as WEIRD-Western, educated, industrialized, rich, and democratic (Arnett, 2008; Henrich et al., 2010; Thalmayer et al., 2021)-has given an impetus to extend the research to more diverse populations. Confucian East Asian societies have relatively strong social and technological infrastructure to advance science and thus have gained much prominence in cross-cultural studies. This has inadvertently fostered another bias: the dominance of WEIRD-Confucian comparisons and a tendency to draw conclusions about "non-WEIRD" cultures in general based on data from Confucian societies. Here, analyzing 1,466,019 scientific abstracts and, separately, coverage of 60 large-scale cross-cultural psychological projects (Nsamples = 2,668 from Ncountries = 153 covering nparticipants = 3,722,940), we quantify the dominance of Confucian over other non-WEIRD cultures in psychological research. Our analysis also reveals the underrepresentation of non-European Union postcommunist societies and the almost total invisibility of Pacific Island, Caribbean, Middle African, and Central Asian societies within the research database of psychology. We call for a shift in cross-cultural studies toward midsize (7+ countries) and ideally large-scale (50+ countries) cross-cultural studies, and we propose mitigations that we believe could aid the inclusion of diverse researchers as well as participants from underrepresented cultures in our field. People in all world regions and cultures deserve psychological knowledge that applies to them. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Structure prediction of linear and cyclic peptides using CABS-flex

The structural modeling of peptides can be a useful aid in the discovery of new drugs and a deeper understanding of the molecular mechanisms of life. Here we present a novel multiscale protocol for the structure prediction of linear and cyclic peptides. The protocol combines two main stages: coarse-grained simulations using the CABS-flex standalone package and an all-atom reconstruction-optimization process using the Modeller program. We evaluated the protocol on a set of linear peptides and two sets of cyclic peptides, with cyclization through the backbone and disulfide bonds. A comparison with other state-of-the-art tools (APPTEST, PEP-FOLD, ESMFold and AlphaFold implementation in ColabFold) shows that for most cases, AlphaFold offers the highest resolution. However, CABS-flex is competitive, particularly when it comes to short linear peptides. As demonstrated, the protocol performance can be further improved by combination with the residue-residue contact prediction method or more efficient scoring. The protocol is included in the CABS-flex standalone package along with online documentation to aid users in predicting the structure of peptides and mini-proteins.

Luminosity determination using Z boson production at the CMS experiment

The measurement of Z boson production is presented as a method to determine the integrated luminosity of CMS data sets. The analysis uses proton-proton collision data, recorded by the CMS experiment at the CERN LHC in 2017 at a center-of-mass energy of 13Te V . Events with Z bosons decaying into a pair of muons are selected. The total number of Z bosons produced in a fiducial volume is determined, together with the identification efficiencies and correlations from the same data set, in small intervals of 20pb - 1 of integrated luminosity, thus facilitating the efficiency and rate measurement as a function of time and instantaneous luminosity. Using the ratio of the efficiency-corrected numbers of Z bosons, the precisely measured integrated luminosity of one data set is used to determine the luminosity of another. For the first time, a full quantitative uncertainty analysis of the use of Z  bosons for the integrated luminosity measurement is performed. The uncertainty in the extrapolation between two data sets, recorded in 2017 at low and high instantaneous luminosity, is less than 0.5%. We show that the Z boson rate measurement constitutes a precise method, complementary to traditional methods, with the potential to improve the measurement of the integrated luminosity.

Measurement of the production cross section for a W boson in association with a charm quark in proton-proton collisions at s=13TeV

The strange quark content of the proton is probed through the measurement of the production cross section for a W boson and a charm (c) quark in proton-proton collisions at a center-of-mass energy of 13Te V . The analysis uses a data sample corresponding to a total integrated luminosity of 138fb - 1 collected with the CMS detector at the LHC. The W bosons are identified through their leptonic decays to an electron or a muon, and a neutrino. Charm jets are tagged using the presence of a muon or a secondary vertex inside the jet. The W + c production cross section and the cross section ratio R c ± = σ ( W + + c ¯ ) / σ ( W - + c ) are measured inclusively and differentially as functions of the transverse momentum and the pseudorapidity of the lepton originating from the W boson decay. The precision of the measurements is improved with respect to previous studies, reaching 1% in R c ± = 0.950 ± 0.005 (stat) ± 0.010 (syst) . The measurements are compared with theoretical predictions up to next-to-next-to-leading order in perturbative quantum chromodynamics.

Brain size mediates the choice of breeding strategy in the red-backed shrike Lanius collurio

The brain size of vertebrates represents a trade-off between natural selection for enhanced cognitive abilities and the energetic constraints of brain tissue production. Processing information efficiently can confer benefits, but it also entails time costs. Breeding strategies, encompassing timing of breeding onset and nest-site selection, may be related to brain size. In this study, we aim to elucidate the relationship between brain size, breeding timing, nest-site choice, and breeding success in the red-backed shrike Lanius collurio. Our findings revealed that the timing of the first egg-laying date was associated with female head size, with larger-headed females tending to lay eggs later in the breeding season. Additionally, we observed that breeding success was positively correlated with increased nest concealment. However, this relationship was stronger in males with smaller heads. In turn, nest concealment was not related to head size but primarily influenced breeding onset. These results suggest that the choice of breeding strategy may be moderated by brain size, with differences between sexes. Larger-headed females may invest more time in selecting nesting sites, leading to delayed breeding onset, while larger-headed males may compensate for suboptimal nest concealment. Our study sheds light on the intricate interplay between brain size, breeding timing, nest-site preferences, and breeding success in passerine birds, underscoring the potential role of cognitive capacity in shaping individual decision-making processes.

Engineering of Ogataea polymorpha strains with ability for high-temperature alcoholic fermentation of cellobiose

Successful conversion of cellulosic biomass into biofuels requires organisms capable of efficiently utilizing xylose as well as cellodextrins and glucose. Ogataea (Hansenula) polymorpha is the natural xylose-metabolizing organism and is one of the most thermotolerant yeasts known, with a maximum growth temperature above 50°C. Cellobiose-fermenting strains, derivatives of an improved ethanol producer from xylose O. polymorpha BEP/cat8∆, were constructed in this work by the introduction of heterologous genes encoding cellodextrin transporters (CDTs) and intracellular enzymes (β-glucosidase or cellobiose phosphorylase) that hydrolyze cellobiose. For this purpose, the genes gh1-1 of β-glucosidase, CDT-1m and CDT-2m of cellodextrin transporters from Neurospora crassa and the CBP gene coding for cellobiose phosphorylase from Saccharophagus degradans, were successfully expressed in O. polymorpha. Through metabolic engineering and mutagenesis, strains BEP/cat8∆/gh1-1/CDT-1m and BEP/cat8∆/CBP-1/CDT-2mAM were developed, showing improved parameters for high-temperature alcoholic fermentation of cellobiose. The study highlights the need for further optimization to enhance ethanol yields and elucidate cellobiose metabolism intricacies in O. polymorpha yeast. This is the first report of the successful development of stable methylotrophic thermotolerant strains of O. polymorpha capable of coutilizing cellobiose, glucose, and xylose under high-temperature alcoholic fermentation conditions at 45°C.

Isolation of a widespread giant virus implicated in cryptophyte bloom collapse

Photosynthetic cryptophytes are ubiquitous protists that are major participants in the freshwater phytoplankton bloom at the onset of spring. Mortality due to change in environmental conditions and grazing have been recognized as key factors contributing to bloom collapse. In contrast, the role of viral outbreaks as factors terminating phytoplankton blooms remains unknown from freshwaters. Here, we isolated and characterized a cryptophyte virus contributing to the annual collapse of a natural cryptophyte spring bloom population. This viral isolate is also representative for a clade of abundant giant viruses (phylum Nucleocytoviricota) found in freshwaters all over the world.

RING1 Inhibition Has a Cell-Specific Antitumoral Role by Promoting Autophagy in Endometrial Cancer Cells

BACKGROUND/AIMS

Factors influencing gene expression through chemical modifications of histones may play an important role in the regulation of the autophagy process in cancers. RING1A or RING1B are responsible for the catalytical activity of Polycomb repressive complex 1 (PRC1) which monoubiquitylate histone H2A. The aim of the study was to determine the effect of the RING1A/B protein inhibition on the autophagy process in endometrial cancer cells and the anticancer effectiveness of RING1 inhibitor PRT4165 in combination with autophagy inhibitors.

METHODS

The expression of autophagy genes and proteins were analyzed in endometrial cancer cells HEC-1A and Ishikawa grown in different glucose concentrations and treated with PRT4165. To assess the effectiveness of PRT4165 used alone or in combination with HCQ or Lys05, IC50 and the combination index (CI) were calculated. Flow cytometry method was used to estimate apoptotic cells after treatment.

RESULTS

The results confirm the impact of RINGs on autophagy and apoptosis in endometrial cancer cells. PRT4165 inhibitor causes changes in the expression of ATG genes and autophagy markers and the effect depends on glucose concentration and cell types. However, the anticancer effectiveness of PRT4165 was lower when it was used in combination with autophagy inhibitors, suggesting that such a combination is not a promising anticancer strategy.

CONCLUSION

The results indicate the importance of the RINGs in the process of autophagy and apoptosis. Further potentially more effective combinations of PRT4165 with autophagy modulators should be sought.

A3D Model Organism Database (A3D-MODB): a database for proteome aggregation predictions in model organisms

Protein aggregation has been associated with aging and different pathologies and represents a bottleneck in the industrial production of biotherapeutics. Numerous past studies performed in Escherichia coli and other model organisms have allowed to dissect the biophysical principles underlying this process. This knowledge fuelled the development of computational tools, such as Aggrescan 3D (A3D) to forecast and re-design protein aggregation. Here, we present the A3D Model Organism Database (A3D-MODB) http://biocomp.chem.uw.edu.pl/A3D2/MODB, a comprehensive resource for the study of structural protein aggregation in the proteomes of 12 key model species spanning distant biological clades. In addition to A3D predictions, this resource incorporates information useful for contextualizing protein aggregation, including membrane protein topology and structural model confidence, as an indirect reporter of protein disorder. The database is openly accessible without any need for registration. We foresee A3D-MOBD evolving into a central hub for conducting comprehensive, multi-species analyses of protein aggregation, fostering the development of protein-based solutions for medical, biotechnological, agricultural and industrial applications.

On Berman Functions

Let Z ( t ) = exp 2 B H ( t ) - t 2 H , t ∈ R with B H ( t ) , t ∈ R a standard fractional Brownian motion (fBm) with Hurst parameter H ∈ ( 0 , 1 ] and define for x non-negative the Berman function B Z ( x ) = E I { ϵ 0 ( R Z ) > x } ϵ 0 ( R Z ) ∈ ( 0 , ∞ ) , where the random variable R independent of Z has survival function 1 / x , x ⩾ 1 and ϵ 0 ( R Z ) = ∫ R I R Z ( t ) > 1 dt . In this paper we consider a general random field (rf) Z that is a spectral rf of some stationary max-stable rf X and derive the properties of the corresponding Berman functions. In particular, we show that Berman functions can be approximated by the corresponding discrete ones and derive interesting representations of those functions which are of interest for Monte Carlo simulations presented in this article.

Conformation-aggregation interplay in the simplest aliphatic ethers probed under high pressure

The structures of the simplest symmetric primary ethers [(CnH2n+1)2O, n = 1-3] determined under high pressure revealed their conformational preferences and intermolecular interactions. In three new polymorphs of diethyl ether (C2H5)2O, high pressure promotes intermolecular CH...O contacts and enforces a conversion from the trans-trans conformer present in the α, β and γ phases to the trans-gauche conformer, which is higher in energy by 6.4 kJ mol-1, in the δ phase. Two new polymorphs of dimethyl ether (CH3)2O display analogous transformations of the CH...O bonds. The crystal structure of di-n-propyl ether (C3H7)2O, determined for the first time, is remarkably stable over the whole pressure range investigated from 1.70 up to 5.30 GPa.

Artificial intelligence in detecting left atrial appendage thrombus by transthoracic echocardiography and clinical features: the Left Atrial Thrombus on Transoesophageal Echocardiography (LATTEE) registry

AIMS

Transoesophageal echocardiography (TOE) is often performed before catheter ablation or cardioversion to rule out the presence of left atrial appendage thrombus (LAT) in patients on chronic oral anticoagulation (OAC), despite associated discomfort. A machine learning model [LAT-artificial intelligence (AI)] was developed to predict the presence of LAT based on clinical and transthoracic echocardiography (TTE) features.

METHODS AND RESULTS

Data from a 13-site prospective registry of patients who underwent TOE before cardioversion or catheter ablation were used. LAT-AI was trained to predict LAT using data from 12 sites (n = 2827) and tested externally in patients on chronic OAC from two sites (n = 1284). Areas under the receiver operating characteristic curve (AUC) of LAT-AI were compared with that of left ventricular ejection fraction (LVEF) and CHA2DS2-VASc score. A decision threshold allowing for a 99% negative predictive value was defined in the development cohort. A protocol where TOE in patients on chronic OAC is performed depending on the LAT-AI score was validated in the external cohort. In the external testing cohort, LAT was found in 5.5% of patients. LAT-AI achieved an AUC of 0.85 [95% confidence interval (CI): 0.82-0.89], outperforming LVEF (0.81, 95% CI 0.76-0.86, P < .0001) and CHA2DS2-VASc score (0.69, 95% CI: 0.63-0.7, P < .0001) in the entire external cohort. Based on the proposed protocol, 40% of patients on chronic OAC from the external cohort would safely avoid TOE.

CONCLUSION

LAT-AI allows accurate prediction of LAT. A LAT-AI-based protocol could be used to guide the decision to perform TOE despite chronic OAC.

Repeat Sampling of Female Passerines During Reproduction Reveals Surprising Higher Plasma Oxidative Damage During Resting Compared to Active State

Traditional models of oxidative stress predict accumulation of damage caused by reactive oxygen species (ROS) production as highly correlated with aerobic metabolism, a prediction under increasing scrutiny. Here, we repeat sampled female great tits (Parus major) at two opposite levels of energy use during the period of maximum food provisioning to nestlings, once at rest and once during activity. Our results were in contrast to the above prediction, namely significantly higher levels of oxidative damage during rest opposed to active phase. This discrepancy could not be explained neither using levels of "first line" antioxidant enzymes activity measured from erythrocytes, nor from total nonenzymatic antioxidant capacity measured from plasma, as no differences were found between states. Significantly higher levels of uric acid, a potent antioxidant, were seen in the plasma during the active phase than in rest phase, which may explain the lower levels of oxidative damage despite high levels of physical activity. Our results challenge the hypothesis that oxidative stress is elevated during times with high energy use and call for more profound understanding of potential drivers of the modulation of oxidative stress such as metabolic state of the animal, and thus also the time of sampling in general.

Identification of the Enterotoxigenic Potential of Staphylococcus spp. from Raw Milk and Raw Milk Cheeses

This study aimed to genotypic and phenotypic analyses of the enterotoxigenic potential of Staphylococcus spp. isolated from raw milk and raw milk cheeses. The presence of genes encoding staphylococcal enterotoxins (SEs), including the classical enterotoxins (sea-see), non-classical enterotoxins (seg-seu), exfoliative toxins (eta-etd) and toxic shock syndrome toxin-1 (tst-1) were investigated. Isolates positive for classical enterotoxin genes were then tested by SET-RPLA methods for toxin expression. Out of 75 Staphylococcus spp. (19 Staphylococcus aureus and 56 CoNS) isolates from raw milk (49/65.3%) and raw milk cheese samples (26/34.7%), the presence of enterotoxin genes was confirmed in 73 (97.3%) of them. Only one isolate from cheese sample (1.3%) was able to produce enterotoxin (SED). The presence of up to eight different genes encoding enterotoxins was determined simultaneously in the staphylococcal genome. The most common toxin gene combination was sek, eta present in fourteen isolates (18.7%). The tst-1 gene was present in each of the analyzed isolates from cheese samples (26/34.7%). Non-classical enterotoxins were much more frequently identified in the genome of staphylococcal isolates than classical SEs. The current research also showed that genes tagged in S. aureus were also identified in CoNS, and the total number of different genes detected in CoNS was seven times higher than in S. aureus. The obtained results indicate that, in many cases, the presence of a gene in Staphylococcus spp. is not synonymous with the ability of enterotoxins production. The differences in the number of isolates with genes encoding SEs and enterotoxin production may be mainly due to the limit of detection of the toxin production method used. This indicates the need to use high specificity and sensitivity methods for detecting enterotoxin in future studies.

Amphiphilic Azo-Functionalized Polyhedral Oligomeric Silsesquioxane; Synthesis and Photo-Switched Efficient Phase Transfer via Host-Guest Encapsulation

A new amphiphilic azo-functionalized polyhedral oligomeric silsesquioxane (POSS) derivative was synthesized by functionalizing octa(3-aminopropyl)silsesquioxane (OAS-POSS) with 4-((4-(dodecyloxy)phenyl)diazenyl)benzoic acid, affording a hydrophilic amino POSS head and hydrophobic dodecyl tail with a diphenyl-azo connector. Prepared amphiphilic azo-functionalized POSS (azo-POSS) exhibited high ability for encapsulation and transferring cationic dyes into the organic phase by vigorously mixing with aqueous solutions of each dye. The photo-controlled encapsulating properties of the synthesized phase transfer reagent was studied using cationic dyes, such as methylene blue (MB), crystal violet (CV) and thymol blue in acidic conditions. Results showed more than 95 % encapsulation of MB. However, no considerable encapsulation was shown in the case of anionic dyes such as eriochrome black T (EBT) and thymol blue in alkaline solutions. By trans/cis isomerization of the azo moiety of the phase transfer reagent by UV irradiation (365 nm), the amount of dye encapsulation was decreased, which could be attributed to the formation of cis isomer that led to the folding of the dodecyl alkyl tail on the POSS moiety, and therefore prevent to lay the 3-aminopropyl moieties of POSS head to the water/DCM interface to adsorb and encapsulate MB molecules.

Machine learning for prediction of all-cause mortality after transcatheter aortic valve implantation

AIMS

Prediction of adverse events in mid-term follow-up after transcatheter aortic valve implantation (TAVI) is challenging. We sought to develop and validate a machine learning model for prediction of 1-year all-cause mortality in patients who underwent TAVI and were discharged following the index procedure.

METHODS AND RESULTS

The model was developed on data of patients who underwent TAVI at a high-volume centre between January 2013 and March 2019. Machine learning by extreme gradient boosting was trained and tested with repeated 10-fold hold-out testing using 34 pre- and 25 peri-procedural clinical variables. External validation was performed on unseen data from two other independent high-volume TAVI centres. Six hundred four patients (43% men, 81 ± 5 years old, EuroSCORE II 4.8 [3.0-6.3]%) in the derivation and 823 patients (46% men, 82 ± 5 years old, EuroSCORE II 4.7 [2.9-6.0]%) in the validation cohort underwent TAVI and were discharged home following the index procedure. Over the 12 months of follow-up, 68 (11%) and 95 (12%) subjects died in the derivation and validation cohorts, respectively. In external validation, the machine learning model had an area under the receiver-operator curve of 0.82 (0.78-0.87) for prediction of 1-year all-cause mortality following hospital discharge after TAVI, which was superior to pre- and peri-procedural clinical variables including age 0.52 (0.46-0.59) and the EuroSCORE II 0.57 (0.51-0.64), P < 0.001 for a difference.

CONCLUSION

Machine learning based on readily available clinical data allows accurate prediction of 1-year all-cause mortality following a successful TAVI.

Dual Role of Vitamin C-Encapsulated Liposomal Berberine in Effective Colon Anticancer Immunotherapy

The aim of the study was to achieve effective colon anticancer immunotherapy using the alkaloid berberine. In the presented paper we attempt to develop a formulation of berberine loaded into liposomal carriers using the vitamin C gradient method, characterized by efficient drug encapsulation, high stability during long-term storage, low drug release in human plasma with specific cytotoxicity towards colon cancer cells. Liposomal berberine was responsible for the induction of oxidative stress, the presence of Ca2+ ions in the cytosol, the reduction of Δψm, and ATP depletion with a simultaneous lack of caspase activity. Moreover, treatment with liposomal berberine led to CRT exposure on the surface of cancer cells, extracellular ATP, and HMGB1 release. The above-described mechanism of action was most likely associated with ICD induction, contributing to the increased number of phagocytic cancer cells. We have shown that cancer cells treated with liposomal berberine were phagocytosed more frequently by macrophages compared to the untreated cancer cells. What is more, we have shown that macrophage pre-treatment with liposomal berberine led to a 3-fold change in the number of phagocytosed SW620 cancer cells. The obtained results provide new insights into the role of berberine in maintaining the immune response against colorectal cancer.

"It was not mentioned": Improving responses to unanswerable questions using retrieval instructions

Previous research shows that posing many questions about an event may lead to asking questions about unwitnessed details and that people sometimes provide substantive and erroneous answers to them. Therefore, two experiments investigated the role of the problem-solving and judgment processes, which are unrelated to memory access, in improving responding to unanswerable questions. Experiment 1 compared the effects of a brief retrieval training with the effects of an instruction to increase the criterion of reporting. As expected, the two manipulations had different effects on participants' answers, which demonstrates that training can do more than just instigate more cautious responding. However, we found evidence against our prediction that an enhancement in metacognitive ability underlies improved responding after training. Experiment 2 investigated, for the first time, the role of constant awareness that questions can be unanswerable and that such questions should be rejected. We compared the effects of training with the effects of a small change in response format that ensured such awareness. The effects of the two manipulations were similar, which supports our prediction that the constant awareness of unanswerable questions is a key factor behind improved responding. Practical implications for the eyewitness memory domain are discussed. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

RNA tertiary structure prediction using RNAComposer in CASP15

As CASP15 participants, in the new category of 3D RNA structure prediction, we applied expert modeling with the support of our proprietary system RNAComposer. Although RNAComposer is primarily known as an automated web server, its features allow it to be used interactively, for example, for homology-based modeling or assembling models from user-provided structural elements. In the paper, we present various scenarios of applying the system to predict the 3D RNA structures that we employed. Their combination with expert input, comparative analysis of models, and routines to select representative resultant structures form a ready-for-reuse workflow. With selected examples, we demonstrate its application for the in silico modeling of natural and synthetic RNA molecules targeted in CASP15.

survex: an R package for explaining machine learning survival models

SUMMARY

Due to their flexibility and superior performance, machine learning models frequently complement and outperform traditional statistical survival models. However, their widespread adoption is hindered by a lack of user-friendly tools to explain their internal operations and prediction rationales. To tackle this issue, we introduce the survex R package, which provides a cohesive framework for explaining any survival model by applying explainable artificial intelligence techniques. The capabilities of the proposed software encompass understanding and diagnosing survival models, which can lead to their improvement. By revealing insights into the decision-making process, such as variable effects and importances, survex enables the assessment of model reliability and the detection of biases. Thus, transparency and responsibility may be promoted in sensitive areas, such as biomedical research and healthcare applications.

AVAILABILITY AND IMPLEMENTATION

survex is available under the GPL3 public license at https://github.com/modeloriented/survex and on CRAN with documentation available at https://modeloriented.github.io/survex.